Microbial community composition and antimicrobial resistance in agricultural soils fertilized with livestock manure from conventional farming in Northern Italy

Laconi, Andrea; Mughini‐Gras, Lapo; Tolosi, Roberta; Grilli, G.; Trocino, A.; Carraro, Lisa; Cesare, Federica Di; Cagnardi, P.; Piccirillo, Alessandra

doi:10.1016/j.scitotenv.2020.143404

Cited by 48 publications

(25 citation statements)

References 56 publications

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“…Finally, no evidence of carbapenem- and colistin- resistance genes was obtained from the investigated flocks, even if Laconi et al. (2021) reported both of them in poultry manure in Northern Italy.…”

Section: Resultsmentioning

confidence: 87%

“…To our knowledge, only few data regarding the environmental ARG distribution in Italian commercial poultry flocks are available ( Laconi et al., 2021 ), so this study can be considered an attempt to improve the knowledge about the occurrence of a wide range of resistance genes in the environment at the farm level, including the critically important antibiotics for human health.…”

Section: Resultsmentioning

confidence: 99%

“…In Italy, studies have reported the antibiotic-resistance profiles of Enterobacteriaceae isolates such as Escherichia coli and Salmonella Infantis, obtained from animals samples ( Cavicchio et al., 2015 ; Carfora et al., 2018 ). More recently, Laconi et al. (2021) examined the ARG composition of soil and livestock manure in Northern Italy, including poultry farms also.…”

Section: Introductionmentioning

confidence: 99%

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Research Note: Detection of antibiotic-resistance genes in commercial poultry and turkey flocks from Italy

et al. 2021

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Antibiotics are routinely used in commercial poultry farms for the treatment of economically important bacterial diseases. Repeated use of antibiotics, usually administered in the feed or drinking water, may also result in the selection of resistant bacteria in animal feces, able to transfer their antimicrobial-resistance genes ( ARG ), residing on mobile elements, to other microorganisms, including human pathogens. In this study, single and multiplex PCR protocols were performed to detect tetracycline-, lincomycin-, chloramphenicol-, aminoglycoside-, colistin-, vancomycin-, and carbapenem-resistance genes, starting from 38 litter samples collected from 6 poultry and 2 turkey Italian flocks. The ARG were confirmed for all investigated classes of antimicrobials, except for colistin ( mcr-1, mcr-2, mcr-3,mcr-4 mcr-5 ) and carbapenem ( IMP, OXA-48, NDM , KPC ), while the vanB gene was only detected for vancomycin. The highest positivity was obtained for tetracycline ( tet[L], tet[M] , tet[K], tetA[P] ] and aminoglycoside ( aadA2 ) ARG, confirming the predominant use of these antimicrobials in the veterinary practice and their potential to enhance the resistance patterns also in humans as a consequence of environmental contamination. On the contrary, the dissemination by poultry of ARG for critically important antimicrobials seems to be of minor concern, suggesting a negligible environmental dissemination by these genes in the Italian poultry industry. Finally, the molecular screening performed in this study using a noninvasive sampling method represents a simple and rapid tool for monitoring the ARG patterns at the farm level.

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Section: Resultsmentioning

confidence: 87%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Research Note: Detection of antibiotic-resistance genes in commercial poultry and turkey flocks from Italy

et al. 2021

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“…The emergence of bacteria resistant to macrolides, (fluoro)quinolones and β-lactams represents a threat for human health, since antimicrobial drugs (AMDs) belonging to these classes are listed among the critically important antimicrobials by the World Health Organization (WHO) [1] . Of great concern is the dissemination in the environment of antimicrobial resistance genes (ARGs) conferring resistance to these AMDs, since they can be transferred to humans through different routes, including the food chain [ 2 , 3 ]. Here, we report the optimization of previously published assays, four end-point PCRs and one probe-based qPCR [4] , [5] , [6] , [7] , for the detection and quantification of five ARGs (i.e.…”

Section: Description Of Protocolmentioning

confidence: 99%

Optimization of five qPCR protocols toward the detection and the quantification of antimicrobial resistance genes in environmental samples

et al. 2021

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Here, we describe the optimization and validation of five quantitative PCR (qPCR) assays by employing the SYBRGreen chemistry paired with melting curve analysis to detect and quantify clinically relevant antimicrobial resistance genes (ARGs) (i.e. ermB, bla CTXM1-like , bla CMY-2 , qnrA and qnrS ) from environmental samples (i.e. soil and manure) . These five protocols accurately detected and quantified the aforementioned ARGs in complex environmental matrices and represent useful tools for both diagnostic and monitoring activities of resistant bacteria and ARGs into the environment.

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“…Many of these appear to be novel in the context of the horse gut, including Deinococcus-Thermus, Thermotogae and the Candidatus phylum Cloacimonetes (also called WWE1), which has been reported almost exclusively from anaerobic fermenters and the aqueous environment (61,62). However, as this phylum has recently been detected in soil fertilised with manure from dairy cattle, chickens and swine and has been implicated in anaerobic digestion of cellulose, it may play important similar roles in the vertebrate gut (62,63). Interestingly, in four of the five samples more than a thousand reads were assigned to Candidatus Saccharibacteria, a phylum from the candidate phyla radiation, which is home to bacteria that live as bacterial epibionts (64).…”

Section: Reference-based Profiling Documents Microbial Diversitymentioning

confidence: 99%

Metagenomic investigation of the equine faecal microbiome reveals extensive taxonomic and functional diversity

Gilroy

Ray

et al. 2021

Preprint

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BackgroundThe horse plays crucial roles across the globe, including in horseracing, as a working and companion animal and as a food animal. The horse hindgut microbiome makes a key contribution in turning a high fiber diet into body mass and horsepower. However, despite its importance, the horse hindgut microbiome remains largely undefined. Here, we applied culture-independent shotgun metagenomics to thoroughbred equine faecal samples to deliver novel insights into this complex microbial community.ResultsWe performed metagenomic sequencing on five equine faecal samples to construct 123 high- or medium-quality metagenome-assembled genomes from Bacteria and Archaea. In addition, we recovered nearly 200 bacteriophage genomes. We document surprising taxonomic and functional diversity, encompassing dozens of novel or unnamed bacterial genera and species, to which we have assigned new Candidatus names. Many of these genera are conserved across a range of mammalian gut microbiomes.ConclusionsOur metagenomic analyses provide new insights into the bacterial, archaeal and bacteriophage components of the horse gut microbiome. The resulting datasets provide a key resource for future high-resolution taxonomic and functional studies on the equine gut microbiome.

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Microbial community composition and antimicrobial resistance in agricultural soils fertilized with livestock manure from conventional farming in Northern Italy

Cited by 48 publications

References 56 publications

Research Note: Detection of antibiotic-resistance genes in commercial poultry and turkey flocks from Italy

Research Note: Detection of antibiotic-resistance genes in commercial poultry and turkey flocks from Italy

Optimization of five qPCR protocols toward the detection and the quantification of antimicrobial resistance genes in environmental samples

Metagenomic investigation of the equine faecal microbiome reveals extensive taxonomic and functional diversity

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