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Habib I, Mohamed MYI, Lakshmi GB, Ghazawi A, Khan M, Abdalla A, Anes F. High prevalence and genomic features of multidrug-resistant Salmonella enterica isolated from chilled broiler chicken on retail sale in the United Arab Emirates. Int J Food Microbiol 2024; 423:110828. [PMID: 39032201 DOI: 10.1016/j.ijfoodmicro.2024.110828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 06/22/2024] [Accepted: 07/15/2024] [Indexed: 07/22/2024]
Abstract
Non-typhoidal Salmonella represents a significant global concern for food safety and One Health. Despite the United Arab Emirates (UAE) being a leading consumer of chicken meat globally, there is a lack of comprehensive understanding regarding the prevalence and genomic characteristics of Salmonella within the country. This study aims to address this gap by conducting a thorough analysis of Salmonella prevalence, antimicrobial resistance, and genomic profiles of isolates obtained from whole broiler carcasses retailed under chilled conditions in the UAE. Our findings reveal that Salmonella was detected in 41.2 % (130/315) of the sampled chilled broiler carcasses, with notable variability observed among samples sourced from six different companies. Phenotypic antimicrobial resistance (AMR) testing, among 105 isolates, highlighted high resistance rates to tetracycline (97.1 %), nalidixic acid (93.3 %), ampicillin (92.4 %), azithromycin (75.2 %), ciprofloxacin (63.8 %), and ceftriaxone (54.3 %). Furthermore, a concerning 99 % (104/105) of the isolates exhibited multidrug resistance. Whole-genome sequencing (WGS) of 60 isolates identified five serovars, with S. infantis/Sequence Type (ST) 32 (55 %) and S. Minnesota/ST-458 (28.3 %) being the most prevalent. WGS analysis unveiled 34 genes associated with antimicrobial resistance, including mcr-1.1 (only in two isolates), conferring resistance to colistin. The two major serovars, Infantis and Minnesota, exhibited significant variation (P-values <0.001) in the distribution of major AMR genes (aadA1, blaCMY-2, blaSHV-12, qnrB19, qnrS1, sul1, and sul2). Notably, the gene qacEdelta, conferring resistance to quaternary ammonium compounds commonly found in disinfectants, was universally present in all S. Infantis isolates (n = 33), compared to only one S. Minnesota isolate. Additionally, all S. Infantis isolates harbored the IncFIB (pN55391) plasmid replicon type. Major serovars exhibited distinct distributions of antimicrobial resistance genes, underscoring the importance of serovar-specific surveillance. These findings emphasize the critical need for continuous surveillance and intervention measures to address Salmonella contamination risks in poultry products, providing valuable insights for public health and regulatory strategies not only in the UAE but also globally.
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Affiliation(s)
- Ihab Habib
- Veterinary Public Health Research Laboratory, Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al Ain, P.O. Box 1555, United Arab Emirates; ASPIRE Research Institute for Food Security in the Drylands (ARIFSID), United Arab Emirates University, Al Ain, P.O. Box 15551, United Arab Emirates.
| | - Mohamed-Yousif Ibrahim Mohamed
- Veterinary Public Health Research Laboratory, Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al Ain, P.O. Box 1555, United Arab Emirates; ASPIRE Research Institute for Food Security in the Drylands (ARIFSID), United Arab Emirates University, Al Ain, P.O. Box 15551, United Arab Emirates
| | - Glindya Bhagya Lakshmi
- Veterinary Public Health Research Laboratory, Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al Ain, P.O. Box 1555, United Arab Emirates; ASPIRE Research Institute for Food Security in the Drylands (ARIFSID), United Arab Emirates University, Al Ain, P.O. Box 15551, United Arab Emirates
| | - Akela Ghazawi
- Department of Medical Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, P.O. Box 1555, United Arab Emirates
| | - Mushtaq Khan
- Department of Medical Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, P.O. Box 1555, United Arab Emirates
| | - Afra Abdalla
- Veterinary Public Health Research Laboratory, Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al Ain, P.O. Box 1555, United Arab Emirates; ASPIRE Research Institute for Food Security in the Drylands (ARIFSID), United Arab Emirates University, Al Ain, P.O. Box 15551, United Arab Emirates
| | - Febin Anes
- Veterinary Public Health Research Laboratory, Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al Ain, P.O. Box 1555, United Arab Emirates
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Yan W, Xu D, Chen L, Wu X. Antimicrobial resistance and genome characteristics of Salmonella enteritidis from Huzhou, China. PLoS One 2024; 19:e0304621. [PMID: 38833480 PMCID: PMC11149840 DOI: 10.1371/journal.pone.0304621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Accepted: 05/14/2024] [Indexed: 06/06/2024] Open
Abstract
Salmonella enteritidis is a main pathogen responsible for sporadic outbreaks of gastroenteritis, and therefore is an important public health problem. This study investigated the drug resistance and genomic characteristics of S. enteritidis isolated from clinical and food sources in Huzhou, Zhejiang Province, China, from February 1, 2021, to December 30, 2023. In total, 43 S. enteritidis strains isolated during the study period were subjected to virulence gene, drug resistance gene, genetic correlation, antibiotic resistance, and multilocus sequence typing analyses. All 43 isolates were identified as ST11, and contained 108 virulence-related genes. Drug sensitivity analysis of the 43 isolates showed resistance rates of 100% to nalidixic acid and 90.70% to ampicillin and ampicillin/sulbactam. Multidrug resistance is a serious issue, with 81.40% of strains resistant to three or more antibacterial drugs. Genome sequencing indicated that S. enteritidis possessed 23 drug resistance genes, of which 14 were common to all 43 isolates. Phylogenetic analysis based on core genome single-nucleotide polymorphisms divided the 43 S. enteritidis strains into three clusters, with the 10 samples from an outbreak forming an independent branch located in cluster 3.
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Affiliation(s)
- Wei Yan
- Huzhou Center for Disease Control and Prevention, Huzhou, China
| | - Deshun Xu
- Huzhou Center for Disease Control and Prevention, Huzhou, China
| | - Liping Chen
- Huzhou Center for Disease Control and Prevention, Huzhou, China
| | - Xiaofang Wu
- Huzhou Center for Disease Control and Prevention, Huzhou, China
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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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Vilela FP, Felice AG, Seribelli AA, Rodrigues DP, Soares SC, Allard MW, Falcão JP. Comparative genomics reveals high genetic similarity among strains of Salmonella enterica serovar Infantis isolated from multiple sources in Brazil. PeerJ 2024; 12:e17306. [PMID: 38784399 PMCID: PMC11114117 DOI: 10.7717/peerj.17306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 04/04/2024] [Indexed: 05/25/2024] Open
Abstract
Background Salmonella enterica serovar Infantis (Salmonella Infantis) is a zoonotic, ubiquitous and foodborne pathogen of worldwide distribution. Despite Brazil's relevance as a major meat exporter, few studies were conducted to characterize strains of this serovar by genomic analyses in this country. Therefore, this study aimed to assess the diversity of 80 Salmonella Infantis strains isolated from veterinary, food and human sources in Brazil between 2013 and 2018 by comparative genomic analyses. Additional genomes of non-Brazilian countries (n = 18) were included for comparison purposes in some analyses. Methods Analyses of whole-genome multi-locus sequence typing (wgMLST), using PGAdb-builder, and of fragmented genomes, using Gegenees, were conducted to compare the 80 Brazilian strains to the 18 non-Brazilian genomes. Pangenome analyses and calculations were performed for all Salmonella Infantis genomes analyzed. The presence of prophages was determined using PHASTER for the 80 Brazilian strains. The genome plasticity using BLAST Ring Image Generator (BRIG) and gene synteny using Mauve were evaluated for 20 selected Salmonella Infantis genomes from Brazil and ten from non-Brazilian countries. Unique orthologous protein clusters were searched in ten selected Salmonella Infantis genomes from Brazil and ten from non-Brazilian countries. Results wgMLST and Gegenees showed a high genomic similarity among some Brazilian Salmonella Infantis genomes, and also the correlation of some clusters with non-Brazilian genomes. Gegenees also showed an overall similarity >91% among all Salmonella Infantis genomes. Pangenome calculations revealed an open pangenome for all Salmonella Infantis subsets analyzed and a high gene content in the core genomes. Fifteen types of prophages were detected among 97.5% of the Brazilian strains. BRIG and Mauve demonstrated a high structural similarity among the Brazilian and non-Brazilian isolates. Unique orthologous protein clusters related to biological processes, molecular functions, and cellular components were detected among Brazilian and non-Brazilian genomes. Conclusion The results presented using different genomic approaches emphasized the significant genomic similarity among Brazilian Salmonella Infantis genomes analyzed, suggesting wide distribution of closely related genotypes among diverse sources in Brazil. The data generated contributed to novel information regarding the genomic diversity of Brazilian and non-Brazilian Salmonella Infantis in comparison. The different genetically related subtypes of Salmonella Infantis from Brazil can either occur exclusively within the country, or also in other countries, suggesting that some exportation of the Brazilian genotypes may have already occurred.
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Affiliation(s)
- Felipe P. Vilela
- School of Pharmaceutical Sciences of Ribeirão Preto, Department of Clinical Analyses, Toxicology and Food Science, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Andrei G. Felice
- Institute of Biological and Natural Sciences, Department of Microbiology, Immunology and Parasitology, Universidade Federal do Triângulo Mineiro, Uberaba, Minas Gerais, Brazil
| | - Amanda A. Seribelli
- Medical School of Ribeirão Preto, Department of Cellular and Molecular Biology, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Dália P. Rodrigues
- Oswaldo Cruz Institute, Fundação Oswaldo Cruz, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Siomar C. Soares
- Institute of Biological and Natural Sciences, Department of Microbiology, Immunology and Parasitology, Universidade Federal do Triângulo Mineiro, Uberaba, Minas Gerais, Brazil
| | - Marc W. Allard
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD, United States of America
| | - Juliana P. Falcão
- School of Pharmaceutical Sciences of Ribeirão Preto, Department of Clinical Analyses, Toxicology and Food Science, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
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Iduu NV, Raiford D, Conley A, Scaria J, Nelson J, Ruesch L, Price S, Yue M, Gong J, Wei L, Wang C. A Retrospective Analysis of Salmonella Isolates across 11 Animal Species (1982-1999) Led to the First Identification of Chromosomally Encoded blaSCO-1 in the USA. Microorganisms 2024; 12:528. [PMID: 38543579 PMCID: PMC10974302 DOI: 10.3390/microorganisms12030528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 02/29/2024] [Accepted: 03/04/2024] [Indexed: 04/01/2024] Open
Abstract
Antimicrobial resistance (AMR) in non-typhoidal Salmonella is a pressing public health concern in the United States, necessitating continuous surveillance. We conducted a retrospective analysis of 251 Salmonella isolates from 11 animal species recovered between 1982 and 1999, utilizing serotyping, antimicrobial susceptibility testing, and whole-genome sequencing (WGS). Phenotypic resistance was observed in 101 isolates, with S. Typhimurium, S. Dublin, S. Agona, and S. Muenster prevailing among 36 identified serovars. Notably, resistance to 12 of 17 antibiotics was detected, with ampicillin being most prevalent (79/251). We identified 38 resistance genes, primarily mediating aminoglycoside (n = 13) and β-lactamase (n = 6) resistance. Plasmid analysis unveiled nine distinct plasmids associated with AMR genes in these isolates. Chromosomally encoded blaSCO-1 was present in three S. Typhimurium and two S. Muenster isolates from equine samples, conferring resistance to amoxicillin/clavulanic acid. Phylogenetic analysis revealed three distinct clusters for these five isolates, indicating evolutionary divergence. This study represents the first report of blaSCO-1 in the USA, and our recovered isolates harboring this gene as early as 1989 precede those of all other reports. The enigmatic nature of blaSCO-1 prompts further research into its function. Our findings highlight the urgency of addressing antimicrobial resistance in Salmonella for effective public health interventions.
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Affiliation(s)
- Nneka Vivian Iduu
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL 36849, USA; (N.V.I.); (D.R.); (S.P.)
| | - Donna Raiford
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL 36849, USA; (N.V.I.); (D.R.); (S.P.)
| | - Austin Conley
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL 36849, USA; (N.V.I.); (D.R.); (S.P.)
| | - Joy Scaria
- Department of Veterinary Pathobiology, Stillwater, Oklahoma State University, Stillwater, OK 74078, USA;
| | - Julie Nelson
- Department of Veterinary & Biomedical Sciences, South Dakota State University, Brookings, SD 57007, USA; (J.N.); (L.R.)
| | - Laura Ruesch
- Department of Veterinary & Biomedical Sciences, South Dakota State University, Brookings, SD 57007, USA; (J.N.); (L.R.)
| | - Stuart Price
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL 36849, USA; (N.V.I.); (D.R.); (S.P.)
| | - Min Yue
- Department of Veterinary Medicine, Zhejiang University, Hangzhou 310027, China
| | - Jiansen Gong
- Poultry Institute, Chinese Academy of Agricultural Sciences, Yangzhou 225125, China;
| | - Lanjing Wei
- Bioengineering Program, The University of Kansas, Lawrence, KS 66045, USA;
| | - Chengming Wang
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL 36849, USA; (N.V.I.); (D.R.); (S.P.)
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Guzinski J, Potter J, Tang Y, Davies R, Teale C, Petrovska L. Geographical and temporal distribution of multidrug-resistant Salmonella Infantis in Europe and the Americas. Front Microbiol 2024; 14:1244533. [PMID: 38414709 PMCID: PMC10896835 DOI: 10.3389/fmicb.2023.1244533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 12/04/2023] [Indexed: 02/29/2024] Open
Abstract
Recently emerged S. Infantis strains carrying resistance to several commonly used antimicrobials have been reported from different parts of the globe, causing human cases of salmonellosis and with occurrence reported predominantly in broiler chickens. Here, we performed phylogenetic and genetic clustering analyses to describe the population structure of 417 S. Infantis originating from multiple European countries and the Americas collected between 1985 and 2019. Of these, 171 were collected from 56 distinct premises located in England and Wales (E/W) between 2009 and 2019, including isolates linked to incursions of multidrug-resistant (MDR) strains from Europe associated with imported poultry meat. The analysis facilitated the comparison of isolates from different E/W sources with isolates originating from other countries. There was a high degree of congruency between the outputs of different types of population structure analyses revealing that the E/W and central European (Germany, Hungary, and Poland) isolates formed several disparate groups, which were distinct from the cluster relating to the United States (USA) and Ecuador/Peru, but that isolates from Brazil were closely related to the E/W and the central European isolates. Nearly half of the analysed strains/genomes (194/417) harboured the IncFIB(pN55391) replicon typical of the "parasitic" pESI-like megaplasmid found in diverse strains of S. Infantis. The isolates that contained the IncFIB(pN55391) replicon clustered together, despite originating from different parts of the globe. This outcome was corroborated by the time-measured phylogeny, which indicated that the initial acquisition of IncFIB(pN55391) likely occurred in Europe in the late 1980s, with a single introduction of IncFIB(pN55391)-carrying S. Infantis to the Americas several years later. Most of the antimicrobial resistance (AMR) genes were identified in isolates that harboured one or more different plasmids, but based on the short-read assemblies, only a minority of the resistance genes found in these isolates were identified as being associated with the detected plasmids, whereas the hybrid assemblies comprising the short and long reads demonstrated that the majority of the identified AMR genes were associated with IncFIB(pN55391) and other detected plasmid replicon types. This finding underlies the importance of applying appropriate methodologies to investigate associations of AMR genes with bacterial plasmids.
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Affiliation(s)
- Jaromir Guzinski
- Animal and Plant Health Agency, Addlestone, Surrey, United Kingdom
| | - Joshua Potter
- Animal and Plant Health Agency, Addlestone, Surrey, United Kingdom
| | - Yue Tang
- Animal and Plant Health Agency, Addlestone, Surrey, United Kingdom
| | - Rob Davies
- Animal and Plant Health Agency, Addlestone, Surrey, United Kingdom
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Saidenberg ABS, Franco LS, Reple JN, Hounmanou YMG, Casas MRT, Cardoso B, Esposito F, Lincopan N, Dalsgaard A, Stegger M, Knöbl T. Salmonella Heidelberg and Salmonella Minnesota in Brazilian broilers: Genomic characterization of third-generation cephalosporin and fluoroquinolone-resistant strains. ENVIRONMENTAL MICROBIOLOGY REPORTS 2023; 15:119-128. [PMID: 36629129 PMCID: PMC10103857 DOI: 10.1111/1758-2229.13132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 10/12/2022] [Indexed: 05/20/2023]
Abstract
Salmonella serovars Heidelberg and Minnesota encoding antimicrobial resistance to third-generation cephalosporins and fluoroquinolones are often detected in poultry/poultry meat. We analysed the genomes of 10 Salmonella Heidelberg (SH) and 4 Salmonella Minnesota (SM) from faecal isolates of Brazilian poultry. These featured virulent and multidrug-resistant characteristics, with AmpC beta-lactamase (blaCMY-2 ) predominance (9/14), for all SM (4/4) and some SH (3/10) located on IncC plasmid replicons. IncC carrying blaCTX-M-2 was only detected among SH (3/10). Mutation in the gyrA/parC genes was present in all SH, whereas SM harboured parC mutation plus qnrB19 on ColRNAI plasmids (3/4). In silico resistance overall corroborated with phenotypic results. Core genome phylogenies showed close clustering and high similarities between the Brazilian and poultry meat/food isolates from Europe, and to human isolates from European countries with documented import of Brazilian poultry meat. Conjugation assays with SM successfully transferred blaCMY-2 , and qnrB19 to an Escherichia coli recipient. The findings reinforce the ongoing antimicrobial resistance acquisition of SH and Minnesota and the risks for disseminating resistant strains and/or mobile elements which may increasingly affect importing countries and the need for controlling AMR in major poultry-exporting countries like Brazil.
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Affiliation(s)
- Andre Becker Simoes Saidenberg
- Department of Veterinary PathologySchool of Veterinary Medicine and Animal ScienceSão PauloBrazil
- Department of Veterinary and Animal Sciences, Section for Food Safety and ZoonosesInstitute for Veterinary and Companion Animal Science, Københavns UniversitetCopenhagenDenmark
- Department of Bacteria, Parasites and FungiStatens Serum InstitutCopenhagenDenmark
| | - Leticia Soares Franco
- Department of Veterinary PathologySchool of Veterinary Medicine and Animal ScienceSão PauloBrazil
| | - Jessica Nacarato Reple
- Department of Veterinary PathologySchool of Veterinary Medicine and Animal ScienceSão PauloBrazil
| | - Yaovi Mahuton Gildas Hounmanou
- Department of Veterinary and Animal Sciences, Section for Food Safety and ZoonosesInstitute for Veterinary and Companion Animal Science, Københavns UniversitetCopenhagenDenmark
| | | | - Brenda Cardoso
- Department of MicrobiologyInstitute of Biomedical Science, University of São PauloSão PauloBrazil
| | - Fernanda Esposito
- Department of Clinical AnalysisSchool of Pharmaceutical Sciences, University of São PauloSão PauloBrazil
| | - Nilton Lincopan
- Department of MicrobiologyInstitute of Biomedical Science, University of São PauloSão PauloBrazil
- Department of Clinical AnalysisSchool of Pharmaceutical Sciences, University of São PauloSão PauloBrazil
| | - Anders Dalsgaard
- Department of Veterinary and Animal Sciences, Section for Food Safety and ZoonosesInstitute for Veterinary and Companion Animal Science, Københavns UniversitetCopenhagenDenmark
| | - Marc Stegger
- Department of Bacteria, Parasites and FungiStatens Serum InstitutCopenhagenDenmark
| | - Terezinha Knöbl
- Department of Veterinary PathologySchool of Veterinary Medicine and Animal ScienceSão PauloBrazil
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Vilela FP, Dos Prazeres Rodrigues D, Allard MW, Falcão JP. Genomic analyses of drug-resistant Salmonella enterica serovar Heidelberg strains isolated from meat and related sources between 2013 and 2017 in the south region of Brazil. Curr Genet 2023; 69:141-152. [PMID: 36920496 DOI: 10.1007/s00294-023-01264-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 02/22/2023] [Accepted: 03/02/2023] [Indexed: 03/16/2023]
Abstract
Salmonella enterica serovar Heidelberg (S. Heidelberg) is a zoonotic, ubiquitous, and worldwide-distributed pathogen, responsible for gastroenteritis in humans caused by the consumption of contaminated food. In this study, 11 S. Heidelberg strains isolated from chicken and bovine meat, drag swab, and animal feed between 2013 and 2017 in states of the southern region of Brazil were characterized by whole-genome sequencing (WGS) analyses. Antimicrobial resistance against 18 antimicrobials was determined by disk-diffusion and ciprofloxacin's minimum inhibitory concentration by Etest®. The search for resistance and virulence genes, plasmids, Salmonella Pathogenicity Islands (SPIs) plus multi-locus sequence typing (MLST), and single-nucleotide polymorphisms (SNPs) analyses was conducted using WGS data. All strains harbored resistance genes fosA7, aac(6')-Iaa, sul2, tet(A), blaCMY-2, mdsA, and mdsB, and point mutations in gyrA and parC. All strains showed a phenotypic multidrug-resistant profile, with resistant or intermediate resistant profiles against 14 antimicrobials tested. Plasmids ColpVC, IncC, IncX1, and IncI1-I(Alpha) were detected. Virulence genes related to adherence, macrophage induction, magnesium uptake, regulation, and type III secretion systems plus 10 SPIs were detected. All strains were assigned to ST15 and belonged to two SNP clusters showing high similarity to isolates from the United Kingdom, Chile, Germany, the Netherlands, China, South Africa, and South Korea. In conclusion, the presence of multidrug-resistant S. Heidelberg strains in Brazil showing a global genomic relationship may alert for the necessity of stronger surveillance measures by food safety and public health authorities to limit its spread to humans and animals through foods.
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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, US 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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Plasmid Composition, Antimicrobial Resistance and Virulence Genes Profiles of Ciprofloxacin- and Third-Generation Cephalosporin-Resistant Foodborne Salmonella enterica Isolates from Russia. Microorganisms 2023; 11:microorganisms11020347. [PMID: 36838312 PMCID: PMC9961839 DOI: 10.3390/microorganisms11020347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 01/25/2023] [Accepted: 01/28/2023] [Indexed: 01/31/2023] Open
Abstract
Salmonella enterica is an important foodborne pathogen worldwide. Ciprofloxacin and extended-spectrum cephalosporins are the common first-line antimicrobial drugs for the treatment of salmonellosis, antimicrobial resistance genes for which are mostly transferred via plasmids. The goal of this work was to perform genomic analysis of plasmids from foodborne S. enterica isolates obtained in Russia based on whole-genome sequencing. In the current study, 11 multidrug-resistant samples isolated in 2021 from 8 regions of Russia were selected based on their resistance to ciprofloxacin and third-generation cephalosporins (CIP-3rd). Whole-genome short-read sequencing (WGS) was performed for all isolates; the samples belonged to five different sequence types (ST32, ST469, ST11, ST142, and ST548) which had different profiles of antimicrobial resistance (AMR) and virulence genes. We have performed additional long-read sequencing of four representative S. enterica isolates, which showed that they carried pESI-like megaplasmids of 202-280 kb length harboring extended-spectrum β-lactamase genes, fluoroquinolone, tetracycline, and aminoglycosides resistance genes, as well as several virulence determinants. We believe that the WGS data obtained will greatly facilitate further studies of foodborne S. enterica isolates epidemiology in terms of their self-transmissible plasmid composition that mediated antimicrobial resistance and virulence determinants conferring selective advantages of this important bacterial pathogen.
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Chaari M, Elhadef K, Akermi S, Hlima HB, Fourati M, Chakchouk Mtibaa A, Sarkar T, Shariati MA, Rebezov M, D’Amore T, Mellouli L, Smaoui S. Multiobjective response and chemometric approaches to enhance the phytochemicals and biological activities of beetroot leaves: an unexploited organic waste. BIOMASS CONVERSION AND BIOREFINERY 2022; 13:1-15. [PMID: 36530596 PMCID: PMC9746593 DOI: 10.1007/s13399-022-03645-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 12/02/2022] [Accepted: 12/05/2022] [Indexed: 06/17/2023]
Abstract
Research on medicinal plants is developing each day due to inborn phytochemicals, which can encourage the progress of novel drugs. Most plant-based phytochemicals have valuable effects on well-being. Among them, beetroot leaves (BL) are known for their therapeutic properties. Here, three solvents, namely, acetonitrile, ethanol, and water, and their combinations were developed for BL extraction and simultaneous assessment of phytochemical compounds and antioxidant and antifoodborne pathogen bacteria activities. By using the augmented simplex-centroid mixture design, 40.40% acetonitrile diluted in water at 38.74% and ethanol at 20.86% favored the recovery of 49.28 mg GAE/mL (total phenolic content (TPC)) and 0.314 mg QE/mL (total flavonoid content (TFC)), respectively. Acetonitrile diluted in water at 50% guarantees the best antioxidant activity, whereas the optimal predicted mixture for the highest antibacterial activity matches 24.58, 50.17, and 25.25% of acetonitrile, ethanol, and water, respectively. These extraction conditions ensured inhibition of Staphylococcus aureus, Salmonella enterica, and Escherichia coli, respectively, at 0.402, 0.497, and 0.207 mg/mL. Under optimized conditions, at three concentrations of BL, minimal inhibitory concentration (MIC), 2 × MIC, and 4 × MIC, a linear model was employed to investigate the inhibition behavior against the three tested bacteria. The early logarithmic growth phase of these bacteria illustrated the bactericidal effect of optimized extracted BL with a logarithmic growth phase inferior to 6 h. Therefore, BL extract at 4 × MIC, which corresponds to 1.608, 1.988, and 0.828 mg/mL, was more efficient against S. aureus, S. enterica, and E. coli.
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Affiliation(s)
- Moufida Chaari
- Laboratory of Microbial Biotechnology and Engineering Enzymes (LMBEE), Center of Biotechnology of Sfax (CBS), University of Sfax, Road of Sidi Mansour Km 6, P.O. Box 1177, 3018 Sfax, Tunisia
| | - Khaoula Elhadef
- Laboratory of Microbial Biotechnology and Engineering Enzymes (LMBEE), Center of Biotechnology of Sfax (CBS), University of Sfax, Road of Sidi Mansour Km 6, P.O. Box 1177, 3018 Sfax, Tunisia
| | - Sarra Akermi
- Laboratory of Microbial Biotechnology and Engineering Enzymes (LMBEE), Center of Biotechnology of Sfax (CBS), University of Sfax, Road of Sidi Mansour Km 6, P.O. Box 1177, 3018 Sfax, Tunisia
| | - Hajer Ben Hlima
- Laboratory of Enzymatic Engineering and Microbiology, Algae Biotechnology Unit, Biological Engineering Department, National School of Engineers of Sfax, University of Sfax, 3038 Sfax, Tunisia
| | - Mariam Fourati
- Laboratory of Microbial Biotechnology and Engineering Enzymes (LMBEE), Center of Biotechnology of Sfax (CBS), University of Sfax, Road of Sidi Mansour Km 6, P.O. Box 1177, 3018 Sfax, Tunisia
| | - Ahlem Chakchouk Mtibaa
- Laboratory of Microbial Biotechnology and Engineering Enzymes (LMBEE), Center of Biotechnology of Sfax (CBS), University of Sfax, Road of Sidi Mansour Km 6, P.O. Box 1177, 3018 Sfax, Tunisia
| | - Tanmay Sarkar
- Department of Food Technology, Malda Polytechnic, West Bengal State Council of Technical Education, Govt. of West Bengal, Malda, 732102 West Bengal India
| | - Mohammed Ali Shariati
- Department of Scientific Research, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Moscow, 127550 Russia
- Department of Scientific Research, K.G. Razumovsky Moscow State University of Technologies and Management (The First Cossack University), 109004 Moscow, Russia
| | - Maksim Rebezov
- Department of Scientific Research, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Moscow, 127550 Russia
- Department of Scientific Research, K.G. Razumovsky Moscow State University of Technologies and Management (The First Cossack University), 109004 Moscow, Russia
- Department of Scientific Research, V. M. Gorbatov Federal Research Center for Food Systems, Moscow, 109316 Russia
| | - Teresa D’Amore
- Chemistry Department, Istituto Zooprofilattico Sperimentale Della Puglia E Della, Foggia, Italy
| | - Lotfi Mellouli
- Laboratory of Microbial Biotechnology and Engineering Enzymes (LMBEE), Center of Biotechnology of Sfax (CBS), University of Sfax, Road of Sidi Mansour Km 6, P.O. Box 1177, 3018 Sfax, Tunisia
| | - Slim Smaoui
- Laboratory of Microbial Biotechnology and Engineering Enzymes (LMBEE), Center of Biotechnology of Sfax (CBS), University of Sfax, Road of Sidi Mansour Km 6, P.O. Box 1177, 3018 Sfax, Tunisia
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11
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Turcotte MR, Smith JT, Li J, Zhang X, Wolfe KL, Gao F, Benton CS, Andam CP. Genome characteristics of clinical Salmonella enterica population from a state public health laboratory, New Hampshire, USA, 2017–2020. BMC Genomics 2022; 23:537. [PMID: 35870884 PMCID: PMC9308939 DOI: 10.1186/s12864-022-08769-1] [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: 02/04/2022] [Accepted: 07/15/2022] [Indexed: 12/27/2022] Open
Abstract
Abstract
Background
The implementation of whole genome sequencing (WGS) by PulseNet, the molecular subtyping network for foodborne diseases, has transformed surveillance, outbreak detection, and public health laboratory practices in the United States. In 2017, the New Hampshire Public Health Laboratories, a member of PulseNet, commenced the use of WGS in tracking foodborne pathogens across the state. We present some of the initial results of New Hampshire’s initiative to transition to WGS in tracking Salmonella enterica, a bacterial pathogen that is responsible for non-typhoidal foodborne infections and enteric fever. We characterize the population structure and evolutionary history of 394 genomes of isolates recovered from human clinical cases in New Hampshire from 2017 to 2020.
Results
The New Hampshire S. enterica population is phylogenetically diverse, consisting of 78 sequence types (ST) and 67 serotypes. Six lineages dominate the population: ST 11 serotype Enteritidis, ST 19 Typhimurium, ST 32 Infantis, ST 118 Newport, ST 22 Braenderup, and ST 26 Thompson. Each lineage is derived from long ancestral branches in the phylogeny, suggesting their extended presence in the region and recent clonal expansion. We detected 61 genes associated with resistance to 14 antimicrobial classes. Of these, unique genes of five antimicrobial classes (aminocoumarins, aminoglycosides, fluoroquinolones, nitroimidazoles, and peptides) were detected in all genomes. Rather than a single clone carrying multiple resistance genes expanding in the state, we found multiple lineages carrying different combinations of independently acquired resistance determinants. We estimate the time to the most recent common ancestor of the predominant lineage ST 11 serotype Enteritidis (126 genomes) to be 1965 (95% highest posterior density intervals: 1927–1982). Its population size expanded until 1978, followed by a population decline until 1990. This lineage has been expanding since then. Comparison with genomes from other states reveal lack of geographical clustering indicative of long-distance dissemination.
Conclusions
WGS studies of standing pathogen diversity provide critical insights into the population and evolutionary dynamics of lineages and antimicrobial resistance, which can be translated to effective public health action and decision-making. We highlight the need to strengthen efforts to implement WGS-based surveillance and genomic data analyses in state public health laboratories.
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12
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dos Santos AM, Panzenhagen P, Ferrari RG, Conte-Junior CA. Large-scale genomic analysis reveals the pESI-like megaplasmid presence in Salmonella Agona, Muenchen, Schwarzengrund, and Senftenberg. Food Microbiol 2022; 108:104112. [DOI: 10.1016/j.fm.2022.104112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 08/01/2022] [Accepted: 08/06/2022] [Indexed: 11/16/2022]
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Vilela FP, Rodrigues DDP, Allard MW, Falcão JP. Prevalence of efflux pump and heavy metal tolerance encoding genes among Salmonella enterica serovar Infantis strains from diverse sources in Brazil. PLoS One 2022; 17:e0277979. [PMID: 36413564 PMCID: PMC9681071 DOI: 10.1371/journal.pone.0277979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 11/08/2022] [Indexed: 11/23/2022] Open
Abstract
Salmonella enterica subspecies enterica serovar Infantis (S. Infantis) is a non-typhoid, zoonotic and foodborne serovar with worldwide distribution, and often associated with increasing antimicrobial resistance. Efflux pumps are antimicrobial resistance mechanisms able to promote and increase resistance levels to multiple distinct drug classes. Heavy metal tolerance genes have been demonstrated to promote resistance against these compounds and act in the co-selection of antimicrobial resistant strains. Despite the relevance of S. Infantis in clinical and non-clinical fields, few studies worldwide have investigated the occurrence of such genes in strains from diverse sources. Therefore, the present study aimed at determining the prevalence of antimicrobial efflux pump and heavy metal tolerance genes and their genomic relatedness through core-genome multi-locus sequence typing (cgMLST) of 80 S. Infantis strains isolated from food, environmental, human and animal sources from 2013 to 2018 in Brazil. Twenty efflux pump encoding genes were detected, with 17 of these (acrA, acrB, baeR, crp, emrB, emrR, hns, kdpE, kpnF, marA, marR, mdtK, msbA, rsmA, sdiA, soxR and soxS) detected in all strains studied, golS in 98.75%, mdfA in 58.75% and tet(A) in 37.5%. Tolerance genes to arsenic (arsR) were detected in 100% of the strains, gold (golS and golT) in 98.75%, silver (silABCDEFPRS) in 36.25% and mercury (merR and merT) in 1.25%. cgMLST demonstrated a closer genetic relationship among strains harboring similar profiles of heavy metal and efflux pump encoding genes, despite their origin. In conclusion, the high prevalence of some efflux pump and heavy metal tolerance encoding genes alert us about the importance of strong surveillance measures to monitor resistance and the transmission of S. Infantis among diverse sources in Brazil.
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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, United States of America
- * E-mail: (JPF); (MWA)
| | - Juliana Pfrimer Falcão
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto–USP, Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Ribeirão Preto, SP, Brazil
- * E-mail: (JPF); (MWA)
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14
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Góes V, Monte DFM, Saraiva MDMS, Maria de Almeida A, Cabrera JM, Rodrigues Alves LB, Ferreira TS, Lima TSD, Benevides VP, Barrow PA, Freitas Neto OCD, Berchieri A. Salmonella Heidelberg side-step gene loss of respiratory requirements in chicken infection model. Microb Pathog 2022; 171:105725. [PMID: 36007847 DOI: 10.1016/j.micpath.2022.105725] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 07/15/2022] [Accepted: 08/14/2022] [Indexed: 11/27/2022]
Abstract
Among the important recent observations involving anaerobic respiration was that an electron acceptor produced as a result of an inflammatory response to Salmonella Typhimurium generates a growth advantage over the competing microbiota in the lumen. In this regard, anaerobically, salmonellae can oxidize thiosulphate (S2O32-) converting it into tetrathionate (S4O62-), the process by which it is encoded by ttr gene cluster (ttrSRttrBCA). Another important pathway under aerobic or anaerobic conditions is the 1,2-propanediol-utilization mediated by the pdu gene cluster that promotes Salmonella expansion during colitis. Therefore, we sought to compare in this study, whether Salmonella Heidelberg strains lacking the ttrA, ttrApduA, and ttrACBSR genes experience a disadvantage during cecal colonization in broiler chicks. In contrast to expectations, we found that the gene loss in S. Heidelberg potentially confers an increase in fitness in the chicken infection model. These data argue that S. Heidelberg may trigger an alternative pathway involving the use of an alternative electron acceptor, conferring a growth advantage for S. Heidelberg in chicks.
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Affiliation(s)
- Vinícius Góes
- São Paulo State University (Unesp), School of Agricultural and Veterinarian Sciences, Jaboticabal, SP, 14884-900, Brazil
| | - Daniel F M Monte
- São Paulo State University (Unesp), School of Agricultural and Veterinarian Sciences, Jaboticabal, SP, 14884-900, Brazil.
| | | | - Adriana Maria de Almeida
- São Paulo State University (Unesp), School of Agricultural and Veterinarian Sciences, Jaboticabal, SP, 14884-900, Brazil
| | - Julia Memrava Cabrera
- São Paulo State University (Unesp), School of Agricultural and Veterinarian Sciences, Jaboticabal, SP, 14884-900, Brazil
| | - Lucas Bocchini Rodrigues Alves
- São Paulo State University (Unesp), School of Agricultural and Veterinarian Sciences, Jaboticabal, SP, 14884-900, Brazil
| | - Taísa Santiago Ferreira
- São Paulo State University (Unesp), School of Agricultural and Veterinarian Sciences, Jaboticabal, SP, 14884-900, Brazil
| | - Tulio Spina de Lima
- São Paulo State University (Unesp), School of Agricultural and Veterinarian Sciences, Jaboticabal, SP, 14884-900, Brazil
| | - Valdinete P Benevides
- São Paulo State University (Unesp), School of Agricultural and Veterinarian Sciences, Jaboticabal, SP, 14884-900, Brazil
| | - Paul A Barrow
- School of Veterinary Medicine and Science, University of Surrey, Guildford, GU2 7AL, United Kingdom
| | - Oliveiro Caetano de Freitas Neto
- Department of Preventive Veterinary Medicine, Veterinary School, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, 31270-901, Brazil
| | - Angelo Berchieri
- São Paulo State University (Unesp), School of Agricultural and Veterinarian Sciences, Jaboticabal, SP, 14884-900, Brazil.
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15
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Kipper D, Mascitti AK, De Carli S, Carneiro AM, Streck AF, Fonseca ASK, Ikuta N, Lunge VR. Emergence, Dissemination and Antimicrobial Resistance of the Main Poultry-Associated Salmonella Serovars in Brazil. Vet Sci 2022; 9:vetsci9080405. [PMID: 36006320 PMCID: PMC9415136 DOI: 10.3390/vetsci9080405] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 07/22/2022] [Accepted: 07/30/2022] [Indexed: 11/19/2022] Open
Abstract
Simple Summary Salmonellosis is a human and animal disease caused by Salmonella, a bacterial genus classified into different species, subspecies, and serological variants (serovars) according to adaptation to one or more different hosts (animals and humans), pathogenicity profiles, and antigenic properties. Some specific Salmonella serovars can spread more easily in the enteric microbiota of avian species, often causing disease in birds and/or being transmitted to humans through food (such as chicken and eggs). Antimicrobial resistance (AMR) has also been reported in poultry-associated Salmonella isolates due to the widespread use of antimicrobials on farms. The availability of comprehensive data on the emergence and spread of Salmonella serovars, as well as their AMR profiles in farms and food products in Brazil (a major producer of poultry in the World), is necessary to understand their relevance in all avian production chains and also occurrence in poultry-derived foods. This article aims to provide an overview of the genus Salmonella and the main serovars that emerged in Brazilian poultry over time (Gallinarum, Typhimurium, Enteritidis, Heidelberg, and Minnesota), reviewing the scientific literature and suggesting more effective prevention and control for the future. Abstract Salmonella infects poultry, and it is also a human foodborne pathogen. This bacterial genus is classified into several serovars/lineages, some of them showing high antimicrobial resistance (AMR). The ease of Salmonella transmission in farms, slaughterhouses, and eggs industries has made controlling it a real challenge in the poultry-production chains. This review describes the emergence, dissemination, and AMR of the main Salmonella serovars and lineages detected in Brazilian poultry. It is reported that few serovars emerged and have been more widely disseminated in breeders, broilers, and layers in the last 70 years. Salmonella Gallinarum was the first to spread on the farms, remaining as a concerning poultry pathogen. Salmonella Typhimurium and Enteritidis were also largely detected in poultry and foods (eggs, chicken, turkey), being associated with several human foodborne outbreaks. Salmonella Heidelberg and Minnesota have been more widely spread in recent years, resulting in frequent chicken/turkey meat contamination. A few more serovars (Infantis, Newport, Hadar, Senftenberg, Schwarzengrund, and Mbandaka, among others) were also detected, but less frequently and usually in specific poultry-production regions. AMR has been identified in most isolates, highlighting multi-drug resistance in specific poultry lineages from the serovars Typhimurium, Heidelberg, and Minnesota. Epidemiological studies are necessary to trace and control this pathogen in Brazilian commercial poultry production chains.
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Affiliation(s)
- Diéssy Kipper
- Institute of Biotechnology, University of Caxias do Sul (UCS), Caxias do Sul 95070-560, Rio Grande do Sul, Brazil; (D.K.); (A.K.M.); (A.M.C.); (A.F.S.)
| | - Andréa Karoline Mascitti
- Institute of Biotechnology, University of Caxias do Sul (UCS), Caxias do Sul 95070-560, Rio Grande do Sul, Brazil; (D.K.); (A.K.M.); (A.M.C.); (A.F.S.)
| | - Silvia De Carli
- Molecular Diagnostics Laboratory, Lutheran University of Brazil (ULBRA), Canoas 92425-350, Rio Grande do Sul, Brazil;
| | - Andressa Matos Carneiro
- Institute of Biotechnology, University of Caxias do Sul (UCS), Caxias do Sul 95070-560, Rio Grande do Sul, Brazil; (D.K.); (A.K.M.); (A.M.C.); (A.F.S.)
| | - André Felipe Streck
- Institute of Biotechnology, University of Caxias do Sul (UCS), Caxias do Sul 95070-560, Rio Grande do Sul, Brazil; (D.K.); (A.K.M.); (A.M.C.); (A.F.S.)
| | | | - Nilo Ikuta
- Simbios Biotecnologia, Cachoeirinha 94940-030, Rio Grande do Sul, Brazil; (A.S.K.F.); (N.I.)
| | - Vagner Ricardo Lunge
- Institute of Biotechnology, University of Caxias do Sul (UCS), Caxias do Sul 95070-560, Rio Grande do Sul, Brazil; (D.K.); (A.K.M.); (A.M.C.); (A.F.S.)
- Molecular Diagnostics Laboratory, Lutheran University of Brazil (ULBRA), Canoas 92425-350, Rio Grande do Sul, Brazil;
- Simbios Biotecnologia, Cachoeirinha 94940-030, Rio Grande do Sul, Brazil; (A.S.K.F.); (N.I.)
- Correspondence: or or
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16
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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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Núncio ASP, Webber B, Pottker ES, Cardoso B, Esposito F, Fontana H, Lincopan N, Girardello R, Pilotto F, dos Santos LR, Rodrigues LB. Genomic characterization of multidrug-resistant Salmonella Heidelberg E2 strain isolated from chicken carcass in southern Brazil. Int J Food Microbiol 2022; 379:109863. [DOI: 10.1016/j.ijfoodmicro.2022.109863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 02/09/2022] [Accepted: 07/27/2022] [Indexed: 10/16/2022]
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18
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Monte DFM, Nethery MA, Berman H, Keelara S, Lincopan N, Fedorka-Cray PJ, Barrangou R, Landgraf M. Clustered Regularly Interspaced Short Palindromic Repeats Genotyping of Multidrug-Resistant Salmonella Heidelberg Strains Isolated From the Poultry Production Chain Across Brazil. Front Microbiol 2022; 13:867278. [PMID: 35783410 PMCID: PMC9248969 DOI: 10.3389/fmicb.2022.867278] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 04/25/2022] [Indexed: 11/19/2022] Open
Abstract
Salmonella enterica subsp. enterica serovar Heidelberg has been associated with a broad host range, such as poultry, dairy calves, swine, wild birds, environment, and humans. The continuous evolution of S. Heidelberg raises a public health concern since there is a global dispersal of lineages harboring a wide resistome and virulome on a global scale. Here, we characterized the resistome, phylogenetic structure and clustered regularly interspaced short palindromic repeats (CRISPR) array composition of 81 S. Heidelberg strains isolated from broiler farms (n = 16), transport and lairage (n = 5), slaughterhouse (n = 22), and retail market (n = 38) of the poultry production chain in Brazil, between 2015 and 2016 using high-resolution approaches including whole-genome sequencing (WGS) and WGS-derived CRISPR genotyping. More than 91% of the S. Heidelberg strains were multidrug-resistant. The total antimicrobial resistance (AMR) gene abundances did not vary significantly across regions and sources suggesting the widespread distribution of antibiotic-resistant strains from farm to market. The highest AMR gene abundance was observed for fosA7, aac(6′)-Iaa, sul2, tet(A), gyrA, and parC for 100% of the isolates, followed by 88.8% for blaCMY–2. The β-lactam resistance was essentially driven by the presence of the plasmid-mediated AmpC (pAmpC) blaCMY–2 gene, given the isolates which did not carry this gene were susceptible to cefoxitin (FOX). Most S. Heidelberg strains were classified within international lineages, which were phylogenetically nested with Salmonella strains from European countries; while CRISPR genotyping analysis revealed that the spacer content was overall highly conserved, but distributed into 13 distinct groups. In summary, our findings underscore the potential role of S. Heidelberg as a key pathogen disseminated from farm to fork in Brazil and reinforce the importance of CRISPR-based genotyping for salmonellae. Hence, we emphasized the need for continuous mitigation programs to monitor the dissemination of this high-priority pathogen.
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Affiliation(s)
- Daniel F. M. Monte
- Department of Food and Experimental Nutrition, Faculty of Pharmaceutical Sciences, Food Research Center, University of São Paulo, São Paulo, Brazil
- Laboratory of Avian Pathology, Department of Pathology, Theriogenology, and One Health, São Paulo State University (FCAV-Unesp), São Paulo, Brazil
- *Correspondence: Daniel F. M. Monte,
| | - Matthew A. Nethery
- Genomic Sciences Graduate Program, North Carolina State University, Raleigh, NC, United States
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC, United States
| | - Hanna Berman
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, United States
| | - Shivaramu Keelara
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, United States
| | - Nilton Lincopan
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
- Department of Clinical Analysis, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Paula J. Fedorka-Cray
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, United States
| | - Rodolphe Barrangou
- Genomic Sciences Graduate Program, North Carolina State University, Raleigh, NC, United States
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC, United States
| | - Mariza Landgraf
- Department of Food and Experimental Nutrition, Faculty of Pharmaceutical Sciences, Food Research Center, University of São Paulo, São Paulo, Brazil
- Mariza Landgraf,
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Alikhan NF, Moreno LZ, Castellanos LR, Chattaway MA, McLauchlin J, Lodge M, O’Grady J, Zamudio R, Doughty E, Petrovska L, Cunha MPV, Knöbl T, Moreno AM, Mather AE. Dynamics of Salmonella enterica and antimicrobial resistance in the Brazilian poultry industry and global impacts on public health. PLoS Genet 2022; 18:e1010174. [PMID: 35653335 PMCID: PMC9162342 DOI: 10.1371/journal.pgen.1010174] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 03/29/2022] [Indexed: 11/19/2022] Open
Abstract
Non-typhoidal Salmonella enterica is a common cause of diarrhoeal disease; in humans, consumption of contaminated poultry meat is believed to be a major source. Brazil is the world’s largest exporter of chicken meat globally, and previous studies have indicated the introduction of Salmonella serovars through imported food products from Brazil. Here we provide an in-depth genomic characterisation and evolutionary analysis to investigate the most prevalent serovars and antimicrobial resistance (AMR) in Brazilian chickens and assess the impact to public health of products contaminated with S. enterica imported into the United Kingdom from Brazil. To do so, we examine 183 Salmonella genomes from chickens in Brazil and 357 genomes from humans, domestic poultry and imported Brazilian poultry products isolated in the United Kingdom. S. enterica serovars Heidelberg and Minnesota were the most prevalent serovars in Brazil and in meat products imported from Brazil into the UK. We extended our analysis to include 1,259 publicly available Salmonella Heidelberg and Salmonella Minnesota genomes for context. The Brazil genomes form clades distinct from global isolates, with temporal analysis suggesting emergence of these Salmonella Heidelberg and Salmonella Minnesota clades in the early 2000s, around the time of the 2003 introduction of the Enteritidis vaccine in Brazilian poultry. Analysis showed genomes within the Salmonella Heidelberg and Salmonella Minnesota clades shared resistance to sulphonamides, tetracyclines and beta-lactams conferred by sul2, tetA and blaCMY-2 genes, not widely observed in other co-circulating serovars despite similar selection pressures. The sul2 and tetA genes were concomitantly carried on IncC plasmids, whereas blaCMY-2 was either co-located with the sul2 and tetA genes on IncC plasmids or independently on IncI1 plasmids. Long-term surveillance data collected in the UK showed no increase in the incidence of Salmonella Heidelberg or Salmonella Minnesota in human cases of clinical disease in the UK following the increase of these two serovars in Brazilian poultry. In addition, almost all of the small number of UK-derived genomes which cluster with the Brazilian poultry-derived sequences could either be attributed to human cases with a recent history of foreign travel or were from imported Brazilian food products. These findings indicate that even should Salmonella from imported Brazilian poultry products reach UK consumers, they are very unlikely to be causing disease. No evidence of the Brazilian strains of Salmonella Heidelberg or Salmonella Minnesota were observed in UK domestic chickens. These findings suggest that introduction of the Salmonella Enteritidis vaccine, in addition to increasing antimicrobial use, could have resulted in replacement of salmonellae in Brazilian poultry flocks with serovars that are more drug resistant, but less associated with disease in humans in the UK. The plasmids conferring resistance to beta-lactams, sulphonamides and tetracyclines likely conferred a competitive advantage to the Salmonella Minnesota and Salmonella Heidelberg serovars in this setting of high antimicrobial use, but the apparent lack of transfer to other serovars present in the same setting suggests barriers to horizontal gene transfer that could be exploited in intervention strategies to reduce AMR. The insights obtained reinforce the importance of One Health genomic surveillance. Non-typhoidal Salmonella enterica is a common cause of diarrhoeal disease; in humans, consumption of contaminated poultry meat is believed to be a major source. Here we determine that S. enterica serovars Heidelberg and Minnesota were the most prevalent serovars in Brazilian poultry and in poultry products imported from Brazil into the UK. However, long-term surveillance data collected by the UK Health Security Agency showed no increase in the incidence of Salmonella Heidelberg or Salmonella Minnesota in human cases of clinical disease in the UK following the increase of these two serovars in Brazilian poultry. Salmonella Heidelberg and Salmonella Minnesota clades shared resistance to sulphonamides, tetracyclines and beta-lactams conferred by sul2, tetA and blaCMY-2 genes, not widely observed in other co-circulating serovars despite similar selection pressures. The sul2 and tetA genes were concomitantly carried on IncC plasmids, whereas blaCMY-2 was either co-located with the sul2 and tetA genes on IncC plasmids or independently on IncI1 plasmids. These findings suggest that introduction of the Salmonella Enteritidis vaccine, in addition to increasing antimicrobial use, could have resulted in replacement of salmonellae in Brazilian poultry flocks with serovars that are more drug resistant, but less associated with disease in humans in the UK.
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Affiliation(s)
| | - Luisa Zanolli Moreno
- Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil
- Centro Universitário Max Planck (UniMax), Indaiatuba, São Paulo, Brazil
| | | | | | - Jim McLauchlin
- UK Health Security Agency National Infection Service, London, United Kingdom
| | - Martin Lodge
- UK Health Security Agency National Infection Service, London, United Kingdom
| | - Justin O’Grady
- Quadram Institute Bioscience, Norwich, United Kingdom
- University of East Anglia, Norwich, United Kingdom
| | | | - Emma Doughty
- Quadram Institute Bioscience, Norwich, United Kingdom
| | - Liljana Petrovska
- Department of Bacteriology and Food Safety, Animal and Plant Health Agency (APHA—Weybridge), Addlestone, United Kingdom
| | - Marcos Paulo Vieira Cunha
- Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil
| | - Terezinha Knöbl
- Department of Pathology, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil
| | - Andrea Micke Moreno
- Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil
- * E-mail: (AMM); (AEM)
| | - Alison E. Mather
- Quadram Institute Bioscience, Norwich, United Kingdom
- University of East Anglia, Norwich, United Kingdom
- * E-mail: (AMM); (AEM)
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20
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Antimicrobial resistance and genetic background of non-typhoidal Salmonella enterica strains isolated from human infections in São Paulo, Brazil (2000-2019). Braz J Microbiol 2022; 53:1249-1262. [PMID: 35446010 PMCID: PMC9433476 DOI: 10.1007/s42770-022-00748-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Accepted: 03/30/2022] [Indexed: 11/02/2022] Open
Abstract
Salmonella enterica causes Salmonellosis, an important infection in humans and other animals. The number of multidrug-resistant (MDR) phenotypes associated with Salmonella spp. isolates is increasing worldwide, causing public health concern. Here, we aim to characterize the antimicrobial-resistant phenotype of 789 non-typhoidal S. enterica strains isolated from human infections in the state of São Paulo, Brazil, along 20 years (2000-2019). Among the non-susceptible isolates, 31.55, 14.06, and 13.18% were resistant to aminoglycosides, tetracycline, and β-lactams, respectively. Moreover, 68 and 11 isolates were considered MDR and Extended Spectrum β-Lactamase (ESBL) producers, respectively, whereas one isolate was colistin-resistant. We selected four strains to obtain a draft of the Genome Sequence; one S. Infantis (ST32), one S. Enteritidis (ST11), one S. I 4,[5],12:i:- (ST19), and one S. Typhimurium (ST313). Among them, three presented at least one of the following antimicrobial resistance genes (AMR) linked to mobile DNA: blaTEM-1B, dfrA1, tetA, sul1, floR, aac(6')-laa, and qnrE1. This is the first description of the plasmid-mediated quinolone resistance (PMQR) gene qnrE1 in a clinical isolate of S. I 4,[5],12:i:-. The S. Typhimurium is a colistin-resistant isolate, but did not harbor mcr genes, but it presented mutations within the mgrB, pmrB, and pmrC regions that might be linked to the colistin-resistant phenotype. The virulence pattern of the four isolates resembled the virulence pattern of the highly pathogenic S. Typhimurium UK-1 reference strain in assays involving the in vivo Galleria mellonella model. In conclusion, most isolates studied here are susceptible, but a small percentage present an MDR or ESBL-producer and pathogenic phenotype. Sequence analyses revealed plasmid-encoded AMR genes, such as β-lactam and fluoroquinolone resistance genes, indicating that these characteristics can be potentially disseminated among other bacterial strains.
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Vogt NA, Hetman BM, Vogt AA, Pearl DL, Reid-Smith RJ, Parmley EJ, Kadykalo S, Janecko N, Bharat A, Mulvey MR, Ziebell K, Robertson J, Nash J, Allen V, Majury A, Ricker N, Bondo KJ, Allen SE, Jardine CM. Rural Raccoons (Procyon lotor) Not Likely to Be a Major Driver of Antimicrobial Resistant Human Salmonella Cases in Southern Ontario, Canada: A One Health Epidemiological Assessment Using Whole-Genome Sequence Data. Front Vet Sci 2022; 9:840416. [PMID: 35280127 PMCID: PMC8914089 DOI: 10.3389/fvets.2022.840416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 01/24/2022] [Indexed: 11/13/2022] Open
Abstract
Non-typhoidal Salmonella infections represent a substantial burden of illness in humans, and the increasing prevalence of antimicrobial resistance among these infections is a growing concern. Using a combination of Salmonella isolate short-read whole-genome sequence data from select human cases, raccoons, livestock and environmental sources, and an epidemiological framework, our objective was to determine if there was evidence for potential transmission of Salmonella and associated antimicrobial resistance determinants between these different sources in the Grand River watershed in Ontario, Canada. Logistic regression models were used to assess the potential associations between source type and the presence of select resistance genes and plasmid incompatibility types. A total of 608 isolates were obtained from the following sources: humans (n = 58), raccoons (n = 92), livestock (n = 329), and environmental samples (n = 129). Resistance genes of public health importance, including blaCMY−2, were identified in humans, livestock, and environmental sources, but not in raccoons. Most resistance genes analyzed were significantly more likely to be identified in livestock and/or human isolates than in raccoon isolates. Based on a 3,002-loci core genome multi-locus sequence typing (cgMLST) scheme, human Salmonella isolates were often more similar to isolates from livestock and environmental sources, than with those from raccoons. Rare instances of serovars S. Heidelberg and S. Enteritidis in raccoons likely represent incidental infections and highlight possible acquisition and dissemination of predominantly poultry-associated Salmonella by raccoons within these ecosystems. Raccoon-predominant serovars were either not identified among human isolates (S. Agona, S. Thompson) or differed by more than 350 cgMLST loci (S. Newport). Collectively, our findings suggest that the rural population of raccoons on swine farms in the Grand River watershed are unlikely to be major contributors to antimicrobial resistant human Salmonella cases in this region.
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Affiliation(s)
- Nadine A. Vogt
- Department of Population Medicine, Ontario Veterinary College, Guelph, ON, Canada
- *Correspondence: Nadine A. Vogt
| | - Benjamin M. Hetman
- Department of Population Medicine, Ontario Veterinary College, Guelph, ON, Canada
| | | | - David L. Pearl
- Department of Population Medicine, Ontario Veterinary College, Guelph, ON, Canada
| | - Richard J. Reid-Smith
- Department of Population Medicine, Ontario Veterinary College, Guelph, ON, Canada
- Centre for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, ON, Canada
| | - E. Jane Parmley
- Department of Population Medicine, Ontario Veterinary College, Guelph, ON, Canada
- Centre for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, ON, Canada
| | - Stefanie Kadykalo
- Centre for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, ON, Canada
| | - Nicol Janecko
- Quadram Institute Bioscience, Norwich, United Kingdom
| | - Amrita Bharat
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
| | - Michael R. Mulvey
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
| | - Kim Ziebell
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, ON, Canada
| | - James Robertson
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, ON, Canada
| | - John Nash
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, ON, Canada
| | | | - Anna Majury
- Public Health Ontario, Kingston, ON, Canada
- Department of Biomedical and Molecular Science, Queen's University, Kingston, ON, Canada
| | - Nicole Ricker
- Department of Pathobiology, Ontario Veterinary College, Guelph, ON, Canada
| | - Kristin J. Bondo
- Department of Pathobiology, Ontario Veterinary College, Guelph, ON, Canada
| | - Samantha E. Allen
- Wyoming Game and Fish Department, Laramie, WY, United States
- Department of Veterinary Sciences, University of Wyoming, Laramie, WY, United States
| | - Claire M. Jardine
- Department of Pathobiology, Ontario Veterinary College, Guelph, ON, Canada
- Canadian Wildlife Health Cooperative, Ontario Veterinary College, Guelph, ON, Canada
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22
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Silva Teixeira MD, Lages DH, Alves VV, Silva Martins NRD, Freitas Neto OCD. Assessment of maternal immunity against Salmonella enterica serovar Heidelberg in progeny of broiler breeders vaccinated with different formulations of bacterins. Avian Pathol 2022; 51:197-205. [PMID: 35130087 DOI: 10.1080/03079457.2022.2039592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Salmonella Heidelberg (SH) has been reported in broiler flocks of many countries. The ability of some SH strains from poultry origin to cause foodborne infections in humans is a concern. Usually infection of broiler flocks by SH occurs in the first days of life. Therefore, control measures should start early post-hatch. One of the strategies is to generate high titers of anti-Salmonella IgY in breeders by using bacterins to provide passive immunity to their progeny. In this study three broiler breeder flocks were submitted to three Salmonella vaccination regimes (two doses of vaccine 1, two doses of vaccine 2 and non-vaccinated). When breeders were 30 and 55 weeks-old, part of their offspring were separated and challenged with a SH strain at three days of age. Dissemination to organs, caecal colonization and faecal excretion of SH were evaluated over 20 days. Chicks from vaccinated 30 week-old breeders presented lower amounts of SH in caecal content at 1, 3 and 6 days-post infection, correlating with high titers of maternal anti-Salmonella IgY in their yolk. In contrast, there were no differences in counts of SH in caecal content of chicks when their parents were 55 weeks-old and titers of IgY were reduced. Amounts of SH in liver and spleen were low and there were no differences among birds over the experiment. Progeny from 30 week-old flock vaccinated with vaccine 1 also showed lower SH faecal shedding than the remaining birds. Apparently, the maternal IgY was associated with reductions in intestinal infection by SH.
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Affiliation(s)
- Mailson da Silva Teixeira
- Department of Preventive Veterinary Medicine, Veterinary School, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG 31270-901, Brazil
| | - Dayse Helena Lages
- Department Veterinary Clinic and Surgery, Veterinary School, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG 31270-901, Brazil
| | - Victória Veiga Alves
- Department of Preventive Veterinary Medicine, Veterinary School, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG 31270-901, Brazil
| | - Nelson Rodrigo da Silva Martins
- Department of Preventive Veterinary Medicine, Veterinary School, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG 31270-901, Brazil
| | - Oliveiro Caetano de Freitas Neto
- Department of Preventive Veterinary Medicine, Veterinary School, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG 31270-901, Brazil
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Moreira JPFF, do Monte DFM, Lima CDA, de Oliveira CJB, da Silva Martins NR, Berchieri Junior A, de Freitas Neto OC. Molecular genotyping reveals inter-regional relatedness among antimicrobial resistant Salmonella Minnesota strains isolated from poultry farm and humans, Brazil. Braz J Microbiol 2022; 53:503-508. [PMID: 35061241 PMCID: PMC8882525 DOI: 10.1007/s42770-021-00666-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 12/24/2021] [Indexed: 01/23/2023] Open
Abstract
Genetic profiles of Salmonella Minnesota isolates were analyzed using pulsed-field gel electrophoresis (PFGE). In total, 13 isolates obtained from the broiler industry collected in the states of Minas Gerais (11) and São Paulo (2), as well as five recovered from cases of foodborne infections in humans in the states of Minas Gerais (2), Santa Catarina (1), and Rio Grande do Sul (2), were submitted to PFGE. These 18 S. Minnesota isolates together with other 12 of poultry origin were also subjected to antimicrobial susceptibility testing. The PFGE analysis of 18 strains of S. Minnesota generated a dendrogram that grouped the isolates with 83-90% similarity into four main clusters. Among them, cluster "A" grouped the majority of isolates (13), including two of human origin that showed 90% similarity with a broiler isolate, both recovered in Minas Gerais. The S. Minnesota isolates showed resistance to tetracycline (80%), cefoxitin (80%), ceftazidime (46.7%), nalidixic acid (23.3%), ciprofloxacin (13.3%), and streptomycin (10%). No resistance to gentamicin, chloramphenicol, meropenem, nitrofurantoin, and sulfamethoxazole-trimethoprim was found. Moreover, 23.3% of the evaluated isolates presented multi-resistance profile, all from Minas Gerais. The results highlight the importance of further studies involving S. Minnesota, which is prevalent in the Brazilian broiler flocks and could provoke foodborne infection in humans.
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Affiliation(s)
- João Paulo Fernandes Ferreira Moreira
- Department of Preventive Veterinary Medicine, School of Veterinary, Federal University of Minas Gerais (UFMG), Avenida Antônio Carlos, 6667 - São Luiz, Belo Horizonte, Minas Gerais, CEP: 31270-010, Brazil
| | - Daniel Farias Marinho do Monte
- Laboratory of Avian Pathology, Department of Pathology, Theriogenology, and One Health, São Paulo State University (FCAV-Unesp), Jaboticabal, São Paulo, Brazil
| | - Camila de Aguiar Lima
- Veterinary Science Graduate Program, School of Veterinary, Federal University of Minas Gerais (UFMG), Belo Horizonte, Minas Gerais, Brazil
| | - Celso José Bruno de Oliveira
- Department of Animal Science, Center for Agricultural Sciences, Federal University of Paraiba (CCA/UFPB), Areia, PB, Brazil
| | - Nelson Rodrigo da Silva Martins
- Department of Preventive Veterinary Medicine, School of Veterinary, Federal University of Minas Gerais (UFMG), Avenida Antônio Carlos, 6667 - São Luiz, Belo Horizonte, Minas Gerais, CEP: 31270-010, Brazil
| | - Angelo Berchieri Junior
- Laboratory of Avian Pathology, Department of Pathology, Theriogenology, and One Health, São Paulo State University (FCAV-Unesp), Jaboticabal, São Paulo, Brazil
| | - Oliveiro Caetano de Freitas Neto
- Department of Preventive Veterinary Medicine, School of Veterinary, Federal University of Minas Gerais (UFMG), Avenida Antônio Carlos, 6667 - São Luiz, Belo Horizonte, Minas Gerais, CEP: 31270-010, Brazil.
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Yang SM, Kim E, Lee W, Kim HY. Genomic characteristics and comparative genomics of Salmonella enterica subsp. enterica serovar Schwarzengrund strain S16 isolated from chicken feces. Gut Pathog 2022; 14:1. [PMID: 34983642 PMCID: PMC8728987 DOI: 10.1186/s13099-021-00476-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 12/13/2021] [Indexed: 01/18/2023] Open
Abstract
Background Salmonella enterica subsp. enterica serovar Schwarzengrund (S. Schwarzengrund) is most frequently isolated from commensals humans or poultry. Here we report S. Schwarzengrund strain S16, the first sequenced genome in the Republic of Korea. Additionally, genome sequencing for strain S16 was performed and compared with other S. Schwarzengrund genomes obtained from public database. Results Strain S16 was isolated from chicken feces. The complete genome consists of one chromosome and one plasmid. The genome size is 4,822,755 bp with 4852 coding sequences. Strain S16 was determined as serovar Schwarzengrund by in silico serotyping and typed as sequence type (ST) 96. Forty-six S. Schwarzengrund genomes yielded a pangenome of 7112 genes, core-genome of 3374 genes, accessory-genome of 2906 genes, and unique-genome of 835 genes. Eighty-one genes were unique to strain S16, including hypothetical proteins and transcriptional regulators. Genotypic analysis of antibiotic resistance of strain S16 confirmed resistance to amikacin, ciprofloxacin, sulfamethoxazole, streptomycin, and tetracycline. Unlike other S. Schwarzengrund genomes, strain S16 had a mutation of gyrB. Moreover, similar to other S. Schwarzengrund genomes reported in other countries, strain S16 was harbored for 153 virulence genes including Saf operon and cdtB gene. All the antibiotic resistance genes and virulence genes were present in the core- or accessory-genomes. Conclusions Complete genome of strain S16 was sequenced. Comparative genomic analysis revealed several genes responsible for antibiotic resistance and specific genomic features of strain S16 and identified virulence factors that might contribute to the human and animal pathogenicity of other S. Schwarzengrund genomes. Supplementary Information The online version contains supplementary material available at 10.1186/s13099-021-00476-8.
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Affiliation(s)
- Seung-Min Yang
- Institute of Life Sciences & Resources and Department of Food Science and Biotechnology, Kyung Hee University, Yongin, 17104, South Korea
| | - Eiseul Kim
- Institute of Life Sciences & Resources and Department of Food Science and Biotechnology, Kyung Hee University, Yongin, 17104, South Korea
| | - Woojung Lee
- Institute of Life Sciences & Resources and Department of Food Science and Biotechnology, Kyung Hee University, Yongin, 17104, South Korea
| | - Hae-Yeong Kim
- Institute of Life Sciences & Resources and Department of Food Science and Biotechnology, Kyung Hee University, Yongin, 17104, South Korea.
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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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Dos Santos Bersot L, Carbonera NR, Rodrigues Valcanaia CD, Viana C, Nero LA. Multidrug-Resistant and Extended-Spectrum β-Lactamase-Producing Salmonella enterica Serotype Heidelberg Is Widespread in a Poultry Processing Facility in Southern Brazil. J Food Prot 2021; 84:2053-2058. [PMID: 34324677 DOI: 10.4315/jfp-21-140] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 07/16/2021] [Indexed: 11/11/2022]
Abstract
ABSTRACT This study was conducted to characterize the distribution of Salmonella isolates in a poultry processing facility and to identify their antibiotic resistance profiles. Salmonella enterica was detected in 146 samples (66.7%), and 125 isolates were identified as Salmonella Heidelberg (n = 123), Salmonella Abony (n = 1), and Salmonella O:4,5 (n = 1). Salmonella Heidelberg isolates were subjected to XbaI macrorestriction analysis and pulsed-field gel electrophoresis. The 66 pulsotypes obtained were grouped into four major clusters, indicating cross-contamination and persistence of this serotype in the processing facility. Selected S. enterica isolates were characterized by their antibiotic resistance, and most (n = 122, 97.6%) were multidrug resistant. Resistance to third-generation cephalosporins ceftazidime (84 isolates, 67.2%) and cefotaxime and ceftriaxone (91 isolates, 72.8%) was particularly prevalent. Production of extended-spectrum β-lactamases (ESBL) was identified in 24 isolates (19.2%), and ESBL-producing isolates were resistant to at least eight antibiotics. This study revealed the high prevalence of Salmonella Heidelberg in the poultry chain, providing insight into the ecology of this pathogen in this facility. The high prevalence of multidrug-resistant S. enterica is a concern due to the potential consequences for public health. HIGHLIGHTS
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Affiliation(s)
- Luciano Dos Santos Bersot
- LACOMA - Laboratório de Inspeção e Controle de Qualidade de Alimentos e Água, Universidade Federal do Paraná, Setor Palotina, Departamento de Ciências Veterinárias, Rua Pioneiro, 2153, Jardim Dallas, 85950-000, Palotina, PR, Brazil
| | - Neila Rita Carbonera
- LACOMA - Laboratório de Inspeção e Controle de Qualidade de Alimentos e Água, Universidade Federal do Paraná, Setor Palotina, Departamento de Ciências Veterinárias, Rua Pioneiro, 2153, Jardim Dallas, 85950-000, Palotina, PR, Brazil
| | - Carolina Dias Rodrigues Valcanaia
- LACOMA - Laboratório de Inspeção e Controle de Qualidade de Alimentos e Água, Universidade Federal do Paraná, Setor Palotina, Departamento de Ciências Veterinárias, Rua Pioneiro, 2153, Jardim Dallas, 85950-000, Palotina, PR, Brazil
| | - Cibeli Viana
- InsPOA - Laboratório de Inspeção de Produtos de Origem Animal, Universidade Federal de Viçosa, Departamento de Veterinária, Avenida PH Rolfs, s/n, Campus Universitário, 36570-900, Viçosa, MG, Brazil
| | - Luís Augusto Nero
- InsPOA - Laboratório de Inspeção de Produtos de Origem Animal, Universidade Federal de Viçosa, Departamento de Veterinária, Avenida PH Rolfs, s/n, Campus Universitário, 36570-900, Viçosa, MG, Brazil
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Vogt NA, Hetman BM, Pearl DL, Vogt AA, Reid-Smith RJ, Parmley EJ, Janecko N, Bharat A, Mulvey MR, Ricker N, Bondo KJ, Allen SE, Jardine CM. Using whole-genome sequence data to examine the epidemiology of Salmonella, Escherichia coli and associated antimicrobial resistance in raccoons (Procyon lotor), swine manure pits, and soil samples on swine farms in southern Ontario, Canada. PLoS One 2021; 16:e0260234. [PMID: 34793571 PMCID: PMC8601536 DOI: 10.1371/journal.pone.0260234] [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: 09/17/2021] [Accepted: 11/04/2021] [Indexed: 11/19/2022] Open
Abstract
To better understand the contribution of wildlife to the dissemination of Salmonella and antimicrobial resistance in Salmonella and Escherichia coli, we examined whole-genome sequence data from Salmonella and E. coli isolates collected from raccoons (Procyon lotor) and environmental sources on farms in southern Ontario. All Salmonella and phenotypically resistant E. coli collected from raccoons, soil, and manure pits on five swine farms as part of a previous study were included. We assessed for evidence of potential transmission of these organisms between different sources and farms utilizing a combination of population structure assessments (using core-genome multi-locus sequence typing), direct comparisons of multi-drug resistant isolates, and epidemiological modeling of antimicrobial resistance (AMR) genes and plasmid incompatibility (Inc) types. Univariable logistic regression models were fit to assess the impact of source type, farm location, and sampling year on the occurrence of select resistance genes and Inc types. A total of 159 Salmonella and 96 resistant E. coli isolates were included. A diversity of Salmonella serovars and sequence types were identified, and, in some cases, we found similar or identical Salmonella isolates and resistance genes between raccoons, soil, and swine manure pits. Certain Inc types and resistance genes associated with source type were consistently more likely to be identified in isolates from raccoons than swine manure pits, suggesting that manure pits are not likely a primary source of those particular resistance determinants for raccoons. Overall, our data suggest that transmission of Salmonella and AMR determinants between raccoons and swine manure pits is uncommon, but soil-raccoon transmission appears to be occurring frequently. More comprehensive sampling of farms, and assessment of farms with other livestock species, as well as additional environmental sources (e.g., rivers) may help to further elucidate the movement of resistance genes between these various sources.
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Affiliation(s)
- Nadine A. Vogt
- Department of Population Medicine, Ontario Veterinary College, Guelph, Ontario, Canada
| | - Benjamin M. Hetman
- Department of Population Medicine, Ontario Veterinary College, Guelph, Ontario, Canada
| | - David L. Pearl
- Department of Population Medicine, Ontario Veterinary College, Guelph, Ontario, Canada
| | - Adam A. Vogt
- Independent Researcher, Mississauga, Ontario, Canada
| | - Richard J. Reid-Smith
- Department of Population Medicine, Ontario Veterinary College, Guelph, Ontario, Canada
- Centre for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - E. Jane Parmley
- Department of Population Medicine, Ontario Veterinary College, Guelph, Ontario, Canada
- Centre for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Nicol Janecko
- Quadram Institute Bioscience, Norwich, United Kingdom
| | - Amrita Bharat
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Michael R. Mulvey
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Nicole Ricker
- Department of Pathobiology, Ontario Veterinary College, Guelph, Ontario, Canada
| | - Kristin J. Bondo
- Department of Pathobiology, Ontario Veterinary College, Guelph, Ontario, Canada
| | - Samantha E. Allen
- Department of Pathobiology, Ontario Veterinary College, Guelph, Ontario, Canada
- Wyoming Game and Fish Department, Laramie, Wyoming, United States of America
- Department of Veterinary Sciences, University of Wyoming, Laramie, Wyoming, United States of America
| | - Claire M. Jardine
- Department of Pathobiology, Ontario Veterinary College, Guelph, Ontario, Canada
- Canadian Wildlife Health Cooperative, Ontario Veterinary College, Guelph, Ontario, Canada
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Agostinho Davanzo EF, dos Santos RL, Castro VHDL, Palma JM, Pribul BR, Dallago BSL, Fuga B, Medeiros M, Titze de Almeida SS, da Costa HMB, Rodrigues DDP, Lincopan N, Perecmanis S, Santana AP. Molecular characterization of Salmonella spp. and Listeria monocytogenes strains from biofilms in cattle and poultry slaughterhouses located in the federal District and State of Goiás, Brazil. PLoS One 2021; 16:e0259687. [PMID: 34767604 PMCID: PMC8589217 DOI: 10.1371/journal.pone.0259687] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 10/23/2021] [Indexed: 10/26/2022] Open
Abstract
Listeria monocytogenes and Salmonella spp. are considered important foodborne pathogens that are commonly associated with foods of animal origin. The aim of this study was to perform molecular characterization of L. monocytogenes and Salmonella spp. isolated from biofilms of cattle and poultry slaughterhouses located in the Federal District and State of Goiás, Brazil. Fourteen L. monocytogenes isolates and one Salmonella sp. were detected in poultry slaughterhouses. No isolates were detected in cattle slaughterhouses. All L. monocytogenes isolates belonged to lineage II, and 11 different pulsotypes were detected. Pulsed-field gel electrophoresis analysis revealed the dissemination of two strains within one plant, in addition to the regional dissemination of one of them. The Salmonella isolate was identified via whole genome sequencing as Salmonella enterica serovar Minnesota ST548. In the sequence analysis, no premature stop codons were detected in the inlA gene of Listeria. All isolates demonstrated the ability to adhere to Caco-2 cells, while 50% were capable of invading them. Antimicrobial resistance was detected in 57.1% of the L. monocytogenes isolates, and resistance to sulfonamide was the most common feature. The tetC, ermB, and tetM genes were detected, and four isolates were classified as multidrug-resistant. Salmonella sp. was resistant to nine antimicrobials and was classified as multidrug-resistant. Resistance genes qnrB19, blaCMY-2, aac(6')-Iaa, sul2, and tetA, and a mutation in the parC gene were detected. The majority (78.5%) of the L. monocytogenes isolates were capable of forming biofilms after incubation at 37°C for 24 h, and 64.3% were capable of forming biofilms after incubation at 12°C for 168 h. There was no statistical difference in the biofilm-forming capacity under the different evaluated conditions. Salmonella sp. was capable of forming biofilms at both tested temperatures. Biofilm characterization was confirmed by collecting the samples consistently, at the same sampling points, and by assessing biofilm formation in vitro. These results highlight the potential risk of cross-contamination in poultry slaughterhouses and the importance of surveillance and pathogen control maintenance programs within the meat production industry.
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Affiliation(s)
| | | | | | - Joana Marchesini Palma
- Faculty of Agronomy and Veterinary Medicine, University of Brasília (UnB), Brasília, DF, Brazil
| | - Bruno Rocha Pribul
- National Reference Laboratory for Bacterial Enteric Infections, Oswaldo Cruz Institute, Manguinhos, Rio de Janeiro, RJ, Brazil
| | | | - Bruna Fuga
- Laboratory of Bacterial Resistance and Therapeutic Alternatives, Biomedical Sciences Institute, University of São Paulo, São Paulo, SP, Brazil
| | - Margareti Medeiros
- Faculty of Agronomy and Veterinary Medicine, University of Brasília (UnB), Brasília, DF, Brazil
| | | | | | - Dália dos Prazeres Rodrigues
- National Reference Laboratory for Bacterial Enteric Infections, Oswaldo Cruz Institute, Manguinhos, Rio de Janeiro, RJ, Brazil
| | - Nilton Lincopan
- Laboratory of Bacterial Resistance and Therapeutic Alternatives, Biomedical Sciences Institute, University of São Paulo, São Paulo, SP, Brazil
| | - Simone Perecmanis
- Faculty of Agronomy and Veterinary Medicine, University of Brasília (UnB), Brasília, DF, Brazil
| | - Angela Patrícia Santana
- Faculty of Agronomy and Veterinary Medicine, University of Brasília (UnB), Brasília, DF, Brazil
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Wan Makhtar WR, Bharudin I, Samsulrizal NH, Yusof NY. Whole Genome Sequencing Analysis of Salmonella enterica Serovar Typhi: History and Current Approaches. Microorganisms 2021; 9:microorganisms9102155. [PMID: 34683476 PMCID: PMC8538346 DOI: 10.3390/microorganisms9102155] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 10/01/2021] [Accepted: 10/12/2021] [Indexed: 12/27/2022] Open
Abstract
In recent years, the advance in whole-genome sequencing technology has changed the study of infectious diseases. The emergence of genome sequencing has improved the understanding of infectious diseases, which has revamped many fields, such as molecular microbiology, epidemiology, infection control, and vaccine production. In this review we discuss the findings of Salmonella enterica serovar Typhi genomes, publicly accessible from the initial complete genome to the recent update of Salmonella enterica serovar Typhi genomes, which has greatly improved Salmonella enterica serovar Typhi and other pathogen genomic research. Significant information on genetic changes, evolution, antimicrobial resistance, virulence, pathogenesis, and investigation from the genome sequencing of S. Typhi is also addressed. This review will gather information on the variation of the Salmonella enterica serovar Typhi genomes and hopefully facilitate our understanding of their genome evolution, dynamics of adaptation, and pathogenesis for the development of the typhoid point-of-care diagnostics, medications, and vaccines.
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Affiliation(s)
- Wan Ratmaazila Wan Makhtar
- Reconstructive Sciences Unit, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Malaysia;
| | - Izwan Bharudin
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia UKM, Bangi 43600, Malaysia;
| | - Nurul Hidayah Samsulrizal
- Department of Plant Science, Kuliyyah of Science, International Islamic University Malaysia, Kuantan 25200, Malaysia;
| | - Nik Yusnoraini Yusof
- Institute for Research in Molecular Medicine (INFORMM), Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Malaysia
- Correspondence:
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Isolation and molecular characterization of multidrug-resistant Salmonella enterica serovars. J Infect Public Health 2021; 14:1767-1776. [PMID: 34690097 DOI: 10.1016/j.jiph.2021.10.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Revised: 10/04/2021] [Accepted: 10/10/2021] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Salmonellosis is a foodborne zoonosis leaving gastrointestinal illness and drug-resistant genes to the consumers. To prevent Salmonella contamination associated health issues in the chicken meat sold in Riyadh city in Saudi Arabia. The evaluation of the Salmonella isolates from the meat sample needs to be screened for the composition of Salmonella serotypes and antimicrobial resistance pattern at the molecular level. METHODS AND RESULTS Using specific growth media for Salmonella spp., swabs taken from the whole-body surfaces of 200 chilled broiler chickens from different vendors in the city of Riyadh, were screened for Salmonella contamination. Biochemical and molecular characterization of the isolates showed the presence of the serovars, Salmonella enterica, Salmonella Enteritidis, S. Typhimurium, S. Kentucky, and S. Tennessee. The isolated serovars exhibited multidrug resistance [MDR] resistance to antibiotics. Molecular characterization of the different serovars shows the presence of sixteen drug-resistant genes. The drug resistance mechanism at the molecular level varied with serotypes according to the nature of the antibiotics they encountered. A comparative study of the nature of the drug-resistant gene and the common antibiotics used in poultry farming in that province matches much, indicating adaptive variation in S. enterica serotypes to survive in the host's gut biome. The resistance genes from the chicken meat have every chance to get into the human system. The native microbes in consumers may acquire drug-resistant genes from S. entericus serovars. Such conditions may lead to treatment complications in the hosts. CONCLUSIONS The results indicated that Salmonella infections constituted a potential risk to consumers through chicken flocks and noted that the genotypic resistance pattern to antibiotics draws attention in terms of both human and animal health. Also, promote other options for poultry farming, avoiding antibiotics supplementation.
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Recent Evolution and Genomic Profile of Salmonella enterica Serovar Heidelberg Isolates from Poultry Flocks in Brazil. Appl Environ Microbiol 2021; 87:e0103621. [PMID: 34406824 DOI: 10.1128/aem.01036-21] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Salmonella enterica serovar Heidelberg is isolated from poultry-producing regions around the world. In Brazil, S. Heidelberg has been frequently detected in poultry flocks, slaughterhouses, and chicken meat. The goal of the present study was to assess the population structure, recent temporal evolution, and some important genetic characteristics of S. Heidelberg isolated from Brazilian poultry farms. Phylogenetic analysis of 68 S. Heidelberg genomes sequenced here and additional whole-genome data from NCBI demonstrated that all isolates from the Brazilian poultry production chain clustered into a monophyletic group, here called S. Heidelberg Brazilian poultry lineage (SH-BPL). Bayesian analysis defined the time of the most recent common ancestor (tMRCA) as 2004, and the overall population size (Ne) was constant until 2008, when an ∼10-fold Ne increase was observed until circa 2013. SH-BPL presented at least two plasmids with replicons ColpVC (n = 68; 100%), IncX1 (n = 66; 97%), IncA/C2 (n = 65; 95.5%), ColRNAI (n = 43; 63.2%), IncI1 (n = 32; 47%), ColMG828, Col156, IncHI2A, IncHI2, IncQ1, IncX4, IncY, and TrfA (each with n < 4; <4% each). Antibiotic resistance genes were found, with high frequencies of fosA7 (n = 68; 100%), mdf(A) (n = 68; 100%), tet(34) (n = 68; 100%), sul2 (n = 64; 94.1%), and blaCMY-2 (n = 56; 82.3%), along with an overall multidrug resistance (MDR) profile. Ten Salmonella pathogenicity islands (SPI1 to SPI5, SPI9, and SPI11 to SPI14) and 139 virulence genes were also detected. The SH-BPL profile was like those of other previous S. Heidelberg isolates from poultry around the world in the 1990s. In conclusion, the present study demonstrates the recent introduction (2004) and high level of dissemination of an MDR S. Heidelberg lineage in Brazilian poultry operations. IMPORTANCE S. Heidelberg is the most frequent serovar in several broiler farms from the main Brazilian poultry-producing regions. Therefore, avian-source foods (mainly chicken carcasses) commercialized in the country and exported to other continents are contaminated with this foodborne pathogen, generating several national and international economic losses. In addition, isolates of this serovar are usually resistant to antibiotics and can cause human invasive and septicemic infection, representing a public health concern. This study demonstrates the use of whole-genome sequencing (WGS) to obtain epidemiological information for one S. Heidelberg lineage highly spread among Brazilian poultry farms. This information will help to define biosecurity measures to control this important Salmonella serovar in Brazilian and worldwide poultry operations.
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Dissection of Highly Prevalent qnrS1-Carrying IncX Plasmid Types in Commensal Escherichia coli from German Food and Livestock. Antibiotics (Basel) 2021; 10:antibiotics10101236. [PMID: 34680816 PMCID: PMC8532951 DOI: 10.3390/antibiotics10101236] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 09/29/2021] [Accepted: 10/08/2021] [Indexed: 11/16/2022] Open
Abstract
Plasmids are mobile genetic elements, contributing to the spread of resistance determinants by horizontal gene transfer. Plasmid-mediated quinolone resistances (PMQRs) are important determinants able to decrease the antimicrobial susceptibility of bacteria against fluoroquinolones and quinolones. The PMQR gene qnrS1, especially, is broadly present in the livestock and food sector. Thus, it is of interest to understand the characteristics of plasmids able to carry and disseminate this determinant and therewith contribute to the resistance development against this class of high-priority, critically important antimicrobials. Therefore, we investigated all commensal Escherichia (E.) coli isolates, with reduced susceptibility to quinolones, recovered during the annual zoonosis monitoring 2017 in the pork and beef production chain in Germany (n = 2799). Through short-read whole-genome sequencing and bioinformatics analysis, the composition of the plasmids and factors involved in their occurrence were determined. We analysed the presence and structures of predominant plasmids carrying the PMQR qnrS1. This gene was most frequently located on IncX plasmids. Although the E. coli harbouring these IncX plasmids were highly diverse in their sequence types as well as their phenotypic resistance profiles, the IncX plasmids-carrying the qnrS1 gene were rather conserved. Thus, we only detected three distinct IncX plasmids carrying qnrS1 in the investigated isolates. The IncX plasmids were assigned either to IncX1 or to IncX3. All qnrS1-carrying IncX plasmids further harboured a β-lactamase gene (bla). In addition, all investigated IncX plasmids were transmissible. Overall, we found highly heterogenic E. coli harbouring conserved IncX plasmids as vehicles for the most prevalent qnr gene qnrS1. These IncX plasmids may play an important role in the dissemination of those two resistance determinants and their presence, transfer and co-selection properties require a deeper understanding for a thorough risk assessment.
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Santos CA, Lima EMF, Franco BDGDM, Pinto UM. Exploring Phenolic Compounds as Quorum Sensing Inhibitors in Foodborne Bacteria. Front Microbiol 2021; 12:735931. [PMID: 34594318 PMCID: PMC8477669 DOI: 10.3389/fmicb.2021.735931] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Accepted: 08/17/2021] [Indexed: 11/13/2022] Open
Abstract
The emergence of multidrug-resistant bacteria stimulates the search for new substitutes to traditional antimicrobial agents, especially molecules with antivirulence properties, such as those that interfere with quorum sensing (QS). This study aimed to evaluate the potential of phenolic compounds for QS inhibition in a QS biosensor strain (Chromobacterium violaceum) and three foodborne bacterial species (Aeromonas hydrophila, Salmonella enterica serovar Montevideo, and Serratia marcescens). Initially, an in silico molecular docking study was performed to select the compounds with the greatest potential for QS inhibition, using structural variants of the CviR QS regulator of C. violaceum as target. Curcumin, capsaicin, resveratrol, gallic acid, and phloridizin presented good affinity to at least four CviR structural variants. These phenolic compounds were tested for antimicrobial activity, inhibition of biofilm formation, and anti-QS activity. The antimicrobial activity when combined with kanamycin was also assessed. Curcumin, capsaicin, and resveratrol inhibited up to 50% of violacein production by C. violaceum. Biofilm formation was inhibited by resveratrol up to 80% in A. hydrophila, by capsaicin and curcumin up to 40% in S. Montevideo and by resveratrol and capsaicin up to 60% in S. marcescens. Curcumin completely inhibited swarming motility in S. marcescens. Additionally, curcumin and resveratrol increased the sensitivity of the tested bacteria to kanamycin. These results indicate that curcumin and resveratrol at concentrations as low as 6μM are potential quorum sensing inhibitors besides having antimicrobial properties at higher concentrations, encouraging applications in the food and pharmaceutical industries.
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Affiliation(s)
| | | | | | - Uelinton Manoel Pinto
- Department of Food and Experimental Nutrition, Food Research Center, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
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Seribelli AA, da Silva P, Frazão MR, Kich JD, Allard MW, Falcão JP. Phylogenetic relationship and genomic characterization of Salmonella Typhimurium strains isolated from swine in Brazil. INFECTION GENETICS AND EVOLUTION 2021; 93:104977. [PMID: 34174480 DOI: 10.1016/j.meegid.2021.104977] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 05/29/2021] [Accepted: 06/21/2021] [Indexed: 02/07/2023]
Abstract
Salmonella Typhimurium has been transmitted between humans and animals. Although, Brazil has been one of the largest pork meat exporters worldwide, there are few studies that characterized epidemiologically S. Typhimurium strains from swine. The aims of this work were to study the phylogenetic relationship of S. Typhimurium genomes isolated from swine in Brazil among themselves and with other genomes isolated from several sources and countries using wgMLST and cgMLST and to perform the search of Salmonella pathogenicity islands (SPIs). In addition, for S. Typhimurium strains from swine to compare the virulence and antimicrobial resistance genes by VFDB and ResFinder, genetic content by BLAST Atlas and orthologous proteins clusters by OrthoVenn. The constructed phylogenetic trees by wgMLST and cgMLST grouped the majority (92.3% and 80.7%, respectively) of the strains isolated from swine in Brazil into the same group. All the isolates contained important SPIs (SPI-1, SPI-2, SPI-3, SPI-5 and SPI-9). A total of 100 and 31 virulence and resistance genes were detected in the S. Typhimurium strains isolated from swine, respectively. The BLAST Atlas and orthologous proteins analysis found regions of phages and differences in metabolic, regulatory and cellular processes among S. Typhimurium LT2 and S. Typhimurium isolates from swine. In conclusion, molecular typing based in the wgMLST and cgMLST suggested that the S. Typhimurium isolates from swine studied were genetically related. The pathogenic potential of the strains studied was corroborated by the presence of important SPIs and virulence genes. The high number of antimicrobial resistance genes detected is worrying and reinforced their potential risk in swine in Brazil. The comparison by BLAST Atlas suggested differences in mobile genetic elements among S. Typhimurium LT2 and S. Typhimurium isolates from swine in Brazil. The orthologous proteins analysis revealed unique genes related to important cellular processes in the strains from swine.
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Affiliation(s)
- Amanda Aparecida Seribelli
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Patrick da Silva
- Faculdade de Ciências Farmacêuticas de Araraquara, UNESP - Departamento de Ciências Biológicas, Rodovia Araraquara-Jaú Km 1, Araraquara, SP, Brazil
| | - Miliane Rodrigues Frazão
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Jalusa Deon Kich
- Empresa Brasileira de Pesquisa Agropecuária - Suínos e Aves - EMBRAPA, Concórdia, SC, Brazil
| | - Marc W Allard
- Food and Drug Administration - FDA, College Park, MD, United States.
| | - Juliana Pfrimer Falcão
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil.
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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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Koutsoumanis K, Allende A, Álvarez‐Ordóñez A, Bolton D, Bover‐Cid S, Chemaly M, Davies R, De Cesare A, Herman L, Hilbert F, Lindqvist R, Nauta M, Ru G, Simmons M, Skandamis P, Suffredini E, Argüello H, Berendonk T, Cavaco LM, Gaze W, Schmitt H, Topp E, Guerra B, Liébana E, Stella P, Peixe L. Role played by the environment in the emergence and spread of antimicrobial resistance (AMR) through the food chain. EFSA J 2021; 19:e06651. [PMID: 34178158 PMCID: PMC8210462 DOI: 10.2903/j.efsa.2021.6651] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The role of food-producing environments in the emergence and spread of antimicrobial resistance (AMR) in EU plant-based food production, terrestrial animals (poultry, cattle and pigs) and aquaculture was assessed. Among the various sources and transmission routes identified, fertilisers of faecal origin, irrigation and surface water for plant-based food and water for aquaculture were considered of major importance. For terrestrial animal production, potential sources consist of feed, humans, water, air/dust, soil, wildlife, rodents, arthropods and equipment. Among those, evidence was found for introduction with feed and humans, for the other sources, the importance could not be assessed. Several ARB of highest priority for public health, such as carbapenem or extended-spectrum cephalosporin and/or fluoroquinolone-resistant Enterobacterales (including Salmonella enterica), fluoroquinolone-resistant Campylobacter spp., methicillin-resistant Staphylococcus aureus and glycopeptide-resistant Enterococcus faecium and E. faecalis were identified. Among highest priority ARGs bla CTX -M, bla VIM, bla NDM, bla OXA -48-like, bla OXA -23, mcr, armA, vanA, cfr and optrA were reported. These highest priority bacteria and genes were identified in different sources, at primary and post-harvest level, particularly faeces/manure, soil and water. For all sectors, reducing the occurrence of faecal microbial contamination of fertilisers, water, feed and the production environment and minimising persistence/recycling of ARB within animal production facilities is a priority. Proper implementation of good hygiene practices, biosecurity and food safety management systems is very important. Potential AMR-specific interventions are in the early stages of development. Many data gaps relating to sources and relevance of transmission routes, diversity of ARB and ARGs, effectiveness of mitigation measures were identified. Representative epidemiological and attribution studies on AMR and its effective control in food production environments at EU level, linked to One Health and environmental initiatives, are urgently required.
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Dutra MC, Moreno LZ, Dias RA, Moreno AM. Antimicrobial Use in Brazilian Swine Herds: Assessment of Use and Reduction Examples. Microorganisms 2021; 9:microorganisms9040881. [PMID: 33924277 PMCID: PMC8074920 DOI: 10.3390/microorganisms9040881] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 04/15/2021] [Accepted: 04/16/2021] [Indexed: 11/16/2022] Open
Abstract
Brazil, as a major pig producer, is currently experiencing the widespread use of antimicrobials as a serious issue to be addressed. For measures to be taken in this direction, the extent of the problem must be known. The goal of this study was to evaluate the use of antimicrobials in 25 Brazilian swine herds. Antimicrobial use from birth to slaughter was correlated with biosecurity and productivity. After the first assessment (2016; M0), 13 herds implemented good practices to reduce antimicrobial use. Four years after the implementation of these measures (2020; M1), data about antimicrobial usage from these herds were collected. The results of the first assessment (M0) demonstrated a troublesome scenario: the mean value of antimicrobials used was 358.4 mg/kg of pig produced; the median of the pig’s lifetime exposure to antimicrobials was 73.7%, and the median number of drugs used was seven. A positive correlation between the antimicrobials consumed and the pig’s antimicrobial exposure time was detected. Nevertheless, these data did not correlate with biosecurity score or productivity. A significant difference was detected in M1, where a median 30% reduction in antimicrobials consumed was detected. There was also a 44.3% reduction of the pig’s lifetime exposure to antimicrobials. The median number of drugs used was reduced from seven to five. Antimicrobial use did not always reflect the sanitary condition or the real therapeutic needs, easily leading to overuse.
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Whole-Genome Sequencing Reveals the Presence of the blaCTX-M-65 Gene in Extended-Spectrum β-Lactamase-Producing and Multi-Drug-Resistant Clones of Salmonella Serovar Infantis Isolated from Broiler Chicken Environments in the Galapagos Islands. Antibiotics (Basel) 2021; 10:antibiotics10030267. [PMID: 33807748 PMCID: PMC8000398 DOI: 10.3390/antibiotics10030267] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 02/19/2021] [Accepted: 02/25/2021] [Indexed: 12/24/2022] Open
Abstract
Salmonella Infantis, a common contaminant of poultry products, is known to harbor mobile genetic elements that confer multi-drug resistance (MDR) and have been detected in many continents. Here, we report four MDR S. Infantis strains recovered from poultry house environments in Santa Cruz Island of the Galapagos showing extended-spectrum β-lactamase (ESBL) resistance and reduced fluoroquinolone susceptibility. Whole-genome sequencing (WGS) revealed the presence of the ESBL-conferring blaCTX-M-65 gene in an IncFIB-like plasmid in three S. Infantis isolates. Multi-locus sequence typing (MLST) and single nucleotide variant/polymorphism (SNP) SNVPhyl analysis showed that the S. Infantis isolates belong to sequence type ST32, likely share a common ancestor, and are closely related (1–3 SNP difference) to blaCTX-M-65-containing clinical and veterinary S. Infantis isolates from the United States and Latin America. Furthermore, phylogenetic analysis of SNPs following core-genome alignment (i.e., ParSNP) inferred close relatedness between the S. Infantis isolates from Galapagos and the United States. Prophage typing confirmed the close relationship among the Galapagos S. Infantis and was useful in distinguishing them from the United States isolates. This is the first report of MDR blaCTX-M-65-containing S. Infantis in the Galapagos Islands and highlights the need for increased monitoring and surveillance programs to determine prevalence, sources, and reservoirs of MDR pathogens.
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Costa P, Nascimento Y, Costa L, Dias S, Ventura N, Yamatogi R, Costa F, Cossi M. Influence of different periods of pre-slaughter fasting on microbiological quality of bullfrog carcasses (Lithobates catesbeianus). ARQ BRAS MED VET ZOO 2021. [DOI: 10.1590/1678-4162-12030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
ABSTRACT The aim of this study was to evaluate the influence of different periods of pre-slaughter fasting (F1: 2 to 24 hours and F2: 48 to 72 hours) on the counts of hygiene indicator microorganisms and the presence of Salmonella spp. in carcasses of bullfrogs. Two different stages of the slaughter process were analyzed: after bleeding (A) and after the final carcasses cleaning (B). Samples from each fasting period were analyzed to count hygiene indicator microorganisms (n=30) and Salmonella spp. (n=140). For aerobic mesophilic microorganisms, the variation in fasting periods caused a reduction of 0.69 log10 CFU / g (P<0.05) in F2 when compared to F1 at point B of the slaughter. Coliforms at 35º C and Escherichia coli showed no differences (P >0.05) between the fasting analyzed periods. Considering the presence of E. coli, it was observed that F2 resulted in a reduction of 30% (P<0.05) positivity on point B. For Salmonella spp., the results showed that F2 contributed to an 11.5% reduction in the presence of this bacteria at point B. (P<0.05). Therefore, it is concluded that 48 to 72 hours of pre-slaughter fasting resulted in a positive impact on the microbiological quality of bullfrog carcasses.
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Affiliation(s)
- P.C. Costa
- Universidade Federal de Uberlândia, Brazil
| | | | | | - S.C. Dias
- Universidade Estadual Paulista, Brazil
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Genomic investigation of antimicrobial resistance determinants and virulence factors in Salmonella enterica serovars isolated from contaminated food and human stool samples in Brazil. Int J Food Microbiol 2021; 343:109091. [PMID: 33639477 DOI: 10.1016/j.ijfoodmicro.2021.109091] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 01/07/2021] [Accepted: 02/02/2021] [Indexed: 12/20/2022]
Abstract
This study investigated the antimicrobial resistance determinants, virulence factors and identified serovars in 37 Salmonella enterica strains isolated from human stool and contaminated foods linked to outbreaks that occurred in Brazil over 7 years using whole genome sequencing (WGS). Phylogenetic analysis of selected serovars (S. Typhimurium, S. Infantis, S. London, and S. Johannesburg) was performed. Ten distinct serovars were identified and, 51% of the tested strains (n = 19) showed disagreement with the previous conventional serotyping. The antimicrobial resistance (AMR) determinants or plasmids varied among the strains. Resistome analysis revealed the presence of resistance genes to aminoglycosides [aac (6')-laa, aph (3″)-lb, aph (6)-ld, aadA1 and aadA2], sulfonamides (sul1), trimethoprin (dfrA8), fosfomycin (fosA7) and tetracyclines (tetA, tetB, tetC), as well as point mutations in parC (T57S) and gyrA (S83F). Plasmidome showed the presence of IncHI2, IncHI2A, IncFIB (S), IncFII (S), IncI1 and p0111 plasmids. Eight Salmonella pathogenicity islands and up to 102 stress and/or virulence genes were identified in the evaluated genomes. Virulence genes of K88 fimbrial adhesin were first reported in S. enterica (S. Pomona, S. Bredeney and S. Mbandaka strains). pilW gene was first identified in S. Pomona. Phylogenetic analysis showed that some serovars circulated in Brazil for decades, primarily within the poultry production chain. Findings highlighted the virulence and AMR determinants in strains that may lead to recurring food outbreaks.
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Jibril AH, Okeke IN, Dalsgaard A, Menéndez VG, Olsen JE. Genomic Analysis of Antimicrobial Resistance and Resistance Plasmids in Salmonella Serovars from Poultry in Nigeria. Antibiotics (Basel) 2021; 10:99. [PMID: 33498344 PMCID: PMC7909428 DOI: 10.3390/antibiotics10020099] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 01/06/2021] [Accepted: 01/19/2021] [Indexed: 12/31/2022] Open
Abstract
Antimicrobial resistance is a global public health concern, and resistance genes in Salmonella, especially those located on mobile genetic elements, are part of the problem. This study used phenotypic and genomic methods to identify antimicrobial resistance and resistance genes, as well as the plasmids that bear them, in Salmonella isolates obtained from poultry in Nigeria. Seventy-four isolates were tested for susceptibility to eleven commonly used antimicrobials. Plasmid reconstruction and identification of resistance and virulence genes were performed with a draft genome using in silico approaches in parallel with plasmid extraction. Phenotypic resistance to ciprofloxacin (50.0%), gentamicin (48.6%), nalidixic acid (79.7%), sulphonamides (71.6%) and tetracycline (59.5%) was the most observed. Antibiotic resistance genes (ARGs) detected in genomes corresponded well with these observations. Commonly observed ARGs included sul1, sul2, sul3, tet (A), tet (M), qnrS1, qnrB19 and a variety of aminoglycoside-modifying genes, in addition to point mutations in the gyrA and parC genes. Multiple ARGs were predicted to be located on IncN and IncQ1 plasmids of S. Schwarzengrund and S. Muenster, and most qnrB19 genes were carried by Col (pHAD28) plasmids. Seventy-two percent (19/24) of S. Kentucky strains carried multidrug ARGs located in two distinct variants of Salmonella genomic island I. The majority of strains carried full SPI-1 and SPI-2 islands, suggesting full virulence potential.
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Affiliation(s)
- Abdurrahman Hassan Jibril
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark; (A.H.J.); (A.D.); (V.G.M.)
- Department of Veterinary Public Health and Preventive Medicine, Faculty of Veterinary Medicine, Usmanu Danfodiyo University Sokoto, Sokoto 234840, Nigeria
| | - Iruka N. Okeke
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan 234200, Nigeria;
| | - Anders Dalsgaard
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark; (A.H.J.); (A.D.); (V.G.M.)
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore 637459, Singapore
| | - Vanesa García Menéndez
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark; (A.H.J.); (A.D.); (V.G.M.)
- Laboratorio de Referencia de Escherichia coli (LREC), Departamento de Microbioloxía e Parasitoloxía, Facultade de Veterinaria, Universidade de Santiago de Compostela (USC), 27002 Lugo, Spain
| | - John Elmerdahl Olsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark; (A.H.J.); (A.D.); (V.G.M.)
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Genomic Characteristics of Colistin-Resistant Salmonella enterica subsp. enterica Serovar Infantis from Poultry Farms in the Republic of Serbia. Antibiotics (Basel) 2020; 9:antibiotics9120886. [PMID: 33321688 PMCID: PMC7762970 DOI: 10.3390/antibiotics9120886] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 12/03/2020] [Accepted: 12/03/2020] [Indexed: 11/17/2022] Open
Abstract
The antimicrobial susceptibility testing was conducted on 174 single isolates from poultry farms in Serbia and it was determined that seven Salmonella spp. were multidrug resistant. Sixteen serotypes were detected, but only serotype Infantis confirmed reduced susceptibility to colistin. Seven colistin resistant Salmonella Infantis were studied in detail using the WGS approach. Three sequence types were identified corresponding to different epizootiology region. The isolate from the Province of Vojvodina 3842 and isolates from Jagodina (92 and 821) are represented by the sequence type ST413 and ST11, respectively. Four isolates from Kraljevo are ST32, a common S. Infantis sequence type in humans, poultry and food. The fosfomycin resistance gene fosA7 in isolate 3842 and the vgaA gene in isolate 8418/2948 encoding resistance to pleuromutilins were reported for the first time in serovar Infantis. The changes in relative expression of the phoP/Q, mgrB and pmrA/B genes were detected. Single nucleotide polymorphisms of the pmrB gene, including transitions Val164Gly or Val164Met, and Arg92Pro are described. Analyses of quinolone resistance determining region revealed substitutions Ser83Tyr in GyrA protein and Thr57Ser and Ser80Arg in ParC protein. Based on WGS data, there are two major clusters among analyzed Salmonella Infantis isolates from central Serbia.
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Genomic Characterization of Salmonella Minnesota Clonal Lineages Associated with Poultry Production in Brazil. Animals (Basel) 2020; 10:ani10112043. [PMID: 33167341 PMCID: PMC7694379 DOI: 10.3390/ani10112043] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 11/02/2020] [Accepted: 11/03/2020] [Indexed: 12/20/2022] Open
Abstract
Salmonella serotype Minnesota has been increasingly detected in Brazilian poultry farms and food products (chicken meat, eggs) in recent years. In addition, S. Minnesota isolates from poultry are generally resistant to several antibiotics and persistent in farm environments. The present study aimed to assess phylogenomic diversity of S. Minnesota isolates from the poultry production chain in Brazil. In total, 107 worldwide S. Minnesota whole genomes (including 12 from Brazil) were analyzed using a comparative approach. Phylogenetic analysis demonstrated two clades more related to poultry production in Brazil: S. Minnesota poultry lineages I and II (SM-PLI and SM-PLII). Phylodynamic analysis demonstrated that SM-PLI had a common ancestor in 1915, while SM-PLII originated circa 1971. SM-PLII encompassed a higher number of isolates and presented a recent increase in effective population size (mainly from 2009 to 2012). Plasmids IncA/C2 and ColRNA, antimicrobial resistance genes (aph(3')-Ia, blaCMY-2, qnrB19, sul2, and tet(A)) and mainly a virulence genetic cluster (including the yersiniabactin operon) were detected in isolates from SM-PLI and/or SM-PLII. This study demonstrates the dissemination of two distinct S. Minnesota lineages with high resistance to antibiotics and important virulence genetic clusters in Brazilian poultry farms.
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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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Leite EL, Araújo WJ, Vieira TR, Zenato KS, Vasconcelos PC, Cibulski S, Givisiez PEN, Cardoso MRI, Oliveira CJB. First reported genome of an mcr-9-mediated colistin-resistant Salmonella Typhimurium isolate from Brazilian livestock. J Glob Antimicrob Resist 2020; 23:394-397. [PMID: 33039597 DOI: 10.1016/j.jgar.2020.09.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 07/13/2020] [Accepted: 09/08/2020] [Indexed: 11/25/2022] Open
Abstract
OBJECTIVES To investigate the genetic context of colistin resistance in anmcr-9-harbouring Salmonella Typhimurium ST19 strain from swine in Brazil. METHODS Minimum inhibitory concentrations (MIC) to colistin were determined by broth microdilution. Whole-genome sequencing was performed on an Illumina MiSeq system, followed by de novo genome assembly using SPAdes 1.13.1. The draft genome sequence was annotated in Prokka using KBase online server. Downstream analyses for resistome and plasmid detection were performed using online tools available at the Center for Genomic Epidemiology. The strain was typed in silico using MLST 2.0. Phylogenetic analysis involving 24 other genomes ofSalmonella Typhimurium ST19 and mcr-9-harbouring Salmonella Typhimurium isolated from humans, livestock and foodstuff in different regions was also performed. RESULTS Assembly of the draft genome resulted in 5245 protein-coding sequences, 14 rRNAs, 83 tRNAs and a GC content of 51.81%. The strain was identified asSalmonella Typhimurium ST19 harbouring a 265.5-kb pN1566-2 plasmid carrying genes encoding resistance to colistin (mcr-9.1), aminoglycosides (aadA1), tetracycline [tet(C)] and sulfonamides (sul1). Our findings indicate that the Salmonella Typhimurium ST19 strain in this study showed low genetic variability compared with Salmonella Typhimurium ST19 isolated from swine and poultry in Brazil, and was less related to those reported in other countries. CONCLUSIONS This is the first reported genome of a phenotypically colistin-resistantSalmonella Typhimurium harbouring the mcr-9 variant in Brazilian livestock. This genome will aid global investigations on epidemiological and evolutionary aspects of plasmid-mediated colistin resistance and the role of colistin-resistant Salmonella Typhimurium ST19 lineage as a zoonotic pathogen.
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Affiliation(s)
- Elma L Leite
- Department of Animal Science, College for Agricultural Sciences, Federal University of Paraiba (CCA/UFPB), Areia, PB 58397-000, Brazil
| | - Wydemberg J Araújo
- Department of Animal Science, College for Agricultural Sciences, Federal University of Paraiba (CCA/UFPB), Areia, PB 58397-000, Brazil
| | - Tatiana R Vieira
- Department of Preventive Veterinary Medicine, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, RS 91540-000, Brazil
| | - Karoline S Zenato
- Department of Preventive Veterinary Medicine, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, RS 91540-000, Brazil
| | - Priscylla C Vasconcelos
- Department of Animal Science, College for Agricultural Sciences, Federal University of Paraiba (CCA/UFPB), Areia, PB 58397-000, Brazil
| | - Samuel Cibulski
- Center for Biotechnology (CBiotec), Federal University of Paraiba (CBiotec/UFPB), João Pessoa, PB 5805-900, Brazil
| | - Patricia E N Givisiez
- Department of Animal Science, College for Agricultural Sciences, Federal University of Paraiba (CCA/UFPB), Areia, PB 58397-000, Brazil
| | - Marisa R I Cardoso
- Department of Preventive Veterinary Medicine, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, RS 91540-000, Brazil
| | - Celso J B Oliveira
- Department of Animal Science, College for Agricultural Sciences, Federal University of Paraiba (CCA/UFPB), Areia, PB 58397-000, Brazil; Global One Health Initiative (GOHi), The Ohio State University (OSU), Columbus, OH 43210, USA.
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Zhao S, Li C, Hsu CH, Tyson GH, Strain E, Tate H, Tran TT, Abbott J, McDermott PF. Comparative Genomic Analysis of 450 Strains of Salmonella enterica Isolated from Diseased Animals. Genes (Basel) 2020; 11:genes11091025. [PMID: 32883017 PMCID: PMC7564550 DOI: 10.3390/genes11091025] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 08/21/2020] [Accepted: 08/24/2020] [Indexed: 12/02/2022] Open
Abstract
Salmonella is a leading cause of bacterial infections in animals and humans. We sequenced a collection of 450 Salmonella strains from diseased animals to better understand the genetic makeup of their virulence and resistance features. The presence of Salmonella pathogenicity islands (SPIs) varied by serotype. S. Enteritidis carried the most SPIs (n = 15), while S. Mbandaka, S. Cerro, S. Meleagridis, and S. Havana carried the least (n = 10). S. Typhimurium, S. Choleraesuis, S. I 4,5,12:i:-, and S. Enteritidis each contained the spv operon on IncFII or IncFII-IncFIB hybrid plasmids. Two S. IIIa carried a spv operon with spvD deletion on the chromosome. Twelve plasmid types including 24 hybrid plasmids were identified. IncA/C was frequently associated with S. Newport (83%) and S. Agona (100%) from bovine, whereas IncFII (100%), IncFIB (100%), and IncQ1 (94%) were seen in S. Choleraesuis from swine. IncX (100%) was detected in all S. Kentucky from chicken. A total of 60 antimicrobial resistance genes (ARGs), four disinfectant resistances genes (DRGs) and 33 heavy metal resistance genes (HMRGs) were identified. The Salmonella strains from sick animals contained various SPIs, resistance genes and plasmid types based on the serotype and source of the isolates. Such complicated genomic structures shed light on the strain characteristics contributing to the severity of disease and treatment failures in Salmonella infections, including those causing illnesses in animals.
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de Carvalho MPN, Fernandes MR, Sellera FP, Lopes R, Monte DF, Hippólito AG, Milanelo L, Raso TF, Lincopan N. International clones of extended-spectrum β-lactamase (CTX-M)-producing Escherichia coli in peri-urban wild animals, Brazil. Transbound Emerg Dis 2020; 67:1804-1815. [PMID: 32239649 PMCID: PMC7540485 DOI: 10.1111/tbed.13558] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 02/29/2020] [Accepted: 03/23/2020] [Indexed: 12/22/2022]
Abstract
CTX-M-type extended-spectrum β-lactamase (ESBL)-producing Escherichia coli clones have been increasingly reported worldwide. In this regard, although discussions of transmission routes of these bacteria are in evidence, molecular data are lacking to elucidate the epidemiological impacts of ESBL producers in wild animals. In this study, we have screened 90 wild animals living in a surrounding area of São Paulo, the largest metropolitan city in South America, to monitor the presence of multidrug-resistant (MDR) Gram-negative bacteria. Using a genomic approach, we have analysed eight ceftriaxone-resistant E. coli. Resistome analyses revealed that all E. coli strains carried blaCTX-M -type genes, prevalent in human infections, besides other clinically relevant resistance genes to aminoglycosides, β-lactams, phenicols, tetracyclines, sulphonamides, trimethoprim, fosfomycin and quinolones. Additionally, E. coli strains belonged to international sequence types (STs) ST38, ST58, ST212, ST744, ST1158 and ST1251, and carried several virulence-associated genes. Our findings suggest spread and adaptation of international clones of CTX-M-producing E. coli beyond urban settings, including wildlife from shared environments.
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Affiliation(s)
| | - Miriam R. Fernandes
- Department of Clinical and Toxicological AnalysisSchool of Pharmaceutical SciencesUniversity of Sao PauloSao PauloBrazil
| | - Fábio P. Sellera
- Department of Internal MedicineSchool of Veterinary Medicine and Animal ScienceUniversity of São PauloSão PauloBrazil
| | - Ralf Lopes
- Department of MicrobiologyInstituto de Ciências BiomédicasUniversidade de São PauloSão PauloBrazil
| | - Daniel F. Monte
- Department of Food and Experimental NutritionFaculty of Pharmaceutical SciencesFood Research CenterUniversity of São PauloSão PauloBrazil
| | - Alícia G. Hippólito
- Department of Veterinary Surgery and AnesthesiologySchool of Veterinary Medicine and Animal ScienceUniversidade Estadual Paulista (UNESP)BotucatuBrazil
| | - Liliane Milanelo
- Reception Center for WildlifeEcological Park TietêSão PauloBrazil
| | - Tânia F. Raso
- Department of PathologySchool of Veterinary Medicine and Animal ScienceUniversity of São PauloSão PauloBrazil
| | - Nilton Lincopan
- Department of Clinical and Toxicological AnalysisSchool of Pharmaceutical SciencesUniversity of Sao PauloSao PauloBrazil
- Department of MicrobiologyInstituto de Ciências BiomédicasUniversidade de São PauloSão PauloBrazil
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Rodrigues GL, Panzenhagen P, Ferrari RG, Dos Santos A, Paschoalin VMF, Conte-Junior CA. Frequency of Antimicrobial Resistance Genes in Salmonella From Brazil by in silico Whole-Genome Sequencing Analysis: An Overview of the Last Four Decades. Front Microbiol 2020; 11:1864. [PMID: 32849452 PMCID: PMC7426471 DOI: 10.3389/fmicb.2020.01864] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 07/15/2020] [Indexed: 12/20/2022] Open
Abstract
Salmonella is a leading human pathogen and a significant public health concern worldwide. Massive food production and distribution have contributed to this pathogen dissemination, which, combined with antimicrobial resistance (AMR), creates new control challenges in food safety. The development of AMR is a natural phenomenon and can occur in the bacterial evolutionary process. However, the overuse and the misuse of antimicrobial drugs in humans and in animals have increased AMR selective pressure. In Brazil, there is an accuracy lack in AMR frequency in Salmonella because too many isolates are under-investigated for genetic and phenotypic AMR by the Brazilian health authorities and the research community. This underreporting situation makes the comprehension of the real level of Salmonella AMR in the country difficult. The present study aimed to use bioinformatics tools for a rapid in silico screening of the genetic antimicrobial resistance profile of Salmonella through whole-genome sequences (WGS). A total of 930 whole-genome sequences of Salmonella were retrieved from the public database of the National Biotechnology Information Center (NCBI). A total of 65 distinct resistance genes were detected, and the most frequent ones were tet(A), sul2, and fosA7. Nine point mutations were detected in total, and parC at the 57 position (threonine → serine) was the highest frequent substitution (26.7%, 249/930), followed by gyrA at the 83 position (serine → phenylalanine) (20.0%, 186/930) and at the 87 position (aspartic acid → asparagine) (15.7%, 146/930). The in silico prediction of resistance phenotype showed that 58.0% (540/930) of the strains can display a multidrug resistance (MDR) profile. Ciprofloxacin and nalidixic acid were the antimicrobial drugs with the highest frequency rates of the predicted phenotype resistance among the strains. The temporal analysis through the last four decades showed increased frequency rates of antimicrobial resistance genes and predicted resistance phenotypes in the 2000s and the 2010s when compared with the 1980s and 1990s. The results presented herein contributed significantly to the understanding of the strategic use of WGS associated with in silico analysis and the predictions for the determination of AMR in Salmonella from Brazil.
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Affiliation(s)
- Grazielle Lima Rodrigues
- Nucleus of Food Analysis (NAL), Laboratory for the Support of Technological Development (LADETEC), Chemistry Institute, Department of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.,Food Science Graduate Program (PPGCAL), Chemistry Institute, Department of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Pedro Panzenhagen
- Nucleus of Food Analysis (NAL), Laboratory for the Support of Technological Development (LADETEC), Chemistry Institute, Department of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.,Food Science Graduate Program (PPGCAL), Chemistry Institute, Department of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Rafaela Gomes Ferrari
- Nucleus of Food Analysis (NAL), Laboratory for the Support of Technological Development (LADETEC), Chemistry Institute, Department of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.,Food Science Graduate Program (PPGCAL), Chemistry Institute, Department of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Anamaria Dos Santos
- Nucleus of Food Analysis (NAL), Laboratory for the Support of Technological Development (LADETEC), Chemistry Institute, Department of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.,Food Science Graduate Program (PPGCAL), Chemistry Institute, Department of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Vania Margaret Flosi Paschoalin
- Food Science Graduate Program (PPGCAL), Chemistry Institute, Department of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Carlos Adam Conte-Junior
- Nucleus of Food Analysis (NAL), Laboratory for the Support of Technological Development (LADETEC), Chemistry Institute, Department of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.,Food Science Graduate Program (PPGCAL), Chemistry Institute, Department of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.,Health Surveillance Graduate Program (PPGVS), National Institute for Quality Control in Health (INCQS), Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
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49
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Monte DFM, Nethery MA, Barrangou R, Landgraf M, Fedorka-Cray PJ. Whole-genome sequencing analysis and CRISPR genotyping of rare antibiotic-resistant Salmonella enterica serovars isolated from food and related sources. Food Microbiol 2020; 93:103601. [PMID: 32912589 DOI: 10.1016/j.fm.2020.103601] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 07/17/2020] [Accepted: 07/21/2020] [Indexed: 11/25/2022]
Abstract
For decades, Salmonella Typhimurium and Salmonella Enteritidis have prevailed in several countries as agents of salmonellosis outbreaks. In Brazil, the largest exporter of poultry meat, relatively little attention has been paid to infrequent serovars. Here, we report the emergence and characterization of rare serovars isolated from food and related sources collected between 2014 and 2016 in Brazil. Twenty-two Salmonella enterica isolates were analyzed through the use of whole-genome sequencing (WGS) and clustered regularly interspaced short palindromic repeats (CRISPR) genotyping. These isolates were classified into 10 infrequent serovars, including S. Abony, S. Isangi, S. Rochdale, S. Saphra, S. Orion, S. Ouakam, S. Grumpensis, S. Carrau, S. Abaetetuba, and S. Idikan. The presence of six antimicrobial resistance (AMR) genes, qnrB19, blaCMY-2, tetA, aac(6')-Iaa, sul2 and fosA7, which encode resistance to quinolones, third-generation cephalosporin, tetracycline, aminoglycoside, sulfonamide and fosfomycin, respectively, were confirmed by WGS. All S. Isangi harbored qnrB19 with conserved genomic context across strains, while S. Abony harbored blaCMY-2. Twelve (54.5%) strains displayed chromosomal mutations in parC (Thr57→Ser). Most serovars were classified as independent lineages, except S. Abony and S. Abaetetuba, which phylogenetically nested with Salmonella strains from different countries. CRISPR analysis revealed that the spacer content was strongly correlated with serovar and multi-locus sequence type for all strains, independently confirming the observed phylogenetic patterns, and highlighting the value of CRISPR-based genotyping for Salmonella. These findings add valuable information to the epidemiology of S. enterica in Brazil, where the emergency of antibiotic-resistant Salmonella continues to evolve.
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Affiliation(s)
- Daniel F M Monte
- Department of Food and Experimental Nutrition, Faculty of Pharmaceutical Sciences, Food Research Center, University of São Paulo, Brazil; Department of Population Health and Pathobiology, North Carolina State University, College of Veterinary Medicine, Raleigh, NC, USA.
| | - Matthew A Nethery
- Genomic Sciences Graduate Program, North Carolina State University, Raleigh, NC, USA; Department of Food, Bioprocessing & Nutrition Sciences, North Carolina State University, Raleigh, NC, USA
| | - Rodolphe Barrangou
- Genomic Sciences Graduate Program, North Carolina State University, Raleigh, NC, USA; Department of Food, Bioprocessing & Nutrition Sciences, North Carolina State University, Raleigh, NC, USA
| | - Mariza Landgraf
- Department of Food and Experimental Nutrition, Faculty of Pharmaceutical Sciences, Food Research Center, University of São Paulo, Brazil
| | - Paula J Fedorka-Cray
- Department of Population Health and Pathobiology, North Carolina State University, College of Veterinary Medicine, Raleigh, NC, USA.
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50
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García-Soto S, Abdel-Glil MY, Tomaso H, Linde J, Methner U. Emergence of Multidrug-Resistant Salmonella enterica Subspecies enterica Serovar Infantis of Multilocus Sequence Type 2283 in German Broiler Farms. Front Microbiol 2020; 11:1741. [PMID: 32765483 PMCID: PMC7380084 DOI: 10.3389/fmicb.2020.01741] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 07/03/2020] [Indexed: 12/18/2022] Open
Abstract
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.
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Affiliation(s)
- Silvia García-Soto
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institute, Jena, Germany
| | - Mostafa Y Abdel-Glil
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institute, Jena, Germany
| | - Herbert Tomaso
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institute, Jena, Germany
| | - Jörg Linde
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institute, Jena, Germany
| | - Ulrich Methner
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institute, Jena, Germany
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