Co-existence of two blaNDM-5 and blaOXA-181 on distinct plasmids in a carbapenem-resistant Klebsiella pneumoniae from a tertiary hospital, Tanzania

Purpose: To understand the mechanisms of carbapenem-resistant Klebsiella pneumoniae (CRKP) from Tanzania and characterize the genomes carrying the carbapenemase genes. Methods: Clinical CRKP isolates were selected from ongoing antimicrobial resistance surveillance at Muhimbili National Hospital, Dar es Salaam, Tanzania. Whole-genome sequencing was performed utilizing Illumina and Nanopore platforms. Results: A total of twelve CRKP were analyzed in this study. Six different multilocus sequence types were detected, six isolates were sequence type ST437 and one belonged to a novel sequence type, ST6258. Resistance to carbapenems was multifactorial with co-existence of blaNDM-5 and blaOXA-181 in six CRKP, and blaNDM-5 and blaOXA-232 in one isolate, and chromosomal mutation of ompK36 and ompK37 in all twelve isolates. All the CRKP carried genes conferring resistance to 3rd generation cephalosporins, penicillin, aminoglycosides, fosfomycin, trimethoprim-sulfamethoxazole, and quinolones. The hybrid assemblies of 001BS and 002PS2 revealed that they harbored seven and six different plasmids, respectively. The 001BS carried two blaNDM-5 on distinct plasmids. The first blaNDM-5 gene was carried on an IncFIB(K) plasmid; and the second blaNDM-5 co-existed with blaOXA-181 on the ColPK3-IncX3 plasmid. In contrast, in 002PS2 the blaNDM-5 and blaOXA-181 were carried on the IncFIB(K)-IncFII(K) and ColPK3-IncX3 plasmids, respectively. The genetic environment of the blaNDM-5 gene on both plasmids was flanked by the same genetic core IS26–IS30–blaNDM-5 –ble–trpF–DsbD–ISCR1–sul1– QacE–IS3000. Conclusion: Clonally related CRKP ST437 with multiple co-existing carbapenemase genes were detected for the first time at the tertiary hospital in Tanzania. The existence of this high-risk clone poses a great risk for further spread at our facility.