Pathogens on Robert A. Petit III, PhD

Mycobacteria Amplicon Sequencing Tool: automated resistance prediction and lineage classification for Mycobacterium tuberculosis

Mon, 27 Apr 2026 00:00:00 +0000

ABSTRACT The Mycobacteria Amplicon Sequencing Tool ( https://github.com/guthrielab/MAST ) is a modular Nextflow pipeline for antimicrobial resistance prediction and lineage classification of…

Pangenome-GWAS analysis of Clostridioides difficile resistant traits from healthcare- and non-healthcare-associated settings

Thu, 01 Jan 2026 00:00:00 +0000

Clostridioides difficile ( C.

Genomic Dynamics of the Emergent Candida auris: Exploring Climate-dependent Trends

Fri, 25 Jul 2025 00:00:00 +0000

Candidozyma auris (formerly known as Candida auris) (C auris) is a multidrug-resistant fungal pathogen that has emerged as a significant threat to global health.

Comparative genomic analysis of emerging non-typeable Haemophilus influenzae (NTHi) causing emerging septic arthritis in Atlanta

Fri, 21 Mar 2025 00:00:00 +0000

Haemophilus influenzae is a Gram-negative bacterium that can exist as a commensal organism or cause a range of diseases, from ear infections to invasive conditions like meningitis.

Strain Differences in Bloodstream and Skin Infection: Methicillin-Resistant Staphylococcus aureus Isolated in 2018–2021 in a Single Health System

Fri, 03 May 2024 00:00:00 +0000

Staphylococcus aureus is a common cause of skin and soft-tissue infections (SSTIs) and has become the most common cause of bloodstream infections (BSIs) in recent years, but whether the strains…

Mycobacterium tuberculosis epidemiology in Oman: whole-genome sequencing uncovers transmission pathways.

Thu, 28 Sep 2023 00:00:00 +0000

We report evidence that WGS can complement epidemiological analysis to achieve the End TB strategy goal in Oman.

Association of Secretor Status and Recent Norovirus Infection With Gut Microbiome Diversity Metrics in a Veterans Affairs Population

Sun, 01 May 2022 00:00:00 +0000

We report the secretor status and associations with recent norovirus infections

Unrecognized introductions of SARS-CoV-2 into the US state of Georgia shaped the early epidemic

Tue, 15 Feb 2022 00:00:00 +0000

We report the early introductions of SARS-CoV-2 in the US state of Georgia

Molecular Epidemiology and Outcomes of Patients with Carbapenem-Resistant Enterobacteriaceae Bacteriuria, Atlanta 2012–2015

Thu, 01 Oct 2020 00:00:00 +0000

Carbapenem-resistant Enterobacteriaceae (CRE) represent a significant antibiotic resistance threat, in part because carbapenemase genes can spread on mobile genetic elements.

Bactopia: a Flexible Pipeline for Complete Analysis of Bacterial Genomes

Tue, 04 Aug 2020 00:00:00 +0000

We created Bactopia, built using Nextflow workflow software, to provide efficient comparative genomic analyses for bacterial species or genera. Analysis of 1,664 public Lactobacillus genomes was conducted to demonstrate the usage of Bactopia.

Genotypic and Phenotypic Diversity of Staphylococcus aureus Isolates from Cystic Fibrosis Patient Lung Infections and Their Interactions with Pseudomonas aeruginosa

Tue, 23 Jun 2020 00:00:00 +0000

Our work provides greater insight into the diversity of Staphylococcus aureus isolates from cystic fibrosis patients, specifically the distribution of important virulence factors and their interaction with Pseudomonas aeruginosa, all of which have implications in patient health.

Invasive Nontypeable Haemophilus influenzae Infection Among Adults With HIV in Metropolitan Atlanta, Georgia, 2008-2018

Sun, 01 Dec 2019 00:00:00 +0000

We show increase in invasive nontypeable Haemophilus influenzae (NTHi) infection from 2017-2018 among HIV-infected men who have sex with men in metropolitan Atlanta, Georgia.

Human mAbs to Staphylococcus aureus IsdA Provide Protection Through Both Heme-Blocking and Fc-Mediated Mechanisms

Mon, 01 Apr 2019 00:00:00 +0000

The iron-regulated surface determinant (Isd) system scavenges heme-iron from the human host, enabling acquisition of iron in iron-deplete conditions in Staphylococcus aureus during infection. We describe the first isolation of fully human IsdA and IsdH monoclonal antibodies (mAbs), as well as cross-reactive Isd monoclonal antibodies (mAbs).

Whole-Genome Sequences of Staphylococcus aureus Isolates from Cystic Fibrosis Lung Infections

Tue, 01 Jan 2019 00:00:00 +0000

we present the whole-genome sequences of 65 Staphylococcus aureus isolates obtained from 50 individuals with cystic fibrosis.

Fine-scale differentiation between Bacillus anthracis and Bacillus cereus group signatures in metagenome shotgun data

Wed, 01 Aug 2018 00:00:00 +0000

We developed a model to differentiate Bacillus anthracis, the etiologic agent of anthrax, from the closely related (>99% average nucleotide identity) Bacillus cereus group members in metagenome sequences.

Genome sequences for five strains of the emerging pathogen Haemophilus haemolyticus

Sat, 01 Oct 2011 00:00:00 +0000

The first whole-genome sequences for five strains, two carried and three pathogenic, of the emerging pathogen Haemophilus haemolyticus

gigatyper

Mon, 01 Jan 0001 00:00:00 +0000

Salmonella serotyping direct from Illumina FASTQ files using multiple schemes