Dataset Information

Genomic Comparison of Eight Closed Genomes of Multidrug-Resistant Salmonella enterica Strains Isolated From Broiler Farms and Processing Plants in Trinidad and Tobago.

ABSTRACT: Salmonella enterica is an important foodborne pathogen worldwide. We used long and short-read sequencing to close genomes of eight multidrug-resistant (MDR) S. enterica strains, belonging to serovars Infantis (2), Albany, Oranienburg, I 4,[5],12:i:-, Javiana, Schwarzengrund, and Kentucky from broiler chicken farms and processing plants in Trinidad and Tobago. They also belonged to seven different sequence types (STs- 32, 292, 1510, 19, 24, 152, and 96). Among the strains, seven had demonstrated multi-drug resistance with the presence of at least three AMR genes, whereas three isolates contained the quinolone resistance gene qnr _B19 in plasmids (CFSAN103840, CFSAN103854, and CFSAN103872). The extended-spectrum β-lactamase genes bla _CTX-M-65 (CFSAN103796) and bla _TEM-1 (CFSAN103852) were detected in this study. The genomes closed in this study will be useful for future source tracking and outbreak investigations in Trinidad and Tobago and worldwide.

SUBMITTER: Maguire M

PROVIDER: S-EPMC9127609 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature

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Genomic Comparison of Eight Closed Genomes of Multidrug-Resistant Salmonella enterica Strains Isolated From Broiler Farms and Processing Plants in Trinidad and Tobago.

Maguire Meghan M Khan Anisa S AS Adesiyun Abiodun A AA Georges Karla K Gonzalez-Escalona Narjol N

Frontiers in microbiology 20220510

Salmonella enterica is an important foodborne pathogen worldwide. We used long and short-read sequencing to close genomes of eight multidrug-resistant (MDR) S. enterica strains, belonging to serovars Infantis (2), Albany, Oranienburg, I 4,[5],12:i:-, Javiana, Schwarzengrund, and Kentucky from broiler chicken farms and processing plants in Trinidad and Tobago. They also belonged to seven different sequence types (STs- 32, 292, 1510, 19, 24, 152, and 96). Among the strains, seven had ...[more]

PMID: 35620095

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Project description:During the last decade, Salmonella enterica subspecies enterica serovar Infantis (S. Infantis) has become more prevalent across Europe with an increased capability to persist in broiler farms. In this study, we aimed to identify potential genetic causes for the increased emergence and longer persistence of S. Infantis in German poultry farms by high-throughput-sequencing. Broiler derived S. Infantis strains from two decades, the 1990s (n = 12) and the 2010s (n = 18), were examined phenotypically and genotypically to detect potential differences responsible for increased prevalence and persistence. S. Infantis organisms were characterized by serotyping and determining antimicrobial susceptibility using the microdilution method. Genotypic characteristics were analyzed by whole genome sequencing (WGS) to detect antimicrobial resistance and virulence genes as well as plasmids. To detect possible clonal relatedness within S. Infantis organisms, 17 accessible genomes from previous studies about emergent S. Infantis were downloaded and analyzed using complete genome sequence of SI119944 from Israel as reference. In contrast to the broiler derived antibiotic-sensitive S. Infantis strains from the 1990s, the majority of strains from the 2010s (15 out of 18) revealed a multidrug-resistance (MDR) phenotype that encodes for at least three antimicrobials families: aminoglycosides [ant(3")-Ia], sulfonamides (sul1), and tetracyclines [tet(A)]. Moreover, these MDR strains carry a virulence gene pattern missing in strains from the 1990s. It includes genes encoding for fimbriae clusters, the yersiniabactin siderophore, mercury and disinfectants resistance and toxin/antitoxin complexes. In depth genomic analysis confirmed that the 15 MDR strains from the 2010s carry a pESI-like megaplasmid with resistance and virulence gene patterns detected in the emerged S. Infantis strain SI119944 from Israel and clones inside and outside Europe. Genotyping analysis revealed two sequence types (STs) among the resistant strains from the 2010s, ST2283 (n = 13) and ST32 (n = 2). The sensitive strains from the 1990s, belong to sequence type ST32 (n = 10) and ST1032 (n = 2). Therefore, this study confirms the emergence of a MDR S. Infantis pESI-like clone of ST2283 in German broiler farms with presumably high tendency of dissemination. Further studies on the epidemiology and control of S. Infantis in broilers are needed to prevent the transfer from poultry into the human food chain.

Project description:BackgroundThe Ministry of Health (hereafter, Ministry) of Trinidad and Tobago is responsible for delivery of all health services in the country. The Ministry takes responsibility for direct delivery of care in the public sector and has initiated a process whereby those seeking HIV test results could obtain confidential reports during a single-visit to a testing location. The Ministry requested technical assistance with this process from the Caribbean Epidemiology Centre (CAREC). The United States Centers for Disease Control and Prevention (CDC) played an important role in this process through its partnership with CAREC.MethodsUnder the technical guidance of CAREC and CDC, the Ministry organized a technical working group which included representatives from key national HIV program services and technical assistance partners. This working group reviewed internationally-recognized best practices for HIV rapid testing and proposed a program that could be integrated into the national HIV programs of Trinidad and Tobago. The working group wrote a consensus protocol, defined certification criteria, prepared training materials and oversaw implementation of "same-visit" HIV testing at two pilot sites.ResultsA Ministry-of-Health-supported program of "same-visit" HIV testing has been established in Trinidad and Tobago. This program provides confidential testing that is independent of laboratory confirmation. The program allows clients who want to know their HIV status to obtain this information during a single-visit to a testing location. Testers who are certified to provide testing on behalf of the Ministry are also counselors. Non-laboratory personnel have been trained to provide HIV testing in non-laboratory locations. The program includes procedures to assure uniform quality of testing across multiple testing sites. Several procedural and training documents were developed during implementation of this program. This report contains links to those documents.ConclusionsThe Ministry of Health has implemented a program of "same-visit" HIV testing in Trinidad and Tobago. This program provides clients confidential HIV test reports during a single visit to a testing location. The program is staffed by non-laboratory personnel who are trained to provide both testing and counseling in decentralized (non-laboratory) settings. This approach may serve as a model for other small countries.

Dataset Information

Genomic Comparison of Eight Closed Genomes of Multidrug-Resistant Salmonella enterica Strains Isolated From Broiler Farms and Processing Plants in Trinidad and Tobago.

Publications

Genomic Comparison of Eight Closed Genomes of Multidrug-Resistant <i>Salmonella enterica</i> Strains Isolated From Broiler Farms and Processing Plants in Trinidad and Tobago.

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