Whole-genome sequencing-based characterization of Salmonella enterica Serovar Enteritidis and Kentucky isolated from laying hens in northwest of Iran, 2022-2023.

IF 4.3 3区医学 Q1 GASTROENTEROLOGY & HEPATOLOGY Gut Pathogens Pub Date : 2025-01-16 DOI:10.1186/s13099-025-00679-3

Shirin Vakili, Mehri Haeili, Adel Feizi, Kiarash Moghaddasi, Maryam Omrani, Arash Ghodousi, Daniela Maria Cirillo

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Abstract

Background: The transmission of Salmonella spp. to human through the consumption of contaminated food products of animal origin, mainly poultry is a significant global public health concern. The emerging multidrug resistant (MDR) clones of non-typhoidal Salmonella (NTS) serovars, have spread rapidly worldwide both in humans and in the food chain. In this study NTS strains were isolated from diseased laying hens in Iran and were further studied by whole-genome sequencing (WGS) to investigate the prevalent serovars, multilocus sequence types, antimicrobial resistance and virulence genes.

Results: Out of eight isolated Salmonella spp. six were identified as S. Enteritidis serovar ST11 (n = 5) or ST5824 (n = 1), and two isolates were recognized as S. Kentucky serotype ST198 lineages. The aminoglycoside resistance gene aac(6')-Iaa was the most frequently detected gene being present in all serovars, but it did not confer phenotypic resistance to corresponding agents (tobramycin and amikacin). All S. Enteritidis isolates carried a single GyrA D87N/Y substitution. Other identified antimicrobial resistance genes (ARGs) including tetA, floR, sul1, dfrA1, aph(3')-Ia and double gyrA and parC mutations conferring high-level ciprofloxacin resistance (CIP^R) (MIC ≥ 16mg/L) were only found in S. Kentucky isolates. The comparison of phenotypic and genotypic antimicrobial resistance (AMR) profiles revealed inconsistent results for some antibiotics. A total of 11 different Salmonella Pathogenicity Islands (SPIs) including SPIs-1, to 5, 9, 10, 13, 14, C63PI, CS54 and several virulence genes related to type III secretion system, adhesins, iron and magnesium uptake, serum and antimicrobial peptide resistance were detected among the isolates.

Conclusions: Our study reports emergence of a highly MDR- CIP^R S. Kentucky ST198 clone form poultry associated sources in Iran. The presence of numerous virulence determinants, SPIs and ARGs in the examined NTS isolates poses a significant risk for food safety. The inconsistencies between the genotypic and phenotypic AMR profiles indicate that WGS data alone may not be always sufficient for guiding therapeutic strategies.

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2022-2023年伊朗西北地区蛋鸡分离的肠炎沙门氏菌血清型和肯塔基菌全基因组测序鉴定

背景：沙门氏菌通过食用受污染的动物源性食品（主要是家禽）传播给人类是一个重大的全球公共卫生问题。新出现的非伤寒沙门氏菌（NTS）血清型多药耐药（MDR）克隆在人类和食物链中迅速在世界范围内传播。本研究从伊朗产病蛋鸡中分离出NTS菌株，采用全基因组测序（WGS）对其流行的血清型、多位点序列类型、耐药和毒力基因进行了研究。结果：8株分离的沙门氏菌中，6株鉴定为肠炎沙门氏菌ST11 （n = 5）或ST5824 (n = 1)， 2株鉴定为肯塔基沙门氏菌ST198。氨基糖苷耐药基因aac（6′）-Iaa是所有血清型中最常检测到的基因，但它并未赋予对相应药物（妥布霉素和阿米卡星）的表型抗性。所有肠炎沙门氏菌分离株均携带单个GyrA D87N/Y替换。其他已鉴定的抗微生物药物耐药性基因（ARGs）包括tetA、floR、sul1、dfrA1、aph（3’）-Ia和双gyrA和parC突变，这些基因具有高水平的环丙沙星耐药性（CIPR）（MIC≥16mg/L），仅在S. Kentucky分离株中发现。表型和基因型抗菌素耐药性（AMR）谱的比较显示，一些抗生素的结果不一致。共检测到11个不同的沙门氏菌致病性岛（SPIs），包括SPIs-1、SPIs- 5、SPIs- 9、SPIs- 10、SPIs- 13、SPIs- 14、C63PI、CS54以及与III型分泌系统、黏附素、铁和镁摄取、血清和抗菌肽耐药性相关的毒力基因。结论：我们的研究报告了在伊朗禽类相关源中出现了高度耐多药- CIPR的肯塔基S. ST198克隆株。在检测的NTS分离株中存在许多毒力决定因素、spi和ARGs，对食品安全构成重大风险。基因型和表型AMR谱之间的不一致性表明，单独的WGS数据可能并不总是足以指导治疗策略。

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来源期刊

Gut Pathogens GASTROENTEROLOGY & HEPATOLOGY-MICROBIOLOGY

CiteScore

7.70

自引率

2.40%

发文量

期刊介绍： Gut Pathogens is a fast publishing, inclusive and prominent international journal which recognizes the need for a publishing platform uniquely tailored to reflect the full breadth of research in the biology and medicine of pathogens, commensals and functional microbiota of the gut. The journal publishes basic, clinical and cutting-edge research on all aspects of the above mentioned organisms including probiotic bacteria and yeasts and their products. The scope also covers the related ecology, molecular genetics, physiology and epidemiology of these microbes. The journal actively invites timely reports on the novel aspects of genomics, metagenomics, microbiota profiling and systems biology. Gut Pathogens will also consider, at the discretion of the editors, descriptive studies identifying a new genome sequence of a gut microbe or a series of related microbes (such as those obtained from new hosts, niches, settings, outbreaks and epidemics) and those obtained from single or multiple hosts at one or different time points (chronological evolution).