Genotypic Characterisation and Risk Assessment of Virulent ESBL-Producing <i>E. coli</i> in Chicken Meat in Tunisia: Insights from Multi-Omics Machine Learning Perspective
Antibiotics are frequently used in the poultry industry, which has led to the emergence of bacterial strains that are resistant to antimicrobial treatments. The main objectives of this research were to conduct a multimodal risk assessment, to determine the extent of contamination of chicken meat wit...
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2025-06-01
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| author | Khaled Abdallah Ghassan Tayh Elaa Maamar Amine Mosbah Omar Abbes Ismail Fliss Lilia Messadi |
| author_facet | Khaled Abdallah Ghassan Tayh Elaa Maamar Amine Mosbah Omar Abbes Ismail Fliss Lilia Messadi |
| author_sort | Khaled Abdallah |
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| description | Antibiotics are frequently used in the poultry industry, which has led to the emergence of bacterial strains that are resistant to antimicrobial treatments. The main objectives of this research were to conduct a multimodal risk assessment, to determine the extent of contamination of chicken meat with <i>Escherichia coli</i>, assess the prevalence of strains resistant to extended-spectrum cephalosporins (ESC), and characterise the genes associated with resistance and virulence. A standardised procedure involving enrichment in buffered peptone water and isolation of <i>E. coli</i> on MacConkey agar was carried out on 100 chicken carcasses. Subsequently, the sensitivity of the strains was tested against 21 antibiotic discs. Additionally, ESBL production was detected using a double synergy test. Specific PCRs were employed to identify resistance to critical antibiotics in human medicine (such as cephalosporins, carbapenems, fluoroquinolones, and colistin), as well as the presence of virulence genes. The contamination rate of chicken meat with <i>E. coli</i> was 82%. The prevalence of ESC-resistant isolates was 91.2%. Furthermore, 76.5% of the isolates exhibited ESBL production, with the different beta-lactamase genes (<i>bla</i><sub>CTXM</sub>, <i>bla</i><sub>TEM</sub>, and <i>bla</i><sub>SHV</sub>). The <i>mcr-1</i> gene, associated with colistin resistance, was detected in four strains (5.9%). Some isolates also carried resistance genes such as <i>sul1</i>, <i>sul2</i>, <i>sul3</i>, <i>tetA</i>, <i>tetB</i>, <i>qnrB</i>, and <i>qnrS</i>. In addition, several virulence genes were detected. In our study, we were able to link the expression of AMR to the iron metabolic regulatory elements using a multimodal machine learning approach; this mechanism could be targeted to mitigate the bacteria virulence and resistance. The high prevalence of ESBL-producing and multi-resistant <i>E. coli</i> strains in poultry presents significant human health risks, with the focus on antibiotic-resistant uropathogenic strains since poultry meat could be an important source of uropathogenic strains, underscoring the danger of hard-to-treat urinary tract infections, stressing the need for controlled antibiotic use and thorough monitoring. |
| format | Article |
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| institution | Kabale University |
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| spelling | doaj-art-c7145ec2c25d4cf6801f3246b933ffa32025-08-20T03:27:21ZengMDPI AGMicrobiology Research2036-74812025-06-0116613110.3390/microbiolres16060131Genotypic Characterisation and Risk Assessment of Virulent ESBL-Producing <i>E. coli</i> in Chicken Meat in Tunisia: Insights from Multi-Omics Machine Learning PerspectiveKhaled Abdallah0Ghassan Tayh1Elaa Maamar2Amine Mosbah3Omar Abbes4Ismail Fliss5Lilia Messadi6University Manouba, Service de Microbiologie et Immunologie, Ecole Nationale de Médecine Vétérinaire, IRESA, Sidi Thabet 2020, TunisiaUniversity Manouba, Service de Microbiologie et Immunologie, Ecole Nationale de Médecine Vétérinaire, IRESA, Sidi Thabet 2020, TunisiaUniversity Manouba, Service de Microbiologie et Immunologie, Ecole Nationale de Médecine Vétérinaire, IRESA, Sidi Thabet 2020, TunisiaUniversity Manouba, Service d’Aquaculture et Ichtyopathologie, Ecole Nationale de Médecine Vétérinaire, IRESA, Sidi Thabet 2020, TunisiaDICK Company, Poulina Group Holding, Ben Arous 2097, TunisiaDepartment of Food Science, Laval University, Quebec City, QC G1V 0A6, CanadaUniversity Manouba, Service de Microbiologie et Immunologie, Ecole Nationale de Médecine Vétérinaire, IRESA, Sidi Thabet 2020, TunisiaAntibiotics are frequently used in the poultry industry, which has led to the emergence of bacterial strains that are resistant to antimicrobial treatments. The main objectives of this research were to conduct a multimodal risk assessment, to determine the extent of contamination of chicken meat with <i>Escherichia coli</i>, assess the prevalence of strains resistant to extended-spectrum cephalosporins (ESC), and characterise the genes associated with resistance and virulence. A standardised procedure involving enrichment in buffered peptone water and isolation of <i>E. coli</i> on MacConkey agar was carried out on 100 chicken carcasses. Subsequently, the sensitivity of the strains was tested against 21 antibiotic discs. Additionally, ESBL production was detected using a double synergy test. Specific PCRs were employed to identify resistance to critical antibiotics in human medicine (such as cephalosporins, carbapenems, fluoroquinolones, and colistin), as well as the presence of virulence genes. The contamination rate of chicken meat with <i>E. coli</i> was 82%. The prevalence of ESC-resistant isolates was 91.2%. Furthermore, 76.5% of the isolates exhibited ESBL production, with the different beta-lactamase genes (<i>bla</i><sub>CTXM</sub>, <i>bla</i><sub>TEM</sub>, and <i>bla</i><sub>SHV</sub>). The <i>mcr-1</i> gene, associated with colistin resistance, was detected in four strains (5.9%). Some isolates also carried resistance genes such as <i>sul1</i>, <i>sul2</i>, <i>sul3</i>, <i>tetA</i>, <i>tetB</i>, <i>qnrB</i>, and <i>qnrS</i>. In addition, several virulence genes were detected. In our study, we were able to link the expression of AMR to the iron metabolic regulatory elements using a multimodal machine learning approach; this mechanism could be targeted to mitigate the bacteria virulence and resistance. The high prevalence of ESBL-producing and multi-resistant <i>E. coli</i> strains in poultry presents significant human health risks, with the focus on antibiotic-resistant uropathogenic strains since poultry meat could be an important source of uropathogenic strains, underscoring the danger of hard-to-treat urinary tract infections, stressing the need for controlled antibiotic use and thorough monitoring.https://www.mdpi.com/2036-7481/16/6/131<i>Escherichia coli</i>chickenvirulence factorsESBLmultimodal machine learningTunisia |
| spellingShingle | Khaled Abdallah Ghassan Tayh Elaa Maamar Amine Mosbah Omar Abbes Ismail Fliss Lilia Messadi Genotypic Characterisation and Risk Assessment of Virulent ESBL-Producing <i>E. coli</i> in Chicken Meat in Tunisia: Insights from Multi-Omics Machine Learning Perspective Microbiology Research <i>Escherichia coli</i> chicken virulence factors ESBL multimodal machine learning Tunisia |
| title | Genotypic Characterisation and Risk Assessment of Virulent ESBL-Producing <i>E. coli</i> in Chicken Meat in Tunisia: Insights from Multi-Omics Machine Learning Perspective |
| title_full | Genotypic Characterisation and Risk Assessment of Virulent ESBL-Producing <i>E. coli</i> in Chicken Meat in Tunisia: Insights from Multi-Omics Machine Learning Perspective |
| title_fullStr | Genotypic Characterisation and Risk Assessment of Virulent ESBL-Producing <i>E. coli</i> in Chicken Meat in Tunisia: Insights from Multi-Omics Machine Learning Perspective |
| title_full_unstemmed | Genotypic Characterisation and Risk Assessment of Virulent ESBL-Producing <i>E. coli</i> in Chicken Meat in Tunisia: Insights from Multi-Omics Machine Learning Perspective |
| title_short | Genotypic Characterisation and Risk Assessment of Virulent ESBL-Producing <i>E. coli</i> in Chicken Meat in Tunisia: Insights from Multi-Omics Machine Learning Perspective |
| title_sort | genotypic characterisation and risk assessment of virulent esbl producing i e coli i in chicken meat in tunisia insights from multi omics machine learning perspective |
| topic | <i>Escherichia coli</i> chicken virulence factors ESBL multimodal machine learning Tunisia |
| url | https://www.mdpi.com/2036-7481/16/6/131 |
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