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Kim MB, Lee YJ. Emergence of Salmonella Infantis carrying the pESI-like plasmid from eggs in egg grading and packing plants in Korea. Food Microbiol 2024; 122:104568. [PMID: 38839227 DOI: 10.1016/j.fm.2024.104568] [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] [Received: 03/04/2024] [Revised: 05/13/2024] [Accepted: 05/24/2024] [Indexed: 06/07/2024]
Abstract
The plasmid of emerging S. Infantis (pESI) or pESI-like plasmid in Salmonella enterica Infantis are consistently reported in poultry and humans worldwide. However, there has been limited research on these plasmids of S. Infantis isolated from eggs. Therefore, this study aimed to analyze the prevalence and characteristics of S. Infantis carrying the pESI-like plasmid from eggs in egg grading and packing plants. In this study, the pESI-like plasmid was only detected in 18 (78.3%) of 23 S. Infantis isolates, and it was absent in the other 9 Salmonella serovars. In particular, S. Infantis isolates carrying the pESI-like plasmid showed the significantly higher resistance to β-lactams, phenicols, cephams, aminoglycosides, quinolones, sulfonamides, and tetracyclines than Salmonella isolates without the pESI-like plasmid (p < 0.05). Moreover, all S. Infantis isolates carrying the pESI-like plasmid were identified as extended-spectrum β-lactamase (ESBL) producer, harboring the blaCTX-M-65 and blaTEM-1 genes, and carried non-β-lactamase resistance genes (ant(3'')-Ia, aph(4)-Ia, aac(3)-IVa, aph(3')-Ic, sul1, tetA, dfrA14, and floR) against five antimicrobial classes. However, all isolates without the pESI-like plasmid only carried the blaTEM-1 gene among the β-lactamase genes, and either had no non-β-lactamase resistance genes or harbored non-β-lactamase resistance genes against one or two antimicrobial classes. Furthermore, all S. Infantis isolates carrying the pESI-like plasmid carried class 1 and 2 integrons and the aadA1 gene cassette, but none of the other isolates without the pESI-like plasmid harbored integrons. In particular, D87Y substitution in the gyrA gene and IncP replicon type were observed in all the S. Infantis isolates carrying the pESI-like plasmid but not in the S. Infantis isolates without the pESI-like plasmid. The distribution of pulsotypes between pESI-positive and pESI-negative S. Infantis isolates was clearly distinguished, but all S. Infantis isolates were classified as sequence type 32, regardless of whether they carried the pESI-like plasmid. This study is the first to report the characteristics of S. Infantis carrying the pESI-like plasmid isolated from eggs and can provide valuable information for formulating strategies to control the spread of Salmonella in the egg industry worldwide.
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Affiliation(s)
- Min Beom Kim
- College of Veterinary Medicine & Institute for Veterinary Biomedical Science, Kyungpook National University, Daegu, 41556, Republic of Korea.
| | - Young Ju Lee
- College of Veterinary Medicine & Institute for Veterinary Biomedical Science, Kyungpook National University, Daegu, 41556, Republic of Korea.
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Molina A, Thye T, Muñoz-Vargas L, Zamora-Sanabria R, Chercos DH, Hernández-Rojas R, Robles N, Aguilar D, May J, Dekker D. Molecular characterization of antibiotic resistant Salmonella enterica across the poultry production chain in Costa Rica: A cross-sectional study. Int J Food Microbiol 2024; 416:110663. [PMID: 38503221 DOI: 10.1016/j.ijfoodmicro.2024.110663] [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] [Received: 09/06/2023] [Revised: 02/07/2024] [Accepted: 03/04/2024] [Indexed: 03/21/2024]
Abstract
Antibiotic resistant Salmonella enterica are on the increase, worldwide. Given the scarcity of data, this study aimed to investigate its occurrence, virulence, and antibiotic resistance in Costa Rica's food chain. In total, 65 chicken meat- and 171 chicken caecal samples were collected and examined for Salmonella. High frequencies of Salmonella were found in chicken meat (58.5 %, n/N = 38/65) and poultry farms (38.0 %, n/N = 65/171). The majority of Salmonella from chicken meat (89.5 %, n/N = 34/38) and caecum samples (93.6 %, n/N = 59/63) exhibited multidrug resistance (MDR). Serovar Infantis was the most prevalent (94 %, n/N = 67/71), followed by serovars Anatum and Kentucky (3 %, n/N = 2/71). A pESI-like plasmid (92 %, n/N = 65/71) containing virulence and resistance markers was found in S. Infantis. Given the high prevalence of MDR Salmonella, this study emphasizes the need to enhance surveillance systems for foodborne pathogens and antimicrobial resistance in Costa Rica's food production chain.
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Affiliation(s)
- Andrea Molina
- Escuela de Zootecnia, Universidad de Costa Rica, 11501-2060 Ciudad Universitaria Rodrigo Facio, San José, Costa Rica; Infectious Diseases Epidemiology Department, Bernhard Nocht Institute for Tropical Medicine (BNITM), 20359 Hamburg, Germany.
| | - Thorsten Thye
- Infectious Diseases Epidemiology Department, Bernhard Nocht Institute for Tropical Medicine (BNITM), 20359 Hamburg, Germany
| | - Lohendy Muñoz-Vargas
- Escuela de Medicina Veterinaria, Universidad Nacional, 304-3000 Heredia, Costa Rica
| | - Rebeca Zamora-Sanabria
- Escuela de Zootecnia, Universidad de Costa Rica, 11501-2060 Ciudad Universitaria Rodrigo Facio, San José, Costa Rica
| | - Daniel Haile Chercos
- Department of Implementation Research, One Health Bacteriology Group, Bernhard Nocht Institute for Tropical Medicine (BNITM), Hamburg, Germany
| | | | - Noelia Robles
- Facultad de Microbiología, Universidad de Costa Rica, 11501-2060 Ciudad Universitaria Rodrigo Facio, San José, Costa Rica
| | - Daniela Aguilar
- Facultad de Microbiología, Universidad de Costa Rica, 11501-2060 Ciudad Universitaria Rodrigo Facio, San José, Costa Rica
| | - Jürgen May
- Infectious Diseases Epidemiology Department, Bernhard Nocht Institute for Tropical Medicine (BNITM), 20359 Hamburg, Germany; German Center for Infection Research (DZIF), Hamburg-Borstel-Luebeck-Riems, Germany; University Medical Centre Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Denise Dekker
- Department of Implementation Research, One Health Bacteriology Group, Bernhard Nocht Institute for Tropical Medicine (BNITM), Hamburg, Germany
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Powell MR, Williams MS. Trends in Salmonella Infantis human illness incidence and chicken carcass prevalence in the United States; 1996-2019. RISK ANALYSIS : AN OFFICIAL PUBLICATION OF THE SOCIETY FOR RISK ANALYSIS 2024. [PMID: 38616416 DOI: 10.1111/risa.14311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 02/22/2024] [Accepted: 04/03/2024] [Indexed: 04/16/2024]
Abstract
The incidence of human illness due to Salmonella Infantis reported to Foodborne Diseases Active Surveillance Network and the prevalence of Infantis on chicken carcasses reported by the United States Department of Agriculture Food Safety and Inspection Service have increased significantly in the past decade. However, the trends do not appear coincident, as would be expected if the increased prevalence in chicken led to the increase in the incidence of human illness. Salmonella Infantis incidence and prevalence trends are analyzed using penalized B-spline methods for generalized additive regression models. The association between the two time series is analyzed using time-lagged rank-order cross-correlation. Geographic variations in reported incidence and trends are also explored. The increase in human incidence of Salmonella Infantis began circa 2011. The increase in chicken carcass prevalence began circa 2015. A 4-year lag on chicken carcass prevalence maximizes the rank-order cross-correlation with the incidence of illness. While chicken consumption undoubtedly contributes to the incidence of human illness due to Salmonella Infantis, the initial increase in reported illness was likely due to one or more other transmission pathways. Other potential transmission pathways include non-chicken foodborne, waterborne, person-to-person, animal contact, and environmental.
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Affiliation(s)
- Mark R Powell
- Office of Risk Assessment and Cost Benefit Analysis, US Department of Agriculture, Washington, DC, USA
| | - Michael S Williams
- Food Safety and Inspection Service, US Department of Agriculture, Fort Collins, Colorado, USA
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4
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Kim MB, Jung HR, Lee YJ. Emergence of Salmonella Infantis carrying the pESI megaplasmid in commercial farms of five major integrated broiler operations in Korea. Poult Sci 2024; 103:103516. [PMID: 38368739 PMCID: PMC10884471 DOI: 10.1016/j.psj.2024.103516] [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] [Received: 12/18/2023] [Revised: 01/25/2024] [Accepted: 01/26/2024] [Indexed: 02/20/2024] Open
Abstract
Considering Salmonella transmission occurs through several routes in integrated broiler operations, control of nontyphoidal Salmonella in commercial farms is essential. This study aimed to compare the distribution of persistent Salmonella serovars in environments and dead chickens between 5 major integrated broiler operations in Korea. The prevalence of Salmonella-positive farms in dust prior to placement by operations was 0 to 25%, but the prevalence in dust and feces at the time of depletion was increased to 16.7 to 41.7% and 16.7 to 66.7%, respectively. Moreover, the prevalence of farms with Salmonella in chickens that died within 1 week old and at 4 to 5 weeks old ranged from 8.3 to 58.3% and 16.7 to 41.7%, respectively. The prevalence of Salmonella enterica serovar Infantis-positive farms in dust prior to placement and in chickens that died within 1 week old was 5.2 and 3.4%, respectively, but the prevalence in dust and feces at the time of depletion and in chickens that died at 4 to 5 weeks old was significantly increased to 27.6, 41.4, and 20.7%, respectively (P < 0.05). Interestingly, the plasmid of emerging S. Infantis (pESI) was only identified in S. Infantis, and the prevalence of multidrug-resistance was significantly higher in pESI-positive S. Infantis (99.2%) than in pESI-negative S. Infantis (6.7%) (P < 0.05). The distribution of pulsotypes between pESI-positive and pESI-negative S. Infantis were varied, but a majority of S. Infantis were clustered only 2 pulsotypes. Moreover, pESI-positive S. Infantis harbored more virulence factors than pESI-negative S. Infantis. This study is the first report on characteristics of S. Infantis carrying the pESI plasmid in commercial broiler farms in Korea.
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Affiliation(s)
- Min Beom Kim
- College of Veterinary Medicine & Institute for Veterinary Biomedical Science, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Hye-Ri Jung
- College of Veterinary Medicine & Institute for Veterinary Biomedical Science, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Young Ju Lee
- College of Veterinary Medicine & Institute for Veterinary Biomedical Science, Kyungpook National University, Daegu 41566, Republic of Korea.
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5
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Mattock J, Chattaway MA, Hartman H, Dallman TJ, Smith AM, Keddy K, Petrovska L, Manners EJ, Duze ST, Smouse S, Tau N, Timme R, Baker DJ, Mather AE, Wain J, Langridge GC. A One Health Perspective on Salmonella enterica Serovar Infantis, an Emerging Human Multidrug-Resistant Pathogen. Emerg Infect Dis 2024; 30:701-710. [PMID: 38526070 PMCID: PMC10977846 DOI: 10.3201/eid3004.231031] [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: 03/26/2024] Open
Abstract
Salmonella enterica serovar Infantis presents an ever-increasing threat to public health because of its spread throughout many countries and association with high levels of antimicrobial resistance (AMR). We analyzed whole-genome sequences of 5,284 Salmonella Infantis strains from 74 countries, isolated during 1989-2020 from a wide variety of human, animal, and food sources, to compare genetic phylogeny, AMR determinants, and plasmid presence. The global Salmonella Infantis population structure diverged into 3 clusters: a North American cluster, a European cluster, and a global cluster. The levels of AMR varied by Salmonella Infantis cluster and by isolation source; 73% of poultry isolates were multidrug resistant, compared with 35% of human isolates. This finding correlated with the presence of the pESI megaplasmid; 71% of poultry isolates contained pESI, compared with 32% of human isolates. This study provides key information for public health teams engaged in reducing the spread of this pathogen.
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Affiliation(s)
| | - Marie Anne Chattaway
- University of East Anglia, Norwich, UK (J. Mattock, E.J. Manners, A.E. Mather, J. Wain)
- UK Health Security Agency, London, UK (M.A. Chattaway, H. Hartman, T.J. Dallman)
- National Institute for Communicable Diseases, Johannesburg, South Africa (A.M. Smith, S. Smouse, N. Tau)
- University of Pretoria, Pretoria, South Africa (K. Keddy)
- Animal and Plant Health Agency, Addlestone, UK (L. Petrovska)
- University of the Witwatersrand, Johannesburg (S.T. Duze)
- US Food and Drug Administration, College Park, Maryland, USA (R. Timme)
- Quadram Institute Bioscience, Norwich (D.J. Baker, A.E. Mather, J. Wain, G.C. Langridge)
| | - Hassan Hartman
- University of East Anglia, Norwich, UK (J. Mattock, E.J. Manners, A.E. Mather, J. Wain)
- UK Health Security Agency, London, UK (M.A. Chattaway, H. Hartman, T.J. Dallman)
- National Institute for Communicable Diseases, Johannesburg, South Africa (A.M. Smith, S. Smouse, N. Tau)
- University of Pretoria, Pretoria, South Africa (K. Keddy)
- Animal and Plant Health Agency, Addlestone, UK (L. Petrovska)
- University of the Witwatersrand, Johannesburg (S.T. Duze)
- US Food and Drug Administration, College Park, Maryland, USA (R. Timme)
- Quadram Institute Bioscience, Norwich (D.J. Baker, A.E. Mather, J. Wain, G.C. Langridge)
| | | | - Anthony M. Smith
- University of East Anglia, Norwich, UK (J. Mattock, E.J. Manners, A.E. Mather, J. Wain)
- UK Health Security Agency, London, UK (M.A. Chattaway, H. Hartman, T.J. Dallman)
- National Institute for Communicable Diseases, Johannesburg, South Africa (A.M. Smith, S. Smouse, N. Tau)
- University of Pretoria, Pretoria, South Africa (K. Keddy)
- Animal and Plant Health Agency, Addlestone, UK (L. Petrovska)
- University of the Witwatersrand, Johannesburg (S.T. Duze)
- US Food and Drug Administration, College Park, Maryland, USA (R. Timme)
- Quadram Institute Bioscience, Norwich (D.J. Baker, A.E. Mather, J. Wain, G.C. Langridge)
| | - Karen Keddy
- University of East Anglia, Norwich, UK (J. Mattock, E.J. Manners, A.E. Mather, J. Wain)
- UK Health Security Agency, London, UK (M.A. Chattaway, H. Hartman, T.J. Dallman)
- National Institute for Communicable Diseases, Johannesburg, South Africa (A.M. Smith, S. Smouse, N. Tau)
- University of Pretoria, Pretoria, South Africa (K. Keddy)
- Animal and Plant Health Agency, Addlestone, UK (L. Petrovska)
- University of the Witwatersrand, Johannesburg (S.T. Duze)
- US Food and Drug Administration, College Park, Maryland, USA (R. Timme)
- Quadram Institute Bioscience, Norwich (D.J. Baker, A.E. Mather, J. Wain, G.C. Langridge)
| | | | | | - Sanelisiwe T. Duze
- University of East Anglia, Norwich, UK (J. Mattock, E.J. Manners, A.E. Mather, J. Wain)
- UK Health Security Agency, London, UK (M.A. Chattaway, H. Hartman, T.J. Dallman)
- National Institute for Communicable Diseases, Johannesburg, South Africa (A.M. Smith, S. Smouse, N. Tau)
- University of Pretoria, Pretoria, South Africa (K. Keddy)
- Animal and Plant Health Agency, Addlestone, UK (L. Petrovska)
- University of the Witwatersrand, Johannesburg (S.T. Duze)
- US Food and Drug Administration, College Park, Maryland, USA (R. Timme)
- Quadram Institute Bioscience, Norwich (D.J. Baker, A.E. Mather, J. Wain, G.C. Langridge)
| | - Shannon Smouse
- University of East Anglia, Norwich, UK (J. Mattock, E.J. Manners, A.E. Mather, J. Wain)
- UK Health Security Agency, London, UK (M.A. Chattaway, H. Hartman, T.J. Dallman)
- National Institute for Communicable Diseases, Johannesburg, South Africa (A.M. Smith, S. Smouse, N. Tau)
- University of Pretoria, Pretoria, South Africa (K. Keddy)
- Animal and Plant Health Agency, Addlestone, UK (L. Petrovska)
- University of the Witwatersrand, Johannesburg (S.T. Duze)
- US Food and Drug Administration, College Park, Maryland, USA (R. Timme)
- Quadram Institute Bioscience, Norwich (D.J. Baker, A.E. Mather, J. Wain, G.C. Langridge)
| | - Nomsa Tau
- University of East Anglia, Norwich, UK (J. Mattock, E.J. Manners, A.E. Mather, J. Wain)
- UK Health Security Agency, London, UK (M.A. Chattaway, H. Hartman, T.J. Dallman)
- National Institute for Communicable Diseases, Johannesburg, South Africa (A.M. Smith, S. Smouse, N. Tau)
- University of Pretoria, Pretoria, South Africa (K. Keddy)
- Animal and Plant Health Agency, Addlestone, UK (L. Petrovska)
- University of the Witwatersrand, Johannesburg (S.T. Duze)
- US Food and Drug Administration, College Park, Maryland, USA (R. Timme)
- Quadram Institute Bioscience, Norwich (D.J. Baker, A.E. Mather, J. Wain, G.C. Langridge)
| | - Ruth Timme
- University of East Anglia, Norwich, UK (J. Mattock, E.J. Manners, A.E. Mather, J. Wain)
- UK Health Security Agency, London, UK (M.A. Chattaway, H. Hartman, T.J. Dallman)
- National Institute for Communicable Diseases, Johannesburg, South Africa (A.M. Smith, S. Smouse, N. Tau)
- University of Pretoria, Pretoria, South Africa (K. Keddy)
- Animal and Plant Health Agency, Addlestone, UK (L. Petrovska)
- University of the Witwatersrand, Johannesburg (S.T. Duze)
- US Food and Drug Administration, College Park, Maryland, USA (R. Timme)
- Quadram Institute Bioscience, Norwich (D.J. Baker, A.E. Mather, J. Wain, G.C. Langridge)
| | - Dave J. Baker
- University of East Anglia, Norwich, UK (J. Mattock, E.J. Manners, A.E. Mather, J. Wain)
- UK Health Security Agency, London, UK (M.A. Chattaway, H. Hartman, T.J. Dallman)
- National Institute for Communicable Diseases, Johannesburg, South Africa (A.M. Smith, S. Smouse, N. Tau)
- University of Pretoria, Pretoria, South Africa (K. Keddy)
- Animal and Plant Health Agency, Addlestone, UK (L. Petrovska)
- University of the Witwatersrand, Johannesburg (S.T. Duze)
- US Food and Drug Administration, College Park, Maryland, USA (R. Timme)
- Quadram Institute Bioscience, Norwich (D.J. Baker, A.E. Mather, J. Wain, G.C. Langridge)
| | - Alison E. Mather
- University of East Anglia, Norwich, UK (J. Mattock, E.J. Manners, A.E. Mather, J. Wain)
- UK Health Security Agency, London, UK (M.A. Chattaway, H. Hartman, T.J. Dallman)
- National Institute for Communicable Diseases, Johannesburg, South Africa (A.M. Smith, S. Smouse, N. Tau)
- University of Pretoria, Pretoria, South Africa (K. Keddy)
- Animal and Plant Health Agency, Addlestone, UK (L. Petrovska)
- University of the Witwatersrand, Johannesburg (S.T. Duze)
- US Food and Drug Administration, College Park, Maryland, USA (R. Timme)
- Quadram Institute Bioscience, Norwich (D.J. Baker, A.E. Mather, J. Wain, G.C. Langridge)
| | - John Wain
- University of East Anglia, Norwich, UK (J. Mattock, E.J. Manners, A.E. Mather, J. Wain)
- UK Health Security Agency, London, UK (M.A. Chattaway, H. Hartman, T.J. Dallman)
- National Institute for Communicable Diseases, Johannesburg, South Africa (A.M. Smith, S. Smouse, N. Tau)
- University of Pretoria, Pretoria, South Africa (K. Keddy)
- Animal and Plant Health Agency, Addlestone, UK (L. Petrovska)
- University of the Witwatersrand, Johannesburg (S.T. Duze)
- US Food and Drug Administration, College Park, Maryland, USA (R. Timme)
- Quadram Institute Bioscience, Norwich (D.J. Baker, A.E. Mather, J. Wain, G.C. Langridge)
| | - Gemma C. Langridge
- University of East Anglia, Norwich, UK (J. Mattock, E.J. Manners, A.E. Mather, J. Wain)
- UK Health Security Agency, London, UK (M.A. Chattaway, H. Hartman, T.J. Dallman)
- National Institute for Communicable Diseases, Johannesburg, South Africa (A.M. Smith, S. Smouse, N. Tau)
- University of Pretoria, Pretoria, South Africa (K. Keddy)
- Animal and Plant Health Agency, Addlestone, UK (L. Petrovska)
- University of the Witwatersrand, Johannesburg (S.T. Duze)
- US Food and Drug Administration, College Park, Maryland, USA (R. Timme)
- Quadram Institute Bioscience, Norwich (D.J. Baker, A.E. Mather, J. Wain, G.C. Langridge)
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6
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Li C, Tate H, Huang X, Hsu CH, Harrison LB, Zhao S, Fortenberry GZ, Dessai U, McDermott PF, Strain EA. The spread of pESI-mediated extended-spectrum cephalosporin resistance in Salmonella serovars-Infantis, Senftenberg, and Alachua isolated from food animal sources in the United States. PLoS One 2024; 19:e0299354. [PMID: 38483966 PMCID: PMC10939224 DOI: 10.1371/journal.pone.0299354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 02/08/2024] [Indexed: 03/17/2024] Open
Abstract
The goal of this study is to investigate the origin, prevalence, and evolution of the pESI megaplasmid in Salmonella isolated from animals, foods, and humans. We queried 510,097 Salmonella genomes under the National Center for Biotechnology Information (NCBI) Pathogen Detection (PD) database for the presence of potential sequences containing the pESI plasmid in animal, food, and environmental sources. The presence of the pESI megaplasmid was confirmed by using seven plasmid-specific markers (rdA, pilL, SogS, TrbA, ipf, ipr2 and IncFIB(pN55391)). The plasmid and chromosome phylogeny of these isolates was inferred from single nucleotide polymorphisms (SNPs). Our search resolved six Salmonella clusters carrying the pESI plasmid. Four were emergent Salmonella Infantis clusters, and one each belonged to serovar Senftenberg and Alachua. The Infantis cluster with a pESI plasmid carrying blaCTX-M-65 gene was the biggest of the four emergent Infantis clusters, with over 10,000 isolates. This cluster was first detected in South America and has since spread widely in United States. Over time the composition of pESI in United States has changed with the average number of resistance genes showing a decrease from 9 in 2014 to 5 in 2022, resulting from changes in gene content in two integrons present in the plasmid. A recent and emerging cluster of Senftenberg, which carries the blaCTX-M-65 gene and is primarily associated with turkey sources, was the second largest in the United States. SNP analysis showed that this cluster likely originated in North Carolina with the recent acquisition of the pESI plasmid. A single Alachua isolate from turkey was also found to carry the pESI plasmid containing blaCTX-M-65 gene. The study of the pESI plasmid, its evolution and mechanism of spread can help us in developing appropriate strategies for the prevention and further spread of this multi-drug resistant plasmid in Salmonella in poultry and humans.
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Affiliation(s)
- Cong Li
- Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, Maryland, United States of America
| | - Heather Tate
- Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, Maryland, United States of America
| | - Xinyang Huang
- Department of Nutrition and Food Science, University of Maryland, College Park, Maryland, United States of America
- Joint Institute for Food Safety and Applied Nutrition, Center for Food Safety Security Systems, University of Maryland,College Park, Maryland, United States of America
| | - Chih-Hao Hsu
- Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, Maryland, United States of America
| | - Lucas B. Harrison
- Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, Maryland, United States of America
| | - Shaohua Zhao
- Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, Maryland, United States of America
| | - Gamola Z. Fortenberry
- Food Safety and Inspection Service, U.S. Department of Agriculture, Athens, Georgia, United States of America
| | - Uday Dessai
- Food Safety and Inspection Service, U.S. Department of Agriculture, Athens, Georgia, United States of America
| | - Patrick F. McDermott
- Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, Maryland, United States of America
| | - Errol A. Strain
- Center for Food Safety and Applied Nutrition, College Park, Maryland, United States of America
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7
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Richards AK, Siceloff AT, Simmons M, Tillman GE, Shariat NW. Poultry Processing Interventions Reduce Salmonella Serovar Complexity on Postchill Young Chicken Carcasses as Determined by Deep Serotyping. J Food Prot 2024; 87:100208. [PMID: 38142825 DOI: 10.1016/j.jfp.2023.100208] [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] [Received: 10/30/2023] [Revised: 12/14/2023] [Accepted: 12/18/2023] [Indexed: 12/26/2023]
Abstract
Nearly 20% of salmonellosis cases are attributed to broilers, with renewed efforts to reduce Salmonella during broiler production and processing. A limitation to Salmonella culture is that often a single colony is picked for characterization, favoring isolation of the most abundant serovar found in a sample, while low abundance serovars can remain undetected. We used a deep serotyping approach, CRISPR-SeroSeq (serotyping by sequencing the clustered regularly interspaced palindromic repeats), to assess Salmonella serovar complexity during broiler processing and to determine the impact of antimicrobial interventions upon serovar population dynamics. Paired hot rehang and postchill young chicken carcasses were collected from establishments across the United States from August to November 2022. CRISPR-SeroSeq was performed on Salmonella culture-positive hot rehang (n = 153) and postchill (n = 38) samples, including 31 paired hot rehang and postchill samples. Multiple serovars were detected in 48.4% (74/153) and 7.9% (3/38) of hot rehang and postchill samples, respectively. On average, hot rehang carcasses contained 1.6 serovars, compared to 1.1 serovars at postchill (Mann Whitney U, p = 0.00018). Nineteen serovars were identified with serovar Kentucky the most common at hot rehang (72.5%; 111/153) and postchill (73.7%; 28/38). Serovar Infantis prevalence was higher at hot rehang (39.9%; 61/153) than in postchill (7.9%; 3/38). At hot rehang, serovar Enteritidis was outnumbered by other serovars 81.3% (13/16) of the time but was always the single or most abundant serovar detected when it was present at postchill (n = 5). We observed 98.4% (188/191) concordance between traditional isolation with serotyping and CRISPR-SeroSeq. Deep serotyping was able to explain serovar discrepancies between paired hot rehang and postchill samples when only traditional isolation and serotyping methods were used. These data demonstrate that processing interventions are effective in reducing Salmonella serovar complexity.
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Affiliation(s)
- Amber K Richards
- Department of Population Health, University of Georgia, Athens, GA, USA
| | - Amy T Siceloff
- Department of Population Health, University of Georgia, Athens, GA, USA
| | - Mustafa Simmons
- Eastern Laboratory, U. S. Department of Agriculture's Food Safety and Inspection Service, Athens, GA, USA
| | - Glenn E Tillman
- Eastern Laboratory, U. S. Department of Agriculture's Food Safety and Inspection Service, Athens, GA, USA
| | - Nikki W Shariat
- Department of Population Health, University of Georgia, Athens, GA, USA; Center for Food Safety, University of Georgia, Griffin, GA, USA.
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8
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Katz TS, Harhay DM, Schmidt JW, Wheeler TL. Identifying a list of Salmonella serotypes of concern to target for reducing risk of salmonellosis. Front Microbiol 2024; 15:1307563. [PMID: 38410382 PMCID: PMC10894960 DOI: 10.3389/fmicb.2024.1307563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 01/25/2024] [Indexed: 02/28/2024] Open
Abstract
There is an increasing awareness in the field of Salmonella epidemiology that focusing control efforts on those serotypes which cause severe human health outcomes, as opposed to broadly targeting all Salmonella, will likely lead to the greatest advances in decreasing the incidence of salmonellosis. Yet, little guidance exists to support validated, scientific selection of target serotypes. The goal of this perspective is to develop an approach to identifying serotypes of greater concern and present a case study using meat- and poultry-attributed outbreaks to examine challenges in developing a standardized framework for defining target serotypes.
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Affiliation(s)
- Tatum S Katz
- U.S. Department of Agriculture, Agricultural Research Service, Roman L. Hruska U.S. Meat Animal Research Center, Clay Center, NE, United States
| | - Dayna M Harhay
- U.S. Department of Agriculture, Agricultural Research Service, Roman L. Hruska U.S. Meat Animal Research Center, Clay Center, NE, United States
| | - John W Schmidt
- U.S. Department of Agriculture, Agricultural Research Service, Roman L. Hruska U.S. Meat Animal Research Center, Clay Center, NE, United States
| | - Tommy L Wheeler
- U.S. Department of Agriculture, Agricultural Research Service, Roman L. Hruska U.S. Meat Animal Research Center, Clay Center, NE, United States
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9
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Russo I, Fischer J, Uelze L, Napoleoni M, Schiavano GF, Andreoni F, Brandi G, Amagliani G. From farm to fork: Spread of a multidrug resistant Salmonella Infantis clone encoding bla CTX-M-1 on pESI-like plasmids in Central Italy. Int J Food Microbiol 2024; 410:110490. [PMID: 37992554 DOI: 10.1016/j.ijfoodmicro.2023.110490] [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] [Received: 08/04/2023] [Revised: 10/24/2023] [Accepted: 11/11/2023] [Indexed: 11/24/2023]
Abstract
Salmonella enterica subsp. enterica serovar Infantis (S. Infantis) is one of the "top five Salmonella serovars" of clinical significance in the European Union (EU). Antimicrobial resistant and extended spectrum β-lactamase (ESBL) AmpC-producing S. Infantis have been described in food production systems and human clinical samples in Italy. Recently, an increase of MDR S. Infantis carrying blaCTX-M genes involved in 3rd generation cephalosporin resistance was noticed in the EU, including Italy, mainly due to the spread of S. Infantis harboring a pESI-like plasmid. The aim of this study was to investigate the occurrence of the S. Infantis pESI-like plasmid among antibiotic resistant S. Infantis strains isolated at different points of the food chain, and to provide a phylogenetic analysis to gain further insight on their transmission pathways from 'farm to fork'. MDR S. Infantis strains (n. 35) isolated from 2016 to 2021 at different stages of the food chain (animals, food, food-related environments, and humans) were investigated with in depth molecular characterization using real-time PCR, S1 nuclease pulsed-field gel electrophoresis (S1-PFGE) and whole genome sequencing (WGS). Our study reported the occurrence of S. Infantis strains harboring pESI-like plasmids, carrying blaCTX-M-1 genes, in Central Italy, at different sampling points along the food chain. Results confirmed the presence of a plasmid with a molecular size around 224-310 kb, thus consistent with the pESI-like, in 97 % of the 35 samples investigated. Two variants of S. Infantis pESI-like IncFIB(K)_1_Kpn3 were detected, one associated with the European clone carrying blaCTX-M-1 (21 isolates) and the other associated with U.S. isolates carrying blaCTX-M-65 (2 isolates, pESI-like U.S. variant). The majority was resistant to 3rd generation cephalosporins but none of the strains tested positive for the carbapenemase encoding genes. A total of 118 virulence genes were identified in isolates harboring the pESI-like plasmid. cgMLST and SNP-based analysis revealed the presence of one main cluster, composed by strains isolated from the environment, animals, food and humans. The results of this investigation underline the importance of phylogenetic studies to monitor and understand pathogen and AMR spread in a One Health approach.
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Affiliation(s)
- Ilaria Russo
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, Urbino, Italy
| | - Jennie Fischer
- BfR, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Laura Uelze
- BfR, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Maira Napoleoni
- Regional Reference Center for Enteric Pathogens Marche, Istituto Zooprofilattico Sperimentale dell'Umbria e delle Marche "Togo Rosati", Perugia, Italy
| | | | - Francesca Andreoni
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, Urbino, Italy; Clinical Pathology, Urbino Hospital, AST Pesaro-Urbino, Marche, Urbino, Italy
| | - Giorgio Brandi
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, Urbino, Italy
| | - Giulia Amagliani
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, Urbino, Italy.
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10
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Abstract
This review is focused on describing and analyzing means by which Salmonella enterica serotype strains have been genetically modified with the purpose of developing safe, efficacious vaccines to present Salmonella-induced disease in poultry and to prevent Salmonella colonization of poultry to reduce transmission through the food chain in and on eggs and poultry meat. Emphasis is on use of recently developed means to generate defined deletion mutations to eliminate genetic sequences conferring antimicrobial resistance or residual elements that might lead to genetic instability. Problems associated with prior means to develop vaccines are discussed with presentation of various means by which these problems have been lessened, if not eliminated. Practical considerations are also discussed in hope of facilitating means to move lab-proven successful vaccination procedures and vaccine candidates to the marketplace to benefit the poultry industry.
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Affiliation(s)
- Roy Curtiss
- College of Veterinary Medicine, University of Florida, Gainesville, Florida,
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11
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Alvarez DM, Barrón-Montenegro R, Conejeros J, Rivera D, Undurraga EA, Moreno-Switt AI. A review of the global emergence of multidrug-resistant Salmonella enterica subsp. enterica Serovar Infantis. Int J Food Microbiol 2023; 403:110297. [PMID: 37406596 DOI: 10.1016/j.ijfoodmicro.2023.110297] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 06/14/2023] [Accepted: 06/18/2023] [Indexed: 07/07/2023]
Abstract
Salmonella enterica serovar Infantis is an emergent foodborne and zoonotic Salmonella serovar with critical implications for global health. In recent years, the prevalence of S. Infantis infections has increased in the United States, Europe, and Latin America, due to contaminated chicken and other foods. An essential trait of S. Infantis is its resistance to multiple antibiotics, including the critically important third-generation cephalosporins and quinolones, undermining effective medical treatment, particularly in low-resource settings. We describe the emergence of multidrug-resistant (MDR) S. Infantis, focusing on humans, animals, the environment, and food. We conducted a systematic review (1979-2021), selected 183 studies, and analyzed the origin, source, antimicrobial resistance, and presence of a conjugative plasmid of emerging S. Infantis (pESI) in reported isolates. S. Infantis has been detected worldwide, with a substantial increase since 2011. We found the highest number of isolations in the Americas (42.9 %), Europe (29.8 %), Western Pacific (17.2 %), Eastern Mediterranean (6.6 %), Africa (3.4 %), and South-East Asia (0.1 %). S. Infantis showed MDR patterns and numerous resistant genes in all sources. The primary source of MDR S. Infantis is broiler and their meat; however, this emerging pathogen is also present in other reservoirs such as food, wildlife, and the environment. Clinical cases of MDR S. Infantis have been reported in children and adults. The global emergence of S. Infantis is related to a plasmid (pESI) with antibiotic and arsenic- and mercury-resistance genes. Additionally, a new megaplasmid (pESI-like), carrying blaCTX-M-65 and antibiotic-resistant genes reported in an ancestral version, was detected in the broiler, human, and chicken meat isolates. Strains harboring pESI-like were primarily observed in the Americas and Europe. MDR S. Infantis has spread globally, potentially becoming a major public health threat, particularly in low- and middle-income countries.
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Affiliation(s)
- Diana M Alvarez
- Escuela de Medicina Veterinaria, Facultad de Agronomía e Ingeniería Forestal, Facultad de Ciencias Biológicas, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Rocío Barrón-Montenegro
- Escuela de Medicina Veterinaria, Facultad de Agronomía e Ingeniería Forestal, Facultad de Ciencias Biológicas, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - José Conejeros
- Escuela de Gobierno, Pontificia Universidad Católica de Chile, Macul, Santiago, Región Metropolitana, Chile
| | - Dácil Rivera
- Escuela de Medicina Veterinaria, Universidad Andres Bello, Santiago, Chile
| | - Eduardo A Undurraga
- Escuela de Gobierno, Pontificia Universidad Católica de Chile, Macul, Santiago, Región Metropolitana, Chile; Research Center for Integrated Disaster Risk Management (CIGIDEN), Av. Vicuña Mackenna 4860, Macul, Santiago, Región Metropolitana, Chile; CIFAR Azrieli Global Scholars program, CIFAR, 661 University Ave., Toronto, ON M5G 1M1, Canada
| | - Andrea I Moreno-Switt
- Escuela de Medicina Veterinaria, Facultad de Agronomía e Ingeniería Forestal, Facultad de Ciencias Biológicas, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile.
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12
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Awosile B, Rahman MK, Levent G, Botero Y, Ajulo S, Ojasanya R, Williams RB, Loneragan GH. Comparing individual antimicrobial resistant and multi-drug resistant Salmonella enterica across serotypes, sampling sources, sampling periods, and food animal types in the United States (2014-2018). Prev Vet Med 2023; 219:106008. [PMID: 37651892 DOI: 10.1016/j.prevetmed.2023.106008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 08/22/2023] [Accepted: 08/25/2023] [Indexed: 09/02/2023]
Abstract
This study aimed to compare the antimicrobial-resistant Salmonella enterica profiles from three sampling sources cecal contents, HACCP (during processing), and retail meat using phenotypic antibiotic susceptibility and serotype data gathered from 2014 and 2018. Antimicrobial resistance data for 29 major Salmonella serotypes from three sampling sources and associated food animal types (cattle, swine, chicken, and turkey) were obtained from the database of the United States National Antimicrobial Resistance Monitoring System. Using multivariable logistic regression models, we compared individual and multi-drug resistance (MDR) in Salmonella enterica between the three sampling sources, food animal types, sampling period, and Salmonella serotypes. Across the three sources and throughout the sampling period, the recovery of antimicrobial-resistant Salmonella enterica - including MDR, MDR-AmpC, and ACSSuT - among food animal types were dependent on the sampling period and, in some cases, sampling sources and period for the selected antimicrobials. The predicted probability of antimicrobial resistance was greater in Salmonella serotypes from turkey compared to other food animal types, conditional on sampling sources. Ceftriaxone-resistant (OR=0.83, 95% CI: 0.69-0.99), and Sulfisoxazole-resistant (OR=0.84, 95% CI: 0.72-0.98) Salmonella serotypes were less likely to be recovered from the Hazard Analysis and Critical Control Point (HACCP) sources than with the cecal sources. Except for Salmonella serotypes Dublin and Newport, most of the Salmonella serotypes were less likely to be resistant to the selected antimicrobials, or found as MDR, compared to serotype Typhimurium. This study offers an integrated view on the predicted probability of MDR Salmonella serotypes, as well as insights into which serotypes are persistent, emerging or declining across sampling sources and food animal types in the United States.
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Affiliation(s)
- Babafela Awosile
- Texas Tech University School of Veterinary Medicine, Amarillo, TX, USA.
| | - Md Kaisar Rahman
- Texas Tech University School of Veterinary Medicine, Amarillo, TX, USA
| | - Gizem Levent
- Texas Tech University School of Veterinary Medicine, Amarillo, TX, USA
| | - Yesica Botero
- Texas Tech University School of Veterinary Medicine, Amarillo, TX, USA
| | - Samuel Ajulo
- Texas Tech University School of Veterinary Medicine, Amarillo, TX, USA
| | - Rasaq Ojasanya
- Ontario Veterinary College, Department of Population Medicine, Guelph, Ontario, Canada
| | - Ryan B Williams
- Texas Tech University School of Veterinary Medicine, Amarillo, TX, USA
| | - Guy H Loneragan
- Texas Tech University School of Veterinary Medicine, Amarillo, TX, USA
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13
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McMillan EA, Hiott LM, Carrico JA, Machado MP, Pouseele H, Jackson CR, Frye JG. Polymerase chain reaction for the in vitro detection of the pESI plasmid associated with the globally circulating Salmonella Infantis outbreak strain. Lett Appl Microbiol 2023; 76:ovad088. [PMID: 37505450 DOI: 10.1093/lambio/ovad088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 07/13/2023] [Accepted: 07/27/2023] [Indexed: 07/29/2023]
Abstract
A globally circulating strain of Salmonella enterica serotype Infantis containing the pESI plasmid has increased in prevalence in poultry meat samples and cases of human infections. In this study, a polymerase chain reaction (PCR) protocol was designed to detect the pESI plasmid and confirm the Infantis serotype of Salmonella isolates. Primers were tested bioinformatically to predict specificity, sensitivity, and precision. A total of 54 isolates of Salmonella serotypes Infantis, Senftenberg, and Alachua were tested, with and without the pESI plasmid carriage. Isolates of 31 additional serotypes were also screened to confirm specificity to Infantis. Specificity, sensitivity, and precision of each primer were >0.95. All isolates tested produced the expected band sizes. This PCR protocol provides a rapid and clear result for the detection of the pESI plasmid and serotype Infantis and will allow for the in vitro detection for epidemiological studies where whole-genome sequencing is not available.
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Affiliation(s)
- Elizabeth A McMillan
- United States Department of Agriculture, Agricultural Research Service, U. S. National Poultry Research Center, Poultry Microbiological Safety and Processing Research Unit, Athens, GA, 30605, United States
| | - Lari M Hiott
- United States Department of Agriculture, Agricultural Research Service, U. S. National Poultry Research Center, Poultry Microbiological Safety and Processing Research Unit, Athens, GA, 30605, United States
| | | | | | - Hannes Pouseele
- bioMérieux, Applied Maths NV, Sint-Martens-Latem, 9830, Belgium
| | - Charlene R Jackson
- United States Department of Agriculture, Agricultural Research Service, U. S. National Poultry Research Center, Poultry Microbiological Safety and Processing Research Unit, Athens, GA, 30605, United States
| | - Jonathan G Frye
- United States Department of Agriculture, Agricultural Research Service, U. S. National Poultry Research Center, Poultry Microbiological Safety and Processing Research Unit, Athens, GA, 30605, United States
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14
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McMillan EA, Berrang ME, Read QD, Rasamsetti S, Richards AK, Shariat NW, Frye JG. Buffered Peptone Water Formulation Does Not Influence Growth of pESI-positive Salmonella enterica Serovar Infantis. J Food Prot 2023; 86:100033. [PMID: 36916571 DOI: 10.1016/j.jfp.2022.100033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/15/2022] [Accepted: 12/20/2022] [Indexed: 12/25/2022]
Abstract
Salmonella enterica is a major cause of human foodborne illness and is often attributed to poultry food sources. S. enterica serovar Infantis, specifically those carrying the pESI plasmid, has become a frequently isolated serotype from poultry meat samples at processing and has caused numerous recent human infections. In 2016, the USDA-Food Safety and Inspection Service changed the official sampling method for raw poultry products from BPW to using neutralizing BPW (nBPW) as the rinsing agent in order to prevent residual antimicrobial effects from acidifying and oxidizing processing aids. This change was contemporaneous to the emergence of pESI-positive ser. Infantis as a prevalent serovar in poultry, prompting some to question if nBPW could be selecting for this prevalent serovar. We performed two experiments: a comparison of ser. Infantis growth in BPW versus nBPW, and a simulation of regulatory sampling methods. We found that when inoculated into both broths, ser. Infantis initially grows slightly slower in nBPW than in BPW but little difference was seen in abundance after 6 h of growth. Additionally, the use of nBPW to simulate poultry rinse sample and overnight cold shipping to a regulatory lab did not affect the survival or subsequent growth of ser. Infantis in BPW. We concluded that the change in USDA-FSIS methodology to include nBPW in sampling procedures has likely not affected the emergence of S. ser. Infantis as a prevalent serovar in chicken and turkey meat product samples.
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Affiliation(s)
- Elizabeth A McMillan
- United States Department of Agriculture- Agricultural Research Service, U.S. National Poultry Research Center, Poultry Microbiological Safety and Processing Research Unit, 950 College Station Road, Athens, GA 30605, USA.
| | - Mark E Berrang
- United States Department of Agriculture- Agricultural Research Service, U.S. National Poultry Research Center, Poultry Microbiological Safety and Processing Research Unit, 950 College Station Road, Athens, GA 30605, USA
| | - Quentin D Read
- United States Department of Agriculture- Agricultural Research Service, Southeast Area, 840 Oval Drive, Raleigh, NC 27606, USA
| | - Surendra Rasamsetti
- Department of Population Health, University of Georgia, 501 D.W. Brooks Drive, Athens, GA 30602, USA
| | - Amber K Richards
- Department of Population Health, University of Georgia, 501 D.W. Brooks Drive, Athens, GA 30602, USA
| | - Nikki W Shariat
- Department of Population Health, University of Georgia, 501 D.W. Brooks Drive, Athens, GA 30602, USA; Center for Food Safety, University of Georgia, 1109 Experiment Street, Griffin, GA 30223, USA
| | - Jonathan G Frye
- United States Department of Agriculture- Agricultural Research Service, U.S. National Poultry Research Center, Poultry Microbiological Safety and Processing Research Unit, 950 College Station Road, Athens, GA 30605, USA
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