APHL 2019 POSTER ABSTRACTS
New York City’s Drinking Water Microbiome — Microbial
Diversity and Distribution
C. Kretz 1 , J. Novak 2 , I. Rubinstein 2 , Y. Chekoff 2 , S. Silver 2 , T. Geiz 2 ,
S. Hughes 2 , A. Capetanakis 3 , S. Feud 3 , J. Rakeman 2 , E. Omoregie 2 ;
1
Centers for Disease Control and Prevention, 2 New York City Public
Health Laboratory, 3 New York City Department of Environmental
Protection
Drinking water is one of our most valuable and closely monitored
resources and its quality can have an immense influence on human
health. Previous studies have reported that drinking water hosts
diverse assemblages of microorganisms. This includes opportunistic
pathogens that can host virulence and antimicrobial resistance
genes, which are capable of many different types of environmental
transformations and affect drinking water quality. New York City’s
(NYC) water distribution system has a unique, comprehensive and
efficient chemical and microbiological water quality monitoring
program. This monitoring has shown the drinking water is high
quality and free from enteric pathogens. However, relatively little is
known about the microbial community composition in NYC’s drinking
water. The project, which is ongoing, is to investigate the microbial
community structure and metabolic functionality of NYC’s drinking
water microbiome in relation to water source and treatment. This
study coupled 16S rRNA gene sequencing, metagenomics sequence
analysis, and physiological measurements. Samples were collected
monthly over a 1-year period from 19 sites that included pretreated
and posttreated waters. Preliminary data analysis of four months
of 16S rRNA gene sequence revealed presence of more than 695
bacterial genera. Many of these genera are known for nutrient
cycling in soil and aquatic systems, including Firmicutes, Azospira
spp., Shewanella spp., and Methylobacter spp. Enteric pathogens,
(e.g., E. coli or Salmonella) were not detected. However, genera that
include opportunistic pathogens and are common in freshwater
aquatic systems (e.g., Legionella spp. and Mycobacterium spp.)
were detected. A comparison between microbial communities based
on 16S rRNA sequences indicated that Actinobacteria sequences
dominated the microbiome of pretreated waters by at 69% of
the total number of sequences, while comprising only 5% from
posttreated waters. Whole genome metagenomics sequencing and
metabolic functionality is in the process of being assessed. Use
of 16S rRNA gene sequencing indicates that NYC’s drinking water
microbiome is diverse and replete with microorganisms common
to other freshwater environments. This study provides a deeper
understanding of the microbiome found in drinking water using
metagenomic tools to investigate presence of potential pathogens,
virulence factors, and antibiotic genes. It can provide new insights
on potential biological processes associated with the microbiome
and pathogen detection of drinking water microbial communities.
The main goal is to ultimately protect public health by laying ground
work for using new metagenomics tools for water surveillance.
Presenter: Cecilia Kretz, Centers for Disease Control and
Prevention, Atlanta, GA, [email protected]
Genetic Characterization of Human Adenoviruses
Associated with Multiple Respiratory Outbreaks
in the United States in 2018
X. Lu, S. Sakthivel, E. Schneider, H. Biggs, J. Watson, S. Gerber and
S. Lindstrom, Centers for Disease Control and Prevention
Background: Human adenoviruses (HAdVs) are medically important
PublicHealthLabs
@APHL
APHL.org
pathogens responsible for substantial human disease burden. HAdV
infections can cause a wide variety of clinical syndromes, including
respiratory, ophthalmic, gastroenteric, neurologic and immuno-
compromised host disease. HAdVs are classified into 7 species
(A-G). Over 85 genotypes have been described by computational
analysis of complete genomic sequences. Species B and E HAdVs,
in particular types 3, 4, 7 and 14 are more commonly associated
with outbreaks of severe acute respiratory infections. In 2018, CDC
provided laboratory support to US public health laboratories to
identify and characterize HAdVs associated with respiratory disease
outbreaks and individual cases occurring in the US.
Objective: To characterize HAdVs associated with human respiratory
cases and outbreaks in multiple states in the US in 2018 using a
comprehensive set of genetic analysis methods developed at CDC.
Methods: Respiratory specimens collected from multiple HAdVs-
associated respiratory disease cases in 2018 were sent to CDC
for further characterization. Specimens were tested by a universal
pan-HAdV real-time PCR (rPCR) assay to confirm HAdV detection
and characterized by HAdV type-specific rPCR assays. Virus isolation
and whole genome sequencing were performed to determine HAdV
genotypes. DNA libraries were constructed using Nextera XT DNA
Library Prep Kit and paired-end sequencing was performed on the
Illumina MiSeq. De novo and reference-guided genome assemblies
were achieved using CLC Genomics Workbench V11.0. Phylogenetic
trees of the complete genome sequences were constructed by
the neighbor-joining method implemented in MEGA V7. In silico
restriction enzyme analysis was performed using Geneious 9.0.5.
Results: HAdV-type specific rPCR identified four different HAdV types
associated with respiratory disease clusters and cases: HAdV-3,
HAdV-4, HAdV-7, HAdV-14, mixed HAdV-4 and HAdV-7. In silico
restriction enzyme analyses identified HAdV-7 outbreak strains as
genotype 7d that recently emerged in the US in 2013. HAdV-14
outbreak strains were identified as genotype 14p1. HAdV-4 strains
were identified as 4a1 genotype. HAdV-3 strains were typed as
genotype 3a2.
Conclusions: In 2018, several US state public health laboratories
reported cases and outbreaks of HAdV associated severe
respiratory disease and CDC provided comprehensive genetic
analysis that identified four different HAdVs types. Application of
these genetic analysis methods permitted detailed characterization
of the virus confirming its etiologic link with the cases and
outbreaks. This demonstrates the value of rapid characterization
of currently circulating HAdV types in supporting the public health
response to control HAdV-associated outbreaks, and improving our
understanding of the prevalence of respiratory illness associated
with HAdVs.
Presenter: Xiaoyan Lu, Centers for Disease Control and Prevention,
Atlanta, GA, [email protected]
Development of a Targeted Next-Generation Sequencing
Method to Detect Drug Resistance in Mycobacterium
tuberculosis
E. Ransom, S. Burns, B. Metchock and J. Posey, Centers for Disease
Control and Prevention
Conventional drug susceptibility testing in Mycobacterium
tuberculosis (Mtb) requires weeks-to-months to complete due
to the slow growth rate of Mtb. Reducing the turnaround time is
Summer 2019 LAB MATTERS
59