Corrigendum: In silico serotyping of E. coli from short read data identifies limited novel O-loci but extensive diversity of O:H serotype combinations within and between pathogenic lineages

Ingle, Danielle J.; Valcanis, Mary; Kuzevski, Alex; Tauschek, Marija; Inouye​, Michael; Stinear, Timothy P.; Levine, Myron M.; Robins-Browne, Roy M.; Holt, Kathryn E.

doi:10.1099/mgen.0.000109

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“…Given the burden of diseases caused by E. coli and its significant public health concern, hospitals should continuously monitor their antimicrobial treatment efficacy. Whole-genome sequencing (WGS)-based in silico approaches are valuable tools in gene analysis of outbreak strains that offer detailed epidemiological investigation and tracing of pathogens ( 5 ). In this study, we used WGS to characterize E. coli C91 (ST38), an extensively drug-resistant clinical outbreak strain isolated from patient zero in the intensive care unit (ICU) of one of the largest hospitals in Kuwait, with the intention of successfully treating the patients and containing its spread.…”

Section: Introductionmentioning

confidence: 99%

Genomic Characteristics of an Extensive-Drug-Resistant Clinical Escherichia coli O99 H30 ST38 Recovered from Wound

Dashti,

Vali,

Shamsah

et al. 2024

Iran J Pharm Res

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Background: Antibiotic-resistant Escherichia coli is one of the major opportunistic pathogens that cause hospital-acquired infections worldwide. These infections include catheter-associated urinary tract infections (UTIs), ventilator-associated pneumonia, surgical wound infections, and bacteraemia. Objectives: To understand the mechanisms of resistance and prevent its spread, we studied E. coli C91 (ST38), a clinical outbreak strain that was extensively drug-resistant. The strain was isolated from an intensive care unit (ICU) in one of Kuwait's largest hospitals from a patient with UTI. Methods: This study used whole-genome sequencing (Illumina, MiSeq) to identify the strain's multi-locus sequence type, resistance genes (ResFinder), and virulence factors. This study also measured the minimum inhibitory concentrations (MIC) of a panel of antibiotics against this isolate. Results: The analysis showed that E. coli C-91 was identified as O99 H30 ST38 and was resistant to all antibiotics tested, including colistin (MIC > 32 mg/L). It also showed intermediate resistance to imipenem and meropenem (MIC = 8 mg/L). Genome analysis revealed various acquired resistance genes, including mcr-1, blaCTX-M-14, blaCTX-M-15, and blaOXA1. However, we did not detect blaNDM or blaVIM. There were also several point mutations resulting in amino acid changes in chromosomal genes: gyrA, parC, pmrB, and ampC promoter. Additionally, we detected several multidrug efflux pumps, including the multidrug efflux pump mdf(A). Eleven prophage regions were identified, and PHAGE_Entero_SfI_NC was detected to contain ISEc46 and ethidium multidrug resistance protein E (emrE), a small multidrug resistance (SMR) protein family. Finally, there was an abundance of virulence factors in this isolate, including fimbriae, biofilm, and capsule formation genes. Conclusions: This isolate has a diverse portfolio of antimicrobial resistance and virulence genes and belongs to ST38 O99 H30, posing a serious challenge to treating infected patients in clinical settings.

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Section: Introductionmentioning

confidence: 99%

Genomic Characteristics of an Extensive-Drug-Resistant Clinical Escherichia coli O99 H30 ST38 Recovered from Wound

Dashti,

Vali,

Shamsah

et al. 2024

Iran J Pharm Res

View full text Add to dashboard Cite

show abstract

Corrigendum: In silico serotyping of E. coli from short read data identifies limited novel O-loci but extensive diversity of O:H serotype combinations within and between pathogenic lineages

Abstract: Corrigendum: In silico serotyping of E. coli from short read data identifies limited novel O-loci but extensive diversity of O:H serotype combinations within and between pathogenic lineages

Cited by 1 publication

References 0 publications

Genomic Characteristics of an Extensive-Drug-Resistant Clinical Escherichia coli O99 H30 ST38 Recovered from Wound

Genomic Characteristics of an Extensive-Drug-Resistant Clinical Escherichia coli O99 H30 ST38 Recovered from Wound

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