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Chen D, Cheng K, Wan L, Cui C, Li G, Zhao D, Yu Y, Liao X, Liu Y, D'Souza AW, Lian X, Sun J. Daily occupational exposure in swine farm alters human skin microbiota and antibiotic resistome. IMETA 2024; 3:e158. [PMID: 38868515 PMCID: PMC10989081 DOI: 10.1002/imt2.158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 10/06/2023] [Accepted: 10/07/2023] [Indexed: 06/14/2024]
Abstract
Antimicrobial resistance (AMR) is a major threat to global public health, and antibiotic resistance genes (ARGs) are widely distributed across humans, animals, and environment. Farming environments are emerging as a key research area for ARGs and antibiotic resistant bacteria (ARB). While the skin is an important reservoir of ARGs and ARB, transmission mechanisms between farming environments and human skin remain unclear. Previous studies confirmed that swine farm environmental exposures alter skin microbiome, but the timeline of these changes is ill defined. To improve understanding of these changes and to determine the specific time, we designed a cohort study of swine farm workers and students through collected skin and environmental samples to explore the impact of daily occupational exposure in swine farm on human skin microbiome. Results indicated that exposure to livestock-associated environments where microorganisms are richer than school environment can reshape the human skin microbiome and antibiotic resistome. Exposure of 5 h was sufficient to modify the microbiome and ARG structure in workers' skin by enriching microorganisms and ARGs. These changes were preserved once formed. Further analysis indicated that ARGs carried by host microorganisms may transfer between the environment with workers' skin and have the potential to expand to the general population using farm workers as an ARG vector. These results raised concerns about potential transmission of ARGs to the broader community. Therefore, it is necessary to take corresponding intervention measures in the production process to reduce the possibility of ARGs and ARB transmission.
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Affiliation(s)
- Dong‐Rui Chen
- State Key Laboratory for Animal Disease Control and PreventionSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary MedicineSouth China Agricultural UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety EvaluationSouth China Agricultural UniversityGuangzhouChina
- Jiangsu Co‐Innovation Center for the Prevention and Control of Important Animal Infectious Disease and ZoonosesYangzhou UniversityYangzhouChina
- Veterinary CenterGuangxi State Farms Yongxin Animal Husbandry Group Co., Ltd.NanningChina
| | - Ke Cheng
- Veterinary CenterGuangxi State Farms Yongxin Animal Husbandry Group Co., Ltd.NanningChina
| | - Lei Wan
- State Key Laboratory for Animal Disease Control and PreventionSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary MedicineSouth China Agricultural UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety EvaluationSouth China Agricultural UniversityGuangzhouChina
- Jiangsu Co‐Innovation Center for the Prevention and Control of Important Animal Infectious Disease and ZoonosesYangzhou UniversityYangzhouChina
| | - Chao‐Yue Cui
- Laboratory Animal CentreWenzhou Medical UniversityWenzhouChina
| | - Gong Li
- State Key Laboratory for Animal Disease Control and PreventionSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary MedicineSouth China Agricultural UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety EvaluationSouth China Agricultural UniversityGuangzhouChina
- Jiangsu Co‐Innovation Center for the Prevention and Control of Important Animal Infectious Disease and ZoonosesYangzhou UniversityYangzhouChina
| | - Dong‐Hao Zhao
- State Key Laboratory for Animal Disease Control and PreventionSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary MedicineSouth China Agricultural UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety EvaluationSouth China Agricultural UniversityGuangzhouChina
- Jiangsu Co‐Innovation Center for the Prevention and Control of Important Animal Infectious Disease and ZoonosesYangzhou UniversityYangzhouChina
| | - Yang Yu
- State Key Laboratory for Animal Disease Control and PreventionSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary MedicineSouth China Agricultural UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety EvaluationSouth China Agricultural UniversityGuangzhouChina
- Jiangsu Co‐Innovation Center for the Prevention and Control of Important Animal Infectious Disease and ZoonosesYangzhou UniversityYangzhouChina
| | - Xiao‐Ping Liao
- State Key Laboratory for Animal Disease Control and PreventionSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary MedicineSouth China Agricultural UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety EvaluationSouth China Agricultural UniversityGuangzhouChina
- Jiangsu Co‐Innovation Center for the Prevention and Control of Important Animal Infectious Disease and ZoonosesYangzhou UniversityYangzhouChina
| | - Ya‐Hong Liu
- State Key Laboratory for Animal Disease Control and PreventionSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary MedicineSouth China Agricultural UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety EvaluationSouth China Agricultural UniversityGuangzhouChina
- Jiangsu Co‐Innovation Center for the Prevention and Control of Important Animal Infectious Disease and ZoonosesYangzhou UniversityYangzhouChina
| | - Alaric W. D'Souza
- Department of PediatricsBoston Children's HospitalBostonMassachusettsUSA
- Harvard Medical SchoolBostonMassachusettsUSA
| | - Xin‐Lei Lian
- State Key Laboratory for Animal Disease Control and PreventionSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary MedicineSouth China Agricultural UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety EvaluationSouth China Agricultural UniversityGuangzhouChina
| | - Jian Sun
- State Key Laboratory for Animal Disease Control and PreventionSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary MedicineSouth China Agricultural UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety EvaluationSouth China Agricultural UniversityGuangzhouChina
- Jiangsu Co‐Innovation Center for the Prevention and Control of Important Animal Infectious Disease and ZoonosesYangzhou UniversityYangzhouChina
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2
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Jiang H, Zeng W, Zhang X, Li Y, Wang Y, Peng A, Cao D. Gut microbiota and its metabolites in non-small cell lung cancer and brain metastasis: from alteration to potential microbial markers and drug targets. Front Cell Infect Microbiol 2024; 13:1211855. [PMID: 38304459 PMCID: PMC10830900 DOI: 10.3389/fcimb.2023.1211855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 12/14/2023] [Indexed: 02/03/2024] Open
Abstract
Background The elevated mortality rate associated with non-small-cell lung cancer (NSCLC) is a well-established global concern. Considerable attention has been directed toward exploring the association between gut microbiota and various malignant tumors. We herein investigated the associations between the intestinal microbiome and its metabolites, particularly short-chain fatty acids (SCFAs), in patients with NSCLC at different stages, including early and brain metastasis (BM) stages. The findings aim to offer a fresh perspective on the diagnosis and management of NSCLC. Methods Fecal samples were collected from 115 participants, comprising healthy controls (n = 35) and patients with treatment-naive NSCLC at the early stage (ELC, n = 40) and the BM stage (n = 40). Characterization of the intestinal microbiome and fecal SCFA levels was performed using 16S rRNA gene sequencing and gas chromatography. Results The microbial diversity in patients with NSCLC was found to be less abundant and uniform, particularly in the BM stage. Significant alterations in the community structure of the gut microbiota were observed in patients with NSCLC, with an increase in pathogens in Fusobacteria and Proteobacteria and a decrease in SCFA-producing bacteria in Firmicutes and Actinobacteria, particularly in the BM stage. Meanwhile, microbial communities displayed intricate associations in patients with NSCLC. A biomarker panel (Faecalibacterium, Bifidobacterium, Butyricicoccus, Klebsiella, Streptococcus, and Blautia) successfully distinguished patients in the ELC and BM stages from healthy controls (area under the curve: 0.884). The overall concentration of fecal SCFAs was significantly lower in patients with BM compared to patients with ELC and healthy controls. Subgroup analysis of acetate and butyrate yielded similar results. Moreover, multiple disrupted pathways in the NSCLC group were identified using the Kyoto Encyclopedia of Genes and Genomes annotation, including lipid metabolism and genetic information processing, specifically in the BM stage. Conclusion Compared with healthy controls, distinct host-microbe interactions were evident in different phases of patients with NSCLC. Furthermore, specific forms of the gut microbiome and SCFAs may serve as valuable biomarkers and therapeutic targets in the diagnosis and treatment of NSCLC.
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Affiliation(s)
- Haixiao Jiang
- Department of Neurosurgery, The Affiliated Hospital of Yangzhou University, Yangzhou, China
| | - Wei Zeng
- Department of Neurosurgery, Yancheng First Hospital, Affiliated Hospital of Nanjing University Medical School, Yancheng, China
| | - Xiaoli Zhang
- Department of Medical Imaging, The Affiliated Hospital of Yangzhou University, Yangzhou, China
| | - Yuping Li
- Department of Neurosurgery, Clinical Medical College of Yangzhou University, Yangzhou, China
| | - Yilun Wang
- Department of Thoracic Surgery, Clinical Medical College of Yangzhou University, Yangzhou, China
| | - Aijun Peng
- Department of Neurosurgery, The Affiliated Hospital of Yangzhou University, Yangzhou, China
| | - Demao Cao
- Department of Neurosurgery, The Affiliated Hospital of Yangzhou University, Yangzhou, China
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3
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Yu S, Li L, Zhao H, Liu M, Jiang L, Zhao Y. Citrus flavonoid extracts alter the profiling of rumen antibiotic resistance genes and virulence factors of dairy cows. Front Microbiol 2023; 14:1201262. [PMID: 37362928 PMCID: PMC10289158 DOI: 10.3389/fmicb.2023.1201262] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 05/22/2023] [Indexed: 06/28/2023] Open
Abstract
Citrus flavonoid extracts (CFE) have the potential to reduce rumen inflammation, improve ruminal function, and enhance production performance in ruminants. Our previous studies have investigated the effects of CFE on the structure and function of rumen microbiota in dairy cows. However, it remains unclear whether CFE affects the prevalence of antibiotic resistance genes (ARG) and virulence factors genes (VFG) in the rumen. Therefore, metagenomics was used to identify the rumen ARG and VFG in lactating dairy cows fed with CFE diets. The results showed that CFE significantly reduced the levels of Multidrug and Antiphagocytosis in the rumen (p < 0.05) and increased the levels of Tetracycline, Iron uptake system, and Magnesium uptake system (p < 0.05). Furthermore, the changes were found to have associations with the phylum Lentisphaerae. It was concluded that CFE could be utilized as a natural plant product to regulate virulence factors and antibiotic resistance of rumen microbiota, thereby improving rumen homeostasis and the health of dairy cows.
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Affiliation(s)
- Shiqiang Yu
- Beijing Key Laboratory of Dairy Cow Nutrition, College of Animal Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Liuxue Li
- Beijing Key Laboratory of Dairy Cow Nutrition, College of Animal Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Huiying Zhao
- Beijing Key Laboratory of Dairy Cow Nutrition, College of Animal Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Ming Liu
- Beijing Key Laboratory of Dairy Cow Nutrition, College of Animal Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Linshu Jiang
- Beijing Key Laboratory of Dairy Cow Nutrition, College of Animal Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Yuchao Zhao
- Beijing Key Laboratory of Dairy Cow Nutrition, College of Animal Science and Technology, Beijing University of Agriculture, Beijing, China
- Beijing Beinong Enterprise Management Co., Ltd., Beijing, China
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4
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Teseo S, Otani S, Brinch C, Leroy S, Ruiz P, Desvaux M, Forano E, Aarestrup FM, Sapountzis P. A global phylogenomic and metabolic reconstruction of the large intestine bacterial community of domesticated cattle. MICROBIOME 2022; 10:155. [PMID: 36155629 PMCID: PMC9511753 DOI: 10.1186/s40168-022-01357-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 08/24/2022] [Indexed: 05/30/2023]
Abstract
BACKGROUND The large intestine is a colonization site of beneficial microbes complementing the nutrition of cattle but also of zoonotic and animal pathogens. Here, we present the first global gene catalog of cattle fecal microbiomes, a proxy of the large intestine microbiomes, from 436 metagenomes from six countries. RESULTS Phylogenomics suggested that the reconstructed genomes and their close relatives form distinct branches and produced clustering patterns that were reminiscent of the metagenomics sample origin. Bacterial taxa had distinct metabolic profiles, and complete metabolic pathways were mainly linked to carbohydrates and amino acids metabolism. Dietary changes affected the community composition, diversity, and potential virulence. However, predicted enzymes, which were part of complete metabolic pathways, remained present, albeit encoded by different microbes. CONCLUSIONS Our findings provide a global insight into the phylogenetic relationships and the metabolic potential of a rich yet understudied bacterial community and suggest that it provides valuable services to the host. However, we tentatively infer that members of that community are not irreplaceable, because similar to previous findings, symbionts of complex bacterial communities of mammals are expendable if there are substitutes that can perform the same task. Video Abstract.
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Affiliation(s)
- S Teseo
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - S Otani
- National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - C Brinch
- National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - S Leroy
- Université Clermont Auvergne, INRAE, UMR 0454 MEDIS, Clermont-Ferrand, France
| | - P Ruiz
- Université Clermont Auvergne, INRAE, UMR 0454 MEDIS, Clermont-Ferrand, France
| | - M Desvaux
- Université Clermont Auvergne, INRAE, UMR 0454 MEDIS, Clermont-Ferrand, France
| | - E Forano
- Université Clermont Auvergne, INRAE, UMR 0454 MEDIS, Clermont-Ferrand, France
| | - F M Aarestrup
- National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - P Sapountzis
- Université Clermont Auvergne, INRAE, UMR 0454 MEDIS, Clermont-Ferrand, France.
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Vinayamohan PG, Locke SR, Portillo-Gonzalez R, Renaud DL, Habing GG. Antimicrobial Use and Resistance in Surplus Dairy Calf Production Systems. Microorganisms 2022; 10:1652. [PMID: 36014070 PMCID: PMC9413162 DOI: 10.3390/microorganisms10081652] [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: 07/12/2022] [Revised: 08/05/2022] [Accepted: 08/10/2022] [Indexed: 11/16/2022] Open
Abstract
Surplus calves, which consist predominately of male calves born on dairy farms, are an underrecognized source of antimicrobial-resistant (AMR) pathogens. Current production systems for surplus calves have important risk factors for the dissemination of pathogens, including the high degree of commingling during auction and transportation and sometimes inadequate care early in life. These circumstances contribute to an increased risk of respiratory and other infectious diseases, resulting in higher antimicrobial use (AMU) and the development of AMR. Several studies have shown that surplus calves harbor AMR genes and pathogens that are resistant to critically important antimicrobials. This is a potential concern as the resistant pathogens and genes can be shared between animal, human and environmental microbiomes. Although knowledge of AMU and AMR has grown substantially in dairy and beef cattle systems, comparable studies in surplus calves have been mostly neglected in North America. Therefore, the overall goal of this narrative review is to summarize the existing literature regarding AMU and AMR in surplus dairy calf production, highlight the management practices contributing to the increased AMU and the resulting AMR, and discuss potential strategies and barriers for improved antimicrobial stewardship in surplus calf production systems.
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Affiliation(s)
- Poonam G. Vinayamohan
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Samantha R. Locke
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Rafael Portillo-Gonzalez
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - David L. Renaud
- Department of Population Medicine, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Gregory G. Habing
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, OH 43210, USA
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6
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Locke SR, Pempek JA, Meyer R, Portillo-Gonzalez R, Sockett D, Aulik N, Habing G. Prevalence and Sources of Salmonella Lymph Node Infection in Special-Fed Veal Calves. J Food Prot 2022; 85:906-917. [PMID: 35146524 DOI: 10.4315/jfp-21-410] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 02/10/2022] [Indexed: 11/11/2022]
Abstract
ABSTRACT Peripheral lymph nodes (LNs) have been implicated as potential contaminants of ground beef, yet the source and timing of Salmonella LN infection in cattle is still unclear, limiting targeted intervention. The aim of this study was to leverage the vertical integration of special-fed veal production to identify preharvest environmental exposures, specifically in livestock trailers and harvest facility holding pens where calves spend 30 min to 4 h, that result in Salmonella LN infection. Ten cohorts of 80 to 82 veal calves were followed through the harvest process, and environmental samples were collected in barns, trailers, and holding pens. Mesenteric LNs from 35 calves were collected at harvest, and 25 prefemoral LNs per cohort were pooled. Within the same cohort, for 12 samples for which the serovar of the environmental and calf LN Salmonella isolates matched, the isolates were submitted for whole genome sequencing to determine whether environmental exposure resulted in LN infection. Cohort-level Salmonella mesenteric LN prevalence ranged from 0% (0 of 35 samples) to 80% (28 of 35 samples), and pooled prefemoral LNs were positive for Salmonella in 3 of the 10 cohorts. Salmonella prevalence in samples from barns, livestock trailers, and harvest facility holding pens was 22% (13 of 60 samples), 74% (59 of 80 samples), and 93% (74 of 80 samples), respectively. Some environmental and LN isolates were multidrug resistant. Four instances of Salmonella transmission from trailers and/or holding pens to calf LNs were supported by sequence data. Salmonella serovars Agona, Give, and Muenster were identified in transmission events. One instance of transmission from the livestock trailer, two instances from holding pens, and one instance from either trailer or holding pens were observed. Further research is needed to evaluate the extent of environmental Salmonella transmission in cattle and to determine whether targeted interventions in trailers or holding pens could reduce novel Salmonella LN infection in veal calves before harvest. HIGHLIGHTS
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Affiliation(s)
- Samantha R Locke
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, Ohio State University, Columbus, Ohio 43210
| | - Jessica A Pempek
- Department of Animal Science, College of Food, Agricultural, and Environmental Science, Ohio State University, Columbus, Ohio 43210
| | - Rachel Meyer
- Wisconsin Veterinary Diagnostic Laboratory, Madison, Wisconsin 53706, USA
| | - Rafael Portillo-Gonzalez
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, Ohio State University, Columbus, Ohio 43210
| | - Donald Sockett
- Wisconsin Veterinary Diagnostic Laboratory, Madison, Wisconsin 53706, USA
| | - Nicole Aulik
- Wisconsin Veterinary Diagnostic Laboratory, Madison, Wisconsin 53706, USA
| | - Gregory Habing
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, Ohio State University, Columbus, Ohio 43210
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Haley BJ, Kim SW, Salaheen S, Hovingh E, Van Kessel JAS. Virulome and genome analyses identify associations between antimicrobial resistance genes and virulence factors in highly drug-resistant Escherichia coli isolated from veal calves. PLoS One 2022; 17:e0265445. [PMID: 35298535 PMCID: PMC8929554 DOI: 10.1371/journal.pone.0265445] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 03/01/2022] [Indexed: 11/19/2022] Open
Abstract
Food animals are known reservoirs of multidrug-resistant (MDR) Escherichia coli, but information regarding the factors influencing colonization by these organisms is lacking. Here we report the genomic analysis of 66 MDR E. coli isolates from non-redundant veal calf fecal samples. Genes conferring resistance to aminoglycosides, β-lactams, sulfonamides, and tetracyclines were the most frequent antimicrobial resistance genes (ARGs) detected and included those that confer resistance to clinically significant antibiotics (blaCMY-2, blaCTX-M, mph(A), erm(B), aac(6’)Ib-cr, and qnrS1). Co-occurrence analyses indicated that multiple ARGs significantly co-occurred with each other, and with metal and biocide resistance genes (MRGs and BRGs). Genomic analysis also indicated that the MDR E. coli isolated from veal calves were highly diverse. The most frequently detected genotype was phylogroup A-ST Cplx 10. A high percentage of isolates (50%) were identified as sequence types that are the causative agents of extra-intestinal infections (ExPECs), such as ST69, ST410, ST117, ST88, ST617, ST648, ST10, ST58, and ST167, and an appreciable number of these isolates encoded virulence factors involved in the colonization and infection of the human urinary tract. There was a significant difference in the presence of multiple accessory virulence factors (VFs) between MDR and susceptible strains. VFs associated with enterohemorrhagic infections, such as stx, tir, and eae, were more likely to be harbored by antimicrobial-susceptible strains, while factors associated with extraintestinal infections such as the sit system, aerobactin, and pap fimbriae genes were more likely to be encoded in resistant strains. A comparative analysis of SNPs between strains indicated that several closely related strains were recovered from animals on different farms indicating the potential for resistant strains to circulate among farms. These results indicate that veal calves are a reservoir for a diverse group of MDR E. coli that harbor various resistance genes and virulence factors associated with human infections. Evidence of co-occurrence of ARGs with MRGs, BRGs, and iron-scavenging genes (sit and aerobactin) may lead to management strategies for reducing colonization of 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, Beltsville, MD, United States of America
- * E-mail:
| | - Seon Woo Kim
- Environmental Microbial and Food Safety Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, United States of America
| | - Serajus Salaheen
- Environmental Microbial and Food Safety Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, United States of America
| | - Ernest Hovingh
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA, United States of America
| | - 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, United States of America
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8
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Jiang H, Zeng W, Zhang X, Pei Y, Zhang H, Li Y. The role of gut microbiota in patients with benign and malignant brain tumors: a pilot study. Bioengineered 2022; 13:7847-7859. [PMID: 35291914 PMCID: PMC9208447 DOI: 10.1080/21655979.2022.2049959] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Gut microbiota is associated with the growth of various tumors, including malignant gliomas, through the brain-gut axis. Moreover, the gut microbiota in patients with malignant tumors may considerably differ from those with benign tumors. However, the associations of gut microbiota with benign and malignant brain tumors remain unclear. Hence, in order to explore these underlying relationships, patients with benign meningioma (n = 32), malignant glioma (n = 27), and healthy individuals (n = 41) were selected to participate in this study. The results showed that the diversity of the microbial ecosystem in brain tumor patients were less than the healthy controls, while no significant differences were observed between the meningioma and glioma groups. The microbial composition also differed significantly between individuals with brain tumors and healthy participants. In meningioma group, pathogenic bacteria like Enterobacteriaceae were increased, whereas certain carcinogenic bacteria were overrepresented in the glioma group, including Fusobacterium and Akkermansia. Furthermore, benign and malignant brain tumor patients lacked SCFA-producing probiotics. Thus, a microbial biomarker panel including Fusobacterium, Akkermansia, Escherichia/Shigella, Lachnospira, Agathobacter, and Bifidobacterium was established. Diagnostic models confirmed that this panel could distinguish between brain tumor patients and healthy patients. Additionally, gut microbiota can affect the differentiation and proliferation of brain tumors via several metabolic pathways based on annotations from the Kyoto Encyclopedia of Genes and Genomes (KEGG). This is the first study designed to investigate whether gut microbiota differs between benign and malignant brain tumor patients, and our work concluded that intestinal flora is a valuable tool for the diagnosis and treatment of brain tumors.
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Affiliation(s)
- Haixiao Jiang
- Department of Clinical Medicine,School of Medicine, Yangzhou University, Yangzhou, Jiangsu, China.,Department of Neurosurgery, Clinical Medical College of Yangzhou University, Yangzhou, Jiangsu, China
| | - Wei Zeng
- Department of Clinical Medicine,School of Medicine, Yangzhou University, Yangzhou, Jiangsu, China.,Department of Neurosurgery, Clinical Medical College of Yangzhou University, Yangzhou, Jiangsu, China
| | - Xiaoli Zhang
- Department of Clinical Medicine,School of Medicine, Yangzhou University, Yangzhou, Jiangsu, China.,Department of Medical Imaging, The Affiliated Hospital of Yangzhou University, Yangzhou, Jiangsu, China
| | - Yunlong Pei
- Department of Neurosurgery, Clinical Medical College of Yangzhou University, Yangzhou, Jiangsu, China
| | - Hengzhu Zhang
- Department of Clinical Medicine,School of Medicine, Yangzhou University, Yangzhou, Jiangsu, China.,Department of Neurosurgery, Clinical Medical College of Yangzhou University, Yangzhou, Jiangsu, China
| | - Yuping Li
- Department of Clinical Medicine,School of Medicine, Yangzhou University, Yangzhou, Jiangsu, China.,Department of Neurosurgery, Clinical Medical College of Yangzhou University, Yangzhou, Jiangsu, China
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9
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Sapountzis P, Teseo S, Otani S, Aarestrup FM, Forano E, Suen G, Tsiamis G, Haley B, Van Kessel JA, Huws SA. FI: The Fecobiome Initiative. Foodborne Pathog Dis 2021; 19:441-447. [PMID: 34936494 PMCID: PMC9297326 DOI: 10.1089/fpd.2021.0082] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Animal husbandry has been key to the sustainability of human societies for millennia. Livestock animals, such as cattle, convert plants to protein biomass due to a compartmentalized gastrointestinal tract (GIT) and the complementary contributions of a diverse GIT microbiota, thereby providing humans with meat and dairy products. Research on cattle gut microbial symbionts has mainly focused on the rumen (which is the primary fermentation compartment) and there is a paucity of functional insight on the intestinal (distal end) microbiota, where most foodborne zoonotic bacteria reside. Here, we present the Fecobiome Initiative (or FI), an international effort that aims at facilitating collaboration on research projects related to the intestinal microbiota, disseminating research results, and increasing public availability of resources. By doing so, the FI can help mitigate foodborne and animal pathogens that threaten livestock and human health, reduce the emergence and spread of antimicrobial resistance in cattle and their proximate environment, and potentially improve the welfare and nutrition of animals. We invite all researchers interested in this type of research to join the FI through our website: www.fecobiome.com
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Affiliation(s)
| | - Serafino Teseo
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Saria Otani
- National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - Evelyne Forano
- Université Clermont Auvergne, INRAE, UMR 0454 MEDIS, Clermont-Ferrand, France
| | - Garett Suen
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - George Tsiamis
- Lab of Systems Microbiology and Applied Genomics, University of Patras, Agrinio, Greece
| | - Bradd Haley
- Environmental Microbial and Food Safety Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, Maryland, USA
| | - Jo Ann Van Kessel
- Environmental Microbial and Food Safety Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, Maryland, USA
| | - Sharon A Huws
- School of Biological Sciences, Institute for Global Food Security, Queens University Belfast (QUB), Belfast, United Kingdom
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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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Tate H, Li C, Nyirabahizi E, Tyson GH, Zhao S, Rice-Trujillo C, Jones SB, Ayers S, M'ikanatha NM, Hanna S, Ruesch L, Cavanaugh ME, Laksanalamai P, Mingle L, Matzinger SR, McDermott PF. A National Antimicrobial Resistance Monitoring System Survey of Antimicrobial-Resistant Foodborne Bacteria Isolated from Retail Veal in the United States. J Food Prot 2021; 84:1749-1759. [PMID: 34015113 DOI: 10.4315/jfp-21-005] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 05/16/2021] [Indexed: 11/11/2022]
Abstract
ABSTRACT Little is known about the prevalence of antimicrobial-resistant (AMR) bacteria in veal meat in the United States. We estimated the prevalence of bacterial contamination and AMR in various veal meats collected during the 2018 U.S. National Antimicrobial Resistance Monitoring System (NARMS) survey of retail outlets in nine states and compared the prevalence with the frequency of AMR bacteria from other cattle sources sampled for NARMS. In addition, we identified genes associated with resistance to medically important antimicrobials and gleaned other genetic details about the resistant organisms. The prevalence of Campylobacter, Salmonella, Escherichia coli, and Enterococcus in veal meats collected from grocery stores in nine states was 0% (0 of 358), 0.6% (2 of 358), 21.1% (49 of 232), and 53.5% (121 of 226), respectively, with ground veal posing the highest risk for contamination. Both Salmonella isolates were resistant to at least one antimicrobial agent as were 65.3% (32 of 49) of E. coli and 73.6% (89 of 121) of Enterococcus isolates. Individual drug and multiple drug resistance levels were significantly higher (P < 0.05) in E. coli and Enterococcus from retail veal than in dairy cattle ceca and retail ground beef samples from 2018 NARMS data. Whole genome sequencing was conducted on select E. coli and Salmonella from veal. Cephalosporin resistance (blaCMY and blaCTX-M), macrolide resistance (mph), and plasmid-mediated quinolone resistance (qnr) genes and gyrA mutations were found. We also identified heavy metal resistance genes ter, ars, mer, fieF, and gol and disinfectant resistance genes qac and emrE. An stx1a-containing E. coli was also found. Sequence types were highly varied among the nine E. coli isolates that were sequenced. Several plasmid types were identified in E. coli and Salmonella, with the majority (9 of 11) of isolates containing IncF. This study illustrates that veal meat is a carrier of AMR bacteria. HIGHLIGHTS
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Affiliation(s)
- Heather Tate
- Center for Veterinary Medicine, U.S. Food and Drug Administration, 8401 Muirkirk Road, Laurel, Maryland 20708
| | - Cong Li
- Center for Veterinary Medicine, U.S. Food and Drug Administration, 8401 Muirkirk Road, Laurel, Maryland 20708
| | - Epiphanie Nyirabahizi
- Center for Veterinary Medicine, U.S. Food and Drug Administration, 8401 Muirkirk Road, Laurel, Maryland 20708
| | - Gregory H Tyson
- Center for Veterinary Medicine, U.S. Food and Drug Administration, 8401 Muirkirk Road, Laurel, Maryland 20708
| | - Shaohua Zhao
- Center for Veterinary Medicine, U.S. Food and Drug Administration, 8401 Muirkirk Road, Laurel, Maryland 20708
| | - Crystal Rice-Trujillo
- Center for Veterinary Medicine, U.S. Food and Drug Administration, 8401 Muirkirk Road, Laurel, Maryland 20708
| | - Sonya Bodeis Jones
- Center for Veterinary Medicine, U.S. Food and Drug Administration, 8401 Muirkirk Road, Laurel, Maryland 20708
| | - Sherry Ayers
- Center for Veterinary Medicine, U.S. Food and Drug Administration, 8401 Muirkirk Road, Laurel, Maryland 20708
| | - Nkuchia M M'ikanatha
- Division of Infectious Disease Epidemiology, Pennsylvania Department of Health, 7th and Forster Streets, Harrisburg, Pennsylvania 17120
| | - Samir Hanna
- Tennessee Department of Health, 710 James Robertson Parkway, Nashville, Tennessee 37243
| | - Laura Ruesch
- Animal Disease Research and Diagnostic Lab, South Dakota State University, Brookings, South Dakota 57007
| | | | - Pongpan Laksanalamai
- Laboratories Administration, Maryland Department of Health, 1770 Ashland Avenue, Baltimore, Maryland 21205
| | - Lisa Mingle
- Wadsworth Center Division of Infectious Diseases, New York State Department of Health, Albany, New York 12208
| | - Shannon R Matzinger
- Colorado Department of Public Health and Environment, 8100 Lowry Boulevard, Denver, Colorado 80230, USA
| | - Patrick F McDermott
- Center for Veterinary Medicine, U.S. Food and Drug Administration, 8401 Muirkirk Road, Laurel, Maryland 20708
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