APHL 2018 Annual Meeting Poster Abstracts
time qPCR assay on the portable Biomeme two3 system, with
isolate confirmation by the VITEK MS. Of the samples tested, 10
detected positive for Salmonella, with the first detection occurring
within 30 hours of collection. Select qPCR positive samples were
also subjected to metagenomic shotgun sequencing on the portable
MinION sequencing platform for sample characterization. The
successful demonstration of these methods is an important step
towards developing and validating field-ready methods aimed at
shortening the sample to answer timelines for routine foodborne
pathogen surveillance and outbreak investigations. not routinely treated with an antibiotic regimen, treatment should be
considered for persistently symptomatic cases. MIC interpretations,
in conjunction with treatment and outcome data representative
of all four species of Shigella, will be used to establish clinical
breakpoint recommendations.
Presenter: Tamar Dickerson, MRIGlobal, Gaithersburg, MD,
Phone: 240.361.4039, Email: [email protected] Routine Utilization of CIDT, FilmArray Gastrointestinal
Panel, with Simultaneous Stool Culture Leads to Increased
Isolate Recovery
Comparison of ETEST ® and Broth Microdilution Methods for
Antimicrobial Susceptibility Testing of Shigella sp. Isolates
in New York City C. Courtney 1 , J. Rakeman 1 , K. Inglima 1 , M. Aguero-Rosenfeld 2 ;
1
New York City Public Health Laboratory, New York NY, 2 New York
University Langone Medical Center, New York, NY
A. DeVito 1 , G. Zayas 1 , J. Rakeman 2 ; 1 New York City Department of
Health and Mental Hygiene, New York, NY, 2 New York City Public
Health Laboratory, New York, NY
The New York City Department of Health and Mental Hygiene
(DOHMH) Public Health Laboratory (PHL) performs antimicrobial
susceptibility testing (AST) on all Shigella isolates submitted by
clinical laboratories (submission is required by the NYC Health
Code). PHL performs antimicrobial susceptibility testing (AST) using
ETEST ® (bioMeriéux) and forwards a sample of the isolates to the
National Antimicrobial Resistance Monitoring System (NARMS)
at the Centers for Disease Control and Prevention (CDC) for AST
by Sensitire ® broth microdilution using dried panels. PHL uses
the Clinical & Laboratory Standards Institute (CLSI) guidelines for
interpretation, while CDC uses NARMS established breakpoints for
susceptibility interpretation (this includes CLSI breakpoints and
proposed Epidemiological Cutoff Values (ECV) if no CLSI breakpoint
is established). In this study, we evaluated the ETEST ® method
versus the broth microdilution method to inform the establishment
and assessment of clinical breakpoints for Shigella. We analyzed
data from 104 Shigella spp. isolates with collection dates of April,
2013 through December, 2016. Antibiotics tested using both
methods were azithromycin (AZM), ciprofloxacin (CIP), ampicillin
(AMP) and trimethoprim/sulfamethoxazole (SXT). Any ETEST MIC
values that fell between standard two-fold dilutions were rounded up
to the next two-fold value for data analysis. CLSI breakpoints were
used for all drugs except AZM; CLSI epidemiological cutoff values
for S. flexneri and S. sonnei were used for AZM, which lacks clinical
breakpoints. Resistance rates, error rates and descriptive statistics
for both methods were determined and categorical and essential
agreements were calculated by methods described in CLSI M23,
4th ed. CIP results had the best categorical agreement (100%) with
no errors, while SXT and AMP results did not meet the required
acceptability of 90% or higher (82.7% and 87.5%). AZM results had
categorical agreements of 89.8% for S. sonnei with four major errors
and 100% for S. flexneri with no errors. SXT results had the most
major (13) and very major errors (5). AMP results showed eight
major errors and one minor error. The highest ess ential agreement
(+/- 1 doubling dilution) results were observed in AZM for S. sonnei
(89.8%), CIP (87.5%) for all species and AZM for S. flexneri (82.8%).
Both SXT and AMP results (81.7%) for all Shigella spp. had the
lowest essential agreement. Results showed that overall, ETEST ®
resulted in higher rates of resistance interpretation for several of the
antibiotics compared to broth microdilution. Although shigellosis is
56
LAB MATTERS Summer 2018
Presenter: Andrea DeVito, MPH, CPH, New York City Department
of Health and Mental Hygiene, New York, NY, Phone: 212.671.5742,
Email: [email protected]
The wide acceptance and adaptation of culture-independent
diagnostic tests (CIDT) for enteric pathogens, while providing
many improvements for clinicians, has introduced challenges to
public health laboratories directly related to recovery of isolates.
For enteric pathogens like Salmonella, culture-based strain
characterization has been the gold standard for decades and
outbreak investigations rely on either pulse-field gel electrophoresis
(PFGE) and/or whole genome sequence (WGS) analysis, both of
which require an isolated organism. However, very little data exists
to examine the impact that CIDT has had on isolate recovery in
clinical laboratories. In our clinical laboratory, which maintains
stool culture in conjunction with the FilmArray Gastrointestinal (GI)
Panel, we have seen an increase in isolate recovery when using
the FilmArray as a screening test. We performed a retrospective
analysis from 2016–2017 of all specimens for which pathogen DNA
was detected by the FilmArray GI Panel and found that, of the 22
targets included in the panel, we detected 18 (not detected were
Rotavirus A, Sapovirus, Entamoeba histolytica and Giardia lamblia).
Ninety-six patient specimens were included in the analysis, age
ranged from one month to 103 years, with an average collection
to receipt time of 2 hours 46 minutes. Of the 13 bacterial targets
included in the panel, 5 are Escherichia coli species, which are
difficult to differentiate in culture and were not included in the
analysis. Of the remaining 8 targets, Campylobacter, Salmonella
and Shigella were recovered in greater than 10 specimens each and
considered for further analysis. The time to recover and identify the
pathogen was determined with each correlating FilmArray result.
The average time from culture-based identification was 65 hrs 25
mins, 58 hrs 39 mins, 83 hrs 58 mins, respectively, all of which
exceeded the standard 48 hour incubation for stool cultures. Prior
to the implementation of the CIDT, these stool culture plates would
have been discarded before the pathogen was recognized. From the
detection and later isolation of these three organisms, our results
also indicate that 28 isolates would have been missed and not
submitted to the NYC Public Health Laboratory for PulseNet analysis
and 34 isolates wound not have been included in the DOHMH NYC
Molecular Typing surveillance project. We have found that when
used in combination with culture, CIDT methods lead to increased
sensitivity of culture. Prior knowledge of the pathogen resulted in
increased efforts by technologists to recover the organism, including
longer hold times or specialized growth conditions. Increased
recovery of isolates, in turn, leads to the improvement of public
health surveillance.
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