Investigating hospital Mycobacterium chelonae infection using whole genome sequencing and hybrid assembly

Autor: Robert N. Baldassano, Kyle Bittinger, Laurel Glaser, Casey E. Hofstaedter, Christopher H Gu, Lisa M. Mattei, Pablo Tebas, Chunyu Zhao, Frederic D. Bushman
Jazyk: angličtina
Rok vydání: 2020
Předmět:
0301 basic medicine
Pulmonology
Nosocomial Infections
Mycobacterium chelonae
Drug resistance
Genome
Medical Conditions
Medicine and Health Sciences
Genome Sequencing
Reptile Genomics
Phylogeny
Philadelphia
Genetics
Cross Infection
Multidisciplinary
biology
High-Throughput Nucleotide Sequencing
Genomics
Drug susceptibility
Infectious Diseases
Medicine
Research Article
DNA
Bacterial
Sequence analysis
Science
030106 microbiology
Opportunistic Infections
Research and Analysis Methods
Microbiology
03 medical and health sciences
Respiratory Disorders
Antibiotic resistance
Phylogenetics
Microbial Control
Humans
Molecular Biology Techniques
Sequencing Techniques
Molecular Biology
Pharmacology
Whole genome sequencing
Mycobacterium Infections
Whole Genome Sequencing
Biology and Life Sciences
Sequence Analysis
DNA
biology.organism_classification
Nontuberculous mycobacterium
030104 developmental biology
Animal Genomics
Antibiotic Resistance
Respiratory Infections
Antimicrobial Resistance
Nanopore sequencing
Genome
Bacterial
Antibiotic resistance genes
Zdroj: PLoS ONE, Vol 15, Iss 11, p e0236533 (2020)
PLoS ONE
ISSN: 1932-6203
Popis: Mycobacterium chelonae is a rapidly growing nontuberculous mycobacterium that is a common cause of nosocomial infections. Here we describe investigation of a possible nosocomial transmission of M. chelonae at the Hospital of the University of Pennsylvania (HUP). M. chelonae strains with similar high-level antibiotic resistance patterns were isolated from two patients who developed post-operative infections at HUP in 2017, suggesting a possible point source infection. The isolates, along with other clinical isolates from other patients, were sequenced using the Illumina and Oxford Nanopore technologies. The resulting short and long reads were hybrid assembled into draft genomes. The genomes were compared by quantifying single nucleotide variants in the core genome and assessed using a control dataset to quantify error rates in comparisons of identical genomes. We show that all M. chelonae isolates tested were highly dissimilar, as indicated by high pairwise SNV values, consistent with environmental acquisition and not a nosocomial point source. Our control dataset determined a threshold for evaluating identity between strains while controlling for sequencing error. Finally, antibiotic resistance genes were predicted for our isolates, and several single nucleotide variants were identified that have the potential to modulated drug resistance.
Databáze: OpenAIRE
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