Genomic Characterization of Arcobacter butzleri Isolated From Shellfish: Novel Insight Into Antibiotic Resistance and Virulence Determinants

Abstract

Arcobacter (A.) butzleri is an emerging pathogenic microorganism, whose taxonomy has been recently suggested to be emended to the Aliarcobacter (Al.) butzleri comb. nov. Despite extensive taxonomic analysis, only few fragmented studies have investigated the occurrence and the prevalence of virulence and antibiotic resistance determinants of this species in strains isolated from shellfish. Herein we report for the first time the whole genome sequencing and genomic characterization of two A. butzleri strains isolated from shellfish, with particular reference to the antibiotic, heavy metals and virulence determinants. This study supported the taxonomic assignment of these strains to the Al. butzleri species, and allowed us to identify antibiotic and metal resistance along with virulence determinants, also additional to those previously reported for the only two A. butzleri strains from different environments genomically characterized. Moreover, both strains showed resistance to β-lactams, vanocomycin, tetracycline and erythromycin and susceptibility to aminoglycosides and ciprofloxacin. Beside enlarging the availability of genomic data to perform comparative studies aimed at correlating phenotypic differences associated with ecological niche and geographic distribution with the genetic diversity of A. butzleri spp., this study reports the endowment of antibiotic and heavy metal resistance and virulence determinants of these shellfish-isolated strains. This leads to hypothesize a relatively high virulence of A. butzleri isolated from shellfish and prompt the need for a wider genomic analysis and for in vitro and in vivo studies of more strains isolated from this and other ecological niches, to unravel the mechanism of pathogenicity of this species, and the potential risk associated to their consumption.

Keywords: Aliarcobacter butzleri; Arcobacter butzleri; antibiotic and heavy metal resistance; emerging foodborne pathogen; food safety; genomics; shellfish; virulence genes.

FIGURE 1

COGs functional classification of genes present in A. butzleri 55 and A. butzleri 6V genomes.

FIGURE 2

Genomic organization of waaC/waaF gene cluster in A. thereius LMG 24486, A. butzleri ED-1, A. butlzeri 6V, A. butzleri 55, and A. butzleri RM4018. Gene clustering is represented by the arrows superposed on the black horizontal line. Intergenic spaces are not drawn in scale. For A. thereius LMG 24486, A. butzleri ED-1, and A. butzleri RM4018, the locus tag of each gene is indicated below the respective gene arrow; for A. butlzeri 6V and A. butzleri 55, protein ID is indicated below the respective gene arrow. Red arrows in A. butlzeri ED-1 and A. butzleri 6V indicate genes with no orthologue in A. butzleri 55 and A. butlzeri RM4018. D3M75_05155 ^∗ indicates pseudogene (frameshifted). lAaT: lipid A biosynthesis acylTransferase; dK: diacylglycerol kinase; yejM: inner membrane protein yejM; O-aL: O-antigen ligase; hP: hypotetical protein; gT: glycosyltransferase; pgaB: poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase; eptA: phosphoethanolamine transferase eptA; rfaF: lipopolysaccharide heptosyltransferase II; aT: acetyltransferase; sunS: glycosyltransferase sunS; aLP: alkaline phosphatase family protein; gPtT: glucose-1-phosphate thymidylyltransferase rfbA; yrbL-phoP: regulatory network protein; degT: DegT/DnrJ/EryC1/StrS family aminotransferase; rfbA: glucose-1-phosphate thymidyl transferase; rfbB: dTDP-glucose 4,6-dehydratase 1; rfbC: dTDP-4-dehydrorhamnose 3,5-epimerase; rfbD: dTDP-4-dehydrorhamnose reductase; mbOat: membrane bound O-acyl transferase; yrbL-phoP: YrbL-PhoP reg domain containing protein.

FIGURE 3

Multialignment of OXA beta-lactamase from Arcobacter butzleri obtained by using T-Coffee web server (Di Tommaso et al., 2011). Ab 55 protein ID: D3M61_10735; Ab 6V: D3M75_10375; OXA-491, Accession: ANW35665.1; OXA-464: ANW35663.1; OXA-490: ANW35664.1. A. butzleri RM4018: WP_012013127.1; A. butzleri S2_012_000_R2_80: PZP12670.1; A. butzleri L348: WP_046997374.1; A. butzleri L353: WP_050071304.1; A. butzleri ED-1: WP_014468976.1; A. buzleri L355: WP_046997672.1; A. butzleri JV22: EFU68937.1; A. butzleri L349: WP_046993700.1; A. butzleri L.: WP_014474670.1; A. skirrowii CCUG 10374: WP_115588490.1.