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Vilela FP, Rodrigues DDP, Allard MW, Falcão JP. CRISPR and CRISPR-MVLST reveal conserved spacer distribution and high similarity among Salmonella enterica serovar Infantis genomes from Brazil and other countries. Mol Genet Genomics 2024; 299:61. [PMID: 38806731 DOI: 10.1007/s00438-024-02147-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 04/24/2024] [Indexed: 05/30/2024]
Abstract
Salmonella enterica serovar Infantis (S. Infantis) is a globally distributed non-typhoid serovar infecting humans and food-producing animals. Considering the zoonotic potential and public health importance of this serovar, strategies to characterizing, monitor and control this pathogen are of great importance. This study aimed to determine the genetic relatedness of 80 Brazilian S. Infantis genomes in comparison to 40 non-Brazilian genomes from 14 countries using Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR-Multi-Locus Virulence Sequence Typing (CRISPR-MVLST). CRISPR spacers were searched using CRISPR-Cas++ and fimH and sseL alleles using BLAST and MEGA X. Results were analyzed using BioNumerics 7.6 in order to obtain similarity dendrograms. A total of 23 CRISPR1 and 11 CRISPR2 alleles formed by 37 and 26 types of spacers, respectively, were detected. MVLST revealed the presence of five fimH and three sseL alleles. CRISPR's similarity dendrogram showed 32 strain subtypes, with an overall similarity ≥ 78.6. The CRISPR-MVLST similarity dendrogram showed 37 subtypes, with an overall similarity ≥ 79.2. In conclusion, S. Infantis strains isolated from diverse sources in Brazil and other countries presented a high genetic similarity according to CRISPR and CRISPR-MVLST, regardless of their source, year, and/or place of isolation. These results suggest that both methods might be useful for molecular typing S. Infantis strains using WGS data.
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Affiliation(s)
- Felipe Pinheiro Vilela
- Departamento de Análises Clínicas, Toxicológicas E Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto - USP, Av. Do Café, s/n. Bloco S - Sala 41, Ribeirão Preto, SP, 14040-903, Brazil
| | | | - Marc William Allard
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD, USA
| | - Juliana Pfrimer Falcão
- Departamento de Análises Clínicas, Toxicológicas E Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto - USP, Av. Do Café, s/n. Bloco S - Sala 41, Ribeirão Preto, SP, 14040-903, Brazil.
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Mattock J, Smith AM, Keddy KH, Manners EJ, Duze ST, Smouse S, Tau N, Baker D, Chattaway MA, Mather AE, Wain J, Langridge GC. Genetic characterization of Salmonella Infantis from South Africa, 2004-2016. Access Microbiol 2022; 4:acmi000371. [PMID: 36003217 PMCID: PMC9394735 DOI: 10.1099/acmi.0.000371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 05/14/2022] [Indexed: 11/26/2022] Open
Abstract
Salmonella Infantis is presenting an increasing risk to public health. Of particular concern are the reports of pESI, a multidrug resistance (MDR) encoding megaplasmid, in isolates from multiple countries, but little is known about its presence or diversity in South Africa. Whole genome sequences of 387 S. Infantis isolates from South Africa (2004-2020) were analysed for genetic phylogeny, recombination frequency, antimicrobial resistance (AMR) determinants, plasmid presence and overall gene content. The population structure of South African S. Infantis was substantially different to S. Infantis reported elsewhere; only two thirds of isolates belonged to eBG31, while the remainder were identified as eBG297, a much rarer group globally. Significantly higher levels of recombination were observed in the eBG297 isolates, which was associated with the presence of prophages. The majority of isolates were putatively susceptible to antimicrobials (335/387) and lacked any plasmids (311/387); the megaplasmid pESI was present in just one isolate. A larger proportion of eBG31 isolates, 19% (49/263), contained at least one AMR determinant, compared to eBG297 at 2% (3/124). Comparison of the pan-genomes of isolates from either eBG identified 943 genes significantly associated with eBG, with 43 found exclusively in eBG31 isolates and 34 in eBG297 isolates. This, along with the single nucleotide polymorphism distance and difference in resistance profiles, suggests that eBG31 and eBG297 isolates occupy different niches within South Africa. If antibiotic-resistant S. Infantis emerges in South Africa, probably through the spread of the pESI plasmid, treatment of this infection would be compromised.
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Affiliation(s)
- Jennifer Mattock
- Norwich Medical School, University of East Anglia, Norwich, UK
- Present address: The Roslin Institute, University of Edinburgh, UK
| | - Anthony M. Smith
- Centre for Enteric Diseases, National Institute for Communicable Diseases, Johannesburg, South Africa
| | | | - Emma J. Manners
- Norwich Medical School, University of East Anglia, Norwich, UK
- Present address: European Molecular Biology Laboratory, European Bioinformatics Institute, UK
| | - Sanelisiwe T. Duze
- Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Shannon Smouse
- Centre for Enteric Diseases, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Nomsa Tau
- Centre for Enteric Diseases, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - David Baker
- Microbes in the Food Chain, Quadram Institute Bioscience, Norwich, UK
| | - Marie Anne Chattaway
- Gastrointestinal Bacteriology Reference Unit, United Kingdom Health Security Agency, London, UK
| | - Alison E. Mather
- Microbes in the Food Chain, Quadram Institute Bioscience, Norwich, UK
- Faculty of Medicine and Health Sciences, University of East Anglia, Norwich, UK
| | - John Wain
- Norwich Medical School, University of East Anglia, Norwich, UK
- Microbes in the Food Chain, Quadram Institute Bioscience, Norwich, UK
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Vilela FP, Rodrigues DDP, Allard MW, Falcão JP. Genomic characterization and antimicrobial resistance profiles of Salmonella enterica serovar Infantis isolated from food, humans and veterinary-related sources in Brazil. J Appl Microbiol 2021; 132:3327-3342. [PMID: 34958707 DOI: 10.1111/jam.15430] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 12/22/2021] [Accepted: 12/23/2021] [Indexed: 01/07/2023]
Abstract
AIMS To characterize the genetic relatedness, phenotypic and genotypic antimicrobial resistance and plasmid content of 80 Salmonella Infantis strains isolated from food, humans and veterinary sources from 2013 to 2018 in Brazil. METHODS AND RESULTS Pulsed-field gel electrophoresis and single-nucleotide polymorphism analysis showed major clusters containing 50% and 38.8% of the strains studied respectively. Multilocus sequence typing assigned all strains to ST32. Disk-diffusion revealed that 90% of the strains presented resistant or intermediate resistant profiles and 38.8% displayed multidrug resistance. Resistance genes for aminoglycosides (aac(6')-Iaa; aadA12; aph(3″-Ib; aph(6)-Id), β-lactams (blaTEM-1 ; blaCTX-M-8 ; blaCMY-2 ), trimethoprim (dfrA8), tetracycline (tet(A)), amphenicols (floR), sulfonamide (sul2), efflux pumps (mdsA; mdsB), chromosomal point mutations in gyrB, parC, acrB and pmrA were detected. Strains harboured IncI, IncF, IncX, IncQ, IncN and IncR plasmids. CONCLUSIONS The presence of a prevalent S. Infantis subtype in Brazil and the high antimicrobial resistance rates reinforced the potential hazard of this serovar for the public health and food safety fields. SIGNIFICANCE AND IMPACT OF THE STUDY This is the first study characterizing a large set of S. Infantis from Brazil by whole-genome sequencing, which provided a better local and global comprehension about the distribution and characteristics of this serovar of importance in the food, human and veterinary fields.
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Affiliation(s)
- Felipe Pinheiro Vilela
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto - USP, Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Ribeirão Preto, SP, Brazil
| | | | - Marc William Allard
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA
| | - Juliana Pfrimer Falcão
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto - USP, Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Ribeirão Preto, SP, Brazil
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Gymoese P, Kiil K, Torpdahl M, Østerlund MT, Sørensen G, Olsen JE, Nielsen EM, Litrup E. WGS based study of the population structure of Salmonella enterica serovar Infantis. BMC Genomics 2019; 20:870. [PMID: 31730461 PMCID: PMC6858691 DOI: 10.1186/s12864-019-6260-6] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 11/05/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Salmonella Infantis (S. Infantis) is one of the most frequent Salmonella serovars isolated from human cases of salmonellosis and the most detected serovar from animal and food sources in Europe. The serovar is commonly associated with poultry and there is increasing concern over multidrug resistant clones spreading worldwide, as the dominating clones are characterized by presence of large plasmids carrying multiple resistance genes. Increasing the knowledge of the S. Infantis population and evolution is important for understanding and preventing further spread. In this study, we analysed a collection of strains representing different decades, sources and geographic locations. We analysed the population structure and the accessory genome, in particular we identified prophages with a view to understand the role of prophages in relation to the evolution of this serovar. RESULTS We sequenced a global collection of 100 S. Infantis strains. A core-genome SNP analysis separated five strains in e-Burst Group (eBG) 297 with a long branch. The remaining strains, all in eBG31, were divided into three lineages that were estimated to have separated approximately 150 years ago. One lineage contained the vast majority of strains. In five of six clusters, no obvious correlation with source or geographical locations was seen. However, one cluster contained mostly strains from human and avian sources, indicating a clone with preference for these sources. The majority of strains within this cluster harboured a pESI-like plasmid with multiple resistance genes. Another lineage contained three genetic clusters with more rarely isolated strains of mainly animal origin, possibly less sampled or less infectious clones. Conserved prophages were identified in all strains, likely representing bacteriophages which integrated into the chromosome of a common ancestor to S. Infantis. We also saw that some prophages were specific to clusters and were probably introduced when the clusters were formed. CONCLUSIONS This study analysed a global S. Infantis population and described its genetic structure. We hypothesize that the population has evolved in three separate lineages, with one more successfully emerging lineage. We furthermore detected conserved prophages present in the entire population and cluster specific prophages, which probably shaped the population structure.
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Affiliation(s)
- Pernille Gymoese
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Artillerivej 5 Denmark
| | - Kristoffer Kiil
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Artillerivej 5 Denmark
| | - Mia Torpdahl
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Artillerivej 5 Denmark
| | - Mark T. Østerlund
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Artillerivej 5 Denmark
| | - Gitte Sørensen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Artillerivej 5 Denmark
| | - John E. Olsen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, Frederiksberg C, Denmark
| | - Eva M. Nielsen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Artillerivej 5 Denmark
| | - Eva Litrup
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Artillerivej 5 Denmark
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Realpe-Quintero M, Barba-León J, Pérez-Montaño JA, Pacheco-Gallardo C, González-Aguilar D, Dominguez-Arias RM, Cabrera-Diaz E. Genetic diversity and antimicrobial resistance of Salmonella serotypes recovered throughout the beef production chain and from patients with salmonellosis. PeerJ 2018; 6:e5482. [PMID: 30155367 PMCID: PMC6109583 DOI: 10.7717/peerj.5482] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 07/30/2018] [Indexed: 11/20/2022] Open
Abstract
Salmonella is one of the major foodborne pathogens worldwide. The antimicrobial resistance (AMR) of this foodborne pathogen has raised a great concern in recent years. Studies on the frequency and characterization of Salmonella serotypes can help to improve our knowledge on the epidemiology of this pathogen. The purpose of this study was to compare the serotypes, AMR and genetic profiles of Salmonella isolates recovered from raw beef throughout the beef production chain and from human feces associated with clinical cases of salmonellosis. The serotype, AMR and pulsed-field gel electrophoresis profile of 243 Salmonella enterica isolates recovered from beef carcasses (n = 78), ground beef (n = 135), and human feces from clinical cases of salmonellosis (n = 30) were compared. Forty-three different Salmonella serotypes were identified and regardless of the source, the top five corresponded to Typhimurium, Give, Group B (partially serotyped), Infantis and Anatum. Twelve serotypes from beef carcasses were also found in ground beef, showing their presence throughout the beef production chain. Salmonella Typhimurium, Infantis, Anatum and Montevideo were the only serotypes identified in all sample types. Resistance to tetracyclines was the most frequent (41.2%) followed by resistance to aminoglycosides (37%), folate pathway inhibitors (21%), quinolones (20.2%), phenicols (17.1%), penicillins (15.6%) and cephems (7%). Multidrug resistance was observed in 28.8% of the isolates, and those from human feces showed resistance to a larger number of antimicrobials. Great concern arises from the resistance and reduced susceptibility observed to quinolones and cephalosporins because these drugs are the first line of treatment for invasive Salmonella infections. Twenty-seven distinct pulse-types were detected among 238 isolates. Clustering analysis for the most frequent serotypes identified groups of isolates with similar AMR profiles. Multidrug resistance spreading throughout the food production chain should be continually monitored and its importance emphasized.
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Affiliation(s)
- Mauricio Realpe-Quintero
- Universidad de Guadalajara, Departamento de Medicina Veterinaria, Centro Universitario de Ciencias Biológicas y Agropecuarias, Zapopan, Jalisco, Mexico
| | - Jeannette Barba-León
- Universidad de Guadalajara, Departamento de Salud Pública, Centro Universitario de Ciencias Biológicas y Agropecuarias, Zapopan, Jalisco, Mexico
| | - Julia A. Pérez-Montaño
- Universidad de Guadalajara, Marcelino García Barragán, Departamento de Farmacobiología, Centro Universitario de Ciencias Exactas e Ingenierías, Guadalajara, Jalisco, Mexico
| | - Carlos Pacheco-Gallardo
- Universidad de Guadalajara, Departamento de Salud Pública, Centro Universitario de Ciencias Biológicas y Agropecuarias, Zapopan, Jalisco, Mexico
| | - Delia González-Aguilar
- Universidad de Guadalajara, Departamento de Salud Pública, Centro Universitario de Ciencias Biológicas y Agropecuarias, Zapopan, Jalisco, Mexico
| | - Rosa M. Dominguez-Arias
- Universidad de Guadalajara, Departamento de Biología Celular y Molecular, Centro Universitario de Ciencias Biológicas y Agropecuarias, Zapopan, Jalisco, Mexico
| | - Elisa Cabrera-Diaz
- Universidad de Guadalajara, Departamento de Salud Pública, Centro Universitario de Ciencias Biológicas y Agropecuarias, Zapopan, Jalisco, Mexico
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Ed-Dra A, Karraouan B, Allaoui AE, Khayatti M, Ossmani HE, Filali FR, ElMdaghri N, Bouchrif B. Antimicrobial resistance and genetic diversity of Salmonella Infantis isolated from foods and human samples in Morocco. J Glob Antimicrob Resist 2018; 14:297-301. [PMID: 29842977 DOI: 10.1016/j.jgar.2018.05.019] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 05/17/2018] [Accepted: 05/18/2018] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVES Genotyping of Salmonella strains is an important molecular tool to discriminate isolates and to improve epidemiological studies when an outbreak occurs. Among the DNA-based genotyping methods, pulsed-field gel electrophoresis (PFGE) is currently used to subtype Salmonella isolates. In this study, the feasibility of genotyping Salmonella enterica serotype Infantis strains using XbaI restriction enzyme was evaluated. Separation of restricted fragments was performed by PFGE. METHODS To test the possibility of applying this methodology to epidemiological investigation, a collection of 26 Salmonella Infantis strains were tested for their susceptibility to 14 antimicrobial agents and were analysed by XbaI macrorestriction followed by PFGE. Detection of class 1 integrons as well as intI1 and blaTEM genes in resistant strains was also studied. RESULTS Antimicrobial susceptibility testing showed that 84.6% (22/26) of Salmonella Infantis isolates were susceptible to all of the antimicrobials tested, whereas 7.7% (2/26) had low-level resistance to β-lactams and harboured the blaTEM gene. A class 1 integron (0.8kb) and the intI1 gene (898bp) were detected in one Salmonella Infantis strain. However, five different PFGE profiles were defined by XbaI macrorestriction. CONCLUSIONS The PFGE method demonstrated adequate typing ability and represents a powerful tool to discriminate the serotype Salmonella Infantis.
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Affiliation(s)
- Abdelaziz Ed-Dra
- Team of Microbiology and Health, Laboratory of Chemistry-Biology Applied to the Environment, Moulay Ismail University Faculty of Science, BP 11201 Zitoune Meknes, Morocco.
| | - Bouchra Karraouan
- Laboratory of Microbiology and Hygiene of Food and Water, Institut Pasteur du Maroc, 1 place Louis Pasteur, Casablanca 20100, Morocco
| | - Abdellah El Allaoui
- Team of Microbiology and Health, Laboratory of Chemistry-Biology Applied to the Environment, Moulay Ismail University Faculty of Science, BP 11201 Zitoune Meknes, Morocco
| | - Meriem Khayatti
- Laboratory of Microbiology and Hygiene of Food and Water, Institut Pasteur du Maroc, 1 place Louis Pasteur, Casablanca 20100, Morocco
| | - Hicham El Ossmani
- Genetics Laboratory of the Royal Gendarmerie, Ibn Sina Street, Rabat, Morocco
| | - Fouzia Rhazi Filali
- Team of Microbiology and Health, Laboratory of Chemistry-Biology Applied to the Environment, Moulay Ismail University Faculty of Science, BP 11201 Zitoune Meknes, Morocco
| | - Naima ElMdaghri
- Laboratory of Microbiology and Hygiene of Food and Water, Institut Pasteur du Maroc, 1 place Louis Pasteur, Casablanca 20100, Morocco
| | - Brahim Bouchrif
- Laboratory of Microbiology and Hygiene of Food and Water, Institut Pasteur du Maroc, 1 place Louis Pasteur, Casablanca 20100, Morocco
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