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Rzymski P, Gwenzi W, Poniedziałek B, Mangul S, Fal A. Climate warming, environmental degradation and pollution as drivers of antibiotic resistance. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 346:123649. [PMID: 38402936 DOI: 10.1016/j.envpol.2024.123649] [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: 10/17/2023] [Revised: 02/17/2024] [Accepted: 02/22/2024] [Indexed: 02/27/2024]
Abstract
Antibiotic resistance is a major challenge to public health, but human-caused environmental changes have not been widely recognized as its drivers. Here, we provide a comprehensive overview of the relationships between environmental degradation and antibiotic resistance, demonstrating that the former can potentially fuel the latter with significant public health outcomes. We describe that (i) global warming favors horizontal gene transfer, bacterial infections, the spread of drug-resistant pathogens due to water scarcity, and the release of resistance genes with wastewater; (ii) pesticide and metal pollution act as co-selectors of antibiotic resistance mechanisms; (iii) microplastics create conditions promoting and spreading antibiotic resistance and resistant bacteria; (iv) changes in land use, deforestation, and environmental pollution reduce microbial diversity, a natural barrier to antibiotic resistance spread. We argue that management of antibiotic resistance must integrate environmental goals, including mitigation of further increases in the Earth's surface temperature, better qualitative and quantitative protection of water resources, strengthening of sewage infrastructure and improving wastewater treatment, counteracting the microbial diversity loss, reduction of pesticide and metal emissions, and plastic use, and improving waste recycling. These actions should be accompanied by restricting antibiotic use only to clinically justified situations, developing novel treatments, and promoting prophylaxis. It is pivotal for health authorities and the medical community to adopt the protection of environmental quality as a part of public health measures, also in the context of antibiotic resistance management.
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Affiliation(s)
- Piotr Rzymski
- Department of Environmental Medicine, Poznan University of Medical Sciences, Poznań, Poland.
| | - Willis Gwenzi
- Biosystems and Environmental Engineering Research Group, 380 New Adylin, Marlborough, Harare, Zimbabwe; Alexander von Humboldt Fellow and Guest Professor, Grassland Science and Renewable Plant Resources, Faculty of Organic Agricultural Sciences, Universität Kassel, Witzenhausen, Germany; Alexander von Humboldt Fellow and Guest Professor, Leibniz Institute for Agricultural Engineering and Bioeconomy, Potsdam, Germany
| | - Barbara Poniedziałek
- Department of Environmental Medicine, Poznan University of Medical Sciences, Poznań, Poland
| | - Serghei Mangul
- Titus Family Department of Clinical Pharmacy, USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, USA
| | - Andrzej Fal
- Department of Allergy, Lung Diseases and Internal Medicine Central Clinical Hospital, Ministry of Interior, Warsaw, Poland; Collegium Medicum, Warsaw Faculty of Medicine, Cardinal Stefan Wyszyński University, Warsaw, Poland
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Mao Y, Zeineldin M, Usmani M, Jutla A, Shisler JL, Whitaker RJ, Nguyen TH. Local and Environmental Reservoirs of Salmonella enterica After Hurricane Florence Flooding. GEOHEALTH 2023; 7:e2023GH000877. [PMID: 37928215 PMCID: PMC10624599 DOI: 10.1029/2023gh000877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 08/28/2023] [Accepted: 10/13/2023] [Indexed: 11/07/2023]
Abstract
In many regions of the world, including the United States, human and animal fecal genetic markers have been found in flood waters. In this study, we use high-resolution whole genomic sequencing to examine the origin and distribution of Salmonella enterica after the 2018 Hurricane Florence flooding. We specifically asked whether S. enterica isolated from water samples collected near swine farms in North Carolina shortly after Hurricane Florence had evidence of swine origin. To investigate this, we isolated and fully sequenced 18 independent S. enterica strains from 10 locations (five flooded and five unflooded). We found that all strains have extremely similar chromosomes with only five single nucleotide polymorphisms (SNPs) and possessed two plasmids assigned bioinformatically to the incompatibility groups IncFIB and IncFII. The chromosomal core genome and the IncFIB plasmid are most closely related to environmental Salmonella strains isolated previously from the southeastern US. In contrast, the IncFII plasmid was found in environmental S. enterica strains whose genomes were more divergent, suggesting the IncFII plasmid is more promiscuous than the IncFIB type. We identified 65 antibiotic resistance genes (ARGs) in each of our 18 S. enterica isolates. All ARGs were located on the Salmonella chromosome, similar to other previously characterized environmental isolates. All isolates with different SNPs were resistant to a panel of commonly used antibiotics. These results highlight the importance of environmental sources of antibiotic-resistant S. enterica after extreme flood events.
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Affiliation(s)
- Yuqing Mao
- Department of Civil and Environmental EngineeringUniversity of Illinois at Urbana‐ChampaignILUrbanaUSA
- Carl R. Woese Institute for Genomic BiologyUniversity of Illinois at Urbana‐ChampaignILUrbanaUSA
| | - Mohamed Zeineldin
- Carl R. Woese Institute for Genomic BiologyUniversity of Illinois at Urbana‐ChampaignILUrbanaUSA
| | - Moiz Usmani
- Engineering School of Sustainable Infrastructure & EnvironmentUniversity of FloridaFLGainesvilleUSA
| | - Antarpreet Jutla
- Engineering School of Sustainable Infrastructure & EnvironmentUniversity of FloridaFLGainesvilleUSA
| | - Joanna L. Shisler
- Carl R. Woese Institute for Genomic BiologyUniversity of Illinois at Urbana‐ChampaignILUrbanaUSA
- Department of MicrobiologyUniversity of Illinois at Urbana‐ChampaignILUrbanaUSA
| | - Rachel J. Whitaker
- Carl R. Woese Institute for Genomic BiologyUniversity of Illinois at Urbana‐ChampaignILUrbanaUSA
- Department of MicrobiologyUniversity of Illinois at Urbana‐ChampaignILUrbanaUSA
| | - Thanh H. Nguyen
- Department of Civil and Environmental EngineeringUniversity of Illinois at Urbana‐ChampaignILUrbanaUSA
- Carl R. Woese Institute for Genomic BiologyUniversity of Illinois at Urbana‐ChampaignILUrbanaUSA
- Carle Illinois College of Medicine, University of Illinois at Urbana‐ChampaignUrbanaILUSA
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Zhang Y, Kitazumi A, Liao YT, de los Reyes BG, Wu VCH. Metagenomic investigation reveals bacteriophage-mediated horizontal transfer of antibiotic resistance genes in microbial communities of an organic agricultural ecosystem. Microbiol Spectr 2023; 11:e0022623. [PMID: 37754684 PMCID: PMC10581182 DOI: 10.1128/spectrum.00226-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 07/10/2023] [Indexed: 09/28/2023] Open
Abstract
Agricultural microbiomes are major reservoirs of antibiotic resistance genes (ARGs), posing continuous risks to human health. To understand the role of bacteriophages as vehicles for the horizontal transfer of ARGs in the agricultural microbiome, we investigated the diversity of bacterial and viral microbiota from fecal and environmental samples on an organic farm. The profiles of the microbiome indicated the highest abundance of Bacteroidetes, Firmicutes, and Proteobacteria phyla in animal feces, with varying Actinobacteria and Spirochaetes abundance across farm animals. The most predominant composition in environmental samples was the phylum Proteobacteria. Compared to the microbiome profiles, the trends in virome indicated much broader diversity with more specific signatures between the fecal and environmental samples. Overall, viruses belonging to the order Caudovirales were the most prevalent across the agricultural samples. Additionally, the similarities within and between fecal and environmental components of the agricultural environment based on ARG-associated bacteria alone were much lower than those of total microbiome composition. However, there were significant similarities in the profiles of ARG-associated viruses across the fecal and environmental components. Moreover, the predictive models of phage-bacterial interactions on bipartite ARG transfer networks indicated that phages belonging to the order Caudovirales, particularly in the Siphoviridae family, contained diverse ARG types in different samples. Their interaction with various bacterial hosts further implied the important role of bacteriophages in ARG transmission across bacterial populations. Our findings provided a novel insight into the potential mechanisms of phage-mediated ARG transmission and their correlation with resistome evolution in natural agricultural environments. IMPORTANCE Antibiotic resistance has become a serious health concern worldwide. The potential impact of viruses, bacteriophages in particular, on spreading antibiotic resistance genes is still controversial due to the complexity of bacteriophage-bacterial interactions within diverse environments. In this study, we determined the microbiome profiles and the potential antibiotic resistance gene (ARG) transfer between bacterial and viral populations in different agricultural samples using a high-resolution analysis of the metagenomes. The results of this study provide compelling genetic evidence for ARG transfer through bacteriophage-bacteria interactions, revealing the inherent risks associated with bacteriophage-mediated ARG transfer across the agricultural microbiome.
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Affiliation(s)
- Yujie Zhang
- U.S. Department of Agriculture, Produce Safety and Microbiology Research Unit, Agricultural Research Service, Western Regional Research Center, Albany, California, USA
| | - Ai Kitazumi
- Department of Plant and Soil Science, Texas Tech University, Lubbock, Texas, USA
| | - Yen-Te Liao
- U.S. Department of Agriculture, Produce Safety and Microbiology Research Unit, Agricultural Research Service, Western Regional Research Center, Albany, California, USA
| | | | - Vivian C. H. Wu
- U.S. Department of Agriculture, Produce Safety and Microbiology Research Unit, Agricultural Research Service, Western Regional Research Center, Albany, California, USA
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Uprety S, Sherchan SP, Narayanan P, Dangol B, Maggos M, Celmer A, Shisler J, Amarasiri M, Sano D, Nguyen TH. Microbial assessment of water, sanitation, and hygiene (WaSH) in temporary and permanent settlements two years after Nepal 2015 earthquake. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 877:162867. [PMID: 36931512 DOI: 10.1016/j.scitotenv.2023.162867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 03/10/2023] [Accepted: 03/10/2023] [Indexed: 05/06/2023]
Abstract
Disaster-induced displacement often causes people to live in temporary settlements that have limited infrastructure and access to water, sanitation, and hygiene (WaSH). Reducing the risk of diarrheal diseases in such situations requires knowing how housing influences the presence of pathogens in water and the interaction between human settlements and exposure to pathogens. A cross-sectional study was conducted in May 2017 in two communities hard-hit by the Nepal 2015 earthquake: one recovered with newly reconstructed houses, and one recovered with residents still living in sheet metal temporary shelters constructed after the earthquake. We collected 60 water (30 drinking water and 30 cleaning water), 30 hand rinse, and 90 environmental swab samples (30 toilet handles, 30 utensils, and 30 water vessels) from selected households in each location and quantified 22 bacterial pathogens using microfluidic quantitative polymerase chain reaction (mfqPCR). A total of 59 samples were randomly selected for amplicon-based sequencing of the 16S rRNA, and it identified bacterial community profiles between these two settlements and their association with target genes of pathogenic bacteria. Target genes like uidA of Escherichia coli and the mip gene of Legionella pnuemophila showed significantly high frequency in specific sample types in temporary settlements than in permanent settlements. A significantly high concentration was observed in temporary settlements for Enterococcus spp. and S. typhimurium, specifically in swab samples. There was a sharp distinction of microbial community profiles between water and hand rinse samples with environmental swab samples, with a large abundance of potentially pathogenic bacteria in swab samples in both settlements. This observation highlighted that fomite could be an important transmission route for pathogens in rural settings and designing key interventions to target different stages of transmission pathways is essential. Overall findings from this study suggest that the recovered settlement with higher quality housing may be less impacted by fecal contamination than recovering settlements and that interventions should be designed to disrupt multiple transmission pathways to reduce pathogen exposure.
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Affiliation(s)
- Sital Uprety
- Department of Civil and Environmental Engineering, University of Illinois at Urbana Champaign, Urbana, IL, USA; Department of Sanitation, Water and Solid Waste for Development (Sandec), Swiss Federal Institute of Aquatic Science and Technology (Eawag), Dübendorf, Zurich, Switzerland; Department of Civil and Environmental Engineering, Tohoku University, Sendai, Japan.
| | - Samendra P Sherchan
- Department of Environmental Health Sciences, School of Public Health and Tropical Medicine, New Orleans, LA, USA; Department of Biology, Morgan State University, Baltimore, MD, USA
| | - Preeti Narayanan
- Department of Chemistry, University of Illinois at Urbana Champaign, Urbana, IL, USA
| | - Bipin Dangol
- Environment and Public Health Organization (ENPHO), Kathmandu, Nepal
| | - Marika Maggos
- Department of Microbiology, University of Illinois at Urbana Champaign, Urbana, IL, USA
| | - Alex Celmer
- Department of Microbiology, University of Illinois at Urbana Champaign, Urbana, IL, USA
| | - Joanna Shisler
- Department of Microbiology, University of Illinois at Urbana Champaign, Urbana, IL, USA; Institute of Genomic Biology, University of Illinois at Urbana Champaign, Urbana, IL, USA
| | - Mohan Amarasiri
- Department of Health Science, School of Allied Health Sciences, Kitasato University, Sagamihara, Japan
| | - Daisuke Sano
- Department of Civil and Environmental Engineering, Tohoku University, Sendai, Japan
| | - Thanh H Nguyen
- Department of Civil and Environmental Engineering, University of Illinois at Urbana Champaign, Urbana, IL, USA; Institute of Genomic Biology, University of Illinois at Urbana Champaign, Urbana, IL, USA
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Mao Y, Akdeniz N, Nguyen TH. Quantification of pathogens and antibiotic resistance genes in backyard and commercial composts. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 797:149197. [PMID: 34311369 DOI: 10.1016/j.scitotenv.2021.149197] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 07/09/2021] [Accepted: 07/18/2021] [Indexed: 06/13/2023]
Abstract
Compost is widely used for gardening. Growers can choose to buy compost from markets or make compost at home. Potential exposure of users to pathogens through composting includes ingesting foodborne pathogens and inhaling airborne pathogens. This study compared the abundances of the genetic markers of five opportunistic foodborne and airborne pathogens in the backyard and commercial composts, as well as an immature swine mortality compost. We found that ttrC of Salmonella enterica and ftsZ of Escherichia coli were absent from all ready-to-use compost samples. In contrast, the genes of airborne pathogens such as groEL2 of Mycobacterium spp., mip of Legionella pneumophila, and gyrB of Pseudomonas aeruginosa were detected in the backyard and commercial composts. The groEL2 gene of Mycobacterium spp. was detected in all samples, including the control soil. The abundance of gyrB of P. aeruginosa was high in the two backyard composts, and it was higher than those in any other compost samples. The relative abundances of ARGs were significantly lower in backyard composts than commercial composts. We found that ftsZ of E. coli co-existed with multiple single-drug resistant ARGs in the immature swine mortality compost. We also found that mip of L. pneumophila and gyrB of P. aeruginosa co-existed with aminoglycoside resistance genes. Our findings suggest that inhaling airborne pathogens may carry more risk than ingesting foodborne pathogens when applying composts.
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Affiliation(s)
- Yuqing Mao
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, IL 61801, USA
| | - Neslihan Akdeniz
- Department of Agricultural and Biological Engineering, University of Illinois at Urbana-Champaign, IL 61801, USA
| | - Thanh H Nguyen
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, IL 61801, USA; Institute for Genomic Biology, University of Illinois at Urbana-Champaign, IL 61801, USA.
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Buddhasiri S, Sukjoi C, Kaewsakhorn T, Nambunmee K, Nakphaichit M, Nitisinprasert S, Thiennimitr P. Anti-inflammatory Effect of Probiotic Limosilactobacillus reuteri KUB-AC5 Against Salmonella Infection in a Mouse Colitis Model. Front Microbiol 2021; 12:716761. [PMID: 34497597 PMCID: PMC8419263 DOI: 10.3389/fmicb.2021.716761] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Accepted: 08/04/2021] [Indexed: 01/31/2023] Open
Abstract
Acute non-typhoidal salmonellosis (NTS) caused by Salmonella enterica Typhimurium (STM) is among the most prevalent of foodborne diseases. A global rising of antibiotic resistance strains of STM raises an urgent need for alternative methods to control this important pathogen. Major human food animals which harbor STM in their gut are cattle, swine, and poultry. Previous studies showed that the probiotic Limosilactobacillus (Lactobacillus) reuteri KUB-AC5 (AC5) exhibited anti-Salmonella activities in chicken by modulating gut microbiota and the immune response. However, the immunobiotic effect of AC5 in a mammalian host is still not known. Here, we investigated the anti-Salmonella and anti-inflammatory effects of AC5 on STM infection using a mouse colitis model. Three groups of C57BL/6 mice (prophylactic, therapeutic, and combined) were fed with 109 colony-forming units (cfu) AC5 daily for 7, 4, and 11 days, respectively. Then, the mice were challenged with STM compared to the untreated group. By using a specific primer pair, we found that AC5 can transiently colonize mouse gut (colon, cecum, and ileum). Interestingly, AC5 reduced STM gut proliferation and invasion together with attenuated gut inflammation and systemic dissemination in mice. The decreased STM numbers in mouse gut lumen, gut tissues, and spleen possibly came from longer AC5 feeding duration and/or the combinatorial (direct and indirect inhibitory) effect of AC5 on STM. However, AC5 attenuated inflammation (both in the gut and in the spleen) with no difference between these three approaches. This study demonstrated that AC5 confers both direct and indirect inhibitory effects on STM in the inflamed gut.
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Affiliation(s)
- Songphon Buddhasiri
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Chutikarn Sukjoi
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Thattawan Kaewsakhorn
- Department of Veterinary Biosciences and Veterinary Public Health, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Kowit Nambunmee
- Major of Occupational Health and Safety, School of Health Science, Mae Fah Luang University, Chiang Rai, Thailand.,Urban Safety Innovation Research Group, Mae Fah Luang University, Chiang Rai, Thailand
| | - Massalin Nakphaichit
- Department of Biotechnology, Faculty of Agro-Industry, Kasetsart University, Bangkok, Thailand
| | - Sunee Nitisinprasert
- Department of Biotechnology, Faculty of Agro-Industry, Kasetsart University, Bangkok, Thailand
| | - Parameth Thiennimitr
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand.,Research Center of Microbial Diversity and Sustainable Utilization, Chiang Mai University, Chiang Mai, Thailand.,Faculty of Medicine, Center of Multidisciplinary Technology for Advanced Medicine, Chiang Mai University, Chiang Mai, Thailand
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