CHICKEN MEAT - AgriFutures Australia

RIRDC Completed Projects in 2007-2008 and Research in Progress as at June 2008

CHICKEN MEAT

November 2008

RIRDC Publication No 08/070

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© 2008 Rural Industries Research and Development Corporation All rights reserved.

ISBN 1 74151 659 5 ISSN 1440-6845 IRDC Completed Projects in 2007-2008 and Research in Progress as at June 2008 - Chicken Meat Publication No 08/070

The information contained in this publication is intended for general use to assist public knowledge and discussion and to help improve the development of sustainable regions. You must not rely on any information contained in this publication without taking specialist advice relevant to your particular circumstances.

While reasonable care has been taken in preparing this publication to ensure that information is true and correct, the Commonwealth of Australia gives no assurance as to the accuracy of any information in this publication.

The Commonwealth of Australia, the Rural Industries Research and Development Corporation (RIRDC), the authors or contributors expressly disclaim, to the maximum extent permitted by law, all responsibility and liability to any person, arising directly or indirectly from any act or omission, or for any consequences of any such act or omission, made in reliance on the contents of this publication, whether or not caused by any negligence on the part of the Commonwealth of Australia, RIRDC, the authors or contributors.

The Commonwealth of Australia does not necessarily endorse the views in this publication.

This publication is copyright. Apart from any use as permitted under the Copyright Act 1968, all other rights are reserved. However, wide dissemination is encouraged. Requests and inquiries concerning reproduction and rights should be addressed to the RIRDC Publications Manager on phone 02 6271 4165.

RIRDC Chicken Meat Program Research Manager

Dr Vivien Kite RIRDC Chicken Meat Program PO Box 579 NORTH SYDNEY NSW 2059 Phone: 02 9929 4077 Fax: 02 9925 0627 Email: [email protected]

RIRDC Publications Manager

Rural Industries Research and Development Corporation Level 2, 15 National Circuit BARTON ACT 2600 PO Box 4776 KINGSTON ACT 2604 Phone: 02 6271 4100 Fax: 02 6271 4199 Email: [email protected] Website: http://www.rirdc.gov.au

Published electronically in November 2008

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Foreword RIRDC produces Research in Progress summaries of continuing projects and those completed during 2007-2008. Our intention is to:

• give stakeholders early access to the results of ongoing and completed work to inform their decisions, and

• inform researchers of results to shape research directions.

The complete report on all programs is on our website at http:www.rirdc.gov.au.

The following report is a hardcopy extract covering the Chicken Meat R&D Program. It contains all entries from continuing and completed Chicken Meat research projects funded by RIRDC in 2007–2008.

The objective of the Chicken Meat Program is to support increased sustainability and profitability in the chicken meat industry.

This research was funded from industry revenue which is matched by funds provided by the Australian Government.

This report is an addition to RIRDC’s diverse range of over 1800 research publications, which are available for viewing, downloading or purchasing online through our website:

• downloads at www.rirdc.gov.au/fullreports/index.html

• purchases at www.rirdc.gov.au/eshop

Peter O’Brien

Managing Director Rural Industries Research and Development Corporation

http://www.rirdc.gov.au/fullreports/index.html

http://www.rirdc.gov.au/eshop

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CHICKEN MEAT PROGRAM ADVISORY COMMITTEE

Chairperson: Mr Barry Shay Food Safety Consultant 27 Uther Street CARINDALE QLD 4152 Ph: (07) 3398 1766 Mobile: 0402 245 744 Fax: (07) 3398 6631 Email: [email protected]

Research Manager: Dr Vivien Kite RIRDC Chicken Meat Program PO Box 579 NORTH SYDNEY NSW 2059 Ph: (02) 9929 4077 Fax: (02) 9929 0627 Email: [email protected]

Committee Members: Dr Pat Blackall Animal Research Institute Department of Primary Industries Locked Mail Bag No 4 MOOROOKA QLD 4015 Ph: (07) 3362 9498 Fax: (07) 3362 9429 E-mail: [email protected]

Dr Rod Jenner Golden Cockerel Pty Ltd PO Box 142 CLEVELAND QLD 4163 Ph: (07) 3206 6444 Fax: (07) 3206 6999 E-mail: [email protected]

Dr Tom Grimes Grimes Consultancy Pty Ltd 29 Tradewinds Avenue PARADISE POINT QLD 4216 Ph/fax: (07) 5529 6146 Mob: 0416 257 524 Email: [email protected]

Dr Ron MacAlpine Inghams Enterprises Pty Ltd Locked Bag 4000 LIVERPOOL BC NSW 1871 Ph: (02) 9606 5666 Fax: (02) 9606 6640 Email: [email protected]

Dr Margaret MacKenzie Inghams Enterprises Pty Ltd PO Box 1100 BROWNS PLAINS QLD 4118 Ph: (07) 3297 4644 Fax: (07) 3290 4471 Email: [email protected]

Mr Gary Sansom 82 Hawkins Road JIMBOOMBA QLD 4280 Ph: (07) 5546 9235 Fax: (07) 5546 0070 E-mail: [email protected]

Ms Margie Thomson RIRDC PO Box 4776 KINGSTON ACT 2604 Ph: (02) 6272 4152 Fax: (02) 6272 5877 Email: [email protected]

Dr Liam Morrisroe Bartter Enterprises Pty Ltd PO Box 616 NORTH RYDE NSW 1670 Ph: (02) 8870 0000 Fax: (02) 8870 0093 E-mail: [email protected]

Program Development and Communication Coordinator: Dr Elisa Heylin RIRDC, PO Box 579, NORTH SYDNEY NSW 2059 Ph: (02) 9929 4077, Fax: (02) 9929 0627, Email: [email protected] Program Coordinator: Ms Lea Edwards RIRDC, PO Box 4776, KINGSTON ACT 2604 Ph: (02) 6271 4132, Fax: (02) 6271 4199, Email: [email protected]

mailto:[email protected]




mailto:elisa.heylin@


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Index To Project Summaries Foreword ...................................................................................................................iii

CHICKEN MEAT PROGRAM ADVISORY COMMITTEE ..........................................iv

Index To Project Summaries .......................................................................................v

Completed Projects...................................................................................................1

Efficiency of Production ...........................................................................................1

Broiler performance on pearl millet based diets .............................................................................. 1

Developing novel biological management strategies for darkling beetle (Alphitobius diaperinus [Panzer]) in Australian broiler houses.............................................................................................. 3

Using antimicrobial proteins to control necrotic enteritis in meat chickens .................................... 5

Nutritional characterisation of sorghums from QLD and NSW for chicken meat........................... 7

Update amino acid digestibility booklet ........................................................................................ 10

Product Quality and Safety.....................................................................................11

Effect of new strategies in Salmonella & Campylobacter during chicken processing .................. 11

Molecular epidemiology of antibiotic resistance in Salmonella from chickens ............................ 13

The Workboot Series - The story of chicken in Australia.............................................................. 15

QA Workshops – Pre-Workshop Microorganism Surveys ............................................................ 17

Sustainable Production Environment....................................................................18

Evaluating risks posed by pathogen emissions from meat chicken sheds ..................................... 18

Monitoring mechanical ventilation rates in poultry buildings for application of odour/dust control technologies ................................................................................................................................... 20

Evaluation of "add-on" technologies for control of odour and dust from chicken sheds............... 21

National Poultry Litter Project - Plan for Stage 1: Initiation Phase ............................................... 23

NTL Poultry Litter PROJ - Literature Review, Market Study and Project .................................... 25

Other.........................................................................................................................27

Nutritional Value of Australian Chicken Meat .............................................................................. 27

RESEARCH IN PROGRESS.....................................................................................29

Efficiency of Production .........................................................................................29

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Trialling natural agents for control of darkling beetles.................................................................. 29

Postgraduate scholarship - David Stephenson: Delivery of therapeutic proteins using lactobacillus........................................................................................................................................................ 30

Physiological & nutritional approaches to alleviate heat stress ..................................................... 31

Subunit vaccine against infectious bursal disease virus................................................................. 32

Improvement of lupins and lathyrus for broilers and egg layers by enzyme treatment (managed by AECL)............................................................................................................................................ 33

Investigation of IBH outbreaks in Australian meat breeder/broiler flocks and establishment of an avian adenovirus typing facility and service .................................................................................. 34

Improved control measures for infectious bursal disease virus (IBDV) ........................................ 35

Product Quality and Safety.....................................................................................36

Differential typing of Campylobacter ............................................................................................ 36

Investigation of the prevalence of chlamydiosis in the Australian chicken meat industry ............ 38

Use of bacteriophage and phage products to control Campylobacter in chickens......................... 39

Smart State Fellowships Program – development of probiotic control measures to combat Campylobacter related food borne disease using glyco array technology..................................... 40

Early feeding of prebiotics on the development of the digestive system and gut microflora of broilers ........................................................................................................................................... 41

Expansion and refinement of a molecular typing system for Salmonella ...................................... 42

Sustainable Production Environment....................................................................44

High Value Products from Hatchery Waste................................................................................... 44

Piloting chicken litter usage in broadacre cropping: setting research directions .......................... 45

Avian influenza: improved diagnostics for detecting antibodies to H5N1 .................................... 47

Managing litter re-use for minimal nutrient runoff to surface water ............................................. 48

Verification of separation distance methods for meat chicken farms ............................................ 49

Other.........................................................................................................................50

Nuffield Scholarship Award 2007 – Rob Kestel............................................................................ 50

OTHER SUPPORTED ACTIVITIES ..........................................................................51

NEW RESEARCH TO BE SUPPORTED IN 2008/2009 ...........................................52

RIRDC CHICKEN MEAT PUBLICATIONS...............................................................53

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Completed Projects

Efficiency of Production

Project Title Broiler performance on pearl millet based diets

RIRDC Project No.:

PRJ-000594

Start Date: 1/04/2006 Finish Date 1/10/2007 Researcher: Mr Danny Singh Organisation: Queensland Department of Primary Industries and

Fisheries Phone: (07) 3820 0515 Fax: (07) 3824 4316 Email: [email protected]

Objectives • To ascertain the effect on broiler performance of a pearl millet (PM) based diet.

• To ascertain the effect on chicken meat quality when pearl millet based diets are fed to birds.

• To promote the benefits and disadvantages of pearl millet as a feed grain to both grain growers and meat chicken industry.

Background RIRDC Project DAQ-302A characterised the nutritive value of PM hybrids. PM hybrids were shown to have higher apparent metabolisable energy (AME) values and their digestible amino acid profile was superior to sorghum. The report recommended that further research was warranted to assess these hybrids in terms of broiler growth, feed efficiency and carcass quality.

Research Two tonnes of PM hybrids (NPM3 and NPM4) were harvested, cleaned and transported to Pork Research and Development Corporation for evaluation in 2005. Twelve tonnes of hybrid PM35 was harvested in 2006. All three PM hybrids analysed for nutrient content, however, AME and amino acid digestibility were conducted on NPM3 and NPM4 only. Two growth experiments were conducted, first to ascertain the maximum inclusion rates in broiler diets. This was conducted in cages under environmentally controlled conditions and the second experiment was conducted in floor pens and under semi-commercial conditions. Treatments for the second experiment were NPM3, PM35 and a good quality sorghum was the control. At the end of 42 days, twenty birds (10 of each sex) from each treatment were sent for carcass evaluation.

Outcomes PM35 had higher protein content and lower starch content than NPM3 and NPM4. The fat content of the pearl millet varieties was similar (6%) which was twice as much as the fat content of sorghum (3%). The AME content of pearl millet was 1.4MJ/kg higher than sorghum (16.1 compared to 14.6 MJ/kg. The amino acid profile of pearl millet hybrids were better than sorghum.. Replacing sorghum with pearl millet had no significant effect on the bodyweight of the broilers compared to the sorghum control when measured at either 21 or 42 days of age although

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birds on sorghum diet had numerically lower bodyweight (P>0.05,). Feed intake of birds during starter and grower periods was not significantly different. However feed intake of birds on sorghum diets over the whole period (0-42 days) were numerically higher than those on pearl millet based diets. Birds on sorghum diet had the poorest feed conversion compared to birds on pearl millet diets in both growth periods. Birds on the PM hybrid diets had higher breast and thigh weights and lower leaf fat than birds on sorghum diets.

Implications Pearl millet hybrids are suitable feed ingredients for broilers and can be substituted for cereal grains in broiler diets. A concerted effort ought to be made by the chicken meat industry to encourage grain producers to include the growing of pearl millet in their crop production cycle.

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Project Title Developing novel biological management strategies for darkling beetle (Alphitobius diaperinus [Panzer]) in Australian broiler houses

RIRDC Project No.:

PRJ-000602

Start Date: 1/08/05 Finish Date 3/08/07 Researcher: Mr Trevor Lambkin Organisation: Queensland Department of Primary Industries and Fisheries Phone: (07) 3362 9606 Fax: (07) 3362 9429 Email: [email protected]

Objectives • To develop protocols for laboratory inoculation and assessment of virulence of entomopathogenic fungi (bio-pesticide) as a litter treatment for darkling beetle management.

• To undertake a preliminary evaluation of entomopathogenic nematodes in the laboratory for beetle management as a litter or floor applicant.

• To investigate in the laboratory the efficacy of entomopathogenic fungi in combination with diatomaceous earth.

Background Previous RIRDC funded research into the management of darkling beetle in Australian broiler houses indicated that high pest numbers predominately occur in broiler house litter and that treatments of earth floors of houses with the two currently registered insecticides (fenitrothion and cyfluthrin) are mostly ineffective. More importantly, this research also pointed out that, in most cases, applying control agents to fresh litter would be much more effective than application to floors. In light of these findings, the aim of this proposed project is to develop and trial in the laboratory a range of insecticide-free litter and earth treatments.

Research The susceptibility of Darkling Beetle, Alphitobius diaperinus to two fungal species, Beauveria bassiana and Metarhizium anisopliae, was evaluated in the laboratory and the most virulent isolates of each species were further tested in laboratory litter assays at 30°C and 55% relative humidity, singly and in combination with diatomaceous earth. In addition, susceptibility of larvae and adults of A. diaperinus was tested against four nematode species (Steinernema feltiae, S. carpocapsae, S. riobrave and Heterorhabditis bacteriofora) at a range of temperatures in the laboratory. The most virulent nematode species was further assessed in laboratory test boxes containing simulated litter and a sand substrate.

Outcomes Litter surface applications of fungal conidia were very effective, with 91 and 88% progeny reductions achieved by B. bassiana and M. anisopliae respectively at relatively low doses (0.49 x 108 and 0.87 x 109 conidia/m2 respectively). At almost all doses of M. anisopliae, combining the fungi with diatomaceous earth (at 0.25 and 0.5 kg/m3) saw an effect greater than using each agent singly. This was not evident with B. bassiana as its efficacy at the tested doses was very good and therefore overall efficacy was not notably enhanced by diatomaceous earth. The most effective and reliable nematode species was S. carpocapsae at 30°C. Results also indicated that a damp environment

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might be required for nematodes to be effective. Implications The results of these laboratory studies indicated that applications of

native Australian isolates of B. bassiana, M. anisopliae, and S. carpocapsae to litter showed promising efficacy for control of A. diaperinus. With this in mind, field trialling of these agents should soon be undertaken to test their efficacy in broiler house conditions.

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Project Title Using antimicrobial proteins to control necrotic enteritis in meat chickens

RIRDC Project No.:

PRJ-000697

Start Date: 02/10/05 Finish Date: 01/10/07 Researcher: Dr Robert Moore Organisation: CSIRO Livestock Industries

Private Bag 24 GEELONG VIC 3220

Phone: (03) 5227 5760 Fax: (03) 5227 5555 Email: [email protected]

Objectives • To develop therapeutic treatments for necrotic enteritis based on the use of antimicrobial proteins such as bacteriocins, delivered to birds by live bacterial vectors.

Background The intensive animal production industries are under pressure to reduce the use of in-feed antibiotics because of the perceived implications of ongoing use on the spread of antibiotic resistant bacteria in the human population. The chicken industry has identified that some pathogens (in particular Clostridium perfringens, the causative agent of necrotic enteritis) may increase in prevalence when in-feed antibiotics are withdrawn and hence are proactively looking for alternative control strategies. This project aims to develop a cost effective, user-friendly, environmentally sustainable biological control strategy.

Research The comparative performance of several antimicrobial proteins when delivered by three different Escherichia coli vector strains was assessed in chickens by scoring disease lesions and determining bacterial numbers in the gut. Expression constructs were manipulated and vector strains were tested for their ability to colonise the chicken gut in higher numbers in order to deliver more of the antimicrobial protein to the appropriate site. After the most suitable vector and antimicrobial proteins were found, a construct expressing multiple antimicrobial proteins was tested to improve performance and reduce the possibility of resistant C. perfringens arising.

Outcomes Two strains of E. coli were identified as suitable vectors to deliver antimicrobial proteins to the gut of chickens due to persistence of the strain and antimicrobial activity at the appropriate site. Delivery of Piscicolin 126 (P126) using the plasmid pRM1503 significantly reduced necrotic lesions and C. perfringens numbers in most of the disease challenge trials in which it was tested. In a few trials protection was not seen. It appears that there is a critical element to the balance in the bird between the live delivered antimicrobials and the C. perfringens pathogen that we do not yet understand.

Implications This project has shown that the delivery of prophylactic proteins to the gut of chickens is possible by the use of suitable live bacterial vectors. Secondly, delivery of specific antimicrobial proteins are a potential solution for the control of necrotic enteritis, although further work is required to determine the exact conditions which are required to

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maximise success of this strategy. Publications Moore, R.J., Rood, J.I., Sheedy, S.A. (2007) "Bacterial delivery of

biologically active polypeptides" patent number WO 2007/025333. Sheedy, S.A., Rood, J.I. & Moore, R.J. (2007) Identification and use of commensal Escherichia coli strains to deliver therapeutic proteins to the gastrointestinal tract of chickens. Applied and Environmental Microbiology (in prep) Keyburn, A.L., Sheedy, S.A., Rood, J.I., & Moore, R.J. (2006) The alpha-toxin of Clostridium perfringens is not an essential virulence factor in necrotic enteritis in chickens. Infection and immunity 74: 11 (6496-6500).

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Project Title Nutritional characterisation of sorghums from QLD and NSW for chicken meat

RIRDC Project No.:

PRJ-000586

Start Date: 1/10/2004 Finish Date: 30/11/2007 Researcher: Dr Rider Perez-Maldonado Organisation: Queensland Department of Primary Industries and


Objectives • To characterise and evaluate the variability of sorghums from QLD and NSW regions.

Background In Australia, early cultivars of sorghum contained considerable anti-nutritional factors (ANF) such as polyphenolic compounds and fungus contaminations that lowered sorghum’s nutritional value with significantly depressed growth, poorer feed and energy utilisation and sometimes with toxic effects when fed to poultry. However, Australian plant breeding programs have paid considerable attention to reduce these ANF in sorghum cultivars producing modern varieties which are able to improve its nutritional value and safeness when feeding livestock. In areas of Australia, improved Australian sorghum lines are the preferred grain for chicken meat production compared to wheat due to its apparent metabolisable energy (AME) consistency and lower price. However, it was recently pointed out that breast meat yield variability can be large and the feed conversion ratio (FCR) slightly depressed compared to values obtained on wheat-based diets. This difference equates to 2 to 3% additional feed cost ($2-3 million) and needs to be addressed. Together with the loss in revenue due to variability in carcass composition, this results in a significant loss to this very competitive industry in Australia. This project was proposed to address these production differences.

Research A total of 38 grain sorghum samples were collected in two rounds harvest periods nominated year 1 (2004-2005) and year 2 (2005-2006) from various areas of NSW and QLD. Each grain was chemically analysed including ANF such as condensed tannins (CT) and ergot contamination. Subsequent evaluations determined the AME and ileal digestibility of amino acids (AA), starch, nitrogen (N), and CT including their interaction affecting sorghum nutritional value in poultry diets. Next, pilot studies in metabolism cages evaluated broiler growth performance for each sorghum variety collected during both harvests. A control wheat-based diet with added xylanase enzyme was included in each pilot study for comparing bird performance between grains. The relationship between sorghum AME intake and live weight gain (LWG) and between Sorghum AME intake and FCR during the starter and grower/finisher period were calculated and plotted and compared with grain feed efficiency obtained in wheat-based diets. Broiler performance parameters comparisons were made between pilot studies conducted in the 2004 sorghums and 2005 sorghums harvest. The effect of AME

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determination methods, feed preparation and the effect of bird age were compared on broiler production performance. The effects of adding commercial xylanase and phytase feed enzymes and synthetic cystine on selected sorghum-based starter diets, compared with wheat-based diets were evaluated. Finally, selected sorghums evaluated in semi-commercial experiments with various feeding strategies were examined to improve sorghum utilisation with emphasis in the starter phase period (0-21 d) by comparison to current industry standard wheat-based diets.

Outcomes • Chemical analyses of sorghum grains were consistent across the two harvest years. Therefore, the data reported here can be valid for at least the next seven years.

• Within each harvest year, there was consistently large grain variability between regions and grain cultivars so that any extrapolation of data needs to be taken with care.

• The total bound phosphorus (P) as phytate-P which represented about 76% of evaluated sorghums, may negatively influence AA, N, DM, minerals and energy utilisation with a high correlation (r=0.70) between grain available P and sorghum AME.

• The lower cystine and tryptophan digestibility found was associated with levels of CT found in sorghum and this may affect bird performance in sorghum based diets particularly during early bird growth.

• The reduction in AME found in young birds (0-21 days old) was negatively correlated with the free CT (r=0.725) and bound CT (r=-0.773) fractions found in sorghum grain.

• Normally in Australia AME values are obtained with older birds, (22-29 days) and are then used to formulate diets for birds between 0-21 days. This large reduction in AME will have a significant consequence nutritionally on birds during the starter phase (0-21 days old).

Implications Recommendations • It is recommended that nutritionists update their databases with

values obtained in this report. • Prior to dietary formulation, chemical analysis of sorghum grain is

needed at least for N, but an overall mean value for other parameters such as P, phytate-P, AME, starch, and amino acids can be used with acceptable results.

• It is recommended that sorghum breeders use international accepted methods for CT determination in important sorghum lines.

• There is a need for reducing CT levels in sorghum lines. • There is a need to evaluate the negative effect of CT on younger birds

(0-7 and 7-14 days old) and its interaction with energy, and other nutrient utilisation.

• The addition of phytase showed an improvement in poultry feed intake and live weight gain without negatively affecting FCR. But subsequent experiments with the use of enzymes and selected AA were not conclusive. Thus it is recommended to continue poultry research on the response of various enzymes levels and types in combination with AA (cystine and trptophan) as indicated in the report.

• Due to the negative effect of CT on young birds, it is necessary for nutritionists to adjust the AME value by -0.8 MJ to be applied in the formulation of broiler starter diets in order to improve sorghum

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utilisation particularly during the early starter period. • The adjustment of AME in sorghum grain diets was linked linked to a

reduction of fat and increased breast meat yield. However more research is needed to investigate the potential effect of CT on AME determined in much younger birds (0-7 days old and 7-14 days old) and when fed these sorghum-based diets.

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Project Title Update amino acid digestibility booklet

RIRDC Project No.:

PRJ-002827

Start Date: 09/04/2008 Finish Date: 31/05/2008 Researcher: Prof Wayne Bryden Organisation: The University of Queensland Phone: (07) 5460 1250 Fax: (07) 5460 1444 Email: [email protected]

Objectives • To update amino acid composition and digestibility tables in the RIRDC booklet.

Background The amino acid composition and digestibility values of 93 Australian feedstuffs were published by RIRDC in 1998 as “Digestible Amino Acids in Poultry Feedstuffs”. During the past decade, additional digestibility data has been generated with broiler chickens. It was decided that compilation of this data with existing data in an updated booklet would be a valuable resource for the poultry industry and those engaged in poultry nutrition research.

Outcomes An updated book “Ileal Digestible Amino Acids in Feedstuffs for Poultry’ has been completed and includes: • the amino acid concentrations and digestibility values of 137 samples

representing 28 feed ingredients • Tryptophan data for selective feed ingredients • linear regression equations describing total and apparent ileal

digestible amino acid content as function of total and apparent ileal digestible crude protein content have been calculated for major feed ingredients.

Implications This publication will be a useful resource for the poultry industry, especially nutritionists and those engaged in protein and amino acid research with poultry. Importantly, differences in amino acid digestibility of feedstuffs can be effectively used to improve the precision of feed formulation.

Publications Bryden,W.L.Li,X., Ravindran,G.,Hew,L.I.and Ravindran,V. (2008). Ileal Digestible Amino Acids in Feedstuffs for Poultry. RIRDC. In press

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Product Quality and Safety

Project Title Effect of new strategies in Salmonella & Campylobacter during chicken processing

RIRDC Project No.:

PRJ-000887

Start Date: 1/06/2007 Finish Date: 18/04/2008 Researcher: Dr Narelle Fegan Organisation: Food Science Australia Phone: (07) 3214 2095 Fax: (07) 3214 2050 Email: [email protected]

Objectives • To determine if new intervention strategies implemented since the previous study have further reduced the prevalence of Campylobacter and Salmonella during processing. Specifically it will seek:

• To establish prevalence and levels of Campylobacter and Salmonella on chickens at eight to twelve points during processing in three representative Australian facilities on three different sampling days.

• To record physical data, such as temperatures and chlorine levels, relevant to sampling points at the same time as microbiological samples are taken.

• To use these data to determine the effectiveness of strategies on levels of the two pathogens.

Background A previous RIRDC project (FSA-3A) was conducted in 2005 to determine the levels of Salmonella and Campylobacter in chicken processing facilities in Australia and to determine the impact of different processing points on the levels of these two pathogens. Further investigation of the impact of sampling on different processing days and establishing if industry changes since 2005 had any effect on the levels of these bacteria on chicken carcases would provide the industry with more detailed information on the most important processing steps for control of these pathogens.

Research The levels of Salmonella and Campylobacter were determined on chicken carcases at various points throughout processing from just after slaughter through to packaging at three chicken processing facilities. Each facility was sampled on three separate days. Various processing parameters, such as chlorine levels and the temperatures of scald and chiller tanks during each visit were provided by the processing plant to determine which steps were important in reducing contamination of chicken carcases.

Outcomes The levels of Salmonella and Campylobacter were highest on carcases at the beginning of processing just after slaughter, and were lowest on carcases after chilling and packaging. Prior to chilling, the levels of Salmonella and Campylobacter varied across different sampling days, even within the same processing plant operating under similar processing conditions. However, after chilling, there was little variation between the levels of either pathogen. Appropriate chilling has the greatest impact on reducing the levels of Salmonella and Campylobacter

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on chicken carcases. Implications Chicken processing facilities need to maintain control over all aspects of

processing, particularly those relating to chilling to ensure the levels of Salmonella and Campylobacter on chicken carcases are kept to a minimum.

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Project Title Molecular epidemiology of antibiotic resistance in Salmonella from chickens

RIRDC Project No.:

PRJ-000750

Start Date: 01/07/05 Finish Date: 31/07/07 Researcher: Dr Michael Heuzenroeder Organisation: Institute of Medical and Veterinary Science

Infectious Diseases Laboratories PO Box 14 Rundle Mall PO ADELAIDE SA 5000


Objectives • To develop an improved understanding of the epidemiology of antibiotic resistance of Salmonella involved in poultry production by (a) determining the molecular epidemiology of resistance genes in Salmonella in humans and chickens; (b) clarifying the role of bacteriophages in the transfer of antibiotic resistance in Salmonella and other enteric organisms such as Escherichia coli, and (c) determining if antibiotic resistance can be transferred in the chicken gastrointestinal tract by bacteriophages.

Background Salmonella strains in chickens and other food-producing animals readily acquire antibiotic resistance genes through a process of horizontal gene transfer and many strains resistant to multiple classes of antibiotics have emerged. Use of any one of the antibiotics to which these multi-resistant strains are resistant exerts selection pressure facilitating the dominance of these resistant strains in the chicken flock. Contamination of carcasses with strains that are multi-resistant poses a risk of difficult-to-treat food borne infections in young children or immuno-compromised adults as antibiotic treatment can be required for treatment of Salmonella infections in these classes of patients. Transfer of bacterial genetic material via bacteriophage (phage transduction) has been shown to be potentially important in the transfer of genes in vitro (Heuzenroeder et al RIRDC Project IMV-3A). However, the role of bacteriophage in transfer of antibiotic resistance genes although suspected has been largely neglected, despite the fact that it has been estimated that 70% -80% of Salmonella of veterinary origin harbour phage capable of genetic transfer by transduction.

A better understanding of the mechanisms of horizontal transfer of resistance genes would lead to improvements in how antibiotics are used in the chicken meat industry. In addition, more knowledge of the molecular epidemiology of resistance genes in enteric Salmonella strains would assist in development of antibiotic resistance surveillance programs.

Research The research suggests that “common” genes chosen on the basis of overseas studies are often not detected in Salmonella that are phenotypically resistant to the antibiotic that the common gene encodes resistance for. No conclusions that the Salmonella isolated from humans

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is potentially derived from either chickens or pigs could be made. The widespread distribution of type I integrons was observed.

This work represents the first Australian study to determine whether Salmonella isolated in Australia contain temperate bacteriophages. Bacteriophages could be induced from most isolates, including from the widespread Salmonella Sofia serovar. Transduction was proven to occur between Salmonella strains with the tetA and blaTEM-1 being transferred in vitro.

Although antibiotic resistance transfer could be demonstrated phenotypically very readily, the transfer of resistance was not stable in the putative transductants; abortive transduction was the most likely explanation. However successful transduction could be demonstrated amongst a small number of strains.

There was strong evidence that genetic transfer of antibiotic resistance genes can occur within the chicken gut. Bacteriophages that could infect a wide range of host bacteria could be routinely isolated from faeces. In some instances there was evidence that the non–Salmonella bacteria within the gut had transferred resistance genes to the administered Salmonella recipients. Both laboratory and natural strains were shown to be capable of transferring resistance genes. In addition, there was strong evidence to suggest that the environment of the chicken gut could mediate the phenomenon of phage type conversion in the recipient strains. It is most likely that this is occurring because of infection with temperate bacteriophages either from the administered donor strain or from pre-existing phages within the gut.

Outcomes • A survey of common antibiotic resistance genes in Salmonella from Australia and the demonstration of integrons.

• In vitro demonstration of bacteriophage mediated transduction of antibiotic resistance genes tetA and blaTEM-1

• In vivo transduction in the chicken gut of tetA and blaTEM-1 and evidence of transfer of antibiotic resistance from commensal bacteria.

• In vivo demonstration of phage type conversion. Implications Integrons appear to be relatively widespread within Salmonella. These

elements are extremely important in the spread of antibiotic resistance and a larger study should be undertaken to fully survey their presence and to determine more fully the genes involved in common resistance profiles.

Bacteriophages have been shown to transfer antibiotic resistance to laboratory chosen bacteria within the chicken gut. This is an important observation. A study should take place where the role of antibiotic resistant Salmonella is examined in the transfer of resistance to natural non-Salmonella bacteria within the chicken gut.

Bacteriophages have been shown to influence phage type within the chicken gut, as phage typing is still a widely used methodology for organism tracing it is recommended that further study be undertaken to investigate phage type conversion and the influence of in vivo conditions on other typing methodologies such as MLVA.

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Project Title The Workboot Series - The story of chicken in Australia

RIRDC Project No.:

PRJ-000753

Start Date: 1/07/2005 Finish Date: 31/05/2008 Researcher: Catriona Nicholls Organisation: Kondinin Group Incorporated Phone: (03) 6374 2300 Fax: (03) 6374 2387 Email: [email protected]

Objectives • To raise awareness of the nutritional value of chicken meat and the importance of the Australian poultry industry, particularly among children, by gathering accurate and up-to-date information about the Australian chicken meat industry, from producer to consumer, and presenting the information as a high-quality educational book which will be marketed nationally.

Background The future profitability of the Australian chicken meat industry depends on improved marketing and education. This project addresses the lack of well-developed and presented educational materials about the Australian chicken meat industry for primary and secondary school-aged children and their teachers and families through the production of a Workboot Series — The Story of Chicken in Australia book.

There is currently limited relevant information available to students and teachers on modern Australian primary industries. The result is low awareness levels about where basic foods come from, as evidenced by Kondinin Group's National Schools Survey.

Kondinin Group Limited is a not-for-profit, independent agricultural research and publishing organisation. The Workboot Series has been developed by Kondinin Group to promote primary industries to tomorrow's consumers. The Series is a high-quality, well-utilised educational resource series encompassing books, teacher resource kits and CD-Roms. To date there are 13 titles in the Series.

A Workboot Series — The Story of chicken in Australia book will be of benefit to all involved in the Australian chicken meat industry by educating consumers from an early age about the production processes and the nutritional benefits of chicken. The Workboot Series — The Story of Chicken in Australia book will address the lack of suitable educational resources available for primary and secondary school age children and their teachers.

Research This book follows the well-regarded and established format of the Workboot Series, with accurate, detailed and lively text and full-colour photographs, illustrators of the Series character, Blunnie the Workboot, graphs charts, diagrams flowcharts, activities, a glossary and index.

In the development of the book, Kondinin Group sourced information about the chicken meat industry from across Australia to produce an initial draft. The draft text was distributed to a wide range of industry and educational specialists to ensure accuracy, suitability and balance and depth of content. Kondinin Group worked with RIRDC for the final

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editing with reference to industry and educational changes. Photographs and diagrams were sourced form industry to ensure technical excellence, relevance to the text and to engage readers.

Outcomes Production of a 68-page hardcover educational Workboot Series book on Australia's chicken meat industry, which meets the educational standards and requirements of children in the 10-13 year-old age group.

Other outcomes include:

Increased awareness of the Australian chicken meat industry by school-aged children, their teachers and parents, increased understanding of the nutritional value of chicken meat, a greater understanding of the production processes involved with the chicken meat industry increased opportunity for teachers to use primary industries, in particular poultry, as a classroom theme through quality teaching resources.

Implications It is hoped that use of this book will result in increased awareness of the meat chicken industry.

Publications The Workboot Series — the Story of Chicken in Australia.

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Project Title QA Workshops – Pre-Workshop Microorganism Surveys

RIRDC Project No.:

PRJ-002966

Start Date: 21/04/2008 Finish Date: 29/01/2009 Researcher: Dr Narelle Fegan Organisation: Food Science Australia Phone: (03) 9731 3284 Fax: (03) 9731 3322 Email: [email protected]

Objectives • To test and report on the incidence and levels of Salmonella and Campylobacter, and TVC, on whole chicken carcasses submitted by chicken processing plants across Australia.

Background The RIRDC Chicken Meat Program has run two Pathogen Reduction workshops aimed at helping industry to improve pathogen control in primary processing plants.

The workshops sought to engage companies in an industry driven commitment to improve the microbiological status of the finished chicken meat product and provided information which will help them to achieve this outcome.

Research TVC and the levels of Salmonella and Campylobacter were determined on chicken carcases after spin or air chill from 24 chicken processing plants. Each plant collected 5 chilled chickens on 2 separate days for analysis of TVC and Campylobacter. Each plant also collected 10 whole chickens, 1 per day (stored frozen) for analysis of Salmonella. Each plant has been informed of their individual results.

Outcomes All participating plants can assess where the microbiological status of their individual processing plants sits in comparison to other plants. This study has fed into the Pathogen reduction Workshops held in Brisbane and Melbourne.

Implications This study and others FSA-9A (2007) and FSA-3A (2005) provide a solid baseline for the industry to demonstrate future improvements.

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Sustainable Production Environment

Project Title Evaluating risks posed by pathogen emissions from meat chicken sheds

RIRDC Project No.:

PRJ-000591

Start Date: 01/01/04 Finish Date: 31/12/06 Researcher: Dr Pat Blackall Organisation: Department of Primary Industries and Fisheries (Qld)

Animal Research Institute Locked Mail Bag No 4 MOOROOKA QLD 4105


Objectives • To quantify emission rates for pathogenic bacteria (Salmonella species, Escherichia coli, Campylobacter jejuni/coli, Staphylococcus) from typical tunnel ventilated meat chicken sheds.

• To evaluate the potential for human health effects caused by these emissions, evaluated by combining measured emissions, gaussian air dispersion models, bacterial survival models and applying quantitative risk assessment methodology.

Background Pathogen and dust emissions in exhaust plumes from meat chicken sheds and the consequential potential for disease and disease transmission to humans are increasingly raised as issues of concern when considering the sustainability and impact of the chicken meat industry. While it is commonly known that bacteria and dust particles are present in the exhaust air from these facilities, the potential for human health effects does not necessarily follow. The absence of valid data collected from Australian meat chicken production facilities has made it a very difficult task for the industry to demonstrate to the public and to regulators that, on a continuing basis, sustainable practices are being pursued by the industry.

Research Pathogenic bacteria – specifically Salmonella and Campylobacter – were measured in the air inside and outside sheds on four meat chicken farms. The project also looked for bacteria that could be regarded as indicators of the effect of shed emissions at distances from the shed. These trials on an “indicator” organism were performed on three meat chicken farms. Dust emission studies were performed on two meat chicken farms. The work was performed using methodologies validated in a preliminary field study.

Outcomes Salmonella was only rarely detected, and then at low levels, in the external air. Campylobacter was never detected in the external environment of the shed. The low levels of Salmonella and absence of Campylobacter indicate that there are no significant issues in terms of infection due to these organisms to humans exposed to aerosols from meat chicken sheds. A group of harmless, non-pathogenic bacteria – the


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staphylococci bacteria – that can be used as indicators of the impact of the chicken sheds on the surrounding environment were identified. These indicator organisms could be detected at levels above background for up to distances of 400 metres from the shed during the meat chicken production cycle.

The highest particle emissions were consistently detected not for the oldest birds but for the ones of 4-5 weeks of age. The majority of particle mass emitted was larger than 2.5 µm and in the range from 10-2.5 µm. We have found that before the first thinning the sheds emit around 7.6 grams of dust (smaller than 10 µm) per hour for every 500 kg of bird mass, while that number drops down to 2.8 grams after the first thinning.

Implications This work has shown that there are bacteria that are associated with poultry production and that the levels of these bacteria which can be relatively easily monitored. This work has also shown that potentially pathogenic bacteria can either only be detected rarely (Salmonella) or appear absent (Campylobacter) in the air immediately outside the meat chicken sheds. The levels of Salmonella, when present, are low and do not pose a realistic health risk to neighbours. The work has found that the levels of air-borne pathogens are linked to the levels of these organisms in the litter inside the shed. Hence, management practices that are designed to reduce the levels of food-borne pathogens in the litter will also reduce the already low levels of these organisms in the air external to the shed.

In the dust component of the work, it was shown that the maximum particle emissions per shed were not observed at the oldest bird age but at the age of bird before the first thinning when the density of birds is highest. This was valid even when the results were presented per kg of bird mass.

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Project Title Monitoring mechanical ventilation rates in poultry buildings for application of odour/dust control technologies

RIRDC Project No.:

PRJ-000599

Start Date: 1/07/2006 Finish Date: 31/05/2008 Researcher: Mr Mark Dunlop Organisation: Queensland Department of Primary Industries and


Objectives • To quantify daily, seasonal and batch-age trends in ventilation rates for mechanically ventilated meat chicken sheds in a range of climatic zones along eastern Australia.

Background The meat chicken industry is under pressure to reduce odour emissions from the production sheds. Add-on technologies to control emissions are being developed to reduce impacts. It may be possible to optimise these technologies to match ventilation requirements during critical times when impacts are most likely. Mechanical ventilation in poultry buildings is automatically controlled to maintain a suitable environment for the chickens. There is currently a lack of information regarding the ventilation requirements in meat chicken sheds. This information needs to be collected to assist with optimising the designs of add-on technologies. This optimisation may reduce the size, running costs and maintenance of such systems.

Research Five meat chicken farms in different climatic regions were selected. Monitoring stations were established at each site to collect fan activity and environmental data. Data was processed to identify climatic, seasonal, diurnal and batch age trends in ventilation rates.

Outcomes Ventilation rate was found to be highly dependent on ambient temperatures (varying seasonally and diurnally) and batch age (including chicken live mass). Fan activity decreased at night time and during periods of cooler weather. This result was not unexpected, however the data demonstrated that reduced fan activity occurred for the vast majority of these times when atmospheric dispersion of odours is reduced. Consequently, control of odour impacts, at these critical times, with an add-on technology need only be undertaken at this reduced level of fan activity.

Implications Producers considering the use of an add-on technology to relieve intermittent periods of odour nuisance will be able to work out the level of expected fan activity at those critical times. They will then be able to design the technology to suit the ventilation rate at that level of fan activity, rather than simply the maximum ventilation rate. This approach may make the adoption of add-on technologies more viable, while still improving environmental performance outcomes.

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Project Title Evaluation of "add-on" technologies for control of odour and dust from chicken sheds

RIRDC Project No.:

PRJ-000600

Start Date: 01/09/06 Finish Date: 30/08/07 Researcher: Mr Mark Dunlop Organisation: Department of Primary Industries and Fisheries (Qld)

PO Box 102 TOOWOOMBA QLD 4350


Objectives • To identify potential add-on technologies for air quality improvement based on scientific and practical validity as well as cost-benefit performance.

• To define the benefits and short-comings of the selected technologies in terms of costs, production performance, environmental performance, amenity factors and workplace health and safety.

• To develop a guide for producers, integrators and regulators defining benefits/limitations of these technologies.

• To develop a spreadsheet/model to assist producers and regulators to calculate the required size for the selected add-on technologies and assist in estimation of costs.

Background There is increasing pressure from regulators and the community to reduce the emission of odour, dust and other gaseous pollutants from meat chicken production facilities. Some producers are considering applying odour and dust control strategies in response to regulation pressure and community concerns. Lack of reliable information regarding the performance, costs and operational requirements for these technologies is hindering this process. Deliverables from this project will provide information to assist in the decision making process for applying odour and dust reducing technologies to meat chicken farms.

Research A review was undertaken to investigate odour reducing technologies/methods appropriate for application to the meat chicken industries. This has built on previous reviews, detailing new options and updating details of existing technologies, especially in relation to costs & compatibility with meat chicken production in Australia. Factors influencing the performance and size of these technologies were assessed. Some of the technologies included in this review were: dry dust filtration; wet wall scrubbing; odour neutralising agents; spray/fogging systems; electrostatic particulate ionisation; dust control structures and litter aeration.

Outcomes A significant amount of information has been collated regarding a selection of add on technologies. Cost analyses have shown that for the technologies included in this report, costs ranged from 0.4 cents per bird to 9 cents per bird (based on 10 year lifespan). Affordability, cost effectiveness and suitability of each technology will be different for each farming operation, and will be influenced by many factors, especially

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external pressures to control odour and dust emissions. For some of the technologies, it would not be possible to treat all of the exhaust air due to practical, physical or costs limitations. In these cases, treating a percentage of this air may be sufficient to provide adequate odour or dust control while improving affordability. Before deciding to install an add-on technology, producers first need to consider their own circumstances, thoroughly understand exactly why odour or dust nuisance is occurring and ensure that all measures have been taken to control these odours. If an add-on technology is required, producers should choose one that is affordable and has a proven track record.

Implications A number of odour and dust control technologies have been identified as compatible for installation in broiler sheds. However, odour and dust control performance, especially under Australia conditions, has not been demonstrated for many of these. Also, affordability of these technologies has not been clearly defined for Australian operating conditions. Consequently, it is difficult to recommend which, if any, of these technologies are the most suitable and affordable for Australian meat chicken producers. Future consultation with industry, technology suppliers and regulators will be required to identify which technologies should undergo further testing and evaluation.

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Project Title National Poultry Litter Project - Plan for Stage 1: Initiation Phase

RIRDC Project No.:

PRJ-000882

Start Date: 2/07/2007 Finish Date: 22/11/2007 Researcher: Dr Chris Dorahy Organisation: New South Wales Department of Primary Industries Phone: (03) 5579 8519 Fax: (03) 5579 8519 Email: [email protected]

Objectives • To identify and address blockages/impediments that prevent or limit the use of litter as fertilizer by potential end-users, and

• To determine and promote the value of litter as fertilizer. Background The Australian Chicken Meat industry produces around 1.6 million m3

of litter each year presenting challenges with respect to sourcing the input material and managing the spent litter. Consequently, the industry has established priorities for:1) identifying and addressing blockages/ impediments that prevent or limit the use of litter (as fertiliser) by potential end-users; and 2) determining and promoting the value of litter as fertiliser.

The Rural Industries Research and Development Corporation (RIRDC) Chicken Meat Program has expressed interest in funding an integrated national program of research (National Poultry Litter Project) for delivering upon these priorities. As the first step in this process (Stage 1), RIRDC engaged Dr Chris Dorahy, from the NSW DPI’s Centre for Recycled Organics in Agriculture to consult with and engage industry stakeholders via a series of meetings, discussions and a workshop, to develop the integrated research program.

Research The objectives of Stage 1 were achieved by undertaking the following activities:

• Searching relevant databases to document relevant poultry litter research being undertaken in Australia (1).

• Liaising with potentially interested parties who may have a role to play in the development of the program (2).

• Organising and co-ordinating a workshop of interested collaborators to initiate the development of a coordinated program of activities / research directed towards the above goal (2).

• Identifying appropriate suppliers of research to deliver upon the program of activities or research that is identified through the workshop (2).

• Co-ordinating the preparation of project proposals in specific areas identified through the above processes (2).

• Establishing realistic milestones for the overall Project and its constituent individual projects (2).

• Identifying a RIRDC/industry Steering Committee which will provide input and oversight of the overall Project following its initiation (2).

• Reporting to the R&D Manager and the R&D Advisory Committee

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of the Chicken Meat Program on the outcomes of the above activities (3).

• Presenting to the R&D Manager and the R&D Advisory Committee of the Chicken Meat Program the overall program of research that has been developed for its consideration (4).

• Delivering the integrated project proposal for Stage 2 in the form of a written report at the time of the presentation to the RIRDC Project Manager and Advisory Committee (4).

Outcomes The key outputs arising from Stage 1 of the National Poultry Litter Workshop were:

• Scoping study cataloguing existing poultry litter research in Australia.

• Strategic Planning workshop: Dorahy, C. (Facilitator) National Poultry Litter Workshop, Rural Industries Research and Development Corporation, Toowoomba, Qld, 11-12 October, 2007.

• Presentation: Dorahy, C.G. (2007) National Poultry Litter Project (Phase 1). Project No. DAN-256A. R&D Advisory Committee for the Chicken Meat Program, Rural Industries Research and Development Corporation, North Sydney, NSW, 12 November, 2007.

• Final report: Dorahy, C.G. (2007) National Poultry Litter Project (Phase 1). Project No. DAN-256A. Internal report prepared for the R&D Advisory Committee for the Chicken Meat Program, Rural Industries Research and Development Corporation, Canberra, ACT.

The principal outcome arising from Stage 1 of the National Poultry Litter Project was the delivery of an integrated research strategy for achieving the stated industry goals of: 1) identifying and addressing blockages/ impediments that prevent or limit the use of litter (as fertiliser) by potential end-users; and 2) determining and promoting the value of litter as fertiliser.

The components of the strategy are:

• A literature review to document what is known about poultry litter and identify knowledge gaps.

• Market research to define the market for poultry litter and investigate why end users do or don’t use poultry litter.

• Commissioned R&D to concentrate efforts on filling knowledge gaps on key product attributes and markets.

• A communications Plan to develop clear and consistent messages about poultry litter and deliver the messages to key influencers in the way they want to receive them.

Preliminary project proposals have been developed via Expressions of Interest around these components and the budget for implementing the program is estimated to be in the order of $580,000 (excl. GST) over 2.5 years.

Implications Implementing this strategy (Stage 2) will enable the industry goals to be achieved in a cost-effective and targeted manner. However, this will require clear communication, coordination and collaboration throughout the value chain. Subject to the R&D Advisory Committee’s endorsement of the proposed strategy, the integrated research program will be initiated in a staged manner, beginning early 2008.

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Project Title NTL Poultry Litter PROJ - Literature Review, Market Study and Project

RIRDC Project No.:

PRJ-002752

Start Date: 1/02/2008 Finish Date: 30/06/2008 Researcher: Dr Chris Dorahy Organisation: Ableblue Pty Ltd Phone: (03) 5579 8519 Fax: (03) 5579 8519 Email: [email protected] Objectives • To conduct a literature review that:

1. Pulls together all currently available information on the nutrient (and other) value of litter for fertilizer

2. Identifies gaps in knowledge that need to be addressed to enable the complete definition of the value of litter as fertilizer

3. Recommends what (if any) further research is needed to address these gaps.

4. Informs subsequent research required to complete the definition of the ‘fertiliser value’ of poultry litter.

• To undertake a market study to: 1. Understand both the supply and demand market metrics and

drivers by estimating the trends in each of these markets over the next five to ten years; and the implications this has for poultry litter i.e. Supply - for the chicken meat industry define the quantities and locations where poultry litter is/ will be produced over the next 5-10 years and identify the key factors driving changes. Demand – what are the current and potential markets and drivers behind these markets?

2. Understand (in the targeted markets for poultry litter products) which attributes are important to growers/farmers when they purchase chicken litter as a fertiliser, and the respective value they place on each of these attributes.

3. Identify the perceived blockages and risks surrounding poultry litter as a fertiliser and what needs to be done to overcome them.

4. Understanding the above information and focusing on key products and markets will enable the chicken meat industry / RIRDC to effectively target its research and development efforts to optimise the value of poultry litter products. It will also enable us to understand what product information end users are looking for the concerns growers currently have and from these key messages for each target market can be developed to inform the communications plan. Likewise, the outcomes could then be used by the chicken meat industry to develop new business models for making poultry litter cost positive, rather than cost negative or neutral.

Background The Australian Chicken Meat industry produces around 1.74 million m3 of litter each year, presenting challenges with respect to sourcing the input material and managing the spent litter. Consequently, the industry has established priorities for:

1. Identifying and addressing blockages/ impediments that prevent or

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limit the use of litter (as fertiliser) by potential end-users.

2. Determining and promoting the value of litter as fertiliser.

This research is the first component of a nationally integrated project aimed at meeting these industry goals.

Research The market research had two components: market metrics and product metrics. The market metrics involved investigating the physical aspects of the market, such as how much litter is produced and where it ends up, as well as defining the poultry litter supply chain and price structures of the current market.

The product metrics component involved interviewing existing, former and potential users of poultry litter to improve understanding of how they value poultry litter and identify the key challenges, which prevent or limit their use of litter as a fertiliser.

The literature review summarised existing knowledge on the use of poultry litter as a fertiliser from an end-users perspective to identify knowledge gaps and determine whether these gaps were significant enough to block the decision making process and prevent adoption. It also examined the value of poultry litter from a technical perspective and examined some approaches for assigning an economic value to poultry litter.

Outcomes The key blockages to adopting poultry litter as a fertiliser by end-users have been identified as:

• Needing to demonstrate the value proposition to potential end-users • Difficulties associated with storing, handling and applying litter • Odour and dust • A perceived lack of information on what is in poultry litter and its

performance benefits.

The key findings in relation to understanding and promoting the value of poultry litter as a fertiliser are that:

• Poultry litter is undervalued in the market place, possibly due to challenges associated with storing, handling and applying litter and uncertainty about product quality and performance.

• End users value the benefits poultry litter provides on soil organic matter/carbon; its cost-effectiveness; and its benefits on crop growth and or yield, above other attributes.

• Based upon these attributes poultry litter is well placed to address soil structural degradation, which is a common constraint identified by potential end users.

• There is significant potential value in poultry litter, with the key drivers for realising this value relating to understanding end-users cross price elasticity of demand for poultry litter.

• The extent to which the Chicken Meat Industry is able to realise this potential value is dependent on its preference to adopt a supply chain or value chain approach.

Implications This report has implications for all stakeholders involved in the poultry litter supply chain, as it is the first step in achieving the industry goal of improving the resource value of poultry litter as a fertiliser.

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Other

Project Title Nutritional Value of Australian Chicken Meat

RIRDC Project No.:

PRJ-001502

Start Date: 1/07/2007 Finish Date: 30/11/2007 Researcher: Prof Linda Tapsell Organisation: University of Wollongong Phone: (02) 4221 3152 Email: [email protected] Objectives • To undertake a review (and reanalysis where necessary) of the

available data from Australia on the nutritional value of Australian chicken meat.

• Where Australian data is deficient, to review, compare and include relevant overseas data which may assist industry to define the nutrient profile of chicken meat in the absence of solid local data.

• To compare nutrient data available for the Ross and Cobb strains of chicken.

• To compare Australian chicken meat data for equivalent cuts (e.g. high value, trimmed cuts such as fillets and breast meat) of beef, lamb, pork and fish.

• To provide recommendations for where additional data is required. • To prepare a significant report, for publication as an RIRDC report,

which presents all the review and nutrient information for the composition analyses for Australia. The report will also include recommendations for additional analytical work that is required and the methodologies recommended.

• To prepare and submit for publication a manuscript based on the work undertaken in a suitable, peer reviewed journal.

Background Australian food composition for chicken meat is quite outdated. RIRDC have previously commissioned analytical work which requires further interpretation and may be used in updating food composition databases. This project utilised this data to produce nutrient composition information for Australian chicken meat.

Research 1. Gaps in the AGAL data were identified. 2. Comparisons were made between the AGAL data and that of the other countries. 3. Mean imputation analyses were conducted if the data was within 10% of the AGAL data and data was ‘borrowed’ from other countries if only one comparable dataset was found. 4. The final data set was compared with high value cuts for beef, lamb, pork and fish.

Outcomes Results showed large differences in values for chicken cuts from Europe and Australia. Each cut needed to be individually compared due to the variability in total fat values. The greatest difference was in available fatty acid data and the range of nutrients listed. Imputation analysis was required for data on the majority of fatty acids, all amino acids and 23 vitamin and mineral categories. Lean breast of chicken also provided

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relatively more Selenium (>25%) than beef, lamb and pork, and more Manganese (>90%) than lamb (data on others not available). Lean fillet of chicken also provided relatively more vitamin E (a tocopherol) than lamb and beef (>40%).

Implications The work of this project addresses the importance of up-to-date food composition data for chicken meat in Australia and identifies the need for standardised food composition information on a worldwide scale.

Publications Probst, Y. Large variability of nutrient data around the world supports the need for standardised food composition information. In preparation for: Journal of Food Composition and Analysis.

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RESEARCH IN PROGRESS

Efficiency of Production

Project Title Trialling natural agents for control of darkling beetles

RIRDC Project No.:

PRJ-000097

Start Date: 1/07/2007 Finish Date: 31/08/2009 Researcher: Mr Trevor Lambkin Organisation: Queensland Department of Primary Industries and Fisheries Phone: (07) 3362 9606 Fax: (07) 3362 9429 Email: [email protected]

Objectives • To undertake laboratory assays to determine the best application regime for using entomopathogenic fungi and nematodes in broiler houses.

• To undertake small field trials to measure fungal and nematode efficacy in reducing darkling beetle populations in broiler houses.

Current Progress Laboratory testing of entomopathogenic fungi and nematodes as biological control agents for Alphitobius diaperinus is nearing completion. The results of fungal assays using Metarhizium anisopliae showed that treating earth floors (90% reduction of larvae at 9.6g of spore/m2 suspension) was as effective as treating litter. This was also the case for nematodes using Steinernema carpocapsae.

Because it is the most practical application method, both agents will be applied to broiler house floors in upcoming field trials. Laboratory fungal assays are continuing, investigating effects of disinfectants on fungal infectivity.

APVMA approval for field-testing of fungi is being finalised. Laboratory testing of nematodes also indicates that nematodes are susceptible to disinfectant exposure with formaldehyde being the most destructive. In addition, the research indicated that nematodes should be applied in relatively large volumes of water to ensure maximum survival and effectiveness. In the upcoming nematode field trial (June 2008), a proof of concept dose rate of 3.875 x 106 nematodes/m2 will be applied in 1000 ml of water/m2 of earth floor. Applications will be only under feed supply lines in 1 and 2 m strips and after disinfectant has dried. The broiler houses will be on a single farm at Gatton in southeast Queensland.

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Project Title Postgraduate scholarship - David Stephenson: Delivery of therapeutic proteins using lactobacillus

RIRDC Project No.:

PRJ-000573

Start Date: 01/04/06 Finish Date: 31/05/09 Researcher: Mr David Stephenson Organisation: Australian National University

School of Biochemistry and Molecular Biology CANBERRA ACT 0200

Phone: (02) 6125 7632 Fax: (02) 6125 0313 Email: [email protected] Objectives To deliver therapeutic proteins targeting Clostridium perfringens to the

gastrointestinal tract of chickens using strains of Lactobacillus, by (a) isolating and characterising a large number of Lactobacillus strains from the chicken gastrointestinal tract; (b) identifying persistent strains by tracking marked strains in chickens; (c) genetically engineering persistent strains to produce antimicrobial peptides and other potentially therapeutic proteins; and (d) testing the performance of these engineered strains in animal disease models.

Current Progress By sampling chickens from a variety of different sources we have acquired a collection of approximately 3000 local Lactobacillus isolates. Strains collected from commercial and research sources were tested for persistence in a chicken trial which identified 26 isolates of interest. These isolates have been recently retested in a second trial, the results of which are currently being analysed. A number of high throughput analytical tools have been developed to identify and track isolates during this work. These tools are currently being used to identify a few highly persistent candidate delivery strains, and have wider applications in the study of the ecology of lactobacilli in the chicken gut. Candidate strains will be modified to deliver antimicrobial proteins against C. perfringens. To this end, recombinant plasmids have been designed to produce the antimicrobial protein using various combinations of Lactobacillus expression and secretion signals. Optimal delivery strain-plasmid combinations will be determined. We will then move on to test the strains antimicrobial efficiency against C. perfringens in vitro.

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Project Title Physiological & nutritional approaches to alleviate heat stress

RIRDC Project No.:

PRJ-000264

Start Date: 1/05/2007 Finish Date: 30/04/2010 Researcher: Dr Jeff Downing Organisation: The University of Sydney Phone: (02) 9036 7748 Email: [email protected]

Objectives • To develop practical management strategies that can be easily applied in commercial sheds to improve broiler performance and thermo-tolerance under summer conditions, particularly prior to marketing, as the susceptibility to heat stress increases with age.

Current Progress For the study into heat conditioning in broilers, the objective was to investigate the effect of early thermal conditioning on broiler performance and thermo-tolerance when exposed to a thermal challenge at week 5-6 of age. Two strains (Cobb and Ross) of broilers were divided into seven treatments as follows; control, thermally conditioned at day 1, 3 or 5 of age using two different temperatures 36-37 or 38-39°C for 6 hours. For Ross birds, thermal conditioning did not significantly affect body weight, daily gain, feed intake and feed conversion ratio through the trial except in the first week, where lower daily gains and feed intakes were observed in thermally conditioned birds. Birds that were thermally conditioned had significantly lower body temperature at 36 days of age, lower plasma T3 concentrations and H/L ratios at day 42. Mortality rate during week 6 tended to be lower in thermally conditioned birds compared to the control birds. Birds thermally conditioned at 3 days of age had the lowest mortality rate and while not significant also the highest body weights. Taken together the results suggest that thermal manipulation at three days of age could provide some protection against high temperature later in life when broilers are more susceptible to heat stress.

For Cobb birds, thermal conditioning provided no advantage to growth performance during week 6. There were no differences in the physiological measures (body temperature, T3 concentration and H/L ratios) at day 42. The data suggest that for Cobb birds’ thermal conditioning for 6 hours early in life is not sufficient for thermotolerance acquisition.

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Project Title: Subunit vaccine against infectious bursal disease virus

RIRDC Project No.:

PRJ-000266

Start Date: 1/07/2007 Finish Date: 30/09/2010 Researcher: Dr Sandra Sapats Organisation: CSIRO Livestock Industries



Objectives • To develop a subunit vaccine against infectious bursal disease virus using a bacterial delivery system based upon Lactobacillus.

Current Progress The development of an oral vaccine for poultry against IBDV was initiated using an E. coli delivery system. Expression cassettes were constructed encoding three different regions of the IBDV genome, including the entire A segment of IBDV (encoding viral proteins VP2, VP3 and VP4) as well as smaller fragments encompassing either the mature VP2 protein or larger precursor VP2 protein known as VPX. Constructs were cloned under the control of two different promoters utilizing either the lambda constitutive promoter for continual high level expression in the chicken gut or the cytomegalovirus immediate early promoter for a DNA vaccination approach.

In an attempt to improve the efficacy of the IBDV vaccine, the incorporation of a chicken cytokine was also initiated. Chicken Il-6 was also cloned under the control of the lambda constitutive promoter and a signal sequence added to enable secretion of the protein. Western blot analysis indicated that the levels of Il-6 expressed were comparable to those obtained using an inducible promoter.

The persistence of two different E. coli vectors isolated in a previous RIRDC project (CSA-20A) were also tested in SPF birds and shown to be present in the chicken gut for up to 26 days confirming their suitability as vaccine delivery vectors.

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Project Title: Improvement of lupins and lathyrus for broilers and egg layers by enzyme treatment (managed by AECL)

RIRDC Project No.:

PRJ-000449

Start Date: 01/12/06 Finish Date: 31/07/08 Researcher: Dr Ian Williams Organisation: University of Western Australia

School of Animal Biology Faculty of Natural and Agricultural Sciences 35 Stirling Hwy CRAWLEY WA 6009


Objectives • To provide the poultry industries with suitable alternatives to animal proteins (eg. meatmeal) and imported soybean meal by improving the nutritive value of locally-grown legumes, lupins and lathyrus.

• To determine whether these legumes can be treated with enzymes that are not present in the digestive tract of birds to achieve a more extensive breakdown of pectin and therefore cell walls.

• To (i) increase the nutritive value of these feed ingredients by making more nutrients available to the bird for digestion; (ii) reduce water-holding capacity of digesta and hence wet droppings, (iii) reduce viscosity of digesta and allow a greater digestibility of released nutrients and, (iv) reduce excretion of nutrients into the environment.

Current Progress We have nearly completed the egg-layer experiment to determine the optimal dose of pectinases, polygalacturonase (PG) and pectin methyl esterase (PME). The main objective of this experiment was to break down completely the pectin in the cell walls of dehulled lupins by a combination of PG and PME. This breakdown should improve the nutritive value of dehulled lupins for egg layers and reduce wet droppings and soiled eggs associated with dehulled lupins, and to allow dehulled lupins to be incorporated into the diet to a level of 30%. Dehulled lupins were added into the diet at either 0, 10, 20 or 30%, treated with or without combination of PME and PG (200 and 2100 g/kg diet) and fed to egg layers for 10 weeks. The effectiveness of combination of PME and PG were tested by measuring feed and water intake, feed conversion ratio (feed : egg), digestibility of dry matter, apparent metabolisable energy of the diet, egg yield and quality (weight, Haugh units, shell weight and thickness, yolk colour and soiled eggs), viscosity of digesta in the intestine, wet droppings, cell-wall polysaccharides, and pectin.

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Project Title: Investigation of IBH outbreaks in Australian meat breeder/broiler flocks and establishment of an avian adenovirus typing facility and service

RIRDC Project No.:

PRJ-000610

Start Date: 01/08/06 Finish Date: 30/11/09 Researcher: Dr Amir H Noormohammadi Organisation: The University of Melbourne

School of Veterinary Science 250 Princes Highway WERRIBEE VIC 3030


Objectives • To establish the necessary diagnostic tools to allow avian adenoviruses (FAdV) to be isolated and typed in Australia.

• To use these tools to investigate outbreaks of inclusion body hepatitis (IBH) in Australian breeder and broiler flocks.

• To establish an avian adenovirus diagnostic facility and ongoing typing service for the Australian chicken industry.

Current Progress Set-up of the conventional immunological serotyping test for all FAdV reference strains is underway. Antisera against each FAdV serotype were raised in SPF birds injected with inactivated viruses and are now under examination for cross neutralisation with other serotypes. Despite the suspected weak antibody response of some birds, antisera for seven of the twelve FAdV reference serotypes have so far been specific in serum microneutralisation tests. The test set-up will be completed by the end of July.

Several field samples have been submitted from different broiler companies in different states and successfully typed using the FAdV PCR and HRM analysis test developed last year. In most cases, samples of bursa and thymus tissues have also been collected and will be tested for the presence of CAV and/or IBDV in future. All these cases were also examined by histopathology.

Several Australian FAV field isolates have been propagated in cell culture and their identities will be confirmed using the conventional immunological serotyping test, once the test set-up is complete.

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Project Title: Improved control measures for infectious bursal disease virus (IBDV)

RIRDC Project No.:

PRJ-000699

Start Date: 01/10/06 Finish Date: 30/09/09 Researcher: Dr Sandra Sapats Organisation: CSIRO Livestock Industries



Objectives • To continue monitoring genetic changes occurring in circulating infectious bursal disease virus (IBDV) field strains.

• To examine the pathogenicity of selected field isolates displaying unusual amino acids changes in SPF flocks.

• To apply the optimised reverse genetic system for IBDV to ascertain the importance of specific mutations within the VP2 gene related to virulence of endemic strains with a focus on understanding changes occurring in Australian strains.

Current Progress Monitoring genetic changes occurring in IBDV strains circulating throughout Australia revealed that 15/53 sites were positive for IBDV, including 3/12 from NSW, 3/21 from Victoria, 7/14 from Queensland and 2/3 from SA. All three sites from WA tested negative for IBDV. Sequence analysis revealed that most field strains were similar to strains isolated previously in each of the states, including classical like strains in NSW and Queensland and variants in Victoria and SA. For the second time, a Queensland isolate was identified bearing an amino acid substitution associated with vvIBDV (isoleucine 256). However, this Queensland isolate was isolated from a healthy flock of birds and we have previously demonstrated using genetically modified viruses that this amino acid substitution alone does not appear to alter the virulence of Australian strains. The pathogenicity of 9 IBDV strains bearing unusual amino acid changes was tested in SPF birds and tissues assessed by histopathology and quantitative real time PCR.

Although none of the strains induced any mortalities, four appeared to induce significantly greater changes in the bursa which correlated with increased viral loads as determined by real time PCR. Two variant strains isolated from Vic (12/07 and 03/06) appeared to be the most virulent followed by two strains from Queensland (27/06) and NSW (02/05). The unusual amino acid changes observed in these four strains are currently being incorporated into our reverse genetics system developed for IBDV to confirm their association with disease.

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Product Quality and Safety

Project Title: Differential typing of Campylobacter

RIRDC Project No.:

PRJ-000605

Start Date: 01/09/05 Finish Date: 31/08/08 Researcher: Ms Jillian Templeton Organisation: Department of Primary Industries and Fisheries Queensland (QDPI&F)

Animal Research Institute Locked Mail Bag No 4 MOOROOKA QLD 4105


Objectives • To establish the technique of single nucleotide polymorphism (SNP) analysis for typing of Campylobacter jejuni and Campylobacter coli.

• To extend the current Campylobacter collection to include poultry isolates from other research groups and industry and to obtain non-poultry isolates from sources such as diary cattle, pets and humans.

• To establish the SNP types of the extended Campylobacter collection.

• To compare and contrast the SNP types of the poultry C. jejuni with the non-poultry types (including human isolates from OzFood that have already been examined by SNP typing by the Queensland node of the CRC for Diagnostics).

• To compare and contrast the capacity of SNP typing with pulsed field gel electrophoresis (PFGE) and flaA typing.

• To establish an on-going typing technique that will function as a national reference service on a user pays basis.

Current Progress SNP typing has been on-going with a selection of C. jejuni isolates from Queensland chickens, feedlot cattle, dairy cattle, chicken factory samples and dog isolates being SNP typed. To date a total of 450 isolates have been SNP typed for the project.

Extension of the current DPI&F Campylobacter culture collection is continuing. We have received 42 pig isolates from interstate collaborators, 37 are C. coli, seven dog isolates and one cat isolate, all being C. jejuni. We are receiving isolates from a private veterinary microbiology laboratory in Queensland who are sampling unhealthy puppies/dogs. To date we have received five isolates, three are C. jejuni and two are C. coli.

A survey of Queensland feedlot cattle has continued over the past 12 months. Samples have been collected from four commercial feedlots in South-East Queensland on multiple sampling occasions. 115/220 samples were Campylobacter-positive, of which 106 are C. jejuni and nine are C. coli.

In addition we continue to expand our collection of isolates from

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Queensland meat chickens. During 2008 we are receiving isolates from the major chicken processors in South East Queensland.

A collaboration with the Queensland Health Department has been formed. Isolates collected from humans in South East Queensland during 2000 and 2008 will be included in our studies.

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Project Title: Investigation of the prevalence of chlamydiosis in the Australian chicken meat industry

RIRDC Project No.:

PRJ-000611

Start Date: 01/08/06 Finish Date: 31/07/09 Researcher: Dr Amir H Noormohammadi Organisation: The University of Melbourne

School of Veterinary Science 250 Princes Highway WERRIBEE VIC 3030


Objectives • To investigate the extent and prevalence of chlamydiosis in Australian poultry flocks.

• To determine the species of Chlamydia/Chlamydophila involved in clinical disease.

• To understand if the role of the pathogen is primary or secondary. • To develop a reliable and sensitive detection test for chlamydiosis in

poultry. Current Progress An rRNA PCR assay has been re-optimised for detection of a wide range

of Chlamydophila/Chlamydia species and is proven to be highly sensitive for field specimens. A real-time PCR assay followed by high resolution melt (HRM) curve analysis has been developed, identifying rRNA in a wide range of Chlamydophila/Chlamydia species from different animals. The HRM curve analysis distinguishes the reference species from one another and also determines the identity of the field species involved.

An important component of the project is to assess the diagnostic assays in suspected chlamydiosis outbreaks in poultry. There have been six suspected cases of chlamydiosis in commercial poultry in NSW since June 2007. Collaboration with researchers at the NSW Department of Primary Industries’ Elizabeth Macarthur Agricultural Institute (EMAI) has allowed samples of faeces and tissue from these cases to be obtained. These are being subjected to diagnostic tests.

Serological testing, including complement fixation test, commercial ELISA and Western blotting, is also being completed on sera from the six NSW cases, as well as on suspected positive chicken sera supplied by the University of Ghent.

A study to confirm Chlamydophila psittaci infection in SPF chickens and to produce definitive positive sample materials for diagnostic test validation has been planned. The isolate to be used in this infection study has been cultured from the liver of a backyard chicken.

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Project Title: Use of bacteriophage and phage products to control Campylobacter in chickens

RIRDC Project No.:

PRJ-000653

Start Date: 01/03/07 Finish Date: 28/02/10 Researcher: Prof Mary Barton Organisation: The University of South Australia

Sansom Institute School of Pharmacy and Medical Sciences GPO Box 2471 ADELAIDE SA 5001


Objectives • To investigate the potential for bacteriophage and bacteriophage products to reduce colonisation of chickens with Campylobacter jejuni.

Current Progress Sampling for the project has extended beyond the time originally thought necessary as we were unable to isolate bacteriophage from indoor birds, despite the birds still being Campylobacter positive. Checking with the Nottingham group revealed that they have experienced the same phenomenon over the last three years (although they have not indicated this in their publications). The extended sampling covered three processing plants (multiple visits), litter (three different producers), backyard chickens, treated sewage (four locations), five free-range egg farms, 1 free-range meat producer (two farms), and some sheep, dairy cattle, ferrets and ducks. Final sampling will re-test backyard chickens, plus cover some other species. Because of the unexpected failure to isolate bacteriophage from shedded chickens we have had to also isolate Campylobacter from a range of settings as well as bacteriophage.

We now have more than 200 Campylobacter isolates (including isolates from Pat Blackall’s laboratory) and 120 samples of bacteriophage. The identity of the field isolates of campylobacter are currently being identified using multiplex PCR and the bacteriophages purified and propagated to assess whether they are temperate or lytic. The lytic strains will be tested against the collected Campylobacter strains and the temperate strains kept for bacteriphage lysine isolation.

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Project Title: Smart State Fellowships Program – development of probiotic control measures to combat Campylobacter related food borne disease using glyco array technology

RIRDC Project No.:

PRJ-000696

Start Date: 01/02/07 Finish Date: 30/06/09 Researcher: Dr Christopher Day Organisation: Griffith University

Institute for Glycomics Microbial Glycobiology PMB 50 GOLD COAST MAIL CENTRE QLD 9726

Phone: (07) 55528189 Fax: (07) 5552-8908 Email: [email protected]

Objectives • To reduce the incidence of Campylobacter gastrointeritis in humans by developing a rapid and effective treatment for patients that have acquired the pathogen from poultry products or from other sources.

• To develop a means to reduce or eliminate C. jejuni from poultry. Current Progress A Glycan Array Facility has been established at the Institute for

Glycomics at Griffith University. The library for the printing of the glycan array consists of 116 sugar compounds, 20 amino acids and 10 cell-surface proteins and has been successfully printed. This is the first Glycan Array Facility to be established in Australia.

Campylobacter strains can be grouped based on how well and for how long they colonise chickens. Groups include strains that immediately colonise and remain present indefinitely (potent chicken colonisers) to strains that cannot colonise chickens. Array analysis of eight strains of C. jejuni identified a range of sugar structures (glycans) that are bound by Campylobacter, including glycans found on mucin and blood group antigens (glycans on the surface of blood cells that interact with the immune system). Strains that have been characterised as potent chicken colonising strains bound sialic acid residues. This is a novel finding suggesting that sialic acid binding is linked to chicken colonisation potential. As Campylobacter does not use sugars as a food source the observed interactions must be for adherence/colonisation purposes. These results indicate a number of lead structures that can potentially be used as universal inhibitors of Campylobacter infection and colonisation.

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Project Title: Early feeding of prebiotics on the development of the digestive system and gut microflora of broilers

RIRDC Project No.:

PRJ-000631

Researcher: Dr Paul Iji Start Date: 01/05/05 Finish Date: 31/07/08 Organisation: The University of New England

Animal Science School of Rural Science and Agriculture ARMIDALE NSW 2351


Objectives • To evaluate whether provision of low-molecular weight carbohydrates (oligomers of mannose, galactose, xylose or glucose) from hatch up to seven days of age will affect development of the digestive system, gut microflora and the immune function of broilers.

Current Progress To date, about seven experiments have been completed. The last experiment was conducted in April/May, 2008 and was semi-commercial in nature. A total of 1053 chicks were involved. The experiment was designed to test the benefit of access to a diet containing trehalose at 1 g/kg fed for 7, 14 or 21 days. Birds were given access to this diet within 8 hours of hatch or delayed access, fed upon receipt of a normal commercial batch from the hatchery. A negative control group was maintained on a diet without trehalose and placed in the pens more than 8 hours (approximately 36 hours) after hatching. Feed consumption and weight gain were assessed at 7, 14 and 21 days. There were 6 replicates per pen and there were about 25 birds per pen. Samples were taken on 21d and assessed for nutrient digestion and digestive enzyme function.

The initial differences in hatching weight of birds used in the semi-commercial trial confounded the results obtained. Birds that were given early access to feed were generally heavier at hatch than the batch that was received as delayed feeding. Differences were observed at subsequent evaluation but these generally disappeared once starting weight was included as a covariate. When duration of access to trehalose was compared within any batch rather than across hatching batches, there were no significant differences between the groups, suggesting that the supplement could be used for a shorter period in the diet, to achieve the same benefits observed in previous experiments.

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Project Title: Expansion and refinement of a molecular typing system for Salmonella

RIRDC Project No.:

PRJ-000751

Start Date: 01/07/06 Finish Date: 31/07/09 Researcher: Dr Michael Heuzenroeder Organisation: Institute of Medical and Veterinary Science

Infectious Diseases Laboratories PO Box 14 Rundle Mall PO ADELAIDE SA 5000


Objectives • To continue to make available to the industry a free (up to 6,000 tests per annum) and discreet conventional and where appropriate, molecular based, typing service.

• To further develop the bacteriophage-based molecular and MLVA typing systems developed in project IMV-5A and expand these typing systems into other serovars of interest to the chicken meat industry.

• To investigate improved turnaround times for MAPLT and MLVA systems by use of real time PCR, multiplexing and to determine the minimal number of primer sets required yielding maximum separation in the most isolates.

Current Progress From 1st July 2007 to 31st May 2008, we have received 5,141 cultures from the poultry industry for serotyping. Salmonella II Sofia, Salmonella Typhimurium and Salmonella Infantis continue to be the three most common serovars in broiler chickens. S. Muenster, mentioned as an emerging serovar in 2006-2007, has become established in broiler flocks (7.8% of broiler isolates in 2007, 1.0% in 2006, not seen in poultry previously). This serovar has also occurred more frequently in human infection in the past year than previously reported. There have also been increased numbers of Salmonella Montevideo in broilers (8.8% of isolates in 2007, 0.9% in 2006).

The MAPLT typing system has been extended to include Salmonella serovars Infantis and Enteritidis. As a comparison established methods such as MLVA and PFGE on 76 Salmonella Infantis isolates. It was shown that MAPLT could divide the isolates into 28 profiles whereas MLVA could only generate 9 profiles and PFGE 8 profiles.

Using Simpson’s Index of Diversity as a measure, MAPLT provided the greatest discrimination of Salmonella Infantis. Even upon simplifying the number of MAPLT primer sets to four, the level of discrimination by MAPLT was similar to PFGE but superior to MLVA.

Development of rapid methodologies for typing Salmonella incorporating the above techniques is continuing using both Salmonella Typhimurium and Salmonella Enteritidis. Both MAPLT and MLVA procedures have been simplified to a two tube method rather than the previous multi-tube methodology. Automated size and detection

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analysis with an eGene® capillary instrument for fast, sensitive and accurate throughput of samples is also being assessed. We have also participated in a national collaboration to develop a harmonious molecular typing scheme for Salmonella initially based upon MLVA.

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Sustainable Production Environment

Project Title High Value Products from Hatchery Waste

RIRDC Project No.:

PRJ-000078

Start Date: 1/07/07 Finish Date: 31/08/08 Researcher: Phil Glatz; Babu Santhanam Organisation: South Australian Research and Development Institute Phone: (08) 8303 7786 Fax: (08) 8303 7689 Email: [email protected]

Objectives • To conduct a survey of hatcheries in Australia to identify bottlenecks in the disposal of hatchery waste and to determine alternate methods of handling and processing that are currently being used.

• To undertake a literature review to establish hatchery waste processing methods that are economically viable, environmentally friendly, comply with regulatory issues and lead to development of useful by-products.

Current Progress The disposal of hatchery waste in Australia is a significant cost restricting growth and expansion of hatcheries in peri-urban regions.

A draft survey form was developed for completion by Australian hatchery managers. The survey included questions on hatchery size and performance. Questions on hatchery waste have been separated into two parts; one for solid waste and the other for wastewater. Details requested on solid waste include how much solid waste is produced weekly, how is the solid waste handled on site, how the solid waste is disposed and any waste treatment techniques used. Questions on wastewater include the volume of water used to clean the hatchery, how the wastewater is treated, if treated wastewater is recycled and how the wastewater is disposed. This survey also includes questions on the manager’s attitudes to waste management and any local environmental issues attributable to hatchery waste.

The literature review has provided information on hatchery waste composition, hatchery waste disposal methods and waste treatment techniques. Hatchery waste can be cooked, boiled, extruded and autoclaved. It also can be treated using lactic acid fermentation,an aerobic digestion to produce methane or by using enzyme or sodium hydroxide pre-treatment prior to fermentation. It can also be composted for 4-6 weeks to reach a stabilised material for use as an organic fertilizer.

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Project Title Piloting chicken litter usage in broadacre cropping: setting research directions

RIRDC Project No.:

PRJ-000226

Start Date: 01/03/07 Finish Date: 30/04/10 Researcher: Mr Tony Craddock Organisation: Rural Directions Pty Ltd Phone: (08) 8564 3300 Fax: (08) 8564 3300 Email: [email protected]

Objectives • To generate base information as to how chicken litter can be incorporated into modern broadacre cropping systems by quantifying crop and soil responses.

• To develop preliminary guidelines for using chicken litter as a nutrient source in broadacre cropping systems.

• To undertake an economic analysis so that costs associated with chicken litter use are understood.

• To gain a deeper understanding of product quality and variation. • To gain an insight into the potential for carryover of pathogens

affecting human health from litter into broadacre crops. • To develop recommendations as to key issues to be targeted for an

expanded field trial. Current Progress Three small plot field trial sites have been established at Freeling,

Mallala and Bowmans in South Australia’s lower-mid North cropping district. Two replicated trials were sown at each site. One investigates the interaction between application timing and the method of incorporation. The second is a rate of application trial comparing different chicken litter application rates to conventional fertilizer. All are tested using 4 different litter types, raw wood based, raw straw based, wood based composted, and wood based multi-batched.

The broadacre farming season in 2007 challenged many crops with the trials being no exception. The season was a major contributor to a low number of statistically significant results. However several trends are evident.

The type of fertilizer and rate of application significantly affected the yield and zinc levels of grain from all sites. Protein, grain size, kernel weight and the level of several macro and micro nutrients were significantly influenced at one or more sites.

Multiple sources of the previously mentioned litter types are currently being tested for their nutritional status. These samples will also be assessed for viable weed seeds.

300 samples of grain from litter treated and untreated plots are being tested for the presence of Salmonella, E. coli and Campylobacter to determine if there are any human health risks.

The 2008 soil sampling is complete, litter treatments have been applied and adequate soil moisture has allowed sowing of the appropriate crops at all sites.

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Additional support is provided by PIRSA, SA Manure Supplies, Poultry Manure Supplies, Nuleaf Organics and Peats Soils and Garden Supplies to fund the inclusion of composted litter in the trials.

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Project Title Avian influenza: improved diagnostics for detecting antibodies to H5N1

RIRDC Project No.:

PRJ-000251

Start Date: 1/07/2007 Finish Date: 30/09/2010 Researcher: Dr Sandra Sapats Organisation: CSIRO Livestock Industries Phone: (03) 5227 5770 Fax: (03) 5227 5377 Email: [email protected] Objectives • To develop a competition ELISA aimed at detecting antibodies

specifically against H5N1. Current Progress In order to develop reagents for a competition based ELISA aimed at

detecting exposure of commercial poultry to H5N1 strains of avian influenza, a recombinant chicken antibody library was initiated. Chickens were immunized against a Vietnamese H5N1 strain and the spleens harvested for the isolation of mRNA encoding antibody genes. Using PCR, genes encoding the antigen binding site of the antibody molecule were amplified and subsequently cloned producing a library containing approximately 7.2 x 107 different antibodies. Antibodies specific for H5N1 were subsequently selecting by panning the library against H5N1 virus coated onto a solid support. Individual antibody clones are currently being tested for their reactivity with the H5N1 virus in ELISA.

In order to express the Heamagglutanin (HA) and Neuraminidase (NA) proteins of a H5N1 strain for use in the same competition based ELISA described above, two different expression systems are being evaluated using either yeast (Pichia pastoris) or baculovirus. The PCR was used to amplify the complete HA and NA genes of a highly pathogenic Vietnamese strain of H5N1. At least 3 independent PCR products were cloned for each gene and a consensus sequence generated. Although it was possible to isolate a single clone containing the consensus sequence for the NA gene, the HA gene had to be genetically manipulated in order to generate a single clone baring the desired consensus sequence.

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Project Title Managing litter re-use for minimal nutrient runoff to surface water

RIRDC Project No.:

PRJ-000596

Start Date: 23/08/2004 Finish Date: 31/12/2008 Researcher: Jarl Devereux Organisation: Queensland Department of Primary Industries and Fisheries Phone: (07) 4688 1096 Fax: (07) 4688 1192 Email: [email protected] Objectives To establish accurate estimates of the contributions of applied meat

chicken litter to catchment nutrient loads at case study farms under conditions of appropriate management, helping to ensure that a realistic representation of this form of nutrient re-cycling is available for local government planners and regulators.

To establish effective management techniques, likely nutrient load outcomes, and costs through application of existing state-of-the-art modelling techniques to case study litter re-use enterprises in sensitive locations.

To extend effective management practices to litter end-users and industry, and provide updates to the National Chicken Industry Environmental Management System.

Current Progress Following the initial hydrological calibration of GLEAMS, the nutrient export was investigated to see if predictions could be improved. It became apparent that during periods where the litter was applied to the soil surface with no incorporation, the model could not account for observed increases in the dissolved reactive phosphorous (DRP) in the runoff. For these periods we are testing a recently developed model for phosphorous loss in runoff from surface applied litters. Initial testing of this model has been promising with the model displaying a good correlation between measured and observed DRP in runoff (y = 1.1177 x - 0.7399, R2 = 0.7472). This model slightly under predicts total DPR losses at 2.2 kg/ha compared to 2.4 kg/ha during the period investigated. Runoff flumes were recently installed at the three study sites to collect further runoff data. This was initiated to provide a second independent data set to assist calibrating GLEAMS and enable further modelling to progress. Over 4 runoff events have been captured at the main study site with the other sites having recorded 2 to 4 events during the period Jan 08 - May 08. Further work investigating ways of reducing phosphorous and nitrogen is underway. A phosphorus management product will be tested for its ability to reduce phosphorous concentrations in runoff. The ability of this product to remove P from solutions is being tested in the laboratory to establish likely removal rates and suitable application rates in the field. However the management solutions have not been finalised at this point.

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Project Title Verification of separation distance methods for meat chicken farms

RIRDC Project No.:

PRJ-002747

Start Date: 10/03/2008 Finish Date: 31/03/2009 Researcher: Mark Dunlop Organisation: Queensland Department of Primary Industries and Fisheries Phone: (07) 4688 1280 Fax: (07) 4688 1192 Email: [email protected]

Objectives • To monitor the temperature of air exhausted from a poultry shed in order to assess temperature gradients with the outside air. This monitoring will also demonstrate how the air temperature changes when poultry exhaust mixes with ambient air. Results from this monitoring program will be used to check the assumptions within CFD and Calpuff models.

• To use computational fluid dynamics (CFD) modelling to demonstrate that Calpuff accurately simulates the emission of odour emissions from tunnel ventilated meat chicken sheds. This will include a sensitivity analysis of emission temperature on plume movement and dispersion due to thermal buoyancy.

• To verify the ‘S-factor’ formula for calculating separation distances and buffer zones, as specified in the Draft best practice technical guide for the meat chicken industry in Queensland, 21 October 2005, using Calpuff.

Current Progress The project started in mid June 2008. A detailed list of modelling scenarios and expected outputs is being prepared. In addition a preliminary methodology has been prepared and additional detail and explanations about some components are being compiled. Temperature data collected in the RIRDC project PRJ-00599 ‘Monitoring mechanical ventilation rates’ (ambient and temperature exhaust air temperatures) was compiled and provided to the CFD modellers to enable them to accurately model the ‘real’ situation, and not use temperature estimates. Preparations are well underway to establish the temperature monitoring grid.

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Other

Project Title Nuffield Scholarship Award 2007 – Rob Kestel

RIRDC Project No.:

PRJ-002031

Start Date: 1/10/2007 Finish Date: 30/11/2009 Researcher: Jim Geltch Organisation: Nuffield Australia Phone: (03) 5480 0755 Fax: (03) 5480 0233 Email: [email protected]

Objectives • To build the capacity of the chicken meat sector to overcome the challenges of a global and internationally competitive environment through the provision of support for one Nuffield Farming Scholarship for a chicken meat farmer.

Current Progress Rob Kestel was selected on the 3rd September 2007 for a Nuffield Scholarship for a chicken meat grower.

He attended the Nuffield Australia Spring Tour in Fremantle and regional WA in early October 2007. The tour entailed a comprehensive briefing on the 3rd October for the 16 newly selected Scholars. The 4th, 6th and 7th October were spent travelling in the environs of Perth and regional WA visiting various primary production and agribusiness operations.

Friday 5th October, Rob attended Innovative Farming Australia where some of the 2006 Nuffield Scholars made their formal presentations of their study topics. Rob was formally presented with his Scholarship at a Gala Dinner held in Fremantle on the 5th October by Gary Sansom – a member of the RIRDC Chicken Meat Committee and President of the Queensland Farmers Federation. Rob attended the Nuffield Contemporary Scholars Conference in Melbourne and regional Victoria in February 2008. This conference bought together the 50 Nuffield Scholars who had been selected in the previous twelve months around the world. Rob was able to network with Scholars from United Kingdom, Ireland, Canada, New Zealand and Australia during the week that included top level briefings, visits to some of Victoria’s top farming operations culminating in listening to the remainder of the 2006 Scholars make their presentations at Moama on the 29th February.

This conference gives each of the Scholars an unprecedented opportunity to meet and develop relationships with like minded farmers from around the globe.

Rob then completed his Global Focus Program took him to California, Canada, Washington DC, Mexico, Brazil and the United Kingdom over a six week period.

He is currently completing a further ten weeks on his personal study tour, before making his formal presentation in Hobart in October 2008.

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OTHER SUPPORTED ACTIVITIES

SCHOLARSHIPS PRJ-000573 Postgraduate scholarship - David Stephenson: Delivery of therapeutic proteins using

Lactobacillus

COLLABORATIVE PROGRAMS

PRJ-000735 CRC for the Australian Poultry Industries funding

TRAVEL/CONFERENCE/WORKSHOPS

PRJ-001481 14th International Workshop on CHRO – Rotterdam September 2007 – Dr Margaret MacKenzie

PRJ-000907 14th International Workshop on CHRO – Rotterdam September 2007 – Mr Barry Shay

PRJ-003220 Pathogen Reduction Workshops

PRJ-002618 XXIII World's Poultry Congress – 29 June to 4 July 2008, Brisbane

PRJ-000849 51st Livestock Insect Workers' Conference – Kentucky USA – Mr Trevor Lambkin

RESEARCH TO BE SUPPORTED IN 2008/2009

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NEW RESEARCH TO BE SUPPORTED IN 2008/2009 Bird Nutrition and Feed Supply

Project Title Project No Principal Investigator Organisation Phone No

The biosecurity of mass poultry mortality composting PRJ-002325 Wilkinson, Kevin Dept Primary Industries (Vic) 03 8341 2412

Chicken Meat R&D Program Evaluation and Five Year R&D Plan 2010-2015 PRJ-003307 Clarke, Michael AgEconPlus Pty Ltd 02 9817 5888

Nutrient Composition of Chicken PRJ-002974 Arcot, Jayashree The University of New South Wales 02 9385 5360

Chicken Meat Usage and Attitude Survey PRJ-002977 Finn, Helen Colmar Brunton Research 02 8873 0804

Epidemiological understanding of prevalence of H6 & AI virus subtypes-waterfowl PRJ-002997 Arzey /NSW Dpt of Primary Industries 02 46406402

Methods to improve the nutritional value of sorghum for broilers PRJ-002967 Bryden, Wayne University of Queensland 07 5460 1250

Accurate, real-time description of available energy in cereal grains PRJ-002973 Hughes, Bob SARDI 08 8303 7788

Pop genetics, mixed species competition of Eimeria necatrix and E. tenella PRJ-002473 Morgan, Jessica Department of Primary Industries and Fisheries 07 336 29494

Life Cycle Analysis Case Studies – Chicken Meat PRJ-002963 McGahan, Eugene FSA Consulting 07 46328230

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RIRDC CHICKEN MEAT PUBLICATIONS

Publication Title Pub No. $

Chicken Litter: Issues associated with sourcing and use (2007, 72pgs) 07/035Web only

Chicken Meat Research in Progress 2006 (2005, 63pgs) 06/069 FreeChicken Meat Research in Progress 2005 – Web Only (2005, 30pgs) 05/067 FreeEvaluation of New Millet Varieties as a Poultry Feed ingredient (2004, 24pgs) 04/173 $16Developing a slope ratio chick assay for amino acid availability (2004, 33pgs) 04/144 $16Control of intestinal Spirochaete infections in Chickens (2004, 65 pgs) 04/141 $16Determination of the genomic sequence of Mycoplasma gallisepticum (2004, 14pgs) 04/140 $16Molecular epidemiology of Newcastle disease virus in Australia (2004, 36pgs) 04/139 $16Salmonella typing and colonisation of chickens (2004, 65pgs) 04/138 $16Avian Leukosis Virus sub-group J (ALV-J) – Developing laboratory technologies for diagnosis in Australia (2004, 80pgs) 04/116 $21Utlisation of digestable amino acids by broilers (2004, 42pgs) 04/030 $16Detection of Virulent Strains of Newcastle Disease Virus (2004, 21pgs) 04/022 $16Live vaccines for three species of Eimeria (2004, 43pgs) 03/143 $16Implementation of the RIRDC broiler welfare audit to industry (2003, 31pgs) 03/093 $16New Fowl Pox Vaccine Evaluation (2003, 13pgs) 03/086 $16National Environmental Management System for the Chicken Meat industry (2003, 185 pgs) 03/035 $35Sustainability Improvements in the VIC Chicken Meat industry (2003, 122pgs) Energy 03/035 $21Metabolism of Chickens (2003, 73pgs) 02/151 $16Investigations into the Management of the Darkling Beetle (2001, 105pgs) 01/151 $21New Therapeutics for Poultry (2001, 35pgs) 01/149 $16Detection of vvIBDV Strains & Australian Variants in Poultry (2001, 12pgs) 01/147 $16Salmonella Sofia in Chickens (2001, 47pgs) 01/106 $16Antibiotic Resistance in Bacteria Isolated from Poultry (2001, 44pgs) 01/105 $16Odour & Ammonia Emission from Broiler Hens (2000, 94pgs) 00/200 $21Improving Serological Diagnosis of Mycoplasma Synoviae (2000, 14pgs) 00/178 $16The New Season Grain Phenomenon (2000, 46pgs) 00/143 $16Chicken Meat and Egg Programs (2000) 00/098 FreeComparison of Total & Digestible Amino Acids in Diets for Broilers & Layers (1998, 25pgs) 98/124 $16Increasing Efficiency of Lean Tissue Deposition in Broiler Chickens (2000, 23pgs) 98/123 $16Diagnosing Avian Respiratory Diseases (1998, 32pgs) 98/105 $16

Ovarian Disease vs Normal Regression in Hens (1998, 20pgs) 98/031Web Only

Digestible Amino Acids in Poultry Feedstuffs (1998, 52pgs) 98/009 $56

All prices include GST and postage and handling. To order any of these publications, please contact RIRDC on (02) 6271 4100 or download them free from our website at http://www.rirdc.gov.au/fullreports/.

http://www.rirdc.gov.au/fullreports/

CHICKEN MEAT - AgriFutures Australia

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