Diverse Antibiotic Resistance Genes in Dairy Cow Manure

Abstract

Application of manure from antibiotic-treated animals to crops facilitates the dissemination of antibiotic resistance determinants into the environment. However, our knowledge of the identity, diversity, and patterns of distribution of these antibiotic resistance determinants remains limited. We used a new combination of methods to examine the resistome of dairy cow manure, a common soil amendment. Metagenomic libraries constructed with DNA extracted from manure were screened for resistance to beta-lactams, phenicols, aminoglycosides, and tetracyclines. Functional screening of fosmid and small-insert libraries identified 80 different antibiotic resistance genes whose deduced protein sequences were on average 50 to 60% identical to sequences deposited in GenBank. The resistance genes were frequently found in clusters and originated from a taxonomically diverse set of species, suggesting that some microorganisms in manure harbor multiple resistance genes. Furthermore, amid the great genetic diversity in manure, we discovered a novel clade of chloramphenicol acetyltransferases. Our study combined functional metagenomics with third-generation PacBio sequencing to significantly extend the roster of functional antibiotic resistance genes found in animal gut bacteria, providing a particularly broad resource for understanding the origins and dispersal of antibiotic resistance genes in agriculture and clinical settings.

Temporal changes of antibiotic-resistance genes and bacterial communities in two contrasting soils treated with cattle manure

“…The abundant and diverse ARGs found in antibiotic-free cattle manure are in line with the similar findings in previous studies (Looft et al 2012;Kyselkova et al 2013Kyselkova et al , 2015Wichmann et al 2014), which prompted us to explore the evolution and movement of these ARGs after manure application. Although land application of cattle manure is a common practice in crop production, current knowledge regarding the temporal patterns of ARGs following manure amendment is limited, which hinders our ability to reliably predict ARG behaviors in soil environment.…”

“…Animal manure is widely used to improve soil fertility levels but is also recognized as a substantial carrier of ARGs and pathogens into soil (Zhu et al 2013;Wichmann et al 2014). Amendment of soils with manure from antibiotic-treated animals has been frequently reported as an important route by which ARGs enter the environment and food system (Ghosh and LaPara 2007;Heuer et al 2008).…”

“…2), suggesting that bacteria resistant to these antibiotics are present in gastrointestinal tracts of cattle that received no administration of antibiotics. These antibiotic-free manure samples have divergent ARG profiles from the swine and cow manure receiving large amount of antibiotics, in which β-lactam, kanamycin and macrolide resistance genes were primarily enriched (Zhu et al 2013;Wichmann et al 2014). Although manure samples can be strikingly different between our study and others' regardless of the history of antibiotic treatment and husbandry practice, we provide further evidence that even in the absence of selective pressure imposed by agricultural use of antibiotics, clinically relevant ARGs are ubiquitous and abundant in cattle manure samples.…”

Prevalence of antibiotic resistant bacteria in healthy adults, foods, food animals, and the environment in selected areas in Thailand

“…However, avoidance of contamination with antibiotic resistant bacteria across the food production chain is also important, because consumption of killed resistant bacteria may induce viable non-resistant bacterial strains to become resistant to antibiotics. 45 Moreover, consumption of foods that contain residual antibiotics could still induce non-resistant bacteria colonizing the gut to become antibiotic-resistant. Therefore, restriction of inappropriate use of antibiotics in animal husbandry, aquaculture, and agriculture is important.…”

“…Consumption of non-viable resistant bacteria can also induce antibiotic resistance in gastrointestinal bacteria in humans and other animals by gene transfer. 45 Furthermore, it is a common practice in many communities in Thailand to use pig and chicken manure to feed fish in ponds or canals, and to fertilize vegetables and fruits. These practices could transfer antibiotic resistant bacteria from the feces of some food animals to other foods and the environment.…”