The resistomes of six carbapenem-resistant pathogens – a critical genotype–phenotype analysis

Abstract

Carbapenem resistance is a rapidly growing threat to our ability to treat refractory bacterial infections. To understand how carbapenem resistance is mobilized and spread between pathogens, it is important to study the genetic context of the underlying resistance mechanisms. In this study, the resistomes of six clinical carbapenem-resistant isolates of five different species – Acinetobacter baumannii, Escherichia coli, two Klebsiella pneumoniae, Proteus mirabilis and Pseudomonas aeruginosa – were characterized using whole genome sequencing. All Enterobacteriaceae isolates and the A. baumannii isolate had acquired a large number of antimicrobial resistance genes (7–18 different genes per isolate), including the following encoding carbapenemases: blaKPC-2, blaOXA-48, blaOXA-72, blaNDM-1, blaNDM-7 and blaVIM-1. In addition, a novel version of blaSHV was discovered. Four new resistance plasmids were identified and their fully assembled sequences were verified using optical DNA mapping. Most of the resistance genes were co-localized on these and other plasmids, suggesting a risk for co-selection. In contrast, five out of six carbapenemase genes were present on plasmids with no or few other resistance genes. The expected level of resistance – based on acquired resistance determinants – was concordant with measured levels in most cases. There were, however, several important discrepancies for four of the six isolates concerning multiple classes of antibiotics. In conclusion, our results further elucidate the diversity of carbapenemases, their mechanisms of horizontal transfer and possible patterns of co-selection. The study also emphasizes the difficulty of using whole genome sequencing for antimicrobial susceptibility testing of pathogens with complex genotypes.

Elucidation of Proteus mirabilis as a Key Bacterium in Crohn’s Disease Inflammation

“…17 This cluster also contains 2 strains from stool samples from a Chinese (GCF_000313255.1) and a Swedish subject (GCF_003194305.1). 18,19 Interestingly, the remaining 2 isolates, both recovered from the patient biopsy sample of patient W19, were assigned to a distinct branch within the P mirabilis lineage, along with an isolate recovered from a stool sample as part of the National Institutes of Health Human Microbiome Project.…”

“…The genome assemblies for all 24 clinical isolates were annotated using Prokka, RAST, and National Center for Biotechnology Information. 19,20 For genomic comparisons, the isolates and publicly available genomes were then uploaded to the software platform EDGAR 21 to determine a core, shared and accessory genome. The average nucleotide identity scores between the orthologs present in a "core genome" from all 57 P mirabilis genomes were also calculated using EDGAR, and a matrix of average nucleotide identity scores generated using RStudio.…”

Identity of blaCTX-M Carrying Plasmids in Sequential ESBL-E. coli Isolates from Patients with Recurrent Urinary Tract Infections

“…In combination with CRISPR/Cas9 restriction, we can obtain information about plasmid size, resistance gene location, and barcode in the same experiment [17]. For the characterization of plasmids, we have previously demonstrated that the ODM results correlate very well with NGS analysis [14,[18][19][20]. We have also showed its usefulness in tracking possible transmission routes in nosocomial outbreak investigations, in a neonatal polyclonal outbreak due to CTX-M-producing bacteria in Sweden, and in an ESBL E. coli ST410 outbreak in a clinical setting in Ethiopia [12,20].…”

A comprehensive survey of integron-associated genes present in metagenomes

“…Vibrio ssp. and Xanthomonas ssp., or on conjugative elements, as is common for in pathogens such as Escherichia coli and Salmonella enterica [7,8]. Since integrons enable incorporation of a wide range of genes, they have been suggested to play a major role in the adaptation and evolution of many forms of bacteria [9][10][11].…”