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Behling AH, Wilson BC, Ho D, Cutfield WS, Vatanen T, O'Sullivan JM. Horizontal gene transfer after faecal microbiota transplantation in adolescents with obesity. MICROBIOME 2024; 12:26. [PMID: 38347627 PMCID: PMC10860221 DOI: 10.1186/s40168-024-01748-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 01/02/2024] [Indexed: 02/15/2024]
Abstract
BACKGROUND Horizontal gene transfer (HGT) describes the transmission of DNA outside of direct ancestral lineages. The process is best characterised within the bacterial kingdom and can enable the acquisition of genetic traits that support bacterial adaptation to novel niches. The adaptation of bacteria to novel niches has particular relevance for faecal microbiota transplantation (FMT), a therapeutic procedure which aims to resolve gut-related health conditions of individuals, through transplanted gut microbiota from healthy donors. RESULTS Three hundred eighty-one stool metagenomic samples from a placebo-controlled FMT trial for obese adolescents (the Gut Bugs Trial) were analysed for HGT, using two complementary methodologies. First, all putative HGT events, including historical HGT signatures, were quantified using the bioinformatics application WAAFLE. Second, metagenomic assembly and gene clustering were used to assess and quantify donor-specific genes transferred to recipients following the intervention. Both methodologies found no difference between the level of putative HGT events in the gut microbiomes of FMT and placebo recipients, post-intervention. HGT events facilitated by engrafted donor species in the FMT recipient gut at 6 weeks post-intervention were identified and characterised. Bacterial strains contributing to this subset of HGT events predominantly belonged to the phylum Bacteroidetes. Engraftment-dependent horizontally transferred genes were retained within recipient microbiomes at 12 and 26 weeks post-intervention. CONCLUSION Our study suggests that novel microorganisms introduced into the recipient gut following FMT have no impact on the basal rate of HGT within the human gut microbiome. Analyses of further FMT studies are required to assess the generalisability of this conclusion across different FMT study designs and for the treatment of different gut-related conditions. Video Abstract.
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Affiliation(s)
- Anna H Behling
- Liggins Institute, University of Auckland, Auckland, New Zealand
| | - Brooke C Wilson
- Liggins Institute, University of Auckland, Auckland, New Zealand
| | - Daniel Ho
- Liggins Institute, University of Auckland, Auckland, New Zealand
| | - Wayne S Cutfield
- Liggins Institute, University of Auckland, Auckland, New Zealand
| | - Tommi Vatanen
- Liggins Institute, University of Auckland, Auckland, New Zealand.
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland.
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Justin M O'Sullivan
- Liggins Institute, University of Auckland, Auckland, New Zealand.
- The Maurice Wilkins Centre, The University of Auckland, Private Bag 92019, Auckland, New Zealand.
- Australian Parkinsons Mission, Garvan Institute of Medical Research, 384 Victoria Street, SydneyDarlinghurst, NSWNSW, 2010, Australia.
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, SO16 6YD, UK.
- Singapore Institute for Clinical Sciences, Agency for Science Technology and Research, Singapore, Singapore.
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Subramaniam S, Joyce P, Ogunniyi AD, Dube A, Sampson SL, Lehr CM, Prestidge CA. Minimum Information for Conducting and Reporting In Vitro Intracellular Infection Assays. ACS Infect Dis 2024; 10:337-349. [PMID: 38295053 DOI: 10.1021/acsinfecdis.3c00613] [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] [Indexed: 02/02/2024]
Abstract
Bacterial pathogens are constantly evolving to outsmart the host immune system and antibiotics developed to eradicate them. One key strategy involves the ability of bacteria to survive and replicate within host cells, thereby causing intracellular infections. To address this unmet clinical need, researchers are adopting new approaches, such as the development of novel molecules that can penetrate host cells, thus exerting their antimicrobial activity intracellularly, or repurposing existing antibiotics using nanocarriers (i.e., nanoantibiotics) for site-specific delivery. However, inconsistency in information reported across published studies makes it challenging for scientific comparison and judgment of experiments for future direction by researchers. Together with the lack of reproducibility of experiments, these inconsistencies limit the translation of experimental results beyond pre-clinical evaluation. Minimum information guidelines have been instrumental in addressing such challenges in other fields of biomedical research. Guidelines and recommendations provided herein have been designed for researchers as essential parameters to be disclosed when publishing their methodology and results, divided into four main categories: (i) experimental design, (ii) establishing an in vitro model, (iii) assessment of efficacy of novel therapeutics, and (iv) statistical assessment. These guidelines have been designed with the intention to improve the reproducibility and rigor of future studies while enabling quantitative comparisons of published studies, ultimately facilitating translation of emerging antimicrobial technologies into clinically viable therapies that safely and effectively treat intracellular infections.
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Affiliation(s)
- Santhni Subramaniam
- UniSA Clinical and Health Sciences, University of South Australia, Adelaide, SA 5000, Australia
| | - Paul Joyce
- UniSA Clinical and Health Sciences, University of South Australia, Adelaide, SA 5000, Australia
| | - Abiodun D Ogunniyi
- Australian Centre for Antimicrobial Resistance Ecology, School of Animal and Veterinary Sciences, Roseworthy Campus, University of Adelaide, Roseworthy, SA 5371, Australia
| | - Admire Dube
- School of Pharmacy, University of the Western Cape, Bellville, 7535 Cape Town, South Africa
| | - Samantha L Sampson
- South African Medical Research Council Centre for Tuberculosis Research, and Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Stellenbosch, 7602 Cape Town, South Africa
| | - Claus-Michael Lehr
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Campus Building E 8.1, 66123 Saarbrücken, Germany
- Department of Pharmacy, Saarland University, Campus Building E8.1, 66123 Saarbrücken, Germany
| | - Clive A Prestidge
- UniSA Clinical and Health Sciences, University of South Australia, Adelaide, SA 5000, Australia
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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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54
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Wang M, Wang C, Yang J, Liu X, Xie B, Ren P, Kong X, Fu Y. Biochar induces different responses of intracellular and extracellular antibiotic resistance genes and suppresses horizontal transfer during lincomycin fermentation dregs composting. BIORESOURCE TECHNOLOGY 2024; 394:130227. [PMID: 38135225 DOI: 10.1016/j.biortech.2023.130227] [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: 12/04/2023] [Revised: 12/18/2023] [Accepted: 12/18/2023] [Indexed: 12/24/2023]
Abstract
This study aims to indicate the influence of biochar on extracellular and intracellular ARGs (e/iARGs) variation and proliferation during lincomycin fermentation dregs (LFDs) compost. Biochar addition made iARGs keep reducing but eARGs increase to the maximum at the middle thermophilic phase and reduce at the end of the compost. Compared to control 3.15-log and 5.42-log reduction of iARGs and eARGs were observed, respectively. Biochar addition, bacterial community, and MGEs were the major contributors to iARGs and eARGs removal, with the contribution percentages of 38.4%, 31.0%, 23.7%, and 27.2%, 29.1%, and 34.9%, respectively. Moreover, biochar significantly inhibited eARGs transformation and RP4 plasmid conjugative transfer among E. coli DH5α and Pseudomonas aeruginosa HLS-6. The underlying mechanism involved in broken cell membranes of bacteria, and altered expression of oxidative stress genes and save our souls (SOS) response-related genes. The results indicated that biochar addition in composting could limit the dissemination of ARGs.
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Affiliation(s)
- Mengmeng Wang
- College of Environment and Safety Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Chenhao Wang
- College of Environment and Safety Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Jie Yang
- College of Environment and Safety Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Xiangyu Liu
- College of Environment and Safety Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Binghan Xie
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai 264209, China
| | - Peng Ren
- Laoshan Laboratory, Qingdao 266061, China
| | - Xiaowei Kong
- College of Environment and Safety Engineering, Qingdao University of Science and Technology, Qingdao 266042, China.
| | - Yunxia Fu
- Key Laboratory of Geological Safety of Coastal Urban Underground Space, Ministry of Natural Resources, Qingdao 266100, China; Qingdao Geo-Engineering Surveying Institute (Qingdao Geological Exploration Development Bureau), Qingdao 266100, China
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55
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Paganini JA, Kerkvliet JJ, Vader L, Plantinga NL, Meneses R, Corander J, Willems RJL, Arredondo-Alonso S, Schürch AC. PlasmidEC and gplas2: an optimized short-read approach to predict and reconstruct antibiotic resistance plasmids in Escherichia coli. Microb Genom 2024; 10:001193. [PMID: 38376388 PMCID: PMC10926690 DOI: 10.1099/mgen.0.001193] [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: 09/19/2023] [Accepted: 01/22/2024] [Indexed: 02/21/2024] Open
Abstract
Accurate reconstruction of Escherichia coli antibiotic resistance gene (ARG) plasmids from Illumina sequencing data has proven to be a challenge with current bioinformatic tools. In this work, we present an improved method to reconstruct E. coli plasmids using short reads. We developed plasmidEC, an ensemble classifier that identifies plasmid-derived contigs by combining the output of three different binary classification tools. We showed that plasmidEC is especially suited to classify contigs derived from ARG plasmids with a high recall of 0.941. Additionally, we optimized gplas, a graph-based tool that bins plasmid-predicted contigs into distinct plasmid predictions. Gplas2 is more effective at recovering plasmids with large sequencing coverage variations and can be combined with the output of any binary classifier. The combination of plasmidEC with gplas2 showed a high completeness (median=0.818) and F1-Score (median=0.812) when reconstructing ARG plasmids and exceeded the binning capacity of the reference-based method MOB-suite. In the absence of long-read data, our method offers an excellent alternative to reconstruct ARG plasmids in E. coli.
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Affiliation(s)
- Julian A. Paganini
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Jesse J. Kerkvliet
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Lisa Vader
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Nienke L. Plantinga
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Rodrigo Meneses
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Jukka Corander
- Department of Biostatistics, Faculty of Medicine, University of Oslo, Oslo, Norway
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK
- Helsinki Institute of Information Technology, Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
| | - Rob J. L. Willems
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Sergio Arredondo-Alonso
- Department of Biostatistics, Faculty of Medicine, University of Oslo, Oslo, Norway
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK
| | - Anita C. Schürch
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
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56
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Bernabeu M, Cabello-Yeves E, Flores E, Samarra A, Kimberley Summers J, Marina A, Collado MC. Role of vertical and horizontal microbial transmission of antimicrobial resistance genes in early life: insights from maternal-infant dyads. Curr Opin Microbiol 2024; 77:102424. [PMID: 38237429 DOI: 10.1016/j.mib.2023.102424] [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: 11/16/2023] [Revised: 12/19/2023] [Accepted: 12/20/2023] [Indexed: 02/12/2024]
Abstract
Early life represents a critical window for metabolic, cognitive and immune system development, which is influenced by the maternal microbiome as well as the infant gut microbiome. Antibiotic exposure, mode of delivery and breastfeeding practices modulate the gut microbiome and the reservoir of antibiotic resistance genes (ARGs). Vertical and horizontal microbial gene transfer during early life and the mechanisms behind these transfers are being uncovered. In this review, we aim to provide an overview of the current knowledge on the transfer of antibiotic resistance in the mother-infant dyad through vertical and horizontal transmission and to highlight the main gaps and challenges in this area.
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Affiliation(s)
- Manuel Bernabeu
- Institute of Agrochemistry and Food Technology - National Research Council (IATA-CSIC), 46980 Valencia, Spain.
| | - Elena Cabello-Yeves
- Instituto de Biomedicina de Valencia-Consejo de Investigaciones Científicas (IBV-CSIC), CIBER de Enfermedades Raras (CIBERER), 46010 Valencia, Spain.
| | - Eduard Flores
- Institute of Agrochemistry and Food Technology - National Research Council (IATA-CSIC), 46980 Valencia, Spain
| | - Anna Samarra
- Institute of Agrochemistry and Food Technology - National Research Council (IATA-CSIC), 46980 Valencia, Spain
| | - Joanna Kimberley Summers
- Wellington Lab, School of Life Sciences, University of Warwick, CV4 7AL Coventry, United Kingdom
| | - Alberto Marina
- Instituto de Biomedicina de Valencia-Consejo de Investigaciones Científicas (IBV-CSIC), CIBER de Enfermedades Raras (CIBERER), 46010 Valencia, Spain
| | - M Carmen Collado
- Institute of Agrochemistry and Food Technology - National Research Council (IATA-CSIC), 46980 Valencia, Spain
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57
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Han Z, Luan X, Feng H, Deng Y, Yang M, Zhang Y. Metagenomic insights into microorganisms and antibiotic resistance genes of waste antibiotic fermentation residues along production, storage and treatment processes. J Environ Sci (China) 2024; 136:45-55. [PMID: 37923454 DOI: 10.1016/j.jes.2022.10.035] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 10/24/2022] [Accepted: 10/24/2022] [Indexed: 11/07/2023]
Abstract
Antibiotic fermentation residue (AFR) is nutrient-rich solid waste generated from fermentative antibiotic production process. It is demonstrated that AFR contains high-concentration of remaining antibiotics, and thus may promote antibiotic resistance development in receiving environment or feeding farmed animals. However, the dominate microorganisms and antibiotic resistance genes (ARGs) in AFRs have not been adequately explored, hampering understanding on the potential antibiotic resistance risk development caused by AFRs. Herein, seven kinds of representative AFRs along their production, storage, and treatment processes were collected, and multiple methods including amplicon sequencing, metagenomic sequencing, and bioinformatic approaches were adopted to explore the biological characteristics of AFRs. As expected, antibiotic fermentation producer was found as the predominant species in raw AFRs, which were collected at the outlet of fermentation tanks. However, except for producer species, more environment-derived species persisted in stored AFRs, which were temporarily stored at a semi-open space. Lactobacillus genus, classified as Firmicutes phylum and Bacilli class, became predominant bacterial taxa in stored AFRs, which might attribute to its tolerance to high concentration of antibiotics. Results from metagenomic sequencing together with assembly and binning approaches showed that these newly-colonizing species (e.g., Lactobacillus genus) tended to carry ARGs conferring resistance to the remaining antibiotic. However, after thermal treatment, remaining antibiotic could be efficiently removed from AFRs, and microorganisms together with DNA could be strongly destroyed. In sum, the main risk from the AFRs was the remaining antibiotic, while environment-derived bacteria which tolerate extreme environment, survived in ARFs with high content antibiotics, and may carry ARGs. Thus, hydrothermal or other harmless treatment technologies are recommended to remove antibiotic content and inactivate bacteria before recycling of AFRs in pharmaceutical industry.
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Affiliation(s)
- Ziming Han
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiao Luan
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Haodi Feng
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Yanqin Deng
- Wuhan Agricultural Inspection Center, Wuhan 430016, China
| | - Min Yang
- National Engineering Research Center of Industrial Wastewater Detoxication and Resource Recovery, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yu Zhang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; National Engineering Research Center of Industrial Wastewater Detoxication and Resource Recovery, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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58
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Djordjevic SP, Jarocki VM, Seemann T, Cummins ML, Watt AE, Drigo B, Wyrsch ER, Reid CJ, Donner E, Howden BP. Genomic surveillance for antimicrobial resistance - a One Health perspective. Nat Rev Genet 2024; 25:142-157. [PMID: 37749210 DOI: 10.1038/s41576-023-00649-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/02/2023] [Indexed: 09/27/2023]
Abstract
Antimicrobial resistance (AMR) - the ability of microorganisms to adapt and survive under diverse chemical selection pressures - is influenced by complex interactions between humans, companion and food-producing animals, wildlife, insects and the environment. To understand and manage the threat posed to health (human, animal, plant and environmental) and security (food and water security and biosecurity), a multifaceted 'One Health' approach to AMR surveillance is required. Genomic technologies have enabled monitoring of the mobilization, persistence and abundance of AMR genes and mutations within and between microbial populations. Their adoption has also allowed source-tracing of AMR pathogens and modelling of AMR evolution and transmission. Here, we highlight recent advances in genomic AMR surveillance and the relative strengths of different technologies for AMR surveillance and research. We showcase recent insights derived from One Health genomic surveillance and consider the challenges to broader adoption both in developed and in lower- and middle-income countries.
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Affiliation(s)
- Steven P Djordjevic
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Sydney, New South Wales, Australia.
- Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Sydney, New South Wales, Australia.
| | - Veronica M Jarocki
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Sydney, New South Wales, Australia
- Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Torsten Seemann
- Centre for Pathogen Genomics, University of Melbourne, Melbourne, Victoria, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, University of Melbourne at the Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Max L Cummins
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Sydney, New South Wales, Australia
- Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Anne E Watt
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, University of Melbourne at the Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Barbara Drigo
- UniSA STEM, University of South Australia, Adelaide, South Australia, Australia
- Future Industries Institute, University of South Australia, Adelaide, South Australia, Australia
| | - Ethan R Wyrsch
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Sydney, New South Wales, Australia
- Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Cameron J Reid
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Sydney, New South Wales, Australia
- Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Erica Donner
- Future Industries Institute, University of South Australia, Adelaide, South Australia, Australia
- Cooperative Research Centre for Solving Antimicrobial Resistance in Agribusiness, Food, and Environments (CRC SAAFE), Adelaide, South Australia, Australia
| | - Benjamin P Howden
- Centre for Pathogen Genomics, University of Melbourne, Melbourne, Victoria, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, University of Melbourne at the Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
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59
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Liu W, Sun C, Ren Z, Hao S, Chen Z, Li T, Wen X. Long-term occurrence, resistance risk and chaotic characteristics of antibiotic resistance genes in sludge anaerobic digestion system. BIORESOURCE TECHNOLOGY 2024; 394:130267. [PMID: 38154733 DOI: 10.1016/j.biortech.2023.130267] [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: 11/07/2023] [Revised: 12/08/2023] [Accepted: 12/25/2023] [Indexed: 12/30/2023]
Abstract
The long-term occurrence, dynamics and risk of antibiotic resistance genes (ARGs) in anaerobic digestion (AD) of excess sludge (ES) are not fully understood. Therefore, 13-month metagenomic monitoring was carried out in a full-scale AD plant. The highest ARG abundance and risk scores were observed in spring. AD achieved a 35 % removal rate for the total ARG abundance, but the risk score of AD sludge was not always lower than ES samples, because of the higher proportion of Rank I ARGs in AD sludge. ARGs showed less obvious patterns under linear models compared with microbial community, implying their chaotic dynamics, which was further confirmed by nonlinearity tests. Empirical dynamic modeling performed better than the autoregressive integrated moving average model for ARG dynamics, especially for those with simple and nonlinear dynamics. This study highlighted spring for its higher ARG abundance and risk, and recommended nonlinear models for revealing the dynamics of ARGs.
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Affiliation(s)
- Wei Liu
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Chenxiang Sun
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Zhengran Ren
- Research and Development Center, Beijing Drainage Group Co. Ltd., Beijing 100080, China
| | - Shan Hao
- Research and Development Center, Beijing Drainage Group Co. Ltd., Beijing 100080, China
| | - Zhan Chen
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Tianle Li
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Xianghua Wen
- School of Environment, Tsinghua University, Beijing 100084, China.
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60
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Gama GSP, Pimenta AS, Feijó FMC, de Azevedo TKB, de Melo RR, de Andrade GS. The Potential of Wood Vinegar to Replace Antimicrobials Used in Animal Husbandry-A Review. Animals (Basel) 2024; 14:381. [PMID: 38338024 PMCID: PMC10854697 DOI: 10.3390/ani14030381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 12/16/2023] [Accepted: 12/27/2023] [Indexed: 02/12/2024] Open
Abstract
The indiscriminate use of antimicrobials in animal husbandry can result in various types of environmental contamination. Part of the dose of these products is excreted, still active, in the animals' feces and urine. These excreta are widely used as organic fertilizers, which results in contamination with antimicrobial molecules. The impacts can occur in several compartments, such as soil, groundwater, and surface watercourses. Also, contamination by antimicrobials fed or administrated to pigs, chickens, and cattle can reach the meat, milk, and other animal products, which calls into question the sustainability of using these products as part of eco-friendly practices. Therefore, a search for alternative natural products is required to replace the conventional antimicrobials currently used in animal husbandry, aiming to mitigate environmental contamination. We thus carried out a review addressing this issue, highlighting wood vinegar (WV), also known as pyroligneous acid, as an alternative antimicrobial with good potential to replace conventional products. In this regard, many studies have demonstrated that WV is a promising product. WV is a nontoxic additive widely employed in the food industry to impart a smoked flavor to foods. Studies have shown that, depending on the WV concentration, good results can be achieved using it as an antimicrobial against pathogenic bacteria and fungi and a valuable growth promoter for poultry and pigs.
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Affiliation(s)
- Gil Sander Próspero Gama
- Graduate Program in Forest Sciences, Forest Engineering, Universidade Federal do Rio Grande do Norte, Rodovia RN 160, km 03 s/n, Distrito de Jundiaí, Macaíba CEP 59.280-000, Brazil; (G.S.P.G.); (A.S.P.); (T.K.B.d.A.); (G.S.d.A.)
| | - Alexandre Santos Pimenta
- Graduate Program in Forest Sciences, Forest Engineering, Universidade Federal do Rio Grande do Norte, Rodovia RN 160, km 03 s/n, Distrito de Jundiaí, Macaíba CEP 59.280-000, Brazil; (G.S.P.G.); (A.S.P.); (T.K.B.d.A.); (G.S.d.A.)
| | - Francisco Marlon Carneiro Feijó
- Graduate Program in Environment, Technology, and Society—PPGATS, Laboratory of Veterinary Microbiology and Laboratory of Wood Technology, Universidade Federal Rural do Semiárido—UFERSA, Av. Francisco Mota, 572—Bairro Costa e Silva, Mossoró CEP 59.625-900, Brazil;
| | - Tatiane Kelly Barbosa de Azevedo
- Graduate Program in Forest Sciences, Forest Engineering, Universidade Federal do Rio Grande do Norte, Rodovia RN 160, km 03 s/n, Distrito de Jundiaí, Macaíba CEP 59.280-000, Brazil; (G.S.P.G.); (A.S.P.); (T.K.B.d.A.); (G.S.d.A.)
| | - Rafael Rodolfo de Melo
- Graduate Program in Environment, Technology, and Society—PPGATS, Laboratory of Veterinary Microbiology and Laboratory of Wood Technology, Universidade Federal Rural do Semiárido—UFERSA, Av. Francisco Mota, 572—Bairro Costa e Silva, Mossoró CEP 59.625-900, Brazil;
| | - Gabriel Siqueira de Andrade
- Graduate Program in Forest Sciences, Forest Engineering, Universidade Federal do Rio Grande do Norte, Rodovia RN 160, km 03 s/n, Distrito de Jundiaí, Macaíba CEP 59.280-000, Brazil; (G.S.P.G.); (A.S.P.); (T.K.B.d.A.); (G.S.d.A.)
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Zhang T, Mu Y, Gao Y, Tang Y, Mao S, Liu J. Fecal microbial gene transfer contributes to the high-grain diet-induced augmentation of aminoglycoside resistance in dairy cattle. mSystems 2024; 9:e0081023. [PMID: 38085089 PMCID: PMC10805029 DOI: 10.1128/msystems.00810-23] [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: 08/02/2023] [Accepted: 10/31/2023] [Indexed: 01/24/2024] Open
Abstract
A high-grain (HG) diet can rapidly lower the rumen pH and thus modify the gastrointestinal microbiome in dairy cattle. Although the prevalence of antibiotic resistance is strongly linked with the gut microbiome, the influences of HG diet on animals' gut resistome remain largely unexplored. Here, we examined the impact and mechanism of an HG diet on the fecal resistome in dairy cattle by metagenomically characterizing the gut microbiome. Eight lactating Holstein cattle were randomly allocated into two groups and fed either a conventional (CON) or HG diet for 3 weeks. The fecal microbiome and resistome were significantly altered in dairy cattle from HG, demonstrating an adaptive response that peaks at day 14 after the dietary transition. Importantly, we determined that feeding an HG diet specifically elevated the prevalence of resistance to aminoglycosides (0.11 vs 0.24 RPKG, P < 0.05). This diet-induced resistance increase is interrelated with the disproportional propagation of microbes in Lachnospiraceae, indicating a potential reservoir of aminoglycosides resistance. We further showed that the prevalence of acquired resistance genes was also modified by introducing a different diet, likely due to the augmented frequency of lateral gene transfer (LGT) in microbes (CON vs HG: 254 vs 287 taxa) such as Lachnospiraceae. Consequently, we present that diet transition is associated with fecal resistome modification in dairy cattle and an HG diet specifically enriched aminoglycosides resistance that is likely by stimulating microbial LGT.IMPORTANCEThe increasing prevalence of antimicrobial resistance is one of the most severe threats to public health, and developing novel mitigation strategies deserves our top priority. High-grain (HG) diet is commonly applied in dairy cattle to enhance animals' performance to produce more high-quality milk. We present that despite such benefits, the application of an HG diet is correlated with an elevated prevalence of resistance to aminoglycosides, and this is a combined effect of the expansion of antibiotic-resistant bacteria and increased frequency of lateral gene transfer in the fecal microbiome of dairy cattle. Our results provided new knowledge in a typically ignored area by showing an unexpected enrichment of antibiotic resistance under an HG diet. Importantly, our findings laid the foundation for designing potential dietary intervention strategies to lower the prevalence of antibiotic resistance in dairy production.
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Affiliation(s)
- Tao Zhang
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Yingyu Mu
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Yunlong Gao
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Yijun Tang
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Shengyong Mao
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Jinxin Liu
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
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Jiang B, Zeng Q, Liu Q, Chai H, Xiang J, Li H, Shi S, Yang A, Chen Z, Cui Y, Hu D, Ge H, Yuan C, Dong J, Han F. Impacts of electric field-magnetic powder coupled membrane bioreactor on phenol wastewater treatment: Performance, synergistic mechanism, antibiotic resistance genes, and eco-environmental benefit evaluation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 909:168607. [PMID: 37981150 DOI: 10.1016/j.scitotenv.2023.168607] [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: 09/01/2023] [Revised: 11/03/2023] [Accepted: 11/14/2023] [Indexed: 11/21/2023]
Abstract
A novel electric field-magnetic powder coupled membrane bioreactor (EM-MBR) was constructed, which was superior on improvement of phenol treatment performance and sludge characteristics, and mitigation of membrane fouling. EM-MBR enhanced the phenol degradation via the improvement activity of phenol degrading enzymes. The EPS contents and SVI of EM-MBR were significantly reduced by 49.3 % and 58.7 % than that of the conventional MBR, respectively. Moreover, EM-MBR successfully reduced fouling rate by 57.0 %, delaying the membrane resistance. The EPS contents were positively correlated with the SVI and fouling rate, implying that the sludge settleability was strengthened by improving the properties of EPS with the assistance of electromagnetic, thus mitigating the membrane fouling. Microbial co-occurrence network demonstrated that EM-MBR enriched phenol-degrading and EPS-degrading genera correlated to Fe redox cycle. Furthermore, the activation of the antioxidant system in the EM-MBR resulted in the suppression of reactive oxygen species (ROS) generation, consequently impeding the dissemination of antibiotic resistance genes (ARGs). Co-occurrence patterns of MGEs and ARGs revealed that intercellular binding facilitated by ist and Integrase may account for the horizontal transfer of ARGs. The reduction of unit capital costs (15.63 %), running costs (53.00 %), and total average carbon emissions (15.18 %) indicated that EM-MBR was environmentally beneficial.
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Affiliation(s)
- Bei Jiang
- College of Environment and Resources, Dalian Minzu University, 18 Liaohe West Road, Dalian Jinpu New District, Dalian 116600, China
| | - Qianzhi Zeng
- School of Life Science, Liaoning Normal University, Dalian 116081, China
| | - Qiangwei Liu
- School of Life Science, Liaoning Normal University, Dalian 116081, China
| | - Huiying Chai
- College of Environment and Resources, Dalian Minzu University, 18 Liaohe West Road, Dalian Jinpu New District, Dalian 116600, China
| | - Jinxun Xiang
- School of Life Science, Liaoning Normal University, Dalian 116081, China
| | - Hongxin Li
- School of Life Science, Liaoning Normal University, Dalian 116081, China
| | - Shengnan Shi
- School of Life Science, Liaoning Normal University, Dalian 116081, China
| | - Aifu Yang
- Technology Center of Dalian Customs District, Dalian 116001, China
| | - Zhaobo Chen
- College of Environment and Resources, Dalian Minzu University, 18 Liaohe West Road, Dalian Jinpu New District, Dalian 116600, China.
| | - Yubo Cui
- College of Environment and Resources, Dalian Minzu University, 18 Liaohe West Road, Dalian Jinpu New District, Dalian 116600, China
| | - Dongxue Hu
- College of Environment and Resources, Dalian Minzu University, 18 Liaohe West Road, Dalian Jinpu New District, Dalian 116600, China
| | - Hui Ge
- College of Environment and Resources, Dalian Minzu University, 18 Liaohe West Road, Dalian Jinpu New District, Dalian 116600, China
| | - Chang Yuan
- Southwest Guizhou Vocational and Technical College for Nationalities, Xingyi 562400, China
| | - Jian Dong
- College of Environment and Resources, Dalian Minzu University, 18 Liaohe West Road, Dalian Jinpu New District, Dalian 116600, China
| | - Fei Han
- College of Environment and Resources, Dalian Minzu University, 18 Liaohe West Road, Dalian Jinpu New District, Dalian 116600, China
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Hinthong W, Thaotumpitak V, Sripradite J, Indrawattana N, Srisook T, Kongngoen T, R. Atwill E, Jeamsripong S. Antimicrobial resistance, virulence profile, and genetic analysis of ESBL-producing Escherichia coli isolated from Nile tilapia in fresh markets and supermarkets in Thailand. PLoS One 2024; 19:e0296857. [PMID: 38215169 PMCID: PMC10786378 DOI: 10.1371/journal.pone.0296857] [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: 07/02/2023] [Accepted: 12/20/2023] [Indexed: 01/14/2024] Open
Abstract
This study investigated the prevalence and antimicrobial resistance (AMR) of Escherichia coli (E. coli) in Nile tilapia from fresh markets and supermarkets. A total of samples (n = 828) were collected from Nile tilapia including fish flesh (n = 276), liver and kidney (n = 276), and intestine (n = 276). Overall prevalence of fecal coliforms (61.6%) and E. coli (53.0%) were observed. High prevalence of E. coli was found in the intestine (71.4%), followed by the liver and kidney (45.7%). The highest prevalence of resistance was commonly found against tetracycline (78.5%), ampicillin (72.8%), and sulfamethoxazole (45.6%) with resistance to only tetracycline (15.2%) as the most common antibiogram. The prevalence of multidrug resistance (MDR) (54.4%) and Extended-spectrum beta-lactamases (ESBLs) (5.7%) were examined. The predominant virulence genes (n = 158) were st (14.6%), followed by eaeA (0.6%). The blaTEM (73.4%), tetA (65.2%), and qnrS (57.6%). There is statistical significance between Nile tilapia from fresh markets and supermarkets. Based on logistic regression analysis, ampicillin-resistant E. coli was statistically associated with the phenotypic resistance to tetracycline and trimethoprim, and the presence of blaTEM and tetA (p < 0.05). Further investigation of AMR transference and their mechanisms is needed for AMR control.
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Affiliation(s)
- Woranich Hinthong
- Princess Srisavangavadhana College of Medicine, Chulabhorn Royal Academy, Bangkok, Thailand
| | - Varangkana Thaotumpitak
- Research Unit in Microbial Food Safety and Antimicrobial Resistance, Department of Veterinary Public Health, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Jarukorn Sripradite
- Department of Social and Applied Science, College of Industrial Technology, King Mongkut’s University of Technology North Bangkok, Bangkok, Thailand
| | - Nitaya Indrawattana
- Department Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Thassanee Srisook
- Princess Srisavangavadhana College of Medicine, Chulabhorn Royal Academy, Bangkok, Thailand
| | - Thida Kongngoen
- Department Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Edward R. Atwill
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States of America
| | - Saharuetai Jeamsripong
- Research Unit in Microbial Food Safety and Antimicrobial Resistance, Department of Veterinary Public Health, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
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64
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Thorn AV, Aarestrup FM, Munk P. Flankophile: a bioinformatic pipeline for prokaryotic genomic synteny analysis. Microbiol Spectr 2024; 12:e0241323. [PMID: 38084973 PMCID: PMC10783016 DOI: 10.1128/spectrum.02413-23] [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: 06/08/2023] [Accepted: 11/08/2023] [Indexed: 12/21/2023] Open
Abstract
IMPORTANCE The Flankophile pipeline enables the analysis and visualization of flanking regions of prokaryotic sequences of interest on large data sets in one step and in a consistent manner. A specific tool for flanking region analysis with automated visualization has not been developed before, and Flankophile will make flanking region analysis easier and accessible to more people. Flankophile will be especially useful in the field of genomic epidemiology of acquired antimicrobial resistance genes. Here, information from flanking region sequences can be instrumental in rejecting or supporting the possibility of a recent common source of the same resistance gene found in different samples.
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Affiliation(s)
- Alix Vincent Thorn
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Frank M. Aarestrup
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Patrick Munk
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
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65
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Parra B, Cockx B, Lutz VT, Brøndsted L, Smets BF, Dechesne A. Isolation and characterization of novel plasmid-dependent phages infecting bacteria carrying diverse conjugative plasmids. Microbiol Spectr 2024; 12:e0253723. [PMID: 38063386 PMCID: PMC10782986 DOI: 10.1128/spectrum.02537-23] [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: 06/19/2023] [Accepted: 11/12/2023] [Indexed: 12/23/2023] Open
Abstract
IMPORTANCE This work was undertaken because plasmid-dependent phages can reduce the prevalence of conjugative plasmids and can be leveraged to prevent the acquisition and dissemination of ARGs by bacteria. The two novel phages described in this study, Lu221 and Hi226, can infect Escherichia coli, Salmonella enterica, Kluyvera sp. and Enterobacter sp. carrying conjugative plasmids. This was verified with plasmids carrying resistance determinants and belonging to the most common plasmid families among Gram-negative pathogens. Therefore, the newly isolated phages could have the potential to help control the spread of ARGs and thus help combat the antimicrobial resistance crisis.
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Affiliation(s)
- Boris Parra
- Department of Environmental Engineering and Resource Engineering, Technical University of Denmark, Kongens Lyngby, Denmark
- Laboratorio de Investigación de Agentes Antibacterianos, Departamento de Microbiología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
- Instituto de Ciencias Naturales, Facultad de Medicina Veterinaria y Agronomía, Universidad de las Américas, Concepción, Chile
| | - Bastiaan Cockx
- Department of Environmental Engineering and Resource Engineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Veronika T. Lutz
- Department of Veterinary and Animal Sciences, University of Copenhagen, København, Denmark
| | - Lone Brøndsted
- Department of Veterinary and Animal Sciences, University of Copenhagen, København, Denmark
| | - Barth F. Smets
- Department of Environmental Engineering and Resource Engineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Arnaud Dechesne
- Department of Environmental Engineering and Resource Engineering, Technical University of Denmark, Kongens Lyngby, Denmark
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Piña-González AM, Castelán-Sánchez HG, Hurtado-Ramírez JM, López-Leal G. Campylobacter prophage diversity reveals pervasive recombination between prophages from different Campylobacter species. Microbiol Spectr 2024; 12:e0279523. [PMID: 38088548 PMCID: PMC10782988 DOI: 10.1128/spectrum.02795-23] [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: 07/07/2023] [Accepted: 11/12/2023] [Indexed: 01/13/2024] Open
Abstract
IMPORTANCE Prophages play an important role in shaping the genetic diversity and evolution of their hosts. Acquisition or loss of prophages can lead to genomic variations, including changes in the bacterial phenotype promoted by recombination events, genetic repertoire exchanges and dissemination of virulence factors, and antibiotic resistance. By studying prophages in Campylobacter species, scientists can gain insights into the evolutionary patterns, pathogenicity mechanisms, epidemiology, and population dynamics of these species. This has implications for public health, antibiotic resistance surveillance, and the development of targeted therapeutic approaches.
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Affiliation(s)
- Adán Manuel Piña-González
- Laboratorio de Biología Computacional y Virómica Integrativa, Centro de Investigación en Dinámica Celular, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | - Hugo G. Castelán-Sánchez
- Grupo de Genómica y Dinámica Evolutiva de Microorganismos Emergentes, Consejo Nacional de Humanidades, Ciudad de México, México
| | | | - Gamaliel López-Leal
- Laboratorio de Biología Computacional y Virómica Integrativa, Centro de Investigación en Dinámica Celular, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
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67
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Cui Y, Gao J, Zeng L, Guo Y, Xu H, Zhao M. Different fates of extracellular and intracellular antibiotic resistance genes in flocs, granular and biofilm nitrification systems under the stress of acetaminophen. JOURNAL OF HAZARDOUS MATERIALS 2024; 461:132675. [PMID: 37806259 DOI: 10.1016/j.jhazmat.2023.132675] [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: 08/08/2023] [Revised: 09/12/2023] [Accepted: 09/28/2023] [Indexed: 10/10/2023]
Abstract
The spread of antibiotic resistance genes (ARGs), including intracellular ARGs (i-ARGs) and extracellular ARGs (e-ARGs), has become a global problem that cannot be ignored. This study clarified the fates of e-ARGs and i-ARGs in floc sludge reactor (FS), granular sludge reactor (GS) and biofilm reactor (BF) under the stress of acetaminophen (APAP). The results showed that the risk of ARGs transmission, especially for e-ARGs, in FS and BF could increase with the increasing times of APAP treatment, except for that in GS. The fates of i-ARGs in three different systems were similar, which were mainly clustered as the efflux pumps mechanism. The secretion and disintegration of extracellular polymeric substances mainly affected the fates of e-ARGs. In the three systems, the complexity of network relationships between ARGs and microbial communities was FS, GS and BF. Partial least-squares path model analysis indicated that bacterial community directly contributed to the variations of e-ARGs and i-ARGs under APAP treatment in the three systems, playing a leading role. And i-ARGs and protein secondary structure showed direct effects on e-ARGs. This study indicated that e-ARGs in complex systems were more susceptible to be influenced, which should be paid more attention to prevent further propagation of ARGs.
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Affiliation(s)
- Yingchao Cui
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, China
| | - Jingfeng Gao
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, China.
| | - Liqin Zeng
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, China
| | - Yi Guo
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, China
| | - Hongxin Xu
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, China
| | - Mingyan Zhao
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, China
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Baker M, Zhang X, Maciel-Guerra A, Babaarslan K, Dong Y, Wang W, Hu Y, Renney D, Liu L, Li H, Hossain M, Heeb S, Tong Z, Pearcy N, Zhang M, Geng Y, Zhao L, Hao Z, Senin N, Chen J, Peng Z, Li F, Dottorini T. Convergence of resistance and evolutionary responses in Escherichia coli and Salmonella enterica co-inhabiting chicken farms in China. Nat Commun 2024; 15:206. [PMID: 38182559 PMCID: PMC10770378 DOI: 10.1038/s41467-023-44272-1] [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: 04/04/2023] [Accepted: 12/06/2023] [Indexed: 01/07/2024] Open
Abstract
Sharing of genetic elements among different pathogens and commensals inhabiting same hosts and environments has significant implications for antimicrobial resistance (AMR), especially in settings with high antimicrobial exposure. We analysed 661 Escherichia coli and Salmonella enterica isolates collected within and across hosts and environments, in 10 Chinese chicken farms over 2.5 years using data-mining methods. Most isolates within same hosts possessed the same clinically relevant AMR-carrying mobile genetic elements (plasmids: 70.6%, transposons: 78%), which also showed recent common evolution. Supervised machine learning classifiers revealed known and novel AMR-associated mutations and genes underlying resistance to 28 antimicrobials, primarily associated with resistance in E. coli and susceptibility in S. enterica. Many were essential and affected same metabolic processes in both species, albeit with varying degrees of phylogenetic penetration. Multi-modal strategies are crucial to investigate the interplay of mobilome, resistance and metabolism in cohabiting bacteria, especially in ecological settings where community-driven resistance selection occurs.
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Affiliation(s)
- Michelle Baker
- School of Veterinary Medicine and Science, University of Nottingham, College Road, Sutton Bonington, Loughborough, Leicestershire, LE12 5RD, UK
| | - Xibin Zhang
- Shandong New Hope Liuhe Group Co. Ltd. and Qingdao Key Laboratory of Animal Feed Safety, Qingdao, Shandong, 266000, P.R. China
| | - Alexandre Maciel-Guerra
- School of Veterinary Medicine and Science, University of Nottingham, College Road, Sutton Bonington, Loughborough, Leicestershire, LE12 5RD, UK
| | - Kubra Babaarslan
- School of Veterinary Medicine and Science, University of Nottingham, College Road, Sutton Bonington, Loughborough, Leicestershire, LE12 5RD, UK
| | - Yinping Dong
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, 100021, P. R. China
| | - Wei Wang
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, 100021, P. R. China
| | - Yujie Hu
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, 100021, P. R. China
| | - David Renney
- Nimrod Veterinary Products Limited, 2, Wychwood Court, Cotswold Business Village, Moreton-in-Marsh, GL56 0JQ, London, UK
| | - Longhai Liu
- Shandong Kaijia Food Co. Ltd, Weifang, P. R. China
| | - Hui Li
- Luoyang Center for Disease Control and Prevention, No. 9, Zhenghe Road, Luolong District, Luoyang City, Henan Province, Luolong, 471000, P. R. China
| | - Maqsud Hossain
- School of Veterinary Medicine and Science, University of Nottingham, College Road, Sutton Bonington, Loughborough, Leicestershire, LE12 5RD, UK
| | - Stephan Heeb
- School of Life Sciences, University of Nottingham, East Drive, Nottingham, Nottinghamshire, NG7 2RD, UK
| | - Zhiqin Tong
- Luoyang Center for Disease Control and Prevention, No. 9, Zhenghe Road, Luolong District, Luoyang City, Henan Province, Luolong, 471000, P. R. China
| | - Nicole Pearcy
- School of Veterinary Medicine and Science, University of Nottingham, College Road, Sutton Bonington, Loughborough, Leicestershire, LE12 5RD, UK
- School of Life Sciences, University of Nottingham, East Drive, Nottingham, Nottinghamshire, NG7 2RD, UK
| | - Meimei Zhang
- Liaoning Provincial Center for Disease Control and Prevention, No. 168, Jinfeng Street, Hunnan District, Shenyang City, Liaoning Province, 110072, P. R. China
| | - Yingzhi Geng
- Liaoning Provincial Center for Disease Control and Prevention, No. 168, Jinfeng Street, Hunnan District, Shenyang City, Liaoning Province, 110072, P. R. China
| | - Li Zhao
- Agricultural Biopharmaceutical Laboratory, College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, No. 700 Changcheng Road, Chengyang District, Qingdao City, Shandong Province, 266109, P. R. China
| | - Zhihui Hao
- Chinese Veterinary Medicine Innovation Center, College of Veterinary Medicine, China Agricultural University, Haidian District, Beijing City, 100193, P. R. China
| | - Nicola Senin
- Department of Engineering, University of Perugia, Perugia, I06125, Italy
| | - Junshi Chen
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, 100021, P. R. China
| | - Zixin Peng
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, 100021, P. R. China.
| | - Fengqin Li
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, 100021, P. R. China.
| | - Tania Dottorini
- School of Veterinary Medicine and Science, University of Nottingham, College Road, Sutton Bonington, Loughborough, Leicestershire, LE12 5RD, UK.
- Centre for Smart Food Research, Nottingham Ningbo China Beacons of Excellence Research and Innovation Institute, University of Nottingham Ningbo China, Ningbo, 315100, P. R. China.
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Zhao Y, Qian C, Ye J, Li Q, Zhao R, Qin L, Mao Q. Convergence of plasmid-mediated Colistin and Tigecycline resistance in Klebsiella pneumoniae. Front Microbiol 2024; 14:1221428. [PMID: 38282729 PMCID: PMC10813211 DOI: 10.3389/fmicb.2023.1221428] [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: 05/12/2023] [Accepted: 11/15/2023] [Indexed: 01/30/2024] Open
Abstract
Objective The co-occurrence of colistin and tigecycline resistance genes in Klebsiella pneumoniae poses a serious public health problem. This study aimed to characterize a K. pneumoniae strain, K82, co-harboring a colistin resistance gene (CoRG) and tigecycline resistance gene (TRG), and, importantly, investigate the genetic characteristics of the plasmid with CoRG or TRG in GenBank. Methods K. pneumoniae strain K82 was subjected to antimicrobial susceptibility testing, conjugation assay, and whole-genome sequencing (WGS). In addition, comparative genomic analysis of CoRG or TRG-harboring plasmids from K82 and GenBank was conducted. K. pneumoniae strain K82 was resistant to all the tested antimicrobials including colistin and tigecycline, except for carbapenems. Results WGS and bioinformatic analysis showed that K82 belonged to the ST656 sequence type and carried multiple drug resistance genes, including mcr-1 and tmexCD1-toprJ1, which located on IncFIA/IncHI2/IncHI2A/IncN/IncR-type plasmid pK82-mcr-1 and IncFIB/IncFII-type plasmid pK82-tmexCD-toprJ, respectively. The pK82-mcr-1 plasmid was capable of conjugation. Analysis of the CoRG/TRG-harboring plasmid showed that mcr-8 and tmexCD1-toprJ1 were the most common CoRG and TRG of Klebsiella spp., respectively. These TRG/CoRG-harboring plasmids could be divided into two categories based on mash distance. Moreover, we found an IncFIB/IncHI1B-type plasmid, pSYCC1_tmex_287k, co-harboring mcr-1 and tmexCD1-toprJ1. To the best of our knowledge, this is the first report on the co-occurrence of mcr-1 and tmexCD1-toprJ1 on a single plasmid. Conclusion Our research expands the known diversity of CoRG and TRG-harboring plasmids in K. pneumoniae. Effective surveillance should be implemented to assess the prevalence of co-harboring CoRG and TRG in a single K. pneumoniae isolate or even a single plasmid.
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Affiliation(s)
- Yujie Zhao
- Department of Clinical Laboratory, The Affiliated Li Huili Hospital, Ningbo University, Ningbo, China
| | - Changrui Qian
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Jianzhong Ye
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Qingcao Li
- Department of Clinical Laboratory, The Affiliated Li Huili Hospital, Ningbo University, Ningbo, China
| | - Rongqing Zhao
- Department of Clinical Laboratory, The Affiliated Li Huili Hospital, Ningbo University, Ningbo, China
| | - Ling Qin
- Department of Clinical Laboratory, The Affiliated Li Huili Hospital, Ningbo University, Ningbo, China
| | - Qifeng Mao
- Department of Clinical Laboratory, Ningbo No. 2 Hospital, Ningbo, China
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Bodus B, O'Malley K, Dieter G, Gunawardana C, McDonald W. Review of emerging contaminants in green stormwater infrastructure: Antibiotic resistance genes, microplastics, tire wear particles, PFAS, and temperature. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 906:167195. [PMID: 37777137 DOI: 10.1016/j.scitotenv.2023.167195] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 09/08/2023] [Accepted: 09/16/2023] [Indexed: 10/02/2023]
Abstract
Green stormwater infrastructure is a growing management approach to capturing, infiltrating, and treating runoff at the source. However, there are several emerging contaminants for which green stormwater infrastructure has not been explicitly designed to mitigate and for which removal mechanisms are not yet well defined. This is an issue, as there is a growing understanding of the impact of emerging contaminants on human and environmental health. This paper presents a review of five emerging contaminants - antibiotic resistance genes, microplastics, tire wear particles, PFAS, and temperature - and seeks to improve our understanding of how green stormwater infrastructure is impacted by and can be designed to mitigate these emerging contaminants. To do so, we present a review of the source and transport of these contaminants to green stormwater infrastructure, specific treatment mechanisms within green infrastructure, and design considerations of green stormwater infrastructure that could lead to their removal. In addition, common removal mechanisms across these contaminants and limitations of green infrastructure for contaminant mitigation are discussed. Finally, we present future research directions that can help to advance the use of green infrastructure as a first line of defense for downstream water bodies against emerging contaminants of concern.
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Affiliation(s)
- Benjamin Bodus
- Department of Civil, Construction and Environmental Engineering, Marquette University, 1637 W. Wisconsin Ave, Milwaukee, WI 53233, USA.
| | - Kassidy O'Malley
- Department of Civil, Construction and Environmental Engineering, Marquette University, 1637 W. Wisconsin Ave, Milwaukee, WI 53233, USA.
| | - Greg Dieter
- Department of Civil, Construction and Environmental Engineering, Marquette University, 1637 W. Wisconsin Ave, Milwaukee, WI 53233, USA.
| | - Charitha Gunawardana
- Department of Civil, Construction and Environmental Engineering, Marquette University, 1637 W. Wisconsin Ave, Milwaukee, WI 53233, USA.
| | - Walter McDonald
- Department of Civil, Construction and Environmental Engineering, Marquette University, 1637 W. Wisconsin Ave, Milwaukee, WI 53233, USA.
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Tamayo-Leiva J, Alcorta J, Sepúlveda F, Fuentes-Alburquenque S, Arroyo JI, González-Pastor JE, Díez B. Structure and dispersion of the conjugative mobilome in surface ocean bacterioplankton. ISME COMMUNICATIONS 2024; 4:ycae059. [PMID: 38770060 PMCID: PMC11104534 DOI: 10.1093/ismeco/ycae059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 04/13/2024] [Accepted: 04/24/2024] [Indexed: 05/22/2024]
Abstract
Mobile genetic elements (MGEs), collectively referred to as the "mobilome", can have a significant impact on the fitness of microbial communities and therefore on ecological processes. Marine MGEs have mainly been associated with wide geographical and phylogenetic dispersal of adaptative traits. However, whether the structure of this mobilome exhibits deterministic patterns in the natural community is still an open question. The aim of this study was to characterize the structure of the conjugative mobilome in the ocean surface bacterioplankton by searching the publicly available marine metagenomes from the TARA Oceans survey, together with molecular markers, such as relaxases and type IV coupling proteins of the type IV secretion system (T4SS). The T4SS machinery was retrieved in more abundance than relaxases in the surface marine bacterioplankton. Moreover, among the identified MGEs, mobilizable elements were the most abundant, outnumbering self-conjugative sequences. Detection of a high number of incomplete T4SSs provides insight into possible strategies related to trans-acting activity between MGEs, and accessory functions of the T4SS (e.g. protein secretion), allowing the host to maintain a lower metabolic burden in the highly dynamic marine system. Additionally, the results demonstrate a wide geographical dispersion of MGEs throughout oceanic regions, while the Southern Ocean appears segregated from other regions. The marine mobilome also showed a high similarity of functions present in known plasmid databases. Moreover, cargo genes were mostly related to DNA processing, but scarcely associated with antibiotic resistance. Finally, within the MGEs, integrative and conjugative elements showed wider marine geographic dispersion than plasmids.
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Affiliation(s)
- Javier Tamayo-Leiva
- Biological Sciences Faculty, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
- Center for Climate and Resilience Research (CR2), University of Chile, Santiago, Chile
| | - Jaime Alcorta
- Biological Sciences Faculty, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
- Millennium Institute Center for Genome Regulation (CRG) , Santiago, Chile
| | - Felipe Sepúlveda
- Biological Sciences Faculty, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
- Millennium Institute Center for Genome Regulation (CRG) , Santiago, Chile
| | - Sebastián Fuentes-Alburquenque
- Centro de Investigación en Recursos Naturales y Sustentabilidad, Universidad Bernardo O’Higgins, Santiago, Chile
- Departamento de Matemáticas y Ciencias de la Ingeniería, Facultad de Ingeniería, Ciencia y Tecnología, Universidad Bernardo O’Higgins, Santiago, Chile
| | - José Ignacio Arroyo
- Biological Sciences Faculty, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
- The Santa Fe Institute, Santa Fe, NM 87131, United States
- Centro de Modelamiento Matemático, Universidad de Chile, IRL 2807 CNRS Beauchef 851, Santiago, Chile
| | - José Eduardo González-Pastor
- Department of Molecular Evolution, Centro de Astrobiología (CAB), CSIC-INTA. Carretera de Ajalvir km 4, Torrejón de Ardoz 28850 Madrid, Spain
| | - Beatriz Díez
- Biological Sciences Faculty, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
- Center for Climate and Resilience Research (CR2), University of Chile, Santiago, Chile
- Millennium Institute Center for Genome Regulation (CRG) , Santiago, Chile
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Zhang C, Saad Z, Zhang S, Chen B, He X, Liu S. Effects of voltage and tetracycline on horizontal transfer of ARGs in microbial electrolysis cells. ENVIRONMENTAL TECHNOLOGY 2024; 45:559-568. [PMID: 35980276 DOI: 10.1080/09593330.2022.2114860] [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: 05/14/2022] [Accepted: 07/28/2022] [Indexed: 06/15/2023]
Abstract
The abuse of antibiotics leads to the production of antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs). Microbial electrolysis cells (MECs) have been widely applicated in the field of degrading antibiotics. ARGs were increased via horizontal transfer in single and two-chamber MECs. As one of the critical parameters in MECs, voltage has a particular impact on the ARGs transfer via horizontal transfer. However, there have been few studies of ARGs transfer under the exposure of antibiotics and voltage in MECs. In this study, five concentrations of tetracycline (0, 1, 5, 10, 20 mg/L) were selected to explore the conjugative transfer frequency of plasmid-encoded the ARGs from the donor (E. coli RP4) to receptor (E. coli HB101) in MECs, two voltages (1.5 and 2.0 V) were used to explore the conjugative transfer frequency of ARGs in MECs, then, the transfer of ARGs in MECs under the co-effect of tetracycline and voltage was explored. The results showed that the conjugative transfer frequency of ARGs was significantly increased with the increase of tetracycline concentration and voltage, respectively (p < 0.05). Under the pressure of tetracycline and voltage, the conjugative transfer frequency of ARGs is significantly enhanced with the co-effect of tetracycline and voltage (p < 0.05). The oxidative response induced by electrical stimulation promotes the overproduction of reactive oxygen species and the enhancement of cell membrane permeability of donor and recipient bacteria in MECs. These findings provide insights for studying the spread of ARGs in MECs.
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Affiliation(s)
- Chenxi Zhang
- Jiangsu Key Laboratory of Atmospheric Environment Monitoring and Pollution Control (AEMPC), Collaborative Innovation Center of Atmospheric Environment and Equipment Technology (CIC-AEET), School of Environmental Science and Engineering, Nanjing University of Information Science & Technology, Nanjing, People's Republic of China
| | - Zouafi Saad
- Jiangsu Key Laboratory of Atmospheric Environment Monitoring and Pollution Control (AEMPC), Collaborative Innovation Center of Atmospheric Environment and Equipment Technology (CIC-AEET), School of Environmental Science and Engineering, Nanjing University of Information Science & Technology, Nanjing, People's Republic of China
| | - Shuai Zhang
- Jiangsu Key Laboratory of Atmospheric Environment Monitoring and Pollution Control (AEMPC), Collaborative Innovation Center of Atmospheric Environment and Equipment Technology (CIC-AEET), School of Environmental Science and Engineering, Nanjing University of Information Science & Technology, Nanjing, People's Republic of China
| | - Bin Chen
- Jiangsu Key Laboratory of Atmospheric Environment Monitoring and Pollution Control (AEMPC), Collaborative Innovation Center of Atmospheric Environment and Equipment Technology (CIC-AEET), School of Environmental Science and Engineering, Nanjing University of Information Science & Technology, Nanjing, People's Republic of China
| | - Xin He
- BDG Water Design &Research Institute Co., Ltd, Beijing, People's Republic of China
| | - Shuai Liu
- College of Environment and Safety Engineering, Qingdao University of Science and Technology, Qingdao, People's Republic of China
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Inglis LK, Roach MJ, Edwards RA. Prophages: an integral but understudied component of the human microbiome. Microb Genom 2024; 10:001166. [PMID: 38264887 PMCID: PMC10868603 DOI: 10.1099/mgen.0.001166] [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: 07/05/2023] [Accepted: 12/07/2023] [Indexed: 01/25/2024] Open
Abstract
Phages integrated into a bacterial genome - called prophages - continuously monitor the vigour of the host bacteria to determine when to escape the genome and to protect their host from other phage infections, and they may provide genes that promote bacterial growth. Prophages are essential to almost all microbiomes, including the human microbiome. However, most human microbiome studies have focused on bacteria, ignoring free and integrated phages, so we know little about how these prophages affect the human microbiome. To address this gap in our knowledge, we compared the prophages identified in 14 987 bacterial genomes isolated from human body sites to characterize prophage DNA in the human microbiome. Here, we show that prophage DNA is ubiquitous, comprising on average 1-5 % of each bacterial genome. The prophage content per genome varies with the isolation site on the human body, the health of the human and whether the disease was symptomatic. The presence of prophages promotes bacterial growth and sculpts the microbiome. However, the disparities caused by prophages vary throughout the body.
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Affiliation(s)
- Laura K. Inglis
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, SA 5042, Australia
| | - Michael J. Roach
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, SA 5042, Australia
| | - Robert A. Edwards
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, SA 5042, Australia
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74
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Ye C, Chen C, Zhang K, Feng M, Yu X. Solar/periodate inhibits ARGs transformation by degradation of DNA without damaging cell membrane. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 340:122766. [PMID: 37865329 DOI: 10.1016/j.envpol.2023.122766] [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: 08/24/2023] [Revised: 10/09/2023] [Accepted: 10/15/2023] [Indexed: 10/23/2023]
Abstract
Antibiotic-resistant bacterial infections are a growing global threat to public health. Chlorine-based water disinfection and some advanced oxidation processes significantly increase the risk of ARGs release and transmission in the aquatic environment. Therefore, it is critical to develop or optimize disinfection methods to reduce the conversion and transmission of ARGs in natural water. This study investigated whether the solar/periodate (PI) system inhibited the natural transmission of ARGs and its mechanism. The results showed that solar/PI systems could effectively inhibit the propagation of ARGs in two simulated natural transformation systems, up to more than 100 times. By characterizing the cellular process of bacteria treated by the solar/PI system, we found that the solar/PI system could directly cause damage to DNA bases and its dual effect with almost no damage to the bacterial cell membrane, which was the main reason why this technology could inhibit natural transformation processes. Specifically, the inhibition effect of solar/PI on bacteria did not result in enhanced membrane permeability under appropriate PI dosage (<200 μM), which greatly reduced the risk of secondary contamination of eARGs released by traditional disinfection. Our findings could help improve existing disinfection strategies to ensure that antibiotic resistance is not spread in the natural water environment.
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Affiliation(s)
- Chengsong Ye
- Fujian Key Laboratory of Coastal Pollution Prevention and Control, College of the Environment & Ecology, Xiamen University, Xiamen, 361102, China
| | - Chenlan Chen
- Fujian Key Laboratory of Coastal Pollution Prevention and Control, College of the Environment & Ecology, Xiamen University, Xiamen, 361102, China
| | - Kaiting Zhang
- Fujian Key Laboratory of Coastal Pollution Prevention and Control, College of the Environment & Ecology, Xiamen University, Xiamen, 361102, China
| | - Mingbao Feng
- Fujian Key Laboratory of Coastal Pollution Prevention and Control, College of the Environment & Ecology, Xiamen University, Xiamen, 361102, China
| | - Xin Yu
- Fujian Key Laboratory of Coastal Pollution Prevention and Control, College of the Environment & Ecology, Xiamen University, Xiamen, 361102, China.
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Zhao M, Gao J, Cui Y, Zhang H, Wang Z, Zhang S, Sun L. The effects of didodecyl dimethyl ammonium chloride on microbial communities and resistance genes in floc, granular and biofilm denitrification sludge. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 906:167618. [PMID: 37804971 DOI: 10.1016/j.scitotenv.2023.167618] [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: 07/16/2023] [Revised: 10/04/2023] [Accepted: 10/04/2023] [Indexed: 10/09/2023]
Abstract
As a type of quaternary ammonium compounds, didodecyl dimethyl ammonium chloride (DADMAC C12) was frequently detected in wastewater treatment plants. Here, floc-based sequencing batch reactor (FSBR), granule-based SBR (GSBR) and biofilm SBR (BSBR) were fed with 0.5, 5 and 10 mg/L of DADMAC C12 for 120 d. Compared with floc sludge and granule sludge, biofilm had the strongest ability to resist the impact of DADMAC C12. Notably, in both FSBR and GSBR systems, 5 mg/L DADMAC C12 promoted denitrification sludge to become hydrophobic and compact due to an increase in α-Helix/(β-Sheet+Random coil), consequently enhancing sludge granulation. Besides,high concentration of DADMAC C12 generally increased the abundances of MGEs in three denitrification systems, except extracellular MGEs in water. The variation of efflux pump ARGs was basically consistent with that of MGEs. The stimulation of DADMAC C12 also increased significantly the abundance of extracellular antibiotics deactivation ARGs in water in three denitrification systems. Besides, DADMAC C12 induced co-selection among various ARGs and promoted the proliferation and spread of sulfonamide ARGs in water.
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Affiliation(s)
- Mingyan Zhao
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, China
| | - Jingfeng Gao
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, China.
| | - Yingchao Cui
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, China
| | - Haoran Zhang
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, China
| | - Zhiqi Wang
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, China
| | - Shujun Zhang
- Research and Development Center of Beijing Drainage Group Co., Ltd, Beijing 100124, China.
| | - Lixin Sun
- D·smart Environmental Technology (Beijing) Co., Ltd., China
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Saula AY, Knight G, Bowness R. Within-Host Mathematical Models of Antibiotic Resistance. Methods Mol Biol 2024; 2833:79-91. [PMID: 38949703 DOI: 10.1007/978-1-0716-3981-8_9] [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] [Indexed: 07/02/2024]
Abstract
Mathematical models have been used to study the spread of infectious diseases from person to person. More recently studies are developing within-host modeling which provides an understanding of how pathogens-bacteria, fungi, parasites, or viruses-develop, spread, and evolve inside a single individual and their interaction with the host's immune system.Such models have the potential to provide a more detailed and complete description of the pathogenesis of diseases within-host and identify other influencing factors that may not be detected otherwise. Mathematical models can be used to aid understanding of the global antibiotic resistance (ABR) crisis and identify new ways of combating this threat.ABR occurs when bacteria respond to random or selective pressures and adapt to new environments through the acquisition of new genetic traits. This is usually through the acquisition of a piece of DNA from other bacteria, a process called horizontal gene transfer (HGT), the modification of a piece of DNA within a bacterium, or through. Bacteria have evolved mechanisms that enable them to respond to environmental threats by mutation, and horizontal gene transfer (HGT): conjugation; transduction; and transformation. A frequent mechanism of HGT responsible for spreading antibiotic resistance on the global scale is conjugation, as it allows the direct transfer of mobile genetic elements (MGEs). Although there are several MGEs, the most important MGEs which promote the development and rapid spread of antimicrobial resistance genes in bacterial populations are plasmids and transposons. Each of the resistance-spread-mechanisms mentioned above can be modeled allowing us to understand the process better and to define strategies to reduce resistance.
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Affiliation(s)
| | - Gwenan Knight
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
| | - Ruth Bowness
- Department of Mathematical Sciences, University of Bath, Bath, UK.
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Muhammad I, Pan S, Elken EM, Zhang H, Wang Y, Xu Y, Wang Y, Kong L, Ma H. Antibiotic resistance of probiotics isolated from Chinese corn stover silage. JOURNAL OF APPLIED ANIMAL RESEARCH 2023. [DOI: 10.1080/09712119.2023.2165088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Inam Muhammad
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, People’s Republic of China
- Department of Zoology, Shaheed Benazir Bhutto University, Shrengal, Pakistan
| | - Siyu Pan
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, People’s Republic of China
| | - Emad Mohammed Elken
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, People’s Republic of China
- Department of Animal Production, Faculty of Agriculture, Al-Azhar University, Nasr City Cairo, Egypt
| | - Haipeng Zhang
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, People’s Republic of China
| | - Yu Wang
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, People’s Republic of China
| | - Yuxuan Xu
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, People’s Republic of China
| | - Yiming Wang
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, People’s Republic of China
| | - Lingcong Kong
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, People’s Republic of China
- The Key Laboratory of New Veterinary Drug Research and Development of Jilin Province, Jilin Agricultural University, Changchun, People’s Republic of China
| | - Hongxia Ma
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, People’s Republic of China
- College of Life Science, Jilin Agricultural University, Changchun, People’s Republic of China
- The Engineering Research Center of Bioreactor and Drug Development, Ministry of Education, Jilin Agricultural University, Changchun, People’s Republic of China
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Unnikrishnan VK, Sundaramoorthy NS, Nair VG, Ramaiah KB, Roy JS, Rajendran M, Srinath S, Kumar S, S PS, S SM, Nagarajan S. Genome analysis of triple phages that curtails MDR E. coli with ML based host receptor prediction and its evaluation. Sci Rep 2023; 13:23040. [PMID: 38155176 PMCID: PMC10754912 DOI: 10.1038/s41598-023-49880-x] [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: 07/16/2023] [Accepted: 12/13/2023] [Indexed: 12/30/2023] Open
Abstract
Infections by multidrug resistant bacteria (MDR) are becoming increasingly difficult to treat and alternative approaches like phage therapy, which is unhindered by drug resistance, are urgently needed to tackle MDR bacterial infections. During phage therapy phage cocktails targeting different receptors are likely to be more effective than monophages. In the present study, phages targeting carbapenem resistant clinical isolate of E. coli U1007 was isolated from Ganges River (U1G), Cooum River (CR) and Hospital waste water (M). Capsid architecture discerned using TEM identified the phage families as Podoviridae for U1G, Myoviridae for CR and Siphoviridae for M phage. Genome sequencing showed the phage genomes varied in size U1G (73,275 bp) CR (45,236 bp) and M (45,294 bp). All three genomes lacked genes encoding tRNA sequence, antibiotic resistant or virulent genes. A machine learning (ML) based multi-class classification model using Random Forest, Logistic Regression, and Decision Tree were employed to predict the host receptor targeted by receptor binding protein of all 3 phages and the best performing algorithm Random Forest predicted LPS O antigen, LamB or OmpC for U1G; FhuA, OmpC for CR phage; and FhuA, LamB, TonB or OmpF for the M phage. OmpC was validated as receptor for U1G by physiological experiments. In vivo intramuscular infection study in zebrafish showed that cocktail of dual phages (U1G + M) along with colsitin resulted in a significant 3.5 log decline in cell counts. Our study highlights the potential of ML tool to predict host receptor and proves the utility of phage cocktail to restrict E. coli U1007 in vivo.
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Affiliation(s)
- Vineetha K Unnikrishnan
- Center for Research On Infectious Diseases (CRID), School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, Tamil Nadu, 613401, India
- Antimicrobial Resistance Lab, ASK-I-312, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, Tamil Nadu, India
| | - Niranjana Sri Sundaramoorthy
- Center for Research On Infectious Diseases (CRID), School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, Tamil Nadu, 613401, India
- Translational Health Sciences Technology Institute, Faridabad, India
| | - Veena G Nair
- Center for Research On Infectious Diseases (CRID), School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, Tamil Nadu, 613401, India
- Antimicrobial Resistance Lab, ASK-I-312, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, Tamil Nadu, India
| | - Kavi Bharathi Ramaiah
- Center for Research On Infectious Diseases (CRID), School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, Tamil Nadu, 613401, India
- Antimicrobial Resistance Lab, ASK-I-312, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, Tamil Nadu, India
| | - Jean Sophy Roy
- Center for Research On Infectious Diseases (CRID), School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, Tamil Nadu, 613401, India
| | - Malarvizhi Rajendran
- Center for Research On Infectious Diseases (CRID), School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, Tamil Nadu, 613401, India
| | - Sneha Srinath
- Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, Tamil Nadu, 613401, India
| | - Santhosh Kumar
- Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, Tamil Nadu, 613401, India
| | - Prakash Sankaran S
- Center for Research On Infectious Diseases (CRID), School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, Tamil Nadu, 613401, India
| | - Suma Mohan S
- Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, Tamil Nadu, 613401, India.
| | - Saisubramanian Nagarajan
- Center for Research On Infectious Diseases (CRID), School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, Tamil Nadu, 613401, India.
- Antimicrobial Resistance Lab, ASK-I-312, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, Tamil Nadu, India.
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Naidoo N, Zishiri OT. Comparative genomics analysis and characterization of Shiga toxin-producing Escherichia coli O157:H7 strains reveal virulence genes, resistance genes, prophages and plasmids. BMC Genomics 2023; 24:791. [PMID: 38124028 PMCID: PMC10731853 DOI: 10.1186/s12864-023-09902-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 12/13/2023] [Indexed: 12/23/2023] Open
Abstract
Escherichia coli O157:H7 is a foodborne pathogen that has been linked to global disease outbreaks. These diseases include hemorrhagic colitis and hemolytic uremic syndrome. It is vital to know the features that make this strain pathogenic to understand the development of disease outbreaks. In the current study, a comparative genomic analysis was carried out to determine the presence of structural and functional features of O157:H7 strains obtained from 115 National Center for Biotechnology Information database. These strains of interest were analysed in the following programs: BLAST Ring Image Generator, PlasmidFinder, ResFinder, VirulenceFinder, IslandViewer 4 and PHASTER. Five strains (ECP19-198, ECP19-798, F7508, F8952, H2495) demonstrated a great homology with Sakai because of a few regions missing. Five resistant genes were identified, however, Macrolide-associated resistance gene mdf(A) was commonly found in all genomes. Majority of the strains (97%) were positive for 15 of the virulent genes (espA, espB, espF, espJ, gad, chuA, eae, iss, nleA, nleB, nleC, ompT, tccP, terC and tir). The plasmid analysis demonstrated that the IncF group was the most prevalent in the strains analysed. The prophage and genomic island analysis showed a distribution of bacteriophages and genomic islands respectively. The results indicated that structural and functional features of the many O157:H7 strains differ and may be a result of obtaining mobile genetic elements via horizontal gene transfer. Understanding the evolution of O157:H7 strains pathogenicity in terms of their structural and functional features will enable the development of detection and control of transmission strategies.
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Affiliation(s)
- Natalie Naidoo
- School of Life Sciences, College of Agriculture, Engineering and Sciences, University of KwaZulu-Natal, Private Bag X54001, Durban, 4000, South Africa.
| | - Oliver T Zishiri
- School of Life Sciences, College of Agriculture, Engineering and Sciences, University of KwaZulu-Natal, Private Bag X54001, Durban, 4000, South Africa
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80
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Ren CY, Zhao HP. Synthetic Nuclease-Producing Microbiome Achieves Efficient Removal of Extracellular Antibiotic Resistance Genes from Wastewater Effluent. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:21224-21234. [PMID: 38059467 DOI: 10.1021/acs.est.3c07974] [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: 12/08/2023]
Abstract
Antibiotic resistance gene (ARG) transmission poses significant threats to human health. The effluent of wastewater treatment plants is demonstrated as a hotspot source of ARGs released into the environment. In this study, a synthetic microbiome containing nuclease-producing Deinococcus radiodurans was constructed to remove extracellular ARGs. Results of quantitative polymerase chain reaction (qPCR) showed significant reduction in plasmid RP4-associated ARGs (by more than 3 orders of magnitude) and reduction of indigenous ARG sul1 and mobile genetic element (MGE) intl1 (by more than 1 order of magnitude) in the synthetic microbiome compared to the control without D. radiodurans. Metagenomic analysis revealed a decrease in ARG and MGE diversity in extracellular DNA (eDNA) of the treated group. Notably, whereas eight antibiotic-resistant plasmids with mobility risk were detected in the control, only one was detected in the synthetic microbiome. The abundance of the nuclease encoding gene exeM, quantified by qPCR, indicated its enrichment in the synthetic microbiome, which ensures stable eDNA degradation even when D. radiodurans decreased. Moreover, intracellular ARGs and MGEs and pathogenic ARG hosts in the river receiving treated effluent were lower than those in the river receiving untreated effluent. Overall, this study presents a new approach for removing extracellular ARGs and further reducing the risk of ARG transmission in receiving rivers.
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Affiliation(s)
- Chong-Yang Ren
- MOE Key Lab of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Science, Zhejiang University, Hangzhou 310058, China
| | - He-Ping Zhao
- MOE Key Lab of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Science, Zhejiang University, Hangzhou 310058, China
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81
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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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82
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Abebe AA, Birhanu AG. Methicillin Resistant Staphylococcus aureus: Molecular Mechanisms Underlying Drug Resistance Development and Novel Strategies to Combat. Infect Drug Resist 2023; 16:7641-7662. [PMID: 38111667 PMCID: PMC10726795 DOI: 10.2147/idr.s428103] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 11/29/2023] [Indexed: 12/20/2023] Open
Abstract
Antimicrobial resistance (AMR) represents a major threat to global health. Infection caused by Methicillin-resistant Staphylococcus aureus (MRSA) is one of the well-recognized global public health problem globally. In some regions, as many as 90% of S. aureus infections are reported to be MRSA, which cannot be treated with standard antibiotics. WHO reports indicated that MRSA is circulating in every province worldwide, significantly increasing the risk of death by 64% compared to drug-sensitive forms of the infection which is attributed to its antibiotic resistance. The emergence and spread of antibiotic-resistant MRSA strains have contributed to its increased prevalence in both healthcare and community settings. The resistance of S. aureus to methicillin is due to expression of penicillin-binding protein 2a (PBP2a), which renders it impervious to the action of β-lactam antibiotics including methicillin. The other is through the production of beta-lactamases. Although the treatment options for MRSA are limited, there are promising alternatives to antibiotics to combat the infections. Innovative therapeutic strategies with wide range of activity and modes of action are yet to be explored. The review highlights the global challenges posed by MRSA, elucidates the mechanisms underlying its resistance development, and explores mitigation strategies. Furthermore, it focuses on alternative therapies such as bacteriophages, immunotherapy, nanobiotics, and antimicrobial peptides, emphasizing their synergistic effects and efficacy against MRSA. By examining these alternative approaches, this review provides insights into the potential strategies for tackling MRSA infections and combatting the escalating threat of AMR. Ultimately, a multifaceted approach encompassing both conventional and novel interventions is imperative to mitigate the impact of MRSA and ensure a sustainable future for global healthcare.
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Affiliation(s)
- Assefa Asnakew Abebe
- Department of Molecular Biology, Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
- Department of Medical laboratory Sciences, Institute of Health, Bule Hora University, Bule Hora, Ethiopia
| | - Alemayehu Godana Birhanu
- Department of Molecular Biology, Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
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83
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Chen Y, Fu X, Ou Z, Li J, Lin S, Wu Y, Wang X, Deng Y, Sun Y. Environmental determinants and demographic influences on global urban microbiomes, antimicrobial resistance and pathogenicity. NPJ Biofilms Microbiomes 2023; 9:94. [PMID: 38062054 PMCID: PMC10703778 DOI: 10.1038/s41522-023-00459-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 11/20/2023] [Indexed: 12/18/2023] Open
Abstract
Urban microbiome plays crucial roles in human health and are related to various diseases. The MetaSUB Consortium has conducted the most comprehensive global survey of urban microbiomes to date, profiling microbial taxa/functional genes across 60 cities worldwide. However, the influence of environmental/demographic factors on urban microbiome remains to be elucidated. We collected 35 environmental and demographic characteristics to examine their effects on global urban microbiome diversity/composition by PERMANOVA and regression models. PM10 concentration was the primary determinant factor positively associated with microbial α-diversity (observed species: p = 0.004, β = 1.66, R2 = 0.46; Fisher's alpha: p = 0.005, β = 0.68, R2 = 0.43), whereas GDP per capita was negatively associated (observed species: p = 0.046, β = -0.70, R2 = 0.10; Fisher's alpha: p = 0.004, β = -0.34, R2 = 0.22). The β-diversity of urban microbiome was shaped by seven environmental characteristics, including Köppen climate type, vegetation type, greenness fraction, soil type, PM2.5 concentration, annual average precipitation and temperature (PERMANOVA, p < 0.001, R2 = 0.01-0.06), cumulatively accounted for 20.3% of the microbial community variance. Canonical correspondence analysis (CCA) identified microbial species most strongly associated with environmental characteristic variation. Cities in East Asia with higher precipitation showed an increased abundance of Corynebacterium metruchotii, and cities in America with a higher greenness fraction exhibited a higher abundance of Corynebacterium casei. The prevalence of antimicrobial resistance (AMR) genes were negatively associated with GDP per capita and positively associated with solar radiation (p < 0.005). Total pathogens prevalence was positively associated with urban population and negatively associated with average temperature in June (p < 0.05). Our study presents the first comprehensive analysis of the influence of environmental/demographic characteristics on global urban microbiome. Our findings indicate that managing air quality and urban greenness is essential for regulating urban microbial diversity and composition. Meanwhile, socio-economic considerations, particularly reducing antibiotic usage in regions with lower GDP, are paramount in curbing the spread of antimicrobial resistance in urban environments.
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Affiliation(s)
- Yang Chen
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, P. R. China
| | - Xi Fu
- Guangdong Provincial Engineering Research Center of Public Health Detection and Assessment, School of Public Health, Guangdong Pharmaceutical University, 510006, Guangzhou, P. R. China.
| | - Zheyuan Ou
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, P. R. China
| | - Jiang Li
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, P. R. China
| | - Simiao Lin
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, P. R. China
| | - Yaoxuan Wu
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, P. R. China
| | - Xuwei Wang
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, P. R. China
| | - Yiqun Deng
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, P. R. China.
| | - Yu Sun
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, P. R. China.
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84
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Tao S, Hu C, Fang Y, Zhang H, Xu Y, Zheng L, Chen L, Liang W. Targeted elimination of Vancomycin resistance gene vanA by CRISPR-Cas9 system. BMC Microbiol 2023; 23:380. [PMID: 38049763 PMCID: PMC10694887 DOI: 10.1186/s12866-023-03136-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: 10/02/2023] [Accepted: 11/28/2023] [Indexed: 12/06/2023] Open
Abstract
OBJECTIVE The purpose of this study is to reduce the spread of the vanA gene by curing the vanA-harboring plasmid of vancomycin-resistant using the CRISPR-Cas9 system. METHODS Two specific spacer sequence (sgRNAs) specific was designed to target the vanA gene and cloned into plasmid CRISPR-Cas9. The role of the CRISPR-Cas system in the plasmid elimination of drug-resistance genes was verified by chemically transformation and conjugation delivery methods. Moreover, the elimination efficiency in strains was evaluated by plate counting, PCR, and quantitative real-time PCR (qPCR). Susceptibility testing was performed by broth microdilution assay and by Etest strips (bioMérieux, France) to detect changes in bacterial drug resistance phenotype after drug resistance plasmid clearance. RESULTS In the study, we constructed a specific prokaryotic CRISPR-Cas9 system plasmid targeting cleavage of the vanA gene. PCR and qPCR results indicated that recombinant pCas9-sgRNA plasmid can efficiently clear vanA-harboring plasmids. There was no significant correlation between sgRNA lengths and curing efficiency. In addition, the drug susceptibility test results showed that the bacterial resistance to vancomycin was significantly reduced after the vanA-containing drug-resistant plasmid was specifically cleaved by the CRISPR-Cas system. The CRISPR-Cas9 system can block the horizontal transfer of the conjugated plasmid pUC19-vanA. CONCLUSION In conclusion, our study demonstrated that CRISPR-Cas9 achieved plasmid clearance and reduced antimicrobial resistance. The CRISPR-Cas9 system could block the horizontal transfer of plasmid carrying vanA. This strategy provided a great potential to counteract the ever-worsening spread of the vanA gene among bacterial pathogens and laid the foundation for subsequent research using the CRISPR-Cas9 system as adjuvant antibiotic therapy.
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Affiliation(s)
- Shuan Tao
- Department of Clinical Laboratory, The First Affiliated Hospital of Ningbo University, No 59. Liuting Road, Haishu District, Ningbo, 315010, China
- School of Medicine, Jiangsu University, Zhenjiang, China
| | - Chunwei Hu
- The Biobank of The First Affiliated Hospital of Ningbo University, Ningbo, China
| | - Yewei Fang
- Department of Clinical Laboratory, The First Affiliated Hospital of Ningbo University, No 59. Liuting Road, Haishu District, Ningbo, 315010, China
| | - He Zhang
- Bengbu Medical College, Bengbu, China
| | - Yao Xu
- School of Medicine, Ningbo University, Ningbo, China
| | - Lin Zheng
- Department of Clinical Laboratory, The First Affiliated Hospital of Ningbo University, No 59. Liuting Road, Haishu District, Ningbo, 315010, China
| | - Luyan Chen
- Department of Blood Transfusion, The First Affiliated Hospital of Ningbo University, Ningbo, China
| | - Wei Liang
- Department of Clinical Laboratory, The First Affiliated Hospital of Ningbo University, No 59. Liuting Road, Haishu District, Ningbo, 315010, China.
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85
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Jung HR, Lee YJ, Hong S, Yoon S, Lim SK, Lee YJ. Current status of β-lactam antibiotic use and characterization of β-lactam-resistant Escherichia coli from commercial farms by integrated broiler chicken operations in Korea. Poult Sci 2023; 102:103091. [PMID: 37839166 PMCID: PMC10587523 DOI: 10.1016/j.psj.2023.103091] [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: 07/25/2023] [Revised: 08/31/2023] [Accepted: 09/01/2023] [Indexed: 10/17/2023] Open
Abstract
β-Lactam antibiotics are one of the most clinical importance in human and veterinary medicine because they are used for both preventive and therapeutic purposes against several gram-positive, gram-negative, and anaerobic organisms. In this study, it was confirmed that β-lactams (81.1%) were found to be significantly prescribed the most among 74 farms in 5 integrated broiler operations, and single prescription (84.6%), 2-day (41.5%) or 3-day (40.0%) administration, and 15 to 22 d of age (67.7%) administration was significantly higher in the farms (P < 0.05). Among the E. coli isolated from 74 farms in 5 integrated broiler operations, β-lactam-resistant E. coli isolates were detected more frequently in fecal sample (94.6%) than in dust sample (60.8%) (P < 0.05). The prevalence of MDR in β-lactam-resistant isolates, ranging from 88.1 to 96.5%, was significantly higher than that in non-β-lactam-resistant isolates (P < 0.05), without significant differences among operations. Of 466 β-lactam-resistant isolates, 432 (92.7%) isolates harbored β-lactamase genes. The non-extended-spectrum β-lactamase (ESBL) gene blaTEM-1 (81.8%) showed the highest prevalence among isolates, followed by the non-ESBL gene blaTEM-135 (6.4%) (P < 0.05). Five ESBL genes, SHV-12, OXA-1, CTX-M-27, CTX-M-55, and CTX-M-65, were found in 0.9 to 6.0% of the isolates. The pAmpC gene blaCMY-2 was detected in 17 isolates (3.6%). These results suggest that feces and dust are important reservoirs of antimicrobial-resistant bacteria, highlighting the need to strengthen farm management regulations, such as cleaning, disinfection, and litter disposal and to reduce the use of antibiotics in broiler operations.
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Affiliation(s)
- Hye-Ri Jung
- College of Veterinary Medicine & Zoonoses Research Institute, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Yu Jin Lee
- College of Veterinary Medicine & Zoonoses Research Institute, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Serim Hong
- College of Veterinary Medicine & Zoonoses Research Institute, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Sunghyun Yoon
- Division of Microbiology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA
| | - Suk-Kyung Lim
- Bacterial Disease Division, Animal and Plant Quarantine Agency, Gimcheon-si 39660, Gyeongsangbuk-do, Republic of Korea
| | - Young Ju Lee
- College of Veterinary Medicine & Zoonoses Research Institute, Kyungpook National University, Daegu 41566, Republic of Korea.
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86
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Ojha AK, Shah NP, Mishra V, Emanuel N, Taneja NK. Prevalence of antibiotic resistance in lactic acid bacteria isolated from traditional fermented Indian food products. Food Sci Biotechnol 2023; 32:2131-2143. [PMID: 37860739 PMCID: PMC10581985 DOI: 10.1007/s10068-023-01305-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 03/15/2023] [Accepted: 03/24/2023] [Indexed: 10/21/2023] Open
Abstract
The emergence of antimicrobial resistance (AMR) in lactic acid bacteria (LAB) raises questions on qualified presumptive safety status and poses challenge of AMR transmission in food milieu. This study focuses on isolation, identification and characterization of AMR in LAB prevalent in traditional fermented Indian food products. The analysis of 16SrRNA based phylogenetic tree showed placements of isolates among four different genera Lactobacillus, Enterococcus, Weissella and Leuconostoc. In E-strip gradient test of susceptibility to 14 different antibiotics, over 50% of isolates showed resistance to ampicillin, chloramphenicol, ciprofloxacin, erythromycin, kanamycin, linezolid, streptomycin, trimethoprim and vancomycin. A multivariate principal component analysis, an antibiogram and multiple antibiotic resistance index-values (> 0.2) indicated presence of multidrug-resistance among the isolates. This study reports prevalence of an alarmingly high rate of AMR LAB strains in traditional fermented foods and is important to regulators and public health authorities for developing strategies to control transmission in food systems. Supplementary Information The online version contains supplementary material available at 10.1007/s10068-023-01305-1.
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Affiliation(s)
- Anup Kumar Ojha
- Department of Basic and Applied Sciences, NIFTEM, Sonipat, Haryana 131028 India
| | - Nagendra Prasad Shah
- Food and Nutritional Sciences, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, SAR China
| | - Vijendra Mishra
- Department of Basic and Applied Sciences, NIFTEM, Sonipat, Haryana 131028 India
| | - Neela Emanuel
- Department of Basic and Applied Sciences, NIFTEM, Sonipat, Haryana 131028 India
| | - Neetu Kumra Taneja
- Department of Basic and Applied Sciences, NIFTEM, Sonipat, Haryana 131028 India
- Centre for Advanced Translational Research in Food Nanobiotechnology (CATR-FNB), NIFTEM, Sonepat, Haryana 131028 India
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87
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Nolan TM, Sala-Comorera L, Reynolds LJ, Martin NA, Stephens JH, O'Hare GMP, O'Sullivan JJ, Meijer WG. Bacteriophages from faecal contamination are an important reservoir for AMR in aquatic environments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 900:165490. [PMID: 37487901 DOI: 10.1016/j.scitotenv.2023.165490] [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: 04/21/2023] [Revised: 07/10/2023] [Accepted: 07/10/2023] [Indexed: 07/26/2023]
Abstract
Bacteriophages have been shown to play an important role in harbouring and propagating antibiotic resistance genes (ARGs). Faecal matter contains high levels of phages, suggesting that faecal contamination of water bodies may lead to increased antimicrobial resistance (AMR) levels due to increased phage loading in aquatic environments. In this study, we assessed whether faecal pollution of three rivers (Rivers Liffey, Tolka, and Dodder) was responsible for increased levels of ARGs in phage particles using established phage-faecal markers, focusing on four ARGs (blaTEM, tet(O), qnrS, and sul1). We observed all four ARGs in phage fractions in all three rivers, with ARGs more frequently observed in agricultural and urban sampling sites compared to their source. These findings highlight the role of faecal pollution in environmental AMR and the impact of agricultural and urban activities on water quality. Furthermore, our results suggest the importance of including phages as indicators when assessing environmental AMR, as they serve as significant reservoirs of resistance genes in aquatic environments. This study provides important insights into the role of faecal pollution and phages in the prevalence of AMR in the environment and the need for their inclusion in future studies to provide a comprehensive understanding of environmental AMR.
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Affiliation(s)
- Tristan M Nolan
- UCD School of Biomolecular and Biomedical Science, UCD Earth Institute and UCD Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Laura Sala-Comorera
- UCD School of Biomolecular and Biomedical Science, UCD Earth Institute and UCD Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Liam J Reynolds
- UCD School of Biomolecular and Biomedical Science, UCD Earth Institute and UCD Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Niamh A Martin
- UCD School of Biomolecular and Biomedical Science, UCD Earth Institute and UCD Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Jayne H Stephens
- UCD School of Biomolecular and Biomedical Science, UCD Earth Institute and UCD Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Gregory M P O'Hare
- School of Computer Science and Statistics, Trinity College Dublin, Dublin 2, Ireland
| | - John J O'Sullivan
- UCD School of Civil Engineering, UCD Dooge Centre for Water Resources Research and UCD Earth Institute, University College Dublin, Dublin 4, Ireland
| | - Wim G Meijer
- UCD School of Biomolecular and Biomedical Science, UCD Earth Institute and UCD Conway Institute, University College Dublin, Dublin 4, Ireland.
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88
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Yadav S, Mehta P, Soni J, Chattopadhyay P, Devi P, Habyarimana T, Tardalkar K, Joshi M, Pandey R. Single-cell RNA-Seq reveals intracellular microbial diversity within immune cells during SARS-CoV-2 infection and recovery. iScience 2023; 26:108357. [PMID: 38026191 PMCID: PMC10663746 DOI: 10.1016/j.isci.2023.108357] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 10/05/2023] [Accepted: 10/25/2023] [Indexed: 12/01/2023] Open
Abstract
Intracellular microorganisms, like viruses, bacteria, and fungi, pose challenges in detection due to their non-culturable forms. Transcriptomic analysis at cellular level enables exploration of distributions and the impact of these microorganisms on host cells, a domain that remains underexplored because of methodological limitations. Single-cell technology shows promise in addressing this by capturing polyadenine-tailed transcripts, because recent studies confirmed polyadenylation in microbial transcriptomes. We utilized single-cell RNA-seq from PBMCs to probe intracellular microbes in healthy, SARS-CoV-2-positive, and recovered individuals. Among 76 bacterial species detected, 16 showed significant abundance differences. Buchnera aphidicola, Streptomyces clavuligerus, and Ehrlichia canis emerged significantly in memory-B, Naïve-T, and Treg cells. Staphylococcus aureus, Mycoplasma mycoides, Leptospira interrogans, and others displayed elevated levels in SARS-CoV-2-positive patients, suggesting possible disease association. This highlights the strength of single-cell technology in revealing potential microorganism's cell-specific functions. Further research is essential for functional understanding of their cell-specific abundance across physiological states.
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Affiliation(s)
- Sunita Yadav
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi 110007, India
| | - Priyanka Mehta
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi 110007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Jyoti Soni
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi 110007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Partha Chattopadhyay
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi 110007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Priti Devi
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi 110007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Thierry Habyarimana
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi 110007, India
- Department of Biomedical Laboratory Sciences, INES-Ruhengeri, Ruhengeri, Rwanda
| | - Kishore Tardalkar
- Dr. D. Y. Patil Medical College, Hospital and Research Institute, Kolhapur, Maharashtra 416003, India
| | - Meghnad Joshi
- Dr. D. Y. Patil Medical College, Hospital and Research Institute, Kolhapur, Maharashtra 416003, India
| | - Rajesh Pandey
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi 110007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
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89
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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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90
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Muteeb G, Rehman MT, Shahwan M, Aatif M. Origin of Antibiotics and Antibiotic Resistance, and Their Impacts on Drug Development: A Narrative Review. Pharmaceuticals (Basel) 2023; 16:1615. [PMID: 38004480 PMCID: PMC10675245 DOI: 10.3390/ph16111615] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 11/08/2023] [Accepted: 11/10/2023] [Indexed: 11/26/2023] Open
Abstract
Antibiotics have revolutionized medicine, saving countless lives since their discovery in the early 20th century. However, the origin of antibiotics is now overshadowed by the alarming rise in antibiotic resistance. This global crisis stems from the relentless adaptability of microorganisms, driven by misuse and overuse of antibiotics. This article explores the origin of antibiotics and the subsequent emergence of antibiotic resistance. It delves into the mechanisms employed by bacteria to develop resistance, highlighting the dire consequences of drug resistance, including compromised patient care, increased mortality rates, and escalating healthcare costs. The article elucidates the latest strategies against drug-resistant microorganisms, encompassing innovative approaches such as phage therapy, CRISPR-Cas9 technology, and the exploration of natural compounds. Moreover, it examines the profound impact of antibiotic resistance on drug development, rendering the pursuit of new antibiotics economically challenging. The limitations and challenges in developing novel antibiotics are discussed, along with hurdles in the regulatory process that hinder progress in this critical field. Proposals for modifying the regulatory process to facilitate antibiotic development are presented. The withdrawal of major pharmaceutical firms from antibiotic research is examined, along with potential strategies to re-engage their interest. The article also outlines initiatives to overcome economic challenges and incentivize antibiotic development, emphasizing international collaborations and partnerships. Finally, the article sheds light on government-led initiatives against antibiotic resistance, with a specific focus on the Middle East. It discusses the proactive measures taken by governments in the region, such as Saudi Arabia and the United Arab Emirates, to combat this global threat. In the face of antibiotic resistance, a multifaceted approach is imperative. This article provides valuable insights into the complex landscape of antibiotic development, regulatory challenges, and collaborative efforts required to ensure a future where antibiotics remain effective tools in safeguarding public health.
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Affiliation(s)
- Ghazala Muteeb
- Department of Nursing, College of Applied Medical Science, King Faisal University, Al-Ahsa 31982, Saudi Arabia
| | - Md Tabish Rehman
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh 11437, Saudi Arabia;
- Center for Medical and Bio-Allied Health Sciences Research, Ajman University, Ajman 346, United Arab Emirates;
| | - Moayad Shahwan
- Center for Medical and Bio-Allied Health Sciences Research, Ajman University, Ajman 346, United Arab Emirates;
- Department of Clinical Sciences, College of Pharmacy and Health Sciences, Ajman University, Ajman 346, United Arab Emirates
| | - Mohammad Aatif
- Department of Public Health, College of Applied Medical Sciences, King Faisal University, Al-Ahsa 31982, Saudi Arabia;
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91
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Karasiński M, Wnorowska U, Durnaś B, Król G, Daniluk T, Skłodowski K, Głuszek K, Piktel E, Okła S, Bucki R. Ceragenins and Ceragenin-Based Core-Shell Nanosystems as New Antibacterial Agents against Gram-Negative Rods Causing Nosocomial Infections. Pathogens 2023; 12:1346. [PMID: 38003809 PMCID: PMC10674730 DOI: 10.3390/pathogens12111346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 10/30/2023] [Accepted: 11/09/2023] [Indexed: 11/26/2023] Open
Abstract
The growing number of infections caused by multidrug-resistant bacterial strains, limited treatment options, multi-species infections, high toxicity of the antibiotics used, and an increase in treatment costs are major challenges for modern medicine. To remedy this, scientists are looking for new antibiotics and treatment methods that will effectively eradicate bacteria while continually developing different resistance mechanisms. Ceragenins are a new group of antimicrobial agents synthesized based on molecular patterns that define the mechanism of antibacterial action of natural antibacterial peptides and steroid-polyamine conjugates such as squalamine. Since ceragenins have a broad spectrum of antimicrobial activity, with little recorded ability of bacteria to develop a resistance mechanism that can bridge their mechanism of action, there are high hopes that this group of molecules can give rise to a new family of drugs effective against bacteria resistant to currently used antibiotics. Experimental data suggests that core-shell nanosystems, in which ceragenins are presented to bacterial cells on metallic nanoparticles, may increase their antimicrobial potential and reduce their toxicity. However, studies should be conducted, among others, to assess potential long-term cytotoxicity and in vivo studies to confirm their activity and stability in animal models. Here, we summarized the current knowledge on ceragenins and ceragenin-containing nanoantibiotics as potential new tools against emerging Gram-negative rods associated with nosocomial infections.
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Affiliation(s)
- Maciej Karasiński
- Department of Medical Microbiology and Nanobiomedical Engineering, Medical University of Białystok, Mickiewicza 2C, 15-222 Bialystok, Poland; (M.K.); (U.W.); (T.D.); (K.S.)
| | - Urszula Wnorowska
- Department of Medical Microbiology and Nanobiomedical Engineering, Medical University of Białystok, Mickiewicza 2C, 15-222 Bialystok, Poland; (M.K.); (U.W.); (T.D.); (K.S.)
| | - Bonita Durnaś
- Department of Microbiology and Immunology, Institute of Medical Science, Collegium Medicum, Jan Kochanowski University in Kielce, IX Wieków Kielc 19A, 25-317 Kielce, Poland; (B.D.); (G.K.); (K.G.)
| | - Grzegorz Król
- Department of Microbiology and Immunology, Institute of Medical Science, Collegium Medicum, Jan Kochanowski University in Kielce, IX Wieków Kielc 19A, 25-317 Kielce, Poland; (B.D.); (G.K.); (K.G.)
| | - Tamara Daniluk
- Department of Medical Microbiology and Nanobiomedical Engineering, Medical University of Białystok, Mickiewicza 2C, 15-222 Bialystok, Poland; (M.K.); (U.W.); (T.D.); (K.S.)
| | - Karol Skłodowski
- Department of Medical Microbiology and Nanobiomedical Engineering, Medical University of Białystok, Mickiewicza 2C, 15-222 Bialystok, Poland; (M.K.); (U.W.); (T.D.); (K.S.)
| | - Katarzyna Głuszek
- Department of Microbiology and Immunology, Institute of Medical Science, Collegium Medicum, Jan Kochanowski University in Kielce, IX Wieków Kielc 19A, 25-317 Kielce, Poland; (B.D.); (G.K.); (K.G.)
| | - Ewelina Piktel
- Independent Laboratory of Nanomedicine, Medical University of Białystok, Mickiewicza 2B, 15-222 Białystok, Poland;
| | - Sławomir Okła
- Holy Cross Oncology Center of Kielce, Artwińskiego 3, 25-734 Kielce, Poland;
| | - Robert Bucki
- Department of Medical Microbiology and Nanobiomedical Engineering, Medical University of Białystok, Mickiewicza 2C, 15-222 Bialystok, Poland; (M.K.); (U.W.); (T.D.); (K.S.)
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92
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Abriouel H, Manetsberger J, Lavilla Lerma L, Pestaña Blanco MD, Martínez Nogueras R, Caballero Gómez N, Benomar N. Metagenomic insights into microbial contamination in critical healthcare environments and the efficacy of a novel "HLE" disinfectant. Infect Dis Health 2023; 28:282-289. [PMID: 37558566 DOI: 10.1016/j.idh.2023.07.002] [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: 05/19/2023] [Revised: 07/09/2023] [Accepted: 07/10/2023] [Indexed: 08/11/2023]
Abstract
BACKGROUND Bacterial contamination on inanimate clinical surfaces is directly linked to severe health problems, especially those caused by multidrug resistant (MDR) pathogens. Here, we evaluated the microbial burden in these environments and tested the efficacy of a novel HLE disinfectant solution. METHODS Microbial contamination of healthcare surfaces [Intensive Care Unit (ICU), Long Period Hospitalization Room (LPHR) and Otolaryngology Consultation (OC)] and the efficacy of HLE disinfectant solution were determined analyzing the viable counts on general and selective media, and also by molecular studies focused on metagenomic and specific qPCR. RESULTS Different contamination loads were detected with LPHR showing the highest contamination. Treatment with the HLE disinfectant solution curbed the spread of well-adapted pathogens on touched surfaces (ICU, LPHR and OC). Metagenomic analysis of microbial diversity of the Patient Table (most contaminated surface in LPHR) revealed the presence of mainly A. johnsonii and P. putida. Furthermore, functional annotation of toxin, virulence and antibiotic resistance sequences showed a high diversity of Acinetobacter spp. and Pseudomonas spp. In this context, specific qPCR analysis confirmed the efficacy of HLE disinfectant solution against the most prevalent and critical pathogens Pseudomonas sp. and Acinetobacter sp. achieving their complete eradication. CONCLUSION Given the persistence of detrimental resistant pathogens, the application of HLE disinfection solution could be a highly beneficial and effective option -used either alone or in combination-for infection prevention and control with the aim to eliminate microbial pathogens and their genes from contaminated contact-surfaces and thus limit the spread to humans and other ecological niches.
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Affiliation(s)
- Hikmate Abriouel
- Área de Microbiología, Departamento de Ciencias de la Salud, Facultad de Ciencias Experimentals, Universidad de Jaén, 23071, Jaén, Spain.
| | - Julia Manetsberger
- Área de Microbiología, Departamento de Ciencias de la Salud, Facultad de Ciencias Experimentals, Universidad de Jaén, 23071, Jaén, Spain
| | - Leyre Lavilla Lerma
- Área de Microbiología, Departamento de Ciencias de la Salud, Facultad de Ciencias Experimentals, Universidad de Jaén, 23071, Jaén, Spain
| | | | | | - Natacha Caballero Gómez
- Área de Microbiología, Departamento de Ciencias de la Salud, Facultad de Ciencias Experimentals, Universidad de Jaén, 23071, Jaén, Spain
| | - Nabil Benomar
- Área de Microbiología, Departamento de Ciencias de la Salud, Facultad de Ciencias Experimentals, Universidad de Jaén, 23071, Jaén, Spain
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93
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Miotti C, Cicotello J, Suarez Archilla G, Neder V, Alvarado Lucero W, Calvinho L, Signorini M, Camussone C, Zbrun MV, Molineri AI. Antimicrobial resistance of Streptococcus uberis isolated from bovine mastitis: Systematic review and meta-analysis. Res Vet Sci 2023; 164:105032. [PMID: 37844492 DOI: 10.1016/j.rvsc.2023.105032] [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: 07/10/2023] [Revised: 09/14/2023] [Accepted: 09/29/2023] [Indexed: 10/18/2023]
Abstract
Streptococcus uberis is one of the most common pathogens associated with bovine mastitis, commonly treated with antimicrobials (AM), favoring the appearance of antimicrobial resistance (AMR). The objective of this work was to determine the proportion of phenotypic AMR among S. uberis isolated worldwide from bovine intramammary infections between the years 1983-2022, and to assess the variables associated by means of a systematic review and metanalysis. Sixty articles were eligible for quantitative review. Ninety-four independent studies were obtained. The antimicrobials evaluated in more S. uberis strains were penicillin (21,987 strains), oxacillin (21,727 strains), erythromycin (20,013 strains), and ampicillin (19,354 strains). Most of the studies included in this meta-analysis were from Europe (44), followed by America (25), Africa (10), Asia (10), and Oceania (5). Among the included articles, 22 were published from 1983 to 2006, 23 from 2007 to 2012, 25 from 2013 to 2015, and the remaining 24 after 2016. Penicillin, erythromycin, and tetracycline were the antimicrobials with >25 studies. Therefore, the following analyses were performed only for these antimicrobials, presenting a high heterogeneity index (I2). The variability observed for penicillin and tetracycline was only explained, partially, by continent of origin. The variability observed for erythromycin was not explained by any of the potential explanatory variables included in this study. The S. uberis proportion of resistance to antimicrobials is highly variable and probably influenced by many factors other than those studied in this meta-analysis, where it was not possible to inform a unique average proportion of resistance.
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Affiliation(s)
- Camila Miotti
- Instituto de Investigación de la Cadena Láctea (INTA-CONICET), Estación Experimental Agropecuaria Rafaela, Ruta 34 Km 227, Rafaela, Santa Fe, Argentina
| | - Joaquín Cicotello
- Instituto de Investigación de la Cadena Láctea (INTA-CONICET), Estación Experimental Agropecuaria Rafaela, Ruta 34 Km 227, Rafaela, Santa Fe, Argentina
| | - Guillermo Suarez Archilla
- Instituto de Investigación de la Cadena Láctea (INTA-CONICET), Estación Experimental Agropecuaria Rafaela, Ruta 34 Km 227, Rafaela, Santa Fe, Argentina
| | - Verónica Neder
- Instituto de Investigación de la Cadena Láctea (INTA-CONICET), Estación Experimental Agropecuaria Rafaela, Ruta 34 Km 227, Rafaela, Santa Fe, Argentina
| | - Wanda Alvarado Lucero
- Instituto de Investigación de la Cadena Láctea (INTA-CONICET), Estación Experimental Agropecuaria Rafaela, Ruta 34 Km 227, Rafaela, Santa Fe, Argentina
| | - Luis Calvinho
- Instituto de Investigación de la Cadena Láctea (INTA-CONICET), Estación Experimental Agropecuaria Rafaela, Ruta 34 Km 227, Rafaela, Santa Fe, Argentina
| | - Marcelo Signorini
- Instituto de Investigación de la Cadena Láctea (INTA-CONICET), Estación Experimental Agropecuaria Rafaela, Ruta 34 Km 227, Rafaela, Santa Fe, Argentina
| | - Cecilia Camussone
- Instituto de Investigación de la Cadena Láctea (INTA-CONICET), Estación Experimental Agropecuaria Rafaela, Ruta 34 Km 227, Rafaela, Santa Fe, Argentina
| | - María Virginia Zbrun
- Instituto de Investigación de la Cadena Láctea (INTA-CONICET), Estación Experimental Agropecuaria Rafaela, Ruta 34 Km 227, Rafaela, Santa Fe, Argentina.
| | - Ana Inés Molineri
- Instituto de Investigación de la Cadena Láctea (INTA-CONICET), Estación Experimental Agropecuaria Rafaela, Ruta 34 Km 227, Rafaela, Santa Fe, Argentina
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94
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Li Y, Du X, Pian H, Fan X, Zhang Y, Wang T, Zhai F, Abro SM, Yu D. Effects of dietary supplement with licorice and rutin mixture on production performance, egg quality, antioxidant capacity, and gut microbiota in quails (Turnix tanki). Poult Sci 2023; 102:103038. [PMID: 37729679 PMCID: PMC10514455 DOI: 10.1016/j.psj.2023.103038] [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: 05/28/2023] [Revised: 08/03/2023] [Accepted: 08/11/2023] [Indexed: 09/21/2023] Open
Abstract
This study was conducted to evaluate the effect of licorice and rutin on production performance, egg quality, and mucosa antioxidant levels in Chinese yellow quail. A total of 240 Chinese Yellow Quail (400-day-old) were randomly distributed into 5 groups: the Control group, fed with a basic diet; the LR1 group, fed with basal diet supplemented with 300 + 100 mg licorice and rutin mixture/kg diet; the LR2 group, fed with basal diet supplemented with 300 + 200 mg licorice and rutin mixture/kg diet; the LR3 group, fed with basal diet supplemented with 600 + 100 mg licorice and rutin mixture/kg diet and the LR4 group, fed with basal diet supplemented with 600 + 200 mg licorice and rutin mixture/kg diet. Compared with the control, supplementation with the licorice and rutin mixture improved the laying rate and eggshell thickness whereas decreased the feed conversion ratio of quails. Moreover, dietary supplementation with the licorice and rutin mixture improved the antioxidant capacity by increasing the activity of the superoxide dismutase (SOD) level and decreasing the concentration of malondialdehyde (MDA) in the jejunal mucosa. The licorice and rutin mixture altered the composition of intestinal microbiota by influencing the relative abundances of Bacteroidetes and Bacteroides. The relative abundances of the Bacteroidetes were significantly related to the laying rate of quails. In addition, the mixture of licorice and rutin was also effective in reducing the relative abundance of intestinal Proteobacteria and Enterobacter in quails, reducing the accumulation of antibiotic-resistance genes. The results revealed that supplementation of licorice and rutin mixture to the diet improved production performance, egg quality, and antioxidant capacity and modified the composition of intestinal microbiota in quails. This study provides a reference for Chinese herbal additives to promote production performance by modulating quail gut microbes.
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Affiliation(s)
- Yan Li
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, PR China
| | - Xubin Du
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, PR China
| | - Huifang Pian
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, PR China
| | - Xiaoji Fan
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, PR China
| | - Yuchen Zhang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, PR China
| | - Tingzhang Wang
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, PR China
| | - Feng Zhai
- Tangrenshen Group Shares Co, Ltd., Zhuzhou, Hunan, PR China
| | - Sarang Mazhar Abro
- Joint International Research Laboratory of Animal Health and Food Safety of Ministry of Education & Single Molecule Nanometry Laboratory, Nanjing Agricultural University, Nanjing, PR China; Department of Veterinary Medicine, Sindh Agriculture University Tandojam, Sindh, Pakistan
| | - Debing Yu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, PR China.
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95
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Tao S, Chen H, Li N, Fang Y, Zhang H, Xu Y, Chen L, Liang W. Elimination of bla KPC-2-mediated carbapenem resistance in Escherichia coli by CRISPR-Cas9 system. BMC Microbiol 2023; 23:310. [PMID: 37884864 PMCID: PMC10601263 DOI: 10.1186/s12866-023-03058-7] [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: 06/27/2023] [Accepted: 10/11/2023] [Indexed: 10/28/2023] Open
Abstract
OBJECTIVE The purpose of this study is to re-sensitive bacteria to carbapenemases and reduce the transmission of the blaKPC-2 gene by curing the blaKPC-2-harboring plasmid of carbapenem-resistant using the CRISPR-Cas9 system. METHODS The single guide RNA (sgRNA) specifically targeted to the blaKPC-2 gene was designed and cloned into plasmid pCas9. The recombinant plasmid pCas9-sgRNA(blaKPC-2) was transformed into Escherichia coli (E.coli) carrying pET24-blaKPC-2. The elimination efficiency in strains was evaluated by polymerase chain reaction (PCR) and quantitative real-time PCR (qPCR). Susceptibility testing was performed by broth microdilution assay and by E-test strips (bioMérieux, France) to detect changes in bacterial drug resistance phenotype after drug resistance plasmid clearance. RESULTS In the present study, we constructed a specific prokaryotic CRISPR-Cas9 system plasmid targeting cleavage of the blaKPC-2 gene. PCR and qPCR results indicated that prokaryotic CRISPR-Cas9 plasmid transforming drug-resistant bacteria can efficiently clear blaKPC-2-harboring plasmids. In addition, the drug susceptibility test results showed that the bacterial resistance to imipenem was significantly reduced and allowed the resistant model bacteria to restore susceptibility to antibiotics after the blaKPC-2-containing drug-resistant plasmid was specifically cleaved by the CRISPR-Cas system. CONCLUSION In conclusion, our study demonstrated that the one plasmid-mediated CRISPR-Cas9 system can be used as a novel tool to remove resistance plasmids and re-sensitize the recipient bacteria to antibiotics. This strategy provided a great potential to counteract the ever-worsening spread of the blaKPC-2 gene among bacterial pathogens and laid the foundation for subsequent research using the CRISPR-Cas9 system as adjuvant antibiotic therapy.
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Affiliation(s)
- Shuan Tao
- Department of Clinical Laboratory, The First Affiliated Hospital of Ningbo University, Ningbo, China
- School of Medicine, Jiangsu University, Zhenjiang, China
| | - Huimin Chen
- Department of Clinical Laboratory, The First Affiliated Hospital of Ningbo University, Ningbo, China
| | - Na Li
- Bengbu Medical College, Bengbu, China
| | - Yewei Fang
- Department of Clinical Laboratory, The First Affiliated Hospital of Ningbo University, Ningbo, China
| | - He Zhang
- Bengbu Medical College, Bengbu, China
| | - Yao Xu
- School of Medicine, Ningbo University, Ningbo, China
| | - Luyan Chen
- Department of Blood Transfusion, The First Affiliated Hospital of Ningbo University, Ningbo, China
| | - Wei Liang
- Department of Clinical Laboratory, The First Affiliated Hospital of Ningbo University, Ningbo, China.
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96
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Wu Y, Li S, Yu K, Hu J, Chen Q, Sun W. Wastewater treatment plant effluents exert different impacts on antibiotic resistome in water and sediment of the receiving river: Metagenomic analysis and risk assessment. JOURNAL OF HAZARDOUS MATERIALS 2023; 460:132528. [PMID: 37713776 DOI: 10.1016/j.jhazmat.2023.132528] [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: 04/22/2023] [Revised: 08/06/2023] [Accepted: 09/09/2023] [Indexed: 09/17/2023]
Abstract
Wastewater treatment plants (WWTPs) are considered as hotspots for the spread of antibiotic resistome into the environment. However, the differential contributions of WWTPs to the antibiotic resistome in the receiving river water and sediment are poorly understood. Here, based on metagenomic analysis, we found that the WWTP effluents significantly elevated the diversities and abundances of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) in the receiving river water from the Qinghai-Tibet Plateau, but showed less interference with the antibiotic resistome in sediment. Estimated by SourceTracker, WWTPs contributed 60.691.8% of ARGs in downstream river water, much higher than those for sediment (7.7568.0%). A holistic comparison of ARG risks based on analysis of ARG combination, mobility risk, ARG hosts and ARG-carrying pathogens further revealed the great impacts of WWTP effluents on downstream river water rather than sediment. Among various MGEs, tnpA exhibited the greatest potential for the dissemination of ARGs, and displayed highest co-occurrence frequency with multiple ARGs. P. aeruginosa, E. cloacae, and E. coli were identified as the critical-priority pathogens of ARG hosts. This study demonstrated the much greater impacts of WWTP effluents on the downstream water compared with sediment, which is significant for developing effective strategies to mitigate ARG risks.
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Affiliation(s)
- Yang Wu
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, China; State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Si Li
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Ke Yu
- Shenzhen Key Laboratory for Heavy Metal Pollution Control and Reutilization, School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Jingrun Hu
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, China; State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Qian Chen
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, China; State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Weiling Sun
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, China; State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China.
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97
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Arbé-Carton K, Rey-Sogo A, Santos-Fernández N, Altube O, Garbisu C, Arana L, Alkorta I. Development of a high-throughput platform to measure plasmid transfer frequency. Front Cell Infect Microbiol 2023; 13:1269732. [PMID: 37886666 PMCID: PMC10598849 DOI: 10.3389/fcimb.2023.1269732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Accepted: 09/25/2023] [Indexed: 10/28/2023] Open
Abstract
Antibiotic resistance represents one of the greatest threats to global health. The spread of antibiotic resistance genes among bacteria occurs mostly through horizontal gene transfer via conjugation mediated by plasmids. This process implies a direct contact between a donor and a recipient bacterium which acquires the antibiotic resistance genes encoded by the plasmid and, concomitantly, the capacity to transfer the acquired plasmid to a new recipient. Classical assays for the measurement of plasmid transfer frequency (i.e., conjugation frequency) are often characterized by a high variability and, hence, they require many biological and technical replicates to reduce such variability and the accompanying uncertainty. In addition, classical conjugation assays are commonly tedious and time-consuming because they typically involve counting colonies on a large number of plates for the quantification of donors, recipients, and transconjugants (i.e., the bacteria that have received the genetic material by conjugation). Due to the magnitude of the antibiotic resistance problem, it is critical to develop reliable and rapid methods for the quantification of plasmid transfer frequency that allow the simultaneous analysis of many samples. Here, we present the development of a high-throughput, reliable, quick, easy, and cost-effective method to simultaneously accomplish and measure multiple conjugation events in 96-well plates, in which the quantification of donors, recipients, and transconjugants is estimated from the time required to reach a specific threshold value (OD600 value) in the bacterial growth curves. Our method successfully discriminates different plasmid transfer frequencies, yielding results that are equivalent to those obtained by a classical conjugation assay.
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Affiliation(s)
- Kepa Arbé-Carton
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Bilbao, Spain
| | - Ana Rey-Sogo
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Bilbao, Spain
| | - Nagore Santos-Fernández
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Bilbao, Spain
| | - Oihane Altube
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Bilbao, Spain
| | - Carlos Garbisu
- Department of Conservation of Natural Resources, NEIKER-Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Derio, Spain
| | - Lide Arana
- Department of Applied Chemistry, University of the Basque Country (UPV/EHU), Donostia, Spain
| | - Itziar Alkorta
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Bilbao, Spain
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98
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Abban MK, Ayerakwa EA, Mosi L, Isawumi A. The burden of hospital acquired infections and antimicrobial resistance. Heliyon 2023; 9:e20561. [PMID: 37818001 PMCID: PMC10560788 DOI: 10.1016/j.heliyon.2023.e20561] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 08/21/2023] [Accepted: 09/29/2023] [Indexed: 10/12/2023] Open
Abstract
The burden of Hospital care-associated infections (HCAIs) is becoming a global concern. This is compounded by the emergence of virulent and high-risk bacterial strains such as "ESKAPE" pathogens - (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter species), especially within Intensive care units (ICUs) that house high-risk and immunocompromised patients. In this review, we discuss the contributions of AMR pathogens to the increasing burden of HCAIs and provide insights into AMR mechanisms, with a particular focus on last-resort antibiotics like polymyxins. We extensively discuss how structural modifications of surface-membrane lipopolysaccharides and cationic interactions influence and inform AMR, and subsequent severity of HCAIs. We highlight some bacterial phenotypic survival mechanisms against polymyxins. Lastly, we discuss the emergence of plasmid-mediated resistance as a phenomenon making mitigation of AMR difficult, especially within the ICUs. This review provides a balanced perspective on the burden of HCAIs, associated pathogens, implication of AMR and factors influencing emerging AMR mechanisms.
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Affiliation(s)
- Molly Kukua Abban
- West African Centre for Cell Biology of Infectious Pathogens, P.O. Box LG 54, Volta Road, University of Ghana, Legon, Accra, Ghana
- Department of Biochemistry, Cell and Molecular Biology, College of Basic and Applied Sciences, P.O. Box LG 54, Volta Road, University of Ghana, Legon, Accra, Ghana
| | - Eunice Ampadubea Ayerakwa
- West African Centre for Cell Biology of Infectious Pathogens, P.O. Box LG 54, Volta Road, University of Ghana, Legon, Accra, Ghana
- Department of Biochemistry, Cell and Molecular Biology, College of Basic and Applied Sciences, P.O. Box LG 54, Volta Road, University of Ghana, Legon, Accra, Ghana
| | - Lydia Mosi
- West African Centre for Cell Biology of Infectious Pathogens, P.O. Box LG 54, Volta Road, University of Ghana, Legon, Accra, Ghana
- Department of Biochemistry, Cell and Molecular Biology, College of Basic and Applied Sciences, P.O. Box LG 54, Volta Road, University of Ghana, Legon, Accra, Ghana
| | - Abiola Isawumi
- West African Centre for Cell Biology of Infectious Pathogens, P.O. Box LG 54, Volta Road, University of Ghana, Legon, Accra, Ghana
- Department of Biochemistry, Cell and Molecular Biology, College of Basic and Applied Sciences, P.O. Box LG 54, Volta Road, University of Ghana, Legon, Accra, Ghana
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99
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Weber M, Göpfert B, von Wezyk S, Savin-Hoffmeyer M, Lipski A. Correlation between Bacterial Cell Density and Abundance of Antibiotic Resistance on Milking Machine Surfaces Assessed by Cultivation and Direct qPCR Methods. MICROBIAL ECOLOGY 2023; 86:1676-1685. [PMID: 37166501 PMCID: PMC10497690 DOI: 10.1007/s00248-023-02225-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 04/18/2023] [Indexed: 05/12/2023]
Abstract
The relative abundance of antibiotic-resistant bacteria and antibiotic-resistance genes was surveyed for different parts of a milking machine. A cultivation approach based on swab samples showed a highly diverse microbiota, harboring resistances against cloxacillin, ampicillin, penicillin, and tetracycline. This approach demonstrated a substantial cloxacillin resistance of numerous taxa within milking machine microbiota coming along with regular use of cloxacillin for dry-off therapy of dairy cows. For the less abundant tetracycline-resistant bacteria we found a positive correlation between microbial cell density and relative abundance of tetracycline-resistant microorganisms (R2 = 0.73). This indicated an accelerated dispersion of resistant cells for sampling locations with high cell density. However, the direct quantification of the tetM gene from the swap samples by qPCR showed the reverse relation to bacterial density if normalized against the abundance of 16S rRNA genes (R2 = 0.88). The abundance of 16S rRNA genes was analyzed by qPCR combined with a propidium monoazide treatment, which eliminates 16S rRNA gene signals in negative controls.
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Affiliation(s)
- Mareike Weber
- Institute of Nutrition and Food Sciences, Department of Food Microbiology and Hygiene, University of Bonn, Friedrich-Hirzebruch-Allee 7, 53115, Bonn, Germany
| | - Bettina Göpfert
- Institute of Nutrition and Food Sciences, Department of Food Microbiology and Hygiene, University of Bonn, Friedrich-Hirzebruch-Allee 7, 53115, Bonn, Germany
| | - Sina von Wezyk
- Institute of Nutrition and Food Sciences, Department of Food Microbiology and Hygiene, University of Bonn, Friedrich-Hirzebruch-Allee 7, 53115, Bonn, Germany
| | - Michael Savin-Hoffmeyer
- Institute for Hygiene and Public Health, University Hospital Bonn, Venusberg-Campus 1, 53127, Bonn, Germany
| | - André Lipski
- Institute of Nutrition and Food Sciences, Department of Food Microbiology and Hygiene, University of Bonn, Friedrich-Hirzebruch-Allee 7, 53115, Bonn, Germany.
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100
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Ashy RA. Functional analysis of bacterial genes accidentally packaged in rhizospheric phageome of the wild plant species Abutilon fruticosum. Saudi J Biol Sci 2023; 30:103789. [PMID: 37680975 PMCID: PMC10480775 DOI: 10.1016/j.sjbs.2023.103789] [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: 08/02/2023] [Revised: 08/11/2023] [Accepted: 08/18/2023] [Indexed: 09/09/2023] Open
Abstract
The study aimed to reveal the structure and function of phageome existing in soil rhizobiome of Abutilon fruticosum in order to detect accidentally-packaged bacterial genes that encode Carbohydrate-Active enZymes (or CAZymes) and those that confer antibiotic resistance (e.g., antibiotic resistance genes or ARGs). Highly abundant genes were shown to mainly exist in members of the genera Pseudomonas, Streptomyces, Mycobacterium and Rhodococcus. Enriched CAZymes belong to glycoside hydrolase families GH4, GH6, GH12, GH15 and GH43 and mainly function in D-glucose biosynthesis via 10 biochemical passages. Another enriched CAZyme, e.g., alpha-galactosidase, of the GH4 family is responsible for the wealth of different carbohydrate forms in rhizospheric soil sink of A. fruticosum. ARGs of this phageome include the soxR and OleC genes that participate in the "antibiotic efflux pump" resistance mechanism, the parY mutant gene that participates in the "antibiotic target alteration" mechanism and the arr-1, iri, and AAC(3)-Ic genes that participate in the "antibiotic inactivation" mechanism. It is claimed that the genera Streptomyces, which harbors phages with oleC and parY mutant genes, and Pseudomonas, which harbors phages with soxR and AAC(3)-Ic genes, are approaching multidrug resistance via newly disseminating phages. These ARGs inhibit many antibiotics including oleandomycin, tetracycline, rifampin and aminoglycoside. The study highlights the possibility of accidental packaging of these ARGs in soil phageome and the risk of their horizontal transfer to human gut pathogens through the food chain as detrimental impacts of soil phageome of A. fruticosum. The study also emphasizes the beneficial impacts of phageome on soil microbiome and plant interacting in storing carbohydrates in the soil sink for use by the two entities upon carbohydrate deprivation.
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Affiliation(s)
- Ruba Abdulrahman Ashy
- Department of Biology, College of Science, University of Jeddah, Jeddah 21493, Saudi Arabia
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