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Background  The  Hafnia  genus is an opportunistic pathogen that has been implicated in both nosocomial and community-acquired infections. Although  Hafnia  is fairly often isolated from clinical material, its taxonomy has remained an unsolved riddle, and the involvement and importance of  Hafnia  in human disease is also uncertain. Here, we used comparative genomic analysis to define the taxonomy of  Hafnia , identify species-specific genes that may be the result of ecological and pathogenic specialization, and reveal virulence-related genetic profiles that may contribute to pathogenesis.    Results  One complete genome sequence and 19 draft genome sequences for  Hafnia  strains were generated and combined with 27 publicly available genomes. We provided high-resolution typing methods by constructing phylogeny and population structure based on single-copy core genes in combination with whole genome average nucleotide identity to identify two distant  Hafnia  species ( alvei  and  paralvei ) and one mislabeled strain. The open pan-genome and the presence of numerous mobile genetic elements reveal that  Hafnia  has undergone massive gene rearrangements. Presence of species-specific core genomes associated with metabolism and transport suggests the putative niche differentiation between  alvei  and  paralvei . We also identified possession of diverse virulence-related profiles in both  Hafnia  species., including the macromolecular secretion system, virulence, and antimicrobial resistance. In the macromolecular system, T1SS, Flagellum 1, Tad pilus and T6SS-1 were conserved in  Hafnia , whereas T4SS, T5SS, and other T6SSs exhibited the evolution of diversity. The virulence factors in  Hafnia  are related to adherence, toxin, iron uptake, stress adaptation, and efflux pump. The identified resistance genes are associated with aminoglycoside, beta-lactam, bacitracin, cationic antimicrobial peptide, fluoroquinolone, and rifampin. These virulence-related profiles identified at the genomic level provide insights into  Hafnia  pathogenesis and the differentiation between  alvei  and  paralvei .    Conclusions  Our research using core genome phylogeny and comparative genomics analysis of a larger collection of strains provides a comprehensive view of the taxonomy and species-specific traits between  Hafnia  species. Deciphering the genome of  Hafnia  strains possessing a reservoir of macromolecular secretion systems, virulence factors, and resistance genes related to pathogenicity may provide insights into addressing its numerous infections and devising strategies to combat the pathogen.

bmc genomics

Comparative genomic analysis of the Hafnia genus reveals an explicit evolutionary relationship between the species alvei and paralvei and provides insights into pathogenicity