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

Abstract

Aliarcobacter cryaerophilus (formerly Arcobacter cryaerophilus) is a globally emerging foodborne and zoonotic pathogen. However, little is known about the species' genomic features and diversity, antibiotic resistance and virulence. In this study, 27 A. cryaerophilus strains from water poultry in Thuringia, Germany, were investigated using whole-genome sequencing. Four of these strains were sequenced using longand short-read sequencing methods to obtain circularized genomes. The German strains belong to the A. cryaerophilus cluster I. Cluster I genomes exhibited a high degree of genetic diversity in which variable sites comprised 9.1% of the core genome. The German strains formed three subgroups that contained 2, 6, and 9 strains, respectively. The genomic analysis of cluster I revealed variable presence of mobile elements and that 65% of the strains lack CRISPR systems. The four circularized genomes carried a ∼2 Mbp chromosome and a single megaplasmid (size 98.1-154.5 Kbp). The chromosome was densely packed with coding sequences (∼92%) and showed inversions and shifts in the gene blocks between different strains. Antimicrobial resistance was assessed using a gradient strip diffusion method and showed that all 27 strains were resistant to cefotaxime and susceptible to erythromycin, gentamicin, and ampicillin. Sixteen strains were also resistant to ciprofloxacin, whereas 23 were resistant to streptomycin. The genetic prediction of antibiotic resistance identified numerous efflux pumps similar to those found in A. butzleri. All strains harbored two beta-lactamase genes which may explain the cefotaxime resistance. A correlation between the gyrA point mutation (Thr-85-Ile) and ciprofloxacin resistance was partially discovered in 15 out of 16 strains. In silico virulence profiling showed a wide range of virulence factors including a full chemotaxis system and most of the flagellar genes. In contrast to A. butzleri, no urease cluster was found. This study provides new insights into the genomic variability of A. cryaerophilus strains of cluster I. The different genetic makeup of these strains may contribute to the virulence of strains and the severity of the infections in humans.

Antimicrobial Resistance and in silico Virulence Profiling of Aliarcobacter butzleri Strains From German Water Poultry

“…The phylogenetic analysis did also not support clustering based on either the isolation source or geographical location of the genomes. Similar observations have been reported before for A. cryaerophilus (Müller et al, 2020b ).…”

“…However, in some genomes ( n = 10) the accurate assignment was not possible due to the presence of paralogs for the gly A and glt A loci (i.e., multiple copies in the same genome). Similar observations were made for strains of the species A. butzleri and A. cryaerophilus (Isidro et al, 2020 ; Müller et al, 2020b ), although the paralogs found here were not identical except for the glt A locus. While developing the first MLST scheme for Aliarcobacter , Miller et al ( 2009 ) reported the presence of two gly A loci, gly A1 and gly A2.…”

“…These were ~12,580 SNPs distant from each other. This phenomenon has also been described before for A. cryaerophilus isolates from German water poultry (Müller et al, 2020b ).…”

“…In that study, allele 1 was assigned to the gly A1 locus and allele 142 to the gly A2 locus (Miller et al, 2009 ). We conclude that the gly A locus is either not suitable for MLST analysis since it can lead to incorrect allele calling, or new bioinformatic approaches need to be developed to tackle this problem (Isidro et al, 2020 ; Müller et al, 2020b ).…”

Data_Sheet_1.xlsx

“…These were ∼12,580 SNPs distant from each other. This phenomenon has also been described before for A. cryaerophilus isolates from German water poultry (Müller et al, 2020b).…”