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Zheng Y, Chai R, Wang T, Xu Z, He Y, Shen P, Liu J. RNA polymerase stalling-derived genome instability underlies ribosomal antibiotic efficacy and resistance evolution. Nat Commun 2024; 15:6579. [PMID: 39097616 PMCID: PMC11297953 DOI: 10.1038/s41467-024-50917-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 07/24/2024] [Indexed: 08/05/2024] Open
Abstract
Bacteria often evolve antibiotic resistance through mutagenesis. However, the processes causing the mutagenesis have not been fully resolved. Here, we find that a broad range of ribosome-targeting antibiotics cause mutations through an underexplored pathway. Focusing on the clinically important aminoglycoside gentamicin, we find that the translation inhibitor causes genome-wide premature stalling of RNA polymerase (RNAP) in a loci-dependent manner. Further analysis shows that the stalling is caused by the disruption of transcription-translation coupling. Anti-intuitively, the stalled RNAPs subsequently induce lesions to the DNA via transcription-coupled repair. While most of the bacteria are killed by genotoxicity, a small subpopulation acquires mutations via SOS-induced mutagenesis. Given that these processes are triggered shortly after antibiotic addition, resistance rapidly emerges in the population. Our work reveals a mechanism of action of ribosomal antibiotics, illustrates the importance of dissecting the complex interplay between multiple molecular processes in understanding antibiotic efficacy, and suggests new strategies for countering the development of resistance.
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Affiliation(s)
- Yayun Zheng
- Center for Infection Biology, School of Basic Medical Sciences, Tsinghua University, Beijing, China
| | - Ruochen Chai
- Center for Infection Biology, School of Basic Medical Sciences, Tsinghua University, Beijing, China
| | - Tianmin Wang
- Center for Infection Biology, School of Basic Medical Sciences, Tsinghua University, Beijing, China.
- Tsinghua-Peking Center for Life Sciences, Beijing, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
| | - Zeqi Xu
- Center for Infection Biology, School of Basic Medical Sciences, Tsinghua University, Beijing, China
| | - Yihui He
- Center for Infection Biology, School of Basic Medical Sciences, Tsinghua University, Beijing, China
| | - Ping Shen
- Center for Infection Biology, School of Basic Medical Sciences, Tsinghua University, Beijing, China
| | - Jintao Liu
- Center for Infection Biology, School of Basic Medical Sciences, Tsinghua University, Beijing, China.
- Tsinghua-Peking Center for Life Sciences, Beijing, China.
- SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, Shanxi Medical University, Taiyuan, Shanxi Province, China.
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Wei X, Guo J, Geng X, Xue B, Huang S, Yuan Z. The Combination of Membrane Disruption and FtsZ Targeting by a Chemotherapeutic Hydrogel Synergistically Combats Pathogens Infections. Adv Healthc Mater 2024; 13:e2304600. [PMID: 38491859 DOI: 10.1002/adhm.202304600] [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: 01/23/2024] [Revised: 02/23/2024] [Indexed: 03/18/2024]
Abstract
The emergence of multidrug-resistant (MDR) bacteria poses a significant challenge to global health. Due to a shortage of antibiotics, alternative therapeutic strategies are urgently needed. Unfortunately, colistin, the last-resort antibiotic, has unavoidable nephrotoxicity and hepatotoxicity, and its single killing mechanism is prone to drug resistance. To address this challenge, a promising combinatorial approach that includes colistin, a membrane-disrupting antimicrobial agent, and chelerythrine (CHE), a FtsZ protein inhibitor is proposed. This approach significantly reduces antibiotic dose and development of resistance, leading to almost complete inactivation of MDR pathogens in vitro. To address solubility issues and ensure transport, the antimicrobial hydrogel system LNP-CHE-CST@hydrogel, which induced reactive oxygen species (ROS) and apoptosis-like cell death by targeting the FtsZ protein, is used. In an in vivo mouse skin infection model, the combination therapy effectively eliminated MDR bacteria within 24 h, as monitored by fluorescence tracking. The findings demonstrate a promising approach for developing multifunctional hydrogels to combat MDR bacterial infections.
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Affiliation(s)
- Xianyuan Wei
- Faculty of Health Sciences and Center for Cognitive and Brain Sciences, University of Macau, Macau, SAR, 999078, China
| | - Jintong Guo
- Faculty of Health Sciences and Center for Cognitive and Brain Sciences, University of Macau, Macau, SAR, 999078, China
| | - Xiaorui Geng
- Faculty of Health Sciences and Center for Cognitive and Brain Sciences, University of Macau, Macau, SAR, 999078, China
| | - Bin Xue
- Faculty of Health Sciences and Center for Cognitive and Brain Sciences, University of Macau, Macau, SAR, 999078, China
- Shenzhen Key Laboratory of Ultraintense Laser and Advanced Material Technology, Center for Intense Laser Application Technology and College of Engineering Physics, Shenzhen Technology University, Shenzhen, 518118, China
| | - Shaohui Huang
- School of Life Sciences, University of Chinese Academy of Sciences, Beijing, 101499, China
- LightEdge Technologies Limited, Zhongshan, Guangdong, 528403, China
| | - Zhen Yuan
- Faculty of Health Sciences and Center for Cognitive and Brain Sciences, University of Macau, Macau, SAR, 999078, China
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3
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Chollet S, Hernandez Padilla AC, Daix T, Gaschet M, François B, Piguet C, Gachard N, Da Re S, Jeannet R, Ploy MC. Phagosomal granulocytic ROS in septic patients induce the bacterial SOS response. iScience 2024; 27:109825. [PMID: 38799552 PMCID: PMC11126768 DOI: 10.1016/j.isci.2024.109825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 09/14/2023] [Accepted: 04/24/2024] [Indexed: 05/29/2024] Open
Abstract
Septic patients with worst clinical prognosis have increased circulating immature granulocytes (IG), displaying limited phagocytosis and reactive oxygen species (ROS) production. Here, we developed an ex vivo model of incubation of human granulocytes, from septic patients or healthy donors, with Escherichia coli. We showed that the ROS production in Sepsis-IG is lower due to decreased activation and protein expression of the NADPH oxidase complex. We also demonstrated that the low level of ROS production and lower phagocytosis of IG in sepsis induce the bacterial SOS response, leading to the expression of the SOS-regulated quinolone resistance gene qnrB2. Without antimicrobial pressure, the sepsis immune response alone may promote antibiotic resistance expression.
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Affiliation(s)
- Stecy Chollet
- University Limoges, Inserm, CHU Limoges, RESINFIT, U 1092, F-87000 Limoges, France
| | | | - Thomas Daix
- University Limoges, Inserm, CHU Limoges, RESINFIT, U 1092, F-87000 Limoges, France
- CHU Limoges, Service de Réanimation Polyvalente, Limoges, France
- Inserm CIC 1435, Limoges, France
| | - Margaux Gaschet
- University Limoges, Inserm, CHU Limoges, RESINFIT, U 1092, F-87000 Limoges, France
| | - Bruno François
- University Limoges, Inserm, CHU Limoges, RESINFIT, U 1092, F-87000 Limoges, France
- CHU Limoges, Service de Réanimation Polyvalente, Limoges, France
- Inserm CIC 1435, Limoges, France
| | | | - Nathalie Gachard
- CHU Limoges, Laboratoire d’hématologie, Limoges, France
- CNRS UMR 7276, Inserm UMR 1262, Université de Limoges, Limoges, France
| | - Sandra Da Re
- University Limoges, Inserm, CHU Limoges, RESINFIT, U 1092, F-87000 Limoges, France
| | - Robin Jeannet
- Inserm CIC 1435, Limoges, France
- CNRS UMR 7276, Inserm UMR 1262, Université de Limoges, Limoges, France
| | - Marie-Cécile Ploy
- University Limoges, Inserm, CHU Limoges, RESINFIT, U 1092, F-87000 Limoges, France
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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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5
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Soto KD, Alcalde-Rico M, Ugalde JA, Olivares-Pacheco J, Quiroz V, Brito B, Rivas LM, Munita JM, García PC, Wozniak A. Ceftazidime/avibactam resistance is associated with PER-3-producing ST309 lineage in Chilean clinical isolates of non-carbapenemase producing Pseudomonas aeruginosa. Front Cell Infect Microbiol 2024; 14:1410834. [PMID: 38903939 PMCID: PMC11188487 DOI: 10.3389/fcimb.2024.1410834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Accepted: 05/13/2024] [Indexed: 06/22/2024] Open
Abstract
Introduction Ceftazidime/avibactam (CZA) is indicated against multidrug-resistant Pseudomonas aeruginosa, particularly those that are carbapenem resistant. CZA resistance in P. aeruginosa producing PER, a class A extended-spectrum β-lactamase, has been well documented in vitro. However, data regarding clinical isolates are scarce. Our aim was to analyze the contribution of PER to CZA resistance in non-carbapenemase-producing P. aeruginosa clinical isolates that were ceftazidime and/or carbapenem non-susceptible. Methods Antimicrobial susceptibility was determined through agar dilution and broth microdilution, while bla PER gene was screened through PCR. All PER-positive isolates and five PER-negative isolates were analyzed through Whole Genome Sequencing. The mutational resistome associated to CZA resistance was determined through sequence analysis of genes coding for PBPs 1b, 3 and 4, MexAB-OprM regulators MexZ, MexR, NalC and NalD, AmpC regulators AmpD and AmpR, and OprD porin. Loss of bla PER-3 gene was induced in a PER-positive isolate by successive passages at 43°C without antibiotics. Results Twenty-six of 287 isolates studied (9.1%) were CZA-resistant. Thirteen of 26 CZA-resistant isolates (50%) carried bla PER. One isolate carried bla PER but was CZA-susceptible. PER-producing isolates had significantly higher MICs for CZA, amikacin, gentamicin, ceftazidime, meropenem and ciprofloxacin than non-PER-producing isolates. All PER-producing isolates were ST309 and their bla PER-3 gene was associated to ISCR1, an insertion sequence known to mobilize adjacent DNA. PER-negative isolates were classified as ST41, ST235 (two isolates), ST395 and ST253. PER-negative isolates carried genes for narrow-spectrum β-lactamases and the mutational resistome showed that all isolates had one major alteration in at least one of the genes analyzed. Loss of bla PER-3 gene restored susceptibility to CZA, ceftolozane/tazobactam and other β-lactamsin the in vitro evolved isolate. Discussion PER-3-producing ST309 P. aeruginosa is a successful multidrug-resistant clone with blaPER-3 gene implicated in resistance to CZA and other β-lactams.
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Affiliation(s)
- Katherine D. Soto
- Laboratory of Microbiology, Department of Clinical Laboratories; Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Manuel Alcalde-Rico
- Instituto de Ciencias e Innovación en Medicina (ICIM), Facultad de Medicina, Universidad del Desarrollo. Millennium Initiative for Collaborative Research on Bacterial Resistance (MICROB-R), Santiago, Chile
- Grupo de Resistencia Antimicrobiana en Bacterias Patógenas y Ambientales (GRABPA), Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen Macarena, Consejo Superior de Investigaciones Científicas (CSIC), Universidad de Sevilla, Sevilla, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - Juan A. Ugalde
- Instituto de Ciencias e Innovación en Medicina (ICIM), Facultad de Medicina, Universidad del Desarrollo. Millennium Initiative for Collaborative Research on Bacterial Resistance (MICROB-R), Santiago, Chile
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Jorge Olivares-Pacheco
- Instituto de Ciencias e Innovación en Medicina (ICIM), Facultad de Medicina, Universidad del Desarrollo. Millennium Initiative for Collaborative Research on Bacterial Resistance (MICROB-R), Santiago, Chile
- Grupo de Resistencia Antimicrobiana en Bacterias Patógenas y Ambientales (GRABPA), Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Valeria Quiroz
- Laboratory of Microbiology, Department of Clinical Laboratories; Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
- Genomics and Resistant Microbes Group (GeRM), Instituto de Ciencias e Innovación en Medicina (ICIM), Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago, Chile
| | - Bárbara Brito
- Australian Institute for Microbiology and Infection, Faculty of Science, University of Technology Sydney, Sydney, NSW, Australia
| | - Lina M. Rivas
- Instituto de Ciencias e Innovación en Medicina (ICIM), Facultad de Medicina, Universidad del Desarrollo. Millennium Initiative for Collaborative Research on Bacterial Resistance (MICROB-R), Santiago, Chile
- Genomics and Resistant Microbes Group (GeRM), Instituto de Ciencias e Innovación en Medicina (ICIM), Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago, Chile
| | - José M. Munita
- Instituto de Ciencias e Innovación en Medicina (ICIM), Facultad de Medicina, Universidad del Desarrollo. Millennium Initiative for Collaborative Research on Bacterial Resistance (MICROB-R), Santiago, Chile
- Genomics and Resistant Microbes Group (GeRM), Instituto de Ciencias e Innovación en Medicina (ICIM), Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago, Chile
| | - Patricia C. García
- Laboratory of Microbiology, Department of Clinical Laboratories; Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
- Instituto de Ciencias e Innovación en Medicina (ICIM), Facultad de Medicina, Universidad del Desarrollo. Millennium Initiative for Collaborative Research on Bacterial Resistance (MICROB-R), Santiago, Chile
- Clinical Laboratories Network, Red de Salud UC-CHRISTUS, Santiago, Chile
| | - Aniela Wozniak
- Laboratory of Microbiology, Department of Clinical Laboratories; Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
- Instituto de Ciencias e Innovación en Medicina (ICIM), Facultad de Medicina, Universidad del Desarrollo. Millennium Initiative for Collaborative Research on Bacterial Resistance (MICROB-R), Santiago, Chile
- Clinical Laboratories Network, Red de Salud UC-CHRISTUS, Santiago, Chile
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Skutel M, Yanovskaya D, Demkina A, Shenfeld A, Musharova O, Severinov K, Isaev A. RecA-dependent or independent recombination of plasmid DNA generates a conflict with the host EcoKI immunity by launching restriction alleviation. Nucleic Acids Res 2024; 52:5195-5208. [PMID: 38567730 PMCID: PMC11109961 DOI: 10.1093/nar/gkae243] [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: 09/19/2023] [Revised: 03/17/2024] [Accepted: 03/22/2024] [Indexed: 05/23/2024] Open
Abstract
Bacterial defence systems are tightly regulated to avoid autoimmunity. In Type I restriction-modification (R-M) systems, a specific mechanism called restriction alleviation (RA) controls the activity of the restriction module. In the case of the Escherichia coli Type I R-M system EcoKI, RA proceeds through ClpXP-mediated proteolysis of restriction complexes bound to non-methylated sites that appear after replication or reparation of host DNA. Here, we show that RA is also induced in the presence of plasmids carrying EcoKI recognition sites, a phenomenon we refer to as plasmid-induced RA. Further, we show that the anti-restriction behavior of plasmid-borne non-conjugative transposons such as Tn5053, previously attributed to their ardD loci, is due to plasmid-induced RA. Plasmids carrying both EcoKI and Chi sites induce RA in RecA- and RecBCD-dependent manner. However, inactivation of both RecA and RecBCD restores RA, indicating that there exists an alternative, RecA-independent, homologous recombination pathway that is blocked in the presence of RecBCD. Indeed, plasmid-induced RA in a RecBCD-deficient background does not depend on the presence of Chi sites. We propose that processing of random dsDNA breaks in plasmid DNA via homologous recombination generates non-methylated EcoKI sites, which attract EcoKI restriction complexes channeling them for ClpXP-mediated proteolysis.
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Affiliation(s)
- Mikhail Skutel
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Daria Yanovskaya
- Skolkovo Institute of Science and Technology, Moscow, Russia
- Moscow Institute of Physics and Technology, Moscow, Russia
| | - Alina Demkina
- Skolkovo Institute of Science and Technology, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | | | - Olga Musharova
- Skolkovo Institute of Science and Technology, Moscow, Russia
- Institute of Molecular Genetics, National Research Center Kurchatov Institute, Moscow, Russia
| | - Konstantin Severinov
- Waksman Institute of Microbiology, Piscataway, USA
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Artem Isaev
- Skolkovo Institute of Science and Technology, Moscow, Russia
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Jing W, Guo R, Zhu X, Peng S, Li H, Xu D, Hu L, Mo H. Ferrous gluconate triggers ferroptosis in Escherichia coli: Implications of lipid peroxidation and DNA damage. Microbiol Res 2024; 284:127711. [PMID: 38636240 DOI: 10.1016/j.micres.2024.127711] [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: 03/13/2024] [Revised: 03/28/2024] [Accepted: 04/01/2024] [Indexed: 04/20/2024]
Abstract
Microbial ferroptosis has been proved to combat drug-resistant pathogens, but whether this pattern can be applied to the prevention and control of Escherichia coli remains to be further explored. In this study, ferrous gluconate (FeGlu) showed remarkable efficacy in killing E. coli MG1655 with a mortality rate exceeding 99.9%, as well as enterotoxigenic E. coli H10407 (ETEC H10407) and enterohemorrhagic E. coli O157:H7 (EHEC O157:H7). Bacteria death was instigated by the infiltration of Fe2+, accompanied by a burst of intracellular reactive oxygen species (ROS) and lipid peroxidation. Notably, mitigating lipid peroxidation failed to alleviate death of E. coli. Further findings confirmed that FeGlu induced DNA damage, and ΔrecA mutant showed more sensitive, implicating that DNA damage was involved in the death of E. coli. The direct interaction of Fe2+ with DNA was demonstrated by fluorescent staining, gel electrophoresis, and circular dichroism (CD). Moreover, proteomic analysis unveiled 50 differentially expressed proteins (DEPs), including 18 significantly down-regulated proteins and 32 significantly up-regulated proteins. Among them, the down-regulation of SOS-responsive transcriptional suppressor LexA indicated DNA damage induced severely by FeGlu. Furthermore, FeGlu influenced pathways such as fatty acid metabolism (FadB, FadE), iron-sulfur cluster assembly (IscA, IscU, YadR), iron binding, and DNA-binding transcription, along with α-linolenic acid metabolism, fatty acid degradation, and pyruvate metabolism. These pathways were related to FeGlu stress, including lipid peroxidation and DNA damage. In summary, FeGlu facilitated ferroptosis in E. coli through mechanisms involving lipid peroxidation and DNA damage, which presents a new strategy for the development of innovative antimicrobial strategies targeting E. coli infections.
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Affiliation(s)
- Wenhui Jing
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China
| | - Rongxian Guo
- Laboratory of Functional Microbiology and Animal Health, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471003, China; Luoyang Key Laboratory of Live Carrier Biomaterial and Animal Disease Prevention and Control, Luoyang 471003, China
| | - Xiaolin Zhu
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China
| | - Shurui Peng
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China
| | - Hongbo Li
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China
| | - Dan Xu
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China
| | - Liangbin Hu
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China.
| | - Haizhen Mo
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China.
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Richard E, Darracq B, Littner E, Millot GA, Conte V, Cokelaer T, Engelstädter J, Rocha EPC, Mazel D, Loot C. Belt and braces: Two escape ways to maintain the cassette reservoir of large chromosomal integrons. PLoS Genet 2024; 20:e1011231. [PMID: 38578806 PMCID: PMC11023631 DOI: 10.1371/journal.pgen.1011231] [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: 10/20/2023] [Revised: 04/17/2024] [Accepted: 03/19/2024] [Indexed: 04/07/2024] Open
Abstract
Integrons are adaptive devices that capture, stockpile, shuffle and express gene cassettes thereby sampling combinatorial phenotypic diversity. Some integrons called sedentary chromosomal integrons (SCIs) can be massive structures containing hundreds of cassettes. Since most of these cassettes are non-expressed, it is not clear how they remain stable over long evolutionary timescales. Recently, it was found that the experimental inversion of the SCI of Vibrio cholerae led to a dramatic increase of the cassette excision rate associated with a fitness defect. Here, we question the evolutionary sustainability of this apparently counter selected genetic context. Through experimental evolution, we find that the integrase is rapidly inactivated and that the inverted SCI can recover its original orientation by homologous recombination between two insertion sequences (ISs) present in the array. These two outcomes of SCI inversion restore the normal growth and prevent the loss of cassettes, enabling SCIs to retain their roles as reservoirs of functions. These results illustrate a nice interplay between gene orientation, genome rearrangement, bacterial fitness and demonstrate how integrons can benefit from their embedded ISs.
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Affiliation(s)
- Egill Richard
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Unité Plasticité du Génome Bactérien, Paris, France
- Sorbonne Université, ED515, Paris, France
| | - Baptiste Darracq
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Unité Plasticité du Génome Bactérien, Paris, France
- Sorbonne Université, ED515, Paris, France
| | - Eloi Littner
- Sorbonne Université, ED515, Paris, France
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris, France
- DGA CBRN Defence, Vert-le-Petit, France
| | - Gael A. Millot
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, Paris, France
| | - Valentin Conte
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Unité Plasticité du Génome Bactérien, Paris, France
| | - Thomas Cokelaer
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, Paris, France
- Institut Pasteur, Université Paris Cité, Plateforme Technologique Biomics, Paris, France
| | - Jan Engelstädter
- School of the Environment, The University of Queensland, Brisbane, Australia
| | - Eduardo P. C. Rocha
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris, France
| | - Didier Mazel
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Unité Plasticité du Génome Bactérien, Paris, France
| | - Céline Loot
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Unité Plasticité du Génome Bactérien, Paris, France
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Fang Y, Chen C, Cui B, Zhou D. Nanoscale zero-valent iron alleviate antibiotic resistance risk during managed aquifer recharge (MAR) by regulating denitrifying bacterial network. JOURNAL OF HAZARDOUS MATERIALS 2024; 465:133238. [PMID: 38134694 DOI: 10.1016/j.jhazmat.2023.133238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 11/05/2023] [Accepted: 12/10/2023] [Indexed: 12/24/2023]
Abstract
The frequent occurrence of antibiotics in reclaimed water is concerning, in the case of managed aquifer recharge (MAR), it inevitably hinders further water purification and accelerates the evolutionary resistance in indigenous bacteria. In this study, we constructed two column reactors and nanoscale zero-valent iron (nZVI) amendment was applied for its effects on water quality variation, microbial community succession, and antibiotic resistance genes (ARGs) dissemination, deciphered the underlying mechanism of resistance risk reduction. Results showed that nZVI was oxidized to iron oxides in the sediment column, and total effluent iron concentration was within permissible limits. nZVI enhanced NO3--N removal by 15.5% through enriching denitrifying bacteria and genes, whereas made no effects on oxacillin (OXA) removal. In addition, nZVI exhibited a pivotal impact on ARGs and plasmids decreasing. Network analysis elucidated that the diversity and richness of ARG host declined with nZVI amendment. Denitrifying bacteria play a key role in suppressing horizontal gene transfer (HGT). The underlying mechanisms of inhibited HGT included the downregulated SOS response, the inhibited Type-Ⅳ secretion system and the weakened driving force. This study afforded vital insights into ARG spread control, providing a reference for future applications of nZVI in MAR.
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Affiliation(s)
- Yuanping Fang
- Engineering Research Center of Low-Carbon Treatment and Green Development of Polluted Water in Northeast China, Ministry of Education, Northeast Normal University, Changchun 130117, China; Jilin Engineering Lab for Water Pollution Control and Resources Recovery, Northeast Normal University, Changchun 130117, China
| | - Congli Chen
- Engineering Research Center of Low-Carbon Treatment and Green Development of Polluted Water in Northeast China, Ministry of Education, Northeast Normal University, Changchun 130117, China; Jilin Engineering Lab for Water Pollution Control and Resources Recovery, Northeast Normal University, Changchun 130117, China
| | - Bin Cui
- Engineering Research Center of Low-Carbon Treatment and Green Development of Polluted Water in Northeast China, Ministry of Education, Northeast Normal University, Changchun 130117, China; Jilin Engineering Lab for Water Pollution Control and Resources Recovery, Northeast Normal University, Changchun 130117, China.
| | - Dandan Zhou
- Engineering Research Center of Low-Carbon Treatment and Green Development of Polluted Water in Northeast China, Ministry of Education, Northeast Normal University, Changchun 130117, China; Jilin Engineering Lab for Water Pollution Control and Resources Recovery, Northeast Normal University, Changchun 130117, China.
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10
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Richard E, Darracq B, Littner E, Vit C, Whiteway C, Bos J, Fournes F, Garriss G, Conte V, Lapaillerie D, Parissi V, Rousset F, Skovgaard O, Bikard D, Rocha EPC, Mazel D, Loot C. Cassette recombination dynamics within chromosomal integrons are regulated by toxin-antitoxin systems. SCIENCE ADVANCES 2024; 10:eadj3498. [PMID: 38215203 DOI: 10.1126/sciadv.adj3498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 12/14/2023] [Indexed: 01/14/2024]
Abstract
Integrons are adaptive bacterial devices that rearrange promoter-less gene cassettes into variable ordered arrays under stress conditions, thereby sampling combinatorial phenotypic diversity. Chromosomal integrons often carry hundreds of silent gene cassettes, with integrase-mediated recombination leading to rampant DNA excision and integration, posing a potential threat to genome integrity. How this activity is regulated and controlled, particularly through selective pressures, to maintain such large cassette arrays is unknown. Here, we show a key role of promoter-containing toxin-antitoxin (TA) cassettes as systems that kill the cell when the overall cassette excision rate is too high. These results highlight the importance of TA cassettes regulating the cassette recombination dynamics and provide insight into the evolution and success of integrons in bacterial genomes.
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Affiliation(s)
- Egill Richard
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Unité Plasticité du Génome Bactérien, 75015 Paris, France
- Sorbonne Université, ED515, F-75005 Paris, France
| | - Baptiste Darracq
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Unité Plasticité du Génome Bactérien, 75015 Paris, France
- Sorbonne Université, ED515, F-75005 Paris, France
| | - Eloi Littner
- Sorbonne Université, ED515, F-75005 Paris, France
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, 75015 Paris, France
- DGA CBRN Defence, 91710 Vert-le-Petit, France
| | - Claire Vit
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Unité Plasticité du Génome Bactérien, 75015 Paris, France
- Sorbonne Université, ED515, F-75005 Paris, France
| | - Clémence Whiteway
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Unité Plasticité du Génome Bactérien, 75015 Paris, France
| | - Julia Bos
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Unité Plasticité du Génome Bactérien, 75015 Paris, France
| | - Florian Fournes
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Unité Plasticité du Génome Bactérien, 75015 Paris, France
| | - Geneviève Garriss
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Unité Plasticité du Génome Bactérien, 75015 Paris, France
| | - Valentin Conte
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Unité Plasticité du Génome Bactérien, 75015 Paris, France
| | - Delphine Lapaillerie
- University of Bordeaux, Fundamental Microbiology and Pathogenicity Laboratory, CNRS, UMR 5234, SFR TransBioMed, Bordeaux, France
- Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), France
| | - Vincent Parissi
- University of Bordeaux, Fundamental Microbiology and Pathogenicity Laboratory, CNRS, UMR 5234, SFR TransBioMed, Bordeaux, France
- Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), France
| | - François Rousset
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Synthetic Biology, 75015 Paris, France
| | - Ole Skovgaard
- Department of Science, Systems and Models, Roskilde University, Roskilde DK-4000, Denmark
| | - David Bikard
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Synthetic Biology, 75015 Paris, France
| | - Eduardo P C Rocha
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, 75015 Paris, France
| | - Didier Mazel
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Unité Plasticité du Génome Bactérien, 75015 Paris, France
| | - Céline Loot
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Unité Plasticité du Génome Bactérien, 75015 Paris, France
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11
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Loot C, Millot GA, Richard E, Littner E, Vit C, Lemoine F, Néron B, Cury J, Darracq B, Niault T, Lapaillerie D, Parissi V, Rocha EPC, Mazel D. Integron cassettes integrate into bacterial genomes via widespread non-classical attG sites. Nat Microbiol 2024; 9:228-240. [PMID: 38172619 DOI: 10.1038/s41564-023-01548-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 11/07/2023] [Indexed: 01/05/2024]
Abstract
Integrons are genetic elements involved in bacterial adaptation which capture, shuffle and express genes encoding adaptive functions embedded in cassettes. These events are governed by the integron integrase through site-specific recombination between attC and attI integron sites. Using computational and molecular genetic approaches, here we demonstrate that the integrase also catalyses cassette integration into bacterial genomes outside of its known att sites. Once integrated, these cassettes can be expressed if located near bacterial promoters and can be excised at the integration point or outside, inducing chromosomal modifications in the latter case. Analysis of more than 5 × 105 independent integration events revealed a very large genomic integration landscape. We identified consensus recombination sequences, named attG sites, which differ greatly in sequence and structure from classical att sites. These results unveil an alternative route for dissemination of adaptive functions in bacteria and expand the role of integrons in bacterial evolution.
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Affiliation(s)
- Céline Loot
- Institut Pasteur, Université Paris Cité, CNRS UMR 3525, Unité Plasticité du Génome Bactérien, Paris, France.
| | - Gael A Millot
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, Paris, France
| | - Egill Richard
- Institut Pasteur, Université Paris Cité, CNRS UMR 3525, Unité Plasticité du Génome Bactérien, Paris, France
- Sorbonne Université, Collège Doctoral, Paris, France
| | - Eloi Littner
- Sorbonne Université, Collège Doctoral, Paris, France
- DGA CBRN Defence, Vert-le-Petit, France
- Institut Pasteur, Université Paris Cité, CNRS UMR 3525, Microbial Evolutionary Genomics, Paris, France
| | - Claire Vit
- Institut Pasteur, Université Paris Cité, CNRS UMR 3525, Unité Plasticité du Génome Bactérien, Paris, France
- Sorbonne Université, Collège Doctoral, Paris, France
| | - Frédéric Lemoine
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, Paris, France
| | - Bertrand Néron
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, Paris, France
| | - Jean Cury
- Université Paris-Saclay, Inria, Laboratoire de Recherche en Informatique, CNRS UMR 8623, Orsay, France
| | - Baptiste Darracq
- Institut Pasteur, Université Paris Cité, CNRS UMR 3525, Unité Plasticité du Génome Bactérien, Paris, France
- Sorbonne Université, Collège Doctoral, Paris, France
| | - Théophile Niault
- Institut Pasteur, Université Paris Cité, CNRS UMR 3525, Unité Plasticité du Génome Bactérien, Paris, France
- Sorbonne Université, Collège Doctoral, Paris, France
| | - Delphine Lapaillerie
- Université de Bordeaux, Fundamental Microbiology and Pathogenicity Laboratory, CNRS UMR 5234, Département de Sciences Biologiques et Médicales, Bordeaux, France
- Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), Bordeaux, France
| | - Vincent Parissi
- Université de Bordeaux, Fundamental Microbiology and Pathogenicity Laboratory, CNRS UMR 5234, Département de Sciences Biologiques et Médicales, Bordeaux, France
- Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), Bordeaux, France
| | - Eduardo P C Rocha
- Institut Pasteur, Université Paris Cité, CNRS UMR 3525, Microbial Evolutionary Genomics, Paris, France
| | - Didier Mazel
- Institut Pasteur, Université Paris Cité, CNRS UMR 3525, Unité Plasticité du Génome Bactérien, Paris, France
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12
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Ghaly TM, Rajabal V, Penesyan A, Coleman NV, Paulsen IT, Gillings MR, Tetu SG. Functional enrichment of integrons: Facilitators of antimicrobial resistance and niche adaptation. iScience 2023; 26:108301. [PMID: 38026211 PMCID: PMC10661359 DOI: 10.1016/j.isci.2023.108301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 10/11/2023] [Accepted: 10/19/2023] [Indexed: 12/01/2023] Open
Abstract
Integrons are genetic elements, found among diverse bacteria and archaea, that capture and rearrange gene cassettes to rapidly generate genetic diversity and drive adaptation. Despite their broad taxonomic and geographic prevalence, and their role in microbial adaptation, the functions of gene cassettes remain poorly characterized. Here, using a combination of bioinformatic and experimental analyses, we examined the functional diversity of gene cassettes from different environments. We find that cassettes encode diverse antimicrobial resistance (AMR) determinants, including those conferring resistance to antibiotics currently in the developmental pipeline. Further, we find a subset of cassette functions is universally enriched relative to their broader metagenomes. These are largely involved in (a)biotic interactions, including AMR, phage defense, virulence, biodegradation, and stress tolerance. The remainder of functions are sample-specific, suggesting that they confer localised functions relevant to their microenvironment. Together, they comprise functional profiles different from bulk metagenomes, representing niche-adaptive components of the prokaryotic pangenome.
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Affiliation(s)
- Timothy M. Ghaly
- School of Natural Sciences, Macquarie University, New South Wales 2109, Australia
| | - Vaheesan Rajabal
- School of Natural Sciences, Macquarie University, New South Wales 2109, Australia
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, New South Wales 2109, Australia
| | - Anahit Penesyan
- School of Natural Sciences, Macquarie University, New South Wales 2109, Australia
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, New South Wales 2109, Australia
| | - Nicholas V. Coleman
- School of Natural Sciences, Macquarie University, New South Wales 2109, Australia
| | - Ian T. Paulsen
- School of Natural Sciences, Macquarie University, New South Wales 2109, Australia
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, New South Wales 2109, Australia
| | - Michael R. Gillings
- School of Natural Sciences, Macquarie University, New South Wales 2109, Australia
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, New South Wales 2109, Australia
| | - Sasha G. Tetu
- School of Natural Sciences, Macquarie University, New South Wales 2109, Australia
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, New South Wales 2109, Australia
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13
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Baltazar-Cruz J, Rojas-Rios R, Larios-Serrato V, Mendoza-Sanchez I, Curiel-Quesada E, Pérez-Valdespino A. A Class 4-like Chromosomal Integron Found in Aeromonas sp. Genomospecies paramedia Isolated from Human Feces. Microorganisms 2023; 11:2548. [PMID: 37894206 PMCID: PMC10609294 DOI: 10.3390/microorganisms11102548] [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: 09/08/2023] [Revised: 09/29/2023] [Accepted: 10/12/2023] [Indexed: 10/29/2023] Open
Abstract
Integrons are genetic elements that store, express and exchange gene cassettes. These elements are characterized by containing a gene that codes for an integrase (intI), a cassette integration site (attI) and a variable region holding the cassettes. Using bioinformatics and molecular biology methods, a functional integron found in Aeromonas sp. 3925, a strain isolated from diarrheal stools, is described. To confirm the integron class, a phylogenetic analysis with amino acid sequences was conducted. The integrase was associated to class 4 integrases; however, it is clearly different from them. Thus, we classified the associated element as a class 4-like integron. We found that the integrase activity is not under the control of the SOS or catabolic repression, since the expression was not increased in the presence of mitomycin or arabinose. The class-4-like integron is located on the chromosome and contains two well-defined gene cassettes: aadA1 that confers resistance to streptomycin and lpt coding for a lipoprotein. It also includes eight Open Reading frames (ORFs) with unknown functions. The strain was characterized through a Multilocus Phylogenetic Analyses (MLPA) of the gyrB, gyrA, rpoD, recA, dnaJ and dnaX genes. The phylogenetic results grouped it into a different clade from the species already reported, making it impossible to assign a species. We resorted to undertaking complete genome sequencing and a phylogenomic analysis. Aeromonas sp. 3925 is related to A. media and A. rivipollensis clusters, but it is clearly different from these species. In silico DNA-DNA hybridization (isDDH) and Average Nucleotide Identity (ANI) analyses suggested that this isolate belongs to the genomospecies paramedia. This paper describes the first class 4-like integron in Aeromonas and contributes to the establishment of genomospecies paramedia.
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Affiliation(s)
- Jesús Baltazar-Cruz
- Department of Biochemistry, Escuela Nacional de Ciencias Biológicas del Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Col. Santo Tomás, Mexico City 11340, Mexico; (J.B.-C.); (R.R.-R.); (V.L.-S.)
| | - Rogelio Rojas-Rios
- Department of Biochemistry, Escuela Nacional de Ciencias Biológicas del Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Col. Santo Tomás, Mexico City 11340, Mexico; (J.B.-C.); (R.R.-R.); (V.L.-S.)
| | - Violeta Larios-Serrato
- Department of Biochemistry, Escuela Nacional de Ciencias Biológicas del Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Col. Santo Tomás, Mexico City 11340, Mexico; (J.B.-C.); (R.R.-R.); (V.L.-S.)
| | - Itza Mendoza-Sanchez
- Department of Environmental & Occupational Health, Texas A&M University School of Public Health, College Station, TX 77843, USA;
| | - Everardo Curiel-Quesada
- Department of Biochemistry, Escuela Nacional de Ciencias Biológicas del Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Col. Santo Tomás, Mexico City 11340, Mexico; (J.B.-C.); (R.R.-R.); (V.L.-S.)
| | - Abigail Pérez-Valdespino
- Department of Biochemistry, Escuela Nacional de Ciencias Biológicas del Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Col. Santo Tomás, Mexico City 11340, Mexico; (J.B.-C.); (R.R.-R.); (V.L.-S.)
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14
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Buelow E, Dauga C, Carrion C, Mathé-Hubert H, Achaibou S, Gaschet M, Jové T, Chesneau O, Kennedy SP, Ploy MC, Da Re S, Dagot C. Hospital and urban wastewaters shape the matrix and active resistome of environmental biofilms. WATER RESEARCH 2023; 244:120408. [PMID: 37678036 DOI: 10.1016/j.watres.2023.120408] [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: 03/12/2023] [Revised: 07/22/2023] [Accepted: 07/24/2023] [Indexed: 09/09/2023]
Abstract
Understanding the dynamics of antibiotic resistance gene (ARG) transfer and dissemination in natural environments remains challenging. Biofilms play a crucial role in bacterial survival and antimicrobial resistance (AMR) dissemination in natural environments, particularly in aquatic systems. This study focused on hospital and urban wastewater (WW) biofilms to investigate the potential for ARG dissemination through mobile genetic elements (MGEs). The analysis included assessing the biofilm extracellular polymeric substances (EPS), microbiota composition as well as metatranscriptomic profiling of the resistome and mobilome. We produced both in vitro and in situ biofilms and performed phenotypic and genomic analyses. In the in vitro setup, untreated urban and hospital WW was used to establish biofilm reactors, with ciprofloxacin added as a selective agent at minimal selective concentration. In the in situ setup, biofilms were developed directly in hospital and urban WW pipes. We first showed that a) the composition of EPS differed depending on the growth environment (in situ and in vitro) and the sampling origin (hospital vs urban WW) and that b) ciprofloxacin impacted the composition of the EPS. The metatranscriptomic approach showed that a) expression of several ARGs and MGEs increased upon adding ciprofloxacin for biofilms from hospital WW only and b) that the abundance and type of plasmids that carried individual or multiple ARGs varied depending on the WW origins of the biofilms. When the same plasmids were present in both, urban and hospital WW biofilms, they carried different ARGs. We showed that hospital and urban wastewaters shaped the structure and active resistome of environmental biofilms, and we confirmed that hospital WW is an important hot spot for the dissemination and selection of antimicrobial resistance. Our study provides a comprehensive assessment of WW biofilms as crucial hotspots for ARG transfer. Hospital WW biofilms exhibited distinct characteristics, including higher eDNA abundance and expression levels of ARGs and MGEs, highlighting their role in antimicrobial resistance dissemination. These findings emphasize the importance of understanding the structural, ecological, functional, and genetic organization of biofilms in anthropized environments and their contribution to antibiotic resistance dynamics.
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Affiliation(s)
- Elena Buelow
- INSERM, CHU Limoges, RESINFIT, U1092, Univ. Limoges, F-87000, Limoges, France; CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, Univ. Grenoble Alpes, 38000, Grenoble, France.
| | - Catherine Dauga
- Institut Pasteur, Département Biologie Computationnelle, Université Paris Cité, F-75015, Paris, France; Biomics Pole, CITECH, Institut Pasteur, F-75015, Paris, France
| | - Claire Carrion
- CNRS, INSERM, CHU Limoges, BISCEm, UAR 2015, US 42, Univ. Limoges, F-87000, Limoges, France
| | - Hugo Mathé-Hubert
- CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, Univ. Grenoble Alpes, 38000, Grenoble, France
| | - Sophia Achaibou
- Biomics Pole, CITECH, Institut Pasteur, F-75015, Paris, France
| | - Margaux Gaschet
- INSERM, CHU Limoges, RESINFIT, U1092, Univ. Limoges, F-87000, Limoges, France
| | - Thomas Jové
- INSERM, CHU Limoges, RESINFIT, U1092, Univ. Limoges, F-87000, Limoges, France
| | - Olivier Chesneau
- Collection de l'Institut Pasteur (CIP), Microbiology Department, Institut Pasteur, Paris, 75015, France
| | - Sean P Kennedy
- Institut Pasteur, Département Biologie Computationnelle, Université Paris Cité, F-75015, Paris, France
| | - Marie-Cecile Ploy
- INSERM, CHU Limoges, RESINFIT, U1092, Univ. Limoges, F-87000, Limoges, France
| | - Sandra Da Re
- INSERM, CHU Limoges, RESINFIT, U1092, Univ. Limoges, F-87000, Limoges, France
| | - Christophe Dagot
- INSERM, CHU Limoges, RESINFIT, U1092, Univ. Limoges, F-87000, Limoges, France
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15
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Pan X, Liu W, Du Q, Zhang H, Han D. Recent Advances in Bacterial Persistence Mechanisms. Int J Mol Sci 2023; 24:14311. [PMID: 37762613 PMCID: PMC10531727 DOI: 10.3390/ijms241814311] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 09/13/2023] [Accepted: 09/15/2023] [Indexed: 09/29/2023] Open
Abstract
The recurrence of bacterial infectious diseases is closely associated with bacterial persisters. This subpopulation of bacteria can escape antibiotic treatment by entering a metabolic status of low activity through various mechanisms, for example, biofilm, toxin-antitoxin modules, the stringent response, and the SOS response. Correspondingly, multiple new treatments are being developed. However, due to their spontaneous low abundance in populations and the lack of research on in vivo interactions between persisters and the host's immune system, microfluidics, high-throughput sequencing, and microscopy techniques are combined innovatively to explore the mechanisms of persister formation and maintenance at the single-cell level. Here, we outline the main mechanisms of persister formation, and describe the cutting-edge technology for further research. Despite the significant progress regarding study techniques, some challenges remain to be tackled.
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Affiliation(s)
- Xiaozhou Pan
- Department of Clinical Laboratory, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200062, China
- Institute of Pediatric Infection, Immunity, and Critical Care Medicine, School of Medicine, Shanghai Jiao Tong University, Shanghai 200062, China
| | - Wenxin Liu
- Department of Clinical Laboratory, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200062, China
- Institute of Pediatric Infection, Immunity, and Critical Care Medicine, School of Medicine, Shanghai Jiao Tong University, Shanghai 200062, China
| | - Qingqing Du
- Department of Clinical Laboratory, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200062, China
- Institute of Pediatric Infection, Immunity, and Critical Care Medicine, School of Medicine, Shanghai Jiao Tong University, Shanghai 200062, China
| | - Hong Zhang
- Department of Clinical Laboratory, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200062, China
- Institute of Pediatric Infection, Immunity, and Critical Care Medicine, School of Medicine, Shanghai Jiao Tong University, Shanghai 200062, China
| | - Dingding Han
- Department of Clinical Laboratory, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200062, China
- Institute of Pediatric Infection, Immunity, and Critical Care Medicine, School of Medicine, Shanghai Jiao Tong University, Shanghai 200062, China
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16
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Weisberg AJ, Chang JH. Mobile Genetic Element Flexibility as an Underlying Principle to Bacterial Evolution. Annu Rev Microbiol 2023; 77:603-624. [PMID: 37437216 DOI: 10.1146/annurev-micro-032521-022006] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/14/2023]
Abstract
Mobile genetic elements are key to the evolution of bacteria and traits that affect host and ecosystem health. Here, we use a framework of a hierarchical and modular system that scales from genes to populations to synthesize recent findings on mobile genetic elements (MGEs) of bacteria. Doing so highlights the role that emergent properties of flexibility, robustness, and genetic capacitance of MGEs have on the evolution of bacteria. Some of their traits can be stored, shared, and diversified across different MGEs, taxa of bacteria, and time. Collectively, these properties contribute to maintaining functionality against perturbations while allowing changes to accumulate in order to diversify and give rise to new traits. These properties of MGEs have long challenged our abilities to study them. Implementation of new technologies and strategies allows for MGEs to be analyzed in new and powerful ways.
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Affiliation(s)
- Alexandra J Weisberg
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA;
| | - Jeff H Chang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA;
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17
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Bhat BA, Mir RA, Qadri H, Dhiman R, Almilaibary A, Alkhanani M, Mir MA. Integrons in the development of antimicrobial resistance: critical review and perspectives. Front Microbiol 2023; 14:1231938. [PMID: 37720149 PMCID: PMC10500605 DOI: 10.3389/fmicb.2023.1231938] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 08/14/2023] [Indexed: 09/19/2023] Open
Abstract
Antibiotic resistance development and pathogen cross-dissemination are both considered essential risks to human health on a worldwide scale. Antimicrobial resistance genes (AMRs) are acquired, expressed, disseminated, and traded mainly through integrons, the key players capable of transferring genes from bacterial chromosomes to plasmids and their integration by integrase to the target pathogenic host. Moreover, integrons play a central role in disseminating and assembling genes connected with antibiotic resistance in pathogenic and commensal bacterial species. They exhibit a large and concealed diversity in the natural environment, raising concerns about their potential for comprehensive application in bacterial adaptation. They should be viewed as a dangerous pool of resistance determinants from the "One Health approach." Among the three documented classes of integrons reported viz., class-1, 2, and 3, class 1 has been found frequently associated with AMRs in humans and is a critical genetic element to serve as a target for therapeutics to AMRs through gene silencing or combinatorial therapies. The direct method of screening gene cassettes linked to pathogenesis and resistance harbored by integrons is a novel way to assess human health. In the last decade, they have witnessed surveying the integron-associated gene cassettes associated with increased drug tolerance and rising pathogenicity of human pathogenic microbes. Consequently, we aimed to unravel the structure and functions of integrons and their integration mechanism by understanding horizontal gene transfer from one trophic group to another. Many updates for the gene cassettes harbored by integrons related to resistance and pathogenicity are extensively explored. Additionally, an updated account of the assessment of AMRs and prevailing antibiotic resistance by integrons in humans is grossly detailed-lastly, the estimation of AMR dissemination by employing integrons as potential biomarkers are also highlighted. The current review on integrons will pave the way to clinical understanding for devising a roadmap solution to AMR and pathogenicity. Graphical AbstractThe graphical abstract displays how integron-aided AMRs to humans: Transposons capture integron gene cassettes to yield high mobility integrons that target res sites of plasmids. These plasmids, in turn, promote the mobility of acquired integrons into diverse bacterial species. The acquisitions of resistant genes are transferred to humans through horizontal gene transfer.
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Affiliation(s)
- Basharat Ahmad Bhat
- Department of Bio-Resources, School of Biological Sciences, University of Kashmir, Srinagar, India
| | - Rakeeb Ahmad Mir
- Department of Biotechnology, School of Life Sciences, Central University of Kashmir, Ganderbal, India
| | - Hafsa Qadri
- Department of Bio-Resources, School of Biological Sciences, University of Kashmir, Srinagar, India
| | - Rohan Dhiman
- Department of Life Sciences, National Institute of Technology (NIT), Rourkela, Odisha, India
| | - Abdullah Almilaibary
- Department of Family and Community Medicine, Faculty of Medicine, Al Baha University, Al Bahah, Saudi Arabia
| | - Mustfa Alkhanani
- Department of Biology, College of Science, Hafr Al Batin University of Hafr Al-Batin, Hafar Al Batin, Saudi Arabia
| | - Manzoor Ahmad Mir
- Department of Bio-Resources, School of Biological Sciences, University of Kashmir, Srinagar, India
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18
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Shin J, Rychel K, Palsson BO. Systems biology of competency in Vibrio natriegens is revealed by applying novel data analytics to the transcriptome. Cell Rep 2023; 42:112619. [PMID: 37285268 DOI: 10.1016/j.celrep.2023.112619] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 04/27/2023] [Accepted: 05/22/2023] [Indexed: 06/09/2023] Open
Abstract
Vibrio natriegens regulates natural competence through the TfoX and QstR transcription factors, which are involved in external DNA capture and transport. However, the extensive genetic and transcriptional regulatory basis for competency remains unknown. We used a machine-learning approach to decompose Vibrio natriegens's transcriptome into 45 groups of independently modulated sets of genes (iModulons). Our findings show that competency is associated with the repression of two housekeeping iModulons (iron metabolism and translation) and the activation of six iModulons; including TfoX and QstR, a novel iModulon of unknown function, and three housekeeping iModulons (representing motility, polycations, and reactive oxygen species [ROS] responses). Phenotypic screening of 83 gene deletion strains demonstrates that loss of iModulon function reduces or eliminates competency. This database-iModulon-discovery cycle unveils the transcriptomic basis for competency and its relationship to housekeeping functions. These results provide the genetic basis for systems biology of competency in this organism.
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Affiliation(s)
- Jongoh Shin
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Kevin Rychel
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Bernhard O Palsson
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark; Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
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Jiang H, Jiao X, Yu T, Wang W, Cheng H, Huang G, Fang J. Contribution of different class 2 integron elements to fitness costs in multi-drug resistant Escherichia coli and evaluation of their adaptability in “farm-to-table” environments. Food Microbiol 2023; 113:104279. [PMID: 37098435 DOI: 10.1016/j.fm.2023.104279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 03/13/2023] [Accepted: 04/03/2023] [Indexed: 04/08/2023]
Abstract
Integrons play a pivotal role in the dissemination of antimicrobial resistance, because they can capture and express exogenous antimicrobial resistance genes. This study aimed to elucidate the structure and contribution of different elements of class 2 integrons to fitness costs in their host bacteria and evaluate their adaptability to the "farm-to-table" process. We mapped 27 typical class 2 integrons of Escherichia coli isolated from aquatic foods and pork products, each harboring an inactive truncated class 2 integrase gene and the gene cassette (GC) array dfrA1-sat2-aadA1 with strong Pc2A/Pc2B promoters. Notably, the fitness costs associated with class 2 integrons depended on the Pc promoter strength and quantity and content of GCs in the array. Additionally, the costs of integrases were activity-dependent, and a balance was identified between GC capture ability and integron stability, which could explain the inactive truncated integrase identified. Although typical class 2 integrons exhibited low-cost structures in E. coli, the bacteria incurred biological costs, including decreasing growth rates and biofilm formation, in farm-to-table environments, especially under low-nutrient conditions. Nevertheless, sub-inhibitory antibiotic concentrations led to the selection of class 2 integron-carrying bacteria. This study provides important insights into how integrons may travel from preharvest to consumer goods.
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Chang Y, Sun W, Murchie AIH, Chen D. Genome-wide identification of Kanamycin B binding RNA in Escherichia coli. BMC Genomics 2023; 24:120. [PMID: 36927548 PMCID: PMC10018874 DOI: 10.1186/s12864-023-09234-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 03/07/2023] [Indexed: 03/18/2023] Open
Abstract
BACKGROUND The aminoglycosides are established antibiotics that inhibit bacterial protein synthesis by binding to ribosomal RNA. Additional non-antibiotic aminoglycoside cellular functions have also been identified through aminoglycoside interactions with cellular RNAs. The full extent, however, of genome-wide aminoglycoside RNA interactions in Escherichia coli has not been determined. Here, we report genome-wide identification and verification of the aminoglycoside Kanamycin B binding to Escherichia coli RNAs. Immobilized Kanamycin B beads in pull-down assays were used for transcriptome-profiling analysis (RNA-seq). RESULTS Over two hundred Kanamycin B binding RNAs were identified. Functional classification analysis of the RNA sequence related genes revealed a wide range of cellular functions. Small RNA fragments (ncRNA, tRNA and rRNA) or small mRNA was used to verify the binding with Kanamycin B in vitro. Kanamycin B and ibsC mRNA was analysed by chemical probing. CONCLUSIONS The results will provide biochemical evidence and understanding of potential extra-antibiotic cellular functions of aminoglycosides in Escherichia coli.
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Affiliation(s)
- Yaowen Chang
- Fudan University Pudong Medical Center, and Institute of Biomedical Sciences, Shanghai Medical College, Key Laboratory of Medical Epigenetics and Metabolism, Fudan University, 200032, Shanghai, China.,Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Wenxia Sun
- Fudan University Pudong Medical Center, and Institute of Biomedical Sciences, Shanghai Medical College, Key Laboratory of Medical Epigenetics and Metabolism, Fudan University, 200032, Shanghai, China.,Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Alastair I H Murchie
- Fudan University Pudong Medical Center, and Institute of Biomedical Sciences, Shanghai Medical College, Key Laboratory of Medical Epigenetics and Metabolism, Fudan University, 200032, Shanghai, China. .,Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China.
| | - Dongrong Chen
- Fudan University Pudong Medical Center, and Institute of Biomedical Sciences, Shanghai Medical College, Key Laboratory of Medical Epigenetics and Metabolism, Fudan University, 200032, Shanghai, China. .,Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China.
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21
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Off-Target Integron Activity Leads to Rapid Plasmid Compensatory Evolution in Response to Antibiotic Selection Pressure. mBio 2023; 14:e0253722. [PMID: 36840554 PMCID: PMC10127599 DOI: 10.1128/mbio.02537-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023] Open
Abstract
Integrons are mobile genetic elements that have played an important role in the dissemination of antibiotic resistance. Under stress, the integron can generate combinatorial variation in resistance cassette expression by cassette reshuffling, accelerating the evolution of resistance. However, the flexibility of the integron integrase site recognition motif hints at potential off-target effects of the integrase on the rest of the genome that may have important evolutionary consequences. Here, we test this hypothesis by selecting for increased-piperacillin-resistance populations of Pseudomonas aeruginosa with a mobile integron containing a difficult-to-mobilize β-lactamase cassette to minimize the potential for adaptive cassette reshuffling. We found that integron activity can decrease the overall survival rate but also improve the fitness of the surviving populations. Off-target inversions mediated by the integron accelerated plasmid adaptation by disrupting costly conjugative genes otherwise mutated in control populations lacking a functional integrase. Plasmids containing integron-mediated inversions were associated with lower plasmid costs and higher stability than plasmids carrying mutations albeit at the cost of a reduced conjugative ability. These findings highlight the potential for integrons to create structural variation that can drive bacterial evolution, and they provide an interesting example showing how antibiotic pressure can drive the loss of conjugative genes. IMPORTANCE Tackling the public health challenge created by antibiotic resistance requires understanding the mechanisms driving its evolution. Mobile integrons are widespread genetic platforms heavily involved in the spread of antibiotic resistance. Through the action of the integrase enzyme, integrons allow bacteria to capture, excise, and shuffle antibiotic resistance gene cassettes. This integrase enzyme is characterized by its ability to recognize a wide range of recombination sites, which allows it to easily capture diverse resistance cassettes but which may also lead to off-target reactions with the rest of the genome. Using experimental evolution, we tested the off-target impact of integron activity. We found that integrons increased the fitness of the surviving bacteria through extensive genomic rearrangements of the plasmids carrying the integrons, reducing their ability to spread horizontally. These results show that integrons not only accelerate resistance evolution but also can generate extensive structural variation, driving bacterial evolution beyond antibiotic resistance.
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Pons MC, Praud K, Da Re S, Cloeckaert A, Doublet B. Conjugative IncC Plasmid Entry Triggers the SOS Response and Promotes Effective Transfer of the Integrative Antibiotic Resistance Element SGI1. Microbiol Spectr 2023; 11:e0220122. [PMID: 36472437 PMCID: PMC9927553 DOI: 10.1128/spectrum.02201-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 11/17/2022] [Indexed: 12/12/2022] Open
Abstract
The broad-host-range IncC plasmid family and the integrative mobilizable Salmonella genomic island 1 (SGI1) and its derivatives enable the spread of medically important antibiotic resistance genes among Gram-negative pathogens. Although several aspects of the complex functional interactions between IncC plasmids and SGI1 have been recently deciphered regarding their conjugative transfer and incompatibility, the biological signal resulting in the hijacking of the conjugative plasmid by the integrative mobilizable element remains unknown. Here, we demonstrate that the conjugative entry of IncC/IncA plasmids is detected at an early stage by SGI1 through the transient activation of the SOS response, which induces the expression of the SGI1 master activators SgaDC, shown to play a crucial role in the complex biology between SGI1 and IncC plasmids. Besides, we developed an original tripartite conjugation approach to directly monitor SGI1 mobilization in a time-dependent manner following conjugative entry of IncC plasmids. Finally, we propose an updated biological model of the conjugative mobilization of the chromosomal resistance element SGI1 by IncC plasmids. IMPORTANCE Antimicrobial resistance has become a major public health issue, particularly with the increase of multidrug resistance (MDR) in both animal and human pathogenic bacteria and with the emergence of resistance to medically important antibiotics. The spread between bacteria of successful mobile genetic elements, such as conjugative plasmids and integrative elements conferring multidrug resistance, is the main driving force in the dissemination of acquired antibiotic resistances among Gram-negative bacteria. Broad-host-range IncC plasmids and their integrative mobilizable SGI1 counterparts contribute to the spread of critically important resistance genes (e.g., extended-spectrum β-lactamases [ESBLs] and carbapenemases). A better knowledge of the complex biology of these broad-host-range mobile elements will help us to understand the dissemination of antimicrobial resistance genes that occurred across Gammaproteobacteria borders.
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Affiliation(s)
| | - Karine Praud
- INRAE, Université de Tours, ISP, Nouzilly, France
| | - Sandra Da Re
- INSERM, Université de Limoges, CHU de Limoges, RESINFIT, Limoges, France
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Bastos MC, Rheinheimer DDS, Le Guet T, Vargas Brunet J, Aubertheau E, Mondamert L, Labanowski J. Presence of pharmaceuticals and bacterial resistance genes in river epilithic biofilms exposed to intense agricultural and urban pressure. ENVIRONMENTAL MONITORING AND ASSESSMENT 2023; 195:328. [PMID: 36697888 DOI: 10.1007/s10661-022-10899-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 12/28/2022] [Indexed: 06/17/2023]
Abstract
The continuous discharge of pharmaceutical compounds into the aquatic environment has raised concerns over the contamination of water resources. Urban activities and intensive animal breeding are important sources of contamination. The accumulation of antibiotics may lead to the transfer or alternatively maintain the presence of resistance genes in natural microbial communities existing in epilithic biofilms. The objective of this study was to evaluate the pharmaceutical contamination levels and the presence of resistance genes in biofilms from a South Brazilian watershed. The Guaporé watershed exhibits a high diversity of land use, including agricultural and urban areas with differing levels of anthropogenic pressure. Seventeen sites along the Guaporé watershed were monitored. Biofilm samples were collected in two seasons (winter and summer), and the pharmaceutical concentration and quantity of resistance genes were analyzed. All monitored sites were contaminated with pharmaceuticals. Agricultural activities contribute through transferring pharmaceuticals derived from the application of animal waste to agricultural fields. The most contaminated site (pharmaceuticals and bacterial resistance genes) was located in an urban area exposed to high pressure. Decreases in the contamination of biofilms were also observed, exemplifying processes of natural attenuation in the watershed. The quality of the biofilms sampled throughout the watershed served as a useful tool to understand and monitor environmental pollution.
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Affiliation(s)
- Marília Camotti Bastos
- Centro de Ciências Rurais, Departamento de Solos, Universidade Federal de Santa Maria, Avenida Roraima, N° 1000, Bairro Camobi, Rio Grande Do Sul, CEP, 97105-900, Brazil.
- Institut de Chimie Des Milieux Et Matériaux de Poitiers, Université de Poitiers, IC2MP, Poitiers, France.
| | - Danilo Dos Santos Rheinheimer
- Centro de Ciências Rurais, Departamento de Solos, Universidade Federal de Santa Maria, Avenida Roraima, N° 1000, Bairro Camobi, Rio Grande Do Sul, CEP, 97105-900, Brazil
| | - Thibaut Le Guet
- Institut de Chimie Des Milieux Et Matériaux de Poitiers, Université de Poitiers, IC2MP, Poitiers, France
| | - Jocelina Vargas Brunet
- Centro de Ciências Rurais, Departamento de Solos, Universidade Federal de Santa Maria, Avenida Roraima, N° 1000, Bairro Camobi, Rio Grande Do Sul, CEP, 97105-900, Brazil
- Institut de Chimie Des Milieux Et Matériaux de Poitiers, Université de Poitiers, IC2MP, Poitiers, France
| | - Elodie Aubertheau
- Institut de Chimie Des Milieux Et Matériaux de Poitiers, Université de Poitiers, IC2MP, Poitiers, France
| | - Leslie Mondamert
- Institut de Chimie Des Milieux Et Matériaux de Poitiers, Université de Poitiers, IC2MP, Poitiers, France
| | - Jérôme Labanowski
- Institut de Chimie Des Milieux Et Matériaux de Poitiers, Université de Poitiers, IC2MP, Poitiers, France
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Haenelt S, Wang G, Kasmanas JC, Musat F, Richnow HH, da Rocha UN, Müller JA, Musat N. The fate of sulfonamide resistance genes and anthropogenic pollution marker intI1 after discharge of wastewater into a pristine river stream. Front Microbiol 2023; 14:1058350. [PMID: 36760511 PMCID: PMC9907086 DOI: 10.3389/fmicb.2023.1058350] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 01/10/2023] [Indexed: 01/26/2023] Open
Abstract
Introduction Currently there are sparse regulations regarding the discharge of antibiotics from wastewater treatment plants (WWTP) into river systems, making surface waters a latent reservoir for antibiotics and antibiotic resistance genes (ARGs). To better understand factors that influence the fate of ARGs in the environment and to foster surveillance of antibiotic resistance spreading in such habitats, several indicator genes have been proposed, including the integrase gene intI1 and the sulfonamide resistance genes sul1 and sul2. Methods Here we used quantitative PCR and long-read nanopore sequencing to monitor the abundance of these indicator genes and ARGs present as class 1 integron gene cassettes in a river system from pristine source to WWTP-impacted water. ARG abundance was compared with the dynamics of the microbial communities determined via 16S rRNA gene amplicon sequencing, conventional water parameters and the concentration of sulfamethoxazole (SMX), sulfamethazine (SMZ) and sulfadiazine (SDZ). Results Our results show that WWTP effluent was the principal source of all three sulfonamides with highest concentrations for SMX (median 8.6 ng/l), and of the indicator genes sul1, sul2 and intI1 with median relative abundance to 16S rRNA gene of 0.55, 0.77 and 0.65%, respectively. Downstream from the WWTP, water quality improved constantly, including lower sulfonamide concentrations, decreasing abundances of sul1 and sul2 and lower numbers and diversity of ARGs in the class 1 integron. The riverine microbial community partially recovered after receiving WWTP effluent, which was consolidated by a microbiome recovery model. Surprisingly, the relative abundance of intI1 increased 3-fold over 13 km of the river stretch, suggesting an internal gene multiplication. Discussion We found no evidence that low amounts of sulfonamides in the aquatic environment stimulate the maintenance or even spread of corresponding ARGs. Nevertheless, class 1 integrons carrying various ARGs were still present 13 km downstream from the WWTP. Therefore, limiting the release of ARG-harboring microorganisms may be more crucial for restricting the environmental spread of antimicrobial resistance than attenuating ng/L concentrations of antibiotics.
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Affiliation(s)
- Sarah Haenelt
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Gangan Wang
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Jonas Coelho Kasmanas
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Florin Musat
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research, Leipzig, Germany,Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Babeş-Bolyai University, Cluj-Napoca, Romania
| | - Hans Hermann Richnow
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research, Leipzig, Germany,Isodetect Umweltmonitoring GmbH, Leipzig, Germany
| | - Ulisses Nunes da Rocha
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Jochen A. Müller
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research, Leipzig, Germany,Institute for Biological Interfaces (IBG 5), Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | - Niculina Musat
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research, Leipzig, Germany,*Correspondence: Niculina Musat,
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Krin E, Baharoglu Z, Sismeiro O, Varet H, Coppée JY, Mazel D. Systematic transcriptome analysis allows the identification of new type I and type II Toxin/Antitoxin systems located in the superintegron of Vibrio cholerae. Res Microbiol 2023; 174:103997. [PMID: 36347445 DOI: 10.1016/j.resmic.2022.103997] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/27/2022] [Accepted: 10/28/2022] [Indexed: 11/07/2022]
Abstract
Vibrio cholerae N16961 genome encodes 18 type II Toxin/Antitoxin (TA) systems, all but one located inside gene cassettes of its chromosomal superintegron (SI). This study aims to investigate additional TA systems in this genome. We screened for all two-genes operons of uncharacterized function by analyzing previous RNAseq data. Assays on nine candidates, revealed one additional functional type II TA encoded by the VCA0497-0498 operon, carried inside a SI cassette. We showed that VCA0498 antitoxin alone and in complex with VCA0497 represses its own operon promoter. VCA0497-0498 is the second element of the recently identified dhiT/dhiA superfamily uncharacterized type II TA system. RNAseq analysis revealed that another SI cassette encodes a novel type I TA system: VCA0495 gene and its two associated antisense non-coding RNAs, ncRNA495 and ncRNA496. Silencing of both antisense ncRNAs lead to cell death, demonstrating the type I TA function. Both VCA0497 and VCA0495 toxins do not show any homology to functionally characterized toxins, however our preliminary data suggest that their activity may end up in mRNA degradation, directly or indirectly. Our findings increase the TA systems number carried in this SI to 19, preferentially located in its distal end, confirming their importance in this large cassette array.
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Affiliation(s)
- Evelyne Krin
- Institut Pasteur, Université Paris Cité, CNRS UMR 3525, Unité de Plasticité du Génome Bactérien, 28 rue du Docteur Roux, F-75015 Paris, France.
| | - Zeynep Baharoglu
- Institut Pasteur, Université Paris Cité, CNRS UMR 3525, Unité de Plasticité du Génome Bactérien, 28 rue du Docteur Roux, F-75015 Paris, France.
| | - Odile Sismeiro
- Institut Pasteur, Université Paris Cité, Transcriptome and EpiGenome, Biomics Center for Innovation and Technological Research, 28 rue du Docteur Roux, F-75015 Paris, France.
| | - Hugo Varet
- Institut Pasteur, Université Paris Cité, Transcriptome and EpiGenome, Biomics Center for Innovation and Technological Research, 28 rue du Docteur Roux, F-75015 Paris, France.
| | - Jean-Yves Coppée
- Institut Pasteur, Université Paris Cité, Transcriptome and EpiGenome, Biomics Center for Innovation and Technological Research, 28 rue du Docteur Roux, F-75015 Paris, France.
| | - Didier Mazel
- Institut Pasteur, Université Paris Cité, CNRS UMR 3525, Unité de Plasticité du Génome Bactérien, 28 rue du Docteur Roux, F-75015 Paris, France.
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Gharbi M, Kamoun S, Hkimi C, Ghedira K, Béjaoui A, Maaroufi A. Relationships between Virulence Genes and Antibiotic Resistance Phenotypes/Genotypes in Campylobacter spp. Isolated from Layer Hens and Eggs in the North of Tunisia: Statistical and Computational Insights. Foods 2022; 11:foods11223554. [PMID: 36429146 PMCID: PMC9689815 DOI: 10.3390/foods11223554] [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: 09/01/2022] [Revised: 09/25/2022] [Accepted: 10/09/2022] [Indexed: 11/10/2022] Open
Abstract
Globally, Campylobacter is a significant contributor to gastroenteritis. Efficient pathogens are qualified by their virulence power, resistance to antibiotics and epidemic spread. However, the correlation between antimicrobial resistance (AR) and the pathogenicity power of pathogens is complex and poorly understood. In this study, we aimed to investigate genes encoding virulence and AR mechanisms in 177 Campylobacter isolates collected from layer hens and eggs in Tunisia and to assess associations between AR and virulence characteristics. Virulotyping was determined by searching 13 virulence genes and AR-encoding genes were investigated by PCR and MAMA-PCR. The following genes were detected in C. jejuni and C. coli isolates: tet(O) (100%/100%), blaOXA-61 (18.82%/6.25%), and cmeB (100%/100%). All quinolone-resistant isolates harbored the Thr-86-Ile substitution in GyrA. Both the A2074C and A2075G mutations in 23S rRNA were found in all erythromycin-resistant isolates; however, the erm(B) gene was detected in 48.38% and 64.15% of the C. jejuni and C. coli isolates, respectively. The machine learning algorithm Random Forest was used to determine the association of virulence genes with AR phenotypes. This analysis showed that C. jejuni virulotypes with gene clusters encompassing the racR, ceuE, virB11, and pldA genes were strongly associated with the majority of phenotypic resistance. Our findings showed high rates of AR and virulence genes among poultry Campylobacter, which is a cause of concern to human health. In addition, the correlations of specific virulence genes with AR phenotypes were established by statistical analysis.
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Affiliation(s)
- Manel Gharbi
- Group of Bacteriology and Biotechnology Development, Laboratory of Epidemiology and Veterinary Microbiology, Institut Pasteur de Tunis, University of Tunis El Manar (UTM), Tunis 1002, Tunisia
- Correspondence: ; Tel.: +216-27310041
| | - Selim Kamoun
- Laboratory of Bioinformatics, Biomathematics and Biostatistics, Institut Pasteur de Tunis, University of Tunis El Manar (UTM), Tunis 1006, Tunisia
| | - Chaima Hkimi
- Laboratory of Bioinformatics, Biomathematics and Biostatistics, Institut Pasteur de Tunis, University of Tunis El Manar (UTM), Tunis 1006, Tunisia
| | - Kais Ghedira
- Laboratory of Bioinformatics, Biomathematics and Biostatistics, Institut Pasteur de Tunis, University of Tunis El Manar (UTM), Tunis 1006, Tunisia
| | - Awatef Béjaoui
- Group of Bacteriology and Biotechnology Development, Laboratory of Epidemiology and Veterinary Microbiology, Institut Pasteur de Tunis, University of Tunis El Manar (UTM), Tunis 1002, Tunisia
| | - Abderrazak Maaroufi
- Group of Bacteriology and Biotechnology Development, Laboratory of Epidemiology and Veterinary Microbiology, Institut Pasteur de Tunis, University of Tunis El Manar (UTM), Tunis 1002, Tunisia
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27
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Zhu W, Wang T, Zhu Y, Xiao L, Liu W, Wei Q. Two-dimensional PCR for detecting class 1, 2 and 3 integrons. Heliyon 2022; 8:e11844. [DOI: 10.1016/j.heliyon.2022.e11844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 09/29/2022] [Accepted: 11/17/2022] [Indexed: 11/27/2022] Open
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Zhang Y, Su YA, Qiu X, Mao Q, Liu H, Liu H, Wen D, Su Z. Temperature affects variations of class 1 integron during sludge anaerobic digestion. BIORESOURCE TECHNOLOGY 2022; 364:128005. [PMID: 36155808 DOI: 10.1016/j.biortech.2022.128005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 09/15/2022] [Accepted: 09/17/2022] [Indexed: 06/16/2023]
Abstract
Revealing class 1 integron characteristics under different operating conditions is of great importance to control antibiotic resistance genes (ARGs) during sludge anaerobic digestion (AD). This study investigated the variations of class 1 integrons and the ARGs carried by class 1 integrons in anaerobic sludge digesters under 25 °C, 35 °C, and 55 °C. The results showed lower intI1 abundance and fewer class I integrons with long gene cassette arrays at 55 °C than at 25 °C and 35 °C. Multi-resistance gene cassette arrays were observed in the digesters at 25 °C and 35 °C. Abundant ARGs were detected on class 1 integrons in all digesters with aminoglycosides as the dominant class. The abundance of ARGs on class 1 integrons in digesters at 55 °C was lower than that at 25 °C and 35 °C. Thermophilic AD is better than mesophilic ones in the control of ARGs carried by class 1 integrons.
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Affiliation(s)
- Yan Zhang
- School of Environment and Civil Engineering, Jiangnan University, Wuxi 214122, China; Jiangsu Key Laboratory of Anaerobic Biotechnology, Wuxi 214122, China; Jiangsu Collaborative Innovation Center of Water Treatment Technology and Material, Suzhou 215011, China
| | - Yu-Ao Su
- School of Environment and Civil Engineering, Jiangnan University, Wuxi 214122, China
| | - Xuyang Qiu
- School of Environment and Civil Engineering, Jiangnan University, Wuxi 214122, China
| | - Qiuyan Mao
- School of Environment and Civil Engineering, Jiangnan University, Wuxi 214122, China
| | - Hongbo Liu
- School of Environment and Civil Engineering, Jiangnan University, Wuxi 214122, China; Jiangsu Key Laboratory of Anaerobic Biotechnology, Wuxi 214122, China; Jiangsu Collaborative Innovation Center of Water Treatment Technology and Material, Suzhou 215011, China
| | - He Liu
- School of Environment and Civil Engineering, Jiangnan University, Wuxi 214122, China; Jiangsu Key Laboratory of Anaerobic Biotechnology, Wuxi 214122, China; Jiangsu Collaborative Innovation Center of Water Treatment Technology and Material, Suzhou 215011, China.
| | - Donghui Wen
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Zhiguo Su
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
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29
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Knecht CA, Krüger M, Kellmann S, Mäusezahl I, Möder M, Adelowo OO, Vollmers J, Kaster AK, Nivala J, Müller JA. Cellular stress affects the fate of microbial resistance to folate inhibitors in treatment wetlands. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 845:157318. [PMID: 35839882 DOI: 10.1016/j.scitotenv.2022.157318] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 06/11/2022] [Accepted: 07/08/2022] [Indexed: 06/15/2023]
Abstract
The environmental prevalence of antimicrobial resistance (AMR) has come into focus under the One Health concept. Wastewater treatment systems are among the significant sources of AMR in the environment. In such systems, it is uncertain to which extent antimicrobials present at sub-inhibitory concentrations constitute a selective pressure for bacterial maintenance and acquisition of antibiotic resistance (AR) genes. Here, we mapped AMR to inhibitors of folate biosynthesis in an aerated and a non-aerated horizontal subsurface flow treatment wetland receiving the same pre-treated municipal wastewater. General water characteristics and the concentrations of folate inhibitors were determined to define the ambient conditions over the longitudinal axis of the two treatment wetlands. Profiling of AMR as well as class 1 integrons, a carrier of AR genes against folate inhibitors and other antimicrobials, was conducted by cultivation-dependent and -independent methods. The wetlands achieved mean reductions of AR gene copy numbers in the effluents of at least 2 log, with the aerated system performing better. The folate inhibitors had no noticeable effect on the prevalence of respective AR genes. However, there was a transient increase of AR gene copy numbers and AR gene cassette composition in class 1 integrons in the aerated wetland. The comparison of all data from both wetlands suggests that higher levels of cellular stress in the aerated system promoted the mobility of AR genes via enhancing the activity of the DNA recombinase of the class 1 integron. The findings highlight that environmental conditions that modulate the activity of this genetic element can be more important for the fate of associated AR genes in treatment wetlands than the ambient concentration of the respective antimicrobial agents. By extrapolation, the results suggest that cellular stress also contributes to the mobility of AR gene in other wastewater treatment systems.
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Affiliation(s)
- Camila A Knecht
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany; Otto-von-Guericke-University Magdeburg, FVST Chair Environmental Technology, Magdeburg, Germany
| | - Markus Krüger
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany; Institute of Biodiversity, Friedrich-Schiller-University Jena, Germany
| | - Simon Kellmann
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Ines Mäusezahl
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Monika Möder
- Department of Analytical Chemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Olawale O Adelowo
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany; Environmental Microbiology and Biotechnology Laboratory, Department of Microbiology, University of Ibadan, Ibadan, Nigeria
| | - John Vollmers
- Institute for Biological Interfaces (IBG5), Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | - Anne-Kristin Kaster
- Institute for Biological Interfaces (IBG5), Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | - Jaime Nivala
- Environmental and Biotechnology Centre (UBZ), Helmholtz Centre for Environmental Research (UFZ), Leipzig, Germany; Research Unit REVERSAAL, National Research Institute for Agriculture, Food and the Environment (INRAE), Villeurbanne, France
| | - Jochen A Müller
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany; Institute for Biological Interfaces (IBG5), Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany.
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Lima-Noronha MA, Fonseca DLH, Oliveira RS, Freitas RR, Park JH, Galhardo RS. Sending out an SOS - the bacterial DNA damage response. Genet Mol Biol 2022; 45:e20220107. [PMID: 36288458 PMCID: PMC9578287 DOI: 10.1590/1678-4685-gmb-2022-0107] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 07/15/2022] [Indexed: 11/04/2022] Open
Abstract
The term “SOS response” was first coined by Radman in 1974, in an intellectual effort to put together the data suggestive of a concerted gene expression program in cells undergoing DNA damage. A large amount of information about this cellular response has been collected over the following decades. In this review, we will focus on a few of the relevant aspects about the SOS response: its mechanism of control and the stressors which activate it, the diversity of regulated genes in different species, its role in mutagenesis and evolution including the development of antimicrobial resistance, and its relationship with mobile genetic elements.
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Affiliation(s)
- Marco A. Lima-Noronha
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Microbiologia, São Paulo, SP, Brazil
| | - Douglas L. H. Fonseca
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Microbiologia, São Paulo, SP, Brazil
| | - Renatta S. Oliveira
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Microbiologia, São Paulo, SP, Brazil
| | - Rúbia R. Freitas
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Microbiologia, São Paulo, SP, Brazil
| | - Jung H. Park
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Microbiologia, São Paulo, SP, Brazil
| | - Rodrigo S. Galhardo
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Microbiologia, São Paulo, SP, Brazil
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Shi X, Xia Y, Wei W, Ni BJ. Accelerated spread of antibiotic resistance genes (ARGs) induced by non-antibiotic conditions: Roles and mechanisms. WATER RESEARCH 2022; 224:119060. [PMID: 36096030 DOI: 10.1016/j.watres.2022.119060] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Revised: 08/28/2022] [Accepted: 09/04/2022] [Indexed: 05/28/2023]
Abstract
The global spread of antibiotic resistance genes (ARGs) has wreaked havoc with the treatment efficiency of antibiotics and, ultimately, anti-microbial chemotherapy, and has been conventionally attributed to the abuse and misuse of antibiotics. However, the ancient ARGs have alterative functions in bacterial physiology and thus they could be co-regulated by non-antibiotic conditions. Recent research has demonstrated that many non-antibiotic chemicals such as microplastics, metallic nanoparticles and non-antibiotic drugs, as well as some non-antibiotic conditions, can accelerate the dissemination of ARGs. These results suggested that the role of antibiotics might have been previously overestimated whereas the effects of non-antibiotic conditions were possibly ignored. Thus, in an attempt to fully understand the fate and behavior of ARGs in the eco-system, it is urgent to critically highlight the role and mechanisms of non-antibiotic chemicals and related environmental factors in the spread of ARGs. To this end, this timely review assessed the evolution of ARGs, especially its function alteration, summarized the non-antibiotic chemicals promoting the spread of ARGs, evaluated the non-antibiotic conditions related to ARG dissemination and analyzed the molecular mechanisms related to spread of ARGs induced by the non-antibiotic factors. Finally, this review then provided several critical perspectives for future research.
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Affiliation(s)
- Xingdong Shi
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Yu Xia
- School of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Wei Wei
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Bing-Jie Ni
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Sydney, NSW 2007, Australia.
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Al Mamun AAM, Kissoon K, Kishida K, Shropshire WC, Hanson B, Christie PJ. IncFV plasmid pED208: Sequence analysis and evidence for translocation of maintenance/leading region proteins through diverse type IV secretion systems. Plasmid 2022; 123-124:102652. [PMID: 36228885 PMCID: PMC10018792 DOI: 10.1016/j.plasmid.2022.102652] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 10/02/2022] [Accepted: 10/04/2022] [Indexed: 12/04/2022]
Abstract
Two phylogenetically distantly-related IncF plasmids, F and pED208, serve as important models for mechanistic and structural studies of F-like type IV secretion systems (T4SSFs) and F pili. Here, we present the pED208 sequence and compare it to F and pUMNF18, the closest match to pED208 in the NCBI database. As expected, gene content of the three cargo regions varies extensively, although the maintenance/leading regions (MLRs) and transfer (Tra) regions also carry novel genes or motifs with predicted modulatory effects on plasmid stability, dissemination and host range. By use of a Cre recombinase assay for translocation (CRAfT), we recently reported that pED208-carrying donors translocate several products of the MLR (ParA, ParB1, ParB2, SSB, PsiB, PsiA) intercellularly through the T4SSF. Here, we extend these findings by reporting that pED208-carrying donors translocate 10 additional MLR proteins during conjugation. In contrast, two F plasmid-encoded toxin components of toxin-antitoxin (TA) modules, CcdB and SrnB, were not translocated at detectable levels through the T4SSF. Remarkably, most or all of the pED208-encoded MLR proteins and CcdB and SrnB were translocated through heterologous T4SSs encoded by IncN and IncP plasmids pKM101 and RP4, respectively. Together, our sequence analyses underscore the genomic diversity of the F plasmid superfamily, and our experimental data demonstrate the promiscuous nature of conjugation machines for protein translocation. Our findings raise intriguing questions about the nature of T4SS translocation signals and of the biological and evolutionary consequences of conjugative protein transfer.
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Affiliation(s)
- Abu Amar M Al Mamun
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center, McGovern School of Medicine, Fannin St, Houston, TX 77030, United States of America.
| | - Kimberly Kissoon
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center, McGovern School of Medicine, Fannin St, Houston, TX 77030, United States of America
| | - Kouhei Kishida
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center, McGovern School of Medicine, Fannin St, Houston, TX 77030, United States of America
| | - William C Shropshire
- Center for Antimicrobial Resistance and Microbial Genomics, University of Texas Health Science Center, McGovern School of Medicine, Houston, TX, USA; Center for Infectious Diseases, University of Texas Health Science Center, School of Public Health, Houston, TX, USA
| | - Blake Hanson
- Center for Antimicrobial Resistance and Microbial Genomics, University of Texas Health Science Center, McGovern School of Medicine, Houston, TX, USA; Center for Infectious Diseases, University of Texas Health Science Center, School of Public Health, Houston, TX, USA
| | - Peter J Christie
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center, McGovern School of Medicine, Fannin St, Houston, TX 77030, United States of America.
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Hipólito A, García-Pastor L, Blanco P, Trigo da Roza F, Kieffer N, Vergara E, Jové T, Álvarez J, Escudero J. The expression of aminoglycoside resistance genes in integron cassettes is not controlled by riboswitches. Nucleic Acids Res 2022; 50:8566-8579. [PMID: 35947699 PMCID: PMC9410878 DOI: 10.1093/nar/gkac662] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 07/11/2022] [Accepted: 07/22/2022] [Indexed: 12/24/2022] Open
Abstract
Regulation of gene expression is a key factor influencing the success of antimicrobial resistance determinants. A variety of determinants conferring resistance against aminoglycosides (Ag) are commonly found in clinically relevant bacteria, but whether their expression is regulated or not is controversial. The expression of several Ag resistance genes has been reported to be controlled by a riboswitch mechanism encoded in a conserved sequence. Yet this sequence corresponds to the integration site of an integron, a genetic platform that recruits genes of different functions, making the presence of such a riboswitch counterintuitive. We provide, for the first time, experimental evidence against the existence of such Ag-sensing riboswitch. We first tried to reproduce the induction of the well characterized aacA5 gene using its native genetic environment, but were unsuccessful. We then broadened our approach and analyzed the inducibility of all AgR genes encoded in integrons against a variety of antibiotics. We could not observe biologically relevant induction rates for any gene in the presence of several aminoglycosides. Instead, unrelated antibiotics produced mild but consistently higher increases in expression, that were the result of pleiotropic effects. Our findings rule out the riboswitch control of aminoglycoside resistance genes in integrons.
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Affiliation(s)
- Alberto Hipólito
- Departamento de Sanidad Animal, Facultad de Veterinaria de la Universidad Complutense de Madrid, Spain,VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Spain
| | - Lucía García-Pastor
- Departamento de Sanidad Animal, Facultad de Veterinaria de la Universidad Complutense de Madrid, Spain,VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Spain
| | | | | | - Nicolas Kieffer
- Departamento de Sanidad Animal, Facultad de Veterinaria de la Universidad Complutense de Madrid, Spain,VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Spain
| | - Ester Vergara
- Departamento de Sanidad Animal, Facultad de Veterinaria de la Universidad Complutense de Madrid, Spain,VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Spain
| | - Thomas Jové
- INSERM, CHU Limoges, RESINFIT, University of Limoges, Limoges, France
| | - Julio Álvarez
- Departamento de Sanidad Animal, Facultad de Veterinaria de la Universidad Complutense de Madrid, Spain,VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Spain
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Pal S, Ahamed Z, Pal P. Removal of antibiotics and pharmaceutically active compounds from water Environment: Experiments towards industrial scale up. Sep Purif Technol 2022. [DOI: 10.1016/j.seppur.2022.121249] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Protozoal food vacuoles enhance transformation in Vibrio cholerae through SOS-regulated DNA integration. THE ISME JOURNAL 2022; 16:1993-2001. [PMID: 35577916 PMCID: PMC9296650 DOI: 10.1038/s41396-022-01249-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 04/20/2022] [Accepted: 04/29/2022] [Indexed: 11/08/2022]
Abstract
Vibrio cholerae, the bacterial pathogen responsible for the diarrheal disease cholera, resides in the aquatic environment between outbreaks. For bacteria, genetic variation by lateral gene transfer (LGT) is important for survival and adaptation. In the aquatic environment, V. cholerae is predominantly found in biofilms associated with chitinous organisms or with chitin "rain". Chitin induces competency in V. cholerae, which can lead to LGT. In the environment, V. cholerae is also subjected to predation pressure by protist. Here we investigated whether protozoal predation affected LGT using the integron as a model. Integrons facilitate the integration of mobile DNA (gene cassettes) into the bacterial chromosome. We report that protozoal predation enhances transformation of a gene cassette by as much as 405-fold. We show that oxidative radicals produced in the protozoal phagosome induces the universal SOS response, which in turn upregulates the integron-integrase, the recombinase that facilitates cassette integration. Additionally, we show that during predation, V. cholerae requires the type VI secretion system to acquire the gene cassette from Escherichia coli. These results show that protozoal predation enhances LGT thus producing genetic variants that may have increased capacity to survive grazing. Additionally, the conditions in the food vacuole may make it a "hot spot" for LGT by accumulating diverse bacteria and inducing the SOS response helping drive genetic diversification and evolution.
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Mutuku C, Gazdag Z, Melegh S. Occurrence of antibiotics and bacterial resistance genes in wastewater: resistance mechanisms and antimicrobial resistance control approaches. World J Microbiol Biotechnol 2022; 38:152. [PMID: 35781751 PMCID: PMC9250919 DOI: 10.1007/s11274-022-03334-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 06/10/2022] [Indexed: 12/14/2022]
Abstract
Antimicrobial pharmaceuticals are classified as emergent micropollutants of concern, implying that even at low concentrations, long-term exposure to the environment can have significant eco-toxicological effects. There is a lack of a standardized regulatory framework governing the permissible antibiotic content for monitoring environmental water quality standards. Therefore, indiscriminate discharge of antimicrobials at potentially active concentrations into urban wastewater treatment facilities is rampant. Antimicrobials may exert selective pressure on bacteria, leading to resistance development and eventual health consequences. The emergence of clinically important multiple antibiotic-resistant bacteria in untreated hospital effluents and wastewater treatment plants (WWTPs) has been linked to the continuous exposure of bacteria to antimicrobials. The levels of environmental exposure to antibiotics and their correlation to the evolution and spread of resistant bacteria need to be elucidated to help in the formulation of mitigation measures. This review explores frequently detected antimicrobials in wastewater and gives a comprehensive coverage of bacterial resistance mechanisms to different antibiotic classes through the expression of a wide variety of antibiotic resistance genes either inherent and/or exchanged among bacteria or acquired from the reservoir of antibiotic resistance genes (ARGs) in wastewater systems. To complement the removal of antibiotics and ARGs from WWTPs, upscaling the implementation of prospective interventions such as vaccines, phage therapy, and natural compounds as alternatives to widespread antibiotic use provides a multifaceted approach to minimize the spread of antimicrobial resistance.
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Affiliation(s)
- Christopher Mutuku
- Department of General and Environmental Microbiology, Faculty of Sciences, University of Pécs, Ifjúság u. 6, Pecs, 7624, Hungary.
| | - Zoltan Gazdag
- Department of General and Environmental Microbiology, Faculty of Sciences, University of Pécs, Ifjúság u. 6, Pecs, 7624, Hungary
| | - Szilvia Melegh
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, 7622, Pecs, Hungary
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Yu D, Ryu K, Zhi S, Otto SJG, Neumann NF. Naturalized Escherichia coli in Wastewater and the Co-evolution of Bacterial Resistance to Water Treatment and Antibiotics. Front Microbiol 2022; 13:810312. [PMID: 35707173 PMCID: PMC9189398 DOI: 10.3389/fmicb.2022.810312] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 05/09/2022] [Indexed: 12/30/2022] Open
Abstract
Antibiotic resistance represents one of the most pressing concerns facing public health today. While the current antibiotic resistance crisis has been driven primarily by the anthropogenic overuse of antibiotics in human and animal health, recent efforts have revealed several important environmental dimensions underlying this public health issue. Antibiotic resistant (AR) microbes, AR genes, and antibiotics have all been found widespread in natural environments, reflecting the ancient origins of this phenomenon. In addition, modern societal advancements in sanitation engineering (i.e., sewage treatment) have also contributed to the dissemination of resistance, and concerningly, may also be promoting the evolution of resistance to water treatment. This is reflected in the recent characterization of naturalized wastewater strains of Escherichia coli-strains that appear to be adapted to live in wastewater (and meat packing plants). These strains carry a plethora of stress-resistance genes against common treatment processes, such as chlorination, heat, UV light, and advanced oxidation, mechanisms which potentially facilitate their survival during sewage treatment. These strains also carry an abundance of common antibiotic resistance genes, and evidence suggests that resistance to some antibiotics is linked to resistance to treatment (e.g., tetracycline resistance and chlorine resistance). As such, these naturalized E. coli populations may be co-evolving resistance against both antibiotics and water treatment. Recently, extraintestinal pathogenic strains of E. coli (ExPEC) have also been shown to exhibit phenotypic resistance to water treatment, seemingly associated with the presence of various shared genetic elements with naturalized wastewater E. coli. Consequently, some pathogenic microbes may also be evolving resistance to the two most important public health interventions for controlling infectious disease in modern society-antibiotic therapy and water treatment.
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Affiliation(s)
- Daniel Yu
- School of Public Health, University of Alberta, Edmonton, AB, Canada
- Antimicrobial Resistance – One Health Consortium, Calgary, AB, Canada
| | - Kanghee Ryu
- School of Public Health, University of Alberta, Edmonton, AB, Canada
- Antimicrobial Resistance – One Health Consortium, Calgary, AB, Canada
| | - Shuai Zhi
- School of Medicine, Ningbo University, Ningbo, China
- The Affiliated Hospital of Medical School, Ningbo University, Ningbo, China
| | - Simon J. G. Otto
- School of Public Health, University of Alberta, Edmonton, AB, Canada
- Antimicrobial Resistance – One Health Consortium, Calgary, AB, Canada
- Human-Environment-Animal Transdisciplinary Antimicrobial Resistance Research Group, School of Public Health, University of Alberta, Edmonton, AB, Canada
- Healthy Environments, Centre for Health Communities, School of Public Health, University of Alberta, Edmonton, AB, Canada
| | - Norman F. Neumann
- School of Public Health, University of Alberta, Edmonton, AB, Canada
- Antimicrobial Resistance – One Health Consortium, Calgary, AB, Canada
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Babosan A, Gaschet M, Muggeo A, Jové T, Skurnik D, Ploy MC, de Champs C, Reffuveille F, Guillard T. A qnrD-Plasmid Promotes Biofilm Formation and Class 1 Integron Gene Cassette Rearrangements in Escherichia coli. Antibiotics (Basel) 2022; 11:antibiotics11060715. [PMID: 35740122 PMCID: PMC9220102 DOI: 10.3390/antibiotics11060715] [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: 05/11/2022] [Revised: 05/20/2022] [Accepted: 05/24/2022] [Indexed: 11/17/2022] Open
Abstract
Bacteria within biofilms may be exposed to sub-minimum inhibitory concentrations (sub-MICs) of antibiotics. Cell-to-cell contact within biofilms facilitates horizontal gene transfers and favors induction of the SOS response. Altogether, it participates in the emergence of antibiotic resistance. Aminoglycosides at sub-MICs can induce the SOS response through NO accumulation in E. coli carrying the small plasmid with the quinolone resistance qnrD gene (pDIJ09-518a). In this study, we show that in E. coli pDIJ09-518a, the SOS response triggered by sub-MICs of aminoglycosides has important consequences, promoting genetic rearrangement in class 1 integrons and biofilm formation. We found that the integrase expression was increased in E. coli carrying pDIJ09-518a in the presence of tobramycin, which was not observed for the WT isogenic strain that did not carry the qnrD-plasmid. Moreover, we showed that biofilm production was significantly increased in E. coli WT/pDIJ09-518a compared to the WT strain. However, such a higher production was decreased when the Hmp-NO detoxification pathway was fully functional by overexpressing Hmp. Our results showing that a qnrD-plasmid can promote biofilm formation in E. coli and potentiate the acquisition and spread of resistance determinants for other antibiotics complicate the attempts to counteract antibiotic resistance and prevention of biofilm development even further. We anticipate that our findings emphasize the complex challenges that will impact the decisions about antibiotic stewardship, and other decisions related to retaining antibiotics as effective drugs and the development of new drugs.
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Affiliation(s)
- Anamaria Babosan
- Inserm UMR-S 1250 P3Cell, SFR CAP-Santé, Université de Reims-Champagne-Ardenne, 51100 Reims, France; (A.B.); (A.M.); (C.d.C.)
| | - Margaux Gaschet
- Université de Limoges, Inserm, CHU Limoges, UMR-S 1092, 87032 Limoges, France; (M.G.); (T.J.); (M.-C.P.)
| | - Anaëlle Muggeo
- Inserm UMR-S 1250 P3Cell, SFR CAP-Santé, Université de Reims-Champagne-Ardenne, 51100 Reims, France; (A.B.); (A.M.); (C.d.C.)
- Laboratoire de Bactériologie-Virologie-Hygiène Hospitalière-Parasitologie-Mycologie, CHU Reims, Hôpital Robert Debré, Avenue du Général Koenig, CEDEX, 51092 Reims, France
| | - Thomas Jové
- Université de Limoges, Inserm, CHU Limoges, UMR-S 1092, 87032 Limoges, France; (M.G.); (T.J.); (M.-C.P.)
| | - David Skurnik
- Institut Necker-Enfants Malades, Inserm U1151-Equipe 11, Université Paris Descartes, 75015 Paris, France;
- Laboratoire de Bactériologie, AP-HP, Hôpital Necker-Enfants Malades, 75015 Paris, France
- Division of Infectious Diseases, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Marie-Cécile Ploy
- Université de Limoges, Inserm, CHU Limoges, UMR-S 1092, 87032 Limoges, France; (M.G.); (T.J.); (M.-C.P.)
| | - Christophe de Champs
- Inserm UMR-S 1250 P3Cell, SFR CAP-Santé, Université de Reims-Champagne-Ardenne, 51100 Reims, France; (A.B.); (A.M.); (C.d.C.)
- Laboratoire de Bactériologie-Virologie-Hygiène Hospitalière-Parasitologie-Mycologie, CHU Reims, Hôpital Robert Debré, Avenue du Général Koenig, CEDEX, 51092 Reims, France
| | - Fany Reffuveille
- EA 4691 BiOS, SFR CAP-Santé, Université de Reims Champagne-Ardenne, 51100 Reims, France;
| | - Thomas Guillard
- Inserm UMR-S 1250 P3Cell, SFR CAP-Santé, Université de Reims-Champagne-Ardenne, 51100 Reims, France; (A.B.); (A.M.); (C.d.C.)
- Laboratoire de Bactériologie-Virologie-Hygiène Hospitalière-Parasitologie-Mycologie, CHU Reims, Hôpital Robert Debré, Avenue du Général Koenig, CEDEX, 51092 Reims, France
- Correspondence: ; Tel.: +33-3-26-78-32-10; Fax: +33-3-26-78-41
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Activation of class 1 integron integrase is promoted in the intestinal environment. PLoS Genet 2022; 18:e1010177. [PMID: 35482826 PMCID: PMC9090394 DOI: 10.1371/journal.pgen.1010177] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 05/10/2022] [Accepted: 03/30/2022] [Indexed: 11/21/2022] Open
Abstract
Class 1 integrons are widespread genetic elements playing a major role in the dissemination of antibiotic resistance. They allow bacteria to capture, express and exchange antibiotic resistance genes embedded within gene cassettes. Acquisition of gene cassettes is catalysed by the class 1 integron integrase, a site-specific recombinase playing a key role in the integron system. In in vitro planktonic culture, expression of intI1 is controlled by the SOS response, a regulatory network which mediates the repair of DNA damage caused by a wide range of bacterial stress, including antibiotics. However, in vitro experimental conditions are far from the real lifestyle of bacteria in natural environments such as the intestinal tract which is known to be a reservoir of integrons. In this study, we developed an in vivo model of intestinal colonization in gnotobiotic mice and used a recombination assay and quantitative real-time PCR, to investigate the induction of the SOS response and expression and activity of the class 1 integron integrase, IntI1. We found that the basal activity of IntI1 was higher in vivo than in vitro. In addition, we demonstrated that administration of a subinhibitory concentration of ciprofloxacin rapidly induced both the SOS response and intI1 expression that was correlated with an increase of the activity of IntI1. Our findings show that the gut is an environment in which the class 1 integron integrase is induced and active, and they highlight the potential role of integrons in the acquisition and/or expression of resistance genes in the gut, particularly during antibiotic therapy. Class 1 integrons are genetic systems allowing bacteria to acquire antibiotic resistance genes through the recombination activity of the IntI1 integrase. These genetic platforms are involved in the spread of antibiotic resistance among bacteria. So far, most of the studies for understanding the mechanistic of integrons have been performed in vitro, experimental conditions which are far from the lifestyle of bacteria in natural environments such as the gut. We developed a new in vivo model using gnotobiotic mice and we showed that in the gut, the basal activity of IntI1 is significantly higher than in in vitro conditions. In addition, we showed that a subinhibitory concentration of ciprofloxacin rapidly triggers the SOS response, leading to increased activity of IntI1 in the mouse gut. Our results demonstrate that the intestinal environment promotes the acquisition/expression of antibiotic resistance genes through the integron system and that this phenomenon can be enhanced by antibiotic therapy.
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Responses of the Soil Bacterial Community, Resistome, and Mobilome to a Decade of Annual Exposure to Macrolide Antibiotics. Appl Environ Microbiol 2022; 88:e0031622. [PMID: 35384705 DOI: 10.1128/aem.00316-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Biosolids that are applied to agricultural soil as an organic fertilizer are frequently contaminated with pharmaceutical residues that have persisted during wastewater treatment and partitioned into the organic phase. Macrolide antibiotics, which serve as a critically important human medicine, have been detected within biosolids. To determine the impacts of macrolide antibiotics on soil bacteria, every year for a decade, a series of replicated field plots received an application of a mixture of erythromycin, clarithromycin, and azithromycin at a realistic (0.1 mg kg soil-1) or an unrealistically high (10 mg kg soil-1) dose or were left untreated. The effects of repeated antibiotic exposure on the soil bacterial community, resistome, mobilome, and integron gene cassette content were evaluated by 16S rRNA and integron gene cassette amplicon sequencing, as well as whole-metagenome sequencing. At the unrealistically high dose, the overall diversity of the resistome and mobilome was altered, as 21 clinically important antibiotic resistance genes predicted to encode resistance to 10 different antibiotic drug classes were increased and 20 mobile genetic element variants (tnpA, intI1, tnpAN, and IS91) were increased. In contrast, at the realistic dose, no effect was observed on the overall diversity of the soil bacterial community, resistome, mobilome, or integron gene cassette-carrying genes. Overall, these results suggest that macrolide antibiotics entrained into soil at concentrations anticipated with biosolid applications would not result in major changes to these endpoints. IMPORTANCE Biosolids, produced from the treatment of sewage sludge, are rich in plant nutrients and are a valuable alternative to inorganic fertilizer when applied to agricultural soil. However, the use of biosolids in agriculture, which are frequently contaminated with pharmaceuticals, such as macrolide antibiotics, may pose a risk to human health by selecting for antibiotic resistance genes that could be transferred to plant-based food destined for human consumption. The consequences of long-term, repeated macrolide antibiotic exposure on the diversity of the soil bacterial community, resistome, and mobilome were evaluated. At unrealistically high concentrations, macrolide antibiotics alter the overall diversity of the resistome and mobilome, enriching for antibiotic resistance genes and mobile genetic elements of concern to human health. However, at realistic antibiotic concentrations, no effect on these endpoints was observed, suggesting that current biosolids land management practices are unlikely to pose a risk to human health due to macrolide antibiotic contamination alone.
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Algarni S, Ricke SC, Foley SL, Han J. The Dynamics of the Antimicrobial Resistance Mobilome of Salmonella enterica and Related Enteric Bacteria. Front Microbiol 2022; 13:859854. [PMID: 35432284 PMCID: PMC9008345 DOI: 10.3389/fmicb.2022.859854] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 03/07/2022] [Indexed: 12/31/2022] Open
Abstract
The foodborne pathogen Salmonella enterica is considered a global public health risk. Salmonella enterica isolates can develop resistance to several antimicrobial drugs due to the rapid spread of antimicrobial resistance (AMR) genes, thus increasing the impact on hospitalization and treatment costs, as well as the healthcare system. Mobile genetic elements (MGEs) play key roles in the dissemination of AMR genes in S. enterica isolates. Multiple phenotypic and molecular techniques have been utilized to better understand the biology and epidemiology of plasmids including DNA sequence analyses, whole genome sequencing (WGS), incompatibility typing, and conjugation studies of plasmids from S. enterica and related species. Focusing on the dynamics of AMR genes is critical for identification and verification of emerging multidrug resistance. The aim of this review is to highlight the updated knowledge of AMR genes in the mobilome of Salmonella and related enteric bacteria. The mobilome is a term defined as all MGEs, including plasmids, transposons, insertion sequences (ISs), gene cassettes, integrons, and resistance islands, that contribute to the potential spread of genes in an organism, including S. enterica isolates and related species, which are the focus of this review.
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Affiliation(s)
- Suad Algarni
- Division of Microbiology, FDA National Center for Toxicological Research, Jefferson, AR, United States
- Cellular and Molecular Biology Graduate Program, University of Arkansas, Fayetteville, AR, United States
| | - Steven C. Ricke
- Meat Science and Animal Biologics Discovery Program, Department of Animal and Dairy Sciences, University of Wisconsin, Madison, WI, United States
| | - Steven L. Foley
- Division of Microbiology, FDA National Center for Toxicological Research, Jefferson, AR, United States
- Cellular and Molecular Biology Graduate Program, University of Arkansas, Fayetteville, AR, United States
| | - Jing Han
- Division of Microbiology, FDA National Center for Toxicological Research, Jefferson, AR, United States
- *Correspondence: Jing Han,
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Ghaly TM, Penesyan A, Pritchard A, Qi Q, Rajabal V, Tetu SG, Gillings MR. Methods for the targeted sequencing and analysis of integrons and their gene cassettes from complex microbial communities. Microb Genom 2022; 8. [PMID: 35298369 PMCID: PMC9176274 DOI: 10.1099/mgen.0.000788] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Integrons are microbial genetic elements that can integrate mobile gene cassettes. They are mostly known for spreading antibiotic resistance cassettes among human pathogens. However, beyond clinical settings, gene cassettes encode an extraordinarily diverse range of functions important for bacterial adaptation. The recovery and sequencing of cassettes has promising applications, including: surveillance of clinically important genes, particularly antibiotic resistance determinants; investigating the functional diversity of integron-carrying bacteria; and novel enzyme discovery. Although gene cassettes can be directly recovered using PCR, there are no standardised methods for their amplification and, importantly, for validating sequences as genuine integron gene cassettes. Here, we present reproducible methods for the amplification, sequence processing, and validation of gene cassette amplicons from complex communities. We describe two different PCR assays that either amplify cassettes together with integron integrases, or gene cassettes together within cassette arrays. We compare the performance of Nanopore and Illumina sequencing, and present bioinformatic pipelines that filter sequences to ensure that they represent amplicons from genuine integrons. Using a diverse set of environmental DNAs, we show that our approach can consistently recover thousands of unique cassettes per sample and up to hundreds of different integron integrases. Recovered cassettes confer a wide range of functions, including antibiotic resistance, with as many as 300 resistance cassettes found in a single sample. In particular, we show that class one integrons are collecting and concentrating resistance genes out of the broader diversity of cassette functions. The methods described here can be applied to any environmental or clinical microbiome sample.
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Affiliation(s)
- Timothy M Ghaly
- School of Natural Sciences, Macquarie University, New South Wales 2109, Australia
| | - Anahit Penesyan
- School of Natural Sciences, Macquarie University, New South Wales 2109, Australia.,ARC Centre of Excellence in Synthetic Biology, Macquarie University, New South Wales 2109, Australia
| | - Alexander Pritchard
- Division of Food Sciences, University of Nottingham, Loughborough LE12 5RD, Australia
| | - Qin Qi
- School of Natural Sciences, Macquarie University, New South Wales 2109, Australia
| | - Vaheesan Rajabal
- School of Natural Sciences, Macquarie University, New South Wales 2109, Australia.,ARC Centre of Excellence in Synthetic Biology, Macquarie University, New South Wales 2109, Australia
| | - Sasha G Tetu
- School of Natural Sciences, Macquarie University, New South Wales 2109, Australia.,ARC Centre of Excellence in Synthetic Biology, Macquarie University, New South Wales 2109, Australia
| | - Michael R Gillings
- School of Natural Sciences, Macquarie University, New South Wales 2109, Australia.,ARC Centre of Excellence in Synthetic Biology, Macquarie University, New South Wales 2109, Australia
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Azithromycin can induce SOS response and horizontal gene transfer of SXT element in Vibrio cholerae. Mol Biol Rep 2022; 49:4737-4748. [DOI: 10.1007/s11033-022-07323-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 03/02/2022] [Indexed: 10/18/2022]
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Unbridled Integrons: A Matter of Host Factors. Cells 2022; 11:cells11060925. [PMID: 35326376 PMCID: PMC8946536 DOI: 10.3390/cells11060925] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 03/03/2022] [Accepted: 03/04/2022] [Indexed: 12/29/2022] Open
Abstract
Integrons are powerful recombination systems found in bacteria, which act as platforms capable of capturing, stockpiling, excising and reordering mobile elements called cassettes. These dynamic genetic machineries confer a very high potential of adaptation to their host and have quickly found themselves at the forefront of antibiotic resistance, allowing for the quick emergence of multi-resistant phenotypes in a wide range of bacterial species. Part of the success of the integron is explained by its ability to integrate various environmental and biological signals in order to allow the host to respond to these optimally. In this review, we highlight the substantial interconnectivity that exists between integrons and their hosts and its importance to face changing environments. We list the factors influencing the expression of the cassettes, the expression of the integrase, and the various recombination reactions catalyzed by the integrase. The combination of all these host factors allows for a very tight regulation of the system at the cost of a limited ability to spread by horizontal gene transfer and function in remotely related hosts. Hence, we underline the important consequences these factors have on the evolution of integrons. Indeed, we propose that sedentary chromosomal integrons that were less connected or connected via more universal factors are those that have been more successful upon mobilization in mobile genetic structures, in contrast to those that were connected to species-specific host factors. Thus, the level of specificity of the involved host factors network may have been decisive for the transition from chromosomal integrons to the mobile integrons, which are now widespread. As such, integrons represent a perfect example of the conflicting relationship between the ability to control a biological system and its potential for transferability.
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Sonbol S, Siam R. Abundance of integrons in halophilic bacteria. Can J Microbiol 2022; 68:435-445. [PMID: 35239425 DOI: 10.1139/cjm-2021-0308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Integrons are genetic platforms used for expressing open reading frames (ORFs) arranged in gene cassettes. Excision and integration of gene cassettes is controlled by their associated integron integrase (IntI). Using IntegronFinder software, we analyzed all complete halophilic genomes available in the HaloDom database, along with selected partial halophilic genomes. We identified 18 new complete bacterial integrons and 46 clusters of attC sites lacking a neighboring integron-integrase (CALINs). Different classes of insertion sequences (ISs) were also identified within and nearby integrons and CALINs; with the abundance of IS1182 elements and different ISs that can presumably mobilize adjacent genomic structures. Different promoters for intI genes (PintI) showed nearby binding sites for arginine repressor (ArgR), raising the possibility that IntIs expression and recombination activity are regulated by these proteins. Our findings reveal the existence of new integrons in halophilic bacteria with possible adaptive roles.
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Affiliation(s)
- Sarah Sonbol
- The American University in Cairo School of Sciences and Engineering, 110156, Biotechnology, New Cairo, Egypt, 11835;
| | - Rania Siam
- The American University in Cairo School of Sciences and Engineering, 110156, Biology department and Biotechnology graduate program, New Cairo, Cairo, Egypt.,University of Medicine and Health Sciences, Basseterre, St. Kitts, West Indies, Saint Kitts and Nevis;
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The evolution of clinical guidelines for antimicrobial photodynamic therapy of skin. Photochem Photobiol Sci 2022; 21:385-395. [PMID: 35132604 PMCID: PMC8821777 DOI: 10.1007/s43630-021-00169-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: 07/13/2021] [Accepted: 12/28/2021] [Indexed: 11/28/2022]
Abstract
Antimicrobial photodynamic therapy has become an important component in the treatment of human infection. This review considers historical guidelines, and the scientific literature to envisage what future clinical guidelines for treating skin infection might include. Antibiotic resistance, vertical and horizontal infection control strategies and a range of technologies effective in eradicating microbes without building up new resistance are described. The mechanism of action of these treatments and examples of their clinical use are also included. The research recommendations of NICE Guidelines on the dermatological manifestations of microbial infection were also reviewed to identify potential applications for PDT. The resistance of some microbes to antibiotics can be halted, or even reversed through the use of supplementary drugs, and so they are likely to persist as a treatment of infection. Conventional PDT will undoubtedly continue to be used for a range of skin conditions given existing healthcare infrastructure and a large evidence base. Daylight PDT may find broader antimicrobial applications than just Acne and Cutaneous Leishmaniasis, and Ambulatory PDT devices could become popular in regions where resources are limited or daylight exposure is not possible or inappropriate. Nanotheranostics were found to be highly relevant, and often include PDT, however, new treatments and novel applications and combinations of existing treatments will be subject to Clinical Trials.
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Fonseca ÉL, Vicente AC. Integron Functionality and Genome Innovation: An Update on the Subtle and Smart Strategy of Integrase and Gene Cassette Expression Regulation. Microorganisms 2022; 10:microorganisms10020224. [PMID: 35208680 PMCID: PMC8876359 DOI: 10.3390/microorganisms10020224] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/14/2022] [Accepted: 01/15/2022] [Indexed: 12/22/2022] Open
Abstract
Integrons are considered hot spots for bacterial evolution, since these platforms allow one-step genomic innovation by capturing and expressing genes that provide advantageous novelties, such as antibiotic resistance. The acquisition and shuffling of gene cassettes featured by integrons enable the population to rapidly respond to changing selective pressures. However, in order to avoid deleterious effects and fitness burden, the integron activity must be tightly controlled, which happens in an elegant and elaborate fashion, as discussed in detail in the present review. Here, we aimed to provide an up-to-date overview of the complex regulatory networks that permeate the expression and functionality of integrons at both transcriptional and translational levels. It was possible to compile strong shreds of evidence clearly proving that these versatile platforms include functions other than acquiring and expressing gene cassettes. The well-balanced mechanism of integron expression is intricately related with environmental signals, host cell physiology, fitness, and survival, ultimately leading to adaptation on the demand.
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Subirats J, Murray R, Yin X, Zhang T, Topp E. Impact of chicken litter pre-application treatment on the abundance, field persistence, and transfer of antibiotic resistant bacteria and antibiotic resistance genes to vegetables. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 801:149718. [PMID: 34425441 DOI: 10.1016/j.scitotenv.2021.149718] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 08/12/2021] [Accepted: 08/13/2021] [Indexed: 06/13/2023]
Abstract
Treatment of manures prior to land application can potentially reduce the abundance of antibiotic resistance genes and thus the risk of contaminating crops or water resources. In this study, raw and composted chicken litter were applied to field plots that were cropped to carrots, lettuce and radishes. Vegetables were washed per normal culinary practice before downstream analysis. The impact of composting on manure microbial composition, persistence of antibiotic resistant bacteria in soil following application, and distribution of antibiotic resistance genes and bacteria on washed vegetables were determined. A subset of samples that were thought likely to reveal the most significant effects were chosen for shotgun sequencing. The absolute abundance of all target genes detected by qPCR decreased after composting except sul1, intI1, incW and erm(F) that remained stable. The shotgun sequencing revealed that some integron integrases were enriched by composting. Composting significantly reduced the abundance of enteric bacteria, including those carrying antibiotic resistance. Manure-amended soil showed significantly higher abundances of sul1, str(A), str(B), erm(B), aad(A), intI1 and incW compared to unmanured soil. At harvest, those genes that were detected in soil samples before the application of manure (intI1, sul1, strA and strB) were quantifiable by qPCR on vegetables, with a larger number of gene targets detected on the radishes than in the carrots or lettuce. Shotgun metagenomic sequencing suggested that the increase of antibiotic resistance genes on radishes produced in soil receiving raw manure may be due to changes to soil microbial communities following manure application, rather than transfer to the radishes of enteric bacteria. Overall, under field conditions there was limited evidence for transfer of antibiotic resistance genes from composted or raw manure to vegetables that then persisted through washing.
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Affiliation(s)
- Jessica Subirats
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, Canada; Department of Biology, University of Western Ontario, London, Ontario, Canada
| | - Roger Murray
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, Canada
| | - Xiaole Yin
- Environmental Biotechnology Lab, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China
| | - Tong Zhang
- Environmental Biotechnology Lab, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China
| | - Edward Topp
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, Canada; Department of Biology, University of Western Ontario, London, Ontario, Canada.
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Liu G, Thomsen LE, Olsen JE. Antimicrobial-induced horizontal transfer of antimicrobial resistance genes in bacteria: a mini-review. J Antimicrob Chemother 2021; 77:556-567. [PMID: 34894259 DOI: 10.1093/jac/dkab450] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The emergence and spread of antimicrobial resistance (AMR) among pathogenic bacteria constitute an accelerating crisis for public health. The selective pressures caused by increased use and misuse of antimicrobials in medicine and livestock production have accelerated the overall selection of resistant bacteria. In addition, horizontal gene transfer (HGT) plays an important role in the spread of resistance genes, for example mobilizing reservoirs of AMR from commensal bacteria into pathogenic ones. Antimicrobials, besides antibacterial function, also result in undesirable effects in the microbial populations, including the stimulation of HGT. The main aim of this narrative review was to present an overview of the current knowledge of the impact of antimicrobials on HGT in bacteria, including the effects of transformation, transduction and conjugation, as well as other less well-studied mechanisms of HGT. It is widely accepted that conjugation plays a major role in the spread of AMR in bacteria, and the focus of this review is therefore mainly on the evidence provided that antimicrobial treatment affects this process. Other mechanisms of HGT have so far been deemed less important in this respect; however, recent discoveries suggest their role may be larger than previously thought, and the review provides an update on the rather limited knowledge currently available regarding the impact of antimicrobial treatment on these processes as well. A conclusion from the review is that there is an urgent need to investigate the mechanisms of antimicrobial-induced HGT, since this will be critical for developing new strategies to combat the spread of AMR.
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Affiliation(s)
- Gang Liu
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao 266109, China.,Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Frederiksberg C, Denmark
| | - Line Elnif Thomsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Frederiksberg C, Denmark
| | - John Elmerdahl Olsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Frederiksberg C, Denmark
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Role of pollution on the selection of antibiotic resistance and bacterial pathogens in the environment. Curr Opin Microbiol 2021; 64:117-124. [PMID: 34700125 DOI: 10.1016/j.mib.2021.10.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 09/28/2021] [Accepted: 10/06/2021] [Indexed: 02/02/2023]
Abstract
There is evidence that human activity causes pollution that contributes to an enhanced selection of bacterial pathogens in the environment. In this review, we consider how environmental pollution can favour the selection of bacterial pathogens in the environment. We specifically discuss pollutants released into the environment by human activities (mainly human waste) that are associated with the selection for genetic features in environmental bacterial populations that lead to the emergence of bacterial pathogens. Finally, we also identify key pollutants that are associated with antibiotic resistance and discuss possibilities of how to prevent their release into the environment.
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