背景:这是一项独特而新颖的研究,描述了霍乱弧菌AMR决定子的基因分型和随后的预测,揭示了当代菌株作为霍乱严重AMR危机的前体的潜力。
结果:代表性菌株的基因分型,VC1和VC2被用来表征抗氯霉素的抗菌素抗性基因(ARGs),SXT,萘啶酸和链霉素在我们之前的研究中通过抗菌谱分析发现它们对它们具有抗性。strAB,sxt,用PCR检测sul2、qaceΔ1-sul1。用WGS对ARGs进行基因组注释和鉴定有助于检测almG的存在,varG,strA(APH(3\'\')-Ib),strB(APH(6)-Id),sul2,catB9,floR,CRP,dfrA1基因。与抗菌素耐药性有关的耐药性决定子和蛋白质结构域的签名,主要是,根据与参考蛋白的30-100%同源性鉴定抗生素的外排。基于与参考蛋白质和核苷酸序列的100%同一性和100%覆盖率,预测这些结构域参与其他代谢功能,并且预测这些结构域具有不同的分类学起源,这突出了微生物群对AMR获取的影响。QRDR(喹诺酮抗性决定区)的序列分析揭示了SNP。Cytoscapev3.8.2用于分析MDR蛋白的蛋白-蛋白相互作用,MdtA和EmrD-2,具有重要的AMR途径节点。发现VC1和VC2中不存在涉及不同类别抗生素外排的重要节点,这证明了这些菌株对大多数抗生素的敏感性。
结论:该研究有助于检查从最近爆发的疫情中分离出的VC的耐药性,以了解对大多数抗生素敏感的根本原因,并表征其基因组中的ARGs。研究表明,VC是抗性决定因素的特征库,是霍乱严重AMR危机的前兆。这是第一项研究,根据我们的知识,它已经系统地审查和介绍了,在生物信息学工具的帮助下,有可能在VC中充当AMR决定因素的前瞻性领域的信息。这种开创性的方法可能有助于预测AMR登陆,并有利于流行病学监测和预警系统。
BACKGROUND: This is a unique and novel study delineating the genotyping and subsequent prediction of AMR determinants of Vibrio cholerae revealing the potential of contemporary strains to serve as precursors of severe AMR crisis in cholera.
RESULTS: Genotyping of representative strains, VC1 and VC2 was undertaken to characterize antimicrobial resistance genes (ARGs) against chloramphenicol, SXT, nalidixic acid and streptomycin against which they were found to be resistant by antibiogram analysis in our previous investigation. strAB, sxt, sul2, qace∆1-sul1 were detected by PCR. Genome annotation and identification of ARGs with WGS helped to detect the presence of almG, varG, strA (APH(3\'\')-Ib), strB (APH(6)-Id), sul2, catB9, floR, CRP, dfrA1 genes. Signatures of resistance determinants and protein domains involved in antimicrobial resistance, primarily, efflux of antibiotics were identified on the basis of 30-100% homology to reference proteins. These domains were predicted to be involved in other metabolic functions on the basis of 100% identity with 100% coverage with reference protein and nucleotide sequences and were predicted to be of a diverse taxonomic origin accentuating the influence of the microbiota on AMR acquisition. Sequence analysis of QRDR (quinolone resistance-determining region) revealed SNPs.
Cytoscape v3.8.2 was employed to analyse protein-protein interaction of MDR proteins, MdtA and EmrD-2, with nodes of vital AMR pathways. Vital nodes involved in efflux of different classes of antibiotics were found to be absent in VC1 and VC2 justifying the sensitivity of these strains to most antibiotics.
CONCLUSIONS: The study helped to examine the resistome of VC isolated from recent outbreaks to understand the underlying reason of sensitivity to most antibiotics and also to characterize the ARGs in their genome. It revealed that VC is a reservoir of signatures of resistance determinants and serving as precursors for severe AMR crisis in cholera. This is the first study, to our knowledge, which has scrutinized and presented systematically, information on prospective domains which bear the potential of serving as AMR determinants in VC with the help of bioinformatic tools. This pioneering approach may help in the prediction of AMR landfalls and benefit epidemiological surveillance and early warning systems.