Antimicrobial resistance (AMR) profiling in Escherichia coli from farmed and wild animals in the

Mekong delta of VietnamNguyen Thi Nhung

Oxford University Clinical Research Unit, HCMC, VietnamBiodiversity and Health Symposium

Phnom Penh, 17-18 Nov 2014

Agenda

• Introduction − Animal production in Mekong Delta of Vietnam• Methods − Sampling − Laboratory methods• Results − Prevalence of AMR E. coli from farmed and wild animals − AMR patterns of E. coli from different species − Risk factors for multidrug resistance• Conclusion

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Animal production in Mekong Delta of Vietnam

• Large poultry and pig population

• Mixed farms

• Small scale production systems including household backyard farms

• Duck production systems integrated with rice production systems (free ranging ducks)

• Low bio-security and bio-containment

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• Commensal bacteria of warm-blooded animals

• High prevalence, simple and efficient isolation procedures

• Useful indicator for the presence of AMR in monitoring and surveillance programs

Use of Escherichia coli as indicator

No studies have investigated the prevalence of AMR E. coli isolated from the farmed and wildlife species in the Mekong Delta of Vietnam

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Aims of study

• To investigate the prevalence of AMR on E. coli indicator bacteria in various food animals and wildlife

• To characterize E. coli phenotypic resistant profiles

• To identify risk factors for fecal carriage of AMR E. coli in animal production

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• Cao Lanh district, Dong Thap province

• 90 pig, duck and chicken farms (30 of each) were stratified by size (small, medium and large)

• Fecal material was collected using a pair of boot swabs

Farm survey design

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• Small wild mammals were trapped from pig and poultry farms, rice fields, forests

• Humanely culled by overdose of isoflurane

• 0.2g caecal contents were collected from large intestines

Small wild mammals trapping and processing

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Laboratory methods

Antimicrobial agents Acronym

Amoxicilin/clavulanic acid (30µg) AMC

Ampicillin (10µg) AMP

Ceftazidime (30µg) CAZ

Chloramphenicol (30µg) C

Ciprofloxacin (5µg) CIP

Gentamicin (10µg) CN

Tetracycline (30µg) TE

Trimethoprim-sulphamethoxazol (25µg)

SXT

AMR E. coli testing

E. coli isolation

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Results

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E. coli isolates

SpeciesNo. samples

No. isolates

Total isolates

Farmed animals

Chicken 30 148

434Duck 30 143

Pig 30 143

Small wild mammals

Rattus argentiventer

9 33

234

Rattus tanezumi 19 62

Rattus exulans 5 16

Rattus norvegicus

10 28

Bandicota indica

16 67

Suncus murinus 7 28

Total 156 668

B. indica

R. argentiventer

R. exulans

R. norvegicus

R. tanezumi

S. murinus

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Prevalence of AMR E. coli from farmed animals

TE: tetracycline, SXT: trimethoprim-sulphamethoxazole, CN: gentamicin, CIP: ciprofloxacin, AMP: ampicillin, AMC: amoxicilin-clavulanic acid, CAZ: ceftazidime , C: chloramphenicol, ESBL: extended spectrum β lactamase, MDR: multidrug resistance, was defined as resistant to at least three different of antimicrobials

Unadjusted data Adjusted data

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Prevalence of AMR E. coli from small wild animals

Farms

Non-farms

TE: tetracycline, SXT: trimethoprim-sulphamethoxazole, CN: gentamicin, CIP: ciprofloxacin AMP: ampicillin, AMC: amoxicilin-clavulanic acid, CAZ: ceftazidime , C: chloramphenicol, ESBL: extended spectrum β lactamase, MDR: multidrug resistance, was defined as resistant to at least three different of antimicrobials

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Minimum spanning tree of AMR patterns from different species

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DAPC of AMR profiles by host type

DAPC= Discriminant Analysis of Principal Components

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Multivariable logistic regression of MDR for isolates from farms

OR 95% CI p-value

Type of farm (baseline=chicken or

duck)

1.0 - -

Small medium pig farm 1.18 1.04-1.35 0.0104

Large pig farm 1.41 1.27-1.57 <0.001

Age farmer (per 10-year period) 0.86 0.82-0.90 <0.001

Well-water: Large pig farm 1.24 1.15-1.33 <0.001

Small medium pig farm 1.55 1.37-1.75 <0.001

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Conclusions

• High levels of resistance to common antimicrobials among farmed animals

− Extensive range of antimicrobial compounds used not according to the dosage, length of treatment of the manufacturers

− Antimicrobials used on farm and human medicine are largely similar

• Small wild mammals trapped on farms seem to have higher prevalence of AMR

− Wildlife contact directly with antimicrobial residuals or resistant bacteria through food and effluent systems

− Useful indicators of the presence of antimicrobial resistant populations in the environment and/or farms

• There are some factors such as farm size (pigs), age of farmers, and water sources that may contribute to the problem of AMR on farms

− The longitudinal studies need to be conducted16

Acknowledgements:•Dr. Juan Carrique-Mas

•Dr. Ngo Thi Hoa

•Mr. James Campbell

•Mr. Nguyen Van Cuong

•Ms. Vo Nhu Thanh Truc

•Dr. Serge Morand

• Sub-Department of Animal Health Dong Thap

•Hospital Tropical Diseases HCMC

Funding: VIZIONS WT/093724

ZoNMW / WOTRO/205100012 (The Netherlands)

Li-Ka-Shing Foundation

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Thank you!