Enterobacter roggenkampii ST422 with highly conjugative IncP plasmid carrying bla _KPC-2 gene from Lebanon: a case...

The Enterobacter cloacae complex (ECC) includes opportunistic pathogens that can be carbapenem resistant, thus complicating treatment regimens. Here, we characterized a carbapenem- and colistin-resistant ECC O89H7 isolate expressing KPC carbapenemase.

ECC O89H7 was isolated in January 2021 from an axillary swab performed during routine screening for multidrug-resistant (MDR) bacteria from a patient after 39 days of hospitalization in the intensive care unit (ICU) for severe COVID-19 pneumonia at Nini hospital (Tripoli, Lebanon). The ECC O89H7 was identified as E. roggenkampii (Er) belonging to sequence type (ST)422 and contained eight different plasmids as revealed by whole-genome sequencing (WGS). Er O89H7 was predicted to be a human pathogen (96.3%), harboring 51 virulence factors as well as genes conferring resistance to heavy metals and quaternary ammonium compounds. Er O89H7 was highly drug resistant, including resistance to carbapenems and colistin. The resistome revealed six β-lactamase genes: the chromosome-encoded bla _MIR-3 cephalosporinase, bla _LAP-2 and bla _SHV-12 encoded on a 115-kb IncM-1 plasmid, and bla _OXA-10 , bla _TEM-40, and bla _KPC-2 on a mobilizable IncP-6 plasmid of 51 kb, as revealed by mating-out assays.

Here, we have characterized a human pathogenic Er ST422 harboring bla _KPC-2 carbapenemase on an IncP-6 plasmid from Lebanon. Er O89H7 represents a major health threat due to limited therapeutic options, especially because novel β-lactam/inhibitor combinations are not available in Lebanon. Our results highlight an urgent need for improved carbapenemase screening and detection capacity in clinical laboratories and for enhanced genomic surveillance of MDR bacteria to implement intervention strategies to control their spread in Lebanon and beyond.