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Huang Z, Li Y, Yu K, Ma L, Pang B, Qin Q, Li J, Wang D, Gao H, Kan B. Genome-wide expanding of genetic evolution and potential pathogenicity in Vibrio alginolyticus. Emerg Microbes Infect 2024; 13:2350164. [PMID: 38687697 PMCID: PMC11132748 DOI: 10.1080/22221751.2024.2350164] [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: 01/18/2024] [Accepted: 04/26/2024] [Indexed: 05/02/2024]
Abstract
Vibrio alginolyticus, an emergent species of Vibrio genus, exists in aquatic and marine environments. It has undergone genetic diversification, but its detailed genomic diversity is still unclear. Here, we performed a multi-dimensional comparative genomic analysis to explore the population phylogeny, virulence-related genes and potential drug resistance genes of 184 V. alginolyticus isolates. Although genetic diversity is complex, we analysed the population structure using three sub-datasets, including the subdivision for three lineages into sublineages and the distribution of strains in the marine ecological niche. Accessory genes, most of which reclassified V. alginolyticus genomes as different but with relatively close affinities, were nonuniformly distributed among these isolates. We demonstrated that the spread of some post-evolutionary isolates (mainly L3 strains isolated from Chinese territorial seas) was likely to be closely related to human activities, whereas other more ancestral strains (strains in the L1 and L2) tended to be locally endemic and formed clonal complex groups. In terms of pathogenicity, the potential virulence factors were mainly associated with toxin, adherence, motility, chemotaxis, and the type III secretion system (T3SS). We also found five types of antibacterial drug resistance genes. The prevalence of β-lactam resistance genes was 100%, which indicated that there may be a potential risk of natural resistance to β-lactam drugs. Our study reveals insights into genomic characteristics, evolution and potential virulence-associated gene profiles of V. alginolyticus.
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Affiliation(s)
- Zhenzhou Huang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
- Hangzhou Center for Disease Control and Prevention, Zhejiang, People’s Republic of China
| | - Yanjun Li
- The Sixth Medical Center of PLA General Hospital, Beijing, People’s Republic of China
| | - Keyi Yu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Lizhi Ma
- The Third Medical Center, Chinese PLA (People’s Liberation Army) General Hospital, Beijing, People’s Republic of China
| | - Bo Pang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Qin Qin
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Jie Li
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Duochun Wang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - He Gao
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Biao Kan
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
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Vuruputoor VS, Starovoitov A, Cai Y, Liu Y, Rahmatpour N, Hedderson TA, Wilding N, Wegrzyn JL, Goffinet B. Crossroads of assembling a moss genome: navigating contaminants and horizontal gene transfer in the moss Physcomitrellopsis africana. G3 (BETHESDA, MD.) 2024; 14:jkae104. [PMID: 38781445 PMCID: PMC11228847 DOI: 10.1093/g3journal/jkae104] [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: 03/18/2024] [Revised: 05/03/2024] [Accepted: 05/09/2024] [Indexed: 05/25/2024]
Abstract
The first chromosome-scale reference genome of the rare narrow-endemic African moss Physcomitrellopsis africana (P. africana) is presented here. Assembled from 73 × Oxford Nanopore Technologies (ONT) long reads and 163 × Beijing Genomics Institute (BGI)-seq short reads, the 414 Mb reference comprises 26 chromosomes and 22,925 protein-coding genes [Benchmarking Universal Single-Copy Ortholog (BUSCO) scores: C:94.8% (D:13.9%)]. This genome holds 2 genes that withstood rigorous filtration of microbial contaminants, have no homolog in other land plants, and are thus interpreted as resulting from 2 unique horizontal gene transfers (HGTs) from microbes. Further, P. africana shares 176 of the 273 published HGT candidates identified in Physcomitrium patens (P. patens), but lacks 98 of these, highlighting that perhaps as many as 91 genes were acquired in P. patens in the last 40 million years following its divergence from its common ancestor with P. africana. These observations suggest rather continuous gene gains via HGT followed by potential losses during the diversification of the Funariaceae. Our findings showcase both dynamic flux in plant HGTs over evolutionarily "short" timescales, alongside enduring impacts of successful integrations, like those still functionally maintained in extant P. africana. Furthermore, this study describes the informatic processes employed to distinguish contaminants from candidate HGT events.
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Affiliation(s)
- Vidya S Vuruputoor
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Andrew Starovoitov
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Yuqing Cai
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake 518004, China
| | - Yang Liu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake 518004, China
| | - Nasim Rahmatpour
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Terry A Hedderson
- Department of Biological Sciences, Bolus Herbarium, University of Cape Town, Private Bag, 7701 Rondebosch, South Africa
| | - Nicholas Wilding
- UMR PVBMT, BP 7151, Université de La Réunion, chemin de l’IRAT, 97410 Saint-Pierre, La Réunion, France
- Missouri Botanical Garden, P.O. Box 299, St. Louis, MO 63166-0299, USA
| | - Jill L Wegrzyn
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
- Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA
| | - Bernard Goffinet
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
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Babajanyan SG, Garushyants SK, Wolf YI, Koonin EV. Microbial diversity and ecological complexity emerging from environmental variation and horizontal gene transfer in a simple mathematical model. BMC Biol 2024; 22:148. [PMID: 38965531 PMCID: PMC11225191 DOI: 10.1186/s12915-024-01937-7] [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: 01/17/2024] [Accepted: 06/13/2024] [Indexed: 07/06/2024] Open
Abstract
BACKGROUND Microbiomes are generally characterized by high diversity of coexisting microbial species and strains, and microbiome composition typically remains stable across a broad range of conditions. However, under fixed conditions, microbial ecology conforms with the exclusion principle under which two populations competing for the same resource within the same niche cannot coexist because the less fit population inevitably goes extinct. Therefore, the long-term persistence of microbiome diversity calls for an explanation. RESULTS To explore the conditions for stabilization of microbial diversity, we developed a simple mathematical model consisting of two competing populations that could exchange a single gene allele via horizontal gene transfer (HGT). We found that, although in a fixed environment, with unbiased HGT, the system obeyed the exclusion principle, in an oscillating environment, within large regions of the phase space bounded by the rates of reproduction and HGT, the two populations coexist. Moreover, depending on the parameter combination, all three major types of symbiosis were obtained, namely, pure competition, host-parasite relationship, and mutualism. In each of these regimes, certain parameter combinations provided for synergy, that is, a greater total abundance of both populations compared to the abundance of the winning population in the fixed environment. CONCLUSIONS The results of this modeling study show that basic phenomena that are universal in microbial communities, namely, environmental variation and HGT, provide for stabilization and persistence of microbial diversity, and emergence of ecological complexity.
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Affiliation(s)
- Sanasar G Babajanyan
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, 20894, MD, USA.
| | - Sofya K Garushyants
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, 20894, MD, USA
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, 20894, MD, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, 20894, MD, USA.
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D'Accolti M, Soffritti I, Bini F, Mazziga E, Caselli E. Tackling transmission of infectious diseases: A probiotic-based system as a remedy for the spread of pathogenic and resistant microbes. Microb Biotechnol 2024; 17:e14529. [PMID: 39045894 PMCID: PMC11267305 DOI: 10.1111/1751-7915.14529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 07/04/2024] [Indexed: 07/25/2024] Open
Abstract
Built environments (BEs) currently represent the areas in which human beings spend most of their life. Consistently, microbes populating BEs mostly derive from human occupants and can be easily transferred from BE to occupants. The hospital microbiome is a paradigmatic example, representing a reservoir for harmful pathogens that can be transmitted to susceptible patients, causing the healthcare-associated infections (HAIs). Environmental cleaning is a crucial pillar in controlling BE pathogens and preventing related infections, and chemical disinfectants have been largely used so far towards this aim. However, despite their immediate effect, chemical-based disinfection is unable to prevent recontamination, has a high environmental impact, and can select/increase antimicrobial resistance (AMR) in treated microbes. To overcome these limitations, probiotic-based sanitation (PBS) strategies were recently proposed, built on the use of detergents added with selected probiotics able to displace surrounding pathogens by competitive exclusion. PBS was reported as an effective and low-impact alternative to chemical disinfection, providing stable rebalance of the BE microbiome and significantly reducing pathogens and HAIs compared to disinfectants, without exacerbating AMR and pollution concerns. This minireview summarizes the most significant results obtained by applying PBS in sanitary and non-sanitary settings, which overall suggest that PBS may effectively tackle the infectious risk meanwhile preventing the further spread of pathogenic and resistant microbes.
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Affiliation(s)
- Maria D'Accolti
- Section of Microbiology, Department of Chemical, Pharmaceutical and Agricultural Sciences, and LTTAUniversity of FerraraFerraraItaly
- CIAS Research CenterUniversity of FerraraFerraraItaly
| | - Irene Soffritti
- Section of Microbiology, Department of Chemical, Pharmaceutical and Agricultural Sciences, and LTTAUniversity of FerraraFerraraItaly
- CIAS Research CenterUniversity of FerraraFerraraItaly
| | - Francesca Bini
- Section of Microbiology, Department of Chemical, Pharmaceutical and Agricultural Sciences, and LTTAUniversity of FerraraFerraraItaly
- CIAS Research CenterUniversity of FerraraFerraraItaly
| | - Eleonora Mazziga
- Section of Microbiology, Department of Chemical, Pharmaceutical and Agricultural Sciences, and LTTAUniversity of FerraraFerraraItaly
- CIAS Research CenterUniversity of FerraraFerraraItaly
| | - Elisabetta Caselli
- Section of Microbiology, Department of Chemical, Pharmaceutical and Agricultural Sciences, and LTTAUniversity of FerraraFerraraItaly
- CIAS Research CenterUniversity of FerraraFerraraItaly
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Dayie NTKD, Egyir B, Amoa-Owusu F, Owusu-Nyantakyi C, Adu B, Kotey FCN, Donkor ES, Stabler RA. Genome Sequences of Extended-Spectrum Beta-Lactamase-Producing Escherichia coli Recovered from Mid-Stream Urine Samples in Accra, Ghana. Microorganisms 2024; 12:1139. [PMID: 38930521 PMCID: PMC11205560 DOI: 10.3390/microorganisms12061139] [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: 05/08/2024] [Revised: 05/25/2024] [Accepted: 05/26/2024] [Indexed: 06/28/2024] Open
Abstract
Escherichia coli, a member of the commensal intestinal microbiota, is a significant aetiology of urinary tract infections (UTIs) and has a propensity for acquiring multidrug resistance characteristics, such as extended-spectrum beta-lactamases (ESBLs). Despite the increase in the incidence of ESBL-producing E. coli infections in sub-Saharan Africa, routine ESBL detection in Ghana is often absent, and molecular data on ESBL genotypes is scarce. Eleven ESBL-producing E. coli recovered from mid-stream urine samples were subjected to antimicrobial susceptibility testing and whole-genome sequence analyses. All isolates exhibited multidrug resistance, demonstrating phenotypic resistance to third-generation cephalosporins, such as cefotaxime, ceftazidime, and cefpodoxime. Three isolates demonstrated resistance to norfloxacin (a fluoroquinolone), and one isolate demonstrated intermediate resistance to ertapenem (a carbapenem). Analysis of the draft genomes identified multiple antimicrobial resistance genes including ESBL genotypes blaTEM-1B/TEM-190 (6/11 and 1/11, respectively), blaCTX-M-15/CTX-M-3 (7/11 and 1/11) and blaOXA-1/OXA-181 (3/11 and 1/11). The strains belong to 10 different serotypes and 10 different multilocus sequence types. This study provides information on phenotypic resistance in 11 ESBL E. coli from Ghana and AMR genotypes within their genomes.
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Affiliation(s)
- Nicholas T. K. D. Dayie
- Department of Medical Microbiology, University of Ghana Medical School, Accra P.O. Box KB 4236, Ghana; (N.T.K.D.D.); (F.C.N.K.); (E.S.D.)
| | - Beverly Egyir
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra P.O. Box LG 581, Ghana; (B.E.); (F.A.-O.); (C.O.-N.)
| | - Felicia Amoa-Owusu
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra P.O. Box LG 581, Ghana; (B.E.); (F.A.-O.); (C.O.-N.)
| | - Christian Owusu-Nyantakyi
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra P.O. Box LG 581, Ghana; (B.E.); (F.A.-O.); (C.O.-N.)
| | - Bright Adu
- Department of Immunology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra P.O. Box LG 581, Ghana;
| | - Fleischer C. N. Kotey
- Department of Medical Microbiology, University of Ghana Medical School, Accra P.O. Box KB 4236, Ghana; (N.T.K.D.D.); (F.C.N.K.); (E.S.D.)
| | - Eric S. Donkor
- Department of Medical Microbiology, University of Ghana Medical School, Accra P.O. Box KB 4236, Ghana; (N.T.K.D.D.); (F.C.N.K.); (E.S.D.)
| | - Richard A. Stabler
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
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Alkorta I, Garbisu C. Expanding the focus of the One Health concept: links between the Earth-system processes of the planetary boundaries framework and antibiotic resistance. REVIEWS ON ENVIRONMENTAL HEALTH 2024; 0:reveh-2024-0013. [PMID: 38815132 DOI: 10.1515/reveh-2024-0013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 03/26/2024] [Indexed: 06/01/2024]
Abstract
The scientific community warns that our impact on planet Earth is so acute that we are crossing several of the planetary boundaries that demarcate the safe operating space for humankind. Besides, there is mounting evidence of serious effects on people's health derived from the ongoing environmental degradation. Regarding human health, the spread of antibiotic resistant bacteria is one of the most critical public health issues worldwide. Relevantly, antibiotic resistance has been claimed to be the quintessential One Health issue. The One Health concept links human, animal, and environmental health, but it is frequently only focused on the risk of zoonotic pathogens to public health or, to a lesser extent, the impact of contaminants on human health, i.e., adverse effects on human health coming from the other two One Health "compartments". It is recurrently claimed that antibiotic resistance must be approached from a One Health perspective, but such statement often only refers to the connection between the use of antibiotics in veterinary practice and the antibiotic resistance crisis, or the impact of contaminants (antibiotics, heavy metals, disinfectants, etc.) on antibiotic resistance. Nonetheless, the nine Earth-system processes considered in the planetary boundaries framework can be directly or indirectly linked to antibiotic resistance. Here, some of the main links between those processes and the dissemination of antibiotic resistance are described. The ultimate goal is to expand the focus of the One Health concept by pointing out the links between critical Earth-system processes and the One Health quintessential issue, i.e., antibiotic resistance.
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Affiliation(s)
- Itziar Alkorta
- Department of Biochemistry and Molecular Biology, 16402 University of the Basque Country (UPV/EHU) , Bilbao, Spain
| | - Carlos Garbisu
- NEIKER - Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Derio, Spain
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Tettey R, Egyir B, Tettey P, Arko-Mensah J, Addo SO, Owusu-Nyantakyi C, Boateng W, Fobil J. Genomic analysis of multidrug-resistant Escherichia coli from Urban Environmental water sources in Accra, Ghana, Provides Insights into public health implications. PLoS One 2024; 19:e0301531. [PMID: 38787855 PMCID: PMC11125565 DOI: 10.1371/journal.pone.0301531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 03/18/2024] [Indexed: 05/26/2024] Open
Abstract
Wastewater discharge into the environment in resource-poor countries poses a threat to public health. Studies in this area within these countries are limited, and the use of high-throughput whole-genome sequencing technologies is lacking. Therefore, understanding of environmental impacts is inadequate. The present study investigated the antibiotic resistance profiles and diversity of beta-lactamases in Escherichia coli strains isolated from environmental water sources in Accra, Ghana. Microbiological analyses were conducted on wastewater samples from three hospitals, a sewage and wastewater treatment plant, and water samples from two urban surface water bodies. Confirmed isolates (N = 57) were selected for phenotypic antibiotic resistance profiles. Multi-drug-resistant isolates (n = 25) were genome sequenced using Illumina MiSeq sequencing technology and screened for sequence types, antibiotic resistance, virulence and beta-lactamase genes, and mobile genetic elements. Isolates were frequently resistant to ampicillin (63%), meropenem (47%), azithromycin (46%), and sulfamethoxazole-trimethoprim (42%). Twenty different sequence types (STs) were identified, including clinically relevant ones such as ST167 and ST21. Five isolates were assigned to novel STs: ST14531 (n = 2), ST14536, ST14537, and ST14538. The isolates belonged to phylogroups A (52%), B1 (44%), and B2 (4%) and carried β-lactamase (TEM-1B, TEM-1C, CTX-M-15, and blaDHA-1) and carbapenemase (OXA-1, OXA-181) resistance genes. Dominant plasmid replicons included Col440I (10.2%) and IncFIB (AP001918) (6.8%). Polluted urban environments in Accra are reservoirs for antibiotic-resistant bacteria, posing a substantial public health risk. The findings underscore the need for targeted public health interventions to mitigate the spread of antibiotic-resistant bacteria and protect public health.
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Affiliation(s)
- Rebecca Tettey
- Department of Biological, Environmental, and Occupational Health Science, School of Public Health, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Beverly Egyir
- West African Center for Global Environmental & Occupational Health, College of Health Sciences, University of Ghana, Accra, Ghana
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Prudence Tettey
- Department of Biological, Environmental, and Occupational Health Science, School of Public Health, College of Health Sciences, University of Ghana, Accra, Ghana
| | - John Arko-Mensah
- Department of Biological, Environmental, and Occupational Health Science, School of Public Health, College of Health Sciences, University of Ghana, Accra, Ghana
- West African Center for Global Environmental & Occupational Health, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Samuel Ofori Addo
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Christian Owusu-Nyantakyi
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | - William Boateng
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Julius Fobil
- West African Center for Global Environmental & Occupational Health, College of Health Sciences, University of Ghana, Accra, Ghana
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Halema AA, El-Beltagi HS, Al-Dossary O, Alsubaie B, Henawy AR, Rezk AA, Almutairi HH, Mohamed AA, Elarabi NI, Abdelhadi AA. Omics technology draws a comprehensive heavy metal resistance strategy in bacteria. World J Microbiol Biotechnol 2024; 40:193. [PMID: 38709343 DOI: 10.1007/s11274-024-04005-y] [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: 03/21/2024] [Accepted: 04/24/2024] [Indexed: 05/07/2024]
Abstract
The rapid industrial revolution significantly increased heavy metal pollution, becoming a major global environmental concern. This pollution is considered as one of the most harmful and toxic threats to all environmental components (air, soil, water, animals, and plants until reaching to human). Therefore, scientists try to find a promising and eco-friendly technique to solve this problem i.e., bacterial bioremediation. Various heavy metal resistance mechanisms were reported. Omics technologies can significantly improve our understanding of heavy metal resistant bacteria and their communities. They are a potent tool for investigating the adaptation processes of microbes in severe conditions. These omics methods provide unique benefits for investigating metabolic alterations, microbial diversity, and mechanisms of resistance of individual strains or communities to harsh conditions. Starting with genome sequencing which provides us with complete and comprehensive insight into the resistance mechanism of heavy metal resistant bacteria. Moreover, genome sequencing facilitates the opportunities to identify specific metal resistance genes, operons, and regulatory elements in the genomes of individual bacteria, understand the genetic mechanisms and variations responsible for heavy metal resistance within and between bacterial species in addition to the transcriptome, proteome that obtain the real expressed genes. Moreover, at the community level, metagenome, meta transcriptome and meta proteome participate in understanding the microbial interactive network potentially novel metabolic pathways, enzymes and gene species can all be found using these methods. This review presents the state of the art and anticipated developments in the use of omics technologies in the investigation of microbes used for heavy metal bioremediation.
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Affiliation(s)
- Asmaa A Halema
- Genetics Department, Faculty of Agriculture, Cairo University, Giza, 12613, Egypt
| | - Hossam S El-Beltagi
- Agricultural Biotechnology Department, College of Agriculture and Food Sciences, King Faisal University, Al-Ahsa, 31982, Saudi Arabia.
- Biochemistry Department, Faculty of Agriculture, Cairo University, Giza, 12613, Egypt.
| | - Othman Al-Dossary
- Agricultural Biotechnology Department, College of Agriculture and Food Sciences, King Faisal University, Al-Ahsa, 31982, Saudi Arabia
| | - Bader Alsubaie
- Agricultural Biotechnology Department, College of Agriculture and Food Sciences, King Faisal University, Al-Ahsa, 31982, Saudi Arabia
| | - Ahmed R Henawy
- Microbiology Department, Faculty of Agriculture, Cairo University, Giza, 12613, Egypt
| | - Adel A Rezk
- Agricultural Biotechnology Department, College of Agriculture and Food Sciences, King Faisal University, Al-Ahsa, 31982, Saudi Arabia
- Plant Virology Department, Plant Pathology Research Institute, Agriculture Research Center, Giza, 12619, Egypt
| | - Hayfa Habes Almutairi
- Chemistry Department, College of Science, King Faisal University, Al-Ahsa, 31982, Saudi Arabia
| | - Amal A Mohamed
- Chemistry Dept, Al-Leith University College, Umm Al-Qura University, P.O. Box 6725- 21955, Makkah, Saudi Arabia
| | - Nagwa I Elarabi
- Genetics Department, Faculty of Agriculture, Cairo University, Giza, 12613, Egypt
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Lin ZJ, Zhou ZC, Shuai XY, Shan XY, Zhou JY, Chen H. Deciphering Multidrug-Resistant Plasmids in Disinfection Residual Bacteria from a Wastewater Treatment Plant. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:6793-6803. [PMID: 38574343 DOI: 10.1021/acs.est.3c10895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/06/2024]
Abstract
Current disinfection processes pose an emerging environmental risk due to the ineffective removal of antibiotic-resistant bacteria, especially disinfection residual bacteria (DRB) carrying multidrug-resistant plasmids (MRPs). However, the characteristics of DRB-carried MRPs are poorly understood. In this study, qPCR analysis reveals that the total absolute abundance of four plasmids in postdisinfection effluent decreases by 1.15 log units, while their relative abundance increases by 0.11 copies/cell compared to investigated wastewater treatment plant (WWTP) influent. We obtain three distinctive DRB-carried MRPs (pWWTP-01-03) from postdisinfection effluent, each carrying 9-11 antibiotic-resistant genes (ARGs). pWWTP-01 contains all 11 ARGs within an ∼25 Kbp chimeric genomic island showing strong patterns of recombination with MRPs from foodborne outbreaks and hospitals. Antibiotic-, disinfectant-, and heavy-metal-resistant genes on the same plasmid underscore the potential roles of disinfectants and heavy metals in the coselection of ARGs. Additionally, pWWTP-02 harbors an adhesin-type virulence operon, implying risks of both antibiotic resistance and pathogenicity upon entering environments. Furthermore, some MRPs from DRB are capable of transferring and could confer selective advantages to recipients under environmentally relevant antibiotic pressure. Overall, this study advances our understanding of DRB-carried MRPs and highlights the imminent need to monitor and control wastewater MRPs for environmental security.
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Affiliation(s)
- Ze-Jun Lin
- Institute of Environmental Technology, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Zhen-Chao Zhou
- Institute of Environmental Technology, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xin-Yi Shuai
- Institute of Environmental Technology, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xiao-Yu Shan
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Jin-Yu Zhou
- Institute of Environmental Technology, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Hong Chen
- Institute of Environmental Technology, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, Hangzhou 310058, China
- International Cooperation Base of Environmental Pollution and Ecological Health, Science and Technology Agency of Zhejiang, Zhejiang University, Hangzhou 310058, China
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10
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Kang Y, Wang J, Li Z. Meta-analysis addressing the characterization of antibiotic resistome in global hospital wastewater. JOURNAL OF HAZARDOUS MATERIALS 2024; 466:133577. [PMID: 38281357 DOI: 10.1016/j.jhazmat.2024.133577] [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: 10/07/2023] [Revised: 12/07/2023] [Accepted: 01/18/2024] [Indexed: 01/30/2024]
Abstract
Hospital wastewater (HWW) is a significant environmental reservoir of antibiotic resistance genes (ARGs). However, currently, no comprehensive understanding exists of the antibiotic resistome in global HWW. In this study, we attempted to address this knowledge gap through an in silico reanalysis of publicly accessible global HWW metagenomic data. We reanalyzed ARGs in 338 HWW samples from 13 countries in Africa, Asia, and Europe. In total, 2420 ARG subtypes belonging to 30 ARG types were detected, dominated by multidrug, beta-lactam, and aminoglycoside resistance genes. ARG composition in Europe differed from that in Asia and Africa. Notably, the ARGs presented co-occurrence with mobile genetic elements (MGEs), metal resistance genes (MRGs), and human bacterial pathogens (HBP), indicating a potential dissemination risk of ARGs in the HWW. Multidrug resistance genes presented co-occurrence with MGEs, MRGs, and HBP, is particularly pronounced. The abundance of contigs that contained ARG, contigs that contained ARG and HBP, contigs that contained ARG and MGE, contigs that contained ARG and MRG were used for health and transmission risk assessment of antibiotic resistome and screened out 40 high risk ARGs in the global HWW. This study first provides a comprehensive characterization and risk of the antibiotic resistome in global HWW.
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Affiliation(s)
- Yutong Kang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases (NITFID), National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102200, China
| | - Jie Wang
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Zhenjun Li
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases (NITFID), National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102200, China.
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11
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Zhuang X, Fan H, Li X, Dong Y, Wang S, Zhao B, Wu S. Transfer and accumulation of antibiotic resistance genes and bacterial pathogens in the mice gut due to consumption of organic foods. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 915:169842. [PMID: 38215844 DOI: 10.1016/j.scitotenv.2023.169842] [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: 09/19/2023] [Revised: 11/27/2023] [Accepted: 12/30/2023] [Indexed: 01/14/2024]
Abstract
Over the last few decades, organic food demand has grown largely because of increasing personal health concerns. Organic farming introduces antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARB) into foods. However, potential effects of organic foods on the gut microbiome and ARGs have been overlooked. Using high-throughput quantitative PCR and 16S rRNA high-throughput sequencing technology, we examined 132 ARGs from major classes, eight transposase genes, universal class I integron-integrase gene (intI), clinical class I integron-integrase gene (cintI), and the bacterial community in mouse gut after 8 weeks with an either organic or inorganic lettuce and wheat diet. A total of 8 types of major ARGs and 10 mobile genetic elements (MGEs) were detected in mice gut, including tetracycline, multidrug, sulfonamide, aminoglycoside, beta-lactamase, chloramphenicol, MLSB and vancomycin resistance genes. We found that abundance and diversity of ARGs, mobile gene elements, and potential ARB in the gut increased with time after consumption of organic foods, whereas no significant changes were observed in inorganic treated groups. Moreover, MGEs, including IS613, Tp614 and tnpA_03 were found to play an important role in regulating ARG profiles in the gut microbiome following consumption of organic foods. Importantly, feeding organic food increased the relative abundance of the potentially antibiotic-resistant pathogens, Bacteroides and Streptococcus. Our results confirm that there is an increasing risk of ARGs and ARB in the gut microbiome, which highlights the importance of organic food industries taking into account the potential accumulation and transmission of ARGs as a risk factor.
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Affiliation(s)
- Xuliang Zhuang
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; State Key Laboratory of Tibetan Plateau Earth System, Environment and Resources (TPESER), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haonan Fan
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xianglong Li
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuzhu Dong
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shijie Wang
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bin Zhao
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shanghua Wu
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China.
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12
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Sheng Q, Xu Q, Lan Z, Wu Z. Comparative Genome Analysis of Two Streptococcus suis Serotype 8 Strains Identifies Two New Virulence-Associated Genes. Animals (Basel) 2024; 14:572. [PMID: 38396540 PMCID: PMC10886379 DOI: 10.3390/ani14040572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 01/18/2024] [Accepted: 02/06/2024] [Indexed: 02/25/2024] Open
Abstract
Streptococcus suis is an important zoonotic pathogen that can cause meningitis and septicemia in swine and humans. Among numerous pathogenic serotypes, S. suis serotype 8 has distinctive characteristics such as a high detection rate and causing multi-host infection. There is no complete genome of serotype 8 strains so far. In this study, the complete genome of two S. suis serotype 8 strains, virulent strain 2018WUSS151 and non-virulent strain WUSS030, were sequenced. Comparative genomic analysis showed that the homology of the two genomes reaches 99.68%, and the main difference is the distinctive prophages. There are 83 genes unique to virulent strain 2018WUSS151, including three putative virulence-associated genes (PVGs). Two PVGs, padR and marR, are passenger genes in ISSsu2 family transposons that are able to form circular DNA intermediates during transposition, indicating the possibility of horizontal transmission among S. suis strains. The deletion mutant of PVGs marR or atpase attenuated the virulence of serotype 2 virulent SC070731 in a mouse infection model, confirming their role in S. suis virulence. These findings contribute to clarifying the genomic characterization of S. suis serotype 8 and S. suis pathogenesis.
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Affiliation(s)
- Qi Sheng
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210014, China; (Q.S.); (Q.X.)
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing 210014, China
- WOAH Reference Lab for Swine Streptococcosis, Nanjing 210014, China
| | - Qiuhua Xu
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210014, China; (Q.S.); (Q.X.)
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing 210014, China
- WOAH Reference Lab for Swine Streptococcosis, Nanjing 210014, China
| | - Zouran Lan
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210014, China; (Q.S.); (Q.X.)
- Shandong Provincial Center for Animal Disease Control, Jinan 250100, China
| | - Zongfu Wu
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210014, China; (Q.S.); (Q.X.)
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing 210014, China
- WOAH Reference Lab for Swine Streptococcosis, Nanjing 210014, China
- Guangdong Provincial Key Laboratory of Research on the Technology of Pig-Breeding and Pig-Disease Prevention, Guangzhou 511400, China
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13
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Babajanyan SG, Garushyants SK, Wolf YI, Koonin EV. Microbial diversity and ecological complexity emerging from environmental variation and horizontal gene transfer in a simple mathematical model. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.17.576128. [PMID: 38313259 PMCID: PMC10836074 DOI: 10.1101/2024.01.17.576128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2024]
Abstract
Microbiomes are generally characterized by high diversity of coexisting microbial species and strains that remains stable within a broad range of conditions. However, under fixed conditions, microbial ecology conforms with the exclusion principle under which two populations competing for the same resource within the same niche cannot coexist because the less fit population inevitably goes extinct. To explore the conditions for stabilization of microbial diversity, we developed a simple mathematical model consisting of two competing populations that could exchange a single gene allele via horizontal gene transfer (HGT). We found that, although in a fixed environment, with unbiased HGT, the system obeyed the exclusion principle, in an oscillating environment, within large regions of the phase space bounded by the rates of reproduction and HGT, the two populations coexist. Moreover, depending on the parameter combination, all three major types of symbiosis obtained, namely, pure competition, host-parasite relationship and mutualism. In each of these regimes, certain parameter combinations provided for synergy, that is, a greater total abundance of both populations compared to the abundance of the winning population in the fixed environments. These findings show that basic phenomena that are universal in microbial communities, environmental variation and HGT, provide for stabilization of microbial diversity and ecological complexity.
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Affiliation(s)
- Sanasar G. Babajanyan
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Sofya K. Garushyants
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Yuri I. Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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14
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Nawata K, Kadoya A, Suzuki S. Persistence of Marine Bacterial Plasmid in the House Fly (Musca domestica): Marine-Derived Antimicrobial Resistance Genes Have a Chance of Invading the Human Environment. MICROBIAL ECOLOGY 2024; 87:30. [PMID: 38191744 PMCID: PMC10774151 DOI: 10.1007/s00248-023-02341-4] [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: 10/18/2023] [Accepted: 12/31/2023] [Indexed: 01/10/2024]
Abstract
The house fly is known to be a vector of antibiotic-resistant bacteria (ARB) in animal farms. It is also possible that the house fly contributes to the spread of ARB and antibiotic resistance genes (ARGs) among various environments. We hypothesized that ARB and ARGs present in marine fish and fishery food may gain access to humans via the house fly. We show herein that pAQU1, a marine bacterial ARG-bearing plasmid, persists in the house fly intestine for 5 days after fly ingestion of marine bacteria. In the case of Escherichia coli bearing the same plasmid, the persistence period exceeded 7 days. This interval is sufficient for transmission to human environments, meaning that the house fly is capable of serving as a vector of marine-derived ARGs. Time course monitoring of the house fly intestinal microflora showed that the initial microflora was occupied abundantly with Enterobacteriaceae. Experimentally ingested bacteria dominated the intestinal environment immediately following ingestion; however, after 72 h, the intestinal microflora recovered to resemble that observed at baseline, when diverse genera of Enterobacteriaceae were seen. Given that pAQU1 in marine bacteria and E. coli were detected in fly excrement (defined here as any combination of feces and regurgitated material) at 7 days post-bacterial ingestion, we hypothesize that the house fly may serve as a vector for transmission of ARGs from marine items and fish to humans via contamination with fly excrement.
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Affiliation(s)
- Kanoko Nawata
- Center for Marine Environmental Studies, Ehime University, Matsuyama, Ehime, Japan
| | - Aya Kadoya
- Center for Marine Environmental Studies, Ehime University, Matsuyama, Ehime, Japan
| | - Satoru Suzuki
- Center for Marine Environmental Studies, Ehime University, Matsuyama, Ehime, Japan.
- Graduate School of Science and Engineering, Ehime University, Matsuyama, Ehime, Japan.
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15
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Tokuda M, Shintani M. Microbial evolution through horizontal gene transfer by mobile genetic elements. Microb Biotechnol 2024; 17:e14408. [PMID: 38226780 PMCID: PMC10832538 DOI: 10.1111/1751-7915.14408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 12/20/2023] [Accepted: 01/02/2024] [Indexed: 01/17/2024] Open
Abstract
Mobile genetic elements (MGEs) are crucial for horizontal gene transfer (HGT) in bacteria and facilitate their rapid evolution and adaptation. MGEs include plasmids, integrative and conjugative elements, transposons, insertion sequences and bacteriophages. Notably, the spread of antimicrobial resistance genes (ARGs), which poses a serious threat to public health, is primarily attributable to HGT through MGEs. This mini-review aims to provide an overview of the mechanisms by which MGEs mediate HGT in microbes. Specifically, the behaviour of conjugative plasmids in different environments and conditions was discussed, and recent methodologies for tracing the dynamics of MGEs were summarised. A comprehensive understanding of the mechanisms underlying HGT and the role of MGEs in bacterial evolution and adaptation is important to develop strategies to combat the spread of ARGs.
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Affiliation(s)
- Maho Tokuda
- Department of Environment and Energy Systems, Graduate School of Science and TechnologyShizuoka UniversityHamamatsuJapan
| | - Masaki Shintani
- Department of Environment and Energy Systems, Graduate School of Science and TechnologyShizuoka UniversityHamamatsuJapan
- Research Institute of Green Science and TechnologyShizuoka UniversityHamamatsuJapan
- Japan Collection of MicroorganismsRIKEN BioResource Research CenterIbarakiJapan
- Graduate School of Integrated Science and TechnologyShizuoka UniversityHamamatsuJapan
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16
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Wang M, Masoudi A, Wang C, Wu C, Zhang Z, Zhao X, Liu Y, Yu Z, Liu J. Impacts of net cages on pollutant accumulation and its consequence on antibiotic resistance genes (ARGs) dissemination in freshwater ecosystems: Insights for sustainable urban water management. ENVIRONMENT INTERNATIONAL 2024; 183:108357. [PMID: 38056093 DOI: 10.1016/j.envint.2023.108357] [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: 06/10/2023] [Revised: 11/08/2023] [Accepted: 11/26/2023] [Indexed: 12/08/2023]
Abstract
There has been increasing interest in the role of human activities in disseminating antibiotic-resistance genes (ARGs) in aquatic ecosystems. However, the influence of pollutant accumulation on anthropogenic pollutant-ARG synergistic actions is limited. This study explored the association of net cages with the propagation of anthropogenic pollutants and their consequences for influencing the enrichment of ARGs using high-throughput metagenomic sequencing. We showed that net cages could substantially impact the ecology of freshwater systems by enhancing i) ARG diversity and the tendency for ARG-horizontal gene transfer and ii) the overlap of mobile genetic elements (MGEs) with biocide-metal resistance genes (BMRGs) and ARGs. These findings suggested that the cotransfer of these three genetic determinants would be favored in net cage plots and that nonantibiotic factors such as metal(loid)s, particularly iron (Fe), displayed robust selective pressures on ARGs exerted by the net cage. The resistome risk scores of net cage sediments and biofilms were higher than those from off-net cage plots, indicating that the net cage-origin antibiotic resistome should be of great concern. The combination of deterministic and stochastic processes acting on bacterial communities could explain the higher ARG variations in cage plots (8.2%) than in off-cage plots (3.4%). Moreover, MGEs and pollutants together explained 43.3% of the total variation in ARG communities, which was higher than that of off-cage plots (8.8%), considering pollutants, environmental variables, MGEs, and assembly processes. These findings will inform the development of policies and guidelines to more effectively limit the spread of antimicrobial resistance and achieve the goal of sustainability in freshwater systems in urban areas.
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Affiliation(s)
- Min Wang
- Hebei Key Laboratory of Animal Physiology, Biochemistry, and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Hebei Research Center of the Basic Discipline of Cell Biology, Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei 050024, PR China
| | - Abolfazl Masoudi
- Hebei Key Laboratory of Animal Physiology, Biochemistry, and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Hebei Research Center of the Basic Discipline of Cell Biology, Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei 050024, PR China.
| | - Can Wang
- Hebei Key Laboratory of Animal Physiology, Biochemistry, and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Hebei Research Center of the Basic Discipline of Cell Biology, Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei 050024, PR China
| | - Changhao Wu
- Hebei Key Laboratory of Animal Physiology, Biochemistry, and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Hebei Research Center of the Basic Discipline of Cell Biology, Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei 050024, PR China
| | - Ze Zhang
- Hebei Key Laboratory of Animal Physiology, Biochemistry, and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Hebei Research Center of the Basic Discipline of Cell Biology, Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei 050024, PR China
| | - Xin Zhao
- Hebei Key Laboratory of Animal Physiology, Biochemistry, and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Hebei Research Center of the Basic Discipline of Cell Biology, Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei 050024, PR China
| | - Yuanjie Liu
- Hebei Key Laboratory of Animal Physiology, Biochemistry, and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Hebei Research Center of the Basic Discipline of Cell Biology, Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei 050024, PR China
| | - Zhijun Yu
- Hebei Key Laboratory of Animal Physiology, Biochemistry, and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Hebei Research Center of the Basic Discipline of Cell Biology, Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei 050024, PR China.
| | - Jingze Liu
- Hebei Key Laboratory of Animal Physiology, Biochemistry, and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Hebei Research Center of the Basic Discipline of Cell Biology, Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei 050024, PR China.
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17
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Wanyan R, Pan M, Mai Z, Xiong X, Wang S, Han Q, Yu Q, Wang G, Wu S, Li H. Fate of high-risk antibiotic resistance genes in large-scale aquaculture sediments: Geographical differentiation and corresponding drivers. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 905:167068. [PMID: 37714353 DOI: 10.1016/j.scitotenv.2023.167068] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 08/22/2023] [Accepted: 09/12/2023] [Indexed: 09/17/2023]
Abstract
Antibiotic resistance genes (ARGs), emerging environmental contaminants, have become challenges of public health security. However, the distribution and drivers of ARGs, especially high-risk ARGs, in large-scale aquaculture sediments remain unknown. Here, we collected sediment samples from 40 crayfish ponds in seven main crayfish culture provinces in China and then investigated the distribution and risk of ARGs based on high-throughput sequencing and quantitative PCR techniques. Our results suggested that aquaculture sediment was potential reservoir of ARGs and the abundance of aadA-02 was the highest. High-risk ARG (floR) was also prevalent in the sediment and was the most abundant in Jiangsu Province, where opportunistic pathogens were also enriched. The abundance of floR was positively correlated with different environmental factors, such as total phosphorus in water and total carbon in sediment. In addition, Mycobacterium sp., opportunistic pathogenic bacteria, might be potential host for floR. Furthermore, the potential propagation pathway of ARGs was from sediment to crayfish gut, and Bacteroidetes and Proteobacteria might be the main bacterial groups responsible for the proliferation of ARGs. Generally, our results illustrate that pond sediment may be an ARG reservoir of aquatic animals. Meanwhile, our study helps develop valuable strategies for accessing risks and managing ARGs.
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Affiliation(s)
- Ruijun Wanyan
- School of Public Health, Lanzhou University, Lanzhou 730000, China; Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Meijing Pan
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Zhan Mai
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiong Xiong
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Sijie Wang
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Qian Han
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Qiaoling Yu
- State Key Laboratory of Grassland Agro-ecosystems, Center for Grassland Microbiome, College of Pastoral Agriculture Science and Technology, Lanzhou University, Gansu 730000, China
| | - Guitang Wang
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shangong Wu
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Huan Li
- School of Public Health, Lanzhou University, Lanzhou 730000, China; State Key Laboratory of Grassland Agro-ecosystems, Center for Grassland Microbiome, College of Pastoral Agriculture Science and Technology, Lanzhou University, Gansu 730000, China.
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18
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Roh H, Kannimuthu D. Comparative resistome analysis of Aeromonas species in aquaculture reveals antibiotic resistance patterns and phylogeographic distribution. ENVIRONMENTAL RESEARCH 2023; 239:117273. [PMID: 37805184 DOI: 10.1016/j.envres.2023.117273] [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: 08/02/2023] [Revised: 09/27/2023] [Accepted: 09/28/2023] [Indexed: 10/09/2023]
Abstract
The overuse of antibiotics in aquaculture drives the emergence of multi-drug-resistant bacteria, and antibiotic-resistant genes (ARGs) can be disseminated to other bacteria through vertical- and horizontal gene transfer (VGT and HGT) under selective pressure. Profiling the antibiotic resistome and understanding the global distribution of ARGs constitutes the first step in developing a control strategy. Hence, this study utilized extensive genomic data from hundreds of Aeromonas strains in aquaculture to profile resistome patterns and explores their association with isolation year, country, and species characteristics. Overall, ∼400 Aeromonas genomes were used to predict the ARGs from A. salmonicida, A. hydrophila, A. veronii, A. media, and A. sobria. ARGs such as sul1, tet(A), and tet(D), which display a similar proportion of positive strains among species, were subjected to phylodynamic and phylogeographic analyses. More than a hundred ARGs were identified, some of which exhibited either species-specific or non-species-specific patterns. A. salmonicida and A. media were found to have a higher proportion of species-specific ARGs than other strains, which might lead to more distinct patterns of ARG acquisition. Overall, ∼25% of strains have either sul1, tet(A), or tet(D) gene(s), but no significant difference was observed in the proportion of positive strains by species. Phylogeographic analysis revealed that the abundant numbers of sul1, tet(A), and/or tet(D) introduced in a few East Asian and North American countries could spread to both adjacent and faraway countries. In recent years, the proportions of these ARGs have dramatically increased, particularly in strains sourced from aquatic environments, suggesting control is required of the overuse of antibiotics in aquaculture. The findings of this research offer significant insights into the global dissemination of ARGs.
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Affiliation(s)
- HyeongJin Roh
- Pathogen Transmission and Disease Research Group, Institute of Marine Research, PO Box 1870, Nordnes, 5870, Bergen, Norway.
| | - Dhamotharan Kannimuthu
- Pathogen Transmission and Disease Research Group, Institute of Marine Research, PO Box 1870, Nordnes, 5870, Bergen, Norway
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19
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Naidoo Y, Pierneef RE, Cowan DA, Valverde A. Characterization of the soil resistome and mobilome in Namib Desert soils. Int Microbiol 2023:10.1007/s10123-023-00454-x. [PMID: 37968548 DOI: 10.1007/s10123-023-00454-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 11/06/2023] [Accepted: 11/10/2023] [Indexed: 11/17/2023]
Abstract
The study of the soil resistome is important in understanding the evolution of antibiotic resistance and its dissemination between the clinic and the environment. However, very little is known about the soil resistome, especially of those from deserts. Here, we characterize the bacterial communities, using targeted sequencing of the 16S rRNA genes, and both the resistome and the mobilome in Namib Desert soils, using shotgun metagenomics. We detected a variety of antibiotic resistance genes (ARGs) that conferred resistance to antibiotics such as elfamycin, rifampicin, and fluoroquinolones, metal/biocide resistance genes (MRGs/BRGs) conferring resistance to metals such as arsenic and copper, and mobile genetic elements (MGEs) such as the ColE1-like plasmid. The presence of metal/biocide resistance genes in close proximity to ARGs indicated a potential for co-selection of resistance to antibiotics and metals/biocides. The co-existence of MGEs and horizontally acquired ARGs most likely contributed to a decoupling between bacterial community composition and ARG profiles. Overall, this study indicates that soil bacterial communities in Namib Desert soils host a diversity of resistance elements and that horizontal gene transfer, rather than host phylogeny, plays an essential role in their dynamics.
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Affiliation(s)
- Yashini Naidoo
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Lynnwood Road, Pretoria, 0002, South Africa.
| | - Rian E Pierneef
- Biotechnology Platform, Agricultural Research Council, Soutpan Road, Onderstepoort Campus, Pretoria, 0110, South Africa
| | - Don A Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Lynnwood Road, Pretoria, 0002, South Africa
| | - Angel Valverde
- IRNASA-CSIC, Cordel de Merinas, 37008, Salamanca, Spain.
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20
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Lin X, Zhang C, Han R, Li S, Peng H, Zhou X, Huang L, Xu Y. Oxytetracycline and heavy metals promote the migration of resistance genes in the intestinal microbiome by plasmid transfer. THE ISME JOURNAL 2023; 17:2003-2013. [PMID: 37700035 PMCID: PMC10579362 DOI: 10.1038/s41396-023-01514-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 09/03/2023] [Accepted: 09/05/2023] [Indexed: 09/14/2023]
Abstract
Horizontal gene transfer (HGT) has been considered the most important pathway to introduce antibiotic resistance genes (ARGs), which seriously threatens human health and biological security. The presence of ARGs in the aquatic environment and their effect on the intestinal micro-ecosystem of aquatic animals can occur easily. To investigate the HGT potential and rule of exogenous ARGs in the intestinal flora, a visual conjugative model was developed, including the donor of dual-fluorescent bacterium and the recipient of Xenopus tropicalis intestinal microbiome. Some common pollutants of oxytetracycline (OTC) and three heavy metals (Zn, Cu and Pb) were selected as the stressor. The multi-techniques of flow cytometry (FCM), scanning electron microscopy (SEM), atomic force microscopy (AFM), single-cell Raman spectroscopy with sorting (SCRSS) and indicator analysis were used in this study. The results showed that ARG transfer could occur more easily under stressors. Moreover, the conjugation efficiency mainly depended on the viability of the intestinal bacteria. The mechanisms of OTC and heavy metal stressing conjugation included the upregulation of ompC, traJ, traG and the downregulation of korA gene. Moreover, the enzymatic activities of SOD, CAT, GSH-PX increased and the bacterial surface appearance also changed. The predominant recipient was identified as Citrobacter freundi by SCRSS, in which the abundance and quantity of ARG after conjugation were higher than those before. Therefore, since the diversity of potential recipients in the intestine are very high, the migration of invasive ARGs in the microbiome should be given more attention to prevent its potential risks to public health.
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Affiliation(s)
- Xiaojun Lin
- School of Environmental Science and Engineering, Guangdong University of Technology, No. 100 Wai Huan Xi Road, Guangzhou Higher Education Mega Center, Panyu District, Guangzhou, 510006, PR China
| | - Chaonan Zhang
- School of Environmental Science and Engineering, Guangdong University of Technology, No. 100 Wai Huan Xi Road, Guangzhou Higher Education Mega Center, Panyu District, Guangzhou, 510006, PR China
| | - Ruiqi Han
- School of Environmental Science and Engineering, Guangdong University of Technology, No. 100 Wai Huan Xi Road, Guangzhou Higher Education Mega Center, Panyu District, Guangzhou, 510006, PR China
| | - Shoupeng Li
- Analysis and Test Center, Guangdong University of Technology, No. 100 Wai Huan Xi Road, Guangzhou Higher Education Mega Center, Panyu District, Guangzhou, 510006, PR China
| | - Huishi Peng
- School of Environmental Science and Engineering, Guangdong University of Technology, No. 100 Wai Huan Xi Road, Guangzhou Higher Education Mega Center, Panyu District, Guangzhou, 510006, PR China
| | - Xiao Zhou
- Analysis and Test Center, Guangdong University of Technology, No. 100 Wai Huan Xi Road, Guangzhou Higher Education Mega Center, Panyu District, Guangzhou, 510006, PR China
| | - Lu Huang
- Analysis and Test Center, Guangdong University of Technology, No. 100 Wai Huan Xi Road, Guangzhou Higher Education Mega Center, Panyu District, Guangzhou, 510006, PR China
| | - Yanbin Xu
- School of Environmental Science and Engineering, Guangdong University of Technology, No. 100 Wai Huan Xi Road, Guangzhou Higher Education Mega Center, Panyu District, Guangzhou, 510006, PR China.
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21
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Bessa LJ, Shaaban M, Aminov R. Editorial: Insights in antimicrobials, resistance & chemotherapy: 2022. Front Microbiol 2023; 14:1310156. [PMID: 37928656 PMCID: PMC10622649 DOI: 10.3389/fmicb.2023.1310156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 10/10/2023] [Indexed: 11/07/2023] Open
Affiliation(s)
- Lucinda J. Bessa
- Egas Moniz Center for Interdisciplinary Research (CiiEM), Egas Moniz School of Health and Science, Almada, Portugal
| | - Mona Shaaban
- Department of Microbiology and Immunology, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Rustam Aminov
- The School of Medicine, Medical Sciences, and Nutrition, University of Aberdeen, Aberdeen, United Kingdom
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22
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Ham H, Park DS. Novel approach toward the understanding of genetic diversity based on the two types of amino acid repeats in Erwinia amylovora. Sci Rep 2023; 13:17876. [PMID: 37857695 PMCID: PMC10587187 DOI: 10.1038/s41598-023-44558-w] [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: 03/29/2023] [Accepted: 10/10/2023] [Indexed: 10/21/2023] Open
Abstract
Erwinia amylovora is a notorious plant pathogenic bacterium of global concern that has devastated the apple and pear production industry worldwide. Nevertheless, the approaches available currently to understand the genetic diversity of E. amylovora remain unsatisfactory because of the lack of a trustworthy index and data covering the globally occurring E. amylovora strains; thus, their origin and distribution pattern remains ambiguous. Therefore, there is a growing need for robust approaches for obtaining this information via the comparison of the genomic structure of Amygdaloideae-infecting strains to understand their genetic diversity and distribution. Here, the whole-genome sequences of 245 E. amylovora strains available from the NCBI database were compared to identify intraspecific genes for use as an improved index for the simple classification of E. amylovora strains regarding their distribution. Finally, we discovered two kinds of strain-typing protein-encoding genes, i.e., the SAM-dependent methyltransferase and electron transport complex subunit RsxC. Interestingly, both of these proteins carried an amino acid repeat in these strains: SAM-dependent methyltransferase comprised a single-amino-acid repeat (asparagine), whereas RsxC carried a 40-amino-acid repeat, which was differentially distributed among the strains. These noteworthy findings and approaches may enable the exploration of the genetic diversity of E. amylovora from a global perspective.
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Affiliation(s)
- Hyeonheui Ham
- Crop Protection Division, Department of Agro-Food Safety and Crop Protection, National Institute of Agricultural Sciences, Rural Development Administration, Wanju, 55365, Republic of Korea
| | - Dong Suk Park
- Crop Protection Division, Department of Agro-Food Safety and Crop Protection, National Institute of Agricultural Sciences, Rural Development Administration, Wanju, 55365, Republic of Korea.
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23
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Devi K, Singh AD, Dhiman S, Kour J, Bhardwaj T, Sharma N, Madaan I, Khanna K, Ohri P, Singh AP, Sirhindi G, Bhardwaj R, Kumar V. Current studies on the degradation of microplastics in the terrestrial and aquatic ecosystem. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:102010-102026. [PMID: 37670091 DOI: 10.1007/s11356-023-29640-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 08/28/2023] [Indexed: 09/07/2023]
Abstract
Soil and water are two important basic ecosystems for the survival of different organisms. The excessive microplastic pollutants in soil have been directly discharged into the terrestrial ecosystems. Microplastic pollutants (MPs) constitute a ubiquitous global menace due to their durability, flexibility, and tough nature. MPs posed threat to the sustainability of the ecosystem due to their small size and easy transportation via ecological series resulting in the accumulation of MPs in aquatic and terrestrial ecosystems. After being emitted into the terrestrial ecosystem, the MPs might be aged by oxidative degeneration (photo/thermal), reprecipitation (bioturbation), and hetero-accumulation. The mechanism of adsorption, degradation, and breakdown of MPs into unaffected plastic debris is accomplished by using several biological, physical, and chemical strategies. This review presents the importance of ecosystems, occurrence and sources of MPs, its toxicity, and the alteration in the ecology of the ecosystems. The inhibitory impact of MPs on the ecosystems also documents to unveil the ecological hazards of MPs. Further research is required to study the immobilization and recovery efficiency of MPs on a larger scale.
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Affiliation(s)
- Kamini Devi
- Department of Botanical and Environmental Sciences, Amritsar, Punjab, 143005, India
| | - Arun Dev Singh
- Department of Botanical and Environmental Sciences, Amritsar, Punjab, 143005, India
| | - Shalini Dhiman
- Department of Botanical and Environmental Sciences, Amritsar, Punjab, 143005, India
| | - Jaspreet Kour
- Department of Botanical and Environmental Sciences, Amritsar, Punjab, 143005, India
| | - Tamanna Bhardwaj
- Department of Botanical and Environmental Sciences, Amritsar, Punjab, 143005, India
| | - Neerja Sharma
- Department of Botanical and Environmental Sciences, Amritsar, Punjab, 143005, India
| | - Isha Madaan
- Government College of Education, Jalandhar, Punjab, 144001, India
- Department of Botany, Punjabi University, Patiala, Punjab, 147002, India
| | - Kanika Khanna
- Department of Botany, D.A.V. University, Jalandhar, Punjab, 144001, India
| | - Puja Ohri
- Department of Zoology, Guru Nanak Dev University, Amritsar, Punjab, 143005, India
| | - Amrit Pal Singh
- Department of Pharmaceutical Sciences, Guru Nanak Dev University, Amritsar, Punjab, 143005, India
| | - Geetika Sirhindi
- Department of Botany, Punjabi University, Patiala, Punjab, 147002, India
| | - Renu Bhardwaj
- Department of Botanical and Environmental Sciences, Amritsar, Punjab, 143005, India
| | - Vinod Kumar
- Department of Botany, Government Degree College, Jammu and Kashmir, Ramban, India.
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24
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Gionchetta G, Snead D, Semerad S, Beck K, Pruden A, Bürgmann H. Dynamics of antibiotic resistance markers and Escherichia coli invasion in riverine heterotrophic biofilms facing increasing heat and flow stagnation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 893:164658. [PMID: 37321511 DOI: 10.1016/j.scitotenv.2023.164658] [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: 03/15/2023] [Revised: 06/02/2023] [Accepted: 06/02/2023] [Indexed: 06/17/2023]
Abstract
As motivation to address environmental dissemination of antimicrobial resistance (AMR) is mounting, there is a need to characterize mechanisms by which AMR can propagate under environmental conditions. Here we investigated the effect of temperature and stagnation on the persistence of wastewater-associated antibiotic resistance markers in riverine biofilms and the invasion success of genetically-tagged Escherichia coli. Biofilms grown on glass slides incubated in-situ downstream of a wastewater treatment plant effluent discharge point were transferred to laboratory-scale flumes fed with filtered river water under potentially stressful temperature and flow conditions: recirculation flow at 20 °C, stagnation at 20 °C, and stagnation at 30 °C. After 14 days, quantitative PCR and amplicon sequencing were used to quantify bacteria, biofilms diversity, resistance markers (sul1, sul2, ermB, tetW, tetM, tetB, blaCTX-M-1, intI1) and E. coli. Resistance markers significantly decreased over time regardless of the treatment applied. Although invading E. coli were initially able to colonize the biofilms, its abundance subsequently declined. Stagnation was associated with a shift in biofilm taxonomic composition, but there was no apparent effect of flow conditions or the simulated river-pool warming (30 °C) on AMR persistence or invasion success of E. coli. Results however indicated that antibiotic resistance markers in the riverine biofilms decreased under the experimental conditions in the absence of exposure to external inputs of antibiotics and AMR.
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Affiliation(s)
- G Gionchetta
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Department of Surface Waters - Research and Management, 6047 Kastanienbaum, Switzerland
| | - D Snead
- Department of Civil & Environmental Engineering, University of Michigan, Ann Arbor, MI, USA; Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, USA
| | - S Semerad
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Department of Surface Waters - Research and Management, 6047 Kastanienbaum, Switzerland
| | - K Beck
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Department of Surface Waters - Research and Management, 6047 Kastanienbaum, Switzerland
| | - A Pruden
- Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, USA
| | - H Bürgmann
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Department of Surface Waters - Research and Management, 6047 Kastanienbaum, Switzerland.
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25
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Byun KH, Kim HJ. Survival strategies of Listeria monocytogenes to environmental hostile stress: biofilm formation and stress responses. Food Sci Biotechnol 2023; 32:1631-1651. [PMID: 37780599 PMCID: PMC10533466 DOI: 10.1007/s10068-023-01427-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 08/29/2023] [Accepted: 08/31/2023] [Indexed: 10/03/2023] Open
Abstract
Listeria monocytogenes is a critical foodborne pathogen that causes listeriosis and threatens public health. This pathogenic microorganism forms a transmission cycle in nature, food industry, and humans, expanding the areas of contamination among them and influencing food safety. L. monocytogenes forms biofilms to protect itself and promotes survival through stress responses to the various stresses (e.g., temperature, pH, and antimicrobial agents) that may be inflicted during food processing. Biofilms and mechanisms of resistance to hostile external or general stresses allow L. monocytogenes to survive despite a variety of efforts to ensure food safety. The current review article focuses on biofilm formation, resistance mechanisms through biofilms, and external specific or general stress responses of L. monocytogenes to help understand the unexpected survival rates of this bacterium; it also proposes the use of obstacle technology to effectively cope with it in the food industry.
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Affiliation(s)
- Kye-Hwan Byun
- Food Safety and Distribution Research Group, Korea Food Research Institute, Jeollabuk-Do, Wanju, 55365 Republic of Korea
| | - Hyun Jung Kim
- Food Safety and Distribution Research Group, Korea Food Research Institute, Jeollabuk-Do, Wanju, 55365 Republic of Korea
- Department of Food Biotechnology, University of Science and Technology, Daejeon, 34113 Republic of Korea
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26
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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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27
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El-Zamkan MA, Ahmed AS, Abdelhafeez HH, Mohamed HMA. Molecular characterization of Vibrio species isolated from dairy and water samples. Sci Rep 2023; 13:15368. [PMID: 37717062 PMCID: PMC10505214 DOI: 10.1038/s41598-023-42334-4] [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: 05/07/2023] [Accepted: 09/08/2023] [Indexed: 09/18/2023] Open
Abstract
Vibrio species can cause foodborne infections and lead to serious gastrointestinal illnesses. The purpose of this research was to detect the Vibrio cholerae and Vibrio parahaemolyticus in raw milk, dairy products, and water samples. Also, it investigated the virulence factors, antibiotic resistance and biofilm formation in isolated bacteria. Conventional and molecular approaches were used to identify the isolates in this study. Vibrio species were detected in 5% of the samples. Vibrio cholerae and Vibrio parahaemolyticus were isolated from 1.25 and 1.5%, respectively, of the total samples. Penicillin resistance was detected in all strains of Vibrio cholerae and Vibrio parahaemolyticus, with a MAR index ranging from 0.16 to 0.5. Four isolates were moderate biofilm producer and three of them were MDR. When Vibrio cholerae was screened for virulence genes, ctxAB, hlyA, and tcpA were found in 80, 60, and 80% of isolates, respectively. However, tdh + /trh + associated-virulence genes were found in 33.3% of Vibrio parahaemolyticus isolates.
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Affiliation(s)
- Mona A El-Zamkan
- Department of Food Hygiene and Control (Milk Hygiene), Faculty of Veterinary Medicine, South Valley University, Qena, 83523, Egypt.
| | - Ahmed Shaban Ahmed
- Department of Food Hygiene and Control (Milk Hygiene), Faculty of Veterinary Medicine, South Valley University, Qena, 83523, Egypt
| | - Hanan H Abdelhafeez
- Department of Cell and Tissues, Faculty of Veterinary Medicine, Assiut University, Assiut, 71526, Egypt.
| | - Hams M A Mohamed
- Department of Microbiology, Faculty of Veterinary Medicine, South Valley University, Qena, 83523, Egypt.
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28
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Liang X, Zhang J, Kim Y, Ho J, Liu K, Keenum I, Gupta S, Davis B, Hepp SL, Zhang L, Xia K, Knowlton KF, Liao J, Vikesland PJ, Pruden A, Heath LS. ARGem: a new metagenomics pipeline for antibiotic resistance genes: metadata, analysis, and visualization. Front Genet 2023; 14:1219297. [PMID: 37811141 PMCID: PMC10558085 DOI: 10.3389/fgene.2023.1219297] [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: 05/08/2023] [Accepted: 09/01/2023] [Indexed: 10/10/2023] Open
Abstract
Antibiotic resistance is of crucial interest to both human and animal medicine. It has been recognized that increased environmental monitoring of antibiotic resistance is needed. Metagenomic DNA sequencing is becoming an attractive method to profile antibiotic resistance genes (ARGs), including a special focus on pathogens. A number of computational pipelines are available and under development to support environmental ARG monitoring; the pipeline we present here is promising for general adoption for the purpose of harmonized global monitoring. Specifically, ARGem is a user-friendly pipeline that provides full-service analysis, from the initial DNA short reads to the final visualization of results. The capture of extensive metadata is also facilitated to support comparability across projects and broader monitoring goals. The ARGem pipeline offers efficient analysis of a modest number of samples along with affordable computational components, though the throughput could be increased through cloud resources, based on the user's configuration. The pipeline components were carefully assessed and selected to satisfy tradeoffs, balancing efficiency and flexibility. It was essential to provide a step to perform short read assembly in a reasonable time frame to ensure accurate annotation of identified ARGs. Comprehensive ARG and mobile genetic element databases are included in ARGem for annotation support. ARGem further includes an expandable set of analysis tools that include statistical and network analysis and supports various useful visualization techniques, including Cytoscape visualization of co-occurrence and correlation networks. The performance and flexibility of the ARGem pipeline is demonstrated with analysis of aquatic metagenomes. The pipeline is freely available at https://github.com/xlxlxlx/ARGem.
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Affiliation(s)
- Xiao Liang
- Department of Computer Science, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Jingyi Zhang
- Department of Computer Science, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Yoonjin Kim
- Department of Computer Science, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Josh Ho
- Department of Computer Science, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Kevin Liu
- Department of Computer Science, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Ishi Keenum
- Department of Civil and Environmental Engineering, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Suraj Gupta
- Interdisciplinary PhD Program in Genetics, Bioinformatics, and Computational Biology, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Benjamin Davis
- Department of Civil and Environmental Engineering, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Shannon L. Hepp
- Department of Civil and Environmental Engineering, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Liqing Zhang
- Department of Computer Science, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Kang Xia
- School of Plant and Environmental Science, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Katharine F. Knowlton
- Department of Dairy Science, Virginia Polytechnic Institute and State University, Blacksburg, VaA, United States
| | - Jingqiu Liao
- Department of Civil and Environmental Engineering, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Peter J. Vikesland
- Department of Civil and Environmental Engineering, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Amy Pruden
- Department of Civil and Environmental Engineering, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Lenwood S. Heath
- Department of Computer Science, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
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29
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Shindoh S, Kadoya A, Kanechi R, Watanabe K, Suzuki S. Marine bacteria harbor the sulfonamide resistance gene sul4 without mobile genetic elements. Front Microbiol 2023; 14:1230548. [PMID: 37779713 PMCID: PMC10539471 DOI: 10.3389/fmicb.2023.1230548] [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: 05/29/2023] [Accepted: 08/31/2023] [Indexed: 10/03/2023] Open
Abstract
Marine bacteria are possible reservoirs of antibiotic-resistance genes (ARGs) originating not only from clinical and terrestrial hot spots but also from the marine environment. We report here for the first time a higher rate of the sulfonamide-resistance gene sul4 in marine bacterial isolates compared with other sul genes. Among four sulfonamide-resistance genes (sul1, sul2, sul3, and sul4), sul4 was most abundant (45%) in 74 sulfonamide-resistant marine isolates by PCR screening. The order of abundance was sul4 (33 isolates) >sul2 (6 isolates) >sul3 (5 isolates) >sul1 (1 isolate). Whole-genome sequencing of 23 isolates of sul4-expressing α- and γ-proteobacteria and bacilli revealed that sul4 was not accompanied by known mobile genetic elements. This suggests that sul4 in these marine isolates is clonally transferred and not horizontally transferable. Folate metabolism genes formed a cluster with sul4, suggesting that the cluster area plays a role in folate metabolism, at which sul4 functions as a dihydropteroate synthase. Thus, sul4 might be expressed in marine species and function in folate synthesis, but it is not a transferable ARG.
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Affiliation(s)
- Suzune Shindoh
- Center for Marine Environmental Studies, Ehime University, Matsuyama, Japan
| | - Aya Kadoya
- Center for Marine Environmental Studies, Ehime University, Matsuyama, Japan
| | - Reo Kanechi
- Center for Marine Environmental Studies, Ehime University, Matsuyama, Japan
| | - Kozo Watanabe
- Center for Marine Environmental Studies, Ehime University, Matsuyama, Japan
- Graduate School of Science and Engineering, Ehime University, Matsuyama, Japan
| | - Satoru Suzuki
- Graduate School of Science and Engineering, Ehime University, Matsuyama, Japan
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30
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Huang C, Pham HQ, Zhu L, Wang R, Law OK, Lin SL, Nie QC, Zhang L, Wang X, Lau TCK. Comparative Analysis of Transcriptome and Proteome Revealed the Common Metabolic Pathways Induced by Prevalent ESBL Plasmids in Escherichia coli. Int J Mol Sci 2023; 24:14009. [PMID: 37762311 PMCID: PMC10531281 DOI: 10.3390/ijms241814009] [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: 07/31/2023] [Revised: 09/11/2023] [Accepted: 09/11/2023] [Indexed: 09/29/2023] Open
Abstract
Antibiotic resistance has emerged as one of the most significant threats to global public health. Plasmids, which are highly efficient self-replicating genetic vehicles, play a critical role in the dissemination of drug-resistant genes. Previous studies have mainly focused on drug-resistant genes only, often neglecting the complete functional role of multidrug-resistant (MDR) plasmids in bacteria. In this study, we conducted a comprehensive investigation of the transcriptomes and proteomes of Escherichia coli J53 transconjugants harboring six major MDR plasmids of different incompatibility (Inc) groups, which were clinically isolated from patients. The RNA-seq analysis revealed that MDR plasmids influenced the gene expression in the bacterial host, in particular, the genes related to metabolic pathways. A proteomic analysis demonstrated the plasmid-induced regulation of several metabolic pathways including anaerobic respiration and the utilization of various carbon sources such as serine, threonine, sialic acid, and galactarate. These findings suggested that MDR plasmids confer a growth advantage to bacterial hosts in the gut, leading to the expansion of plasmid-carrying bacteria over competitors without plasmids. Moreover, this study provided insights into the versatility of prevalent MDR plasmids in moderating the cellular gene network of bacteria, which could potentially be utilized in therapeutics development for bacteria carrying MDR plasmids.
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Affiliation(s)
- Chuan Huang
- Department of Biomedical Sciences, College of Veterinary Medicine and Life Science, City University of Hong Kong, Hong Kong SAR, China; (C.H.); (H.-Q.P.); (L.Z.); (R.W.); (O.-K.L.); (S.-L.L.); (Q.-C.N.); (L.Z.)
- Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong SAR, China
| | - Hoa-Quynh Pham
- Department of Biomedical Sciences, College of Veterinary Medicine and Life Science, City University of Hong Kong, Hong Kong SAR, China; (C.H.); (H.-Q.P.); (L.Z.); (R.W.); (O.-K.L.); (S.-L.L.); (Q.-C.N.); (L.Z.)
- Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong SAR, China
| | - Lina Zhu
- Department of Biomedical Sciences, College of Veterinary Medicine and Life Science, City University of Hong Kong, Hong Kong SAR, China; (C.H.); (H.-Q.P.); (L.Z.); (R.W.); (O.-K.L.); (S.-L.L.); (Q.-C.N.); (L.Z.)
- Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong SAR, China
| | - Rui Wang
- Department of Biomedical Sciences, College of Veterinary Medicine and Life Science, City University of Hong Kong, Hong Kong SAR, China; (C.H.); (H.-Q.P.); (L.Z.); (R.W.); (O.-K.L.); (S.-L.L.); (Q.-C.N.); (L.Z.)
- Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong SAR, China
| | - Oi-Kwan Law
- Department of Biomedical Sciences, College of Veterinary Medicine and Life Science, City University of Hong Kong, Hong Kong SAR, China; (C.H.); (H.-Q.P.); (L.Z.); (R.W.); (O.-K.L.); (S.-L.L.); (Q.-C.N.); (L.Z.)
- Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong SAR, China
| | - Shu-Ling Lin
- Department of Biomedical Sciences, College of Veterinary Medicine and Life Science, City University of Hong Kong, Hong Kong SAR, China; (C.H.); (H.-Q.P.); (L.Z.); (R.W.); (O.-K.L.); (S.-L.L.); (Q.-C.N.); (L.Z.)
- Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong SAR, China
| | - Qi-Chang Nie
- Department of Biomedical Sciences, College of Veterinary Medicine and Life Science, City University of Hong Kong, Hong Kong SAR, China; (C.H.); (H.-Q.P.); (L.Z.); (R.W.); (O.-K.L.); (S.-L.L.); (Q.-C.N.); (L.Z.)
- Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong SAR, China
| | - Liang Zhang
- Department of Biomedical Sciences, College of Veterinary Medicine and Life Science, City University of Hong Kong, Hong Kong SAR, China; (C.H.); (H.-Q.P.); (L.Z.); (R.W.); (O.-K.L.); (S.-L.L.); (Q.-C.N.); (L.Z.)
- Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong SAR, China
| | - Xin Wang
- Department of Surgery, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China;
| | - Terrence Chi-Kong Lau
- Department of Biomedical Sciences, College of Veterinary Medicine and Life Science, City University of Hong Kong, Hong Kong SAR, China; (C.H.); (H.-Q.P.); (L.Z.); (R.W.); (O.-K.L.); (S.-L.L.); (Q.-C.N.); (L.Z.)
- Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong SAR, China
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Ivanova O, Blumenkrants D, Krylova E, Soltynskaya I, Goncharova A, Chaikin E, Akhmetzyanova A, Panin A. Founding of the culture collection of antibiotic-resistant strains of zoonotic bacteria in the Russian Federation. Vet World 2023; 16:1451-1460. [PMID: 37621551 PMCID: PMC10446724 DOI: 10.14202/vetworld.2023.1451-1460] [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: 11/14/2022] [Accepted: 05/29/2023] [Indexed: 08/26/2023] Open
Abstract
Background and Aim The main purpose of a national bioresource center is to standardize, centralize, preserve, and ensure accessibility of microbial bioresources that accumulate there because of state research programs. The establishment of national bioresource centers for antibiotic-resistant microorganisms allows to solve practical problems in the field of veterinary service, as well as to develop effective chemotherapeutic and disinfectant drugs to overcome the mechanisms of resistance. This study aimed to outline the process of forming a national culture collection of antibiotic-resistant strains of zoonotic bacteria in the Russian Federation using two microbial strains. Materials and Methods The object of research was isolates of Salmonella spp., Escherichia coli, Enterococcus spp., Campylobacter spp., Listeria monocytogenes, and Staphylococcus spp., all of which were obtained from biomaterials of farm animals, feed samples, bedding, water from livestock buildings, washouts from environmental objects, and food products. The resistance of bacterial isolates was determined using microbiological and molecular-genetic research methods. Results During monitoring studies, 1489 bacterial isolates were isolated. In total, 408 bacterial isolates were tested for sensitivity to antimicrobial agents, including E. coli (47.6%), Salmonella spp. (30.4%), Enterococcus spp. (11.3%), and Campylobacter spp. (10.8%). For genetic characterization, 95 isolates of Salmonella enterica, E. coli, Campylobacter spp., L. monocytogenes, Staphylococcus spp., Enterococcus spp. were chosen from the research collection, which was formed as part of the monitoring program for antibiotic resistance. Conclusion Deposited isolates that underwent whole-genome analysis can be used as positive control samples both in the development and use of methods or test systems for the detection of various resistance genes in zoonotic bacteria. In addition, such isolates can also be used for microbiological studies related to determining the sensitivity of microorganisms to antibacterial drugs, for phenotypic studies in the diagnosis of various bacterial infections in animals and birds, and retrospective analysis of strains from numerous collections.
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Affiliation(s)
- Olga Ivanova
- Federal State Budgetary Institution, The Russian State Center for Animal Feed and Drug Standardization and Quality, Moscow, Russia
| | - Dmitry Blumenkrants
- Federal State Budgetary Institution, The Russian State Center for Animal Feed and Drug Standardization and Quality, Moscow, Russia
| | - Ekaterina Krylova
- Federal State Budgetary Institution, The Russian State Center for Animal Feed and Drug Standardization and Quality, Moscow, Russia
| | - Irina Soltynskaya
- Federal State Budgetary Institution, The Russian State Center for Animal Feed and Drug Standardization and Quality, Moscow, Russia
| | - Anastasia Goncharova
- Federal State Budgetary Institution, The Russian State Center for Animal Feed and Drug Standardization and Quality, Moscow, Russia
| | - Evgeny Chaikin
- Federal State Budgetary Institution, The Russian State Center for Animal Feed and Drug Standardization and Quality, Moscow, Russia
| | - Anna Akhmetzyanova
- Federal State Budgetary Institution, The Russian State Center for Animal Feed and Drug Standardization and Quality, Moscow, Russia
| | - Alexander Panin
- Federal State Budgetary Institution, The Russian State Center for Animal Feed and Drug Standardization and Quality, Moscow, Russia
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32
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Řezanka T, Kyselová L, Murphy DJ. Archaeal lipids. Prog Lipid Res 2023; 91:101237. [PMID: 37236370 DOI: 10.1016/j.plipres.2023.101237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 04/25/2023] [Accepted: 05/19/2023] [Indexed: 05/28/2023]
Abstract
The major archaeal membrane glycerolipids are distinguished from those of bacteria and eukaryotes by the contrasting stereochemistry of their glycerol backbones, and by the use of ether-linked isoprenoid-based alkyl chains rather than ester-linked fatty acyl chains for their hydrophobic moieties. These fascinating compounds play important roles in the extremophile lifestyles of many species, but are also present in the growing numbers of recently discovered mesophilic archaea. The past decade has witnessed significant advances in our understanding of archaea in general and their lipids in particular. Much of the new information has come from the ability to screen large microbial populations via environmental metagenomics, which has revolutionised our understanding of the extent of archaeal biodiversity that is coupled with a strict conservation of their membrane lipid compositions. Significant additional progress has come from new culturing and analytical techniques that are gradually enabling archaeal physiology and biochemistry to be studied in real time. These studies are beginning to shed light on the much-discussed and still-controversial process of eukaryogenesis, which probably involved both bacterial and archaeal progenitors. Puzzlingly, although eukaryotes retain many attributes of their putative archaeal ancestors, their lipid compositions only reflect their bacterial progenitors. Finally, elucidation of archaeal lipids and their metabolic pathways have revealed potentially interesting applications that have opened up new frontiers for biotechnological exploitation of these organisms. This review is concerned with the analysis, structure, function, evolution and biotechnology of archaeal lipids and their associated metabolic pathways.
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Affiliation(s)
- Tomáš Řezanka
- Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, 142 00 Prague, Czech Republic
| | - Lucie Kyselová
- Research Institute of Brewing and Malting, Lípová 511, 120 44 Prague, Czech Republic
| | - Denis J Murphy
- School of Applied Sciences, University of South Wales, Pontypridd, CF37 1DL, United Kingdom.
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Nikulin N, Nikulina A, Zimin A, Aminov R. Phages for treatment of Escherichia coli infections. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 200:171-206. [PMID: 37739555 DOI: 10.1016/bs.pmbts.2023.03.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/24/2023]
Abstract
Diseases due to infections by pathogenic Escherichia coli strains are on the rise and with the growing antimicrobial resistance among bacterial pathogens, including this group. Thus, alternative therapeutic options are actively investigated. Among these alternatives is phage therapy. In the case of E. coli, the combination of the well understood biology of this species and its bacteriophages represents a good guiding example for the establishment of phage therapy principles against this and other pathogenic bacteria. In this chapter, the procedures toward the development of phage therapy against pathogenic E. coli with the use of T-even group of phages are discussed. These steps involve the isolation, purification, characterisation and large-scale production of these phages, with formulation of phage cocktails for in vitro and in vivo studies. The main emphasis is made on phage therapy of enteropathogenic E. coli O157:H, which is one of the prominent human pathogens but persists as a commensal bacterium in many food animals. The implementation of phage therapy against E. coli O157:H within the One Health framework in carrier animals and for treatment of meat, vegetables, fruits and other agricultural produce thus would allow controlling and interrupting the transmission routes of this pathogen to the human food chain and preventing human disease. Examples of successful control and elimination of E. coli O157:H are given, while the problems encountered in phage treatment of this pathogen are also discussed.
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Affiliation(s)
- Nikita Nikulin
- Laboratory of Molecular Microbiology, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Federal Research Center, Pushchino, Russia
| | - Alexandra Nikulina
- Laboratory of Molecular Microbiology, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Federal Research Center, Pushchino, Russia
| | - Andrei Zimin
- Laboratory of Molecular Microbiology, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Federal Research Center, Pushchino, Russia
| | - Rustam Aminov
- The School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, United Kingdom.
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Tripathi A, Kumar D, Chavda P, Rathore DS, Pandit R, Blake D, Tomley F, Joshi M, Joshi CG, Dubey SK. Resistome profiling reveals transmission dynamics of antimicrobial resistance genes from poultry litter to soil and plant. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 327:121517. [PMID: 36990341 DOI: 10.1016/j.envpol.2023.121517] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 02/26/2023] [Accepted: 03/25/2023] [Indexed: 06/19/2023]
Abstract
Poultry farming is a major livelihood in South and Southeast Asian economies where it is undergoing rapid intensification to meet the growing human demand for dietary protein. Intensification of poultry production systems is commonly supported by increased antimicrobial drug use, risking greater selection and dissemination of antimicrobial resistance genes (ARGs). Transmission of ARGs through food chains is an emerging threat. Here, we investigated transmission of ARGs from chicken (broiler and layer) litter to soil and Sorghum bicolor (L.) Moench plants based on field and pot experiments. The results demonstrate ARGs transmission from poultry litter to plant systems under field as well as experimental pot conditions. The most common ARGs could be tracked for transmission from litter to soil to plants were identified as detected were cmx, ErmX, ErmF, lnuB, TEM-98 and TEM-99, while common microorganisms included Escherichia coli, Staphylococcus aureus, Enterococcus faecium, Pseudomonas aeruginosa, and Vibrio cholerae. Using next generation sequencing and digital PCR assays we detected ARGs transmitted from poultry litter in both the roots and stems of S. bicolor (L.) Moench plants. Poultry litter is frequently used as a fertiliser because of its high nitrogen content; our studies show that ARGs can transmit from litter to plants and illustrates the risks posed to the environment by antimicrobial treatment of poultry. This knowledge is useful for formulating intervention strategies that can reduce or prevent ARGs transmission from one value chain to another, improving understanding of impacts on human and environmental health. The research outcome will help in further understanding the transmission and risks posed by ARGs from poultry to environmental and human/animal health.
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Affiliation(s)
- Animesh Tripathi
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, 221005, India
| | - Dinesh Kumar
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology; (DST), Government of Gujarat, Gandhinagar, Gujarat, 382011, India
| | - Priyank Chavda
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology; (DST), Government of Gujarat, Gandhinagar, Gujarat, 382011, India
| | - Dalip Singh Rathore
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology; (DST), Government of Gujarat, Gandhinagar, Gujarat, 382011, India
| | - Ramesh Pandit
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology; (DST), Government of Gujarat, Gandhinagar, Gujarat, 382011, India
| | - Damer Blake
- Pathobiology and Population Sciences, The Royal Veterinary College, Hawkshead Lane, North Mymms, Hertfordshire, UK
| | - Fiona Tomley
- Pathobiology and Population Sciences, The Royal Veterinary College, Hawkshead Lane, North Mymms, Hertfordshire, UK
| | - Madhvi Joshi
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology; (DST), Government of Gujarat, Gandhinagar, Gujarat, 382011, India
| | - Chaitanya G Joshi
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology; (DST), Government of Gujarat, Gandhinagar, Gujarat, 382011, India
| | - Suresh Kumar Dubey
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, 221005, India.
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Piscon B, Pia Esposito E, Fichtman B, Samburski G, Efremushkin L, Amselem S, Harel A, Rahav G, Zarrilli R, Gal-Mor O. The Effect of Outer Space and Other Environmental Cues on Bacterial Conjugation. Microbiol Spectr 2023; 11:e0368822. [PMID: 36995224 PMCID: PMC10269834 DOI: 10.1128/spectrum.03688-22] [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: 09/12/2022] [Accepted: 03/11/2023] [Indexed: 03/31/2023] Open
Abstract
Bacterial conjugation is one of the most abundant horizontal gene transfer (HGT) mechanisms, playing a fundamental role in prokaryote evolution. A better understanding of bacterial conjugation and its cross talk with the environment is needed for a more complete understanding of HGT mechanisms and to fight the dissemination of malicious genes between bacteria. Here, we studied the effect of outer space, microgravity, and additional key environmental cues on transfer (tra) gene expression and conjugation efficiency, using the under studied broad-host range plasmid pN3, as a model. High resolution scanning electron microscopy revealed the morphology of the pN3 conjugative pili and mating pair formation during conjugation. Using a nanosatellite carrying a miniaturized lab, we studied pN3 conjugation in outer space, and used qRT-PCR, Western blotting and mating assays to determine the effect of ground physicochemical parameters on tra gene expression and conjugation. We showed for the first time that bacterial conjugation can occur in outer space and on the ground, under microgravity-simulated conditions. Furthermore, we demonstrated that microgravity, liquid media, elevated temperature, nutrient depletion, high osmolarity and low oxygen significantly reduce pN3 conjugation. Interestingly, under some of these conditions we observed an inverse correlation between tra gene transcription and conjugation frequency and found that induction of at least traK and traL can negatively affect pN3 conjugation frequency in a dose-dependent manner. Collectively, these results uncover pN3 regulation by various environmental cues and highlight the diversity of conjugation systems and the different ways in which they may be regulated in response to abiotic signals. IMPORTANCE Bacterial conjugation is a highly ubiquitous and promiscuous process, by which a donor bacterium transfers a large portion of genetic material to a recipient cell. This mechanism of horizontal gene transfer plays an important role in bacterial evolution and in the ability of bacteria to acquire resistance to antimicrobial drugs and disinfectants. Bacterial conjugation is a complex and energy-consuming process, that is tightly regulated and largely affected by various environmental signals sensed by the bacterial cell. Comprehensive knowledge about bacterial conjugation and the ways it is affected by environmental cues is required to better understand bacterial ecology and evolution and to find new effective ways to counteract the threating dissemination of antibiotic resistance genes between bacterial populations. Moreover, characterizing this process under stress or suboptimal growth conditions such as elevated temperatures, high salinity or in the outer space, may provide insights relevant to future habitat environmental conditions.
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Affiliation(s)
- Bar Piscon
- The Infectious Diseases Research Laboratory, Sheba Medical Center, Tel-Hashomer, Israel
- Department of Clinical Microbiology and Immunology, Tel Aviv University, Tel Aviv, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Eliana Pia Esposito
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Boris Fichtman
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Guy Samburski
- SpacePharma R&D Israel LTD., Herzliya Pituach, Israel & SpacePharma SA, Courgenay, Switzerland
| | - Lihi Efremushkin
- SpacePharma R&D Israel LTD., Herzliya Pituach, Israel & SpacePharma SA, Courgenay, Switzerland
| | - Shimon Amselem
- SpacePharma R&D Israel LTD., Herzliya Pituach, Israel & SpacePharma SA, Courgenay, Switzerland
| | - Amnon Harel
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Galia Rahav
- The Infectious Diseases Research Laboratory, Sheba Medical Center, Tel-Hashomer, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Raffaele Zarrilli
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Ohad Gal-Mor
- The Infectious Diseases Research Laboratory, Sheba Medical Center, Tel-Hashomer, Israel
- Department of Clinical Microbiology and Immunology, Tel Aviv University, Tel Aviv, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
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Wang J, Xu S, Zhao K, Song G, Zhao S, Liu R. Risk control of antibiotics, antibiotic resistance genes (ARGs) and antibiotic resistant bacteria (ARB) during sewage sludge treatment and disposal: A review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 877:162772. [PMID: 36933744 DOI: 10.1016/j.scitotenv.2023.162772] [Citation(s) in RCA: 32] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 02/14/2023] [Accepted: 03/06/2023] [Indexed: 05/06/2023]
Abstract
Sewage sludge is an important reservoir of antibiotics, antibiotic resistance genes (ARGs), and antibiotic resistant bacteria (ARB) in wastewater treatment plants (WWTPs), and the reclamation of sewage sludge potentially threats human health and environmental safety. Sludge treatment and disposal are expected to control these risks, and this review summarizes the fate and controlling efficiency of antibiotics, ARGs, and ARB in sludge involved in different processes, i.e., disintegration, anaerobic digestion, aerobic composting, drying, pyrolysis, constructed wetland, and land application. Additionally, the analysis and characterization methods of antibiotics, ARGs, and ARB in complicate sludge are reviewed, and the quantitative risk assessment approaches involved in land application are comprehensively discussed. This review benefits process optimization of sludge treatment and disposal, with regard to environmental risks control of antibiotics, ARGs, and ARB in sludge. Furthermore, current research limitations and gaps, e.g., the antibiotic resistance risk assessment in sludge-amended soil, are proposed to advance the future studies.
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Affiliation(s)
- Jiaqi Wang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Yangze Eco-Environment Engineering Research Center, China Three Gorges Corporation, Beijing 100038, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Siqi Xu
- Center for Water and Ecology, State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Kai Zhao
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ge Song
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shunan Zhao
- Center for Water and Ecology, State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Ruiping Liu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Center for Water and Ecology, State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Fujihara H, Hirose J, Suenaga H. Evolution of genetic architecture and gene regulation in biphenyl/PCB-degrading bacteria. Front Microbiol 2023; 14:1168246. [PMID: 37350784 PMCID: PMC10282184 DOI: 10.3389/fmicb.2023.1168246] [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: 02/17/2023] [Accepted: 05/16/2023] [Indexed: 06/24/2023] Open
Abstract
A variety of bacteria in the environment can utilize xenobiotic compounds as a source of carbon and energy. The bacterial strains degrading xenobiotics are suitable models to investigate the adaptation and evolutionary processes of bacteria because they appear to have emerged relatively soon after the release of these compounds into the natural environment. Analyses of bacterial genome sequences indicate that horizontal gene transfer (HGT) is the most important contributor to the bacterial evolution of genetic architecture. Further, host bacteria that can use energy effectively by controlling the expression of organized gene clusters involved in xenobiotic degradation will have a survival advantage in harsh xenobiotic-rich environments. In this review, we summarize the current understanding of evolutionary mechanisms operative in bacteria, with a focus on biphenyl/PCB-degrading bacteria. We then discuss metagenomic approaches that are useful for such investigation.
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Affiliation(s)
- Hidehiko Fujihara
- Department of Food and Fermentation Sciences, Faculty of Food and Nutrition Sciences, Beppu University, Beppu, Japan
| | - Jun Hirose
- Department of Applied Chemistry, Faculty of Engineering, University of Miyazaki, Miyazaki, Japan
| | - Hikaru Suenaga
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
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Pan J, Zheng N, An Q, Li Y, Sun S, Zhang W, Song X. Effects of cadmium and copper mixtures on antibiotic resistance genes in rhizosphere soil. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 259:115008. [PMID: 37196522 DOI: 10.1016/j.ecoenv.2023.115008] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 05/08/2023] [Accepted: 05/10/2023] [Indexed: 05/19/2023]
Abstract
The evolvement and development of antibiotic resistance in microorganisms may be influenced by metals; however, it is still unclear how cadmium (Cd) and copper (Cu) combined affect the distribution and presence of antibiotic-resistance genes (ARGs) in rhizosphere soil. The aims of this research were to (1) compare the distribution patterns of bacterial communities and ARGs in response to the effects of Cd and Cu both separately and combined; (2) explore the possible mechanisms underlying the variation in soil bacterial communities and ARGs in addition to the combined effects of Cd, Cu, and various environmental variables (nutrients, pH, etc.); and (3) provide a reference for assessing the risks of metals (Cd and Cu) and ARGs. The findings showed that the multidrug resistance genes acrA and acrB and the transposon gene intI-1 were present in high relative abundance in bacterial communities. Cadmium and Cu had a substantial interaction effect on the abundance of acrA, whereas Cu had a notable main effect on the abundance of intI-1. According to the network analysis, the strong links between bacterial taxa and specific ARGs revealed that most ARGs were hosted by Proteobacteria, Actinobacteria, and Bacteroidetes. According to structural equation modeling, Cd had a larger effect on ARGs than Cu. Compared to previous analyses of ARGs, bacterial community diversity had little effect on ARGs in this study. Overall, the results may have important consequences for determining the possible hazard of soil metals and extend the understanding of how Cd and Cu co-select ARGs in rhizosphere soils.
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Affiliation(s)
- Jiamin Pan
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Na Zheng
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China; Key Laboratory of Groundwater Resources and Environment of the Ministry of Education, College of New Energy and Environment, Jilin University 130021, China.
| | - Qirui An
- Key Laboratory of Groundwater Resources and Environment of the Ministry of Education, College of New Energy and Environment, Jilin University 130021, China
| | - Yunyang Li
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Siyu Sun
- Key Laboratory of Groundwater Resources and Environment of the Ministry of Education, College of New Energy and Environment, Jilin University 130021, China
| | - Wenhui Zhang
- Key Laboratory of Groundwater Resources and Environment of the Ministry of Education, College of New Energy and Environment, Jilin University 130021, China
| | - Xue Song
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
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Calderón-Franco D, van Loosdrecht MCM, Abeel T, Weissbrodt DG. Catch me if you can: capturing microbial community transformation by extracellular DNA using Hi-C sequencing. Antonie Van Leeuwenhoek 2023:10.1007/s10482-023-01834-z. [PMID: 37156983 DOI: 10.1007/s10482-023-01834-z] [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: 02/24/2023] [Accepted: 04/24/2023] [Indexed: 05/10/2023]
Abstract
The transformation of environmental microorganisms by extracellular DNA is an overlooked mechanism of horizontal gene transfer and evolution. It initiates the acquisition of exogenous genes and propagates antimicrobial resistance alongside vertical and conjugative transfers. We combined mixed-culture biotechnology and Hi-C sequencing to elucidate the transformation of wastewater microorganisms with a synthetic plasmid encoding GFP and kanamycin resistance genes, in the mixed culture of chemostats exposed to kanamycin at concentrations representing wastewater, gut and polluted environments (0.01-2.5-50-100 mg L-1). We found that the phylogenetically distant Gram-negative Runella (102 Hi-C links), Bosea (35), Gemmobacter (33) and Zoogloea (24) spp., and Gram-positive Microbacterium sp. (90) were transformed by the foreign plasmid, under high antibiotic exposure (50 mg L-1). In addition, the antibiotic pressure shifted the origin of aminoglycoside resistance genes from genomic DNA to mobile genetic elements on plasmids accumulating in microorganisms. These results reveal the power of Hi-C sequencing to catch and surveil the transfer of xenogenetic elements inside microbiomes.
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Affiliation(s)
| | | | - Thomas Abeel
- Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - David G Weissbrodt
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands.
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Trondheim, Norway.
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Song J, Zhang H, Wu Z, Qiu M, Zhan X, Zheng C, Shi N, Zhang Q, Zhang L, Yu Y, Fang H. A novel bidirectional regulation mechanism of mancozeb on the dissemination of antibiotic resistance. JOURNAL OF HAZARDOUS MATERIALS 2023; 455:131559. [PMID: 37163893 DOI: 10.1016/j.jhazmat.2023.131559] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 04/06/2023] [Accepted: 05/01/2023] [Indexed: 05/12/2023]
Abstract
The high abundance of antibiotic resistance genes (ARGs) in the fungicide residual environment, posing a threat to the environment and human health, raises the question of whether and how fungicide promotes the prevalence and dissemination of antibiotic resistance. Here, we reported a novel mechanism underlying bidirectional regulation of a typical heavy-metal-containing fungicide mancozeb on the horizontal transfer of ARGs. Our findings revealed that mancozeb exposure significantly exerted oxidative and osmotic stress on the microbes and facilitated plasmid-mediated ARGs transfer, but its metallic portions (Mn and Zn) were potentially utilized as essential ions by microbes for metalating enzymes to deal with cellular stress and thus reduce the transfer. The results of transcriptome analysis with RT-qPCR confirmed that the expression levels of cellular stress responses and conjugation related genes were drastically altered. It can be concluded mancozeb bidirectionally regulated the ARGs dissemination which may be attributed to the diverse effects on the microbes by its different portions. This novel mechanism provides an updated understanding of neglected fungicide-triggered ARGs dissemination and crucial insight for comprehensive risk assessment of fungicides.
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Affiliation(s)
- Jiajin Song
- Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Houpu Zhang
- Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; College of Resources and Environment, Anhui Agricultural University, Key Laboratory of Agri-food Safety of Anhui Province, Hefei 230036, China
| | - Zishan Wu
- Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Mengting Qiu
- Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Xiuping Zhan
- Shanghai Agricultural Technology Extension Service Center, Shanghai 201103, China
| | - Conglai Zheng
- Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Nan Shi
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92697, United States
| | - Qianke Zhang
- Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Luqing Zhang
- Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, China
| | - Yunlong Yu
- Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, China
| | - Hua Fang
- Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, China.
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41
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Moshe M, Gupta CL, Sela N, Minz D, Banin E, Frenkel O, Cytryn E. Comparative genomics of Bacillus cereus sensu lato spp. biocontrol strains in correlation to in-vitro phenotypes and plant pathogen antagonistic capacity. Front Microbiol 2023; 14:996287. [PMID: 36846749 PMCID: PMC9947482 DOI: 10.3389/fmicb.2023.996287] [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: 07/17/2022] [Accepted: 01/12/2023] [Indexed: 02/11/2023] Open
Abstract
Bacillus cereus sensu lato (Bcsl) strains are widely explored due to their capacity to antagonize a broad range of plant pathogens. These include B. cereus sp. UW85, whose antagonistic capacity is attributed to the secondary metabolite Zwittermicin A (ZwA). We recently isolated four soil and root-associated Bcsl strains (MO2, S-10, S-25, LSTW-24) that displayed different growth profiles and in-vitro antagonistic effects against three soilborne plant pathogens models: Pythium aphanidermatum (oomycete) Rhizoctonia solani (basidiomycete), and Fusarium oxysporum (ascomycete). To identify genetic mechanisms potentially responsible for the differences in growth and antagonistic phenotypes of these Bcsl strains, we sequenced and compared their genomes, and that of strain UW85 using a hybrid sequencing pipeline. Despite similarities, specific Bcsl strains had unique secondary metabolite and chitinase-encoding genes that could potentially explain observed differences in in-vitro chitinolytic potential and anti-fungal activity. Strains UW85, S-10 and S-25 contained a (~500 Kbp) mega-plasmid that harbored the ZwA biosynthetic gene cluster. The UW85 mega-plasmid contained more ABC transporters than the other two strains, whereas the S-25 mega-plasmid carried a unique cluster containing cellulose and chitin degrading genes. Collectively, comparative genomics revealed several mechanisms that can potentially explain differences in in-vitro antagonism of Bcsl strains toward fungal plant pathogens.
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Affiliation(s)
- Maya Moshe
- Institute of Soil, Water and Environmental Sciences, Agricultural Research Organization, Rishon-Lezion, Israel
- Institute of Plant Pathology and Weed Research, Agricultural Research Organization, Rishon-Lezion, Israel
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Chhedi Lal Gupta
- Institute of Soil, Water and Environmental Sciences, Agricultural Research Organization, Rishon-Lezion, Israel
| | - Noa Sela
- Institute of Plant Pathology and Weed Research, Agricultural Research Organization, Rishon-Lezion, Israel
| | - Dror Minz
- Institute of Soil, Water and Environmental Sciences, Agricultural Research Organization, Rishon-Lezion, Israel
| | - Ehud Banin
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Omer Frenkel
- Institute of Plant Pathology and Weed Research, Agricultural Research Organization, Rishon-Lezion, Israel
| | - Eddie Cytryn
- Institute of Soil, Water and Environmental Sciences, Agricultural Research Organization, Rishon-Lezion, Israel
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42
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Emara Y, Jolliet O, Finkbeiner M, Heß S, Kosnik M, Siegert MW, Fantke P. Comparative selective pressure potential of antibiotics in the environment. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 318:120873. [PMID: 36529346 DOI: 10.1016/j.envpol.2022.120873] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 12/11/2022] [Accepted: 12/12/2022] [Indexed: 06/17/2023]
Abstract
To guide both environmental and public health policy, it is important to assess the degree of antibiotic resistance selection pressure under measured environmental concentrations (MECs), and to compare the efficacy of different mitigation strategies to minimize the spread of resistance. To this end, the resistance selection and enrichment potential due to antibiotic emissions into the environment must be analysed from a life cycle perspective, for a wide range of antibiotics, and considering variations in the underlying fitness costs between different resistance mutations and genes. The aim of this study is to consistently derive fitness cost-dependent minimum selective concentrations (MSCs) from readily available bacterial inhibition data and to build MSC-based species sensitivity distributions (SSDs). These are then used to determine antibiotic-specific resistance selection concentrations predicted to promote resistance in 5% of exposed bacterial species (RSC5). Using a previously developed competition model, we provide estimated MSC10 endpoints for 2,984 antibiotic and bacterial species combinations; the largest set of modelled MSCs available to date. Based on constructed SSDs, we derive RSC5 for 128 antibiotics with four orders of magnitude difference in their 'selective pressure potential' in the environment. By comparing our RSC5 to MECs, we highlight specific environmental compartments (e.g. hospital and wastewater effluents, lakes and rivers), as well as several antibiotics (e.g. ciprofloxacin, norfloxacin, enrofloxacin, and tetracycline), to be scrutinized for their potential role in resistance selection and dissemination. In addition to enabling comparative risk screening of the selective pressure potential of multiple antibiotics, our SSD-derived RSC5 provide the point of departure for calculating new life cycle-based characterization factors for antibiotics to compare mitigation strategies, thereby contributing towards a 'One-Health' approach to tackling the global antibiotic resistance crisis.
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Affiliation(s)
- Yasmine Emara
- Quantitative Sustainability Assessment, Department of Environmental and Resource Engineering, Technical University of Denmark, 2800 Kgs, Lyngby, Denmark
| | - Olivier Jolliet
- Quantitative Sustainability Assessment, Department of Environmental and Resource Engineering, Technical University of Denmark, 2800 Kgs, Lyngby, Denmark; Department of Environmental Health Sciences, School of Public Health, University of Michigan, 1415 Washington Heights, Ann Arbor, MI, 48109, USA.
| | - Matthias Finkbeiner
- Department of Environmental Technology, Technical University Berlin, 10623, Berlin, Germany.
| | - Stefanie Heß
- Institute of Microbiology, Technische Universität Dresden, 01847, Dresden, Germany.
| | - Marissa Kosnik
- Quantitative Sustainability Assessment, Department of Environmental and Resource Engineering, Technical University of Denmark, 2800 Kgs, Lyngby, Denmark.
| | - Marc-William Siegert
- Department of Environmental Technology, Technical University Berlin, 10623, Berlin, Germany
| | - Peter Fantke
- Quantitative Sustainability Assessment, Department of Environmental and Resource Engineering, Technical University of Denmark, 2800 Kgs, Lyngby, Denmark.
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43
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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: 0] [Impact Index Per Article: 0] [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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44
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Baral B. Phages against killer superbugs: An enticing strategy against antibiotics-resistant pathogens. Front Pharmacol 2023; 14:1036051. [PMID: 36762109 PMCID: PMC9902939 DOI: 10.3389/fphar.2023.1036051] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 01/12/2023] [Indexed: 01/26/2023] Open
Abstract
The emerging resistivity of antibiotic resistance superbugs desire the need to resolve the global problem of antibiotic resistance. Among several other methods currently being adopted, one possible solution may be the development of supplemental therapies for antibiotics. The use of the normal and advanced bactericidal properties of bacteriophages (bacteriophage therapy) may be one of the viable infection control options. It is evident, however, that the safe and regulated application of phage treatment will need extensive knowledge of the characteristics and behaviour of certain phage-bacterium systems. This mini review offers an overview of the potential for phage therapy as well as the constraints and obstacles it faces in becoming a commonly accepted infection management strategy.
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Conjugative RP4 Plasmid-Mediated Transfer of Antibiotic Resistance Genes to Commensal and Multidrug-Resistant Enteric Bacteria In Vitro. Microorganisms 2023; 11:microorganisms11010193. [PMID: 36677486 PMCID: PMC9860721 DOI: 10.3390/microorganisms11010193] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 12/30/2022] [Accepted: 01/05/2023] [Indexed: 01/15/2023] Open
Abstract
Many antibiotic-resistant bacteria carry resistance genes on conjugative plasmids that are transferable to commensals and pathogens. We determined the ability of multiple enteric bacteria to acquire and retransfer a broad-host-range plasmid RP4. We used human-derived commensal Escherichia coli LM715-1 carrying a chromosomal red fluorescent protein gene and green fluorescent protein (GFP)-labeled broad-host-range RP4 plasmid with ampR, tetR, and kanR in in vitro matings to rifampicin-resistant recipients, including Escherichia coli MG1655, Dec5α, Vibrio cholerae, Pseudomonas putida, Pseudomonas aeruginosa, Klebsiella pneumoniae, Citrobacter rodentium, and Salmonella Typhimurium. Transconjugants were quantified on selective media and confirmed using fluorescence microscopy and PCR for the GFP gene. The plasmid was transferred from E. coli LM715-1 to all tested recipients except P. aeruginosa. Transfer frequencies differed between specific donor-recipient pairings (10-2 to 10-8). Secondary retransfer of plasmid from transconjugants to E. coli LM715-1 occurred at frequencies from 10-2 to 10-7. A serial passage plasmid persistence assay showed plasmid loss over time in the absence of antibiotics, indicating that the plasmid imposed a fitness cost to its host, although some plasmid-bearing cells persisted for at least ten transfers. Thus, the RP4 plasmid can transfer to multiple clinically relevant bacterial species without antibiotic selection pressure.
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Iweriebor BC, Egbule OS, Obi LC. The Emergence of Colistin- and Imipenem-Associated Multidrug Resistance in Escherichia coli Isolates from Retail Meat. Pol J Microbiol 2022; 71:519-528. [PMID: 36473114 PMCID: PMC9944967 DOI: 10.33073/pjm-2022-046] [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: 07/15/2022] [Accepted: 09/19/2022] [Indexed: 12/12/2022] Open
Abstract
To determine the prevalence of Escherichia coli and their drug resistance profiles in fresh pork sold at two retail outlets (open-air market and closed retail stores) in Alice, South Africa. Retail meat samples (n = 176) collected from four shops (two from open-air markets and two from closed stores) were analyzed by conventional biochemical and PCR-based molecular confirmatory tests. The confirmed isolates were profiled for antimicrobial susceptibility to a panel of 12 commercial antibiotics: tetracycline, ampicillin, sulphamethoxazole trimethoprim, erythromycin, gentamycin, colistin sulphate, cefotaxime, chloramphenicol, norfloxacin, ciprofloxacin, cefuroxime, and imipenem. Colistin, ampicillin, and erythromycin resistance genes were profiled with the gene-specific primers. Multidrug resistance (MDR) and the association of imipenem and colistin in the MDR profile were determined. A total of 68 (39.08%) E. coli isolates were confirmed by PCR analysis. Resistance was most common to erythromycin (100%), followed by cefotaxime (95.58%), ampicillin (88.23%), cefuroxime (88.23%), trimethoprim-sulphamethoxazole (88.23%), and tetracycline (60.29%). Overall, 27/68 (39.70%) were MDR (≥ 3antibiotics classes). MDR E. coli isolates associated with imipenem resistance (50.00%) and colistin resistance (33.82%) were detected. The resistance genes were detected among the isolates though not in all the phenotypically resistant isolates. The detection of colistin resistance among MDR E. coli isolates from retail meat is troubling as the drug is a last resort antibiotic. Overall, the epidemiological implications of the findings are of public health importance.
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Affiliation(s)
- Benson Chuks Iweriebor
- School of Science and Technology, Sefako Makgatho Health Sciences University, Ga‑Rankuwa, South Africa, B.C. Iweriebor, School of Science and Technology, Sefako Makgatho Health Sciences University, Ga-Rankuwa, South Africa
| | | | - Larry C. Obi
- School of Science and Technology, Sefako Makgatho Health Sciences University, Ga‑Rankuwa, South Africa
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47
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Nava AR, Daneshian L, Sarma H. Antibiotic resistant genes in the environment-exploring surveillance methods and sustainable remediation strategies of antibiotics and ARGs. ENVIRONMENTAL RESEARCH 2022; 215:114212. [PMID: 36037921 DOI: 10.1016/j.envres.2022.114212] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 08/05/2022] [Accepted: 08/22/2022] [Indexed: 06/15/2023]
Abstract
Antibiotic Resistant Genes (ARGs) are an emerging environmental health threat due to the potential change in the human microbiome and selection for the emergence of antibiotic resistant bacteria. The rise of antibiotic resistant bacteria has caused a global health burden. The WHO (world health organization) predicts a rise in deaths due to antibiotic resistant infections. Since bacteria can acquire ARGs through horizontal transmission, it is important to assess the dissemination of antibioticresistant genes from anthropogenic sources. There are several sources of antibiotics, antibiotic resistant bacteria and genes in the environment. These include wastewater treatment plants, landfill leachate, agricultural, animal industrial sources and estuaries. The use of antibiotics is a worldwide practice that has resulted in the evolution of resistance to antibiotics. Our review provides a more comprehensive look into multiple sources of ARG's and antibiotics rather than one. Moreover, we focus on effective surveillance methods of ARGs and antibiotics and sustainable abiotic and biotic remediation strategies for removal and reduction of antibiotics and ARGs from both terrestrial and aquatic environments. Further, we consider the impact on public health as this problem cannot be addressed without a global transdisciplinary effort.
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Affiliation(s)
- Amy R Nava
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, 94305, USA.
| | - Leily Daneshian
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, 94305, USA.
| | - Hemen Sarma
- Bioremediation Technology Research Group, Department of Botany, Bodoland University, Rangalikhata, Deborgaon, Kokrajhar (BTR), Assam, 783370, India.
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48
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Orata FD, Hussain NAS, Liang KYH, Hu D, Boucher YF. Genomes of Vibrio metoecus co-isolated with Vibrio cholerae extend our understanding of differences between these closely related species. Gut Pathog 2022; 14:42. [PMID: 36404338 PMCID: PMC9677704 DOI: 10.1186/s13099-022-00516-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 11/04/2022] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Vibrio cholerae, the causative agent of cholera, is a well-studied species, whereas Vibrio metoecus is a recently described close relative that is also associated with human infections. The availability of V. metoecus genomes provides further insight into its genetic differences from V. cholerae. Additionally, both species have been co-isolated from a cholera-free brackish coastal pond and have been suggested to interact with each other by horizontal gene transfer (HGT). RESULTS The genomes of 17 strains from each species were sequenced. All strains share a large core genome (2675 gene families) and very few genes are unique to each species (< 3% of the pan-genome of both species). This led to the identification of potential molecular markers-for nitrite reduction, as well as peptidase and rhodanese activities-to further distinguish V. metoecus from V. cholerae. Interspecies HGT events were inferred in 21% of the core genes and 45% of the accessory genes. A directional bias in gene transfer events was found in the core genome, where V. metoecus was a recipient of three times (75%) more genes from V. cholerae than it was a donor (25%). CONCLUSION V. metoecus was misclassified as an atypical variant of V. cholerae due to their resemblance in a majority of biochemical characteristics. More distinguishing phenotypic assays can be developed based on the discovery of potential gene markers to avoid any future misclassifications. Furthermore, differences in relative abundance or seasonality were observed between the species and could contribute to the bias in directionality of HGT.
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Affiliation(s)
- Fabini D. Orata
- grid.17089.370000 0001 2190 316XDepartment of Biological Sciences, University of Alberta, Edmonton, Alberta Canada ,grid.17089.370000 0001 2190 316XDepartment of Chemical and Materials Engineering, University of Alberta, Edmonton, Alberta Canada
| | - Nora A. S. Hussain
- grid.17089.370000 0001 2190 316XDepartment of Biological Sciences, University of Alberta, Edmonton, Alberta Canada
| | - Kevin Y. H. Liang
- grid.17089.370000 0001 2190 316XDepartment of Biological Sciences, University of Alberta, Edmonton, Alberta Canada ,grid.14709.3b0000 0004 1936 8649Department of Quantitative Life Sciences, McGill University, Montréal, Québec Canada ,grid.14709.3b0000 0004 1936 8649Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec Canada
| | - Dalong Hu
- grid.4280.e0000 0001 2180 6431Saw Swee Hock School of Public Health, National University of Singapore and National University Hospital System, Singapore, Singapore ,grid.4280.e0000 0001 2180 6431Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore, Singapore
| | - Yann F. Boucher
- grid.17089.370000 0001 2190 316XDepartment of Biological Sciences, University of Alberta, Edmonton, Alberta Canada ,grid.4280.e0000 0001 2180 6431Saw Swee Hock School of Public Health, National University of Singapore and National University Hospital System, Singapore, Singapore ,grid.4280.e0000 0001 2180 6431Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore, Singapore ,grid.4280.e0000 0001 2180 6431Infectious Diseases Translational Research Program, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore and National University Hospital System, Singapore, Singapore
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Abstract
Gene-by-environment interactions play a crucial role in horizontal gene transfer by affecting how the transferred genes alter host fitness. However, how the environment modulates the fitness effect of transferred genes has not been tested systematically in an experimental study. We adapted a high-throughput technique for obtaining very precise estimates of bacterial fitness, in order to measure the fitness effects of 44 orthologs transferred from Salmonella Typhimurium to Escherichia coli in six physiologically relevant environments. We found that the fitness effects of individual genes were highly dependent on the environment, while the distributions of fitness effects across genes were not, with all tested environments resulting in distributions of same shape and spread. Furthermore, the extent to which the fitness effects of a gene varied between environments depended on the average fitness effect of that gene across all environments, with nearly neutral and nearly lethal genes having more consistent fitness effects across all environments compared to deleterious genes. Put together, our results reveal the unpredictable nature of how environmental conditions impact the fitness effects of each individual gene. At the same time, distributions of fitness effects across environments exhibit consistent features, pointing to the generalizability of factors that shape horizontal gene transfer of orthologous genes.
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Affiliation(s)
- Hande Acar Kirit
- Veterinary and Ecological Sciences, Institute of Infection, University of Liverpool, Liverpool, Merseyside, United Kingdom
- Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, Norman, OK
- Department of Anthropology, University of Oklahoma, Norman, OK
| | - Jonathan P Bollback
- Veterinary and Ecological Sciences, Institute of Infection, University of Liverpool, Liverpool, Merseyside, United Kingdom
| | - Mato Lagator
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
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50
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Yu Z, Zhang L, Huang Q, Dong S, Wang X, Yan C. Combined effects of micro-/nano-plastics and oxytetracycline on the intestinal histopathology and microbiome in zebrafish (Danio rerio). THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 843:156917. [PMID: 35772560 DOI: 10.1016/j.scitotenv.2022.156917] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 05/23/2022] [Accepted: 06/19/2022] [Indexed: 06/15/2023]
Abstract
Accumulated evidence has demonstrated that microplastics and oxytetracycline (OTC) affect organisms, but few studies have investigated their combined effects on aquatic organisms. In this study, adult zebrafish (Danio rerio) were exposed to single and binary-combined contamination of micro-, nano-sized polystyrene plastics and OTC for 30 days, and the intestinal histopathology, gut microbiota and antibiotic resistance genes (ARGs) of zebrafish were measured. The results showed that the intestinal epithelial damage increase with the decrease of plastic sizes. Nano-sized plastics, OTC and their combined exposure caused intestinal epithelial damage, and co-exposure with micro-sized plastics reduced the intestinal damage caused by single OTC exposure. The gut microbial communities were affected by the combined exposure to microplastics and OTC. Compared with the blank control, the relative abundance of Fusobacteria increased 12.7 % and 21.1 % in OTC combined with 45-85 μm micro-plastics (MOTC) and 40-54 nm nano-plastics (NOTC), respectively, and that of Bacteroidetes increased 26.2 % and 18.6 % in the MOTC and NOTC treatments, respectively. The effects of MOTC and NOTC on the biodiversity of the zebrafish gut microbiome were different; MOTC increased the biodiversity by 11.3 % compared with the blank control, whereas NOTC decreased the biodiversity by 8.8 % compared with the blank control. Furthermore, the abundance of ARGs in 40-54 nm nano-plastics, MOTC and NOTC treatments was increased 96.9 %, 96.6 % and 68.8 % compared with the control group, respectively. Additionally, significant differences were observed in ARGs characteristics between the micro- and nano-plastics treated groups whether combined with OTC or not. These results are essential to further understand the combined ecotoxicological effects of micro- or nano-plastics and antibiotics on aquatic organisms.
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Affiliation(s)
- Ziyue Yu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ling Zhang
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qiansheng Huang
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Sijun Dong
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002, China
| | - Xinhong Wang
- College of the Environment and Ecology, Xiamen University, Xiamen 361102, China
| | - Changzhou Yan
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.
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