Pathogenomic Characterization of Multidrug-Resistant <i>Escherichia coli</i> Strains Carrying Wide Efflux-Associated and Virulence Genes from the Dairy Farm Environment in Xinjiang, China
<b>Background/Objectives</b>: Livestock species, particularly dairy animals, can serve as important reservoirs of <i>E. coli</i>, carrying antibiotic resistance and virulence genes under constant selective pressure and their spread in the environment. In this study, we perfor...
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2025-05-01
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| author | Muhammad Shoaib Sehrish Gul Sana Majeed Zhuolin He Baocheng Hao Minjia Tang Xunjing Zhang Zhongyong Wu Shengyi Wang Wanxia Pu |
| author_facet | Muhammad Shoaib Sehrish Gul Sana Majeed Zhuolin He Baocheng Hao Minjia Tang Xunjing Zhang Zhongyong Wu Shengyi Wang Wanxia Pu |
| author_sort | Muhammad Shoaib |
| collection | DOAJ |
| description | <b>Background/Objectives</b>: Livestock species, particularly dairy animals, can serve as important reservoirs of <i>E. coli</i>, carrying antibiotic resistance and virulence genes under constant selective pressure and their spread in the environment. In this study, we performed the pathogenomic analysis of seven multidrug resistant (MDR) <i>E. coli</i> strains carrying efflux-associated and virulence genes from the dairy farm environment in Xinjiang Province, China. <b>Methods</b>: First, we processed the samples using standard microbiological techniques followed by species identification with MALDI-TOF MS. Then, we performed whole genome sequencing (WGS) on the Illumina NovaSeq PE150 platform and conducted pathogenomic analysis using multiple bioinformatics tools. <b>Results</b>: WGS analysis revealed that the <i>E. coli</i> strains harbored diverse antibiotic efflux-associated genes, including conferring resistance to fluoroquinolones, aminoglycosides, aminocoumarins, macrolides, peptides, phosphonic acid, nitroimidazole, tetracyclines, disinfectants/antiseptics, and multidrug resistance. The phylogenetic analysis classified seven <i>E. coli</i> strains into B1 (<i>n</i> = 4), C (<i>n</i> = 2), and F (<i>n</i> = 1) phylogroups. PathogenFinder predicted all <i>E. coli</i> strains as potential human pathogens belonging to distinct serotypes and carrying broad virulence genes (ranging from 12 to 27), including the Shiga toxin-producing gene (<i>stx1</i>, <i>n</i> = 1). However, we found that a few of the virulence genes were associated with prophages and genomic islands in the <i>E. coli</i> strains. Moreover, all <i>E. coli</i> strains carried a diverse bacterial secretion systems and biofilm-associated genes. <b>Conclusions</b>: The present study highlights the need for large-scale genomic surveillance of antibiotic-resistant bacteria in dairy farm environments to identify AMR reservoir spillover and pathogenic risks to humans and design targeted interventions to further stop their spread under a One Health framework. |
| format | Article |
| id | doaj-art-ff711ca532394738a4e28b619cafcc60 |
| institution | OA Journals |
| issn | 2079-6382 |
| language | English |
| publishDate | 2025-05-01 |
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| series | Antibiotics |
| spelling | doaj-art-ff711ca532394738a4e28b619cafcc602025-08-20T01:56:24ZengMDPI AGAntibiotics2079-63822025-05-0114551110.3390/antibiotics14050511Pathogenomic Characterization of Multidrug-Resistant <i>Escherichia coli</i> Strains Carrying Wide Efflux-Associated and Virulence Genes from the Dairy Farm Environment in Xinjiang, ChinaMuhammad Shoaib0Sehrish Gul1Sana Majeed2Zhuolin He3Baocheng Hao4Minjia Tang5Xunjing Zhang6Zhongyong Wu7Shengyi Wang8Wanxia Pu9Key Laboratory of New Animal Drug Project Gansu Province, Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Lanzhou 730050, ChinaInstitute of Microbiology, University of Agriculture, Faisalabad 38000, PakistanLaboratory of Aquatic Animal Medicine, College of Veterinary Medicine, Chungbuk National University, Cheongju 28644, Republic of KoreaKey Laboratory of New Animal Drug Project Gansu Province, Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Lanzhou 730050, ChinaKey Laboratory of New Animal Drug Project Gansu Province, Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Lanzhou 730050, ChinaKey Laboratory of New Animal Drug Project Gansu Province, Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Lanzhou 730050, ChinaKey Laboratory of New Animal Drug Project Gansu Province, Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Lanzhou 730050, ChinaKey Laboratory of New Animal Drug Project Gansu Province, Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Lanzhou 730050, ChinaKey Laboratory of New Animal Drug Project Gansu Province, Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Lanzhou 730050, ChinaKey Laboratory of New Animal Drug Project Gansu Province, Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Lanzhou 730050, China<b>Background/Objectives</b>: Livestock species, particularly dairy animals, can serve as important reservoirs of <i>E. coli</i>, carrying antibiotic resistance and virulence genes under constant selective pressure and their spread in the environment. In this study, we performed the pathogenomic analysis of seven multidrug resistant (MDR) <i>E. coli</i> strains carrying efflux-associated and virulence genes from the dairy farm environment in Xinjiang Province, China. <b>Methods</b>: First, we processed the samples using standard microbiological techniques followed by species identification with MALDI-TOF MS. Then, we performed whole genome sequencing (WGS) on the Illumina NovaSeq PE150 platform and conducted pathogenomic analysis using multiple bioinformatics tools. <b>Results</b>: WGS analysis revealed that the <i>E. coli</i> strains harbored diverse antibiotic efflux-associated genes, including conferring resistance to fluoroquinolones, aminoglycosides, aminocoumarins, macrolides, peptides, phosphonic acid, nitroimidazole, tetracyclines, disinfectants/antiseptics, and multidrug resistance. The phylogenetic analysis classified seven <i>E. coli</i> strains into B1 (<i>n</i> = 4), C (<i>n</i> = 2), and F (<i>n</i> = 1) phylogroups. PathogenFinder predicted all <i>E. coli</i> strains as potential human pathogens belonging to distinct serotypes and carrying broad virulence genes (ranging from 12 to 27), including the Shiga toxin-producing gene (<i>stx1</i>, <i>n</i> = 1). However, we found that a few of the virulence genes were associated with prophages and genomic islands in the <i>E. coli</i> strains. Moreover, all <i>E. coli</i> strains carried a diverse bacterial secretion systems and biofilm-associated genes. <b>Conclusions</b>: The present study highlights the need for large-scale genomic surveillance of antibiotic-resistant bacteria in dairy farm environments to identify AMR reservoir spillover and pathogenic risks to humans and design targeted interventions to further stop their spread under a One Health framework.https://www.mdpi.com/2079-6382/14/5/511<i>Escherichia coli</i>antibiotic efflux genesvirulence genesserotypingprophagesgenomic islands |
| spellingShingle | Muhammad Shoaib Sehrish Gul Sana Majeed Zhuolin He Baocheng Hao Minjia Tang Xunjing Zhang Zhongyong Wu Shengyi Wang Wanxia Pu Pathogenomic Characterization of Multidrug-Resistant <i>Escherichia coli</i> Strains Carrying Wide Efflux-Associated and Virulence Genes from the Dairy Farm Environment in Xinjiang, China Antibiotics <i>Escherichia coli</i> antibiotic efflux genes virulence genes serotyping prophages genomic islands |
| title | Pathogenomic Characterization of Multidrug-Resistant <i>Escherichia coli</i> Strains Carrying Wide Efflux-Associated and Virulence Genes from the Dairy Farm Environment in Xinjiang, China |
| title_full | Pathogenomic Characterization of Multidrug-Resistant <i>Escherichia coli</i> Strains Carrying Wide Efflux-Associated and Virulence Genes from the Dairy Farm Environment in Xinjiang, China |
| title_fullStr | Pathogenomic Characterization of Multidrug-Resistant <i>Escherichia coli</i> Strains Carrying Wide Efflux-Associated and Virulence Genes from the Dairy Farm Environment in Xinjiang, China |
| title_full_unstemmed | Pathogenomic Characterization of Multidrug-Resistant <i>Escherichia coli</i> Strains Carrying Wide Efflux-Associated and Virulence Genes from the Dairy Farm Environment in Xinjiang, China |
| title_short | Pathogenomic Characterization of Multidrug-Resistant <i>Escherichia coli</i> Strains Carrying Wide Efflux-Associated and Virulence Genes from the Dairy Farm Environment in Xinjiang, China |
| title_sort | pathogenomic characterization of multidrug resistant i escherichia coli i strains carrying wide efflux associated and virulence genes from the dairy farm environment in xinjiang china |
| topic | <i>Escherichia coli</i> antibiotic efflux genes virulence genes serotyping prophages genomic islands |
| url | https://www.mdpi.com/2079-6382/14/5/511 |
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