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Wang N, Zheng X, Leptihn S, Li Y, Cai H, Zhang P, Wu W, Yu Y, Hua X. Characteristics and phylogenetic distribution of megaplasmids and prediction of a putative chromid in Pseudomonas aeruginosa. Comput Struct Biotechnol J 2024; 23:1418-1428. [PMID: 38616963 PMCID: PMC11015739 DOI: 10.1016/j.csbj.2024.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 04/01/2024] [Accepted: 04/01/2024] [Indexed: 04/16/2024] Open
Abstract
Research on megaplasmids that contribute to the spread of antimicrobial resistance (AMR) in Pseudomonas aeruginosa strains has grown in recent years due to the now widely used technologies allowing long-read sequencing. Here, we systematically analyzed distinct and consistent genetic characteristics of megaplasmids found in P. aeruginosa. Our data provide information on their phylogenetic distribution and hypotheses tracing the potential evolutionary paths of megaplasmids. Most of the megaplasmids we found belong to the IncP-2-type, with conserved and syntenic genetic backbones carrying modules of genes associated with chemotaxis apparatus, tellurite resistance and plasmid replication, segregation, and transmission. Extensively variable regions harbor abundant AMR genes, especially those encoding β-lactamases such as VIM-2, IMP-45, and KPC variants, which are high-risk elements in nosocomial infection. IncP-2 megaplasmids act as effective vehicles transmitting AMR genes to diverse regions. One evolutionary model of the origin of megaplasmids claims that chromids can develop from megaplasmids. These chromids have been characterized as an intermediate between a megaplasmid and a chromosome, also containing core genes that can be found on the chromosome but not on the megaplasmid. Using in silico prediction, we identified the "PABCH45 unnamed replicon" as a putative chromid in P. aeruginosa, which shows a much higher similarity and closer phylogenetic relationship to chromosomes than to megaplasmids while also encoding plasmid-like partition genes. We propose that such a chromid could facilitate genome expansion, allowing for more rapid adaptations to novel ecological niches or selective conditions, in comparison to megaplasmids.
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Affiliation(s)
- Nanfei Wang
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xuan Zheng
- Department of Nephrology, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Sebastian Leptihn
- HMU Health and Medical University, Am Anger 64/73 – 99084, Erfurt, Germany
- Deutsches Zentrum für Infektionsforschung (DZIF) Translational Phage-Network, Inhoffenstraße 7 – 38124, Braunschweig, Germany
- University of Southern Denmark,Department of Biochemistry and Molecular Biology, Campusvej 55 – 5230, Odense, Denmark
| | - Yue Li
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Heng Cai
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Piaopiao Zhang
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Wenhao Wu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yunsong Yu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaoting Hua
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
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Lu N, Du Z, Chu F, Xiao R, Wu Z, Wang M, Jia R, Chu W. Tracking the impact of perfluoroalkyl acid emissions on antibiotic resistance gene profiles in receiving water by metagenomic analysis. WATER RESEARCH 2024; 261:121931. [PMID: 38924952 DOI: 10.1016/j.watres.2024.121931] [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: 02/01/2024] [Revised: 05/17/2024] [Accepted: 06/11/2024] [Indexed: 06/28/2024]
Abstract
The ecological risks posed by perfluoroalkyl acids (PFAAs) to the aquatic environment have recently been of great concern. However, little information was available on the impact of PFAAs on antibiotic resistance genes (ARGs) profiles. In this study, the receiving river of the largest fluoropolymer production facility in China was selected to investigate the effects of PFAAs on ARGs profiles. The highest PFAAs concentration for water samples near the industrial effluent discharge point was 310.9 μg/L, which was thousands times of higher than the average concentration collected at upstream sites. Perfluorooctanoic acid accounted for more than 67.2 % of ∑PFAAs concentration in water samples collected at the downstream sites, followed by perfluorohexanoic acid (3.6 %-15.9 %). 145 ARG subtypes including high-risk ARGs were detected by metagenomic technology. The results indicated that the discharge of PFAA-containing effluents had a significant impact on the abundance and diversity of ARGs in receiving waters, and PFAAs and water quality parameters (e.g., pH, NH3N, CODMn, TP) could largely affect ARG profiles. Specifically, short-chain PFAAs had similar impacts on ARG profiles compared to the restricted long-chain PFAAs. This study confirmed the potential effects of PFAAs on ARGs in aquatic environment and provided more insights into the ecological risk raised by PFAAs.
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Affiliation(s)
- Nannan Lu
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, China; Shandong Provincial Water Supply and Drainage Monitoring Centre, Jinan, 250101, China
| | - Zhenqi Du
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, China; Shandong Provincial Water Supply and Drainage Monitoring Centre, Jinan, 250101, China
| | - Fumin Chu
- Shandong Provincial Water Supply and Drainage Monitoring Centre, Jinan, 250101, China
| | - Rong Xiao
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, China
| | - Zhengdi Wu
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, China
| | - Mingquan Wang
- Shandong Provincial Water Supply and Drainage Monitoring Centre, Jinan, 250101, China
| | - Ruibao Jia
- Shandong Provincial Water Supply and Drainage Monitoring Centre, Jinan, 250101, China.
| | - Wenhai Chu
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, China; Key Laboratory of Yangtze River Water Environment, Ministry of Education, Tongji University, Shanghai, 200092, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai, 200092, China.
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Abbas A, Barkhouse A, Hackenberger D, Wright GD. Antibiotic resistance: A key microbial survival mechanism that threatens public health. Cell Host Microbe 2024; 32:837-851. [PMID: 38870900 DOI: 10.1016/j.chom.2024.05.015] [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: 03/18/2024] [Revised: 05/13/2024] [Accepted: 05/17/2024] [Indexed: 06/15/2024]
Abstract
Antibiotic resistance (AMR) is a global public health threat, challenging the effectiveness of antibiotics in combating bacterial infections. AMR also represents one of the most crucial survival traits evolved by bacteria. Antibiotics emerged hundreds of millions of years ago as advantageous secondary metabolites produced by microbes. Consequently, AMR is equally ancient and hardwired into the genetic fabric of bacteria. Human use of antibiotics for disease treatment has created selection pressure that spurs the evolution of new resistance mechanisms and the mobilization of existing ones through bacterial populations in the environment, animals, and humans. This integrated web of resistance elements is genetically complex and mechanistically diverse. Addressing this mode of bacterial survival requires innovation and investment to ensure continued use of antibiotics in the future. Strategies ranging from developing new therapies to applying artificial intelligence in monitoring AMR and discovering new drugs are being applied to manage the growing AMR crisis.
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Affiliation(s)
- Amna Abbas
- David Braley Center for Antibiotic Discovery, Michael G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
| | - Alexandra Barkhouse
- David Braley Center for Antibiotic Discovery, Michael G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
| | - Dirk Hackenberger
- David Braley Center for Antibiotic Discovery, Michael G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
| | - Gerard D Wright
- David Braley Center for Antibiotic Discovery, Michael G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada.
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Neff SL, Doing G, Reiter T, Hampton TH, Greene CS, Hogan DA. Pseudomonas aeruginosa transcriptome analysis of metal restriction in ex vivo cystic fibrosis sputum. Microbiol Spectr 2024; 12:e0315723. [PMID: 38385740 PMCID: PMC10986534 DOI: 10.1128/spectrum.03157-23] [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: 08/24/2023] [Accepted: 01/22/2024] [Indexed: 02/23/2024] Open
Abstract
Chronic Pseudomonas aeruginosa lung infections are a feature of cystic fibrosis (CF) that many patients experience even with the advent of highly effective modulator therapies. Identifying factors that impact P. aeruginosa in the CF lung could yield novel strategies to eradicate infection or otherwise improve outcomes. To complement published P. aeruginosa studies using laboratory models or RNA isolated from sputum, we analyzed transcripts of strain PAO1 after incubation in sputum from different CF donors prior to RNA extraction. We compared PAO1 gene expression in this "spike-in" sputum model to that for P. aeruginosa grown in synthetic cystic fibrosis sputum medium to determine key genes, which are among the most differentially expressed or most highly expressed. Using the key genes, gene sets with correlated expression were determined using the gene expression analysis tool eADAGE. Gene sets were used to analyze the activity of specific pathways in P. aeruginosa grown in sputum from different individuals. Gene sets that we found to be more active in sputum showed similar activation in published data that included P. aeruginosa RNA isolated from sputum relative to corresponding in vitro reference cultures. In the ex vivo samples, P. aeruginosa had increased levels of genes related to zinc and iron acquisition which were suppressed by metal amendment of sputum. We also found a significant correlation between expression of the H1-type VI secretion system and CFTR corrector use by the sputum donor. An ex vivo sputum model or synthetic sputum medium formulation that imposes metal restriction may enhance future CF-related studies.IMPORTANCEIdentifying the gene expression programs used by Pseudomonas aeruginosa to colonize the lungs of people with cystic fibrosis (CF) will illuminate new therapeutic strategies. To capture these transcriptional programs, we cultured the common P. aeruginosa laboratory strain PAO1 in expectorated sputum from CF patient donors. Through bioinformatic analysis, we defined sets of genes that are more transcriptionally active in real CF sputum compared to a synthetic cystic fibrosis sputum medium. Many of the most differentially active gene sets contained genes related to metal acquisition, suggesting that these gene sets play an active role in scavenging for metals in the CF lung environment which may be inadequately represented in some models. Future studies of P. aeruginosa transcript abundance in CF may benefit from the use of an expectorated sputum model or media supplemented with factors that induce metal restriction.
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Affiliation(s)
- Samuel L. Neff
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Georgia Doing
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Taylor Reiter
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Thomas H. Hampton
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Casey S. Greene
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Deborah A. Hogan
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
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Zhang J, Li T, Tao S, Shen M. Microplastic pollution interaction with disinfectant resistance genes: research progress, environmental impacts, and potential threats. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:16241-16255. [PMID: 38340302 DOI: 10.1007/s11356-024-32225-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 01/23/2024] [Indexed: 02/12/2024]
Abstract
The consumption of disposable plastic products and disinfectants has surged during the global COVID-19 pandemic, as they play a vital role in effectively preventing and controlling the spread of the virus. However, microplastic pollution and the excessive or improper use of disinfectants contribute to the increased environmental tolerance of microorganisms. Microplastics play a crucial role as vectors for microorganisms and plankton, facilitating energy transfer and horizontal gene exchange. The increase in the use of disinfectants has become a driving force for the growth of disinfectant resistant bacteria (DRB). A large number of microorganisms can have intense gene exchange, such as plasmid loss and capture, phage transduction, and cell fusion. The reproduction and diffusion rate of DRB in the environment is significantly higher than that of ordinary microorganisms, which will greatly increase the environmental tolerance of DRB. Unfortunately, there is still a huge knowledge gap in the interaction between microplastics and disinfectant resistance genes (DRGs). Accordingly, it is critical to comprehensively summarize the formation and transmission routes of DRGs on microplastics to address the problem. This paper systematically analyzed the process and mechanisms of DRGs formed by microbes. The interaction between microplastics and DRGs and the contribution of microplastic on the diffusion and spread of DRGs were expounded. The potential threats to the ecological environment and human health were also discussed. Additionally, some challenges and future priorities were also proposed with a view to providing useful basis for further research.
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Affiliation(s)
- Jiahao Zhang
- School of Energy and Environment, Anhui University of Technology, Maanshan, Anhui, 243002, People's Republic of China
| | - Tianhao Li
- School of Energy and Environment, Anhui University of Technology, Maanshan, Anhui, 243002, People's Republic of China
| | - Shiyu Tao
- School of Energy and Environment, Anhui University of Technology, Maanshan, Anhui, 243002, People's Republic of China
| | - Maocai Shen
- School of Energy and Environment, Anhui University of Technology, Maanshan, Anhui, 243002, People's Republic of China.
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Ashworth EA, Wright RCT, Shears RK, Wong JKL, Hassan A, Hall JPJ, Kadioglu A, Fothergill JL. Exploiting lung adaptation and phage steering to clear pan-resistant Pseudomonas aeruginosa infections in vivo. Nat Commun 2024; 15:1547. [PMID: 38378698 PMCID: PMC10879199 DOI: 10.1038/s41467-024-45785-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 02/05/2024] [Indexed: 02/22/2024] Open
Abstract
Pseudomonas aeruginosa is a major nosocomial pathogen that causes severe disease including sepsis. Carbapenem-resistant P. aeruginosa is recognised by the World Health Organisation as a priority 1 pathogen, with urgent need for new therapeutics. As such, there is renewed interest in using bacteriophages as a therapeutic. However, the dynamics of treating pan-resistant P. aeruginosa with phage in vivo are poorly understood. Using a pan-resistant P. aeruginosa in vivo infection model, phage therapy displays strong therapeutic potential, clearing infection from the blood, kidneys, and spleen. Remaining bacteria in the lungs and liver displays phage resistance due to limiting phage adsorption. Yet, resistance to phage results in re-sensitisation to a wide range of antibiotics. In this work, we use phage steering in vivo, pre-exposing a pan resistant P. aeruginosa infection with a phage cocktail to re-sensitise bacteria to antibiotics, clearing the infection from all organs.
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Affiliation(s)
- Eleri A Ashworth
- Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, Liverpool, UK
| | - Rosanna C T Wright
- Division of Evolution & Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester, UK
| | - Rebecca K Shears
- Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, Liverpool, UK
- Centre for Bioscience, Manchester Metropolitan University, Manchester, M1 5DG, UK
| | - Janet K L Wong
- Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, Liverpool, UK
| | - Akram Hassan
- Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, Liverpool, UK
| | - James P J Hall
- Department of Evolution, Ecology and Behaviour, University of Liverpool, Liverpool, UK
| | - Aras Kadioglu
- Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, Liverpool, UK.
| | - Joanne L Fothergill
- Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, Liverpool, UK.
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Lee JH, Kim NH, Jang KM, Jin H, Shin K, Jeong BC, Kim DW, Lee SH. Prioritization of Critical Factors for Surveillance of the Dissemination of Antibiotic Resistance in Pseudomonas aeruginosa: A Systematic Review. Int J Mol Sci 2023; 24:15209. [PMID: 37894890 PMCID: PMC10607276 DOI: 10.3390/ijms242015209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 10/13/2023] [Accepted: 10/13/2023] [Indexed: 10/29/2023] Open
Abstract
Pseudomonas aeruginosa is the primary opportunistic human pathogen responsible for a range of acute and chronic infections; it poses a significant threat to immunocompromised patients and is the leading cause of morbidity and mortality for nosocomial infections. Its high resistance to a diverse array of antimicrobial agents presents an urgent health concern. Among the mechanisms contributing to resistance in P. aeruginosa, the horizontal acquisition of antibiotic resistance genes (ARGs) via mobile genetic elements (MGEs) has gained recognition as a substantial concern in clinical settings, thus indicating that a comprehensive understanding of ARG dissemination within the species is strongly required for surveillance. Here, two approaches, including a systematic literature analysis and a genome database survey, were employed to gain insights into ARG dissemination. The genome database enabled scrutinizing of all the available sequence information and various attributes of P. aeruginosa isolates, thus providing an extensive understanding of ARG dissemination within the species. By integrating both approaches, with a primary focus on the genome database survey, mobile ARGs that were linked or correlated with MGEs, important sequence types (STs) carrying diverse ARGs, and MGEs responsible for ARG dissemination were identified as critical factors requiring strict surveillance. Although human isolates play a primary role in dissemination, the importance of animal and environmental isolates has also been suggested. In this study, 25 critical mobile ARGs, 45 critical STs, and associated MGEs involved in ARG dissemination within the species, are suggested as critical factors. Surveillance and management of these prioritized factors across the One Health sectors are essential to mitigate the emergence of multidrug-resistant (MDR) and extensively resistant (XDR) P. aeruginosa in clinical settings.
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Affiliation(s)
- Jung Hun Lee
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, Yongin 17058, Republic of Korea; (J.H.L.); (K.-M.J.); (H.J.); (K.S.); (B.C.J.)
| | - Nam-Hoon Kim
- Division of Life Sciences, Jeonbuk National University, Jeonju 54896, Republic of Korea;
| | - Kyung-Min Jang
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, Yongin 17058, Republic of Korea; (J.H.L.); (K.-M.J.); (H.J.); (K.S.); (B.C.J.)
| | - Hyeonku Jin
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, Yongin 17058, Republic of Korea; (J.H.L.); (K.-M.J.); (H.J.); (K.S.); (B.C.J.)
| | - Kyoungmin Shin
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, Yongin 17058, Republic of Korea; (J.H.L.); (K.-M.J.); (H.J.); (K.S.); (B.C.J.)
| | - Byeong Chul Jeong
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, Yongin 17058, Republic of Korea; (J.H.L.); (K.-M.J.); (H.J.); (K.S.); (B.C.J.)
| | - Dae-Wi Kim
- Division of Life Sciences, Jeonbuk National University, Jeonju 54896, Republic of Korea;
| | - Sang Hee Lee
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, Yongin 17058, Republic of Korea; (J.H.L.); (K.-M.J.); (H.J.); (K.S.); (B.C.J.)
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Eladawy M, Thomas JC, Hoyles L. Phenotypic and genomic characterization of Pseudomonas aeruginosa isolates recovered from catheter-associated urinary tract infections in an Egyptian hospital. Microb Genom 2023; 9:001125. [PMID: 37902186 PMCID: PMC10634444 DOI: 10.1099/mgen.0.001125] [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: 07/20/2023] [Accepted: 10/12/2023] [Indexed: 10/31/2023] Open
Abstract
Catheter-associated urinary tract infections (CAUTIs) represent one of the major healthcare-associated infections, and Pseudomonas aeruginosa is a common Gram-negative bacterium associated with catheter infections in Egyptian clinical settings. The present study describes the phenotypic and genotypic characteristics of 31 P. aeruginosa isolates recovered from CAUTIs in an Egyptian hospital over a 3 month period. Genomes of isolates were of good quality and were confirmed to be P. aeruginosa by comparison to the type strain (average nucleotide identity, phylogenetic analysis). Clonal diversity among the isolates was determined; eight different sequence types were found (STs 244, 357, 381, 621, 773, 1430, 1667 and 3765), of which ST357 and ST773 are considered to be high-risk clones. Antimicrobial resistance (AMR) testing according to European Committee on Antimicrobial Susceptibility Testing (EUCAST) guidelines showed that the isolates were highly resistant to quinolones [ciprofloxacin (12/31, 38.7 %) and levofloxacin (9/31, 29 %) followed by tobramycin (10/31, 32.5 %)] and cephalosporins (7/31, 22.5 %). Genotypic analysis of resistance determinants predicted all isolates to encode a range of AMR genes, including those conferring resistance to aminoglycosides, β-lactamases, fluoroquinolones, fosfomycin, sulfonamides, tetracyclines and chloramphenicol. One isolate was found to carry a 422 938 bp pBT2436-like megaplasmid encoding OXA-520, the first report from Egypt of this emerging family of clinically important mobile genetic elements. All isolates were able to form biofilms and were predicted to encode virulence genes associated with adherence, antimicrobial activity, anti-phagocytosis, phospholipase enzymes, iron uptake, proteases, secretion systems and toxins. The present study shows how phenotypic analysis alongside genomic analysis may help us understand the AMR and virulence profiles of P. aeruginosa contributing to CAUTIs in Egypt.
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Affiliation(s)
- Mohamed Eladawy
- Department of Biosciences, School of Science and Technology, Nottingham Trent University, Nottingham, UK
- Department of Microbiology and Immunology, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Jonathan C. Thomas
- Department of Biosciences, School of Science and Technology, Nottingham Trent University, Nottingham, UK
| | - Lesley Hoyles
- Department of Biosciences, School of Science and Technology, Nottingham Trent University, Nottingham, UK
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Mataseje LF, Pitout J, Croxen M, Mulvey MR, Dingle TC. Three separate acquisitions of bla NDM-1 in three different bacterial species from a single patient. Eur J Clin Microbiol Infect Dis 2023; 42:1275-1280. [PMID: 37688673 PMCID: PMC10511597 DOI: 10.1007/s10096-023-04651-4] [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: 05/26/2023] [Accepted: 08/07/2023] [Indexed: 09/11/2023]
Abstract
To investigate the acquisition and relatedness of New Delhi Metallo-beta-lactamase among multiple separate species from one patient. Five isolates from three species (Pseudomonas aeruginosa; Pa, Acinetobacter baumannii; Ab and Proteus mirabilis; Pm) suspected of harbouring a carbapenemase were investigated by phenotype (antimicrobial susceptibilities) and whole genome sequencing. Epidemiological data was collected on this patient. Three different carbapenemase genes were detected; blaVIM-1 (Pa; ST773), blaOXA-23 (Ab, ST499) and blaNDM-1 identified in all isolates. NDM regions were found chromosomally integrated in all isolates. Data showed no evidence of NDM-1 transfer within this patient suggesting the enzyme was acquired in three separate events.
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Affiliation(s)
- L F Mataseje
- National Microbiology laboratory, Winnipeg, MB, Canada
| | - J Pitout
- Alberta Precision Laboratories, Public Health Laboratory, 3030 Hospital Drive N.W, Calgary, AB, T2N 4W4, Canada
- University of Calgary, Calgary, AB, Canada
- University of Pretoria, Pretoria, Gauteng, South Africa
| | - M Croxen
- Alberta Precision Laboratories, Public Health Laboratory, 3030 Hospital Drive N.W, Calgary, AB, T2N 4W4, Canada
- University of Alberta, Edmonton, AB, Canada
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB, Canada
- Women and Children's Health Research Institute, University of Alberta, Edmonton, AB, Canada
| | - M R Mulvey
- National Microbiology laboratory, Winnipeg, MB, Canada
| | - T C Dingle
- Alberta Precision Laboratories, Public Health Laboratory, 3030 Hospital Drive N.W, Calgary, AB, T2N 4W4, Canada.
- University of Calgary, Calgary, AB, Canada.
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Weisberg AJ, Chang JH. Mobile Genetic Element Flexibility as an Underlying Principle to Bacterial Evolution. Annu Rev Microbiol 2023; 77:603-624. [PMID: 37437216 DOI: 10.1146/annurev-micro-032521-022006] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/14/2023]
Abstract
Mobile genetic elements are key to the evolution of bacteria and traits that affect host and ecosystem health. Here, we use a framework of a hierarchical and modular system that scales from genes to populations to synthesize recent findings on mobile genetic elements (MGEs) of bacteria. Doing so highlights the role that emergent properties of flexibility, robustness, and genetic capacitance of MGEs have on the evolution of bacteria. Some of their traits can be stored, shared, and diversified across different MGEs, taxa of bacteria, and time. Collectively, these properties contribute to maintaining functionality against perturbations while allowing changes to accumulate in order to diversify and give rise to new traits. These properties of MGEs have long challenged our abilities to study them. Implementation of new technologies and strategies allows for MGEs to be analyzed in new and powerful ways.
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Affiliation(s)
- Alexandra J Weisberg
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA;
| | - Jeff H Chang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA;
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Wang N, Lei T, Zhu Y, Li Y, Cai H, Zhang P, Leptihn S, Zhou J, Ke H, Gao B, Feng Y, Hua X, Qu T. Characterization of two novel VIM-type metallo-β-lactamases, VIM-84 and VIM-85, associated with the spread of IncP-2 megaplasmids in Pseudomonas aeruginosa. Microbiol Spectr 2023; 11:e0154423. [PMID: 37707305 PMCID: PMC10580930 DOI: 10.1128/spectrum.01544-23] [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: 04/17/2023] [Accepted: 07/17/2023] [Indexed: 09/15/2023] Open
Abstract
This study aimed to characterize two novel VIM-type metallo-β-lactamases, VIM-84 and VIM-85, and reveal the important role of the IncP-2 type megaplasmids in the spread of antimicrobial resistance (AMR) genes. VIM-84 and VIM-85 were encoded by two novel genes bla VIM-84 and bla VIM-85 which showed similarity to bla VIM-24. Both bla VIM-84 and bla VIM-85 are harbored into class 1 integrons embedded into the Tn1403 transposon. The bla VIM-85 gene was identified in a megaplasmid, which was related to 17 megaplasmid sequences with sizes larger than 430 kb, deposited previously in Genbank. A comparative analysis of complete plasmid sequences showed highly similar backbone regions and various AMR genes. A phylogenetic tree revealed that these megaplasmids, which were widely distributed globally, were vehicles for the spread of AMR genes. The bla VIM-24, bla VIM-84, and bla VIM-85 genes were cloned into pGK1900, and the recombinant vectors were further transformed into Escherichia coli DH5α and Pseudomonas aeruginosa PAO1. The antimicrobial susceptibility test of the cloning strains showed high levels of resistance to β-lactams while they remained susceptible to aztreonam. Enzymatic tests revealed that both, VIM-84 and VIM-85, exhibited higher activity in hydrolyzing β-lactams compared to VIM-24. A D117N mutation found in VIM-24 affected binding to the antibiotics. IMPORTANCE The metallo-β-lactamases-producing Pseudomonas aeruginosa strains play an important role in hospital outbreaks and the VIM-type enzyme is the most prevalent in European countries. Two novel VIM-type enzymes in our study, VIM-84 and VIM-85, have higher levels of resistance to β-lactams and greater hydrolytic activities for most β-lactams compared with VIM-24. Both bla VIM-84 and bla VIM-85 are harbored into class 1 integrons embedded into the Tn1403 transposon. Notably, the genes bla VIM-85 are carried by three different IncP-2-type megaplasmids which are distributed locally and appear responsible for the spread of antimicrobial resistance genes in hospital settings.
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Affiliation(s)
- Nanfei Wang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Tailong Lei
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yiwei Zhu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yue Li
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Heng Cai
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Piaopiao Zhang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Sebastian Leptihn
- Department of Biochemistry, Health and Medical University, Erfurt, Germany
- Department of Antimicrobial Biotechnology, Fraunhofer Institute for Cell Therapy & Immunology, Leipzig, Germany
| | - Junxin Zhou
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Huanhuan Ke
- Department of Biophysics, and Department of Infectious Disease of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Bo Gao
- Department of Biophysics, and Department of Infectious Disease of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yu Feng
- Department of Biophysics, and Department of Infectious Disease of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaoting Hua
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou, Zhejiang, China
| | - Tingting Qu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
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Shikov AE, Savina IA, Nizhnikov AA, Antonets KS. Recombination in Bacterial Genomes: Evolutionary Trends. Toxins (Basel) 2023; 15:568. [PMID: 37755994 PMCID: PMC10534446 DOI: 10.3390/toxins15090568] [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: 08/08/2023] [Revised: 09/02/2023] [Accepted: 09/07/2023] [Indexed: 09/28/2023] Open
Abstract
Bacterial organisms have undergone homologous recombination (HR) and horizontal gene transfer (HGT) multiple times during their history. These processes could increase fitness to new environments, cause specialization, the emergence of new species, and changes in virulence. Therefore, comprehensive knowledge of the impact and intensity of genetic exchanges and the location of recombination hotspots on the genome is necessary for understanding the dynamics of adaptation to various conditions. To this end, we aimed to characterize the functional impact and genomic context of computationally detected recombination events by analyzing genomic studies of any bacterial species, for which events have been detected in the last 30 years. Genomic loci where the transfer of DNA was detected pertained to mobile genetic elements (MGEs) housing genes that code for proteins engaged in distinct cellular processes, such as secretion systems, toxins, infection effectors, biosynthesis enzymes, etc. We found that all inferences fall into three main lifestyle categories, namely, ecological diversification, pathogenesis, and symbiosis. The latter primarily exhibits ancestral events, thus, possibly indicating that adaptation appears to be governed by similar recombination-dependent mechanisms.
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Affiliation(s)
- Anton E. Shikov
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia; (A.E.S.); (I.A.S.); (A.A.N.)
- Faculty of Biology, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia
| | - Iuliia A. Savina
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia; (A.E.S.); (I.A.S.); (A.A.N.)
| | - Anton A. Nizhnikov
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia; (A.E.S.); (I.A.S.); (A.A.N.)
- Faculty of Biology, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia
| | - Kirill S. Antonets
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia; (A.E.S.); (I.A.S.); (A.A.N.)
- Faculty of Biology, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia
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Neff SL, Doing G, Reiter T, Hampton TH, Greene CS, Hogan DA. Analysis of Pseudomonas aeruginosa transcription in an ex vivo cystic fibrosis sputum model identifies metal restriction as a gene expression stimulus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.21.554169. [PMID: 37662412 PMCID: PMC10473638 DOI: 10.1101/2023.08.21.554169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Chronic Pseudomonas aeruginosa lung infections are a distinctive feature of cystic fibrosis (CF) pathology, that challenge adults with CF even with the advent of highly effective modulator therapies. Characterizing P. aeruginosa transcription in the CF lung and identifying factors that drive gene expression could yield novel strategies to eradicate infection or otherwise improve outcomes. To complement published P. aeruginosa gene expression studies in laboratory culture models designed to model the CF lung environment, we employed an ex vivo sputum model in which laboratory strain PAO1 was incubated in sputum from different CF donors. As part of the analysis, we compared PAO1 gene expression in this "spike-in" sputum model to that for P. aeruginosa grown in artificial sputum medium (ASM). Analyses focused on genes that were differentially expressed between sputum and ASM and genes that were most highly expressed in sputum. We present a new approach that used sets of genes with correlated expression, identified by the gene expression analysis tool eADAGE, to analyze the differential activity of pathways in P. aeruginosa grown in CF sputum from different individuals. A key characteristic of P. aeruginosa grown in expectorated CF sputum was related to zinc and iron acquisition, but this signal varied by donor sputum. In addition, a significant correlation between P. aeruginosa expression of the H1-type VI secretion system and corrector use by the sputum donor was observed. These methods may be broadly useful in looking for variable signals across clinical samples.
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Affiliation(s)
- Samuel L. Neff
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Georgia Doing
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Taylor Reiter
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Thomas H. Hampton
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Casey S. Greene
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Deborah A. Hogan
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
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Avakh A, Grant GD, Cheesman MJ, Kalkundri T, Hall S. The Art of War with Pseudomonas aeruginosa: Targeting Mex Efflux Pumps Directly to Strategically Enhance Antipseudomonal Drug Efficacy. Antibiotics (Basel) 2023; 12:1304. [PMID: 37627724 PMCID: PMC10451789 DOI: 10.3390/antibiotics12081304] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 07/26/2023] [Accepted: 08/07/2023] [Indexed: 08/27/2023] Open
Abstract
Pseudomonas aeruginosa (P. aeruginosa) poses a grave clinical challenge due to its multidrug resistance (MDR) phenotype, leading to severe and life-threatening infections. This bacterium exhibits both intrinsic resistance to various antipseudomonal agents and acquired resistance against nearly all available antibiotics, contributing to its MDR phenotype. Multiple mechanisms, including enzyme production, loss of outer membrane proteins, target mutations, and multidrug efflux systems, contribute to its antimicrobial resistance. The clinical importance of addressing MDR in P. aeruginosa is paramount, and one pivotal determinant is the resistance-nodulation-division (RND) family of drug/proton antiporters, notably the Mex efflux pumps. These pumps function as crucial defenders, reinforcing the emergence of extensively drug-resistant (XDR) and pandrug-resistant (PDR) strains, which underscores the urgency of the situation. Overcoming this challenge necessitates the exploration and development of potent efflux pump inhibitors (EPIs) to restore the efficacy of existing antipseudomonal drugs. By effectively countering or bypassing efflux activities, EPIs hold tremendous potential for restoring the antibacterial activity against P. aeruginosa and other Gram-negative pathogens. This review focuses on concurrent MDR, highlighting the clinical significance of efflux pumps, particularly the Mex efflux pumps, in driving MDR. It explores promising EPIs and delves into the structural characteristics of the MexB subunit and its substrate binding sites.
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Affiliation(s)
| | | | | | | | - Susan Hall
- School of Pharmacy and Medical Sciences, Griffith University, Gold Coast, QLD 4222, Australia; (A.A.); (G.D.G.); (M.J.C.); (T.K.)
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15
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Li H, Li X, Chen T, Yang Z, Shi D, Yin J, Yang D, Zhou S, Li J, Jin M. Antidepressant exposure as a source of disinfectant resistance in waterborne bacteria. JOURNAL OF HAZARDOUS MATERIALS 2023; 452:131371. [PMID: 37030229 DOI: 10.1016/j.jhazmat.2023.131371] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 03/25/2023] [Accepted: 04/03/2023] [Indexed: 05/03/2023]
Abstract
The emergence of disinfectant-resistant pathogens in water is a major threat to public health. However, whether human-consumed pharmaceuticals can induce bacterial resistance to disinfectants remains unclear. Herein, Escherichia coli was exposed to 12 antidepressants, and susceptibility of antidepressant-induced chloramphenicol (CHL)-resistant mutants to disinfectants was tested. Whole genome sequencing, global transcriptomic sequencing, and real-time quantitative polymerase chain reaction were used to elucidate the underlying mechanisms. We observed that duloxetine, fluoxetine, amitriptyline, and sertraline significantly increased the mutation frequency of E. coli against CHL by 15- to 2948-fold. The resultant mutants increased the average MIC50 of sodium hypochlorite, benzalkonium bromide, and triclosan roughly 2- to 8-fold. Consistently, marRAB and acrAB-tolC genes, together with ABC transporter genes (e.g., yddA, yadG, yojI, and mdlA), were triggered to increase the efflux of disinfectants out of the cell, while ompF was inhibited, reducing disinfectant penetration into the cell. Additionally, the occurrence of DNA mutations in marR and acrR in the mutants was observed, potentially resulting in increased synthesis of the AcrAB-TolC pump. This study indicates that pharmaceutical exposure may create disinfectant-resistant bacteria, which may then be released into water systems, providing novel insights into the potential source of water-borne disinfectant-resistant pathogens.
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Affiliation(s)
- Haibei Li
- Department of Environment and Health, Tianjin Institute of Environmental & Operational Medicine, Key Laboratory of Risk Assessment and Control for Environment & Food Safety, Tianjin 300050, China
| | - Xinmei Li
- Department of Environment and Health, Tianjin Institute of Environmental & Operational Medicine, Key Laboratory of Risk Assessment and Control for Environment & Food Safety, Tianjin 300050, China
| | - Tianjiao Chen
- Department of Environment and Health, Tianjin Institute of Environmental & Operational Medicine, Key Laboratory of Risk Assessment and Control for Environment & Food Safety, Tianjin 300050, China
| | - Zhongwei Yang
- Department of Environment and Health, Tianjin Institute of Environmental & Operational Medicine, Key Laboratory of Risk Assessment and Control for Environment & Food Safety, Tianjin 300050, China
| | - Danyang Shi
- Department of Environment and Health, Tianjin Institute of Environmental & Operational Medicine, Key Laboratory of Risk Assessment and Control for Environment & Food Safety, Tianjin 300050, China
| | - Jing Yin
- Department of Environment and Health, Tianjin Institute of Environmental & Operational Medicine, Key Laboratory of Risk Assessment and Control for Environment & Food Safety, Tianjin 300050, China
| | - Dong Yang
- Department of Environment and Health, Tianjin Institute of Environmental & Operational Medicine, Key Laboratory of Risk Assessment and Control for Environment & Food Safety, Tianjin 300050, China
| | - Shuqing Zhou
- Department of Environment and Health, Tianjin Institute of Environmental & Operational Medicine, Key Laboratory of Risk Assessment and Control for Environment & Food Safety, Tianjin 300050, China
| | - Junwen Li
- Department of Environment and Health, Tianjin Institute of Environmental & Operational Medicine, Key Laboratory of Risk Assessment and Control for Environment & Food Safety, Tianjin 300050, China
| | - Min Jin
- Department of Environment and Health, Tianjin Institute of Environmental & Operational Medicine, Key Laboratory of Risk Assessment and Control for Environment & Food Safety, Tianjin 300050, China.
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16
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Ge H, Qiao J, Zheng J, Xu H, Liu R, Zhao J, Chen R, Li C, Guo X, Zheng B. Emergence and clonal dissemination of KPC-3-producing Pseudomonas aeruginosa in China with an IncP-2 megaplasmid. Ann Clin Microbiol Antimicrob 2023; 22:31. [PMID: 37120531 PMCID: PMC10149002 DOI: 10.1186/s12941-023-00577-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 03/28/2023] [Indexed: 05/01/2023] Open
Abstract
BACKGROUND Despite the global prevalence of Klebsiella pneumoniae Carbapenemase (KPC)-type class A β-lactamases, occurrences of KPC-3-producing isolates in China remain infrequent. This study aims to explore the emergence, antibiotic resistance profiles, and plasmid characteristics of blaKPC-3-carrying Pseudomonas aeruginosa. METHODS Species identification was performed by MALDI-TOF-MS, and antimicrobial resistance genes (ARGs) were identified by polymerase chain reaction (PCR). The characteristics of the target strain were detected by whole-genome sequencing (WGS) and antimicrobial susceptibility testing (AST). Plasmids were analyzed by S1-nuclease pulsed-field gel electrophoresis(S1-PFGE), Southern blotting and transconjugation experiment. RESULTS Five P. aeruginosa strains carrying blaKPC-3 were isolated from two Chinese patients without a history of travelling to endemic areas. All strains belonged to the novel sequence type ST1076. The blaKPC-3 was carried on a 395-kb IncP-2 megaplasmid with a conserved structure (IS6100-ISKpn27-blaKPC-3-ISKpn6-korC-klcA), and this genetic sequence was identical to many plasmid-encoded KPC of Pseudomonas species. By further analyzing the genetic context, it was supposed that the original of blaKPC-3 in our work was a series of mutation of blaKPC-2. CONCLUSIONS The emergence of a multidrug resistance IncP-2 megaplasmid and clonal transmission of blaKPC-3-producing P. aeruginosa in China underlined the crucial need for continuous monitoring of blaKPC-3 for prevention and control of its further dissemination in China.
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Affiliation(s)
- Haoyu Ge
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, College of Medicine, the First Affiliated Hospital, Zhejiang University, Hangzhou, China
- Department of Laboratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jie Qiao
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, College of Medicine, the First Affiliated Hospital, Zhejiang University, Hangzhou, China
- Department of Laboratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jiahao Zheng
- Institute of Animal Quarantine, Chinese Academy of Inspection and Quarantine, Beijing, 100176, China
| | - Hao Xu
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, College of Medicine, the First Affiliated Hospital, Zhejiang University, Hangzhou, China
| | - Ruishan Liu
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, College of Medicine, the First Affiliated Hospital, Zhejiang University, Hangzhou, China
| | - Junhui Zhao
- School of Basic Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Ruyan Chen
- Department of Laboratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Chenyu Li
- Department of Laboratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xiaobing Guo
- Department of Laboratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.
| | - Beiwen Zheng
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, College of Medicine, the First Affiliated Hospital, Zhejiang University, Hangzhou, China.
- Department of Structure and Morphology, Jinan Microecological Biomedicine Shandong Laboratory, Jinan, Shandong, China.
- Research Units of Infectious Diseases and Microecology, Chinese Academy of Medical Sciences, Beijing, China.
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17
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Xie Z, Huang J, Zhang S, Xu B, Zhang Q, Li B. Genomic and functional characterization of carbapenem-resistant Klebsiella pneumoniae from hospital wastewater. BMC Microbiol 2023; 23:115. [PMID: 37095431 PMCID: PMC10124015 DOI: 10.1186/s12866-023-02862-5] [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: 01/23/2023] [Accepted: 04/15/2023] [Indexed: 04/26/2023] Open
Abstract
BACKGROUND The emergence of carbapenem-resistant Klebsiella pneumoniae (CRKP) attracted extensive attention. Information on CRKP from hospital wastewater (HWW) is limited. The aims of this study were to investigate the genomic characteristics and to evaluate the survivability characteristics of 11 CRKP from HWW in a Chinese teaching hospital in Fujian province. RESULTS A total of 11 CRKP from HWW were recovered in this study. All CRKP from HWW were resistant to most antibiotics. Comparative genetic analysis demonstrated that all CRKP isolates were clustered into the three distinct phylogenetic clades and clade 2 and clade 3 were mixtures of samples collected from both HWW and clinical settings. Varieties of resistance genes, virulence genes and plasmid replicon types were detected in CRKP from HWW. In vitro transfer of blaKPC-2 was successful for 3 blaKPC-2-positive CRKP from HWW with high conjugation frequency. Our study demonstrated that the genetic environments of blaKPC-2 shared core structure with ISKpn27-blaKPC-2-ISKpn6. Group analysis showed that CRKP from HWW had a lower survivability in serum compared to clinical CRKP (p < 005); and CRKP from HWW had no significant difference in survivability in HWW compared to clinical CRKP (p > 005). CONCLUSIONS We analyzed the genomic and survivability characteristics of CRKP from HWW in a Chinese teaching hospital. These genomes represent a significant addition of genomic data from the genus and could serve as a valuable resource for future genomic studies about CRKP from HWW.
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Affiliation(s)
- Zhiqiang Xie
- Department of Clinical Laboratory, Fujian Medical University Union Hospital, 29 Xinquan Rd, Fuzhou, 350001, Fujian, China
| | - Jiangqing Huang
- Department of Clinical Laboratory, Fujian Medical University Union Hospital, 29 Xinquan Rd, Fuzhou, 350001, Fujian, China
| | - Shengcen Zhang
- Department of Clinical Laboratory, Fujian Medical University Union Hospital, 29 Xinquan Rd, Fuzhou, 350001, Fujian, China
| | - BinBin Xu
- Department of Clinical Laboratory, Fujian Medical University Union Hospital, 29 Xinquan Rd, Fuzhou, 350001, Fujian, China
| | - Qianwen Zhang
- Department of Clinical Laboratory, Fujian Medical University Union Hospital, 29 Xinquan Rd, Fuzhou, 350001, Fujian, China
| | - Bin Li
- Department of Clinical Laboratory, Fujian Medical University Union Hospital, 29 Xinquan Rd, Fuzhou, 350001, Fujian, China.
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18
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Dop RA, Neill DR, Hasell T. Sulfur-Polymer Nanoparticles: Preparation and Antibacterial Activity. ACS APPLIED MATERIALS & INTERFACES 2023; 15:20822-20832. [PMID: 37074085 PMCID: PMC10165599 DOI: 10.1021/acsami.3c03826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
High sulfur content polymers prepared by inverse vulcanization have many reported potential applications, including as novel antimicrobial materials. High sulfur content polymers usually have limited water-solubility and dispersibility due to their hydrophobic nature, which could limit the development of their applications. Herein, we report the formulation of high sulfur content polymeric nanoparticles by a nanoprecipitation and emulsion-based method. High sulfur content polymeric nanoparticles were found to have an inhibitory effect against important bacterial pathogens, including Gram-positive methicillin-resistant Staphylococcus aureus and Gram-negative Pseudomonas aeruginosa. Salt-stable particles were formulated with the addition of a surfactant, which did not inhibit the antibacterial activity of the polymeric particles. Furthermore, the polymeric nanoparticles were found to inhibit S. aureus biofilm formation and exhibited low cytotoxicity against mammalian liver cells. Interaction of the polymeric particles with cellular thiols could be a potential mechanism of action against bacterial cells, as demonstrated by reaction with cysteine as a model thiol. The findings presented demonstrate methods of preparing aqueous dispersions of high sulfur content polymeric nanoparticles that could have useful biological applications.
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Affiliation(s)
- Romy A Dop
- Department of Chemistry, University of Liverpool, Liverpool L69 7ZD, United Kingdom
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L69 7ZD, United Kingdom
| | - Daniel R Neill
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L69 7ZD, United Kingdom
| | - Tom Hasell
- Department of Chemistry, University of Liverpool, Liverpool L69 7ZD, United Kingdom
- College of Chemistry and Chemical Engineering, Gansu International Scientific and Technological Cooperation Base of Water-Retention Chemical Functional Materials, Northwest Normal University, Lanzhou 730070, P. R. China
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An XDR Pseudomonas aeruginosa ST463 Strain with an IncP-2 Plasmid Containing a Novel Transposon Tn 6485f Encoding blaIMP-45 and blaAFM-1 and a Second Plasmid with Two Copies of blaKPC-2. Microbiol Spectr 2023; 11:e0446222. [PMID: 36651737 PMCID: PMC9927494 DOI: 10.1128/spectrum.04462-22] [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] [Indexed: 01/19/2023] Open
Abstract
The increased carbapenem resistance among Pseudomonas aeruginosa has become a serious health issue worldwide. We reported an extensively drug-resistant (XDR) P. aeruginosa PA30 isolate which belonged to sequence type ST463 and contained an IncP-2 plasmid (pPA30_1) carrying two genes, namely, blaIMP-45 and blaAFM-1, which encoded the metallo-β-lactamases AFM-1 and IMP-45, respectively. Additionally, the strain had a plasmid (pPA30_2) with two copies of the blaKPC-2 genes embedded. The plasmid pPA30_1 was highly similar to the previously reported plasmid pHS17-127, which has the same genetic architecture. This plasmid contained blaIMP-45, located in a second gene cassette of the integron In786, carried by a Tn1403-derivative transposon acquiring an ISCR27n3-blaAFM-1 structure. Interestingly, the transposon in pPA30_1 acquired an extra ISCR1-qnrVC6 module and formed a novel transposon, which was subsequently annotated as Tn6485f. The blaKPC-2 genes in pPA30_2 underwent duplication due to the inversion of the IS26-blaKPC-2-IS26 element, which resulted in two copies of blaKPC-2. IMPORTANCE The ST463 clone is an emerging high-risk sequence type that is spreading with blaKPC-2-containing plasmids. The core blaKPC-2 genetic platform is ISKpn27-blaKPC-2-ISKpn6 in almost all samples, and the adjacent region beyond the core platform varies by IS26-mediated inversion or duplication events, amplifying the blaKPC-2 gene copies. The ST463 P. aeruginosa strain PA30 in our study contains another two metallo-β-lactamase genes, namely, blaIMP-45 and blaAFM-1, in a novel transposon Tn6485f that is harbored by the IncP-2 megaplasmid. The pPA30_1 carrying blaIMP-45 and blaAFM-1 is highly related to pHS17-127 from the ST369 P. aeruginosa strain, indicating the putative dissemination of the megaplasmid between different clones.
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Wu RA, Feng J, Yue M, Liu D, Ding T. Overuse of food-grade disinfectants threatens a global spread of antimicrobial-resistant bacteria. Crit Rev Food Sci Nutr 2023; 64:6870-6879. [PMID: 36756870 DOI: 10.1080/10408398.2023.2176814] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Food-grade disinfectants are extensively used for microbial decontamination of food processing equipment. In recent years, food-grade disinfectants have been increasingly used. However, the overuse of disinfectants causes another major issue, which is the emergence and spread of antimicrobial-resistant bacteria on a global scale. As the ongoing pandemic takes global attention, bacterial infections with antibiotic resistance are another ongoing pandemic that often goes unnoticed and will be the next real threat to humankind. Here, the effects of food-grade disinfectant overuse on the global emergence and spread of antimicrobial-resistant bacteria were reviewed. It was found that longtime exposure to the most common food-grade disinfectants promoted resistance to clinically important antibiotics in pathogenic bacteria, namely cross-resistance. Currently, the use of disinfectants is largely unregulated. The mechanisms of cross-resistance are regulated by intrinsic molecular mechanisms including efflux pumps, DNA repair system, modification of the molecular target, and metabolic adaptation. Cross-resistance can also be acquired by mobile genetic elements. Long-term exposure to disinfectants has an impact on the dissemination of antimicrobial resistance in soil, plants, animals, water, and human gut environments.
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Affiliation(s)
- Ricardo A Wu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, China
| | - Jinsong Feng
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, China
| | - Min Yue
- College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Donghong Liu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, China
- Ningbo Research Institute, Zhejiang University, Ningbo, China
| | - Tian Ding
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, China
- Ningbo Research Institute, Zhejiang University, Ningbo, China
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21
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Thompson CMA, Hall JPJ, Chandra G, Martins C, Saalbach G, Panturat S, Bird SM, Ford S, Little RH, Piazza A, Harrison E, Jackson RW, Brockhurst MA, Malone JG. Plasmids manipulate bacterial behaviour through translational regulatory crosstalk. PLoS Biol 2023; 21:e3001988. [PMID: 36787297 PMCID: PMC9928087 DOI: 10.1371/journal.pbio.3001988] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 01/04/2023] [Indexed: 02/15/2023] Open
Abstract
Beyond their role in horizontal gene transfer, conjugative plasmids commonly encode homologues of bacterial regulators. Known plasmid regulator homologues have highly targeted effects upon the transcription of specific bacterial traits. Here, we characterise a plasmid translational regulator, RsmQ, capable of taking global regulatory control in Pseudomonas fluorescens and causing a behavioural switch from motile to sessile lifestyle. RsmQ acts as a global regulator, controlling the host proteome through direct interaction with host mRNAs and interference with the host's translational regulatory network. This mRNA interference leads to large-scale proteomic changes in metabolic genes, key regulators, and genes involved in chemotaxis, thus controlling bacterial metabolism and motility. Moreover, comparative analyses found RsmQ to be encoded on a large number of divergent plasmids isolated from multiple bacterial host taxa, suggesting the widespread importance of RsmQ for manipulating bacterial behaviour across clinical, environmental, and agricultural niches. RsmQ is a widespread plasmid global translational regulator primarily evolved for host chromosomal control to manipulate bacterial behaviour and lifestyle.
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Affiliation(s)
- Catriona M. A. Thompson
- Department of Molecular Microbiology, John Innes Centre, Colney Lane, Norwich, United Kingdom
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk, United Kingdom
| | - James P. J. Hall
- Department of Evolution, Ecology and Behaviour Institute of Infection, Veterinary and Ecological Sciences University of Liverpool, Crown Street, Liverpool, United Kingdom
| | - Govind Chandra
- Department of Molecular Microbiology, John Innes Centre, Colney Lane, Norwich, United Kingdom
| | - Carlo Martins
- Department of Molecular Microbiology, John Innes Centre, Colney Lane, Norwich, United Kingdom
| | - Gerhard Saalbach
- Department of Molecular Microbiology, John Innes Centre, Colney Lane, Norwich, United Kingdom
| | - Supakan Panturat
- Department of Molecular Microbiology, John Innes Centre, Colney Lane, Norwich, United Kingdom
| | - Susannah M. Bird
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Samuel Ford
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Richard H. Little
- Department of Molecular Microbiology, John Innes Centre, Colney Lane, Norwich, United Kingdom
| | - Ainelen Piazza
- Department of Molecular Microbiology, John Innes Centre, Colney Lane, Norwich, United Kingdom
| | - Ellie Harrison
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Robert W. Jackson
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Michael A. Brockhurst
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
- Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester, United Kingdom
| | - Jacob G. Malone
- Department of Molecular Microbiology, John Innes Centre, Colney Lane, Norwich, United Kingdom
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk, United Kingdom
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22
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Chukamnerd A, Pomwised R, Chusri S, Singkhamanan K, Chumtong S, Jeenkeawpiam K, Sakunrang C, Saroeng K, Saengsuwan P, Wonglapsuwan M, Surachat K. Antimicrobial Susceptibility and Molecular Features of Colonizing Isolates of Pseudomonas aeruginosa and the Report of a Novel Sequence Type (ST) 3910 from Thailand. Antibiotics (Basel) 2023; 12:antibiotics12010165. [PMID: 36671367 PMCID: PMC9854967 DOI: 10.3390/antibiotics12010165] [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: 12/19/2022] [Revised: 01/09/2023] [Accepted: 01/11/2023] [Indexed: 01/15/2023] Open
Abstract
Pseudomonas aeruginosa is an important pathogen as it can cause hospital-acquired infections. Additionally, it can also colonize in patients and in other various environments. Hence, this study aimed to investigate the antimicrobial susceptibility, and to study the molecular features, of colonizing isolates of P. aeruginosa from Songklanagarind Hospital, Thailand. Genomic DNA extraction, whole-genome sequencing (WGS), and bioinformatics analysis were performed in all studied isolates. The findings demonstrated that the majority of isolates were non-susceptible to colistin and carbapenem. For in silico study, multilocus sequence typing (MLST) revealed one novel sequence type (ST) 3910 and multiple defined STs. The isolates carried several antimicrobial resistance genes (blaOXA-50, aph(3')-IIb, etc.) and virulence-associated genes (fleN, waaA, etc.). CRISPR-Cas sequences with different spacers and integrated bacteriophage sequences were also identified in these isolates. Very high SNPs were found in the alignments of the novel ST-3910 isolate with other isolates. A comparative genomic analysis exhibited phylogenetic clustering of our colonizing isolates with clinical isolates from many countries. Interestingly, ST-3981, ST-3982, ST-3983, ST-3984, ST-3985, ST-3986, ST-3986, ST-3986, ST-3987, and ST-3988, the new STs from published genomes, were assigned in this study. In conclusion, this WGS data might be useful for tracking the spread of P. aeruginosa colonizing isolates.
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Affiliation(s)
- Arnon Chukamnerd
- Division of Infectious Diseases, Department of Internal Medicine, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand
| | - Rattanaruji Pomwised
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Songkhla 90110, Thailand
| | - Sarunyou Chusri
- Division of Infectious Diseases, Department of Internal Medicine, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand
| | - Kamonnut Singkhamanan
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand
| | - Sanicha Chumtong
- Division of Animal Production Innovation and Management, Faculty of Natural Resources, Prince of Songkla University, Songkhla 90110, Thailand
| | - Kongpop Jeenkeawpiam
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand
| | - Chanida Sakunrang
- Molecular Evolution and Computational Biology Research Unit, Faculty of Science, Prince of Songkla University, Songkhla 90110, Thailand
| | - Kuwanhusna Saroeng
- Molecular Evolution and Computational Biology Research Unit, Faculty of Science, Prince of Songkla University, Songkhla 90110, Thailand
| | - Phanvasri Saengsuwan
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand
| | - Monwadee Wonglapsuwan
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Songkhla 90110, Thailand
| | - Komwit Surachat
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand
- Molecular Evolution and Computational Biology Research Unit, Faculty of Science, Prince of Songkla University, Songkhla 90110, Thailand
- Translational Medicine Research Center, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand
- Correspondence:
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23
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Role of Efflux Pumps on Antimicrobial Resistance in Pseudomonas aeruginosa. Int J Mol Sci 2022; 23:ijms232415779. [PMID: 36555423 PMCID: PMC9779380 DOI: 10.3390/ijms232415779] [Citation(s) in RCA: 60] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 12/02/2022] [Accepted: 12/05/2022] [Indexed: 12/15/2022] Open
Abstract
Antimicrobial resistance is an old and silent pandemic. Resistant organisms emerge in parallel with new antibiotics, leading to a major global public health crisis over time. Antibiotic resistance may be due to different mechanisms and against different classes of drugs. These mechanisms are usually found in the same organism, giving rise to multidrug-resistant (MDR) and extensively drug-resistant (XDR) bacteria. One resistance mechanism that is closely associated with the emergence of MDR and XDR bacteria is the efflux of drugs since the same pump can transport different classes of drugs. In Gram-negative bacteria, efflux pumps are present in two configurations: a transmembrane protein anchored in the inner membrane and a complex formed by three proteins. The tripartite complex has a transmembrane protein present in the inner membrane, a periplasmic protein, and a porin associated with the outer membrane. In Pseudomonas aeruginosa, one of the main pathogens associated with respiratory tract infections, four main sets of efflux pumps have been associated with antibiotic resistance: MexAB-OprM, MexXY, MexCD-OprJ, and MexEF-OprN. In this review, the function, structure, and regulation of these efflux pumps in P. aeruginosa and their actions as resistance mechanisms are discussed. Finally, a brief discussion on the potential of efflux pumps in P. aeruginosa as a target for new drugs is presented.
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24
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Selection of Relevant Bacterial Strains for Novel Therapeutic Testing: a Guidance Document for Priority Cystic Fibrosis Lung Pathogens. CURRENT CLINICAL MICROBIOLOGY REPORTS 2022. [DOI: 10.1007/s40588-022-00182-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Abstract
Purpose of Review
People with cystic fibrosis (CF) suffer chronic lung infections with a range of antimicrobial-resistant bacterial pathogens. There is an urgent need for researchers to develop novel anti-infectives to treat these problematic infections, but how can we select bacterial strains which are relevant for robust testing and comparative research?
Recent Findings
Pseudomonas aeruginosa, Burkholderia cepacia complex and Burkholderia gladioli, Mycobacterium abscessus complex, Staphylococcus aureus, Haemophilus influenza, and several multidrug-resistant Gram-negative species were selected as key CF infections that urgently require new therapeutics. Reference isolates and strain panels were identified, and a summary of the known genotypic diversity of each pathogen was provided.
Summary
Here, we summarise the current strain resources available for priority CF bacterial pathogens and highlight systematic selection criteria that researchers can use to select strains for use in therapeutic testing.
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25
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Kusumawardhani H, Hosseini R, Verschoor JA, de Winde JH. Comparative analysis reveals the modular functional structure of conjugative megaplasmid pTTS12 of Pseudomonas putida S12: A paradigm for transferable traits, plasmid stability, and inheritance? Front Microbiol 2022; 13:1001472. [PMID: 36212887 PMCID: PMC9537497 DOI: 10.3389/fmicb.2022.1001472] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 09/06/2022] [Indexed: 11/26/2022] Open
Abstract
Originating from various environmental niches, large numbers of bacterial plasmids have been found carrying heavy metal and antibiotic resistance genes, degradation pathways and specific transporter genes for organic solvents or aromatic compounds. Such genes may constitute promising candidates for novel synthetic biology applications. Our systematic analysis of gene clusters encoded on megaplasmid pTTS12 from Pseudomonas putida S12 underscores that a large portion of its genes is involved in stress response to increase survival under harsh conditions like the presence of heavy metal and organic solvent. We investigated putative roles of genes encoded on pTTS12 and further elaborated on their roles in the establishment and maintenance under several stress conditions, specifically focusing on solvent tolerance in P. putida strains. The backbone of pTTS12 was found to be closely related to that of the carbapenem-resistance plasmid pOZ176, member of the IncP-2 incompatibility group, although the carbapenem resistance cassette is absent from pTTS12. Megaplasmid pTTS12 contains multiple transposon-flanked cassettes mediating resistance to various heavy metals such as tellurite, chromate (Tn7), and mercury (Tn5053 and Tn5563). Additionally, pTTS12 also contains a P-type, Type IV secretion system (T4SS) supporting self-transfer to other P. putida strains. This study increases our understanding in the modular structure of pTTS12 as a member of IncP-2 plasmid family and several promising exchangeable gene clusters to construct robust microbial hosts for biotechnology applications.
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Affiliation(s)
- Hadiastri Kusumawardhani
- Institute of Biology Leiden, Leiden University, Leiden, Netherlands
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Rohola Hosseini
- Institute of Biology Leiden, Leiden University, Leiden, Netherlands
| | | | - Johannes H. de Winde
- Institute of Biology Leiden, Leiden University, Leiden, Netherlands
- *Correspondence: Johannes H. de Winde,
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26
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Zhang T, Ding Y, Peng J, Dai Y, Luo S, Liu W, Ma Y. Effects of Broad-Spectrum Antibiotic (Florfenicol) on Resistance Genes and Bacterial Community Structure of Water and Sediments in an Aquatic Microcosm Model. Antibiotics (Basel) 2022; 11:1299. [PMID: 36289957 PMCID: PMC9598473 DOI: 10.3390/antibiotics11101299] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/19/2022] [Accepted: 09/21/2022] [Indexed: 11/16/2022] Open
Abstract
This study evaluates the effects of a broad-spectrum antibiotic (florfenicol) on antibiotic resistance genes (ARGs) and bacterial community structure in aquatic environments. We constructed an indoor aquatic microcosm model, adding different concentrations of florfenicol (0.1, 1, 10, 100 mg L-1), and water and sediment samples were collected after 0, 7, 30, and 60 days. qPCR and 16S rDNA amplicon sequencing were used to study the changes in the ARGs and bacterial community structure of the collected samples. The results show that the inclusion of florfenicol resulted in an increased abundance of the floR and optrA genes. Adding 100 mg L-1 florfenicol to the water increased the abundance of optrA gene copies with the maximum on the Day 7, and increased the abundance of floR gene copies with the maximum on Day 30. Adding 100 mg L-1 florfenicol to the sediment increased the abundance of floR and optrA genes by one order of magnitude on Day 60. Meanwhile, the average number of operational taxonomic units (OTUs) in the water samples was 257, and the average number of OTUs in sediment samples was 823. The bacterial community diversity and richness in sediments were higher than those in water. The difference between the maximal and minimal values of the Shannon diversity index in the water and sediment samples was 4.36 and 1.95, respectively. The effect of florfenicol on the bacterial community structure in water was much higher than that in sediment. At 30 days, the diversity index and richness index of the florfenicol treatment groups with 1 and 10 mg L-1 concentrations began to increase; at 60 days, the diversity and richness indices of the 100 mg L-1 florfenicol treatment group began to increase. The samples at the same sampling time in the sediments clustered closer together. The results of this study provide a scientific basis for guiding the rational use of florfenicol in aquaculture, maintaining a healthy and stable microecological environment in aquaculture, and provide theoretical data for environmental ecological risk assessment and safety management caused by microbial resistance under the abuse of florfenicol.
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Affiliation(s)
- Tengyue Zhang
- Department of Veterinary Medicine, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, China
| | - Yuexia Ding
- Department of Veterinary Medicine, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, China
| | - Jinju Peng
- Department of Veterinary Medicine, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, China
| | - Yue Dai
- Department of Veterinary Medicine, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, China
| | - Shuaishuai Luo
- Department of Veterinary Medicine, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, China
| | - Wenchao Liu
- Department of Animal Science, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, China
| | - Yi Ma
- Department of Veterinary Medicine, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming 525000, China
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27
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Quezada-Aguiluz M, Opazo-Capurro A, Lincopan N, Esposito F, Fuga B, Mella-Montecino S, Riedel G, Lima CA, Bello-Toledo H, Cifuentes M, Silva-Ojeda F, Barrera B, Hormazábal JC, González-Rocha G. Novel Megaplasmid Driving NDM-1-Mediated Carbapenem Resistance in Klebsiella pneumoniae ST1588 in South America. Antibiotics (Basel) 2022; 11:antibiotics11091207. [PMID: 36139987 PMCID: PMC9494972 DOI: 10.3390/antibiotics11091207] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 08/22/2022] [Accepted: 08/31/2022] [Indexed: 11/16/2022] Open
Abstract
Carbapenem-resistant Enterobacterales (CRE) is a critical public health problem in South America, where the prevalence of NDM metallo-betalactamases has increased substantially in recent years. In this study, we used whole genome sequencing to characterize a multidrug-resistant (MDR) Klebsiella pneumoniae (UCO-361 strain) clinical isolate from a teaching hospital in Chile. Using long-read (Nanopore) and short-read (Illumina) sequence data, we identified a novel un-typeable megaplasmid (314,976 kb, pNDM-1_UCO-361) carrying the blaNDM-1 carbapenem resistance gene within a Tn3000 transposon. Strikingly, conjugal transfer of pNDM-1_UCO-361 plasmid only occurs at low temperatures with a high frequency of 4.3 × 10−6 transconjugants/receptors at 27 °C. UCO-361 belonged to the ST1588 clone, previously identified in Latin America, and harbored aminoglycoside, extended-spectrum β-lactamases (ESBLs), carbapenem, and quinolone-resistance determinants. These findings suggest that blaNDM-1-bearing megaplasmids can be adapted to carriage by some K. pneumoniae lineages, whereas its conjugation at low temperatures could contribute to rapid dissemination at the human–environmental interface.
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Affiliation(s)
- Mario Quezada-Aguiluz
- Laboratorio de Investigación en Agentes Antibacterianos (LIAA-UdeC), Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción 4030000, Chile
- Departamento de Medicina Interna, Facultad de Medicina, Universidad de Concepción, Concepción 4030000, Chile
- Millennium Nucleus for Collaborative Research on Bacterial Resistance (MICROB-R), Santiago 8320000, Chile
- Centro Regional de Telemedicina y Telesalud del Biobío (CRT Biobío), Concepción 4030000, Chile
| | - Andrés Opazo-Capurro
- Laboratorio de Investigación en Agentes Antibacterianos (LIAA-UdeC), Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción 4030000, Chile
- Millennium Nucleus for Collaborative Research on Bacterial Resistance (MICROB-R), Santiago 8320000, Chile
| | - Nilton Lincopan
- Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo 05508-000, Brazil
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil
| | - Fernanda Esposito
- Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo 05508-000, Brazil
| | - Bruna Fuga
- Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo 05508-000, Brazil
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil
| | - Sergio Mella-Montecino
- Departamento de Medicina Interna, Facultad de Medicina, Universidad de Concepción, Concepción 4030000, Chile
- Unidad de Infectología, Hospital Regional “Dr. Guillermo Grant Benavente”, Concepción 4030000, Chile
| | - Gisela Riedel
- Departamento de Medicina Interna, Facultad de Medicina, Universidad de Concepción, Concepción 4030000, Chile
- Unidad de Infectología, Hospital Regional “Dr. Guillermo Grant Benavente”, Concepción 4030000, Chile
| | - Celia A. Lima
- Laboratorio de Investigación en Agentes Antibacterianos (LIAA-UdeC), Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción 4030000, Chile
| | - Helia Bello-Toledo
- Laboratorio de Investigación en Agentes Antibacterianos (LIAA-UdeC), Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción 4030000, Chile
| | - Marcela Cifuentes
- Servicio de Laboratorio Clínico, Hospital Clínico Universidad de Chile, Santiago 8320000, Chile
| | - Francisco Silva-Ojeda
- Servicio de Laboratorio Clínico, Hospital Clínico Universidad de Chile, Santiago 8320000, Chile
| | - Boris Barrera
- Servicio de Laboratorio Clínico, Hospital Clínico Universidad de Chile, Santiago 8320000, Chile
| | - Juan C. Hormazábal
- Subdepartamento de Enfermedades Infecciosas, Instituto de Salud Pública de Chile (ISP), Santiago 8320000, Chile
| | - Gerardo González-Rocha
- Laboratorio de Investigación en Agentes Antibacterianos (LIAA-UdeC), Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción 4030000, Chile
- Millennium Nucleus for Collaborative Research on Bacterial Resistance (MICROB-R), Santiago 8320000, Chile
- Correspondence: ; Tel.: +56-41-2661527; Fax: +56-41-2245975
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28
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Zou H, Berglund B, Wang S, Zhou Z, Gu C, Zhao L, Meng C, Li X. Emergence of bla NDM-1, bla NDM-5, bla KPC-2 and bla IMP-4 carrying plasmids in Raoultella spp. in the environment. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 306:119437. [PMID: 35537555 DOI: 10.1016/j.envpol.2022.119437] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 05/02/2022] [Accepted: 05/05/2022] [Indexed: 06/14/2023]
Abstract
To date, carbapenem-resistant Enterobacteriaceae have been found predominantly in clinical settings worldwide. Raoultella belongs to the Enterobacteriaceae family which can cause hospital-acquired infections, and carbapenem-resistant Raoultella spp. (CRR) is sporadically reported in the environment. We investigated the distribution and underlying resistance mechanisms of CRR in a wastewater treatment plant (WWTP) from eastern China between January 2018 and February 2019. A total of 17 CRR were isolated from 324 environmental samples, including Raoultella ornithinolytica (n = 15) and Raoultella planticola (n = 2). The detection of CRR was more frequent in the water inlet compared to anaerobic tank, aerobic tank, sludge thickener, activated sludge, mud cake storage area, and water outlet, and CRR was detected in mud cake stacking area. All CRR were resistant to imipenem, meropenem, ampicillin, piperacillin-tazobactam, cefotaxime, ceftazidime, trimethoprim-sulfamethoxazole and fosfomycin. Four different carbapenemase genes were identified, including blaKPC-2 (n = 13), blaNDM-1 (n = 8), blaNDM-5 (n = 1), blaIMP-4 (n = 1). Interestingly, isolated R. ornithinolytica from the WWTP were closely related to those reported from human samples in China. Plasmid analysis indicated that IncFII(Yp), IncP6, and IncU mediated blaKPC-2 spread, IncX3 and IncN2 mediated blaNDM spread in the environment. The core structure of the Tn3-ISKpn27-blaKPC-2-ISKpn6, ISAba125-blaNDM-bleMBL-trpF-dsbD were identified. The study provides evidence that Raoultella spp. may spread alarming carbapenem resistance in the environment and, therefore, the continuous surveillance for carbapenem resistance in the WWTP should be conducted, especially sludge.
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Affiliation(s)
- Huiyun Zou
- Department of Environment and Health, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Björn Berglund
- Department of Clinical and Experimental Medicine, Linköping University, 581 85, Linköping, Sweden
| | - Shuang Wang
- Institute of Infection Disease Control, Shandong Centre for Disease Control and Prevention, Jinan, China
| | - Ziyu Zhou
- Department of Environment and Health, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Congcong Gu
- Department of Environment and Health, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Ling Zhao
- Department of Environment and Health, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Chen Meng
- Department of Environment and Health, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Xuewen Li
- Department of Environment and Health, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China.
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29
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Menck-Costa MF, Baptista AAS, Gazal LEDS, Justino L, Sanches MS, de Souza M, Nishio EK, Queiroz Dos Santos B, Cruz VD, Berbert JVM, Gonçalves BC, Andrade G, Vespero EC, Nakazato G, Kobayashi RKT. High-Frequency Detection of fosA3 and bla CTX-M-55 Genes in Escherichia coli From Longitudinal Monitoring in Broiler Chicken Farms. Front Microbiol 2022; 13:846116. [PMID: 35663865 PMCID: PMC9158547 DOI: 10.3389/fmicb.2022.846116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 04/11/2022] [Indexed: 11/13/2022] Open
Abstract
Considering the worrying emergence of multidrug resistance, including in animal husbandry and especially in food-producing animals, the need to detect antimicrobial resistance strains in poultry environments is relevant, mainly considering a One Health approach. Thus, this study aimed to conduct longitudinal monitoring of antimicrobial resistance in broiler chicken farms, with an emphasis on evaluating the frequency of resistance to fosfomycin and β-lactams. Escherichia coli was isolated from broiler chicken farms (cloacal swabs, meconium, poultry feed, water, poultry litter, and Alphitobius diaperinus) in northern Paraná from 2019 to 2020 during three periods: the first period (1st days of life), the second period (20th to 25th days of life), and third period (40th to 42nd days of life). Antibiogram tests and the detection of phenotypic extended-spectrum β-lactamase (ESBL) were performed, and they were confirmed by seaching for genes from the blaCTX–M group. The other resistance genes searched were mcr-1 and fosA3. Some ESBL blaCTX–M–1 group strains were selected for ESBL identification by sequencing and enterobacterial repetitive intergenic consensus-polymerase chain reaction analysis. To determine the transferability of the blaCTX–M–1– and fosA3-carrying plasmids, strains were subjected to conjugation experiments. A total of 507 E. coli were analyzed: 360 from cloacal swabs, 24 from meconium samples, 3 from poultry feed samples, 18 from water samples, 69 from poultry litter samples, and 33 from A. diaperinus samples. Among the strain isolate, 80% (406/507) were multidrug-resistant (MDR), and 51% (260/507) were ESBL-positive, with the blaCTX–M–1 group being the most frequent. For the fosA3 gene, 68% (344/507) of the strains isolated were positive, deserves to be highlighted E. coli isolated from day-old chickens (OR 6.34, CI 2.34–17.17), when compared with strains isolated from other origins (poultry litter, A. diaperinus, water, and poultry feed). This work alerts us to the high frequency of the fosA3 gene correlated with the CTX-M-1 group (OR 3.57, CI 95% 2.7–4.72, p < 0.05), especially the blaCTX–M–55 gene, in broiler chickens. This profile was observed mainly in day-old chicken, with a high percentage of E. coli that were MDR. The findings emphasize the importance of conducting longitudinal monitoring to detect the primary risk points during poultry production.
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Affiliation(s)
- Maísa Fabiana Menck-Costa
- Department of Microbiology, Biological Sciences Center, State University of Londrina, Londrina, Brazil
| | - Ana Angelita Sampaio Baptista
- Department of Preventive Veterinary Medicine, Avian Medicine Laboratory, State University of Londrina, Londrina, Brazil
| | | | - Larissa Justino
- Department of Preventive Veterinary Medicine, Avian Medicine Laboratory, State University of Londrina, Londrina, Brazil
| | - Matheus Silva Sanches
- Department of Microbiology, Biological Sciences Center, State University of Londrina, Londrina, Brazil
| | - Marielen de Souza
- Department of Preventive Veterinary Medicine, Avian Medicine Laboratory, State University of Londrina, Londrina, Brazil
| | - Erick Kenji Nishio
- Department of Microbiology, Biological Sciences Center, State University of Londrina, Londrina, Brazil
| | - Beatriz Queiroz Dos Santos
- Department of Preventive Veterinary Medicine, Avian Medicine Laboratory, State University of Londrina, Londrina, Brazil
| | - Victor Dellevedove Cruz
- Department of Microbiology, Biological Sciences Center, State University of Londrina, Londrina, Brazil
| | - João Vitor Monteiro Berbert
- Department of Preventive Veterinary Medicine, Avian Medicine Laboratory, State University of Londrina, Londrina, Brazil
| | - Bruna Carolina Gonçalves
- Department of Microbiology, Biological Sciences Center, State University of Londrina, Londrina, Brazil
| | - Galdino Andrade
- Department of Microbiology, Biological Sciences Center, State University of Londrina, Londrina, Brazil
| | - Eliana Carolina Vespero
- Department of Pathology, Clinical Analysis and Toxicology, Health Sciences Center, State University of Londrina, Londrina, Brazil
| | - Gerson Nakazato
- Department of Microbiology, Biological Sciences Center, State University of Londrina, Londrina, Brazil
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Lang J, Li Y, Yang W, Dong R, Liang Y, Liu J, Chen L, Wang W, Ji B, Tian G, Che N, Meng B. Genomic and resistome analysis of Alcaligenes faecalis strain PGB1 by Nanopore MinION and Illumina Technologies. BMC Genomics 2022; 23:316. [PMID: 35443609 PMCID: PMC9022240 DOI: 10.1186/s12864-022-08507-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 03/28/2022] [Indexed: 12/24/2022] Open
Abstract
Background Drug-resistant bacteria are important carriers of antibiotic-resistant genes (ARGs). This fact is crucial for the development of precise clinical drug treatment strategies. Long-read sequencing platforms such as the Oxford Nanopore sequencer can improve genome assembly efficiency particularly when they are combined with short-read sequencing data. Results Alcaligenes faecalis PGB1 was isolated and identified with resistance to penicillin and three other antibiotics. After being sequenced by Nanopore MinION and Illumina sequencer, its entire genome was hybrid-assembled. One chromosome and one plasmid was assembled and annotated with 4,433 genes (including 91 RNA genes). Function annotation and comparison between strains were performed. A phylogenetic analysis revealed that it was closest to A. faecalis ZD02. Resistome related sequences was explored, including ARGs, Insert sequence, phage. Two plasmid aminoglycoside genes were determined to be acquired ARGs. The main ARG category was antibiotic efflux resistance and β-lactamase (EC 3.5.2.6) of PGB1 was assigned to Class A, Subclass A1b, and Cluster LSBL3. Conclusions The present study identified the newly isolated bacterium A. faecalis PGB1 and systematically annotated its genome sequence and ARGs. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08507-7.
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Affiliation(s)
- Jidong Lang
- Geneis (Beijing) Co., Ltd, Beijing, 100102, China.,Qingdao Geneis Institute of Big Data Mining and Precision Medicine, Qingdao, People's Republic of China
| | - Yanju Li
- School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Wenjuan Yang
- Geneis (Beijing) Co., Ltd, Beijing, 100102, China
| | - Ruyi Dong
- Geneis (Beijing) Co., Ltd, Beijing, 100102, China.,Qingdao Geneis Institute of Big Data Mining and Precision Medicine, Qingdao, People's Republic of China
| | - Yuebin Liang
- Geneis (Beijing) Co., Ltd, Beijing, 100102, China.,Qingdao Geneis Institute of Big Data Mining and Precision Medicine, Qingdao, People's Republic of China
| | - Jia Liu
- Geneis (Beijing) Co., Ltd, Beijing, 100102, China
| | - Lanyou Chen
- Geneis (Beijing) Co., Ltd, Beijing, 100102, China
| | - Weiwei Wang
- Geneis (Beijing) Co., Ltd, Beijing, 100102, China
| | - Binbin Ji
- Geneis (Beijing) Co., Ltd, Beijing, 100102, China
| | - Geng Tian
- Geneis (Beijing) Co., Ltd, Beijing, 100102, China.,Qingdao Geneis Institute of Big Data Mining and Precision Medicine, Qingdao, People's Republic of China
| | - Nanying Che
- Department of Pathology, Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, 101149, China.
| | - Bo Meng
- Geneis (Beijing) Co., Ltd, Beijing, 100102, China.
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Fang Y, Baloch Z, Zhang W, Hu Y, Zheng R, Song Y, Tai W, Xia X. Emergence of Carbapenem-Resistant ST244, ST292, and ST2446 Pseudomonas aeruginosa Clones in Burn Patients in Yunnan Province. Infect Drug Resist 2022; 15:1103-1114. [PMID: 35321081 PMCID: PMC8935738 DOI: 10.2147/idr.s353130] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 03/08/2022] [Indexed: 12/13/2022] Open
Abstract
Introduction The prevalence of carbapenem-resistant Pseudomonas aeruginosa is increasing persistently, particularly in burn ward isolates. Here, we investigate the prevalence of carbapenem-resistant Pseudomonas aeruginosa in a burn ward of a provincial-level hospital at Kunming, Yunnan province, China. Methods A total of 118 P. aeruginosa strains were isolated from 57 hospitalized patients, and their MICs were measured. Carbapenem-resistant isolates were selected for multilocus sequence typing (MLST). Carbapenem-resistance mechanisms were identified by examining carbapenemase genes and OprD protein and Carba-NP testing. Representative isolates were further characterized by de novo sequencing for carbapenemase molecular background. Results Among 118 P. aeruginosa isolates, 54 (54/118,45.8%) were carbapenem-resistant Pseudomonas aeruginosa, and 3 genotypes were found (ST292, ST244, and ST2446). Non-carbapenemase-producing ST292 was the most prevalent ST, followed by ST2446 and ST244. A novel 13-bp oprD deletion was found in the ST292 clone, which formed the truncated outer membrane protein and may cause carbapenem resistance. ST244 and ST2446 harbored blaIMP-45 and blaIMP-87, respectively. blaIMP-45 is located in a megaplasmid, together with aac(6’)-Ib3, blaOXA-1, catB3, qnrVC6, armA, msr(E), mph(E), aph(3’)-Ia, tetC/tetR, aac(6’)-Ib3, floR, mexC-mexD-oprJ, fosA and lead to extensive drug resistance. ST2446 contains a carbapenem-resistant gene blaIMP-87 on the chromosome and is acquired by a novel gene cassette array (blaIMP-87-ant(2”)-Ia-blaOXA-10-aac(6’)-Ib3) of class 1 integron. Discussion For the first time, ST244, ST292 and ST2446 are reported emerging in burn patients, with distinctive carbapenem-resistance mechanisms, respectively. The obtained results highlight the need to surveillance carbapenem-resistant isolates in burn patients.
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Affiliation(s)
- Yue Fang
- The Affiliated AnNing First Hospital & Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, 650500, People’s Republic of China
| | - Zulqarnain Baloch
- The Affiliated AnNing First Hospital & Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, 650500, People’s Republic of China
| | - Wei Zhang
- The 2nd Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, 650101, People’s Republic of China
| | - Ying Hu
- The 2nd Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, 650101, People’s Republic of China
| | - Rui Zheng
- The First Hospital of Yunnan Province & The Affiliated Hospital, Kunming University of Science and Technology, Kunming, Yunnan, 650034, People’s Republic of China
| | - Yuzhu Song
- The Affiliated AnNing First Hospital & Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, 650500, People’s Republic of China
- Correspondence: Yuzhu Song; Xueshan Xia, Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, 650500, People’s Republic of China, Tel +86-871-65920756, Fax +86-871-65920570, Email ;
| | - Wenlin Tai
- The 2nd Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, 650101, People’s Republic of China
| | - Xueshan Xia
- The Affiliated AnNing First Hospital & Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, 650500, People’s Republic of China
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Characterization of a Conjugative Multidrug Resistance IncP-2 Megaplasmid, pPAG5, from a Clinical Pseudomonas aeruginosa Isolate. Microbiol Spectr 2022; 10:e0199221. [PMID: 35171033 PMCID: PMC8849076 DOI: 10.1128/spectrum.01992-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The spread of resistance genes via horizontal plasmid transfer plays a significant role in the formation of multidrug-resistant (MDR) Pseudomonas aeruginosa strains. Here, we identified a megaplasmid (ca. 513 kb), designated pPAG5, which was recovered from a clinical multidrug-resistant P. aeruginosa PAG5 strain. The pPAG5 plasmid belonged to the IncP-2 incompatibility group. Two large multidrug resistance regions (MDR-1 and MDR-2) and two heavy metal resistance operons (merEDACPTR and terZABCDE) were identified in the pPAG5 plasmid. Genetic analysis demonstrated that the formation of MDR regions was mediated by several homologous recombination events. Further conjugation assays identified that pPAG5 could be transferred to P. aeruginosa but not Escherichia coli. Antimicrobial susceptibility testing on transconjugants demonstrated that pPAG5 was capable of transferring resistance genes to transconjugants and producing a multidrug-resistant phenotype. Comparative analysis revealed that pPAG5 and related plasmids shared an overall similar backbone, including genes essential for replication (repA), partition (par), and conjugal transfer (tra). Further phylogenetic analysis showed that pPAG5 was closely related to plasmids pOZ176 and pJB37, both of which are members of the IncP-2-type plasmid group. IMPORTANCE The emergence and spread of plasmid-associated multidrug resistance in bacterial pathogens is a key global threat to public health. It is important to understand the mechanisms of the formation and evolution of these plasmids in patients, hospitals, and the environment. In this study, we detailed the genetic characteristics of a multidrug resistance IncP-2 megaplasmid, pPAG5, and investigated the formation of its MDR regions and evolution. To the best of our knowledge, plasmid pPAG5 is the largest multidrug resistance plasmid ever sequenced in the Pseudomonas genus. Our results may provide further insight into the formation of multidrug resistance plasmids in bacteria and the molecular evolution of plasmids.
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Jin X, Chen Z, Shi Y, Gui J, Zhao Z. Response of gut microbiota to feed-borne bacteria depends on fish growth rate: a snapshot survey of farmed juvenile Takifugu obscurus. Microb Biotechnol 2022; 15:683-702. [PMID: 33393737 PMCID: PMC8867974 DOI: 10.1111/1751-7915.13741] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 12/07/2020] [Accepted: 12/12/2020] [Indexed: 02/06/2023] Open
Abstract
Environmental bacteria have a great impact on fish gut microbiota, yet little is known as to where fish acquire their gut symbionts, and how gut microbiota response to the disturbance from environmental bacteria. Through the integrative analysis by community profiling and source tracking, we show that feed-associated bacteria can impose a strong disturbance upon the hindgut microbiota of cultured fugu. Consequently, marked alterations in the composition and function of gut microbiota in slow growth fugu were observed, implying a reduced stability upon bacterial disturbance from feed. Moreover, quantitative ecological analyses indicated that homogeneous selection and dispersal limitation largely contribute to the community stability and partial variations among hosts in the context of lower degree of disturbance. While the disturbance peaked, variable selection leads to an augmented interaction within gut microbiota, entailing community unstability and shift. Our findings emphasized the intricate linkage between feed and gut microbiota and highlighted the importance of resolving the feed source signal before the conclusion of comparative analysis of microbiota can be drawn. Our results provide a deeper insight into aquaculture of fugu and other economically important fishes and have further implications for an improved understanding of host-microbe interactions in the vertebrate gastrointestinal tract.
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Affiliation(s)
- Xingkun Jin
- Department of Marine BiologyCollege of OceanographyHohai UniversityNanjing210098China
| | - Ziwei Chen
- Department of Marine BiologyCollege of OceanographyHohai UniversityNanjing210098China
| | - Yan Shi
- Department of Marine BiologyCollege of OceanographyHohai UniversityNanjing210098China
| | - Jian‐Fang Gui
- Department of Marine BiologyCollege of OceanographyHohai UniversityNanjing210098China
- State Key Laboratory of Freshwater Ecology and BiotechnologyInstitute of HydrobiologyThe Innovation Academy of Seed DesignChinese Academy of SciencesWuhan430072China
| | - Zhe Zhao
- Department of Marine BiologyCollege of OceanographyHohai UniversityNanjing210098China
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Ghaly TM, Gillings MR. New perspectives on mobile genetic elements: a paradigm shift for managing the antibiotic resistance crisis. Philos Trans R Soc Lond B Biol Sci 2022; 377:20200462. [PMID: 34839710 PMCID: PMC8628067 DOI: 10.1098/rstb.2020.0462] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Mobile genetic elements (MGEs) are primary facilitators in the global spread of antibiotic resistance. Here, we present novel ecological and evolutionary perspectives to understand and manage these elements: as selfish entities that exhibit biological individuality, as pollutants that replicate and as invasive species that thrive under human impact. Importantly, each viewpoint suggests new means to control their activity and spread. When seen as biological individuals, MGEs can be regarded as therapeutic targets in their own right. We highlight promising conjugation-inhibiting compounds that could be administered alongside antibiotic treatment. Viewed as pollutants, sewage treatment methods could be modified to efficiently remove antimicrobials and the resistance genes that they select. Finally, by recognizing the invasive characteristics of MGEs, we might apply strategies developed for the management of invasive species. These include environmental restoration to reduce antimicrobial selection, early detection to help inform appropriate antibiotic usage, and biocontrol strategies that target MGEs, constituting precision antimicrobials. These actions, which embody the One Health approach, target different characteristics of MGEs that are pertinent at the cellular, community, landscape and global levels. The strategies could act on multiple fronts and, together, might provide a more fruitful means to combat the global resistance crisis. This article is part of the theme issue ‘The secret lives of microbial mobile genetic elements’.
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Affiliation(s)
- Timothy M Ghaly
- Department of Biological Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Michael R Gillings
- Department of Biological Sciences, Macquarie University, Sydney, NSW, 2109, Australia.,ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW, 2109, Australia
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Abstract
Naturally occurring plasmids come in different sizes. The smallest are less than a kilobase of DNA, while the largest can be over three orders of magnitude larger. Historically, research has tended to focus on smaller plasmids that are usually easier to isolate, manipulate and sequence, but with improved genome assemblies made possible by long-read sequencing, there is increased appreciation that very large plasmids—known as megaplasmids—are widespread, diverse, complex, and often encode key traits in the biology of their host microorganisms. Why are megaplasmids so big? What other features come with large plasmid size that could affect bacterial ecology and evolution? Are megaplasmids 'just' big plasmids, or do they have distinct characteristics? In this perspective, we reflect on the distribution, diversity, biology, and gene content of megaplasmids, providing an overview to these large, yet often overlooked, mobile genetic elements. This article is part of the theme issue ‘The secret lives of microbial mobile genetic elements’.
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Affiliation(s)
- James P J Hall
- Department of Evolution, Ecology and Behaviour, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - João Botelho
- Antibiotic Resistance Evolution Group, Max Planck Institute for Evolutionary Biology, Plön, Germany.,Department of Evolutionary Ecology and Genetics, Zoological Institute, Christian Albrechts University, Kiel, Germany
| | - Adrian Cazares
- EMBL's European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, UK.,Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - David A Baltrus
- School of Plant Sciences, University of Arizona, Tucson, AZ, USA
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Abstract
Horizontal transfer of bacterial plasmids generates genetic variability and contributes to the dissemination of the genes that enable bacterial cells to develop antimicrobial resistance (AMR). Several aspects of the conjugative process have long been known, namely, those related to the proteins that participate in the establishment of cell-to-cell contact and to the enzymatic processes associated with the processing of plasmid DNA and its transfer to the recipient cell. In this work, we describe the roles of newly identified proteins that influence the conjugation of several plasmids. Genes encoding high-molecular-weight bacterial proteins that contain one or several immunoglobulin-like domains (Big) are located in the transfer regions of several plasmids that usually harbor AMR determinants. These Big proteins are exported to the external medium and target two extracellular organelles: the flagella and conjugative pili. The plasmid gene-encoded Big proteins facilitate conjugation by reducing cell motility and facilitating cell-to-cell contact by binding both to the flagella and to the conjugative pilus. They use the same export machinery as that used by the conjugative pilus components. In the examples characterized in this paper, these proteins influence conjugation at environmental temperatures (i.e., 25°C). This suggests that they may play relevant roles in the dissemination of plasmids in natural environments. Taking into account that they interact with outer surface organelles, they could be targeted to control the dissemination of different bacterial plasmids carrying AMR determinants. IMPORTANCE Transmission of a plasmid from one bacterial cell to another, in several instances, underlies the dissemination of antimicrobial resistance (AMR) genes. The process requires well-characterized enzymatic machinery that facilitates cell-to-cell contact and the transfer of the plasmid. Our paper identifies novel plasmid gene-encoded high-molecular-weight proteins that contain an immunoglobulin-like domain and are required for plasmid transmission. They are encoded by genes on different groups of plasmids. These proteins are exported outside the cell. They bind to extracellular cell appendages such as the flagella and conjugative pili. Expression of these proteins reduces cell motility and increases the ability of the bacterial cells to transfer the plasmid. These proteins could be targeted with specific antibodies to combat infections caused by AMR microorganisms that harbor these plasmids.
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Laborda P, Hernando-Amado S, Martínez JL, Sanz-García F. Antibiotic Resistance in Pseudomonas. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1386:117-143. [DOI: 10.1007/978-3-031-08491-1_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Yi B, Dalpke AH. Revisiting the intrageneric structure of the genus Pseudomonas with complete whole genome sequence information: Insights into diversity and pathogen-related genetic determinants. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 97:105183. [PMID: 34920102 DOI: 10.1016/j.meegid.2021.105183] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 08/09/2021] [Accepted: 12/08/2021] [Indexed: 06/14/2023]
Abstract
Pseudomonas spp. exhibit considerable differences in host specificity and virulence. Most Pseudomonas species were isolated exclusively from environmental sources, ranging from soil to plants, but some Pseudomonas species have been detected from versatile sources, including both human host and environmental sources. Understanding genome variations that generate the tremendous diversity in Pseudomonas biology is important in controlling the incidence of infections. With a data set of 704 Pseudomonas complete whole genome sequences representing 186 species, Pseudomonas intrageneric structure was investigated by hierarchical clustering based on average nucleotide identity, and by phylogeny analysis based on concatenated core-gene alignment. Further comparative functional analyses indicated that Pseudomonas species only living in natural habitats lack multiple functions that are important in the regulation of bacterial pathogenesis, indicating the possession of these functions might be characteristic of Pseudomonas human pathogens. Moreover, we have performed pan-genome based homogeneity analyses, and detected genes with conserved structures but diversified functions across the Pseudomonas genomes, suggesting these genes play a role in driving diversity. In summary, this study provided insights into the dynamics of genome diversity and pathogen-related genetic determinants in Pseudomonas, which might help the development of more targeted antibiotics for the treatment of Pseudomonas infections.
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Affiliation(s)
- Buqing Yi
- Institute of Medical Microbiology and Virology, Medical Faculty, Technische Universität Dresden, Dresden, Germany.
| | - Alexander H Dalpke
- Institute of Medical Microbiology and Virology, Medical Faculty, Technische Universität Dresden, Dresden, Germany.
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Affiliation(s)
- Masaki Shintani
- Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, Japan
- Green Energy Research Division, Research Institute of Green Science and Technology, Shizuoka University, Shizuoka, Japan
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, Ibaraki, Japan
| | - Haruo Suzuki
- Faculty of Environment and Information Studies, Keio University, Fujisawa, Kanagawa, Japan
| | - Hideaki Nojiri
- Agro-Biotechnology Research Center (AgTECH), Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Masato Suzuki
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
- Corresponding author. E-mail:
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Peng W, Wang Y, Fu Y, Deng Z, Lin S, Liang R. Characterization of the Tellurite-Resistance Properties and Identification of the Core Function Genes for Tellurite Resistance in Pseudomonas citronellolis SJTE-3. Microorganisms 2022; 10:microorganisms10010095. [PMID: 35056544 PMCID: PMC8779313 DOI: 10.3390/microorganisms10010095] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 12/27/2021] [Accepted: 12/30/2021] [Indexed: 11/16/2022] Open
Abstract
Tellurite is highly toxic to bacteria and commonly used in the clinical screening for pathogens; it is speculated that there is a potential relationship between tellurite resistance and bacterial pathogenicity. Until now, the core function genes of tellurite resistance and their characteristics are still obscure. Pseudomonas citronellolis SJTE-3 was found able to resist high concentrations of tellurite (250 μg/mL) and formed vacuole-like tellurium nanostructures. The terZABCDE gene cluster located in the large plasmid pRBL16 endowed strain SJTE-3 with the tellurite resistance of high levels. Although the terC and terD genes were identified as the core function genes for tellurite reduction and resistance, the inhibition of cell growth was observed when they were used solely. Interestingly, co-expression of the terA gene or terZ gene could relieve the burden caused by the expression of the terCD genes and recover normal cell growth. TerC and TerD proteins commonly shared the conserved sequences and are widely distributed in many pathogenic bacteria, highly associated with the pathogenicity factors.
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Affiliation(s)
- Wanli Peng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; (W.P.); (Y.W.); (Y.F.); (Z.D.); (S.L.)
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yanqiu Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; (W.P.); (Y.W.); (Y.F.); (Z.D.); (S.L.)
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yali Fu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; (W.P.); (Y.W.); (Y.F.); (Z.D.); (S.L.)
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; (W.P.); (Y.W.); (Y.F.); (Z.D.); (S.L.)
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Shuangjun Lin
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; (W.P.); (Y.W.); (Y.F.); (Z.D.); (S.L.)
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Rubing Liang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; (W.P.); (Y.W.); (Y.F.); (Z.D.); (S.L.)
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Correspondence: ; Tel./Fax: +86-21-34204192
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Wardell SJT, Gauthier J, Martin LW, Potvin M, Brockway B, Levesque RC, Lamont IL. Genome evolution drives transcriptomic and phenotypic adaptation in Pseudomonas aeruginosa during 20 years of infection. Microb Genom 2021; 7. [PMID: 34826267 PMCID: PMC8743555 DOI: 10.1099/mgen.0.000681] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The opportunistic pathogen Pseudomonas aeruginosa chronically infects the lungs of patients with cystic fibrosis (CF). During infection the bacteria evolve and adapt to the lung environment. Here we use genomic, transcriptomic and phenotypic approaches to compare multiple isolates of P. aeruginosa collected more than 20 years apart during a chronic infection in a CF patient. Complete genome sequencing of the isolates, using short- and long-read technologies, showed that a genetic bottleneck occurred during infection and was followed by diversification of the bacteria. A 125 kb deletion, an 0.9 Mb inversion and hundreds of smaller mutations occurred during evolution of the bacteria in the lung, with an average rate of 17 mutations per year. Many of the mutated genes are associated with infection or antibiotic resistance. RNA sequencing was used to compare the transcriptomes of an earlier and a later isolate. Substantial reprogramming of the transcriptional network had occurred, affecting multiple genes that contribute to continuing infection. Changes included greatly reduced expression of flagellar machinery and increased expression of genes for nutrient acquisition and biofilm formation, as well as altered expression of a large number of genes of unknown function. Phenotypic studies showed that most later isolates had increased cell adherence and antibiotic resistance, reduced motility, and reduced production of pyoverdine (an iron-scavenging siderophore), consistent with genomic and transcriptomic data. The approach of integrating genomic, transcriptomic and phenotypic analyses reveals, and helps to explain, the plethora of changes that P. aeruginosa undergoes to enable it to adapt to the environment of the CF lung during a chronic infection.
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Affiliation(s)
| | - Jeff Gauthier
- Institut de biologie intégrative et des Systèmes, Université Laval, Québec, Canada
| | - Lois W Martin
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Marianne Potvin
- Institut de biologie intégrative et des Systèmes, Université Laval, Québec, Canada
| | - Ben Brockway
- Department of Medicine, University of Otago, Dunedin, New Zealand
| | - Roger C Levesque
- Institut de biologie intégrative et des Systèmes, Université Laval, Québec, Canada
| | - Iain L Lamont
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
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Huang J, Zhao Z, Zhang Q, Zhang S, Zhang S, Chen M, Qiu H, Cao Y, Li B. Phylogenetic Analysis Reveals Distinct Evolutionary Trajectories of the Fluoroquinolones-Resistant Escherichia coli ST1193 From Fuzhou, China. Front Microbiol 2021; 12:746995. [PMID: 34803966 PMCID: PMC8602892 DOI: 10.3389/fmicb.2021.746995] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 10/13/2021] [Indexed: 01/27/2023] Open
Abstract
Escherichia coli (E. coli) ST1193 is an emerging fluoroquinolones-resistant and virulent lineage. Large gaps remain in our understanding of the evolutionary processes and differences of this lineage. Therefore, we used 76 E. coli ST1193 genomes to detect strain-level genetic diversity and phylogeny of this lineage globally. All E. coli ST1193 possessed fimH64, filCH5, and fumC14. There was 94.7% of isolates classified as O-type O75. There was 9.33% of E. coli ST1193 that possessed K5 capsular, while 90.67% of isolates possessed K1 capsular. The core genome analysis revealed that all isolates were divided into two phylogenetic clades (clade A and B). Clade A included 25 non-Chinese E. coli ST1193, and clade B contained all isolates collected from Fuzhou, China, respectively. The results of comparative genomics indicated Indels were identified in 150 clade-specific genes, which were enriched into the biological process and molecular function. Accessory genome phylogenetic tree showed a high degree of correlation between accessory genome clusters and core genome clades. There was significant difference in antibiotic resistance genes (ARGs) [bla CTX-M-55 , bla TEM-1 , sul2, tet(B), tet(R), APH(6)-Id, and AAC(3)-IId], virulence factors (cia, neuC, gad, and traT), and plasmid replicon types (IncQ1, Col156, and IncB/O/K/Z) between clade A (non-Chinese isolates) and clade B (Chinese isolates) (p < 0.05). Further analysis of the genetic environments of bla CTX-M-55 demonstrated that the flanking contexts of bla CTX-M-55 were diverse. In conclusion, our results reveal the distinct evolutionary trajectories of the spread of E. coli ST1193 in Fuzhou, China and non-China regions. This supports both global transmission and localized lineage expansion of this lineage following specific introductions into a geographic locality.
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Affiliation(s)
- Jiangqing Huang
- Department of Clinical Laboratory, Fujian Medical University Union Hospital, Fuzhou, China
| | - Zhichang Zhao
- Department of Pharmacy, Fujian Medical University Union Hospital, Fuzhou, China
| | - Qianwen Zhang
- Department of Clinical Laboratory, Fujian Medical University Union Hospital, Fuzhou, China
| | - Shengcen Zhang
- Department of Clinical Laboratory, Fujian Medical University Union Hospital, Fuzhou, China
| | - Shuyu Zhang
- Department of Laboratory Medicine, Fujian Medical University, Fuzhou, China
| | - Min Chen
- Department of Laboratory Medicine, Fujian Medical University, Fuzhou, China
| | - Hongqiang Qiu
- Department of Pharmacy, Fujian Medical University Union Hospital, Fuzhou, China
| | - Yingping Cao
- Department of Clinical Laboratory, Fujian Medical University Union Hospital, Fuzhou, China
| | - Bin Li
- Department of Clinical Laboratory, Fujian Medical University Union Hospital, Fuzhou, China
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Li Y, Zhu Y, Zhou W, Chen Z, Moran RA, Ke H, Feng Y, van Schaik W, Shen H, Ji J, Ruan Z, Hua X, Yu Y. Alcaligenes faecalis metallo-β-lactamase in extensively drug-resistant Pseudomonas aeruginosa isolates. Clin Microbiol Infect 2021; 28:880.e1-880.e8. [PMID: 34826621 DOI: 10.1016/j.cmi.2021.11.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 08/24/2021] [Accepted: 11/06/2021] [Indexed: 12/24/2022]
Abstract
OBJECTIVES This study aimed to characterize Alcaligenes faecalis metallo-β-lactamases AFM-2 and AFM-3 from clinical P. aeruginosa isolates NDTH10366, NDTH9845 and WTJH17. METHODS Clinical isolates were whole-genome sequenced using the Illumina and Oxford Nanopore platforms. Minimum inhibitory concentrations (MICs) of clinical isolates and transformants containing MBL genes were determined using broth microdilution methods. Kinetic parameters of purified AFM and NDM-1 were measured using a spectrophotometer. The AFM structure was modelled with SWISS-MODEL. RESULTS NDTH10366 and NDTH9845 were extensively drug-resistant (XDR) isolates carrying blaAFM-2 and multiple copies of blaKPC-2, while WTJH17 was an XDR isolate carrying blaAFM-3. The plasmid-borne blaAFM-2 and blaAFM-3 genes are associated with a novel ISCR element, ISCR29. AFM-2 and AFM-3, differing from AFM-1 by one amino acid substitution each, shared 86.2% and 86.6% amino acid sequence identity with NDM-1, respectively. Phylogenetic analysis confirmed the close relationship between AFM and NDM. Expression of AFM and NDM-1 under their native promoters in DH5α and PAO1 led to elevated MICs for all tested β-lactams except aztreonam. Comparable catalytic abilities were observed for AFM and NDM-1 when hydrolyzing nitrocefin, cefepime, imipenem and biapenem, while for other tested β-lactams AFM displayed weaker enzymatic activities. Modelling AFM structure revealed a characteristic αβ/βα fold with two zinc-binding active sites. CONCLUSIONS AFM from clinical P. aeruginosa isolates demonstrated β-lactamase activity comparable to NDM-1. Co-carriage of blaAFM and blaKPC renders clinical P. aeruginosa isolates non-susceptible to all antipseudomonal β-lactams. The association of blaAFM genes with translocatable genetic elements and plasmids highlights their concerning potential for dissemination.
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Affiliation(s)
- Yue Li
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China; Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China; Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yiwei Zhu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China; Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China; Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Wanqing Zhou
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, Nanjing University Medical School, Nanjing, China
| | - Zhongju Chen
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Robert A Moran
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Huanhuan Ke
- Department of Biophysics, Zhejiang University School of Medicine, Hangzhou, China
| | - Yu Feng
- Department of Biophysics, Zhejiang University School of Medicine, Hangzhou, China
| | - Willem van Schaik
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Han Shen
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, Nanjing University Medical School, Nanjing, China
| | - Jingshu Ji
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China; Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China; Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhi Ruan
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaoting Hua
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China; Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China; Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.
| | - Yunsong Yu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China; Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China; Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.
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Oberlé K, Bouju-Albert A, Helsens N, Pangga G, Prevost H, Magras C, Calvez S. No evidence for a relationship between farm or transformation process locations and antibiotic resistance patterns of Pseudomonas population associated with rainbow trout (Oncorhynchus mykiss). J Appl Microbiol 2021; 132:1738-1750. [PMID: 34719087 PMCID: PMC9299046 DOI: 10.1111/jam.15344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 09/10/2021] [Accepted: 10/15/2021] [Indexed: 11/30/2022]
Abstract
AIMS Study the relationship between antibiotic resistance patterns of Pseudomonas isolated from farmed rainbow trout fillets and farm or transformation process locations. METHODS AND RESULTS Pseudomonas strains were isolated from rainbow trout sampled in two differently located farms and filleted in laboratory or in a processing factory. One hundred and twenty-five isolates were confirmed as belonging to Pseudomonas using CFC selective media, Gram staining, oxidase test and quantitative polymerase chain reaction methods. Fifty-one isolates from separate fish fillets were further identified using MALDI-TOF mass spectrometry, and the minimal inhibitory concentrations (MIC) of 11 antibiotics were also determined by microdilution method. Most of the isolates belonged to the Pseudomonas fluorescens group (94.1%), and no relationship was established between antibiotic resistance patterns and sampling locations (farms or filleting areas). Multiple resistance isolates with high MIC values (from 64 µg ml-1 to more than 1024 µg ml-1 ) were identified. CONCLUSIONS Antibiotic resistance patterns found in Pseudomonas isolates were not influenced by farms or transformation process locations. Seven isolates were found highly resistant to four different antibiotic classes. SIGNIFICANCE AND IMPACT OF THE STUDY This study does not provide evidence of a relationship between farm or transformation process locations on antibiotic resistance patterns of Pseudomonas population.
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Affiliation(s)
| | | | - Nicolas Helsens
- INRAE, Oniris, BIOEPAR, Nantes, France.,INRAE, Oniris, SECALIM, Nantes, France
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Hall JPJ, Wright RCT, Harrison E, Muddiman KJ, Wood AJ, Paterson S, Brockhurst MA. Plasmid fitness costs are caused by specific genetic conflicts enabling resolution by compensatory mutation. PLoS Biol 2021; 19:e3001225. [PMID: 34644303 PMCID: PMC8544851 DOI: 10.1371/journal.pbio.3001225] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 10/25/2021] [Accepted: 09/20/2021] [Indexed: 12/13/2022] Open
Abstract
Plasmids play an important role in bacterial genome evolution by transferring genes between lineages. Fitness costs associated with plasmid carriage are expected to be a barrier to gene exchange, but the causes of plasmid fitness costs are poorly understood. Single compensatory mutations are often sufficient to completely ameliorate plasmid fitness costs, suggesting that such costs are caused by specific genetic conflicts rather than generic properties of plasmids, such as their size, metabolic burden, or gene expression level. By combining the results of experimental evolution with genetics and transcriptomics, we show here that fitness costs of 2 divergent large plasmids in Pseudomonas fluorescens are caused by inducing maladaptive expression of a chromosomal tailocin toxin operon. Mutations in single genes unrelated to the toxin operon, and located on either the chromosome or the plasmid, ameliorated the disruption associated with plasmid carriage. We identify one of these compensatory loci, the chromosomal gene PFLU4242, as the key mediator of the fitness costs of both plasmids, with the other compensatory loci either reducing expression of this gene or mitigating its deleterious effects by up-regulating a putative plasmid-borne ParAB operon. The chromosomal mobile genetic element Tn6291, which uses plasmids for transmission, remained up-regulated even in compensated strains, suggesting that mobile genetic elements communicate through pathways independent of general physiological disruption. Plasmid fitness costs caused by specific genetic conflicts are unlikely to act as a long-term barrier to horizontal gene transfer (HGT) due to their propensity for amelioration by single compensatory mutations, helping to explain why plasmids are so common in bacterial genomes.
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Affiliation(s)
- James P. J. Hall
- Department of Evolution, Ecology and Behaviour, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Rosanna C. T. Wright
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
- Division of Evolution and Genomic Sciences, University of Manchester, Manchester, United Kingdom
| | - Ellie Harrison
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Katie J. Muddiman
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - A. Jamie Wood
- Department of Biology, University of York, York, United Kingdom
- Department of Mathematics, University of York, York, United Kingdom
| | - Steve Paterson
- Department of Evolution, Ecology and Behaviour, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Michael A. Brockhurst
- Division of Evolution and Genomic Sciences, University of Manchester, Manchester, United Kingdom
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G. C. Rodrigues J, Nair HP, O'Kane C, Walker CA. Prevalence of multidrug resistance in Pseudomonas spp. isolated from wild bird feces in an urban aquatic environment. Ecol Evol 2021; 11:14303-14311. [PMID: 34707856 PMCID: PMC8525170 DOI: 10.1002/ece3.8146] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 08/25/2021] [Accepted: 09/01/2021] [Indexed: 01/18/2023] Open
Abstract
Antimicrobial resistance (AMR) has been detected in the microbiota of wildlife, yet little is known about the origin and impact within the ecosystem. Due to the shortage of nonepizootic surveillance, there is limited understanding of the natural prevalence and circulation of AMR bacteria in the wild animal population, including avian species. In this surveillance study, feces from wild birds in proximity to the River Cam, Cambridge, England, were collected and Pseudomonas spp. were isolated. Of the 115 samples collected, 24 (20.9%; 95% CI, 12.6%‒29.2%) harbored Pseudomonas spp. of which 18 (75%; 95% CI, 58%‒92%) had a multiple antibiotic resistance (MAR) index greater than 0.2. No Pseudomonas spp. isolate in this study was pansusceptible. Resistance was found among the 24 isolates against ciprofloxacin (87.5%; 95% CI, 74.3%‒100%) and cefepime (83.3%; 95% CI, 68.4%‒98.2%), both of which are extensively used to treat opportunistic Pseudomonas spp. infections. The prevalence of Pseudomonas spp. in the wild bird feces sampled during this study is greater than previous, similar studies. Additionally, their multidrug resistance profile provides insight into the potential risk for ecosystem contamination. It further highlights the importance of a One Health approach, including ongoing surveillance efforts that help to develop the understanding of how wildlife, including avifauna, may contribute and disperse AMR across the ecosystem.
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Affiliation(s)
- Joana G. C. Rodrigues
- School of Life SciencesFaculty of Science & EngineeringAnglia Ruskin UniversityCambridgeUK
| | - Harisree P. Nair
- School of Life SciencesFaculty of Science & EngineeringAnglia Ruskin UniversityCambridgeUK
| | - Christopher O'Kane
- School of Life SciencesFaculty of Science & EngineeringAnglia Ruskin UniversityCambridgeUK
| | - Caray A. Walker
- School of Life SciencesFaculty of Science & EngineeringAnglia Ruskin UniversityCambridgeUK
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V M Starling MC, Mendonça Neto RPD, Pires GFF, Vilela PB, Amorim CC. Combat of antimicrobial resistance in municipal wastewater treatment plant effluent via solar advanced oxidation processes: Achievements and perspectives. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 786:147448. [PMID: 33965817 DOI: 10.1016/j.scitotenv.2021.147448] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 04/11/2021] [Accepted: 04/26/2021] [Indexed: 06/12/2023]
Abstract
This review aims to gather main achievements and limitations associated to the application of solar photocatalytic processes with regard to the removal of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) from municipal wastewater treatment plant effluent (MWWTPE). Solar photocatalytic processes were chosen considering the context of developing tropical countries. Among these processes, solar photo-Fenton has been proved effective for the elimination of ARB from MWWTPE at neutral pH in bench and pilot scale and also under continuous flow. Yet, ARG removal varies as according to the gene. Irradiation intensity and matrix composition play a key role on treatment efficiency for this purpose. The use of sulfate radical in modified solar photo-Fenton is still incipient for ARB and ARG removal. Also, investigations related to ARB resistance profile and horizontal gene transfer rates after solar photo-Fenton treatment must be further analyzed. Regarding solar heterogeneous photocatalysis, TiO2 and TiO2-composites applied in suspension are the most commonly investigated for the removal of ARB and ARGs. Irradiation intensity, temperature and catalyst dosage affect treatment efficiency. However, most studies were performed in synthetic solutions using reduced sample volumes. Extended exposition times and addition of H2O2 to the system (solar/TiO2/H2O2) are required to prevent bacteria regrowth and ensure ARG abatement. In addition, enhancement of TiO2 with graphene or (semi)metals improved ARB elimination. Differences concerning irradiation intensity, matrix composition, catalyst dosage, and model ARB and ARGs used in studies analyzed in this review hinder the comparison of photocatalysts synthesized by various research groups. Finally, future research should aim at evaluating the efficiency of solar photocatalytic processes in real matrices originated from sewage treatment systems applied in developing countries; determining indicators of antimicrobial resistance in MWWTPE; and investigating ARB mutation rate as well as the removal of cell-free ARGs present in suspension in MWWTPE.
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Affiliation(s)
- Maria Clara V M Starling
- Universidade Federal de Minas Gerais, Research Group on Environmental Applications of Advanced Oxidation Processes, Av. Antônio Carlos 6627, 31270-901, Pampulha, Belo Horizonte, Brazil
| | - Rondon P de Mendonça Neto
- Universidade Federal de Minas Gerais, Research Group on Environmental Applications of Advanced Oxidation Processes, Av. Antônio Carlos 6627, 31270-901, Pampulha, Belo Horizonte, Brazil; Universidade Federal de Minas Gerais, Instituto de Ciências Biológicas, Departamento de Bioquímica e Imunologia, Pampulha, Belo Horizonte, MG, Brazil
| | - Giovanna F F Pires
- Universidade Federal de Minas Gerais, Research Group on Environmental Applications of Advanced Oxidation Processes, Av. Antônio Carlos 6627, 31270-901, Pampulha, Belo Horizonte, Brazil
| | - Pâmela Beccalli Vilela
- Universidade Federal de Minas Gerais, Research Group on Environmental Applications of Advanced Oxidation Processes, Av. Antônio Carlos 6627, 31270-901, Pampulha, Belo Horizonte, Brazil
| | - Camila C Amorim
- Universidade Federal de Minas Gerais, Research Group on Environmental Applications of Advanced Oxidation Processes, Av. Antônio Carlos 6627, 31270-901, Pampulha, Belo Horizonte, Brazil.
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Urbanowicz P, Izdebski R, Baraniak A, Żabicka D, Hryniewicz W, Gniadkowski M. Molecular and genomic epidemiology of VIM/IMP-like metallo-β-lactamase-producing Pseudomonas aeruginosa genotypes in Poland. J Antimicrob Chemother 2021; 76:2273-2284. [PMID: 34179963 DOI: 10.1093/jac/dkab188] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 05/06/2021] [Indexed: 12/31/2022] Open
Abstract
OBJECTIVES To identify key factors of the expansion of metallo-β-lactamase (MBL)-producing Pseudomonas aeruginosa (MPPA) in Poland, focusing on the role of clonal epidemic(s). METHODS MPPA isolates were typed by PFGE, followed by MLST. blaVIM/IMP MBL genes were amplified and sequenced within class 1 integrons. Their location was assessed by S1 nuclease-hybridization assays. Short-read WGS was performed, and genomes were subjected to SNP-based phylogenetic and resistome analyses. RESULTS Of 1314 MPPA isolates collected in 2005-15 from 212 hospitals, 454 representatives were selected. The isolates belonged to 120 pulsotypes and 52 STs, of which ST235 (∼31%), ST111 (∼17%), ST273 (∼16%) and ST654 (∼9%) prevailed, followed by ST244, ST17, ST395, ST175 and ST1567. The isolates produced seven VIM variants (97.5%) and four IMPs encoded by 46 integrons, most of which were observed only or mainly in Poland. Around 60% of the isolates resulted from (inter)regional clonal outbreaks of 10 individual ST235, ST111, ST273 and ST654 genotypes. The phylogenetic analysis of 163 genomes revealed heterogeneity of ST235 and ST111 populations, arising from transnational circulation and on-site differentiation of several clades/branches. Contrarily, ST273 and ST654 formed relatively homogeneous and apparently Poland-specific lineages, and a unique ST273 genotype with integron In249 was the most expansive organism. CONCLUSIONS Together with a previous report on self-transmissible In461-carrying IncP-2-type plasmids, this study revealed the molecular/genomic background of the rapid MPPA increase in Poland in 2001-15, evidencing multi-clonal spread as its leading factor. Numerous novel/specific MPPA characteristics were identified.
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Affiliation(s)
- P Urbanowicz
- Department of Molecular Microbiology, National Medicines Institute, 00-725, Warsaw, Poland
| | - R Izdebski
- Department of Molecular Microbiology, National Medicines Institute, 00-725, Warsaw, Poland
| | - A Baraniak
- Department of Molecular Microbiology, National Medicines Institute, 00-725, Warsaw, Poland
| | - D Żabicka
- Department of Epidemiology and Clinical Microbiology, The National Reference Centre for Susceptibility Testing, National Medicines Institute, 00-725, Warsaw, Poland
| | - W Hryniewicz
- Department of Epidemiology and Clinical Microbiology, The National Reference Centre for Susceptibility Testing, National Medicines Institute, 00-725, Warsaw, Poland
| | - M Gniadkowski
- Department of Molecular Microbiology, National Medicines Institute, 00-725, Warsaw, Poland
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Sanz-García F, Gil-Gil T, Laborda P, Ochoa-Sánchez LE, Martínez JL, Hernando-Amado S. Coming from the Wild: Multidrug Resistant Opportunistic Pathogens Presenting a Primary, Not Human-Linked, Environmental Habitat. Int J Mol Sci 2021; 22:8080. [PMID: 34360847 PMCID: PMC8347278 DOI: 10.3390/ijms22158080] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 07/22/2021] [Accepted: 07/24/2021] [Indexed: 12/24/2022] Open
Abstract
The use and misuse of antibiotics have made antibiotic-resistant bacteria widespread nowadays, constituting one of the most relevant challenges for human health at present. Among these bacteria, opportunistic pathogens with an environmental, non-clinical, primary habitat stand as an increasing matter of concern at hospitals. These organisms usually present low susceptibility to antibiotics currently used for therapy. They are also proficient in acquiring increased resistance levels, a situation that limits the therapeutic options for treating the infections they cause. In this article, we analyse the most predominant opportunistic pathogens with an environmental origin, focusing on the mechanisms of antibiotic resistance they present. Further, we discuss the functions, beyond antibiotic resistance, that these determinants may have in the natural ecosystems that these bacteria usually colonize. Given the capacity of these organisms for colonizing different habitats, from clinical settings to natural environments, and for infecting different hosts, from plants to humans, deciphering their population structure, their mechanisms of resistance and the role that these mechanisms may play in natural ecosystems is of relevance for understanding the dissemination of antibiotic resistance under a One-Health point of view.
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Affiliation(s)
| | | | | | | | - José L. Martínez
- Centro Nacional de Biotecnología, CSIC, 28049 Madrid, Spain; (F.S.-G.); (T.G.-G.); (P.L.); (L.E.O.-S.); (S.H.-A.)
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Evolution of Subfamily I.1 Lipases in Pseudomonas aeruginosa. Curr Microbiol 2021; 78:3494-3504. [PMID: 34279672 DOI: 10.1007/s00284-021-02589-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 06/21/2021] [Indexed: 10/20/2022]
Abstract
The gram-negative Pseudomonas aeruginosa is an opportunistic human pathogen that contains two different types of strains: the "classical" and the "outlier". In the "classical" strain, its bacterial subfamily I.1 lipases, such as LipA and LipC in P. aeruginosa PAO1, play critical roles in its pathogenicity. However, less is known about the subfamily I.1 lipases in the "outlier" strain, nor the evolution paths of those lipases in both types of P. aeruginosa strains. Our genome-scale investigation on I.1 lipases across different bacterial strains demonstrates the presence of one LipA-like and one new type of I.1 lipase (LipC2) in those "outlier" strains. The related genomic islands analyses further suggest that the LipC counterpart gene in the "outlier" strain was lost by gene truncation. In addition, the evolutionary analyses also indicates the horizontal LipC2 gene transfer from other gammaproteobacterial species, as well as the horizontal LipA gene transfer between two different phyla, both suggesting that the gene transfer of bacterial I.1 lipases might occur in different taxonomical levels. Our results not only provide an evidence to understand the pathogenicity among different P. aeruginosa strains, but add to the knowledge of I.1 lipase evolution in bacteria.
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