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Kujat Choy S, Neumann EM, Romero-Barrios P, Tamber S. Contribution of Food to the Human Health Burden of Antimicrobial Resistance. Foodborne Pathog Dis 2024; 21:71-82. [PMID: 38099924 PMCID: PMC10877391 DOI: 10.1089/fpd.2023.0099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2024] Open
Abstract
The impact of foodborne antimicrobial resistance (AMR) on the human health burden of AMR infections is unknown. The aim of this review was to evaluate and summarize the scientific literature investigating all potential sources of human AMR infections related to food. A literature search was conducted in Embase (Ovid) and MEDLINE (Ovid) databases to identify appropriate studies published between 2010 and 2023. The results of the search were reviewed and categorized based on the primary subject matter. Key concepts from each category are described from the perspective of food safety as a public health objective. The search yielded 3457 references, 1921 remained after removal of duplicates, abstracts, editorials, comments, notes, retractions, and errata. No properly designed source attribution studies were identified, but 383 journal articles were considered relevant and were classified into eight subcategories and discussed in the context of four streams of evidence: prevalence data, epidemiological studies, outbreak investigations and human health impact estimates. There was sufficient evidence to conclude that AMR genes, whether present in pathogenic or nonpathogenic bacteria, constitute a foodborne hazard. The level of consumer risk owing to this hazard cannot be accurately estimated based on the data summarized here. Key gaps in the literature are noted.
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Affiliation(s)
- Sonya Kujat Choy
- Bureau of Microbial Hazards, Health Products and Food Branch, Health Canada, Ottawa, Canada
| | - Eva-Marie Neumann
- Library Services Division, Corporate Services Branch, Health Canada, Ottawa, Canada
| | - Pablo Romero-Barrios
- Bureau of Microbial Hazards, Health Products and Food Branch, Health Canada, Ottawa, Canada
| | - Sandeep Tamber
- Bureau of Microbial Hazards, Health Products and Food Branch, Health Canada, Ottawa, Canada
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2
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Souza SSR, Turcotte MR, Li J, Zhang X, Wolfe KL, Gao F, Benton CS, Andam CP. Population analysis of heavy metal and biocide resistance genes in Salmonella enterica from human clinical cases in New Hampshire, United States. Front Microbiol 2022; 13:983083. [PMID: 36338064 PMCID: PMC9626534 DOI: 10.3389/fmicb.2022.983083] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 10/03/2022] [Indexed: 11/24/2022] Open
Abstract
Microbes frequently encounter heavy metals and other toxic compounds generated from natural biogeochemical processes and anthropogenic activities. Here, we analyzed the prevalence and association of genes conferring resistance to heavy metals, biocides, and antimicrobial compounds in 394 genome sequences of clinical human-derived S. enterica from New Hampshire, USA. The most prevalent was the gold operon (gesABC-golTSB), which was present in 99.2% of the genomes. In contrast, the other five heavy metal operons (arsenic, copper, mercury, silver, tellurite) were present in 0.76% (3/394)–5.58% (22/394) of the total population. The heavy metal operons and three biocide resistance genes were differentially distributed across 15 sequence types (STs) and 16 serotypes. The number of heavy metal operons and biocide resistance genes per genome was significantly associated with high number of antimicrobial resistance (AMR) genes per genome. Notable is the mercury operon which exhibited significant association with genes conferring resistance to aminoglycosides, cephalosporins, diaminopyrimidine, sulfonamide, and fosfomycin. The mercury operon was co-located with the AMR genes aac(3)-IV, ant(3”)-IIa, aph(3’)-Ia, and aph(4)-Ia, CTX-M-65, dfrA14, sul1, and fosA3 genes within the same plasmid types. Lastly, we found evidence for negative selection of individual genes of each heavy metal operon and the biocide resistance genes (dN/dS < 1). Our study highlights the need for continued surveillance of S. enterica serotypes that carry those genes that confer resistance to heavy metals and biocides that are often associated with mobile AMR genes. The selective pressures imposed by heavy metals and biocides on S. enterica may contribute to the co-selection and spread of AMR in human infections.
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Affiliation(s)
- Stephanie S. R. Souza
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, United States
- *Correspondence: Stephanie S. R. Souza, ; orcid.org/0000-0002-4207-8231
| | - Madison R. Turcotte
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, United States
| | - Jinfeng Li
- New Hampshire Department of Health and Human Services, Concord, NH, United States
| | - Xinglu Zhang
- New Hampshire Department of Health and Human Services, Concord, NH, United States
| | - Kristin L. Wolfe
- New Hampshire Department of Health and Human Services, Concord, NH, United States
| | - Fengxiang Gao
- New Hampshire Department of Health and Human Services, Concord, NH, United States
| | | | - Cheryl P. Andam
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, United States
- Cheryl P. Andam, ; orcid.org/0000-0003-4428-0924
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Khajanchi BK, Foley SL. Antimicrobial Resistance and Increased Virulence of Salmonella. Microorganisms 2022; 10:microorganisms10091829. [PMID: 36144431 PMCID: PMC9504589 DOI: 10.3390/microorganisms10091829] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 09/11/2022] [Indexed: 11/25/2022] Open
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4
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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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5
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Genomic analysis of Salmonella Typhimurium from humans and food sources accurately predicts phenotypic multi-drug resistance. Food Microbiol 2022; 103:103957. [DOI: 10.1016/j.fm.2021.103957] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 10/17/2021] [Accepted: 11/24/2021] [Indexed: 02/01/2023]
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Yu J, Xu X, Wang Y, Zhai X, Pan Z, Jiao X, Zhang Y. Prophage-mediated genome differentiation of the Salmonella Derby ST71 population. Microb Genom 2022; 8. [PMID: 35451954 PMCID: PMC9453062 DOI: 10.1099/mgen.0.000817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Although Salmonella Derby ST71 strains have been recognized as poultry-specific by previous studies, multiple swine-associated S. Derby ST71 strains were identified in this long-term, multi-site epidemic study. Here, 15 representative swine-associated S. Derby ST71 strains were sequenced and compared with 65 (one swine-associated and 64 poultry-associated) S. Derby ST71 strains available in the NCBI database at a pangenomic level through comparative genomics analysis to identify genomic features related to the differentiation of swine-associated strains and previously reported poultry-associated strains. The distribution patterns of known Salmonella pathogenicity islands (SPIs) and virulence factor (VF) encoding genes were not capable of differentiating between the two strain groups. The results demonstrated that the S. Derby ST71 population harbours an open pan-genome, and swine-associated ST71 strains contain many more genes than the poultry-associated strains, mainly attributed to the prophage sequence contents in the genomes. The numbers of prophage sequences identified in the swine-associated strains were higher than those in the poultry-associated strains. Prophages specifically harboured by the swine-associated strains were found to contain genes that facilitate niche adaptation for the bacterial hosts. Gene deletion experiments revealed that the dam gene specifically present in the prophage of the swine-associated strains is important for S. Derby to adhere onto the host cells. This study provides novel insights into the roles of prophages during the genome differentiation of Salmonella.
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Affiliation(s)
- Jinyan Yu
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, PR China.,Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, PR China.,Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, PR China.,Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou 225009, PR China
| | - Xiaomeng Xu
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, PR China.,Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, PR China.,Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, PR China.,Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou 225009, PR China
| | - Yu Wang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, PR China.,Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, PR China.,Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, PR China.,Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou 225009, PR China
| | - Xianyue Zhai
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, PR China.,Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, PR China.,Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, PR China.,Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou 225009, PR China
| | - Zhiming Pan
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, PR China.,Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, PR China.,Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, PR China.,Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou 225009, PR China
| | - Xinan Jiao
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, PR China.,Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, PR China.,Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, PR China.,Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou 225009, PR China
| | - Yunzeng Zhang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, PR China.,Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, PR China.,Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, PR China.,Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou 225009, PR China
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Karanth S, Tanui CK, Meng J, Pradhan AK. Exploring the predictive capability of advanced machine learning in identifying severe disease phenotype in Salmonella enterica. Food Res Int 2022; 151:110817. [PMID: 34980422 DOI: 10.1016/j.foodres.2021.110817] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 11/12/2021] [Accepted: 11/17/2021] [Indexed: 11/26/2022]
Abstract
The past few years have seen a significant increase in availability of whole genome sequencing information, allowing for its incorporation in predictive modeling for foodborne pathogens to account for inter- and intra-species differences in their virulence. However, this is hindered by the inability of traditional statistical methods to analyze such large amounts of data compared to the number of observations/isolates. In this study, we have explored the applicability of machine learning (ML) models to predict the disease outcome, while identifying features that exert a significant effect on the prediction. This study was conducted on Salmonella enterica, a major foodborne pathogen with considerable inter- and intra-serovar variation. WGS of isolates obtained from various sources (i.e., human, chicken, and swine) were used as input in four machine learning models (logistic regression with ridge, random forest, support vector machine, and AdaBoost) to classify isolates based on disease severity (extraintestinal vs. gastrointestinal) in the host. The predictive performances of all models were tested with and without Elastic Net regularization to combat dimensionality issues. Elastic Net-regularized logistic regression model showed the best area under the receiver operating characteristic curve (AUC-ROC; 0.86) and outcome prediction accuracy (0.76). Additionally, genes coding for transcriptional regulation, acidic, oxidative, and anaerobic stress response, and antibiotic resistance were found to be significant predictors of disease severity. These genes, which were significantly associated with each outcome, could possibly be input in amended, gene-expression-specific predictive models to estimate virulence pattern-specific effect of Salmonella and other foodborne pathogens on human health.
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Affiliation(s)
- Shraddha Karanth
- Department of Nutrition and Food Science, University of Maryland, College Park, MD 20742, USA
| | - Collins K Tanui
- Department of Nutrition and Food Science, University of Maryland, College Park, MD 20742, USA; Center for Food Safety and Security Systems, University of Maryland, College Park, MD 20742, USA
| | - Jianghong Meng
- Department of Nutrition and Food Science, University of Maryland, College Park, MD 20742, USA; Center for Food Safety and Security Systems, University of Maryland, College Park, MD 20742, USA; Joint Institute for Food Safety and Applied Nutrition, University of Maryland, College Park, MD 20742, USA
| | - Abani K Pradhan
- Department of Nutrition and Food Science, University of Maryland, College Park, MD 20742, USA; Center for Food Safety and Security Systems, University of Maryland, College Park, MD 20742, USA.
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Brown EW, Bell R, Zhang G, Timme R, Zheng J, Hammack TS, Allard MW. Salmonella Genomics in Public Health and Food Safety. EcoSal Plus 2021; 9:eESP00082020. [PMID: 34125583 PMCID: PMC11163839 DOI: 10.1128/ecosalplus.esp-0008-2020] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 03/16/2021] [Indexed: 12/26/2022]
Abstract
The species Salmonella enterica comprises over 2,600 serovars, many of which are known to be intracellular pathogens of mammals, birds, and reptiles. It is now apparent that Salmonella is a highly adapted environmental microbe and can readily persist in a number of environmental niches, including water, soil, and various plant (including produce) species. Much of what is known about the evolution and diversity of nontyphoidal Salmonella serovars (NTS) in the environment is the result of the rise of the genomics era in enteric microbiology. There are over 340,000 Salmonella genomes available in public databases. This extraordinary breadth of genomic diversity now available for the species, coupled with widespread availability and affordability of whole-genome sequencing (WGS) instrumentation, has transformed the way in which we detect, differentiate, and characterize Salmonella enterica strains in a timely way. Not only have WGS data afforded a detailed and global examination of the molecular epidemiological movement of Salmonella from diverse environmental reservoirs into human and animal hosts, but they have also allowed considerable consolidation of the diagnostic effort required to test for various phenotypes important to the characterization of Salmonella. For example, drug resistance, serovar, virulence determinants, and other genome-based attributes can all be discerned using a genome sequence. Finally, genomic analysis, in conjunction with functional and phenotypic approaches, is beginning to provide new insights into the precise adaptive changes that permit persistence of NTS in so many diverse and challenging environmental niches.
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Affiliation(s)
- Eric W. Brown
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA
| | - Rebecca Bell
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA
| | - Guodong Zhang
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA
| | - Ruth Timme
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA
| | - Jie Zheng
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA
| | - Thomas S. Hammack
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA
| | - Marc W. Allard
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA
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Whole-Genome Analysis of Multidrug-Resistant Salmonella Enteritidis Strains Isolated from Poultry Sources in Korea. Pathogens 2021; 10:pathogens10121615. [PMID: 34959570 PMCID: PMC8707440 DOI: 10.3390/pathogens10121615] [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: 11/22/2021] [Revised: 12/08/2021] [Accepted: 12/09/2021] [Indexed: 11/17/2022] Open
Abstract
The Salmonella Enterica subsp. Enterica serovar Enteritidis is one of main serovars isolated from human patients with food poisoning and poultry without clinical signs. Consumption of poultry products contaminated with Salmonella Enteritidis is a common source of human salmonellosis; 82 Salmonella spp. were isolated from 291 samples of retail chicken meat, 201 one-day-old chicks, 30 internal organs of chickens, 156 chicken eggs, 100 duck eggs, 38 straw bedding samples, 18 samples of retail duck meat, and 19 swab samples from slaughterhouses in 2019 and 2020. An antibiotic susceptibility test was performed for all isolates, revealing 33 multidrug-resistant (MDR) strains. The whole genome of 33 MDR strains isolated in 2019 and 2020 and 10 strains isolated in 2011, 2012, and 2017 was sequenced using the MinION sequencing protocol. Within these 43 samples, 5 serovars were identified: S. Enteritidis, S. Agona, S. Virchow, S. Albany, and S. Bareilly. The most common serovar was S. Enteritidis (26/43), which showed the highest resistance to ampicillin (100%), followed by nalidixic acid (90%) and colistin (83%). Core genome multilocus sequence typing analysis showed that the S. Enteritidis strains isolated from different sources and in different years were clustered together. In addition, the S. Enteritidis strains isolated since 2011 consistently harbored the same antibiotic resistance patterns.
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Gu Y, Huang L, Wu C, Huang J, Hao H, Yuan Z, Cheng G. The Evolution of Fluoroquinolone Resistance in Salmonella under Exposure to Sub-Inhibitory Concentration of Enrofloxacin. Int J Mol Sci 2021; 22:ijms222212218. [PMID: 34830098 PMCID: PMC8619427 DOI: 10.3390/ijms222212218] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 10/25/2021] [Accepted: 11/02/2021] [Indexed: 02/04/2023] Open
Abstract
The evolution of resistance in Salmonella to fluoroquinolones (FQs) under a broad range of sub-inhibitory concentrations (sub-MICs) has not been systematically studied. This study investigated the mechanism of resistance development in Salmonella enterica serovar Enteritidis (S. Enteritidis) under sub-MICs of 1/128×MIC to 1/2×MIC of enrofloxacin (ENR), a widely used veterinary FQ. It was shown that the resistance rate and resistance level of S. Enteritidis varied with the increase in ENR concentration and duration of selection. qRT-PCR results demonstrated that the expression of outer membrane porin (OMP) genes, ompC, ompD and ompF, were down-regulated first to rapidly adapt and develop the resistance of 4×MIC, and as the resistance level increased (≥8×MIC), the up-regulated expression of efflux pump genes, acrB, emrB amd mdfA, along with mutations in quinolone resistance-determining region (QRDR) gradually played a decisive role. Cytohubba analysis based on transcriptomic profiles demonstrated that purB, purC, purD, purF, purH, purK, purL, purM, purN and purT were the hub genes for the FQs resistance. The 'de novo' IMP biosynthetic process, purine ribonucleoside monophosphate biosynthetic process and purine ribonucleotide biosynthetic process were the top three biological processes screened by MCODE. This study first described the dynamics of FQ resistance evolution in Salmonella under a long-term selection of sub-MICs of ENR in vitro. In addition, this work offers greater insight into the transcriptome changes of S. Enteritidis under the selection of ENR and provides a framework for FQs resistance of Salmonella for further studies.
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Affiliation(s)
- Yufeng Gu
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (Y.G.); (L.H.); (C.W.); (J.H.); (H.H.); (Z.Y.)
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan 430070, China
| | - Lulu Huang
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (Y.G.); (L.H.); (C.W.); (J.H.); (H.H.); (Z.Y.)
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan 430070, China
| | - Cuirong Wu
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (Y.G.); (L.H.); (C.W.); (J.H.); (H.H.); (Z.Y.)
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan 430070, China
| | - Junhong Huang
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (Y.G.); (L.H.); (C.W.); (J.H.); (H.H.); (Z.Y.)
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan 430070, China
| | - Haihong Hao
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (Y.G.); (L.H.); (C.W.); (J.H.); (H.H.); (Z.Y.)
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan 430070, China
| | - Zonghui Yuan
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (Y.G.); (L.H.); (C.W.); (J.H.); (H.H.); (Z.Y.)
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan 430070, China
| | - Guyue Cheng
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (Y.G.); (L.H.); (C.W.); (J.H.); (H.H.); (Z.Y.)
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan 430070, China
- Correspondence: ; Tel.: +86-027-8728-7165
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11
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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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12
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Zhang K, Ge H, He J, Hu M, Xu Z, Jiao X, Chen X. Salmonella Typhimurium ST34 Isolate Was More Resistant than the ST19 Isolate in China, 2007 - 2019. Foodborne Pathog Dis 2021; 19:62-69. [PMID: 34520252 DOI: 10.1089/fpd.2021.0047] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
To disclose the antimicrobial susceptibility and wide adaptability of commonly occurring genotypes of Salmonella enterica serovar Typhimurium, the antimicrobial resistance and multilocus sequence typing (MLST) profiles of 196 Salmonella Typhimurium isolates (136 from food-producing animals, 19 from environments, 15 from markets, and 26 from humans) in China between 2007 and 2019 were analyzed. Tests of susceptibility to 19 antimicrobial agents using the broth microdilution method showed that 84.7% of the isolates were resistant to at least one antimicrobial. Antimicrobial susceptibility analysis demonstrated that 66.8% of the isolates were multidrug-resistant (MDR) strains, with resistance to three or more antimicrobials. The highest antidrug resistance was to ampicillin, amoxicillin/clavulanic acid, and tetracycline. Three MLST types were detected, and sequence type (ST) 19 was the most common ST. However, ST34 was associated with a higher MDR rate and more complex MDR patterns, than ST19 and ST99, although the exact mechanism has not been reported. Our study highlights the variation of drug resistance and STs from different sources and the association between STs and drug resistance, providing useful information for epidemiological research and developing a public health strategy.
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Affiliation(s)
- Kai Zhang
- Jiangsu Key Laboratory of Zoonosis, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality of Ministry of Agriculture and Rural Affairs, Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education, Yangzhou University, Yangzhou, China
| | - Haojie Ge
- Jiangsu Key Laboratory of Zoonosis, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality of Ministry of Agriculture and Rural Affairs, Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education, Yangzhou University, Yangzhou, China
| | - Jingjing He
- Jiangsu Key Laboratory of Zoonosis, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality of Ministry of Agriculture and Rural Affairs, Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education, Yangzhou University, Yangzhou, China
| | - Maozhi Hu
- Jiangsu Key Laboratory of Zoonosis, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality of Ministry of Agriculture and Rural Affairs, Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education, Yangzhou University, Yangzhou, China
| | - Zhengzhong Xu
- Jiangsu Key Laboratory of Zoonosis, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality of Ministry of Agriculture and Rural Affairs, Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education, Yangzhou University, Yangzhou, China
| | - Xin'an Jiao
- Jiangsu Key Laboratory of Zoonosis, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality of Ministry of Agriculture and Rural Affairs, Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education, Yangzhou University, Yangzhou, China
| | - Xiang Chen
- Jiangsu Key Laboratory of Zoonosis, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality of Ministry of Agriculture and Rural Affairs, Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education, Yangzhou University, Yangzhou, China
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13
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Uelze L, Borowiak M, Deneke C, Fischer J, Flieger A, Simon S, Szabó I, Tausch SH, Malorny B. Comparative genomics of Salmonella enterica subsp. diarizonae serovar 61:k:1,5,(7) reveals lineage-specific host adaptation of ST432. Microb Genom 2021; 7. [PMID: 34338625 PMCID: PMC8549363 DOI: 10.1099/mgen.0.000604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Unlike most Salmonella enterica subsp. diarizonae, which are predominantly associated with cold-blooded animals such as reptiles, the serovar IIIb 61:k:1,5,(7) (termed SASd) is regarded as host-adapted to sheep. The bacterium is rarely associated with disease in humans but, nevertheless, SASd isolates are sporadically obtained from human clinical samples. It is unclear whether these transmissions are directly linked to sheep or whether transmissions may, for example, occur through other domestic animals also carrying SASd. For this reason, we utilized whole-genome sequencing to investigate a set of 119 diverse SASd isolates, including sheep-associated and human-associated isolates, as well as isolates obtained from other matrices. We discovered that serovar IIIb 61:k:1,5,(7) is composed of two distinct lineages defined by their sequence types ST432 and ST439. These two lineages are distinguished by a number of genetic features, as well as their prevalence and reservoir. ST432 appears to be the more prevalent sequence type, with the majority of isolates investigated in this study belonging to ST432. In contrast, only a small number of isolates were attributed to ST439. While ST432 isolates were of sheep, human or other origin, all ST439 isolates with source information available, were obtained from human clinical samples. Regarding their genetic features, lineage ST432 shows increased pseudogenization, harbours a virB/D4 plasmid that encodes a type IV secretion system (T4SS) and does not possess the iro gene cluster, which encodes a salmochelin siderophore for iron acquisition. These characteristics likely contribute to the ability of ST432 to persistently colonize the intestines of sheep. Furthermore, we found isolates of the lineage ST432 to be highly clonal, with little variation over the sampling period of almost 20 years. We conclude from the genomic comparisons that SASd underlies a microevolutionary process and that it is specifically lineage ST432 that should be considered as host-adapted to sheep.
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Affiliation(s)
- Laura Uelze
- Department of Biological Safety, German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Straße 8-10, 10589 Berlin, Germany
| | - Maria Borowiak
- Department of Biological Safety, German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Straße 8-10, 10589 Berlin, Germany
| | - Carlus Deneke
- Department of Biological Safety, German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Straße 8-10, 10589 Berlin, Germany
| | - Jennie Fischer
- Department of Biological Safety, German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Straße 8-10, 10589 Berlin, Germany
| | - Antje Flieger
- Unit for Enteropathogenic Bacteria and Legionella (FG11)/National Reference Centre for Salmonella and Other Bacterial Enteric Pathogens, Robert Koch Institute (RKI), Burgstraße 37, 38855 Wernigerode, Germany
| | - Sandra Simon
- Unit for Enteropathogenic Bacteria and Legionella (FG11)/National Reference Centre for Salmonella and Other Bacterial Enteric Pathogens, Robert Koch Institute (RKI), Burgstraße 37, 38855 Wernigerode, Germany
| | - István Szabó
- Department of Biological Safety, German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Straße 8-10, 10589 Berlin, Germany
| | - Simon H Tausch
- Department of Biological Safety, German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Straße 8-10, 10589 Berlin, Germany
| | - Burkhard Malorny
- Department of Biological Safety, German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Straße 8-10, 10589 Berlin, Germany
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14
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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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15
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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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16
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Appel A, Zuffo JP, Wolf J, Stahlhofer SR, Lopes PD, Correia B, Moreira F, Millezi AF, Bianchi I, Oliveira Júnior JM, Peripolli V. Photohydroionisation for disinfection of poultry litter. Br Poult Sci 2021; 62:695-700. [PMID: 33949900 DOI: 10.1080/00071668.2021.1925225] [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: 10/21/2022]
Abstract
1. This study evaluated photohydroionisation efficiency on the disinfection of new shavings used as substrate for litter in the poultry industry, pre-inoculated with bacterial, fungal and viral agents.2. Each replicate consisted of 250 g of new shavings sterilised by autoclaving, challenged with bacterial (Escherichia coli, Staphylococcus aureus, and Salmonella enterica, serovar Abony), fungal (Saccharomyces cerevisiae) and viral inoculum (Gumboro disease virus). The experiment consisted of six replicates at four times (0, 1, 5 or 10 min exposure) of photohydroionisation. The disinfection process was performed in a bench photohydroionisation device with four ultraviolet lamps. The agents inoculated in the shavings were analysed after the disinfection process.3. The counts of enterobacteria and total bacteria showed a quadratic effect. In contrast, the counts of fungi and viruses showed a negative linear effect with an increase in the time of photohydroionisation. The enterobacteria showed a linear response plateau effect (LRP), with a minimum time point of 5.498 minutes at a minimum contamination of 0.666 CFU/g and a reduction of 82.27% of the pre-established inoculum. Total bacteria had an LRP effect with a minimum time point of 1.902 minutes at minimum contamination of 1.739 CFU/g and a reduction of 50.0% of the pre-established inoculum. An LRP effect was found for fungi, with a minimum time point of 7.931 minutes in minimum contamination of 3.380 CFU/g, and with a reduction of 11.0% of the pre-established inoculum. For viruses, there was an LRP effect with a minimum time point of 5.012 minutes in minimum contamination of 0.000 viral titre per 100 g of shavings, which was reduced by 100% of the pre-established inoculum.4. Photohydroionisation in the disinfection of new shavings used as poultry litter has partial potential as a microbiological control tool, as a complete reduction occurred only for the viruses, whereas for bacteria and fungi only partial reductions of these microorganisms were observed.
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Affiliation(s)
- A Appel
- Post-Graduation Program in Animal Production and Health, Instituto Federal Catarinense, Araquari, Brazil.,Seara Alimentos Ltda, Itajaí, Brazil
| | - J P Zuffo
- Seara Alimentos Ltda, Itajaí, Brazil
| | - J Wolf
- Seara Alimentos Ltda, Itajaí, Brazil
| | - S R Stahlhofer
- Post-Graduation Program in Animal Production and Health, Instituto Federal Catarinense, Araquari, Brazil.,Seara Alimentos Ltda, Itajaí, Brazil
| | - P D Lopes
- Seara Alimentos Ltda, Itajaí, Brazil
| | - B Correia
- Education, Extension, and Research Group in Animal Production, Instituto Federal Catarinense, Araquari, Brazil
| | - F Moreira
- Post-Graduation Program in Animal Production and Health, Instituto Federal Catarinense, Araquari, Brazil.,Education, Extension, and Research Group in Animal Production, Instituto Federal Catarinense, Araquari, Brazil
| | - A F Millezi
- Post-Graduation Program in Animal Production and Health, Instituto Federal Catarinense, Concórdia, Brazil
| | - I Bianchi
- Post-Graduation Program in Animal Production and Health, Instituto Federal Catarinense, Araquari, Brazil.,Education, Extension, and Research Group in Animal Production, Instituto Federal Catarinense, Araquari, Brazil
| | - J M Oliveira Júnior
- Post-Graduation Program in Animal Production and Health, Instituto Federal Catarinense, Araquari, Brazil.,Education, Extension, and Research Group in Animal Production, Instituto Federal Catarinense, Araquari, Brazil
| | - V Peripolli
- Post-Graduation Program in Animal Production and Health, Instituto Federal Catarinense, Araquari, Brazil.,Education, Extension, and Research Group in Animal Production, Instituto Federal Catarinense, Araquari, Brazil
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17
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Pightling AW, Pettengill J, Luo Y, Strain E, Rand H. Genomic diversity of Salmonella enterica isolated from papaya samples collected during multiple outbreaks in 2017. MICROBIOLOGY-SGM 2021; 166:453-459. [PMID: 32100709 DOI: 10.1099/mic.0.000895] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
In 2017, the US Food and Drug Administration investigated the sources of multiple outbreaks of salmonellosis. Epidemiologic and traceback investigations identified Maradol papayas as the suspect vehicles. During the investigations, the genomes of 55 Salmonella enterica that were isolated from papaya samples were sequenced. Serovar assignments and phylogenetic analysis placed the 55 isolates into ten distinct groups, each representing a different serovar. Within-serovar SNP differences are generally between 0 and 20 SNPs, while the median between-serovar distance is 51 812 SNPs. We observed two groups with SNP distances between 21 and 100 SNPs. These relatively large within-serovar SNP distances may indicate that the isolates represent either diverse populations or multiple, genetically distinct subpopulations. Further inspection of these cases with traceback evidence allowed us to identify an 11th population. We observed that high levels of genomic diversity from individual firms is possible, with one firm yielding five of the ten serovars. Also, high levels of diversity are possible within small geographic regions, as five of the serovars were isolated from papayas that originated from farms located in Armería and Tecomán, Colima. In addition, we identified AMR genes that are present in three of the serovars studied here (aph(3')-lb, aph(6)-ld, tet(C), fosA7, and qnrB19) and we detected the presence of the plasmid IncHI2A among S. Urbana isolates.
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Affiliation(s)
| | | | - Yan Luo
- US Food and Drug Administration, Maryland, USA
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18
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Yao K, González-Escalona N, Hoffmann M. Multiple Displacement Amplification as a Solution for Low Copy Number Plasmid Sequencing. Front Microbiol 2021; 12:617487. [PMID: 33643244 PMCID: PMC7904871 DOI: 10.3389/fmicb.2021.617487] [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: 10/14/2020] [Accepted: 01/13/2021] [Indexed: 11/13/2022] Open
Abstract
Plasmids play a major role in bacterial adaptation to environmental stress and often contribute to antibiotic resistance and disease virulence. Although the complete sequence of each plasmid is essential for studying plasmid biology, most antibiotic resistance and virulence plasmids in Salmonella are present only in a low copy number, making extraction and sequencing difficult. Long read sequencing technologies require higher concentrations of DNA to provide optimal results. To resolve this problem, we assessed the sufficiency of multiple displacement amplification (MDA) for replicating Salmonella plasmid DNA to a satisfactory concentration for accurate sequencing and multiplexing. Nine Salmonella enterica isolates, representing nine different serovars carrying plasmids for which sequence data are already available at NCBI, were cultured and their plasmids isolated using an alkaline lysis extraction protocol. We then used the Phi29 polymerase to perform MDA, thereby obtaining enough plasmid DNA for long read sequencing. These amplified plasmids were multiplexed and sequenced on one single molecule, real-time (SMRT) cell with the Pacific Biosciences (Pacbio) Sequel sequencer. We were able to close all Salmonella plasmids (sizes ranged from 38 to 166 Kb) with sequencing coverage from 24 to 2,582X. This protocol, consisting of plasmid isolation, MDA, and multiplex sequencing, is an effective and fast method for closing high-molecular weight and low-copy-number plasmids. This high throughput protocol reduces the time and cost of plasmid closure.
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Affiliation(s)
- Kuan Yao
- Division of Microbiology, Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, United States
| | - Narjol González-Escalona
- Division of Microbiology, Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, United States
| | - Maria Hoffmann
- Division of Microbiology, Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, United States
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19
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Tassinari E, Bawn M, Thilliez G, Charity O, Acton L, Kirkwood M, Petrovska L, Dallman T, Burgess CM, Hall N, Duffy G, Kingsley RA. Whole-genome epidemiology links phage-mediated acquisition of a virulence gene to the clonal expansion of a pandemic Salmonella enterica serovar Typhimurium clone. Microb Genom 2020; 6:mgen000456. [PMID: 33112226 PMCID: PMC7725340 DOI: 10.1099/mgen.0.000456] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 10/01/2020] [Indexed: 01/10/2023] Open
Abstract
Epidemic and pandemic clones of bacterial pathogens with distinct characteristics continually emerge, replacing those previously dominant through mechanisms that remain poorly characterized. Here, whole-genome-sequencing-powered epidemiology linked horizontal transfer of a virulence gene, sopE, to the emergence and clonal expansion of a new epidemic Salmonella enterica serovar Typhimurium (S. Typhimurium) clone. The sopE gene is sporadically distributed within the genus Salmonella and rare in S. enterica Typhimurium lineages, but was acquired multiple times during clonal expansion of the currently dominant pandemic monophasic S. Typhimurium sequence type (ST) 34 clone. Ancestral state reconstruction and time-scaled phylogenetic analysis indicated that sopE was not present in the common ancestor of the epidemic clade, but later acquisition resulted in increased clonal expansion of sopE-containing clones that was temporally associated with emergence of the epidemic, consistent with increased fitness. The sopE gene was mainly associated with a temperate bacteriophage mTmV, but recombination with other bacteriophage and apparent horizontal gene transfer of the sopE gene cassette resulted in distribution among at least four mobile genetic elements within the monophasic S. enterica Typhimurium ST34 epidemic clade. The mTmV prophage lysogenic transfer to other S. enterica serovars in vitro was limited, but included the common pig-associated S. enterica Derby (S. Derby). This may explain mTmV in S. Derby co-circulating on farms with monophasic S. Typhimurium ST34, highlighting the potential for further transfer of the sopE virulence gene in nature. We conclude that whole-genome epidemiology pinpoints potential drivers of evolutionary and epidemiological dynamics during pathogen emergence, and identifies targets for subsequent research in epidemiology and bacterial pathogenesis.
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Affiliation(s)
- Eleonora Tassinari
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
- Teagasc Food Research Centre, Ashtown, Dublin 15, Ireland
| | - Matt Bawn
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
- Earlham Institute, Norwich Research Park, Norwich, UK
| | - Gaetan Thilliez
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Oliver Charity
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Luke Acton
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Mark Kirkwood
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | | | - Timothy Dallman
- Gastrointestinal Bacteria Reference Unit, National Infection Service, Public Health England, London, UK
| | | | - Neil Hall
- Earlham Institute, Norwich Research Park, Norwich, UK
| | | | - Robert A. Kingsley
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
- University of East Anglia, Norwich, UK
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20
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Allard MW, Zheng J, Cao G, Timme R, Stevens E, Brown EW. Food Safety Genomics and Connections to One Health and the Clinical Microbiology Laboratory. Clin Lab Med 2020; 40:553-563. [PMID: 33121622 DOI: 10.1016/j.cll.2020.08.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
This article describes the potential for one health surveillance of foodborne pathogens and disease using the revolutionary methodologies of whole genome sequencing. Whole genome sequencing of viral and bacterial pathogens is a natural fit to a one health perspective because these pathogens reside and are shared by humans, animals, and the environment and their genomes are compared easily regardless of where or from what host the pathogen was isolated. A genome provides a huge amount of data that can be analyzed for numerous applications. Sharing data coordinates surveillance efforts across the various disciplines.
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Affiliation(s)
- Marc W Allard
- US Food and Drug Administration, Center for Food Safety and Applied Nutrition, 5001 Campus Drive, College Park, MD 20740, USA.
| | - Jie Zheng
- US Food and Drug Administration, Center for Food Safety and Applied Nutrition, 5001 Campus Drive, College Park, MD 20740, USA
| | - Guojie Cao
- US Food and Drug Administration, Center for Food Safety and Applied Nutrition, 5001 Campus Drive, College Park, MD 20740, USA
| | - Ruth Timme
- US Food and Drug Administration, Center for Food Safety and Applied Nutrition, 5001 Campus Drive, College Park, MD 20740, USA
| | - Eric Stevens
- US Food and Drug Administration, Center for Food Safety and Applied Nutrition, 5001 Campus Drive, College Park, MD 20740, USA
| | - Eric W Brown
- US Food and Drug Administration, Center for Food Safety and Applied Nutrition, 5001 Campus Drive, College Park, MD 20740, USA
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21
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McDermott PF, Davis JJ. Predicting antimicrobial susceptibility from the bacterial genome: A new paradigm for one health resistance monitoring. J Vet Pharmacol Ther 2020; 44:223-237. [PMID: 33010049 DOI: 10.1111/jvp.12913] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 08/25/2020] [Accepted: 09/09/2020] [Indexed: 12/11/2022]
Abstract
The laboratory identification of antibacterial resistance is a cornerstone of infectious disease medicine. In vitro antimicrobial susceptibility testing has long been based on the growth response of organisms in pure culture to a defined concentration of antimicrobial agents. By comparing individual isolates to wild-type susceptibility patterns, strains with acquired resistance can be identified. Acquired resistance can also be detected genetically. After many decades of research, the inventory of genes underlying antimicrobial resistance is well known for several pathogenic genera including zoonotic enteric organisms such as Salmonella and Campylobacter and continues to grow substantially for others. With the decline in costs for large scale DNA sequencing, it is now practicable to characterize bacteria using whole genome sequencing, including the carriage of resistance genes in individual microorganisms and those present in complex biological samples. With genomics, we can generate comprehensive, detailed information on the bacterium, the mechanisms of antibiotic resistance, clues to its source, and the nature of mobile DNA elements by which resistance spreads. These developments point to a new paradigm for antimicrobial resistance detection and tracking for both clinical and public health purposes.
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Affiliation(s)
- Patrick F McDermott
- Office of Research, Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, MD, USA
| | - James J Davis
- Division of Data Science and Learning, Argonne National Laboratory, Argonne, IL, USA.,University of Chicago Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, USA
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22
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Wellawa DH, Allan B, White AP, Köster W. Iron-Uptake Systems of Chicken-Associated Salmonella Serovars and Their Role in Colonizing the Avian Host. Microorganisms 2020; 8:E1203. [PMID: 32784620 PMCID: PMC7465098 DOI: 10.3390/microorganisms8081203] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 07/30/2020] [Accepted: 07/31/2020] [Indexed: 01/09/2023] Open
Abstract
Iron is an essential micronutrient for most bacteria. Salmonella enterica strains, representing human and animal pathogens, have adopted several mechanisms to sequester iron from the environment depending on availability and source. Chickens act as a major reservoir for Salmonella enterica strains which can lead to outbreaks of human salmonellosis. In this review article we summarize the current understanding of the contribution of iron-uptake systems to the virulence of non-typhoidal S. enterica strains in colonizing chickens. We aim to address the gap in knowledge in this field, to help understand and define the interactions between S. enterica and these important hosts, in comparison to mammalian models.
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Affiliation(s)
- Dinesh H. Wellawa
- Vaccine & Infectious Disease Organization-International Vaccine Centre, University of Saskatchewan, 120 Veterinary Rd., Saskatoon, SK S7N 5E3, Canada; (D.H.W.); (B.A.); (A.P.W.)
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada
| | - Brenda Allan
- Vaccine & Infectious Disease Organization-International Vaccine Centre, University of Saskatchewan, 120 Veterinary Rd., Saskatoon, SK S7N 5E3, Canada; (D.H.W.); (B.A.); (A.P.W.)
| | - Aaron P. White
- Vaccine & Infectious Disease Organization-International Vaccine Centre, University of Saskatchewan, 120 Veterinary Rd., Saskatoon, SK S7N 5E3, Canada; (D.H.W.); (B.A.); (A.P.W.)
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada
| | - Wolfgang Köster
- Vaccine & Infectious Disease Organization-International Vaccine Centre, University of Saskatchewan, 120 Veterinary Rd., Saskatoon, SK S7N 5E3, Canada; (D.H.W.); (B.A.); (A.P.W.)
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada
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Yousfi K, Usongo V, Berry C, Khan RH, Tremblay DM, Moineau S, Mulvey MR, Doualla-Bell F, Fournier E, Nadon C, Goodridge L, Bekal S. Source Tracking Based on Core Genome SNV and CRISPR Typing of Salmonella enterica Serovar Heidelberg Isolates Involved in Foodborne Outbreaks in Québec, 2012. Front Microbiol 2020; 11:1317. [PMID: 32625190 PMCID: PMC7311582 DOI: 10.3389/fmicb.2020.01317] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 05/25/2020] [Indexed: 12/22/2022] Open
Abstract
Whole-genome sequencing (WGS) is the method of choice for bacterial subtyping and it is rapidly replacing the more traditional methods such as pulsed-field gel electrophoresis (PFGE). Here we used the high-resolution core genome single nucleotide variant (cgSNV) typing method to characterize clinical and food from Salmonella enterica serovar Heidelberg isolates in the context of source attribution. Additionally, clustered regularly interspaced short palindromic repeats (CRISPR) analysis was included to further support this method. Our results revealed that cgSNV was highly discriminatory and separated the outbreak isolates into distinct clusters (0-4 SNVs). CRISPR analysis was also able to distinguish outbreak strains from epidemiologically unrelated isolates. Specifically, our data clearly demonstrated the strength of these two methods to determine the probable source(s) of a 2012 epidemiologically characterized outbreak of S. Heidelberg. Using molecular cut-off of 0-10 SNVs, the cgSNV analysis of 246 clinical and food isolates of S. Heidelberg collected in Québec, in the same year of the outbreak event, revealed that retail and abattoir chicken isolates likely represent an important source of human infection to S. Heidelberg. Interestingly, the isolates genetically related by cgSNV also harbored the same CRISPR as outbreak isolates and clusters. This indicates that CRISPR profiles can be useful as a complementary approach to determine source attribution in foodborne outbreaks. Use of the genomic analysis also allowed to identify a large number of cases that were missed by PFGE, indicating that most outbreaks are probably underestimated. Although epidemiological information must still support WGS-based results, cgSNV method is a highly discriminatory method for the resolution of outbreak events and the attribution of these events to their respective sources. CRISPR typing can serve as a complimentary tool to this analysis during source tracking.
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Affiliation(s)
- Khadidja Yousfi
- Laboratoire de Santé Publique du Québec, Institut National de Santé Publique du Québec, Sainte-Anne-de-Bellevue, QC, Canada
- Department of Food Science and Agricultural Chemistry, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
| | - Valentine Usongo
- Laboratoire de Santé Publique du Québec, Institut National de Santé Publique du Québec, Sainte-Anne-de-Bellevue, QC, Canada
- Department of Food Science and Agricultural Chemistry, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
| | - Chrystal Berry
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Rufaida H. Khan
- Laboratoire de Santé Publique du Québec, Institut National de Santé Publique du Québec, Sainte-Anne-de-Bellevue, QC, Canada
- Department of Food Science and Agricultural Chemistry, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
| | - Denise M. Tremblay
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Faculté des Sciences et de Génie, Université Laval, Quebec City, QC, Canada
| | - Sylvain Moineau
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Faculté des Sciences et de Génie, Université Laval, Quebec City, QC, Canada
| | - Michael R. Mulvey
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Florence Doualla-Bell
- Laboratoire de Santé Publique du Québec, Institut National de Santé Publique du Québec, Sainte-Anne-de-Bellevue, QC, Canada
| | - Eric Fournier
- Laboratoire de Santé Publique du Québec, Institut National de Santé Publique du Québec, Sainte-Anne-de-Bellevue, QC, Canada
| | - Celine Nadon
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Lawrence Goodridge
- Department of Food Science and Agricultural Chemistry, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
| | - Sadjia Bekal
- Laboratoire de Santé Publique du Québec, Institut National de Santé Publique du Québec, Sainte-Anne-de-Bellevue, QC, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC, Canada
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Silveira L, Nunes A, Pista Â, Isidro J, Belo Correia C, Saraiva M, Batista R, Castanheira I, Machado J, Gomes JP. Characterization of Multidrug-Resistant Isolates of Salmonella enterica Serovars Heidelberg and Minnesota from Fresh Poultry Meat Imported to Portugal. Microb Drug Resist 2020; 27:87-98. [PMID: 32460607 DOI: 10.1089/mdr.2019.0384] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Salmonella enterica serovars Heidelberg and Minnesota frequently display several genetic mobile elements making them potential spreaders of resistance genes. Here, we phenotypically determined the antibiotic resistance profile and subsequently performed whole-genome sequencing on 36 isolates recovered from samples of fresh poultry meat, within the Portuguese Official Inspection Plan for Imported Foodstuffs. Several isolates of both serovars showed high genetic relatedness either with isolates from raw poultry meat imported to the Netherlands from Brazil or with isolates from samples from the broiler production chain in Brazil. The multidrug-resistant (MDR) character was common to the vast majority (94.4%) of isolates from both serovars, and several isolates carried the plasmid IncA/C2 containing the β-lactamase gene blaCMY-2 and IncX1 containing a type IV secretion system. These results somehow mirror the scenario observed in the Netherlands, showing the introduction, through fresh imported poultry meat in compliance with European legislation, of MDR Salmonella enterica serovars Heidelberg and Minnesota in Europe, with the potential spread of resistance markers. These data suggest the need to revise the hygiene criteria for foodstuffs monitoring before its placement on the market, with the determination of the resistome being an invaluable contribute to limit the dissemination of resistance markers.
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Affiliation(s)
- Leonor Silveira
- National Reference Laboratory of Gastrointestinal Infections, Department of Infectious Diseases, National Institute of Health, Lisbon, Portugal
| | - Alexandra Nunes
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health (INSA), Lisbon, Portugal
| | - Ângela Pista
- National Reference Laboratory of Gastrointestinal Infections, Department of Infectious Diseases, National Institute of Health, Lisbon, Portugal
| | - Joana Isidro
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health (INSA), Lisbon, Portugal
| | - Cristina Belo Correia
- Food Microbiology Laboratory, Reference Unit, Department of Food and Nutrition, National Institute of Health, Lisbon, Portugal
| | - Margarida Saraiva
- Food Microbiology Laboratory, Reference Unit, Department of Food and Nutrition, National Institute of Health, Porto, Portugal
| | - Rita Batista
- Food Microbiology Laboratory, Reference Unit, Department of Food and Nutrition, National Institute of Health, Lisbon, Portugal
| | - Isabel Castanheira
- Food Microbiology Laboratory, Reference Unit, Department of Food and Nutrition, National Institute of Health, Lisbon, Portugal
| | - Jorge Machado
- National Reference Laboratory of Gastrointestinal Infections, Department of Infectious Diseases, National Institute of Health, Lisbon, Portugal
| | - João Paulo Gomes
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health (INSA), Lisbon, Portugal
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25
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Hoffmann M, Miller J, Melka D, Allard MW, Brown EW, Pettengill JB. Temporal Dynamics of Salmonella enterica subsp. enterica Serovar Agona Isolates From a Recurrent Multistate Outbreak. Front Microbiol 2020; 11:478. [PMID: 32265893 PMCID: PMC7104706 DOI: 10.3389/fmicb.2020.00478] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 03/05/2020] [Indexed: 11/19/2022] Open
Abstract
The largest outbreak of Salmonella Agona in the United States occurred in 1998. It affected more than 400 patients and was linked to toasted oat cereal. Ten years later, a similar outbreak occurred with the same outbreak strain linked to the same production facility. In this study, whole-genome sequence (WGS) data from a set of 46 Salmonella Agona including five isolates associated with the 1998 outbreak and 25 isolates associated with the 2008 outbreak were analyzed. From each outbreak one isolate was sequenced on the Pacific Biosciences RS II Sequencer to determine the complete genome sequence. We reconstructed a phylogenetic hypothesis of the samples using a reference-based method for identifying variable sites. Using Single Nucleotide Polymorphism (SNP) analyses, we were able to distinguish and separate Salmonella Agona isolates from both outbreaks with only a mean of eight SNP differences between them. The phylogeny illustrates that the 2008 outbreak involves direct descendants from the 1998 outbreak rather than a second independent contamination event. Based on these results, there is evidence supporting the persistence of Salmonella over time in food processing facilities and highlights the need for consistent monitoring and control of organisms in the supply chain to minimize the risk of successive outbreaks.
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Affiliation(s)
- Maria Hoffmann
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, U.S. Food & Drug Administration, College Park, MD, United States
| | - John Miller
- Division of Public Health and Biostatistics, Office of Food Defense, Communication and Emergency Response, Center for Food Safety and Applied Nutrition, U.S. Food & Drug Administration, College Park, MD, United States
| | - David Melka
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, U.S. Food & Drug Administration, College Park, MD, United States
| | - Marc W Allard
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, U.S. Food & Drug Administration, College Park, MD, United States
| | - Eric W Brown
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, U.S. Food & Drug Administration, College Park, MD, United States
| | - James B Pettengill
- Division of Public Health and Biostatistics, Office of Food Defense, Communication and Emergency Response, Center for Food Safety and Applied Nutrition, U.S. Food & Drug Administration, College Park, MD, United States
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26
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Gymoese P, Kiil K, Torpdahl M, Østerlund MT, Sørensen G, Olsen JE, Nielsen EM, Litrup E. WGS based study of the population structure of Salmonella enterica serovar Infantis. BMC Genomics 2019; 20:870. [PMID: 31730461 PMCID: PMC6858691 DOI: 10.1186/s12864-019-6260-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 11/05/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Salmonella Infantis (S. Infantis) is one of the most frequent Salmonella serovars isolated from human cases of salmonellosis and the most detected serovar from animal and food sources in Europe. The serovar is commonly associated with poultry and there is increasing concern over multidrug resistant clones spreading worldwide, as the dominating clones are characterized by presence of large plasmids carrying multiple resistance genes. Increasing the knowledge of the S. Infantis population and evolution is important for understanding and preventing further spread. In this study, we analysed a collection of strains representing different decades, sources and geographic locations. We analysed the population structure and the accessory genome, in particular we identified prophages with a view to understand the role of prophages in relation to the evolution of this serovar. RESULTS We sequenced a global collection of 100 S. Infantis strains. A core-genome SNP analysis separated five strains in e-Burst Group (eBG) 297 with a long branch. The remaining strains, all in eBG31, were divided into three lineages that were estimated to have separated approximately 150 years ago. One lineage contained the vast majority of strains. In five of six clusters, no obvious correlation with source or geographical locations was seen. However, one cluster contained mostly strains from human and avian sources, indicating a clone with preference for these sources. The majority of strains within this cluster harboured a pESI-like plasmid with multiple resistance genes. Another lineage contained three genetic clusters with more rarely isolated strains of mainly animal origin, possibly less sampled or less infectious clones. Conserved prophages were identified in all strains, likely representing bacteriophages which integrated into the chromosome of a common ancestor to S. Infantis. We also saw that some prophages were specific to clusters and were probably introduced when the clusters were formed. CONCLUSIONS This study analysed a global S. Infantis population and described its genetic structure. We hypothesize that the population has evolved in three separate lineages, with one more successfully emerging lineage. We furthermore detected conserved prophages present in the entire population and cluster specific prophages, which probably shaped the population structure.
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Affiliation(s)
- Pernille Gymoese
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Artillerivej 5 Denmark
| | - Kristoffer Kiil
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Artillerivej 5 Denmark
| | - Mia Torpdahl
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Artillerivej 5 Denmark
| | - Mark T. Østerlund
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Artillerivej 5 Denmark
| | - Gitte Sørensen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Artillerivej 5 Denmark
| | - John E. Olsen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, Frederiksberg C, Denmark
| | - Eva M. Nielsen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Artillerivej 5 Denmark
| | - Eva Litrup
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Artillerivej 5 Denmark
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Carson C, Li XZ, Agunos A, Loest D, Chapman B, Finley R, Mehrotra M, Sherk LM, Gaumond R, Irwin R. Ceftiofur-resistant Salmonella enterica serovar Heidelberg of poultry origin - a risk profile using the Codex framework. Epidemiol Infect 2019; 147:e296. [PMID: 31679543 PMCID: PMC6836576 DOI: 10.1017/s0950268819001778] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 07/26/2019] [Accepted: 09/23/2019] [Indexed: 12/16/2022] Open
Abstract
Codex published the 'Guidelines for Risk Analysis of Foodborne Antimicrobial Resistance' to standardise the approach for evaluating risk posed by foodborne antimicrobial-resistant bacteria. One of the first steps in the guidelines is to compile a risk profile, which provides the current state of knowledge regarding a food safety issue, describes risk management options and recommends next steps. In Canada, ceftiofur/ceftriaxone-resistant Salmonella enterica subsp. enterica serovar Heidelberg from poultry was identified as an antimicrobial resistance (AMR) food safety issue. The first objective of this article was to contextualise this food safety issue, using the risk profile format of the Codex Guidelines. A second objective was to evaluate the applicability of the Codex Guidelines. This risk profile indicated that ceftiofur/ceftriaxone-resistant S. Heidelberg (CSH) was commonly isolated from poultry and was associated with severe disease in humans. Ceftiofur use in poultry hatcheries temporally mirrored the prevalence of CSH from poultry meat at retail and from people with salmonellosis. The evidence was sufficient to indicate the need for risk management options, such as restricting the use of ceftiofur in poultry. The Codex Guidelines provided a useful approach to summarise data for decision-makers to evaluate an AMR food safety issue.
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Affiliation(s)
- Carolee Carson
- Centre for Food-borne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Xian-Zhi Li
- Veterinary Drugs Directorate, Health Products and Food Branch, Health Canada, Ottawa, Ontario, Canada
| | - Agnes Agunos
- Centre for Food-borne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Daleen Loest
- Centre for Food-borne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Brennan Chapman
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Rita Finley
- Centre for Food-borne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Manisha Mehrotra
- Veterinary Drugs Directorate, Health Products and Food Branch, Health Canada, Ottawa, Ontario, Canada
| | | | - Réjean Gaumond
- Market and Industry Services Branch, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Rebecca Irwin
- Centre for Food-borne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, Ontario, Canada
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Hendriksen RS, Bortolaia V, Tate H, Tyson GH, Aarestrup FM, McDermott PF. Using Genomics to Track Global Antimicrobial Resistance. Front Public Health 2019; 7:242. [PMID: 31552211 PMCID: PMC6737581 DOI: 10.3389/fpubh.2019.00242] [Citation(s) in RCA: 198] [Impact Index Per Article: 39.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 08/13/2019] [Indexed: 11/30/2022] Open
Abstract
The recent advancements in rapid and affordable DNA sequencing technologies have revolutionized diagnostic microbiology and microbial surveillance. The availability of bioinformatics tools and online accessible databases has been a prerequisite for this. We conducted a scientific literature review and here we present a description of examples of available tools and databases for antimicrobial resistance (AMR) detection and provide future perspectives and recommendations. At least 47 freely accessible bioinformatics resources for detection of AMR determinants in DNA or amino acid sequence data have been developed to date. These include, among others but not limited to, ARG-ANNOT, CARD, SRST2, MEGARes, Genefinder, ARIBA, KmerResistance, AMRFinder, and ResFinder. Bioinformatics resources differ for several parameters including type of accepted input data, presence/absence of software for search within a database of AMR determinants that can be specific to a tool or cloned from other resources, and for the search approach employed, which can be based on mapping or on alignment. As a consequence, each tool has strengths and limitations in sensitivity and specificity of detection of AMR determinants and in application, which for some of the tools have been highlighted in benchmarking exercises and scientific articles. The identified tools are either available at public genome data centers, from GitHub or can be run locally. NCBI and European Nucleotide Archive (ENA) provide possibilities for online submission of both sequencing and accompanying phenotypic antimicrobial susceptibility data, allowing for other researchers to further analyze data, and develop and test new tools. The advancement in whole genome sequencing and the application of online tools for real-time detection of AMR determinants are essential to identify control and prevention strategies to combat the increasing threat of AMR. Accessible tools and DNA sequence data are expanding, which will allow establishing global pathogen surveillance and AMR tracking based on genomics. There is however, a need for standardization of pipelines and databases as well as phenotypic predictions based on the data.
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Affiliation(s)
- Rene S. Hendriksen
- European Union Reference Laboratory for Antimicrobial Resistance, World Health Organisation, Collaborating Center for Antimicrobial Resistance and Genomics in Food borne Pathogens, FAO Reference Laboratory for Antimicrobial Resistance, National Food Institute, Technical University of Denmark, Lyngby, Denmark
| | - Valeria Bortolaia
- European Union Reference Laboratory for Antimicrobial Resistance, World Health Organisation, Collaborating Center for Antimicrobial Resistance and Genomics in Food borne Pathogens, FAO Reference Laboratory for Antimicrobial Resistance, National Food Institute, Technical University of Denmark, Lyngby, Denmark
| | - Heather Tate
- Center for Veterinary Medicine, Office of Research, United States Food and Drug Administration, Laurel, MD, United States
| | - Gregory H. Tyson
- Center for Veterinary Medicine, Office of Research, United States Food and Drug Administration, Laurel, MD, United States
| | - Frank M. Aarestrup
- European Union Reference Laboratory for Antimicrobial Resistance, World Health Organisation, Collaborating Center for Antimicrobial Resistance and Genomics in Food borne Pathogens, FAO Reference Laboratory for Antimicrobial Resistance, National Food Institute, Technical University of Denmark, Lyngby, Denmark
| | - Patrick F. McDermott
- Center for Veterinary Medicine, Office of Research, United States Food and Drug Administration, Laurel, MD, United States
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Biswas S, Li Y, Elbediwi M, Yue M. Emergence and Dissemination of mcr-Carrying Clinically Relevant Salmonella Typhimurium Monophasic Clone ST34. Microorganisms 2019; 7:E298. [PMID: 31466338 PMCID: PMC6780495 DOI: 10.3390/microorganisms7090298] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 08/26/2019] [Accepted: 08/27/2019] [Indexed: 02/07/2023] Open
Abstract
Antibiotic resistance in bacteria is one of the urgent threats to both public and global health. The Salmonella Typhimurium monophasic sequence type 34 (ST34) clone, with its rapid dissemination and resistance to numerous critical antimicrobials, has raised global concerns. Here, we present an updated overview on the emerging infections caused by mobile colistin resistance (mcr)-carrying colistin-resistant ST34 isolates, covering their global dissemination and virulence-associated efficacy. The higher rates of mcr-1-positive ST34 in children in China highlights the increasing threat caused by this pathogen. Most of the ST34 isolates carrying the mcr-1 gene were isolated from animals and food products, indicating the role of foodborne transmission of mcr-1. The emergence of multidrug resistance genes along with various virulence factors and many heavy metal resistance genes on the chromosome and plasmid from ST34 isolates will challenge available therapeutic options. The presence of the colistin resistance gene (mcr-1, mcr-3, and mcr-5) with the multidrug-resistant phenotype in ST34 has spread across different countries, and most of the mcr-1 genes in ST34 isolates were detected in plasmid type IncHI2 followed by IncI2, and IncX4. Together, mcr-carrying S. Typhimurium ST34 may become a new pandemic clone. The fast detection and active surveillance in community, hospital, animal herds, food products and environment are urgently warranted.
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Affiliation(s)
- Silpak Biswas
- CATG Microbiology & Food Safety Laboratory, Institute of Preventive Veterinary Sciences, Zhejiang University College of Animal Sciences, Hangzhou 310058, China
| | - Yan Li
- CATG Microbiology & Food Safety Laboratory, Institute of Preventive Veterinary Sciences, Zhejiang University College of Animal Sciences, Hangzhou 310058, China
| | - Mohammed Elbediwi
- CATG Microbiology & Food Safety Laboratory, Institute of Preventive Veterinary Sciences, Zhejiang University College of Animal Sciences, Hangzhou 310058, China
| | - Min Yue
- CATG Microbiology & Food Safety Laboratory, Institute of Preventive Veterinary Sciences, Zhejiang University College of Animal Sciences, Hangzhou 310058, China.
- Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Hangzhou 310058, China.
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Salmonella enterica subsp. enterica Serovar Heidelberg Food Isolates Associated with a Salmonellosis Outbreak Have Enhanced Stress Tolerance Capabilities. Appl Environ Microbiol 2019; 85:AEM.01065-19. [PMID: 31175193 DOI: 10.1128/aem.01065-19] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 06/03/2019] [Indexed: 11/20/2022] Open
Abstract
Salmonella enterica serovar Heidelberg is currently the 12th most common serovar of Salmonella enterica causing salmonellosis in the United States and results in twice the average incidence of blood infections caused by nontyphoidal salmonellae. Multiple outbreaks of salmonellosis caused by Salmonella Heidelberg resulted from the same poultry processor, which infected 634 people during 2013 and 2014. The hospitalization and invasive illness rates were 38% and 15%, respectively. We hypothesized that the outbreak strains of Salmonella Heidelberg had enhanced stress tolerance and virulence capabilities. We sourced nine food isolates collected during the outbreak investigation and three reference isolates to assess their tolerance to heat and sanitizers, ability to attach to abiotic surfaces, and invasiveness in vitro We performed RNA sequencing on three isolates (two outbreak-associated isolates and a reference Salmonella Heidelberg strain) with various levels of heat tolerance to gain insight into the mechanism behind the isolates' enhanced heat tolerance. We also performed genomic analyses to determine the genetic relationships among the outbreak isolates. Ultimately, we determined that (i) six Salmonella Heidelberg isolates associated with the foodborne outbreak had enhanced heat tolerance, (ii) one outbreak isolate with enhanced heat tolerance also had an enhanced biofilm-forming ability under stressful conditions, (iii) exposure to heat stress increased the expression of Salmonella Heidelberg multidrug efflux and virulence genes, and (iv) outbreak-associated isolates were likely transcriptionally primed to better survive processing stresses and, potentially, to cause illness.IMPORTANCE This study provides a deep analysis of the intrinsic stress tolerance and virulence capabilities of Salmonella Heidelberg that may have contributed to the length and severity of a recent salmonellosis outbreak. Additionally, this study provides a comprehensive analysis of the transcriptomic response of S. enterica strains to heat stress conditions and compares baseline stationary-phase gene expression among outbreak- and non-outbreak-associated Salmonella Heidelberg isolates. These data can be used in assay development to screen isolates for stress tolerance and subsequent survival. This study adds to our understanding of the strains associated with the outbreak and informs ongoing regulatory discussions on Salmonella in poultry.
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31
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van den Berg RR, Dissel S, Rapallini MLBA, van der Weijden CC, Wit B, Heymans R. Characterization and whole genome sequencing of closely related multidrug-resistant Salmonella enterica serovar Heidelberg isolates from imported poultry meat in the Netherlands. PLoS One 2019; 14:e0219795. [PMID: 31329622 PMCID: PMC6645675 DOI: 10.1371/journal.pone.0219795] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 07/01/2019] [Indexed: 02/01/2023] Open
Abstract
Multidrug-resistant Salmonella enterica serovar Heidelberg isolates are frequently recovered in the Netherlands from poultry meat imported from South America. Our aim was to retrospectively assess the characteristics of the antimicrobial determinants, gene content and the clonal relatedness of 122 unique S. Heidelberg isolates from chicken meat from Brazil (n = 119) and Argentina (n = 3) that were imported between 2010 and 2015. These isolates were subjected to antimicrobial susceptibility testing, PCR and Illumina HiSeq2500 whole genome sequencing. Draft genomes were assembled to assess the gene content, and the phylogenetic relationships between isolates were determined using single nucleotide polymorphisms. Ciprofloxacin-resistance was identified in 98.4% of the isolates and 83.7% isolates showed resistance to the extended-spectrum cephalosporins cefotaxime and ceftazidime (83.6% and 82.8% respectively). Of the latter, 97.1% exhibited an AmpC phenotype and contained blaCMY-2, whereas the remaining three isolates contained an extended spectrum beta-lactamase. Of the 99 extended-spectrum cephalosporins-resistant isolates harboring CMY-2 plasmids, 56.6% contained the incompatibility group I1 replicon. Phylogenetic cluster analysis showed that all isolates from Brazil clustered together, with 49% occurring in clusters larger than 5 isolates that revealed intra-cluster similarities based on geographical location and/or resistance profiles. The remaining isolates were classified in smaller clusters or as singletons, highlighting the large diversity of S. Heidelberg in the poultry chain in Brazil that was revealed by this study. Considering the potential public health risk associated with multidrug-resistant S. Heidelberg in imported poultry, collaborative whole genome sequencing-based surveillance is needed to monitor the spread, pathogenic properties and epidemiological distribution of these isolates.
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Affiliation(s)
- Redmar R. van den Berg
- Netherlands Food and Consumer Product Safety Authority, Consumer and Safety Division, Laboratory Food and Feed Safety, WB Wageningen, the Netherlands
| | - Serge Dissel
- Netherlands Food and Consumer Product Safety Authority, Consumer and Safety Division, Laboratory Food and Feed Safety, WB Wageningen, the Netherlands
| | - Michel L. B. A. Rapallini
- Netherlands Food and Consumer Product Safety Authority, Consumer and Safety Division, Laboratory Food and Feed Safety, WB Wageningen, the Netherlands
| | - Coen C. van der Weijden
- Netherlands Food and Consumer Product Safety Authority, Consumer and Safety Division, Laboratory Food and Feed Safety, WB Wageningen, the Netherlands
| | - Ben Wit
- Netherlands Food and Consumer Product Safety Authority, Consumer and Safety Division, Laboratory Food and Feed Safety, WB Wageningen, the Netherlands
| | - Raymond Heymans
- Netherlands Food and Consumer Product Safety Authority, Consumer and Safety Division, Laboratory Food and Feed Safety, WB Wageningen, the Netherlands
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Whole genome sequencing uses for foodborne contamination and compliance: Discovery of an emerging contamination event in an ice cream facility using whole genome sequencing. INFECTION GENETICS AND EVOLUTION 2019; 73:214-220. [PMID: 31039448 DOI: 10.1016/j.meegid.2019.04.026] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 04/25/2019] [Accepted: 04/26/2019] [Indexed: 11/21/2022]
Abstract
We review how FDA surveillance identifies several ways that whole genome sequencing (WGS) improves actionable outcomes for public health and compliance in a case involving Listeria monocytogenes contamination in an ice cream facility. In late August 2017 FDA conducted environmental sampling inside an ice cream facility. These isolates were sequenced and deposited into the GenomeTrakr databases. In September 2018 the Centers for Disease Control and Prevention contacted the Florida Department of Health after finding that the pathogen analyses of three clinical cases of listeriosis (two in 2013, one in 2018) were highly related to the aforementioned L. monocytogenes isolates collected from the ice cream facility. in 2017. FDA returned to the ice cream facility in late September 2018 and conducted further environmental sampling and again recovered L. monocytogenes from environmental subsamples that were genetically related to the clinical cases. A voluntary recall was issued to include all ice cream manufactured from August 2017 to October 2018. Subsequently, FDA suspended this food facility's registration. WGS results for L. monocytogenes found in the facility and from clinical samples clustered together by 0-31 single nucleotide polymorphisms (SNPs). The FDA worked together with the Centers for Disease Control and Prevention, as well as the Florida Department of Health, and the Florida Department of Agriculture and Consumer Services to recall all ice cream products produced by this facility. Our data suggests that when available isolates from food facility inspections are subject to whole genome sequencing and the subsequent sequence data point to linkages between these strains and recent clinical isolates (i.e., <20 nucleotide differences), compliance officials should take regulatory actions early to prevent further potential illness. The utility of WGS for applications related to enforcement of FDA compliance programs in the context of foodborne pathogens is reviewed.
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Longitudinal study reveals persistent environmental Salmonella Heidelberg in Brazilian broiler farms. Vet Microbiol 2019; 233:118-123. [PMID: 31176397 DOI: 10.1016/j.vetmic.2019.04.004] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 04/03/2019] [Accepted: 04/05/2019] [Indexed: 11/21/2022]
Abstract
The vast capacity for maintenance and dissemination in the environment are major challenges for the control of Salmonella spp. in poultry farms. The aim of this study was to assess environmental contamination by non-typhoidal Salmonella in successive broiler flocks in nine commercial broiler farms integrated with three companies in the south of Brazil, for a twelve-month production period. Recycled broiler litter, feed and swabs from the evaporative cooling system pads were analyzed, and the total enterobacteria count in the litter samples was ascertained. Positive broiler houses were identified in two of the three broiler companies studied, in which non-typhoidal Salmonella were detected for the first time in the first or second flock, and recurred in the recycled litter of subsequent flocks. Feed and evaporative cooling pad swab samples were also positive in at least one of the assessed flocks. The majority of the isolates (87.5%) originating from different flocks, broiler houses and companies that were sampled were identified as S. Heidelberg, with the prevalence of one single genotype. The total enterobacteria levels in the litter diminished as the flocks progressed, but the presence of Salmonella spp. was constant over the course of time, indicating that the litter management procedures were not capable of interrupting the cycle of residual contamination. The predominance of S. Heidelberg highlights its emergence and dissemination in this region, as well as its resistance and maintenance in the environment, and reinforces the need to improve prevention and recycled litter management measures.
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Hu L, Stones R, Brown EW, Allard MW, Ma LM, Zhang G. DNA sequences and predicted protein structures of prot6E and sefA genes for Salmonella ser. Enteritidis detection. Food Control 2019. [DOI: 10.1016/j.foodcont.2018.09.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Keefer AB, Xiaoli L, M'ikanatha NM, Yao K, Hoffmann M, Dudley EG. Retrospective whole-genome sequencing analysis distinguished PFGE and drug-resistance-matched retail meat and clinical Salmonella isolates. MICROBIOLOGY-SGM 2019; 165:270-286. [PMID: 30672732 DOI: 10.1099/mic.0.000768] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Non-typhoidal Salmonella is a leading cause of outbreak and sporadic-associated foodborne illnesses in the United States. These infections have been associated with a range of foods, including retail meats. Traditionally, pulsed-field gel electrophoresis (PFGE) and antibiotic susceptibility testing (AST) have been used to facilitate public health investigations of Salmonella infections. However, whole-genome sequencing (WGS) has emerged as an alternative tool that can be routinely implemented. To assess its potential in enhancing integrated surveillance in Pennsylvania, USA, WGS was used to directly compare the genetic characteristics of 7 retail meat and 43 clinical historic Salmonella isolates, subdivided into 3 subsets based on PFGE and AST results, to retrospectively resolve their genetic relatedness and identify antimicrobial resistance (AMR) determinants. Single nucleotide polymorphism (SNP) analyses revealed that the retail meat isolates within S. Heidelberg, S. Typhimurium var. O5- subset 1 and S. Typhimurium var. O5- subset 2 were separated from each primary PFGE pattern-matched clinical isolate by 6-12, 41-96 and 21-81 SNPs, respectively. Fifteen resistance genes were identified across all isolates, including fosA7, a gene only recently found in a limited number of Salmonella and a ≥95 % phenotype to genotype correlation was observed for all tested antimicrobials. Moreover, AMR was primarily plasmid-mediated in S. Heidelberg and S. Typhimurium var. O5- subset 2, whereas AMR was chromosomally carried in S. Typhimurium var. O5- subset 1. Similar plasmids were identified in both the retail meat and clinical isolates. Collectively, these data highlight the utility of WGS in retrospective analyses and enhancing integrated surveillance for Salmonella from multiple sources.
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Affiliation(s)
- Andrea B Keefer
- 1Department of Food Science, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Lingzi Xiaoli
- 1Department of Food Science, The Pennsylvania State University, University Park, Pennsylvania, USA
| | | | - Kuan Yao
- 3Center for Food Safety and Applied Nutrition (CFSAN), Food and Drug Administration (FDA), College Park, Maryland, USA
| | - Maria Hoffmann
- 3Center for Food Safety and Applied Nutrition (CFSAN), Food and Drug Administration (FDA), College Park, Maryland, USA
| | - Edward G Dudley
- 4E. coli Reference Center, The Pennsylvania State University, University Park, Pennsylvania, USA.,1Department of Food Science, The Pennsylvania State University, University Park, Pennsylvania, USA
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Kuijpers AFA, Bonacic Marinovic AA, Wijnands LM, Delfgou-van Asch EHM, van Hoek AHAM, Franz E, Pielaat A. Phenotypic Prediction: Linking in vitro Virulence to the Genomics of 59 Salmonella enterica Strains. Front Microbiol 2019; 9:3182. [PMID: 30687242 PMCID: PMC6333659 DOI: 10.3389/fmicb.2018.03182] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 12/07/2018] [Indexed: 11/17/2022] Open
Abstract
The increased availability of whole-genome-sequencing techniques generates a wealth of DNA data on numerous organisms, including foodborne pathogens such as Salmonella. However, how these data can be used to improve microbial risk assessment and understanding of Salmonella epidemiology remains a challenge. The aim of this study was to assess variability in in vitro virulence and genetic characteristics between and within different serovars. The phenotypic behavior of 59 strains of 32 different Salmonella enterica serovars from animal, human and food origin was assessed in an in vitro gastro-intestinal tract (GIT) system and they were analyzed for the presence of 233 putative virulence genes as markers for phenotypic prediction. The probability of in vitro infection, P(inf), defined as the fraction of infectious cells passing from inoculation to host cell invasion at the last stage of the GIT system, was interpreted as the in vitro virulence. Results showed that the (average) P(inf) of Salmonella serovars ranged from 5.3E-05 (S. Kedougou) to 5.2E-01 (S. Typhimurium). In general, a higher P(inf) on serovar level corresponded to higher reported human incidence from epidemiological reporting data. Of the 233 virulence genes investigated, only 101 showed variability in presence/absence among the strains. In vitro P(inf) was found to be positively associated with the presence of specific plasmid related virulence genes (mig-5, pef, rck, and spv). However, not all serovars with a relatively high P(inf), > 1E-02, could be linked with these specific genes. Moreover, some outbreak related strains (S. Heidelberg and S. Thompson) did not reveal this association with P(inf). No clear association with in vitro virulence P(inf) was identified when grouping serovars with the same virulence gene profile (virulence plasmid, Typhoid toxin, peg operon and stk operon). This study shows that the in vitro P(inf) variation among individual strains from the same serovar is larger than that found between serovars. Therefore, ranking P(inf) of S. enterica on serovar level alone, or in combination with a serovar specific virulence gene profile, cannot be recommended. The attribution of single biological phenomena to individual strains or serovars is not sufficient to improve the hazard characterization for S. enterica. Future microbial risk assessments, including virulence gene profiles, require a systematic approach linked to epidemiological studies rather than revealing differences in characteristics on serovar level alone.
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Wahl A, Battesti A, Ansaldi M. Prophages in Salmonella enterica: a driving force in reshaping the genome and physiology of their bacterial host? Mol Microbiol 2018; 111:303-316. [PMID: 30466179 PMCID: PMC7380047 DOI: 10.1111/mmi.14167] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/10/2018] [Indexed: 12/11/2022]
Abstract
Thanks to the exponentially increasing number of publicly available bacterial genome sequences, one can now estimate the important contribution of integrated viral sequences to the diversity of bacterial genomes. Indeed, temperate bacteriophages are able to stably integrate the genome of their host through site‐specific recombination and transmit vertically to the host siblings. Lysogenic conversion has been long acknowledged to provide additional functions to the host, and particularly to bacterial pathogen genomes where prophages contribute important virulence factors. This review aims particularly at highlighting the current knowledge and questions about lysogeny in Salmonella genomes where functional prophages are abundant, and where genetic interactions between host and prophages are of particular importance for human health considerations.
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Affiliation(s)
- Astrid Wahl
- Laboratoire de Chimie Bactérienne, UMR7283, Institut de Microbiologie de la Méditerranée, Centre National de la Recherche Scientifique, Aix-Marseille Université, Marseille, France
| | - Aurélia Battesti
- Laboratoire de Chimie Bactérienne, UMR7283, Institut de Microbiologie de la Méditerranée, Centre National de la Recherche Scientifique, Aix-Marseille Université, Marseille, France
| | - Mireille Ansaldi
- Laboratoire de Chimie Bactérienne, UMR7283, Institut de Microbiologie de la Méditerranée, Centre National de la Recherche Scientifique, Aix-Marseille Université, Marseille, France
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Antony L, Behr M, Sockett D, Miskimins D, Aulik N, Christopher-Hennings J, Nelson E, Allard MW, Scaria J. Genome divergence and increased virulence of outbreak associated Salmonella enterica subspecies enterica serovar Heidelberg. Gut Pathog 2018; 10:53. [PMID: 30603048 PMCID: PMC6304783 DOI: 10.1186/s13099-018-0279-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 12/15/2018] [Indexed: 11/20/2022] Open
Abstract
Salmonella enterica serotype Heidelberg is primarily a poultry adapted serotype of Salmonella that can also colonize other hosts and cause human disease. In this study, we compared the genomes of outbreak associated non-outbreak causing Salmonella ser. Heidelberg strains from diverse hosts and geographical regions. Human outbreak associated strains in this study were from a 2015 multistate outbreak of Salmonella ser. Heidelberg involving 15 states in the United States which originated from bull calves. Our clinicopathologic examination revealed that cases involving Salmonella ser. Heidelberg strains were predominantly young, less than weeks-old, dairy calves. Pre-existing or concurrent disease was found in the majority of the calves. Detection of Salmonella ser. Heidelberg correlated with markedly increased death losses clinically comparable to those seen in herds infected with S. Dublin, a known serious pathogen of cattle. Whole genome based single nucleotide polymorphism based analysis revealed that these calf isolates formed a distinct cluster along with outbreak associated human isolates. The defining feature of the outbreak associated strains, when compared to older isolates of S. Heidelberg, is that all isolates in this cluster contained Saf fimbrial genes which are generally absent in S. Heidelberg. The acquisition of several single nucleotide polymorphisms and the gain of Saf fimbrial genes may have contributed to the increased disease severity of these Salmonella ser. Heidelberg strains.
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Affiliation(s)
- Linto Antony
- 1Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD USA.,South Dakota Center for Biologics Research and Commercialization, Brookings, SD USA
| | - Melissa Behr
- 1Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD USA
| | - Donald Sockett
- 3Wisconsin Veterinary Diagnostic Laboratory, University of Wisconsin, Madison, WI USA
| | - Dale Miskimins
- 1Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD USA
| | - Nicole Aulik
- 3Wisconsin Veterinary Diagnostic Laboratory, University of Wisconsin, Madison, WI USA
| | - Jane Christopher-Hennings
- 1Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD USA.,South Dakota Center for Biologics Research and Commercialization, Brookings, SD USA
| | - Eric Nelson
- 1Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD USA.,South Dakota Center for Biologics Research and Commercialization, Brookings, SD USA
| | - Marc W Allard
- 4Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Nutrition, U.S. Food and Drug Administration, College Park, MD USA
| | - Joy Scaria
- 1Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD USA.,South Dakota Center for Biologics Research and Commercialization, Brookings, SD USA
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Pornsukarom S, van Vliet AHM, Thakur S. Whole genome sequencing analysis of multiple Salmonella serovars provides insights into phylogenetic relatedness, antimicrobial resistance, and virulence markers across humans, food animals and agriculture environmental sources. BMC Genomics 2018; 19:801. [PMID: 30400810 PMCID: PMC6218967 DOI: 10.1186/s12864-018-5137-4] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 10/02/2018] [Indexed: 11/13/2022] Open
Abstract
Background Salmonella enterica is a significant foodborne pathogen, which can be transmitted via several distinct routes, and reports on acquisition of antimicrobial resistance (AMR) are increasing. To better understand the association between human Salmonella clinical isolates and the potential environmental/animal reservoirs, whole genome sequencing (WGS) was used to investigate the epidemiology and AMR patterns within Salmonella isolates from two adjacent US states. Results WGS data of 200 S. enterica isolates recovered from human (n = 44), swine (n = 32), poultry (n = 22), and farm environment (n = 102) were used for in silico prediction of serovar, distribution of virulence genes, and phylogenetically clustered using core genome single nucleotide polymorphism (SNP) and feature frequency profiling (FFP). Furthermore, AMR was studied both by genotypic prediction using five curated AMR databases, and compared to phenotypic AMR using broth microdilution. Core genome SNP-based and FFP-based phylogenetic trees showed consistent clustering of isolates into the respective serovars, and suggested clustering of isolates based on the source of isolation. The overall correlation of phenotypic and genotypic AMR was 87.61% and 97.13% for sensitivity and specificity, respectively. AMR and virulence genes clustered with the Salmonella serovars, while there were also associations between the presence of virulence genes in both animal/environmental isolates and human clinical samples. Conclusions WGS is a helpful tool for Salmonella phylogenetic analysis, AMR and virulence gene predictions. The clinical isolates clustered closely with animal and environmental isolates, suggesting that animals and environment are potential sources for dissemination of AMR and virulence genes between Salmonella serovars. Electronic supplementary material The online version of this article (10.1186/s12864-018-5137-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Suchawan Pornsukarom
- Faculty of Veterinary Medicine, Rajamangala University of Technology Tawan-ok, Chonburi, Thailand
| | - Arnoud H M van Vliet
- School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Surrey, UK
| | - Siddhartha Thakur
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA. .,Comparative Medicine Institute, North Carolina State University, Raleigh, NC, USA.
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Gad AH, Abo-Shama UH, Harclerode KK, Fakhr MK. Prevalence, Serotyping, Molecular Typing, and Antimicrobial Resistance of Salmonella Isolated From Conventional and Organic Retail Ground Poultry. Front Microbiol 2018; 9:2653. [PMID: 30455678 PMCID: PMC6230656 DOI: 10.3389/fmicb.2018.02653] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 10/17/2018] [Indexed: 01/23/2023] Open
Abstract
Ground poultry is marketed as a healthier alternative to ground beef despite the fact that poultry is a major source of foodborne Salmonella. The objectives of this study were to determine the prevalence of Salmonella in Oklahoma retail ground poultry and to characterize representative isolates by serotyping, antimicrobial resistance, PFGE patterns, and large plasmid profiling. A total of 199 retail ground poultry samples (150 ground turkey and 49 ground chicken) were investigated. The overall prevalence of Salmonella in ground poultry was 41% (82/199), and the incidence in conventional samples (47%, 66/141) was higher than in organic samples (27%, 16/58). The prevalence of Salmonella in organic ground chicken and organic ground turkey was 33% (3/9) and 26% (13/49), respectively. Twenty six Salmonella isolates (19 conventional and 7 organic) were chosen for further characterization. The following six serotypes and number of isolates per serotype were identified as follows: Tennessee, 8; Saintpaul, 4; Senftenberg, 4; Anatum, 4 (one was Anatum_var._15+); Ouakam, 3; and Enteritidis, 3. Resistance to 16 tested antimicrobials was as follows: gentamycin, 100% (26/26); ceftiofur, 100% (26/26); amoxicillin/clavulanic acid, 96% (25/26); streptomycin, 92% (24/26); kanamycin, 88% (23/26); ampicillin, 85% (22/26); cephalothin, 81% (21/26); tetracycline, 35% (9/26); sulfisoxazole, 27% (7/26); nalidixic acid, 15% (4/26); and cefoxitin, 15% (4/26). All isolates were susceptible to amikacin, chloramphenicol, ceftriaxone, and trimethoprim/sulfamethoxazole. All screened isolates were multidrug resistant (MDR) and showed resistance to 4-10 antimicrobials; isolates from organic sources showed resistance to 5-7 antimicrobials. PFGE was successful in clustering the Salmonella isolates into distinct clusters that each represented one serotype. PFGE was also used to investigate the presence of large plasmids using S1 nuclease digestion. A total of 8/26 (31%) Salmonella isolates contained a ∼100 Kb plasmid that was present in all Anatum and Ouakam isolates. In conclusion, the presence of multidrug resistant Salmonella with various serotypes, PFGE profiles, and large plasmids in ground poultry stresses the importance of seeking novel interventions to reduce the risk of this foodborne pathogen. Multidrug resistance (MDR) is considered a high additional risk and continued surveillance at the retail level could minimize the risk for the consumer.
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Affiliation(s)
- Ahmed H. Gad
- Department of Biological Science, The University of Tulsa, Tulsa, OK, United States
| | - Usama H. Abo-Shama
- Department of Biological Science, The University of Tulsa, Tulsa, OK, United States
- Microbiology and Immunology Department, Faculty of Veterinary Medicine, Sohag University, Sohag, Egypt
| | | | - Mohamed K. Fakhr
- Department of Biological Science, The University of Tulsa, Tulsa, OK, United States
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Weinroth MD, Britton BC, Belk KE. Genetics and microbiology of meat. Meat Sci 2018; 144:15-21. [DOI: 10.1016/j.meatsci.2018.04.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 04/18/2018] [Accepted: 04/18/2018] [Indexed: 10/17/2022]
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Oladeinde A, Cook K, Orlek A, Zock G, Herrington K, Cox N, Plumblee Lawrence J, Hall C. Hotspot mutations and ColE1 plasmids contribute to the fitness of Salmonella Heidelberg in poultry litter. PLoS One 2018; 13:e0202286. [PMID: 30169497 PMCID: PMC6118388 DOI: 10.1371/journal.pone.0202286] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 07/31/2018] [Indexed: 12/14/2022] Open
Abstract
Salmonella enterica subsp. enterica serovar Heidelberg (S. Heidelberg) is a clinically-important serovar linked to food-borne illness, and commonly isolated from poultry. Investigations of a large, multistate outbreak in the USA in 2013 identified poultry litter (PL) as an important extra-intestinal environment that may have selected for specific S. Heidelberg strains. Poultry litter is a mixture of bedding materials and chicken excreta that contains chicken gastrointestinal (GI) bacteria, undigested feed, feathers, and other materials of chicken origin. In this study, we performed a series of controlled laboratory experiments which assessed the microevolution of two S. Heidelberg strains (SH-2813 and SH-116) in PL previously used to raise 3 flocks of broiler chickens. The strains are closely related at the chromosome level, differing from the reference genome by 109 and 89 single nucleotide polymorphisms/InDels, respectively. Whole genome sequencing was performed on 86 isolates recovered after 0, 1, 7 and 14 days of microevolution in PL. Only strains carrying an IncX1 (37kb), 2 ColE1 (4 and 6kb) and 1 ColpVC (2kb) plasmids survived more than 7 days in PL. Competition experiments showed that carriage of these plasmids was associated with increased fitness. This increased fitness was associated with an increased copy number of IncX1 and ColE1 plasmids. Further, all Col plasmid-bearing strains had hotspot mutations in 37 loci on the chromosome and in 3 loci on the IncX1 plasmid. Additionally, we observed a decrease in susceptibility to tobramycin, kanamycin, gentamicin, neomycin and fosfomycin for Col plasmid-bearing strains. Our study demonstrates how positive selection from poultry litter can change the evolutionary path of S. Heidelberg.
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Affiliation(s)
- Adelumola Oladeinde
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, U.S. National Poultry Research Center, USDA-ARS, Athens, GA, United States of America
| | - Kimberly Cook
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, U.S. National Poultry Research Center, USDA-ARS, Athens, GA, United States of America
| | - Alex Orlek
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Greg Zock
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, U.S. National Poultry Research Center, USDA-ARS, Athens, GA, United States of America
| | - Kyler Herrington
- Department of Microbiology, University of Georgia, Athens, GA, United States of America
| | - Nelson Cox
- Poultry Microbiological Safety and Processing Research Unit, U.S. National Poultry Research Center, USDA-ARS, Athens, GA, United States of America
| | - Jodie Plumblee Lawrence
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, U.S. National Poultry Research Center, USDA-ARS, Athens, GA, United States of America
| | - Carolina Hall
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, U.S. National Poultry Research Center, USDA-ARS, Athens, GA, United States of America
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Almeida F, Seribelli AA, Medeiros MIC, Rodrigues DDP, de MelloVarani A, Luo Y, Allard MW, Falcão JP. Phylogenetic and antimicrobial resistance gene analysis of Salmonella Typhimurium strains isolated in Brazil by whole genome sequencing. PLoS One 2018; 13:e0201882. [PMID: 30102733 PMCID: PMC6089434 DOI: 10.1371/journal.pone.0201882] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 07/24/2018] [Indexed: 12/02/2022] Open
Abstract
Whole genome sequencing (WGS) has been used as a powerful technology for molecular epidemiology, surveillance, identification of species and serotype, identification of the sources of outbreaks, among other purposes. In Brazil, there is relatively few epidemiological data on Salmonella. In this study, 90 Salmonella Typhimurium strains had their genome sequenced to uncover the diversity of Salmonella Typhimurium isolated from humans and food, between 1983 and 2013, from different geographic regions in Brazil based on single nucleotide polymorphism (SNP) analysis. A total of 39 resistance genes were identified, such as aminoglycoside, tetracycline, sulfonamide, trimethoprim, beta-lactam, fluoroquinolone, phenicol and macrolide, as well as the occurrence of point mutations in some of the genes such as gyrA, gyrB, parC and parE. A total of 65 (72.2%) out of 90 S. Typhimurium strains studied were phenotypically resistant to sulfonamides, 44 (48.9%) strains were streptomycin resistant, 27 (30%) strains were resistant to tetracycline, 21 (23.3%) strains were gentamicin resistant, and seven (7.8%) strains were resistant to ceftriaxone. In the gyrA gene, it was observed the following amino acid substitutions: Asp(87)→Gly, Asp(87)→Asn, Ser(83)→Phe, Ser(83)→Tyr. Phylogenetic results placed the 90 S. Typhimurium strains into two major clades suggesting the existence of a prevalent subtype, likely more adapted, among strains isolated from humans, with some diversity in subtypes in foods. The variety and prevalence of resistant genes found in these Salmonella Typhimurium strains reinforces their potential hazard for humans and the risk in foods in Brazil.
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Affiliation(s)
- Fernanda Almeida
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas–Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. do Café s/ nº, Ribeirão Preto, SP Brasil
| | - Amanda Aparecida Seribelli
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas–Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. do Café s/ nº, Ribeirão Preto, SP Brasil
| | | | - Dália dos Prazeres Rodrigues
- Laboratório de Enterobactérias, FIOCRUZ/Fundação Instituto Oswaldo Cruz, Avenida Brasil, Pavilhão Rocha Lima, 3°andar, Manguinhos, Rio de Janeiro, RJ, Brasil
| | - Alessandro de MelloVarani
- Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (UNESP), Jaboticabal, Brazil
| | - Yan Luo
- Division of Microbiology, Office of Regular Science, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, United States of America
| | - Marc W. Allard
- Division of Microbiology, Office of Regular Science, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, United States of America
- * E-mail: (JPF); (MA)
| | - Juliana Pfrimer Falcão
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas–Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. do Café s/ nº, Ribeirão Preto, SP Brasil
- * E-mail: (JPF); (MA)
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Sequencing of pT5282-CTXM, p13190-KPC and p30860-NR, and comparative genomics analysis of IncX8 plasmids. Int J Antimicrob Agents 2018; 52:210-217. [DOI: 10.1016/j.ijantimicag.2018.04.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 04/08/2018] [Accepted: 04/11/2018] [Indexed: 01/31/2023]
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Nair DVT, Kollanoor Johny A. Characterizing the Antimicrobial Function of a Dairy-Originated Probiotic, Propionibacterium freudenreichii, Against Multidrug-Resistant Salmonella enterica Serovar Heidelberg in Turkey Poults. Front Microbiol 2018; 9:1475. [PMID: 30050507 PMCID: PMC6052351 DOI: 10.3389/fmicb.2018.01475] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 06/13/2018] [Indexed: 01/29/2023] Open
Abstract
Antimicrobial potential of a dairy-origin probiotic bacteria, Propionibacterium freudenreichii, against multidrug-resistant Salmonella Heidelberg (SH) in turkey poults was determined in the current study. Employing in vitro experiments, two strains (subsp.) of P. freudenreichii: P. freudenreichii freudenreichii B3523 (PF) and P. freudenreichii shermanii B4327 (PS) were tested for their ability to resist low pH (2.5) and bile salts (0.3%). In addition, the ability of the strains to adhere to and invade avian epithelial cells was determined after exposure to Propionibacterium strains followed by SH challenge. Moreover, the antibacterial activity of the strains' cell-free culture supernatants (CFCSs) were tested against three major foodborne pathogens, including SH. Furthermore, the susceptibility of the strains to common antibiotics used for human therapy was determined. The hemolytic properties of the strains were determined in comparison to Streptococcus pyogenes, a known hemolysis-causing pathogen. Appropriate controls were kept in all studies. Using two in vivo experiments, PF was tested against SH colonization of poult ceca and dissemination to liver and spleen. The four treatment groups were: negative control, PF control (PFC), SH control (SC), and a test group (PFS; PF + SH). The poults in the PFC and PFS groups were inoculated with 1010 CFU ml-1 PF on day 1 through crop gavage and subsequently supplemented through drinking water. On day 7, SC and PFS groups were challenged with SH at 106 CFU ml-1, and after 7 days, cecum, liver, and spleen were collected for determining surviving SH populations. Results indicated that both PF and PS resisted pH = 2.5 and 0.3% bile salts with surviving populations comparable to the control and adhered well onto the avian epithelial cell lines. The strains were susceptible to antibiotics and did not invade the epithelial cells or exhibit hemolytic properties. The CFCSs were highly bactericidal against all tested pathogens. In turkey poults, PF significantly reduced cecal colonization of SH and the dissemination of the pathogen to the liver, compared to the SH challenge controls (P < 0.05). Results revealed that PF, a non-host gastrointestinal tract-derived probiotic, could be an antibiotic alternative to prevent the early colonization of SH in poults, improving the preharvest safety of turkeys.
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Affiliation(s)
| | - Anup Kollanoor Johny
- Department of Animal Science, University of Minnesota, Saint Paul, MN, United States
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Delgado-Suárez EJ, Selem-Mojica N, Ortiz-López R, Gebreyes WA, Allard MW, Barona-Gómez F, Rubio-Lozano MS. Whole genome sequencing reveals widespread distribution of typhoidal toxin genes and VirB/D4 plasmids in bovine-associated nontyphoidal Salmonella. Sci Rep 2018; 8:9864. [PMID: 29959369 PMCID: PMC6026178 DOI: 10.1038/s41598-018-28169-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 05/23/2018] [Indexed: 01/23/2023] Open
Abstract
Nontyphoidal Salmonella (NTS) is a common pathogen in food-producing animals and a public health concern worldwide. Various NTS serovars may be present in apparently healthy animals. This could result in carcass contamination during the slaughter process leading to human exposure. While most genomic research has focused on Salmonella pathogenesis, little is known on the factors associated with subclinical infections and environmental persistence. We report here the widespread distribution of typhoidal toxin genes (i. e. the cdtB islet, hlyE, taiA), among NTS strains from a beef slaughter operation (n = 39) and from epidemiologically unconnected ground beef (n = 20). These genes were present in 76% of the strains, regardless of serovar, isolation source or geographical location. Moreover, strains that predominated in the slaughterhouse carry plasmid-borne type IV secretion systems (T4SS), which have been linked to persistent infections in numerous pathogens. Population genomics supports clonal dissemination of NTS along the food production chain, highlighting its role as reservoir of genetic variability in the environment. Overall, the study provides a thorough characterization of serovar diversity and genomic features of beef-associated NTS in Mexico. Furthermore, it reveals how common genetic factors could partially explain the emergence and persistence of certain NTS serovars in the beef industry.
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Affiliation(s)
- Enrique Jesús Delgado-Suárez
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Mexico City, 04510, Mexico.
| | - Nelly Selem-Mojica
- Evolution of Metabolic Diversity Laboratory, Unidad de Genómica Avanzada (Langebio), Cinvestav-IPN, Irapuato, 36821, Mexico
| | - Rocío Ortiz-López
- Centro de Investigación y Desarrollo en Ciencias de la Salud, Universidad Autónoma de Nuevo León, Monterrey, 66460, Mexico
- Tecnológico de Monterrey, School of Medicine and Health Sciences, Monterrey, 64710, Mexico
| | | | - Marc W Allard
- Office of Regulatory Science, Center for Food Safety and Applied Nutrition, U. S. Food and Drug Administration, College Park, 20740, USA
| | - Francisco Barona-Gómez
- Evolution of Metabolic Diversity Laboratory, Unidad de Genómica Avanzada (Langebio), Cinvestav-IPN, Irapuato, 36821, Mexico.
| | - María Salud Rubio-Lozano
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Mexico City, 04510, Mexico
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Ricke SC, Kim SA, Shi Z, Park SH. Molecular-based identification and detection of Salmonella in food production systems: current perspectives. J Appl Microbiol 2018; 125:313-327. [PMID: 29675864 DOI: 10.1111/jam.13888] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Revised: 04/03/2018] [Accepted: 04/10/2018] [Indexed: 12/25/2022]
Abstract
Salmonella remains a prominent cause of foodborne illnesses and can originate from a wide range of food products. Given the continued presence of pathogenic Salmonella in food production systems, there is a consistent need to improve identification and detection methods that can identify this pathogen at all stages in food systems. Methods for subtyping have evolved over the years, and the introduction of whole genome sequencing and advancements in PCR technologies have greatly improved the resolution for differentiating strains within a particular serovar. This, in turn, has led to the continued improvement in Salmonella detection technologies for utilization in food production systems. In this review, the focus will be on recent advancements in these technologies, as well as potential issues associated with the application of these tools in food production. In addition, the recent and emerging research developments on Salmonella detection and identification methodologies and their potential application in food production systems will be discussed.
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Affiliation(s)
- S C Ricke
- Department of Food Science, Center for Food Safety, University of Arkansas, Fayetteville, AR, USA
| | - S A Kim
- Department of Food Science, Center for Food Safety, University of Arkansas, Fayetteville, AR, USA
| | - Z Shi
- Department of Food Science, Center for Food Safety, University of Arkansas, Fayetteville, AR, USA
| | - S H Park
- Department of Food Science, Center for Food Safety, University of Arkansas, Fayetteville, AR, USA
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Abstract
The genus Lactobacillus encompasses a diversity of species that occur widely in nature and encode a plethora of metabolic pathways reflecting their adaptation to various ecological niches, including humans, animals, plants and food products. Accordingly, their functional attributes have been exploited industrially and several strains are commonly formulated as probiotics or starter cultures in the food industry. Although divergent evolutionary processes have yielded the acquisition and evolution of specialized functionalities, all Lactobacillus species share a small set of core metabolic properties, including the glycolysis pathway. Thus, the sequences of glycolytic enzymes afford a means to establish phylogenetic groups with the potential to discern species that are too closely related from a 16S rRNA standpoint. Here, we identified and extracted glycolysis enzyme sequences from 52 species, and carried out individual and concatenated phylogenetic analyses. We show that a glycolysis-based phylogenetic tree can robustly segregate lactobacilli into distinct clusters and discern very closely related species. We also compare and contrast evolutionary patterns with genome-wide features and transcriptomic patterns, reflecting genomic drift trends. Overall, results suggest that glycolytic enzymes provide valuable phylogenetic insights and may constitute practical targets for evolutionary studies.
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Affiliation(s)
- Katelyn Brandt
- 1Genomic Sciences Graduate Program, North Carolina State University, Raleigh, NC 27695, USA.,2Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - Rodolphe Barrangou
- 1Genomic Sciences Graduate Program, North Carolina State University, Raleigh, NC 27695, USA.,2Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC 27695, USA
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Ngueng Feze I, Dalpé G, Song L, Farber J, Goodridge L, Levesque RC, Joly Y. For the Safety of Fresh Produce: Regulatory Considerations for Canada on the Use of Whole Genome Sequencing to Subtype Salmonella. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2018. [DOI: 10.3389/fsufs.2018.00021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Oniciuc EA, Likotrafiti E, Alvarez-Molina A, Prieto M, Santos JA, Alvarez-Ordóñez A. The Present and Future of Whole Genome Sequencing (WGS) and Whole Metagenome Sequencing (WMS) for Surveillance of Antimicrobial Resistant Microorganisms and Antimicrobial Resistance Genes across the Food Chain. Genes (Basel) 2018; 9:E268. [PMID: 29789467 PMCID: PMC5977208 DOI: 10.3390/genes9050268] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Revised: 05/14/2018] [Accepted: 05/15/2018] [Indexed: 12/21/2022] Open
Abstract
Antimicrobial resistance (AMR) surveillance is a critical step within risk assessment schemes, as it is the basis for informing global strategies, monitoring the effectiveness of public health interventions, and detecting new trends and emerging threats linked to food. Surveillance of AMR is currently based on the isolation of indicator microorganisms and the phenotypic characterization of clinical, environmental and food strains isolated. However, this approach provides very limited information on the mechanisms driving AMR or on the presence or spread of AMR genes throughout the food chain. Whole-genome sequencing (WGS) of bacterial pathogens has shown potential for epidemiological surveillance, outbreak detection, and infection control. In addition, whole metagenome sequencing (WMS) allows for the culture-independent analysis of complex microbial communities, providing useful information on AMR genes occurrence. Both technologies can assist the tracking of AMR genes and mobile genetic elements, providing the necessary information for the implementation of quantitative risk assessments and allowing for the identification of hotspots and routes of transmission of AMR across the food chain. This review article summarizes the information currently available on the use of WGS and WMS for surveillance of AMR in foodborne pathogenic bacteria and food-related samples and discusses future needs that will have to be considered for the routine implementation of these next-generation sequencing methodologies with this aim. In particular, methodological constraints that impede the use at a global scale of these high-throughput sequencing (HTS) technologies are identified, and the standardization of methods and protocols is suggested as a measure to upgrade HTS-based AMR surveillance schemes.
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Affiliation(s)
- Elena A Oniciuc
- Faculty of Food Science and Engineering, Dunarea de Jos University of Galati, Galati 800008, Romania.
| | - Eleni Likotrafiti
- Laboratory of Food Microbiology, Department of Food Technology, Alexander Technological Educational Institute of Thessaloniki, Thessaloniki T.K. 57400, Greece.
| | - Adrián Alvarez-Molina
- Department of Food Hygiene and Technology and Institute of Food Science and Technology, Universidad de León, 24071 León, Spain.
| | - Miguel Prieto
- Department of Food Hygiene and Technology and Institute of Food Science and Technology, Universidad de León, 24071 León, Spain.
| | - Jesús A Santos
- Department of Food Hygiene and Technology and Institute of Food Science and Technology, Universidad de León, 24071 León, Spain.
| | - Avelino Alvarez-Ordóñez
- Department of Food Hygiene and Technology and Institute of Food Science and Technology, Universidad de León, 24071 León, Spain.
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