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:
[email protected]
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: [email protected]
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
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