Shared Multidrug Resistance Patterns in Chicken-Associated Escherichia coli Identified by Association Rule Mining
Using multiple antimicrobials in food animals may incubate genetically-linked multidrug-resistance (MDR) in enteric bacteria, which can contaminate meat at slaughter. The U.S. National Antimicrobial Resistance Monitoring System tested 14,418 chicken-associated Escherichia coli between 2004 and 2012...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2019-04-01
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| Series: | Frontiers in Microbiology |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/article/10.3389/fmicb.2019.00687/full |
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| author | Casey L. Cazer Mohammad A. Al-Mamun Karun Kaniyamattam William J. Love James G. Booth Cristina Lanzas Yrjö T. Gröhn |
| author_facet | Casey L. Cazer Mohammad A. Al-Mamun Karun Kaniyamattam William J. Love James G. Booth Cristina Lanzas Yrjö T. Gröhn |
| author_sort | Casey L. Cazer |
| collection | DOAJ |
| description | Using multiple antimicrobials in food animals may incubate genetically-linked multidrug-resistance (MDR) in enteric bacteria, which can contaminate meat at slaughter. The U.S. National Antimicrobial Resistance Monitoring System tested 14,418 chicken-associated Escherichia coli between 2004 and 2012 for resistance to 15 antimicrobials, resulting in >32,000 possible MDR patterns. We analyzed MDR patterns in this dataset with association rule mining, also called market-basket analysis. The association rules were pruned with four quality measures resulting in a <1% false-discovery rate. MDR rules were more stable across consecutive years than between slaughter and retail. Rules were decomposed into networks with antimicrobials as nodes and rules as edges. A strong subnetwork of beta-lactam resistance existed in each year and the beta-lactam resistances also had strong associations with sulfisoxazole, gentamicin, streptomycin and tetracycline resistances. The association rules concur with previously identified E. coli resistance patterns but provide significant flexibility for studying MDR in large datasets. |
| first_indexed | 2024-12-13T00:26:52Z |
| format | Article |
| id | doaj.art-51ed0c39c74942adb807436999d04b6a |
| institution | Directory Open Access Journal |
| issn | 1664-302X |
| language | English |
| last_indexed | 2024-12-13T00:26:52Z |
| publishDate | 2019-04-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj.art-51ed0c39c74942adb807436999d04b6a2022-12-22T00:05:24ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2019-04-011010.3389/fmicb.2019.00687446995Shared Multidrug Resistance Patterns in Chicken-Associated Escherichia coli Identified by Association Rule MiningCasey L. Cazer0Mohammad A. Al-Mamun1Karun Kaniyamattam2William J. Love3James G. Booth4Cristina Lanzas5Yrjö T. Gröhn6Department of Population Medicine and Diagnostic Sciences, Cornell University College of Veterinary Medicine, Ithaca, NY, United StatesDepartment of Epidemiology of Microbial Diseases, Yale University School of Public Health, New Haven, CT, United StatesDepartment of Population Medicine and Diagnostic Sciences, Cornell University College of Veterinary Medicine, Ithaca, NY, United StatesDepartment of Population Health and Pathobiology, North Carolina State University College of Veterinary Medicine, Raleigh, NC, United StatesDepartment of Biological Statistics and Computational Biology, Cornell University College of Agriculture and Life Sciences, Ithaca, NY, United StatesDepartment of Population Health and Pathobiology, North Carolina State University College of Veterinary Medicine, Raleigh, NC, United StatesDepartment of Population Medicine and Diagnostic Sciences, Cornell University College of Veterinary Medicine, Ithaca, NY, United StatesUsing multiple antimicrobials in food animals may incubate genetically-linked multidrug-resistance (MDR) in enteric bacteria, which can contaminate meat at slaughter. The U.S. National Antimicrobial Resistance Monitoring System tested 14,418 chicken-associated Escherichia coli between 2004 and 2012 for resistance to 15 antimicrobials, resulting in >32,000 possible MDR patterns. We analyzed MDR patterns in this dataset with association rule mining, also called market-basket analysis. The association rules were pruned with four quality measures resulting in a <1% false-discovery rate. MDR rules were more stable across consecutive years than between slaughter and retail. Rules were decomposed into networks with antimicrobials as nodes and rules as edges. A strong subnetwork of beta-lactam resistance existed in each year and the beta-lactam resistances also had strong associations with sulfisoxazole, gentamicin, streptomycin and tetracycline resistances. The association rules concur with previously identified E. coli resistance patterns but provide significant flexibility for studying MDR in large datasets.https://www.frontiersin.org/article/10.3389/fmicb.2019.00687/fullassociation rule miningantimicrobial resistanceEscherichia colimachine learningmultidrug resistancefoodborne bacteria |
| spellingShingle | Casey L. Cazer Mohammad A. Al-Mamun Karun Kaniyamattam William J. Love James G. Booth Cristina Lanzas Yrjö T. Gröhn Shared Multidrug Resistance Patterns in Chicken-Associated Escherichia coli Identified by Association Rule Mining Frontiers in Microbiology association rule mining antimicrobial resistance Escherichia coli machine learning multidrug resistance foodborne bacteria |
| title | Shared Multidrug Resistance Patterns in Chicken-Associated Escherichia coli Identified by Association Rule Mining |
| title_full | Shared Multidrug Resistance Patterns in Chicken-Associated Escherichia coli Identified by Association Rule Mining |
| title_fullStr | Shared Multidrug Resistance Patterns in Chicken-Associated Escherichia coli Identified by Association Rule Mining |
| title_full_unstemmed | Shared Multidrug Resistance Patterns in Chicken-Associated Escherichia coli Identified by Association Rule Mining |
| title_short | Shared Multidrug Resistance Patterns in Chicken-Associated Escherichia coli Identified by Association Rule Mining |
| title_sort | shared multidrug resistance patterns in chicken associated escherichia coli identified by association rule mining |
| topic | association rule mining antimicrobial resistance Escherichia coli machine learning multidrug resistance foodborne bacteria |
| url | https://www.frontiersin.org/article/10.3389/fmicb.2019.00687/full |
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