Genomic analysis of antibiotic resistance genes and mobile genetic elements in eight strains of nontyphoid Salmonella.

IF 5 2区生物学 Q1 MICROBIOLOGY

mSystems Pub Date : 2024-09-17 Epub Date: 2024-08-19 DOI:10.1128/msystems.00586-24

Haibing Liu, Lijie Zheng, Huimin Fan, Ji Pang

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Abstract

Nontyphoidal Salmonella (NTS) is the main etiological agent of human nontyphoidal salmonellosis. The aim of this study was to analyze the epidemiological characteristics and horizontal transfer mechanisms of antimicrobial resistance (AMR) genes from eight strains of NTS detected in Zhenjiang City, Jiangsu Province, China. Fecal samples from outpatients with food-borne diarrhea were collected in 2022. The NTS isolates were identified, and their susceptibility was tested with the Vitek 2 Compact system. The genomes of the NTS isolates were sequenced with the Illumina NovaSeq platform and Oxford Nanopore Technologies platform. The AMR genes and mobile genetic elements (MGEs) were predicted with the relevant open access resources. Eight strains of NTS were isolated from 153 specimens, and Salmonella Typhimurium ST19 was the most prevalent serotype. The AMR gene with the highest detection rate was AAC(6')-Iaa (10.5%) followed by TEM-1 (7.9%), sul2 (6.6%), and tet(A) (5.3%). Eleven MGEs carrying 34 AMR genes were identified on the chromosomes of 3 of the 8 NTS, including 3 resistance islands, 6 composite transposons (Tns), and 2 integrons. Eighteen plasmids carrying 40 AMR genes were detected in the 8 NTS strains, including 6 mobilizable plasmids, 3 conjugative plasmids, and 9 nontransferable plasmids, 7 of which carried 10 composite Tns and 3 integrons. This study provided a theoretical basis, from a genetic perspective, for the prevention and control of NTS resistance in Zhenjiang City.

Importance: Human nontyphoidal salmonellosis is one of the common causes of bacterial food-borne illnesses, with significant social and economic impacts, especially those caused by invasive multidrug-resistant nontyphoidal Salmonella, which entails high morbidity and mortality. Antimicrobial resistance is mainly mediated by drug resistance genes, and mobile genetic elements play key roles in the capture, accumulation, and dissemination of antimicrobial resistance genes. Therefore, it is necessary to study the epidemiological characteristics and horizontal transfer mechanisms of antimicrobial resistance genes of nontyphoidal Salmonella to prevent the spread of multidrug-resistant nontyphoidal Salmonella.

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八株非伤寒沙门氏菌耐抗生素基因和移动遗传因子的基因组分析。

非伤寒沙门氏菌（NTS）是人类非伤寒沙门氏菌病的主要病原菌。本研究旨在分析中国江苏省镇江市检出的8株NTS的流行病学特征和抗菌药耐药性（AMR）基因的水平转移机制。该研究收集了 2022 年食源性腹泻门诊患者的粪便样本。对 NTS 分离物进行了鉴定，并使用 Vitek 2 Compact 系统检测了它们的药敏性。用 Illumina NovaSeq 平台和 Oxford Nanopore Technologies 平台对 NTS 分离物的基因组进行了测序。利用相关开放资源对 AMR 基因和移动遗传元件（MGEs）进行了预测。从 153 份标本中分离出 8 株 NTS 菌株，伤寒沙门氏菌 ST19 是最常见的血清型。检出率最高的 AMR 基因是 AAC(6')-Iaa (10.5%)，其次是 TEM-1 (7.9%)、sul2 (6.6%) 和 tet(A) (5.3%)。在 8 个 NTS 中的 3 个的染色体上发现了 11 个携带 34 个 AMR 基因的 MGE，包括 3 个抗性岛、6 个复合转座子（Tns）和 2 个整合子。在 8 株 NTS 中检测到携带 40 个 AMR 基因的 18 个质粒，包括 6 个可迁移质粒、3 个共轭质粒和 9 个不可迁移质粒，其中 7 个质粒携带 10 个复合转座子和 3 个整合子。该研究从遗传学角度为镇江市防控NTS耐药性提供了理论依据：人类非伤寒沙门氏菌病是细菌性食源性疾病的常见病因之一，具有重大的社会和经济影响，尤其是由具有多重耐药性的侵袭性非伤寒沙门氏菌引起的非伤寒沙门氏菌病，具有很高的发病率和死亡率。抗菌药耐药性主要是由耐药基因介导的，而移动遗传因子在抗菌药耐药基因的捕获、积累和传播中起着关键作用。因此，有必要研究非伤寒沙门氏菌抗菌基因的流行病学特征和水平转移机制，以防止耐多药非伤寒沙门氏菌的传播。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

mSystems Biochemistry, Genetics and Molecular Biology-Biochemistry

CiteScore

10.50

自引率

3.10%

发文量

308

审稿时长

13 weeks

期刊介绍： mSystems™ will publish preeminent work that stems from applying technologies for high-throughput analyses to achieve insights into the metabolic and regulatory systems at the scale of both the single cell and microbial communities. The scope of mSystems™ encompasses all important biological and biochemical findings drawn from analyses of large data sets, as well as new computational approaches for deriving these insights. mSystems™ will welcome submissions from researchers who focus on the microbiome, genomics, metagenomics, transcriptomics, metabolomics, proteomics, glycomics, bioinformatics, and computational microbiology. mSystems™ will provide streamlined decisions, while carrying on ASM''s tradition of rigorous peer review.