In-depth analysis ofKlebsiella aerogenesresistome, virulome and mobilome worldwide

Klebsiella aerogenes is an emergent pathogen associated with outbreaks of carbapenem-resistant strains. To date, studies focusing on K. aerogenes have been small-scale and/or geographically restricted. Here, we analyzed the epidemiology, resistome, virulome, and mobilome of this species based on 561 genomes, spanning all continents. Furthermore, we sequenced four new strains from Brazil (mostly from the Amazon region). Dozens of STs occur worldwide, but the pandemic clones ST93 and ST4 have prevailed in several countries. Almost all genomes were clinical, however, most of them did not carry ESBL or carbapenemases, instead, they carried chromosomal alterations ( omp 36, amp D, amp G, amp R) associated with resistance to β-lactams. Integrons were also identified, presenting gene cassettes not yet reported in this species ( bla IMP, bla VIM, bla GES). Considering the virulence loci, the yersiniabactin and colibactin operons were found in the ICEKp10 element, which is disseminated in genomes of several STs, as well as an incomplete salmochelin cluster. In contrast, the aerobactin hypervirulence trait was observed only in one ST432 genome. Plasmids were common, mainly from the ColRNAI replicon, with some carrying resistance genes ( mcr, bla TEM, bla NDM, bla IMP, bla KPC, bla VIM) and virulence genes (EAST1, sen B). Interestingly, plasmids containing the colicin gene occurred in hundreds of genomes of different STs.