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Genomic analysis unveils important aspects of population structure, virulence, and antimicrobial resistance in Klebsiella aerogenes
Author(s) -
PassarelliAraujo Hemanoel,
Palmeiro Jussara K.,
Moharana Kanhu C.,
PedrosaSilva Francisnei,
DallaCosta Libera M.,
Venancio Thiago M.
Publication year - 2019
Publication title -
the febs journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.981
H-Index - 204
eISSN - 1742-4658
pISSN - 1742-464X
DOI - 10.1111/febs.15005
Subject(s) - virulence , enterobacter aerogenes , biology , genetics , population , klebsiella pneumoniae , antibiotic resistance , multilocus sequence typing , genome , microbiology and biotechnology , genotype , gene , virology , antibiotics , escherichia coli , medicine , environmental health
Klebsiella aerogenes is an important pathogen in healthcare‐associated infections. Nevertheless, in comparison to other clinically important pathogens, K. aerogenes population structure, genetic diversity, and pathogenicity remain poorly understood. Here, we elucidate K. aerogenes clonal complexes ( CC s) and genomic features associated with resistance and virulence. We present a detailed description of the population structure of K. aerogenes based on 97 publicly available genomes by using both multilocus sequence typing and single‐nucleotide polymorphisms extracted from the core genome. We also assessed virulence and resistance profiles using Virulence Finder Database and Comprehensive Antibiotic Resistance Database, respectively. We show that K. aerogenes has an open pangenome and a large effective population size, which account for its high genomic diversity and support that negative selection prevents fixation of most deleterious alleles. The population is structured in at least 10 CC s, including two novel ones identified here, CC 9 and CC 10. The repertoires of resistance genes comprise a high number of antibiotic efflux proteins as well as narrow‐ and extended‐spectrum β‐lactamases. Regarding the population structure, we identified two clusters based on virulence profiles because of the presence of the toxin‐encoding clb operon and the siderophore production genes, irp and ybt . Notably, CC 3 comprises the majority of K. aerogenes isolates associated with hospital outbreaks, emphasizing the importance of constant monitoring of this pathogen. Collectively, our results may provide a foundation for the development of new therapeutic and surveillance strategies worldwide.