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

Abstract

BackgroundThe 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.ResultsOne 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.ConclusionsOur 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.

A combination ofLactobacillus buchneriandPediococcus pentosaceusextended the aerobic stability of conventional and brown midrib mutants–corn hybrids ensiled at low dry matter concentrations by causing a major shift in their bacterial and fungal community

“…The genus Hafnia has been reported in Italian ryegrass silage (Heron et al, 1993), but few studies describe it as part of the phyllosphere microbiome of fresh corn. Some Hafnia species are known to be gut pathogens (Yin et al, 2019). Romero et al (2018) and Ni et al (2017) also Downloaded from https://academic.oup.com/jas/article/99/8/skab141/6271125 by UNIVERSITA DEGLI STUDI DI FIRENZE, BIBLIOTECA BIOMEDICA user on 24 February 2022 reported Erwinia and Sphingobacterium in fresh whole-crop corn, but other studies differ in the main genera identified, including Acinetobacter, Klebsiella, and Weissella (Keshri et al, 2018) and Agrobacterium, Microbacterium, and Sphingobacterium (Xu et al, 2019).…”

First Characterization of a Hafnia Phage Reveals Extraordinarily Large Burst Size and Unusual Plaque Polymorphism

“…It is normally isolated from the gastrointestinal tract of animals and humans and from food (Osuka et al, 2011). There are a number of reports on diseases associated with H. alvei and H. paralvei involved in a variety of animal and human infections (Real et al, 1997;Casagrande Proietti et al, 2004;Casanova-Román et al, 2004;Janda and Abbott, 2006;Osuka et al, 2011;Padilla et al, 2013;Orozova et al, 2014;Jayol et al, 2017;Litrenta and Oetgen, 2017;Rodríguez-Alarcón et al, 2019;Yin et al, 2019;Zhang et al, 2019;Cutuli et al, 2021). The main symptoms of H. alvei diseases included hepatosplenomegaly, multifocal nectrotizing hepatitis, and splenitis (Real et al, 1997;Casagrande Proietti et al, 2004;Orozova et al, 2014).…”

The complete genome sequence of Hafnia alvei A23BA; a potential antibiotic-producing rhizobacterium

“…It is almost never associated with antibiotic production except for the antimicrobial activities reported for a strain isolated from the gut of honeybees [ 7 ]. Phylogenetic studies of this little-known species have shown its pan-genome to be open and dynamic with each strain possessing sets of unique genes [ 8 ]. Unique gene acquisition is mainly by horizontal gene transfer, and it reflects the adaptation of strains to their remarkably diverse natural habitats.…”