Spatial and temporal dynamics of microbiomes and resistomes in broiler litter stockpiles

Farmers apply broiler chicken litter to soils to enrich organic matter and provide crops with nutrients, following varying periods of stockpiling. However, litter frequently harbors fecal-derived microbial pathogens and associated antibiotic resistance genes (ARGs), and may be a source of microbial...

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Autores principales:	Chhedi Lal Gupta, Ran Avidov, Karuppasamy Kattusamy, Ibrahim Saadi, Vempalli Sudharsan Varma, Shlomo E. Blum, Yong‑Guan Zhu, Xin‑Yuan Zhou, Jian‑Qiang Su, Yael Laor, Eddie Cytryn
Formato:	article
Lenguaje:	EN
Publicado:	Elsevier 2021
Materias:	Microbiome Antibiotic resistance gene Antibiotic resistance bacteria Broiler litter Bioinformatics Long-read sequencing Biotechnology TP248.13-248.65
Acceso en línea:	https://doaj.org/article/10295c7884fa498e8b1efe876c88e8e2
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spelling	oai:doaj.org-article:10295c7884fa498e8b1efe876c88e8e22021-11-26T04:26:49ZSpatial and temporal dynamics of microbiomes and resistomes in broiler litter stockpiles2001-037010.1016/j.csbj.2021.11.020https://doaj.org/article/10295c7884fa498e8b1efe876c88e8e22021-01-01T00:00:00Zhttp://www.sciencedirect.com/science/article/pii/S2001037021004852https://doaj.org/toc/2001-0370Farmers apply broiler chicken litter to soils to enrich organic matter and provide crops with nutrients, following varying periods of stockpiling. However, litter frequently harbors fecal-derived microbial pathogens and associated antibiotic resistance genes (ARGs), and may be a source of microbial contamination of produce. We coupled a cutting-edge Loop Genomics long-read 16S rRNA amplicon-sequencing platform with high-throughput qPCR that targeted a suite of ARGs, to assess temporal (five time points over a 60-day period) and spatial (top, middle and bottom layers) microbiome and resistome dynamics in a broiler litter stockpile. We focused on potentially pathogenic species from the Enterobacteriaceae, Enterococcaceae and Staphylococcaceae families associated with food-borne disease. Bacterial diversity was significantly lower in the middle of the stockpile, where targeted pathogens were lowest and Bacillaceae were abundant. E. coli was the most abundant Enterobacteriaceae species, and high levels of the opportunistic pathogen Enterococcus faecium were detected. Correlation analyses revealed that the latter was significantly associated with aminoglycoside (aac(6′)-Ib(aka aacA4), aadA5), tetracycline (tetG), vancomycin (vanC), phenicol (floR) and MLSB (mphB) resistance genes. Staphylococcaceae were primarily non-pathogenic, but extremely low levels of the opportunistic pathogen S. aureus were detected, as was the opportunistic pathogen S. saprophyticus, which was linked to vancomycin (vanSA, vanC1), MLSB (vatE, ermB) and tetracycline (tetK) resistance genes. Collectively, we found that stockpile microbiomes and resistomes are strongly dictated by temporal fluctuations and spatial heterogeneity. Insights from this study can be exploited to improve stockpile management practice to support sustainable antimicrobial resistance mitigation policies in the future.Chhedi Lal GuptaRan AvidovKaruppasamy KattusamyIbrahim SaadiVempalli Sudharsan VarmaShlomo E. BlumYong‑Guan ZhuXin‑Yuan ZhouJian‑Qiang SuYael LaorEddie CytrynElsevierarticleMicrobiomeAntibiotic resistance geneAntibiotic resistance bacteriaBroiler litterBioinformaticsLong-read sequencingBiotechnologyTP248.13-248.65ENComputational and Structural Biotechnology Journal, Vol 19, Iss , Pp 6201-6211 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Microbiome Antibiotic resistance gene Antibiotic resistance bacteria Broiler litter Bioinformatics Long-read sequencing Biotechnology TP248.13-248.65
spellingShingle	Microbiome Antibiotic resistance gene Antibiotic resistance bacteria Broiler litter Bioinformatics Long-read sequencing Biotechnology TP248.13-248.65 Chhedi Lal Gupta Ran Avidov Karuppasamy Kattusamy Ibrahim Saadi Vempalli Sudharsan Varma Shlomo E. Blum Yong‑Guan Zhu Xin‑Yuan Zhou Jian‑Qiang Su Yael Laor Eddie Cytryn Spatial and temporal dynamics of microbiomes and resistomes in broiler litter stockpiles
description	Farmers apply broiler chicken litter to soils to enrich organic matter and provide crops with nutrients, following varying periods of stockpiling. However, litter frequently harbors fecal-derived microbial pathogens and associated antibiotic resistance genes (ARGs), and may be a source of microbial contamination of produce. We coupled a cutting-edge Loop Genomics long-read 16S rRNA amplicon-sequencing platform with high-throughput qPCR that targeted a suite of ARGs, to assess temporal (five time points over a 60-day period) and spatial (top, middle and bottom layers) microbiome and resistome dynamics in a broiler litter stockpile. We focused on potentially pathogenic species from the Enterobacteriaceae, Enterococcaceae and Staphylococcaceae families associated with food-borne disease. Bacterial diversity was significantly lower in the middle of the stockpile, where targeted pathogens were lowest and Bacillaceae were abundant. E. coli was the most abundant Enterobacteriaceae species, and high levels of the opportunistic pathogen Enterococcus faecium were detected. Correlation analyses revealed that the latter was significantly associated with aminoglycoside (aac(6′)-Ib(aka aacA4), aadA5), tetracycline (tetG), vancomycin (vanC), phenicol (floR) and MLSB (mphB) resistance genes. Staphylococcaceae were primarily non-pathogenic, but extremely low levels of the opportunistic pathogen S. aureus were detected, as was the opportunistic pathogen S. saprophyticus, which was linked to vancomycin (vanSA, vanC1), MLSB (vatE, ermB) and tetracycline (tetK) resistance genes. Collectively, we found that stockpile microbiomes and resistomes are strongly dictated by temporal fluctuations and spatial heterogeneity. Insights from this study can be exploited to improve stockpile management practice to support sustainable antimicrobial resistance mitigation policies in the future.
format	article
author	Chhedi Lal Gupta Ran Avidov Karuppasamy Kattusamy Ibrahim Saadi Vempalli Sudharsan Varma Shlomo E. Blum Yong‑Guan Zhu Xin‑Yuan Zhou Jian‑Qiang Su Yael Laor Eddie Cytryn
author_facet	Chhedi Lal Gupta Ran Avidov Karuppasamy Kattusamy Ibrahim Saadi Vempalli Sudharsan Varma Shlomo E. Blum Yong‑Guan Zhu Xin‑Yuan Zhou Jian‑Qiang Su Yael Laor Eddie Cytryn
author_sort	Chhedi Lal Gupta
title	Spatial and temporal dynamics of microbiomes and resistomes in broiler litter stockpiles
title_short	Spatial and temporal dynamics of microbiomes and resistomes in broiler litter stockpiles
title_full	Spatial and temporal dynamics of microbiomes and resistomes in broiler litter stockpiles
title_fullStr	Spatial and temporal dynamics of microbiomes and resistomes in broiler litter stockpiles
title_full_unstemmed	Spatial and temporal dynamics of microbiomes and resistomes in broiler litter stockpiles
title_sort	spatial and temporal dynamics of microbiomes and resistomes in broiler litter stockpiles
publisher	Elsevier
publishDate	2021
url	https://doaj.org/article/10295c7884fa498e8b1efe876c88e8e2
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Spatial and temporal dynamics of microbiomes and resistomes in broiler litter stockpiles

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