Characterizing multidrug resistance plasmids from Botswanan bacterial isolates

Antimicrobial resistance is a disseminated global health challenge because many of the genes that cause resistance can transfer horizontally between bacteria. Resistance genes often accumulate and coalesce on extrachromosomal DNA elements called plasmids. Despite the central role of plasmids in driving the spread of resistance, detection and surveillance of plasmids remains a significant barrier in molecular epidemiology because the modularity of gene cassettes and the abundance of repetitive DNA elements hampers the assembly of plasmids from genomic datasets. We sought to assemble the plasmid complements of two extensively drug resistant bacterial isolates, Escherichia coli HUM3355 and Klebsiella pneumoniae HUM7199, that were isolated from human feces in Botswana. All five plasmids encoded one or more antibiotic resistance genes, and four were found to encode genes for conjugative transfer. Two plasmids were almost identical to antibiotic resistance plasmids sequenced in Europe and North America from human infections and a pig farm, illustrating the One Health connections that enable resistance determinants to move between hosts and continents. The other three plasmids contained large and novel gene islands containing multiple resistance genes. Altogether, whole genome assemblies demonstrated the benefits of genomics for infectious disease tracking and antibiotic resistance gene identification and surveillance in low- and middle-income countries.