A genetic cluster of OXA-244 carbapenemase-producing Escherichia coli ST38 with putative uropathogenicity factors in the Netherlands

Abstract

Emergence of urine-associated Escherichia coli ST38 producing OXA-244 harbouring putative uropathogenicity factors in the Netherlands.

Large hospital outbreak caused by OXA-244-producing Escherichia coli sequence type 38, Poland, 2023

“…The expansion of OXA-244-Ec ST38 has been one of the most worrying phenomena in recent epidemiology of CPE in Europe, addressed in two consecutive ECDC RRAs in February 2020 and July 2021 [11] and in several reports from different countries [12][13][14][15][16]. This concern has arisen from the significance of E. coli as a major human pathogen which causes community-acquired infections [1] and from the role of carbapenems as the last line drugs in the treatment of severe MDR Gramnegative infections [3].…”

“…This sub-lineage, notably homogeneous and co-expressing the cefotaximase (CTX)-M-27 ESBL was first identified in 2016. Another sub-lineage, Cluster B, detected in 2013, is less frequent, more diversified genetically and correlates with the CTX-M-14 enzyme [11][12][13][14][15][16].…”

OXA-48–Producing Uropathogenic Escherichia coli Sequence Type 127, the Netherlands, 2015–2022

“…A variety of PUFs, associated with UPEC, were detected in cluster isolates ( Appendix 2 Table 5, Appendix 1 Figure, panel E), including adhesins (e.g., sfaH , pili papGII / papGIII ), toxins (e.g., α-hemolysin, cytotoxic necrotizing factor-1, and E. coli uropathogenic-specific protein) ( 4 , 7 , 8 ). Cluster isolates carried significantly more (mean 18) PUFs, than the other E. coli isolates from CPE surveillance (mean nonurine isolates, 7; urine isolates, 9; previously reported OXA-244 E. coli ST38 isolates, 8; p<0.001 by Mann-Whitney U-test) ( Appendix 1 Figure, panel F) ( 1 ). We identified additional uropathogenicity determinants curli, type-I fimbriae, S-fimbriae, flagella, and group 2 capsule genes but not group 3 capsule genes.…”

“…We recently described OXA-244 carbapenemase-producing Escherichia coli sequence type (ST) 38 with putative uropathogenicity factors ( 1 ). Here we report a genetic cluster of 20 OXA-48–producing uropathogenic Escherichia coli (UPEC) ST127 isolates in the Netherlands.…”

“…For all isolates, we perform meropenem Etest, carbapenem inactivation method, next-generation sequencing (NGS; lllumina, https://www.illumina.com ), and long-read sequencing (Oxford Nanopore Technologies, https://www.nanoporetech.com ). We use NGS data to analyze the Clermont phylotype ( 2 ), core-genome single-nucleotide polymorphisms, classical multilocus sequence typing (MLST) STs, and in-house E. coli whole-genome MLST (wgMLST) types ( 1 , 3 ). We also evaluated presence of antimicrobial resistance genes (AMRfinder, https://www.ncbi.nlm.nih.gov/pathogens/antimicrobial-resistance/AMRFinder ), plasmid replicons (PlasmidFinder, https://cge.food.dtu.dk/services/PlasmidFinder ), and 31 previously described putative uropathogenicity factors (PUFs) using an in-house PUFfinder ( 4 ).…”