Resistome analysis of global livestock and soil microbiomes
Date
2022-07-07
Journal Title
Journal ISSN
Volume Title
Publisher
Frontiers Media
Abstract
Antimicrobial resistance (AMR) is a serious threat to public health globally; it is estimated
that AMR bacteria caused 1.27 million deaths in 2019, and this is set to rise to 10 million
deaths annually. Agricultural and soil environments act as antimicrobial resistance gene
(ARG) reservoirs, operating as a link between different ecosystems and enabling the mixing
and dissemination of resistance genes. Due to the close interactions between humans
and agricultural environments, these AMR gene reservoirs are a major risk to both human
and animal health. In this study, we aimed to identify the resistance gene reservoirs present
in four microbiomes: poultry, ruminant, swine gastrointestinal (GI) tracts coupled with
those from soil. This large study brings together every poultry, swine, ruminant, and soil
shotgun metagenomic sequence available on the NCBI sequence read archive for the
first time. We use the ResFinder database to identify acquired antimicrobial resistance
genes in over 5,800 metagenomes. ARGs were diverse and widespread within the
metagenomes, with 235, 101, 167, and 182 different resistance genes identified in the
poultry, ruminant, swine, and soil microbiomes, respectively. The tetracycline resistance
genes were the most widespread in the livestock GI microbiomes, including tet(W)_1,
tet(Q)_1, tet(O)_1, and tet(44)_1. The tet(W)_1 resistance gene was found in 99% of
livestock GI tract microbiomes, while tet(Q)_1 was identified in 93%, tet(O)_1 in 82%, and
finally tet(44)_1 in 69%. Metatranscriptomic analysis confirmed these genes were “real”
and expressed in one or more of the livestock GI tract microbiomes, with tet(40)_1 and
tet(O)_1 expressed in all three livestock microbiomes. In soil, the most abundant ARG
was the oleandomycin resistance gene, ole(B)_1. A total of 55 resistance genes were
shared by the four microbiomes, with 11 ARGs actively expressed in two or more
microbiomes. By using all available metagenomes we were able to mine a large number
of samples and describe resistomes in 37 countries. This study provides a global insight
into the diverse and abundant antimicrobial resistance gene reservoirs present in both
livestock and soil microbiomes.
Description
Publication history: Accepted - 24 May 2022: Published online - 7 July 2022
item.page.type
Article
item.page.format
Keywords
ruminant, poultry, swine, soil, metagenome, resistome, antimicrobial resistance gene, antimicrobial resistance
Citation
Lawther, K., Santos, F.G., Oyama, L.B., Rubino, F., Morrison, S., Creevey, C.J., McGrath, J.W. and Huws, S.A. (2022) ‘Resistome Analysis of Global Livestock and Soil Microbiomes’, Frontiers in Microbiology. Frontiers Media SA. doi:10.3389/fmicb.2022.897905.