Ultra-deep long-read sequencing detects IS-mediated gene duplications as a potential trigger to generate arrays of resistance genes and a mechanism to induce novel gene variants such as blaCTX-M-243. (2nd December 2021)

• Record Type: Journal Article
• Authors: Schuster, Christopher F.; Weber, Robert E.; Weig, Michael; Werner, Guido; Pfeifer, Yvonne
• Is Part Of: Journal of antimicrobial chemotherapy. Volume 77:Number 2(2022)
• Page Start: 381
• Page End: 390
• Publication Date: 2021-12-02
• Subjects: Anti-infective agents -- Periodicals; Chemotherapy -- Periodicals; 615.58
• DOI: 10.1093/jac/dkab407
• Languages: English
• ISSNs: 0305-7453

Abstract

Abstract: Background: Extended-spectrum β-lactamases (ESBLs) are enzymes that can render their hosts resistant to various β-lactam antibiotics. CTX-M-type enzymes are the most prevalent ESBLs and the main cause of resistance to third-generation cephalosporins in Enterobacteriaceae. The number of described CTX-M types is continuously rising, currently comprising over 240 variants. During routine screening we identified a novel bla CTX-M gene. Objectives: To characterize a novel bla CTX-M variant harboured by a multidrug-resistant Escherichia coli isolate of sequence type ST354. Methods: Antibiotic susceptibilities were determined using broth microdilution. Genome and plasmid sequences were reconstructed using short- and long-read sequencing. The novel bla CTX-M locus was analysed using long-read and Sanger sequencing. Plasmid polymorphisms were determined in silico on a single plasmid molecule level. Results: The novel bla CTX-M-243 allele was discovered alongside a nearly identical bla CTX-M-104 -containing gene array on a 219 kbp IncHI2A plasmid. CTX-M-243 differed from CTX-M-104 by only one amino acid substitution (N109S). Ultra-deep (2300-fold coverage) long-read sequencing revealed dynamic scaling of the bla CTX-M genetic contexts from one to five copies. Further antibiotic resistance genes such as bla TEM-1 also exhibited sequence heterogeneity but were stable in copy number. Conclusions: We identified the novel ESBL gene bla CTX-M-243 and illustrate a dynamic system of varying bla CTX-M copy numbers. Our results highlight the constant emergence of new CTX-M family enzymes and demonstrate a potential evolutionary platform to generate novel ESBL variants and possibly other antibiotic resistance genes.