1
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Liu Y, Song X, Hou X, Wang Y, Cao X. Effect of Mn-HA on ARGs and MRGs in nitrogen-culturing sludge. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 365:121615. [PMID: 38936019 DOI: 10.1016/j.jenvman.2024.121615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Revised: 06/21/2024] [Accepted: 06/23/2024] [Indexed: 06/29/2024]
Abstract
The simultaneous escalation in ARGs (antibiotic resistance genes) and MRGs (metal resistance genes) further complicates the intricate network of factors contributing to the proliferation of microbial resistance. Manganese, which has been reported to affect the resistance of bacteria to antibiotics and metals, plays a vital role in microbial nitrogen metabolism. Moreover, nitrifying and denitrifying populations are potential hosts for ARGs. In this study, manganese was introduced in its prevalent organic chelated form in the environment (Manganese humus chelates, Mn-HA) to a N metabolism sludge to explore the effect of manganese on MRGs and ARGs dissemination. Metagenomics results revealed that manganese availability enhances nitrogen metabolism, while a decrease in ARGs was noted which may be attributed to the inhibition of horizontal gene transfer (HGT), reflected in the reduced integrase -encoded gene int. Population analysis revealed that nitrifier and denitrifier genus harbor MRGs and ARGs, indicating that nitrifier and denitrifier are hosts of MRGs and ARGs. This raises the question of whether the prevalence of ARGs is always increased in metal-contained environments.
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Affiliation(s)
- Yingying Liu
- College of Environmental Science and Engineering, State Environmental Protection Engineering Center for Pollution Treatment and Control in Textile Industry, Donghua University, Shanghai, 201620, China
| | - Xinshan Song
- College of Environmental Science and Engineering, State Environmental Protection Engineering Center for Pollution Treatment and Control in Textile Industry, Donghua University, Shanghai, 201620, China.
| | - Xiaoxiao Hou
- College of Environmental Science and Engineering, State Environmental Protection Engineering Center for Pollution Treatment and Control in Textile Industry, Donghua University, Shanghai, 201620, China
| | - Yuhui Wang
- College of Environmental Science and Engineering, State Environmental Protection Engineering Center for Pollution Treatment and Control in Textile Industry, Donghua University, Shanghai, 201620, China
| | - Xin Cao
- College of Environmental Science and Engineering, State Environmental Protection Engineering Center for Pollution Treatment and Control in Textile Industry, Donghua University, Shanghai, 201620, China
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2
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Dauvergne E, Lacquemant C, Mullié C. Antibacterial Activity of Brass against Antibiotic-Resistant Bacteria following Repeated Exposure to Hydrogen Peroxide/Peracetic Acid and Quaternary Ammonium Compounds. Microorganisms 2024; 12:1393. [PMID: 39065161 PMCID: PMC11279221 DOI: 10.3390/microorganisms12071393] [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: 06/21/2024] [Revised: 07/03/2024] [Accepted: 07/04/2024] [Indexed: 07/28/2024] Open
Abstract
Copper-containing materials are attracting attention as self-disinfecting surfaces, suitable for helping healthcare settings in reducing healthcare-associated infections. However, the impact of repeated exposure to disinfectants frequently used in biocleaning protocols on their antibacterial activity remains insufficiently characterized. This study aimed at evaluating the antibacterial efficiency of copper (positive control), a brass alloy (AB+®) and stainless steel (negative control) after repeated exposure to a quaternary ammonium compound and/or a mix of peracetic acid/hydrogen peroxide routinely used in healthcare settings. A panel of six antibiotic-resistant strains (clinical isolates) was selected for this assessment. After a short (5 min) exposure time, the copper and brass materials retained significantly better antibacterial efficiencies than stainless steel, regardless of the bacterial strain or disinfectant treatment considered. Moreover, post treatment with both disinfectant products, copper-containing materials still reached similar levels of antibacterial efficiency to those obtained before treatment. Antibiotic resistance mechanisms such as efflux pump overexpression did not impair the antibacterial efficiency of copper-containing materials, nor did the presence of one or several genes related to copper homeostasis/resistance. In light of these results, surfaces made out of copper and brass remain interesting tools in the fight against the dissemination of antibiotic-resistant strains that might cause healthcare-associated infections.
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Affiliation(s)
- Emilie Dauvergne
- Laboratoire AGIR—UR UPJV 4294, UFR de Pharmacie, Université de Picardie Jules Verne, 80037 Amiens, France
- FAVI SA, 80490 Hallencourt, France;
| | | | - Catherine Mullié
- Laboratoire AGIR—UR UPJV 4294, UFR de Pharmacie, Université de Picardie Jules Verne, 80037 Amiens, France
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3
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Zhu Y, Yan S, Chen X, Li Y, Xie S. Thallium spill shifts the structural and functional characteristics of viral communities with different lifestyles in river sediments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 947:174531. [PMID: 38971241 DOI: 10.1016/j.scitotenv.2024.174531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Revised: 06/10/2024] [Accepted: 07/03/2024] [Indexed: 07/08/2024]
Abstract
Thallium (Tl), a highly toxic heavy metal, can affect microbial community, while little is known about its effect on viral community. The present study investigated the variation of viral communities, as well as their interactions with microbial hosts under Tl stress. Tl in sediments significantly altered the composition and diversity of the viral communities, but showed no significant links with the prokaryotic communities, which may reveal a potential discrepancy in the sensitivity of the viral and prokaryotic communities to heavy metal stress. Auxiliary metabolic genes (AMGs) involved in denitrification, methane oxidation and organic sulfur transformation were enriched at T1-contaminated sites, while the abundance of AMGs related to methanogenesis and sulfate reduction were higher at pristine sites. Specially, the enrichment of AMGs involved in assimilatory sulfate reduction in Tl-contaminated sites could possibly reduce Tl bioavailability by enhancing the microbially-driven sulfur cycling to generate sulfides that could be complexed with Tl. Moreover, there was a significantly positive correlation between virus-carrying metal resistant genes and the sedimentary Tl concentration, implying that Tl contamination might enhance the metal resistant potential of the viruses. Serving as the functional gene reservoir, the response of viral AMGs to Tl stress could represent a potential pathway for microorganisms to be adapted to the metal-polluted environments. Our study provided novel insights into the impact of Tl spill on viral communities, shedding light on functional characteristics and the links of virus-host interaction with Tl level.
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Affiliation(s)
- Ying Zhu
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Shuang Yan
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Xiuli Chen
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Yangyang Li
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Shuguang Xie
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China.
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4
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Xu Z, Lin X. Metal-regulated antibiotic resistance and its implications for antibiotic therapy. Microb Biotechnol 2024; 17:e14537. [PMID: 39045888 PMCID: PMC11267348 DOI: 10.1111/1751-7915.14537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Accepted: 07/09/2024] [Indexed: 07/25/2024] Open
Abstract
Antibiotic resistance, one of the major medical threats worldwide, can be selected and induced by metals through multiple mechanisms such as co-resistance, cross-resistance, and co-regulation. Compared with co-resistance and cross-resistance which are attributed to the physically or functionally linked metal and antibiotic resistance genes, co-regulation of antibiotic resistance genes by metal-responsive regulators and pathways is much more complex and elusive. Here, we discussed the main mechanisms by which antibiotic resistance is regulated in response to metals and showed recent attempts to combat antibiotic resistance by interfering with metal-based signalling pathways. Further efforts to depict the intricate metal-based regulatory network of antibiotic resistance will provide tremendous opportunities for the discovery of novel anti-resistance targets, and blocking or rewiring the metal-based signalling pathways is emerging as a promising stratagem to reverse bacterial resistance to antibiotics and rejuvenate the efficacy of conventional antibiotics.
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Affiliation(s)
- Zeling Xu
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research CentreSouth China Agricultural UniversityGuangzhouChina
| | - Xiaoshan Lin
- The Fifth Affiliated HospitalSouthern Medical UniversityGuangzhouChina
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5
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Gillieatt BF, Coleman NV. Unravelling the mechanisms of antibiotic and heavy metal resistance co-selection in environmental bacteria. FEMS Microbiol Rev 2024; 48:fuae017. [PMID: 38897736 PMCID: PMC11253441 DOI: 10.1093/femsre/fuae017] [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: 11/27/2023] [Revised: 06/09/2024] [Accepted: 06/18/2024] [Indexed: 06/21/2024] Open
Abstract
The co-selective pressure of heavy metals is a contributor to the dissemination and persistence of antibiotic resistance genes in environmental reservoirs. The overlapping range of antibiotic and metal contamination and similarities in their resistance mechanisms point to an intertwined evolutionary history. Metal resistance genes are known to be genetically linked to antibiotic resistance genes, with plasmids, transposons, and integrons involved in the assembly and horizontal transfer of the resistance elements. Models of co-selection between metals and antibiotics have been proposed, however, the molecular aspects of these phenomena are in many cases not defined or quantified and the importance of specific metals, environments, bacterial taxa, mobile genetic elements, and other abiotic or biotic conditions are not clear. Co-resistance is often suggested as a dominant mechanism, but interpretations are beset with correlational bias. Proof of principle examples of cross-resistance and co-regulation has been described but more in-depth characterizations are needed, using methodologies that confirm the functional expression of resistance genes and that connect genes with specific bacterial hosts. Here, we comprehensively evaluate the recent evidence for different models of co-selection from pure culture and metagenomic studies in environmental contexts and we highlight outstanding questions.
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Affiliation(s)
- Brodie F Gillieatt
- School of Life and Environmental Sciences, The University of Sydney, F22 - LEES Building, NSW 2006, Australia
| | - Nicholas V Coleman
- School of Natural Sciences, and ARC Centre of Excellence in Synthetic Biology, Macquarie University, 6 Wally’s Walk, Macquarie Park, NSW 2109, Australia
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6
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Madden DE, Baird T, Bell SC, McCarthy KL, Price EP, Sarovich DS. Keeping up with the pathogens: improved antimicrobial resistance detection and prediction from Pseudomonas aeruginosa genomes. Genome Med 2024; 16:78. [PMID: 38849863 PMCID: PMC11157771 DOI: 10.1186/s13073-024-01346-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: 10/29/2023] [Accepted: 05/20/2024] [Indexed: 06/09/2024] Open
Abstract
BACKGROUND Antimicrobial resistance (AMR) is an intensifying threat that requires urgent mitigation to avoid a post-antibiotic era. Pseudomonas aeruginosa represents one of the greatest AMR concerns due to increasing multi- and pan-drug resistance rates. Shotgun sequencing is gaining traction for in silico AMR profiling due to its unambiguity and transferability; however, accurate and comprehensive AMR prediction from P. aeruginosa genomes remains an unsolved problem. METHODS We first curated the most comprehensive database yet of known P. aeruginosa AMR variants. Next, we performed comparative genomics and microbial genome-wide association study analysis across a Global isolate Dataset (n = 1877) with paired antimicrobial phenotype and genomic data to identify novel AMR variants. Finally, the performance of our P. aeruginosa AMR database, implemented in our AMR detection and prediction tool, ARDaP, was compared with three previously published in silico AMR gene detection or phenotype prediction tools-abritAMR, AMRFinderPlus, ResFinder-across both the Global Dataset and an analysis-naïve Validation Dataset (n = 102). RESULTS Our AMR database comprises 3639 mobile AMR genes and 728 chromosomal variants, including 75 previously unreported chromosomal AMR variants, 10 variants associated with unusual antimicrobial susceptibility, and 281 chromosomal variants that we show are unlikely to confer AMR. Our pipeline achieved a genotype-phenotype balanced accuracy (bACC) of 85% and 81% across 10 clinically relevant antibiotics when tested against the Global and Validation Datasets, respectively, vs. just 56% and 54% with abritAMR, 58% and 54% with AMRFinderPlus, and 60% and 53% with ResFinder. ARDaP's superior performance was predominantly due to the inclusion of chromosomal AMR variants, which are generally not identified with most AMR identification tools. CONCLUSIONS Our ARDaP software and associated AMR variant database provides an accurate tool for predicting AMR phenotypes in P. aeruginosa, far surpassing the performance of current tools. Implementation of ARDaP for routine AMR prediction from P. aeruginosa genomes and metagenomes will improve AMR identification, addressing a critical facet in combatting this treatment-refractory pathogen. However, knowledge gaps remain in our understanding of the P. aeruginosa resistome, particularly the basis of colistin AMR.
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Affiliation(s)
- Danielle E Madden
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, QLD, Australia
- Sunshine Coast Health Institute, Birtinya, Queensland, Australia
| | - Timothy Baird
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, QLD, Australia
- Sunshine Coast Health Institute, Birtinya, Queensland, Australia
- Respiratory Department, Sunshine Coast University Hospital, Birtinya, Queensland, Australia
| | - Scott C Bell
- Adult Cystic Fibrosis Centre, The Prince Charles Hospital, Chermside, Queensland, Australia
- Children's Health Research Centre, Faculty of Medicine, The University of Queensland, South Brisbane, Queensland, Australia
| | - Kate L McCarthy
- University of Queensland Medical School, Herston, QLD, Australia
- Royal Brisbane and Women's Hospital, Herston, Queensland, Australia
| | - Erin P Price
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, QLD, Australia
- Sunshine Coast Health Institute, Birtinya, Queensland, Australia
| | - Derek S Sarovich
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, QLD, Australia.
- Sunshine Coast Health Institute, Birtinya, Queensland, Australia.
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7
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Guruge KS, Goswami P, Kanda K, Abeynayaka A, Kumagai M, Watanabe M, Tamamura-Andoh Y. Plastiome: Plastisphere-enriched mobile resistome in aquatic environments. JOURNAL OF HAZARDOUS MATERIALS 2024; 471:134353. [PMID: 38678707 DOI: 10.1016/j.jhazmat.2024.134353] [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: 02/08/2024] [Revised: 03/28/2024] [Accepted: 04/17/2024] [Indexed: 05/01/2024]
Abstract
Aquatic microplastics (MPs) act as reservoirs for microbial communities, fostering the formation of a mobile resistome encompassing diverse antibiotic (ARGs) and biocide/metal resistance genes (BMRGs), and mobile genetic elements (MGEs). This collective genetic repertoire, referred to as the "plastiome," can potentially perpetuate environmental antimicrobial resistance (AMR). Our study examining two Japanese rivers near Tokyo revealed that waterborne MPs are primarily composed of polyethylene and polypropylene fibers and sheets of diverse origin. Clinically important genera like Exiguobacterium and Eubacterium were notably enriched on MPs. Metagenomic analysis uncovered a 3.46-fold higher enrichment of ARGs on MPs than those in water, with multidrug resistance genes (MDRGs) and BMRGs prevailing, particularly within MPs. Specific ARG and BMRG subtypes linked to resistance to vancomycin, beta-lactams, biocides, arsenic, and mercury showed selective enrichment on MPs. Network analysis revealed intense associations between host genera with ARGs, BMRGs, and MGEs on MPs, emphasizing their role in coselection. In contrast, river water exhibited weaker associations. This study underscores the complex interactions shaping the mobile plastiome in aquatic environments and emphasizes the global imperative for research to comprehend and effectively control AMR within the One Health framework.
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Affiliation(s)
- Keerthi S Guruge
- Hygiene Management Group, National Institute of Animal Health, National Agriculture and Food Research Organization, 3-1-5 Kannondai, Tsukuba, Ibaraki 305-0856, Japan.
| | - Prasun Goswami
- Hygiene Management Group, National Institute of Animal Health, National Agriculture and Food Research Organization, 3-1-5 Kannondai, Tsukuba, Ibaraki 305-0856, Japan
| | - Kazuki Kanda
- Hygiene Management Group, National Institute of Animal Health, National Agriculture and Food Research Organization, 3-1-5 Kannondai, Tsukuba, Ibaraki 305-0856, Japan
| | - Amila Abeynayaka
- Pirika Inc., 1 Chome-7-2, Ebisu, Shibuya City, Tokyo 150-6018, Japan; Quantitative Sustainability Assessment, Department of Environmental and Resource Engineering, Technical University of Denmark, Kongens Lyngby 2800, Denmark
| | - Masahiko Kumagai
- Bioinformatics Team, Research Center for Advanced Analysis, National Agriculture and Food Research Organization, 3-1-5 Kannondai, Tsukuba, Ibaraki 305-0856, Japan
| | - Mafumi Watanabe
- Hygiene Management Group, National Institute of Animal Health, National Agriculture and Food Research Organization, 3-1-5 Kannondai, Tsukuba, Ibaraki 305-0856, Japan
| | - Yukino Tamamura-Andoh
- Enteric Pathogen Group, National Institute of Animal Health, National Agriculture and Food Research Organization, 3-1-5 Kannondai, Tsukuba, Ibaraki 305-0856, Japan
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8
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Sharma M, Sharma S, Paavan, Gupta M, Goyal S, Talukder D, Akhtar MS, Kumar R, Umar A, Alkhanjaf AAM, Baskoutas S. Mechanisms of microbial resistance against cadmium - a review. JOURNAL OF ENVIRONMENTAL HEALTH SCIENCE & ENGINEERING 2024; 22:13-30. [PMID: 38887775 PMCID: PMC11180082 DOI: 10.1007/s40201-023-00887-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Accepted: 11/15/2023] [Indexed: 06/20/2024]
Abstract
The escalating cadmium influx from industrial activities and anthropogenic sources has raised serious environmental concerns due to its toxic effects on ecosystems and human health. This review delves into the intricate mechanisms underlying microbial resistance to cadmium, shedding light on the multifaceted interplay between microorganisms and this hazardous heavy metal. Cadmium overexposure elicits severe health repercussions, including renal carcinoma, mucous membrane degradation, bone density loss, and kidney stone formation in humans. Moreover, its deleterious impact extends to animal and plant metabolism. While physico-chemical methods like reverse osmosis and ion exchange are employed to mitigate cadmium contamination, their costliness and incomplete efficacy necessitate alternative strategies. Microbes, particularly bacteria and fungi, exhibit remarkable resilience to elevated cadmium concentrations through intricate resistance mechanisms. This paper elucidates the ingenious strategies employed by these microorganisms to combat cadmium stress, encompassing metal ion sequestration, efflux pumps, and enzymatic detoxification pathways. Bioremediation emerges as a promising avenue for tackling cadmium pollution, leveraging microorganisms' ability to transform toxic cadmium forms into less hazardous derivatives. Unlike conventional methods, bioremediation offers a cost-effective, environmentally benign, and efficient approach. This review amalgamates the current understanding of microbial cadmium resistance mechanisms, highlighting their potential for sustainable remediation strategies. By unraveling the intricate interactions between microorganisms and cadmium, this study contributes to advancing our knowledge of bioremediation approaches, thereby paving the way for safer and more effective cadmium mitigation practices.
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Affiliation(s)
- Monu Sharma
- Department of Biosciences and Technology, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, 133207 Haryana India
| | - Sonu Sharma
- Department of Biosciences and Technology, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, 133207 Haryana India
| | - Paavan
- Department of Biotechnology, Ambala College of Engineering and Applied Research, Devsthali, Ambala, 133101 Haryana India
| | - Mahiti Gupta
- Department of Biosciences and Technology, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, 133207 Haryana India
| | - Soniya Goyal
- Department of Biosciences and Technology, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, 133207 Haryana India
| | - Daizee Talukder
- Department of Biosciences and Technology, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, 133207 Haryana India
| | - Mohd. Sayeed Akhtar
- Department of Botany, Gandhi Faiz-E-Aam College, Shahjahanpur, 242001 Uttar Pradesh India
| | - Raman Kumar
- Department of Biosciences and Technology, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, 133207 Haryana India
| | - Ahmad Umar
- Department of Chemistry, Faculty of Science and ArtsPromising Centre for Sensors and Electronic Devices (PCSED), Najran University, Najran, 11001 Kingdom of Saudi Arabia
- Department of Materials Science and Engineering, The Ohio State University, Columbus, OH 43210 USA
| | - Abdulrab Ahmed M. Alkhanjaf
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, 11001 Najran, Saudi Arabia
| | - Sotirios Baskoutas
- Department of Materials Science, University of Patras, 26500 Patras, Greece
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9
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Novelli M, Bolla JM. RND Efflux Pump Induction: A Crucial Network Unveiling Adaptive Antibiotic Resistance Mechanisms of Gram-Negative Bacteria. Antibiotics (Basel) 2024; 13:501. [PMID: 38927168 PMCID: PMC11200565 DOI: 10.3390/antibiotics13060501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 05/22/2024] [Accepted: 05/27/2024] [Indexed: 06/28/2024] Open
Abstract
The rise of multi-drug-resistant (MDR) pathogenic bacteria presents a grave challenge to global public health, with antimicrobial resistance ranking as the third leading cause of mortality worldwide. Understanding the mechanisms underlying antibiotic resistance is crucial for developing effective treatments. Efflux pumps, particularly those of the resistance-nodulation-cell division (RND) superfamily, play a significant role in expelling molecules from bacterial cells, contributing to the emergence of multi-drug resistance. These are transmembrane transporters naturally produced by Gram-negative bacteria. This review provides comprehensive insights into the modulation of RND efflux pump expression in bacterial pathogens by numerous and common molecules (bile, biocides, pharmaceuticals, additives, plant extracts, etc.). The interplay between these molecules and efflux pump regulators underscores the complexity of antibiotic resistance mechanisms. The clinical implications of efflux pump induction by non-antibiotic compounds highlight the challenges posed to public health and the urgent need for further investigation. By addressing antibiotic resistance from multiple angles, we can mitigate its impact and preserve the efficacy of antimicrobial therapies.
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Affiliation(s)
- Marine Novelli
- Aix Marseille Univ, INSERM, SSA, MCT, 13385 Marseille, France;
- Université Paris Cité, CNRS, Biochimie des Protéines Membranaires, F-75005 Paris, France
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10
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Zhang Y, Zhou Q, Gao C, Lu Y, Sheng Y, Xiao M, Yun Y, Selvaraj JN, Zhang X, Li Y, Yu X. Endophytic bacteria for Cd remediation in rice: Unraveling the Cd tolerance mechanisms of Cupriavidus metallidurans CML2. JOURNAL OF HAZARDOUS MATERIALS 2024; 469:133846. [PMID: 38412644 DOI: 10.1016/j.jhazmat.2024.133846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 01/30/2024] [Accepted: 02/18/2024] [Indexed: 02/29/2024]
Abstract
The utility of endophytic bacteria in Cadmium (Cd) remediation has gained significant attention due to their ability to alleviate metal-induced stress and enhance plant growth. Here, we investigate C. metallidurans CML2, an endophytic bacterial strain prevalent in rice, showing resilience against 2400 mg/L of Cd(II). We conducted an in-depth integrated morphological and transcriptomic analysis illustrating the multifarious mechanisms CML2 employs to combat Cd, including the formation of biofilm and CdO nanoparticles, upregulation of genes involved in periplasmic immobilization, and the utilization of RND efflux pumps to extract excess Cd ions. Beyond Cd, CML2 exhibited robust tolerance to an array of heavy metals, including Mn2+, Se4+, Ni2+, Cu2+, and Hg2+, demonstrating effective Cd(II) removal capacity. Furthermore, CML2 has exhibited plant growth-promoting properties through the production of indole-3-acetic acid (IAA) at 0.93 mg/L, soluble phosphorus compounds at 1.11 mg/L, and siderophores at 22.67%. Supportively, pot experiments indicated an increase in root lengths and a decrease in Cd bioaccumulation in rice seedlings inoculated with CML2, consequently reducing Cd translocation rates from 43% to 31%. These findings not only contribute to the understanding of Cd resistance mechanisms in C. metallidurans, but also underscore CML2's promising application in Cd remediation within rice farming ecosystems.
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Affiliation(s)
- Yuan Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, PR China
| | - Qi Zhou
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, PR China
| | - Chang Gao
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, PR China
| | - Yue Lu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, PR China
| | - Yang Sheng
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, PR China
| | - Ming Xiao
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, PR China
| | - Yueli Yun
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, PR China
| | - Jonathan Nimal Selvaraj
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, PR China
| | - Xianhua Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, PR China
| | - Yadong Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, PR China
| | - Xuejing Yu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, PR China.
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11
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Wu W, Huang J, Xu Z. Antibiotic influx and efflux in Pseudomonas aeruginosa: Regulation and therapeutic implications. Microb Biotechnol 2024; 17:e14487. [PMID: 38801351 PMCID: PMC11129675 DOI: 10.1111/1751-7915.14487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 05/06/2024] [Accepted: 05/09/2024] [Indexed: 05/29/2024] Open
Abstract
Pseudomonas aeruginosa is a notorious multidrug-resistant pathogen that poses a serious and growing threat to the worldwide public health. The expression of resistance determinants is exquisitely modulated by the abundant regulatory proteins and the intricate signal sensing and transduction systems in this pathogen. Downregulation of antibiotic influx porin proteins and upregulation of antibiotic efflux pump systems owing to mutational changes in their regulators or the presence of distinct inducing molecular signals represent two of the most efficient mechanisms that restrict intracellular antibiotic accumulation and enable P. aeruginosa to resist multiple antibiotics. Treatment of P. aeruginosa infections is extremely challenging due to the highly inducible mechanism of antibiotic resistance. This review comprehensively summarizes the regulatory networks of the major porin proteins (OprD and OprH) and efflux pumps (MexAB-OprM, MexCD-OprJ, MexEF-OprN, and MexXY) that play critical roles in antibiotic influx and efflux in P. aeruginosa. It also discusses promising therapeutic approaches using safe and efficient adjuvants to enhance the efficacy of conventional antibiotics to combat multidrug-resistant P. aeruginosa by controlling the expression levels of porins and efflux pumps. This review not only highlights the complexity of the regulatory network that induces antibiotic resistance in P. aeruginosa but also provides important therapeutic implications in targeting the inducible mechanism of resistance.
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Affiliation(s)
- Weiyan Wu
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research CentreSouth China Agricultural UniversityGuangzhouChina
| | - Jiahui Huang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research CentreSouth China Agricultural UniversityGuangzhouChina
| | - Zeling Xu
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research CentreSouth China Agricultural UniversityGuangzhouChina
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12
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Li T, Cao H, Duan C, Chen S, Xu Z. Activation of CzcS/CzcR during zinc excess regulates copper tolerance and pyochelin biosynthesis of Pseudomonas aeruginosa. Appl Environ Microbiol 2024; 90:e0232723. [PMID: 38376236 PMCID: PMC10952498 DOI: 10.1128/aem.02327-23] [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: 12/21/2023] [Accepted: 01/24/2024] [Indexed: 02/21/2024] Open
Abstract
Zinc is an important transition metal that is essential for numerous physiological processes while excessive zinc is cytotoxic. Pseudomonas aeruginosa is a ubiquitous opportunistic human pathogen equipped with an exquisite zinc homeostatic system, and the two-component system CzcS/CzcR plays a key role in zinc detoxification. Although an increasing number of studies have shown the versatility of CzcS/CzcR, its physiological functions are still not fully understood. In this study, transcriptome analysis was performed, which revealed that CzcS/CzcR is silenced in the absence of the zinc signal but modulates global gene expression when the pathogen encounters zinc excess. CzcR was demonstrated to positively regulate the copper tolerance gene ptrA and negatively regulate the pyochelin biosynthesis regulatory gene pchR through direct binding to their promoters. Remarkably, the upregulation of ptrA and downregulation of pchR were shown to rescue the impaired capacity of copper tolerance and prevent pyochelin overproduction, respectively, caused by zinc excess. This study not only advances our understanding of the regulatory spectrum of CzcS/CzcR but also provides new insights into stress adaptation mediated by two-component systems in bacteria to balance the cellular processes that are disturbed by their signals. IMPORTANCE CzcS/CzcR is a two-component system that has been found to modulate zinc homeostasis, quorum sensing, and antibiotic resistance in Pseudomonas aeruginosa. To fully understand the physiological functions of CzcS/CzcR, we performed a comparative transcriptome analysis in this study and discovered that CzcS/CzcR controls global gene expression when it is activated during zinc excess. In particular, we demonstrated that CzcS/CzcR is critical for maintaining copper tolerance and iron homeostasis, which are disrupted during zinc excess, by inducing the expression of the copper tolerance gene ptrA and repressing the pyochelin biosynthesis genes through pchR. This study revealed the global regulatory functions of CzcS/CzcR and described a new and intricate adaptive mechanism in response to zinc excess in P. aeruginosa. The findings of this study have important implications for novel anti-infective interventions by incorporating metal-based drugs.
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Affiliation(s)
- Ting Li
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Huiluo Cao
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Cheng Duan
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Shuzhen Chen
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Zeling Xu
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
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13
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Carlsen ECL, Hjelset S, Gomes T, Igartua A, Sørensen L, Booth AM, Hylland K, Eiler A. Synthetic and natural rubber associated chemicals drive functional and structural changes as well as adaptations to antibiotics in in vitro marine microbiomes. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 273:116134. [PMID: 38387143 DOI: 10.1016/j.ecoenv.2024.116134] [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: 10/13/2023] [Revised: 02/06/2024] [Accepted: 02/18/2024] [Indexed: 02/24/2024]
Abstract
The leaching of additives from plastics and elastomers (rubbers) has raised concerns due to their potential negative impacts on the environment and the development of antibiotic resistance. In this study, we investigated the effects of chemicals extracted from two types of rubber on microbiomes derived from a benthic sea urchin and two pelagic fish species. Additionally, we examined whether bacterial communities preconditioned with rubber-associated chemicals displayed adaptations to antibiotics. At the highest tested concentrations of chemicals, we observed reduced maximum growth rates and yields, prolonged lag phases, and increased alpha diversity. While the effects on alpha and beta diversity were not always conclusive, several bacterial genera were significantly influenced by chemicals from the two rubber sources. Subsequent exposure of sea urchin microbiomes preconditioned with rubber chemicals to the antibiotic ciprofloxacin resulted in decreased maximum growth rates. This indicates a more sensitive microbiome to ciprofloxacin when preconditioned with rubber chemicals. Although no significant interaction effects between rubber chemicals and ciprofloxacin exposure were observed in bacterial alpha and beta diversity, we observed log-fold changes in two bacterial genera in response to ciprofloxacin exposure. These findings highlight the structural and functional alterations in microbiomes originating from various marine species when exposed to rubber-associated chemicals and underscore the potential risks posed to marine life.
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Affiliation(s)
- Eira Catharine Lødrup Carlsen
- Section for Aquatic Biology and Toxicology, Centre for Biogeochemistry in the Anthropocene, Department of Biosciences, University of Oslo, Blindernveien 31, Oslo 0371, Norway
| | - Sverre Hjelset
- Section for Aquatic Biology and Toxicology, Centre for Biogeochemistry in the Anthropocene, Department of Biosciences, University of Oslo, Blindernveien 31, Oslo 0371, Norway; Norwegian Institute for Water Research (NIVA), Section of Ecotoxicology and Risk Assessment, Økernveien 94, Oslo 0579, Norway
| | - Tânia Gomes
- Norwegian Institute for Water Research (NIVA), Section of Ecotoxicology and Risk Assessment, Økernveien 94, Oslo 0579, Norway
| | - Amaia Igartua
- Department of Climate and Environment, SINTEF Ocean, SINTEF Sealab, Brattørkaia 17C, Trondheim 7010, Norway
| | - Lisbet Sørensen
- Department of Climate and Environment, SINTEF Ocean, SINTEF Sealab, Brattørkaia 17C, Trondheim 7010, Norway
| | - Andy M Booth
- Department of Climate and Environment, SINTEF Ocean, SINTEF Sealab, Brattørkaia 17C, Trondheim 7010, Norway
| | - Ketil Hylland
- Section for Aquatic Biology and Toxicology, Department of Biosciences, University of Oslo, Blindernveien 31, Oslo 0371, Norway
| | - Alexander Eiler
- Section for Aquatic Biology and Toxicology, Centre for Biogeochemistry in the Anthropocene, Department of Biosciences, University of Oslo, Blindernveien 31, Oslo 0371, Norway.
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14
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Ramnarine SDB, Ali O, Jayaraman J, Ramsubhag A. Early transcriptional changes of heavy metal resistance and multiple efflux genes in Xanthomonas campestris pv. campestris under copper and heavy metal ion stress. BMC Microbiol 2024; 24:81. [PMID: 38461228 PMCID: PMC10924375 DOI: 10.1186/s12866-024-03206-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 01/28/2024] [Indexed: 03/11/2024] Open
Abstract
BACKGROUND Copper-induced gene expression in Xanthomonas campestris pv. campestris (Xcc) is typically evaluated using targeted approaches involving qPCR. The global response to copper stress in Xcc and resistance to metal induced damage is not well understood. However, homologs of heavy metal efflux genes from the related Stenotrophomonas genus are found in Xanthomonas which suggests that metal related efflux may also be present. METHODS AND RESULTS Gene expression in Xcc strain BrA1 exposed to 0.8 mM CuSO4.5H2O for 15 minutes was captured using RNA-seq analysis. Changes in expression was noted for genes related to general stress responses and oxidoreductases, biofilm formation, protein folding chaperones, heat-shock proteins, membrane lipid profile, multiple drug and efflux (MDR) transporters, and DNA repair were documented. At this timepoint only the cohL (copper homeostasis/tolerance) gene was upregulated as well as a chromosomal czcCBA efflux operon. An additional screen up to 4 hrs using qPCR was conducted using a wider range of heavy metals. Target genes included a cop-containing heavy metal resistance island and putative metal efflux genes. Several efflux pumps, including a copper resistance associated homolog from S. maltophilia, were upregulated under toxic copper stress. However, these pumps were also upregulated in response to other toxic heavy metals. Additionally, the temporal expression of the coh and cop operons was also observed, demonstrating co-expression of tolerance responses and later activation of part of the cop operon. CONCLUSIONS Overall, initial transcriptional responses focused on combating oxidative stress, mitigating protein damage and potentially increasing resistance to heavy metals and other biocides. A putative copper responsive efflux gene and others which might play a role in broader heavy metal resistance were also identified. Furthermore, the expression patterns of the cop operon in conjunction with other copper responsive genes allowed for a better understanding of the fate of copper ions in Xanthomonas. This work provides useful evidence for further evaluating MDR and other efflux pumps in metal-specific homeostasis and tolerance phenotypes in the Xanthomonas genus. Furthermore, non-canonical copper tolerance and resistance efflux pumps were potentially identified. These findings have implications for interpreting MIC differences among strains with homologous copLAB resistance genes, understanding survival under copper stress, and resistance in disease management.
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Affiliation(s)
- Stephen D B Ramnarine
- Department of Life Sciences, Faculty of Science and Technology, The University of The West Indies, St. Augustine campus, St. Augustine, Trinidad and Tobago, W. I
| | - Omar Ali
- Department of Life Sciences, Faculty of Science and Technology, The University of The West Indies, St. Augustine campus, St. Augustine, Trinidad and Tobago, W. I
| | - Jayaraj Jayaraman
- Department of Life Sciences, Faculty of Science and Technology, The University of The West Indies, St. Augustine campus, St. Augustine, Trinidad and Tobago, W. I
| | - Adesh Ramsubhag
- Department of Life Sciences, Faculty of Science and Technology, The University of The West Indies, St. Augustine campus, St. Augustine, Trinidad and Tobago, W. I.
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15
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Chatterjee D, Panda AP, Daya Manasi AR, Ghosh AS. P-type ATPase zinc transporter Rv3270 of Mycobacterium tuberculosis enhances multi-drug efflux activity. MICROBIOLOGY (READING, ENGLAND) 2024; 170:001441. [PMID: 38373028 PMCID: PMC10924464 DOI: 10.1099/mic.0.001441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 02/08/2024] [Indexed: 02/20/2024]
Abstract
Metal homeostasis is maintained by the uptake, storage and efflux of metal ions that are necessary for the survival of the bacterium. Homeostasis is mostly regulated by a group of transporters categorized as ABC transporters and P-type ATPases. On the other hand, efflux pumps often play a role in drug-metal cross-resistance. Here, with the help of antibiotic sensitivity, antibiotic/dye accumulation and semi-quantitative biofilm formation assessments we report the ability of Rv3270, a P-type ATPase known for its role in combating Mn2+ and Zn2+ metal ion toxicity in Mycobacterium tuberculosis, in influencing the extrusion of multiple structurally unrelated drugs and enhancing the biofilm formation of Escherichia coli and Mycobacterium smegmatis. Overexpression of Rv3270 increased the tolerance of host cells to norfloxacin, ofloxacin, sparfloxacin, ampicillin, oxacillin, amikacin and isoniazid. A significantly lower accumulation of norfloxacin, ethidium bromide, bocillin FL and levofloxacin in cells harbouring Rv3270 as compared to host cells indicated its role in enhancing efflux activity. Although over-expression of Rv3270 did not alter the susceptibility levels of levofloxacin, rifampicin and apramycin, the presence of a sub-inhibitory concentration of Zn2+ resulted in low-level tolerance towards these drugs. Of note, the expression of Rv3270 enhanced the biofilm-forming ability of the host cells strengthening its role in antimicrobial resistance. Therefore, the study indicated that the over-expression of Rv3270 enhances the drug efflux activity of the micro-organism where zinc might facilitate drug-metal cross-resistance for some antibiotics.
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Affiliation(s)
- Debasmita Chatterjee
- Department of Bioscience and Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal 721302, India
| | - Aditya Prasad Panda
- Department of Bioscience and Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal 721302, India
| | - A. R. Daya Manasi
- Department of Bioscience and Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal 721302, India
| | - Anindya S. Ghosh
- Department of Bioscience and Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal 721302, India
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16
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Olaya‐Abril A, Biełło K, Rodríguez‐Caballero G, Cabello P, Sáez LP, Moreno‐Vivián C, Luque‐Almagro VM, Roldán MD. Bacterial tolerance and detoxification of cyanide, arsenic and heavy metals: Holistic approaches applied to bioremediation of industrial complex wastes. Microb Biotechnol 2024; 17:e14399. [PMID: 38206076 PMCID: PMC10832572 DOI: 10.1111/1751-7915.14399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 12/19/2023] [Accepted: 12/22/2023] [Indexed: 01/12/2024] Open
Abstract
Cyanide is a highly toxic compound that is found in wastewaters generated from different industrial activities, such as mining or jewellery. These residues usually contain high concentrations of other toxic pollutants like arsenic and heavy metals that may form different complexes with cyanide. To develop bioremediation strategies, it is necessary to know the metabolic processes involved in the tolerance and detoxification of these pollutants, but most of the current studies are focused on the characterization of the microbial responses to each one of these environmental hazards individually, and the effect of co-contaminated wastes on microbial metabolism has been hardly addressed. This work summarizes the main strategies developed by bacteria to alleviate the effects of cyanide, arsenic and heavy metals, analysing interactions among these toxic chemicals. Additionally, it is discussed the role of systems biology and synthetic biology as tools for the development of bioremediation strategies of complex industrial wastes and co-contaminated sites, emphasizing the importance and progress derived from meta-omic studies.
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Affiliation(s)
- Alfonso Olaya‐Abril
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa, Campus de RabanalesUniversidad de CórdobaCórdobaSpain
| | - Karolina Biełło
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa, Campus de RabanalesUniversidad de CórdobaCórdobaSpain
| | - Gema Rodríguez‐Caballero
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa, Campus de RabanalesUniversidad de CórdobaCórdobaSpain
| | - Purificación Cabello
- Departamento de Botánica, Ecología y Fisiología Vegetal, Edificio Celestino Mutis, Campus de RabanalesUniversidad de CórdobaCórdobaSpain
| | - Lara P. Sáez
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa, Campus de RabanalesUniversidad de CórdobaCórdobaSpain
| | - Conrado Moreno‐Vivián
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa, Campus de RabanalesUniversidad de CórdobaCórdobaSpain
| | - Víctor Manuel Luque‐Almagro
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa, Campus de RabanalesUniversidad de CórdobaCórdobaSpain
| | - María Dolores Roldán
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa, Campus de RabanalesUniversidad de CórdobaCórdobaSpain
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17
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Chukwu KB, Abafe OA, Amoako DG, Essack SY, Abia ALK. Environmental concentrations of antibiotics, biocides, and heavy metals fail to induce phenotypic antimicrobial resistance in Escherichia coli. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 899:165721. [PMID: 37482346 DOI: 10.1016/j.scitotenv.2023.165721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 07/19/2023] [Accepted: 07/20/2023] [Indexed: 07/25/2023]
Abstract
Most anthropogenically affected environments contain mixtures of pollutants from different sources. The impact of these pollutants is usually the combined effect of the individual polluting constituents. However, how these stressors contribute to the development of antimicrobial resistance in environmental microorganisms is poorly understood. Thus, a 30-day exposure experiment to environmental and sub-inhibitory concentrations of oxytetracycline, amoxicillin, zinc, copper, BAC (benzalkonium chloride) 10 and DADMAC (diallyldimethylammonium chloride) 12, was conducted using fully susceptible E. coli ATCC 25922 to ascertain any development of phenotypic or genotypic resistance. Furthermore, wild-type isolates were collected from the same aquatic environment as the stressors, analysed for phenotypic resistance using the disk diffusion method and genotypically through whole genome sequencing. Exposure to the various concentrations and combinations of the stressors did not trigger phenotypic resistance in the experimental bacteria. Furthermore, genotypic analysis of the WGS on the exposed isolates only found the macrolide resistance mdf(A) gene (also present in the control strain) and the disinfectant resistance gene sitABCD. With further analysis for single nucleotide variants (SNV), mutations were detected for 19 genes that encoded for oxidative stress, DNA repair, membrane proteins efflux systems, growth and persister formations except for the robA, a transcription protein subset of the ArcC/XylS family of proteins, which confer multidrug resistance in E. coli. This indicates that exposure to sub-inhibitory concentrations of antibiotics, heavy metals and biocide residues in the aquatic environmental concentrations of the stressors identified in the current study could not induce phenotypic or genotypic resistance but encoded for genes responsible for the development of persistence and tolerance in bacteria, which could be a precursor to the development of resistance in environmental bacteria.
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Affiliation(s)
- Kelechi B Chukwu
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Ovokeroye A Abafe
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa; School of Geography, Earth and Environmental Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom; Residue Laboratory, Agricultural Research Council - Onderstepoort Veterinary Research Campus, Onderstepoort 0110, South Africa
| | - Daniel G Amoako
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa; Department of Integrative Biology and Bioinformatics, University of Guelph, Ontario N1G 2W1, Canada
| | - Sabiha Y Essack
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.
| | - Akebe L K Abia
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa; Environmental Research Foundation, Westville 3630, Kwazulu-Natal, South Africa.
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Zhang SP, Ye YP, Hou J, Ye ZR, Wang ZS, Yu XQ, Guo DD, Wang Y, He YX. Antitoxin MqsA decreases antibiotic susceptibility through the global regulator AgtR in Pseudomonas fluorescens. Antimicrob Agents Chemother 2023; 67:e0081223. [PMID: 37877694 PMCID: PMC10649091 DOI: 10.1128/aac.00812-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 08/31/2023] [Indexed: 10/26/2023] Open
Abstract
Type II toxin-antitoxin systems are highly prevalent in bacterial genomes and play crucial roles in the general stress response. Previously, we demonstrated that the type II antitoxin PfMqsA regulates biofilm formation through the global regulator AgtR in Pseudomonas fluorescens. Here, we found that both the C-terminal DNA-binding domain of PfMqsA and AgtR are involved in bacterial antibiotic susceptibility. Electrophoretic mobility shift assay (EMSA) analyses revealed that AgtR, rather than PfMqsA, binds to the intergenic region of emhABC-emhR, in which emhABC encodes an resistance-nodulation-cell division efflux pump and emhR encodes a repressor. Through quantitative real-time reverse-transcription PCR and EMSA analysis, we showed that AgtR directly activates the expression of the emhR by binding to the DNA motif [5´-CTAAGAAATATACTTAC-3´], leading to repression of the emhABC. Furthermore, we demonstrated that PfMqsA modulates the expression of EmhABC and EmhR. These findings enhance our understanding of the mechanism by which antitoxin PfMqsA contributes to antibiotic susceptibility.
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Affiliation(s)
- Si-Ping Zhang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, China
| | - Yi-Ping Ye
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, China
| | - Jun Hou
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, China
| | - Zi-Rui Ye
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, China
| | - Zhi-Song Wang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, China
| | - Xiao-Quan Yu
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, China
| | - Ding-Ding Guo
- School of Pharmacy, Lanzhou University, Lanzhou, Gansu, China
| | - Yong Wang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, China
| | - Yong-Xing He
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, China
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Petit M, Tessier J, Sahli C, Schmitzer AR. Confronting the Threat: Designing Highly Effective bis-Benzimidazolium Agents to Overcome Biofilm Persistence and Antimicrobial Resistance. ACS Infect Dis 2023; 9:2202-2214. [PMID: 37882623 DOI: 10.1021/acsinfecdis.3c00289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2023]
Abstract
The objective of this study is to take the initial steps toward developing novel antibiotics to counteract the escalating problem of antimicrobial and bacterial persistence, particularly in relation to biofilms. Our approach involves emulating the structural characteristics of cationic antimicrobial peptides. To circumvent resistance development, we have designed a library of bis-benzimidazolium salts that selectively target the microbial membranes in a nonspecific manner. To explore their structure-activity relationship, we conducted experiments using these compounds on various pathogens known for their resistance to conventional antibiotics, including Gram-positive methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant Enterococcus faecium (VRE), and Gram-negative Escherichia coli (E. coli). Notably, two bis-benzimidazolium salts exhibited robust antimicrobial activity while maintaining a high level of selectivity compared with mammalian cells. Our investigations revealed significant antibiofilm activity, as these compounds rapidly acted against established biofilms. In addition, bis-benzimidazolium compounds exhibited consistent results in resistance development and cross-resistance studies. Consequently, amphiphilic bis-benzimidazolium salts hold promise as potential candidates to combat resistance-associated infections.
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Affiliation(s)
- Maude Petit
- Département de Chimie, Faculté des Arts et des Sciences, Université de Montréal, Campus MIL, 1375, Ave. Thérèse Lavoie-Roux, Montréal, Québec H2 V 0B3, Canada
| | - Jérémie Tessier
- Département de Chimie, Faculté des Arts et des Sciences, Université de Montréal, Campus MIL, 1375, Ave. Thérèse Lavoie-Roux, Montréal, Québec H2 V 0B3, Canada
- Collège Bois-de-Boulogne, 10555 Ave. de Bois-de-Boulogne, Montréal H4N 1L4, Canada
| | - Célia Sahli
- Département de Chimie, Faculté des Arts et des Sciences, Université de Montréal, Campus MIL, 1375, Ave. Thérèse Lavoie-Roux, Montréal, Québec H2 V 0B3, Canada
- CNRS-UMR 7086, Interfaces, Traitements, Organisation et Dynamique des Systèmes (ITODYS), Université Paris Cité, Paris 75013 , France
| | - Andreea R Schmitzer
- Département de Chimie, Faculté des Arts et des Sciences, Université de Montréal, Campus MIL, 1375, Ave. Thérèse Lavoie-Roux, Montréal, Québec H2 V 0B3, Canada
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20
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Chen S, Cao H, Xu Z, Huang J, Liu Z, Li T, Duan C, Wu W, Wen Y, Zhang LH, Xu Z. A type I-F CRISPRi system unveils the novel role of CzcR in modulating multidrug resistance of Pseudomonas aeruginosa. Microbiol Spectr 2023; 11:e0112323. [PMID: 37646520 PMCID: PMC10581170 DOI: 10.1128/spectrum.01123-23] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 07/16/2023] [Indexed: 09/01/2023] Open
Abstract
Pseudomonas aeruginosa has abundant signaling systems that exquisitely control its antibiotic resistance in response to different environmental cues. Understanding the regulation of antibiotic resistance will provide important implications for precise antimicrobial interventions. However, efficient genetic tools for functional gene characterizations are sometimes not available, particularly, in clinically isolated strains. Here, we established a type I-F CRISPRi (CSYi) system for programmable gene silencing. By incorporating anti-CRISPR proteins, this system was even applicable to bacterial hosts encoding a native type I-F CRISPR-Cas system. With the newly developed gene-silencing system, we revealed that the response regulator CzcR from the zinc (Zn2+)-responsive two-component system CzcS/CzcR is a repressor of efflux pumps MexAB-OprM and MexGHI-OpmD, which inhibits the expression of both operons by directly interacting with their promoters. Repression of MexAB-OprM consequently increases the susceptibility of P. aeruginosa to multiple antibiotics such as levofloxacin and amikacin. Together, this study provided a simple approach to study gene functions, which enabled us to unveil the novel role of CzcR in modulating efflux pump genes and multidrug resistance in P. aeruginosa. IMPORTANCE P. aeruginosa is a ubiquitous opportunistic pathogen frequently causing chronic infections. In addition to being an important model organism for antibiotic-resistant research, this species is also important for understanding and exploiting CRISPR-Cas systems. In this study, we established a gene-silencing system based on the most abundant type I-F CRISPR-Cas system in this species, which can be readily employed to achieve targeted gene repression in multiple bacterial species. Using this gene-silencing system, the physiological role of Zn2+ and its responsive regulator CzcR in modulating multidrug resistance was unveiled with great convenience. This study not only displayed a new framework to expand the abundant CRISPR-Cas and anti-CRISPR systems for functional gene characterizations but also provided new insights into the regulation of multidrug resistance in P. aeruginosa and important clues for precise anti-pseudomonal therapies.
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Affiliation(s)
- Shuzhen Chen
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Huiluo Cao
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Zirui Xu
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Jiahui Huang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Zhiqing Liu
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Ting Li
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Cheng Duan
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Weiyan Wu
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Yongqi Wen
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Lian-Hui Zhang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
| | - Zeling Xu
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
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21
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Paredes A, Iheacho C, Smith AT. Metal Messengers: Communication in the Bacterial World through Transition-Metal-Sensing Two-Component Systems. Biochemistry 2023; 62:2339-2357. [PMID: 37539997 PMCID: PMC10530140 DOI: 10.1021/acs.biochem.3c00296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Abstract
Bacteria survive in highly dynamic and complex environments due, in part, to the presence of systems that allow the rapid control of gene expression in the presence of changing environmental stimuli. The crosstalk between intra- and extracellular bacterial environments is often facilitated by two-component signal transduction systems that are typically composed of a transmembrane histidine kinase and a cytosolic response regulator. Sensor histidine kinases and response regulators work in tandem with their modular domains containing highly conserved structural features to control a diverse array of genes that respond to changing environments. Bacterial two-component systems are widespread and play crucial roles in many important processes, such as motility, virulence, chemotaxis, and even transition metal homeostasis. Transition metals are essential for normal prokaryotic physiological processes, and the presence of these metal ions may also influence pathogenic virulence if their levels are appropriately controlled. To do so, bacteria use transition-metal-sensing two-component systems that bind and respond to rapid fluctuations in extracytosolic concentrations of transition metals. This perspective summarizes the structural and metal-binding features of bacterial transition-metal-sensing two-component systems and places a special emphasis on understanding how these systems are used by pathogens to establish infection in host cells and how these systems may be targeted for future therapeutic developments.
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Affiliation(s)
- Alexander Paredes
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland 21250, United States
| | - Chioma Iheacho
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland 21250, United States
| | - Aaron T Smith
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland 21250, United States
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22
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Lear L, Hesse E, Newsome L, Gaze W, Buckling A, Vos M. The effect of metal remediation on the virulence and antimicrobial resistance of the opportunistic pathogen Pseudomonas aeruginosa. Evol Appl 2023; 16:1377-1389. [PMID: 37492145 PMCID: PMC10363854 DOI: 10.1111/eva.13576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 05/18/2023] [Accepted: 06/19/2023] [Indexed: 07/27/2023] Open
Abstract
Anthropogenic metal pollution can result in co-selection for antibiotic resistance and potentially select for increased virulence in bacterial pathogens. Metal-polluted environments can select for the increased production of siderophore molecules to detoxify non-ferrous metals. However, these same molecules also aid the uptake of ferric iron, a limiting factor for within-host pathogen growth, and are consequently a virulence factor. Anthropogenic methods to remediate environmental metal contamination commonly involve amendment with lime-containing materials. However, whether this reduces in situ co-selection for antibiotic resistance and siderophore-mediated virulence remains unknown. Here, using microcosms containing non-sterile metal-contaminated river water and sediment, we test whether liming reduces co-selection for these pathogenicity traits in the opportunistic pathogen Pseudomonas aeruginosa. To account for the effect of environmental structure, which is known to impact siderophore production, microcosms were incubated under either static or shaking conditions. Evolved P. aeruginosa populations had greater fitness in the presence of toxic concentrations of copper than the ancestral strain and showed increased resistance to the clinically relevant antibiotics apramycin, cefotaxime and trimethoprim, regardless of lime addition or environmental structure. Although we found virulence to be significantly associated with siderophore production, neither virulence nor siderophore production significantly differed between the four treatments. Furthermore, liming did not mitigate metal-imposed selection for antibiotic resistance or virulence in P. aeruginosa. Consequently, metal-contaminated environments may select for antibiotic resistance and virulence traits even when treated with lime.
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Affiliation(s)
- Luke Lear
- College of Life and Environmental ScienceUniversity of ExeterPenrynUK
| | - Elze Hesse
- College of Life and Environmental ScienceUniversity of ExeterPenrynUK
| | - Laura Newsome
- College of Engineering, Mathematics and Physical SciencesUniversity of ExeterPenrynUK
| | - William Gaze
- European Centre for Environment and Human HealthUniversity of Exeter Medical SchoolPenrynUK
| | - Angus Buckling
- College of Life and Environmental ScienceUniversity of ExeterPenrynUK
| | - Michiel Vos
- European Centre for Environment and Human HealthUniversity of Exeter Medical SchoolPenrynUK
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23
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Yamasaki S, Zwama M, Yoneda T, Hayashi-Nishino M, Nishino K. Drug resistance and physiological roles of RND multidrug efflux pumps in Salmonella enterica, Escherichia coli and Pseudomonas aeruginosa. MICROBIOLOGY (READING, ENGLAND) 2023; 169:001322. [PMID: 37319001 PMCID: PMC10333786 DOI: 10.1099/mic.0.001322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 03/18/2023] [Indexed: 06/17/2023]
Abstract
Drug efflux pumps transport antimicrobial agents out of bacteria, thereby reducing the intracellular antimicrobial concentration, which is associated with intrinsic and acquired bacterial resistance to these antimicrobials. As genome analysis has advanced, many drug efflux pump genes have been detected in the genomes of bacterial species. In addition to drug resistance, these pumps are involved in various essential physiological functions, such as bacterial adaptation to hostile environments, toxin and metabolite efflux, biofilm formation and quorum sensing. In Gram-negative bacteria, efflux pumps in the resistance–nodulation–division (RND) superfamily play a clinically important role. In this review, we focus on Gram-negative bacteria, including Salmonella enterica , Escherichia coli and Pseudomonas aeruginosa , and discuss the role of RND efflux pumps in drug resistance and physiological functions.
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Affiliation(s)
- Seiji Yamasaki
- SANKEN (The Institute of Scientific and Industrial Research), Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
- Institute for Advanced Co-Creation Studies, Osaka University, 1-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Martijn Zwama
- SANKEN (The Institute of Scientific and Industrial Research), Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Tomohiro Yoneda
- SANKEN (The Institute of Scientific and Industrial Research), Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Mitsuko Hayashi-Nishino
- SANKEN (The Institute of Scientific and Industrial Research), Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Kunihiko Nishino
- SANKEN (The Institute of Scientific and Industrial Research), Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
- Center for Infectious Disease Education and Research, 2-8 Yamadaoka, Osaka University, Suita, Osaka 565-0871, Japan
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24
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De Gaetano GV, Lentini G, Famà A, Coppolino F, Beninati C. Antimicrobial Resistance: Two-Component Regulatory Systems and Multidrug Efflux Pumps. Antibiotics (Basel) 2023; 12:965. [PMID: 37370284 DOI: 10.3390/antibiotics12060965] [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: 05/05/2023] [Revised: 05/22/2023] [Accepted: 05/24/2023] [Indexed: 06/29/2023] Open
Abstract
The number of multidrug-resistant bacteria is rapidly spreading worldwide. Among the various mechanisms determining resistance to antimicrobial agents, multidrug efflux pumps play a noteworthy role because they export extraneous and noxious substrates from the inside to the outside environment of the bacterial cell contributing to multidrug resistance (MDR) and, consequently, to the failure of anti-infective therapies. The expression of multidrug efflux pumps can be under the control of transcriptional regulators and two-component systems (TCS). TCS are a major mechanism by which microorganisms sense and reply to external and/or intramembrane stimuli by coordinating the expression of genes involved not only in pathogenic pathways but also in antibiotic resistance. In this review, we describe the influence of TCS on multidrug efflux pump expression and activity in some Gram-negative and Gram-positive bacteria. Taking into account the strict correlation between TCS and multidrug efflux pumps, the development of drugs targeting TCS, alone or together with already discovered efflux pump inhibitors, may represent a beneficial strategy to contribute to the fight against growing antibiotic resistance.
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Affiliation(s)
| | - Germana Lentini
- Department of Human Pathology, University of Messina, 98124 Messina, Italy
| | - Agata Famà
- Department of Human Pathology, University of Messina, 98124 Messina, Italy
| | - Francesco Coppolino
- Department of Biomedical, Dental and Imaging Sciences, University of Messina, 98124 Messina, Italy
| | - Concetta Beninati
- Department of Human Pathology, University of Messina, 98124 Messina, Italy
- Scylla Biotech Srl, 98124 Messina, Italy
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25
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Chettri U, Nongkhlaw M, Joshi SR. Molecular Evidence for Occurrence of Heavy Metal and Antibiotic Resistance Genes Among Predominant Metal Tolerant Pseudomonas sp. and Serratia sp. Prevalent in the Teesta River. Curr Microbiol 2023; 80:226. [PMID: 37227565 DOI: 10.1007/s00284-023-03334-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 05/15/2023] [Indexed: 05/26/2023]
Abstract
Riverine ecosystems polluted by pharmaceutical and metal industries are potential incubators of bacteria with dual resistance to heavy metals and antibiotics. The processes of co-resistance and cross resistance that empower bacteria to negotiate these challenges, strongly endorse dangers of antibiotic resistance generated by metal stress. Therefore, investigation into the molecular evidence of heavy metal and antibiotic resistance genes was the prime focus of this study. The selected Pseudomonas and Serratia species isolates evinced by their minimum inhibitory concentration and multiple antibiotic resistance (MAR) index showed significant heavy metal tolerance and multi-antibiotic resistance capability, respectively. Consequently, isolates with higher tolerance for the most toxic metal cadmium evinced high MAR index value (0.53 for Pseudomonas sp., and 0.46 for Serratia sp.) in the present investigation. Metal tolerance genes belonging to PIB-type and resistance nodulation division family of proteins were evident in these isolates. The antibiotic resistance genes like mexB, mexF and mexY occurred in Pseudomonas isolates while sdeB genes were present in Serratia isolates. Phylogenetic incongruency and GC composition analysis of PIB-type genes suggested that some of these isolates had acquired resistance through horizontal gene transfer (HGT). Therefore, the Teesta River has become a reservoir for resistant gene exchange or movement via selective pressure exerted by metals and antibiotics. The resultant adaptive mechanisms and altered phenotypes are potential tools to track metal tolerant strains with clinically significant antibiotic resistance traits.
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Affiliation(s)
- Upashna Chettri
- Department of Biotechnology and Bioinformatics, North-Eastern Hill University, Shillong, Meghalaya, India
| | - Macmillan Nongkhlaw
- Department of Biotechnology and Bioinformatics, North-Eastern Hill University, Shillong, Meghalaya, India
| | - Santa R Joshi
- Department of Biotechnology and Bioinformatics, North-Eastern Hill University, Shillong, Meghalaya, India.
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26
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Zhang Q, Zhou H, Jiang P, Xiao X. Metal-based nanomaterials as antimicrobial agents: A novel driveway to accelerate the aggravation of antibiotic resistance. JOURNAL OF HAZARDOUS MATERIALS 2023; 455:131658. [PMID: 37209560 DOI: 10.1016/j.jhazmat.2023.131658] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 05/05/2023] [Accepted: 05/16/2023] [Indexed: 05/22/2023]
Abstract
The consequences of antibiotic tolerance directly affect human health and result in socioeconomic loss. Nanomaterials as antimicrobial agents are considered a promising alternative to antibiotics and have been blended with various medical applications. However, with increasing evidence that metal-based nanomaterials may induce antibiotic tolerance, there is an urgent need to scrutinize how nanomaterial-induced microbial adaption affects the evolution and spread of antibiotic tolerance. Accordingly, within this investigation, we summarized the principal factors influencing the resistance development exposed to metal-based nanomaterials, including physicochemical properties, exposure scenario, as well as bacterial response. Furthermore, the mechanisms of metal-based nanomaterial-induced antibiotic resistance development were comprehensively elucidated from acquired resistance by horizontal transfer of antibiotic resistance genes (ARGs), intrinsic resistance by genetic mutation or upregulated resistance-related gene expression, and adaptive resistance by global evolution. Overall, our review raises concerns about the safety of nanomaterials as antimicrobial agents, which will facilitate assistance in the safe development of antibiotic-free antibacterial strategies.
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Affiliation(s)
- Qiurong Zhang
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei 230601, China
| | - Huixian Zhou
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei 230601, China
| | - Ping Jiang
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei 230601, China
| | - Xiang Xiao
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei 230601, China; School of Resources and Environmental Engineering, Anhui University, Hefei 230601, China.
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27
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Markowicz A, Borymski S, Adamek A, Sułowicz S. The influence of ZnO nanoparticles on horizontal transfer of resistance genes in lab and soil conditions. ENVIRONMENTAL RESEARCH 2023; 223:115420. [PMID: 36764431 DOI: 10.1016/j.envres.2023.115420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 11/14/2022] [Accepted: 02/01/2023] [Indexed: 06/18/2023]
Abstract
Antibiotic resistance is a severe problem that threatens the achievements of modern medicine. Metallic nanoparticles may promote the horizontal transfer of resistance genes due to their toxicity to bacterial cells and metal-induced co-selection mechanisms. In this study, we investigated the toxicity of ZnO nanoparticles to E. coli DH5α laboratory strain and the abundance of soil microbial community. Moreover, the influence of ZnO nanoparticles on resistance gene transfer in laboratory and soil conditions was evaluated. ZnO nanoparticles at concentrations up to 10 mg L-1 reduced the survival of E. coli cells by 14.6% and increased the transformation frequency by almost 1.8 fold. In soil, ZnO nanoparticles at a concentration of 1000 mg kg-1 affected the total abundance of bacteria, causing a decrease in the 16S rRNA gene copy number. We did not detect the presence of 11 target antibiotic resistance genes (sul1, sul2, imp2, imp5, blaCTX-M, ermB, mefA, strB, aadA1, tetA1, tetB), which confer resistance to five classes of antibiotics in soil treated with ZnO nanoparticles. No elevated conjugation frequency was observed in soil microbial communities treated with ZnO nanoparticles. However, the increase in czcA gene copies indicates the spread of genetic elements harbouring metal resistance. The data shows that metallic nanoparticles promote the spread of antibiotic and metal resistance genes. The broad implication of the present research is that the inevitable nanoparticles environmental pollution may lead to the further dissemination of antibiotic resistance and profoundly influence public health.
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Affiliation(s)
- Anna Markowicz
- University of Silesia, Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, Jagiellonska 28, 40-032, Katowice, Poland.
| | - Sławomir Borymski
- University of Silesia, Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, Jagiellonska 28, 40-032, Katowice, Poland
| | - Anna Adamek
- University of Silesia, Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, Jagiellonska 28, 40-032, Katowice, Poland
| | - Sławomir Sułowicz
- University of Silesia, Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, Jagiellonska 28, 40-032, Katowice, Poland
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28
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Yan S, Zhang Z, Wang J, Xia Y, Chen S, Xie S. River sediment microbial community composition and function impacted by thallium spill. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 880:163101. [PMID: 36996985 DOI: 10.1016/j.scitotenv.2023.163101] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/20/2023] [Accepted: 03/23/2023] [Indexed: 04/14/2023]
Abstract
Thallium (Tl) is widely used in various industries, which increases the risk of leakage into the environment. Since Tl is highly toxic, it can do a great harm to human health and ecosystem. In order to explore the response of freshwater sediment microorganisms to sudden Tl spill, metagenomic technique was used to elucidate the changes of microbial community composition and functional genes in river sediments. Tl pollution could have profound impacts on microbial community composition and function. Proteobacteria remained the dominance in contaminated szediments, indicating that it had a strong resistance to Tl contamination, and Cyanobacteria also showed a certain resistance. Tl pollution also had a certain screening effect on resistance genes and affected the abundance of resistance genes. Metal resistance genes (MRGs) and antibiotic resistance genes (ARGs) were enriched at the site near the spill site, where Tl concentration was relatively low among polluted sites. When Tl concentration was higher, the screening effect was not obvious and the resistance genes even became lower. Moreover, there was a significant correlation between MRGs and ARGs. In addition, co-occurrence network analysis showed that Sphingopyxis had the most links with resistance genes, indicating that it was the biggest potential host of resistance genes. This study provided new insight towards the shifts in the composition and function of microbial communities after sudden serious Tl contamination.
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Affiliation(s)
- Shuang Yan
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Zhengke Zhang
- South China Institute of Environmental Sciences (SCIES), Ministry of Ecology and Environment (MEE), Guangzhou 510655, China
| | - Ji Wang
- South China Institute of Environmental Sciences (SCIES), Ministry of Ecology and Environment (MEE), Guangzhou 510655, China
| | - Yulin Xia
- South China Institute of Environmental Sciences (SCIES), Ministry of Ecology and Environment (MEE), Guangzhou 510655, China
| | - Sili Chen
- South China Institute of Environmental Sciences (SCIES), Ministry of Ecology and Environment (MEE), Guangzhou 510655, China.
| | - Shuguang Xie
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
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29
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Nguyen THT, Nguyen HD, Le MH, Nguyen TTH, Nguyen TD, Nguyen DL, Nguyen QH, Nguyen TKO, Michalet S, Dijoux-Franca MG, Pham HN. Efflux Pump Inhibitors in Controlling Antibiotic Resistance: Outlook under a Heavy Metal Contamination Context. Molecules 2023; 28:molecules28072912. [PMID: 37049674 PMCID: PMC10095785 DOI: 10.3390/molecules28072912] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 03/10/2023] [Accepted: 03/18/2023] [Indexed: 04/14/2023] Open
Abstract
Multi-drug resistance to antibiotics represents a growing challenge in treating infectious diseases. Outside the hospital, bacteria with the multi-drug resistance (MDR) phenotype have an increased prevalence in anthropized environments, thus implying that chemical stresses, such as metals, hydrocarbons, organic compounds, etc., are the source of such resistance. There is a developing hypothesis regarding the role of metal contamination in terrestrial and aquatic environments as a selective agent in the proliferation of antibiotic resistance caused by the co-selection of antibiotic and metal resistance genes carried by transmissible plasmids and/or associated with transposons. Efflux pumps are also known to be involved in either antibiotic or metal resistance. In order to deal with these situations, microorganisms use an effective strategy that includes a range of expressions based on biochemical and genetic mechanisms. The data from numerous studies suggest that heavy metal contamination could affect the dissemination of antibiotic-resistant genes. Environmental pollution caused by anthropogenic activities could lead to mutagenesis based on the synergy between antibiotic efficacy and the acquired resistance mechanism under stressors. Moreover, the acquired resistance includes plasmid-encoded specific efflux pumps. Soil microbiomes have been reported as reservoirs of resistance genes that are available for exchange with pathogenic bacteria. Importantly, metal-contaminated soil is a selective agent that proliferates antibiotic resistance through efflux pumps. Thus, the use of multi-drug efflux pump inhibitors (EPIs) originating from natural plants or synthetic compounds is a promising approach for restoring the efficacy of existing antibiotics, even though they face a lot of challenges.
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Affiliation(s)
- Thi Huyen Thu Nguyen
- Department of Life Sciences, University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi 10072, Vietnam
- Saint Paul Hospital, 12 Chu Van An, Hanoi 11114, Vietnam
| | - Hai Dang Nguyen
- Department of Academic Affairs, University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi 10072, Vietnam
| | - Mai Huong Le
- Institute of Natural Products Chemistry, Vietnam Academy of Science and Technology, 1H Building, 18 Hoang Quoc Viet, Cau Giay, Hanoi 10072, Vietnam
| | - Thi Thu Hien Nguyen
- Institute of Biological and Food Technology, Hanoi Open University, 101B Nguyen Hien, Hanoi 11615, Vietnam
| | - Thi Dua Nguyen
- Saint Paul Hospital, 12 Chu Van An, Hanoi 11114, Vietnam
| | | | - Quang Huy Nguyen
- Department of Life Sciences, University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi 10072, Vietnam
| | - Thi Kieu Oanh Nguyen
- Department of Life Sciences, University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi 10072, Vietnam
| | - Serge Michalet
- UMR 5557, Ecologie Microbienne, CNRS, INRAe, VetagroSup, UCBL, Université de Lyon, 43 Boulevard du 11 Novembre, F-69622 Villeurbanne, France
| | - Marie-Geneviève Dijoux-Franca
- UMR 5557, Ecologie Microbienne, CNRS, INRAe, VetagroSup, UCBL, Université de Lyon, 43 Boulevard du 11 Novembre, F-69622 Villeurbanne, France
| | - Hoang Nam Pham
- Department of Life Sciences, University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi 10072, Vietnam
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30
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Goswami A, Adkins-Jablonsky SJ, Barreto Filho MM, Shilling MD, Dawson A, Heiser S, O’Connor A, Walker M, Roberts Q, Morris JJ. Heavy Metal Pollution Impacts Soil Bacterial Community Structure and Antimicrobial Resistance at the Birmingham 35th Avenue Superfund Site. Microbiol Spectr 2023; 11:e0242622. [PMID: 36951567 PMCID: PMC10101053 DOI: 10.1128/spectrum.02426-22] [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: 07/11/2022] [Accepted: 02/23/2023] [Indexed: 03/24/2023] Open
Abstract
Heavy metals (HMs) are known to modify bacterial communities both in the laboratory and in situ. Consequently, soils in HM-contaminated sites such as the U.S. Environmental Protection Agency (EPA) Superfund sites are predicted to have altered ecosystem functioning, with potential ramifications for the health of organisms, including humans, that live nearby. Further, several studies have shown that heavy metal-resistant (HMR) bacteria often also display antimicrobial resistance (AMR), and therefore HM-contaminated soils could potentially act as reservoirs that could disseminate AMR genes into human-associated pathogenic bacteria. To explore this possibility, topsoil samples were collected from six public locations in the zip code 35207 (the home of the North Birmingham 35th Avenue Superfund Site) and in six public areas in the neighboring zip code, 35214. 35027 soils had significantly elevated levels of the HMs As, Mn, Pb, and Zn, and sequencing of the V4 region of the bacterial 16S rRNA gene revealed that elevated HM concentrations correlated with reduced microbial diversity and altered community structure. While there was no difference between zip codes in the proportion of total culturable HMR bacteria, bacterial isolates with HMR almost always also exhibited AMR. Metagenomes inferred using PICRUSt2 also predicted significantly higher mean relative frequencies in 35207 for several AMR genes related to both specific and broad-spectrum AMR phenotypes. Together, these results support the hypothesis that chronic HM pollution alters the soil bacterial community structure in ecologically meaningful ways and may also select for bacteria with increased potential to contribute to AMR in human disease. IMPORTANCE Heavy metals cross-select for antimicrobial resistance in laboratory experiments, but few studies have documented this effect in polluted soils. Moreover, despite decades of awareness of heavy metal contamination at the EPA Superfund site in North Birmingham, Alabama, this is the first analysis of the impact of this pollution on the soil microbiome. Specifically, this work advances the understanding of the relationship between heavy metals, microbial diversity, and patterns of antibiotic resistance in North Birmingham soils. Our results suggest that polluted soils carry a risk of increased exposure to antibiotic-resistant infections in addition to the direct health consequences of heavy metals. Our work provides important information relevant to both political and scientific efforts to advance environmental justice for the communities that call Superfund neighborhoods home.
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Affiliation(s)
- Anuradha Goswami
- Department of Biology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Sarah J. Adkins-Jablonsky
- Department of Biology, University of Alabama at Birmingham, Birmingham, Alabama, USA
- Alabama College of Osteopathic Medicine, Dothan, Alabama, USA
| | | | - Michelle D. Shilling
- Department of Biology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Alex Dawson
- Department of Biology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Sabrina Heiser
- Department of Biology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Aisha O’Connor
- Department of Biology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Melissa Walker
- Department of Biology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Qutia Roberts
- Department of Biology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - J. Jeffrey Morris
- Department of Biology, University of Alabama at Birmingham, Birmingham, Alabama, USA
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31
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Chen X, Wang J, Pan C, Feng L, Chen S, Xie S. Metagenomic insights into the influence of thallium spill on sediment microbial community. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 317:120660. [PMID: 36436665 DOI: 10.1016/j.envpol.2022.120660] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 11/03/2022] [Accepted: 11/11/2022] [Indexed: 06/16/2023]
Abstract
Thallium (Tl) is an extremely toxic metal. The release of Tl into the natural environment can pose a potential threat to organisms. So far, information about the impact of Tl on indigenous microorganisms is still very limited. In addition, there has been no report on how sudden Tl spill influences the structure and function of the microbial community. Therefore, this study explored the response of river sediment microbiome to a Tl spill. Residual T1 in the sediment significantly decreased bacterial community diversity. The increase in the abundance of Bacteroidetes in all Tl- impacted sediments suggested the advantage of Bacteroidetes to resist Tl pressure. Under T1 stress, microbial genes related to carbon fixation and gene cysH participating in assimilatory sulfate reduction were down-regulated, while genes related to nitrogen cycling were up-regulated. After T1 spill, increase in both metal resistance genes (MRGs) and antibiotic resistance genes (ARGs) was observed in Tl-impacted sediments. Moreover, the abundance of MRGs and ARGs was significantly correlated with sediment Tl concentration, implying the positive effect of Tl contamination on the proliferation of these resistance genes. Procrustes analysis suggested a significant congruence between profiles of MRGs and bacterial communities. Through LEfSe and co-occurrence network analysis, Trichococcus, Polaromonas, and Arenimonas were identified to be tolerant and resistant to Tl pollution. The colocalization analysis of contigs indicated the co-effects of selection and transfer for MRGs/ARGs were important reasons for the increase in the microbial resistance in Tl-impacted sediments. This study added new insights into the effect of Tl spill on microbial community and highlighted the role of heavy metal spill in the increase of both heavy metal and antibiotic resistance genes.
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Affiliation(s)
- Xiuli Chen
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Ji Wang
- South China Institute of Environmental Sciences (SCIES), Ministry of Ecology and Environment (MEE), Guangzhou, 510655, China
| | - Chaoyi Pan
- South China Institute of Environmental Sciences (SCIES), Ministry of Ecology and Environment (MEE), Guangzhou, 510655, China
| | - Lishi Feng
- South China Institute of Environmental Sciences (SCIES), Ministry of Ecology and Environment (MEE), Guangzhou, 510655, China
| | - Sili Chen
- South China Institute of Environmental Sciences (SCIES), Ministry of Ecology and Environment (MEE), Guangzhou, 510655, China.
| | - Shuguang Xie
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
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Ducret V, Gonzalez D, Leoni S, Valentini M, Perron K. A Zur-mediated transcriptional regulation of the zinc export system in Pseudomonas aeruginosa. BMC Microbiol 2023; 23:6. [PMID: 36617571 PMCID: PMC9827704 DOI: 10.1186/s12866-022-02750-4] [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: 10/12/2022] [Accepted: 12/28/2022] [Indexed: 01/10/2023] Open
Abstract
The control of cellular zinc (Zn) concentrations by dedicated import and export systems is essential for the survival and virulence of Pseudomonas aeruginosa. The transcription of its many Zn transporters is therefore tightly regulated by a known set of transcription factors involved in either the import or the export of Zn. In this work, we show that the Zur protein, a well-known repressor of Zn import, plays a dual role and functions in both import and export processes. In a situation of Zn excess, Zur represses Zn entry, but also activates the transcription of czcR, a positive regulator of the Zn export system. To achieve this, Zur binds at two sites, located by DNA footprinting in the region downstream the czcR transcription start site. In agreement with this regulation, a delay in induction of the efflux system is observed in the absence of Zur and Zn resistance is reduced. The discovery of this regulation highlights a new role of Zur as global regulator of Zn homeostasis in P. aeruginosa disclosing an important link between Zur and zinc export.
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Affiliation(s)
- Verena Ducret
- grid.8591.50000 0001 2322 4988Department of Plant Sciences, Microbiology Unit, University of Geneva, Quai Ernest-Ansermet 30, 1211 Geneva 4, Switzerland
| | - Diego Gonzalez
- grid.10711.360000 0001 2297 7718Laboratory of Microbiology, Institute of Biology, Faculty of Sciences, University of Neuchâtel, Rue Emile-Argand 11, 2000 Neuchâtel, Switzerland
| | - Sara Leoni
- grid.8591.50000 0001 2322 4988Department of Plant Sciences, Microbiology Unit, University of Geneva, Quai Ernest-Ansermet 30, 1211 Geneva 4, Switzerland
| | - Martina Valentini
- grid.8591.50000 0001 2322 4988Department of Microbiology and Molecular Medicine, Faculty of Medicine, CMU, University of Geneva, Geneva, Switzerland
| | - Karl Perron
- grid.8591.50000 0001 2322 4988Department of Plant Sciences, Microbiology Unit, University of Geneva, Quai Ernest-Ansermet 30, 1211 Geneva 4, Switzerland ,grid.8591.50000 0001 2322 4988Section of Pharmaceutical Sciences, University of Geneva, Rue Michel-Servet 1, 1205 Geneva, Switzerland
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Evans L, Kotar A, Valentini M, Filloux A, Jamshidi S, Plavec J, Rahman KM, Vilar R. Identification and characterisation of G-quadruplex DNA-forming sequences in the Pseudomonas aeruginosa genome. RSC Chem Biol 2023; 4:94-100. [PMID: 36685252 PMCID: PMC9811510 DOI: 10.1039/d2cb00205a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 11/13/2022] [Indexed: 11/16/2022] Open
Abstract
A number of Gram-negative bacteria such as Pseudomonas aeruginosa are becoming resistant to front-line antibiotics. Consequently, there is a pressing need to find alternative bio-molecular targets for the development of new drugs. Since non-canonical DNA structures such as guanine-quadruplexes (G4s) have been implicated in regulating transcription, we were interested in determining whether there are putative quadruplex-forming sequences (PQS) in the genome of Pseudomonas aeruginosa. Using bioinformatic tools, we screened 36 genes potentially relevant to drug resistance for the presence of PQS and 10 of these were selected for biophysical characterisation (i.e. circular dichroism and thermal difference UV/Vis spectroscopy). These studies showed that three of these G-rich sequences (linked to murE, ftsB and mexC genes) form stable guanine-quadruplexes which were studied by NMR spectroscopy; detailed analysis of one of the sequences (mexC) confirmed that it adopts a two-quartet antiparallel quadruplex structure in the presence of K+ ions. We also show by FRET melting assays that small molecules can stabilise these three new G4 DNA structures under physiological conditions. These initial results could be of future interest in the development of new antibiotics with alternative bio-molecular targets which in turn would help tackle antimicrobial resistance.
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Affiliation(s)
- Lindsay Evans
- Department of Chemistry, Imperial College London, White City CampusLondon W12 OBZUK
| | - Anita Kotar
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 191000 LjubljanaSlovenia
| | - Martina Valentini
- Department of Life Sciences, MRC Centre for Molecular Microbiology and Infection, Imperial College London, South Kensington CampusLondon SW7 2AZUK
| | - Alain Filloux
- Department of Life Sciences, MRC Centre for Molecular Microbiology and Infection, Imperial College London, South Kensington CampusLondon SW7 2AZUK
| | - Shirin Jamshidi
- Institute of Pharmaceutical Science, King's College London, Franklin-Wilkins Building150 Stamford StreetLondon SE1 9NHUK
| | - Janez Plavec
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 191000 LjubljanaSlovenia
| | - Khondaker Miraz Rahman
- Institute of Pharmaceutical Science, King's College London, Franklin-Wilkins Building150 Stamford StreetLondon SE1 9NHUK
| | - Ramon Vilar
- Department of Chemistry, Imperial College London, White City CampusLondon W12 OBZUK
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Sandoz A, Ducret V, Gottwald GA, Vilmart G, Perron K. SINDy for delay-differential equations: application to model bacterial zinc response. Proc Math Phys Eng Sci 2023. [DOI: 10.1098/rspa.2022.0556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
We extend the data-driven method of sparse identification of nonlinear dynamics (SINDy) developed by Brunton
et al.
,
Proc. Natl Acad. Sci. USA
113
(2016) to the case of delay differential equations (DDEs). This is achieved in a bilevel optimization procedure by first applying SINDy for fixed delay and then subsequently optimizing the error of the reconstructed SINDy model over delay times. We test the SINDy-delay method on a noisy short dataset from a toy DDE and show excellent agreement. We then apply the method to experimental data of gene expressions in the bacterium
Pseudomonas aeruginosa
subject to the influence of zinc. The derived SINDy model suggests that the increase in zinc concentration mainly affects the time delay and not the strengths of the interactions between the different agents controlling the zinc export mechanism.
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Affiliation(s)
- Antoine Sandoz
- Department of Plant Sciences, Microbiology Unit, and Section of Mathematics, Microbiology Unit, and Section of Pharmaceutical Sciences, University of Geneva, CP64, 1211 Geneva 4, Switzerland
| | - Verena Ducret
- Department of Plant Sciences, Microbiology Unit, Microbiology Unit, and Section of Pharmaceutical Sciences, University of Geneva, CP64, 1211 Geneva 4, Switzerland
| | - Georg A. Gottwald
- School of Mathematics and Statistics, University of Sydney, Sydney, NSW 2006, Australia
| | - Gilles Vilmart
- Section of Mathematics, Microbiology Unit, and Section of Pharmaceutical Sciences, University of Geneva, CP64, 1211 Geneva 4, Switzerland
| | - Karl Perron
- Department of Plant Sciences, Microbiology Unit, and Section of Pharmaceutical Sciences, University of Geneva, CP64, 1211 Geneva 4, Switzerland
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Li J, Guo YK, Zhao QX, He JZ, Zhang Q, Cao HY, Liang CQ. Microbial cell wall sorption and Fe-Mn binding in rhizosphere contribute to the obstruction of cadmium from soil to rice. Front Microbiol 2023; 14:1162119. [PMID: 37138638 PMCID: PMC10149983 DOI: 10.3389/fmicb.2023.1162119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 03/07/2023] [Indexed: 05/05/2023] Open
Abstract
Screening high-tolerant microorganisms to cadmium (Cd) and revealing their bio-obstruction mechanism could be significant for Cd regulation from farmland to the food chain. We examined the tolerance and bio-removal efficiency of Cd ions of two bacterial strains, Pseudomonas putida 23483 and Bacillus sp. GY16, and measured the accumulation of Cd ions in rice tissues and its different chemical forms in soil. The results showed that the two strains had high tolerance to Cd, but the removal efficiency was decreased successively with increasing Cd concentrations (0.05 to 5 mg kg-1). Cell-sorption accounted for the major proportion of Cd removal compared with excreta binding in both strains, which was conformed to the pseudo-second-order kinetics. At the subcellular level, Cd was mostly taken up by the cell mantle and cell wall, and only a small amount entered into the cytomembrane and cytoplasmic with time progressed (0 to 24 h) in each concentration. The cell mantle and cell wall sorption decreased with increasing Cd concentration, especially in the cytomembrane and cytoplasmic. The scanning electron microscope (SEM) and energy dispersive X-ray (EDS) analysis verified that Cd ions were attached to the cell surface, and the functional groups of C-H, C-N, C=O, N-H, and O-H in the cell surface may participate in cell-sorption process tested by the FTIR analysis. Furthermore, inoculation of the two strains significantly decreased Cd accumulation in rice straw and grain but increased in the root, increased Cd enrichment ratio in root from soil, decreased Cd translocation ratio from root to straw and grain, and increased the Cd concentrations of Fe-Mn binding form and residual form in rhizosphere soil. This study highlights that the two strains mainly removed Cd ions in solution through biosorption and passivated soil Cd as Fe-Mn combined form ascribe to its characteristics of manganese-oxidizing, eventually achieving bio-obstruction of Cd from soil to rice grain.
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Affiliation(s)
- Jie Li
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yi-Kai Guo
- Ecological Environment Planning and Environmental Protection Technology Center of Qinghai Province, Xining, China
| | - Qing-Xia Zhao
- Institute of New Rural Development, Guizhou University, Guiyang, China
| | - Ji-Zheng He
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia
| | - Qian Zhang
- Key Laboratory of Land Surface Pattern and Simulation, Beijing Key Laboratory of Environmental Damage Assessment and Remediation, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China
| | - Hong-Ying Cao
- Key Laboratory of Land Surface Pattern and Simulation, Beijing Key Laboratory of Environmental Damage Assessment and Remediation, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China
- *Correspondence: Hong-Ying Cao
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Liu Z, Xu Z, Chen S, Huang J, Li T, Duan C, Zhang LH, Xu Z. CzcR Is Essential for Swimming Motility in Pseudomonas aeruginosa during Zinc Stress. Microbiol Spectr 2022; 10:e0284622. [PMID: 36416561 PMCID: PMC9769499 DOI: 10.1128/spectrum.02846-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 11/04/2022] [Indexed: 11/25/2022] Open
Abstract
Two-component system (TCS) plays a vital role in modulating target gene expression in response to the changing environments. Pseudomonas aeruginosa is a ubiquitous opportunistic pathogen that can survive under diverse stress conditions. The great adaptability of P. aeruginosa relies heavily on the abundant TCSs encoded by its genome. However, most TCSs in P. aeruginosa have not been well-characterized. CzcS/CzcR is a metal responsive TCS which displays multiple regulatory functions associated with metal hemostasis, quorum sensing activity and antibiotic resistance. In this study, we found that swimming motility of P. aeruginosa was completely abolished during zinc (Zn2+) stress when the czcR gene from the TCS CzcS/CzcR was deleted. Noticeably, CzcR was dispensable for swimming without the stress of Zn2+ excess. CzcR was shown to be activated by Zn2+ stress possibly through inducing its expression level and triggering its phosphorylation to positively regulate swimming which was abolished by Zn2+ stress in a CzcR-independent manner. Further TEM analyses and promoter activity examinations revealed that CzcR was required for the expression of genes involved in flagellar biosynthesis during Zn2+ stress. In vitro protein-DNA interaction assay showed that CzcR was capable of specifically recognizing and binding to the promoters of operons flgBCDE, flgFGHIJK, and PA1442/FliMNOPQR/flhB. Together, this study demonstrated a novel function of CzcR in regulating flagellar gene expression and motility in P. aeruginosa when the pathogen encounters Zn2+ stress conditions. IMPORTANCE The fitness of bacterial cells depends largely on their ability to sense and respond quickly to the changing environments. P. aeruginosa expresses a great number of signal sensing and transduction systems that enable the pathogen to grow and survive under diverse stress conditions and cause serious infections at different sites in many hosts. In addition to the previously characterized functions to regulate metal homeostasis, quorum sensing activity, and antibiotic resistance, here we report that CzcR is a novel regulator essential for flagellar gene expression and swimming motility in P. aeruginosa during Zn2+ stress. Since swimming motility is important for the virulence of P. aeruginosa, findings in this study might provide a new target for the treatment of P. aeruginosa infections with Zn2+-based antimicrobial agents in the future.
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Affiliation(s)
- Zhiqing Liu
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, People’s Republic of China
| | - Zirui Xu
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, People’s Republic of China
| | - Shuzhen Chen
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, People’s Republic of China
| | - Jiahui Huang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, People’s Republic of China
| | - Ting Li
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, People’s Republic of China
| | - Cheng Duan
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, People’s Republic of China
| | - Lian-Hui Zhang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, People’s Republic of China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, People’s Republic of China
| | - Zeling Xu
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, People’s Republic of China
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37
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Ducret V, Gonzalez D, Perron K. Zinc homeostasis in Pseudomonas. Biometals 2022:10.1007/s10534-022-00475-5. [PMID: 36472780 PMCID: PMC10393844 DOI: 10.1007/s10534-022-00475-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 11/21/2022] [Indexed: 12/12/2022]
Abstract
AbstractIn the genus Pseudomonas, zinc homeostasis is mediated by a complete set of import and export systems, whose expression is precisely controlled by three transcriptional regulators: Zur, CzcR and CadR. In this review, we describe in detail our current knowledge of these systems, their regulation, and the biological significance of zinc homeostasis, taking Pseudomonas aeruginosa as our paradigm. Moreover, significant parts of this overview are dedicated to highlight interactions and cross-regulations between zinc and copper import/export systems, and to shed light, through a review of the literature and comparative genomics, on differences in gene complement and function across the whole Pseudomonas genus. The impact and importance of zinc homeostasis in Pseudomonas and beyond will be discussed throughout this review.
Graphical abstract
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38
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Bianco K, de Farias BO, Gonçalves-Brito AS, Alves do Nascimento AP, Magaldi M, Montenegro K, Flores C, Oliveira S, Monteiro MA, Spisso BF, Pereira MU, Ferreira RG, Albano RM, Cardoso AM, Clementino MM. Mobile resistome of microbial communities and antimicrobial residues from drinking water supply systems in Rio de Janeiro, Brazil. Sci Rep 2022; 12:19050. [PMID: 36351942 PMCID: PMC9646821 DOI: 10.1038/s41598-022-21040-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 09/22/2022] [Indexed: 11/10/2022] Open
Abstract
Antibiotic resistance genes (ARGs) are widespread in the environment due to the overuse of antibiotics and other pollutants, posing a threat to human and animal health. In this study, we evaluated antimicrobial residues, bacterial diversity and ARGs in two important watersheds, Guandu and São João, that supply drinking water to Rio de Janeiro city, Brazil. In addition, tap water samples were collected from three different cities in Rio de Janeiro State, including the metropolitan area of Rio de Janeiro city. Clarithromycin, sulfamethoxazole and azithromycin were found in untreated water and drinking water in all samples. A greater abundance of Proteobacteria was observed in Guandu and São João watersheds, with most of the sequences belonging to the Gammaproteobacteria class. A plasmidome-focused metagenomics approach revealed 4881 (Guandu), 3705 (São João) and 3385 (drinking water) ARGs mainly associated with efflux systems. The genes encoding metallo-β-lactamase enzymes (blaAIM, blaGIM, blaIMP, and blaVIM) were detected in the two watersheds and in drinking water samples. Moreover, we demonstrated the presence of the colistin resistance genes mcr-3 and mcr-4 (both watersheds) and mcr-9 (drinking water and Guandu) for the first time in Brazil. Our data emphasize the importance of introducing measures to reduce the disposal of antibiotics and other pollutants capable of promoting the occurrence and spread of the microbial resistome on aquatic environments and predicting possible negative impacts on human health.
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Affiliation(s)
- Kayo Bianco
- Instituto Nacional de Controle de Qualidade Em Saúde INCQS/FIOCRUZ, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, 4365, Brazil.
| | - Beatriz Oliveira de Farias
- Instituto Nacional de Controle de Qualidade Em Saúde INCQS/FIOCRUZ, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, 4365, Brazil
| | - Andressa Silva Gonçalves-Brito
- Instituto Nacional de Controle de Qualidade Em Saúde INCQS/FIOCRUZ, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, 4365, Brazil
| | - Ana Paula Alves do Nascimento
- Instituto Nacional de Controle de Qualidade Em Saúde INCQS/FIOCRUZ, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, 4365, Brazil
| | - Mariana Magaldi
- Instituto Nacional de Controle de Qualidade Em Saúde INCQS/FIOCRUZ, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, 4365, Brazil
| | - Kaylanne Montenegro
- Instituto Nacional de Controle de Qualidade Em Saúde INCQS/FIOCRUZ, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, 4365, Brazil
| | - Claudia Flores
- Instituto Nacional de Controle de Qualidade Em Saúde INCQS/FIOCRUZ, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, 4365, Brazil
| | - Samara Oliveira
- Instituto Nacional de Controle de Qualidade Em Saúde INCQS/FIOCRUZ, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, 4365, Brazil
| | - Mychelle Alves Monteiro
- Instituto Nacional de Controle de Qualidade Em Saúde INCQS/FIOCRUZ, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, 4365, Brazil
| | - Bernardete Ferraz Spisso
- Instituto Nacional de Controle de Qualidade Em Saúde INCQS/FIOCRUZ, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, 4365, Brazil
| | - Mararlene Ulberg Pereira
- Instituto Nacional de Controle de Qualidade Em Saúde INCQS/FIOCRUZ, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, 4365, Brazil
| | - Rosana Gomes Ferreira
- Instituto Nacional de Controle de Qualidade Em Saúde INCQS/FIOCRUZ, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, 4365, Brazil
| | | | | | - Maysa Mandetta Clementino
- Instituto Nacional de Controle de Qualidade Em Saúde INCQS/FIOCRUZ, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, 4365, Brazil
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Wand ME, Sutton JM. Efflux-mediated tolerance to cationic biocides, a cause for concern? MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 36748532 DOI: 10.1099/mic.0.001263] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
AbstractWith an increase in the number of isolates resistant to multiple antibiotics, infection control has become increasingly important to help combat the spread of multi-drug-resistant pathogens. An important component of this is through the use of disinfectants and antiseptics (biocides). Antibiotic resistance has been well studied in bacteria, but little is known about potential biocide resistance genes and there have been few reported outbreaks in hospitals resulting from a breakdown in biocide effectiveness. Development of increased tolerance to biocides has been thought to be more difficult due to the mode of action of biocides which affect multiple cellular targets compared with antibiotics. Very few genes which contribute towards increased biocide tolerance have been identified. However, the majority of those that have are components or regulators of different efflux pumps or genes which modulate membrane function/modification. This review will examine the role of efflux in increased tolerance towards biocides, focusing on cationic biocides and heavy metals against Gram-negative bacteria. As many efflux pumps which are upregulated by biocide presence also contribute towards an antimicrobial resistance phenotype, the role of these efflux pumps in cross-resistance to both other biocides and antibiotics will be explored.
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Affiliation(s)
- Matthew E Wand
- Technology Development Group, UK Health Security Agency, Research and Evaluation, Porton Down, Salisbury, Wiltshire, SP4 0JG, UK
| | - J Mark Sutton
- Technology Development Group, UK Health Security Agency, Research and Evaluation, Porton Down, Salisbury, Wiltshire, SP4 0JG, UK
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Environmental complexity is more important than mutation in driving the evolution of latent novel traits in E. coli. Nat Commun 2022; 13:5904. [PMID: 36202805 PMCID: PMC9537139 DOI: 10.1038/s41467-022-33634-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 09/26/2022] [Indexed: 11/23/2022] Open
Abstract
Recent experiments show that adaptive Darwinian evolution in one environment can lead to the emergence of multiple new traits that provide no immediate benefit in this environment. Such latent non-adaptive traits, however, can become adaptive in future environments. We do not know whether mutation or environment-driven selection is more important for the emergence of such traits. To find out, we evolve multiple wild-type and mutator E. coli populations under two mutation rates in simple (single antibiotic) environments and in complex (multi-antibiotic) environments. We then assay the viability of evolved populations in dozens of new environments and show that all populations become viable in multiple new environments different from those they had evolved in. The number of these new environments increases with environmental complexity but not with the mutation rate. Genome sequencing demonstrates the reason: Different environments affect pleiotropic mutations differently. Our experiments show that the selection pressure provided by an environment can be more important for the evolution of novel traits than the mutational supply experienced by a wild-type and a mutator strain of E. coli. Novel traits without immediate fitness benefit evolve frequently but we don’t know whether mutation or environment-driven selection drives this evolution. Here, using experimental evolution of E. coli populations, the authors demonstrate the importance of selection in the evolution of latent novel traits.
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Adhikary A, Biswal S, Chatterjee D, Ghosh AS. A NiCoT family metal transporter of Mycobacterium tuberculosis (Rv2856/NicT) behaves as a drug efflux pump that facilitates cross-resistance to antibiotics. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 36282241 DOI: 10.1099/mic.0.001260] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Metals often act as a facilitator in the proliferation and persistence of antibiotic resistance. Efflux pumps play key roles in the co-selection of metal and antibiotic resistance. Here, we report the ability of a putative nickel/cobalt transporter (NiCoT family), Rv2856 or NicT of Mycobacterium tuberculosis (Mtb), to transport metal and antibiotics and identified some key amino acid residues that are important for its function. Ectopic expression of NicT in Escherichia coli CS109 resulted in the increase of intracellular nickel uptake. Additionally, enhanced tolerance towards several antibiotics (norfloxacin, sparfloxacin, ofloxacin, gentamicin, nalidixic acid and isoniazid) was observed with NicT overexpression in E. coli and Mycobacterium smegmatis. A comparatively lower intracellular accumulation of norfloxacin upon NicT overexpression than that of the cells without NicT indicated the involvement of NicT in an active efflux process. Although expression of NicT did not alter the sensitivity towards kanamycin, doxycycline, tetracycline, apramycin, neomycin and ethambutol, the presence of a sub-inhibitory dose of Ni2+ resulted in the manifestation of low-level tolerance towards these drugs. Further, substitution of four residues (H77I, D82I, H83L and D227I) in the conserved regions of NicT by isoleucine and leucine resulted in reduced to nearly complete loss of the transport function for both metals and antimicrobials. Therefore, the study suggests that nickel transporter Rv2856/NicT may actively export different drugs and the presence of nickel might drive the cross-resistance to some of the antibiotics.
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Affiliation(s)
- Anwesha Adhikary
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal-721302, India
| | - Sarmistha Biswal
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal-721302, India
| | - Debasmita Chatterjee
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal-721302, India
| | - Anindya S Ghosh
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal-721302, India
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Wesseling CJ, Martin NI. Synergy by Perturbing the Gram-Negative Outer Membrane: Opening the Door for Gram-Positive Specific Antibiotics. ACS Infect Dis 2022; 8:1731-1757. [PMID: 35946799 PMCID: PMC9469101 DOI: 10.1021/acsinfecdis.2c00193] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
New approaches to target antibacterial agents toward Gram-negative bacteria are key, given the rise of antibiotic resistance. Since the discovery of polymyxin B nonapeptide as a potent Gram-negative outer membrane (OM)-permeabilizing synergist in the early 1980s, a vast amount of literature on such synergists has been published. This Review addresses a range of peptide-based and small organic compounds that disrupt the OM to elicit a synergistic effect with antibiotics that are otherwise inactive toward Gram-negative bacteria, with synergy defined as a fractional inhibitory concentration index (FICI) of <0.5. Another requirement for the inclusion of the synergists here covered is their potentiation of a specific set of clinically used antibiotics: erythromycin, rifampicin, novobiocin, or vancomycin. In addition, we have focused on those synergists with reported activity against Gram-negative members of the ESKAPE family of pathogens namely, Escherichia coli, Pseudomonas aeruginosa, Klebsiella pneumoniae, and/or Acinetobacter baumannii. In cases where the FICI values were not directly reported in the primary literature but could be calculated from the published data, we have done so, allowing for more direct comparison of potency with other synergists. We also address the hemolytic activity of the various OM-disrupting synergists reported in the literature, an effect that is often downplayed but is of key importance in assessing the selectivity of such compounds for Gram-negative bacteria.
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43
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Xu F, Liu S, Naren N, Li L, Ma LZ, Zhang X. Experimental evolution of bacterial survival on metallic copper. Ecol Evol 2022. [DOI: 10.1002/ece3.9225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Affiliation(s)
- Feng Xu
- School of Natural Sciences Massey University Auckland New Zealand
| | - Sha Liu
- School of Natural Sciences Massey University Auckland New Zealand
| | - Naran Naren
- School of Natural Sciences Massey University Auckland New Zealand
| | - Lily Li
- School of Natural Sciences Massey University Auckland New Zealand
| | - Luyan Z. Ma
- State Key Laboratory of Microbial Resources, Institute of Microbiology Chinese Academy of Sciences Beijing China
| | - Xue‐Xian Zhang
- School of Natural Sciences Massey University Auckland New Zealand
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Gupta S, Graham DW, Sreekrishnan TR, Ahammad SZ. Effects of heavy metals pollution on the co-selection of metal and antibiotic resistance in urban rivers in UK and India. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 306:119326. [PMID: 35491000 DOI: 10.1016/j.envpol.2022.119326] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 04/06/2022] [Accepted: 04/15/2022] [Indexed: 06/14/2023]
Abstract
Heavy metal pollution and the potential for co-selection of resistance to antibiotics in the environment is growing concern. However, clear associations between heavy metals and antibiotic resistance in river systems have not been developed. Here we investigated relationships between total and bioavailable heavy metals concentrations; metal resistance gene (MRG) and antibiotic resistance gene (ARG) abundances; mobile genetic elements; and the composition of local bacterial communities in low and high metal polluted rivers in UK and India. The results indicated that MRGs conferring resistance to cobalt (Co) and nickel (Ni) (rcnA), and Co, zinc (Zn), and cadmium (Cd) (czcA), and ARGs conferring resistance to carbapenem and erythromycin were the dominating resistant genes across the samples. The relative MRGs, ARGs, and integrons abundances tended to increase at high metal polluted environments, suggesting high metals concentrations have a strong potential to promote metal and antibiotic resistance by horizontal gene transmission and affecting bacterial communities, leading to the development of multi-metal and multi-antibiotic resistance. Network analysis demonstrated the positive and significant relationships between MRGs and ARGs as well as the potential for integrons playing a role in the co-transmission of MRGs and ARGs (r > 0.80, p < 0.05). Additionally, the major host bacteria of various MRGs and ARGs that could be accountable for greater MRGs and ARGs levels at high metal polluted environments were also identified by network analysis. Spearman's rank-order correlations and RDA analysis further confirm relationships between total and bioavailable heavy metals concentrations and the relative MRG, ARG, and integron abundances, as well as the composition of related bacterial communities (r > 0.80 (or < -0.80), p < 0.05). These findings are critical for assessing the possible human health concerns associated with metal-driven antibiotic resistance and highlight the need of considering metal pollution for developing appropriate measures to control ARG transmission.
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Affiliation(s)
- Sonia Gupta
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India
| | - David W Graham
- School of Engineering, Newcastle University, Newcastle Upon Tyne, NE1 7RU, United Kingdom
| | - T R Sreekrishnan
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India
| | - Shaikh Ziauddin Ahammad
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India.
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45
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Zhang K, Liu L, Yan M, Chen C, Li X, Tian J, Luo C, Wang X, Wang M. Reduced porin expression with EnvZ-OmpR, PhoPQ, BaeSR two-component system down-regulation in carbapenem resistance of Klebsiella Pneumoniae based on proteomic analysis. Microb Pathog 2022; 170:105686. [PMID: 35917986 DOI: 10.1016/j.micpath.2022.105686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 07/15/2022] [Accepted: 07/17/2022] [Indexed: 11/30/2022]
Abstract
Carbapenem-resistant Klebsiella pneumoniae (CRKP) has proven to be an urgent threat to human health. Proteomics (TMT/LC-MS/MS) and bioinformatics approaches were employed to explore the potential mechanisms underlying carbapenem resistance. Proteomic profiling of CRKP and susceptible KP (sKP) isolates revealed the involvement of outer membrane, beta-lactam resistance pathway, and two-component systems (TCSs) in carbapenem resistance. 27 CRKP strains and 27 susceptible Klebsiella pneumoniae strains were isolated from inpatients at the Second Xiangya Hospital, China to verify the mechanisms. Modified carbapenem inactivation method (mCIM) and PCR of common carbapenem resistance genes confirmed that 77.8% (21/27) of CRKP isolates were carbapenemase-producing. Porin decrease in CRKP isolates was found by SDS-PAGE and mRNA levels of major porins (OmpK35 and OmpK36). RT-qPCR detection of two-component systems (envZ, ompR, phoP, phoQ, baeS and baeR) revealed down-regulation of EnvZ-OmpR, PhoPQ, BaeSR TCSs. Expression of the TCSs, except ompR, were closely correlated with OMPs with the R-value >0.7. Together, this study reaffirmed the significance of the β-lactam resistance pathway in CRKP based on proteomic analysis. OmpK35/36 porin reduction and the controversial downregulation of EnvZ-OmpR, PhoPQ, and BaeSR TCSs were confirmed in carbapenem resistance of Klebsiella pneumoniae.
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Affiliation(s)
- Kan Zhang
- Department of Laboratory Medicine, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China.
| | - Lei Liu
- Department of Laboratory Medicine, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China.
| | - Min Yan
- Department of Laboratory Medicine, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China.
| | - Chunmei Chen
- Department of Laboratory Medicine, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China.
| | - Xianping Li
- Department of Laboratory Medicine, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China.
| | - Jingjing Tian
- Department of Laboratory Medicine, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China.
| | - Can Luo
- Department of Laboratory Medicine, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China.
| | - Xiaofan Wang
- Department of Laboratory Medicine, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China.
| | - Min Wang
- Department of Laboratory Medicine, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China.
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46
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Liu C, Yu H, Zhang B, Liu S, Liu CG, Li F, Song H. Engineering whole-cell microbial biosensors: Design principles and applications in monitoring and treatment of heavy metals and organic pollutants. Biotechnol Adv 2022; 60:108019. [PMID: 35853551 DOI: 10.1016/j.biotechadv.2022.108019] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 07/13/2022] [Accepted: 07/13/2022] [Indexed: 01/18/2023]
Abstract
Biosensors have been widely used as cost-effective, rapid, in situ, and real-time analytical tools for monitoring environments. The development of synthetic biology has enabled emergence of genetically engineered whole-cell microbial biosensors. This review updates the design and optimization principles for a diverse array of whole-cell biosensors based on transcription factors (TF) including activators or repressors derived from heavy metal resistance systems, alkanes, and aromatics metabolic pathways of bacteria. By designing genetic circuits, the whole-cell biosensors could be engineered to intelligently sense heavy metals (Hg2+, Zn2+, Pb2+, Au3+, Cd2+, As3+, Ni2+, Cu2+, and UO22+) or organic compounds (alcohols, alkanes, phenols, and benzenes) through one-component or two-component system-based TFs, transduce signals through genetic amplifiers, and response as various outputs such as cell fluorescence and bioelectricity for monitoring heavy metals and organic pollutants in real conditions, synthetic curli and surface metal-binding peptides for in situ bio-sorption of heavy metals. We further review strategies that have been implemented to optimize the selectivity and correlation between ligand concentration and output signal of the TF-based biosensors, so as to meet requirements of practical applications. The optimization strategies include protein engineering to change specificities, promoter engineering to improve sensitivities, and genetic circuit-based amplification to enhance dynamic ranges via designing transcriptional amplifiers, logic gates, and feedback loops. At last, we outlook future trends in developing novel forms of biosensors.
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Affiliation(s)
- Changjiang Liu
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Huan Yu
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Baocai Zhang
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Shilin Liu
- Collaborative Innovation Center of Chemical Science and Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Chen-Guang Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences of Ministry of Education, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Feng Li
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China.
| | - Hao Song
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China.
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Fang L, Zhu H, Geng Y, Zhang G, Zhang H, Shi T, Wu X, Li QX, Hua R. Resistance properties and adaptation mechanism of cadmium in an enriched strain, Cupriavidus nantongensis X1 T. JOURNAL OF HAZARDOUS MATERIALS 2022; 434:128935. [PMID: 35461001 DOI: 10.1016/j.jhazmat.2022.128935] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 04/12/2022] [Accepted: 04/12/2022] [Indexed: 06/14/2023]
Abstract
Bacterial adaption to heavy metal stress is a complex and comprehensive process of multi-response regulation. However, the mechanism is largely unexplored. In this study, cadmium (Cd) resistance and adaptation mechanism in Cupriavidus nantongensis X1T were investigated. Strain X1T could resist the stress of 307 mg/L Cd2+ and remove 70% Cd2+ in 48 h. Spectroscopic analyses suggested interactions between Cd2+ with C-N, -COOH, and -NH ligands of extracellular polymeric substances. Whole-genome sequencing found that the resistance of Cd2+ in strain X1T was caused by the joint action of Czc and Cad systems. Cd2+ at 20 mg/L elicited differential expression of 1157 genes in strain X1T. In addition to the reported effects of uptake, adsorption, effluxion, and accumulation system, the oxidative stress system, Type-VI secretory protein system, Fe-S protein synthesis, and cysteine synthesis system in strain X1T were involved in the Cd2+ resistance and accumulation. The intracellular accumulation content of Cd2+ in strain X1T was higher than the extracellular adsorption content made strain X1T to be an important resource strain in the bioremediation of Cd-contaminated sewage. The results provide a theoretical network for understanding the complex regulatory system of bacterial resistance and adaptation of Cd against stressful environments.
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Affiliation(s)
- Liancheng Fang
- Anhui Provincial Key Laboratory for Quality and Safety of Agri-Products, School of Resource & Environment, Anhui Agricultural University, Hefei, Anhui 230036, China; Institute for Green Development, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Hao Zhu
- Anhui Provincial Key Laboratory for Quality and Safety of Agri-Products, School of Resource & Environment, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Yuehan Geng
- Anhui Provincial Key Laboratory for Quality and Safety of Agri-Products, School of Resource & Environment, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Genrong Zhang
- Anhui Provincial Key Laboratory for Quality and Safety of Agri-Products, School of Resource & Environment, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Houpu Zhang
- Anhui Provincial Key Laboratory for Quality and Safety of Agri-Products, School of Resource & Environment, Anhui Agricultural University, Hefei, Anhui 230036, China; Institute for Green Development, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Taozhong Shi
- Anhui Provincial Key Laboratory for Quality and Safety of Agri-Products, School of Resource & Environment, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Xiangwei Wu
- Anhui Provincial Key Laboratory for Quality and Safety of Agri-Products, School of Resource & Environment, Anhui Agricultural University, Hefei, Anhui 230036, China; Institute for Green Development, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Qing X Li
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, 1955 East-West Road, Honolulu, HI 96822, United States
| | - Rimao Hua
- Anhui Provincial Key Laboratory for Quality and Safety of Agri-Products, School of Resource & Environment, Anhui Agricultural University, Hefei, Anhui 230036, China; Institute for Green Development, Anhui Agricultural University, Hefei, Anhui 230036, China.
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48
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Saha J, Dey S, Pal A. Whole genome sequencing and comparative genomic analyses of Pseudomonas aeruginosa strain isolated from arable soil reveal novel insights into heavy metal resistance and codon biology. Curr Genet 2022; 68:481-503. [PMID: 35763098 DOI: 10.1007/s00294-022-01245-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 05/14/2022] [Accepted: 06/06/2022] [Indexed: 11/03/2022]
Abstract
Elevated concentration of non-essential persistent heavy metals and metalloids in the soil is detrimental to essential soil microbes and plants, resulting in diminished diversity and biomass. Thus, isolation, screening, and whole genomic analysis of potent strains of bacteria from arable lands with inherent capabilities of heavy metal resistance and plant growth promotion hold the key for bio remedial applications. This study is an attempt to do the same. In this study, a potent strain of Pseudomonas aeruginosa was isolated from paddy fields, followed by metabolic profiling using FTIR, metal uptake analysis employing ICP-MS, whole genome sequencing and comparative codon usage analysis. ICP-MS study provided insights into a high degree of Cd uptake during the exponential phase of growth under cumulative metal stress to Cd, Zn and Co, which was further corroborated by the detection of cadA gene along with czcCBA operon in the genome upon performing whole-genome sequencing. This potent strain of Pseudomonas aeruginosa also harboured genes, such as copA, chrA, znuA, mgtE, corA, and others conferring resistance against different heavy metals, such as Cd, Zn, Co, Cu, Cr, etc. A comparative codon usage bias analysis at the genomic and genic level, whereby several heavy metal resistant genes were considered in the backdrop of two housekeeping genes among 40 Pseudomonas spp. indicated the presence of a relatively strong codon usage bias in the studied strain. With this work, an effort was made to explore heavy metal-resistant bacteria (isolated from arable soil) and whole genome sequence analysis to get insight into metal resistance for future bio remedial applications.
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Affiliation(s)
- Jayanti Saha
- Microbiology and Computational Biology Laboratory, Department of Botany, Raiganj University, Raiganj, West Bengal, 733134, India
| | - Sourav Dey
- Microbiology and Computational Biology Laboratory, Department of Botany, Raiganj University, Raiganj, West Bengal, 733134, India
| | - Ayon Pal
- Microbiology and Computational Biology Laboratory, Department of Botany, Raiganj University, Raiganj, West Bengal, 733134, India.
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49
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Targeting the Holy Triangle of Quorum Sensing, Biofilm Formation, and Antibiotic Resistance in Pathogenic Bacteria. Microorganisms 2022; 10:microorganisms10061239. [PMID: 35744757 PMCID: PMC9228545 DOI: 10.3390/microorganisms10061239] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 06/12/2022] [Accepted: 06/14/2022] [Indexed: 12/12/2022] Open
Abstract
Chronic and recurrent bacterial infections are frequently associated with the formation of biofilms on biotic or abiotic materials that are composed of mono- or multi-species cultures of bacteria/fungi embedded in an extracellular matrix produced by the microorganisms. Biofilm formation is, among others, regulated by quorum sensing (QS) which is an interbacterial communication system usually composed of two-component systems (TCSs) of secreted autoinducer compounds that activate signal transduction pathways through interaction with their respective receptors. Embedded in the biofilms, the bacteria are protected from environmental stress stimuli, and they often show reduced responses to antibiotics, making it difficult to eradicate the bacterial infection. Besides reduced penetration of antibiotics through the intricate structure of the biofilms, the sessile biofilm-embedded bacteria show reduced metabolic activity making them intrinsically less sensitive to antibiotics. Moreover, they frequently express elevated levels of efflux pumps that extrude antibiotics, thereby reducing their intracellular levels. Some efflux pumps are involved in the secretion of QS compounds and biofilm-related materials, besides being important for removing toxic substances from the bacteria. Some efflux pump inhibitors (EPIs) have been shown to both prevent biofilm formation and sensitize the bacteria to antibiotics, suggesting a relationship between these processes. Additionally, QS inhibitors or quenchers may affect antibiotic susceptibility. Thus, targeting elements that regulate QS and biofilm formation might be a promising approach to combat antibiotic-resistant biofilm-related bacterial infections.
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50
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Giddings LA, Kunstman K, Moumen B, Asiama L, Green S, Delafont V, Brockley M, Samba-Louaka A. Isolation and Genome Analysis of an Amoeba-Associated Bacterium Dyella terrae Strain Ely Copper Mine From Acid Rock Drainage in Vermont, United States. Front Microbiol 2022; 13:856908. [PMID: 35677904 PMCID: PMC9169046 DOI: 10.3389/fmicb.2022.856908] [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: 01/17/2022] [Accepted: 04/21/2022] [Indexed: 11/13/2022] Open
Abstract
Protozoa play important roles in microbial communities, regulating populations via predation and contributing to nutrient cycling. While amoebae have been identified in acid rock drainage (ARD) systems, our understanding of their symbioses in these extreme environments is limited. Here, we report the first isolation of the amoeba Stemonitis from an ARD environment as well as the genome sequence and annotation of an associated bacterium, Dyella terrae strain Ely Copper Mine, from Ely Brook at the Ely Copper Mine Superfund site in Vershire, Vermont, United States. Fluorescent in situ hybridization analysis showed this bacterium colonizing cells of Stemonitis sp. in addition to being outside of amoebal cells. This amoeba-resistant bacterium is Gram-negative with a genome size of 5.36 Mbp and GC content of 62.5%. The genome of the D. terrae strain Ely Copper Mine encodes de novo biosynthetic pathways for amino acids, carbohydrates, nucleic acids, and lipids. Genes involved in nitrate (1) and sulfate (7) reduction, metal (229) and antibiotic resistance (37), and secondary metabolite production (6) were identified. Notably, 26 hydrolases were identified by RAST as well as other biomass degradation genes, suggesting roles in carbon and energy cycling within the microbial community. The genome also contains type IV secretion system genes involved in amoebae resistance, revealing how this bacterium likely survives predation from Stemonitis sp. This genome analysis and the association of D. terrae strain Ely Copper Mine with Stemonitis sp. provide insight into the functional roles of amoebae and bacteria within ARD environments.
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Affiliation(s)
- Lesley-Ann Giddings
- Department of Chemistry, Smith College, Northampton, MA, United States.,Department of Chemistry and Biochemistry, Middlebury College, Middlebury, VT, United States
| | - Kevin Kunstman
- Research Resources Center, University of Illinois at Chicago, Chicago, IL, United States
| | - Bouziane Moumen
- Laboratoire Ecologie et Biologie des Interactions, Université de Poitiers, UMR7267, Poitiers, France
| | - Laurent Asiama
- Department of Chemistry and Biochemistry, Middlebury College, Middlebury, VT, United States
| | - Stefan Green
- Research Resources Center, University of Illinois at Chicago, Chicago, IL, United States
| | - Vincent Delafont
- Laboratoire Ecologie et Biologie des Interactions, Université de Poitiers, UMR7267, Poitiers, France
| | - Matthew Brockley
- Department of Chemistry and Biochemistry, Middlebury College, Middlebury, VT, United States
| | - Ascel Samba-Louaka
- Laboratoire Ecologie et Biologie des Interactions, Université de Poitiers, UMR7267, Poitiers, France
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