Shewanella species as the origin of blaOXA-48 genes: insights into gene diversity, associated phenotypes and possible transfer mechanisms

Abstract

Chromosome-encoded beta-lactamases of Shewanella spp. have been indicated as probable progenitors of bla_OXA-48-like genes. However, these have been detected in few Shewanella spp. and dissemination mechanisms are unclear. Thus, our main objective was to confirm the role of Shewanella species as progenitors of bla_OXA-48-like genes. In silico analysis of Shewanella genomes was performed to detect bla_OXA-48-like genes and context, and 43 environmental Shewanella spp. were characterised. Clonal relatedness was determined by BOX-PCR. Phylogenetic affiliation was assessed by 16S rDNA and gyrB sequencing. Antibiotic susceptibility phenotypes were determined. The bla_OXA-48-like genes and genetic context were inspected by PCR, hybridisation and sequence analysis. Gene variants were cloned in Escherichia coli and MICs were determined. Shewanella isolates were screened for integrons, plasmids and insertion sequences. Analysis of Shewanella spp. genomes showed that putative bla_OXA-48-like is present in the majority and in an identical context. Isolates presenting unique BOX profiles affiliated with 11 Shewanella spp. bla_OXA-48-like genes were detected in 22 isolates from 6 species. Genes encoded enzymes identical to OXA-48, OXA-204, OXA-181, and 7 new variants differing from OXA-48 from 2 to 82 amino acids. IS1999 was detected in 24 isolates, although not in the vicinity of bla_OXA-48 genes. Recombinant E. coli strains presented altered MICs. The presence/absence of bla_OXA-48-like genes was species-related. Gene variants encoded enzymes with hydrolytic spectra similar to OXA-48-like from non-shewanellae. From the mobile elements previously described in association with bla_OXA-48-like genes, only the IS1999 was found in Shewanella, which indicates its relevance in bla_OXA-48-like genes transfer to other hosts.

Keywords: Class D carbapenemases; OXA-48-like; Origin; Shewanella.