Robustness in quantifying the abundance of antimicrobial resistance genes in pooled faeces samples from batches of slaughter pigs using metagenomics analysis

被引:5
作者
Andersen, Vibe Dalhoff [1 ]
Jensen, Marie Stengaard [1 ]
Munk, Patrick [1 ]
Vigre, Hakan [1 ]
机构
[1] Tech Univ Denmark, Natl Food Inst, Res Grp Genom Epidemiol, Lyngby, Denmark
关键词
Pigs; Antimicrobial resistance; Sampling; Pooled sample; Sequencing; Measurement error; SEQUENCING DEPTH; ASSOCIATION;
D O I
10.1016/j.jgar.2021.02.005
中图分类号
R51 [传染病];
学科分类号
100401 ;
摘要
Objectives: With the continued spread of antimicrobial resistance (AMR) in animals, it is important to assess its occurrence throughout a microbiome quantitatively in order to evaluate significantly affecting factors, e.g. antimicrobial usage. Metagenomics methods make it possible to measure the abundance of AMR genes in complex samples such as pooled faeces samples from batches of slaughter pigs. This study was performed to determine the random error in pooled samples from batches of pigs at slaughter and the measurement error from the metagenomics processes. Methods: In four farms, two pooled samples were obtained from a batch of slaughter pigs by two individual samplers, and each pooled sample was thereafter processed twice. Hierarchically clustered heatmaps were applied to evaluate dissimilarities between samples. The coefficient of variation was used to calculate the percentage difference between samples from the same farm. Results: Results of the analysis revealed that it was not possible to quantitatively separate the variation arising from sampling and metagenomics processes. They both contributed to the overall measurement error in batches of slaughter pigs. Conclusion: Sampling of single pigs in 30 randomly selected pig pens within the farms provides a composition representative for frequently occurring AMR genes present within the farms, while rare genes were not dispersed in a similar manner. Aggregating the resistance abundance at gene family or antimicrobial class level will reduce the apparent variation originating from errors in sampling and metagenomics processing. ? 2021 The Authors. Published by Elsevier Ltd on behalf of International Society for Antimicrobial Chemotherapy. This is an open access article under the CC BY-NC-ND license (http://creativecommons. Objectives: With the continued spread of antimicrobial resistance (AMR) in animals, it is important to assess its occurrence throughout a microbiome quantitatively in order to evaluate significantly affecting factors, e.g. antimicrobial usage. Metagenomics methods make it possible to measure the abundance of AMR genes in complex samples such as pooled faeces samples from batches of slaughter pigs. This study was performed to determine the random error in pooled samples from batches of pigs at slaughter and the measurement error from the metagenomics processes. Methods: In four farms, two pooled samples were obtained from a batch of slaughter pigs by two individual samplers, and each pooled sample was thereafter processed twice. Hierarchically clustered heatmaps were applied to evaluate dissimilarities between samples. The coefficient of variation was used to calculate the percentage difference between samples from the same farm. Results: Results of the analysis revealed that it was not possible to quantitatively separate the variation arising from sampling and metagenomics processes. They both contributed to the overall measurement error in batches of slaughter pigs. Conclusion: Sampling of single pigs in 30 randomly selected pig pens within the farms provides a composition representative for frequently occurring AMR genes present within the farms, while rare genes were not dispersed in a similar manner. Aggregating the resistance abundance at gene family or antimicrobial class level will reduce the apparent variation originating from errors in sampling and metagenomics processing. (c) 2021 The Authors. Published by Elsevier Ltd on behalf of International Society for Antimicrobial Chemotherapy. This is an open access article under the CC BY-NC-ND license (http://creativecommons. org/licenses/by-nc-nd/4.0/).
引用
收藏
页码:398 / 402
页数:5
相关论文
共 19 条
[1]   Predicting effects of changed antimicrobial usage on the abundance of antimicrobial resistance genes in finisher' gut microbiomes [J].
Andersen, V. D. ;
Aarestrup, F. M. ;
Munk, P. ;
Jensen, M. S. ;
de Knegt, L., V ;
Bortolaia, V ;
Knudsen, B. E. ;
Lukjancenko, O. ;
Birkegard, A. C. ;
Vigre, H. .
PREVENTIVE VETERINARY MEDICINE, 2020, 174
[2]  
Andersen VD, 2017, EPIDEMIOL INFECT, V145, P2827, DOI [10.1017/S0950268817001285, 10.1017/s0950268817001285]
[3]  
[Anonymous], 2004, RANDOM ORG TRUE RAND
[4]   The indigenous gastrointestinal microflora [J].
Berg, RD .
TRENDS IN MICROBIOLOGY, 1996, 4 (11) :430-435
[5]   Association between selected antimicrobial resistance genes and antimicrobial exposure in Danish pig farms [J].
Birkegard, Anna Camilla ;
Halasa, Tariq ;
Grsboll, Kaare ;
Clasen, Julie ;
Folkesson, Anders ;
Toft, Nils .
SCIENTIFIC REPORTS, 2017, 7
[6]   Determining the optimal number of individual samples to pool for quantification of average herd levels of antimicrobial resistance genes in Danish pig herds using high-throughput qPCR [J].
Clasen, Julie ;
Mellerup, Anders ;
Olsen, John Elmerdahl ;
Angen, Oystein ;
Folkesson, Anders ;
Halasa, Tariq ;
Toft, Nils ;
Birkegard, Anna Camilla .
VETERINARY MICROBIOLOGY, 2016, 189 :46-51
[7]   Rapid and precise alignment of raw reads against redundant databases with KMA [J].
Clausen, Philip T. L. C. ;
Aarestrup, Frank M. ;
Lund, Ole .
BMC BIOINFORMATICS, 2018, 19
[8]   What is antibiotic resistance and how can we measure it? [J].
Davison, HC ;
Low, JC ;
Woolhouse, MEJ .
TRENDS IN MICROBIOLOGY, 2000, 8 (12) :554-559
[9]   Antimicrobial resistance: harmonisation of national antimicrobial resistance monitoring and surveillance programmes in animals and in animal-derived food [J].
Franklin, A ;
Acar, J ;
Anthony, F ;
Gupta, R ;
Nicholls, T ;
Tamura, Y ;
Thompson, S ;
Threlfall, EJ ;
Vose, D ;
van Vuuren, M ;
White, DG ;
Wegener, HC ;
Costarrica, ML .
REVUE SCIENTIFIQUE ET TECHNIQUE-OFFICE INTERNATIONAL DES EPIZOOTIES, 2001, 20 (03) :859-870
[10]   Global monitoring of antimicrobial resistance based on metagenomics analyses of urban sewage [J].
Hendriksen, Rene S. ;
Munk, Patrick ;
Njage, Patrick ;
van Bunnik, Bram ;
McNally, Luke ;
Lukjancenko, Oksana ;
Roder, Timo ;
Nieuwenhuijse, David ;
Pedersen, Susanne Karlsmose ;
Kjeldgaard, Jette ;
Kaas, Rolf S. ;
Clausen, Philip Thomas Lanken Conradsen ;
Vogt, Josef Korbinian ;
Leekitcharoenphon, Pimlapas ;
van de Schans, Milou G. M. ;
Zuidema, Tina ;
Husman, Ana Maria de Roda ;
Rasmussen, Simon ;
Petersen, Bent ;
Amid, Clara ;
Cochrane, Guy ;
Sicheritz-Ponten, Thomas ;
Schmitt, Heike ;
Alvarez, Jorge Raul Matheu ;
Aidara-Kane, Awa ;
Pamp, Sunje J. ;
Lund, Ole ;
Hald, Tine ;
Woolhouse, Mark ;
Koopmans, Marion P. ;
Vigre, Hakan ;
Petersen, Thomas Nordahl ;
Aarestrup, Frank M. ;
Bego, Artan ;
Rees, Catherine ;
Cassar, Susan ;
Coventry, Kris ;
Collignon, Peter ;
Allerberger, Franz ;
Rahube, Teddie O. ;
Oliveira, Guilherme ;
Ivanov, Ivan ;
Vuthy, Yith ;
Sopheak, Thet ;
Yost, Christopher K. ;
Ke, Changwen ;
Zheng, Huanying ;
Li Baisheng ;
Jiao, Xiaoyang ;
Donado-Godoy, Pilar .
NATURE COMMUNICATIONS, 2019, 10 (1)