Lab Matters Summer 2018 - Page 58

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: tdickerson@mriglobal.org 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: adevito@health.nyc.gov 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. PublicHealthLabs @APHL APHL.org