Hidden in the community: poly-clonal spread of KPC- or NDM-producing Klebsiella pneumoniae revealed by whole-genome sequencing in Southeastern Brazil

OBJECTIVES: Carbapenemase-producing Klebsiella pneumoniae remains a major driver of multidrug resistance, traditionally linked to healthcare-associated infections but its detection in community-acquired infections represents a worrying shift. We aimed to characterize community-origin KPC- or NDM-producing K. pneumoniae isolates from two cities in São Paulo State, Brazil. METHODS: A laboratory-based surveillance was conducted, including 111 non-duplicate K. pneumoniae isolates from urine of non-hospitalized patients. Polymyxin B MICs were determined by broth microdilution. All isolates underwent Illumina WGS. In silico analyses used Kleborate and Roary were used for bioinformatics analyses. RESULTS: 76% of the isolates were susceptible to polymyxin. The most frequent carbapenemase gene detected was KPC-2 (94.5%), but KPC-3, NDM-1 and NDM-5 were detected. MLST showed high clonal diversity (14 STs), dominated by ST11 (n = 34) and ST437 (n = 20), followed by ST16 (n = 12), ST6386 (n = 10), ST258 (n = 9), ST147 (n = 6), ST307 (n = 5), among others. Core-genome phylogeny revealed a polyclonal structure with multiple subclusters, consistent with community dissemination, grouped by ST. No classic hvKp plasmid markers were detected by Kleborate. Resistome were diverse. CONCLUSIONS: . The detection of secondary complexes such as CC16, CC147, and CC307, and the identification of NDM-producing isolates, highlight the polyclonal nature of dissemination and suggest ongoing genomic adaptation in community settings. The genomic diversity observed here reinforces the potential of environmental and community as non-obvious reservoirs contributing to KPC and NDM spread beyond hospital boundaries.