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Bergum OET, Singleton AH, Røst LM, Bodein A, Scott-Boyer MP, Rye MB, Droit A, Bruheim P, Otterlei M. SOS genes are rapidly induced while translesion synthesis polymerase activity is temporally regulated. Front Microbiol 2024; 15:1373344. [PMID: 38596376 PMCID: PMC11002266 DOI: 10.3389/fmicb.2024.1373344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 03/11/2024] [Indexed: 04/11/2024] Open
Abstract
The DNA damage inducible SOS response in bacteria serves to increase survival of the species at the cost of mutagenesis. The SOS response first initiates error-free repair followed by error-prone repair. Here, we have employed a multi-omics approach to elucidate the temporal coordination of the SOS response. Escherichia coli was grown in batch cultivation in bioreactors to ensure highly controlled conditions, and a low dose of the antibiotic ciprofloxacin was used to activate the SOS response while avoiding extensive cell death. Our results show that expression of genes involved in error-free and error-prone repair were both induced shortly after DNA damage, thus, challenging the established perception that the expression of error-prone repair genes is delayed. By combining transcriptomics and a sub-proteomics approach termed signalomics, we found that the temporal segregation of error-free and error-prone repair is primarily regulated after transcription, supporting the current literature. Furthermore, the heterology index (i.e., the binding affinity of LexA to the SOS box) was correlated to the maximum increase in gene expression and not to the time of induction of SOS genes. Finally, quantification of metabolites revealed increasing pyrimidine pools as a late feature of the SOS response. Our results elucidate how the SOS response is coordinated, showing a rapid transcriptional response and temporal regulation of mutagenesis on the protein and metabolite levels.
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Affiliation(s)
| | - Amanda Holstad Singleton
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Lisa Marie Røst
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Antoine Bodein
- Department of Molecular Medicine, CHU de Québec Research Center, Université Laval, Québec, QC, Canada
| | - Marie-Pier Scott-Boyer
- Department of Molecular Medicine, CHU de Québec Research Center, Université Laval, Québec, QC, Canada
| | - Morten Beck Rye
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Clinic of Surgery, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
- Clinic of Laboratory Medicine, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
- BioCore - Bioinformatics Core Facility, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Arnaud Droit
- Department of Molecular Medicine, CHU de Québec Research Center, Université Laval, Québec, QC, Canada
| | - Per Bruheim
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Marit Otterlei
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Clinic of Laboratory Medicine, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
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2
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Li Q, Tian P, Xu C, Peng Z, Xu P, Zhang H, Chen L. Increased expression of Mycobacterium tuberculosis Rv3737 gene associated with low-level amikacin resistance. J Infect Chemother 2024; 30:208-212. [PMID: 38012984 DOI: 10.1016/j.jiac.2023.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 08/17/2023] [Accepted: 10/10/2023] [Indexed: 11/29/2023]
Abstract
INTRODUCTION As an infectious disease, tuberculosis (TB) poses a serious threat to public health. Although amikacin (AMK) is an important antibiotic for the treatment of drug-resistant TB, its resistance mechanisms are not fully understood. METHODS To investigate the role of Rv3737 gene on AMK drug susceptibility, a Mycobacterium tuberculosis (M.tb) Rv3737 knockout strain (H37Rv△Rv3737) and a Mycobacterium smegmatis (M.sm) Rv3737 overexpressing strain (Msm/pMV261-Rv3737) were used to detect their minimal inhibitory concentrations (MICs) in this study. RESULTS The AMK MICs of Rv3737 knockout and overexpressing strains were 4-fold lower and 2-fold higher than those of the wild-type and empty plasmid strains, respectively. The results of clinical isolates showed that no Rv3737 gene mutation was found to be associated with AMK susceptibility, while the rrs A1401G mutation remained the main mechanism of high level of AMK resistance (MIC>32 μg/ml). There was a positive correlation between Rv3737 mRNA expression level and AMK MIC. In the isolates with low-level AMK resistance (MIC = 4 μg/ml) without rrs A1401G mutation, the expression level of Rv3737 gene was significantly higher than those of susceptible isolates. CONCLUSIONS In this study, the Rv3737 gene was reported for the first time for its effect on AMK susceptibility in M.tb. Although the rrs A1401G mutation remains the main reason of high-level AMK resistance, high expression of the Rv3737 gene was associated with low-level AMK resistance in clinical isolates.
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Affiliation(s)
- Qiong Li
- Department of Tuberculosis, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou Province, 563003, China
| | - Peng Tian
- Department of Tuberculosis, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou Province, 563003, China
| | - Chao Xu
- Department of Tuberculosis, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou Province, 563003, China
| | - Zhangli Peng
- Department of Tuberculosis, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou Province, 563003, China
| | - Peng Xu
- School of Basic Medicine, Zunyi Medical University, Zunyi, Guizhou Province, 563000, China.
| | - Hong Zhang
- Department of Tuberculosis, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou Province, 563003, China; 3Z-BioMed, Inc., Rockville, MD, 20855, USA.
| | - Ling Chen
- Department of Tuberculosis, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou Province, 563003, China.
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Qi W, Jonker MJ, de Leeuw W, Brul S, ter Kuile BH. Reactive oxygen species accelerate de novo acquisition of antibiotic resistance in E. coli. iScience 2023; 26:108373. [PMID: 38025768 PMCID: PMC10679899 DOI: 10.1016/j.isci.2023.108373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 09/06/2023] [Accepted: 10/27/2023] [Indexed: 12/01/2023] Open
Abstract
Reactive oxygen species (ROS) produced as a secondary effect of bactericidal antibiotics are hypothesized to play a role in killing bacteria. If correct, ROS may play a role in development of de novo resistance. Here we report that single-gene knockout strains with reduced ROS scavenging exhibited enhanced ROS accumulation and more rapid acquisition of resistance when exposed to sublethal levels of bactericidal antibiotics. Consistent with this observation, the ROS scavenger thiourea in the medium decelerated resistance development. Thiourea downregulated the transcriptional level of error-prone DNA polymerase and DNA glycosylase MutM, which counters the incorporation and accumulation of 8-hydroxy-2'-deoxyguanosine (8-HOdG) in the genome. The level of 8-HOdG significantly increased following incubation with bactericidal antibiotics but decreased after treatment with the ROS scavenger thiourea. These observations suggest that in E. coli sublethal levels of ROS stimulate de novo development of resistance, providing a mechanistic basis for hormetic responses induced by antibiotics.
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Affiliation(s)
- Wenxi Qi
- Laboratory for Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
| | - Martijs J. Jonker
- RNA Biology & Applied Bioinformatics, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
| | - Wim de Leeuw
- RNA Biology & Applied Bioinformatics, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
| | - Stanley Brul
- Laboratory for Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
| | - Benno H. ter Kuile
- Laboratory for Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
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4
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Merino N, Berdejo D, Pagán E, Girard C, Kerros S, Spinozzi E, Pagán R, García-Gonzalo D. Phenotypic and Genotypic Comparison of Antimicrobial-Resistant Variants of Escherichia coli and Salmonella Typhimurium Isolated from Evolution Assays with Antibiotics or Commercial Products Based on Essential Oils. Pharmaceuticals (Basel) 2023; 16:1443. [PMID: 37895914 PMCID: PMC10610042 DOI: 10.3390/ph16101443] [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: 09/14/2023] [Revised: 10/06/2023] [Accepted: 10/07/2023] [Indexed: 10/29/2023] Open
Abstract
On account of the widespread development and propagation of antimicrobial-resistant (AMR) bacteria, essential oils (EOs) have emerged as potential alternatives to antibiotics. However, as already observed for antibiotics, recent studies have raised concerns regarding the potential emergence of resistant variants (RVs) to EOs. In this study, we assessed the emergence of RVs in Escherichia coli and Salmonella enterica Typhimurium after evolution assays under extended exposure to subinhibitory doses of two commercial EOs (AEN and COLIFIT) as well as to two antibiotics (amoxicillin and colistin). Phenotypic characterization of RVs from evolution assays with commercial EOs yielded no relevant increases in the minimum inhibitory concentration (MIC) of E. coli and did not even modify MIC values in S. Typhimurium. Conversely, RVs of E. coli and S. Typhimurium isolated from evolution assays with antibiotics showed increased resistance. Genotypic analysis demonstrated that resistance to commercial EOs was associated with enhanced protection against oxidative stress and redirection of cell energy toward efflux activity, while resistance to antibiotics was primarily linked to modifications in the cell binding sites of antibiotics. These findings suggest that AEN and COLIFIT could serve as safe alternatives to antibiotics in combating the emergence and dissemination of antimicrobial resistance within the agrifood system.
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Affiliation(s)
- Natalia Merino
- Departamento de Producción Animal y Ciencia de los Alimentos, Facultad de Veterinaria, Instituto Agroalimentario de Aragón-IA2 (Universidad de Zaragoza-CITA), 50013 Zaragoza, Spain
| | - Daniel Berdejo
- Departamento de Producción Animal y Ciencia de los Alimentos, Facultad de Veterinaria, Instituto Agroalimentario de Aragón-IA2 (Universidad de Zaragoza-CITA), 50013 Zaragoza, Spain
| | - Elisa Pagán
- Departamento de Producción Animal y Ciencia de los Alimentos, Facultad de Veterinaria, Instituto Agroalimentario de Aragón-IA2 (Universidad de Zaragoza-CITA), 50013 Zaragoza, Spain
| | | | | | - Eleonora Spinozzi
- Chemistry Interdiscplinary Project (ChIP), School of Pharmacy, University of Camerino, 62032 Camerino, Italy
| | - Rafael Pagán
- Departamento de Producción Animal y Ciencia de los Alimentos, Facultad de Veterinaria, Instituto Agroalimentario de Aragón-IA2 (Universidad de Zaragoza-CITA), 50013 Zaragoza, Spain
| | - Diego García-Gonzalo
- Departamento de Producción Animal y Ciencia de los Alimentos, Facultad de Veterinaria, Instituto Agroalimentario de Aragón-IA2 (Universidad de Zaragoza-CITA), 50013 Zaragoza, Spain
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5
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Prentiss M, Wang D, Fu J, Prévost C, Godoy-Carter V, Kleckner N, Danilowicz C. Highly mismatch-tolerant homology testing by RecA could explain how homology length affects recombination. PLoS One 2023; 18:e0288611. [PMID: 37440583 PMCID: PMC10343044 DOI: 10.1371/journal.pone.0288611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 07/02/2023] [Indexed: 07/15/2023] Open
Abstract
In E. coli, double strand breaks (DSBs) are resected and loaded with RecA protein. The genome is then rapidly searched for a sequence that is homologous to the DNA flanking the DSB. Mismatches in homologous partners are rare, suggesting that RecA should rapidly reject mismatched recombination products; however, this is not the case. Decades of work have shown that long lasting recombination products can include many mismatches. In this work, we show that in vitro RecA forms readily observable recombination products when 16% of the bases in the product are mismatched. We also consider various theoretical models of mismatch-tolerant homology testing. The models test homology by comparing the sequences of Ltest bases in two single-stranded DNAs (ssDNA) from the same genome. If the two sequences pass the homology test, the pairing between the two ssDNA becomes permanent. Stringency is the fraction of permanent pairings that join ssDNA from the same positions in the genome. We applied the models to both randomly generated genomes and bacterial genomes. For both randomly generated genomes and bacterial genomes, the models show that if no mismatches are accepted stringency is ∼ 99% when Ltest = 14 bp. For randomly generated genomes, stringency decreases with increasing mismatch tolerance, and stringency improves with increasing Ltest. In contrast, in bacterial genomes when Ltest ∼ 75 bp, stringency is ∼ 99% for both mismatch-intolerant and mismatch-tolerant homology testing. Furthermore, increasing Ltest does not improve stringency because most incorrect pairings join different copies of repeats. In sum, for bacterial genomes highly mismatch tolerant homology testing of 75 bp provides the same stringency as homology testing that rejects all mismatches and testing more than ∼75 base pairs is not useful. Interestingly, in vivo commitment to recombination typically requires homology testing of ∼ 75 bp, consistent with highly mismatch intolerant testing.
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Affiliation(s)
- Mara Prentiss
- Department of Physics, Harvard University, Cambridge, Massachusetts, United States of America
| | - Dianzhuo Wang
- Department of Physics, Harvard University, Cambridge, Massachusetts, United States of America
| | - Jonathan Fu
- Department of Physics, Harvard University, Cambridge, Massachusetts, United States of America
| | - Chantal Prévost
- Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, Paris, France
| | - Veronica Godoy-Carter
- Department of Biology, Northeastern University, Boston, Massachusetts, United States of America
| | - Nancy Kleckner
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Claudia Danilowicz
- Department of Physics, Harvard University, Cambridge, Massachusetts, United States of America
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6
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Gifford DR, Berríos-Caro E, Joerres C, Suñé M, Forsyth JH, Bhattacharyya A, Galla T, Knight CG. Mutators can drive the evolution of multi-resistance to antibiotics. PLoS Genet 2023; 19:e1010791. [PMID: 37311005 DOI: 10.1371/journal.pgen.1010791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 05/18/2023] [Indexed: 06/15/2023] Open
Abstract
Antibiotic combination therapies are an approach used to counter the evolution of resistance; their purported benefit is they can stop the successive emergence of independent resistance mutations in the same genome. Here, we show that bacterial populations with 'mutators', organisms with defects in DNA repair, readily evolve resistance to combination antibiotic treatment when there is a delay in reaching inhibitory concentrations of antibiotic-under conditions where purely wild-type populations cannot. In populations of Escherichia coli subjected to combination treatment, we detected a diverse array of acquired mutations, including multiple alleles in the canonical targets of resistance for the two drugs, as well as mutations in multi-drug efflux pumps and genes involved in DNA replication and repair. Unexpectedly, mutators not only allowed multi-resistance to evolve under combination treatment where it was favoured, but also under single-drug treatments. Using simulations, we show that the increase in mutation rate of the two canonical resistance targets is sufficient to permit multi-resistance evolution in both single-drug and combination treatments. Under both conditions, the mutator allele swept to fixation through hitch-hiking with single-drug resistance, enabling subsequent resistance mutations to emerge. Ultimately, our results suggest that mutators may hinder the utility of combination therapy when mutators are present. Additionally, by raising the rates of genetic mutation, selection for multi-resistance may have the unwanted side-effect of increasing the potential to evolve resistance to future antibiotic treatments.
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Affiliation(s)
- Danna R Gifford
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
- Department of Earth and Environmental Sciences, School of Natural Sciences, Faculty of Science and Engineering, The University of Manchester, Manchester, United Kingdom
| | - Ernesto Berríos-Caro
- Department of Physics and Astronomy, School of Natural Sciences, Faculty of Science and Engineering, The University of Manchester, Manchester, United Kingdom
- Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology, Plön, Germany
- Department of Evolutionary Ecology and Genetics, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Christine Joerres
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
| | - Marc Suñé
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
| | - Jessica H Forsyth
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
| | - Anish Bhattacharyya
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
| | - Tobias Galla
- Department of Physics and Astronomy, School of Natural Sciences, Faculty of Science and Engineering, The University of Manchester, Manchester, United Kingdom
- Instituto de Física Interdisciplinar y Sistemas Complejos, IFISC (CSIC-UIB), Campus Universitat Illes Balears, Palma de Mallorca, Spain
| | - Christopher G Knight
- Department of Earth and Environmental Sciences, School of Natural Sciences, Faculty of Science and Engineering, The University of Manchester, Manchester, United Kingdom
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7
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Xu N, Du LH, Chen YC, Zhang JH, Zhu QF, Chen R, Peng GP, Wang QM, Yu HZ, Rao LQ. Lonicera japonica Thunb. as a promising antibacterial agent for Bacillus cereus ATCC14579 based on network pharmacology, metabolomics, and in vitro experiments. RSC Adv 2023; 13:15379-15390. [PMID: 37223411 PMCID: PMC10201548 DOI: 10.1039/d3ra00802a] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 05/15/2023] [Indexed: 05/25/2023] Open
Abstract
Lonicera japonica Thunb. has attracted much attention for its treatment of bacterial and viral infectious diseases, while its active ingredients and potential mechanisms of action have not been fully elucidated. Here, we combined metabolomics, and network pharmacology to explore the molecular mechanism of Bacillus cereus ATCC14579 inhibition by Lonicera japonica Thunb. In vitro inhibition experiments showed that the Lonicera japonica Thunb.'s water extracts, ethanolic extract, luteolin, quercetin, and kaempferol strongly inhibited Bacillus cereus ATCC14579. In contrast, chlorogenic acid and macranthoidin B had no inhibitory effect on Bacillus cereus ATCC14579. Meanwhile, the minimum inhibitory concentrations of luteolin, quercetin, and kaempferol against Bacillus cereus ATCC14579 were 15.625 μg mL-1, 31.25 μg mL-1, and 15.625 μg mL-1. Based on the previous experimental basis, the metabolomic analysis showed the presence of 16 active ingredients in Lonicera japonica Thunb.'s water extracts and ethanol extracts, with differences in the luteolin, quercetin, and kaempferol contents between the water extracts and ethanol extracts. Network pharmacology studies indicated that fabZ, tig, glmU, secA, deoD, nagB, pgi, rpmB, recA, and upp were potential key targets. Active ingredients of Lonicera japonica Thunb. may exert their inhibitory effects by inhibiting ribosome assembly, the peptidoglycan biosynthesis process, and the phospholipid biosynthesis process of Bacillus cereus ATCC14579. An alkaline phosphatase activity assay, peptidoglycan concentration assay, and protein concentration assay showed that luteolin, quercetin, and kaempferol disrupted the Bacillus cereus ATCC14579 cell wall and cell membrane integrity. Transmission electron microscopy results showed significant changes in the morphology and ultrastructure of the cell wall and cell membrane of Bacillus cereus ATCC14579, further confirming the disruption of the cell wall and cell membrane integrity of Bacillus cereus ATCC14579 by luteolin, quercetin, and kaempferol. In conclusion, Lonicera japonica Thunb. can be used as a potential antibacterial agent for Bacillus cereus ATCC14579, which may exert its antibacterial activity by destroying the integrity of the cell wall and membrane.
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Affiliation(s)
- Nan Xu
- Hunan Engineering Laboratory for Good Agricultural Practice and Comprehensive Utilization of Famous-Region Medicinal Plants, Hunan Agricultural University Changsha China
| | - Li-Hua Du
- Hunan Engineering Laboratory for Good Agricultural Practice and Comprehensive Utilization of Famous-Region Medicinal Plants, Hunan Agricultural University Changsha China
| | - Yan-Chao Chen
- Hunan Engineering Laboratory for Good Agricultural Practice and Comprehensive Utilization of Famous-Region Medicinal Plants, Hunan Agricultural University Changsha China
| | - Jin-Hao Zhang
- Hunan Engineering Laboratory for Good Agricultural Practice and Comprehensive Utilization of Famous-Region Medicinal Plants, Hunan Agricultural University Changsha China
| | - Qian-Feng Zhu
- Hunan Engineering Laboratory for Good Agricultural Practice and Comprehensive Utilization of Famous-Region Medicinal Plants, Hunan Agricultural University Changsha China
| | - Rong Chen
- Hunan Engineering Laboratory for Good Agricultural Practice and Comprehensive Utilization of Famous-Region Medicinal Plants, Hunan Agricultural University Changsha China
| | - Guo-Ping Peng
- Hunan Engineering Laboratory for Good Agricultural Practice and Comprehensive Utilization of Famous-Region Medicinal Plants, Hunan Agricultural University Changsha China
| | - Qi-Ming Wang
- Hunan Engineering Laboratory for Good Agricultural Practice and Comprehensive Utilization of Famous-Region Medicinal Plants, Hunan Agricultural University Changsha China
| | - Hua-Zhong Yu
- Key Laboratory of Hunan Forest Products and Chemical Industry Engineering, Jishou University Jishou China
| | - Li-Qun Rao
- Hunan Engineering Laboratory for Good Agricultural Practice and Comprehensive Utilization of Famous-Region Medicinal Plants, Hunan Agricultural University Changsha China
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8
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Chen P, Yu K, He Y. The dynamics and transmission of antibiotic resistance associated with plant microbiomes. ENVIRONMENT INTERNATIONAL 2023; 176:107986. [PMID: 37257204 DOI: 10.1016/j.envint.2023.107986] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 05/17/2023] [Accepted: 05/17/2023] [Indexed: 06/02/2023]
Abstract
Antibiotic resistance genes (ARGs) have been widely found and studied in soil and water environments. However, the propagation of ARGs in plant microbiomes has attracted insufficient attention. Plant microbiomes, especially the rhizosphere microorganisms, are closely connected with water, soil, and air, which allows ARGs to spread widely in ecosystems and pose a threat to human health after entering the human body with bacteria. Therefore, it is necessary to deeply understand and explore the dynamics and the transmission of ARGs in rhizosphere microorganisms and endophytes of plants. In this review, the transmission and influencing factors of ARGs in the microorganisms associated with plants, especially the influence of root exudates on plant microbiomes, are analyzed. Notably, the role of intrinsic genes of plants in determining root exudates and their potential effects on ARGs are proposed and analyzed. The important role of phyllosphere microorganisms and endophytes in the transmission of ARGs and co-resistance of antibiotics and other substances are also emphasized. The proliferation and transmission of ARGs associated with plant microbiomes addressed in this review is conducive to revealing the fate of ARGs in plant microorganisms and alleviating ARG pollution.
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Affiliation(s)
- Ping Chen
- School of Environmental Science & Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Kaifeng Yu
- School of Environmental Science & Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Yiliang He
- School of Environmental Science & Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China.
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9
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Lu R, Zhu H, Wu X. Estimating mutation rates in a Markov branching process using approximate Bayesian computation. J Theor Biol 2023; 565:111467. [PMID: 36963627 DOI: 10.1016/j.jtbi.2023.111467] [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: 07/14/2022] [Revised: 02/15/2023] [Accepted: 03/15/2023] [Indexed: 03/26/2023]
Abstract
Estimating microbial mutation rates is an essential task in evolutionary biology, with wide range applications in related fields such as virology, epidemiology, clinic and public health, and antibiotic research. Significant progress has been made on this research since 1943 when Luria-Delbrück fluctuation analysis was first introduced. However, existing estimators of mutation rates are heavily reliant on model assumptions in fluctuation analysis, and become less applicable to real microbial experiments which deviate from the model assumptions. To overcome this difficulty, we propose to model fluctuation experimental data by a two-type Markov branching process (MBP) and use approximate Bayesian computation (ABC) to estimate the mutation probability parameters. Such an ABC-based mutation rate estimator is based on intensive simulations from the mutation process, thereby taking advantage of modern computing power. Most importantly, its likelihood-free feature allows more complex and realistic setups of the mutation process, especially when the distribution of the number of mutants cannot be easily derived. To further improve computation efficiency, we use a Gaussian process surrogate to substitute the simulator in the ABC algorithm, and call the resulting estimator GPS-ABC. Simulation studies show that, when used to estimate constant mutation rate in MBP, ABC-based estimators generally outperform traditional moment or likelihood-based estimators. When mutations occur in two stages, i.e., in MBP with a piece-wise constant mutation rate function, traditional mutation rate estimators become not applicable, yet GPS-ABC still achieves reasonable estimates. Finally, the proposed GPS-ABC estimator is used to analyze real fluctuation experimental datasets for studying drug resistance.
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Affiliation(s)
- Ruijin Lu
- Department of Statistics, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, United States of America
| | - Hongxiao Zhu
- Department of Statistics, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, United States of America
| | - Xiaowei Wu
- Department of Statistics, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, United States of America.
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10
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Diaz-Diaz S, Recacha E, Pulido MR, Romero-Muñoz M, de Gregorio-Iaria B, Docobo-Pérez F, Pascual A, Rodríguez-Martínez JM. Synergistic Effect of SOS Response and GATC Methylome Suppression on Antibiotic Stress Survival in Escherichia coli. Antimicrob Agents Chemother 2023; 67:e0139222. [PMID: 36802234 PMCID: PMC10019295 DOI: 10.1128/aac.01392-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 01/22/2023] [Indexed: 02/23/2023] Open
Abstract
The suppression of the SOS response has been shown to enhance the in vitro activity of quinolones. Furthermore, Dam-dependent base methylation has an impact on susceptibility to other antimicrobials affecting DNA synthesis. Here, we investigated the interplay between these two processes, alone and in combination, in terms of antimicrobial activity. A genetic strategy was used employing single- and double-gene mutants for the SOS response (recA gene) and the Dam methylation system (dam gene) in isogenic models of Escherichia coli both susceptible and resistant to quinolones. Regarding the bacteriostatic activity of quinolones, a synergistic sensitization effect was observed when the Dam methylation system and the recA gene were suppressed. In terms of growth, after 24 h in the presence of quinolones, the Δdam ΔrecA double mutant showed no growth or delayed growth compared to the control strain. In bactericidal terms, spot tests showed that the Δdam ΔrecA double mutant was more sensitive than the ΔrecA single mutant (about 10- to 102-fold) and the wild type (about 103- to 104-fold) in both susceptible and resistant genetic backgrounds. Differences between the wild type and the Δdam ΔrecA double mutant were confirmed by time-kill assays. The suppression of both systems, in a strain with chromosomal mechanisms of quinolone resistance, prevents the evolution of resistance. This genetic and microbiological approach demonstrated the enhanced sensitization of E. coli to quinolones by dual targeting of the recA (SOS response) and Dam methylation system genes, even in a resistant strain model.
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Affiliation(s)
- S. Diaz-Diaz
- Unidad de Enfermedades Infecciosas y Microbiología, Hospital Universitario Virgen Macarena, Seville, Spain
- Departamento de Microbiología, Facultad de Medicina, Universidad de Sevilla, Seville, Spain
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen Macarena/CSIC/Universidad de Sevilla, Seville, Spain
| | - E. Recacha
- Unidad de Enfermedades Infecciosas y Microbiología, Hospital Universitario Virgen Macarena, Seville, Spain
- Departamento de Microbiología, Facultad de Medicina, Universidad de Sevilla, Seville, Spain
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen Macarena/CSIC/Universidad de Sevilla, Seville, Spain
| | - Marina R. Pulido
- Departamento de Microbiología, Facultad de Medicina, Universidad de Sevilla, Seville, Spain
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen Macarena/CSIC/Universidad de Sevilla, Seville, Spain
| | - María Romero-Muñoz
- Departamento de Microbiología, Facultad de Medicina, Universidad de Sevilla, Seville, Spain
| | - B. de Gregorio-Iaria
- Departamento de Microbiología, Facultad de Medicina, Universidad de Sevilla, Seville, Spain
| | - F. Docobo-Pérez
- Departamento de Microbiología, Facultad de Medicina, Universidad de Sevilla, Seville, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen Macarena/CSIC/Universidad de Sevilla, Seville, Spain
| | - A. Pascual
- Unidad de Enfermedades Infecciosas y Microbiología, Hospital Universitario Virgen Macarena, Seville, Spain
- Departamento de Microbiología, Facultad de Medicina, Universidad de Sevilla, Seville, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen Macarena/CSIC/Universidad de Sevilla, Seville, Spain
| | - J. M. Rodríguez-Martínez
- Departamento de Microbiología, Facultad de Medicina, Universidad de Sevilla, Seville, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen Macarena/CSIC/Universidad de Sevilla, Seville, Spain
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11
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Cory MB, Li A, Hurley CM, Hostetler ZM, Venkatesh Y, Jones CM, Petersson EJ, Kohli RM. Engineered RecA Constructs Reveal the Minimal SOS Activation Complex. Biochemistry 2022; 61:2884-2896. [PMID: 36473084 PMCID: PMC9982712 DOI: 10.1021/acs.biochem.2c00505] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The SOS response is a bacterial DNA damage response pathway that has been heavily implicated in bacteria's ability to evolve resistance to antibiotics. Activation of the SOS response is dependent on the interaction between two bacterial proteins, RecA and LexA. RecA acts as a DNA damage sensor by forming lengthy oligomeric filaments (RecA*) along single-stranded DNA (ssDNA) in an ATP-dependent manner. RecA* can then bind to LexA, the repressor of SOS response genes, triggering LexA degradation and leading to induction of the SOS response. Formation of the RecA*-LexA complex therefore serves as the key "SOS activation signal." Given the challenges associated with studying a complex involving multiple macromolecular interactions, the essential constituents of RecA* that allow LexA cleavage are not well defined. Here, we leverage head-to-tail linked and end-capped RecA constructs as tools to define the minimal RecA* filament that can engage LexA. In contrast to previously postulated models, we found that as few as three linked RecA units are capable of ssDNA binding, LexA binding, and LexA cleavage. We further demonstrate that RecA oligomerization alone is insufficient for LexA cleavage, with an obligate requirement for ATP and ssDNA binding to form a competent SOS activation signal with the linked constructs. Our minimal system for RecA* highlights the limitations of prior models for the SOS activation signal and offers a novel tool that can inform efforts to slow acquired antibiotic resistance by targeting the SOS response.
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Affiliation(s)
- Michael B. Cory
- Graduate Group in Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Allen Li
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Christina M. Hurley
- Graduate Group in Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Zachary M. Hostetler
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Yarra Venkatesh
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Chloe M. Jones
- Graduate Group in Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - E. James Petersson
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Rahul M. Kohli
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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12
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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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13
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Revitt‐Mills SA, Wright EK, Vereker M, O'Flaherty C, McPherson F, Dawson C, van Oijen AM, Robinson A. Defects in DNA double‐strand break repair resensitize antibiotic‐resistant
Escherichia coli
to multiple bactericidal antibiotics. Microbiologyopen 2022; 11:e1316. [PMCID: PMC9500592 DOI: 10.1002/mbo3.1316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 09/03/2022] [Accepted: 09/03/2022] [Indexed: 11/11/2022] Open
Affiliation(s)
- Sarah A. Revitt‐Mills
- School of Chemistry and Molecular Bioscience, Molecular Horizons Institute University of Wollongong Wollongong New South Wales Australia
- Illawarra Health and Medical Research Institute Wollongong New South Wales Australia
| | - Elizabeth K. Wright
- School of Chemistry and Molecular Bioscience, Molecular Horizons Institute University of Wollongong Wollongong New South Wales Australia
- Illawarra Health and Medical Research Institute Wollongong New South Wales Australia
| | - Madaline Vereker
- School of Chemistry and Molecular Bioscience, Molecular Horizons Institute University of Wollongong Wollongong New South Wales Australia
- Illawarra Health and Medical Research Institute Wollongong New South Wales Australia
| | - Callum O'Flaherty
- School of Chemistry and Molecular Bioscience, Molecular Horizons Institute University of Wollongong Wollongong New South Wales Australia
- Illawarra Health and Medical Research Institute Wollongong New South Wales Australia
| | - Fairley McPherson
- School of Chemistry and Molecular Bioscience, Molecular Horizons Institute University of Wollongong Wollongong New South Wales Australia
- Illawarra Health and Medical Research Institute Wollongong New South Wales Australia
| | - Catherine Dawson
- School of Chemistry and Molecular Bioscience, Molecular Horizons Institute University of Wollongong Wollongong New South Wales Australia
- Illawarra Health and Medical Research Institute Wollongong New South Wales Australia
| | - Antoine M. van Oijen
- School of Chemistry and Molecular Bioscience, Molecular Horizons Institute University of Wollongong Wollongong New South Wales Australia
- Illawarra Health and Medical Research Institute Wollongong New South Wales Australia
| | - Andrew Robinson
- School of Chemistry and Molecular Bioscience, Molecular Horizons Institute University of Wollongong Wollongong New South Wales Australia
- Illawarra Health and Medical Research Institute Wollongong New South Wales Australia
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14
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Schmidt SBI, Rodríguez-Rojas A, Rolff J, Schreiber F. Biocides used as material preservatives modify rates of de novo mutation and horizontal gene transfer in bacteria. JOURNAL OF HAZARDOUS MATERIALS 2022; 437:129280. [PMID: 35714537 DOI: 10.1016/j.jhazmat.2022.129280] [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: 12/13/2021] [Revised: 05/20/2022] [Accepted: 05/30/2022] [Indexed: 06/15/2023]
Abstract
Antimicrobial resistance (AMR) is a global health problem with the environment being an important compartment for the evolution and transmission of AMR. Previous studies showed that de-novo mutagenesis and horizontal gene transfer (HGT) by conjugation or transformation - important processes underlying resistance evolution and spread - are affected by antibiotics, metals and pesticides. However, natural microbial communities are also frequently exposed to biocides used as material preservatives, but it is unknown if these substances induce mutagenesis and HGT. Here, we show that active substances used in material preservatives can increase rates of mutation and conjugation in a species- and substance-dependent manner, while rates of transformation are not increased. The bisbiguanide chlorhexidine digluconate, the quaternary ammonium compound didecyldimethylammonium chloride, the metal copper, the pyrethroid-insecticide permethrin, and the azole-fungicide propiconazole increase mutation rates in Escherichia coli, whereas no increases were identified for Bacillus subtilis and Acinetobacter baylyi. Benzalkonium chloride, chlorhexidine and permethrin increased conjugation in E. coli. Moreover, our results show a connection between the RpoS-mediated general stress and the RecA-linked SOS response with increased rates of mutation and conjugation, but not for all biocides. Taken together, our data show the importance of assessing the contribution of material preservatives on AMR evolution and spread.
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Affiliation(s)
- Selina B I Schmidt
- Division of Biodeterioration and Reference Organisms (4.1), Department of Materials and the Environment, Federal Institute for Materials Research and Testing (BAM), Unter den Eichen 87, 12205 Berlin, Germany.
| | - Alexandro Rodríguez-Rojas
- Evolutionary Biology, Institute of Biology, Freie Universität Berlin, Königin-Luise-Straße 1-3, 14195 Berlin, Germany; Internal Medicine - Vetmeduni Vienna, Veterinärplatz 1, 1210 Vienna, Austria.
| | - Jens Rolff
- Evolutionary Biology, Institute of Biology, Freie Universität Berlin, Königin-Luise-Straße 1-3, 14195 Berlin, Germany.
| | - Frank Schreiber
- Division of Biodeterioration and Reference Organisms (4.1), Department of Materials and the Environment, Federal Institute for Materials Research and Testing (BAM), Unter den Eichen 87, 12205 Berlin, Germany.
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15
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Vasse M, Bonhoeffer S, Frenoy A. Ecological effects of stress drive bacterial evolvability under sub-inhibitory antibiotic treatments. ISME COMMUNICATIONS 2022; 2:80. [PMID: 37938266 PMCID: PMC9723650 DOI: 10.1038/s43705-022-00157-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 07/20/2022] [Accepted: 07/29/2022] [Indexed: 11/09/2023]
Abstract
Stress is thought to increase mutation rate and thus to accelerate evolution. In the context of antibiotic resistance, sub-inhibitory treatments could then lead to enhanced evolvability, thereby fuelling the adaptation of pathogens. Combining wet-lab experiments, stochastic simulations and a meta-analysis of the literature, we found that the increase in mutation rates triggered by antibiotic treatments is often cancelled out by reduced population size, resulting in no overall increase in genetic diversity. A careful analysis of the effect of ecological factors on genetic diversity showed that the potential for regrowth during recovery phase after treatment plays a crucial role in evolvability, being the main factor associated with increased genetic diversity in experimental data.
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Affiliation(s)
- Marie Vasse
- Institute for Integrative Biology, ETH Zürich, Zurich, Switzerland
| | | | - Antoine Frenoy
- Institute for Integrative Biology, ETH Zürich, Zurich, Switzerland.
- Université Grenoble Alpes, CNRS UMR 5525, Grenoble, France.
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16
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Jaramillo AVC, Cory MB, Li A, Kohli RM, Wuest WM. Exploration of inhibitors of the bacterial LexA repressor-protease. Bioorg Med Chem Lett 2022; 65:128702. [PMID: 35351585 DOI: 10.1016/j.bmcl.2022.128702] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 03/17/2022] [Accepted: 03/24/2022] [Indexed: 11/25/2022]
Abstract
Resistant and tolerant bacterial infections lead to billions in healthcare costs and cause hundreds of thousands of deaths each year. The bulk of current antibiotic research efforts focus on molecules which, although novel, are not immune from acquired resistance and seldomly affect tolerant populations. The bacterial SOS response has been implicated in several resistance and tolerance mechanisms, making it an attractive antibiotic target. Using small molecule inhibitors targeting a key step in the deployment of the SOS response, our approach focused on preventing the deployment of mechanisms such as biofilm formation, horizontal gene transfer, and error-prone DNA repair. Herein we report the synthesis and testing of analogs of a triazole-containing tricyclic inhibitor of LexA proteolysis, the key event in the SOS response. Our results hint that our inhibitor's may function by adopting a β-hairpin conformation, reminiscent of the native cleavage loop of LexA.
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Affiliation(s)
| | - Michael B Cory
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Allen Li
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Rahul M Kohli
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - William M Wuest
- Department of Chemistry, Emory University, Atlanta, GA, USA.
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17
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Transcriptomic profiling of Escherichia coli K-12 in response to a compendium of stressors. Sci Rep 2022; 12:8788. [PMID: 35610252 PMCID: PMC9130244 DOI: 10.1038/s41598-022-12463-3] [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: 12/18/2021] [Accepted: 05/05/2022] [Indexed: 11/09/2022] Open
Abstract
Environmental perturbations impact multiple cellular traits, including gene expression. Bacteria respond to these stressful situations through complex gene interaction networks, thereby inducing stress tolerance and survival of cells. In this paper, we study the response mechanisms of E. coli when exposed to different environmental stressors via differential expression and co-expression analysis. Gene co-expression networks were generated and analyzed via Weighted Gene Co-expression Network Analysis (WGCNA). Based on the gene co-expression networks, genes with similar expression profiles were clustered into modules. The modules were analysed for identification of hub genes, enrichment of biological processes and transcription factors. In addition, we also studied the link between transcription factors and their differentially regulated targets to understand the regulatory mechanisms involved. These networks validate known gene interactions and provide new insights into genes mediating transcriptional regulation in specific stress environments, thus allowing for in silico hypothesis generation.
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18
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Ma Y, Khan MZ, Xiao J, Alugongo GM, Chen X, Li S, Wang Y, Cao Z. An Overview of Waste Milk Feeding Effect on Growth Performance, Metabolism, Antioxidant Status and Immunity of Dairy Calves. Front Vet Sci 2022; 9:898295. [PMID: 35656173 PMCID: PMC9152456 DOI: 10.3389/fvets.2022.898295] [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: 03/20/2022] [Accepted: 04/19/2022] [Indexed: 11/15/2022] Open
Abstract
Waste milk (WM) is a part of the milk produced on dairy farms, which is usually unsuitable for human consumption. The WM contains transition milk, mastitis milk, colostrum, milk with somatic cells, blood (Hemolactia), harmful pathogens, pathogenic and antibiotic residues. Due to the high cost of milk replacer (MR), dairy farmers prefer raw WM to feed their calves. It has been well established that WM has a greater nutritive value than MR. Hence WM can contribute to improved growth, rumen development, and immune-associated parameters when fed to dairy calves. However, feeding raw WM before weaning has continuously raised some critical concerns. The pathogenic load and antibiotic residues in raw WM may increase the risk of diseases and antibacterial resistance in calves. Thus, pasteurization has been recommended as an effective method to decrease the risk of diseases in calves by killing/inhibiting the pathogenic microorganisms in the raw WM. Altogether, the current review provides a brief overview of the interplay between the positive role of raw WM in the overall performance of dairy calves, limitations of raw WM as a feed source and how to overcome these issues arising from feeding raw WM.
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Affiliation(s)
- Yulin Ma
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Muhammad Zahoor Khan
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
- University of Agriculture, Dera Ismail Khan, Khyber Pakhtunkhwa, Pakistan
| | - Jianxin Xiao
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Gibson Maswayi Alugongo
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xu Chen
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Shengli Li
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yajing Wang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Zhijun Cao
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
- *Correspondence: Zhijun Cao
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19
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Mercolino J, Lo Sciuto A, Spinnato MC, Rampioni G, Imperi F. RecA and Specialized Error-Prone DNA Polymerases are not Required for Mutagenesis and Antibiotic Resistance Induced by Fluoroquinolones in Pseudomonas aeruginosa. Antibiotics (Basel) 2022; 11:antibiotics11030325. [PMID: 35326787 PMCID: PMC8944484 DOI: 10.3390/antibiotics11030325] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 02/24/2022] [Accepted: 02/26/2022] [Indexed: 02/05/2023] Open
Abstract
To cope with stressful conditions, including antibiotic exposure, bacteria activate the SOS response, a pathway that induces error-prone DNA repair and mutagenesis mechanisms. In most bacteria, the SOS response relies on the transcriptional repressor LexA and the co-protease RecA, the latter being also involved in homologous recombination. The role of the SOS response in stress- and antibiotic-induced mutagenesis has been characterized in detail in the model organism Escherichia coli. However, its effect on antibiotic resistance in the human pathogen Pseudomonas aeruginosa is less clear. Here, we analyzed a recA deletion mutant and confirmed, by conjugation and gene expression assays, that RecA is required for homologous recombination and SOS response induction in P. aeruginosa. MIC assays demonstrated that RecA affects P. aeruginosa resistance only towards fluoroquinolones and genotoxic agents. The comparison of antibiotic-resistant mutant frequency between treated and untreated cultures revealed that, among the antibiotics tested, only fluoroquinolones induced mutagenesis in P. aeruginosa. Notably, both RecA and error-prone DNA polymerases were found to be dispensable for this process. These data demonstrate that the SOS response is not required for antibiotic-induced mutagenesis in P. aeruginosa, suggesting that RecA inhibition is not a suitable strategy to target antibiotic-induced emergence of resistance in this pathogen.
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Affiliation(s)
- Jessica Mercolino
- Department of Science, Roma Tre University, 00146 Rome, Italy; (J.M.); (A.L.S.); (M.C.S.); (G.R.)
| | - Alessandra Lo Sciuto
- Department of Science, Roma Tre University, 00146 Rome, Italy; (J.M.); (A.L.S.); (M.C.S.); (G.R.)
| | - Maria Concetta Spinnato
- Department of Science, Roma Tre University, 00146 Rome, Italy; (J.M.); (A.L.S.); (M.C.S.); (G.R.)
| | - Giordano Rampioni
- Department of Science, Roma Tre University, 00146 Rome, Italy; (J.M.); (A.L.S.); (M.C.S.); (G.R.)
- IRCCS Fondazione Santa Lucia, 00179 Rome, Italy
| | - Francesco Imperi
- Department of Science, Roma Tre University, 00146 Rome, Italy; (J.M.); (A.L.S.); (M.C.S.); (G.R.)
- IRCCS Fondazione Santa Lucia, 00179 Rome, Italy
- Correspondence:
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20
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de Lastours V, El Meouche I, Chau F, Beghain J, Chevret D, Aubert-Frambourg A, Clermont O, Royer G, Bouvet O, Denamur E, Fantin B. Evolution of fluoroquinolone-resistant Escherichia coli in the gut after ciprofloxacin treatment. Int J Med Microbiol 2022; 312:151548. [PMID: 35030401 DOI: 10.1016/j.ijmm.2022.151548] [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: 06/10/2021] [Revised: 12/14/2021] [Accepted: 01/03/2022] [Indexed: 10/19/2022] Open
Abstract
BACKGROUND Three healthy volunteers carried similar quinolone-resistant E. coli (QREC) (pulsed field gel electrophoresis profiles) in their gut before and after 14 days ciprofloxacin treatment. Given the intensity of the selective pressure and the mutagenic properties of quinolones, we determined whether these strains had evolved at the phenotypic and/or genomic levels. MATERIAL AND METHODS Commensal QREC from before day-0 (D0), and a month after 14 days of ciprofloxacin (D42) were compared in 3 volunteers. Growth experiments were performed; acetate levels, mutation frequencies, quinolone MICs and antibiotic tolerance were measured at D0 and D42. Genomes were sequenced and single nucleotide polymorphisms (SNPs) between D0 and D42 were analyzed using DiscoSNP and breseq methods. Cytoplasmic proteins were extracted, HPLC performed and proteins identified using X!tandem software; abundances were measured by mass spectrometry using the Spectral Counting (SC) and eXtraction Ion Chromatograms (XIC) integration methods. RESULTS No difference was found in MICs, growth characteristics, acetate concentrations, mutation frequencies, tolerance profiles, phylogroups, O-and H-types, fimH alleles and sequence types between D0 and D42. No SNP variation was evidenced between D0 and D42 isolates for 2/3 subjects; 2 SNP variations were evidenced in one. At the protein level, very few significant protein abundance differences were identified between D0 and D42. CONCLUSION No fitness, tolerance, metabolic or genomic evolution of commensal QREC was observed overtime, despite massive exposure to ciprofloxacin in the gut. The three strains behaved as if they had been unaffected by ciprofloxacin, suggesting that gut may act as a sanctuary where bacteria would be protected from the effect of antibiotics and survive without any detrimental effect of stress.
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Affiliation(s)
- V de Lastours
- Service de Médecine Interne, Hôpital Beaujon, Assistance-Publique Hôpitaux de Paris, F-92100 Clichy, France; IAME Research Group, UMR 1137, Université de Paris and INSERM, F-75018 Paris, France.
| | - I El Meouche
- IAME Research Group, UMR 1137, Université de Paris and INSERM, F-75018 Paris, France
| | - F Chau
- IAME Research Group, UMR 1137, Université de Paris and INSERM, F-75018 Paris, France
| | - J Beghain
- IAME Research Group, UMR 1137, Université de Paris and INSERM, F-75018 Paris, France
| | - D Chevret
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, F-78150 Jouy-en-Josas, France
| | - A Aubert-Frambourg
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, F-78150 Jouy-en-Josas, France
| | - O Clermont
- IAME Research Group, UMR 1137, Université de Paris and INSERM, F-75018 Paris, France
| | - G Royer
- IAME Research Group, UMR 1137, Université de Paris and INSERM, F-75018 Paris, France
| | - O Bouvet
- IAME Research Group, UMR 1137, Université de Paris and INSERM, F-75018 Paris, France
| | - E Denamur
- IAME Research Group, UMR 1137, Université de Paris and INSERM, F-75018 Paris, France; Laboratoire de Génétique Moléculaire, Hôpital Bichat, Assistance-Publique Hôpitaux de Paris, F-75018 Paris, France
| | - B Fantin
- Service de Médecine Interne, Hôpital Beaujon, Assistance-Publique Hôpitaux de Paris, F-92100 Clichy, France; IAME Research Group, UMR 1137, Université de Paris and INSERM, F-75018 Paris, France
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21
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Adefisayo OO, Dupuy P, Nautiyal A, Bean JM, Glickman MS. Division of labor between SOS and PafBC in mycobacterial DNA repair and mutagenesis. Nucleic Acids Res 2021; 49:12805-12819. [PMID: 34871411 PMCID: PMC8682763 DOI: 10.1093/nar/gkab1169] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 09/30/2021] [Accepted: 11/10/2021] [Indexed: 11/15/2022] Open
Abstract
DNA repair systems allow microbes to survive in diverse environments that compromise chromosomal integrity. Pathogens such as Mycobacterium tuberculosis must contend with the genotoxic host environment, which generates the mutations that underlie antibiotic resistance. Mycobacteria encode the widely distributed SOS pathway, governed by the LexA repressor, but also encode PafBC, a positive regulator of the transcriptional DNA damage response (DDR). Although the transcriptional outputs of these systems have been characterized, their full functional division of labor in survival and mutagenesis is unknown. Here, we specifically ablate the PafBC or SOS pathways, alone and in combination, and test their relative contributions to repair. We find that SOS and PafBC have both distinct and overlapping roles that depend on the type of DNA damage. Most notably, we find that quinolone antibiotics and replication fork perturbation are inducers of the PafBC pathway, and that chromosomal mutagenesis is codependent on PafBC and SOS, through shared regulation of the DnaE2/ImuA/B mutasome. These studies define the complex transcriptional regulatory network of the DDR in mycobacteria and provide new insight into the regulatory mechanisms controlling the genesis of antibiotic resistance in M. tuberculosis.
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Affiliation(s)
- Oyindamola O Adefisayo
- Immunology and Microbial Pathogenesis Graduate Program, Weill Cornell Graduate School, 1300 York Avenue, New York, NY 10065, USA.,Immunology Program, Sloan Kettering Institute, 1275 York Avenue, New York, NY 10025, USA
| | - Pierre Dupuy
- Immunology Program, Sloan Kettering Institute, 1275 York Avenue, New York, NY 10025, USA
| | - Astha Nautiyal
- Immunology Program, Sloan Kettering Institute, 1275 York Avenue, New York, NY 10025, USA
| | - James M Bean
- Immunology Program, Sloan Kettering Institute, 1275 York Avenue, New York, NY 10025, USA
| | - Michael S Glickman
- Immunology and Microbial Pathogenesis Graduate Program, Weill Cornell Graduate School, 1300 York Avenue, New York, NY 10065, USA.,Immunology Program, Sloan Kettering Institute, 1275 York Avenue, New York, NY 10025, USA
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22
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Diaz-Diaz S, Recacha E, García-Duque A, Docobo-Pérez F, Blázquez J, Pascual A, Rodríguez-Martínez JM. Effect of RecA inactivation and detoxification systems on the evolution of ciprofloxacin resistance in Escherichia coli. J Antimicrob Chemother 2021; 77:641-645. [PMID: 34878138 PMCID: PMC8864997 DOI: 10.1093/jac/dkab445] [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: 07/02/2021] [Accepted: 11/09/2021] [Indexed: 11/16/2022] Open
Abstract
Background Suppression of SOS response and overproduction of reactive oxygen species (ROS) through detoxification system suppression enhance the activity of fluoroquinolones. Objectives To evaluate the role of both systems in the evolution of resistance to ciprofloxacin in an isogenic model of Escherichia coli. Methods Single-gene deletion mutants of E. coli BW25113 (wild-type) (ΔrecA, ΔkatG, ΔkatE, ΔsodA, ΔsodB), double-gene (ΔrecA-ΔkatG, ΔrecA-ΔkatE, ΔrecA-ΔsodA, ΔrecA-ΔsodB, ΔkatG-ΔkatE, ΔsodB-ΔsodA) and triple-gene (ΔrecA-ΔkatG-ΔkatE) mutants were included. The response to sudden high ciprofloxacin pressure was evaluated by mutant prevention concentration (MPC). The gradual antimicrobial pressure response was evaluated through experimental evolution and antibiotic resistance assays. Results For E. coli BW25113 strain, ΔkatE, ΔsodB and ΔsodB/ΔsodA mutants, MPC values were 0.25 mg/L. The ΔkatG, ΔsodA, ΔkatG/katE and ΔrecA mutants showed 2-fold reductions (0.125 mg/L). The ΔkatG/ΔrecA, ΔkatE/ΔrecA, ΔsodA/ΔrecA, ΔsodB/ΔrecA and ΔkatG/ΔkatE/ΔrecA strains showed 4–8-fold reductions (0.03–0.06 mg/L) relative to the wild-type. Gradual antimicrobial pressure increased growth capacity for ΔsodA and ΔsodB and ΔsodB/ΔsodA mutants (no growth in 4 mg/L) compared with the wild-type (no growth in the range of 0.5–2 mg/L). Accordingly, increased growth was observed with the mutants ΔrecA/ΔkatG (no growth in 2 mg/L), ΔrecA/ΔkatE (no growth in 2 mg/L), ΔrecA/ΔsodA (no growth in 0.06 mg/L), ΔrecA/ΔsodB (no growth in 0.25 mg/L) and ΔrecA/ΔkatG/ΔkatE (no growth in 0.5 mg/L) compared with ΔrecA (no growth in the range of 0.002–0.015 mg/L). Conclusions After RecA inactivation, gradual exposure to ciprofloxacin reduces the evolution of resistance. After suppression of RecA and detoxification systems, sudden high exposure to ciprofloxacin reduces the evolution of resistance in E. coli.
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Affiliation(s)
- S Diaz-Diaz
- Unidad de Enfermedades Infecciosas, Microbiología y Medicina Preventiva, Hospital Universitario Virgen Macarena, Seville, Spain.,Departamento de Microbiología, Facultad de Medicina, Universidad de Sevilla, Sevilla, Spain.,Red Española de Investigación en Patología Infecciosa (REIPI), Instituto de Salud Carlos III, Madrid, Spain.,Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Sevilla, Spain
| | - E Recacha
- Unidad de Enfermedades Infecciosas, Microbiología y Medicina Preventiva, Hospital Universitario Virgen Macarena, Seville, Spain.,Departamento de Microbiología, Facultad de Medicina, Universidad de Sevilla, Sevilla, Spain.,Red Española de Investigación en Patología Infecciosa (REIPI), Instituto de Salud Carlos III, Madrid, Spain.,Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Sevilla, Spain
| | - A García-Duque
- Unidad de Enfermedades Infecciosas, Microbiología y Medicina Preventiva, Hospital Universitario Virgen Macarena, Seville, Spain
| | - F Docobo-Pérez
- Departamento de Microbiología, Facultad de Medicina, Universidad de Sevilla, Sevilla, Spain.,Red Española de Investigación en Patología Infecciosa (REIPI), Instituto de Salud Carlos III, Madrid, Spain.,Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Sevilla, Spain
| | - J Blázquez
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - A Pascual
- Unidad de Enfermedades Infecciosas, Microbiología y Medicina Preventiva, Hospital Universitario Virgen Macarena, Seville, Spain.,Departamento de Microbiología, Facultad de Medicina, Universidad de Sevilla, Sevilla, Spain.,Red Española de Investigación en Patología Infecciosa (REIPI), Instituto de Salud Carlos III, Madrid, Spain.,Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Sevilla, Spain
| | - J M Rodríguez-Martínez
- Departamento de Microbiología, Facultad de Medicina, Universidad de Sevilla, Sevilla, Spain.,Red Española de Investigación en Patología Infecciosa (REIPI), Instituto de Salud Carlos III, Madrid, Spain.,Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Sevilla, Spain
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23
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Gu Y, Huang L, Wu C, Huang J, Hao H, Yuan Z, Cheng G. The Evolution of Fluoroquinolone Resistance in Salmonella under Exposure to Sub-Inhibitory Concentration of Enrofloxacin. Int J Mol Sci 2021; 22:ijms222212218. [PMID: 34830098 PMCID: PMC8619427 DOI: 10.3390/ijms222212218] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 10/25/2021] [Accepted: 11/02/2021] [Indexed: 02/04/2023] Open
Abstract
The evolution of resistance in Salmonella to fluoroquinolones (FQs) under a broad range of sub-inhibitory concentrations (sub-MICs) has not been systematically studied. This study investigated the mechanism of resistance development in Salmonella enterica serovar Enteritidis (S. Enteritidis) under sub-MICs of 1/128×MIC to 1/2×MIC of enrofloxacin (ENR), a widely used veterinary FQ. It was shown that the resistance rate and resistance level of S. Enteritidis varied with the increase in ENR concentration and duration of selection. qRT-PCR results demonstrated that the expression of outer membrane porin (OMP) genes, ompC, ompD and ompF, were down-regulated first to rapidly adapt and develop the resistance of 4×MIC, and as the resistance level increased (≥8×MIC), the up-regulated expression of efflux pump genes, acrB, emrB amd mdfA, along with mutations in quinolone resistance-determining region (QRDR) gradually played a decisive role. Cytohubba analysis based on transcriptomic profiles demonstrated that purB, purC, purD, purF, purH, purK, purL, purM, purN and purT were the hub genes for the FQs resistance. The 'de novo' IMP biosynthetic process, purine ribonucleoside monophosphate biosynthetic process and purine ribonucleotide biosynthetic process were the top three biological processes screened by MCODE. This study first described the dynamics of FQ resistance evolution in Salmonella under a long-term selection of sub-MICs of ENR in vitro. In addition, this work offers greater insight into the transcriptome changes of S. Enteritidis under the selection of ENR and provides a framework for FQs resistance of Salmonella for further studies.
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Affiliation(s)
- Yufeng Gu
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (Y.G.); (L.H.); (C.W.); (J.H.); (H.H.); (Z.Y.)
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan 430070, China
| | - Lulu Huang
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (Y.G.); (L.H.); (C.W.); (J.H.); (H.H.); (Z.Y.)
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan 430070, China
| | - Cuirong Wu
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (Y.G.); (L.H.); (C.W.); (J.H.); (H.H.); (Z.Y.)
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan 430070, China
| | - Junhong Huang
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (Y.G.); (L.H.); (C.W.); (J.H.); (H.H.); (Z.Y.)
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan 430070, China
| | - Haihong Hao
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (Y.G.); (L.H.); (C.W.); (J.H.); (H.H.); (Z.Y.)
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan 430070, China
| | - Zonghui Yuan
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (Y.G.); (L.H.); (C.W.); (J.H.); (H.H.); (Z.Y.)
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan 430070, China
| | - Guyue Cheng
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (Y.G.); (L.H.); (C.W.); (J.H.); (H.H.); (Z.Y.)
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan 430070, China
- Correspondence: ; Tel.: +86-027-8728-7165
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24
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Chen P, Guo X, Li S, Li F. A review of the bioelectrochemical system as an emerging versatile technology for reduction of antibiotic resistance genes. ENVIRONMENT INTERNATIONAL 2021; 156:106689. [PMID: 34175779 DOI: 10.1016/j.envint.2021.106689] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 05/31/2021] [Accepted: 06/02/2021] [Indexed: 06/13/2023]
Abstract
Antibiotic contamination and the resulting resistance genes have attracted worldwide attention because of the extensive overuse and abuse of antibiotics, which seriously affects the environment as well as human health. Bioelectrochemical system (BES), a potential avenue to be explored, can alleviate antibiotic pollution and reduce antibiotic resistance genes (ARGs). This review mainly focuses on analyzing the possible reasons for the good performance of ARG reduction by BESs and potential ways to improve its performance on the basis of revealing the generation and transmission of ARGs in BES. This system reduces ARGs through two pathways: (1) the contribution of BES to the low selection pressure of ARGs caused by the efficient removal of antibiotics, and (2) inhibition of ARG transmission caused by low sludge yield. To promote the reduction of ARGs, incorporating additives, improving the removal rate of antibiotics by adjusting the environmental conditions, and controlling the microbial community in BES are proposed. Furthermore, this review also provides an overview of bioelectrochemical coupling systems including the BES coupled with the Fenton system, BES coupled with constructed wetland, and BES coupled with photocatalysis, which demonstrates that this method is applicable in different situations and conditions and provides inspiration to improve these systems to control ARGs. Finally, the challenges and outlooks are addressed, which is constructive for the development of technologies for antibiotic and ARG contamination remediation and blocking risk migration.
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Affiliation(s)
- Ping Chen
- Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China; Key Laboratory of Pollution Processes and Environmental Criteria, Ministry of Education, Tianjin 300350, China
| | - Xiaoyan Guo
- Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China; Key Laboratory of Pollution Processes and Environmental Criteria, Ministry of Education, Tianjin 300350, China
| | - Shengnan Li
- Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China; Key Laboratory of Pollution Processes and Environmental Criteria, Ministry of Education, Tianjin 300350, China; State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, Heilongjiang Province 150090, China
| | - Fengxiang Li
- Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China; Key Laboratory of Pollution Processes and Environmental Criteria, Ministry of Education, Tianjin 300350, China.
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25
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Koutsoumanis K, Allende A, Alvarez‐Ordóñez A, Bolton D, Bover‐Cid S, Chemaly M, Davies R, De Cesare A, Herman L, Hilbert F, Lindqvist R, Nauta M, Ru G, Simmons M, Skandamis P, Suffredini E, Andersson DI, Bampidis V, Bengtsson‐Palme J, Bouchard D, Ferran A, Kouba M, López Puente S, López‐Alonso M, Nielsen SS, Pechová A, Petkova M, Girault S, Broglia A, Guerra B, Innocenti ML, Liébana E, López‐Gálvez G, Manini P, Stella P, Peixe L. Maximum levels of cross-contamination for 24 antimicrobial active substances in non-target feed.
Part 4: β-Lactams: amoxicillin and penicillin V. EFSA J 2021; 19:e06855. [PMID: 34729084 PMCID: PMC8547409 DOI: 10.2903/j.efsa.2021.6855] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The specific concentrations of amoxicillin and penicillin V in non-target feed for food-producing animals, below which there would not be an effect on the emergence of, and/or selection for, resistance in bacteria relevant for human and animal health, as well as the specific antimicrobial concentrations in feed which have an effect in terms of growth promotion/increased yield were assessed by EFSA in collaboration with EMA. Details of the methodology used for this assessment, associated data gaps and uncertainties, are presented in a separate document. To address antimicrobial resistance, the Feed Antimicrobial Resistance Selection Concentration (FARSC) model developed specifically for the assessment was applied. However, due to the lack of data on the parameters required to calculate the FARSC, it was not possible to conclude the assessment until further experimental data become available. To address growth promotion, data from scientific publications obtained from an extensive literature review were used. Levels in feed that showed to have an effect on growth promotion/increased yield were reported for amoxicillin, whilst for penicillin V no suitable data for the assessment were available. It was recommended to carry out studies to generate the data that are required to fill the gaps which prevented the calculation of the FARSC for these two antimicrobials.
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26
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Koutsoumanis K, Allende A, Alvarez‐Ordóñez A, Bolton D, Bover‐Cid S, Chemaly M, Davies R, De Cesare A, Herman L, Hilbert F, Lindqvist R, Nauta M, Ru G, Simmons M, Skandamis P, Suffredini E, Andersson DI, Bampidis V, Bengtsson‐Palme J, Bouchard D, Ferran A, Kouba M, López Puente S, López‐Alonso M, Nielsen SS, Pechová A, Petkova M, Girault S, Broglia A, Guerra B, Innocenti ML, Liébana E, López‐Gálvez G, Manini P, Stella P, Peixe L. Maximum levels of cross-contamination for 24 antimicrobial active substances in non-target feed. Part 11: Sulfonamides. EFSA J 2021; 19:e06863. [PMID: 34729091 PMCID: PMC8546515 DOI: 10.2903/j.efsa.2021.6863] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
The specific concentrations of sulfonamides in non-target feed for food-producing animals, below which there would not be an effect on the emergence of, and/or selection for, resistance in bacteria relevant for human and animal health, as well as the specific antimicrobial concentrations in feed which have an effect in terms of growth promotion/increased yield were assessed by EFSA in collaboration with EMA. Details of the methodology used for this assessment, associated data gaps and uncertainties, are presented in a separate document. To address antimicrobial resistance, the Feed Antimicrobial Resistance Selection Concentration (FARSC) model developed specifically for the assessment was applied. However, due to the lack of data on the parameters required to calculate the FARSC, it was not possible to conclude the assessment until further experimental data are available. To address growth promotion, data from scientific publications obtained from an extensive literature review were used. Levels in feed that showed to have an effect on growth promotion/increased yield were identified for three sulfonamides: sulfamethazine, sulfathiazole and sulfamerazine. It was recommended to carry out studies to generate the data that are required to fill the gaps which prevented the calculation of the FARSC for these antimicrobials.
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27
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A Perspective on the Role of Microbiome for Colorectal Cancer Treatment. Cancers (Basel) 2021; 13:cancers13184623. [PMID: 34572850 PMCID: PMC8468110 DOI: 10.3390/cancers13184623] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/13/2021] [Accepted: 09/13/2021] [Indexed: 02/07/2023] Open
Abstract
Simple Summary Colorectal cancer is the third most diagnosed cancer worldwide and contributes significantly to global mortality and morbidity. The gut microbiome, composed of the trillions of microbes endemic to the human gastrointestinal tract, has been shown to be implicated in colorectal cancer oncogenesis; however, the roles of microbiota and dysbiosis in CRC treatment remain poorly understood. This review sought to characterize this relationship and in doing so, identify how these interactions may inform future treatments in the form of synbiotics designed to alter the host microbiota to achieve optimized treatment outcomes. Abstract In healthy hosts, trillions of microbes colonise the gut and oral cavity in a well-balanced state, maintaining a mutually beneficial relationship. Loss of this balance, termed dysbiosis, is strongly implicated in the pathogenesis of colorectal cancer (CRC). However, the roles of microbiota and dysbiosis in CRC treatment remain poorly understood. Recent studies suggest that the gut microbiota has the ability to affect the host response to chemotherapeutic agents by enhancing drug efficacy, promoting chemoresistance and mediating chemotherapy-induced toxicity and side effects via a variety of mechanisms. Several other studies have also proposed manipulation of the microbiota to optimise CRC treatment. In this review, we summarise the current advancement of knowledge on how microbiota and CRC treatments interact with each other and how this interaction may shed some light on the development of personalised microbiota manipulations that improve CRC treatment outcomes.
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28
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Kiran K, Patil KN. Expression and Characterization of the Staphylococcus aureus RecA protein: A mapping of canonical functions. Protein Expr Purif 2021; 189:105967. [PMID: 34481085 DOI: 10.1016/j.pep.2021.105967] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 07/27/2021] [Accepted: 08/27/2021] [Indexed: 11/16/2022]
Abstract
Recombinases are responsible for homologous recombination (HR), proper genome maintenance, and accurate deoxyribonucleic acid (DNA) duplication. Moreover, HR plays a determining role in DNA transaction processes such as DNA replication, repair, recombination, and transcription. Staphylococcus aureus, an opportunistic pathogen, usually causes respiratory infections such as sinusitis, skin infections, and food poisoning. To date, the role of the RecA gene product in S. aureus remains obscure. In this study, we attempted to map the functional properties of the RecA protein. S. aureus expresses the recA gene product in vivo upon exposure to the DNA-damaging agents, ultraviolet radiation, and methyl methanesulfonate. The recombinant purified S. aureus RecA protein displayed strong single-stranded DNA affinity compared to feeble binding to double-stranded DNA. Interestingly, the RecA protein is capable of invasion and formed displacement loops and readily performed strand-exchange activities with an oligonucleotide-based substrate. Notably, the S. aureus RecA protein hydrolyzed the DNA-dependent adenosine triphosphate and cleaved LexA, showing the conserved function of coprotease. This study provides the functional characterization of the S. aureus RecA protein and sheds light on the canonical processes of homologous recombination, which are conserved in the gram-positive foodborne pathogen S. aureus.
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Affiliation(s)
- Kajal Kiran
- Department of Protein Chemistry and Technology, Council of Scientific & Industrial Research-Central Food Technological Research Institute (CSIR-CFTRI), Mysuru, 570 020, Karnataka, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, Uttar Pradesh, India
| | - K Neelakanteshwar Patil
- Department of Protein Chemistry and Technology, Council of Scientific & Industrial Research-Central Food Technological Research Institute (CSIR-CFTRI), Mysuru, 570 020, Karnataka, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, Uttar Pradesh, India.
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29
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Piatti G, De Ferrari L, Schito AM, Riccio AM, Penco S, Cassia S, Bruzzone M, Ceppi M. In Vitro Reduction of Interleukin-8 Response to Enterococcus faecalis by Escherichia coli Strains Isolated from the Same Polymicrobial Urines. Microorganisms 2021; 9:microorganisms9071501. [PMID: 34361936 PMCID: PMC8307267 DOI: 10.3390/microorganisms9071501] [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: 05/12/2021] [Revised: 07/05/2021] [Accepted: 07/05/2021] [Indexed: 11/16/2022] Open
Abstract
Urinary tract infections are often polymicrobial and are mainly due to uropathogenic Escherichia coli (UPEC). We previously demonstrated a link among clinical fluoroquinolone susceptible E. coli reducing in vitro urothelial interleukin-8 (CXCL8) induced by E. coli K-12, polymicrobial cystitis, and pyuria absence. Here, we evaluated whether fifteen clinical fluoroquinolone susceptible UPEC were able to reduce CXCL8 induced by Enterococcus faecalis that had been isolated from the same mixed urines, other than CXCL8 induced by E. coli K-12. We also evaluated the connection between fluoroquinolone susceptibility and pathogenicity by evaluating the immune modulation of isogenic gyrA, a mutant UPEC resistant to ciprofloxacin. Using the 5637 bladder epithelial cell line, we observed that lower CXCL8 induced the most UPEC isolates than K-12 and the corresponding E. faecalis. During coinfections of UPEC/K-12 and UPEC/E. faecalis, we observed lower CXCL8 than during infections caused by K-12 and E. faecalis alone. UPEC strains showed host–pathogen and pathogen–pathogen interaction, which in part explained their persistence in the human urinary tract and coinfections, respectively. Mutant UPEC showed lower modulating activity with respect to the wildtypes, confirming the connection between acquired fluoroquinolone resistance and the decrease of innate microbial properties.
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Affiliation(s)
- Gabriella Piatti
- Department of Surgical Sciences and Integrated Diagnostics (DISC), University of Genoa, 16132 Genova, Italy;
- Correspondence: ; Tel.: +39-0105555193
| | - Laura De Ferrari
- Department of Internal Medicine, University of Genoa, 16132 Genova, Italy; (L.D.F.); (A.M.R.); (S.C.)
| | - Anna Maria Schito
- Department of Surgical Sciences and Integrated Diagnostics (DISC), University of Genoa, 16132 Genova, Italy;
| | - Anna Maria Riccio
- Department of Internal Medicine, University of Genoa, 16132 Genova, Italy; (L.D.F.); (A.M.R.); (S.C.)
| | - Susanna Penco
- Department of Experimental Medicine, University of Genoa, 16132 Genova, Italy;
| | - Sebastiano Cassia
- Department of Internal Medicine, University of Genoa, 16132 Genova, Italy; (L.D.F.); (A.M.R.); (S.C.)
| | - Marco Bruzzone
- Unit of Clinical Epidemiology, Ospedale Policlinico San Martino-IRCCS per l’Oncologia, 16132 Genova, Italy; (M.B.); (M.C.)
| | - Marcello Ceppi
- Unit of Clinical Epidemiology, Ospedale Policlinico San Martino-IRCCS per l’Oncologia, 16132 Genova, Italy; (M.B.); (M.C.)
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30
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Antioxidant Molecules as a Source of Mitigation of Antibiotic Resistance Gene Dissemination. Antimicrob Agents Chemother 2021; 65:AAC.02658-20. [PMID: 33753335 DOI: 10.1128/aac.02658-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 03/16/2021] [Indexed: 11/20/2022] Open
Abstract
Escherichia coli is the most commonly identified human pathogen and a prominent microorganism of the gut microbiota. Acquired resistance to antibiotics in this species is driven mainly by horizontal gene transfer and plasmid acquisition. Currently, the main concern is the acquisition of extended-spectrum β-lactamases of the CTX-M type in E. coli, a worldwide-observed phenomenon. Plasmids encoding CTX-M enzymes have different scaffolds and conjugate at different frequencies. Here, we show that the conjugation rates of several plasmid types encoding broad-spectrum β-lactamases are increased when the E. coli donor strain is exposed to subinhibitory concentrations of diverse orally given antibiotics, including fluoroquinolones, such as ciprofloxacin and levofloxacin, but also trimethoprim and nitrofurantoin. This study provides insights into underlying mechanisms leading to increased plasmid conjugation frequency in relation to DNA synthesis inhibitor-type antibiotics, involving reactive oxygen species (ROS) production and probably increased expression of genes involved in the SOS response. Furthermore, we show that some antioxidant molecules currently approved for unrelated clinical uses, such as edaravone, p-coumaric acid, and N-acetylcysteine, may antagonize the ability of antibiotics to increase plasmid conjugation rates. These results suggest that several antioxidative molecules might be used in combination with these "inducer" antibiotics to mitigate the unwanted increased resistance plasmid dissemination.
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31
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Xu G, Liu H, Jia X, Wang X, Xu P. Mechanisms and detection methods of Mycobacterium tuberculosis rifampicin resistance: The phenomenon of drug resistance is complex. Tuberculosis (Edinb) 2021; 128:102083. [PMID: 33975262 DOI: 10.1016/j.tube.2021.102083] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Revised: 03/30/2021] [Accepted: 04/25/2021] [Indexed: 10/21/2022]
Abstract
Tuberculosis (TB) is an infectious disease that poses a serious threat to human health. Rifampin (RIF) is an important first-line anti-TB drug, and rifampin resistance (RIF-R) is a key factor in formulating treatment regimen and evaluating the prognosis of TB. Compared with other drugs resistance, the RIF-R mechanism of Mycobacterium tuberculosis (M. tuberculosis) is one of the clearest, which is mainly caused by RIF resistance-related mutations in the rpoB gene. This provides a convenient condition for developing rapid detection methods, and also an ideal object for studying the general drug resistance mechanisms of M. tuberculosis. This review focuses on the mechanisms that influence the RIF resistance of M. tuberculosis and related detection methods. Besides the mutations in rpoB, M. tuberculosis can decrease the amount of drugs entering the cells, enhance the drugs efflux, and be heterogeneous RIF susceptibility to resist drug pressure. Based on the results of current researches, many genes participate in influencing the susceptibility to RIF, which indicates the phenomenon of M. tuberculosis drug resistance is very complex.
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Affiliation(s)
- Ge Xu
- Key Laboratory of Characteristic Infectious Disease & Bio-safety Development of Guizhou Province Education Department, Institute of Life Sciences, Zunyi Medical University, No.6 West Xuefu Road, Xinpu District, Zunyi, Guizhou Province, 563000, China
| | - Hangchi Liu
- Key Laboratory of Characteristic Infectious Disease & Bio-safety Development of Guizhou Province Education Department, Institute of Life Sciences, Zunyi Medical University, No.6 West Xuefu Road, Xinpu District, Zunyi, Guizhou Province, 563000, China
| | - Xudong Jia
- Key Laboratory of Characteristic Infectious Disease & Bio-safety Development of Guizhou Province Education Department, Institute of Life Sciences, Zunyi Medical University, No.6 West Xuefu Road, Xinpu District, Zunyi, Guizhou Province, 563000, China
| | - Xiaomin Wang
- Department of Microbiology, Zunyi Medical University, No.6 West Xuefu Road, Xinpu District, Zunyi, Guizhou Province, 563000, China.
| | - Peng Xu
- Key Laboratory of Characteristic Infectious Disease & Bio-safety Development of Guizhou Province Education Department, Institute of Life Sciences, Zunyi Medical University, No.6 West Xuefu Road, Xinpu District, Zunyi, Guizhou Province, 563000, China.
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Inactivation of UmuC Protein Significantly Reduces Resistance to Ciprofloxacin and SOS Mutagenesis in Escherichia coli Mutants Harboring Intact umuD Gene. Jundishapur J Microbiol 2021. [DOI: 10.5812/jjm.111828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Background: Ciprofloxacin induces SOS response and mutagenesis by activation of UmuD’2C (DNA polymerase V) and DinB (DNA polymerase IV) in Escherichia coli, leading to antibiotic resistance during therapy. Inactivation of DNA polymerase V can result in the inhibition of mutagenesis in E. coli. Objectives: The aim of this research was to investigate the effect of UmuC inactivation on resistance to ciprofloxacin and SOS mutagenesis in E. coli mutants. Methods: Ciprofloxacin-resistant mutants were produced in a umuC- genetic background in the presence of increasing concentrations of ciprofloxacin. The minimum inhibitory concentration of umuC-mutants was measured by broth dilution method. Alterations in the rifampin resistance-determing region of rpoB gene were assessed by PCR amplification and DNA sequencing. The expression of SOS genes was measured by quantitative real-time PCR assay. Results: Results showed that despite the induction of SOS response (overexpression of recA, dinB, and umuD genes) following exposure to ciprofloxacin in E. coli umuC mutants, resistance to ciprofloxacin and SOS mutagenesis significantly decreased. However, rifampicin-resistant clones emerged in this genetic background. One of these clones showed mutations in the rifampicin resistance-determining region of rpoB (cluster II). The low mutation frequency of E. coli might be associated with the presence and overexpression of umuD gene, which could somehow limit the activity of DinB, the location and type of mutations in the β subunit of RNA polymerase. Conclusions: In conclusion, for increasing the efficiency of ciprofloxacin against Gram-negative bacteria, use of an inhibitor of umuC, along with ciprofloxacin, would be helpful.
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Synergistic Quinolone Sensitization by Targeting the recA SOS Response Gene and Oxidative Stress. Antimicrob Agents Chemother 2021; 65:AAC.02004-20. [PMID: 33526493 DOI: 10.1128/aac.02004-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 01/28/2021] [Indexed: 12/24/2022] Open
Abstract
Suppression of the recA SOS response gene and reactive oxygen species (ROS) overproduction have been shown, separately, to enhance fluoroquinolone activity and lethality. Their putative synergistic impact as a strategy to potentiate the efficacy of bactericidal antimicrobial agents such as fluoroquinolones is unknown. We generated Escherichia coli mutants that exhibited a suppressed ΔrecA gene in combination with inactivated ROS detoxification system genes (ΔsodA, ΔsodB, ΔkatG, ΔkatE, and ΔahpC) or inactivated oxidative stress regulator genes (ΔoxyR and ΔrpoS) to evaluate the interplay of both DNA repair and detoxification systems in drug response. Synergistic sensitization effects, ranging from 7.5- to 30-fold relative to the wild type, were observed with ciprofloxacin in double knockouts of recA and inactivated detoxification system genes. Compared to recA knockout, inactivation of an additional detoxification system gene reduced MIC values up to 8-fold. In growth curves, no growth was evident in mutants doubly deficient for recA gene and oxidative detoxification systems at subinhibitory concentrations of ciprofloxacin, in contrast to the recA-deficient strain. There was a marked reduction of viable bacteria in a short period of time when the recA gene and other detoxification system genes (katG, sodA, or ahpC) were inactivated (using absolute ciprofloxacin concentrations). At 4 h, a bactericidal effect of ciprofloxacin was observed for ΔkatG ΔrecA and ΔahpC ΔrecA double mutants compared to the single ΔrecA mutant (Δ3.4 log10 CFU/ml). Synergistic quinolone sensitization, by targeting the recA gene and oxidative detoxification stress systems, reinforces the role of both DNA repair systems and ROS in antibiotic-induced bacterial cell death, opening up a new pathway for antimicrobial sensitization.
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Tiwari P, Khare T, Shriram V, Bae H, Kumar V. Plant synthetic biology for producing potent phyto-antimicrobials to combat antimicrobial resistance. Biotechnol Adv 2021; 48:107729. [PMID: 33705914 DOI: 10.1016/j.biotechadv.2021.107729] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 01/22/2021] [Accepted: 03/04/2021] [Indexed: 12/14/2022]
Abstract
Inappropriate and injudicious use of antimicrobial drugs in human health, hygiene, agriculture, animal husbandry and food industries has contributed significantly to rapid emergence and persistence of antimicrobial resistance (AMR), one of the serious global public health threats. The crisis of AMR versus slower discovery of newer antibiotics put forth a daunting task to control these drug-resistant superbugs. Several phyto-antimicrobials have been identified in recent years with direct-killing (bactericidal) and/or drug-resistance reversal (re-sensitization of AMR phenotypes) potencies. Phyto-antimicrobials may hold the key in combating AMR owing to their abilities to target major microbial drug-resistance determinants including cell membrane, drug-efflux pumps, cell communication and biofilms. However, limited distribution, low intracellular concentrations, eco-geographical variations, beside other considerations like dynamic environments, climate change and over-exploitation of plant-resources are major blockades in full potential exploration phyto-antimicrobials. Synthetic biology (SynBio) strategies integrating metabolic engineering, RNA-interference, genome editing/engineering and/or systems biology approaches using plant chassis (as engineerable platforms) offer prospective tools for production of phyto-antimicrobials. With expanding SynBio toolkit, successful attempts towards introduction of entire gene cluster, reconstituting the metabolic pathway or transferring an entire metabolic (or synthetic) pathway into heterologous plant systems highlight the potential of this field. Through this perspective review, we are presenting herein the current situation and options for addressing AMR, emphasizing on the significance of phyto-antimicrobials in this apparently post-antibiotic era, and effective use of plant chassis for phyto-antimicrobial production at industrial scales along with major SynBio tools and useful databases. Current knowledge, recent success stories, associated challenges and prospects of translational success are also discussed.
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Affiliation(s)
- Pragya Tiwari
- Molecular Metabolic Engineering Lab, Department of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk 38541, Republic of Korea
| | - Tushar Khare
- Department of Biotechnology, Modern College of Arts, Science and Commerce, Savitribai Phule Pune University, Ganeshkhind, Pune 411016, India; Department of Environmental Science, Savitribai Phule Pune University, Pune 411007, India
| | - Varsha Shriram
- Department of Botany, Prof. Ramkrishna More Arts, Commerce and Science College, Savitribai Phule Pune University, Akurdi, Pune 411044, India
| | - Hanhong Bae
- Molecular Metabolic Engineering Lab, Department of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk 38541, Republic of Korea.
| | - Vinay Kumar
- Department of Biotechnology, Modern College of Arts, Science and Commerce, Savitribai Phule Pune University, Ganeshkhind, Pune 411016, India; Department of Environmental Science, Savitribai Phule Pune University, Pune 411007, India.
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35
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Bacterial phenotypic heterogeneity in DNA repair and mutagenesis. Biochem Soc Trans 2021; 48:451-462. [PMID: 32196548 PMCID: PMC7200632 DOI: 10.1042/bst20190364] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 02/26/2020] [Accepted: 02/28/2020] [Indexed: 02/06/2023]
Abstract
Genetically identical cells frequently exhibit striking heterogeneity in various phenotypic traits such as their morphology, growth rate, or gene expression. Such non-genetic diversity can help clonal bacterial populations overcome transient environmental challenges without compromising genome stability, while genetic change is required for long-term heritable adaptation. At the heart of the balance between genome stability and plasticity are the DNA repair pathways that shield DNA from lesions and reverse errors arising from the imperfect DNA replication machinery. In principle, phenotypic heterogeneity in the expression and activity of DNA repair pathways can modulate mutation rates in single cells and thus be a source of heritable genetic diversity, effectively reversing the genotype-to-phenotype dogma. Long-standing evidence for mutation rate heterogeneity comes from genetics experiments on cell populations, which are now complemented by direct measurements on individual living cells. These measurements are increasingly performed using fluorescence microscopy with a temporal and spatial resolution that enables localising, tracking, and counting proteins with single-molecule sensitivity. In this review, we discuss which molecular processes lead to phenotypic heterogeneity in DNA repair and consider the potential consequences on genome stability and dynamics in bacteria. We further inspect these concepts in the context of DNA damage and mutation induced by antibiotics.
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Machuca J, Recacha E, Gallego-Mesa B, Diaz-Diaz S, Rojas-Granado G, García-Duque A, Docobo-Pérez F, Blázquez J, Rodríguez-Rojas A, Pascual A, Rodríguez-Martínez JM. Effect of RecA inactivation on quinolone susceptibility and the evolution of resistance in clinical isolates of Escherichia coli. J Antimicrob Chemother 2021; 76:338-344. [PMID: 33147333 DOI: 10.1093/jac/dkaa448] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Accepted: 09/30/2020] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND SOS response suppression (by RecA inactivation) has been postulated as a therapeutic strategy for potentiating antimicrobials against Enterobacterales. OBJECTIVES To evaluate the impact of RecA inactivation on the reversion and evolution of quinolone resistance using a collection of Escherichia coli clinical isolates. METHODS Twenty-three E. coli clinical isolates, including isolates belonging to the high-risk clone ST131, were included. SOS response was suppressed by recA inactivation. Susceptibility to fluoroquinolones was determined by broth microdilution, growth curves and killing curves. Evolution of quinolone resistance was evaluated by mutant frequency and mutant prevention concentration (MPC). RESULTS RecA inactivation resulted in 2-16-fold reductions in fluoroquinolone MICs and modified EUCAST clinical category for several isolates, including ST131 clone isolates. Growth curves and time-kill curves showed a clear disadvantage (up to 10 log10 cfu/mL after 24 h) for survival in strains with an inactivated SOS system. For recA-deficient mutants, MPC values decreased 4-8-fold, with values below the maximum serum concentration of ciprofloxacin. RecA inactivation led to a decrease in mutant frequency (≥103-fold) compared with isolates with unmodified SOS responses at ciprofloxacin concentrations of 4×MIC and 1 mg/L. These effects were also observed in ST131 clone isolates. CONCLUSIONS While RecA inactivation does not reverse existing resistance, it is a promising strategy for increasing the effectiveness of fluoroquinolones against susceptible clinical isolates, including high-risk clone isolates.
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Affiliation(s)
- J Machuca
- Unidad Clínica de Enfermedades Infecciosas, Microbiología y Medicina Preventiva, Hospital Universitario Virgen Macarena, Seville, Spain.,Red Española de Investigación en Patología Infecciosa (REIPI), Instituto de Salud Carlos III, Madrid, Spain.,Instituto de Biomedicina de Sevilla IBIS, Hospital Universitario Virgen Macarena/CSIC/Departamento de Microbiología, Universidad de Sevilla, Seville, Spain
| | - E Recacha
- Unidad Clínica de Enfermedades Infecciosas, Microbiología y Medicina Preventiva, Hospital Universitario Virgen Macarena, Seville, Spain.,Red Española de Investigación en Patología Infecciosa (REIPI), Instituto de Salud Carlos III, Madrid, Spain.,Instituto de Biomedicina de Sevilla IBIS, Hospital Universitario Virgen Macarena/CSIC/Departamento de Microbiología, Universidad de Sevilla, Seville, Spain
| | - B Gallego-Mesa
- Departamento de Microbiología, Facultad de Medicina, Universidad de Sevilla, Sevilla, Spain
| | - S Diaz-Diaz
- Red Española de Investigación en Patología Infecciosa (REIPI), Instituto de Salud Carlos III, Madrid, Spain.,Instituto de Biomedicina de Sevilla IBIS, Hospital Universitario Virgen Macarena/CSIC/Departamento de Microbiología, Universidad de Sevilla, Seville, Spain.,Departamento de Microbiología, Facultad de Medicina, Universidad de Sevilla, Sevilla, Spain
| | - G Rojas-Granado
- Departamento de Microbiología, Facultad de Medicina, Universidad de Sevilla, Sevilla, Spain
| | - A García-Duque
- Unidad Clínica de Enfermedades Infecciosas, Microbiología y Medicina Preventiva, Hospital Universitario Virgen Macarena, Seville, Spain
| | - F Docobo-Pérez
- Red Española de Investigación en Patología Infecciosa (REIPI), Instituto de Salud Carlos III, Madrid, Spain.,Instituto de Biomedicina de Sevilla IBIS, Hospital Universitario Virgen Macarena/CSIC/Departamento de Microbiología, Universidad de Sevilla, Seville, Spain.,Departamento de Microbiología, Facultad de Medicina, Universidad de Sevilla, Sevilla, Spain
| | - J Blázquez
- Red Española de Investigación en Patología Infecciosa (REIPI), Instituto de Salud Carlos III, Madrid, Spain.,Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | | | - A Pascual
- Unidad Clínica de Enfermedades Infecciosas, Microbiología y Medicina Preventiva, Hospital Universitario Virgen Macarena, Seville, Spain.,Red Española de Investigación en Patología Infecciosa (REIPI), Instituto de Salud Carlos III, Madrid, Spain.,Instituto de Biomedicina de Sevilla IBIS, Hospital Universitario Virgen Macarena/CSIC/Departamento de Microbiología, Universidad de Sevilla, Seville, Spain.,Departamento de Microbiología, Facultad de Medicina, Universidad de Sevilla, Sevilla, Spain
| | - J M Rodríguez-Martínez
- Red Española de Investigación en Patología Infecciosa (REIPI), Instituto de Salud Carlos III, Madrid, Spain.,Instituto de Biomedicina de Sevilla IBIS, Hospital Universitario Virgen Macarena/CSIC/Departamento de Microbiología, Universidad de Sevilla, Seville, Spain.,Departamento de Microbiología, Facultad de Medicina, Universidad de Sevilla, Sevilla, Spain
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Morgan RN, Farrag HA, Aboulwafa MM, Saleh SE. "Effect of Subinhibitory Concentrations of Some Antibiotics and Low Doses of Gamma Radiation on the Cytotoxicity and Expression of Colibactin by an Uropathogenic Escherichia coli isolate". Curr Microbiol 2021; 78:544-557. [PMID: 33388934 DOI: 10.1007/s00284-020-02331-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 12/10/2020] [Indexed: 01/10/2023]
Abstract
Colibactin and cytotoxic necrotizing factor 1 (Cnf 1) are cyclomodulins secreted by uropathogenic E. coli. In this study, uropathogenic E. coli expressing colibactin and Cnf 1 was exposed to antibiotics subMICs and gamma radiation to investigate their effects on its cytotoxicity and expression of colibactin. The test isolate was exposed to three subMIC levels of levofloxacin, ciprofloxacin, trimethoprim/sulfamethoxazole and ceftriaxone and irradiated with gamma rays at 10 and 24.4 Gy. The cytotoxicity for either antibiotic or gamma rays treated cultures was measured using MTT assay and the expression of colibactin encoding genes was determined by RT-PCR. Treatment with fluoroquinolones nearly abolished the cytotoxicity of E. coli isolate and significantly downregulated clbA gene expression at the tested subMICs (P ≤ 0.05) while trimethoprim/sulfamethoxazole treated cultures exerted significant downregulation of clbA and clbQ genes at 0.5 MIC only (P ≤ 0.05). Ceftriaxone treated cultured exhibited reduction in the cytotoxicity and insignificant effects on expression of clbA, clbQ and clbM genes. On contrast, significant upregulation in the expression of clbA and clbQ genes was observed in irradiated cultures (P ≤ 0.05). Fluoroquinolones reduced both the cytotoxicity of UPEC isolate and colibactin expression at different subMICs while ceftriaxone at subMICs failed to suppress the expression of genotoxin, colibactin, giving an insight to the risks associated upon their choice for UTI treatment. Colibactin expression was enhanced by gamma irradiation at doses resembling these received during pelvic radiotherapy which might contribute to post-radiotherapy complications.
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Affiliation(s)
- Radwa N Morgan
- National Centre for Radiation Research and Technology (NCRRT), Drug Radiation Research Department, Egyptian Atomic Energy Authority (EAEA), Ahmed El-Zomor Street, Nasr city, Cairo, 11787, Egypt
| | - Hala A Farrag
- National Centre for Radiation Research and Technology (NCRRT), Drug Radiation Research Department, Egyptian Atomic Energy Authority (EAEA), Ahmed El-Zomor Street, Nasr city, Cairo, 11787, Egypt
| | - Mohammad M Aboulwafa
- Microbiology and Immunology Department, Faculty of Pharmacy, Ain Shams University, African union organization Street, Abbassia, Cairo, 11566, Egypt.
- Faculty of Pharmacy, King Salman International University, South Sinai, Ras-Sedr, Egypt.
| | - Sarra E Saleh
- Microbiology and Immunology Department, Faculty of Pharmacy, Ain Shams University, African union organization Street, Abbassia, Cairo, 11566, Egypt
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Neves HI, Machado GT, Ramos TCDS, Yang HM, Yagil E, Spira B. Competition for nutritional resources masks the true frequency of bacterial mutants. BMC Biol 2020; 18:194. [PMID: 33317515 PMCID: PMC7737367 DOI: 10.1186/s12915-020-00913-1] [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: 07/22/2020] [Accepted: 11/03/2020] [Indexed: 12/02/2022] Open
Abstract
Background It is widely assumed that all mutant microorganisms present in a culture are able to grow and form colonies, provided that they express the features required for selection. Unlike wild-type Escherichia coli, PHO-constitutive mutants overexpress alkaline phosphatase and hence can hydrolyze glycerol-2-phosphate (G2P) to glycerol and form colonies on plates having G2P as the sole carbon source. These mutations mostly occur in the pst operon. However, the frequency of PHO-constitutive colonies on the G2P selective plate is exceptionally low. Results We show that the rate in which spontaneous PHO-constitutive mutations emerge is about 8.0 × 10−6/generation, a relatively high rate, but the growth of most existing mutants is inhibited by their neighboring wild-type cells. This inhibition is elicited only by non-mutant viable bacteria that can take up and metabolize glycerol formed by the mutants. Evidence indicates that the few mutants that do form colonies derive from microclusters of mutants on the selective plate. A mathematical model that describes the fate of the wild-type and mutant populations under these circumstances supports these results. Conclusion This scenario in which neither the wild-type nor the majority of the mutants are able to grow resembles an unavoidable “tragedy of the commons” case which results in the collapse of the majority of the population. Cooperation between rare adjacent mutants enables them to overcome the competition and eventually form mutant colonies. The inhibition of PHO-constitutive mutants provides an example of mutant frequency masked by orders of magnitude due to a competition between mutants and their ancestral wild-type cells. Similar “tragedy of the commons-like” cases may occur in other settings and should be taken into consideration while estimating true mutant frequencies and mutation rates. Supplementary Information The online version contains supplementary material available at (doi:10.1186/s12915-020-00913-1).
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Affiliation(s)
- Henrique Iglesias Neves
- Departamento de Microbiologia, Instituto de Ciências Biomédicas Universidade de São Paulo, São Paulo, SP, Brazil
| | - Gabriella Trombini Machado
- Departamento de Microbiologia, Instituto de Ciências Biomédicas Universidade de São Paulo, São Paulo, SP, Brazil
| | | | - Hyun Mo Yang
- Departamento de Matemática Aplicada, Instituto de Matemática, Estatística e Computação Científica, Campinas, SP, Brazil
| | - Ezra Yagil
- Departament of Biochemistry and Molecular Biology, Faculty of Life Sciences, Tel-Aviv University, Tel Aviv, Israel
| | - Beny Spira
- Departamento de Microbiologia, Instituto de Ciências Biomédicas Universidade de São Paulo, São Paulo, SP, Brazil.
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Dörr T. Understanding tolerance to cell wall-active antibiotics. Ann N Y Acad Sci 2020; 1496:35-58. [PMID: 33274447 PMCID: PMC8359209 DOI: 10.1111/nyas.14541] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 11/02/2020] [Accepted: 11/04/2020] [Indexed: 12/19/2022]
Abstract
Antibiotic tolerance-the ability of bacteria to survive for an extended time in the presence of bactericidal antibiotics-is an understudied contributor to antibiotic treatment failure. Herein, I review the manifestations, mechanisms, and clinical relevance of tolerance to cell wall-active (CWA) antibiotics, one of the most important groups of antibiotics at the forefront of clinical use. I discuss definitions of tolerance and assays for tolerance detection, comprehensively discuss the mechanism of action of β-lactams and other CWA antibiotics, and then provide an overview of how cells mitigate the potentially lethal effects of CWA antibiotic-induced cell damage to become tolerant. Lastly, I discuss evidence for a role of CWA antibiotic tolerance in clinical antibiotic treatment failure.
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Affiliation(s)
- Tobias Dörr
- Weill Institute for Cell and Molecular Biology, Department of Microbiology, and Cornell Institute of Host-Pathogen Interactions and Disease, Cornell University, Ithaca, New York
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40
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Bush NG, Diez-Santos I, Abbott LR, Maxwell A. Quinolones: Mechanism, Lethality and Their Contributions to Antibiotic Resistance. Molecules 2020; 25:E5662. [PMID: 33271787 PMCID: PMC7730664 DOI: 10.3390/molecules25235662] [Citation(s) in RCA: 125] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/27/2020] [Accepted: 11/28/2020] [Indexed: 12/05/2022] Open
Abstract
Fluoroquinolones (FQs) are arguably among the most successful antibiotics of recent times. They have enjoyed over 30 years of clinical usage and become essential tools in the armoury of clinical treatments. FQs target the bacterial enzymes DNA gyrase and DNA topoisomerase IV, where they stabilise a covalent enzyme-DNA complex in which the DNA is cleaved in both strands. This leads to cell death and turns out to be a very effective way of killing bacteria. However, resistance to FQs is increasingly problematic, and alternative compounds are urgently needed. Here, we review the mechanisms of action of FQs and discuss the potential pathways leading to cell death. We also discuss quinolone resistance and how quinolone treatment can lead to resistance to non-quinolone antibiotics.
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Affiliation(s)
| | | | | | - Anthony Maxwell
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK; (N.G.B.); (I.D.-S.); (L.R.A.)
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High-throughput laboratory evolution reveals evolutionary constraints in Escherichia coli. Nat Commun 2020; 11:5970. [PMID: 33235191 PMCID: PMC7686311 DOI: 10.1038/s41467-020-19713-w] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 10/28/2020] [Indexed: 01/19/2023] Open
Abstract
Understanding the constraints that shape the evolution of antibiotic resistance is critical for predicting and controlling drug resistance. Despite its importance, however, a systematic investigation of evolutionary constraints is lacking. Here, we perform a high-throughput laboratory evolution of Escherichia coli under the addition of 95 antibacterial chemicals and quantified the transcriptome, resistance, and genomic profiles for the evolved strains. Utilizing machine learning techniques, we analyze the phenotype–genotype data and identified low dimensional phenotypic states among the evolved strains. Further analysis reveals the underlying biological processes responsible for these distinct states, leading to the identification of trade-off relationships associated with drug resistance. We also report a decelerated evolution of β-lactam resistance, a phenomenon experienced by certain strains under various stresses resulting in higher acquired resistance to β-lactams compared to strains directly selected by β-lactams. These findings bridge the genotypic, gene expression, and drug resistance gap, while contributing to a better understanding of evolutionary constraints for antibiotic resistance. Understanding evolutionary constraints in antibiotic resistance is crucial for prediction and control. Here, the authors use high-throughput laboratory evolution of Escherichia coli alongside machine learning to identify trade-off relationships associated with drug resistance.
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Revitt-Mills SA, Robinson A. Antibiotic-Induced Mutagenesis: Under the Microscope. Front Microbiol 2020; 11:585175. [PMID: 33193230 PMCID: PMC7642495 DOI: 10.3389/fmicb.2020.585175] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 09/28/2020] [Indexed: 11/24/2022] Open
Abstract
The development of antibiotic resistance poses an increasing threat to global health. Understanding how resistance develops in bacteria is critical for the advancement of new strategies to combat antibiotic resistance. In the 1980s, it was discovered that certain antibiotics induce elevated rates of mutation in bacteria. From this, an “increased evolvability” hypothesis was proposed: antibiotic-induced mutagenesis increases the genetic diversity of bacterial populations, thereby increasing the rate at which bacteria develop antibiotic resistance. However, antibiotic-induced mutagenesis is one of multiple competing factors that act on bacterial populations exposed to antibiotics. Its relative importance in shaping evolutionary outcomes, including the development of antibiotic resistance, is likely to depend strongly on the conditions. Presently, there is no quantitative model that describes the relative contribution of antibiotic-induced mutagenesis to bacterial evolution. A far more complete understanding could be reached if we had access to technology that enabled us to study antibiotic-induced mutagenesis at the molecular-, cellular-, and population-levels simultaneously. Direct observations would, in principle, allow us to directly link molecular-level events with outcomes in individual cells and cell populations. In this review, we highlight microscopy studies which have allowed various aspects of antibiotic-induced mutagenesis to be directly visualized in individual cells for the first time. These studies have revealed new links between error-prone DNA polymerases and recombinational DNA repair, evidence of spatial regulation occurring during the SOS response, and enabled real-time readouts of mismatch and mutation rates. Further, we summarize the recent discovery of stochastic population fluctuations in cultures exposed to sub-inhibitory concentrations of bactericidal antibiotics and discuss the implications of this finding for the study of antibiotic-induced mutagenesis. The studies featured here demonstrate the potential of microscopy to provide direct observation of phenomena relevant to evolution under antibiotic-induced mutagenesis.
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Affiliation(s)
- Sarah A Revitt-Mills
- Molecular Horizons Institute and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia.,Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia
| | - Andrew Robinson
- Molecular Horizons Institute and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia.,Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia
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Rodríguez-Rosado AI, Valencia EY, Rodríguez-Rojas A, Costas C, Galhardo RS, Rodríguez-Beltrán J, Blázquez J. N-acetylcysteine blocks SOS induction and mutagenesis produced by fluoroquinolones in Escherichia coli. J Antimicrob Chemother 2020; 74:2188-2196. [PMID: 31102529 DOI: 10.1093/jac/dkz210] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 04/15/2019] [Accepted: 04/17/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Fluoroquinolones such as ciprofloxacin induce the mutagenic SOS response and increase the levels of intracellular reactive oxygen species (ROS). Both the SOS response and ROS increase bacterial mutagenesis, fuelling the emergence of resistant mutants during antibiotic treatment. Recently, there has been growing interest in developing new drugs able to diminish the mutagenic effect of antibiotics by modulating ROS production and the SOS response. OBJECTIVES To test whether physiological concentrations of N-acetylcysteine, a clinically safe antioxidant drug currently used in human therapy, is able to reduce ROS production, SOS induction and mutagenesis in ciprofloxacin-treated bacteria without affecting antibiotic activity. METHODS The Escherichia coli strain IBDS1 and its isogenic mutant deprived of SOS mutagenesis (TLS-) were treated with different concentrations of ciprofloxacin, N-acetylcysteine or both drugs in combination. Relevant parameters such as MICs, growth rates, ROS production, SOS induction, filamentation and antibiotic-induced mutation rates were evaluated. RESULTS Treatment with N-acetylcysteine reduced intracellular ROS levels (by ∼40%), as well as SOS induction (by up to 75%) and bacterial filamentation caused by subinhibitory concentrations of ciprofloxacin, without affecting ciprofloxacin antibacterial activity. Remarkably, N-acetylcysteine completely abolished SOS-mediated mutagenesis. CONCLUSIONS Collectively, our data strongly support the notion that ROS are a key factor in antibiotic-induced SOS mutagenesis and open the possibility of using N-acetylcysteine in combination with antibiotic therapy to hinder the development of antibiotic resistance.
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Affiliation(s)
| | - Estela Ynés Valencia
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | | | - Coloma Costas
- Instituto de Biomedicina de Sevilla (IBiS), Seville, Spain
| | - Rodrigo S Galhardo
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | | | - Jesús Blázquez
- Centro Nacional de Biotecnología (CNB), Madrid, Spain.,Clinical Unit of Infectious Diseases, Microbiology and Preventive Medicine, University Hospital Virgen del Rocio, Seville, Spain
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44
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Ching C, Orubu ESF, Sutradhar I, Wirtz VJ, Boucher HW, Zaman MH. Bacterial antibiotic resistance development and mutagenesis following exposure to subinhibitory concentrations of fluoroquinolones in vitro: a systematic review of the literature. JAC Antimicrob Resist 2020; 2:dlaa068. [PMID: 34223024 PMCID: PMC8210091 DOI: 10.1093/jacamr/dlaa068] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 07/15/2020] [Indexed: 12/09/2022] Open
Abstract
BACKGROUND Understanding social and scientific drivers of antibiotic resistance is critical to help preserve antibiotic efficacy. These drivers include exposure to subinhibitory antibiotic concentrations in the environment and clinic. OBJECTIVES To summarize and quantify the relationship between subinhibitory fluoroquinolone exposure and antibiotic resistance and mutagenesis to better understand resistance patterns and mechanisms. METHODS Following PRISMA guidelines, PubMed, Web of Science and Embase were searched for primary in vitro experimental studies on subinhibitory fluoroquinolone exposure and bacterial antibiotic resistance and mutagenesis, from earliest available dates through to 2018 without language limitation. A specifically developed non-weighted tool was used to assess risk of bias. RESULTS Evidence from 62 eligible studies showed that subinhibitory fluoroquinolone exposure results in increased resistance to the selecting fluoroquinolone. Most increases in MIC were low (median minimum of 3.7-fold and median maximum of 32-fold) and may not be considered clinically relevant. Mechanistically, resistance is partly explained by target mutations but also changes in drug efflux. Collaterally, resistance to other fluoroquinolones and unrelated antibiotic classes also develops. The mean ± SD quality score for all studies was 2.6 ± 1.8 with a range of 0 (highest score) to 7 (lowest score). CONCLUSIONS Low and moderate levels of resistance and efflux changes can create an opportunity for higher-level resistance or MDR. Future studies, to elucidate the genetic regulation of specific resistance mechanisms, and increased policies, including surveillance of low-level resistance changes or genomic surveillance of efflux pump genes and regulators, could serve as a predictor of MDR development.
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Affiliation(s)
- Carly Ching
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Ebiowei S F Orubu
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
- Institute for Health System Innovation & Policy, Boston University, Boston, MA, USA
| | - Indorica Sutradhar
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Veronika J Wirtz
- Department of Global Health, Boston University School of Public Health, Boston, MA, USA
| | - Helen W Boucher
- Division of Geographic Medicine and Infectious Diseases, Tufts Medical Center, Boston, MA, USA
| | - Muhammad H Zaman
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
- Howard Hughes Medical Institute, Boston University, Boston, MA, USA
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45
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Gudda FO, Waigi MG, Odinga ES, Yang B, Carter L, Gao Y. Antibiotic-contaminated wastewater irrigated vegetables pose resistance selection risks to the gut microbiome. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 264:114752. [PMID: 32417582 DOI: 10.1016/j.envpol.2020.114752] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 05/03/2020] [Accepted: 05/05/2020] [Indexed: 06/11/2023]
Abstract
Wastewater reuse in food crop irrigation has led to agroecosystem pollution concerns and human health risks. However, there is limited attention on the relationship of sub-lethal antibiotic levels in vegetables and resistance selection. Most risk assessment studies show non-significant toxicity, but overlook the link between antibiotics in crops and propagation of gut microbiome resistance selection. The review highlights the risk of antibiotics in treated water used for irrigation, uptake, and accumulation in edible vegetable parts. Moreover, it elucidates the risks to the adaptive resistance selection of the gut microbiome from sub-lethal antibiotic levels, as a result of dietary contaminated vegetables. Experiments have reported that bacterial resistance selection is possible at concentrations that are several hundred-folds lower than lethal effect levels on susceptible cells. Consequently, mutants selected at low antibiotic levels, such as those from vegetables, are fitter and more resistant compared to those selected at high concentrations. Necessary standardization, such as the development of minimum acceptable antibiotic limits allowable in food crop irrigation water, with a focus on minimum selection concentration, and not only toxicity, has been proposed. Wastewater irrigation offers environmental benefits and can contribute to food security, but it has non-addressed risks. Research gaps, future perspectives, and frameworks of mitigating the potential risks are discussed.
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Affiliation(s)
- Fredrick Owino Gudda
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China; Faculty of Environment and Resource Development, Department of Environmental Sciences, Egerton University, Box 536, Egerton, 20115, Kenya
| | - Michael Gatheru Waigi
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Emmanuel Stephen Odinga
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Bing Yang
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Laura Carter
- School of Geography, University of Leeds, Leeds, LS2 9JT, UK
| | - Yanzheng Gao
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China.
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46
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Goneau LW, Delport J, Langlois L, Poutanen SM, Razvi H, Reid G, Burton JP. Issues beyond resistance: inadequate antibiotic therapy and bacterial hypervirulence. FEMS MICROBES 2020; 1:xtaa004. [PMID: 37333955 PMCID: PMC10117437 DOI: 10.1093/femsmc/xtaa004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 10/15/2020] [Indexed: 10/15/2023] Open
Abstract
The administration of antibiotics while critical for treatment, can be accompanied by potentially severe complications. These include toxicities associated with the drugs themselves, the selection of resistant organisms and depletion of endogenous host microbiota. In addition, antibiotics may be associated with less well-recognized complications arising through changes in the pathogens themselves. Growing evidence suggests that organisms exposed to antibiotics can respond by altering the expression of toxins, invasins and adhesins, as well as biofilm, resistance and persistence factors. The clinical significance of these changes continues to be explored; however, it is possible that treatment with antibiotics may inadvertently precipitate a worsening of the clinical course of disease. Efforts are needed to adjust or augment antibiotic therapy to prevent the transition of pathogens to hypervirulent states. Better understanding the role of antibiotic-microbe interactions and how these can influence disease course is critical given the implications on prescription guidelines and antimicrobial stewardship policies.
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Affiliation(s)
- Lee W Goneau
- Department of Microbiology and Immunology, Western University, London, Ontario, Canada
- Lawson Health Research Institute, 268 Grosvenor St, London, Ontario, N6A 4V2 Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto,1 King's College Cir, Toronto, ON M5S 1A8 Ontario, Canada
| | - Johannes Delport
- Department of Pathology, London Health Sciences Center - Victoria Hospital, 800 Commissioners Rd E, London, Ontario, Canada N6A 5W9
| | - Luana Langlois
- Department of Microbiology and Immunology, Western University, London, Ontario, Canada
| | - Susan M Poutanen
- Department of Laboratory Medicine and Pathobiology, University of Toronto,1 King's College Cir, Toronto, ON M5S 1A8 Ontario, Canada
- Department of Medicine, University of Toronto, 1 King's College Cir, Toronto, ON M5S 1A8 Toronto, Ontario, Canada
- Department of Microbiology, University Health Network and Sinai Health, 190 Elizabeth St. Toronto, ON M5G 2C4, Ontario, Canada
| | - Hassan Razvi
- Lawson Health Research Institute, 268 Grosvenor St, London, Ontario, N6A 4V2 Canada
- Division of Urology, Department of Surgery, Western University, 1151 Richmond St, London, Ontario, N6A 3K7 Canada
| | - Gregor Reid
- Department of Microbiology and Immunology, Western University, London, Ontario, Canada
- Lawson Health Research Institute, 268 Grosvenor St, London, Ontario, N6A 4V2 Canada
- Division of Urology, Department of Surgery, Western University, 1151 Richmond St, London, Ontario, N6A 3K7 Canada
| | - Jeremy P Burton
- Department of Microbiology and Immunology, Western University, London, Ontario, Canada
- Lawson Health Research Institute, 268 Grosvenor St, London, Ontario, N6A 4V2 Canada
- Division of Urology, Department of Surgery, Western University, 1151 Richmond St, London, Ontario, N6A 3K7 Canada
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47
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Hernando-Amado S, Coque TM, Baquero F, Martínez JL. Antibiotic Resistance: Moving From Individual Health Norms to Social Norms in One Health and Global Health. Front Microbiol 2020; 11:1914. [PMID: 32983000 PMCID: PMC7483582 DOI: 10.3389/fmicb.2020.01914] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 07/21/2020] [Indexed: 12/16/2022] Open
Abstract
Antibiotic resistance is a problem for human health, and consequently, its study had been traditionally focused toward its impact for the success of treating human infections in individual patients (individual health). Nevertheless, antibiotic-resistant bacteria and antibiotic resistance genes are not confined only to the infected patients. It is now generally accepted that the problem goes beyond humans, hospitals, or long-term facility settings and that it should be considered simultaneously in human-connected animals, farms, food, water, and natural ecosystems. In this regard, the health of humans, animals, and local antibiotic-resistance-polluted environments should influence the health of the whole interconnected local ecosystem (One Health). In addition, antibiotic resistance is also a global problem; any resistant microorganism (and its antibiotic resistance genes) could be distributed worldwide. Consequently, antibiotic resistance is a pandemic that requires Global Health solutions. Social norms, imposing individual and group behavior that favor global human health and in accordance with the increasingly collective awareness of the lack of human alienation from nature, will positively influence these solutions. In this regard, the problem of antibiotic resistance should be understood within the framework of socioeconomic and ecological efforts to ensure the sustainability of human development and the associated human-natural ecosystem interactions.
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Affiliation(s)
- Sara Hernando-Amado
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Teresa M. Coque
- Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS) and Centro de Investigación Biomédica en Red Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Fernando Baquero
- Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS) and Centro de Investigación Biomédica en Red Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - José L. Martínez
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
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48
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Ribeiro ÁCDS, Martins WMBDS, Silva AAD, Gales AC, Rando DGG, Minarini LADR. Exposure to sub-inhibitory ciprofloxacin and nitrofurantoin concentrations increases recA gene expression in uropathogenic Escherichia coli: The role of RecA protein as a drug target. Eur J Pharm Sci 2020; 146:105268. [PMID: 32081832 DOI: 10.1016/j.ejps.2020.105268] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 02/03/2020] [Accepted: 02/15/2020] [Indexed: 01/01/2023]
Abstract
Sub-inhibitory concentrations (sub-MIC) of antimicrobial agents can lead to genetic changes in bacteria, modulating the expression of genes related to bacterial stress and leading to drug resistance. Herein we describe the impact of sub-MIC of ciprofloxacin and nitrofurantoin on three uropathogenic Escherichia coli strains. Disk-diffusion assays with different antimicrobial agents were tested to detect phenotype alterations, and quantitative real-time PCR (qRT-PCR) was performed to analyze the expression of ompF and recA genes. Significant reduction on the susceptibility to ciprofloxacin and nitrofurantoin was detected on disk diffusion test. The qRT-PCR results revealed a 1.2-4.7 increase in recA expression in all E. coli studied, while the ompF expression varied. Because RecA was pointed as an important component to the development of drug resistance, molecular docking studies were performed with three experimentally known inhibitors of this enzyme. These studies aimed to understand the inhibitory binding mode of such compounds. The results confirmed the ADP/ATP binding site as a potential site of inhibitor recognition and a binding mode based on π-stacking interactions with Tyr103 and hydrogen bonds with Tyr264. These findings can be useful for guiding the search and design of new antimicrobial agents, mainly concerning the treatment of infections with resistant bacterial strains.
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Affiliation(s)
- Ághata Cardoso da Silva Ribeiro
- Universidade Federal de São Paulo - UNIFESP, Instituto de Ciências Ambientais, Químicas e Farmacêuticas, Laboratório Multidisciplinar em Saúde e Meio Ambiente, Departamento de Ciências Farmacêuticas, Rua São Nicolau, 210 Diadema, SP, Brazil
| | - Willames Marcos Brasileiro da Silva Martins
- Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina/Universidade Federal de São Paulo - UNIFESP, Rua Pedro de Toledo, 781 São Paulom, SP, Brazil
| | - Adilson Aderito da Silva
- Universidade Presbiteriana Mackenzie, Centro de Ciências Sociais e Aplicadas, Rua da Consolação, 930, São Paulo, SP, Brazil
| | - Ana Cristina Gales
- Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina/Universidade Federal de São Paulo - UNIFESP, Rua Pedro de Toledo, 781 São Paulom, SP, Brazil
| | - Daniela Gonçales Galasse Rando
- Universidade Federal de São Paulo - UNIFESP, Instituto de Ciências Ambientais, Químicas e Farmacêuticas, Grupo de Pesquisas Químico-Farmacêuticas da UNIFESP, Departamento de Ciências Farmacêuticas, Rua São Nicolau, 210, Diadema, SP, Brazil
| | - Luciene Andrade da Rocha Minarini
- Universidade Federal de São Paulo - UNIFESP, Instituto de Ciências Ambientais, Químicas e Farmacêuticas, Laboratório Multidisciplinar em Saúde e Meio Ambiente, Departamento de Ciências Farmacêuticas, Rua São Nicolau, 210 Diadema, SP, Brazil.
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49
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Penesyan A, Nagy SS, Kjelleberg S, Gillings MR, Paulsen IT. Rapid microevolution of biofilm cells in response to antibiotics. NPJ Biofilms Microbiomes 2019; 5:34. [PMID: 31728201 PMCID: PMC6834608 DOI: 10.1038/s41522-019-0108-3] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 10/03/2019] [Indexed: 02/08/2023] Open
Abstract
Infections caused by Acinetobacter baumannii are increasingly antibiotic resistant, generating a significant public health problem. Like many bacteria, A. baumannii adopts a biofilm lifestyle that enhances its antibiotic resistance and environmental resilience. Biofilms represent the predominant mode of microbial life, but research into antibiotic resistance has mainly focused on planktonic cells. We investigated the dynamics of A. baumannii biofilms in the presence of antibiotics. A 3-day exposure of A. baumannii biofilms to sub-inhibitory concentrations of antibiotics had a profound effect, increasing biofilm formation and antibiotic resistance in the majority of biofilm dispersal isolates. Cells dispersing from biofilms were genome sequenced to identify mutations accumulating in their genomes, and network analysis linked these mutations to their phenotypes. Transcriptomics of biofilms confirmed the network analysis results, revealing novel gene functions of relevance to both resistance and biofilm formation. This approach is a rapid and objective tool for investigating resistance dynamics of biofilms.
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Affiliation(s)
- Anahit Penesyan
- 1Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW 2109 Australia.,2School of Chemical Engineering, University of New South Wales, Sydney, NSW 2052 Australia
| | - Stephanie S Nagy
- 1Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW 2109 Australia
| | - Staffan Kjelleberg
- 3Singapore Centre for Environmental Life Sciences Engineering, 60 Nanyang Drive, SBS-01N-27, Singapore, 637551 Singapore.,4School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551 Singapore.,5School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW 2052 Australia
| | - Michael R Gillings
- 6Department of Biological Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW 2109 Australia
| | - Ian T Paulsen
- 1Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW 2109 Australia
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50
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Blázquez J, Rodríguez-Beltrán J, Matic I. Antibiotic-Induced Genetic Variation: How It Arises and How It Can Be Prevented. Annu Rev Microbiol 2019; 72:209-230. [PMID: 30200850 DOI: 10.1146/annurev-micro-090817-062139] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
By targeting essential cellular processes, antibiotics provoke metabolic perturbations and induce stress responses and genetic variation in bacteria. Here we review current knowledge of the mechanisms by which these molecules generate genetic instability. They include production of reactive oxygen species, as well as induction of the stress response regulons, which lead to enhancement of mutation and recombination rates and modulation of horizontal gene transfer. All these phenomena influence the evolution and spread of antibiotic resistance. The use of strategies to stop or decrease the generation of resistant variants is also discussed.
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Affiliation(s)
- Jesús Blázquez
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), 28049 Madrid, Spain; .,Unidad de Enfermedades Infecciosas, Microbiologia y Medicina Preventiva, Hospital Universitario Virgen del Rocio, 41013 Seville, Spain.,Red Española de Investigacion en Patologia Infecciosa, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | | | - Ivan Matic
- Faculté de Médecine Paris Descartes, INSERM 1001, CNRS, Université Paris-Descartes-Sorbonne Paris Cité, 75014 Paris, France;
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