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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...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Frontiers Media S.A.
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6473086/ https://www.ncbi.nlm.nih.gov/pubmed/31031716 http://dx.doi.org/10.3389/fmicb.2019.00687 |
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author | Cazer, Casey L. Al-Mamun, Mohammad A. Kaniyamattam, Karun Love, William J. Booth, James G. Lanzas, Cristina Gröhn, Yrjö T. |
author_facet | Cazer, Casey L. Al-Mamun, Mohammad A. Kaniyamattam, Karun Love, William J. Booth, James G. Lanzas, Cristina Gröhn, Yrjö T. |
author_sort | Cazer, Casey L. |
collection | PubMed |
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. |
format | Online Article Text |
id | pubmed-6473086 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-64730862019-04-26 Shared Multidrug Resistance Patterns in Chicken-Associated Escherichia coli Identified by Association Rule Mining Cazer, Casey L. Al-Mamun, Mohammad A. Kaniyamattam, Karun Love, William J. Booth, James G. Lanzas, Cristina Gröhn, Yrjö T. Front Microbiol Microbiology 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. Frontiers Media S.A. 2019-04-12 /pmc/articles/PMC6473086/ /pubmed/31031716 http://dx.doi.org/10.3389/fmicb.2019.00687 Text en Copyright © 2019 Cazer, Al-Mamun, Kaniyamattam, Love, Booth, Lanzas and Gröhn. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Microbiology Cazer, Casey L. Al-Mamun, Mohammad A. Kaniyamattam, Karun Love, William J. Booth, James G. Lanzas, Cristina Gröhn, Yrjö T. Shared Multidrug Resistance Patterns in Chicken-Associated Escherichia coli Identified by Association Rule Mining |
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 | Microbiology |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6473086/ https://www.ncbi.nlm.nih.gov/pubmed/31031716 http://dx.doi.org/10.3389/fmicb.2019.00687 |
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