scholarly journals On-Farm Anaerobic Digestion of Dairy Manure Reduces the Abundance of Antibiotic Resistance-Associated Gene Targets, and the Potential for Plasmid Transfer

2021 ◽  
Author(s):  
Tam T. Tran ◽  
Andrew Scott ◽  
Yuan-Ching Tien ◽  
Roger Murray ◽  
Patrick Boerlin ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Anaerobic Digestion ◽  
Resistance Genes ◽  
Dairy Farms ◽  
Dairy Manure ◽  
Coliform Bacteria ◽  
E Coli ◽  
On Farm ◽  
The Impact ◽  
Transfer Potential

The present study investigated the impact of on-farm anaerobic digestion on the abundance of enteric bacteria, antibiotic resistance-associated gene targets and the horizontal transfer potential of extended-spectrum β-lactamase (ESBL) genes. Samples of raw and digested manure were obtained from six commercial dairy farms in Ontario, Canada. Digestion significantly abated populations of viable coliforms in all six farms. Conjugative transfer of plasmids carrying β-lactamase genes from manure bacteria enriched overnight with buffered peptone containing 4 mg/l cefotaxime into a β-lactam sensitive gfp-labelled E. coli as a recipient strain was evaluated in patch matings. Digestion significantly decreased the frequency of the horizontal transfer potential of ESBL genes. Twenty-five transconjugants were sequenced revealing six distinct plasmids with a size range of 40 – 180kb. A variety of ESBL genes were identified: blaCTX-M-1, blaCTX-M-14, blaCTX-M-15, blaCTX-M-27, blaCTX-M-55, blaPER-1. The blaCTX-M-15 was the most prevalent ESBL gene detected on plasmids harboured by transconjugants. Various mobile genetic elements were found located proximal to resistance genes. Ten gene targets including sul1, strA, strB, ermB, ermF, intI1, aadA, incW, blaPSE and blaOXA-20 were quantified by quantitative PCR on a subset of 18 raw and 18 digested samples. Most targets were significantly more abundant in raw manure, however ermB and ermF targets were more abundant in digested samples. Overall, on-farm digestion of dairy manure abated coliform bacteria, a number of antibiotic resistance-associated gene targets, and the potential for in vitro conjugation of plasmids conferring resistance to extended-spectrum β-lactams and other classes of antibiotics into E. coli CV601. IMPORTANCE Using livestock manure for fertilization can entrain antibiotic resistant bacteria into soil. Manure on some dairy farms is anaerobically digested before being land applied. Recommending the widespread implementation of the practice should be founded on understanding the impact of this treatment on various endpoints of human health concern. Although lab-scale anaerobic treatments have showed potential of reducing antibiotic resistance genes, there are very few data from commercial farms. Anaerobic digestion of manure on six dairy farms efficiently abated coliform bacteria and E. coli and a majority of antibiotic resistance-associated gene targets. In addition, the conjugation potential of plasmids carrying ESBL genes into introduced E. coli CV601 was reduced. Overall, anaerobic digestion abated coliform bacteria, the genes that they carry and the potential for ESBL-carrying plasmid transfer.

scholarly journals Degradation of antibiotic resistance genes and mobile gene elements in dairy manure anerobic digestion

PLoS ONE ◽  
2021 ◽  
Vol 16 (8) ◽  
pp. e0254836
Author(s):  
Yi Wang ◽  
Pramod K. Pandey ◽  
Sundaram Kuppu ◽  
Richard Pereira ◽  
Sharif Aly ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Anaerobic Digestion ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes ◽  
Dairy Manure ◽  
Health Concern ◽  
Animal Origin ◽  
Rrna Gene ◽  
Transposase Gene ◽  
Integrase Gene

Antibiotic resistance genes (ARGs) are emerging contaminants causing serious global health concern. Interventions to address this concern include improving our understanding of methods for treating waste material of human and animal origin that are known to harbor ARGs. Anaerobic digestion is a commonly used process for treating dairy manure, and although effective in reducing ARGs, its mechanism of action is not clear. In this study, we used three ARGs to conducted a longitudinal bench scale anaerobic digestion experiment with various temperatures (28, 36, 44, and 52°C) in triplicate using fresh dairy manure for 30 days to evaluate the reduction of gene abundance. Three ARGs and two mobile genetic elements (MGEs) were studied: sulfonamide resistance gene (sulII), tetracycline resistance genes (tetW), macrolide-lincosamide-streptogramin B (MLSB) superfamily resistance genes (ermF), class 1 integrase gene (intI1), and transposase gene (tnpA). Genes were quantified by real-time quantitative PCR. Results show that the thermophilic anaerobic digestion (52°C) significantly reduced (p < 0.05) the absolute abundance of sulII (95%), intI1 (95%), tnpA (77%) and 16S rRNA gene (76%) after 30 days of digestion. A modified Collins–Selleck model was used to fit the decay curve, and results suggest that the gene reduction during the startup phase of anaerobic digestion (first 5 days) was faster than the later stage, and reductions in the first five days were more than 50% for most genes.

scholarly journals Anaerobic Digestion of Tetracycline Spiked Livestock Manure and Poultry Litter Increased the Abundances of Antibiotic and Heavy Metal Resistance Genes

2020 ◽  
Vol 11 ◽  
Author(s):  
Getahun E. Agga ◽  
John Kasumba ◽  
John H. Loughrin ◽  
Eric D. Conte
Keyword(s):  
Heavy Metals ◽  
Heavy Metal ◽  
Anaerobic Digestion ◽  
Resistance Genes ◽  
Poultry Litter ◽  
Heavy Metal Resistance ◽  
Animal Manure ◽  
Metal Resistance ◽  
E Coli ◽  
The Impact

Anaerobic digestion is used for the treatment of animal manure by generating biogas. Heavy metals cause environmental pollutions and co-select for antimicrobial resistance. We evaluated the impact of mesophilic anaerobic digestion of cattle manure (CM), swine manure (SM) and poultry litter (PL) on the concentrations of seven tetracycline [tet(A), tet(B), tet(G), tet(M), tet(O), tet(Q), and tet(W)], macrolide [erm(B)], methicillin (mecA and mecC), copper (copB, pcoA, pcoD, and tcrB) and zinc (czrC) resistance genes, and three bacterial species (E. coli, Enterococcus spp. and Staphylococcus aureus). The total bacterial population and total abundance of the seven tet genes significantly increased in the three manure types after digestion. Concentration of tet(M) was strongly correlated with that of erm(B) and enterococci. As concentration of tetracyclines declined during anaerobic digestion, that of four tet genes (A, B, Q, and W) and 16S rRNA increased, that of tet(M) decreased, and that of tet(G) and tet(O) did not change. Concentrations of copB and pcoA did not change; while that of pcoD did not change in the PL, it increased in the SM and CM. While the concentration of enterococci remained unchanged in CM, it significantly increased in the PL and SM. Concentrations of tcrB significantly increased in the three manure types. While concentrations of S. aureus significantly increased in the CM and PL, that of SM was not affected. Concentrations of mecC significantly increased in all manure types after digestion; while mecA concentrations did not change in the SM, they significantly increased in CM and PL. While concentration of czrC remained low in the CM, it increased in the PL but declined in the SM. In conclusion, while mesophilic anaerobic digestion of animal manure decreased concentration of tetracyclines, it increased the concentrations of total bacteria, tet genes, E. coli, enterococci and S. aureus and methicillin resistance genes. It did not have any effect on concentrations of heavy metals; concentrations of heavy metal resistance genes either increased or remained unaffected depending on the animal species. This study showed the need for post-digestion treatments of animal manure to remove bacteria, antibiotic resistance genes, heavy metals and their resistance genes.

scholarly journals Detection and drug resistance profile of Escherichia coli from subclinical mastitis cows and water supply in dairy farms in Saraburi Province, Thailand

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3431 ◽  
Author(s):  
Woranich Hinthong ◽  
Natapol Pumipuntu ◽  
Sirijan Santajit ◽  
Suphang Kulpeanprasit ◽  
Shutipen Buranasinsup ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Water Samples ◽  
Antibiotic Resistance Genes ◽  
Dairy Farms ◽  
Subclinical Mastitis ◽  
Persistent Problem ◽  
E Coli ◽  
Milk Samples

Subclinical mastitis is a persistent problem in dairy farms worldwide. Environmental Escherichia coli is the bacterium predominantly responsible for this condition. In Thailand, subclinical mastitis in dairy cows is usually treated with various antibiotics, which could lead to antibiotic resistance in bacteria. E. coli is also a reservoir of many antibiotic resistance genes, which can be conveyed to other bacteria. In this study, the presence of E. coli in milk and water samples was reported, among which enteropathogenic E. coli was predominant, followed by enteroaggregative E. coli and enterohemorrhagic E. coli, which was found only in milk samples. Twenty-one patterns of antibiotic resistance were identified in this study. Ampicillin- and carbenicillin-resistant E. coli was the most common among the bacterial isolates from water samples. Meanwhile, resistance to ampicillin, carbenicillin, and sulfamethoxazole-trimethoprim was the pattern found most commonly in the E. coli from milk samples. Notably, only the E. coli from water samples possessed ESBL phenotype and carried antibiotic resistance genes, blaTEM and blaCMY-2. This indicates that pathogenic E. coli in dairy farms is also exposed to antibiotics and could potentially transfer these genes to other pathogenic bacteria under certain conditions.

scholarly journals Effect of Urban Wastewater Discharge on the Abundance of Antibiotic Resistance Genes and Antibiotic-Resistant Escherichia coli in Two Italian Rivers

2020 ◽  
Vol 17 (18) ◽  
pp. 6813 ◽  
Author(s):  
Fabrizio Pantanella ◽  
Itziar Lekunberri ◽  
Antonella Gagliardi ◽  
Giuseppe Venuto ◽  
Alexandre Sànchez-Melsió ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes ◽  
Treated Wastewater ◽  
Flow Volume ◽  
Antibiotic Resistant ◽  
E Coli ◽  
Absolute Concentrations ◽  
The Impact

Background: Wastewater treatment plants (WWTPs) are microbial factories aimed to reduce the amount of nutrients and pathogenic microorganisms in the treated wastewater before its discharge into the environment. We studied the impact of urban WWTP effluents on the abundance of antibiotic resistance genes (ARGs) and antibiotic-resistant Escherichia coli (AR-E. coli) in the last stretch of two rivers (Arrone and Tiber) in Central Italy that differ in size and flow volume. Methods: Water samples were collected in three seasons upstream and downstream of the WWTP, at the WWTP outlet, and at sea sites near the river mouth, and analyzed for the abundance of ARGs by qPCR and AR-E. coli using cultivation followed by disk diffusion assays. Results: For all studied genes (16S rRNA, intI1, sul1, ermB, blaTEM, tetW and qnrS), absolute concentrations were significantly higher in the Tiber than in the Arrone at all sampling sites, despite their collection date, but the prevalence of target ARGs within bacterial communities in both rivers was similar. The absolute concentrations of most ARGs were also generally higher in the WWTP effluent with median levels between log 4 and log 6 copies per ml but did not show differences along the studied stretches of rivers. Statistically significant site effect was found for E. coli phenotypic resistance to tetracycline and ciprofloxacin in the Arrone but not in the Tiber. Conclusions: In both rivers, diffuse or point pollution sources other than the studied WWTP effluents may account for the observed resistance pattern, although the Arrone appears as more sensitive to the wastewater impact considering its lower flow volume.

scholarly journals Quantification of antibiotic resistance genes and mobile genetic elements in manure from dairy farms in California

2020 ◽  
Author(s):  
Yi Wang ◽  
Pramod Pandey ◽  
Colleen Chiu ◽  
Richard Jeannotte ◽  
Sundaram Kuppu ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Management Practices ◽  
Animal Health ◽  
Antibiotic Resistance Genes ◽  
Dairy Farms ◽  
Mobile Genetic Elements ◽  
Dairy Manure ◽  
Manure Management ◽  
Genetic Elements

Abstract Antibiotic resistance genes (ARGs) are emerging environmental contaminants of concern to both human and animal health. Dairy manure is considered reservoir of ARGs. This study is focused on investigating prevalence of ARGs in California dairy farm manure under current common manure management. A total of 33 manure samples were collected from multiple manure treatment conditions: 1) flushed manure (FM), 2) fresh pile (FP), 3) compost pile (CP), 4) primary lagoon (PL), and 5) secondary lagoon (SL). After DNA extraction, all fecal samples were screened by PCR for the presence of 8 ARGs: four sulfonamide ARGs (sulI, sulII, sulIII, sulA), two tetracycline ARGs (tetW, tetO), two macrolide-lincosamide-streptogramin B (MLSB) ARGs (ermB, ermF). Samples were also screened for two mobile genetic elements (MGEs) (intI1, tnpA), which are responsible for dissemination of ARGs. Quantitative PCR was then used to screen all samples for five ARGs (sulII, tetW, ermF, tnpA and intI1). Prevalence of genes varied among sample types, but all genes were detectable in different manure types. Results showed that liquid-solid separation, piling, and lagoon conditions had limited effects on reducing ARGs and MGEs, and the effect was only found significant on tetW (p = 0.01). Besides, network analysis indicated that sulII was associated with tnpA (p < 0.05), and Psychrobacter and Pseudomonas as opportunistic human pathogens, were potential ARG/MGE hosts (p < 0.05). This research indicated current manure management practices in California dairy farms has limited effects on reducing ARGs and MGEs. Improvement of manure management in dairy farms is thus important to mitigate dissemination of ARGs into the environment.

scholarly journals Quantification of antibiotic resistance genes and mobile genetic in dairy manure

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12408
Author(s):  
Yi Wang ◽  
Pramod Pandey ◽  
Colleen Chiu ◽  
Richard Jeannotte ◽  
Sundaram Kuppu ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Management Practices ◽  
Animal Health ◽  
Dairy Farm ◽  
Antibiotic Resistance Genes ◽  
Dairy Farms ◽  
Dairy Manure ◽  
Manure Management ◽  
Human Pathogens

Background Antibiotic resistance genes (ARGs) are considered to be emerging environmental contaminants of concern potentially posing risks to human and animal health, and this research studied the prevalence of antimicrobial resistance in dairy manure. Methods This study is focused on investigating prevalence of ARGs in California dairy farm manure under current common different manure management. A total of 33 manure samples were collected from multiple manure treatment conditions: (1) flushed manure (FM), (2) fresh pile (FP), (3) compost pile (CP), (4) primary lagoon (PL), and (5) secondary lagoon (SL). After DNA extraction, all fecal samples were screened by PCR for the presence of eight ARGs: four sulfonamide ARGs (sulI, sulII, sulIII, sulA), two tetracycline ARGs (tetW, tetO), two macrolide-lincosamide-streptogramin B (MLSB) ARGs (ermB, ermF). Samples were also screened for two mobile genetic elements (MGEs) (intI1, tnpA), which are responsible for dissemination of ARGs. Quantitative PCR was then used to screen all samples for five ARGs (sulII, tetW, ermF, tnpA and intI1). Results Prevalence of genes varied among sample types, but all genes were detectable in different manure types. Results showed that liquid-solid separation, piling, and lagoon conditions had limited effects on reducing ARGs and MGEs, and the effect was only found significant on tetW (p = 0.01). Besides, network analysis indicated that sulII was associated with tnpA (p < 0.05), and Psychrobacter and Pseudomonas as opportunistic human pathogens, were potential ARG/MGE hosts (p < 0.05). This research indicated current different manure management practices in California dairy farms has limited effects on reducing ARGs and MGEs. Improvement of different manure management in dairy farms is thus important to mitigate dissemination of ARGs into the environment.

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