Molecular genetic characteristics of Vibrio cholerae nono1/nono139 strain, the causative agent of a new case of acute intestinal infection in Rostov-on-Don

During more than 50 years, a heterogeneous population of Vibrio cholerae non-O1/non-O139 (NAGs) exists in Rostov region of Russia, whose representatives periodically cause acute human intestinal infections; the last case was registered in 2018. In 2022, a sick child was again revealed in Rostov, from whom 2 NAG subcultures were isolated. Aim of the study: bioinformatics analysis of whole genome sequences (WGSs) of the 2022 clinical NAG isolates, genetic determinants of pathogenicity factors and relevant products. Materials and methods. Isolation, identification of cultures, as well as antibiotic sensitivity were carried out according to the MUK 4.2.3745-22. SNP analysis of WGSs obtained on the MiSeq Illumina platform were analyzed by means of designed software; BioEdit 7.2.5, Vector NTI Advance 11 package, CARD database were used to identify and analyze genes and relevant deduced products. Results. The isolated cultures with identical phenotypic features, PCR-genotypes and results of SNP analysis, were identified as a non-toxigenic NAG. The agent showed sensitivity to chloramphenicol, ceftriaxone, streptomycin, gentamicin, nalidixic acid, ciprofloxacin, ampicillin, amikacin and intermediate resistance to tetracycline, doxycycline, furazolidon and co-trimoxazole. WGSs lacked CTX and preCTX prophages, pathogenicity island VPI, thermostable and cholix toxin genes, pandemic islands VSP-I and VSP-II. The determinants of the type 6 secretion system (T6SS) were not presented completely, which evidenced in favor of the loss of its functionality. An intact T3SS cluster was revealed, which was adjacent to the nan-nag region of the VPI-2 pathogenicity island in the absence of the proximal and distal parts of the latter. Other determinants of pathogenicity factors were revealed: RTX cluster responsible for synthesis of MARTX cytotoxin, genes for hemolysin HlyA, cytotonic toxin Cef, several serine and metalloproteases. The nucleotide compositions of most determinants differed from the prototypes, but their putative products preserved characteristic active domains. The adhesive activity might be provided by mannose-insensitive MSHA-like pili, since the msh-cluster included all the genes necessary for their production, as well as flagella, as both clusters responsible for their assembling were 99% identical to the prototype. From antibiotic resistance determinants only β-lactamase VarG gene was found. Conclusion. The NAG strain examined here contains a sufficient set of intact virulence-associated genetic determinants, expression of which could contribute to the development of the disease.