Community and Clinical Resistomes and Mobilomes: A Correlation

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 (WGS) and bioinformatic pipelines. Resistome analysis revealed that bla _CTX−M−15 predominated in clinical isolates, whereas bla _TEM−1B was more common in community E. coli , and all K. pneumoniae isolates carried a bla _SHV variant. 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 ARG 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, and STs suggest potential AMR transmission between settings, highlighting the importance of AMR surveillance in community settings.