Virulence and antibiotic resistance plasticity ofArcobacter butzleri: insights on the genomic diversity of an emerging human pathogen

Abstract

Arcobacter butzleri is a food and waterborne bacteria and an emerging human pathogen, frequently displaying a multidrug resistant character. Still, no comprehensive genome-scale comparative analysis has been performed so far, which has limited our knowledge on A. butzleri diversification and pathogenicity. Here, we performed a deep genome analysis of A. butzleri focused on decoding its core-and pan-genome diversity and specific genetic traits underlying its pathogenic potential and diverse ecology. In total, 49 A. butzleri strains (collected from human, animal, food and environmental sources) were screened.A. butzleri (genome size 2.07-2.58 Mbp) revealed a large open pan-genome with 7474 genes (about 50% being singletons) and a small core-genome with 1165 genes. The core-genome is highly diverse (≥55% of the core genes presenting at least 40/49 alleles), being enriched with genes associated with housekeeping functions. In contrast, the accessory genome presented a high proportion of loci with an unknown function, also being particularly overrepresented by genes associated with defence mechanisms. A. butzleri revealed a plastic virulome (including newly identified determinants), marked by the differential presence of multiple adaptationrelated virulence factors, such as the urease cluster ureD(AB)CEFG (phenotypically confirmed), the hypervariable hemagglutinin-encoding hecA, a putative type I secretion system (T1SS) harboring another agglutinin potentially related to adherence and a novel VirB/D4 T4SS likely linked to interbacterial competition and cytotoxicity. In addition, A. butzleri harbors a large repertoire of efflux pumps (EPs) (ten "core" and nine differentially present) and other antibiotic resistant determinants. We provide the first description of a genetic determinant of macrolides resistance in A. butzleri, by associating the inactivation of a TetR repressor (likely regulating an EP) with erythromycin resistance. Fluoroquinolones resistance correlated with the Thr-85-Ile substitution in GyrA and ampicillin resistance was linked to an OXA-15-like β-lactamase. Remarkably, by decoding the polymorphism pattern of the porin-and adhesin-encoding main antigen PorA, this study strongly supports that this pathogen is able to exchange porA as a whole and/or hypervariable epitope-encoding regions separately, leading to a multitude of chimeric PorA presentations that can impact pathogen-host interaction during infection. Ultimately, our unprecedented screening of short sequence repeats detected potential phasevariable genes related to adaptation and host/environment interaction, such as lipopolysaccharide modification and motility/chemotaxis, suggesting that phase variation likely modulate A. butzleri key adaptive functions.In summary, this study constitutes a turning point on A. butzleri comparative genomics revealing that this human gastrointestinal pathogen is equipped with vast virulence and antibiotic resistance arsenals, which, coupled with its remarkable core-and pan-genome diversity, opens a multitude of ...

Genomic Analysis and Antimicrobial Resistance of Aliarcobacter cryaerophilus Strains From German Water Poultry

“…The glyA paralogs were identical in two genomes [17CS1055-B and L401(accession: GCF_001572845.1 )] but showed variants in one genome (ATCC 49165). Isidro et al (2020) also observed this for the glyA gene in strains of the species A. butzleri . Thus, this specific locus may not be suitable for MLST typing because it may lead to an incorrect allele calling as it has been reported for Acinetobacter baumanii ( Gaiarsa et al, 2019 ).…”

“…Utilizing the genomes of cluster I the genetic prediction of antimicrobial resistance genes was done using the custom database created by Isidro et al (2020) . Out of 19 efflux pump (EP) systems which have been detected in A. butzleri genomes, 16 were found in the A. cryaerophilus genomes belonging to cluster I ( n = 44) ( Figure 4 ).…”

“…Those findings showed that A. cryaerophilus harbors all major families of efflux transporters that are present in prokaryotes apart from the multidrug and toxic efflux (MATE) family ( Webber and Piddock, 2003 ). Since the protein size of regulator TetR (RM4018p_22360) from EP16 is supposed to correlate with the erythromycin resistance, Isidro et al (2020) hypothesized that truncating mutations in TetR lead to an overexpression of EP16 and thus to increased erythromycin excretion and ultimately cause resistance or tolerance to this antibiotic. The regulator TetR was not present in our 27 German A. cryaerophilus strains, which were all susceptible to erythromycin.…”

“…For further investigations, the virulence and antimicrobial resistance determinants from the corresponding A. butzleri strains described by Isidro et al (2020) were extracted with Geneious Prime ® 2019.2.3 ( Kearse et al, 2012 ). All extracted genes were grouped in a custom database and searched within the genomes.…”

“…For that, a pangenome was constructed for all strains using Roary v3.12.0 (options -i 90 -s) ( Page et al, 2015 ). Then, the sequences of the pangenome were BLASTed against the custom database from Isidro et al (2020) using BLASTP ( Altschul et al, 1990 ) with the following thresholds: coverage 70% and E -value 1–20e. BLAST hits with more than 40% identity at the protein level were reported ( Pearson, 2013 ).…”