![A Molecular Biology: Open Access · 2020-01-09 · reverse transcription polymerase chain reaction (RT-PCR) [16,17], Multiplex RT-PCR (mRT-PCR) [18] and real-time RT-PCR [19,20].](https://static.fdocuments.us/doc/165x107/5f0cc7037e708231d43714b2/a-molecular-biology-open-access-2020-01-09-reverse-transcription-polymerase-chain.jpg)
Use of Multiplex Polymerase Chain Reaction (PCR)-Based ...
23
Use of Multiplex Polymerase Chain Reaction (PCR)-Based Diagnostic Testing for Enteric Infections in New York City (NYC), 2014–2016 Julia Latash, MPH CDC/CSTE Applied Epidemiology Fellow New York City Department of Health and Mental Hygiene
Transcript of Use of Multiplex Polymerase Chain Reaction (PCR)-Based ...
Use of Multiplex Polymerase Chain Reaction (PCR)-Based Diagnostic
Testing for Enteric Infections in New York City (NYC), 2014–2016
Julia Latash, MPHCDC/CSTE Applied Epidemiology Fellow
New York City Department of Health and Mental Hygiene
Enteric Disease Surveillance• Based on bacterial culture
– Cases defined as culture-confirmed– Isolation necessary for
• antimicrobial susceptibility testing • serotyping • pulsed-field gel electrophoresis• whole genome sequencing
Multiplex PCR Testing in NYC
• Began receiving multiplex results in 2014• Gastrointestinal syndromic panels• No isolation of microorganism
Multiplex PCR GI Testing in NYC, 2014–2016
• NYC residents diagnosed in 2014–2016 • Positive laboratory test for selected enteric
bacteria and parasites
Routinely investigated pathogens Non-routinely investigated pathogensCryptosporidium (CSP) Entamoeba (AMB)
Cyclospora (CYC) Campylobacter (CAM)Non-typhoidal Salmonella (SAL) Giardia (GIA)
Shiga toxin-producing E. coli (STEC) Shigella (SHG)Non-cholera Vibrio (VIB) Non-plague Yersinia (YER)
Percentage of labs testing NYC residents using multiplex tests, 2014–
2016
2%
8%
13%
0%
2%
4%
6%
8%
10%
12%
14%
2014 2015 2016
Perc
enta
ge
Diagnosis year
Reported infections with multiplex testing — NYC, 2014–2016
4,611
4,723
4,092
3440 1,005
<1%
9%
20%
0%
5%
10%
15%
20%
25%
0
1,000
2,000
3,000
4,000
5,000
6,000
2014 2015 2016 Infe
ctio
ns w
ith m
ultip
lex
test
ing
Infe
ctio
ns
Diagnosis Year
Number of infections diagnosed with a multiplex testNumber of ifections diagnosed without a multiplex testPercentage of infections diagnosed with a multiplex test
Testing cascade, reported infections —NYC, 2014–2016
Additional testing performed at public health lab (PHL)n = 713
Positive result at public health labn = 458
Any additional testing performedn = 816
Multiplex testing performedn = 1,448
Infections reported to NYCn = 14,874
Any additional testing performed —NYC, 2014–2016
89% 87%93%
87%92%
33%
21%12%
77%
63%
0%10%20%30%40%50%60%70%80%90%100%
0
50
100
150
200
250
300
350
400
450
CSP CYC SAL STEC VIB AMB CAM GIA SHG YER
Infe
ctio
ns w
ith a
dditi
onal
test
ing
Infe
ctio
ns
Pathogen
Number of infections with multiplex and additional testingNumber of infections with only multiplex testingPercentage of infections with multiplex and additional testing
Additional testing performed at a PHL— NYC, 2014–2016
99% 100% 99% 99% 100%100%
7% 25%
99% 98%
0%
20%
40%
60%
80%
100%
0
50
100
150
200
CSP CYC SAL STEC VIB AMB CAM GIA SHG YER
Infe
ctio
ns w
ith c
onfir
mat
ory
test
ing
at a
PH
LInfe
ctio
ns
Pathogen
Number of infections with confirmatory testing at a PHLNumber of infections with confirmatory testing at a reference labPercentage of infections with confirmatory testing at a PHL
Positive confirmatory test at a PHL —NYC, 2014–2016
79%
100%91%
27%
50%
67%
100%
60%67%
34%
0%10%20%30%40%50%60%70%80%90%100%
020406080
100120140160180200
CSP CYC SAL STEC VIB AMB CAM GIA SHG YER
Infe
ctio
ns w
ith a
pos
itive
conf
irmat
ory
test
Infe
ctio
ns
Pathogen
Number of infections with a positive confirmatory testNumber of infections with a negative or indeterminate confirmatory testPercentage of infections with a positive confirmatory test
Median (interquartile range) time between specimen collection, result
notification—NYC, 2014–2016 5 (IQR: 3-6)
2 (IQR: 2-3)
0
1
2
3
4
5
6
7
Multiplex tests Non-multiplex tests
Days
Factors Associated with Multiplex PCR GI Test Receipt in NYC, 2014–2016
• Infection with routinely investigated pathogens (CSP, CYC, SAL, STEC, VIB)
• Specimens tested at labs using multiplex tests
Factors consideredDiagnosis year Age
Sex RaceEthnicity County of residence
Hospitalization status Exclusion statusInternational travel Area-based poverty
Factors Associated with Multiplex PCR GI Test Receipt in NYC, 2014–2016
Factors strongly associated with multiplex test receipt
Diagnosis in 2016Hispanic ethnicity
Residence in Bronx, Manhattan
Hospitalization
• Multivariable logistic regression
Factors Associated with Multiplex PCR GI Test Receipt in NYC, 2014–2016
Factors strongly associated with multiplex test receipt
Diagnosis in 2016Hispanic ethnicity*Residence in Bronx,
Manhattan*Hospitalization*
• Multivariable logistic regression
*likely due to types and locations of labs performing testing
Use of Multiplex PCR GI Tests in NYC –Findings
• Multiplex use increased over time• Timelier reporting, but additional testing
needed for public health action• Proportions of infections with reflex testing,
positive confirmatory tests varied by pathogen
Use of Multiplex PCR GI Tests in NYC –Follow Up
• NYC Health Code amended December 5, 2016– Reflex to culture if positive culture-independent
result– Report positive and negative reflex culture result– Submit isolates/broth to public health lab
Acknowledgements
Sharon BalterVasudha ReddyHaeNa WaechterBruce Gutelius
This study/report was supported in part by an appointment to the Applied Epidemiology Fellowship Program administered by the Council of State and Territorial Epidemiologists (CSTE) and funded by the Centers for Disease Control and Prevention
(CDC) Cooperative Agreement Number 1U38OT000143-04.
NYC Bureau of Communicable Disease
NYC Public Health Laboratory
NYS Wadsworth Center
Many others…
Ana Maria FireteanuRobert FitzhenryLisa AlleyneMarcelle Layton
Erlinda AmorosoLan LiKatelynn DevinneyGeneral Surveillance Unit
Morgan MoyColleen CourtneyMicrobiology Section
Jennifer Rakeman
Thank you!Questions: [email protected]
Additional slides
Positive confirmatory test at a public health lab: STECs — NYC, 2014–2016
27%
68%
0%
10%
20%
30%
40%
50%
60%
70%
80%
020406080
100120140160180
All STECs Shiga toxin-positive STECs
Infe
ctio
ns w
ith a
pos
itive
conf
irmat
ory
test
Infe
ctio
ns
STEC infections
Number of infections with a positive confirmatory testNumber of infections with a negative or indeterminate confirmatory testPercentage of infections with a positive confirmatory test
Criteria for excluded food handlers to return to work in NYC
Disease 2 follow-up stools
2 sets of 2 follow-up stools taken 30
days apart
3 follow-up stools
Campylobacteriosis X
Cholera X
Salmonellosis X
Shigellosis X
STEC infection X
Typhoid / paratyphoid fever X
Yersiniosis X
Amebiasis X
Cryptosporidiosis X
Giardiasis X
Criteria for excluded child care worker or attendee to return to school in NYC
Disease Until asymptomatic
2 follow-up stools
2 sets of 2 follow-up
stools, taken 30 days apart
3 follow-up stools
Campylobacteriosis X
Cholera XSalmonellosis X
Shigellosis XSTEC infection X
Typhoid / paratyphoid fever
X
Yersiniosis XAmebiasis X
Cryptosporidiosis XGiardiasis X
Criteria for excluded health care workers to return to work in NYC
Disease Until asymptomatic
2 follow-up stools
2 sets of 2 follow-up
stools, taken 30 days apart
3 follow-up stools
Campylobacteriosis X
Cholera XSalmonellosis X
Shigellosis XSTEC infection X
Typhoid / paratyphoid fever
X
Yersiniosis XAmebiasis X
Cryptosporidiosis XGiardiasis X
![QIAGEN Multiplex PCR Handbook[1]](https://static.fdocuments.us/doc/165x107/577cc7781a28aba711a107f5/qiagen-multiplex-pcr-handbook1.jpg)
