Clonal diversity and zoonotic potential of MDR Escherichia coli isolated from poultry at different age intervals

References

• Abdi-Hachesoo, B., K. Asasi, and H. Sharifiyazdi. 2013. “Rapid Detection of Escherichia coli gyrA and parC Mutants in One-Day-Old Broiler Chicks in Iran.” Veterinaria Italiana 49 (3): 291–297.
   PubMed Web of Science ®Google Scholar
• Bahman, A. H., A. Derakhshandeh, M. Motamedifar, and N. Azimzadeh. 2020. “Antimicrobial Resistance Profiles and Clonal Relationship Among Non-ESBL Avian Pathogenic Escherichia coli Isolates and ESBL Producing E. Coli Isolates from Human Urinary Tract Infections.” Iranian Journal of Public Health 49 (3): 530–538.
   Web of Science ®Google Scholar
• Ballou, A. L., R. A. Ali, M. A. Mendoza, J. C. Ellis, H. M. Hassan, W. J. Croom, and M. D. Koci. 2016. “Development of the Chick Microbiome: How Early Exposure Influences Future Microbial Diversity.” Frontiers in Veterinary Science 3: 2. https://doi.org/10.3389/fvets.2016.00002.
   PubMed Web of Science ®Google Scholar
• Card, R. M., S. A. Cawthraw, J. Nunez-Garcia, R. J. Ellis, G. Kay, M. J. Pallen, and M. F. Anjum. 2017. “An In Vitro Chicken Gut Model Demonstrates Transfer of a Multidrug Resistance Plasmid from Salmonella to Commensal Escherichia coli.” MBio 8 (4): e00777–17. https://doi.org/10.1128/mBio.00777-17.
   PubMed Web of Science ®Google Scholar
• Carter, M. E., P. J. Quinu, B. K. Markey, and G. R. Carter. 1994. Clinical Veterinary Microbiology, 1–645. USA: Wolf Publishing Company.
   Google Scholar
• Clancy, M. M., M. Davis, M. Valitutto, K. Nelson, and J. M. Sykes. 2016. “Infection and Carriage in Reptiles in a Zoological Collection.” Zoo Animals 248 (9): 1050–1059. https://doi.org/10.2460/javma.248.9.1050.
   Google Scholar
• Clinical and Laboratory Standards Institute. 2010. Performance Standards for Antimicrobial Susceptibility Testing: Twentieth Informational Supplement (M100-S20U). Clinical and Laboratory Standards Institute.
   Google Scholar
• Danicke, S., W. Vahjen, O. Simon, and H. Jeroch. 1999. “Effects of Dietary Fat Source and Xylanase Supplementation to Rye-Based Broiler Diets on Selected Bacterial Groups Adhering to the Intestinal Epithelium, on Transit Time of Feed, and on Nutrient Digestibility.” Poultry Science 78 (9): 1292–1299. https://doi.org/10.1093/ps/78.9.1292.
   PubMed Web of Science ®Google Scholar
• Ewers, C., I. Stamm, Y. Pfeifer, L. H. Wieler, P. A. Kopp, K. Schønning, and A. Bethe. 2014. “Clonal Spread of Highly Successful ST15-CTX-M-15 Klebsiella pneumoniae in Companion Animals and Horses.” Journal of Antimicrobial Chemotherapy 69 (10): 2676–2680. https://doi.org/10.1093/jac/dku217.
   PubMed Web of Science ®Google Scholar
• Fricke, W. F., M. S. Wright, A. H. Lindell, D. M. Harkins, C. Baker-Austin, J. Ravel, and R. Stepanauskas. 2008. “Insights into the Environmental Resistance Gene Pool from the Genome Sequence of the Multidrug-Resistant Environmental Isolate Escherichia coli SMS-3-5.” Journal of Bacteriology 190 (20): 6779–6794. https://doi.org/10.1128/JB.00661-08.
   PubMed Web of Science ®Google Scholar
• Garud, N. R., B. H. Good, O. Hallatschek, K. S. Pollard, and I. Gordo. 2019. “Evolutionary Dynamics of Bacteria in the Gut Microbiome within and Across Hosts.” PLoS Biology 17 (1): e3000102. https://doi.org/10.1371/journal.pbio.3000102.
   PubMed Web of Science ®Google Scholar
• Gordon, D. M. 1997. “The Genetic Structure of Escherichia coli Populations in Feral House Mice.” Microbiology (Reading, England) 143 (6): 2039–2046. https://doi.org/10.1099/00221287-143-6-2039.
   PubMedGoogle Scholar
• Hammerum, A. M., and O. E. Heuer. 2009. “Human Health Hazards from Antimicrobial-Resistant Escherichia coli of Animal Origin.” Clinical Infectious Diseases 48 (7): 916–921. https://doi.org/10.1086/597292.
   PubMed Web of Science ®Google Scholar
• Helmy, Y. A., H. El-Adawy, and E. M. Abdelwhab. 2017. “A Comprehensive Review of Common Bacterial, Parasitic and Viral Zoonoses at the Human-Animal Interface in Egypt.” Pathogens 6 (3): 33. https://doi.org/10.3390/pathogens6030033.
   PubMed Web of Science ®Google Scholar
• Jakobsson, H. E., C. Jernberg, A. F. Andersson, M. Sjölundkarlsson, J. K. Jansson, and L. Engstrand. 2010. “Short-Term Antibiotic Treatment Has Differing Longterm Impacts on the Human Throat and Gut Microbiome.” PLoS ONE 5 (3): e9836. https://doi.org/10.1371/journal.pone.0009836.
   PubMed Web of Science ®Google Scholar
• Johnson, J. R., S. Miller, B. Johnston, C. Clabots, and C. DebRoy. 2009. “Sharing of Escherichia coli Sequence Type ST131 and Other Multidrug-Resistant and Urovirulent E. Coli Strains Among Dogs and Cats within a Household.” Journal of Clinical Microbiology 47 (11): 3721–3725. https://doi.org/10.1128/JCM.01581-09.
   PubMed Web of Science ®Google Scholar
• Johnson, T. J., J. L. Thorsness, C. P. Anderson, A. M. Lynne, S. L. Foley, J. Han, and R. S. Singer. 2010. “Horizontal Gene Transfer of a ColV Plasmid Has Resulted in a Dominant Avian Clonal Type of Salmonella enterica Serovar Kentucky.” PLoS One 5 (12): e15524. https://doi.org/10.1371/journal.pone.0015524.
   PubMed Web of Science ®Google Scholar
• Jones, G. P. D., and D. R. Taylor. 2001. “The Incorporation of Whole Grain into Pelleted Broiler Chicken Diets: Production and Physiological Responses.” British Poultry Science 42 (4): 477–483. https://doi.org/10.1080/00071660120070587.
   PubMed Web of Science ®Google Scholar
• Kluytmans, J. A. J. W., I. T. M. A. Overdevest, I. Willemsen, M. F. Q. Kluytmans-Van Den Bergh, and K. Van Der Zwaluw. 2013. “Extended-Spectrum β-Lactamase–Producing Escherichia coli from Retail Chicken Meat and Humans: Comparison of Strains, Plasmids, Resistance Genes, and Virulence Factors.” Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America 56 (4): 478–487. https://doi.org/10.1093/cid/cis929.
   PubMed Web of Science ®Google Scholar
• Knarreborg, A., M. A. Simon, R. M. Engberg, B. B. Jensen, and G. W. Tannock. 2002. “Effects of Dietary Fat Source and Subtherapeutic Levels of Antibiotic on the Bacterial Community in the Ileum of Broiler Chickens at Various Ages.” Applied and Environmental Microbiology 68 (12): 5918–5924. https://doi.org/10.1128/AEM.68.12.5918-5924.2002.
   PubMed Web of Science ®Google Scholar
• Kostman, J. R., T. D. Edlind, J. J. LiPuma, and T. L. Stull. 1992. “Molecular Epidemiology of Pseudomonas Cepacia Determined by Polymerase Chain Reaction Ribotyping.” Journal of Clinical Microbiology 30 (8): 2084–2087. https://doi.org/10.1128/jcm.30.8.2084-2087.1992.
   PubMed Web of Science ®Google Scholar
• Krumperman, P. H. 1983. “Multiple Antibiotic Resistance Indexing of Escherichia coli to Identify High-Risk Sources of Fecal Contamination of Foods.” Applied and Environmental Microbiology 46 (1): 165–170. https://doi.org/10.1128/aem.46.1.165-170.1983.
   PubMed Web of Science ®Google Scholar
• Lu, J., U. Idris, B. Harmon, C. Hofacre, J. J. Maurer, and M. D. Lee. 2003. “Diversity and Succession of the Intestinal Bacterial Community of the Maturing Broiler Chicken.” Applied and Environmental Microbiology 69 (11): 6816–6824. https://doi.org/10.1128/AEM.69.11.6816-6824.2003.
   PubMed Web of Science ®Google Scholar
• Manges, A. R., J. R. Johnson, B. Foxman, T. T. O’Bryan, K. E. Fullerton, and L. W. Riley. 2001. “Widespread Distribution of Urinary Tract Infections Caused by a Multidrug-Resistant Escherichia coli Clonal Group.” New England Journal of Medicine 345 (14): 1007–1013. https://doi.org/10.1056/NEJMoa011265.
   PubMed Web of Science ®Google Scholar
• Moawad, A. A., H. Hotzel, H. Neubauer, R. Ehricht, S. Monecke, H. Tomaso, and H. El-Adawy. 2018. “Antimicrobial Resistance in Enterobacteriaceae from Healthy Broilers in Egypt: Emergence of Colistin-Resistant and Extended-Spectrum β-Lactamase-Producing Escherichia coli.” Gut Pathogens 10 (1): 1–12. https://doi.org/10.1186/s13099-018-0266-5.
   PubMedGoogle Scholar
• Muloi, D., M. J. Ward, A. B. Pedersen, E. M. Fevre, M. E. Woolhouse, and B. A. Van Bunnik. 2018. “Are Food Animals Responsible for Transfer of Antimicrobial-Resistant Escherichia coli or Their Resistance Determinants to Human Populations? A Systematic Review.” Foodborne Pathogens and Disease 15 (8): 467–474. https://doi.org/10.1089/fpd.2017.2411.
   PubMed Web of Science ®Google Scholar
• Ngeleka, M., J. K. Kwaga, D. G. White, T. S. Whittam, C. Riddell, R. Goodhope, A. A. Potter, and B. Allan. 1996. “Escherichia coli Cellulitis in Broiler Chickens: Clonal Relationships Among Strains and Analysis of Virulence-Associated Factors of Isolates from Diseased Birds.” Infection and Immunity 64 (8): 3118–3126. https://doi.org/10.1128/iai.64.8.3118-3126.1996.
   PubMed Web of Science ®Google Scholar
• Nitsan, Z., G. Ben‐Avraham, Z. Zoref, and I. Nir. 1991. “Growth and Development of the Digestive Organs and Some Enzymes in Broiler Chicks After Hatching.” British Poultry Science 32 (3): 515–523. https://doi.org/10.1080/00071669108417376.
   PubMed Web of Science ®Google Scholar
• Ochman, H., and R. K. Selander. 1984. “Evidence for Clonal Population Structure in Escherichia coli.” Proceedings of the National Academy of Sciences 81 (1): 198–201. https://doi.org/10.1073/pnas.81.1.198.
   PubMed Web of Science ®Google Scholar
• Pavel, A. B., and C. I. Vasile. 2012. “PyElph-A Software Tool for Gel Images Analysis and Phylogenetics.” BMC Bioinformatics 13 (1): 1–6. https://doi.org/10.1186/1471-2105-13-9.
   PubMedGoogle Scholar
• Poulsen, L. L., I. Thøfner, M. Bisgaard, J. P. Christensen, R. H. Olsen, and H. Christensen. 2017. “Longitudinal Study of Transmission of Escherichia coli from Broiler Breeders to Broilers.” Veterinary Microbiology 207:13–18. https://doi.org/10.1016/j.vetmic.2017.05.029.
   PubMed Web of Science ®Google Scholar
• Rahmani, M., S. M. Peighambari, C. A. Svendsen, L. M. Cavaco, Y. Agersø, and R. S. Hendriksen. 2013. “Molecular Clonality and Antimicrobial Resistance in Salmonella enterica Serovars Enteritidis and Infantis from Broilers in Three Northern Regions of Iran.” BMC Veterinary Research 9 (1): 1–9. https://doi.org/10.1186/1746-6148-9-66.
   PubMedGoogle Scholar
• Salinas, L., P. Cárdenas, T. J. Johnson, K. Vasco, J. Graham, G. Trueba, and M. Castanheira. 2019. “Diverse Commensal Escherichia coli Clones and Plasmids Disseminate Antimicrobial Resistance Genes in Domestic Animals and Children in a Semirural Community in Ecuador.” MSphere [Internet] 4 (3): e00316–19. https://doi.org/10.1128/mSphere.00316-19.
   PubMed Web of Science ®Google Scholar
• Schroeder, C. M., D. G. White, and J. Meng. 2004. “Retail Meat and Poultry as a Reservoir of Antimicrobial-Resistant Escherichia coli.” Food Microbiology 21 (3): 249–255. https://doi.org/10.1016/S0740-0020_03_00074-1.
   Web of Science ®Google Scholar
• Seiffert, S. N., M. Hilty, V. Perreten, and A. Endimiani. 2013. “Extended-Spectrum Cephalosporin-Resistant Gram-Negative Organisms in Livestock: An Emerging Problem for Human Health.” Drug Resistance Updates 16 (1–2): 22–45. https://doi.org/10.1016/j.drup.2012.12.001.
   PubMed Web of Science ®Google Scholar
• Whittam, T. S. 1989. “Clonal Dynamics of Escherichia coli in Its Natural Habitat.” Antonie Van Leeuwenhoek 55 (1): 23–32. https://doi.org/10.1007/BF02309616.
   PubMedGoogle Scholar
• Wirth, T., D. Falush, R. Lan, F. Colles, P. Mensa, L. H. Wieler, and M. Achtman. 2006. “Sex and Virulence in Escherichia coli: An Evolutionary Perspective.” Molecular Microbiology 60 (5): 1136–1151. https://doi.org/10.1111/j.1365-2958.2006.05172.x.
   PubMed Web of Science ®Google Scholar
• Zhang, X., S. Xiao, X. Jiang, Y. Li, Z. Fan, Y. Yu, and C. Liu. 2019. “Genomic Characterization of Escherichia coli LCT-EC001, an Extremely Multidrug-Resistant Strain with an Amazing Number of Resistance Genes.” Gut Pathogens 11 (1): 1–8. https://doi.org/10.1186/s13099-019-0298-5.
   PubMedGoogle Scholar