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Genome-Wide Searching Single Nucleotide-Polymorphisms (SNPs) and SNPs-Targeting a Multiplex Primer for Identification of Common Salmonella Serotypes. Pathogens 2022; 11:pathogens11101075. [PMID: 36297133 PMCID: PMC9611365 DOI: 10.3390/pathogens11101075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 09/15/2022] [Accepted: 09/16/2022] [Indexed: 12/04/2022] Open
Abstract
A rapid and high-quality single-nucleotide polymorphisms (SNPs)-based method was developed to improve detection and reduce salmonellosis burden. In this study, whole-genome sequence (WGS) was used to investigate SNPs, the most common genetic marker for identifying bacteria. SNP-sites encompassing 15 sets of primers (666–863 bp) were selected and used to amplify the target Salmonella serovar strains, and the amplified products were sequenced. The prevalent Salmonella enterica subspecies enterica serovars, including Typhimurium; Enteritidis, Agona, enterica, Typhi, and Abony, were amplified and sequenced. The amplified sequences of six Salmonella serovars with 15 sets of SNP-sites encompassing primers were aligned, explored SNPs, and SNPs-carrying primers (23 sets) were designed to develop a multiplex PCR marker (m-PCR). Each primer exists in at least two SNPs bases at the 3′ end of each primer, such as one was wild, and another was a mismatched base by transition or transversion mutation. Thus, twenty-three sets of SNP primers (242–670 bp), including 13 genes (SBG, dedA, yacG, mrcB, mesJ, metN, rihA/B, modA, hutG, yehX, ybiY, moeB, and sopA), were developed for PCR confirmation of target Salmonella serovar strains. Finally, the SNPs in four genes, including fliA gene (S. Enteritidis), modA (S. Agona and S. enterica), sopA (S. Abony), and mrcB (S. Typhimurium and S. Typhi), were used for detection markers of six target Salmonella serotypes. We developed an m-PCR primer set in which Salmonella serovars were detected in a single reaction. Nevertheless, m-PCR was validated with 21 Salmonella isolates (at least one isolate was taken from one positive animal fecal, and n = 6 reference Salmonella strains) and non-Salmonella bacteria isolates. The SNP-based m-PCR method would identify prevalent Salmonella serotypes, minimize the infection, and control outbreaks.
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Guard J. Through the Looking Glass: Genome, Phenome, and Interactome of Salmonella enterica. Pathogens 2022; 11:pathogens11050581. [PMID: 35631102 PMCID: PMC9144603 DOI: 10.3390/pathogens11050581] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/10/2022] [Accepted: 05/11/2022] [Indexed: 11/16/2022] Open
Abstract
This review revisits previous concepts on biological phenomenon contributing to the success of the Salmonella enterica subspecies I as a pathogen and expands upon them to include progress in epidemiology based on whole genome sequencing (WGS). Discussion goes beyond epidemiological uses of WGS to consider how phenotype, which is the biological character of an organism, can be correlated with its genotype to develop a knowledge of the interactome. Deciphering genome interactions with proteins, the impact of metabolic flux, epigenetic modifications, and other complex biochemical processes will lead to new therapeutics, control measures, environmental remediations, and improved design of vaccines.
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Affiliation(s)
- Jean Guard
- U. S. Department of Agriculture, Agricultural Research Service, U. S. National Poultry Research Center, 950 College Station Road, Athens, GA 30605, USA
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Shah DH, Board MM, Crespo R, Guard J, Paul NC, Faux C. The occurrence of Salmonella, extended-spectrum β-lactamase producing Escherichia coli and carbapenem resistant non-fermenting Gram-negative bacteria in a backyard poultry flock environment. Zoonoses Public Health 2020; 67:742-753. [PMID: 32710700 DOI: 10.1111/zph.12756] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 04/30/2020] [Accepted: 06/15/2020] [Indexed: 12/15/2022]
Abstract
Increase in the number of small-scale backyard poultry flocks in the USA has substantially increased human-to-live poultry contact, leading to increased public health risks of the transmission of multi-drug resistant (MDR) zoonotic and food-borne bacteria. The objective of this study was to detect the occurrence of Salmonella and MDR Gram-negative bacteria (GNB) in the backyard poultry flock environment. A total of 34 backyard poultry flocks in Washington State (WA) were sampled. From each flock, one composite coop sample and three drag swabs from nest floor, waterer-feeder, and a random site with visible faecal smearing, respectively, were collected. The samples were processed for isolation of Salmonella and other fermenting and non-fermenting GNB under ceftiofur selection. Each isolate was identified to species level using MALDI-TOFF and tested for resistance against 16 antibiotics belonging to eight antibiotic classes. Salmonella serovar 1,4,[5],12:i:- was isolated from one (3%) out of 34 flocks. Additionally, a total of 133 ceftiofur resistant (CefR ) GNB including Escherichia coli (53), Acinetobacter spp. (45), Pseudomonas spp. (22), Achromobacter spp. (8), Bordetella trematum (1), Hafnia alvei (1), Ochrobactrum intermedium (1), Raoultella ornithinolytica (1), and Stenotrophomonas maltophilia (1) were isolated. Of these, 110 (82%) isolates displayed MDR. Each flock was found positive for the presence of one or more CefR GNB. Several MDR E. coli (n = 15) were identified as extended-spectrum β-lactamase (ESBL) positive. Carbapenem resistance was detected in non-fermenting GNB including Acinetobacter spp. (n = 20), Pseudomonas spp. (n = 11) and Stenotrophomonas maltophila (n = 1). ESBL positive E. coli and carbapenem resistant non-fermenting GNB are widespread in the backyard poultry flock environment in WA State. These GNB are known to cause opportunistic infections, especially in immunocompromised hosts. Better understanding of the ecology and epidemiology of these GNB in the backyard poultry flock settings is needed to identify potential risks of transmission to people in proximity.
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Affiliation(s)
- Devendra H Shah
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA, USA
| | - Melissa M Board
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA, USA
| | - Rocio Crespo
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA, USA
| | - Jean Guard
- US National Poultry Research Center, United States Department of Agriculture, Athens, GA, USA
| | - Narayan C Paul
- Texas A & M Veterinary Medical Diagnostic Laboratory, College Station, TX, USA
| | - Cynthia Faux
- Integrative Physiology and Neuroscience, Washington State University, Pullman, WA, USA
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Ducey TF, Durso LM, Ibekwe AM, Dungan RS, Jackson CR, Frye JG, Castleberry BL, Rashash DMC, Rothrock MJ, Boykin D, Whitehead TR, Ramos Z, McManus M, Cook KL. A newly developed Escherichia coli isolate panel from a cross section of U.S. animal production systems reveals geographic and commodity-based differences in antibiotic resistance gene carriage. JOURNAL OF HAZARDOUS MATERIALS 2020; 382:120991. [PMID: 31446353 DOI: 10.1016/j.jhazmat.2019.120991] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 08/08/2019] [Accepted: 08/08/2019] [Indexed: 06/10/2023]
Abstract
There are limited numbers of Escherichia coli isolate panels that represent United States food animal production. The majority of existing Escherichia coli isolate panels are typically designed: (i) to optimize genetic and/or phenotypic diversity; or (ii) focus on human isolates. To address this shortfall in agriculturally-related resources, we have assembled a publicly-available isolate panel (AgEc) from the four major animal production commodities in the United States, including beef, dairy, poultry, and swine, as well as isolates from agriculturally-impacted environments, and other commodity groups. Diversity analyses by phylotyping and Pulsed-field Gel Electrophoresis revealed a highly diverse composition, with the 300 isolates clustered into 71 PFGE sub-types based upon an 80% similarity cutoff. To demonstrate the panel's utility, tetracycline and sulfonamide resistance genes were assayed, which identified 131 isolates harboring genes involved in tetracycline resistance, and 41 isolates containing sulfonamide resistance genes. There was strong overlap in the two pools of isolates, 38 of the 41 isolates harboring sulfonamide resistance genes also contained tetracycline resistance genes. Analysis of antimicrobial resistance gene patterns revealed significant differences along commodity and geographical lines. This panel therefore provides the research community an E. coli isolate panel for study of issues pertinent to U.S. food animal production.
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Affiliation(s)
- Thomas F Ducey
- Coastal Plains Soil, Water, and Plant Research Center, Agricultural Research Service, Department of Agriculture, Florence, SC, United States.
| | - Lisa M Durso
- Agroecosystem Management Research Unit, Agricultural Research Service, Department of Agriculture, Lincoln, NE, United States
| | - Abasiofiok M Ibekwe
- U.S. Salinity Laboratory, Agricultural Research Service, Department of Agriculture, Riverside, CA, United States
| | - Robert S Dungan
- Northwest Irrigation and Soils Research Laboratory, Agricultural Research Service, Department of Agriculture, Kimberly, ID, United States
| | - Charlene R Jackson
- Bacterial Epidemiology & Antimicrobial Resistance Research Unit, U.S. National Poultry Research Center, Agricultural Research Service, Department of Agriculture, Athens, GA, United States
| | - Jonathan G Frye
- Bacterial Epidemiology & Antimicrobial Resistance Research Unit, U.S. National Poultry Research Center, Agricultural Research Service, Department of Agriculture, Athens, GA, United States
| | - B Lana Castleberry
- Livestock Nutrient Management Research Unit, Agricultural Research Service, Department of Agriculture, Bushland, TX, United States
| | - Diana M C Rashash
- North Carolina Cooperative Extension Service, Jacksonville, NC, United States
| | - Michael J Rothrock
- Egg Safety & Quality Research Unit, U.S. National Poultry Research Center, Agricultural Research Service, Department of Agriculture, Athens, GA, United States
| | - Debbie Boykin
- Jamie Whitten Delta States Research Center, Agricultural Research Service, Department of Agriculture, Stoneville, MS, United States
| | - Terence R Whitehead
- Bioenergy Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, Department of Agriculture, Peoria, IL, United States
| | - Zeanmarj Ramos
- South Carolina Governor's School for Science and Mathematics, Hartsville, SC, United States
| | - Morgan McManus
- South Carolina Governor's School for Science and Mathematics, Hartsville, SC, United States
| | - Kimberly L Cook
- Bacterial Epidemiology & Antimicrobial Resistance Research Unit, U.S. National Poultry Research Center, Agricultural Research Service, Department of Agriculture, Athens, GA, United States
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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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Serotyping of Salmonella Enterica Isolated from Mice Caught on US Poultry Farms 1995 through 1998. Food Saf (Tokyo) 2018; 6:44-50. [PMID: 32231946 DOI: 10.14252/foodsafetyfscj.2017022] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 03/06/2018] [Indexed: 11/21/2022] Open
Abstract
In this study, a collection of Salmonella enterica subspecies obtained from live mice caught on 32 poultry farms in the Northeast US between 1995 to 1998 was evaluated to provide a historical reference for serotype distribution during a time when egg contamination by serotype Enteritidis was at its peak. Of 821 mice cultured, 157 were positive (19.1%). Seven mice harbored two serotypes of Salmonella. Nine serotypes were detected, eight of which are often associated with foodborne illness. The three most prevalent serotypes were Enteritidis, Heidelberg, and Typhimurium. Enteritidis and Typhimurium were obtained from both spleens and intestines without preference according to type of sample. In contrast, Heidelberg was isolated most often from intestines and Schwarzengrund was most often obtained from spleens. These results support that the house mouse Mus musculus was a risk factor for introduction of multiple pathogenic Salmonella serotypes in poultry raised in the Northeast US during the mid-1990s. Isolates were submitted to the Food and Drug Administration and draft genomes for 64 isolates of Salmonella enterica serovar Enteritidis data have been released through the National Center for Biotechnology Information via the GenomeTrakr network.
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