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Zelalem A, Koran T, Abegaz K, Abera Z, Mummed B, Olani A, Aliy A, Chimdessa M, Fentahun S, Schwan CL, Vipham JL. Hygienic status of beef butcher shop facilities and antibiotic resistance profile of Salmonella enterica in Ethiopia. Braz J Microbiol 2024; 55:1703-1714. [PMID: 38592593 PMCID: PMC11153418 DOI: 10.1007/s42770-024-01312-2] [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: 11/08/2023] [Accepted: 03/21/2024] [Indexed: 04/10/2024] Open
Abstract
The microbiological quality of meat is influenced by the conditions of hygiene prevailing during production and handling. Thus, this study aimed to assess the prevalence of Salmonella enterica and its antimicrobial resistance, load of hygiene indicator bacteria including E. coli (ECC), coliforms (CC), total coliform (TCC), Enterobacteriaceae (EB) and aerobic plate count (APC), and meat handler's food safety knowledge and hygiene practices in butcher shops in two cities, Addis Ababa and Hawassa in Ethiopia, during 2020 and 2021. A total of 360 samples of beef carcasses (n = 120), knives (n = 60), chopping boards (n = 60), weighing balance (n = 60), and personnel's hands (n = 60) were randomly collected for microbial analysis. Besides, 120 participants were selected to participate in a food safety knowledge and hygiene practices assessment. The S. enterica isolates were identified by agglutination test followed by qPCR targeting invA gene. Phenotypic antimicrobial resistance profiles of S. enterica were determined using disk diffusion assays as described in CLSI. The ECC, CC, TCC, EB, and APC populations were quantified by plating onto petrifilm plates. A structured questionnaire was used to determine food safety knowledge and hygiene practices of participants. Overall prevalence of S. enterica was 16.7% (95% CI, 8.3-26.7) and location seems to have no effect (p = 0.806). Only 20% of the S. enterica were resistant to ampicillin and tetracycline. However, the majority (80%) of S. enterica isolates were susceptible to the panel of 11 antimicrobials tested. The overall mean ± SD (log CFU/cm2) of ECC, CC, TCC, EB, and APC were 4.31 ± 1.15; 4.61 ± 1.33; 4.77 ± 1.32; 4.59 ± 1.38 and 5.87 ± 1.52, respectively. No significant difference (p = 0.123) in E. coli contamination was observed between samples of beef carcasses and chopping boards. The EB contamination showed no significant difference (p > 0.05) among sample sources. The APC contamination levels on beef carcass were significantly higher (p > 0.05) than other sample sources. A total of 56% (95% CI: 46.7 - 65.0) of the participants had poor knowledge and 65% (95% CI: 56.7 - 73.3) had poor hygiene practices towards food safety. This study highlighted the poor hygiene status of butcher facilities with a potential risk of beef safety. Thus, appropriate food safety control strategies and inspection is needed at retail establishments.
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Affiliation(s)
- Andarge Zelalem
- School of Biological Sciences and Biotechnology, College of Natural and Computational Sciences, Haramaya University, Dire Dawa, Ethiopia.
| | | | - Kebede Abegaz
- Department of Food Science & Technology, College of Agriculture, Hawassa University, Hawassa, Ethiopia
| | - Zelalem Abera
- Univeristy Laboratory Management Directorate, Central Laboratories, Haramaya University, Dire Dawa, Ethiopia
| | - Bahar Mummed
- College of Veterinary Medicine, Haramaya University, Dire Dawa, Ethiopia
| | | | - Abde Aliy
- Animal Health Institute, Sebeta, Ethiopia
| | - Meseret Chimdessa
- School of Biological Sciences and Biotechnology, College of Natural and Computational Sciences, Haramaya University, Dire Dawa, Ethiopia
| | - Selam Fentahun
- School of Public Health, College of Medicine and Health Sciences, Hawassa University, Hawassa, Ethiopia
| | - Carla L Schwan
- Department of Nutritional Sciences, College of Family and Consumer Sciences, University of Georgia, Athens, GA, 30602, USA
| | - Jessie L Vipham
- Department of Animal Sciences and Industry, Kansas State University, Manhattan, KS, USA
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Jia M, Li P, Zhang J, Chen Z, Gao L, Sun Y, Zhang X, Yan Y, Zhu G. Characteristics of Two mcr-1-Harboring IncHI2 Plasmids from Clinical Salmonella Isolates in Jiaxing City. Foodborne Pathog Dis 2023; 20:467-476. [PMID: 37699240 DOI: 10.1089/fpd.2023.0051] [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: 09/14/2023] Open
Abstract
Salmonella is a primary cause of foodborne diseases, and the increasing prevalence of mcr-1-carrying plasmids, which confer colistin resistance to Salmonella, poses significant global health concerns. As the frequency of occurrence of the mcr-1 gene is increasing globally, we studied the prevalence of mcr-1 in clinical Salmonella isolates by analyzing 195 clinical strains isolated in 2020. Of the 195 Salmonella isolates, 41 isolates were resistant to colistin. We found mcr-1 in two strains (Salmonella Typhimurium ZJJX20006 and Salmonella Kentucky ZJJX20014), which we analyzed in detail via whole-genome sequencing and antibiotic susceptibility testing. Two strains displayed resistance to ampicillin, ampicillin-sulbactam, tetracycline, chloramphenicol, and cotrimoxazole, while ZJJX20006 displayed resistance to colistin and ZJJX20014 was sensitive. Genomic analysis revealed that these strains had plasmid-encoded mcr-1 in IncHI2 plasmids, which were not similar to the mcr-1-IncX4 identified in 2016. These two strains also harbored other drug resistance genes, including blaOXA-1 and blaCTX-M-14. Our findings may help clarify the molecular mechanisms of mcr-1 dissemination among Salmonella strains in Jiaxing City and offer insights into the evolution of mcr-1 in Salmonella.
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Affiliation(s)
- Miaomiao Jia
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Center for Disease Control and Prevention, Jiaxing, China
| | - Ping Li
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Center for Disease Control and Prevention, Jiaxing, China
| | - Junyan Zhang
- Institute of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Zhongwen Chen
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Center for Disease Control and Prevention, Jiaxing, China
| | - Lei Gao
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Center for Disease Control and Prevention, Jiaxing, China
| | - Yangming Sun
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Center for Disease Control and Prevention, Jiaxing, China
| | - Xiaofei Zhang
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Center for Disease Control and Prevention, Jiaxing, China
| | - Yong Yan
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Center for Disease Control and Prevention, Jiaxing, China
| | - Guoying Zhu
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Center for Disease Control and Prevention, Jiaxing, China
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Rebelo A, Almeida A, Peixe L, Antunes P, Novais C. Unraveling the Role of Metals and Organic Acids in Bacterial Antimicrobial Resistance in the Food Chain. Antibiotics (Basel) 2023; 12:1474. [PMID: 37760770 PMCID: PMC10525130 DOI: 10.3390/antibiotics12091474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 08/02/2023] [Accepted: 08/08/2023] [Indexed: 09/29/2023] Open
Abstract
Antimicrobial resistance (AMR) has a significant impact on human, animal, and environmental health, being spread in diverse settings. Antibiotic misuse and overuse in the food chain are widely recognized as primary drivers of antibiotic-resistant bacteria. However, other antimicrobials, such as metals and organic acids, commonly present in agri-food environments (e.g., in feed, biocides, or as long-term pollutants), may also contribute to this global public health problem, although this remains a debatable topic owing to limited data. This review aims to provide insights into the current role of metals (i.e., copper, arsenic, and mercury) and organic acids in the emergence and spread of AMR in the food chain. Based on a thorough literature review, this study adopts a unique integrative approach, analyzing in detail the known antimicrobial mechanisms of metals and organic acids, as well as the molecular adaptive tolerance strategies developed by diverse bacteria to overcome their action. Additionally, the interplay between the tolerance to metals or organic acids and AMR is explored, with particular focus on co-selection events. Through a comprehensive analysis, this review highlights potential silent drivers of AMR within the food chain and the need for further research at molecular and epidemiological levels across different food contexts worldwide.
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Affiliation(s)
- Andreia Rebelo
- UCIBIO—Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (A.R.); (L.P.)
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
- School of Medicine and Biomedical Sciences (ICBAS), University of Porto, 4050-313 Porto, Portugal
- ESS, Polytechnic of Porto, 4200-072 Porto, Portugal
| | - Agostinho Almeida
- LAQV/REQUIMTE, Laboratory of Applied Chemistry, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal;
| | - Luísa Peixe
- UCIBIO—Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (A.R.); (L.P.)
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
| | - Patrícia Antunes
- UCIBIO—Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (A.R.); (L.P.)
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
- Faculty of Nutrition and Food Sciences (FCNAUP), University of Porto, 4150-180 Porto, Portugal
| | - Carla Novais
- UCIBIO—Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (A.R.); (L.P.)
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
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Jiang M, Li X, Xie CL, Chen P, Luo W, Lin CX, Wang Q, Shu DM, Luo CL, Qu H, Ji J. Fructose-enabled killing of antibiotic-resistant Salmonella enteritidis by gentamicin: Insight from reprogramming metabolomics. Int J Antimicrob Agents 2023; 62:106907. [PMID: 37385564 DOI: 10.1016/j.ijantimicag.2023.106907] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 05/29/2023] [Accepted: 06/25/2023] [Indexed: 07/01/2023]
Abstract
Salmonella enterica is a food-borne pathogen that poses a severe threat to both poultry production and human health. Antibiotics are critical for the initial treatment of bacterial infections. However, the overuse and misuse of antibiotics results in the rapid evolution of antibiotic-resistant bacteria, and the discovery and development of new antibiotics are declining. Therefore, understanding antibiotic resistance mechanisms and developing novel control measures are essential. In the present study, GC-MS-based metabolomics analysis was performed to determine the metabolic profile of gentamicin sensitive (SE-S) and resistant (SE-R) S. enterica. Fructose was identified as a crucial biomarker. Further analysis demonstrated a global depressed central carbon metabolism and energy metabolism in SE-R. The decrease in the pyruvate cycle reduces the production of NADH and ATP, causing a decrease in membrane potential, which contributes to gentamicin resistance. Exogenous fructose potentiated the effectiveness of gentamicin in killing SE-R by promoting the pyruvate cycle, NADH, ATP and membrane potential, thereby increasing gentamicin intake. Further, fructose plus gentamicin improved the survival rate of chicken infected with gentamicin-resistant Salmonella in vivo. Given that metabolite structures are conserved across species, fructose identified from bacteria could be used as a biomarker for breeding disease-resistant phenotypes in chicken. Therefore, a novel strategy is proposed for fighting against antibiotic-resistant S. enterica, including exploring molecules suppressed by antibiotics and providing a new approach to find pathogen targets for disease resistance in chicken breeding.
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Affiliation(s)
- Ming Jiang
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China; The Third Affiliated Hospital, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Xia Li
- The Third Affiliated Hospital, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Chun-Lin Xie
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Peng Chen
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Wei Luo
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Chu-Xiao Lin
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Qiao Wang
- Institute of Animal Sciences of Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ding-Ming Shu
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Cheng-Long Luo
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Hao Qu
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China.
| | - Jian Ji
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China.
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Schwan CL, Bastos LM, Young S, Domesle K, Ge B, Hsu CH, Li C, Strain E, Vipham J, Jones C, Amachawadi R, Nagaraja TG, Trinetta V. Graphical abstractGenotypic and Phenotypic Characterization of Antimicrobial and Heavy Metal tolerance in Salmonella enterica and Escherichia coli Isolates from Swine Feed Mills. J Food Prot 2023:100113. [PMID: 37290750 DOI: 10.1016/j.jfp.2023.100113] [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: 01/25/2023] [Revised: 05/29/2023] [Accepted: 05/31/2023] [Indexed: 06/10/2023]
Abstract
Antimicrobials and heavy metals are commonly used in the animal feed industry. The role of in-feed antimicrobials on the evolution and persistence of resistance in enteric bacteria is not well described. Whole-Genome Sequencing (WGS) is widely used for genetic characterizations of bacterial isolates, including antimicrobial resistance, heavy metal tolerance, virulence factors, and relatedness to other sequenced isolates. The goals of this study were to i) use WGS to characterize Salmonella enterica (n = 33) and Escherichia coli (n = 30) isolated from swine feed and feed mill environments; and ii) investigate their genotypic and phenotypic antimicrobial and heavy metal tolerance. Salmonella isolates belonged to 10 serovars, the most common being Cubana, Senftenberg, and Tennessee. E. coli isolates were grouped into 22 O groups. Phenotypic resistance to at least one antimicrobial was observed in 19 Salmonella (57.6%) and 17 E. coli (56.7%) isolates, whereas multidrug resistance (resistant to ≥ 3 antimicrobial classes) was observed in four Salmonella (12%) and two E. coli (7%) isolates. Antimicrobial resistance genes were identified in 17 Salmonella (51%) and 29 E. coli (97%), with 11 and 29 isolates possessing genes conferring resistance to multiple antimicrobial classes. Phenotypically, 53% Salmonella and 58% E. coli presented resistance to copper and arsenic. All isolates that possessed the copper resistance operon were resistant to the highest concentration tested (40 mM). Heavy metal tolerance genes to copper and silver were present in 26 Salmonella isolates. Our study showed a strong agreement between predicted and measured resistances when comparing genotypic and phenotypic data for antimicrobial resistance, with an overall concordance of 99% and 98.3% for Salmonella and E. coli, respectively.
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Affiliation(s)
- Carla L Schwan
- Department of Nutritional Sciences, University of Georgia, Athens, GA, USA
| | - Leonardo M Bastos
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, USA
| | - Shenia Young
- Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, MD, USA
| | - Kelly Domesle
- Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, MD, USA
| | - Beilei Ge
- Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, MD, USA
| | - Chih-Hao Hsu
- Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, MD, USA
| | - Cong Li
- Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, MD, USA
| | - Errol Strain
- Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, MD, USA
| | - Jessie Vipham
- Department of Animal Sciences and Industry, College of Agriculture, Kansas State University, Manhattan, KS, USA
| | - Cassandra Jones
- Department of Animal Sciences and Industry, College of Agriculture, Kansas State University, Manhattan, KS, USA
| | - Raghavendra Amachawadi
- Department of Clinical Sciences, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Tiruvoor G Nagaraja
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Valentina Trinetta
- Department of Animal Sciences and Industry, College of Agriculture, Kansas State University, Manhattan, KS, USA.
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Anedda E, Farrell ML, Morris D, Burgess CM. Evaluating the impact of heavy metals on antimicrobial resistance in the primary food production environment: A scoping review. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 320:121035. [PMID: 36623784 DOI: 10.1016/j.envpol.2023.121035] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 01/03/2023] [Accepted: 01/06/2023] [Indexed: 06/17/2023]
Abstract
Heavy metals are naturally occurring environmental compounds, which can influence antimicrobial resistance (AMR) dissemination. However, there is limited information on how heavy metals may act as a selective pressure on AMR in the primary food production environment. This review aims to examine the literature on this topic in order to identify knowledge gaps. A total of 73 studies, which met pre-established criteria, were included. These investigations were undertaken between 2008 and 2021, with a significant increase in the last three years. The majority of studies included were undertaken in China. Soil, water and manure were the most common samples analysed, and the sampling locations varied from areas with a natural presence of heavy metals, areas intentionally amended with heavy metals or manure, to areas close to industrial activity or mines. Fifty-four per cent of the investigations focused on the analysis of four or more heavy metals, and copper and zinc were the metals most frequently analysed (n = 59, n = 49, respectively). The findings of this review highlight a link between heavy metals and AMR in the primary food production environment. Heavy metals impacted the abundance and dissemination of mobile genetic elements (MGEs) and antimicrobial resistance genes (ARGs), with MGEs also observed as playing a key role in the spread of ARGs and metal resistance genes (MRGs). Harmonization of methodologies used in future studies would increase the opportunity for comparison between studies. Further research is also required to broaden the availability of data at a global level.
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Affiliation(s)
- Elena Anedda
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Ireland; Food Safety Department, Teagasc Food Research Centre Ashtown, Dublin, Ireland.
| | - Maeve Louise Farrell
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Ireland; Centre for One Health, Ryan Institute, University of Galway, Ireland.
| | - Dearbháile Morris
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Ireland; Centre for One Health, Ryan Institute, University of Galway, Ireland.
| | - Catherine M Burgess
- Food Safety Department, Teagasc Food Research Centre Ashtown, Dublin, Ireland.
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The Occurrence and Genomic Characteristics of mcr-1-Harboring Salmonella from Retail Meats and Eggs in Qingdao, China. Foods 2022; 11:foods11233854. [PMID: 36496661 PMCID: PMC9739812 DOI: 10.3390/foods11233854] [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: 09/22/2022] [Revised: 11/15/2022] [Accepted: 11/26/2022] [Indexed: 12/02/2022] Open
Abstract
Salmonella are widely distributed foodborne pathogens and are often associated with food animal products. Colistin resistance mediated by mcr-1 is an increasing threat; however, data on the characteristics of mcr-1-harboring Salmonella among retail foods are still lacking. In this study, retail meats from 24 supermarkets and eggs from nine markets in Qingdao city were investigated to determine the presence and genomic characteristics of mcr-1-harboring Salmonella. We found the retail meats and eggs were highly contaminated by Salmonella, with detection rates of 17.5% (31/177) and 12.3% (16/130), respectively. A total of 76 Salmonella isolates were obtained in this study, and 77.6% showed multidrug resistance (MDR). The MDR proportion of egg isolates (97.5%) was significantly higher than that in meat isolates (55.6%) (p < 0.05). The most prevalent Salmonella serotypes were Typhimurium (56.6%) and Enteritidis (17.1%). Of the 76 Salmonella isolates, 40 possessed mcr-1. All 40 mcr-1-positive isolates were ST34 S. Typhimurium and were from eggs of eight brands. Different mcr-1-harboring isolates existed in the same egg, and some isolates from different egg samples or brands showed clonal relationships. The mcr-1 was located on similar IncHI2/HI2A MDR non-conjugative plasmids lacking transfer region, resulting in the failure of conjugation. The phylogenetic tree using genome sequences showed that the mcr-1-positive isolates from eggs clustered together with mcr-1-positive isolates from chicken and humans in China, revealing that mcr-1-positive egg-borne Salmonella might be derived from chicken and could potentially trigger outbreaks in humans. The high occurrence of mcr-1-harboring Salmonella in fresh eggs is alarming, and there is an urgent need to monitor mcr-1-harboring Salmonella in retail meats and eggs. We report for the first time the role of retail eggs in disseminating mcr-1-positive Salmonella and the risk of transmission of these MDR pathogens from retail food to humans should be evaluated comprehensively.
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Bloomfield S, Duong VT, Tuyen HT, Campbell JI, Thomson NR, Parkhill J, Le Phuc H, Chau TTH, Maskell DJ, Perron GG, Ngoc NM, Vi LL, Adriaenssens EM, Baker S, Mather AE. Mobility of antimicrobial resistance across serovars and disease presentations in non-typhoidal Salmonella from animals and humans in Vietnam. Microb Genom 2022; 8. [PMID: 35511231 PMCID: PMC9465066 DOI: 10.1099/mgen.0.000798] [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
Non-typhoidal Salmonella (NTS) is a major cause of bacterial enterocolitis globally but also causes invasive bloodstream infections. Antimicrobial resistance (AMR) hampers the treatment of these infections and understanding how AMR spreads between NTS may help in developing effective strategies. We investigated NTS isolates associated with invasive disease, diarrhoeal disease and asymptomatic carriage in animals and humans from Vietnam. Isolates included multiple serovars and both common and rare phenotypic AMR profiles; long- and short-read sequencing was used to investigate the genetic mechanisms and genomic backgrounds associated with phenotypic AMR profiles. We demonstrate concordance between most AMR genotypes and phenotypes but identified large genotypic diversity in clinically relevant phenotypes and the high mobility potential of AMR genes (ARGs) in this setting. We found that 84 % of ARGs identified were located on plasmids, most commonly those containing IncHI1A_1 and IncHI1B(R27)_1_R27 replicons (33%), and those containing IncHI2_1 and IncHI2A_1 replicons (31%). The vast majority (95%) of ARGS were found within 10 kbp of IS6/IS26 elements, which provide plasmids with a mechanism to exchange ARGs between plasmids and other parts of the genome. Whole genome sequencing with targeted long-read sequencing applied in a One Health context identified a comparatively limited number of insertion sequences and plasmid replicons associated with AMR. Therefore, in the context of NTS from Vietnam and likely for other settings as well, the mechanisms by which ARGs move contribute to a more successful AMR profile than the specific ARGs, facilitating the adaptation of bacteria to different environments or selection pressures.
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Affiliation(s)
| | | | - Ha Thanh Tuyen
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - James I Campbell
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | | | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | | | - Tran Thi Hong Chau
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | | | - Gabriel G Perron
- Department of Biology, Bard College, Annandale-on-Hudson, New York, USA
| | | | - Lu Lan Vi
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | | | - Stephen Baker
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK
| | - Alison E Mather
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK.,University of East Anglia, Norwich, UK
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Sallami I, Turki Y, Werheni Ammeri R, Khelifi N, Hassen A. Effects of heavy metals on growth and biofilm-producing abilities of Salmonella enterica isolated from Tunisia. Arch Microbiol 2022; 204:225. [DOI: 10.1007/s00203-022-02836-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 02/19/2022] [Accepted: 03/10/2022] [Indexed: 11/30/2022]
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Storey N, Cawthraw S, Turner O, Rambaldi M, Lemma F, Horton R, Randall L, Duggett NA, AbuOun M, Martelli F, Anjum MF. Use of genomics to explore AMR persistence in an outdoor pig farm with low antimicrobial usage. Microb Genom 2022; 8:000782. [PMID: 35344479 PMCID: PMC9176276 DOI: 10.1099/mgen.0.000782] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Food animals may be reservoirs of antimicrobial resistance (AMR) passing through the food chain, but little is known about AMR prevalence in bacteria when selective pressure from antimicrobials is low or absent. We monitored antimicrobial-resistant Escherichia coli over 1 year in a UK outdoor pig farm with low antimicrobial usage (AMU) compared to conventional pig farms in the United Kingdom. Short and selected long-read whole-genome sequencing (WGS) was performed to identify AMR genes, phylogeny and mobile elements in 385 E. coli isolates purified mainly from pig and some seagull faeces. Generally, low levels of antimicrobial-resistant E. coli were present, probably due to low AMU. Those present were likely to be multi-drug resistant (MDR) and belonging to particular Sequence Types (STs) such as ST744, ST88 or ST44, with shared clones (<14 Single Nucleotide Polymorphisms (SNPs) apart) isolated from different time points indicating epidemiological linkage within pigs of different ages, and between pig and the wild bird faeces. Although importance of horizontal transmission of AMR is well established, there was limited evidence of plasmid-mediated dissemination between different STs. Non-conjugable MDR plasmids or large AMR gene-bearing transposons were stably integrated within the chromosome and remained associated with particular STs/clones over the time period sampled. Heavy metal resistance genes were also detected within some genetic elements. This study highlights that although low levels of antimicrobial-resistant E. coli correlates with low AMU, a basal level of MDR E. coli can still persist on farm potentially due to transmission and recycling of particular clones within different pig groups. Environmental factors such as wild birds and heavy metal contaminants may also play important roles in the recycling and dissemination, and hence enabling persistence of MDR E. coli. All such factors need to be considered as any rise in AMU on low usage farms, could in future, result in a significant increase in their AMR burden.
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Affiliation(s)
- Nathaniel Storey
- Animal and Plant Health Agency, Weybridge, New Haw, Addlestone, Surrey KT15 3NB, UK
- Great Ormond Street Hospital for Children, London WC1N 3JH, UK
| | - Shaun Cawthraw
- Animal and Plant Health Agency, Weybridge, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Olivia Turner
- Animal and Plant Health Agency, Weybridge, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Margherita Rambaldi
- Animal and Plant Health Agency, Weybridge, New Haw, Addlestone, Surrey KT15 3NB, UK
- University of Bologna, Via Zamboni, 33, 40126 Bologna BO, Italy
| | - Fabrizio Lemma
- Animal and Plant Health Agency, Weybridge, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Robert Horton
- Animal and Plant Health Agency, Weybridge, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Luke Randall
- Animal and Plant Health Agency, Weybridge, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Nicholas A. Duggett
- Animal and Plant Health Agency, Weybridge, New Haw, Addlestone, Surrey KT15 3NB, UK
- Teeside University, Campus Heart, Middlesbrough TS1 3BX, UK
| | - Manal AbuOun
- Animal and Plant Health Agency, Weybridge, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Francesca Martelli
- Animal and Plant Health Agency, Weybridge, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Muna F. Anjum
- Animal and Plant Health Agency, Weybridge, New Haw, Addlestone, Surrey KT15 3NB, UK
- *Correspondence: Muna F. Anjum,
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11
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Manakhov AM, Sitnikova NA, Tsygankova AR, Alekseev AY, Adamenko LS, Permyakova E, Baidyshev VS, Popov ZI, Blahová L, Eliáš M, Zajíčková L, Solovieva AO. Electrospun Biodegradable Nanofibers Coated Homogenously by Cu Magnetron Sputtering Exhibit Fast Ion Release. Computational and Experimental Study. MEMBRANES 2021; 11:965. [PMID: 34940466 PMCID: PMC8708309 DOI: 10.3390/membranes11120965] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/03/2021] [Accepted: 12/04/2021] [Indexed: 11/30/2022]
Abstract
Copper-coated nanofibrous materials are desirable for catalysis, electrochemistry, sensing, and biomedical use. The preparation of copper or copper-coated nanofibers can be pretty challenging, requiring many chemical steps that we eliminated in our robust approach, where for the first time, Cu was deposited by magnetron sputtering onto temperature-sensitive polymer nanofibers. For the first time, the large-scale modeling of PCL films irradiation by molecular dynamics simulation was performed and allowed to predict the ions penetration depth and tune the deposition conditions. The Cu-coated polycaprolactone (PCL) nanofibers were thoroughly characterized and tested as antibacterial agents for various Gram-positive and Gram-negative bacteria. Fast release of Cu2+ ions (concentration up to 3.4 µg/mL) led to significant suppression of E. coli and S. aureus colonies but was insufficient against S. typhimurium and Ps. aeruginosa. The effect of Cu layer oxidation upon contact with liquid media was investigated by X-ray photoelectron spectroscopy revealing that, after two hours, 55% of Cu atoms are in form of CuO or Cu(OH)2. The Cu-coated nanofibers will be great candidates for wound dressings thanks to an interesting synergistic effect: on the one hand, the rapid release of copper ions kills bacteria, while on the other hand, it stimulates the regeneration with the activation of immune cells. Indeed, copper ions are necessary for the bacteriostatic action of cells of the immune system. The reactive CO2/C2H4 plasma polymers deposited onto PCL-Cu nanofibers can be applied to grafting of viable proteins, peptides, or drugs, and it further explores the versatility of developed nanofibers for biomedical applications use.
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Affiliation(s)
- Anton M. Manakhov
- Research Institute of Clinical and Experimental Lymphology—Branch of the ICG SB RAS, 2 Timakova St., 630060 Novosibirsk, Russia; (N.A.S.); (E.P.)
| | - Natalya A. Sitnikova
- Research Institute of Clinical and Experimental Lymphology—Branch of the ICG SB RAS, 2 Timakova St., 630060 Novosibirsk, Russia; (N.A.S.); (E.P.)
| | - Alphiya R. Tsygankova
- Nikolaev Institute of Inorganic Chemistry SB RAS, 3 Acad. Lavrentiev Ave., 630090 Novosibirsk, Russia;
| | - Alexander Yu. Alekseev
- Research Institute of Virology, The Federal Research Center of Fundamental and Translational Medicine, 2 Timakova St., 630060 Novosibirsk, Russia; (A.Y.A.); (L.S.A.)
- Research Institute of Applied Ecology, Dagestan State University, Dahadaeva 21, 367000 Makhachkala, Russia
| | - Lyubov S. Adamenko
- Research Institute of Virology, The Federal Research Center of Fundamental and Translational Medicine, 2 Timakova St., 630060 Novosibirsk, Russia; (A.Y.A.); (L.S.A.)
| | - Elizaveta Permyakova
- Research Institute of Clinical and Experimental Lymphology—Branch of the ICG SB RAS, 2 Timakova St., 630060 Novosibirsk, Russia; (N.A.S.); (E.P.)
- Laboratory of Inorganic Nanomaterials, National University of Science and Technology “MISiS”, Leninsky Prospekt 4, 119071 Moscow, Russia
| | - Victor S. Baidyshev
- Department of Computer Engineering and Automated Systems Software, Katanov Khakas State University, Pr. Lenin, 90, 655017 Abakan, Russia;
| | - Zakhar I. Popov
- Laboratory of Acoustic Microscopy, Emanuel Institute of Biochemical Physics RAS, Kosygina 4, 119334 Moscow, Russia;
| | - Lucie Blahová
- Central European Institute of Technology CEITEC-BUT, Purkyňova 123, 61200 Brno, Czech Republic; (L.B.); (M.E.); (L.Z.)
| | - Marek Eliáš
- Central European Institute of Technology CEITEC-BUT, Purkyňova 123, 61200 Brno, Czech Republic; (L.B.); (M.E.); (L.Z.)
| | - Lenka Zajíčková
- Central European Institute of Technology CEITEC-BUT, Purkyňova 123, 61200 Brno, Czech Republic; (L.B.); (M.E.); (L.Z.)
- Department Condensed Matter Physics, Faculty of Science, Masaryk University, Kotlářská 2, 61137 Brno, Czech Republic
| | - Anastasiya O. Solovieva
- Research Institute of Clinical and Experimental Lymphology—Branch of the ICG SB RAS, 2 Timakova St., 630060 Novosibirsk, Russia; (N.A.S.); (E.P.)
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12
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Bearson SMD. Salmonella in Swine: Prevalence, Multidrug Resistance, and Vaccination Strategies. Annu Rev Anim Biosci 2021; 10:373-393. [PMID: 34699256 DOI: 10.1146/annurev-animal-013120-043304] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
An estimated 1.3 million Salmonella infections and 420 deaths occur annually in the United States, with an estimated economic burden of $3.7 billion. More than 50% of US swine operations test positive for Salmonella according to the National Animal Health Monitoring System, and 20% of Salmonella from swine are multidrug resistant (resistant to ≥3 antimicrobial classes) as reported by the National Antimicrobial Resistance Monitoring System. This review on Salmonella in swine addresses the current status of these topics by discussing antimicrobial resistance and metal tolerance in Salmonella and the contribution of horizontal gene transfer. A major challenge in controlling Salmonella is that Salmonella is a foodborne pathogen in humans but is often a commensal in food animals and thereby establishes an asymptomatic reservoir state in such animals, including swine. As food animal production systems continue to expand and antimicrobial usage becomes more limited, the need for Salmonella interventions has intensified. A promising mitigation strategy is vaccination against Salmonella in swine to limit animal, environmental, and food contamination. Expected final online publication date for the Annual Review of Animal Biosciences, Volume 10 is February 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Shawn M D Bearson
- Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, Agricultural Research Center, US Department of Agriculture, Ames, Iowa, USA;
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13
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Portes AB, Rodrigues G, Leitão MP, Ferrari R, Conte Junior CA, Panzenhagen P. Global distribution of plasmid-mediated colistin resistance mcr gene in Salmonella: A systematic review. J Appl Microbiol 2021; 132:872-889. [PMID: 34480840 DOI: 10.1111/jam.15282] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 08/04/2021] [Accepted: 08/31/2021] [Indexed: 11/28/2022]
Abstract
This systematic review focuses on obtaining the most relevant information from multiple studies that detected a mobilized colistin resistance mcr gene in Salmonella for a better comprehension of its global distribution. A group of strategic and systematic keywords were combined to retrieve research data on the detection frequency of the mcr gene globally from four database platforms (Google Scholar, Science Direct, PubMed and Scielo). Forty-eight studies attended all the eligibility criteria and were selected. China was the country with the highest frequency of Salmonella strains with the mcr gene, and Europe exhibited a wide diversity of countries with positive mcr strains. In addition, animals and humans carried the highest frequency of positive strains for the mcr gene. Salmonella Typhimurium was the most frequent serovar carrying the mcr gene. Apparently, colistin overuse in animal husbandry has increased the selective pressure of antimicrobial resistance, resulting in the emergence of a plasmid-mediated colistin resistance mcr gene in China. The mcr-positive Salmonella strains are recently predominant worldwide, which is probably due to the capacity of this gene to be swiftly horizontally transmissible. The transmission ability of mcr-positive Salmonella strains to humans through the consumption of contaminated animal-based food is a public health concern.
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Affiliation(s)
- Ana Beatriz Portes
- Center for Food Analysis (NAL), Technological Development Support Laboratory (LADETEC), Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ, Brazil.,Laboratory of Advanced Analysis in Biochemistry and Molecular Biology (LAABBM), Department of Biochemistry, Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ, Brazil
| | - Grazielle Rodrigues
- Center for Food Analysis (NAL), Technological Development Support Laboratory (LADETEC), Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ, Brazil.,Laboratory of Advanced Analysis in Biochemistry and Molecular Biology (LAABBM), Department of Biochemistry, Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ, Brazil
| | - Mylenna Palma Leitão
- Laboratory of Advanced Analysis in Biochemistry and Molecular Biology (LAABBM), Department of Biochemistry, Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ, Brazil
| | - Rafaela Ferrari
- Center for Food Analysis (NAL), Technological Development Support Laboratory (LADETEC), Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ, Brazil.,Laboratory of Advanced Analysis in Biochemistry and Molecular Biology (LAABBM), Department of Biochemistry, Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ, Brazil
| | - Carlos Adam Conte Junior
- Center for Food Analysis (NAL), Technological Development Support Laboratory (LADETEC), Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ, Brazil.,Laboratory of Advanced Analysis in Biochemistry and Molecular Biology (LAABBM), Department of Biochemistry, Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ, Brazil.,Graduate Program in Food Science (PPGCAL), Institute of Chemistry (IQ), Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ, Brazil.,Graduate Program in Veterinary Hygiene (PPGHV), Faculty of Veterinary Medicine, Fluminense Federal University (UFF), Vital Brazil Filho, Niterói, RJ, Brazil.,Graduate Program in Sanitary Surveillance (PPGVS), National Institute of Health Quality Control (INCQS), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, RJ, Brazil.,Graduate Program in Chemistry (PGQu), Institute of Chemistry (IQ), Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ, Brazil
| | - Pedro Panzenhagen
- Center for Food Analysis (NAL), Technological Development Support Laboratory (LADETEC), Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ, Brazil.,Laboratory of Advanced Analysis in Biochemistry and Molecular Biology (LAABBM), Department of Biochemistry, Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ, Brazil
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14
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Mustafa GR, Zhao K, He X, Chen S, Liu S, Mustafa A, He L, Yang Y, Yu X, Penttinen P, Ao X, Liu A, Shabbir MZ, Xu X, Zou L. Heavy Metal Resistance in Salmonella Typhimurium and Its Association With Disinfectant and Antibiotic Resistance. Front Microbiol 2021; 12:702725. [PMID: 34421860 PMCID: PMC8371916 DOI: 10.3389/fmicb.2021.702725] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 07/05/2021] [Indexed: 11/29/2022] Open
Abstract
Metals are widely used in animal feed for their growth-stimulating and antimicrobial effects, yet their use may potentially promote the proliferation of antibiotic resistance through co-selection. We studied the prevalence and associations of metal, antibiotic, and disinfectant resistances of 300 Salmonella Typhimurium isolates from pig meat, pig manure, chicken meat, poultry manure, and human stool from Sichuan, China. Seventy four percent of the 300 Salmonella Typhimurium isolates were considered resistant to Cu, almost 50% to Zn and Cr, over 25% to Mn and Cd, and almost 10% to Co. Most of the isolates carried at least one heavy metal resistance gene (HMRG). The Cr-Zn-Cd-resistance gene czcD was carried by 254 isolates and the Cu-resistance genes pcoR and pcoC by 196 and 179 isolates, respectively. Most of the isolates were resistant to at least one antibiotic and almost 80% were multidrug-resistant. The prevalence of resistance to six antibiotics was higher among the pig meat and manure isolates than among other isolates, and that of streptomycin and ampicillin were highest among the pig meat isolates and that of ciprofloxacin and ofloxacin among the pig manure isolates. From 55 to 79% of the isolates were considered resistant to disinfectants triclosan, trichloroisocyanuric acid, or benzalkonium chloride. The metal resistances and HMRGs were associated with resistance to antibiotics and disinfectants. Especially, Cu-resistance genes were associated with resistance to several antibiotics and disinfectants. The transfer of the Cr-Zn-Cd-resistance gene czcD, Cu-resistance gene pcoC, and Co-Ni-resistance gene cnrA into Escherichia coli and the increased Cu-resistance of the transconjugants implied that the resistance genes were located on conjugative plasmids. Thus, the excessive use of metals and disinfectants as feed additives and in animal care may have the potential to promote antibiotic resistance through co-selection and maintain and promote antibiotic resistance even in the absence of antibiotics.
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Affiliation(s)
| | - Ke Zhao
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Xueping He
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Shujuan Chen
- College of Food Science, Sichuan Agricultural University, Ya'an, China
| | - Shuliang Liu
- College of Food Science, Sichuan Agricultural University, Ya'an, China
| | - Ahsan Mustafa
- Key Laboratory for Animal Disease-Resistance Nutrition of China, Ministry of Education, Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, China
| | - Li He
- College of Food Science, Sichuan Agricultural University, Ya'an, China
| | - Yong Yang
- College of Food Science, Sichuan Agricultural University, Ya'an, China
| | - Xiumei Yu
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Petri Penttinen
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Xiaolin Ao
- College of Food Science, Sichuan Agricultural University, Ya'an, China
| | - Aiping Liu
- College of Food Science, Sichuan Agricultural University, Ya'an, China
| | | | - Xuebin Xu
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Likou Zou
- College of Resources, Sichuan Agricultural University, Chengdu, China
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15
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Hu Y, Fanning S, Nguyen SV, Wang W, Liu C, Cui X, Dong Y, Gan X, Xu J, Li F. Emergence of a Salmonella enterica serovar Typhimurium ST34 isolate, CFSA629, carrying a novel mcr-1.19 variant cultured from egg in China. J Antimicrob Chemother 2021; 76:1776-1785. [PMID: 33822965 DOI: 10.1093/jac/dkab090] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 02/26/2021] [Indexed: 01/05/2023] Open
Abstract
OBJECTIVES This study aimed to characterize the genomic features of a Salmonella enterica serovar Typhimurium ST34 isolate, CFSA629, which carried a novel mcr-1 variant, designated as mcr-1.19, mapped to an ESBL-encoding IncHI2 plasmid. METHODS Antimicrobial susceptibility assays as well as WGS were carried out on isolate CFSA629. The complete closed genome was obtained and then explored to obtain genomic features. Plasmid sequence comparison was performed for pCFSA629 with similar plasmids and the mcr-1 genetic environment was analysed. RESULTS S. Typhimurium ST34 CFSA629 expressed an MDR phenotype to six classes of compound and consisted of a single circular chromosome and one plasmid. It possessed 11 resistance genes including 2 ESBL genes that mapped to the chromosome and the plasmid; an IS26-flanked composite-like transposon was identified. A novel mcr-1 variant (mcr-1.19) was identified, which had a unique SNP (G1534A) that gave rise to a novel MCR-1 protein containing a Val512Ile amino acid substitution. Plasmid pCFSA629 possessed a conjugative plasmid transfer gene cluster as well as an antimicrobial resistance-encoding gene cluster-containing region that contained two IS26 composite-like transposonal modules, but was devoid of any plasmid-mediated quinolone resistance genes. The background of mcr-1.19 consisted of an ISApl1-mcr-1-PAP2-ter module. CONCLUSIONS We report on an MDR S. Typhimurium ST34 CFSA629 isolate cultured from egg in China, harbouring an mcr-1.19 variant mapped to an IncHI2 plasmid. This highlights the importance of surveillance to mitigate dissemination of mcr-encoding genes among foodborne Salmonella. Improved surveillance is important for tackling the dissemination of mcr genes among foodborne Salmonella around the world.
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Affiliation(s)
- Yujie Hu
- NHC Key Laboratory of Food Safety Risk Assessment, Food Safety Research Unit (2019RU014) of Chinese Academy of Medical Science, China National Center for Food Safety Risk Assessment, Beijing, China.,UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Population Science, University College Dublin, Belfield, Dublin, Ireland
| | - Séamus Fanning
- NHC Key Laboratory of Food Safety Risk Assessment, Food Safety Research Unit (2019RU014) of Chinese Academy of Medical Science, China National Center for Food Safety Risk Assessment, Beijing, China.,UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Population Science, University College Dublin, Belfield, Dublin, Ireland.,Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Chlorine Gardens, Belfast, UK
| | - Scott V Nguyen
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Population Science, University College Dublin, Belfield, Dublin, Ireland
| | - Wei Wang
- NHC Key Laboratory of Food Safety Risk Assessment, Food Safety Research Unit (2019RU014) of Chinese Academy of Medical Science, China National Center for Food Safety Risk Assessment, Beijing, China
| | - Chang Liu
- Food Science and Engineering College, Beijing University of Agriculture, Beijing, China
| | - Xinnan Cui
- Food Science and Engineering College, Beijing University of Agriculture, Beijing, China.,China Center of Industrial Culture Collection, China National Research Institute of Food and Fermentation Industries, Beijing, China
| | - Yinping Dong
- NHC Key Laboratory of Food Safety Risk Assessment, Food Safety Research Unit (2019RU014) of Chinese Academy of Medical Science, China National Center for Food Safety Risk Assessment, Beijing, China.,UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Population Science, University College Dublin, Belfield, Dublin, Ireland
| | - Xin Gan
- NHC Key Laboratory of Food Safety Risk Assessment, Food Safety Research Unit (2019RU014) of Chinese Academy of Medical Science, China National Center for Food Safety Risk Assessment, Beijing, China
| | - Jin Xu
- NHC Key Laboratory of Food Safety Risk Assessment, Food Safety Research Unit (2019RU014) of Chinese Academy of Medical Science, China National Center for Food Safety Risk Assessment, Beijing, China
| | - Fengqin Li
- NHC Key Laboratory of Food Safety Risk Assessment, Food Safety Research Unit (2019RU014) of Chinese Academy of Medical Science, China National Center for Food Safety Risk Assessment, Beijing, China
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16
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Li W, Yan Y, Chen J, Sun R, Wang Y, Wang T, Feng Z, Peng K, Wang J, Chen S, Luo Y, Li R, Yang B. Genomic characterization of conjugative plasmids carrying the mcr-1 gene in foodborne and clinical strains of Salmonella and Escherichia coli. Food Control 2021. [DOI: 10.1016/j.foodcont.2021.108032] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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17
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Overview on the role of heavy metals tolerance on developing antibiotic resistance in both Gram-negative and Gram-positive bacteria. Arch Microbiol 2021; 203:2761-2770. [PMID: 33811263 DOI: 10.1007/s00203-021-02275-w] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 02/11/2021] [Accepted: 03/10/2021] [Indexed: 12/26/2022]
Abstract
Environmental health is a critical concern, continuously contaminated by physical and biological components (viz., anthropogenic activity), which adversely affect on biodiversity, ecosystems and human health. Nonetheless, environmental pollution has great impact on microbial communities, especially bacteria, which try to evolve in changing environment. For instance, during the course of adaptation, bacteria easily become resistance to antibiotics and heavy metals. Antibiotic resistance genes are now one of the most vital pollutants, provided as a source of frequent horizontal gene transfer. In this review, the environmental cause of multidrug resistance (MDR) that was supposed to be driven by either heavy metals or combination of environmental factors was essentially reviewed, especially focussed on the correlation between accumulation of heavy metals and development of MDR by bacteria. This kind of correlation was seemed to be non-significant, i.e. paradoxical. Gram-positive bacteria accumulating much of toxic heavy metal (i.e. highly stress tolerance) were unlikely to become MDR, whereas Gram-negative bacteria that often avoid accumulation of toxic heavy metal by efflux pump systems were come out to be more prone to MDR. So far, other than antibiotic contaminant, no such available data strongly support the direct influence of heavy metals in bacterial evolution of MDR; combinations of factors may drive the evolution of antibiotic resistance. Therefore, Gram-positive bacteria are most likely to be an efficient member in treatment of industrial waste water, especially in the removal of heavy metals, perhaps inducing the less chance of antibiotic resistance pollution in the environment.
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18
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Donoso A, Paredes N, Retamal P. Detection of Antimicrobial Resistant Salmonella enterica Strains in Larval and Adult Forms of Lesser Mealworm ( Alphitobius diaperinus) From Industrial Poultry Farms. Front Vet Sci 2020; 7:577848. [PMID: 33195584 PMCID: PMC7581672 DOI: 10.3389/fvets.2020.577848] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 09/01/2020] [Indexed: 11/13/2022] Open
Abstract
The lesser mealworms (Alphitobius diaperinus) constitute a common cosmopolitan pest in poultry flocks and may colonize the litter in adult and larval forms. Previous studies have documented their potential as carriers of enteric pathogens. In this context, S. enterica constitutes a prioritized zoonotic agent in the poultry industry due to the sanitary risks and economic losses associated with its presence. The aim of this study is to describe the presence of S. enterica strains in larval and adult forms of A. diaperinus collected from poultry litter belonging to industrial farms located in the central zone of Chile. A total of 403 specimens (203 adults and 200 larvae) were sampled from three farms and 25 flocks. For bacteriological isolation, beetles were processed to differentiate external and internal contamination. Then, isolates were serotyped according to the Kauffman-White scheme and antimicrobial resistance phenotypes were determined using the disk diffusion method. Gene sequences from the megaplasmid pESI were identified through a PCR based test. These procedures led to the detection of 15 S. enterica isolates, belonging to serotypes Infantis (14) and Livingstone (1), from both adults (6) and larval (9) specimens, with a similar external (7) and internal (8) distribution. Furthermore, all S. Infantis isolates showed antimicrobial resistance and evidence of megaplasmid pESI carriage, with all possessing multidrug-resistant phenotypes. Our results confirm that A. diaperinus constitutes a potential reservoir of zoonotic Salmonella strains of sanitary and economic concern for the industry and for public health.
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Affiliation(s)
- Alvaro Donoso
- Laboratorio de Enfermedades Infecciosas, Departamento de Medicina Preventiva Animal, Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
| | - Natalia Paredes
- Laboratorio de Enfermedades Infecciosas, Departamento de Medicina Preventiva Animal, Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
| | - Patricio Retamal
- Laboratorio de Enfermedades Infecciosas, Departamento de Medicina Preventiva Animal, Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
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19
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AbuOun M, O'Connor HM, Stubberfield EJ, Nunez-Garcia J, Sayers E, Crook DW, Smith RP, Anjum MF. Characterizing Antimicrobial Resistant Escherichia coli and Associated Risk Factors in a Cross-Sectional Study of Pig Farms in Great Britain. Front Microbiol 2020; 11:861. [PMID: 32523560 PMCID: PMC7261845 DOI: 10.3389/fmicb.2020.00861] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 04/09/2020] [Indexed: 12/18/2022] Open
Abstract
Combatting antimicrobial resistant (AMR) using a One-Health approach is essential as various bacteria, including Escherichia coli, a common bacteria, are becoming increasingly resistant and livestock may be a reservoir. The AMR gene content of 492 E. coli, isolated from 56 pig farms across Great Britain in 2014–2015, and purified on antibiotic selective and non-selective plates, was determined using whole genome sequencing (WGS). The E. coli were phylogenetically diverse harboring a variety of AMR profiles with widespread resistance to “old” antibiotics; isolates harbored up to seven plasmid Inc-types. None showed concurrent resistance to third-generation cephalosporins, fluoroquinolones and clinically relevant aminoglycosides, although ∼3% harbored AMR genes to both the former two. Transferable resistance to carbapenem and colistin were absent, and six of 117 E. coli STs belonged to major types associated with human disease. Prevalence of genotypically MDR E. coli, gathered from non-selective media was 35% and that of extended-spectrum-beta-lactamase E. coli was low (∼2% from non-selective). Approximately 72.6% of E. coli from ciprofloxacin plates and only 8.5% from the other plates harbored fluoroquinolone resistance due to topoisomerase mutations; the majority were MDR. In fact, multivariable analysis confirmed E. coli purified from CIP enrichment plates were more likely to be MDR, and suggested MDR isolates were also more probable from farms with high antibiotic usage, specialist finisher farms, and farms emptying their manure pits only after each batch. Additionally, farms from the South East were more likely to have MDR E. coli, whereas farms in Yorkshire and the Humber were less likely. Future investigations will determine whether suggested improvements such as better biosecurity or lower antimicrobial use decreases MDR E. coli on pig farms. Although this study focuses on pig farms, we believe the methodology and findings can be applied more widely to help livestock farmers in the United Kingdom and elsewhere to tackle AMR.
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Affiliation(s)
- Manal AbuOun
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, United Kingdom.,National Institute for Health Research, Health Protection Research Unit, University of Oxford in Partnership with Public Health England (PHE), Oxford, United Kingdom
| | - Heather M O'Connor
- Department of Epidemiological Sciences, Animal and Plant Health Agency, Weybridge, United Kingdom
| | - Emma J Stubberfield
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, United Kingdom
| | - Javier Nunez-Garcia
- Department of Epidemiological Sciences, Animal and Plant Health Agency, Weybridge, United Kingdom
| | - Ellie Sayers
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, United Kingdom
| | - Derick W Crook
- National Institute for Health Research, Health Protection Research Unit, University of Oxford in Partnership with Public Health England (PHE), Oxford, United Kingdom.,Modernising Medical Microbiology Consortium, Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Richard P Smith
- Department of Epidemiological Sciences, Animal and Plant Health Agency, Weybridge, United Kingdom
| | - Muna F Anjum
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, United Kingdom.,National Institute for Health Research, Health Protection Research Unit, University of Oxford in Partnership with Public Health England (PHE), Oxford, United Kingdom
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Mourão J, Rebelo A, Ribeiro S, Peixe L, Novais C, Antunes P. Tolerance to arsenic contaminant among multidrug‐resistant and copper‐tolerant
Salmonella
successful clones is associated with diverse
ars
operons and genetic contexts. Environ Microbiol 2020; 22:2829-2842. [DOI: 10.1111/1462-2920.15016] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 03/13/2020] [Accepted: 04/08/2020] [Indexed: 11/28/2022]
Affiliation(s)
- Joana Mourão
- UCIBIO/REQUIMTEDepartment of Biological Sciences, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto Porto Portugal
- Center for Innovative Biomedicine and BiotechnologyUniversity of Coimbra Coimbra Portugal
- Center for Neuroscience and Cell BiologyUniversity of Coimbra Coimbra Portugal
- Institute for Interdisciplinary Research, University of Coimbra Coimbra Portugal
| | - Andreia Rebelo
- UCIBIO/REQUIMTEDepartment of Biological Sciences, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto Porto Portugal
- Scientific Area of Environmental HealthSchool of Health, Polytechnic Institute of Porto Porto Portugal
| | - Sofia Ribeiro
- UCIBIO/REQUIMTEDepartment of Biological Sciences, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto Porto Portugal
| | - Luísa Peixe
- UCIBIO/REQUIMTEDepartment of Biological Sciences, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto Porto Portugal
| | - Carla Novais
- UCIBIO/REQUIMTEDepartment of Biological Sciences, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto Porto Portugal
| | - Patrícia Antunes
- UCIBIO/REQUIMTEDepartment of Biological Sciences, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto Porto Portugal
- Faculty of Nutrition and Food SciencesUniversity of Porto Porto Portugal
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21
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Stubberfield E, AbuOun M, Sayers E, O'Connor HM, Card RM, Anjum MF. Use of whole genome sequencing of commensal Escherichia coli in pigs for antimicrobial resistance surveillance, United Kingdom, 2018. Euro Surveill 2019; 24:1900136. [PMID: 31847943 PMCID: PMC6918588 DOI: 10.2807/1560-7917.es.2019.24.50.1900136] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 08/01/2019] [Indexed: 12/19/2022] Open
Abstract
BackgroundSurveillance of commensal Escherichia coli, a possible reservoir of antimicrobial resistance (AMR) genes, is important as they pose a risk to human and animal health. Most surveillance activities rely on phenotypic characterisation, but whole genome sequencing (WGS) presents an alternative.AimIn this retrospective study, we tested 515 E. coli isolated from pigs to evaluate the use of WGS to predict resistance phenotype.MethodsMinimum inhibitory concentration (MIC) was determined for nine antimicrobials of clinical and veterinary importance. Deviation from wild-type, fully-susceptible MIC was assessed using European Committee on Antimicrobial Susceptibility Testing (EUCAST) epidemiological cut-off (ECOFF) values. Presence of AMR genes and mutations were determined using APHA SeqFinder. Statistical two-by-two table analysis and Cohen's kappa (k) test were applied to assess genotype and phenotype concordance.ResultsOverall, correlation of WGS with susceptibility to the nine antimicrobials was 98.9% for test specificity, and 97.5% for the positive predictive value of a test. The overall kappa score (k = 0.914) indicated AMR gene presence was highly predictive of reduced susceptibility and showed excellent correlation with MIC. However, there was variation for each antimicrobial; five showed excellent correlation; four very good and one moderate. Suggested ECOFF adjustments increased concordance between genotypic data and kappa values for four antimicrobials.ConclusionWGS is a powerful tool for accurately predicting AMR that can be used for national surveillance purposes. Additionally, it can detect resistance genes from a wider panel of antimicrobials whose phenotypes are currently not monitored but may be of importance in the future.
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Affiliation(s)
- Emma Stubberfield
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, Surrey, United Kingdom
| | - Manal AbuOun
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, Surrey, United Kingdom
| | - Ellie Sayers
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, Surrey, United Kingdom
- University of East Anglia/Quadram Institute Bioscience, Norwich Research Park, Norwich, United Kingdom
| | - Heather M O'Connor
- Department of Epidemiological Sciences, Animal and Plant Health Agency, Weybridge, Surrey, United Kingdom
| | - Roderick M Card
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, Surrey, United Kingdom
| | - Muna F Anjum
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, Surrey, United Kingdom
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22
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Koutsoumanis K, Allende A, Alvarez-Ordóñez A, Bolton D, Bover-Cid S, Chemaly M, De Cesare A, Herman L, Hilbert F, Lindqvist R, Nauta M, Peixe L, Ru G, Simmons M, Skandamis P, Suffredini E, Dewulf J, Hald T, Michel V, Niskanen T, Ricci A, Snary E, Boelaert F, Messens W, Davies R. Salmonella control in poultry flocks and its public health impact. EFSA J 2019; 17:e05596. [PMID: 32626222 PMCID: PMC7009056 DOI: 10.2903/j.efsa.2019.5596] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
An increase in confirmed human salmonellosis cases in the EU after 2014 triggered investigation of contributory factors and control options in poultry production. Reconsideration of the five current target serovars for breeding hens showed that there is justification for retaining Salmonella Enteritidis, Salmonella Typhimurium (including monophasic variants) and Salmonella Infantis, while Salmonella Virchow and Salmonella Hadar could be replaced by Salmonella Kentucky and either Salmonella Heidelberg, Salmonella Thompson or a variable serovar in national prevalence targets. However, a target that incorporates all serovars is expected to be more effective as the most relevant serovars in breeding flocks vary between Member State (MS) and over time. Achievement of a 1% target for the current target serovars in laying hen flocks is estimated to be reduced by 254,400 CrI95[98,540; 602,700] compared to the situation in 2016. This translates to a reduction of 53.4% CrI95[39.1; 65.7] considering the layer-associated human salmonellosis true cases and 6.2% considering the overall human salmonellosis true cases in the 23 MSs included in attribution modelling. A review of risk factors for Salmonella in laying hens revealed that overall evidence points to a lower occurrence in non-cage compared to cage systems. A conclusion on the effect of outdoor access or impact of the shift from conventional to enriched cages could not be reached. A similar review for broiler chickens concluded that the evidence that outdoor access affects the occurrence of Salmonella is inconclusive. There is conclusive evidence that an increased stocking density, larger farms and stress result in increased occurrence, persistence and spread of Salmonella in laying hen flocks. Based on scientific evidence, an impact of Salmonella control programmes, apart from general hygiene procedures, on the prevalence of Campylobacter in broiler flocks at the holding and on broiler meat at the end of the slaughter process is not expected.
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