Diversity within species: interpreting strains in microbiomes

T Van Rossum, P Ferretti, OM Maistrenko… - Nature Reviews …, 2020 - nature.com
Studying within-species variation has traditionally been limited to culturable bacterial
isolates and low-resolution microbial community fingerprinting. Metagenomic sequencing …

[HTML][HTML] Whole genome sequencing options for bacterial strain typing and epidemiologic analysis based on single nucleotide polymorphism versus gene-by-gene …

AC Schürch, S Arredondo-Alonso, RJL Willems… - Clinical microbiology …, 2018 - Elsevier
Background Whole genome sequence (WGS)-based strain typing finds increasing use in the
epidemiologic analysis of bacterial pathogens in both public health as well as more …

[HTML][HTML] Surveillance of Enterococcus spp. reveals distinct species and antimicrobial resistance diversity across a One-Health continuum

R Zaheer, SR Cook, R Barbieri, N Goji, A Cameron… - Scientific reports, 2020 - nature.com
Abstract For a One-Health investigation of antimicrobial resistance (AMR) in Enterococcus
spp., isolates from humans and beef cattle along with abattoirs, manured fields, natural …

[HTML][HTML] Cooperative recognition of internationally disseminated ceftriaxone-resistant Neisseria gonorrhoeae strain

MM Lahra, I Martin, W Demczuk… - Emerging infectious …, 2018 - ncbi.nlm.nih.gov
Ceftriaxone remains a first-line treatment for patients infected by Neisseria gonorrhoeae in
most settings. We investigated the possible spread of a ceftriaxone-resistant FC428 N …

[HTML][HTML] Standardized phylogenetic and molecular evolutionary analysis applied to species across the microbial tree of life

M Shakya, SA Ahmed, KW Davenport, MC Flynn… - Scientific reports, 2020 - nature.com
There is growing interest in reconstructing phylogenies from the copious amounts of
genome sequencing projects that target related viral, bacterial or eukaryotic organisms. To …

[HTML][HTML] One is not enough: on the effects of reference genome for the mapping and subsequent analyses of short-reads

C Valiente-Mullor, B Beamud, I Ansari… - PLoS computational …, 2021 - journals.plos.org
Mapping of high-throughput sequencing (HTS) reads to a single arbitrary reference genome
is a frequently used approach in microbial genomics. However, the choice of a reference …

[HTML][HTML] A comparative analysis of the Lyve-SET phylogenomics pipeline for genomic epidemiology of foodborne pathogens

LS Katz, T Griswold, AJ Williams-Newkirk… - Frontiers in …, 2017 - frontiersin.org
Modern epidemiology of foodborne bacterial pathogens in industrialized countries relies
increasingly on whole genome sequencing (WGS) techniques. As opposed to profiling …

Building phylogenetic trees from genome sequences With kSNP4

BG Hall, J Nisbet - Molecular Biology and Evolution, 2023 - academic.oup.com
Performing phylogenetic analysis with genome sequences maximizes the information used
to estimate phylogenies and the resolution of closely related taxa. The use of single …

[HTML][HTML] Multistate outbreak of listeriosis associated with packaged leafy green salads, United States and Canada, 2015–2016

JL Self, A Conrad, S Stroika, A Jackson… - Emerging infectious …, 2019 - ncbi.nlm.nih.gov
We investigated an outbreak of listeriosis detected by whole-genome multilocus sequence
typing and associated with packaged leafy green salads. Nineteen cases were identified in …

[HTML][HTML] Posttransfusion sepsis attributable to bacterial contamination in platelet collection set manufacturing facility, United States

I Kracalik, AG Kent, CH Villa, P Gable… - Emerging Infectious …, 2023 - ncbi.nlm.nih.gov
Abstract During May 2018‒December 2022, we reviewed transfusion-transmitted sepsis
cases in the United States attributable to polymicrobial contaminated apheresis platelet …