Clinical Features, Genome Epidemiology, and Antimicrobial Resistance Profiles of spp. Causing Human Infections: A Multicenter Prospective Cohort Study.

Background: The genus is increasingly implicated in human infections, but knowledge of its clinical characteristics and antimicrobial resistance profiles has been limited owing to its complex taxonomy.

Methods: We conducted a multicenter prospective cohort study of patients with infections at hospitals across Japan. Patients were eligible for inclusion if they had an spp. strain in a clinical culture and were considered infected at the culture site. Clinical data were collected, and isolates underwent susceptibility testing and whole-genome sequencing.

Results: A total of 144 patients were included. Hepatobiliary infection accounted for a majority of infections (73% [105 of 144]), which mostly occurred in elderly patients with comorbid conditions, including hepatobiliary complications. The all-cause 30-day mortality rate was 10.0% (95% confidence interval, 4.9%-14.8%). By whole-genome sequencing, 141 strains (98%) belonged to 4 species, , , and with significant intraspecies diversity. was predominant in all infection sites except skin and soft tissue, for which was the prevailing species. The genes encoding chromosomally mediated class B, C, and D β-lactamases were harbored by 92%-100% of the isolates in a species-specific manner, but they often lacked association with resistance phenotypes. The activity of cefepime was reliable. All isolates of and carried an like colistin resistance gene and showed reduced susceptibility to colistin.

Conclusions: Hepatobiliary tract was the most common infection site of spp., with being the dominant causative species. The resistance genotype and phenotype were often incongruent for β-lactam agents.