Genetic Characterization of an ST5571 Hypervirulent Strain Co-Producing NDM-1, MCR-1, and OXA-10 Causing Bacteremia.

PURPOSE

To investigate the phenotypic and genomic characteristics of the multi-drug resistant and hypervirulent strain recovered from bacteremia.

METHODS

Antimicrobial susceptibility testing (AST) was performed by the microdilution method. Antimicrobial resistance genes, virulence-associated genes, multilocus sequence typing (MLST), and plasmid replicon were characterized by next-generation sequencing (NGS) and nanopore sequencing. S1 nuclease-pulsed field gel electrophoresis (S1-PFGE) and Southern blotting were performed to characterize the plasmid profile.

RESULTS

The hypervirulent colistin- and carbapenem-resistant strain DY2009 was identified as ST5571, co-carrying , and . In silico analysis found that it was K2 serotype. AST results revealed that DY2009 was resistant to carbapenems, cephalosporins, ciprofloxacin, chloramphenicol, and colistin but remained susceptible to aztreonam, gentamicin, amikacin, and tigecycline. Through the whole-genome analysis, a variety of virulence determinants were identified, including . Plasmid analysis confirmed that the and gene harbored a ~33 kb IncX4 plasmid and a ~44 kb IncX3 plasmid. In contrast, was encoded by chromosome.

CONCLUSION

To the best of our knowledge, we first report the clinical hypervirulent isolate co-producing MCR-1, NDM-1, and OXA-10 causing bacteremia. We found that and genes were located on two self-conjugative epidemic plasmids, contributing to the widespread MCR-1 and NDM-1 in China. The results of this work improve our understanding of the genetic background of colistin- and carbapenem-resistant isolate from bacteremia and the resistance mechanisms. Our findings highlight the urgent need for infection control of such strain to prevent it from becoming an extensive-drug resistant clone.