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Gómez-Baltazar A, Godínez-Oviedo A, Vázquez-Marrufo G, Vázquez-Garcidueñas MS, Hernández-Iturriaga M. Genomic analysis of the MLST population structure and antimicrobial resistance genes associated with Salmonella enterica in Mexico. Genome 2023; 66:319-332. [PMID: 37478495 DOI: 10.1139/gen-2023-0007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/23/2023]
Abstract
Salmonella enterica is one of the most commonly reported foodborne pathogens by public health agencies worldwide. In this study, the multilocus sequence typing (MLST) population structure and frequency of antimicrobial resistance (AMR) genes were evaluated in S. enterica strains from Mexico (n = 2561). The most common sources of isolation were food (44.28%), environment (27.41%), animal-related (24.83%), and human (3.48%). The most prevalent serovars were Newport (8.51%), Oranienburg (7.03%), Anatum (5.78%), Typhimurium (5.12%), and Infantis (4.57%). As determined by the 7-gene MLST scheme, the most frequent sequence types were ST23, ST64, and ST32. The core genome MLST scheme identified 132 HC2000 and 195 HC900 hierarchical clusters, with the HC2000_2 cluster being the most prevalent in Mexico (n = 256). A total of 78 different AMR genes belonging to 13 antimicrobial classes were detected in 638 genomic assemblies of S. enterica. The most frequent class was aminoglycosides (31.76%), followed by tetracyclines (12.53%) and sulfonamides (11.91%). These results can help public health agencies in Mexico prioritize their efforts and resources to increase the genomic sequencing of circulating Salmonella strains. Additionally, they provide valuable information for local and global public health efforts to reduce the impact of foodborne diseases and AMR.
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Affiliation(s)
- Adrián Gómez-Baltazar
- Departamento de Investigación y Posgrado en Alimentos, Facultad de Química, Universidad Autónoma de Querétaro, Santiago de Querétaro C.P. 76010, Querétaro, Mexico
| | - Angélica Godínez-Oviedo
- Departamento de Investigación y Posgrado en Alimentos, Facultad de Química, Universidad Autónoma de Querétaro, Santiago de Querétaro C.P. 76010, Querétaro, Mexico
| | - Gerardo Vázquez-Marrufo
- Centro Multidisciplinario de Estudios en Biotecnología, Facultad de Medicina Veterinaria y Zootecnia, Universidad Michoacana de San Nicolás de Hidalgo, Tarímbaro C.P. 58893, Michoacán, Mexico
| | - Ma Soledad Vázquez-Garcidueñas
- División de Estudios de Posgrado, Facultad de Ciencias Médicas y Biológicas "Dr. Ignacio Chávez," Universidad Michoacana de San Nicolás de Hidalgo, Morelia C.P. 58020, Michoacán, Mexico
| | - Montserrat Hernández-Iturriaga
- Departamento de Investigación y Posgrado en Alimentos, Facultad de Química, Universidad Autónoma de Querétaro, Santiago de Querétaro C.P. 76010, Querétaro, Mexico
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Prasertsee T, Pascoe B, Patchanee P. Colistin resistance and resistance determinants are mobile among Salmonella enterica isolates from diseased and healthy pigs in Thailand. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.31.526471. [PMID: 36778303 PMCID: PMC9915662 DOI: 10.1101/2023.01.31.526471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Salmonella is an important enteric pathogen that poses a threat to human and livestock animal health, with emerging multidrug resistance (MDR) a major public health issue globally. We investigated the prevalence of Salmonella in healthy and diseased pigs from Thai pig farms and determined their phenotypic and genotypic antimicrobial resistance profiles. A total of 150 fecal samples were collected from pigs housed in pens from four separate pig farms in southern Thailand and tested for the presence of Salmonella. Confirmed Salmonella isolates were tested for their susceptibility to 11 antimicrobials, and PCR used to detect known antimicrobial resistance genes (ARGs). Salmonella isolates were cultured from 69% (103/150) of all fecal samples, with higher prevalence in disease pigs (12/15; 80%), compared with healthy pigs (91/135; 67%). Serotype Rissen was the most frequently identified serotype among the Salmonella isolates. Resistance to ampicillin (AMP) (97%), sulfonamide-trimethoprim (SXT) (97%), and tetracycline (TET) (94%) were the most common phenotypes observed. The most common ARGs identified were blaTEM gene (99.%), tetA (87%), sul1 (77%), and dfrA1 (74%), and more than 95% of the Salmonella isolates tested were MDR - based on resistance to three or more antimicrobial classes. The most common antimicrobial resistance pattern exhibited was AMP-TET-SXT (76%), and resistance to colistin (via the mcr-1 gene) was observed in both healthy and diseased pigs. The clonal groups of PFGE analysis in serotype Typhimurium revealed the genetic relationship among Salmonella isolated from healthy and diseased pigs from different pig farms.
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Affiliation(s)
- Teerarat Prasertsee
- Faculty of Veterinary Science, Prince of Songkla University, Songkhla, Thailand
| | - Ben Pascoe
- Centre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Old Road Campus, Oxford, United Kingdom
- Ineos Oxford Institute of Antimicrobial Research, Department of Biology, University of Oxford, Oxford, United Kingdom
- Integrative Research Center for Veterinary Preventive Medicine, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Prapas Patchanee
- Integrative Research Center for Veterinary Preventive Medicine, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, Thailand
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Hernández-Díaz EA, Vázquez-Garcidueñas MS, Negrete-Paz AM, Vázquez-Marrufo G. Comparative Genomic Analysis Discloses Differential Distribution of Antibiotic Resistance Determinants between Worldwide Strains of the Emergent ST213 Genotype of Salmonella Typhimurium. Antibiotics (Basel) 2022; 11:antibiotics11070925. [PMID: 35884180 PMCID: PMC9312005 DOI: 10.3390/antibiotics11070925] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/06/2022] [Accepted: 07/07/2022] [Indexed: 12/17/2022] Open
Abstract
Salmonella enterica constitutes a global public health concern as one of the main etiological agents of human gastroenteritis. The Typhimurium serotype is frequently isolated from human, animal, food, and environmental samples, with its sequence type 19 (ST19) being the most widely distributed around the world as well as the founder genotype. The replacement of the ST19 genotype with the ST213 genotype that has multiple antibiotic resistance (MAR) in human and food samples was first observed in Mexico. The number of available genomes of ST213 strains in public databases indicates its fast worldwide dispersion, but its public health relevance is unknown. A comparative genomic analysis conducted as part of this research identified the presence of 44 genes, 34 plasmids, and five point mutations associated with antibiotic resistance, distributed across 220 genomes of ST213 strains, indicating the MAR phenotype. In general, the grouping pattern in correspondence to the presence/absence of genes/plasmids that confer antibiotic resistance cluster the genomes according to the geographical origin where the strain was isolated. Genetic determinants of antibiotic resistance group the genomes of North America (Canada, Mexico, USA) strains, and suggest a dispersion route to reach the United Kingdom and, from there, the rest of Europe, then Asia and Oceania. The results obtained here highlight the worldwide public health relevance of the ST213 genotype, which contains a great diversity of genetic elements associated with MAR.
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Affiliation(s)
- Elda Araceli Hernández-Díaz
- Centro Multidisciplinario de Estudios en Biotecnología, Facultad de Medicina Veterinaria y Zootecnia, Universidad Michoacana de San Nicolás de Hidalgo, Km 9.5 Carretera Morelia-Zinapécuaro, Col. La Palma Tarímbaro, Morelia 58893, Michoacán, Mexico; (E.A.H.-D.); (A.M.N.-P.)
| | - Ma. Soledad Vázquez-Garcidueñas
- División de Estudios de Posgrado, Facultad de Ciencias Médicas y Biológicas “Dr. Ignacio Chávez”, Universidad Michoacana de San Nicolás de Hidalgo, Ave. Rafael Carrillo esq. Dr. Salvador González Herrejón, Col. Cuauhtémoc, Morelia 58020, Michoacán, Mexico;
| | - Andrea Monserrat Negrete-Paz
- Centro Multidisciplinario de Estudios en Biotecnología, Facultad de Medicina Veterinaria y Zootecnia, Universidad Michoacana de San Nicolás de Hidalgo, Km 9.5 Carretera Morelia-Zinapécuaro, Col. La Palma Tarímbaro, Morelia 58893, Michoacán, Mexico; (E.A.H.-D.); (A.M.N.-P.)
| | - Gerardo Vázquez-Marrufo
- Centro Multidisciplinario de Estudios en Biotecnología, Facultad de Medicina Veterinaria y Zootecnia, Universidad Michoacana de San Nicolás de Hidalgo, Km 9.5 Carretera Morelia-Zinapécuaro, Col. La Palma Tarímbaro, Morelia 58893, Michoacán, Mexico; (E.A.H.-D.); (A.M.N.-P.)
- Correspondence: ; Tel./Fax: +52-01-443-2-95-80-29
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Melo RT, Galvão NN, Guidotti-Takeuchi M, Peres PABM, Fonseca BB, Profeta R, Azevedo VAC, Monteiro GP, Brenig B, Rossi DA. Molecular Characterization and Survive Abilities of Salmonella Heidelberg Strains of Poultry Origin in Brazil. Front Microbiol 2021; 12:674147. [PMID: 34220757 PMCID: PMC8253257 DOI: 10.3389/fmicb.2021.674147] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 05/12/2021] [Indexed: 12/02/2022] Open
Abstract
The aim of the study was to evaluate the genotypic and phenotypic characteristics of 20 strains of S. Heidelberg (SH) isolated from broilers produced in southern Brazil. The similarity and presence of genetic determinants linked to virulence, antimicrobial resistance, biofilm formation, and in silico-predicted metabolic interactions revealed this serovar as a threat to public health. The presence of the ompC, invA, sodC, avrA, lpfA, and agfA genes was detected in 100% of the strains and the luxS gene in 70% of them. None of the strains carries the blaSHV, mcr-1, qnrA, qnrB, and qnrS genes. All strains showed a multidrug-resistant profile to at least three non-β-lactam drugs, which include colistin, sulfamethoxazole, and tetracycline. Resistance to penicillin, ceftriaxone (90%), meropenem (25%), and cefoxitin (25%) were associated with the presence of blaCTX–M and blaCMY–2 genes. Biofilm formation reached a mature stage at 25 and 37°C, especially with chicken juice (CJ) addition. The sodium hypochlorite 1% was the least efficient in controlling the sessile cells. Genomic analysis of two strains identified more than 100 virulence genes and the presence of resistance to 24 classes of antibiotics correlated to phenotypic tests. Protein-protein interaction (PPI) prediction shows two metabolic pathways correlation with biofilm formation. Virulence, resistance, and biofilm determinants must be constant monitoring in SH, due to the possibility of occurring infections extremely difficult to cure and due risk of the maintenance of the bacterium in production environments.
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Affiliation(s)
- Roberta T Melo
- Faculty of Veterinary Medicine, Federal University of Uberlândia, Uberlândia, Brazil
| | - Newton N Galvão
- Ministry of Agriculture, Livestock and Supply, Rio de Janeiro, Brazil
| | | | - Phelipe A B M Peres
- Faculty of Veterinary Medicine, Federal University of Uberlândia, Uberlândia, Brazil
| | - Belchiolina B Fonseca
- Faculty of Veterinary Medicine, Federal University of Uberlândia, Uberlândia, Brazil
| | - Rodrigo Profeta
- Department of Genetics, Ecology and Evolution (GEE), Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Vasco A C Azevedo
- Department of Genetics, Ecology and Evolution (GEE), Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Guilherme P Monteiro
- Faculty of Veterinary Medicine, Federal University of Uberlândia, Uberlândia, Brazil
| | - Bertram Brenig
- Institute of Veterinary Medicine, University of Göttingen, Göttingen, Germany
| | - Daise A Rossi
- Faculty of Veterinary Medicine, Federal University of Uberlândia, Uberlândia, Brazil
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Delgado-Suárez EJ, Palós-Guitérrez T, Ruíz-López FA, Hernández Pérez CF, Ballesteros-Nova NE, Soberanis-Ramos O, Méndez-Medina RD, Allard MW, Rubio-Lozano MS. Genomic surveillance of antimicrobial resistance shows cattle and poultry are a moderate source of multi-drug resistant non-typhoidal Salmonella in Mexico. PLoS One 2021; 16:e0243681. [PMID: 33951039 PMCID: PMC8099073 DOI: 10.1371/journal.pone.0243681] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 04/15/2021] [Indexed: 12/22/2022] Open
Abstract
Multi-drug resistant (MDR) non-typhoidal Salmonella (NTS) is a public health concern globally. This study reports the phenotypic and genotypic antimicrobial resistance (AMR) profiles of NTS isolates from bovine lymph nodes (n = 48) and ground beef (n = 29). Furthermore, we compared genotypic AMR data of our isolates with those of publicly available NTS genomes from Mexico (n = 2400). The probability of finding MDR isolates was higher in ground beef than in lymph nodes:χ2 = 12.0, P = 0.0005. The most common resistant phenotypes involved tetracycline (40.3%), carbenicillin (26.0%), amoxicillin-clavulanic acid (20.8%), chloramphenicol (19.5%) and trimethoprim-sulfamethoxazole (16.9%), while more than 55% of the isolates showed decreased susceptibility to ciprofloxacin and 26% were MDR. Conversely, resistance to cephalosporins and carbapenems was infrequent (0-9%). MDR phenotypes were strongly associated with NTS serovar (χ2 = 24.5, P<0.0001), with Typhimurium accounting for 40% of MDR strains. Most of these (9/10), carried Salmonella genomic island 1, which harbors a class-1 integron with multiple AMR genes (aadA2, blaCARB-2, floR, sul1, tetG) that confer a penta-resistant phenotype. MDR phenotypes were also associated with mutations in the ramR gene (χ2 = 17.7, P<0.0001). Among public NTS isolates from Mexico, those from cattle and poultry had the highest proportion of MDR genotypes. Our results suggest that attaining significant improvements in AMR meat safety requires the identification and removal (or treatment) of product harboring MDR NTS, instead of screening for Salmonella spp. or for isolates showing resistance to individual antibiotics. In that sense, massive integration of whole genome sequencing (WGS) technologies in AMR surveillance provides the shortest path to accomplish these goals.
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Affiliation(s)
| | - Tania Palós-Guitérrez
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Ciudad de México, México
| | | | - Cindy Fabiola Hernández Pérez
- Centro Nacional de Referencia de Plaguicidas y Contaminantes, Dirección General de Inocuidad Agroalimentaria, Acuícola y Pesquera, Servicio Nacional de Sanidad, Inocuidad y Calidad Agroalimentaria, Estado de México, México
| | | | - Orbelín Soberanis-Ramos
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Rubén Danilo Méndez-Medina
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Marc W. Allard
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, U. S. Food and Drug Administration, College Park, Maryland, United States of America
| | - María Salud Rubio-Lozano
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Ciudad de México, México
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Class 1 integron-borne cassettes harboring blaCARB-2 gene in multidrug-resistant and virulent Salmonella Typhimurium ST19 strains recovered from clinical human stool samples, United States. PLoS One 2020; 15:e0240978. [PMID: 33125394 PMCID: PMC7598458 DOI: 10.1371/journal.pone.0240978] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Accepted: 10/06/2020] [Indexed: 02/07/2023] Open
Abstract
International lineages, such as Salmonella Typhimurium sequence type (ST) 19, are most often associated with foodborne diseases and deaths in humans. In this study, we compared the whole-genome sequences of five S. Typhimurium strains belonging to ST19 recovered from clinical human stool samples in North Carolina, United States. Overall, S. Typhimurium strains displayed multidrug-resistant profile, being resistance to critically and highly important antimicrobials including ampicillin, ticarcillin/clavulanic acid, streptomycin and sulfisoxazole, chloramphenicol, tetracycline, respectively. Interestingly, all S. Typhimurium strains carried class 1 integron (intl1) and we were able to describe two genomic regions surrounding blaCARB-2 gene, size 4,062 bp and 4,422 bp for S. Typhimurium strains (HS5344, HS5437, and HS5478) and (HS5302 and HS5368), respectively. Genomic analysis for antimicrobial resistome confirmed the presence of clinically important genes, including blaCARB-2, aac(6’)-Iaa, aadA2b, sul1, tetG, floR, and biocide resistance genes (qacEΔ1). S. Typhimurium strains harbored IncFIB plasmid containing spvRABCD operon, as well as rck and pef virulence genes, which constitute an important apparatus for spreading the virulence plasmid. In addition, we identified several virulence genes, chromosomally located, while the phylogenetic analysis revealed clonal relatedness among these strains with S. enterica isolated from human and non-human sources obtained in European and Asian countries. Our results provide new insights into this unusual class 1 integron in virulent S. Typhimurium strains that harbors a pool of genes acting as potential hotspots for horizontal gene transfer providing readily adaptation to new surrounds, as well as being crucially required for virulence in vivo. Therefore, continuous genomic surveillance is an important tool for safeguarding human health.
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Obaidat MM. Prevalence and antimicrobial resistance of Listeria monocytogenes, Salmonella enterica and Escherichia coli O157:H7 in imported beef cattle in Jordan. Comp Immunol Microbiol Infect Dis 2020; 70:101447. [PMID: 32105836 DOI: 10.1016/j.cimid.2020.101447] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 02/07/2020] [Accepted: 02/12/2020] [Indexed: 01/30/2023]
Abstract
This study characterized Listeria monocytogenes, Salmonella enterica, and E. coli O157:H7 by collecting rectoanal mucosal swabs and fecal samples from 518 imported beef cattle at Jordan's major abattoir. A unique 53 L. monocytogenes, 287 S. enterica, and 17 E. coli O157:H7 were isolated from 37, 120 and 9 different animals; respectively. The prevalence of S. enterica, L. monocytogenes and E. coli O157:H7 were 23.2 % (95 % CI, 19.7-27.0 %), 7.1 % (95 % CI, 5.2-9.7 %) and 1.7 % (95 % CI, 0.9-3.3 %); respectively. All L. monocytogenes, all E. coli O157:H7 and 93.0 % of S. enterica isolates resisted at least one antimicrobial class. All L. monocytogenes, 94.1 % of E. coli O157:H7 and 69.7 % of S. enterica isolates exhibited multidrug resistance (resistant to ≥3 antimicrobials classes). Moreover, high percentages of L. monocytogenes (98.1 %), E. coli O157:H7 (64.7 %) and S. enterica (45.3 %) isolates resisted ≥5 antimicrobial classes. More than 90 % of the L. monocytogenes isolates resisted ampicillin, penicillin and erythromycin and more than 75 % resisted vancomycin. S. enterica isolates resisted several treatment-of-choice antimicrobials such as nalidixic acid (85.4 %), ciprofloxacin (26.8 %) and ceftriaxone (19.5 %). Furthermore, greater than 50 % of the E. coli O157:H7 isolates resisted streptomycin, nalidixic acid, tetracycline, ampicillin, sulfamethoxazole-trimethoprim, kanamycin, chloramphenicol and ciprofloxacin. The high prevalence and the high resistance percentages of the studied pathogens toward clinically important antimicrobials is alarming. Thus, applying strict sanitation procedures at the abattoirs in Jordan is crucial to lower the risk of carcasses contamination.
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Affiliation(s)
- Mohammad M Obaidat
- Department of Veterinary Pathology and Public Health, Faculty of Veterinary Medicine, Jordan University of Science and Technology, Irbid, Jordan.
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