Community and clinical resistomes and mobilomes: a comparative genomic snapshot of Escherichia coli and Klebsiella pneumoniae

Abstract

Abstract Escherichia coli and Klebsiella pneumoniae are major contributors to antimicrobial resistance (AMR)-related mortality globally. The resistomes, mobilomes, clonalities, and phylogenies of 32 E. coli (15 clinical, 17 community) and 14 K. pneumoniae (6 clinical, 8 community) isolates from KwaZulu-Natal were compared to ascertain similarities and differences between healthcare-related pathogens and community commensals using whole genome sequencing and bioinformatic pipelines. Resistome analysis revealed that bla CTX−M−15 predominated in clinical isolates of both E. coli and K. pneumoniae , whereas bla TEM−1B was more common in community E. coli . Two clinical E. coli harboured bla OXA−181 , and one K. pneumoniae carried bla OXA−181 and bla NDM−5 ; none were detected in community isolates. IncF plasmid replicons were most frequent, and gene cassettes within class 1 integrons, insertion sequences, and transposons contributed to resistome mobilization across both settings. A broad range of sequence types (STs) were detected across both settings, with shared STs limited to ST131, ST10, and ST1193 in E. coli , and ST17 in K. pneumoniae . Phylogeny showed that clinical E. coli clustered with some community isolates, while K. pneumoniae showed limited clustering. The overlap of resistomes, mobilomes, STs and phylogenies suggests genomic relatedness between isolates from both settings, highlighting the importance of AMR surveillance in community settings.