Klebsiella Spp. Isolated from Chlorinated Sewage Are Similar to Pathogenic Strains but with a Limited Resistome

Previous studies have described the potential emergence of treatment-resistant pathogenic E. coli in municipal sewage. This study sought to characterize a group of chlorine-tolerant Klebsiella pneumoniae species complex (KpSC) isolates based on antimicrobial resistance genes (ARGs), phylogenetic relationships to clinical strains, and other genomic traits associated with pathogenicity. Sewage samples collected from various wastewater treatment plants in Alberta, Canada, were treated with chlorine bleach at doses sufficient to reduce coliform bacteria by 4 log10 (i.e., 99.99% reduction), yielding 21 chlorine-tolerant KpSC isolates. Comparative genomics was used to characterize these chlorine-tolerant KpSC isolates against publicly available genomes from clinical and non-clinical KpSC strains. Chlorine-tolerant KpSC isolates belonged to 15 different sequence types and included Klebsiella pneumoniae, Klebsiella quasipneumoniae, and Klebsiella variicola, which are among the most common and clinically relevant KpSC phylogroups. Phylogenetically, chlorine-tolerant isolates from sewage were genetically diverse, clustering with clinical genomes according to species and sequence type, and reflecting significant strain diversity. Of the 21 chlorine-tolerant sewage isolates, eight resolved into a clade with one or more exclusively clinical genomes. Six isolates differed by < 80 single nucleotide polymorphisms from at least one clinical isolate, implying high genetic similarity to clinical strains. Virulence gene profiles were also remarkably similar, albeit the resistomes of the chlorine-tolerant sewage isolates lacked many relevant ARGs frequently detected in related clinical genomes. Collectively, these data suggest that chlorine-tolerant KpSC sewage isolates may be clinically important.