Understanding the genomic landscape of Klebsiella pneumoniae: insights into bacteraemia across North-West London hospitals between April 2020-December 2021

Introduction: Klebsiella pneumoniae is an opportunistic pathogen causing hospital-acquired antimicrobial-resistant (AMR) bacteraemia. The rise of multidrug-resistant strains of invasive K. pneumoniae, particularly those producing extended-spectrum β-lactamases or carbapenemases, necessitates comprehensive genomic investigation. Here, we characterise the genomes of K. pneumoniae causing bacteraemia in North-West London to identify common AMR and virulence determinants. Methods: We investigated 354 blood isolates collected at three tertiary hospitals across North-West London between April 2020 and December 2021. Genomic characterisation was completed using Kraken2, Bracken, MLST, PopPUNK, Kleborate, and ABRicate. Core-gene phylogenetic analysis was completed using ggCaller, SNP-sites, and IQ-TREE. Characterisation of plasmids was completed using MOB-suite. Results: Genomic diversity was high, with 140 sequence types (STs) identified throughout 2020-2021 (2020, 50 STs [n=78]; 2021, 113 STs [n=276]). Just 32 STs comprised ≥3 isolates, with ST15 commonest (6.8%, 24/354), followed by ST37 (5.6%, 20/354), and ST307 (5.1%, 18/354). Critically, four distinct carbapenemase genes were identified (n=11), with two OXA-48-like genes (blaOXA-181 [n=2] and blaOXA-48 [n=6]) detected in eight isolates (two from ST15), consistent with national data to suggest a predominance of OXA-48-like genes among carbapenemase genes in England. blaCTX-M-15 (n=92), which confers cefotaxime resistance, was the most common β-lactamase gene, followed by variants of blaTEM-1-D (n=82), which confer resistance to penicillins/first-generation cephalosporins. Altogether, 24 β-lactamase genes were carried by plasmids across 129 isolates from 123 distinct patients. 62.8% (91/145) of plasmids carrying such genes were positive for the replicon types, IncFIB or IncFII, which frequently co-occurred, underscoring the major role of IncF plasmids in disseminating AMR determinants among Enterobacteriaceae. 67.6% (98/145) of plasmids carrying β-lactamase genes were conjugative, with 49.7% (72/145) of these plasmids encoding MOBF-family relaxases, including a plasmid carrying blaNDM-5. However, all six blaOXA-48 genes were carried by an IncL/M MOBP conjugative plasmid, whilst other OXA-48-like genes (n=2) were carried on MOBP conjugative plasmids of two replicon types, and both blaNDM-1 genes carried on InC MOBH conjugative plasmids. Carriage of carbapenemase genes on multiple conjugative plasmids is concerning, and, despite a maximum prevalence of 3.1% (11/354) here, underpins the importance of their surveillance nationally. 149 isolates (56 STs) carried 50 other AMR genes, including streptomycin-resistance gene, strA (n=76), and trimethoprim-resistance gene, dfrA14 (n=77). No isolates carried colistin-resistance genes. Three key virulence loci (ybt, clb, and iuc) were prevalent even among isolates carrying β-lactamase genes (ST23 [n=3]), highlighting the potential of AMR and virulence determinants to jointly increase patient morbidity. Notably, the ybt locus, which encodes the iron-scavenging siderophore yersiniabactin, was commonest at the population level, with gene ybtX found in 151 isolates. Conclusion: All such insights may inform targeted interventions and the development of urgently needed therapeutics to combat the emergence and spread of multidrug-resistant K. pneumoniae in healthcare settings.