Gene clusters of Hafnia alvei strain FB1 important in survival and pathogenesis: a draft genome perspective

Abstract

BackgroundHafnia alvei is an opportunistic pathogen involved in various types of nosocomical infections. The species has been found to inhabit food and mammalian guts. However, its status as an enteropathogen, and whether the food-inhabiting strains could be a source of gastrointestinal infection remains obscure. In this report we present a draft genome of H. alvei strain FB1 isolated from fish paste meatball, a food popular among Malaysian and Chinese populations. The data was generated on the Illumina MiSeq platform.ResultsA comparative study was carried out on FB1 against two other previously sequenced H. alvei genomes. Several gene clusters putatively involved in survival and pathogenesis of H. alvei FB1 in food and gut environment were characterised in this study. These include the widespread colonisation island (WCI), the tad locus that is known to play an essential role in biofilm formation, a eut operon that might contribute to advantage in nutrient acquisition in gut environment, and genes responsible for siderophore production This features enable the bacteria to successful colonise in the host gut environment.ConclusionWith the whole genome data of H. alvei FB1 presented in this study, we hope to provide an insight into future studies on this candidate of enteropathogen by looking into the possible mechanisms employed to survive stresses and gain advantage in competitions, which eventually leads to successful colonisation and pathogenesis. This is to serve as the basis for more effective clinical diagnosis and treatment.

Sequencing and Genomic Diversity Analysis of IncHI5 Plasmids

“…As observed in the chromosome (Accession No. CP009706) of Hafnia alvei FB1 (Tan et al, 2014), Tn 6535 was assembled from integration of an ars region with a Tn 3 -family core transposition module tnpA – res – tnpR .…”

“…Numbers in brackets indicate nucleotide positions within corresponding plasmids. The accession numbers of Tn 6535 (Tan et al, 2014), Tn 6399a (Murata et al, 2002), Tn 1722 (Allmeier et al, 1992), Tn 6029 (Cain et al, 2010), Tn 6292 (Wei et al, 2016), Tn 1548 (Galimand et al, 2005), IS 26 – catA2 –IS 26 unit (Xiang et al, 2015), Tn 2 (Bailey et al, 2011), aacC2 – tmrB region (Partridge et al, 2012), and Tn 6339 (Liang et al, 2017) for reference are CP009706, AP004237, X61367, HQ840942, KU886034, AF550415, KY270851, HM749967, JX101693, and CP003684, respectively. Arrowheads indicated location of PCR primers and expected amplicons.…”

Transcriptome analysis ofPseudomonas aeruginosaPAO1 grown at both body and elevated temperatures

“…Next Generation sequencing (NGS) has been proven to be an invaluable technology to study bacteria genomes ( Chan, Yin & Lim, 2014 ; Chan et al, 2013 ; Chan et al, 2012 ; Forde et al, 2014 ; Lau, Yin & Chan, 2014 ; Tan, Yin & Chan, 2014 ). In particular RNA-seq can provide a complete coverage of protein-coding genes, intergenic regions and non-coding RNA and small, regulatory RNA populations in a given genome ( Wang, Gerstein & Snyder, 2009 ).…”

Effect of the luxI/R gene on AHL-signaling molecules and QS regulatory mechanism in Hafnia alvei H4

“…To date, only three other H. alvei genomes have been sequenced, one is from strain ATCC 51873, isolated from the gut; another is BIDMC 31, which was investigated as part of the carbapenem resistance study, and was isolated from unspecified clinical source (http://www.ncbi.nlm.nih.gov/genome) (Tan et al 2014). The third genome sequencing was performed for H. alvei FB1 isolated from fish meatballs, also a marine source, similar to H. alvei H4, which was isolated from instant sea cucumbers.…”