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

Abstract

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.

Hybrid Assembly Provides Improved Resolution of Plasmids, Antimicrobial Resistance Genes, and Virulence Factors in Escherichia coli and Klebsiella pneumoniae Clinical Isolates

“…We concluded that results are heavily dependent on the database of choice therefore, Hyb ASM might be a better approach for in depth analyses of WGS data. Although Hyb ASM has been used to study hospital Mycobacterium chelonae infections [59], extraintestinal pathogenic E. coli isolates [52] and one pan-drug-resistant K. pneumoniae isolate [60], the application of Hyb ASM for studying pathogenic factors in clinical samples is somewhat limited. In the current study, Hyb ASM showed reliable results for studying the clinical samples, specifically for the mixed culture as compared to Illum ASM and MinION ASM .…”

Evaluating the potential for respiratory metagenomics to improve treatment of secondary infection and detection of nosocomial transmission on expanded COVID-19 intensive care units

“…Genomes with a genetic similarity of ≥ 99.99% were considered related, and plausible outbreaks were investigated using traditional epidemiological methods. The threshold for genetic similarity was based on previous studies [ 32 , 33 ] and the latest nanopore accuracy data ( https://nanoporetech.com/accuracy ).…”

Infrequent intrahousehold transmission of Clostridioides difficile between pet owners and their pets

“…The human‐ and dog‐derived strains differed by only 1 SNV among the single copy core genes. Using the negative binomial distribution of SNVs from the assembly of Vibrio campbellii technical replicates as reference (Gu et al, 2020), the binomial test of 1 SNV between genomes results in a p ‐value >0.91, implying that these two isolates are identical. These microorganisms were genetically distinct (>50 SNPs difference) from C .…”

“…The human-and dogderived strains differed by only 1 SNV among the single copy core genes. Using the negative binomial distribution of SNVs from the assembly of Vibrio campbellii technical replicates as reference (Gu et al, 2020) 2).…”