Table_1_Genomic Analysis and Antimicrobial Resistance of Aliarcobacter cryaerophilus Strains From German Water Poultry.XLSX

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 long- and 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.

嗜冷阿里弧菌（Aliarcobacter cryaerophilus，前称嗜冷弓形杆菌Arcobacter cryaerophilus）是一种在全球范围内逐渐受到关注的食源性人兽共患病原菌。目前学界对该物种的基因组特征、遗传多样性、抗生素耐药性及毒力特征仍知之甚少。本研究针对采自德国图林根州水禽体内的27株嗜冷阿里弧菌展开全基因组测序分析，其中4株采用长读长与短读长联合测序策略，成功获得了环状闭合的完整基因组。此次研究的德国菌株均隶属于嗜冷阿里弧菌I群。该群菌株的基因组呈现高度遗传多样性，核心基因组内可变位点占比高达9.1%。德国菌株可划分为3个亚群，各亚群分别包含2株、6株及9株菌株。对I群菌株的基因组解析结果显示，其移动遗传元件的携带情况存在显著差异，且65%的菌株缺失成簇规律间隔短回文重复序列（CRISPR）系统。4株闭合基因组均包含一条长度约2 Mb的染色体及1个巨型质粒（质粒大小为98.1~154.5 Kbp）。该染色体编码序列密度极高，占比约92%，且不同菌株间的基因块存在倒位与移位现象。采用梯度扩散条法开展抗菌药物敏感性试验，结果显示27株菌株均对头孢噻肟耐药，对红霉素、庆大霉素及氨苄西林敏感；另有16株菌株对环丙沙星耐药，23株对链霉素耐药。对抗生素耐药性的遗传预测分析发现，存在大量与布氏阿里弧菌（A. butzleri）同源的外排泵编码基因。所有菌株均携带2个β-内酰胺酶基因，这或许可解释其对头孢噻肟的耐药性。在16株环丙沙星耐药菌株中，有15株被检出存在gyrA基因的点突变（苏氨酸85→异亮氨酸，Thr-85-Ile），该突变与环丙沙星耐药性存在部分关联。计算机辅助毒力因子预测分析显示，该菌携带多种毒力因子，包括完整的趋化系统及绝大多数鞭毛相关基因。与布氏阿里弧菌不同，本研究未检测到脲酶基因簇。本研究为解析嗜冷阿里弧菌I群菌株的基因组变异提供了新视角。这些菌株间的遗传差异或许会影响其毒力强弱及人类感染后的病情严重程度。