PDF(Pubmed)
Abstract：
UNASSIGNED: Multidrug-resistant (MDR) Salmonella Infantis has disseminated worldwide, mainly linked to the consumption of poultry products. Evidence shows dissemination of this pathogen in Chile; however, studies are primarily limited to phenotypic data or involve few isolates. As human cases of Salmonella Infantis infections have substantially increased in recent years, this study aimed to characterise the genomic epidemiology and antimicrobial-resistance profiles of isolates obtained from different sources, aiming to inform effective surveillance and control measures.
UNASSIGNED: We sequenced 396 Salmonella Infantis genomes and analysed them with all publicly available genomes of this pathogen from Chile (440 genomes in total), representing isolates from environmental, food, animal, and human sources obtained from 2009 to 2022. Based on bioinformatic and phenotypic methods, we assessed the population structure, dissemination among different niches, and antimicrobial resistance (AMR) profiles of Salmonella Infantis in the country.
UNASSIGNED: The genomic and phylogenetic analyses showed that Salmonella Infantis from Chile comprised several clusters of highly related isolates dominated by sequence type 32. The HC20_343 cluster grouped an important proportion of all isolates. This was the only cluster associated with pESI-like megaplasmids, and up to 12 acquired AMR genes/mutations predicted to result in an MDR phenotype. Accordingly, antimicrobial-susceptibility testing revealed a strong concordance between the AMR genetic determinants and their matching phenotypic expression, indicating that a significant proportion of HC20_343 isolates produce extended-spectrum β-lactamases and have intermediate fluoroquinolone resistance. HC20_343 Salmonella Infantis were spread among environmental, animal, food, and human niches, showing a close relationship between isolates from different years and sources, and a low intra-source genomic diversity.
UNASSIGNED: Our findings show a widespread dissemination of MDR Salmonella Infantis from the HC20_343 cluster in Chile. The high proportion of isolates with resistance to first-line antibiotics and the evidence of active transmission between the environment, animals, food, and humans highlight the urgency of improved surveillance and control measures in the country. As HC20_343 isolates predominate in the Americas, our results suggest a high prevalence of ESBL-producing Salmonella Infantis with intermediate fluoroquinolone resistance in the continent.
UNASSIGNED: Partially supported by the Food and Drug Administration (FDA) of the U.S. Department of Health and Human Services as part of an award, FDU001818, with 30% percent funded by FDA/HHS; and by Agencia de Investigación y Desarrollo de Chile (ANID) through FONDECYT de Postdoctorado Folio 3230796 and Folio 3210317, FONDECYT Regular Folio 1231082, and ANID-Millennium Science Initiative Program-ICN2021_044.
UNASSIGNED: We sequenced 396 Salmonella Infantis genomes and analysed them with all publicly available genomes of this pathogen from Chile (440 genomes in total), representing isolates from environmental, food, animal, and human sources obtained from 2009 to 2022. Based on bioinformatic and phenotypic methods, we assessed the population structure, dissemination among different niches, and antimicrobial resistance (AMR) profiles of Salmonella Infantis in the country.
UNASSIGNED: The genomic and phylogenetic analyses showed that Salmonella Infantis from Chile comprised several clusters of highly related isolates dominated by sequence type 32. The HC20_343 cluster grouped an important proportion of all isolates. This was the only cluster associated with pESI-like megaplasmids, and up to 12 acquired AMR genes/mutations predicted to result in an MDR phenotype. Accordingly, antimicrobial-susceptibility testing revealed a strong concordance between the AMR genetic determinants and their matching phenotypic expression, indicating that a significant proportion of HC20_343 isolates produce extended-spectrum β-lactamases and have intermediate fluoroquinolone resistance. HC20_343 Salmonella Infantis were spread among environmental, animal, food, and human niches, showing a close relationship between isolates from different years and sources, and a low intra-source genomic diversity.
UNASSIGNED: Our findings show a widespread dissemination of MDR Salmonella Infantis from the HC20_343 cluster in Chile. The high proportion of isolates with resistance to first-line antibiotics and the evidence of active transmission between the environment, animals, food, and humans highlight the urgency of improved surveillance and control measures in the country. As HC20_343 isolates predominate in the Americas, our results suggest a high prevalence of ESBL-producing Salmonella Infantis with intermediate fluoroquinolone resistance in the continent.
UNASSIGNED: Partially supported by the Food and Drug Administration (FDA) of the U.S. Department of Health and Human Services as part of an award, FDU001818, with 30% percent funded by FDA/HHS; and by Agencia de Investigación y Desarrollo de Chile (ANID) through FONDECYT de Postdoctorado Folio 3230796 and Folio 3210317, FONDECYT Regular Folio 1231082, and ANID-Millennium Science Initiative Program-ICN2021_044.
摘要：
■多药耐药（MDR）婴儿沙门氏菌已在全球范围内传播，主要与家禽产品的消费有关。证据表明这种病原体在智利传播；然而，研究主要限于表型数据或涉及很少的分离株。由于近年来人类感染沙门氏菌的病例大幅增加，这项研究旨在表征从不同来源获得的分离株的基因组流行病学和抗菌素耐药性概况，旨在提供有效的监测和控制措施。
■我们对396个婴儿沙门氏菌的基因组进行了测序，并对其进行了分析，这些基因组来自智利的该病原体的所有公开基因组（总共440个基因组）。代表来自环境的分离物，食物,动物,和2009年至2022年获得的人类来源。基于生物信息学和表型方法，我们评估了人口结构，在不同的利基之间传播，以及该国婴儿沙门氏菌的抗菌素耐药性（AMR）概况。
■基因组和系统发育分析表明，来自智利的婴儿沙门氏菌包含几簇高度相关的分离株，这些分离株以32型序列为主。HC20_343簇在所有分离株中占重要比例。这是唯一与pESI类巨型质粒相关的簇，和多达12个获得的AMR基因/突变预测导致MDR表型。因此，抗微生物药敏试验揭示了AMR遗传决定子与其匹配的表型表达之间的强烈一致性，表明显著比例的HC20_343分离物产生超广谱β-内酰胺酶并且具有中等氟喹诺酮抗性。HC20_343婴儿沙门氏菌在环境中传播，动物,食物,和人类生态位，显示不同年份和来源的分离株之间的密切关系，和低来源内基因组多样性。
■我们的研究结果表明，智利HC20_343集群中的MDR沙门氏菌在智利广泛传播。对一线抗生素耐药的分离株比例较高，环境间有活跃传播的证据，动物,食物,和人类强调了在该国改善监视和控制措施的紧迫性。由于HC20_343分离株在美洲占主导地位，我们的研究结果表明,产ESBL的婴儿沙门氏菌在非洲大陆的流行率很高,对氟喹诺酮类具有中等耐药性.
■部分由美国卫生与人类服务部食品和药物管理局（FDA）支持，作为奖项的一部分，FDU001818，其中30％由FDA/HHS资助；智利调查机构（ANID）通过FONDECYTdePostdoctoradoFolio3230796和Folio3210317，FONDECYTRegularFolio1231082和ANID-MillenniumScienceInitiative-ICN2021_044。
■我们对396个婴儿沙门氏菌的基因组进行了测序，并对其进行了分析，这些基因组来自智利的该病原体的所有公开基因组（总共440个基因组）。代表来自环境的分离物，食物,动物,和2009年至2022年获得的人类来源。基于生物信息学和表型方法，我们评估了人口结构，在不同的利基之间传播，以及该国婴儿沙门氏菌的抗菌素耐药性（AMR）概况。
■基因组和系统发育分析表明，来自智利的婴儿沙门氏菌包含几簇高度相关的分离株，这些分离株以32型序列为主。HC20_343簇在所有分离株中占重要比例。这是唯一与pESI类巨型质粒相关的簇，和多达12个获得的AMR基因/突变预测导致MDR表型。因此，抗微生物药敏试验揭示了AMR遗传决定子与其匹配的表型表达之间的强烈一致性，表明显著比例的HC20_343分离物产生超广谱β-内酰胺酶并且具有中等氟喹诺酮抗性。HC20_343婴儿沙门氏菌在环境中传播，动物,食物,和人类生态位，显示不同年份和来源的分离株之间的密切关系，和低来源内基因组多样性。
■我们的研究结果表明，智利HC20_343集群中的MDR沙门氏菌在智利广泛传播。对一线抗生素耐药的分离株比例较高，环境间有活跃传播的证据，动物,食物,和人类强调了在该国改善监视和控制措施的紧迫性。由于HC20_343分离株在美洲占主导地位，我们的研究结果表明,产ESBL的婴儿沙门氏菌在非洲大陆的流行率很高,对氟喹诺酮类具有中等耐药性.
■部分由美国卫生与人类服务部食品和药物管理局（FDA）支持，作为奖项的一部分，FDU001818，其中30％由FDA/HHS资助；智利调查机构（ANID）通过FONDECYTdePostdoctoradoFolio3230796和Folio3210317，FONDECYTRegularFolio1231082和ANID-MillenniumScienceInitiative-ICN2021_044。
