CTX-M-15-producing Shewanella sp. clinical isolate expressing OXA-535, a chromosome-encoded OXA-48 variant, putative progenitor of the plasmid-encoded OXA-436 [PublishAheadOfPrint]

Shewanella spp. constitute a reservoir of antibiotic resistance determinants. In a bile sample, we have identified three Extended Spectrum β-lactamase (ESBL)-producing bacteria (Escherichia coli, Klebsiella pneumoniae and Shewanella sp. JAB-1) isolated from a child suffering from cholangitis. Our objectives were to characterize the genome and the resistome of the first ESBL-producing isolate of the genus Shewanella and determine whether plasmidic exchange occurred between the three-bacterial species. Bacterial isolates were characterized using MALDI-TOF, standard biochemical tools and antimicrobial susceptibility testing. Shewanella sp JAB-1 and ESBL gene-carrying plasmids were characterized using PacBio and Illumina whole genome sequencing, respectively. The Shewanella sp JAB-1 chromosome-encoded OXA-48-variant was cloned and functionally characterized.

Whole genome sequencing (WGS) of the Shewanella sp. clinical isolate JAB-1 revealed the presence of a 193-kb plasmid belonging to IncA/C incompatibility group and harboring two ESBL genes: bla_CTX-M-15 and bla_SHV-2a. bla_CTX-M-15 gene carrying plasmids belonging to IncY and IncR incompatibility groups were also found in the E. coli and K. pneumoniae isolates from the same patient, respectively. Comparison of the bla_CTX-M-15 genetic environment indicated the independent origin of these plasmids and dismissed in vivo transfers. Furthermore, characterization of the resistome of Shewanella sp. JAB-1 revealed the presence of a chromosome-encoded bla_OXA-535 gene, likely the progenitor of the plasmid-encoded bla_OXA-436 gene, a novel bla_OXA-48-like gene. Expression of bla_OXA-535 in E. coli showed the carbapenem-hydrolyzing activity of OXA-535. The production of OXA-535 in Shewanella sp. JAB-1 could be evidenced using molecular and immuno-enzymatic tests, but not with biochemical tests that monitor carbapenem-hydrolysis. In this study, we have identified a CTX-M-15-producing Shewanella species that was responsible of an hepatobiliary infection and that is likely the progenitor of OXA-436, a novel plasmid-encoded OXA-48-like class D carbapenemases.

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