Whole-genome analysis of a multidrug-resistant Klebsiella michiganensis environmental isolate from an orthopedic ward in Mwanza, Tanzania reveals IncF-family plasmid replicon signatures associated with resistance determinants

Abstract

BACKGROUND: Klebsiella michiganensis, a member of the Klebsiella oxytoca species complex, is increasingly recognized in healthcare-associated infection and can persist in hospital environmental reservoirs. However, genome-resolved data on environmental K. michiganensis from Africa remain limited. METHODS: We performed short-read whole-genome sequencing (WGS) of an isolate recovered from a wheelchair handle in the orthopedic ward of a tertiary hospital in Mwanza, Tanzania. The isolate was initially recorded during routine surveillance as an unidentified Gram-negative ESBL bacterium and was provisionally identified phenotypically as K. oxytoca using routine laboratory methods. Draft assemblies were analyzed using the rMAP-2.0 bioinformatics pipeline. Genome-based taxonomic assignment using GTDB-Tk and ANI reclassified the study isolate as Klebsiella michiganensis. We then contextualized this genome with publicly available African K. michiganensis genomes and generated a core-genome phylogeny visualized in iTOL. RESULTS: GTDB-Tk reclassified the study isolate A55848, and the comparator public genomes included in the final revised phylogeny as Klebsiella michiganensis, with the closest GTDB reference genome being GCF_002925905.1 and an ANI of 98.97% for A55848. The Tanzanian environmental isolate carried IncFIB(K) and IncFII(K) plasmid replicons, together with Col440I/Col440II. ResFinder-based screening identified a multidrug resistance gene repertoire including blaOXY family alleles (e.g., blaOXY-1-2), blaTEM-1B, oqxA/oqxB, aph(3')-Ia, aac(6')-Ib, and aadA2, consistent with an MDR genotype. Phenotypic testing demonstrated an ESBL profile with reduced susceptibility to oximino-cephalosporins and piperacillin-tazobactam, while susceptibility to meropenem, amikacin, and ciprofloxacin was retained. MLST did not assign a recognized sequence type. Comparative analysis showed that African genomes frequently harbored IncFIB(K)/IncFII(K) replicons and clinically important β-lactamases, including blaCTX-M-15 and blaOXA-1, with one isolate carrying blaNDM-1. Core-genome phylogeny further indicated that related K. michiganensis lineages occur across multiple African countries and that MDR is not confined to a single lineage, supporting resistance acquisition within shared genomic backgrounds. CONCLUSIONS: Recovery of an MDR Klebsiella michiganensis from an orthopedic ward wheelchair handle, carrying IncF-family plasmid replicon signatures together with multiple antimicrobial resistance determinants, underscores the potential for hospital environmental surfaces to serve as reservoirs of resistance. These findings highlight the value of strengthening targeted environmental hygiene and integrating routine genome-informed surveillance to detect, monitor, and mitigate transmission risks in African hospital settings.