Table 5.

Virulence gene profiles of Vibrio cholerae non-O1, non-O139 isolates from German coastal waters and from German clinical samples based on WGS data.

CP-CRVc, carbapenemase producing carbapenem-resistant Vibrio cholerae; ET, El Tor; FVG, few virulence-associated genes/gene clusters (according to PCR data); MVG, many virulence-associated genes/gene clusters (according to PCR data); SA ME, sialic acid metabolism. ^aThe MLST groups are explained in section “Materials and Methods”. Clinical STs are marked in red. ^bAll strains of the MLST groups selected for whole genome sequencing were compared regarding sequence type, year of isolation, geographical origin, sample type, and PCR-based virulence gene profile. Presumably identical strains were summarized in subgroups. One strain from each subgroup was selected for whole genome sequencing. Clinical strains are marked in red. ^cAll strains were negative for VSP-1 and stn. Reference sequences for WGS analysis are given in section “Materials and Methods”. In general, strains showing >90% sequence similarity to a specific reference sequence were defined as positive for the respective virulence-associated trait. Further details are given in the “Results” section. ^∗Virulence-associated gene/gene cluster initially investigated by PCR. ^∗∗Virulence-associated gene only investigated by PCR. ^dStrain belonging to more than one MLST group.