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Feng Y, Li T, Zhao S, Zheng M, Shen J, Wu X, Li X, Zhai Y, Yuan L, Liu J, Hu G, Pan Y, He D. Identification and evolution of novel cfr-carrying plasmids in XDR Klebsiella pneumoniae strains from a chicken farm. Microbiol Spectr 2025; 13:e0262824. [PMID: 40130857 PMCID: PMC12054152 DOI: 10.1128/spectrum.02628-24] [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: 01/03/2025] [Accepted: 02/26/2025] [Indexed: 03/26/2025] Open
Abstract
The cfr gene is typically located on plasmids, playing a crucial role in both intra-species and inter-species transmission among bacteria. This study focused on two cfr-positive Klebsiella pneumoniae strains, J21CTR26 and J21CTR30, isolated from environmental samples of a chicken farm. Antimicrobial susceptibility testing showed that these strains exhibited an extensively drug-resistant (XDR) phenotype, including resistance to 16 antibiotics across nine classes, notably tigecycline and colistin. Sequence analysis identified both strains as belonging to K10-ST6262, harboring 32 resistance genes and 5 virulence genes. Despite their genetic similarity, hybridization and whole-genome sequencing revealed distinct plasmid profiles. Strain J21CTR26 harbored a 5,404,868 bp chromosome and three plasmids: pCTR26-1 (485,030 bp), pCTR26-2 (141,660 bp) carrying cfr, and pCTR26-3 (106,823 bp). In contrast, J21CTR30 possessed a 5,405,166 bp chromosome and three plasmids: pCTR30-1 (394,261 bp) carrying cfr, pCTR30-2 (234,624 bp), and pCTR30-3 (106,770 bp). Conjugation experiments demonstrated the transferability of the cfr-positive plasmid pCTR26-2 from J21CTR26 to Escherichia coli J53, with a conjugation frequency of 4.2 × 10-6. Reverse PCR indicated the formation of a circular intermediate, IS26-cfr, in both cfr-positive strains. Sequence analysis suggested that pCTR30-1 likely originated from a recombination event between pCTR26-1 and pCTR26-2 facilitated by TnAs1-mediated homologous recombination. Identification of a fusion plasmid and its daughter plasmids in different XDR K. pneumoniae strains underscored the dynamic recombination and spread of resistance plasmids in agricultural environments. In conclusion, this study provided insights into the dissemination and evolution of cfr-positive plasmids in husbandry, shedding light on their critical role in antibiotic resistance persistence.IMPORTANCEThis study highlights the alarming role of K. pneumoniae in the spread of antibiotic resistance within agricultural environments. Two strains isolated from a chicken farm were found to carry the cfr gene, conferring resistance to multiple critical antibiotics, including tigecycline and colistin. Despite their genetic similarity, the strains exhibited distinct plasmid structures, emphasizing the complexity of plasmid evolution. The identification of a fusion plasmid and its derived plasmids underscores the dynamic nature of resistance gene transfer facilitated by recombination events. Importantly, the transferability of the cfr-positive plasmid to E. coli demonstrates the potential for cross-species dissemination. This work sheds light on how agricultural practices contribute to the persistence and evolution of resistance genes, with significant implications for public health and the global fight against antimicrobial resistance.
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Affiliation(s)
- Yiming Feng
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Tiantian Li
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Shiyun Zhao
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Mengxiang Zheng
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Jiaxing Shen
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Xiaoying Wu
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Xuexue Li
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Yajun Zhai
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
- Ministry of Education Key Laboratory for Animal Pathogens and Biosafety, Zhengzhou, Henan Province, China
- Henan Province Key Laboratory of Animal Food Pathogens Surveillance, Zhengzhou, China
| | - Li Yuan
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
- Ministry of Education Key Laboratory for Animal Pathogens and Biosafety, Zhengzhou, Henan Province, China
- Henan Province Key Laboratory of Animal Food Pathogens Surveillance, Zhengzhou, China
| | - Jianhua Liu
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Gongzheng Hu
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
- Ministry of Education Key Laboratory for Animal Pathogens and Biosafety, Zhengzhou, Henan Province, China
- Henan Province Key Laboratory of Animal Food Pathogens Surveillance, Zhengzhou, China
| | - Yushan Pan
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Dandan He
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
- Ministry of Education Key Laboratory for Animal Pathogens and Biosafety, Zhengzhou, Henan Province, China
- Henan Province Key Laboratory of Animal Food Pathogens Surveillance, Zhengzhou, China
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Xue W, Hong J, Zhao R, Yao H, Zhang Y, Dai Z, Wang T. Spatial entropy drives the maintenance and dissemination of transferable plasmids. Mol Syst Biol 2025:10.1038/s44320-025-00110-8. [PMID: 40301564 DOI: 10.1038/s44320-025-00110-8] [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: 10/21/2024] [Revised: 03/31/2025] [Accepted: 04/11/2025] [Indexed: 05/01/2025] Open
Abstract
The dissemination of transferable plasmids, a major type of mobile genetic elements (MGEs), is one main driver of antibiotic resistance outbreaks. While the plasmid persistence condition in well-mixed environments has been extensively studied, most microbiota in nature are spatially heterogeneous. However, our knowledge regarding how spatial landscape shapes plasmid maintenance and dissemination remains limited. Here we establish a theoretical framework describing plasmid spread over a metacommunity of multiple patches. By analyzing the gene flow dynamics on randomly generated landscapes, we show that plasmid survival and dispersal are dictated by a simple feature of the landscape, spatial entropy. Reducing entropy speeds up plasmid range expansion and allows the global maintenance of many plasmids that are predicted to be lost by classic theories. The entropy's effects are experimentally validated in E. coli metacommunities transferring a conjugative plasmid. We further examine a vast collection of prokaryotic genomes and show that prokaryotes from low-entropy environments indeed carry more abundant MGEs and antibiotic resistance genes. Our work provides critical insights into the management and control of antimicrobial resistance.
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Affiliation(s)
- Wenzhi Xue
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Juken Hong
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Runmeng Zhao
- School of Mathematics, Jilin University, Changchun, 130012, China
| | - Huaxiong Yao
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Yi Zhang
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Zhuojun Dai
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Teng Wang
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
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3
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Sun J, Wang X, He Y, Han M, Li M, Wang S, Chen J, Zhang Q, Yang B. Environmental fate of antibiotic resistance genes in livestock farming. Arch Microbiol 2025; 207:120. [PMID: 40214801 DOI: 10.1007/s00203-025-04320-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2025] [Accepted: 03/28/2025] [Indexed: 04/30/2025]
Abstract
As emerging environmental pollutants, antibiotic resistance genes (ARGs) are prevalent in livestock farms and their surrounding environments. Although existing studies have focused on ARGs in specific environmental media, comprehensive research on ARGs within farming environments and their adjacent areas remains scarce. This review explores the sources, pollution status, and transmission pathways of ARGs from farms to the surrounding environment. Drawing on the "One Health" concept, it also discusses the potential risks of ARGs transmission from animals to human pathogens and the resulting impact on human health. Our findings suggest that the emergence of ARGs in livestock farming environments primarily results from intrinsic resistance and genetic mutations, while their spread is largely driven by horizontal gene transfer. The distribution of ARGs varies according to the type of resistance genes, seasonal changes, and the medium in which they are present. ARGs are disseminated into the surrounding environment via pathways such as manure application, wastewater discharge, and aerosol diffusion. They may be absorbed by humans, accumulating in the intestinal microbiota and subsequently affecting human health. The spread of ARGs is influenced by the interplay of microbial communities, antibiotics, heavy metals, emerging pollutants, and environmental factors. Additionally, we have outlined three control strategies: reducing the emergence of ARGs at the source, controlling their spread, and minimizing human exposure. This article provides a theoretical framework and scientific guidance for understanding the cross-media migration of microbial resistance in livestock farming environments.
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Affiliation(s)
- Jiali Sun
- College of Food Science and Engineering, Northwest A&F University, 22# Xi'nong Road, Yangling, Shaanxi, 712100, China
| | - Xiaoqi Wang
- College of Food Science and Engineering, Northwest A&F University, 22# Xi'nong Road, Yangling, Shaanxi, 712100, China
| | - Yuanjie He
- College of Life Science, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Mengting Han
- College of Food Science and Engineering, Northwest A&F University, 22# Xi'nong Road, Yangling, Shaanxi, 712100, China
| | - Mei Li
- College of Food Science and Engineering, Northwest A&F University, 22# Xi'nong Road, Yangling, Shaanxi, 712100, China
| | - Siyue Wang
- College of Food Science and Engineering, Northwest A&F University, 22# Xi'nong Road, Yangling, Shaanxi, 712100, China
| | - Jia Chen
- Shijiazhuang University, Shijiazhuang, 050035, China
| | - Qiang Zhang
- National Institutes for Food and Drug Control, Beijing, 100050, China.
| | - Baowei Yang
- College of Food Science and Engineering, Northwest A&F University, 22# Xi'nong Road, Yangling, Shaanxi, 712100, China.
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Changkaew K, Wongsoonthornchai M, Thitanuwat B, Changkwanyeun R, Yoogate P. Efficacy of anaerobic digestion wastewater treatment systems in reducing antimicrobial resistance bacteria in wastewater from swine farms in Thailand. JOURNAL OF WATER AND HEALTH 2025; 23:384-396. [PMID: 40156216 DOI: 10.2166/wh.2025.323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2024] [Accepted: 02/24/2025] [Indexed: 04/01/2025]
Abstract
The study aimed to evaluate the antimicrobial resistance (AMR) patterns among the fecal indicator bacteria and analyze the characteristics of wastewater from anaerobic digestion (AD) wastewater treatment systems in swine farms. Escherichia coli and Enterococcus spp. were identified by conventional and molecular methods. AMR profiles and wastewater quality were analyzed using standard methods. The results indicated that the primary resistances observed in E. coli were against AM, TE, SXT, and DO. Among Enterococcus spp., the highest resistance was noted for TE, followed by E, CIP, and NX. Enterococcus faecium showed the highest resistance to CIP, NX, and TE. Multidrug-resistant-E. coli and enterococci were 64.2 and 32.6%, respectively. Furthermore, CL-resistant E. coli and VA-resistant Enterococcus spp. were reported. Compared with influent, the proportion of AMR E. coli and Enterococcus spp. in effluent was decreased. This decline suggested that AD effectively removed antimicrobial-resistant bacteria (ARB). However, high influent biochemical oxygen demand, total suspended solids, and chemical oxygen demand levels demonstrated significant pollution. Therefore, swine farms should prioritize waste management and regular maintenance of treatment systems to enhance the removal of ARB and pollutants. This study analyzed data from only three farms, highlighting the need for future research with a larger sample.
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Affiliation(s)
- Kanjana Changkaew
- Faculty of Public Health, Thammasat University (Rangsit Campus), Klong Luang, Pathum Thani 12121, Thailand; Thammasat University Research Unit in Modern Microbiology and Public Health Genomics, Thammasat University (Rangsit Campus), Klong Luang, Pathum Thani 12121, Thailand E-mail:
| | - Manaporn Wongsoonthornchai
- Faculty of Public Health, Thammasat University (Rangsit Campus), Klong Luang, Pathum Thani 12121, Thailand
| | - Bussarakam Thitanuwat
- Faculty of Public Health, Thammasat University (Rangsit Campus), Klong Luang, Pathum Thani 12121, Thailand
| | - Ruchirada Changkwanyeun
- Faculty of Public Health, Thammasat University (Lampang Campus), Hang Chat, Lampang 52190, Thailand
| | - Phashararat Yoogate
- Faculty of Public Health, Thammasat University (Rangsit Campus), Klong Luang, Pathum Thani 12121, Thailand
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Choi JM, Rumi MA, Vikesland PJ, Pruden A, Zhang L. ARGfore: A multivariate framework for forecasting antibiotic resistance gene abundances using time-series metagenomic datasets. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.01.13.632008. [PMID: 39868304 PMCID: PMC11761695 DOI: 10.1101/2025.01.13.632008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2025]
Abstract
Background The global spread of antibiotic resistance presents a significant threat to human, animal, and plant health. Metagenomic sequencing is increasingly being utilized to profile antibiotic resistance genes (ARGs) in various environments, but presently a mechanism for predicting future trends in ARG occurrence patterns is lacking. Capability of forecasting ARG abundance trends could be extremely valuable towards informing policy and practice aimed at mitigating the evolution and spread of ARGs. Results Here we propose ARGfore, a multivariate forecasting model for predicting ARG abundances from time-series metagenomic data. ARGfore extracts features that capture inherent relationships among ARGs and is trained to recognize patterns in ARG trends and seasonality. Conclusion ARGfore outperformed standard time-series forecasting methods, such as N-HiTS, LSTM, and ARIMA, exhibiting the lowest mean absolute percentage error when applied to different wastewater datasets. Additionally, ARGfore demonstrated enhanced computational efficiency, making it a promising candidate for a variety of ARG surveillance applications. The rapid prediction of future trends can facilitate early detection and deployment of mitigation efforts if necessary. ARGfore is publicly available at https://github.com/joungmin-choi/ARGfore .
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Taylor W, Bohm K, Dyet K, Weaver L, Pattis I. Comparative analysis of qPCR and metagenomics for detecting antimicrobial resistance in wastewater: a case study. BMC Res Notes 2025; 18:5. [PMID: 39773654 PMCID: PMC11705827 DOI: 10.1186/s13104-024-07027-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 12/03/2024] [Indexed: 01/11/2025] Open
Abstract
OBJECTIVE The World Health Organization (WHO) has declared antimicrobial resistance (AMR) as one of the top threats to global public health. While AMR surveillance of human clinical isolates is well-established in many countries, the increasing threat of AMR has intensified efforts to detect antibiotic resistance genes (ARGs) accurately and sensitively in environmental samples, wastewater, animals, and food. Using five ARGs and the 16S rRNA gene, we compared quantitative PCR (qPCR) and metagenomic sequencing (MGS), two commonly used methods to uncover the wastewater resistome. We compared both methods by evaluating ARG detection through a municipal wastewater treatment chain. RESULTS Our results demonstrate that qPCR was more sensitive than MGS, particularly in diluted samples with low ARG concentrations such as oxidation pond water. However, MGS was potentially more specific and has less risk of off-target binding in concentrated samples such as raw sewage. MGS analysis revealed multiple subtypes of each gene which could not be distinguished by qPCR; these subtypes varied across different sample types. Our findings affect the conclusions that can be drawn when comparing different sample types, particularly in terms of inferring removal rates or origins of genes. We conclude that both methods appear suitable to profile the resistome of wastewater and other environmental samples, depending on the research question and type of sample.
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Affiliation(s)
- William Taylor
- Institute of Environmental Science and Research Ltd, Christchurch, New Zealand
| | - Kristin Bohm
- Institute of Environmental Science and Research Ltd, Kenepuru, Wellington, New Zealand
| | - Kristin Dyet
- Institute of Environmental Science and Research Ltd, Kenepuru, Wellington, New Zealand
| | - Louise Weaver
- Institute of Environmental Science and Research Ltd, Christchurch, New Zealand
| | - Isabelle Pattis
- Institute of Environmental Science and Research Ltd, Christchurch, New Zealand.
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7
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Masarikova M, Sukkar I, Jamborova I, Medvecky M, Papousek I, Literak I, Cizek A, Dolejska M. Antibiotic-resistant Escherichia coli from treated municipal wastewaters and Black-headed Gull nestlings on the recipient river. One Health 2024; 19:100901. [PMID: 39399230 PMCID: PMC11470789 DOI: 10.1016/j.onehlt.2024.100901] [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: 08/30/2023] [Revised: 08/20/2024] [Accepted: 09/20/2024] [Indexed: 10/15/2024] Open
Abstract
Wastewaters belong among the most important sources of environmental pollution, including antibiotic-resistant bacteria. The aim of the study was to evaluate treated wastewaters as a possible transmission pathway for bacterial colonisation of gulls occupying the receiving river. A collection of antibiotic-resistant Escherichia coli originating both from treated municipal wastewaters discharged to the river Svratka (Czech Republic) and nestlings of Black-headed Gull (Chroicocephalus ridibundus) living 35 km downstream of the outlet was obtained using selective cultivation. Isolates were further characterised by various phenotyping and genotyping methods. From a total of 670 E. coli isolates (450 from effluents, 220 from gulls), 86 isolates (41 from effluents, 45 from gulls) showed identical antibiotic resistance phenotype and genotype and were further analysed for clonal relatedness using pulsed-field gel electrophoresis (PFGE). Despite the overall high diversity of the isolates, 21 isolates from both sources showed similar PFGE profiles. Isolates belonging to epidemiologically important sequence types (ST131, 15 isolates; ST23, three isolates) were subjected to whole-genome sequencing. Subsequent phylogenetic analysis did not reveal any close clonal relationship between the isolates from the effluents and gulls' nestlings with the closest strains showing 90 SNPs difference. Although our study did not provide direct evidence of transmission of antibiotic-resistant E. coli to wild gulls via treated wastewaters, we observed gull chicks as carriers of diverse multi-resistant E. coli, including high-risk clones, posing risk of further bacterial contamination of the surrounding environment.
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Affiliation(s)
- Martina Masarikova
- Department of Infectious Diseases and Microbiology, Faculty of Veterinary Medicine, University of Veterinary Sciences Brno, Brno, Czech Republic
- Central European Institute of Technology, University of Veterinary Sciences Brno, Brno, Czech Republic
| | - Iva Sukkar
- Central European Institute of Technology, University of Veterinary Sciences Brno, Brno, Czech Republic
- Biomedical Center, Faculty of Medicine, Charles University, Pilsen, Czech Republic
| | - Ivana Jamborova
- Central European Institute of Technology, University of Veterinary Sciences Brno, Brno, Czech Republic
| | - Matej Medvecky
- Central European Institute of Technology, University of Veterinary Sciences Brno, Brno, Czech Republic
| | - Ivo Papousek
- Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary Sciences Brno, Brno, Czech Republic
| | - Ivan Literak
- Central European Institute of Technology, University of Veterinary Sciences Brno, Brno, Czech Republic
- Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary Sciences Brno, Brno, Czech Republic
| | - Alois Cizek
- Department of Infectious Diseases and Microbiology, Faculty of Veterinary Medicine, University of Veterinary Sciences Brno, Brno, Czech Republic
- Central European Institute of Technology, University of Veterinary Sciences Brno, Brno, Czech Republic
| | - Monika Dolejska
- Central European Institute of Technology, University of Veterinary Sciences Brno, Brno, Czech Republic
- Biomedical Center, Faculty of Medicine, Charles University, Pilsen, Czech Republic
- Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary Sciences Brno, Brno, Czech Republic
- Division of Clinical Microbiology and Immunology, Department of Laboratory Medicine, The University Hospital Brno, Czech Republic
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Nguyen SH, Tran MT. Enzyme-free biosensor utilizing chitosan-capped ZnS doped by Mn nanomaterials for tetracycline hydrochloride detection. Heliyon 2024; 10:e40340. [PMID: 39605817 PMCID: PMC11600035 DOI: 10.1016/j.heliyon.2024.e40340] [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: 07/31/2024] [Revised: 11/11/2024] [Accepted: 11/11/2024] [Indexed: 11/29/2024] Open
Abstract
Tetracycline hydrochloride is a widely used antibiotic for treating bacterial infections, but its misuse poses serious health risks. Therefore, it is crucial to accurately detect tetracycline in complex matrices. In this study, we propose a simple, enzyme-free absorbance biosensor for tetracycline detection based on the optical properties of chitosan-capped ZnS doped with Mn nanomaterials. The biosensor can detect tetracycline in a range from 13.1 pM to 72.2 pM, with the best detection limit being 2.13 pM in deionized water. It can also differentiate tetracycline from ampicillin, penicillin, cephalexin, amoxicillin, and glucose within the aforementioned range. Moreover, this novel sensor has proven reliable over time, and its performance has been demonstrated in tap water and milk. The results have the potential to revolutionize antibiotic monitoring in clinical and environmental settings, thus contributing to the global fight against antibiotic resistance.
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Affiliation(s)
- Son Hai Nguyen
- School of Mechanical Engineering, Hanoi University of Science and Technology, Hanoi, 100000, Viet Nam
| | - Mai Thi Tran
- College of Engineering and Computer Science, VinUniversity, Hanoi, 100000, Viet Nam
- VinUni-Illinois Smart Health Center, VinUniversity, Hanoi, 100000, Viet Nam
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Ortiz-Severín J, Hodar C, Stuardo C, Aguado-Norese C, Maza F, González M, Cambiazo V. Impact of salmon farming in the antibiotic resistance and structure of marine bacterial communities from surface seawater of a northern Patagonian area of Chile. Biol Res 2024; 57:84. [PMID: 39523335 PMCID: PMC11552226 DOI: 10.1186/s40659-024-00556-4] [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: 04/16/2024] [Accepted: 10/14/2024] [Indexed: 11/16/2024] Open
Abstract
BACKGROUND Aquaculture and salmon farming can cause environmental problems due to the pollution of the surrounding waters with nutrients, solid wastes and chemicals, such as antibiotics, which are used for disease control in the aquaculture facilities. Increasing antibiotic resistance in human-impacted environments, such as coastal waters with aquaculture activity, is linked to the widespread use of antibiotics, even at sub-lethal concentrations. In Chile, the world's second largest producer of salmon, aquaculture is considered the primary source of antibiotics residues in the coastal waters of northern Patagonia. Here, we evaluated whether the structure and diversity of marine bacterial community, the richness of antibiotic resistance bacteria and the frequency of antibiotic resistance genes increase in communities from the surface seawater of an area with salmon farming activities, in comparison with communities from an area without major anthropogenic disturbance. RESULTS The taxonomic structure of bacterial community was significantly different between areas with and without aquaculture production. Growth of the culturable fraction under controlled laboratory conditions showed that, in comparison with the undisturbed area, the bacterial community from salmon farms displayed a higher frequency of colonies resistant to the antibiotics used by the salmon industry. A higher adaptation to antibiotics was revealed by a greater proportion of multi-resistant bacteria isolated from the surface seawater of the salmon farming area. Furthermore, metagenomics data revealed a significant higher abundance of antibiotic resistant genes conferring resistance to 11 antibiotic families in the community from salmon farms, indicating that the proportion of bacteria carrying the resistance determinants was overall higher in salmon farms than in the undisturbed site. CONCLUSIONS Our results revealed an association between bacterial communities and antibiotic resistance from surface seawater of a coastal area of Chile. Although the total bacterial community may appear comparable between sites, the cultivation technique allowed to expose a higher prevalence of antibiotic resistant bacteria in the salmon farming area. Moreover, we demonstrated that metagenomics (culture-independent) and phenotypic (culture-dependent) methods are complementary to evaluate the bacterial communities' risk for antibiotic resistance, and that a human-influenced environment (such as salmon farms) can potentiate bacteria to adapt to environmental stresses, such as antibiotics.
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Affiliation(s)
- Javiera Ortiz-Severín
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, El Líbano, 5524, Santiago, Chile
| | - Christian Hodar
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, El Líbano, 5524, Santiago, Chile
- Laboratorio de Bioinformática y Bioestadística del Genoma, INTA, Universidad de Chile, Santiago, Chile
| | - Camila Stuardo
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, El Líbano, 5524, Santiago, Chile
| | - Constanza Aguado-Norese
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, El Líbano, 5524, Santiago, Chile
- Millennium Institute Center for Genome Regulation (CRG), Santiago, Chile
| | - Felipe Maza
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, El Líbano, 5524, Santiago, Chile
| | - Mauricio González
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, El Líbano, 5524, Santiago, Chile
- Millennium Institute Center for Genome Regulation (CRG), Santiago, Chile
| | - Verónica Cambiazo
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, El Líbano, 5524, Santiago, Chile.
- Millennium Institute Center for Genome Regulation (CRG), Santiago, Chile.
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10
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Tsai MA, Chen IC, Chen ZW, Li TH. Further Evidence of Anthropogenic Impact: High Levels of Multiple-Antimicrobial-Resistant Bacteria Found in Neritic-Stage Sea Turtles. Antibiotics (Basel) 2024; 13:998. [PMID: 39596693 PMCID: PMC11591244 DOI: 10.3390/antibiotics13110998] [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: 09/09/2024] [Revised: 10/20/2024] [Accepted: 10/21/2024] [Indexed: 11/29/2024] Open
Abstract
BACKGROUND/OBJECTIVES Marine turtles are globally threatened and face daily anthropogenic threats, including pollution. Water pollution from emerging contaminants such as antimicrobials is a major and current environmental concern. METHODS This study investigated the phenotypic antimicrobial resistance and heavy metal resistance genes of 47 Vibrio isolates from different stages of sea turtles (oceanic stage vs neritic stage) from the Taiwanese coast. RESULTS The results show that a high proportion (48.9%; 23/47) of the Vibrio species isolated from sea turtles in our study had a multiple antimicrobial resistance (MAR) pattern. It was found that Vibrio spp. isolates with a MAR pattern and those with a MAR index value greater than 0.2 were both more likely to be observed in neritic-stage sea turtles. Furthermore, isolates from neritic-stage sea turtles exhibited greater resistance to the majority of antimicrobials tested (with the exception of beta-lactams and macrolides) than isolates from the oceanic-stage groups. Isolates from neritic sea turtles were found to be more resistant to nitrofurans and aminoglycosides than isolates from oceanic sea turtles. Furthermore, isolates with a MAR pattern (p = 0.010) and those with a MAR index value greater than 0.2 (p = 0.027) were both found to be significantly positively associated with the mercury reductase (merA) gene. CONCLUSIONS The findings of our study indicate that co-selection of heavy metals and antimicrobial resistance may occur in aquatic bacteria in the coastal foraging habitats of sea turtles in Taiwan.
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Affiliation(s)
- Ming-An Tsai
- Department of Veterinary Medicine, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung 91201, Taiwan;
- International Program in Ornamental Fish Technology and Aquatic Animal Health, International College, National Pingtung University of Science and Technology, Pingtung 91201, Taiwan
| | - I-Chun Chen
- National Museum of Marine Biology and Aquarium, Pingtung 94450, Taiwan;
| | - Zeng-Weng Chen
- Animal Technology Research Center, Agricultural Technology Research Institute, Miaoli 340401, Taiwan;
| | - Tsung-Hsien Li
- National Museum of Marine Biology and Aquarium, Pingtung 94450, Taiwan;
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung 804201, Taiwan
- Institute of Marine Ecology and Conservation, National Sun Yat-sen University, Kaohsiung 804201, Taiwan
- IUCN Species Survival Commission, Marine Turtle Specialist Group for the East Asia Region, Taiwan
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11
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Karpenko A, Shelenkov A, Manzeniuk I, Kulikova N, Gevorgyan A, Mikhaylova Y, Akimkin V. Whole genome analysis of multidrug-resistant Escherichia coli isolate collected from drinking water in Armenia revealed the plasmid-borne mcr-1.1-mediated colistin resistance. Microbiol Spectr 2024; 12:e0075124. [PMID: 39166856 PMCID: PMC11448411 DOI: 10.1128/spectrum.00751-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 07/19/2024] [Indexed: 08/23/2024] Open
Abstract
The rate of polymyxin-resistant Enterobacteriaceae, as well as human and animal infections caused by them, is increasing worldwide, posing a high epidemiological threat since colistin represents a last-resort antibiotic to treat complicated infections. The study of environmental niches, in particular, aquatic ecosystems in terms of genome analysis of inhabiting antimicrobial-resistant (AMR) microorganisms as reservoirs of acquired resistance determinants (AMR genes), represents a specific concern from a One Health approach. Here, we present a phenotypic AMR analysis and molecular characterization of Escherichia coli isolate found in municipal drinking water after an accident in the water supply system of a residential building in Armenia in 2021. CrieF1144 E. coli isolate was resistant to ampicillin, ampicillin/sulbactam, cefuroxime, ciprofloxacin, levofloxacin, trimethoprim/sulfamethoxazole, colistin, and tigecycline, whereas whole genome sequencing (WGS) revealed blaTEM-1B, tet(A), and a combination of dfrA14 with sul1 resistance determinants, which corresponds well with phenotypic resistance above. Moreover, the multidrug-resistant isolate studied harbored mcr-1.1 gene on a conjugative 251 Kb IncHI2 plasmid, whose structure was determined using hybrid short- and long-reads assembly. CrieF1141_p1 plasmid carried all antimicrobial resistance genes revealed in the isolate and did not harbor any virulence determinants, so it could contribute to the spread of AMR genes in the bacterial population. Two copies of ISApl1 transposase-encoding element, which is likely to mediate mcr-1.1 gene mobilization, were revealed surrounding this gene in a plasmid. IMPORTANCE Evolutionary patterns of Escherichia coli show that they usually develop into highly pathogenic forms by acquiring fitness advantages such as antimicrobial resistance (AMR) and various virulence factors through horizontal gene transfer mediated by mobile elements. This has led to high prevalence of multidrug-resistant (MDR) strains, which highlights the relevancy of enhanced surveillance to monitor and prevent transmission of the MDR bacteria to human and animal populations. However, the limited number of reports regarding the whole genome sequencing (WGS) investigation of MDR E. coli strains isolated from drinking water and harboring mcr genes hampers the adoption of a comprehensive approach to address the relationship between environmental E. coli populations and human and veterinary infections. Our results highlight the relevance of analyzing the environment, especially water, as a part of the surveillance programs to understand the origins and dissemination of antimicrobial resistance within the One Health concept.
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Affiliation(s)
- Anna Karpenko
- Department of Molecular Diagnostics and Epidemiology, Central Research Institute of Epidemiology, Moscow, Russia
| | - Andrey Shelenkov
- Department of Molecular Diagnostics and Epidemiology, Central Research Institute of Epidemiology, Moscow, Russia
| | - Igor Manzeniuk
- Administrative and Management Department – Directorate, Central Research Institute of Epidemiology, Moscow, Russia
| | - Nina Kulikova
- Department of Molecular Diagnostics and Epidemiology, Central Research Institute of Epidemiology, Moscow, Russia
| | - Arman Gevorgyan
- Republican Veterinary and Phytosanitary Laboratory Services Center, Yerevan, Armenia
| | - Yulia Mikhaylova
- Department of Molecular Diagnostics and Epidemiology, Central Research Institute of Epidemiology, Moscow, Russia
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12
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Mahazu S, Prah I, Ota Y, Hayashi T, Suzuki M, Yoshida M, Hoshino Y, Akeda Y, Suzuki T, Ishino T, Ablordey AS, Saito R. Colistin Resistance Mediated by Mcr-3-Related Phosphoethanolamine Transferase Genes in Aeromonas Species Isolated from Aquatic Environments in Avaga and Pakro Communities in the Eastern Region of Ghana. Infect Drug Resist 2024; 17:3011-3023. [PMID: 39050833 PMCID: PMC11268572 DOI: 10.2147/idr.s468000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 06/24/2024] [Indexed: 07/27/2024] Open
Abstract
Purpose Colistin is classified by the World Health Organization (WHO) as a critically important and last-resort antibiotic for the treatment of infections caused by carbapenem-resistant bacteria. However, colistin resistance mediated by chromosomal mutations or plasmid-linked mobilized colistin resistance (mcr) genes has emerged. Methods Thirteen mcr-positive Aeromonas species isolated from water samples collected in Eastern Ghana were analyzed using whole-genome sequencing (WGS). Antimicrobial susceptibility was tested using the broth microdilution method. Resistome analysis was performed in silico using a web-based platform. Results The minimum inhibitory concentration (MIC) of colistin for all except three isolates was >4 µg/mL. Nine new sequence types were identified and whole-genome analysis revealed that the isolates harbored genes (mcr-3-related genes) that code for Lipid A phosphoethanolamine transferases on their chromosomes. BLAST analysis indicated that the amino acid sequences of the mcr-3-related genes detected varied from those previously reported and shared 79.04-99.86% nucleotide sequence identity with publicly available mcr-3 variants and mcr-3-related phosphoethanolamine transferases. Analysis of the genetic context of mcr-3-related genes revealed that the genetic environment surrounding mcr-3-related genes was diverse among the different species of Aeromonas but conserved among isolates of the same species. Mcr-3-related-gene-IS-mcr-3-related-gene segment was identified in three Aeromonas caviae strains. Conclusion The presence of mcr-3-related genes close to insertion elements is important for continuous monitoring to better understand how to control the mobilization and dissemination of antibiotic resistance genes.
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Affiliation(s)
- Samiratu Mahazu
- Department of Molecular Microbiology, Tokyo Medical and Dental University, Tokyo, Japan
- Department of Parasitology and Tropical Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Isaac Prah
- Department of Molecular Microbiology, Tokyo Medical and Dental University, Tokyo, Japan
- Department of Molecular Virology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yusuke Ota
- Department of Molecular Microbiology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Takaya Hayashi
- Department of Molecular Virology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Masato Suzuki
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Mitsunori Yoshida
- Department of Mycobacteriology, Leprosy Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yoshihiko Hoshino
- Department of Mycobacteriology, Leprosy Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yukihiro Akeda
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Toshihiko Suzuki
- Department of Bacterial Pathogenesis, Tokyo Medical and Dental University, Tokyo, Japan
| | - Tomoko Ishino
- Department of Parasitology and Tropical Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Anthony Samuel Ablordey
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Ryoichi Saito
- Department of Molecular Microbiology, Tokyo Medical and Dental University, Tokyo, Japan
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13
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McConn BR, Kraft AL, Durso LM, Ibekwe AM, Frye JG, Wells JE, Tobey EM, Ritchie S, Williams CF, Cook KL, Sharma M. An analysis of culture-based methods used for the detection and isolation of Salmonella spp., Escherichia coli, and Enterococcus spp. from surface water: A systematic review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 927:172190. [PMID: 38575025 DOI: 10.1016/j.scitotenv.2024.172190] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 03/14/2024] [Accepted: 04/01/2024] [Indexed: 04/06/2024]
Abstract
Identification of methods for the standardized assessment of bacterial pathogens and antimicrobial resistance (AMR) in environmental water can improve the quality of monitoring and data collected, support global surveillance efforts, and enhance the understanding of environmental water sources. We conducted a systematic review to assemble and synthesize available literature that identified methods for assessment of prevalence and abundance of bacterial fecal indicators and pathogens in water for the purposes of monitoring bacterial pathogens and AMR. After screening for quality, 175 unique publications were identified from 15 databases, and data were extracted for analysis. This review identifies the most common and robust methods, and media used to isolate target organisms from surface water sources, summarizes methodological trends, and recognizes knowledge gaps. The information presented in this review will be useful when establishing standardized methods for monitoring bacterial pathogens and AMR in water in the United States and globally.
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Affiliation(s)
- Betty R McConn
- Oak Ridge Institute of Science and Education/U.S. Department of Agriculture (USDA), Agricultural Research Service, Beltsville, MD, United States of America
| | - Autumn L Kraft
- Oak Ridge Institute of Science and Education/U.S. Department of Agriculture (USDA), Agricultural Research Service, Beltsville, MD, United States of America
| | - Lisa M Durso
- USDA ARS Agroecoystem Management Research, Lincoln, NE, United States of America
| | - Abasiofiok M Ibekwe
- USDA ARS, Agricultural Water Efficiency and Salinity Research Unit, Riverside, CA, United States of America
| | - Jonathan G Frye
- USDA ARS, U.S. National Poultry Research Center, Poultry Microbiological Safety and Processing Research Unit, Athens, GA, United States of America
| | - James E Wells
- USDA ARS, U.S. Meat Animal Research Center, Meat Safety and Quality, Clay Center, NE, United States of America
| | - Elizabeth M Tobey
- USDA National Agricultural Library, Beltsville, MD, United States of America
| | - Stephanie Ritchie
- USDA National Agricultural Library, Beltsville, MD, United States of America
| | - Clinton F Williams
- USDA ARS, US Arid-Land Agricultural Research Center, Maricopa, AZ, United States of America
| | - Kimberly L Cook
- USDA ARS, Nutrition, Food Safety and Quality National Program Staff, Beltsville, MD, United States of America
| | - Manan Sharma
- USDA ARS Environmental Microbial and Food Safety Laboratory, Beltsville, MD, United States of America.
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14
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Xu Y, Anker Y, Talawar MP. Degradation of tetracycline, oxytetracycline & ampicillin by purified multiple copper oxidase like laccase from Stentrophomonas sp. YBX1. Braz J Microbiol 2024; 55:1529-1543. [PMID: 38340257 PMCID: PMC11153415 DOI: 10.1007/s42770-024-01247-8] [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: 03/15/2023] [Accepted: 01/02/2024] [Indexed: 02/12/2024] Open
Abstract
Multiple copper oxidase (MCO) like laccase is widely distributed in higher plant, fungi and bacteria. This study identified MCO like laccase producing bacterium isolated from a wastewater treatment plant based on 16S rRNA sequence analysis, and they were further confirmed by phylogenetic reconstruction. Biochemical and gene characterization of MCO like laccase from Stenotrophomonas sp. YBX1 is presented. Purification of MCO like laccase was carried out by ion exchange HQ Trap column and followed by gel filtration spheracryl S-100 column. The purified MCO like laccase from Stenotrophomonas sp. YBX1 shows a total activity of 1252 units and specific activity 391.2 U/mg and protein concentration 0.32 mg/mL. In SDS PAGE, the approximate molecular mass was found at 66 kDa and further confirmed from an MS spectrum of MALDI-TOF. The purified MCO like laccase is capable of degradation of antibiotics such as tetracycline completely, whereas oxytetracycline (78%) and ampicillin (62%) degraded within 96 min without any redox mediators at pH 5 and 30 ºC. Its degradation pathway was based on identification of metabolites by LC-MS spectrum. The enzymatic degradation may be used in advanced treatment of antibiotics containing wastewater.
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Affiliation(s)
- Yanbin Xu
- School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou, 510006, China
| | - Yaakov Anker
- Department of Chemical Engineering, Ariel University, 40700, Ariel, Israel
| | - Manjunatha P Talawar
- School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou, 510006, China.
- Department of Chemical Engineering, Ariel University, 40700, Ariel, Israel.
- Department of Life Science, Garden City University, Bangalore, 580049, India.
- School of Chemical Engineering and Light Industry, Guangdong University of Technology, Guangzhou, 510 006, China.
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15
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Pourrostami Niavol K, Bordoloi A, Suri R. An overview of the occurrence, impact of process parameters, and the fate of antibiotic resistance genes during anaerobic digestion processes. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:41745-41774. [PMID: 38853230 PMCID: PMC11219439 DOI: 10.1007/s11356-024-33844-3] [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: 01/22/2024] [Accepted: 05/24/2024] [Indexed: 06/11/2024]
Abstract
Antibiotic resistance genes (ARGs) have emerged as a significant global health threat, contributing to fatalities worldwide. Wastewater treatment plants (WWTPs) and livestock farms serve as primary reservoirs for these genes due to the limited efficacy of existing treatment methods and microbial adaptation to environmental stressors. Anaerobic digestion (AD) stands as a prevalent biological treatment for managing sewage sludge and manure in these settings. Given the agricultural utility of AD digestate as biofertilizers, understanding ARGs' fate within AD processes is essential to devise effective mitigation strategies. However, understanding the impact of various factors on ARGs occurrence, dissemination, and fate remains limited. This review article explores various AD treatment parameters and correlates to various resistance mechanisms and hotspots of ARGs in the environment. It further evaluates the dissemination and occurrence of ARGs in AD feedstocks and provides a comprehensive understanding of the fate of ARGs in AD systems. This review explores the influence of key AD parameters such as feedstock properties, pretreatments, additives, and operational strategies on ARGs. Results show that properties such as high solid content and optimum co-digestion ratios can enhance ARG removal, while the presence of heavy metals, microplastics, and antibiotics could elevate ARG abundance. Also, operational enhancements, such as employing two-stage digestion, have shown promise in improving ARG removal. However, certain pretreatment methods, like thermal hydrolysis, may exhibit a rebounding effect on ARG levels. Overall, this review systematically addresses current challenges and offers future perspectives associated with the fate of ARGs in AD systems.
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Affiliation(s)
- Kasra Pourrostami Niavol
- Department of Civil and Environmental Engineering, Temple University, Philadelphia, PA, 19122, USA
| | - Achinta Bordoloi
- Department of Civil and Environmental Engineering, Temple University, Philadelphia, PA, 19122, USA
| | - Rominder Suri
- Department of Civil and Environmental Engineering, Temple University, Philadelphia, PA, 19122, USA.
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16
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Zhao YC, Sun ZH, Li JK, Liu HY, Cai HL, Cao W, Yu F, Zhang BK, Yan M. Exploring the causes of the prevalence of vancomycin-resistant Enterococcus faecalis. ENVIRONMENTAL SCIENCES EUROPE 2024; 36:92. [DOI: 10.1186/s12302-024-00923-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Accepted: 04/28/2024] [Indexed: 01/04/2025]
Abstract
Abstract
Background
Bacterial drug resistance represents a significant global concern, with vancomycin-resistant Enterococcus faecalis posing a particularly grave threat to contemporary healthcare systems. This study aims to reveal the reasons for the prevalence of VRE in China.
Methods
This study collected data from the China Antimicrobial Resistance Detection System, China Statistical Yearbook, and China Meteorological Network. The collected data are meticulously organized and subjected to both single-factor and multi-factor analyses. An accurate multiple linear regression model was developed by utilizing this comprehensive dataset.
Results
Single-factor analysis revealed significant regional variations in the resistance rate of vancomycin-resistant Enterococcus faecalis (P = 0.003). Specifically, there were noteworthy disparities observed between regions experiencing temperate and monsoon climates (P = 0.029; P = 0.005). Furthermore, multi-factor regression analysis demonstrated a negative correlation between the drug resistance rate and both rainfall and rGDP, while a positive correlation was observed with nPI.
Conclusion
We successfully established a prediction model for the VRE and found that the resistance rate was low in areas with high rainfall and high per capita economic income, but high in areas with many specialized public health institutions. This is critical for public health strategies and helps policymakers and healthcare practitioners tailor antibiotic resistance approaches to local geography, meteorology, economic conditions.
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17
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de Fátima NG, Barriga A, Cáceres JC, Pinto E, Cabrera R. Oxidation of chlortetracycline and its isomers by Botrytis aclada laccase in the absence of mediators: pH dependence and identification of transformation products by LC-MS. Biodegradation 2024; 35:155-171. [PMID: 37428416 DOI: 10.1007/s10532-023-10046-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 06/09/2023] [Indexed: 07/11/2023]
Abstract
Tetracyclines are antibiotics considered emerging pollutants and currently, wastewater treatment plants are not able to remove them efficiently. Laccases are promising enzymes for bioremediation because they can oxidize a wide variety of substrates. The aim of this study was to evaluate the Botrytis aclada laccase for the oxidation of chlortetracycline and its isomers in the absence of a mediator molecule, at a pH range between 3.0 to 7.0, and to characterize the transformation products by LC-MS. Chlortetracycline and three isomers were detected in both, controls and reaction mixtures at 0 h and in controls after 48 h of incubation but in different proportions depending on pH. An additional isomer was also detected, but only in the presence of BaLac. Based on the transformation products identified in the enzymatic reactions and information from literature, we assembled a network of transformation pathways starting from chlortetracycline and its isomers. The spectrometric analysis of the products indicated the probable occurrence of oxygen insertion, dehydrogenation, demethylation and deamination reactions. Four new products were identified, and we also described a novel transformation product without the chloro group. We observed that increasing pH led to higher diversity of main products. This is the first study using the laccase from fungi Botrytis aclada to oxidate chlortetracycline and its isomers and it can be considered as an ecological alternative to be used in bioremediation processes such as wastewater.
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Affiliation(s)
- Nadia Gavilán de Fátima
- Laboratorio de Bioquímica y Biología Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago, Chile
- Unidad de Espectrometría de Masas-CEPEDEQ, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santos Dumont 964, Independencia, Santiago, Chile
| | - Andrés Barriga
- Unidad de Espectrometría de Masas-CEPEDEQ, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santos Dumont 964, Independencia, Santiago, Chile
| | - Juan Carlos Cáceres
- Laboratorio de Bioquímica y Biología Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago, Chile
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, USA
| | - Ernani Pinto
- Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Av. Pádua Dias 11, Piracicaba, SP, Brasil
| | - Ricardo Cabrera
- Laboratorio de Bioquímica y Biología Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago, Chile.
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18
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Lagerstrom KM, Scales NC, Hadly EA. Impressive pan-genomic diversity of E. coli from a wild animal community near urban development reflects human impacts. iScience 2024; 27:109072. [PMID: 38375235 PMCID: PMC10875580 DOI: 10.1016/j.isci.2024.109072] [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: 08/28/2023] [Revised: 11/22/2023] [Accepted: 01/26/2024] [Indexed: 02/21/2024] Open
Abstract
Human and domesticated animal waste infiltrates global freshwater, terrestrial, and marine environments, widely disseminating fecal microbes, antibiotics, and other chemical pollutants. Emerging evidence suggests that guts of wild animals are being invaded by our microbes, including Escherichia coli, which face anthropogenic selective pressures to gain antimicrobial resistance (AMR) and increase virulence. However, wild animal sources remain starkly under-represented among genomic sequence repositories. We sequenced whole genomes of 145 E. coli isolates from 55 wild and 13 domestic animal fecal samples, averaging 2 (ranging 1-7) isolates per sample, on a preserve imbedded in a human-dominated landscape in California Bay Area, USA, to assess AMR, virulence, and pan-genomic diversity. With single nucleotide polymorphism analyses we predict potential transmission routes. We illustrate the usefulness of E. coli to aid our understanding of and ability to surveil the emergence of zoonotic pathogens created by the mixing of human and wild bacteria in the environment.
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Affiliation(s)
| | - Nicholas C. Scales
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA, USA
| | - Elizabeth A. Hadly
- Department of Biology, Stanford University, Stanford, CA, USA
- Stanford Woods Institute for the Environment, Stanford University, Stanford, CA, USA
- Center for Innovation in Global Health, Stanford University, Stanford, CA, USA
- Department of Earth Systems Science, Stanford University, Stanford, CA, USA
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19
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Ajayi AO, Odeyemi AT, Akinjogunla OJ, Adeyeye AB, Ayo-ajayi I. Review of antibiotic-resistant bacteria and antibiotic resistance genes within the one health framework. Infect Ecol Epidemiol 2024; 14:2312953. [PMID: 38371518 PMCID: PMC10868463 DOI: 10.1080/20008686.2024.2312953] [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: 05/02/2023] [Accepted: 01/29/2024] [Indexed: 02/20/2024] Open
Abstract
Background: The interdisciplinary One Health (OH) approach recognizes that human, animal, and environmental health are all interconnected. Its ultimate goal is to promote optimal health for all through the exploration of these relationships. Antibiotic resistance (AR) is a public health challenge that has been primarily addressed within the context of human health and clinical settings. However, it has become increasingly evident that antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) that confer resistance are transmitted and circulated within humans, animals, and the environment. Therefore, to effectively address this issue, antibiotic resistance must also be considered an environmental and livestock/wildlife problem. Objective: This review was carried out to provide a broad overview of the existence of ARB and ARGs in One Health settings. Methods: Relevant studies that placed emphasis on ARB and ARGs were reviewed and key findings were accessed that illustrate the importance of One Health as a measure to tackle growing public and environmental threats. Results: In this review, we delve into the complex interplay of the three components of OH in relation to ARB and ARGs. Antibiotics used in animal husbandry and plants to promote growth, treat, and prevent infectious diseases lead to the development of antibiotic-resistant bacteria in animals. These bacteria are transmitted from animals to humans through food and environmental exposure. The environment plays a critical role in the circulation and persistence of antibiotic-resistant bacteria and genes, posing a significant threat to human and animal health. This article also highlights how ARGs are spread in the environment through the transfer of genetic material between bacteria. This transfer can occur naturally or through human activities such as the use of antibiotics in agriculture and waste management practices. Conclusion: It is important to integrate the One Health approach into the public health system to effectively tackle the emergence and spread of ARB and genes that code for resistance to different antibiotics.
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Affiliation(s)
| | - Adebowale Toba Odeyemi
- Department of Microbiology, Landmark University SDG Groups 2 and 3, Omu-Aran, Kwara State, Nigeria
| | | | | | - Ibiwumi Ayo-ajayi
- Department of Computer Science, Afe Babalola University, Ado Ekiti, Ekiti State, Nigeria
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Han S, Shin R, Ryu SH, Unno T, Hur HG, Shin H. A Potential Indicator Gene, tetM, to Assess Contamination by Antibiotic Resistance Genes in Greenhouses in South Korea. Microbes Environ 2024; 39:ME24053. [PMID: 39756985 PMCID: PMC11821766 DOI: 10.1264/jsme2.me24053] [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: 06/23/2024] [Accepted: 09/07/2024] [Indexed: 01/07/2025] Open
Abstract
Antibiotic resistance genes (ARGs) have been emerging as a concerning threat to both environment and public health. The continuous input of manure, irrigation water, and fertilizers increases the abundance of ARGs in agricultural environments. However, current risk assessments have focused on clinical settings, which are not applicable to environmental settings. Therefore, we herein aimed to identify and assess indicator genes to reduce the time and effort required for ARG surveillance. A nationwide ana-lysis of 322 ARGs and 58 mobile genetic elements (MGEs) was performed on 42 greenhouse and 19 control soil samples. The chemical properties and pH of soil were also investigated to characterize differences between greenhouse and control soil samples. The results obtained showed that the abundance of ARGS was significantly higher and ion concentrations were higher in greenhouse samples than in control samples. These results indicate that agricultural activities increased the abundance of ARGs. Furthermore, the abundance of core genes was significantly higher in greenhouse samples than in control samples, and the chemical characteristics of soil significantly differed between these samples. Among the discriminatory genes selected, tetM was identified as an ARG surveillance indicator gene based on its clinical relevance, prevalence in the soil resistome, and relationship with mobile genetic elements. The present results will contribute to the continuous and rapid surveillance of antibiotic resistance dissemination and proliferation in greenhouses in South Korea.
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Affiliation(s)
- Seunggyun Han
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju, 61005, Republic of Korea
| | - Raan Shin
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju, 61005, Republic of Korea
| | - Song-Hee Ryu
- Residual Agrochemical Assessment Division, National Institute of Agricultural Sciences, Wanju-gun, South Korea
| | - Tatsuya Unno
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju, Republic of Korea
| | - Hor-Gil Hur
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju, 61005, Republic of Korea
| | - Hanseob Shin
- Center for Health Effects of Environmental Contamination, University of Iowa, W195 Chemistry Building, University of Iowa, Iowa city, Iowa, United States
- State Hygienic Laboratory, University of Iowa, Coralville, Iowa, United States
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21
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Fresno M, Pavez L, Poblete Y, Cortez A, Del Pozo T. Unveiling antimicrobial resistance in Chilean fertilized soils: a One Health perspective on environmental AMR surveillance. Front Microbiol 2023; 14:1239761. [PMID: 38107869 PMCID: PMC10722175 DOI: 10.3389/fmicb.2023.1239761] [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: 06/14/2023] [Accepted: 11/09/2023] [Indexed: 12/19/2023] Open
Abstract
Antimicrobial resistance (AMR) poses a significant threat to humans and animals as well as the environment. Within agricultural settings, the utilization of antimicrobial agents in animal husbandry can lead to the emergence of antimicrobial resistance. In Chile, the widespread use of animal-derived organic amendments, including manure and compost, requires an examination of the potential emergence of AMR resulting from their application. The aim of this research was to identify and compare AMR genes found in fertilized soils and manure in Los Andes city, Chile. Soil samples were collected from an agricultural field, comprising unamended soils, amended soils, and manure used for crop fertilization. The selected genes (n = 28) included genes associated with resistance to beta-lactams, tetracyclines, sulfonamides, polymyxins, macrolides, quinolones, aminoglycosides, as well as mobile genetic elements and multidrug resistance genes. Twenty genes were successfully identified in the samples. Tetracycline resistance genes displayed the highest prevalence, followed by MGE and sulfonamides, while quinolone resistance genes were comparatively less abundant. Notably, blaOXA, sulA, tetO, tetW, tetM, aac (6) ib., and intI1, exhibited higher frequencies in unamended soils, indicating their potential persistence within the soil microbiome and contribution to the perpetuation of AMR over time. Given the complex nature of AMR, it is crucial to adopt an integrated surveillance framework that embraces the One Health approach, involving multiple sectors, to effectively address this challenge. This study represents the first investigation of antimicrobial resistance genes in agricultural soils in Chile, shedding light on the presence and dynamics of AMR in this context.
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Affiliation(s)
- Marcela Fresno
- Núcleo de Investigaciones Aplicadas en Ciencias Veterinarias y Agronómicas, Facultad de Medicina Veterinaria y Agronomía, Universidad de Las Américas, Providencia, Santiago, Chile
- Red CYTED-USCC. CYTED 412RT0117: Una Salud en Iberoamérica y El Caribe frente al cambio climático y la pérdida de biodiversidad, Santiago, Chile
| | - Leonardo Pavez
- Núcleo de Investigación en Ciencias Biológicas (NICB), Facultad de Medicina Veterinaria y Agronomía, Universidad de Las Américas, Providencia, Santiago, Chile
- Departamento de Ciencias Humanas, Universidad Bernardo O’Higgins, Santiago, Chile
| | - Yanina Poblete
- Núcleo de Investigaciones Aplicadas en Ciencias Veterinarias y Agronómicas, Facultad de Medicina Veterinaria y Agronomía, Universidad de Las Américas, Providencia, Santiago, Chile
| | - Alexandra Cortez
- Facultad de Medicina Veterinaria y Agronomía, Universidad de Las Américas, Santiago, Chile
| | - Talía Del Pozo
- Núcleo de Investigaciones Aplicadas en Ciencias Veterinarias y Agronómicas, Facultad de Medicina Veterinaria y Agronomía, Universidad de Las Américas, Providencia, Santiago, Chile
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Ashy RA, Jalal RS, Sonbol HS, Alqahtani MD, Sefrji FO, Alshareef SA, Alshehrei FM, Abuauf HW, Baz L, Tashkandi MA, Hakeem IJ, Refai MY, Abulfaraj AA. Functional annotation of rhizospheric phageome of the wild plant species Moringa oleifera. Front Microbiol 2023; 14:1166148. [PMID: 37260683 PMCID: PMC10227523 DOI: 10.3389/fmicb.2023.1166148] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 04/10/2023] [Indexed: 06/02/2023] Open
Abstract
Introduction The study aims to describe phageome of soil rhizosphere of M.oleifera in terms of the genes encoding CAZymes and other KEGG enzymes. Methods Genes of the rhizospheric virome of the wild plant species Moringa oleifera were investigated for their ability to encode useful CAZymes and other KEGG (Kyoto Encyclopedia of Genes and Genomes) enzymes and to resist antibiotic resistance genes (ARGs) in the soil. Results Abundance of these genes was higher in the rhizospheric microbiome than in the bulk soil. Detected viral families include the plant viral family Potyviridae as well as the tailed bacteriophages of class Caudoviricetes that are mainly associated with bacterial genera Pseudomonas, Streptomyces and Mycobacterium. Viral CAZymes in this soil mainly belong to glycoside hydrolase (GH) families GH43 and GH23. Some of these CAZymes participate in a KEGG pathway with actions included debranching and degradation of hemicellulose. Other actions include biosynthesizing biopolymer of the bacterial cell wall and the layered cell wall structure of peptidoglycan. Other CAZymes promote plant physiological activities such as cell-cell recognition, embryogenesis and programmed cell death (PCD). Enzymes of other pathways help reduce the level of soil H2O2 and participate in the biosynthesis of glycine, malate, isoprenoids, as well as isoprene that protects plant from heat stress. Other enzymes act in promoting both the permeability of bacterial peroxisome membrane and carbon fixation in plants. Some enzymes participate in a balanced supply of dNTPs, successful DNA replication and mismatch repair during bacterial cell division. They also catalyze the release of signal peptides from bacterial membrane prolipoproteins. Phages with the most highly abundant antibiotic resistance genes (ARGs) transduce species of bacterial genera Pseudomonas, Streptomyces, and Mycobacterium. Abundant mechanisms of antibiotic resistance in the rhizosphere include "antibiotic efflux pump" for ARGs soxR, OleC, and MuxB, "antibiotic target alteration" for parY mutant, and "antibiotic inactivation" for arr-1. Discussion These ARGs can act synergistically to inhibit several antibiotics including tetracycline, penam, cephalosporin, rifamycins, aminocoumarin, and oleandomycin. The study highlighted the issue of horizontal transfer of ARGs to clinical isolates and human gut microbiome.
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Affiliation(s)
- Ruba A. Ashy
- Department of Biology, College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Rewaa S. Jalal
- Department of Biology, College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Hana S. Sonbol
- Department of Biology, College of Sciences, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Mashael D. Alqahtani
- Department of Biology, College of Sciences, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Fatmah O. Sefrji
- Department of Biology, College of Science, Taibah University, Al-Madinah Al-Munawwarah, Saudi Arabia
| | - Sahar A. Alshareef
- Department of Biology, College of Science and Arts at Khulis, University of Jeddah, Jeddah, Saudi Arabia
| | - Fatimah M. Alshehrei
- Department of Biology, Jumum College University, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Haneen W. Abuauf
- Department of Biology, Faculty of Applied Science, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Lina Baz
- Department of Biochemistry, Faculty of Science, King AbdulAziz University, Jeddah, Saudi Arabia
| | - Manal A. Tashkandi
- Department of Biochemistry, College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Israa J. Hakeem
- Department of Biochemistry, College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Mohammed Y. Refai
- Department of Biochemistry, College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Aala A. Abulfaraj
- Biological Sciences Department, College of Science & Arts, King AbdulAziz University, Rabigh, Saudi Arabia
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Bydalek F, Webster G, Barden R, Weightman AJ, Kasprzyk-Hordern B, Wenk J. Microplastic biofilm, associated pathogen and antimicrobial resistance dynamics through a wastewater treatment process incorporating a constructed wetland. WATER RESEARCH 2023; 235:119936. [PMID: 37028211 DOI: 10.1016/j.watres.2023.119936] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 03/05/2023] [Accepted: 04/01/2023] [Indexed: 06/19/2023]
Abstract
Microplastics in wastewater are colonized by biofilms containing pathogens and antimicrobial resistance (AMR) genes that can be exported into receiving water bodies. This study investigated establishment and changes in microplastic-associated biofilm and AMR during a conventional full-scale 2100 population equivalent wastewater treatment process combined with a free water surface polishing constructed wetland. Sequential microplastic colonization experiments were conducted at different stages of the wastewater treatment process, including in raw sewage, treated effluent and the constructed wetland. Two scenarios were tested in which the constructed wetland served as either (i) a polishing step or (ii) as primary recipient of sewage inoculated microplastics. Bacterial 16S rRNA gene sequencing was carried out for qualitative bacterial community analysis. qPCR was applied for quantitative analysis of AMR genes (sul1, ermB, tetW, intiI1), bacterial biomass (16S rRNA) and a human fecal marker (HF183). Microbial diversity on microplastics increased with incubation time. The initial sewage-derived biofilm composition changed more significantly in the wastewater effluent compared to the constructed wetland. Pathogen and AMR load decreased by up to two orders of magnitude after coupled conventional and constructed wetland treatment, while less impact was observed when sewage-inoculated microplastic material was directly transferred into the constructed wetland. Aeromonas, Klebsiella, and Streptococcus were key pathogenic genera correlated with AMR in microplastic-associated biofilms. Despite decreasing trends on human pathogens and AMR load along the treatment process, microplastic-associated biofilms were a considerable potential hotspot for AMR (intI1 gene) and accommodated Cyanobacteria and fish pathogens.
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Affiliation(s)
- Franciszek Bydalek
- Department of Chemical Engineering, University of Bath, Claverton Down, Bath BA2 7AY, UK; Water Innovation and Research Centre (WIRC), University of Bath, Bath BA2 7AY, UK; GW4 NERC CDT in Freshwater Biosciences and Sustainability, Cardiff University, Cardiff CF10 3AX, UK; Microbiomes, Microbes and Informatics Group, Organisms and Environment Division, School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK
| | - Gordon Webster
- Microbiomes, Microbes and Informatics Group, Organisms and Environment Division, School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK
| | | | - Andrew J Weightman
- Microbiomes, Microbes and Informatics Group, Organisms and Environment Division, School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK
| | - Barbara Kasprzyk-Hordern
- Water Innovation and Research Centre (WIRC), University of Bath, Bath BA2 7AY, UK; Department of Chemistry, University of Bath, Bath BA2 7AY, UK
| | - Jannis Wenk
- Department of Chemical Engineering, University of Bath, Claverton Down, Bath BA2 7AY, UK; Water Innovation and Research Centre (WIRC), University of Bath, Bath BA2 7AY, UK.
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de Souza ZN, de Moura DF, de Almeida Campos LA, Córdula CR, Cavalcanti IMF. Antibiotic resistance profiles on pathogenic bacteria in the Brazilian environments. Arch Microbiol 2023; 205:185. [PMID: 37043091 DOI: 10.1007/s00203-023-03524-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 03/18/2023] [Accepted: 03/28/2023] [Indexed: 04/13/2023]
Abstract
The present study aimed to elaborate a review of multidrug-resistant (MDR) bacteria in soil, food, aquatic environments, cattle, poultry, and swine farms in Brazil. Initially, the literature database for published papers from 2012 to 2023 was Scientific Electronic Library Online (SciELO), U.S. National Library of Medicine (PubMed), and Google Scholar, through the descriptors: antimicrobial resistance, resistance profile, multidrug resistance, environmental bacteria, and pathogenic bacteria. The studies demonstrated the prevalence of pathogenic and resistant bacteria in environments that favor their rapid dissemination. Bacteria of medical importance, such as Staphylococcus aureus, Escherichia coli, Pseudomonas aeruginosa, Listeria monocytogenes, Salmonella spp., Shigella spp., Vibrio spp., were present in samples from animal farms and foods, including cheese and milk, urban aquatic environments, hospital effluents, and shrimp farms. Studies suggested that important bacteria have been disseminated through different niches with easy contact with humans, animals, and food, demonstrating the danger of the emergence of increasingly difficult conditions for treating and controlling these infections. Thus, better understanding and characterizing the resistance profiles of bacteria in these regions, mainly referring to MDR bacteria, can help develop solutions to prevent the progression of this public health problem.
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Affiliation(s)
- Zion Nascimento de Souza
- Keizo Asami Institute (iLIKA), Federal University of Pernambuco (UFPE), Av. Prof. Moraes Rego, 1235, Cidade Universitária, Recife, PE, 50670-901, Brazil
| | - Danielle Feijó de Moura
- Laboratory of Microbiology and Immunology, Academic Center of Vitória (CAV), Federal University of Pernambuco (UFPE), Rua do Alto do Reservatório s/n, Bela Vista, Vitória de Santo Antão, Pernambuco, 55608-680, Brazil
| | - Luís André de Almeida Campos
- Keizo Asami Institute (iLIKA), Federal University of Pernambuco (UFPE), Av. Prof. Moraes Rego, 1235, Cidade Universitária, Recife, PE, 50670-901, Brazil
| | - Carolina Ribeiro Córdula
- Keizo Asami Institute (iLIKA), Federal University of Pernambuco (UFPE), Av. Prof. Moraes Rego, 1235, Cidade Universitária, Recife, PE, 50670-901, Brazil
| | - Isabella Macário Ferro Cavalcanti
- Keizo Asami Institute (iLIKA), Federal University of Pernambuco (UFPE), Av. Prof. Moraes Rego, 1235, Cidade Universitária, Recife, PE, 50670-901, Brazil.
- Laboratory of Microbiology and Immunology, Academic Center of Vitória (CAV), Federal University of Pernambuco (UFPE), Rua do Alto do Reservatório s/n, Bela Vista, Vitória de Santo Antão, Pernambuco, 55608-680, Brazil.
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Fatimazahra S, Latifa M, Laila S, Monsif K. Review of hospital effluents: special emphasis on characterization, impact, and treatment of pollutants and antibiotic resistance. ENVIRONMENTAL MONITORING AND ASSESSMENT 2023; 195:393. [PMID: 36780024 PMCID: PMC9923651 DOI: 10.1007/s10661-023-11002-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 02/01/2023] [Indexed: 06/18/2023]
Abstract
Health care institutions generate large volumes of liquid effluents from specific activities related to healthcare, analysis, and research. Their direct discharge into the environment has various negative effects on aquatic environments and human health, due to their high organic matter charges and the presence of various emerging contaminants such as disinfectants, drugs, bacteria, viruses, and parasites. Moreover, hospital effluents, by carrying antibiotics, contribute to the development of antibiotic-resistant microorganisms in the environment. This resistance has become a global issue that manifests itself variously in different countries, causing the transmission of different infections. In this respect, an effort is provided to protect water resources by current treatment methods that imply physical-chemical processes such as adsorption and advanced oxidation processes, biological processes such as activated sludge and membrane bioreactors and other hybrid techniques. The purpose of this review is to improve the knowledge on the composition and impact of hospital wastewater on man and the environment, highlighting the different treatment techniques appropriate to this type of disposal before discharge into the environment.
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Affiliation(s)
- Sayerh Fatimazahra
- Process Engineering and Environment Laboratory, Faculty of Science and Technology of Mohammedia, Hassan II University, Casablanca, Morocco
| | - Mouhir Latifa
- Process Engineering and Environment Laboratory, Faculty of Science and Technology of Mohammedia, Hassan II University, Casablanca, Morocco
| | - Saafadi Laila
- Process Engineering and Environment Laboratory, Faculty of Science and Technology of Mohammedia, Hassan II University, Casablanca, Morocco
| | - Khazraji Monsif
- Process Engineering and Environment Laboratory, Faculty of Science and Technology of Mohammedia, Hassan II University, Casablanca, Morocco
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26
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Bastos MC, Rheinheimer DDS, Le Guet T, Vargas Brunet J, Aubertheau E, Mondamert L, Labanowski J. Presence of pharmaceuticals and bacterial resistance genes in river epilithic biofilms exposed to intense agricultural and urban pressure. ENVIRONMENTAL MONITORING AND ASSESSMENT 2023; 195:328. [PMID: 36697888 DOI: 10.1007/s10661-022-10899-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 12/28/2022] [Indexed: 06/17/2023]
Abstract
The continuous discharge of pharmaceutical compounds into the aquatic environment has raised concerns over the contamination of water resources. Urban activities and intensive animal breeding are important sources of contamination. The accumulation of antibiotics may lead to the transfer or alternatively maintain the presence of resistance genes in natural microbial communities existing in epilithic biofilms. The objective of this study was to evaluate the pharmaceutical contamination levels and the presence of resistance genes in biofilms from a South Brazilian watershed. The Guaporé watershed exhibits a high diversity of land use, including agricultural and urban areas with differing levels of anthropogenic pressure. Seventeen sites along the Guaporé watershed were monitored. Biofilm samples were collected in two seasons (winter and summer), and the pharmaceutical concentration and quantity of resistance genes were analyzed. All monitored sites were contaminated with pharmaceuticals. Agricultural activities contribute through transferring pharmaceuticals derived from the application of animal waste to agricultural fields. The most contaminated site (pharmaceuticals and bacterial resistance genes) was located in an urban area exposed to high pressure. Decreases in the contamination of biofilms were also observed, exemplifying processes of natural attenuation in the watershed. The quality of the biofilms sampled throughout the watershed served as a useful tool to understand and monitor environmental pollution.
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Affiliation(s)
- Marília Camotti Bastos
- Centro de Ciências Rurais, Departamento de Solos, Universidade Federal de Santa Maria, Avenida Roraima, N° 1000, Bairro Camobi, Rio Grande Do Sul, CEP, 97105-900, Brazil.
- Institut de Chimie Des Milieux Et Matériaux de Poitiers, Université de Poitiers, IC2MP, Poitiers, France.
| | - Danilo Dos Santos Rheinheimer
- Centro de Ciências Rurais, Departamento de Solos, Universidade Federal de Santa Maria, Avenida Roraima, N° 1000, Bairro Camobi, Rio Grande Do Sul, CEP, 97105-900, Brazil
| | - Thibaut Le Guet
- Institut de Chimie Des Milieux Et Matériaux de Poitiers, Université de Poitiers, IC2MP, Poitiers, France
| | - Jocelina Vargas Brunet
- Centro de Ciências Rurais, Departamento de Solos, Universidade Federal de Santa Maria, Avenida Roraima, N° 1000, Bairro Camobi, Rio Grande Do Sul, CEP, 97105-900, Brazil
- Institut de Chimie Des Milieux Et Matériaux de Poitiers, Université de Poitiers, IC2MP, Poitiers, France
| | - Elodie Aubertheau
- Institut de Chimie Des Milieux Et Matériaux de Poitiers, Université de Poitiers, IC2MP, Poitiers, France
| | - Leslie Mondamert
- Institut de Chimie Des Milieux Et Matériaux de Poitiers, Université de Poitiers, IC2MP, Poitiers, France
| | - Jérôme Labanowski
- Institut de Chimie Des Milieux Et Matériaux de Poitiers, Université de Poitiers, IC2MP, Poitiers, France
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Leistikow KR, Beattie RE, Hristova KR. Probiotics beyond the farm: Benefits, costs, and considerations of using antibiotic alternatives in livestock. FRONTIERS IN ANTIBIOTICS 2022; 1:1003912. [PMID: 39816405 PMCID: PMC11732145 DOI: 10.3389/frabi.2022.1003912] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 09/22/2022] [Indexed: 01/18/2025]
Abstract
The increasing global expansion of antimicrobial resistant infections warrants the development of effective antibiotic alternative therapies, particularly for use in livestock production, an agricultural sector that is perceived to disproportionately contribute to the antimicrobial resistance (AMR) crisis by consuming nearly two-thirds of the global antibiotic supply. Probiotics and probiotic derived compounds are promising alternative therapies, and their successful use in disease prevention, treatment, and animal performance commands attention. However, insufficient or outdated probiotic screening techniques may unintentionally contribute to this crisis, and few longitudinal studies have been conducted to determine what role probiotics play in AMR dissemination in animal hosts and the surrounding environment. In this review, we briefly summarize the current literature regarding the efficacy, feasibility, and limitations of probiotics, including an evaluation of their impact on the animal microbiome and resistome and their potential to influence AMR in the environment. Probiotic application for livestock is often touted as an ideal alternative therapy that might reduce the need for antibiotic use in agriculture and the negative downstream impacts. However, as detailed in this review, limited research has been conducted linking probiotic usage with reductions in AMR in agricultural or natural environments. Additionally, we discuss the methods, including limitations, of current probiotic screening techniques across the globe, highlighting approaches aimed at reducing antibiotic usage and ensuring safe and effective probiotic mediated health outcomes. Based on this information, we propose economic and logistical considerations for bringing probiotic therapies to market including regulatory roadblocks, future innovations, and the significant gaps in knowledge requiring additional research to ensure probiotics are suitable long-term options for livestock producers as an antibiotic alternative therapy.
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Affiliation(s)
- Kyle R. Leistikow
- Department of Biological Sciences, Marquette University, Milwaukee, WI, United States
| | - Rachelle E. Beattie
- U.S. Geological Survey, Columbia Environmental Research Center, Columbia, MO, United States
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Abraham TJ, Qureshi QA, Bardhan A. Enteric Pathogenic and Multiple Antibiotic-Resistant Escherichia coli in Farmed Indian Major Carps and Their Environments in Peri-Urban Kolkata, India. JOURNAL OF AQUATIC FOOD PRODUCT TECHNOLOGY 2022. [DOI: 10.1080/10498850.2022.2133585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Thangapalam Jawahar Abraham
- Department of Aquatic Animal Health, Faculty of Fishery Sciences, West Bengal University of Animal and Fishery Sciences, Kolkata, India
| | - Qurratul Ain Qureshi
- Department of Aquatic Animal Health, Faculty of Fishery Sciences, West Bengal University of Animal and Fishery Sciences, Kolkata, India
| | - Avishek Bardhan
- Department of Aquatic Animal Health, Faculty of Fishery Sciences, West Bengal University of Animal and Fishery Sciences, Kolkata, India
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Czatzkowska M, Wolak I, Harnisz M, Korzeniewska E. Impact of Anthropogenic Activities on the Dissemination of ARGs in the Environment-A Review. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph191912853. [PMID: 36232152 PMCID: PMC9564893 DOI: 10.3390/ijerph191912853] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 09/28/2022] [Accepted: 10/03/2022] [Indexed: 05/07/2023]
Abstract
Over the past few decades, due to the excessive consumption of drugs in human and veterinary medicine, the antimicrobial resistance (AR) of microorganisms has risen considerably across the world, and this trend is predicted to intensify. Many worrying research results indicate the occurrence of pools of AR, both directly related to human activity and environmental factors. The increase of AR in the natural environment is mainly associated with the anthropogenic activity. The dissemination of AR is significantly stimulated by the operation of municipal facilities, such as wastewater treatment plants (WWTPs) or landfills, as well as biogas plants, agriculture and farming practices, including animal production and land application of manure. These activities entail a risk to public health by spreading bacteria resistant to antimicrobial products (ARB) and antibiotic resistance genes (ARGs). Furthermore, subinhibitory concentrations of antimicrobial substances additionally predispose microbial consortia and resistomes to changes in particular environments that are permeated by these micropollutants. The current state of knowledge on the fate of ARGs, their dissemination and the complexity of the AR phenomenon in relation to anthropogenic activity is inadequate. This review summarizes the state-of-the-art knowledge on AR in the environment, in particular focusing on AR spread in an anthropogenically altered environment and related environmental consequences.
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Shin M, Kang JW, Kang DH. A study on antibiotic resistance gene degradation in fresh produce using peracetic acid combined with an ultraviolet-C light-emitting-diode. Food Control 2022. [DOI: 10.1016/j.foodcont.2022.109478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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The Resistome of ESKAPEE Pathogens in Untreated and Treated Wastewater: A Polish Case Study. Biomolecules 2022; 12:biom12081160. [PMID: 36009054 PMCID: PMC9405806 DOI: 10.3390/biom12081160] [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: 07/07/2022] [Revised: 08/11/2022] [Accepted: 08/19/2022] [Indexed: 11/16/2022] Open
Abstract
The aim of this study was to quantify ESKAPEE bacteria, genes encoding resistance to antibiotics targeting this group of pathogens, as well as integrase genes in municipal wastewater and river water. Environmental DNA was extracted from the collected samples and used in deep sequencing with the Illumina TruSeq kit. The abundance of bacterial genera and species belonging to the ESKAPEE group, 400 ARGs associated with this microbial group, and three classes of integrase genes were determined. A taxonomic analysis revealed that Acinetobacter was the dominant bacterial genus, whereas Acinetobacter baumannii and Escherichia coli were the dominant bacterial species. The analyzed samples were characterized by the highest concentrations of the following ARGs: blaGES, blaOXA-58, blaTEM, qnrB, and qnrS. Acinetobacter baumannii, E. coli, and genes encoding resistance to β-lactams (blaVEB-1, blaIMP-1, blaGES, blaOXA-58, blaCTX-M, and blaTEM) and fluoroquinolones (qnrS) were detected in samples of river water collected downstream from the wastewater discharge point. The correlation analysis revealed a strong relationship between A. baumannii (bacterial species regarded as an emerging human pathogen) and genes encoding resistance to all tested groups of antimicrobials. The transmission of the studied bacteria (in particular A. baumannii) and ARGs to the aquatic environment poses a public health risk.
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Liguori K, Keenum I, Davis BC, Calarco J, Milligan E, Harwood VJ, Pruden A. Antimicrobial Resistance Monitoring of Water Environments: A Framework for Standardized Methods and Quality Control. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:9149-9160. [PMID: 35732277 DOI: 10.1080/10643389.2021.2024739] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Antimicrobial resistance (AMR) is a grand societal challenge with important dimensions in the water environment that contribute to its evolution and spread. Environmental monitoring could provide vital information for mitigating the spread of AMR; this includes assessing antibiotic resistance genes (ARGs) circulating among human populations, identifying key hotspots for evolution and dissemination of resistance, informing epidemiological and human health risk assessment models, and quantifying removal efficiencies by domestic wastewater infrastructure. However, standardized methods for monitoring AMR in the water environment will be vital to producing the comparable data sets needed to address such questions. Here we sought to establish scientific consensus on a framework for such standardization, evaluating the state of the science and practice of AMR monitoring of wastewater, recycled water, and surface water, through a literature review, survey, and workshop leveraging the expertise of academic, governmental, consulting, and water utility professionals.
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Affiliation(s)
- Krista Liguori
- The Charles Edward Via, Jr., Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24060, United States
| | - Ishi Keenum
- The Charles Edward Via, Jr., Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24060, United States
| | - Benjamin C Davis
- The Charles Edward Via, Jr., Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24060, United States
| | - Jeanette Calarco
- Department of Integrative Biology, University of South Florida, Tampa, Florida 33620, United States
| | - Erin Milligan
- The Charles Edward Via, Jr., Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24060, United States
| | - Valerie J Harwood
- Department of Integrative Biology, University of South Florida, Tampa, Florida 33620, United States
| | - Amy Pruden
- The Charles Edward Via, Jr., Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24060, United States
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Liguori K, Keenum I, Davis BC, Calarco J, Milligan E, Harwood VJ, Pruden A. Antimicrobial Resistance Monitoring of Water Environments: A Framework for Standardized Methods and Quality Control. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:9149-9160. [PMID: 35732277 PMCID: PMC9261269 DOI: 10.1021/acs.est.1c08918] [Citation(s) in RCA: 108] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Antimicrobial resistance (AMR) is a grand societal challenge with important dimensions in the water environment that contribute to its evolution and spread. Environmental monitoring could provide vital information for mitigating the spread of AMR; this includes assessing antibiotic resistance genes (ARGs) circulating among human populations, identifying key hotspots for evolution and dissemination of resistance, informing epidemiological and human health risk assessment models, and quantifying removal efficiencies by domestic wastewater infrastructure. However, standardized methods for monitoring AMR in the water environment will be vital to producing the comparable data sets needed to address such questions. Here we sought to establish scientific consensus on a framework for such standardization, evaluating the state of the science and practice of AMR monitoring of wastewater, recycled water, and surface water, through a literature review, survey, and workshop leveraging the expertise of academic, governmental, consulting, and water utility professionals.
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Affiliation(s)
- Krista Liguori
- The
Charles Edward Via, Jr., Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24060, United States
| | - Ishi Keenum
- The
Charles Edward Via, Jr., Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24060, United States
| | - Benjamin C. Davis
- The
Charles Edward Via, Jr., Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24060, United States
| | - Jeanette Calarco
- Department
of Integrative Biology, University of South
Florida, Tampa, Florida 33620, United States
| | - Erin Milligan
- The
Charles Edward Via, Jr., Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24060, United States
| | - Valerie J. Harwood
- Department
of Integrative Biology, University of South
Florida, Tampa, Florida 33620, United States
| | - Amy Pruden
- The
Charles Edward Via, Jr., Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24060, United States
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Mutuku C, Gazdag Z, Melegh S. Occurrence of antibiotics and bacterial resistance genes in wastewater: resistance mechanisms and antimicrobial resistance control approaches. World J Microbiol Biotechnol 2022; 38:152. [PMID: 35781751 PMCID: PMC9250919 DOI: 10.1007/s11274-022-03334-0] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 06/10/2022] [Indexed: 12/14/2022]
Abstract
Antimicrobial pharmaceuticals are classified as emergent micropollutants of concern, implying that even at low concentrations, long-term exposure to the environment can have significant eco-toxicological effects. There is a lack of a standardized regulatory framework governing the permissible antibiotic content for monitoring environmental water quality standards. Therefore, indiscriminate discharge of antimicrobials at potentially active concentrations into urban wastewater treatment facilities is rampant. Antimicrobials may exert selective pressure on bacteria, leading to resistance development and eventual health consequences. The emergence of clinically important multiple antibiotic-resistant bacteria in untreated hospital effluents and wastewater treatment plants (WWTPs) has been linked to the continuous exposure of bacteria to antimicrobials. The levels of environmental exposure to antibiotics and their correlation to the evolution and spread of resistant bacteria need to be elucidated to help in the formulation of mitigation measures. This review explores frequently detected antimicrobials in wastewater and gives a comprehensive coverage of bacterial resistance mechanisms to different antibiotic classes through the expression of a wide variety of antibiotic resistance genes either inherent and/or exchanged among bacteria or acquired from the reservoir of antibiotic resistance genes (ARGs) in wastewater systems. To complement the removal of antibiotics and ARGs from WWTPs, upscaling the implementation of prospective interventions such as vaccines, phage therapy, and natural compounds as alternatives to widespread antibiotic use provides a multifaceted approach to minimize the spread of antimicrobial resistance.
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Affiliation(s)
- Christopher Mutuku
- Department of General and Environmental Microbiology, Faculty of Sciences, University of Pécs, Ifjúság u. 6, Pecs, 7624, Hungary.
| | - Zoltan Gazdag
- Department of General and Environmental Microbiology, Faculty of Sciences, University of Pécs, Ifjúság u. 6, Pecs, 7624, Hungary
| | - Szilvia Melegh
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, 7622, Pecs, Hungary
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Ramalho R, Mezzomo LC, Machado W, da Silva Morais Hein C, Müller CZ, da Silva TCB, Jank L, Lamas AE, da Costa Ballestrin RA, Wink PL, Lima AAD, Corção G, Martins AF. The occurrence of antimicrobial residues and antimicrobial resistance genes in urban drinking water and sewage in Southern Brazil. Braz J Microbiol 2022; 53:1483-1489. [PMID: 35764766 DOI: 10.1007/s42770-022-00786-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 06/18/2022] [Indexed: 11/25/2022] Open
Abstract
Antimicrobial resistance (AMR) is currently discussed as an important issue worldwide, and the presence of antimicrobial residues (ARs) and antimicrobial resistance genes (ARGs) in the environment, especially in the water sources, is a challenge for public health. This study was conducted to evaluate the occurrence and diversity of AR and ARG in water sources from an urban center, in Southern Brazil. A total of thirty-two water samples from drinking water treatment plants (24) and sewage systems (8) were collected during two annual samplings, winter and summer. The PCR was performed by 18 ARGs, and the detection of 47 ARs was performed by LC-MS/MS. All sewage samples presented carbapenemases, ESBL, and mcr-1 genes as well as quinolones and sulfamethoxazole residues. In drinking water, we just detected blaTEM and tetB genes and doxycycline residues in samples before treatment. This study provides data about AR and ARG in drinking water and sewage systems showing that these sources are important reservoirs of both. The limited effectiveness of wastewater treatment processes to remove mainly AR demonstrates the need to implement better protocols of disinfection, in order to limit the spread of AMR in the environment.
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Affiliation(s)
- Rafaela Ramalho
- Programa de Pós-Graduação Em Ciências Farmacêuticas, Universidade Federal Do Rio Grande Do Sul, Porto Alegre, Brazil
| | - Lisiane Cervieri Mezzomo
- Programa de Pós-Graduação Em Ciências Farmacêuticas, Universidade Federal Do Rio Grande Do Sul, Porto Alegre, Brazil
| | - William Machado
- Programa de Pós-Graduação Em Microbiologia Agrícola E Do Ambiente, Universidade Federal Do Rio Grande Do Sul, Porto Alegre, Brazil
| | - Camila da Silva Morais Hein
- Programa de Pós-Graduação Em Microbiologia Agrícola E Do Ambiente, Universidade Federal Do Rio Grande Do Sul, Porto Alegre, Brazil
| | | | | | - Louise Jank
- Laboratório Federal de Defesa Agropecuária - LFDA/RS, Ministério da Agricultura, Pecuária e Abastecimento,, Porto Alegre, Brazil
| | | | | | - Priscila Lamb Wink
- Laboratório de Pesquisa Em Resistência Bacteriana, LABRESIS, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
| | | | - Gertrudes Corção
- Programa de Pós-Graduação Em Microbiologia Agrícola E Do Ambiente, Universidade Federal Do Rio Grande Do Sul, Porto Alegre, Brazil
| | - Andreza Francisco Martins
- Programa de Pós-Graduação Em Ciências Farmacêuticas, Universidade Federal Do Rio Grande Do Sul, Porto Alegre, Brazil.
- Programa de Pós-Graduação Em Microbiologia Agrícola E Do Ambiente, Universidade Federal Do Rio Grande Do Sul, Porto Alegre, Brazil.
- Laboratório de Pesquisa Em Resistência Bacteriana, LABRESIS, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil.
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Prevalence and Molecular Characterisation of Extended-Spectrum Beta-Lactamase-Producing Shiga Toxin-Producing Escherichia coli, from Cattle Farm to Aquatic Environments. Pathogens 2022; 11:pathogens11060674. [PMID: 35745529 PMCID: PMC9230396 DOI: 10.3390/pathogens11060674] [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] [Received: 05/19/2022] [Revised: 06/02/2022] [Accepted: 06/07/2022] [Indexed: 01/23/2023] Open
Abstract
Extended-spectrum beta-lactamase (ESBL)-producing bacteria are a major problem for public health worldwide because of limited treatment options. Currently, only limited information is available on ESBL-producing Shiga toxin-producing Escherichia coli (STEC) in cattle farms and the surrounding aquatic environment. This study sought to track and characterise ESBL-producing STEC disseminating from a cattle farm into the water environment. Animal husbandry soil (HS), animal manure (AM), animal drinking water (ADW), and nearby river water (NRW) samples were collected from the cattle farm. Presumptive ESBL-producing STEC were isolated and identified using chromogenic media and mass spectrophotometry methods (MALDI-TOF-MS), respectively. The isolates were subjected to molecular analysis, and all confirmed ESBL-producing STEC isolates were serotyped for their O serogroups and assessed for antibiotic resistance genes (ARGs) and for the presence of selected virulence factors (VFs). A phylogenetic tree based on the multilocus sequences was constructed to determine the relatedness among isolates of ESBL-producing STEC. The highest prevalence of ESBL-producing STEC of 83.33% was observed in HS, followed by ADW with 75%, NRW with 68.75%, and the lowest was observed in AM with 64.58%. Out of 40 randomly selected isolates, 88% (n = 35) belonged to the serogroup O45 and 13% (n = 5) to the serogroup O145. The multilocus sequence typing (MLST) analysis revealed four different sequence types (STs), namely ST10, ST23, ST165, and ST117, and the predominant ST was found to be ST10. All 40 isolates carried sul1 (100%), while blaOXA, blaCTX-M, sul2, blaTEM, and qnrS genes were found in 98%, 93%, 90%, 83%, and 23% of the 40 isolates, respectively. For VFs, only stx2 was detected in ESBL-producing STEC isolates. The results of the present study indicated that a cattle environment is a potential reservoir of ESBL-producing STEC, which may disseminate into the aquatic environment through agricultural runoff, thus polluting water sources. Therefore, continual surveillance of ESBL-producing STEC non-O157 would be beneficial for controlling and preventing STEC-related illnesses originating from livestock environments.
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Das S, Bombaywala S, Srivastava S, Kapley A, Dhodapkar R, Dafale NA. Genome plasticity as a paradigm of antibiotic resistance spread in ESKAPE pathogens. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:40507-40519. [PMID: 35349073 DOI: 10.1007/s11356-022-19840-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 03/17/2022] [Indexed: 06/14/2023]
Abstract
The major reason behind the spread of antibiotic resistance genes (ARGs) is persistent selective pressure in the environment encountered by bacteria. Genome plasticity plays a crucial role in dissemination of antibiotic resistance among bacterial pathogens. Mobile genetic elements harboring ARGs are reported to dodge bacterial immune system and mediate horizontal gene transfer (HGT) under selective pressure. Residual antibiotic pollutants develop selective pressures that force the bacteria to lose their defense mechanisms (CRISPR-cas) and acquire resistance. The present study targets the ESKAPE organisms (namely, Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter spp.) causing various nosocomial infections and emerging multidrug-resistant species. The role of CRISPR-cas systems in inhibition of HGT in prokaryotes and its loss due to presence of various stressors in the environment is also focused in the study. IncF and IncH plasmids were identified in all strains of E. faecalis and K. pneumoniae, carrying Beta-lactam and fluoroquinolone resistance genes, whereas sal3, phiCTX, and SEN34 prophages harbored aminoglycoside resistance genes (aadA, aac). Various MGEs present in selected environmental niches that aid the bacterial genome plasticity and transfer of ARGs contributing to its spread are also identified.
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Affiliation(s)
- Sanchita Das
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute (CSIR-NEERI), Nehru Marg, Nagpur, 4400 20, India
| | - Sakina Bombaywala
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute (CSIR-NEERI), Nehru Marg, Nagpur, 4400 20, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 2010 20, India
| | - Shweta Srivastava
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute (CSIR-NEERI), Nehru Marg, Nagpur, 4400 20, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 2010 20, India
| | - Atya Kapley
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute (CSIR-NEERI), Nehru Marg, Nagpur, 4400 20, India
| | - Rita Dhodapkar
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute (CSIR-NEERI), Nehru Marg, Nagpur, 4400 20, India
| | - Nishant A Dafale
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute (CSIR-NEERI), Nehru Marg, Nagpur, 4400 20, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 2010 20, India.
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Dead but Not Forgotten: How Extracellular DNA, Moisture, and Space Modulate the Horizontal Transfer of Extracellular Antibiotic Resistance Genes in Soil. Appl Environ Microbiol 2022; 88:e0228021. [PMID: 35323025 DOI: 10.1128/aem.02280-21] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Antibiotic-resistant bacteria and the spread of antibiotic resistance genes (ARGs) pose a serious risk to human and veterinary health. While many studies focus on the movement of live antibiotic-resistant bacteria to the environment, it is unclear whether extracellular ARGs (eARGs) from dead cells can transfer to live bacteria to facilitate the evolution of antibiotic resistance in nature. Here, we use eARGs from dead, antibiotic-resistant Pseudomonas stutzeri cells to track the movement of eARGs to live P. stutzeri cells via natural transformation, a mechanism of horizontal gene transfer involving the genomic integration of eARGs. In sterile, antibiotic-free agricultural soil, we manipulated the eARG concentration, soil moisture, and proximity to eARGs. We found that transformation occurred in soils inoculated with just 0.25 μg of eDNA g-1 soil, indicating that even low concentrations of soil eDNA can facilitate transformation (previous estimates suggested ∼2 to 40 μg eDNA g-1 soil). When eDNA was increased to 5 μg g-1 soil, there was a 5-fold increase in the number of antibiotic-resistant P. stutzeri cells. We found that eARGs were transformed under soil moistures typical of terrestrial systems (5 to 30% gravimetric water content) but inhibited at very high soil moistures (>30%). Overall, this work demonstrates that dead bacteria and their eARGs are an overlooked path to antibiotic resistance. More generally, the spread of eARGs in antibiotic-free soil suggests that transformation allows genetic variants to establish in the absence of antibiotic selection and that the soil environment plays a critical role in regulating transformation. IMPORTANCE Bacterial death can release eARGs into the environment. Agricultural soils can contain upwards of 109 ARGs g-1 soil, which may facilitate the movement of eARGs from dead to live bacteria through a mechanism of horizontal gene transfer called natural transformation. Here, we track the spread of eARGs from dead, antibiotic-resistant Pseudomonas stutzeri cells to live antibiotic-susceptible P. stutzeri cells in sterile agricultural soil. Transformation increased with the abundance of eARGs and occurred in soils ranging from 5 to 40% gravimetric soil moisture but was lowest in wet soils (>30%). Transformants appeared in soil after 24 h and persisted for up to 15 days even when eDNA concentrations were only a fraction of those found in field soils. Overall, our results show that natural transformation allows eARGs to spread and persist in antibiotic-free soils and that the biological activity of eDNA after bacterial death makes environmental eARGs a public health concern.
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Magaña-Lizárraga JA, Gómez-Gil B, Rendón-Maldonado JG, Delgado-Vargas F, Vega-López IF, Báez-Flores ME. Genomic Profiling of Antibiotic-Resistant Escherichia coli Isolates from Surface Water of Agricultural Drainage in North-Western Mexico: Detection of the International High-Risk Lineages ST410 and ST617. Microorganisms 2022; 10:microorganisms10030662. [PMID: 35336237 PMCID: PMC8948617 DOI: 10.3390/microorganisms10030662] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/10/2022] [Accepted: 03/15/2022] [Indexed: 11/16/2022] Open
Abstract
Aquatic environments are recognized as one of the main reservoirs for the emergence and dissemination of high-risk lineages of multidrug-resistant (MDR) bacteria of public health concern. However, the genomic characteristics of antibiotic-resistant Escherichia coli isolates from aquatic origins remain limited. Herein, we examined the antibiotic resistance and virulence genomic profiles of three E. coli recovered from surface water in northwest Mexico. Antimicrobial susceptibility testing, whole-genome sequencing (WGS), and in-depth in silico analysis were performed. Two E. coli exhibited MDR phenotypes. WGS-based typing revealed genetic diversity, and phylogenetic analysis corroborated a notable divergent relationship among the studied E. coli. One E. coli strain, harboring enterotoxigenic and extraintestinal pathogenic-associated virulence genes, was assigned to the ST4 lineage. MDR E. coli, belonging to the international high-risk clones ST410 and ST617, carried genes and mutations conferring resistance to aminoglycosides, β-lactams, quinolones, sulfonamides, tetracyclines, and trimethoprim. This study describes, for the first time, the detection and genomic profiling of high-risk lineages of E. coli ST410 and ST617 from surface water in Mexico. Additionally, our results underscore the role of surface water as a reservoir for critical pathogenic and MDR E. coli clones and the need for the surveillance and monitoring of aquatic environments via WGS from the One Health perspective.
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Affiliation(s)
- José Antonio Magaña-Lizárraga
- Unidad de Investigaciones en Salud Pública “Dra. Kaethe Willms”, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Sinaloa, Ciudad Universitaria, Culiacan 80013, Mexico; (J.A.M.-L.); (J.G.R.-M.); (F.D.-V.)
| | - Bruno Gómez-Gil
- Centro de Investigación en Alimentación y Desarrollo, A. C. (CIAD), Unidad Mazatlán en Acuicultura y Manejo Ambiental, AP.711, Mazatlan 82112, Mexico;
| | - José Guadalupe Rendón-Maldonado
- Unidad de Investigaciones en Salud Pública “Dra. Kaethe Willms”, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Sinaloa, Ciudad Universitaria, Culiacan 80013, Mexico; (J.A.M.-L.); (J.G.R.-M.); (F.D.-V.)
| | - Francisco Delgado-Vargas
- Unidad de Investigaciones en Salud Pública “Dra. Kaethe Willms”, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Sinaloa, Ciudad Universitaria, Culiacan 80013, Mexico; (J.A.M.-L.); (J.G.R.-M.); (F.D.-V.)
| | | | - María Elena Báez-Flores
- Unidad de Investigaciones en Salud Pública “Dra. Kaethe Willms”, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Sinaloa, Ciudad Universitaria, Culiacan 80013, Mexico; (J.A.M.-L.); (J.G.R.-M.); (F.D.-V.)
- Correspondence: ; Tel.: +52-667-752-0460
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40
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Wang L, Chai B. Fate of Antibiotic Resistance Genes and Changes in Bacterial Community With Increasing Breeding Scale of Layer Manure. Front Microbiol 2022; 13:857046. [PMID: 35356511 PMCID: PMC8959713 DOI: 10.3389/fmicb.2022.857046] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 02/22/2022] [Indexed: 11/24/2022] Open
Abstract
The use of antimicrobials in intensive poultry production is becoming increasingly common because of its high throughput of meat and egg products. However, the profile of antibiotic resistance genes (ARGs) and the underlying mechanisms in different breeding scale farms were not fully explored. The study examined the profiles of ARGs in layer manure from three free-range and 12 intensive layer farms with different scales (N500, N5000, N10000, and N20000). A quantitative PCR (qPCR) array was used to quantify ARGs, and microbial community structure was analyzed by 16S rRNA gene sequencing. A total of 48 ARGs, belonging to seven major types, were identified in the layer manure samples, with sul2, tetM-01, and ermB being the predominant ones. The abundance, diversity, and mobility potential of ARGs in layer manure changed significantly with the increasing of the breeding scale. The abundances of total ARGs had significantly positive correlations with mobile genetic elements (MGEs), suggesting the mobility potential of ARGs in layer manure samples. Bacterial abundance did not show significant differences among the five group manure samples. However, bacterial diversity showed an increasing trend along the breeding scale. Pathogenic Bacteroidetes increased in the largest-scale layer manure samples and showed significant positive correlations with most ARGs. Network analysis revealed significant co-occurrence patterns between ARGs and microbial taxa, indicating ARGs had a wide range of bacterial hosts. Proteobacteria and Firmicutes were potential hosts for tetracycline and macrolide-lincosamide-streptogramin B (MLSB) resistant genes. Our results indicated that the expansion of the breeding scale of a farm promotes the abundance, diversity, and mobility potential of ARGs in layer manure.
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Goh SG, Jiang P, Ng C, Le TH, Haller L, Chen H, Charles FR, Chen H, Liu X, He Y, Gin KYH. A new modelling framework for assessing the relative burden of antimicrobial resistance in aquatic environments. JOURNAL OF HAZARDOUS MATERIALS 2022; 424:127621. [PMID: 34763923 DOI: 10.1016/j.jhazmat.2021.127621] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 09/30/2021] [Accepted: 10/25/2021] [Indexed: 06/13/2023]
Abstract
The infections caused by antibiotic resistant bacteria (ARB) can lead to higher medical costs, prolonged hospital stays, and increased mortality compared to bacteria that are susceptible to antibiotics. Challenges exist in quantifying the potential risk/burden associated with antimicrobial resistance (AMR) as there is a lack of dose-response models available for pathogens which are resistant to antibiotics, in addition to the fact that very little is known regarding the health risks posed by antibiotic resistant genes (ARG). In this paper, we proposed a new modelling framework to evaluate the relative burden of AMR in natural aquatic environments. With this framework, an AMR burden score for each sample was calculated based on burden coefficients assigned for each ARB and ARG, as well as weighted burdens for the separate ARBs and ARGs components. The method developed in this study was applied to assess the relative burden of AMR in local aquatic environments with different land uses at different seasons. The collected filed data were used to verify the applicability of the proposed relative burden assessment method. Through the established method, the spatial and temporal hotspots of AMR were identified, which could provide useful information to agencies for better control and management of AMR emergence in natural aquatic environments.
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Affiliation(s)
- Shin Giek Goh
- NUS Environmental Research Institute, National University of Singapore, 117411, Singapore
| | - Peng Jiang
- Department of Industrial Engineering and Engineering Management, Business School, Sichuan University, Chengdu 610064, China; Department of Industrial Engineering & Management, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Charmaine Ng
- NUS Environmental Research Institute, National University of Singapore, 117411, Singapore
| | - Thai-Hoang Le
- NUS Environmental Research Institute, National University of Singapore, 117411, Singapore
| | - Laurence Haller
- NUS Environmental Research Institute, National University of Singapore, 117411, Singapore
| | - Hongjie Chen
- NUS Environmental Research Institute, National University of Singapore, 117411, Singapore
| | | | - Huiting Chen
- NUS Environmental Research Institute, National University of Singapore, 117411, Singapore
| | - Xiao Liu
- Department of Industrial Engineering & Management, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yiliang He
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Karina Yew-Hoong Gin
- NUS Environmental Research Institute, National University of Singapore, 117411, Singapore; Department of Civil & Environmental Engineering, National University of Singapore, 117576, Singapore.
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Saraiva MMS, Silva NMV, Ferreira VA, Moreira Filho ALB, Givisiez PEN, Freitas Neto OC, Berchieri Júnior A, Gebreyes WA, Oliveira CJB. Residual concentrations of antimicrobial growth promoters in poultry litter favour plasmid conjugation among Escherichia coli. Lett Appl Microbiol 2022; 74:831-838. [PMID: 35138674 DOI: 10.1111/lam.13671] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 02/01/2022] [Accepted: 02/04/2022] [Indexed: 11/28/2022]
Abstract
Considering that plasmid conjugation is a major driver for the dissemination of antimicrobial resistance in bacteria, this study aimed to investigate the effects of residual concentrations of antimicrobial growth promoters (AGPs) in poultry litter on the frequencies of IncFII-FIB plasmid conjugation among Escherichia coli organisms. A 2x5 factorial trial was performed in vitro, using two types of litter materials (sugarcane bagasse and wood shavings) and five treatments of litter: non-treated (CON), herbal alkaloid sanguinarine (SANG), and AGPs monensin (MON), lincomycin (LCM), and virginiamycin (VIR). E. coli H2332 and E. coli J62 were used as donor and recipient strains, respectively.The presence of residues of monensin, lincomycin and virginiamycin increased the frequency of plasmid conjugation among E. coli in both types of litter materials. On the contrary, sanguinarine significantly reduced the frequency of conjugation among E. coli in sugarcane bagasse litter. The conjugation frequencies were significantly higher in wood shavings compared to sugarcane bagasse only in the presence of AGPs. Considering that the presence of AGPs in the litter can increase the conjugation of IncFII-FIB plasmids carrying antimicrobial resistance genes, the real impact of this phenomenon on the dissemination of antimicrobial resistant bacteria in the poultry production chain must be investigated.
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Affiliation(s)
- M M S Saraiva
- Department of Animal Science, Center for Agricultural Sciences, Federal University of Paraiba (CCA/UFPB), Areia, PB, Brazil.,Department of Pathology, Theriogenology and One Health, Laboratory of Ornithopathology, São Paulo State University (FCAV/Unesp), Jaboticabal, SP, Brazil
| | - N M V Silva
- Department of Animal Science, Center for Agricultural Sciences, Federal University of Paraiba (CCA/UFPB), Areia, PB, Brazil.,Instituto Federal do Sertão Pernambucano - Campus Petrolina
| | - V A Ferreira
- Department of Pathology, Theriogenology and One Health, Laboratory of Ornithopathology, São Paulo State University (FCAV/Unesp), Jaboticabal, SP, Brazil
| | - A L B Moreira Filho
- Department of Animal Science, Center for Human, Social and Agricultural Sciences, Federal University of Paraiba (CCHSA/UFPB), Bananeiras, PB, Brazil
| | - P E N Givisiez
- Department of Animal Science, Center for Agricultural Sciences, Federal University of Paraiba (CCA/UFPB), Areia, PB, Brazil
| | - O C Freitas Neto
- Department of Preventive Veterinary Medicine, Veterinary School, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - A Berchieri Júnior
- Department of Pathology, Theriogenology and One Health, Laboratory of Ornithopathology, São Paulo State University (FCAV/Unesp), Jaboticabal, SP, Brazil
| | - W A Gebreyes
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, OH, USA.,Global One health initiative (GOHi), The Ohio State University, Columbus, OH, USA
| | - C J B Oliveira
- Department of Animal Science, Center for Agricultural Sciences, Federal University of Paraiba (CCA/UFPB), Areia, PB, Brazil.,Global One health initiative (GOHi), The Ohio State University, Columbus, OH, USA
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O'Malley K, McNamara P, McDonald W. Antibiotic resistance genes in an urban stream before and after a state fair. JOURNAL OF WATER AND HEALTH 2021; 19:885-894. [PMID: 34874897 DOI: 10.2166/wh.2021.151] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The global spread of antibiotic resistance genes (ARGs) concomitant with a decrease in antibiotic effectiveness is a major public health issue. While research has demonstrated the impact of various urban sources, such as wastewater treatment plant (WWTP) effluent, stormwater runoff, and industrial discharge on ARG abundance in receiving waters, the impact of short-term gatherings such as state fairs is not comprehensively understood. The objective of this research was to explore the impact of a 2-week Wisconsin State Fair gathering - over 1.1 million visitors and 7,100 farm animals - on the abundance of the ARG blaTEM, the integrase of the class 1 integron (intI1), a marker for horizontal gene transfer, and the 16S rRNA gene, a marker for total biomass, in an urban stream receiving runoff from the state fair. Stream samples downstream of the state fair were taken before and after the event and quantified via a droplet digital polymerase chain reaction. The absolute abundance of all genes was significantly higher (p<0.05) following the event. This research showcases the prevalence and persistence of ARG contamination in an urban stream before and after a state fair gathering, suggesting that short-term events can be a significant source of ARGs into the environment.
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Affiliation(s)
- Kassidy O'Malley
- Department of Civil, Construction, and Environmental Engineering, Marquette University, Milwaukee, WI 53233, USA E-mail:
| | - Patrick McNamara
- Department of Civil, Construction, and Environmental Engineering, Marquette University, Milwaukee, WI 53233, USA E-mail:
| | - Walter McDonald
- Department of Civil, Construction, and Environmental Engineering, Marquette University, Milwaukee, WI 53233, USA E-mail:
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Jauregi L, Epelde L, González A, Lavín JL, Garbisu C. Reduction of the resistome risk from cow slurry and manure microbiomes to soil and vegetable microbiomes. Environ Microbiol 2021; 23:7643-7660. [PMID: 34792274 DOI: 10.1111/1462-2920.15842] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 11/04/2021] [Indexed: 11/30/2022]
Abstract
In cow farms, the interaction between animal and environmental microbiomes creates hotspots for antibiotic resistance dissemination. A shotgun metagenomic approach was used to survey the resistome risk in five dairy cow farms. To this purpose, 10 environmental compartments were sampled: 3 of them linked to productive cows (fresh slurry, stored slurry, slurry-amended pasture soil); 6 of them to non-productive heifers and dry cows (faeces, fresh manure, aged manure, aged manure-amended orchard soil, vegetables-lettuces and grazed soil); and, finally, unamended control soil. The resistome risk was assessed using MetaCompare, a computational pipeline which scores the resistome risk according to possible links between antibiotic resistance genes (ARGs), mobile genetic elements (MGEs) and human pathogens. The resistome risk decreased from slurry and manure microbiomes to soil and vegetable microbiomes. In total (sum of all the compartments), 18,157 ARGs were detected: 24% related to ansamycins, 21% to multidrugs, 14% to aminoglycosides, 12% to tetracyclines, 9% to β-lactams, and 9% to macrolide-lincosamide-streptogramin B. All but two of the MGE-associated ARGs were only found in the animal dejections (not in soil or vegetable samples). Several ARGs with potential as resistome risk markers (based on their presence in hubs of co-occurrence networks and high dissemination potential) were identified. As a precautionary principle, improved management of livestock dejections is necessary to minimize the risk of antibiotic resistance.
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Affiliation(s)
- Leire Jauregi
- NEIKER, Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Parque Científico y Tecnológico de Bizkaia, P812, E-48160 Derio, Spain
| | - Lur Epelde
- NEIKER, Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Parque Científico y Tecnológico de Bizkaia, P812, E-48160 Derio, Spain
| | - Aitor González
- NEIKER, Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Parque Científico y Tecnológico de Bizkaia, P812, E-48160 Derio, Spain
| | - José Luis Lavín
- NEIKER, Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Parque Científico y Tecnológico de Bizkaia, P812, E-48160 Derio, Spain
| | - Carlos Garbisu
- NEIKER, Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Parque Científico y Tecnológico de Bizkaia, P812, E-48160 Derio, Spain
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Al-Otaibi WA, AlMotwaa SM. Preparation, characterization, optimization, and antibacterial evaluation of nano-emulsion incorporating essential oil extracted from Teucrium polium L. J DISPER SCI TECHNOL 2021. [DOI: 10.1080/01932691.2021.1980000] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Waad A. Al-Otaibi
- Department of Chemistry, College of Science and Humanities, Shaqra University, Shaqra, Saudi Arabia
| | - Sahar M. AlMotwaa
- Department of Chemistry, College of Science and Humanities, Shaqra University, Shaqra, Saudi Arabia
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Bornbusch SL, Drea CM. Antibiotic Resistance Genes in Lemur Gut and Soil Microbiota Along a Gradient of Anthropogenic Disturbance. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.704070] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The overuse of man-made antibiotics has facilitated the global propagation of antibiotic resistance genes in animals, across natural and anthropogenically disturbed environments. Although antibiotic treatment is the most well-studied route by which resistance genes can develop and spread within host-associated microbiota, resistomes also can be acquired or enriched via more indirect routes, such as via transmission between hosts or via contact with antibiotic-contaminated matter within the environment. Relatively little is known about the impacts of anthropogenic disturbance on reservoirs of resistance genes in wildlife and their environments. We therefore tested for (a) antibiotic resistance genes in primate hosts experiencing different severities and types of anthropogenic disturbance (i.e., non-wildlife animal presence, human presence, direct human contact, and antibiotic treatment), and (b) covariation between host-associated and environmental resistomes. We used shotgun metagenomic sequencing of ring-tailed lemur (Lemur catta) gut resistomes and associated soil resistomes sampled from up to 10 sites: seven in the wilderness of Madagascar and three in captivity in Madagascar or the United States. We found that, compared to wild lemurs, captive lemurs harbored greater abundances of resistance genes, but not necessarily more diverse resistomes. Abundances of resistance genes were positively correlated with our assessments of anthropogenic disturbance, a pattern that was robust across all ten lemur populations. The composition of lemur resistomes was site-specific and the types of resistance genes reflected antibiotic usage in the country of origin, such as vancomycin use in Madagascar. We found support for multiple routes of ARG enrichment (e.g., via human contact, antibiotic treatment, and environmental acquisition) that differed across lemur populations, but could result in similar degrees of enrichment. Soil resistomes varied across natural habitats in Madagascar and, at sites with greater anthropogenic disturbance, lemurs and soil resistomes covaried. As one of the broadest, single-species investigations of wildlife resistomes to date, we show that the transmission and enrichment of antibiotic resistance genes varies across environments, thereby adding to the mounting evidence that the resistance crisis extends outside of traditional clinical settings.
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Qureshi KA, Bholay AD, Rai PK, Mohammed HA, Khan RA, Azam F, Jaremko M, Emwas AH, Stefanowicz P, Waliczek M, Kijewska M, Ragab EA, Rehan M, Elhassan GO, Anwar MJ, Prajapati DK. Isolation, characterization, anti-MRSA evaluation, and in-silico multi-target anti-microbial validations of actinomycin X 2 and actinomycin D produced by novel Streptomyces smyrnaeus UKAQ_23. Sci Rep 2021; 11:14539. [PMID: 34267232 PMCID: PMC8282855 DOI: 10.1038/s41598-021-93285-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 06/23/2021] [Indexed: 12/31/2022] Open
Abstract
Streptomyces smyrnaeus UKAQ_23, isolated from the mangrove-sediment, collected from Jubail,Saudi Arabia, exhibited substantial antimicrobial activity against methicillin-resistant Staphylococcus aureus (MRSA), including non-MRSA Gram-positive test bacteria. The novel isolate, under laboratory-scale conditions, produced the highest yield (561.3 ± 0.3 mg/kg fermented agar) of antimicrobial compounds in modified ISP-4 agar at pH 6.5, temperature 35 °C, inoculum 5% v/w, agar 1.5% w/v, and an incubation period of 7 days. The two major compounds, K1 and K2, were isolated from fermented medium and identified as Actinomycin X2 and Actinomycin D, respectively, based on their structural analysis. The antimicrobial screening showed that Actinomycin X2 had the highest antimicrobial activity compared to Actinomycin D, and the actinomycins-mixture (X2:D, 1:1, w/w) against MRSA and non-MRSA Gram-positive test bacteria, at 5 µg/disc concentrations. The MIC of Actinomycin X2 ranged from 1.56-12.5 µg/ml for non-MRSA and 3.125-12.5 µg/ml for MRSA test bacteria. An in-silico molecular docking demonstrated isoleucyl tRNA synthetase as the most-favored antimicrobial protein target for both actinomycins, X2 and D, while the penicillin-binding protein-1a, was the least-favorable target-protein. In conclusion, Streptomyces smyrnaeus UKAQ_23 emerged as a promising source of Actinomycin X2 with the potential to be scaled up for industrial production, which could benefit the pharmaceutical industry.
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Affiliation(s)
- Kamal A Qureshi
- Faculty of Biosciences and Biotechnology, Invertis University, Bareilly, UP, 243123, India.
- Department of Pharmaceutics, Unaizah College of Pharmacy, Qassim University, Unaizah, Qassim, 51911, Saudi Arabia.
| | - Avinash D Bholay
- Department of Microbiology, KTHM College, Savitribai Phule Pune University, Nashik, MS, 422002, India
| | - Pankaj K Rai
- Faculty of Biosciences and Biotechnology, Invertis University, Bareilly, UP, 243123, India
| | - Hamdoon A Mohammed
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, Qassim University, Buraydah, Qassim, 51452, Saudi Arabia
- Department of Pharmacognosy, Faculty of Pharmacy, Al-Azhar University, Cairo, 11371, Egypt
| | - Riaz A Khan
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, Qassim University, Buraydah, Qassim, 51452, Saudi Arabia
| | - Faizul Azam
- Department of Pharmaceutical Chemistry and Pharmacognosy, Unaizah College of Pharmacy, Qassim University, Unaizah, Qassim, 51911, Saudi Arabia
| | - Mariusz Jaremko
- Biological and Environmental Sciences and Engineering Division (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.
| | - Abdul-Hamid Emwas
- Core Labs, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Piotr Stefanowicz
- Faculty of Chemistry, University of Wroclaw, F. Joliot-Curie, Street-14, 50-383, Wroclaw, Poland
| | - Mateusz Waliczek
- Faculty of Chemistry, University of Wroclaw, F. Joliot-Curie, Street-14, 50-383, Wroclaw, Poland
| | - Monika Kijewska
- Faculty of Chemistry, University of Wroclaw, F. Joliot-Curie, Street-14, 50-383, Wroclaw, Poland
| | - Ehab A Ragab
- Department of Pharmacognosy, Faculty of Pharmacy, Al-Azhar University, Cairo, 11371, Egypt
| | - Medhat Rehan
- Department of Genetics, Faculty of Agriculture, Kafr El-Sheikh University, Kafr El-Sheikh, 33516, Egypt
- Department of Plant Production and Protection, College of Agriculture and Veterinary Medicine, Qassim University, Buraydah, Qassim, 51452, Saudi Arabia
| | - Gamal O Elhassan
- Department of Pharmaceutics, Unaizah College of Pharmacy, Qassim University, Unaizah, Qassim, 51911, Saudi Arabia
| | - Md Jamir Anwar
- Department of Pharmacology and Toxicology, Unaizah College of Pharmacy, Qassim University, Unaizah, Qassim, 51911, Saudi Arabia
| | - Dinesh K Prajapati
- Faculty of Biosciences and Biotechnology, Invertis University, Bareilly, UP, 243123, India.
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Hubeny J, Harnisz M, Korzeniewska E, Buta M, Zieliński W, Rolbiecki D, Giebułtowicz J, Nałęcz-Jawecki G, Płaza G. Industrialization as a source of heavy metals and antibiotics which can enhance the antibiotic resistance in wastewater, sewage sludge and river water. PLoS One 2021; 16:e0252691. [PMID: 34086804 PMCID: PMC8177550 DOI: 10.1371/journal.pone.0252691] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 05/19/2021] [Indexed: 11/22/2022] Open
Abstract
The spread of antibiotic resistance is closely related with selective pressure in the environment. Wastewater from industrialized regions is characterized by higher concentrations of these pollutants than sewage from less industrialized areas. The aim of this study was to compare the concentrations of contaminants such as antibiotics and heavy metals (HMs), and to evaluate their impact on the spread of genes encoding resistance to antimicrobial drugs in samples of wastewater, sewage sludge and river water in two regions with different levels of industrialization. The factors exerting selective pressure, which significantly contributed to the occurrence of the examined antibiotic resistance genes (ARGs), were identified. The concentrations of selected gene copy numbers conferring resistance to four groups of antibiotics as well as class 1 and 2 integron-integrase genes were determined in the analyzed samples. The concentrations of six HMs and antibiotics corresponding to genes mediated resistance from 3 classes were determined. Based on network analysis, only some of the analyzed antibiotics correlated with ARGs, while HM levels were correlated with ARG concentrations, which can confirm the important role of HMs in promoting drug resistance. The samples from a wastewater treatment plant (WWTP) located an industrialized region were characterized by higher HM contamination and a higher number of significant correlations between the analyzed variables than the samples collected from a WWTP located in a less industrialized region. These results indicated that treated wastewater released into the natural environment can pose a continuous threat to human health by transferring ARGs, antibiotics and HMs to the environment. These findings shed light on the impact of industrialization on antibiotic resistance dissemination.
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Affiliation(s)
- Jakub Hubeny
- Department of Water Protection Engineering and Environmental Microbiology, Faculty of Geoengineering, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Monika Harnisz
- Department of Water Protection Engineering and Environmental Microbiology, Faculty of Geoengineering, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
- * E-mail: ,
| | - Ewa Korzeniewska
- Department of Water Protection Engineering and Environmental Microbiology, Faculty of Geoengineering, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Martyna Buta
- Department of Water Protection Engineering and Environmental Microbiology, Faculty of Geoengineering, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Wiktor Zieliński
- Department of Water Protection Engineering and Environmental Microbiology, Faculty of Geoengineering, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Damian Rolbiecki
- Department of Water Protection Engineering and Environmental Microbiology, Faculty of Geoengineering, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Joanna Giebułtowicz
- Department of Bioanalysis and Drug Analysis, Faculty of Pharmacy, Medical University of Warsaw, Warszawa, Poland
| | - Grzegorz Nałęcz-Jawecki
- Department of Environmental Health Sciences, Faculty of Pharmacy, Medical University of Warsaw, Warszawa, Poland
| | - Grażyna Płaza
- Faculty of Organization and Management, Silesian University of Technology, Zabrze, Poland
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Kim M, Park J, Kang M, Yang J, Park W. Gain and loss of antibiotic resistant genes in multidrug resistant bacteria: One Health perspective. J Microbiol 2021; 59:535-545. [PMID: 33877574 DOI: 10.1007/s12275-021-1085-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 02/26/2021] [Accepted: 03/02/2021] [Indexed: 12/17/2022]
Abstract
The emergence of multidrug resistance (MDR) has become a global health threat due to the increasing unnecessary use of antibiotics. Multidrug resistant bacteria occur mainly by accumulating resistance genes on mobile genetic elements (MGEs), made possible by horizontal gene transfer (HGT). Humans and animal guts along with natural and engineered environments such as wastewater treatment plants and manured soils have proven to be the major reservoirs and hotspots of spreading antibiotic resistance genes (ARGs). As those environments support the dissemination of MGEs through the complex interactions that take place at the human-animal-environment interfaces, a growing One Health challenge is for multiple sectors to communicate and work together to prevent the emergence and spread of MDR bacteria. However, maintenance of ARGs in a bacterial chromosome and/or plasmids in the environments might place energy burdens on bacterial fitness in the absence of antibiotics, and those unnecessary ARGs could eventually be lost. This review highlights and summarizes the current investigations into the gain and loss of ARG genes in MDR bacteria among human-animal-environment interfaces. We also suggest alternative treatments such as combinatory therapies or sequential use of different classes of antibiotics/adjuvants, treatment with enzyme-inhibitors, and phage therapy with antibiotics to solve the MDR problem from the perspective of One Health issues.
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Affiliation(s)
- Misung Kim
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Jaeeun Park
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Mingyeong Kang
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Jihye Yang
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Woojun Park
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, 02841, Republic of Korea.
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van den Honert MS, Gouws PA, Hoffman LC. Escherichia coli Antibiotic Resistance Patterns from Co-Grazing and Non-Co-Grazing Livestock and Wildlife Species from Two Farms in the Western Cape, South Africa. Antibiotics (Basel) 2021; 10:antibiotics10060618. [PMID: 34067232 PMCID: PMC8224584 DOI: 10.3390/antibiotics10060618] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 05/14/2021] [Accepted: 05/17/2021] [Indexed: 01/22/2023] Open
Abstract
Although limited, studies have found conflicting results on whether co-grazing results in significant antibiotic resistance transfer between species. This type of farming system can act as a vector in the geographical spread of antibiotic-resistant bacteria in the environment. The aim of this study was to determine the antibiotic-resistant patterns between co-grazing and non-co-grazing livestock and wildlife species in South Africa. Escherichia coli was isolated from the faeces of various wildlife and livestock species from two farms in South Africa and was tested for antibiotic resistance using the Kirby–Bauer disk diffusion method against chloramphenicol, nalidixic acid, ampicillin, streptomycin, sulphafurazole, and tetracycline. A selection of some common antibiotic-resistant genes (blaCMY, aadA1, sul1, sul2, tetA, and tetB) were detected using PCR. The E. coli isolates from wildlife and livestock that co-grazed showed no significant differences in antibiotic resistance patterns. However, this was not the case for tetracycline resistance as the livestock isolates were significantly more resistant than the co-grazing wildlife isolates. The E. coli isolates from the non-co-grazing livestock and wildlife had significant differences in their antibiotic susceptibility patterns; the wildlife E. coli isolates were significantly more resistant to sulphafurazole and streptomycin than the livestock isolates, whilst those isolated from the cattle were significantly more resistant to ampicillin than the wildlife and sheep isolates. The results of this study suggest that there could be an exchange of antibiotic-resistant bacteria and genes between livestock and wildlife that co-graze.
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Affiliation(s)
- Michaela Sannettha van den Honert
- Centre for Food Safety, Department of Food Science, University of Stellenbosch, Private Bag X1, Matieland 7602, South Africa;
- Department of Animal Sciences, University of Stellenbosch, Private Bag X1, Matieland 7602, South Africa;
| | - Pieter Andries Gouws
- Centre for Food Safety, Department of Food Science, University of Stellenbosch, Private Bag X1, Matieland 7602, South Africa;
- Correspondence:
| | - Louwrens Christiaan Hoffman
- Department of Animal Sciences, University of Stellenbosch, Private Bag X1, Matieland 7602, South Africa;
- Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Digital Agricultural Building, 8115, Office 110, Gatton 4343, Australia
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