Lab Matters Summer 2018 - Page 74

APHL 2018 Annual Meeting Poster Abstracts Performance Evaluation and Clinical Application of the GeneXpert MTB/RIF Assay in a Local Public Health Laboratory M. Zhowandai, M. Ghajar, S. Prabhu, J. Low and M. Crumpler, Orange County Public Health Laboratory, Santa Ana, CA Background: 1. The objective of this study was to analyze the performance of the Cepheid GeneXpert ® MTB/RIF Assay in comparison to culture results and patient diagnostic and treatment information to establish effective protocols to maximize efficiency of performing a Nucleic Acid Amplification Test (NAAT) for appropriate Tuberculosis (TB) suspects. 2. This research was funded through a grant from the CDC through the Association of Public Health Laboratories (APHL) to evaluate the performance of molecular diagnostic tests for TB and increase evidence-based knowledge regarding the most appropriate use of these assays. Methods: 1. NAAT was performed on at least one respiratory specimen from each patient, along with conventional culture and broth-based antimicrobial susceptibility testing (AST). 2. Six-hundred seventy specimens from 632 patients were tested. 3. GeneXpert results were compared to culture results and patient diagnostic and treatment information. Results/Key Findings: 1. Of the 670 specimens evaluated, GeneXpert had an overall sensitivity, specificity, positive and negative predictive values of 82.8%, 97.9%, 80.3% and 98.2%, respectively. The sensitivity was higher (97.7 %) in acid fast bacilli (AFB) smear positive specimens. 2. GeneXpert had better correlation (sensitivity) (85.7%) with culture results if Mycobacterium tuberculosis complex (MTB) detected in any cultur e from that patient was considered. 3. For the detection of Rifampin (RIF) resistance, the GeneXpert had sensitivity, specificity, positive and negative predictive values of 100%. 4. The average TAT for GeneXpert to detect MTB and RIF-resistance was 2 days. 5. The average TAT by culture was 22 days for identification of MTB and an additional 15 days for RIF-resistance results. Conclusions: 1. For smear-positive specimens, a negative NAAT result yielded a shorter period of patient isolation (average 17 days) than a positive NAAT result (average 63 days). 2. In 19 cases, negative NAAT results were used to remove patients from isolation by the TB control program. 3. There were 103 pulmonary TB cases and 81 contact investigations. Twenty-nine of the 81 contact investigations were initiated based on the NAAT results. 4. Overall, GeneXpert showed good correlation with culture results for detection of MTB and RIF-resistance. Performance was better in specimens with a positive AFB smear. Presenter: Minoo Ghajar, MPH, Orange County Public Health Laboratory, Santa Ana, CA, Phone: 714.834.8292, Email: Transition of a Manually-Performed Laboratory-Developed Test (LDT) to the Fully Automated cobas ® 6800/8800 Systems Using the cobas ® omni Utility Channel (complete abstract in PHL Capacity, p. 82) 72 LAB MATTERS Summer 2018 Next Generation Sequencing of the Hepatitis A Virus Outbreak in San Diego County S. Steele, T. Basler and B. Austin, San Diego County Health and Human Services Agency, San Diego, CA In San Diego County, California, a Hepatitis A Virus (HAV) outbreak developed, with the first case identified in November of 2016 and affecting over 575 people since then. Unlike other HAV outbreaks, the nature and size of this particular outbreak was unique as it has circulated in the homeless and illicit drug user population. The County of San Diego declared a local public health emergency from September 1, 2017 to January 23, 2018. The declaration significantly increased the involvement of the San Diego Public Health Laboratory (SDPHL) for diagnostic testing. Collaborating with public health partners, such as the California Department of Public Health Viral and Rickettsial Disease Laboratory (VRDL) and the Centers for Disease Control and Prevention (CDC), allowed SDPHL to implement both PCR screening and sequencing to increase the testing capacity, improve detection and focus on prevention efforts for HAV in San Diego County. SDPHL created a testing workflow that first screens suspect patient specimens with a laboratory developed TaqMan assay to determine if the HAV RNA is present. If detected, the virus is sequenced using Sanger sequencing of the VP1/P2B region of the HAV genome, which demonstrates high sequence variability compared to other regions in the genome. Genotyping and cluster identification showed that the outbreak was caused by HAV genotype IB, with the majority in one main cluster and 16 other additional sub-clusters identified. Sequencing the VP1/2PB region has been performed on all specimens during the outbreak by either VRDL or the CDC using Sanger sequencing technology. SDPHL will use the GHOST next generation sequencing (NGS) protocol and compare the NGS data to the Sanger sequence data to determine if there is a better picture of the transmission in the community during the outbreak. Presenter: Tracy Basler, San Diego County Health and Human Services Agency, Public Health Laboratory, San Diego, CA, Phone: 619.692.8500, Email: Molecular Epidemiology of Rabies Virus in New Mexico: Identification of Novel Variants and Their Associated Hosts K. Pesko, M. Breckenridge, L. Washington, A. Aragon and L. Liu, New Mexico Scientific Laboratory Division, Albuquerque, NM Rabies is a fatal viral disease enzootic to the United States, with serious public health implications. Currently, different rabies virus (RABV) variants circulate in New Mexico, associated with different mammalian species. Recent and historic evidence suggest that RABV is capable of jumping from one host to another and can successfully establish emerging enzootics in novel reservoir hosts. We present results from sequencing of nucleoprotein genes from RABV positive samples, along with cytochrome oxidase sequencing to identify host species. We have sequenced many of the host species submitted for RABV testing in New Mexico over the past 10 years and have identified 11 different bat species, two different skunk species and 27 unique species total among the animals tested for RABV. Eight unique strains of RABV were identified in the state over the past 10 years, with Arizona gray fox and south- central skunk as the most commonly identified strains. Phylogenetic analysis of RABV variants is combined with geographic distribution of both host species and RABV variants from New Mexico and PublicHealthLabs @APHL