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Chung M, Dudley E, Kittana H, Thompson AC, Scott M, Norman K, Valeris-Chacin R. Genomic Profiling of Antimicrobial Resistance Genes in Clinical Salmonella Isolates from Cattle in the Texas Panhandle, USA. Antibiotics (Basel) 2024; 13:843. [PMID: 39335016 PMCID: PMC11428942 DOI: 10.3390/antibiotics13090843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2024] [Revised: 08/18/2024] [Accepted: 08/28/2024] [Indexed: 09/30/2024] Open
Abstract
Rising antimicrobial resistance (AMR) in Salmonella serotypes host-adapted to cattle is of increasing concern to the beef and dairy industry. The bulk of the existing literature focuses on AMR post-slaughter. In comparison, the understanding of AMR in Salmonella among pre-harvest cattle is still limited, particularly in Texas, which ranks top five in beef and dairy exports in the United States; inherently, the health of Texas cattle has nationwide implications for the health of the United States beef and dairy industry. In this study, long-read whole genome sequencing and bioinformatic methods were utilized to analyze antimicrobial resistance genes (ARGs) in 98 isolates from beef and dairy cattle in the Texas Panhandle. Fisher exact tests and elastic net models accounting for population structure were used to infer associations between genomic ARG profiles and antimicrobial phenotypic profiles and metadata. Gene mapping was also performed to assess the role of mobile genetic elements in harboring ARGs. Antimicrobial resistance genes were found to be statistically different between the type of cattle operation and Salmonella serotypes. Beef operations were statistically significantly associated with more ARGs compared to dairy operations. Salmonella Heidelberg, followed by Salmonella Dublin isolates, were associated with the most ARGs. Additionally, specific classes of ARGs were only present within mobile genetic elements.
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Affiliation(s)
- Max Chung
- College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, Canyon, TX 79015, USA
| | - Ethan Dudley
- College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, Canyon, TX 79015, USA
| | - Hatem Kittana
- College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA
| | - Alexis C Thompson
- Texas A&M Veterinary Medical Diagnostic Laboratory, Canyon, TX 79015, USA
| | - Matthew Scott
- College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, Canyon, TX 79015, USA
| | - Keri Norman
- College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Robert Valeris-Chacin
- College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, Canyon, TX 79015, USA
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Lee KY, Schlesener CL, Aly SS, Huang BC, Li X, Atwill ER, Weimer BC. Whole genome sequence analysis reveals high genomic diversity and potential host-driven adaptations among multidrug-resistant Escherichia coli from pre-weaned dairy calves. Front Microbiol 2024; 15:1420300. [PMID: 39296303 PMCID: PMC11409426 DOI: 10.3389/fmicb.2024.1420300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Accepted: 08/16/2024] [Indexed: 09/21/2024] Open
Abstract
Food-producing animals such as dairy cattle are potential reservoirs of antimicrobial resistance (AMR), with multidrug-resistant (MDR) organisms such as Escherichia coli observed in higher frequency in young calves compared to older cattle. In this study, we characterized the genomes of enteric MDR E. coli from pre-weaned dairy calves with and without diarrhea and evaluated the influence of host-level factors on genomic composition. Whole genome sequence comparative analysis of E. coli (n = 43) revealed substantial genomic diversity that primarily clustered by sequence type and was minimally driven by calf diarrheal disease status (healthy, diarrheic, or recovered), antimicrobial exposure, and dietary zinc supplementation. Diverse AMR genes (ARGs)-including extended-spectrum beta-lactamase genes and quinolone resistance determinants-were identified (n = 40), with unique sets of ARGs co-occurring in gene clusters with large AMR plasmids IncA/C2 and IncFIB(AP001918). Zinc supplementation was not significantly associated with the selection of individual ARGs in E. coli, however analysis of ARG and metal resistance gene pairs identified positive associations between certain aminoglycoside, beta-lactam, sulfonamide, and trimethoprim ARGs with acid, tellurium and mercury resistance genes. Although E. coli in this study lacked the typical virulence factors of diarrheagenic strains, virulence genes overlapping with those in major pathotypes were identified. Among the 103 virulence genes detected, the highest abundance and diversity of genes corresponded to iron acquisition (siderophores and heme uptake). Our findings indicate that the host-level factors evaluated in this study were not key drivers of genomic variability, but that certain accessory genes in enteric MDR E. coli may be enriched. Collectively, this work provides insight into the genomic diversity and host-microbe interface of MDR E. coli from pre-weaned dairy calves.
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Affiliation(s)
- Katie Y Lee
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Cory L Schlesener
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
- 100K Pathogen Genome Project, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Sharif S Aly
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
- Veterinary Medicine Teaching and Research Center, School of Veterinary Medicine, University of California, Davis, Tulare, CA, United States
| | - Bihua C Huang
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
- 100K Pathogen Genome Project, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Xunde Li
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Edward R Atwill
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Bart C Weimer
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
- 100K Pathogen Genome Project, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
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Wang Z, Fu Y, Zheng YL, Jiang N, Jiang H, Wu C, Lv Z, Krüger-Haker H, Feßler AT, Schwarz S, Wang Y. Fate of florfenicol and linezolid resistance genes and their bacterial hosts during two waste treatment models in swine feedlots. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 939:173645. [PMID: 38821272 DOI: 10.1016/j.scitotenv.2024.173645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 05/16/2024] [Accepted: 05/28/2024] [Indexed: 06/02/2024]
Abstract
Florfenicol resistance genes (FRGs) are widely present in livestock farms. The aim of this study was to evaluate the removal efficiencies of FRGs as well as the relationships between FRGs, mobile genetic elements (MGEs) and bacterial communities during the natural drying (ND) and anaerobic digestion (AD) processes of manure treatment in swine farms by combining bacterial isolation, quantitative PCR and metagenomic approaches. Solid manure showed a higher abundance of FRGs than fresh manure and was the main contamination source of fexA and fexB in ND farms, whilst biogas slurry displayed a lower abundance of FRGs than the wastewater in AD farms. Moreover, fresh manure and wastewater showed a high abundance of optrA, and wastewater was the main contamination source of cfr in both ND and AD farms. Both optrA/fexA-positive enterococci and cfr/fexA-positive staphylococci were mainly isolated along the farms' treatment processes. The cfr-positive staphylococci were highly prevalent in wastewater (57.14 % - 100 %) and may be associated with nasal-derived cfr-positive porcine staphylococci. An increased abundance of Enterococcus, Jeotgalibaca and Vagococcus in the bacterial community structures may account for the high optrA abundance in wastewater and Jeotgalibaca may be another potential host of optrA. Furthermore, the abundance of FRG-related MGEs increased by 22.63 % after the ND process and decreased by 66.96 % in AD farms. A significant correlation was observed between cfr and ISEnfa4, whereas no significance was found between optrA and IS1216E, although IS1216E is the predominant insertion sequence involved in the transfer of optrA. In conclusion, manure and wastewater represented independent pollution sources of FRGs in swine farms. Associated MGEs might play a key role in the transfer and persistence of FRGs. The AD process was more efficient in the removal of FRGs than the ND method, nevertheless a longer storage of slurry may be required for a complete removal.
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Affiliation(s)
- Zheng Wang
- College of Biology and Agricultural Resources, Huanggang Normal University, Huanggang, China.
| | - Yulin Fu
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China; Central Laboratory Department, Shenzhen Centre for Disease Control and Prevention, Shenzhen, Guangdong, China
| | - Yong-Liang Zheng
- College of Biology and Agricultural Resources, Huanggang Normal University, Huanggang, China
| | - Nansong Jiang
- Research Center for Poultry Diseases of Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Haiyang Jiang
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Congming Wu
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Ziquan Lv
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Henrike Krüger-Haker
- Institute of Microbiology and Epizootics, Center for Infection Medicine, School of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany; Veterinary Centre for Resistance Research, School of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Andrea T Feßler
- Institute of Microbiology and Epizootics, Center for Infection Medicine, School of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany; Veterinary Centre for Resistance Research, School of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Stefan Schwarz
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China; Institute of Microbiology and Epizootics, Center for Infection Medicine, School of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany; Veterinary Centre for Resistance Research, School of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany.
| | - Yang Wang
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China.
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Drake MJ, Daniel SG, Baker LD, Indugu N, Bittinger K, Dickens C, Zackular JP, Pitta D, Redding LE. Effects of dietary zinc on the gut microbiome and resistome of the gestating cow and neonatal calf. Anim Microbiome 2024; 6:39. [PMID: 39030654 PMCID: PMC11264502 DOI: 10.1186/s42523-024-00326-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Accepted: 06/20/2024] [Indexed: 07/21/2024] Open
Abstract
Zinc is an essential trace element required in the diet of all species. While the effects of zinc have been studied in growing calves, little is known about the effect of zinc on the microbiota of the gestating cow or her neonatal calf. Understanding factors that shape the gut health of neonatal animals and evaluating the effect of dietary supplements in adult gestating animals is important in promoting animal health and informing feeding practices. The aims of this study were to determine the effect of dietary zinc on the microbiota and resistome of the gestating cow and calf. Gestating cows received standard (40 ppm) or high (205 ppm) dietary zinc levels from dry off to calving. Fecal samples were collected from cows upon enrollment and at calving and from neonatal calves. Fecal samples underwent 16S rRNA sequencing and a subset also underwent shotgun metagenomic sequencing. The effect of zinc supplementation on the diversity and composition of the cow and calf microbiome and resistome was assessed. Alpha and beta diversity and composition of the microbiota were significantly altered over time but not by treatment in the cows, with alpha diversity decreasing and 14 genera found at significantly higher relative abundances at calving compared to enrollment. Levels of 27 antimicrobial resistance genes significantly increased over time. Only a small number of taxa were differentially expressed at calving in treatment and control groups, including Faecalibacterium, Bacteroides, Turicibacter, and Bifidobacterium pseudolongum. No effect of the dam's treatment group was observed on the diversity or composition of the neonatal calf microbiota. The calf resistome, which was relatively rich and diverse compared to the cow, was also unaffected by the dam's treatment group. The impact of high levels of dietary zinc thus appeared to be minimal, with no observed changes in alpha or beta diversity, and few changes in the relative abundance of a small number of taxa and antimicrobial resistance genes.
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Affiliation(s)
- Mary Jane Drake
- Clinical Studies - New Bolton Center, School of Veterinary Medicine, University of Pennsylvania, Kennett Square, PA, USA.
| | - Scott G Daniel
- Division of Gastroenterology, Hepatology and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Linda D Baker
- Clinical Studies - New Bolton Center, School of Veterinary Medicine, University of Pennsylvania, Kennett Square, PA, USA
| | - Nagaraju Indugu
- Clinical Studies - New Bolton Center, School of Veterinary Medicine, University of Pennsylvania, Kennett Square, PA, USA
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Charlene Dickens
- Clinical Studies - New Bolton Center, School of Veterinary Medicine, University of Pennsylvania, Kennett Square, PA, USA
| | - Joseph P Zackular
- Division of Protective Immunity, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Dipti Pitta
- Clinical Studies - New Bolton Center, School of Veterinary Medicine, University of Pennsylvania, Kennett Square, PA, USA
| | - Laurel E Redding
- Clinical Studies - New Bolton Center, School of Veterinary Medicine, University of Pennsylvania, Kennett Square, PA, USA
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Ravelo AD, Ferm P, Guo Y, Omontese BO, Morley PS, Chen C, Noyes NR, Caixeta LS. Using a multi-omics approach to explore potential associations with rumen content and serum of cows with different milk production levels based on genomic predicted transmitting ability for milk and phenotypic milk production. PLoS One 2024; 19:e0305674. [PMID: 39024228 PMCID: PMC11257365 DOI: 10.1371/journal.pone.0305674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 06/03/2024] [Indexed: 07/20/2024] Open
Abstract
This study aims to compare rumen microbiome and metabolites between second lactation dairy cows in the 75th percentile (n = 12; 57.2 ± 5.08 kg/d) of production according to genomic predicted transmitting ability for milk (GPTAM) and their counterparts in the 25th percentile (n = 12; 47.2 ± 8.61 kg/d). It was hypothesized that the metagenome and metabolome would differ between production levels. Cows were matched by days in milk (DIM), sire, occurrence of disease, and days open in previous lactation. For an additional comparison, the cows were also divided by phenotype into high (n = 6; 61.3 ± 2.8 kg/d), medium (n = 10; 55 ± 1.2 kg/d), and low (n = 8; 41.9 ± 5.6 kg/d) based on their milk production. Samples were collected 65 ± 14 DIM. Rumen content was collected using an oro-gastric tube and serum samples were collected from the coccygeal vessels. High-resolution liquid chromatography-mass spectrometry (LC-MS) was used for rumen and serum metabolite profiling. Shotgun metagenomics was used for rumen microbiome profiling. Microbiome sample richness and diversity were used to determine alpha and Bray-Curtis dissimilarity index was used to estimate beta diversity. Differences in metabolites were determined using t-tests or ANOVA. Pearson correlations were used to consider associations between serum metabolites and milk production. There was no evidence of a difference in rumen metabolites or microbial communities by GPTAM or phenotype. Cows in the phenotypic low group had greater serum acetate to propionate ratio and acetate proportion compared to the cows in the phenotypic medium group. Likewise, serum propionate proportion was greater in the medium compared to the low phenotypic group. Serum acetate, butyrate, and propionate concentrations had a weak positive correlation with milk production. When investigating associations between rumen environment and milk production, future studies must consider the impact of the ruminal epithelium absorption and post-absorption processes in relation to milk production.
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Affiliation(s)
- Anay D. Ravelo
- Department of Veterinary Population Medicine, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Peter Ferm
- Department of Veterinary Population Medicine, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Yue Guo
- Department of Food Science and Nutrition, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Bobwealth O. Omontese
- Department of Veterinary Population Medicine, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Paul S. Morley
- Veterinary Education, Research, and Outreach Program, Texas A&M University, Canyon, Texas, United States of America
| | - Chi Chen
- Department of Food Science and Nutrition, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Noelle R. Noyes
- Department of Veterinary Population Medicine, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Luciano S. Caixeta
- Department of Veterinary Population Medicine, University of Minnesota, Saint Paul, Minnesota, United States of America
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Neculai-Valeanu AS, Ariton AM, Radu C, Porosnicu I, Sanduleanu C, Amariții G. From Herd Health to Public Health: Digital Tools for Combating Antibiotic Resistance in Dairy Farms. Antibiotics (Basel) 2024; 13:634. [PMID: 39061316 PMCID: PMC11273838 DOI: 10.3390/antibiotics13070634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Revised: 07/04/2024] [Accepted: 07/06/2024] [Indexed: 07/28/2024] Open
Abstract
The emergence of antimicrobial resistance (AMR) is a significant threat to global food security, human health, and the future of livestock production. Higher rates of antimicrobial use in dairy farming and the sheer lack of new antimicrobials available for use focused attention on the question of how the dairy production sector contributed to the development of AMR and paved the path toward taking action to curtail it on the targeted type of farms. This paper aims to provide an introduction to a phenomenon that has gained considerable attention in the recent past due to its ever-increasing impact, the use of antimicrobial drugs, the emergence of antimicrobial resistance (AMR) on dairy farms, and seeks to discuss the possibilities of approaches such as digital health monitoring and precision livestock farming. Using sensors, data, knowledge, automation, etc., digital health monitoring, as well as Precision Livestock Farming (PLF), is expected to enhance health control and minimize disease and antimicrobial usage. The work presents a literature review on the current status and trends of AMR in dairy farms, an understanding of the concept of digital health monitoring and PLF, and the presentation and usefulness of digital health monitoring and PLF in preventing AMR. The study also analyses the strengths and weaknesses of adopting and incorporating digital technologies and artificial intelligence for dairy farming and presents areas for further study and level of use.
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Affiliation(s)
- Andra-Sabina Neculai-Valeanu
- Research and Development Station for Cattle Breeding Dancu, 707252 Iasi, Romania; (A.-S.N.-V.); (A.-M.A.)
- The Academy of Romanian Scientists, Str. Ilfov No. 3, Sector 5, 050045 Bucharest, Romania
| | - Adina-Mirela Ariton
- Research and Development Station for Cattle Breeding Dancu, 707252 Iasi, Romania; (A.-S.N.-V.); (A.-M.A.)
| | - Ciprian Radu
- Research and Development Station for Cattle Breeding Dancu, 707252 Iasi, Romania; (A.-S.N.-V.); (A.-M.A.)
| | - Ioana Porosnicu
- Research and Development Station for Cattle Breeding Dancu, 707252 Iasi, Romania; (A.-S.N.-V.); (A.-M.A.)
- The Academy of Romanian Scientists, Str. Ilfov No. 3, Sector 5, 050045 Bucharest, Romania
- Faculty of Veterinary Medicine, Iasi University of Life Science, 700490 Iasi, Romania
| | - Catalina Sanduleanu
- Research and Development Station for Cattle Breeding Dancu, 707252 Iasi, Romania; (A.-S.N.-V.); (A.-M.A.)
- Faculty of Food and Animal Resources, Iasi University of Life Science, 700490 Iasi, Romania
| | - Gabriela Amariții
- Research and Development Station for Cattle Breeding Dancu, 707252 Iasi, Romania; (A.-S.N.-V.); (A.-M.A.)
- Faculty of Food and Animal Resources, Iasi University of Life Science, 700490 Iasi, Romania
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Fukuda A, Suzuki M, Makita K, Usui M. Low-frequency transmission and persistence of antimicrobial-resistant bacteria and genes from livestock to agricultural soil and crops through compost application. PLoS One 2024; 19:e0301972. [PMID: 38771763 PMCID: PMC11108225 DOI: 10.1371/journal.pone.0301972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 03/26/2024] [Indexed: 05/23/2024] Open
Abstract
Livestock excrement is composted and applied to agricultural soils. If composts contain antimicrobial-resistant bacteria (ARB), they may spread to the soil and contaminate cultivated crops. Therefore, we investigated the degree of transmission of ARB and related antimicrobial resistance genes (ARGs) and, as well as clonal transmission of ARB from livestock to soil and crops through composting. This study was conducted at Rakuno Gakuen University farm in Hokkaido, Japan. Samples of cattle feces, solid and liquid composts, agricultural soil, and crops were collected. The abundance of Escherichia coli, coliforms, β-lactam-resistant E. coli, and β-lactam-resistant coliforms, as well as the copy numbers of ARG (specifically the bla gene related to β-lactam-resistant bacteria), were assessed using qPCR through colony counts on CHROMagar ECC with or without ampicillin, respectively, 160 days after compost application. After the application of the compost to the soil, there was an initial increase in E. coli and coliform numbers, followed by a subsequent decrease over time. This trend was also observed in the copy numbers of the bla gene. In the soil, 5.0 CFU g-1 E. coli was detected on day 0 (the day post-compost application), and then, E. coli was not quantified on 60 days post-application. Through phylogenetic analysis involving single nucleotide polymorphisms (SNPs) and using whole-genome sequencing, it was discovered that clonal blaCTX-M-positive E. coli and blaTEM-positive Escherichia fergusonii were present in cattle feces, liquid compost, and soil on day 0 as well as 7 days post-application. This showed that livestock-derived ARB were transmitted from compost to soil and persisted for at least 7 days in soil. These findings indicate a potential low-level transmission of livestock-associated bacteria to agricultural soil through composts was observed at low frequency, dissemination was detected. Therefore, decreasing ARB abundance during composting is important for public health.
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Affiliation(s)
- Akira Fukuda
- Food Microbiology and Food Safety Unit, Division of Preventive Veterinary Medicine, School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu, Japan
| | - Masato Suzuki
- Department of Bacteriology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kohei Makita
- Veterinary Epidemiology Unit, Division of Preventive Veterinary Medicine, School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu, Japan
| | - Masaru Usui
- Food Microbiology and Food Safety Unit, Division of Preventive Veterinary Medicine, School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu, Japan
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Strickland AH, Murray SA, Vinasco J, Auvermann BW, Bush KJ, Sawyer JE, Scott HM, Norman KN. Comparative microbiome analysis of beef cattle, the feedyard environment, and airborne particulate matter as a function of probiotic and antibiotic use, and change in pen environment. Front Microbiol 2024; 15:1348171. [PMID: 38389541 PMCID: PMC10883649 DOI: 10.3389/fmicb.2024.1348171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 01/22/2024] [Indexed: 02/24/2024] Open
Abstract
Introduction Intensive beef cattle production systems are frequently implicated as a source of bacteria that can be transferred to nearby humans and animals via effluent water, manure used as fertilizer, or airborne particulate matter. It is crucial to understand microbial population dynamics due to manure pack desiccation, antibiotic usage, and antibiotic alternatives within beef cattle and their associated feedyard environment. Understanding how bacterial communities change in the presence of antibiotics can also improve management practices for reducing the spread of foodborne bacteria. Methods In this study, we aimed to compare the microbiomes within cattle feces, the feedyard environment and artificially produced airborne particulate matter as a function of pen change and treatment with tylosin or probiotics. We utilized 16S rRNA sequencing to compare bacterial communities among sample types, study days, and treatment groups. Results Bacterial community diversity varied as a function of sampling day and pen change (old or new) within fecal and manure pack samples. Manure pack samples from old pens and new pens contained diverse communities of bacteria on days 0 and 84; however, by day 119 of the study these taxonomic differences were less evident. Particulate matter samples exhibited significant differences in community diversity and predominant bacterial taxa compared to the manure pack they originated from. Treatment with tylosin did not meaningfully impact bacterial communities among fecal, environmental, or particulate matter samples; however, minor differences in bacterial community structure were observed in feces from cattle treated with probiotics. Discussion This study was the first to characterize and compare microbial communities within feces, manure pack, and airborne particulate matter from the same location and as a function of tylosin and probiotic treatment, and pen change. Although fecal and environmental samples are commonly used in research studies and other monitoring programs to infer public health risk of bacteria and antimicrobial resistance determinants from feedyard environments, our study suggests that these samples may not be appropriate to infer public health risk associated with airborne particulate matter.
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Affiliation(s)
- A. H. Strickland
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, United States
| | - S. A. Murray
- Department of Veterinary Pathobiology, Texas A&M University, College Station, TX, United States
| | - J. Vinasco
- Department of Veterinary Pathobiology, Texas A&M University, College Station, TX, United States
| | - B. W. Auvermann
- Texas A&M AgriLife Research and Extension Center at Amarillo, Amarillo, TX, United States
| | - K. J. Bush
- Texas A&M AgriLife Research and Extension Center at Amarillo, Amarillo, TX, United States
| | - J. E. Sawyer
- Department of Animal Sciences, Texas A&M University, College Station, TX, United States
| | - H. M. Scott
- Department of Veterinary Pathobiology, Texas A&M University, College Station, TX, United States
| | - K. N. Norman
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, United States
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Cabral LDS, Weimer PJ. Megasphaera elsdenii: Its Role in Ruminant Nutrition and Its Potential Industrial Application for Organic Acid Biosynthesis. Microorganisms 2024; 12:219. [PMID: 38276203 PMCID: PMC10819428 DOI: 10.3390/microorganisms12010219] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 01/15/2024] [Accepted: 01/19/2024] [Indexed: 01/27/2024] Open
Abstract
The Gram-negative, strictly anaerobic bacterium Megasphaera elsdenii was first isolated from the rumen in 1953 and is common in the mammalian gastrointestinal tract. Its ability to use either lactate or glucose as its major energy sources for growth has been well documented, although it can also ferment amino acids into ammonia and branched-chain fatty acids, which are growth factors for other bacteria. The ruminal abundance of M. elsdenii usually increases in animals fed grain-based diets due to its ability to use lactate (the product of rapid ruminal sugar fermentation), especially at a low ruminal pH (<5.5). M. elsdenii has been proposed as a potential dietary probiotic to prevent ruminal acidosis in feedlot cattle and high-producing dairy cows. However, this bacterium has also been associated with milk fat depression (MFD) in dairy cows, although proving a causative role has remained elusive. This review summarizes the unique physiology of this intriguing bacterium and its functional role in the ruminal community as well as its role in the health and productivity of the host animal. In addition to its effects in the rumen, the ability of M. elsdenii to produce C2-C7 carboxylic acids-potential precursors for industrial fuel and chemical production-is examined.
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Affiliation(s)
- Luciano da Silva Cabral
- Department of Animal Science and Rural Extension, Agronomy and Animal Science School, Federal University of Mato Grosso, Cuiabá 780600-900, Mato Grosso, Brazil;
| | - Paul J. Weimer
- Department of Bacteriology, University of Wisconsin, Madison, WI 53706, USA
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Diaz GR, Gaire TN, Ferm P, Case L, Caixeta LS, Goldsmith TJ, Armstrong J, Noyes NR. Effect of castration timing and weaning strategy on the taxonomic and functional profile of ruminal bacteria and archaea of beef calves. Anim Microbiome 2023; 5:61. [PMID: 38041127 PMCID: PMC10691087 DOI: 10.1186/s42523-023-00284-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 11/28/2023] [Indexed: 12/03/2023] Open
Abstract
BACKGROUND Beef cattle experience several management challenges across their lifecycle. Castration and weaning, two major interventions in the early life of beef cattle, can have a substantial impact on animal performance. Despite the key role of the rumen microbiome on productive traits of beef cattle, the effect of castration timing and weaning strategy on this microbial community has not been formally described. We assessed the effect of four castration time windows (at birth, turnout, pre-weaning and weaning) and two weaning strategies (fence-line and truck transportation) on the rumen microbiome in a randomized controlled study with 32 male calves across 3 collection days (i.e., time points). Ruminal fluid samples were submitted to shotgun metagenomic sequencing and changes in the taxonomic (microbiota) and functional profile (metagenome) of the rumen microbiome were described. RESULTS Using a comprehensive yet stringent taxonomic classification approach, we identified 10,238 unique taxa classified under 40 bacterial and 7 archaeal phyla across all samples. Castration timing had a limited long-term impact on the rumen microbiota and was not associated with changes in alpha and beta diversity. The interaction of collection day and weaning strategy was associated with changes in the rumen microbiota, which experienced a significant decrease in alpha diversity and shifts in beta diversity within 48 h post-weaning, especially in calves abruptly weaned by truck transportation. Calves weaned using a fence-line weaning strategy had lower relative abundance of Bacteroides, Lachnospira, Fibrobacter and Ruminococcus genera compared to calves weaned by truck transportation. Some genes involved in the hydrogenotrophic methanogenesis pathway (fwdB and fwdF) had higher relative abundance in fence-line-weaned calves post-weaning. The antimicrobial resistance gene tetW consistently represented more than 50% of the resistome across time, weaning and castration groups, without significant changes in relative abundance. CONCLUSIONS Within the context of this study, castration timing had limited long-term effects on the rumen microbiota, while weaning strategy had short-term effects on the rumen microbiota and methane-associated metagenome, but not on the rumen resistome.
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Affiliation(s)
- Gerardo R Diaz
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, 55108, USA
| | - Tara N Gaire
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, 55108, USA
| | - Peter Ferm
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, 55108, USA
| | - Lacey Case
- North Central Research and Outreach Center, Department of Animal Science, University of Minnesota, St. Paul, MN, 55108, USA
| | - Luciano S Caixeta
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, 55108, USA
| | - Timothy J Goldsmith
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, 55108, USA
| | - Joe Armstrong
- Agricultural and Natural Resource Systems, University of Minnesota Extension, University of Minnesota, St. Paul, MN, 55108, USA
| | - Noelle R Noyes
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, 55108, USA.
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11
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Agarwal V, Yue Y, Zhang X, Feng X, Tao Y, Wang J. Spatial and temporal distribution of endotoxins, antibiotic resistance genes and mobile genetic elements in the air of a dairy farm in Germany. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 336:122404. [PMID: 37625772 DOI: 10.1016/j.envpol.2023.122404] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 08/15/2023] [Accepted: 08/16/2023] [Indexed: 08/27/2023]
Abstract
Antimicrobial resistance (AMR) is a serious issue that is continuously growing and spreading, leading to a dwindling number of effective treatments for infections that were easily treatable with antibiotics in the past. Animal farms are a major hotspot for AMR, where antimicrobials are often overused, misused, and abused, in addition to overcrowding of animals. In this study, we investigated the risk of AMR transmission from a farm to nearby residential areas by examining the overall occurrence of endotoxins, antibiotic resistance genes (ARGs), and mobile genetic elements (MGEs) in the air of a cattle farm. We assessed various factors, including the season and year, day and nighttime, and different locations within the farm building and its vicinity. The most abundant ARGs detected were tetW, aadA1, and sul2, genes that encode for resistances towards antibiotics commonly used in veterinary medicine. While there was a clear concentration gradient for endotoxin from the middle of the farm building to the outside areas, the abundance of ARGs and MGEs was relatively uniform among all locations within the farm and its vicinity. This suggests that endotoxins preferentially accumulated in the coarse particle fraction, which deposited quickly, as opposed to the ARGs and MGEs, which might concentrate in the fine particle fraction and remain longer in the aerosol phase. The occurrence of the same genes found in the air samples and in the manure indicated that ARGs and MGEs in the air mostly originated from the cows, continuously being released from the manure to the air. Although our atmospheric dispersion model indicated a relatively low risk for nearby residential areas, farm workers might be at greater risk of getting infected with resistant bacteria and experiencing overall respiratory tract issues due to continuous exposure to elevated concentrations of endotoxins, ARGs and MGEs in the air of the farm.
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Affiliation(s)
- V Agarwal
- Institute of Environmental Engineering, ETH Zurich, Switzerland; Laboratory for Advanced Analytical Technologies, Empa, Swiss Federal Laboratories for Materials Science and Technology, Dübendorf, 8600, Switzerland
| | - Y Yue
- Institute of Environmental Engineering, ETH Zurich, Switzerland; Laboratory for Advanced Analytical Technologies, Empa, Swiss Federal Laboratories for Materials Science and Technology, Dübendorf, 8600, Switzerland
| | - X Zhang
- Institute of Environmental Engineering, ETH Zurich, Switzerland; Laboratory for Advanced Analytical Technologies, Empa, Swiss Federal Laboratories for Materials Science and Technology, Dübendorf, 8600, Switzerland
| | - X Feng
- Institute of Environmental Engineering, ETH Zurich, Switzerland; Laboratory for Advanced Analytical Technologies, Empa, Swiss Federal Laboratories for Materials Science and Technology, Dübendorf, 8600, Switzerland
| | - Y Tao
- Institute of Environmental Engineering, ETH Zurich, Switzerland; Laboratory for Advanced Analytical Technologies, Empa, Swiss Federal Laboratories for Materials Science and Technology, Dübendorf, 8600, Switzerland
| | - J Wang
- Institute of Environmental Engineering, ETH Zurich, Switzerland; Laboratory for Advanced Analytical Technologies, Empa, Swiss Federal Laboratories for Materials Science and Technology, Dübendorf, 8600, Switzerland.
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12
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Haley BJ, Kim SW, Salaheen S, Hovingh E, Van Kessel JAS. Genome-Wide Analysis of Escherichia coli Isolated from Dairy Animals Identifies Virulence Factors and Genes Enriched in Multidrug-Resistant Strains. Antibiotics (Basel) 2023; 12:1559. [PMID: 37887260 PMCID: PMC10604827 DOI: 10.3390/antibiotics12101559] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Revised: 10/16/2023] [Accepted: 10/16/2023] [Indexed: 10/28/2023] Open
Abstract
The gastrointestinal tracts of dairy calves and cows are reservoirs of antimicrobial-resistant bacteria (ARB), which are present regardless of previous antimicrobial therapy. Young calves harbor a greater abundance of resistant bacteria than older cows, but the factors driving this high abundance are unknown. Here, we aimed to fully characterize the genomes of multidrug-resistant (MDR) and antimicrobial-susceptible Escherichia coli strains isolated from pre-weaned calves, post-weaned calves, dry cows, and lactating cows and to identify the accessory genes that are associated with the MDR genotype to discover genetic targets that can be exploited to mitigate antimicrobial resistance in dairy farms. Results indicated that both susceptible and resistant E. coli isolates recovered from animals on commercial dairy operations were highly diverse and encoded a large pool of virulence factors. In total, 838 transferrable antimicrobial resistance genes (ARGs) were detected, with genes conferring resistance to aminoglycosides being the most common. Multiple sequence types (STs) associated with mild to severe human gastrointestinal and extraintestinal infections were identified. A Fisher's Exact Test identified 619 genes (ARGs and non-ARGs) that were significantly enriched in MDR isolates and 147 genes that were significantly enriched in susceptible isolates. Significantly enriched genes in MDR isolates included the iron scavenging aerobactin synthesis and receptor genes (iucABCD-iutA) and the sitABCD system, as well as the P fimbriae pap genes, myo-inositol catabolism (iolABCDEG-iatA), and ascorbate transport genes (ulaABC). The results of this study demonstrate a highly diverse population of E. coli in commercial dairy operations, some of which encode virulence genes responsible for severe human infections and resistance to antibiotics of human health significance. Further, the enriched accessory genes in MDR isolates (aerobactin, sit, P fimbriae, and myo-inositol catabolism and ascorbate transport genes) represent potential targets for reducing colonization of antimicrobial-resistant bacteria in the calf gut.
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Affiliation(s)
- Bradd J. Haley
- Environmental Microbial and Food Safety Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, 307 Center Drive, Beltsville, MD 20705, USA; (S.W.K.)
| | - Seon Woo Kim
- Environmental Microbial and Food Safety Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, 307 Center Drive, Beltsville, MD 20705, USA; (S.W.K.)
| | - Serajus Salaheen
- Environmental Microbial and Food Safety Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, 307 Center Drive, Beltsville, MD 20705, USA; (S.W.K.)
| | - Ernest Hovingh
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Jo Ann S. Van Kessel
- Environmental Microbial and Food Safety Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, 307 Center Drive, Beltsville, MD 20705, USA; (S.W.K.)
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13
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Zhang X, Li H, Wang Y, Kang Y, Li Z. Metagenomic analysis reveals antibiotic resistance profiles in tissue samples from patients with diabetic foot infections. J Glob Antimicrob Resist 2023; 34:202-210. [PMID: 37307951 DOI: 10.1016/j.jgar.2023.05.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 05/08/2023] [Accepted: 05/22/2023] [Indexed: 06/14/2023] Open
Abstract
OBJECTIVES Treating patients with diabetic foot infection (DFI) is challenging because of high rates of antibiotic resistance. Therefore, to administer a suitable antibiotic treatment, it is necessary to know the antibiotic resistance patterns in DFIs. METHODS To explore this question, we selected metagenomic data of 36 tissue samples from patients with DFI in the National Center for Biotechnology Information Sequence Read Archive database. RESULTS A total of 229 antibiotic-resistant gene (ARG) subtypes belonging to 20 ARG types were detected. The antibiotic resistome of 229 different genes in the tissue samples of patients with DFI comprised 24 core and 205 accessory resistance genes. Among the core antibiotic resistome, multidrug, tetracycline, macrolide-lincosamide-streptogramin, and beta-lactam resistance genes were the dominant categories. Procrustes analysis indicated that both the microbial community composition and mobile genetic elements (MGEs) were determinants of the ARGs. In the network analysis, 29 species were speculated to be potential hosts of 28 ARGs based on the co-occurrence results. Plasmids and transposons were the most common elements that co-occurred with ARGs. CONCLUSIONS Our study provided detailed information about antibiotic resistance patterns in DFI, which has practical implications for suggesting a more specific antibiotic choice.
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Affiliation(s)
- Xiujuan Zhang
- Department of Endocrinology, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Haihui Li
- Department of Endocrinology, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Yonghui Wang
- Department of Endocrinology, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Yutong Kang
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Zhenjun Li
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.
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14
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Ibekwe AM, Bhattacharjee AS, Phan D, Ashworth D, Schmidt MP, Murinda SE, Obayiuwana A, Murry MA, Schwartz G, Lundquist T, Ma J, Karathia H, Fanelli B, Hasan NA, Yang CH. Potential reservoirs of antimicrobial resistance in livestock waste and treated wastewater that can be disseminated to agricultural land. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 872:162194. [PMID: 36781130 DOI: 10.1016/j.scitotenv.2023.162194] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 02/06/2023] [Accepted: 02/08/2023] [Indexed: 06/18/2023]
Abstract
Livestock manure, dairy lagoon effluent, and treated wastewater are known reservoirs of antibiotic resistance genes (ARGs), antibiotic-resistant bacteria (ARB), and virulence factor genes (VFGs), and their application to agricultural farmland could be a serious public health threat. However, their dissemination to agricultural lands and impact on important geochemical pathways such as the nitrogen (N) cycle have not been jointly explored. In this study, shotgun metagenomic sequencing and analyses were performed to examine the diversity and composition of microbial communities, ARGs, VFGs, and N cycling genes in different livestock manure/lagoon and treated wastewater collected from concentrated animal feeding operations (CAFOs) and a municipal wastewater treatment plant along the west coast of the United States. Multivariate analysis showed that diversity indices of bacterial taxa from the different microbiomes were not significantly different based on InvSimpson (P = 0.05), but differences in ARG mechanisms were observed between swine manure and other microbiome sources. Comparative resistome profiling showed that ARGs in microbiome samples belonged to four core resistance classes: aminoglycosides (40-55 %), tetracyclines (30-45 %), beta-lactam-resistance (20-35 %), macrolides (18-30 %), and >50 % of the VFGs that the 24 microbiomes harbored were phyletically affiliated with two bacteria, Bacteroidetes fragilis and Enterobacter aerogenes. Network analysis based on Spearman correlation showed co-occurrence patterns between several genes such as transporter-gene and regulator, efflux pump and involved-in-polymyxin- resistance, aminoglycoside, beta-lactam, and macrolide with VFGs and bacterial taxa such as Firmicutes, Candidatus Themoplasmatota, Actinobacteria, and Bacteroidetes. Metabolic reconstruction of metagenome-assembled genome (MAGs) analysis showed that the most prevalent drug resistance mechanisms were associated with carbapenem resistance, multidrug resistance (MDR), and efflux pump. Bacteroidales was the main taxa involved in dissimilatory nitrate reduction (DNRA) in dairy lagoon effluent. This study demonstrates that the dissemination of waste from these sources can increase the spread of ARGs, ARB, and VFGs into agricultural lands, negatively impacting both soil and human health.
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Affiliation(s)
- Abasiofiok M Ibekwe
- US Salinity Laboratory, USDA-ARS, 450 W. Big Springs Rd., Riverside, CA 92507, USA.
| | - Ananda S Bhattacharjee
- US Salinity Laboratory, USDA-ARS, 450 W. Big Springs Rd., Riverside, CA 92507, USA; Department of Environmental Sciences, University of California, Riverside, CA 92507, USA
| | - Duc Phan
- US Salinity Laboratory, USDA-ARS, 450 W. Big Springs Rd., Riverside, CA 92507, USA; Department of Chemical and Environmental Engineering, University of California, Riverside, 92507, CA, USA
| | - Daniel Ashworth
- US Salinity Laboratory, USDA-ARS, 450 W. Big Springs Rd., Riverside, CA 92507, USA
| | - Michael P Schmidt
- US Salinity Laboratory, USDA-ARS, 450 W. Big Springs Rd., Riverside, CA 92507, USA
| | - Shelton E Murinda
- Animal and Veterinary Sciences Department, California State Polytechnic University, Pomona, CA 91768, USA
| | - Amarachukwu Obayiuwana
- Department of Biological Sciences, Augustine University Ilara-Epe, Lagos State 106101, Nigeria
| | - Marcia A Murry
- Biological Sciences Department, California State Polytechnic University, Pomona, CA 91768, USA
| | - Gregory Schwartz
- BioResource and Agricultural Engineering Department, College of Agriculture, California Polytechnic State University, San Luis Obispo, CA, USA
| | - Tryg Lundquist
- Civil and Environmental Engineering Department, College of Engineering, California Polytechnic State University, San Luis Obispo, CA, USA
| | - Jincai Ma
- College of New Energy and Environment, Jilin University, Changchun 130021, PR China
| | | | | | - Nur A Hasan
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA; EzBiome Inc, MD, USA
| | - Ching-Hong Yang
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA
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15
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Multilayer networks of plasmid genetic similarity reveal potential pathways of gene transmission. THE ISME JOURNAL 2023; 17:649-659. [PMID: 36759552 PMCID: PMC10119158 DOI: 10.1038/s41396-023-01373-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 01/11/2023] [Accepted: 01/16/2023] [Indexed: 02/11/2023]
Abstract
Antimicrobial resistance (AMR) is a significant threat to public health. Plasmids are principal vectors of AMR genes, significantly contributing to their spread and mobility across hosts. Nevertheless, little is known about the dynamics of plasmid genetic exchange across animal hosts. Here, we use theory and methodology from network and disease ecology to investigate the potential of gene transmission between plasmids using a data set of 21 plasmidomes from a single dairy cow population. We constructed a multilayer network based on pairwise plasmid genetic similarity. Genetic similarity is a signature of past genetic exchange that can aid in identifying potential routes and mechanisms of gene transmission within and between cows. Links between cows dominated the transmission network, and plasmids containing mobility genes were more connected. Modularity analysis revealed a network cluster where all plasmids contained a mobM gene, and one where all plasmids contained a beta-lactamase gene. Cows that contain both clusters also share transmission pathways with many other cows, making them candidates for super-spreading. In support, we found signatures of gene super-spreading in which a few plasmids and cows are responsible for most gene exchange. An agent-based transmission model showed that a new gene invading the cow population will likely reach all cows. Finally, we showed that edge weights contain a non-random signature for the mechanisms of gene transmission, allowing us to differentiate between dispersal and genetic exchange. These results provide insights into how genes, including those providing AMR, spread across animal hosts.
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16
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Morris C, Wickramasingha D, Abdelfattah EM, Pereira RV, Okello E, Maier G. Prevalence of antimicrobial resistance in fecal Escherichia coli and Enterococcus spp. isolates from beef cow-calf operations in northern California and associations with farm practices. Front Microbiol 2023; 14:1086203. [PMID: 36910206 PMCID: PMC9996069 DOI: 10.3389/fmicb.2023.1086203] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 02/06/2023] [Indexed: 02/25/2023] Open
Abstract
Antimicrobials are necessary for the treatment of bacterial infections in animals, but increased antimicrobial resistance (AMR) is becoming a concern for veterinarians and livestock producers. This cross-sectional study was conducted on cow-calf operations in northern California to assess prevalence of AMR in Escherichia coli and Enterococcus spp. shed in feces of beef cattle of different life stages, breeds, and past antimicrobial exposures and to evaluate if any significant factors could be identified that are associated with AMR status of the isolates. A total of 244 E. coli and 238 Enterococcus isolates were obtained from cow and calf fecal samples, tested for susceptibility to 19 antimicrobials, and classified as resistant or non-susceptible to the antimicrobials for which breakpoints were available. For E. coli, percent of resistant isolates by antimicrobial were as follows: ampicillin 100% (244/244), sulfadimethoxine 25.4% (62/244), trimethoprim-sulfamethoxazole 4.9% (12/244), and ceftiofur 0.4% (1/244) while percent of non-susceptible isolates by antimicrobial were: tetracycline 13.1% (32/244), and florfenicol 19.3% (47/244). For Enterococcus spp., percent of resistant isolates by antimicrobial were as follows: ampicillin 0.4% (1/238) while percent of non-susceptible isolates by antimicrobial were tetracycline 12.6% (30/238) and penicillin 1.7% (4/238). No animal level or farm level management practices, including antimicrobial exposures, were significantly associated with differences in isolate resistant or non-susceptible status for either E. coli or Enterococcus isolates. This is contrary to the suggestion that administration of antibiotics is solely responsible for development of AMR in exposed bacteria and demonstrates that there are other factors involved, either not captured in this study or not currently well understood. In addition, the overall use of antimicrobials in this cow-calf study was lower than other sectors of the livestock industry. Limited information is available on cow-calf AMR from fecal bacteria, and the results of this study serve as a reference for future studies to support a better understanding and estimation of drivers and trends for AMR in cow-calf operations.
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Affiliation(s)
- Celeste Morris
- William R. Pritchard Veterinary Medical Teaching Hospital, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Devinda Wickramasingha
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Essam M Abdelfattah
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States.,Veterinary Medicine Teaching and Research Center, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States.,Department of Animal Hygiene, and Veterinary Management, Faculty of Veterinary Medicine, Benha University, Benha, Egypt
| | - Richard V Pereira
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Emmanuel Okello
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States.,Veterinary Medicine Teaching and Research Center, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Gabriele Maier
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
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17
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Li Y, Shi X, Zuo Y, Li T, Liu L, Shen Z, Shen J, Zhang R, Wang S. Multiplexed Target Enrichment Enables Efficient and In-Depth Analysis of Antimicrobial Resistome in Metagenomes. Microbiol Spectr 2022; 10:e0229722. [PMID: 36287061 PMCID: PMC9769626 DOI: 10.1128/spectrum.02297-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 10/04/2022] [Indexed: 01/06/2023] Open
Abstract
Antibiotic resistance genes (ARGs) pose a serious threat to public health and ecological security in the 21st century. However, the resistome only accounts for a tiny fraction of metagenomic content, which makes it difficult to investigate low-abundance ARGs in various environmental settings. Thus, a highly sensitive, accurate, and comprehensive method is needed to describe ARG profiles in complex metagenomic samples. In this study, we established a high-throughput sequencing method based on targeted amplification, which could simultaneously detect ARGs (n = 251), mobile genetic element genes (n = 8), and metal resistance genes (n = 19) in metagenomes. The performance of amplicon sequencing was compared with traditional metagenomic shotgun sequencing (MetaSeq). A total of 1421 primer pairs were designed, achieving extremely high coverage of target genes. The amplicon sequencing significantly improved the recovery of target ARGs (~9 × 104-fold), with higher sensitivity and diversity, less cost, and computation burden. Furthermore, targeted enrichment allows deep scanning of single nucleotide polymorphisms (SNPs), and elevated SNPs detection was shown in this study. We further performed this approach for 48 environmental samples (37 feces, 20 soils, and 7 sewage) and 16 clinical samples. All samples tested in this study showed high diversity and recovery of targeted genes. Our results demonstrated that the approach could be applied to various metagenomic samples and served as an efficient tool in the surveillance and evolution assessment of ARGs. Access to the resistome using the enrichment method validated in this study enabled the capture of low-abundance resistomes while being less costly and time-consuming, which can greatly advance our understanding of local and global resistome dynamics. IMPORTANCE ARGs, an increasing global threat to human health, can be transferred into health-related microorganisms in the environment by horizontal gene transfer, posing a serious threat to public health. Advancing profiling methods are needed for monitoring and predicting the potential risks of ARGs in metagenomes. Our study described a customized amplicon sequencing assay that could enable a high-throughput, targeted, in-depth analysis of ARGs and detect a low-abundance portion of resistomes. This method could serve as an efficient tool to assess the variation and evolution of specific ARGs in the clinical and natural environment.
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Affiliation(s)
- Yiming Li
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Xiaomin Shi
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Yang Zuo
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Tian Li
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Lu Liu
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Zhangqi Shen
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Jianzhong Shen
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Rong Zhang
- The Second Affiliated Hospital of Zhejiang University, Zhejiang University, Hangzhou, China
| | - Shaolin Wang
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
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18
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Cifuentes SG, Graham J, Loayza F, Saraiva C, Salinas L, Trueba G, Cárdenas PA. Evaluation of changes in the faecal resistome associated with children's exposure to domestic animals and food animal production. J Glob Antimicrob Resist 2022; 31:212-215. [PMID: 36202201 PMCID: PMC9850782 DOI: 10.1016/j.jgar.2022.09.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 08/02/2022] [Accepted: 09/19/2022] [Indexed: 12/12/2022] Open
Abstract
OBJECTIVES The paediatric gut microbiota is a reservoir of antimicrobial resistance genes. Environmental factors such as a child's exposure to faecal contamination and antimicrobial resistance genes of animal origin likely shape the resistome of infants and children. This study measured how different levels of exposure to domestic or food animals affect the structure of the intestinal resistome in children between 1 and 7 years of age. METHODS One hundred nineteen faecal samples from 39 children were analysed according to the level of exposure to domestic or food animals and categorized into three risk groups. Using high-throughput sequencing with an Illumina NovaSeq 6000 SP platform, we performed faecal resistome analyses using the ResFinder database. Additionally, ResistoXplorer was used to characterize the resistomes of children differentially exposed to domestic animals. RESULTS Our data indicated that specific antimicrobial resistance genes such as those that confer resistance to MATFPR (macrolide, aminoglycoside, tetracycline, fluoroquinolone, phenicol, and rifamycin) and tetracyclines were statistically less abundant in the group of children without exposure to animals (group 2), compared with the groups exposed to domestic and food animals (groups 1 and 3). However, the overall resistome structure among the children was not affected by the different levels of exposure to animals. CONCLUSIONS This study suggests that animal exposure is a risk factor for young children acquiring specific antimicrobial resistance genes from domestic animals or animal production areas. However, the overall resistome structure was not affected.
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Affiliation(s)
- Sara G. Cifuentes
- Universidad San Francisco de Quito USFQ, Colegio de Ciancias Biológicas y Ambientales, Instituto de Microbiología, Quito, Pichincha, Ecuador
| | - Jay Graham
- Environmental Health Sciences Division, University of California, Berkeley, California
| | - Fernanda Loayza
- Universidad San Francisco de Quito USFQ, Colegio de Ciancias Biológicas y Ambientales, Instituto de Microbiología, Quito, Pichincha, Ecuador
| | - Carlos Saraiva
- Universidad San Francisco de Quito USFQ, Colegio de Ciancias Biológicas y Ambientales, Instituto de Microbiología, Quito, Pichincha, Ecuador
| | - Liseth Salinas
- Universidad San Francisco de Quito USFQ, Colegio de Ciancias Biológicas y Ambientales, Instituto de Microbiología, Quito, Pichincha, Ecuador
| | - Gabriel Trueba
- Universidad San Francisco de Quito USFQ, Colegio de Ciancias Biológicas y Ambientales, Instituto de Microbiología, Quito, Pichincha, Ecuador
| | - Paúl A. Cárdenas
- Universidad San Francisco de Quito USFQ, Colegio de Ciancias Biológicas y Ambientales, Instituto de Microbiología, Quito, Pichincha, Ecuador,Corresponding author. Universidad San Francisco de Quito USFQ, Instituto de Microbiología, Vía Interoceánica y Diego de Robles, Cumbayá, Ecuador., (P.A. Cárdenas)
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19
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Stebliankin V, Sazal M, Valdes C, Mathee K, Narasimhan G. A novel approach for combining the metagenome, metaresistome, metareplicome and causal inference to determine the microbes and their antibiotic resistance gene repertoire that contribute to dysbiosis. Microb Genom 2022; 8:mgen000899. [PMID: 36748547 PMCID: PMC9837561 DOI: 10.1099/mgen.0.000899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 09/11/2022] [Indexed: 12/24/2022] Open
Abstract
The use of whole metagenomic data to infer the relative abundance of all its microbes is well established. The same data can be used to determine the replication rate of all eubacterial taxa with circular chromosomes. Despite their availability, the replication rate profiles (metareplicome) have not been fully exploited in microbiome analyses. Another relatively new approach is the application of causal inferencing to analyse microbiome data that goes beyond correlational studies. A novel scalable pipeline called MeRRCI (Metagenome, metaResistome, and metaReplicome for Causal Inferencing) was developed. MeRRCI combines efficient computation of the metagenome (bacterial relative abundance), metaresistome (antimicrobial gene abundance) and metareplicome (replication rates), and integrates environmental variables (metadata) for causality analysis using Bayesian networks. MeRRCI was applied to an infant gut microbiome data set to investigate the microbial community's response to antibiotics. Our analysis suggests that the current treatment stratagem contributes to preterm infant gut dysbiosis, allowing a proliferation of pathobionts. The study highlights the specific antibacterial resistance genes that may contribute to exponential cell division in the presence of antibiotics for various pathogens, namely Klebsiella pneumoniae, Citrobacter freundii, Staphylococcus epidermidis, Veilonella parvula and Clostridium perfringens. These organisms often contribute to the harmful long-term sequelae seen in these young infants.
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Affiliation(s)
- Vitalii Stebliankin
- Bioinformatics Research Group (BioRG), Knight Foundation School of Computing and Information Sciences, Florida International University, Miami, FL, USA
| | - Musfiqur Sazal
- Bioinformatics Research Group (BioRG), Knight Foundation School of Computing and Information Sciences, Florida International University, Miami, FL, USA
- Present address: Microsoft Corporation, GA, Atlanta, USA
| | - Camilo Valdes
- Bioinformatics Research Group (BioRG), Knight Foundation School of Computing and Information Sciences, Florida International University, Miami, FL, USA
- Present address: Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA 94550, USA
| | - Kalai Mathee
- Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
- Biomolecular Sciences Institute, Florida International University, Miami, FL, USA
| | - Giri Narasimhan
- Bioinformatics Research Group (BioRG), Knight Foundation School of Computing and Information Sciences, Florida International University, Miami, FL, USA
- Biomolecular Sciences Institute, Florida International University, Miami, FL, USA
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20
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Baker M, Williams AD, Hooton SPT, Helliwell R, King E, Dodsworth T, María Baena-Nogueras R, Warry A, Ortori CA, Todman H, Gray-Hammerton CJ, Pritchard ACW, Iles E, Cook R, Emes RD, Jones MA, Kypraios T, West H, Barrett DA, Ramsden SJ, Gomes RL, Hudson C, Millard AD, Raman S, Morris C, Dodd CER, Kreft JU, Hobman JL, Stekel DJ. Antimicrobial resistance in dairy slurry tanks: A critical point for measurement and control. ENVIRONMENT INTERNATIONAL 2022; 169:107516. [PMID: 36122459 DOI: 10.1016/j.envint.2022.107516] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 09/09/2022] [Accepted: 09/09/2022] [Indexed: 06/15/2023]
Abstract
Waste from dairy production is one of the largest sources of contamination from antimicrobial resistant bacteria (ARB) and genes (ARGs) in many parts of the world. However, studies to date do not provide necessary evidence to inform antimicrobial resistance (AMR) countermeasures. We undertook a detailed, interdisciplinary, longitudinal analysis of dairy slurry waste. The slurry contained a population of ARB and ARGs, with resistances to current, historical and never-used on-farm antibiotics; resistances were associated with Gram-negative and Gram-positive bacteria and mobile elements (ISEcp1, Tn916, Tn21-family transposons). Modelling and experimental work suggested that these populations are in dynamic equilibrium, with microbial death balanced by fresh input. Consequently, storing slurry without further waste input for at least 60 days was predicted to reduce ARB spread onto land, with > 99 % reduction in cephalosporin resistant Escherichia coli. The model also indicated that for farms with low antibiotic use, further reductions are unlikely to reduce AMR further. We conclude that the slurry tank is a critical point for measurement and control of AMR, and that actions to limit the spread of AMR from dairy waste should combine responsible antibiotic use, including low total quantity, avoidance of human critical antibiotics, and choosing antibiotics with shorter half-lives, coupled with appropriate slurry storage.
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Affiliation(s)
- Michelle Baker
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK; School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK
| | - Alexander D Williams
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK
| | - Steven P T Hooton
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK; (a)Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Richard Helliwell
- School of Sociology and Social Policy, University of Nottingham, University Park Campus, Nottingham NG7 2RD, UK; School of Geography, University of Nottingham, University Park Campus, Nottingham NG7 2RD, UK; Ruralis, University Centre Dragvoll, N-7491 Trondheim, Norway
| | - Elizabeth King
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK
| | - Thomas Dodsworth
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK; ResChem Analytical Ltd, 8 Jubilee Parkway, Jubilee Business Park, Stores Road, Derby DE21 4BJ, UK
| | - Rosa María Baena-Nogueras
- Food Water Waste Research Group, Faculty of Engineering, University of Nottingham, University Park Campus, Nottingham NG7 2RD, UK
| | - Andrew Warry
- Advanced Data Analysis Centre, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK
| | - Catherine A Ortori
- School of Pharmacy, University of Nottingham, University Park Campus, Nottingham NG7 2RD, UK
| | - Henry Todman
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK; School of Mathematical Sciences, University of Nottingham, University Park Campus, Nottingham NG7 2RD, UK
| | - Charlotte J Gray-Hammerton
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK; Department of Zoology, University of Oxford, 11a Mansfield Road, Oxford OX1 3SZ, UK
| | - Alexander C W Pritchard
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK
| | - Ethan Iles
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK
| | - Ryan Cook
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK
| | - Richard D Emes
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK
| | - Michael A Jones
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK
| | - Theodore Kypraios
- School of Mathematical Sciences, University of Nottingham, University Park Campus, Nottingham NG7 2RD, UK
| | - Helen West
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK
| | - David A Barrett
- School of Pharmacy, University of Nottingham, University Park Campus, Nottingham NG7 2RD, UK
| | - Stephen J Ramsden
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK
| | - Rachel L Gomes
- Food Water Waste Research Group, Faculty of Engineering, University of Nottingham, University Park Campus, Nottingham NG7 2RD, UK
| | - Chris Hudson
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK
| | - Andrew D Millard
- (a)Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Sujatha Raman
- School of Sociology and Social Policy, University of Nottingham, University Park Campus, Nottingham NG7 2RD, UK; Centre for Public Awareness of Science, Australian National University, Linnaeus Way, Acton ACT 2601, Canberra, Australia
| | - Carol Morris
- School of Geography, University of Nottingham, University Park Campus, Nottingham NG7 2RD, UK
| | - Christine E R Dodd
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK
| | - Jan-Ulrich Kreft
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT
| | - Jon L Hobman
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK
| | - Dov J Stekel
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK; Department of Mathematics and Applied Mathematics, University of Johannesburg, Auckland Park Kingsway Campus, Rossmore, Johannesburg, South Africa.
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21
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Kang J, Liu Y, Chen X, Xu F, Wang H, Xiong W, Li X. Metagenomic insights into the antibiotic resistomes of typical Chinese dairy farm environments. Front Microbiol 2022; 13:990272. [PMID: 36246251 PMCID: PMC9555277 DOI: 10.3389/fmicb.2022.990272] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 08/24/2022] [Indexed: 11/13/2022] Open
Abstract
Antibiotic resistance genes (ARGs) in the environment pose a threat to human and animal health. Dairy cows are important livestock in China; however, a comprehensive understanding of antibiotic resistance in their production environment has not been well clarified. In this study, we used metagenomic methods to analyze the resistomes, microbiomes, and potential ARG bacterial hosts in typical dairy farm environments (including feces, wastewater, and soil). The ARGs resistant to tetracyclines, MLS, β-lactams, aminoglycoside, and multidrug was dominant in the dairy farm ecosystem. The abundance and diversity of total ARGs in dairy feces and wastewater were significantly higher than in soil (P < 0.05). The same environmental samples from different dairy have similar resistomes and microbiomes. A high detection rate of tet(X) in wastewater and feces (100% and 71.4%, respectively), high abundance (range from 5.74 to 68.99 copies/Gb), and the finding of tet(X5) challenged the clinical application of the last antibiotics resort of tigecycline. Network analysis identified Bacteroides as the dominant genus in feces and wastewater, which harbored the greatest abundance of their respective total ARG coverage and shared ARGs. These results improved our understanding of ARG profiles and their bacterial hosts in dairy farm environments and provided a basis for further surveillance.
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Affiliation(s)
- Jijun Kang
- Key Laboratory of Animal Antimicrobial Resistance Surveillance, Ministry of Agriculture and Rural Affairs, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
- Laboratory of Quality and Safety Risk Assessment for Products on Feed-origin Risk Factor, Ministry of Agriculture and Rural Affairs, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yiming Liu
- Key Laboratory of Animal Antimicrobial Resistance Surveillance, Ministry of Agriculture and Rural Affairs, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
- Laboratory of Quality and Safety Risk Assessment for Products on Feed-origin Risk Factor, Ministry of Agriculture and Rural Affairs, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaojie Chen
- Key Laboratory of Animal Antimicrobial Resistance Surveillance, Ministry of Agriculture and Rural Affairs, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
- Laboratory of Quality and Safety Risk Assessment for Products on Feed-origin Risk Factor, Ministry of Agriculture and Rural Affairs, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Fei Xu
- Key Laboratory of Animal Antimicrobial Resistance Surveillance, Ministry of Agriculture and Rural Affairs, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
- Laboratory of Quality and Safety Risk Assessment for Products on Feed-origin Risk Factor, Ministry of Agriculture and Rural Affairs, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Honglei Wang
- Key Laboratory of Animal Antimicrobial Resistance Surveillance, Ministry of Agriculture and Rural Affairs, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
- Laboratory of Quality and Safety Risk Assessment for Products on Feed-origin Risk Factor, Ministry of Agriculture and Rural Affairs, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wenguang Xiong
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutic Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
| | - Xiubo Li
- Key Laboratory of Animal Antimicrobial Resistance Surveillance, Ministry of Agriculture and Rural Affairs, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
- Laboratory of Quality and Safety Risk Assessment for Products on Feed-origin Risk Factor, Ministry of Agriculture and Rural Affairs, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
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22
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Tello M, Ocejo M, Oporto B, Lavín JL, Hurtado A. Within-farm dynamics of ESBL-producing Escherichia coli in dairy cattle: Resistance profiles and molecular characterization by long-read whole-genome sequencing. Front Microbiol 2022; 13:936843. [PMID: 35966684 PMCID: PMC9366117 DOI: 10.3389/fmicb.2022.936843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 06/29/2022] [Indexed: 11/13/2022] Open
Abstract
A longitudinal study was designed in five dairy cattle farms to assess the within-farm dynamics of ESBL-/AmpC-/carbapenemase-producing E. coli and their resistance profiles, along with the genes conferring the resistance phenotypes. Twelve samplings were performed over a period of 16 months, collecting rectal feces from apparently healthy animals in three age groups (calves, heifers, and lactating cows) that were subjected to selective isolation in cefotaxime-containing media. Minimum inhibitory concentrations were determined by broth microdilution for 197 cefotaxime-resistant E. coli (1-3 isolates per age group and sampling date), and 41 of them were selected for long-read whole-genome sequencing. Cefotaxime-resistant E. coli were detected in the five farms, but isolation frequency and resistance profiles varied among farms and age groups. The genetic profiling of a selection of isolates recovered in two of the farms was described in full detail, showing the predominance of a few genomic subtypes of E. coli in one farm (F1) and great variability of strains in another one (F4). Two predominant distinct strains carrying the bla CTX-M-1 gene in IncX1 plasmids successively spread and persisted in F1 over a prolonged period. In F4, 13 different MLST types carrying a high diversity of ESBL-encoding genes in 6 different plasmid types were observed, probably as the result of multiple source contamination events. In both farms, the presence of certain plasmid types with the same repertoire of ARGs in different E. coli STs strongly suggested the occurrence of horizontal transfer of such plasmids among strains circulating within the farms. Considering the public health importance of ESBL-producing E. coli both as pathogens and as vectors for resistance mechanisms, the presence of β-lactamase- and other AMR-encoding genes in plasmids that can be readily transferred between bacteria is a concern that highlights the need for One Health surveillance.
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Affiliation(s)
- Maitane Tello
- Department of Animal Health, NEIKER – Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Derio, Bizkaia, Spain
| | - Medelin Ocejo
- Department of Animal Health, NEIKER – Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Derio, Bizkaia, Spain
| | - Beatriz Oporto
- Department of Animal Health, NEIKER – Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Derio, Bizkaia, Spain
| | - José Luis Lavín
- Department of Applied Mathematics, NEIKER – Basque Institute for Agricultural Research and Development, Bioinformatics Unit, Basque Research and Technology Alliance (BRTA), Derio, Bizkaia, Spain
| | - Ana Hurtado
- Department of Animal Health, NEIKER – Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Derio, Bizkaia, Spain
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23
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Cason C, D’Accolti M, Soffritti I, Mazzacane S, Comar M, Caselli E. Next-generation sequencing and PCR technologies in monitoring the hospital microbiome and its drug resistance. Front Microbiol 2022; 13:969863. [PMID: 35966671 PMCID: PMC9370071 DOI: 10.3389/fmicb.2022.969863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 07/12/2022] [Indexed: 11/13/2022] Open
Abstract
The hospital environment significantly contributes to the onset of healthcare-associated infections (HAIs), which represent one of the most frequent complications occurring in healthcare facilities worldwide. Moreover, the increased antimicrobial resistance (AMR) characterizing HAI-associated microbes is one of the human health’s main concerns, requiring the characterization of the contaminating microbial population in the hospital environment. The monitoring of surface microbiota in hospitals is generally addressed by microbial cultural isolation. However, this has some important limitations mainly relating to the inability to define the whole drug-resistance profile of the contaminating microbiota and to the long time period required to obtain the results. Hence, there is an urgent need to implement environmental surveillance systems using more effective methods. Molecular approaches, including next-generation sequencing and PCR assays, may be useful and effective tools to monitor microbial contamination, especially the growing AMR of HAI-associated pathogens. Herein, we summarize the results of our recent studies using culture-based and molecular analyses in 12 hospitals for adults and children over a 5-year period, highlighting the advantages and disadvantages of the techniques used.
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Affiliation(s)
- Carolina Cason
- Department of Advanced Translational Microbiology, Institute for Maternal and Child Health, IRCCS “Burlo Garofolo”, Trieste, Italy
| | - Maria D’Accolti
- Department of Chemical, Pharmaceutical and Agricultural Sciences, Section of Microbiology and LTTA, University of Ferrara, Ferrara, Italy
- CIAS Research Centre, University of Ferrara, Ferrara, Italy
| | - Irene Soffritti
- Department of Chemical, Pharmaceutical and Agricultural Sciences, Section of Microbiology and LTTA, University of Ferrara, Ferrara, Italy
- CIAS Research Centre, University of Ferrara, Ferrara, Italy
| | | | - Manola Comar
- Department of Advanced Translational Microbiology, Institute for Maternal and Child Health, IRCCS “Burlo Garofolo”, Trieste, Italy
- Department of Medical Sciences, University of Trieste, Trieste, Italy
| | - Elisabetta Caselli
- Department of Chemical, Pharmaceutical and Agricultural Sciences, Section of Microbiology and LTTA, University of Ferrara, Ferrara, Italy
- CIAS Research Centre, University of Ferrara, Ferrara, Italy
- *Correspondence: Elisabetta Caselli,
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24
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Casseri E, Bulut E, Llanos Soto S, Wemette M, Stout A, Greiner Safi A, Lynch R, Moroni P, Ivanek R. Understanding Antibiotic Resistance as a Perceived Threat towards Dairy Cattle through Beliefs and Practices: A Survey-Based Study of Dairy Farmers. Antibiotics (Basel) 2022; 11:antibiotics11080997. [PMID: 35892387 PMCID: PMC9330383 DOI: 10.3390/antibiotics11080997] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/16/2022] [Accepted: 07/20/2022] [Indexed: 02/05/2023] Open
Abstract
Antibiotic use is an important component in dairy herd management both to treat bacterial diseases and to maximize animal welfare. However, there is concern among scientists that antibiotic misuse and/or overuse by farmers might promote the emergence of resistant pathogens. We conducted a cross-sectional web-based questionnaire study with dairy farmers/managers in New York, USA to evaluate their (i) level of concern about antibiotic resistance and (ii) interest in adopting new judicious antibiotic use practices regarding mastitis treatment. A total of 118 responses were subjected to statistical analysis. The findings revealed that nearly half (45%) of study participants were undecided or disagreed that antibiotic resistance due to antibiotic use in dairy farming may negatively impact the health of dairy cattle. In contrast, the majority (78%) of participants self-reported that they do not treat with antibiotics at the first sign of mastitis, and the majority (66%) have either fully or partially implemented culture-based mastitis treatment on their farm. The self-reported adoption of culture-based mastitis treatment practices was statistically significantly associated with higher numbers of injectable and intramammary doses of antibiotics used on the participants' farms. These findings will aid future research investigations on how to promote sustainable antibiotic use practices in dairy cattle.
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Affiliation(s)
- Eleni Casseri
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA; (E.B.); (S.L.S.); (M.W.); (A.S.); (P.M.); (R.I.)
- Correspondence:
| | - Ece Bulut
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA; (E.B.); (S.L.S.); (M.W.); (A.S.); (P.M.); (R.I.)
| | - Sebastian Llanos Soto
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA; (E.B.); (S.L.S.); (M.W.); (A.S.); (P.M.); (R.I.)
| | - Michelle Wemette
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA; (E.B.); (S.L.S.); (M.W.); (A.S.); (P.M.); (R.I.)
| | - Alison Stout
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA; (E.B.); (S.L.S.); (M.W.); (A.S.); (P.M.); (R.I.)
| | - Amelia Greiner Safi
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA;
- Department of Communication, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Robert Lynch
- College of Agriculture and Life Sciences, Cornell University, Ithaca, NY 14853, USA;
| | - Paolo Moroni
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA; (E.B.); (S.L.S.); (M.W.); (A.S.); (P.M.); (R.I.)
- Dipartimento di Medicina Veterinaria e Scienze Animali, Università degli Studi di Milano, Via dell’Università 6, 26900 Lodi, Italy
| | - Renata Ivanek
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA; (E.B.); (S.L.S.); (M.W.); (A.S.); (P.M.); (R.I.)
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25
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Weinroth MD, Thomas KM, Doster E, Vikram A, Schmidt JW, Arthur TM, Wheeler TL, Parker JK, Hanes AS, Alekoza N, Wolfe C, Metcalf JL, Morley PS, Belk KE. Resistomes and microbiome of meat trimmings and colon content from culled cows raised in conventional and organic production systems. Anim Microbiome 2022; 4:21. [PMID: 35272712 PMCID: PMC8908682 DOI: 10.1186/s42523-022-00166-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 02/04/2022] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND The potential to distribute bacteria resistant to antimicrobial drugs in the meat supply is a public health concern. Market cows make up a fifth of the U.S. beef produced but little is known about the entire population of bacteria (the microbiome) and entirety of all resistance genes (the resistome) that are found in this population. The objective of this study was to characterize and compare the resistomes and microbiome of beef, dairy, and organic dairy market cows at slaughter. METHODS Fifty-four (N = 54) composite samples of both colon content and meat trimmings rinsate samples were collected over six visits to two harvest facilities from cows raised in three different production systems: conventional beef, conventional dairy, and organic dairy (n = 3 samples per visit per production system). Metagenomic DNA obtained from samples were analyzed using target-enriched sequencing (resistome) and 16S rRNA gene sequencing (microbiome). RESULTS All colon content samples had at least one identifiable antimicrobial resistance gene (ARG), while 21 of the 54 meat trimmings samples harbored at least one identifiable ARGs. Tetracycline ARGs were the most abundant class in both colon content and carcass meat trimmings. The resistome found on carcass meat trimmings was not significantly different by production system (P = 0.84, R2 = 0.00) or harvest facility (P = 0.10, R2 = 0.09). However, the resistome of colon content differed (P = 0.01; R2 = 0.05) among production systems, but not among the harvest facilities (P = 0.41; R2 = 0.00). Amplicon sequencing revealed differences (P < 0.05) in microbial populations in both meat trimmings and colon content between harvest facilities but not production systems (P > 0.05). CONCLUSIONS These data provide a baseline characterization of an important segment of the beef industry and highlight the effect that the production system where cattle are raised and the harvest facilities where an animal is processed can impact associated microbiome and resistomes.
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Affiliation(s)
- Margaret D Weinroth
- Department of Animal Sciences, Colorado State University, Fort Collins, CO, USA
- U.S. Department of Agriculture, Agricultural Research Service, U.S. National Poultry Research Center, Athens, GA, USA
| | - Kevin M Thomas
- Department of Animal Sciences, Colorado State University, Fort Collins, CO, USA
| | - Enrique Doster
- Department of Microbiology Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Amit Vikram
- U.S. Department of Agriculture, Agricultural Research Service, Roman L. Hruska U.S. Meat Animal Research Center, Clay Center, NE, USA
- Intralytix, Columbia, MD, 21046, USA
| | - John W Schmidt
- U.S. Department of Agriculture, Agricultural Research Service, Roman L. Hruska U.S. Meat Animal Research Center, Clay Center, NE, USA
| | - Terrance M Arthur
- U.S. Department of Agriculture, Agricultural Research Service, Roman L. Hruska U.S. Meat Animal Research Center, Clay Center, NE, USA
| | - Tommy L Wheeler
- U.S. Department of Agriculture, Agricultural Research Service, Roman L. Hruska U.S. Meat Animal Research Center, Clay Center, NE, USA
| | - Jennifer K Parker
- Department of Clinical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Ayanna S Hanes
- Department of Clinical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Najla Alekoza
- Department of Clinical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Cory Wolfe
- Department of Clinical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Jessica L Metcalf
- Department of Animal Sciences, Colorado State University, Fort Collins, CO, USA
| | - Paul S Morley
- Veterinary Education, Research, and Outreach Program, Texas A&M University and West Texas A&M University, Canyon, TX, 79105, USA.
| | - Keith E Belk
- Department of Animal Sciences, Colorado State University, Fort Collins, CO, USA
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26
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Liang C, Wei D, Yan W, Zhang S, Shi J, Liu L. Fates of intracellular and extracellular antibiotic resistance genes during the cattle farm wastewater treatment process. BIORESOURCE TECHNOLOGY 2022; 344:126272. [PMID: 34737048 DOI: 10.1016/j.biortech.2021.126272] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 10/25/2021] [Accepted: 10/29/2021] [Indexed: 06/13/2023]
Abstract
Cattle farm wastewater, as a significant reservoir for antibiotic resistance genes (ARGs), has received wide attention. Intracellular and extracellular ARGs (iARGs and eARGs) were detected during wastewater treatment, including solid-liquid separation, anaerobic regulation, upflow anaerobic sludge blanket (UASB) digestion, an anoxic-oxic-anoxic-oxic (A2O2) process, a membrane bioreactor (MBR), and ozone disinfection. Ten abundant ARGs were chosen as the target ARGs according to metagenomic sequencing. The concentrations of the total target iARGs and eARGs were 6.12 × 107 and 3.24 × 106 copy numbers/mL in raw wastewater, and then 3.79 × 103 and 3.95 × 105 copy numbers/mL in final effluent, because UASB, A2O2, MBR and ozone disinfection can gradually reduce the concentrations of most ARGs. The concentrations of ARGs were positively correlated with almost all wastewater quality indicators. Positive correlation was also observed between iARGs and Bacteroidetes, Firmicutes and Spirochaetes, indicating that the bacteria in these three phyla might be the main hosts of ARGs. Wastewater quality indicators and bacterial community composition affected the distribution and removal of ARGs during cattle wastewater treatment.
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Affiliation(s)
- Chengyu Liang
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Dong Wei
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, PR China; Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, Shanghai 200241, PR China
| | - Weizhi Yan
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Siying Zhang
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Jiping Shi
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, PR China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, PR China; Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, Shanghai 200241, PR China
| | - Li Liu
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, PR China.
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Tariq M, Jameel F, Ijaz U, Abdullah M, Rashid K. Biofertilizer microorganisms accompanying pathogenic attributes: a potential threat. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2022; 28:77-90. [PMID: 35221573 PMCID: PMC8847475 DOI: 10.1007/s12298-022-01138-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Revised: 11/30/2021] [Accepted: 01/14/2022] [Indexed: 05/04/2023]
Abstract
Application of biofertilizers containing living or dormant plant growth promoting bacterial cells is considered to be an ecofriendly alternative of chemical fertilizers for improved crop production. Biofertilizers opened myriad doors towards sustainable agriculture as they effectively reduce heavy use of chemical fertilizers and pesticides by keeping soils profuse in micro and macronutrients, regulating plant hormones and restraining infections caused by the pests present in soil without inflicting environmental damage. Generally, pathogenicity and biosafety testing of potential plant growth promoting bacteria (PGPB) are not performed, and the bacteria are reported to be beneficial solely on testing plant growth promoting characteristics. Unfortunately, some rhizosphere and endophytic PGPB are reported to be involved in various diseases. Such PGPB can also spread virulence and multidrug resistance genes carried by them through horizontal gene transfer to other bacteria in the environment. Therefore, deployment of such microbial populations in open fields could lead to disastrous side effects on human health and environment. Careless declaration of bacteria as PGPB is more pronounced in research publications. Here, we present a comprehensive report of declared PGPB which are reported to be pathogenic in other studies. This review also suggests the employment of some additional safety assessment protocols before reporting a bacteria as beneficial and product development.
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Affiliation(s)
- Mohsin Tariq
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Farwah Jameel
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
| | - Usman Ijaz
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Muhammad Abdullah
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Kamran Rashid
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
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Black Z, Balta I, Black L, Naughton PJ, Dooley JSG, Corcionivoschi N. The Fate of Foodborne Pathogens in Manure Treated Soil. Front Microbiol 2021; 12:781357. [PMID: 34956145 PMCID: PMC8702830 DOI: 10.3389/fmicb.2021.781357] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 11/22/2021] [Indexed: 12/25/2022] Open
Abstract
The aim of this review was to provide an update on the complex relationship between manure application, altered pathogen levels and antibiotic resistance. This is necessary to protect health and improve the sustainability of this major farming practice in agricultural systems based on high levels of manure production. It is important to consider soil health in relation to environment and land management practices in the context of the soil microflora and the introduction of pathogens on the health of the soil microbiome. Viable pathogens in manure spread on agricultural land may be distributed by leaching, surface run-off, water source contamination and contaminated crop removal. Thus it is important to understand how multiple pathogens can persist in manures and on soil at farm-scale and how crops produced under these conditions could be a potential transfer route for zoonotic pathogens. The management of pathogen load within livestock manure is a potential mechanism for the reduction and prevention of outbreaks infection with Escherichia coli, Listeria Salmonella, and Campylobacter. The ability of Campylobacter, E. coli, Listeria and Salmonella to combat environmental stress coupled with their survival on food crops and vegetables post-harvest emphasizes the need for further study of these pathogens along with the emerging pathogen Providencia given its link to disease in the immunocompromised and its’ high levels of antibiotic resistance. The management of pathogen load within livestock manure has been widely recognized as a potential mechanism for the reduction and prevention of outbreaks infection but any studies undertaken should be considered as region specific due to the variable nature of the factors influencing pathogen content and survival in manures and soil. Mediocre soils that require nutrients could be one template for research on manure inputs and their influence on soil health and on pathogen survival on grassland and in food crops.
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Affiliation(s)
- Zoe Black
- Grassland and Plant Sciences Branch, AFBI Crossnacreevy, Sustainable Agri-Food Sciences Division, Agri-Food and Biosciences Institute, Belfast, United Kingdom.,Bacteriology Branch, Veterinary Sciences Division, Agri-Food and Biosciences Institute, Belfast, United Kingdom.,Nutrition Innovation Centre for Food and Health (NICHE), School of Biomedical Sciences, Ulster University, Coleraine, United Kingdom
| | - Igori Balta
- Bacteriology Branch, Veterinary Sciences Division, Agri-Food and Biosciences Institute, Belfast, United Kingdom.,Faculty of Bioengineering of Animal Resources, Banat University of Animal Sciences and Veterinary Medicine, King Michael I of Romania, Timisoara, Romania
| | - Lisa Black
- Grassland and Plant Sciences Branch, AFBI Crossnacreevy, Sustainable Agri-Food Sciences Division, Agri-Food and Biosciences Institute, Belfast, United Kingdom
| | - Patrick J Naughton
- Nutrition Innovation Centre for Food and Health (NICHE), School of Biomedical Sciences, Ulster University, Coleraine, United Kingdom
| | - James S G Dooley
- Nutrition Innovation Centre for Food and Health (NICHE), School of Biomedical Sciences, Ulster University, Coleraine, United Kingdom
| | - Nicolae Corcionivoschi
- Bacteriology Branch, Veterinary Sciences Division, Agri-Food and Biosciences Institute, Belfast, United Kingdom.,Faculty of Bioengineering of Animal Resources, Banat University of Animal Sciences and Veterinary Medicine, King Michael I of Romania, Timisoara, Romania
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Ma T, McAllister TA, Guan LL. A review of the resistome within the digestive tract of livestock. J Anim Sci Biotechnol 2021; 12:121. [PMID: 34763729 PMCID: PMC8588621 DOI: 10.1186/s40104-021-00643-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 10/07/2021] [Indexed: 12/25/2022] Open
Abstract
Antimicrobials have been widely used to prevent and treat infectious diseases and promote growth in food-production animals. However, the occurrence of antimicrobial resistance poses a huge threat to public and animal health, especially in less developed countries where food-producing animals often intermingle with humans. To limit the spread of antimicrobial resistance from food-production animals to humans and the environment, it is essential to have a comprehensive knowledge of the role of the resistome in antimicrobial resistance (AMR), The resistome refers to the collection of all antimicrobial resistance genes associated with microbiota in a given environment. The dense microbiota in the digestive tract is known to harbour one of the most diverse resistomes in nature. Studies of the resistome in the digestive tract of humans and animals are increasing exponentially as a result of advancements in next-generation sequencing and the expansion of bioinformatic resources/tools to identify and describe the resistome. In this review, we outline the various tools/bioinformatic pipelines currently available to characterize and understand the nature of the intestinal resistome of swine, poultry, and ruminants. We then propose future research directions including analysis of resistome using long-read sequencing, investigation in the role of mobile genetic elements in the expression, function and transmission of AMR. This review outlines the current knowledge and approaches to studying the resistome in food-producing animals and sheds light on future strategies to reduce antimicrobial usage and control the spread of AMR both within and from livestock production systems.
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Affiliation(s)
- Tao Ma
- Key laboratory of Feed Biotechnology of the Ministry of Agriculture, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.,Department of Agricultural, Food and Nutritional Science, University of Alberta, T6G2P5, Edmonton, AB, Canada
| | - Tim A McAllister
- Lethbridge Research and Development Centre, Lethbridge, AB, T1J 4P4, Canada
| | - Le Luo Guan
- Department of Agricultural, Food and Nutritional Science, University of Alberta, T6G2P5, Edmonton, AB, Canada.
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Microbiome Studies from Saudi Arabia over the Last 10 Years: Achievements, Gaps, and Future Directions. Microorganisms 2021; 9:microorganisms9102021. [PMID: 34683342 PMCID: PMC8537179 DOI: 10.3390/microorganisms9102021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 09/13/2021] [Accepted: 09/16/2021] [Indexed: 11/17/2022] Open
Abstract
In the past ten years, microbiome studies have shown tremendous potentiality for implementation of understanding microbiome structures and functions of various biomes and application of this knowledge for human betterment. Saudi Arabia is full of geographical, ecological, ethnical, and industrial diversities and scientific capacities. Therefore, there is a great potential in Saudi Arabia to conduct and implement microbiome-based research and applications. However, there is no review available on where Saudi Arabia stands with respect to global microbiome research trends. This review highlights the metagenome-assisted microbiome research from Saudi Arabia compared to the global focuses on microbiome research. Further, it also highlights the gaps and areas that should be focused on by Saudi microbiome researchers and the possible initiatives to be taken by Saudi government and universities. This literature review shows that the global trends of microbiome research cover a broad spectrum of human and animal health conditions and diseases, environmental and antimicrobial resistance surveillance, surveillance of food and food processing, production of novel industrial enzymes and bioactive pharmaceutical products, and space applications. However, Saudi microbiome studies are mostly confined to very few aspects of health (human and animal) and environment/ecology in last ten years, without much application. Therefore, Saudi Arabia should focus more on applied microbiome research through government, academic, and industry initiatives and global cooperation to match the global trends.
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31
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Haley BJ, Van Kessel JAS. The resistome of the bovine gastrointestinal tract. Curr Opin Biotechnol 2021; 73:213-219. [PMID: 34492620 DOI: 10.1016/j.copbio.2021.07.025] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 07/21/2021] [Indexed: 01/13/2023]
Abstract
The gastrointestinal tracts of beef and dairy cattle are reservoirs of antimicrobial-resistant bacteria, and our knowledge of the ecology of resistance in these animals has changed with the advent of novel molecular technologies. Application of metagenomics and qPCR to the study of bovine gut ecology has demonstrated that there is overlap, with some differences, between beef and dairy cattle fecal resistomes, that treatment with antimicrobials often transiently influences the resistome, and young calves carry a high abundance of ARGs. Future work should harness emerging metagenome sequencing technologies to better describe the taxa harboring ARGs and collocated non-resistance genes and use these data along with identifying the multiplicity of factors driving resistance to develop strategies to reduce AMR carriage in cattle.
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Affiliation(s)
- Bradd J Haley
- Environmental Microbial and Food Safety Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, USA.
| | - Jo Ann S Van Kessel
- Environmental Microbial and Food Safety Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, USA
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Mizrahi I, Wallace RJ, Moraïs S. The rumen microbiome: balancing food security and environmental impacts. Nat Rev Microbiol 2021; 19:553-566. [PMID: 33981031 DOI: 10.1038/s41579-021-00543-6] [Citation(s) in RCA: 143] [Impact Index Per Article: 47.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/09/2021] [Indexed: 02/03/2023]
Abstract
Ruminants produce edible products and contribute to food security. They house a complex rumen microbial community that enables the host to digest their plant feed through microbial-mediated fermentation. However, the rumen microbiome is also responsible for the production of one of the most potent greenhouse gases, methane, and contributes about 18% of its total anthropogenic emissions. Conventional methods to lower methane production by ruminants have proved successful, but to a limited and often temporary extent. An increased understanding of the host-microbiome interactions has led to the development of new mitigation strategies. In this Review we describe the composition, ecology and metabolism of the rumen microbiome, and the impact on host physiology and the environment. We also discuss the most pertinent methane mitigation strategies that emerged to balance food security and environmental impacts.
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Affiliation(s)
- Itzhak Mizrahi
- Department of Life Sciences, Ben-Gurion University of the Negev and the National Institute for Biotechnology in the Negev, Marcus Family Campus, Be'er-Sheva, Israel.
| | - R John Wallace
- The Rowett Institute, University of Aberdeen, Aberdeen, UK
| | - Sarah Moraïs
- Department of Life Sciences, Ben-Gurion University of the Negev and the National Institute for Biotechnology in the Negev, Marcus Family Campus, Be'er-Sheva, Israel
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33
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Antibiotic Resistance Genes and Associated Phenotypes in Escherichia coli and Enterococcus from Cattle at Different Production Stages on a Dairy Farm in Central California. Antibiotics (Basel) 2021; 10:antibiotics10091042. [PMID: 34572624 PMCID: PMC8471271 DOI: 10.3390/antibiotics10091042] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/21/2021] [Accepted: 08/24/2021] [Indexed: 11/19/2022] Open
Abstract
The objectives of this study were to characterize overall genomic antibiotic resistance profiles of fecal Escherichia coli and Enterococcus spp. from dairy cattle at different production stages using whole-genome sequencing and to determine the association between antimicrobial resistance (AMR) phenotypes and their corresponding genotypes. The Comprehensive Antibiotic Resistance Database (CARD) and ResFinder, two publicly available databases of antimicrobial resistance genes, were used to annotate isolates. Based on the ResFinder database, 27.5% and 20.0% of tested E. coli isolates (n = 40) harbored single and ≥3 antimicrobial resistance genes, respectively; for Enterococcus spp., we observed 87.8% and 8.2%, respectively. The highest prevalence of AMR genes in E. coli was for resistance to tetracycline (27.5%), followed by sulphonamide (22.5%) and aminoglycoside (20.0%); the predominant antimicrobial resistance genes in Enterococcus spp. targeted macrolide drugs (77.6%). Based on the CARD database, resistance to ≥3 antimicrobial classes was observed in all E. coli and 77.6% in Enterococcus spp. isolates. A high degree of agreement existed between the resistance phenotype and the presence of resistance genes for various antimicrobial classes for E. coli but much less so for isolates of Enterococcus. Consistent with prior work, fecal E. coli and Enterococcus spp. isolates from calves harbored a wide spectrum of resistance genes, compared to those from cattle at other production stages, based on the cross-sectional samples from the studied farm.
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Kang Y, Sun B, Chen Y, Lou Y, Zheng M, Li Z. Dental Plaque Microbial Resistomes of Periodontal Health and Disease and Their Changes after Scaling and Root Planing Therapy. mSphere 2021; 6:e0016221. [PMID: 34287005 PMCID: PMC8386447 DOI: 10.1128/msphere.00162-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 05/23/2021] [Indexed: 11/20/2022] Open
Abstract
The human oral microbial community has been considered a reservoir of antibiotic resistance. Currently, the effects of periodontitis and the scaling and root planing (SRP) treatment on the performance of antibiotic-resistant genes (ARGs) and metal-resistant genes (MRGs) in the dental plaque microbiota are not well characterized. To explore this issue, we selected 48 healthy-state (HS), 40 periodontitis-state (PS; before treatment), and 24 resolved-state (RS; after SRP treatment) metagenomic data of dental plaque samples from the Sequence Read Archive (SRA) database. NetShift analysis identified Fretibacterium fastidiosum, Tannerella forsythia, and Campylobacter rectus as key drivers during dental plaque microbiota alteration in the progression of periodontitis. Periodontitis and SRP treatment resulted in an increase in the number of ARGs and MRGs in dental plaque and significantly altered the composition of ARG and MRG profiles. Bacitracin, beta-lactam, macrolide-lincosamide-streptogramin (MLS), tetracycline, and multidrug resistance genes were the main classes of ARGs with high relative abundance, whereas multimetal, iron, chromium, and copper resistance genes were the primary types of MRGs in dental plaque microbiota. The cooccurrence of ARGs, MRGs, and mobile genetic elements (MGEs) indicated that a coselection phenomenon exists in the resistomes of dental plaque microbiota. Overall, our data provide new insights into the standing of the distribution of ARGs and MRGs in oral microbiota of periodontitis patients, and it was possible to contribute to the understanding of the complicated correlations among microorganisms, resistomes, and MGEs. IMPORTANCE The emergence and development of resistance to antibiotics in periodontal pathogens have affected the success rate of treatment for periodontitis. The development of new antibacterial strategies is urgently needed to help control and treat periodontal disease, and dental plaque microbiome studies offer a promising new angle of attack. In this study, we investigated the dental plaque microbiota and resistomes in periodontal health and disease states and their changes after SRP therapy. This is the first analysis of the profile of the microbial community and antibiotic and metal resistance genes in dental plaque by the metagenomic approach, to the best of our knowledge. Monitoring the profile of these resistomes has huge potential to provide reference levels for proper antibiotics use and the development of new antimicrobial strategies in periodontitis therapy and thereby improve actual efficacy of the treatment regimens.
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Affiliation(s)
- Yutong Kang
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Bianjin Sun
- Eye Hospital and School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, Zhejiang, China
- National Clinical Research Center for Ocular Diseases, Wenzhou, Zhejiang, China
| | - Yiju Chen
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Yongliang Lou
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Meiqin Zheng
- Eye Hospital and School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, Zhejiang, China
- National Clinical Research Center for Ocular Diseases, Wenzhou, Zhejiang, China
| | - Zhenjun Li
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
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Rothrock MJ, Min BR, Castleberry L, Waldrip H, Parker D, Brauer D, Pitta D, Indugu N. Antibiotic resistance, antimicrobial residues, and bacterial community diversity in pasture-raised poultry, swine, and beef cattle manures. J Anim Sci 2021; 99:6263936. [PMID: 33944927 DOI: 10.1093/jas/skab144] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 04/29/2021] [Indexed: 12/15/2022] Open
Abstract
Animal manure can be a source of antibiotic-resistant genes (ARGs) and pharmaceutical residues; however, few studies have evaluated the presence of ARG in pasture-raised animal production systems. The objective of this study was to examine changes in microbiome diversity and the presence of antibiotic residues (ABRs) on three farms that contained a diverse range of animal species: pasture-raised poultry (broiler and layer), swine, and beef cattle. Total bacterial communities were determined using 16S rRNA microbiome analysis, while specific ARGs (sulfonamide [Sul; Sul1] and tetracycline [Tet; TetA]) were enumerated by qPCR (real-time PCR). Results indicated that the ARG abundances (Sul1 [P < 0.05] and TetA [P < 0.001]) were higher in layer hen manures (16.5 × 10-4 and 1.4 × 10-4 µg kg-1, respectively) followed by broiler chickens (2.9 × 10-4 and 1.7 × 10-4 µg kg-1, respectively), swine (0.22 × 10-4 and 0.20 × 10-4 µg kg-1, respectively) and beef cattle (0.19 × 10-4 and 0.02 × 10-4 µg kg-1, respectively). Average fecal TetA ABR tended to be greater (P = 0.09) for broiler chickens (11.4 µg kg-1) than for other animal species (1.8 to 0.06 µg kg-1), while chlortetracycline, lincomycin, and oxytetracycline ABRs were similar among animal species. Furthermore, fecal microbial richness and abundances differed significantly (P < 0.01) both among farms and specific species of animal. This study indicated that the microbial diversity, ABR, ARG concentrations, and types in feces varied from farm-to-farm and from animal species-to-animal species. Future studies are necessary to perform detailed investigations of the horizontal transfer mechanism of antibiotic-resistant microorganisms (ARMs) and ARG.
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Affiliation(s)
| | - Byeng Ryel Min
- USDA-ARS, Conservation and Production Research Laboratory, Bushland, TX 79012, USA
| | - Lana Castleberry
- USDA-ARS, Conservation and Production Research Laboratory, Bushland, TX 79012, USA
| | - Heidi Waldrip
- USDA-ARS, Conservation and Production Research Laboratory, Bushland, TX 79012, USA
| | - David Parker
- USDA-ARS, Conservation and Production Research Laboratory, Bushland, TX 79012, USA
| | - David Brauer
- USDA-ARS, Conservation and Production Research Laboratory, Bushland, TX 79012, USA
| | - Dipti Pitta
- School of Veterinary Medicine, University of Pennsylvania, Kennett Square, PA 16802, USA
| | - Nagaraju Indugu
- School of Veterinary Medicine, University of Pennsylvania, Kennett Square, PA 16802, USA
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36
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Macedo G, van Veelen HPJ, Hernandez-Leal L, van der Maas P, Heederik D, Mevius D, Bossers A, Schmitt H. Targeted metagenomics reveals inferior resilience of farm soil resistome compared to soil microbiome after manure application. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 770:145399. [PMID: 33736375 DOI: 10.1016/j.scitotenv.2021.145399] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 01/18/2021] [Accepted: 01/20/2021] [Indexed: 05/26/2023]
Abstract
Application of animal manure to soils results in the introduction of manure-derived bacteria and their antimicrobial resistance genes (ARGs) into soils. ResCap is a novel targeted-metagenomic approach that allows the detection of minority components of the resistome gene pool without the cost-prohibitive coverage depths and can provide a valuable tool to study the spread of antimicrobial resistance (AMR) in the environment. We used high-throughput sequencing and qPCR for 16S rRNA gene fragments as well as ResCap to explore the dynamics of bacteria, and ARGs introduced to soils and adjacent water ditches, both at community and individual scale, over a period of three weeks. The soil bacteriome and resistome showed strong resilience to the input of manure, as manuring did not impact the overall structure of the bacteriome, and its effects on the resistome were transient. Initially, manure application resulted in a substantial increase of ARGs in soils and adjacent waters, while not affecting the overall bacterial community composition. Still, specific families increased after manure application, either through the input of manure (e.g., Dysgonomonadaceae) or through enrichment after manuring (e.g., Pseudomonadaceae). Depending on the type of ARG, manure application resulted mostly in an increase (e.g., aph(6)-Id), but occasionally also in a decrease (e.g., dfrB3) of the absolute abundance of ARG clusters (FPKM/kg or L). This study shows that the structures of the bacteriome and resistome are shaped by different factors, where the bacterial community composition could not explain the changes in ARG diversity or abundances. Also, it highlights the potential of applying targeted metagenomic techniques, such as ResCap, to study the fate of AMR in the environment.
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Affiliation(s)
- Gonçalo Macedo
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CL Utrecht, the Netherlands; Wetsus, European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, 8911 MA Leeuwarden, the Netherlands.
| | - H Pieter J van Veelen
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, 8911 MA Leeuwarden, the Netherlands
| | - Lucia Hernandez-Leal
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, 8911 MA Leeuwarden, the Netherlands
| | - Peter van der Maas
- Van Hall Larenstein, University of Applied Sciences, Agora 1, 8901 BV Leeuwarden, the Netherlands
| | - Dick Heederik
- Institute for Risk Assessment Sciences, Utrecht University, Yalelaan 2, 3584, CM, Utrecht, the Netherlands
| | - Dik Mevius
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CL Utrecht, the Netherlands; Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Houtribweg 39, 8221 RA Lelystad, the Netherlands
| | - Alex Bossers
- Institute for Risk Assessment Sciences, Utrecht University, Yalelaan 2, 3584, CM, Utrecht, the Netherlands; Department of Infection Biology, Wageningen Bioveterinary Research, Houtribweg 39, 8221 RA Lelystad, the Netherlands
| | - Heike Schmitt
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Antonie van Leeuwenhoeklaan 9, 3721 MA Bilthoven, the Netherlands
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Keenum I, Williams RK, Ray P, Garner ED, Knowlton KF, Pruden A. Combined effects of composting and antibiotic administration on cattle manure-borne antibiotic resistance genes. MICROBIOME 2021; 9:81. [PMID: 33795006 PMCID: PMC8017830 DOI: 10.1186/s40168-021-01006-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 02/02/2021] [Indexed: 05/23/2023]
Abstract
BACKGROUND Research is needed to delineate the relative and combined effects of different antibiotic administration and manure management practices in either amplifying or attenuating the potential for antibiotic resistance to spread. Here, we carried out a comprehensive parallel examination of the effects of small-scale (> 55 °C × 3 days) static and turned composting of manures from dairy and beef cattle collected during standard antibiotic administration (cephapirin/pirlimycin or sulfamethazine/chlortetracycline/tylosin, respectively), versus from untreated cattle, on "resistomes" (total antibiotic resistance genes (ARGs) determined via shotgun metagenomic sequencing), bacterial microbiota, and indicator ARGs enumerated via quantitative polymerase chain reaction. To gain insight into the role of the thermophilic phase, compost was also externally heated to > 55 °C × 15 days. RESULTS Progression of composting with time and succession of the corresponding bacterial microbiota was the overarching driver of the resistome composition (ANOSIM; R = 0.424, p = 0.001, respectively) in all composts at the small-scale. Reduction in relative abundance (16S rRNA gene normalized) of total ARGs in finished compost (day 42) versus day 0 was noted across all conditions (ANOSIM; R = 0.728, p = 0.001), except when externally heated. Sul1, intI1, beta-lactam ARGs, and plasmid-associated genes increased in all finished composts as compared with the initial condition. External heating more effectively reduced certain clinically relevant ARGs (blaOXA, blaCARB), fecal coliforms, and resistome risk scores, which take into account putative pathogen annotations. When manure was collected during antibiotic administration, taxonomic composition of the compost was distinct according to nonmetric multidimensional analysis and tet(W) decayed faster in the dairy manure with antibiotic condition and slower in the beef manure with antibiotic condition. CONCLUSIONS This comprehensive, integrated study revealed that composting had a dominant effect on corresponding resistome composition, while little difference was noted as a function of collecting manure during antibiotic administration. Reduction in total ARGs, tet(W), and resistome risk suggested that composting reduced some potential for antibiotic resistance to spread, but the increase and persistence of other indicators of antibiotic resistance were concerning. Results indicate that composting guidelines intended for pathogen reduction do not necessarily provide a comprehensive barrier to ARGs or their mobility prior to land application and additional mitigation measures should be considered. Video Abstract.
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Affiliation(s)
- Ishi Keenum
- Department of Civil and Environmental Engineering, Virginia Tech, 418 Durham Hall, 1145 Perry Street, Blacksburg, VA, 24061, USA
| | - Robert K Williams
- Department of Civil and Environmental Engineering, Virginia Tech, 418 Durham Hall, 1145 Perry Street, Blacksburg, VA, 24061, USA
| | - Partha Ray
- Department of Animal Sciences, School of Agriculture, Policy and Development, University of Reading, Reading, RG6 6EU, UK
| | - Emily D Garner
- Department of Civil and Environmental Engineering, Virginia Tech, 418 Durham Hall, 1145 Perry Street, Blacksburg, VA, 24061, USA
- Department of Civil and Environmental Engineering, West Virginia University, Morgantown, WV, USA
| | | | - Amy Pruden
- Department of Civil and Environmental Engineering, Virginia Tech, 418 Durham Hall, 1145 Perry Street, Blacksburg, VA, 24061, USA.
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Sazykin IS, Khmelevtsova LE, Seliverstova EY, Sazykina MA. Effect of Antibiotics Used in Animal Husbandry on the Distribution of Bacterial Drug Resistance (Review). APPL BIOCHEM MICRO+ 2021. [DOI: 10.1134/s0003683821010166] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Hill D, Morra MJ, Stalder T, Jechalke S, Top E, Pollard AT, Popova I. Dairy manure as a potential source of crop nutrients and environmental contaminants. J Environ Sci (China) 2021; 100:117-130. [PMID: 33279025 DOI: 10.1016/j.jes.2020.07.016] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 07/15/2020] [Accepted: 07/15/2020] [Indexed: 06/12/2023]
Abstract
Although animal manure is applied to agricultural fields for its nutrient value, it may also contain potential contaminants. To determine the variability in such contaminants as well as in valuable nutrients, nine uncomposted manure samples from Idaho dairies collected during 2.5 years were analyzed for macro- and micro-nutrients, hormones, phytoestrogens, antibiotics, veterinary drugs, antibiotic resistance genes, and genetic elements involved in the spread of antibiotic resistance. Total N ranged from 6.8 to 30.7 (C:N of 10 to 21), P from 2.4 to 9.0, and K from 10.2 to 47.7 g/kg manure. Zn (103 - 348 mg/kg) was more abundant than Cu (56 - 127 mg/kg) in all samples. Phytoestrogens were the most prevalent contaminants detected, with concentrations fluctuating over time, reflecting animal diets. This is the first study to document the presence of flunixin, a non-steroidal anti-inflammatory drug, in solid stacked manure from regular dairy operations. Monensin was the most frequently detected antibiotic. Progesterones and sulfonamides were regularly detected. We also investigated the relative abundance of several types of plasmids involved in the spread of antibiotic resistance in clinical settings. Plasmids belonging to the IncI, IncP, and IncQ1 incompatibility groups were found in almost all manure samples. IncQ1 plasmids, class 1 integrons, and sulfonamide resistance genes were the most widespread and abundant genetic element surveyed, emphasizing their potential role in the spread of antibiotic resistance. The benefits associated with amending agricultural soils with dairy manure must be carefully weighed against the potential negative consequences of any manure contaminants.
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Affiliation(s)
- Danika Hill
- Department of Soil & Water Systems, University of Idaho, ID 83844-2340, USA
| | - Matthew J Morra
- Department of Soil & Water Systems, University of Idaho, ID 83844-2340, USA
| | | | - Sven Jechalke
- Justus Liebig University Giessen, Institute for Phytopathology, 35392 Gießen, Germany
| | - Eva Top
- Department of Biology, University of Idaho, ID 83844-3051, USA
| | - Anne T Pollard
- Department of Soil & Water Systems, University of Idaho, ID 83844-2340, USA
| | - Inna Popova
- Department of Soil & Water Systems, University of Idaho, ID 83844-2340, USA.
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Raw Cow Milk Bacterial Consortium as Bioindicator of Circulating Anti-Microbial Resistance (AMR). Animals (Basel) 2020; 10:ani10122378. [PMID: 33322611 PMCID: PMC7763537 DOI: 10.3390/ani10122378] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 12/07/2020] [Accepted: 12/08/2020] [Indexed: 12/11/2022] Open
Abstract
The environment, including animals and animal products, is colonized by bacterial species that are typical and specific of every different ecological niche. Natural and human-related ecological pressure promotes the selection and expression of genes related to antimicrobial resistance (AMR). These genes might be present in a bacterial consortium but might not necessarily be expressed. Their expression could be induced by the presence of antimicrobial compounds that could originate from a given ecological niche or from human activity. In this work, we applied (meta)proteomics analysis of bacterial compartment of raw milk in order to obtain a method that provides a measurement of circulating AMR involved proteins and gathers information about the whole bacterial composition. Results from milk analysis revealed the presence of 29 proteins/proteoforms linked to AMR. The detection of mainly β-lactamases suggests the possibility of using the milk microbiome as a bioindicator for the investigation of AMR. Moreover, it was possible to achieve a culture-free qualitative and functional analysis of raw milk bacterial consortia.
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Pitta DW, Indugu N, Toth JD, Bender JS, Baker LD, Hennessy ML, Vecchiarelli B, Aceto H, Dou Z. The distribution of microbiomes and resistomes across farm environments in conventional and organic dairy herds in Pennsylvania. ENVIRONMENTAL MICROBIOME 2020; 15:21. [PMID: 33902716 PMCID: PMC8066844 DOI: 10.1186/s40793-020-00368-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 11/20/2020] [Indexed: 05/07/2023]
Abstract
BACKGROUND Antimicrobial resistance is a serious concern. Although the widespread use of antimicrobials in livestock has exacerbated the emergence and dissemination of antimicrobial resistance genes (ARG) in farm environments, little is known about whether antimicrobial use affects distribution of ARG in livestock systems. This study compared the distribution of microbiomes and resistomes (collections of ARG) across different farm sectors in dairy herds that differed in their use of antimicrobials. Feces from heifers, non-lactating, and lactating cows, manure storage, and soil from three conventional (antimicrobials used to treat cows) and three organic (no antimicrobials used for at least four years) farms in Pennsylvania were sampled. Samples were extracted for genomic DNA, processed, sequenced on the Illumina NextSeq platform, and analyzed for microbial community and resistome profiles using established procedures. RESULTS Microbial communities and resistome profiles clustered by sample type across all farms. Overall, abundance and diversity of ARG in feces was significantly higher in conventional herds compared to organic herds. The ARG conferring resistance to betalactams, macrolide-lincosamide-streptogramin (MLS), and tetracyclines were significantly higher in fecal samples of dairy cows from conventional herds compared to organic herds. Regardless of farm type, all manure storage samples had greater diversity (albeit low abundance) of ARG conferring resistance to aminoglycosides, tetracyclines, MLS, multidrug resistance, and phenicol. All soil samples had lower abundance of ARG compared to feces, manure, and lagoon samples and were comprised of ARG conferring resistance to aminoglycosides, glycopeptides, and multi-drug resistance. The distribution of ARG is likely driven by the composition of microbiota in the respective sample types. CONCLUSIONS Antimicrobial use on farms significantly influenced specific groups of ARG in feces but not in manure storage or soil samples.
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Affiliation(s)
- Dipti W. Pitta
- Department of Clinical Studies, School of Veterinary Medicine, University of Pennsylvania, Kennett Square, PA USA
| | - Nagaraju Indugu
- Department of Clinical Studies, School of Veterinary Medicine, University of Pennsylvania, Kennett Square, PA USA
| | - John D. Toth
- Department of Clinical Studies, School of Veterinary Medicine, University of Pennsylvania, Kennett Square, PA USA
| | - Joseph S. Bender
- Department of Clinical Studies, School of Veterinary Medicine, University of Pennsylvania, Kennett Square, PA USA
| | - Linda D. Baker
- Department of Clinical Studies, School of Veterinary Medicine, University of Pennsylvania, Kennett Square, PA USA
| | - Meagan L. Hennessy
- Department of Clinical Studies, School of Veterinary Medicine, University of Pennsylvania, Kennett Square, PA USA
| | - Bonnie Vecchiarelli
- Department of Clinical Studies, School of Veterinary Medicine, University of Pennsylvania, Kennett Square, PA USA
| | - Helen Aceto
- Department of Clinical Studies, School of Veterinary Medicine, University of Pennsylvania, Kennett Square, PA USA
| | - Zhengxia Dou
- Department of Clinical Studies, School of Veterinary Medicine, University of Pennsylvania, Kennett Square, PA USA
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Mencía-Ares O, Cabrera-Rubio R, Cobo-Díaz JF, Álvarez-Ordóñez A, Gómez-García M, Puente H, Cotter PD, Crispie F, Carvajal A, Rubio P, Argüello H. Antimicrobial use and production system shape the fecal, environmental, and slurry resistomes of pig farms. MICROBIOME 2020; 8:164. [PMID: 33213522 PMCID: PMC7678069 DOI: 10.1186/s40168-020-00941-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 10/17/2020] [Indexed: 05/19/2023]
Abstract
BACKGROUND The global threat of antimicrobial resistance (AMR) is a One Health problem impacted by antimicrobial use (AMU) for human and livestock applications. Extensive Iberian swine production is based on a more sustainable and eco-friendly management system, providing an excellent opportunity to evaluate how sustained differences in AMU impact the resistome, not only in the animals but also on the farm environment. Here, we evaluate the resistome footprint of an extensive pig farming system, maintained for decades, as compared to that of industrialized intensive pig farming by analyzing 105 fecal, environmental and slurry metagenomes from 38 farms. RESULTS Our results evidence a significantly higher abundance of antimicrobial resistance genes (ARGs) on intensive farms and a link between AMU and AMR to certain antimicrobial classes. We observed differences in the resistome across sample types, with a higher richness and dispersion of ARGs within environmental samples than on those from feces or slurry. Indeed, a deeper analysis revealed that differences among the three sample types were defined by taxa-ARGs associations. Interestingly, mobilome analyses revealed that the observed AMR differences between intensive and extensive farms could be linked to differences in the abundance of mobile genetic elements (MGEs). Thus, while there were no differences in the abundance of chromosomal-associated ARGs between intensive and extensive herds, a significantly higher abundance of integrons in the environment and plasmids, regardless of the sample type, was detected on intensive farms. CONCLUSIONS Overall, this study shows how AMU, production system, and sample type influence, mainly through MGEs, the profile and dispersion of ARGs in pig production. Video Abstract.
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Affiliation(s)
- Oscar Mencía-Ares
- Department of Animal Health, Faculty of Veterinary, Universidad de León, León, Spain
| | - Raúl Cabrera-Rubio
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
- APC Microbiome Institute, University College Cork, Co. Cork, Ireland
| | - José Francisco Cobo-Díaz
- Department of Food Hygiene and Technology, Faculty of Veterinary, Universidad de León, León, Spain
- Institute of Food Science and Technology, Universidad de León, León, Spain
| | - Avelino Álvarez-Ordóñez
- Department of Food Hygiene and Technology, Faculty of Veterinary, Universidad de León, León, Spain
- Institute of Food Science and Technology, Universidad de León, León, Spain
| | - Manuel Gómez-García
- Department of Animal Health, Faculty of Veterinary, Universidad de León, León, Spain
| | - Héctor Puente
- Department of Animal Health, Faculty of Veterinary, Universidad de León, León, Spain
| | - Paul D Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
- APC Microbiome Institute, University College Cork, Co. Cork, Ireland
- VistaMilk SFI Research Centre, Fermoy, Co. Cork, Ireland
| | - Fiona Crispie
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
- APC Microbiome Institute, University College Cork, Co. Cork, Ireland
| | - Ana Carvajal
- Department of Animal Health, Faculty of Veterinary, Universidad de León, León, Spain.
| | - Pedro Rubio
- Department of Animal Health, Faculty of Veterinary, Universidad de León, León, Spain
| | - Héctor Argüello
- Department of Animal Health, Faculty of Veterinary, Universidad de León, León, Spain
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Yang Y, Ashworth AJ, DeBruyn JM, Durso LM, Savin M, Cook K, Moore Jr. PA, Owens PR. Antimicrobial resistant gene prevalence in soils due to animal manure deposition and long-term pasture management. PeerJ 2020; 8:e10258. [PMID: 33194426 PMCID: PMC7646296 DOI: 10.7717/peerj.10258] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 10/06/2020] [Indexed: 02/01/2023] Open
Abstract
The persistence of antimicrobial resistant (AMR) genes in the soil-environment is a concern, yet practices that mitigate AMR are poorly understood, especially in grasslands. Animal manures are widely deposited on grasslands, which are the largest agricultural land-use in the United States. These nutrient-rich manures may contain AMR genes. The aim of this study was to enumerate AMR genes in grassland soils following 14-years of poultry litter and cattle manure deposition and evaluate if best management practices (rotationally grazed with a riparian (RBR) area and a fenced riparian buffer strip (RBS), which excluded cattle grazing and poultry litter applications) relative to standard pasture management (continuously grazed (CG) and hayed (H)) minimize the presence and amount of AMR genes. Quantitative PCR (Q-PCR) was performed to enumerate four AMR genes (ermB, sulI, intlI, and blactx-m-32 ) in soil, cattle manure, and poultry litter environments. Six soil samples were additionally subjected to metagenomic sequencing and resistance genes were identified from assembled sequences. Following 14-years of continuous management, ermB, sulI, and intlI genes in soil were greatest (P < 0.05) in samples collected under long-term continuous grazing (relative to conservation best management practices), under suggesting overgrazing and continuous cattle manure deposition may increase AMR gene presence. In general, AMR gene prevalence increased downslope, suggesting potential lateral movement and accumulation based on landscape position. Poultry litter had lower abundance of AMR genes (ermB, sulI, and intlI) relative to cattle manure. Long-term applications of poultry litter increased the abundance of sulI and intlI genes in soil (P < 0.05). Similarly, metagenomic shotgun sequencing revealed a greater total number of AMR genes under long-term CG, while fewer AMR genes were found in H (no cattle manure) and RBS (no animal manure or poultry litter). Results indicate long-term conservation pasture management practices (e.g., RBS and RBR) and select animal manure (poultry litter inputs) may minimize the presence and abundance of AMR genes in grassland soils.
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Affiliation(s)
- Yichao Yang
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas at Fayetteville, Fayetteville, AR, United States of America
| | - Amanda J. Ashworth
- Poultry Production and Product Safety Research Unit, United States Department of Agriculture, Agricultural Research Service, Fayetteville, AR, United States of America
| | - Jennifer M. DeBruyn
- Department of Biosystems Engineering & Soil Science, University of Tennessee - Knoxville, Knoxville, TN, United States of America
| | - Lisa M. Durso
- Agroecosystem Management Research Unit, United States Department of Agriculture, Agricultural Research Service, Lincoln, NE, United States of America
| | - Mary Savin
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas at Fayetteville, Fayetteville, AR, United States of America
| | - Kim Cook
- United States Department of Agriculture, Agriculture Research Service, Beltsville, MD, United States of America
| | - Philip A. Moore Jr.
- Poultry Production and Product Safety Research Unit, United States Department of Agriculture, Agricultural Research Service, Fayetteville, AR, United States of America
| | - Phillip R. Owens
- Dale Bumpers Small Farms Research Center, United States Department of Agriculture, Agricultural Research Service, Booneville, AR, United States of America
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Zhang X, Ma C, Zhang W, Li W, Yu J, Xue D, Wu X, Deng G. Shifts in microbial community, pathogenicity-related genes and antibiotic resistance genes during dairy manure piled up. Microb Biotechnol 2020; 13:1039-1053. [PMID: 32202696 PMCID: PMC7264890 DOI: 10.1111/1751-7915.13551] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 02/15/2020] [Accepted: 02/17/2020] [Indexed: 01/02/2023] Open
Abstract
The uncomposted faeces of dairy cow are usually stacked on cow breeding farms, dried under natural conditions and then used as cow bedding material or they may be continuously piled up. However, no information is available to evaluate variations in the human and animal pathogen genes and antibiotic resistance during the accumulation of fresh faeces of dairy cow to manure. Here, we present the metagenomic analysis of fresh faeces and manure from a dairy farm in Ning Xia, showing a unique enrichment of human and animal pathogen genes and antibiotic resistance genes (ARGs) in manure. We found that manure accumulation could significantly increase the diversity and abundance of the pathogenic constituents. Furthermore, pathogens from manure could spread to the plant environment and enphytotic pathogens could affect the yield and quality of crops during the use of manure as a fertilizer. Levels of virulence genes and ARGs increased with the enrichment of microbes and pathogens when faeces accumulated to manure. Accumulated manure was also the transfer station of ARGs to enrich the ARGs in the environment, indicating the ubiquitous presence of environmental antibiotic resistance genes. Our results demonstrate that manure accumulation and usage without effective manure management is an unreasonable approach that could enrich pathogenic microorganisms and ARGs in the environment. The manure metagenome structure allows us to appreciate the overall influence and interaction of animal waste on water, soil and other areas impacted by faecal accumulation and the factors that influence pathogen occurrence in products from dairy cows.
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Affiliation(s)
- Xu Zhang
- Key Lab of Ministry of Education for Protection and Utilization of Special Biological Resources in Western ChinaNingxia UniversityNingxiaChina
- School of Life ScienceNingxia UniversityNingxiaChina
| | - Chenjie Ma
- Key Lab of Ministry of Education for Protection and Utilization of Special Biological Resources in Western ChinaNingxia UniversityNingxiaChina
- School of Life ScienceNingxia UniversityNingxiaChina
| | - Wen Zhang
- Key Lab of Ministry of Education for Protection and Utilization of Special Biological Resources in Western ChinaNingxia UniversityNingxiaChina
- School of Life ScienceNingxia UniversityNingxiaChina
| | - Wu Li
- Key Lab of Ministry of Education for Protection and Utilization of Special Biological Resources in Western ChinaNingxia UniversityNingxiaChina
- School of Life ScienceNingxia UniversityNingxiaChina
| | - Jialin Yu
- Key Lab of Ministry of Education for Protection and Utilization of Special Biological Resources in Western ChinaNingxia UniversityNingxiaChina
- School of Life ScienceNingxia UniversityNingxiaChina
| | - Di Xue
- Key Lab of Ministry of Education for Protection and Utilization of Special Biological Resources in Western ChinaNingxia UniversityNingxiaChina
- School of Life ScienceNingxia UniversityNingxiaChina
| | - Xiaolin Wu
- Key Lab of Ministry of Education for Protection and Utilization of Special Biological Resources in Western ChinaNingxia UniversityNingxiaChina
- School of Life ScienceNingxia UniversityNingxiaChina
| | - Guangcun Deng
- Key Lab of Ministry of Education for Protection and Utilization of Special Biological Resources in Western ChinaNingxia UniversityNingxiaChina
- School of Life ScienceNingxia UniversityNingxiaChina
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Environmental and Sex Effects on Bacterial Carriage by Adult House Flies ( Musca domestica L.). INSECTS 2020; 11:insects11070401. [PMID: 32605295 PMCID: PMC7412185 DOI: 10.3390/insects11070401] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 06/25/2020] [Accepted: 06/25/2020] [Indexed: 12/31/2022]
Abstract
Adult house flies frequent microbe-rich sites such as urban dumpsters and animal facilities, and encounter and ingest bacteria during feeding and reproductive activities. Due to unique nutritional and reproductive needs, male and female flies demonstrate different interactions with microbe-rich substrates and therefore dissemination potential. We investigated culturable aerobic bacteria and coliform abundance in male and female flies (n = 107) collected from urban (restaurant dumpsters) and agricultural (dairy farm) sites. Whole-fly homogenate was aerobically cultured and enumerated on nonselective (tryptic soy agar; culturable bacteria) and selective (violet-red bile agar, VRBA; coliforms) media. Unique morphotypes from VRBA cultures of agricultural flies were identified and tested for susceptibility to 14 antimicrobials. Female flies harbored more bacteria than males and there was a sex by site interaction with sex effects on bacterial abundance at the urban site. Coliform abundance did not differ by sex, site or sex within site. Both male and female flies carried antimicrobial-resistant (AMR) bacteria: 36/38 isolates (95%) were resistant to ≥1 antimicrobial, 33/38 were multidrug-resistant (≥2), and 24/38 isolates were resistant to ≥4 antimicrobials. Our results emphasize the role of house flies in harboring bacteria including AMR strains that pose a risk to human and animal health.
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Abstract
The human gut is home to a myriad of organisms. While some are harmless commensals, others are transient, pathogenic flora. The gut microbiome is composed of diverse bacterial flora, and apart from playing a major role in protecting from various infectious and non-infectious diseases, it plays an important role in resistance to antimicrobials. The collection of genes or genetic material that confers antimicrobial resistance constitutes the gut resistome, and it may involve the pathogens or commensals of the intestinal tract. The diversity of this gut resistome is influenced by various environmental factors including the diet and antibiotic exposure. This review highlights the recent concepts pertaining to the human gut resistome, factors affecting it, how it impacts human health and diseases, methods to study the resistome and potential therapeutic approaches.
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Affiliation(s)
- Shreya Singh
- Department of Medical Microbiology, Postgraduate Institute of Medical Education & Research, Chandigarh, India
| | - Nipun Verma
- Department of Hepatology, Postgraduate Institute of Medical Education & Research, Chandigarh, India
| | - Neelam Taneja
- Department of Medical Microbiology, Postgraduate Institute of Medical Education & Research, Chandigarh, India
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Lim SK, Kim D, Moon DC, Cho Y, Rho M. Antibiotic resistomes discovered in the gut microbiomes of Korean swine and cattle. Gigascience 2020; 9:5829833. [PMID: 32369165 PMCID: PMC7317084 DOI: 10.1093/gigascience/giaa043] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 03/02/2020] [Accepted: 04/07/2020] [Indexed: 12/14/2022] Open
Abstract
Background Antibiotics administered to farm animals have led to increasing prevalence of resistance genes in different microbiomes and environments. While antibiotic treatments help cure infectious diseases in farm animals, the possibility of spreading antibiotic resistance genes into the environment and human microbiomes raises significant concerns. Through long-term evolution, antibiotic resistance genes have mutated, thereby complicating the resistance problems. Results In this study, we performed deep sequencing of the gut microbiomes of 36 swine and 41 cattle in Korean farms, and metagenomic analysis to understand the diversity and prevalence of antibiotic resistance genes. We found that aminoglycoside, β-lactam, lincosamide, streptogramin, and tetracycline were the prevalent resistance determinants in both swine and cattle. Tetracycline resistance was abundant and prevalent in cattle and swine. Specifically, tetQ, tetW, tetO, tet32, and tet44 were the 5 most abundant and prevalent tetracycline resistance genes. Their prevalence was almost 100% in swine and cattle. While tetQ was similarly abundant in both swine and cattle, tetW was more abundant in swine than in cattle. Aminoglycoside was the second highest abundant resistance determinant in swine, but not in cattle. In particular, ANT(6) and APH(3′′) were the dominant resistance gene families in swine. β-lactam was also an abundant resistance determinant in both swine and cattle. Cfx was the major contributing gene family conferring resistance against β-lactams. Conclusions Antibiotic resistome was more pervasive in swine than in cattle. Specifically, prevalent antibiotic resistance genes (prevalence >50%) were found more in swine than in cattle. Genomic investigation of specific resistance genes from the gut microbiomes of swine and cattle in this study should provide opportunities to better understand the exchange of antibiotic resistance genes in farm animals.
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Affiliation(s)
- Suk-Kyung Lim
- Animal and Plant Quarantine Agency, Bacterial Disease Division, 177 Hyeoksin 8-ro, Gimcheon-si, Gyeongsangbuk-do, 39660, Republic of Korea
| | - Dongjun Kim
- Hanyang University, 222 Wangsimni-ro, Seongdong-gu, Seoul, 04763, Republic of Korea, Department of Computer Science and Engineering
| | - Dong-Chan Moon
- Animal and Plant Quarantine Agency, Bacterial Disease Division, 177 Hyeoksin 8-ro, Gimcheon-si, Gyeongsangbuk-do, 39660, Republic of Korea
| | - Youna Cho
- Hanyang University, 222 Wangsimni-ro, Seongdong-gu, Seoul, 04763, Republic of Korea, Department of Computer Science and Engineering
| | - Mina Rho
- Hanyang University, 222 Wangsimni-ro, Seongdong-gu, Seoul, 04763, Republic of Korea, Department of Computer Science and Engineering.,Hanyang University, 222 Wangsimni-ro, Seongdong-gu, Seoul, 04763, Republic of Korea, Department of Biomedical Informatics
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Li MM, Ray P, Knowlton KF, Pruden A, Xia K, Teets C, Du P. Fate of pirlimycin and antibiotic resistance genes in dairy manure slurries in response to temperature and pH adjustment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 710:136310. [PMID: 32050366 DOI: 10.1016/j.scitotenv.2019.136310] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 12/20/2019] [Accepted: 12/22/2019] [Indexed: 06/10/2023]
Abstract
Quantifying the fate of antibiotics and antibiotic resistance genes (ARGs) in response to physicochemical factors during storage of manure slurries will aid in efforts to reduce the spread of resistance when manure is land-applied. The objectives of this study were to determine the effects of temperature (10, 35, and 55 °C) and initial pH (5, 7, 9, and 12) on the removal of pirlimycin and prevalence of ARGs during storage of dairy manure slurries. We collected and homogenized feces and urine from five lactating dairy cows treated with pirlimycin and prepared slurries by mixing manure and sterile water. Aliquots (200 mL) of slurry were transferred and incubated in 400 mL glass beakers under different temperatures (10, 35, and 55 °C) or initial pH (5, 7, 9, and 12). Pirlimycin concentration and abundances of 16S rRNA, mefA, tet(W), and cfxA as indicators of total bacteria and ARGs corresponding to macrolide, tetracycline, and β-lactam resistance, respectively, were analyzed during manure incubation. The thermophilic environment (55 °C) increased the deconjugation and removal of pirlimycin, while the acidic shock at pH 5 increased deconjugation but inhibited removal of pirlimycin, suggesting that the chemical stability of pirlimycin could be affected by temperature and pH. The thermophilic environment decreased mefA relative abundance on day 7 and 28 (P = 0.02 and 0.04), which indicates that the bacteria that encoded mefA gene were not thermotolerant. Although mefA relative abundance was greater at the pH 9 shock than the rest of pH treatments on day 7 (P = 0.04), no significant pH effect was observed on day 28. The tet(W) abundance under initial pH 12 shock was less than other pH shocks on day 28 (P = 0.01), while no temperature effect was observed on day 28. There was no significant temperature and initial pH effect on cfxA abundance at any time point during incubation, implying that the bacteria that carrying cfxA gene are relatively insensitive to these environmental factors. Overall, directly raising temperature and pH can facilitate pirlimycin removal and decrease mefA and tet(W) relative abundances during storage of manure slurries.
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Affiliation(s)
- Meng M Li
- Department of Dairy Science, Virginia Tech, Blacksburg, VA, USA.
| | - Partha Ray
- Department of Animal Sciences, School of Agriculture, Policy and Development, University of Reading, Reading RG6 6AR, UK
| | | | - Amy Pruden
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Kang Xia
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, USA
| | - Christy Teets
- Department of Dairy Science, Virginia Tech, Blacksburg, VA, USA
| | - Pang Du
- Department of Statistics, Virginia Tech, Blacksburg, VA, USA
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Adator EH, Walker M, Narvaez-Bravo C, Zaheer R, Goji N, Cook SR, Tymensen L, Hannon SJ, Church D, Booker CW, Amoako K, Nadon CA, Read R, McAllister TA. Whole Genome Sequencing Differentiates Presumptive Extended Spectrum Beta-Lactamase Producing Escherichia coli along Segments of the One Health Continuum. Microorganisms 2020; 8:microorganisms8030448. [PMID: 32235751 PMCID: PMC7143971 DOI: 10.3390/microorganisms8030448] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 03/19/2020] [Accepted: 03/19/2020] [Indexed: 12/15/2022] Open
Abstract
Antimicrobial resistance (AMR) has important implications for the continued use of antibiotics to control infectious diseases in both beef cattle and humans. AMR along the One Health continuum of the beef production system is largely unknown. Here, whole genomes of presumptive extended-spectrum β-lactamase E. coli (ESBL-EC) from cattle feces (n = 40), feedlot catch basins (n = 42), surrounding streams (n = 21), a beef processing plant (n = 4), municipal sewage (n = 30), and clinical patients (n = 25) are described. ESBL-EC were isolated from ceftriaxone selective plates and subcultured on ampicillin selective plates. Agreement of genotype-phenotype prediction of AMR ranged from 93.2% for ampicillin to 100% for neomycin, trimethoprim/sulfamethoxazole, and enrofloxacin resistance. Overall, β-lactam (100%; blaEC, blaTEM-1, blaSHV, blaOXA, blaCTX-M-), tetracycline (90.1%; tet(A), tet(B)) and folate synthesis (sul2) antimicrobial resistance genes (ARGs) were most prevalent. The ARGs tet(C), tet(M), tet(32),blaCTX-M-1, blaCTX-M-14, blaOXA-1, dfrA18, dfrA19, catB3, and catB4 were exclusive to human sources, while blaTEM-150, blaSHV-11–12,dfrA12, cmlA1, and cmlA5 were exclusive to beef cattle sources. Frequently encountered virulence factors across all sources included adhesion and type II and III secretion systems, while IncFIB(AP001918) and IncFII plasmids were also common. Specificity and prevalence of ARGs between cattle-sourced and human-sourced presumptive ESBL-EC likely reflect differences in antimicrobial use in cattle and humans. Comparative genomics revealed phylogenetically distinct clusters for isolates from human vs. cattle sources, implying that human infections caused by ESBL-EC in this region might not originate from beef production sources.
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Affiliation(s)
- Emelia H. Adator
- Department of Food and Human Nutritional Sciences, University of Manitoba, Winnipeg, MB R3T 2N2, Canada; (E.H.A.); (C.N.-B.)
| | - Matthew Walker
- National Microbiology Laboratory, Winnipeg, MB R3E 3R2, Canada; (M.W.); (C.A.N.)
| | - Claudia Narvaez-Bravo
- Department of Food and Human Nutritional Sciences, University of Manitoba, Winnipeg, MB R3T 2N2, Canada; (E.H.A.); (C.N.-B.)
| | - Rahat Zaheer
- Lethbridge Research and Development Centre, Lethbridge, AB T1J 4B1, Canada;
| | - Noriko Goji
- Canadian Food Inspection Agency, National Center for Animal Disease, Lethbridge Laboratory, Lethbridge, AB T1J 3Z4, Canada; (N.G.); (K.A.)
| | - Shaun R. Cook
- Alberta Agriculture and Forestry, Lethbridge, AB T1J 4V6, Canada; (S.R.C.); (L.T.)
| | - Lisa Tymensen
- Alberta Agriculture and Forestry, Lethbridge, AB T1J 4V6, Canada; (S.R.C.); (L.T.)
| | - Sherry J. Hannon
- Feedlot Health Management Services Ltd., Okotoks, AB T1S 2A2, Canada; (S.J.H.); (D.C.); (C.W.B.)
| | - Deirdre Church
- Feedlot Health Management Services Ltd., Okotoks, AB T1S 2A2, Canada; (S.J.H.); (D.C.); (C.W.B.)
| | - Calvin W. Booker
- Feedlot Health Management Services Ltd., Okotoks, AB T1S 2A2, Canada; (S.J.H.); (D.C.); (C.W.B.)
| | - Kingsley Amoako
- Canadian Food Inspection Agency, National Center for Animal Disease, Lethbridge Laboratory, Lethbridge, AB T1J 3Z4, Canada; (N.G.); (K.A.)
| | - Celine A. Nadon
- National Microbiology Laboratory, Winnipeg, MB R3E 3R2, Canada; (M.W.); (C.A.N.)
| | - Ron Read
- Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1 Canada;
| | - Tim A. McAllister
- Department of Food and Human Nutritional Sciences, University of Manitoba, Winnipeg, MB R3T 2N2, Canada; (E.H.A.); (C.N.-B.)
- Lethbridge Research and Development Centre, Lethbridge, AB T1J 4B1, Canada;
- Correspondence:
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Haley BJ, Kim SW, Salaheen S, Hovingh E, Van Kessel JAS. Differences in the Microbial Community and Resistome Structures of Feces from Preweaned Calves and Lactating Dairy Cows in Commercial Dairy Herds. Foodborne Pathog Dis 2020; 17:494-503. [PMID: 32176535 DOI: 10.1089/fpd.2019.2768] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Preweaned dairy calves and lactating dairy cows are known reservoirs of antibiotic-resistant bacteria. To further understand the differences in the resistomes and microbial communities between the two, we sequenced the metagenomes of fecal composite samples from preweaned dairy calves and lactating dairy cows on 17 commercial dairy farms (n = 34 samples). Results indicated significant differences in the structures of the microbial communities (analysis of similarities [ANOSIM] R = 0.81, p = 0.001) and resistomes (ANOSIM R = 0.93 to 0.96, p = 0.001) between the two age groups. Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria were the predominant members of the communities, but when the groups were compared, Bacteroidetes and Verrumicrobia were significantly more abundant in calf fecal composite samples, whereas Firmicutes, Spirochaetes, Deinococcus-Thermus, Lentisphaerae, Planctomycetes, Chlorofexi, and Saccharibacteria-(TM7) were more abundant in lactating cow samples. Diverse suites of antibiotic resistance genes (ARGs) were identified in all samples, with the most frequently detected being assigned to tetracycline and aminoglycoside resistance. When the two groups were compared, ARGs were significantly more abundant in composite fecal samples from calves than those from lactating cows (calf median ARG abundance = 1.8 × 100 ARG/16S ribosomal RNA [rRNA], cow median ARG abundance = 1.7 × 10-1 ARG/16S rRNA) and at the antibiotic resistance class level, the relative abundance of tetracycline, trimethoprim, aminoglycoside, macrolide-lincosamide-streptogramin B, β-lactam, and phenicol resistance genes was significantly higher in calf samples than in cow samples. Results of this study indicate that composite feces from preweaned calves harbor different bacterial communities and resistomes than composite feces from lactating cows, with a greater abundance of resistance genes detected in preweaned calf feces.
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Affiliation(s)
- Bradd J Haley
- Environmental Microbial and Food Safety Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, Maryland
| | - Seon-Woo Kim
- Environmental Microbial and Food Safety Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, Maryland
| | - Serajus Salaheen
- Environmental Microbial and Food Safety Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, Maryland
| | - Ernest Hovingh
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, Pennsylvania
| | - Jo Ann S Van Kessel
- Environmental Microbial and Food Safety Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, Maryland
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