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Heidarian S, Guliaev A, Nicoloff H, Hjort K, Andersson DI. High prevalence of heteroresistance in Staphylococcus aureus is caused by a multitude of mutations in core genes. PLoS Biol 2024; 22:e3002457. [PMID: 38175839 PMCID: PMC10766187 DOI: 10.1371/journal.pbio.3002457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 11/30/2023] [Indexed: 01/06/2024] Open
Abstract
Heteroresistance (HR) is an enigmatic phenotype where, in a main population of susceptible cells, small subpopulations of resistant cells exist. This is a cause for concern, as this small subpopulation is difficult to detect by standard antibiotic susceptibility tests, and upon antibiotic exposure the resistant subpopulation may increase in frequency and potentially lead to treatment complications or failure. Here, we determined the prevalence and mechanisms of HR for 40 clinical Staphylococcus aureus isolates, against 6 clinically important antibiotics: daptomycin, gentamicin, linezolid, oxacillin, teicoplanin, and vancomycin. High frequencies of HR were observed for gentamicin (69.2%), oxacillin (27%), daptomycin (25.6%), and teicoplanin (15.4%) while none of the isolates showed HR toward linezolid or vancomycin. Point mutations in various chromosomal core genes, including those involved in membrane and peptidoglycan/teichoic acid biosynthesis and transport, tRNA charging, menaquinone and chorismite biosynthesis and cyclic-di-AMP biosynthesis, were the mechanisms responsible for generating the resistant subpopulations. This finding is in contrast to gram-negative bacteria, where increased copy number of bona fide resistance genes via tandem gene amplification is the most prevalent mechanism. This difference can be explained by the observation that S. aureus has a low content of resistance genes and absence of the repeat sequences that allow tandem gene amplification of these genes as compared to gram-negative species.
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Affiliation(s)
- Sheida Heidarian
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Andrei Guliaev
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Hervé Nicoloff
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Karin Hjort
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Dan I. Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
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Fox V, Santoro F, Apicella C, Diaz-Diaz S, Rodriguez-Martínez JM, Iannelli F, Pozzi G. The mef(A)/ msr(D)-carrying streptococcal prophage Φ1207.3 encodes an SOS-like system, induced by UV-C light, responsible for increased survival and increased mutation rate. J Bacteriol 2023; 205:e0019123. [PMID: 37695857 PMCID: PMC10521357 DOI: 10.1128/jb.00191-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 08/04/2023] [Indexed: 09/13/2023] Open
Abstract
Bacterial SOS response is an inducible system of DNA repair and mutagenesis. Streptococci lack a canonical SOS response, but an SOS-like response was reported in some species. The mef(A)-msr(D)-carrying prophage Ф1207.3 of Streptococcus pyogenes contains a region, spanning orf6 to orf11, showing homology to characterized streptococcal SOS-like cassettes. Genome-wide homology search showed the presence of the whole Φ1207.3 SOS-like cassette in three S. pyogenes prophages, while parts of it were found in other bacterial species. To investigate whether this cassette confers an SOS-mutagenesis phenotype, we constructed Streptococcus pneumoniae R6 isogenic derivative strains: (i) FR172, streptomycin resistant, (ii) FR173, carrying Φ1207.3, and (iii) FR174, carrying a recombinant Φ1207.3, where the SOS-like cassette was deleted. These strains were used in survival and mutation rate assays using a UV-C LED instrument, for which we designed and 3D-printed a customized equipment, constituted of an instrument support and swappable-autoclavable mini-plates and lids. Upon exposure to UV fluences ranging from 0 to 6,400 J/m2 at four different wavelengths, 255, 265, 275, and 285 nm, we found that the presence of Φ1207.3 SOS-like cassette increases bacterial survival up to 34-fold. Mutation rate was determined by measuring rifampicin resistance acquisition upon exposure to UV fluence of 50 J/m2 at the four wavelengths by fluctuation test. The presence of Φ1207.3 SOS-like cassette resulted in a significant increase in the mutation rate (up to 18-fold) at every wavelength. In conclusion, we demonstrated that Φ1207.3 carries a functional SOS-like cassette responsible for an increased survival and increased mutation rate in S. pneumoniae. IMPORTANCE Bacterial mutation rate is generally low, but stress conditions and DNA damage can induce stress response systems, which allow for improved survival and continuous replication. The SOS response is a DNA repair mechanism activated by some bacteria in response to stressful conditions, which leads to a temporary hypermutable phenotype and is usually absent in streptococcal genomes. Here, using a reproducible and controlled UV irradiation system, we demonstrated that the SOS-like gene cassette of prophage Φ1207.3 is functional, responsible for a temporary hypermutable phenotype, and enhances bacterial survival to UV irradiation. Prophage Φ1207.3 also carries erythromycin resistance genes and can lysogenize different pathogenic bacteria, constituting an example of a mobile genetic element which can confer multiple phenotypes to its host.
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Affiliation(s)
- Valeria Fox
- Laboratory of Molecular Microbiology and Biotechnology, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Francesco Santoro
- Laboratory of Molecular Microbiology and Biotechnology, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Carmen Apicella
- Laboratory of Molecular Microbiology and Biotechnology, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Sara Diaz-Diaz
- Unidad Clínica de Enfermedades Infecciosas, Microbiología y Medicina Preventiva, Hospital Universitario Virgen Macarena, Sevilla, Spain
| | | | - Francesco Iannelli
- Laboratory of Molecular Microbiology and Biotechnology, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Gianni Pozzi
- Laboratory of Molecular Microbiology and Biotechnology, Department of Medical Biotechnologies, University of Siena, Siena, Italy
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Cai N, Chen J, Gao N, Ni X, Lei Y, Pu W, Wang L, Che B, Fan L, Zhou W, Feng J, Wang Y, Zheng P, Sun J. Engineering of the DNA replication and repair machinery to develop binary mutators for rapid genome evolution of Corynebacterium glutamicum. Nucleic Acids Res 2023; 51:8623-8642. [PMID: 37449409 PMCID: PMC10484736 DOI: 10.1093/nar/gkad602] [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: 08/22/2022] [Revised: 06/29/2023] [Accepted: 07/06/2023] [Indexed: 07/18/2023] Open
Abstract
Corynebacterium glutamicum is an important industrial workhorse for production of amino acids and chemicals. Although recently developed genome editing technologies have advanced the rational genetic engineering of C. glutamicum, continuous genome evolution based on genetic mutators is still unavailable. To address this issue, the DNA replication and repair machinery of C. glutamicum was targeted in this study. DnaQ, the homolog of ϵ subunit of DNA polymerase III responsible for proofreading in Escherichia coli, was proven irrelevant to DNA replication fidelity in C. glutamicum. However, the histidinol phosphatase (PHP) domain of DnaE1, the α subunit of DNA polymerase III, was characterized as the key proofreading element and certain variants with PHP mutations allowed elevated spontaneous mutagenesis. Repression of the NucS-mediated post-replicative mismatch repair pathway or overexpression of newly screened NucS variants also impaired the DNA replication fidelity. Simultaneous interference with the DNA replication and repair machinery generated a binary genetic mutator capable of increasing the mutation rate by up to 2352-fold. The mutators facilitated rapid evolutionary engineering of C. glutamicum to acquire stress tolerance and protein overproduction phenotypes. This study provides efficient tools for evolutionary engineering of C. glutamicum and could inspire the development of mutagenesis strategy for other microbial hosts.
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Affiliation(s)
- Ningyun Cai
- Tianjin University of Science and Technology, Tianjin 300457, China
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Jiuzhou Chen
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Ning Gao
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaomeng Ni
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Yu Lei
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Wei Pu
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Lixian Wang
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Bin Che
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Liwen Fan
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Wenjuan Zhou
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Jinhui Feng
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Yu Wang
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
- Haihe Laboratory of Synthetic Biology, Tianjin 300308, China
| | - Ping Zheng
- Tianjin University of Science and Technology, Tianjin 300457, China
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
| | - Jibin Sun
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
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Transcription-coupled DNA repair underlies variation in persister awakening and the emergence of resistance. Cell Rep 2022; 38:110427. [PMID: 35235801 DOI: 10.1016/j.celrep.2022.110427] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 01/12/2022] [Accepted: 02/01/2022] [Indexed: 11/21/2022] Open
Abstract
Persisters constitute a population of temporarily antibiotic-tolerant variants in an isogenic bacterial population and are considered an important cause of relapsing infections. It is currently unclear how cellular damage inflicted by antibiotic action is reversed upon persister state exit and how this relates to antibiotic resistance development at the molecular level. We demonstrate that persisters, upon fluoroquinolone treatment, accumulate oxidative DNA damage, which is repaired through nucleotide excision repair. Detection of the damage occurs via transcription-coupled repair using UvrD-mediated backtracking or Mfd-controlled displacement of the RNA polymerase. This competition results in heterogeneity in persister awakening lags. Most persisters repair the oxidative DNA damage, displaying a mutation rate equal to the untreated population. However, the promutagenic factor Mfd increases the mutation rate in a persister subpopulation. Our data provide in-depth insight into the molecular mechanisms underlying persister survival and pinpoint Mfd as an important molecular factor linking persistence to resistance development.
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Abstract
Mutations conferring resistance to one antibiotic can increase (cross-resistance) or decrease (collateral sensitivity) resistance to others. Antibiotic combinations displaying collateral sensitivity could be used in treatments that slow resistance evolution. However, lab-to-clinic translation requires understanding whether collateral effects are robust across different environmental conditions. Here, we isolated and characterized resistant mutants of Escherichia coli using five antibiotics, before measuring collateral effects on resistance to other paired antibiotics. During both isolation and phenotyping, we varied conditions in ways relevant in nature (pH, temperature, and bile). This revealed that local abiotic conditions modified expression of resistance against both the antibiotic used during isolation and other antibiotics. Consequently, local conditions influenced collateral sensitivity in two ways: by favoring different sets of mutants (with different collateral sensitivities) and by modifying expression of collateral effects for individual mutants. These results place collateral sensitivity in the context of environmental variation, with important implications for translation to real-world applications. IMPORTANCE When bacteria become resistant to an antibiotic, the genetic changes involved sometimes increase (cross-resistance) or decrease (collateral sensitivity) their resistance to other antibiotics. Antibiotic combinations showing repeatable collateral sensitivity could be used in treatment to slow resistance evolution. However, collateral sensitivity interactions may depend on the local environmental conditions that bacteria experience, potentially reducing repeatability and clinical application. Here, we show that variation in local conditions (pH, temperature, and bile salts) can influence collateral sensitivity in two ways: by favoring different sets of mutants during bacterial resistance evolution (with different collateral sensitivities to other antibiotics) and by modifying expression of collateral effects for individual mutants. This suggests that translation from the lab to the clinic of new approaches exploiting collateral sensitivity will be influenced by local abiotic conditions.
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Wang X, Han X, Li C, Chen Z, Huang H, Chen J, Wu C, Fan T, Li T, Huang W, Al-Hartomy OA, Al-Ghamdi A, Wageh S, Zheng F, Al-Sehemi AG, Wang G, Xie Z, Zhang H. 2D materials for bone therapy. Adv Drug Deliv Rev 2021; 178:113970. [PMID: 34509576 DOI: 10.1016/j.addr.2021.113970] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 08/24/2021] [Accepted: 09/07/2021] [Indexed: 12/12/2022]
Abstract
Due to their prominent physicochemical properties, 2D materials are broadly applied in biomedicine. Currently, 2D materials have achieved great success in treating many diseases such as cancer and tissue engineering as well as bone therapy. Based on their different characteristics, 2D materials could function in various ways in different bone diseases. Herein, the application of 2D materials in bone tissue engineering, joint lubrication, infection of orthopedic implants, bone tumors, and osteoarthritis are firstly reviewed comprehensively together. Meanwhile, different mechanisms by which 2D materials function in each disease reviewed below are also reviewed in detail, which in turn reveals the versatile functions and application of 2D materials. At last, the outlook on how to further broaden applications of 2D materials in bone therapies based on their excellent properties is also discussed.
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Affiliation(s)
- Xiangjiang Wang
- The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan 511518, Guangdong, China
| | - Xianjing Han
- The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan 511518, Guangdong, China
| | - Chaozhou Li
- Shenzhen Engineering Laboratory of Phosphorene and Optoelectronics, International Collaborative Laboratory of 2D Materials for Optoelectronics Science and Technology of Ministry of Education, College of Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Zhi Chen
- Shenzhen Engineering Laboratory of Phosphorene and Optoelectronics, International Collaborative Laboratory of 2D Materials for Optoelectronics Science and Technology of Ministry of Education, College of Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Hao Huang
- Shenzhen Engineering Laboratory of Phosphorene and Optoelectronics, International Collaborative Laboratory of 2D Materials for Optoelectronics Science and Technology of Ministry of Education, College of Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Jindong Chen
- The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan 511518, Guangdong, China
| | - Chenshuo Wu
- Shenzhen Engineering Laboratory of Phosphorene and Optoelectronics, International Collaborative Laboratory of 2D Materials for Optoelectronics Science and Technology of Ministry of Education, College of Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Taojian Fan
- College of Health Science and Environmental Engineering, Shenzhen Technology University, Shenzhen 518118, China
| | - Tianzhong Li
- Shenzhen International Institute for Biomedical Research, Shenzhen 518116, Guangdong, China
| | - Weichun Huang
- Nantong Key Lab of Intelligent and New Energy Materials, School of Chemistry and Chemical Engineering, Nantong University, Nantong 226019, Jiangsu, PR China
| | - Omar A Al-Hartomy
- Department of Physics, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Ahmed Al-Ghamdi
- Department of Physics, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Swelm Wageh
- Department of Physics, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Fei Zheng
- Shenzhen Engineering Laboratory of Phosphorene and Optoelectronics, International Collaborative Laboratory of 2D Materials for Optoelectronics Science and Technology of Ministry of Education, College of Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Abdullah G Al-Sehemi
- Department of Chemistry, Faculty of Science, Research Center for Advanced Materials Science (RCAMS), King Khalid University, Abha 61413, P.O. Box 9004, Saudi Arabia
| | - Guiqing Wang
- The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan 511518, Guangdong, China
| | - Zhongjian Xie
- Institute of Pediatrics, Shenzhen Children's Hospital, Shenzhen 518038, Guangdong, PR China; Shenzhen International Institute for Biomedical Research, Shenzhen 518116, Guangdong, China
| | - Han Zhang
- Shenzhen Engineering Laboratory of Phosphorene and Optoelectronics, International Collaborative Laboratory of 2D Materials for Optoelectronics Science and Technology of Ministry of Education, College of Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China.
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Ning Q, Wang D, You J. Joint effects of antibiotics and quorum sensing inhibitors on resistance development in bacteria. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2021; 23:995-1005. [PMID: 34060581 DOI: 10.1039/d1em00047k] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Quorum sensing inhibitors (QSIs) are promising alternatives to antibiotics. While QSIs have great application potential in a variety of fields, their joint effects with antibiotics on bacteria, especially on antibiotic resistance mutations, remain largely unexplored. Herein, we report the joint effects of four commonly used antibiotics and two QSIs on bacterial growth and resistance mutations in E. coli. It was found that QSIs presented antagonistic or additive effects with antibiotics on bacterial growth, and more importantly, QSIs exhibited an attenuating effect on antibiotic-induced resistance mutations. Further analysis demonstrated that antibiotics might enhance resistance mutations by promoting the expressions of rpoS, lexA and recA, while QSIs attenuated the mutations by promoting the expressions of mutS and uvrD. The present research provides a comprehensive understanding of the joint effects of antibiotics and QSIs on bacteria, which may benefit the risk assessment of their combined exposure.
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Affiliation(s)
- Qing Ning
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 511443, China.
| | - Dali Wang
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 511443, China.
| | - Jing You
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 511443, China.
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Jánošíková L, Pálková L, Šalát D, Klepanec A, Soltys K. Response of Escherichia coli minimal ter operon to UVC and auto-aggregation: pilot study. PeerJ 2021; 9:e11197. [PMID: 34026346 PMCID: PMC8123226 DOI: 10.7717/peerj.11197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 03/09/2021] [Indexed: 11/20/2022] Open
Abstract
Aim The study of minimal ter operon as a determinant of tellurium resistance (TeR) is important for the purpose of confirming the relationship of these genes to the pathogenicity of microorganisms. The ter operon is widespread among bacterial species and pathogens, implicated also in phage inhibition, oxidative stress and colicin resistance. So far, there is no experimental evidence for the role of the Escherichia coli (E. coli) minimal ter operon in ultraviolet C (UVC) resistance, biofilm formation and auto-aggregation. To identify connection with UVC resistance of the minimal ter operon, matched pairs of Ter-positive and -negative E. coli cells were stressed and differences in survival and whole genome sequence analysis were performed. This study was aimed also to identify differences in phenotype of cells induced by environmental stress. Methods In the current study, a minimal ter operon(terBCDEΔF) originating from the uropathogenic strain E. coli KL53 was used. Clonogenic assay was the method of choice to determine cell reproductive death after treatment with UVC irradiation at certain time intervals. Bacterial suspensions were irradiated with 254 nm UVC-light (germicidal lamp in biological safety cabinet) in vitro. UVC irradiance output was 2.5 mW/cm2 (calculated at the UVC device aperture) and plate-lamp distance of 60 cm. DNA damage analysis was performed using shotgun sequencing on Illumina MiSeq platform. Biofilm formation was measured by a crystal violet retention assay. Auto-aggregation assay was performed according to the Ghane, Babaeekhou & Ketabi (2020). Results A large fraction of Ter-positive E. coli cells survived treatment with 120-s UVC light (300 mJ/cm2) compared to matched Ter-negative cells; ∼5-fold higher resistance of Ter-positive cells to UVC dose (p = 0.0007). Moreover, UVC surviving Ter-positive cells showed smaller mutation rate as Ter-negative cells. The study demonstrated that a 1200-s exposure to UVC (3,000 mJ/cm2) was sufficient for 100% inhibition of growth for all the Ter-positive and -negative E. coli cells. The Ter-positive strain exhibited of 26% higher auto-aggregation activities and was able to inhibit biofilm formation over than Ter- negative strain (**** P < 0.0001). Conclusion Our study shows that Ter-positive cells display lower sensitivity to UVC radiation, corresponding to a presence in minimal ter operon. In addition, our study suggests that also auto-aggregation ability is related to minimal ter operon. The role of the minimal ter operon (terBCDEΔF) in resistance behavior of E. coli under environmental stress is evident.
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Affiliation(s)
- Lenka Jánošíková
- Faculty of Health Sciences, University of St. Cyril and Methodius in Trnava, Trnava, Slovak Republic
| | | | - Dušan Šalát
- Faculty of Health Sciences, University of St. Cyril and Methodius in Trnava, Trnava, Slovak Republic
| | - Andrej Klepanec
- Faculty of Health Sciences, University of St. Cyril and Methodius in Trnava, Trnava, Slovak Republic
| | - Katarina Soltys
- Department of Microbiology and Virology, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovak Republic.,Comenius University Science Park, Comenius University in Bratislava, Bratislava, Slovak Republic
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Ma P, He LL, Pironti A, Laibinis HH, Ernst CM, Manson AL, Bhattacharyya RP, Earl AM, Livny J, Hung DT. Genetic determinants facilitating the evolution of resistance to carbapenem antibiotics. eLife 2021; 10:e67310. [PMID: 33871353 PMCID: PMC8079144 DOI: 10.7554/elife.67310] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 04/15/2021] [Indexed: 02/07/2023] Open
Abstract
In this era of rising antibiotic resistance, in contrast to our increasing understanding of mechanisms that cause resistance, our understanding of mechanisms that influence the propensity to evolve resistance remains limited. Here, we identified genetic factors that facilitate the evolution of resistance to carbapenems, the antibiotic of 'last resort', in Klebsiella pneumoniae, the major carbapenem-resistant species. In clinical isolates, we found that high-level transposon insertional mutagenesis plays an important role in contributing to high-level resistance frequencies in several major and emerging carbapenem-resistant lineages. A broader spectrum of resistance-conferring mutations for select carbapenems such as ertapenem also enables higher resistance frequencies and, importantly, creates stepping-stones to achieve high-level resistance to all carbapenems. These mutational mechanisms can contribute to the evolution of resistance, in conjunction with the loss of systems that restrict horizontal resistance gene uptake, such as the CRISPR-Cas system. Given the need for greater antibiotic stewardship, these findings argue that in addition to considering the current efficacy of an antibiotic for a clinical isolate in antibiotic selection, considerations of future efficacy are also important. The genetic background of a clinical isolate and the exact antibiotic identity can and should also be considered as they are determinants of a strain's propensity to become resistant. Together, these findings thus provide a molecular framework for understanding acquisition of carbapenem resistance in K. pneumoniae with important implications for diagnosing and treating this important class of pathogens.
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Affiliation(s)
- Peijun Ma
- The Broad Institute of MIT and HarvardCambridgeUnited States
- Department of Molecular Biology, Massachusetts General HospitalBostonUnited States
- Department of Genetics, Harvard Medical SchoolBostonUnited States
- Center for Computational and Integrative Biology, Massachusetts General HospitalBostonUnited States
| | - Lorrie L He
- The Broad Institute of MIT and HarvardCambridgeUnited States
| | | | | | - Christoph M Ernst
- The Broad Institute of MIT and HarvardCambridgeUnited States
- Department of Molecular Biology, Massachusetts General HospitalBostonUnited States
- Department of Genetics, Harvard Medical SchoolBostonUnited States
- Center for Computational and Integrative Biology, Massachusetts General HospitalBostonUnited States
| | | | - Roby P Bhattacharyya
- The Broad Institute of MIT and HarvardCambridgeUnited States
- Division of Infectious Diseases, Massachusetts General HospitalBostonUnited States
| | - Ashlee M Earl
- The Broad Institute of MIT and HarvardCambridgeUnited States
| | - Jonathan Livny
- The Broad Institute of MIT and HarvardCambridgeUnited States
| | - Deborah T Hung
- The Broad Institute of MIT and HarvardCambridgeUnited States
- Department of Molecular Biology, Massachusetts General HospitalBostonUnited States
- Department of Genetics, Harvard Medical SchoolBostonUnited States
- Center for Computational and Integrative Biology, Massachusetts General HospitalBostonUnited States
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10
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Santos J, Moschetta M, Rodrigues J, Alpuim P, Capasso A. Interactions Between 2D Materials and Living Matter: A Review on Graphene and Hexagonal Boron Nitride Coatings. Front Bioeng Biotechnol 2021; 9:612669. [PMID: 33585432 PMCID: PMC7873463 DOI: 10.3389/fbioe.2021.612669] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 01/04/2021] [Indexed: 12/24/2022] Open
Abstract
Two-dimensional material (2DM) coatings exhibit complex and controversial interactions with biological matter, having shown in different contexts to induce bacterial cell death and contribute to mammalian cell growth and proliferation in vitro and tissue differentiation in vivo. Although several reports indicate that the morphologic and electronic properties of the coating, as well as its surface features (e.g., crystallinity, wettability, and chemistry), play a key role in the biological interaction, these kinds of interactions have not been fully understood yet. In this review, we report and classify the cellular interaction mechanisms observed in graphene and hexagonal boron nitride (hBN) coatings. Graphene and hBN were chosen as study materials to gauge the effect of two atomic-thick coatings with analogous lattice structure yet dissimilar electrical properties upon contact with living matter, allowing to discern among the observed effects and link them to specific material properties. In our analysis, we also considered the influence of crystallinity and surface roughness, detailing the mechanisms of interaction that make specific coatings of these 2DMs either hostile toward bacterial cells or innocuous for mammalian cells. In doing this, we discriminate among the material and surface properties, which are often strictly connected to the 2DM production technique, coating deposition and post-processing method. Building on this knowledge, the selection of 2DM coatings based on their specific characteristics will allow to engineer desired functionalities and devices. Antibacterial coatings to prevent biofouling, biocompatible platforms suitable for biomedical applications (e.g., wound healing, tissue repairing and regeneration, and novel biosensing devices) could be realized in the next future. Overall, a clear understanding on how the 2DM coating's properties may modulate a specific bacterial or cellular response is crucial for any future innovation in the field.
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Affiliation(s)
- João Santos
- International Iberian Nanotechnology Laboratory, Braga, Portugal
| | - Matteo Moschetta
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Genova, Italy
| | - João Rodrigues
- International Iberian Nanotechnology Laboratory, Braga, Portugal
| | - Pedro Alpuim
- International Iberian Nanotechnology Laboratory, Braga, Portugal
- Centro de Física das Universidades do Minho e do Porto, Braga, Portugal
| | - Andrea Capasso
- International Iberian Nanotechnology Laboratory, Braga, Portugal
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Gerstein AC, Sharp NP. The population genetics of ploidy change in unicellular fungi. FEMS Microbiol Rev 2021; 45:6121427. [PMID: 33503232 DOI: 10.1093/femsre/fuab006] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 01/14/2021] [Indexed: 12/23/2022] Open
Abstract
Changes in ploidy are a significant type of genetic variation, describing the number of chromosome sets per cell. Ploidy evolves in natural populations, clinical populations, and lab experiments, particularly in fungi. Despite a long history of theoretical work on this topic, predicting how ploidy will evolve has proven difficult, as it is often unclear why one ploidy state outperforms another. Here, we review what is known about contemporary ploidy evolution in diverse fungal species through the lens of population genetics. As with typical genetic variants, ploidy evolution depends on the rate that new ploidy states arise by mutation, natural selection on alternative ploidy states, and random genetic drift. However, ploidy variation also has unique impacts on evolution, with the potential to alter chromosomal stability, the rate and patterns of point mutation, and the nature of selection on all loci in the genome. We discuss how ploidy evolution depends on these general and unique factors and highlight areas where additional experimental evidence is required to comprehensively explain the ploidy transitions observed in the field and the lab.
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Affiliation(s)
- Aleeza C Gerstein
- Dept. of Microbiology, Dept. of Statistics, University of Manitoba Canada
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12
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Pieranski M, Sitkiewicz I, Grinholc M. Increased photoinactivation stress tolerance of Streptococcus agalactiae upon consecutive sublethal phototreatments. Free Radic Biol Med 2020; 160:657-669. [PMID: 32916279 DOI: 10.1016/j.freeradbiomed.2020.09.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 08/24/2020] [Accepted: 09/02/2020] [Indexed: 02/08/2023]
Abstract
Streptococcus agalactiae (Group B Streptococcus, GBS) is a common commensal bacterium in adults but remains a leading source of invasive infections in newborns, pregnant women, and the elderly, and more recently, causes an increased incidence of invasive disease in nonpregnant adults. Reduced penicillin susceptibility and emerging resistance to non-β-lactams pose challenges for the development and implementation of novel, nonantimicrobial strategies to reduce the burden of GBS infections. Antimicrobial photodynamic inactivation (aPDI) via the production of singlet oxygen or other reactive oxygen species leads to the successful eradication of pathogenic bacteria, affecting numerous cellular targets of microbial pathogens and indicating a low risk of resistance development. Nevertheless, we have previously reported possible aPDI tolerance development upon repeated sublethal aPDI applications; thus, the current work was aimed at investigating whether aPDI tolerance could be observed for GBS and what mechanisms could cause it. To address this problem, 10 cycles of sublethal aPDI treatments employing rose bengal as a photosensitizer, were applied to the S. agalactiae ATCC 27956 reference strain and two clinical isolates (2306/02 and 2974/07, serotypes III and V, respectively). We demonstrated aPDI tolerance development and stability after 5 cycles of subculturing with no aPDI exposure. Though the treatment resulted in a stable phenotype, no increases in mutation rate or accumulated genetic alterations were observed (employing a RIF-, CIP-, STR-resistant mutant selection assay and cyl sequencing, respectively). qRT-PCR analysis demonstrated that 10 sublethal aPDI exposures led to increased expression of all tested major oxidative stress response elements; changes in sodA, ahpC, npx, cylE, tpx and recA expression indicate possible mechanisms of developed tolerance. Increased expression upon sublethal aPDI treatment was reported for all but two genes, namely, ahpC and cylE. aPDI targeting cylE was further supported by colony morphology changes induced with 10 cycles of aPDI (increased SCV population, increased hemolysis, increased numbers of dark- and unpigmented colonies). In oxidant killing assays, aPDI-tolerant strains demonstrated no increased tolerance to hypochlorite, superoxide (paraquat), singlet oxygen (new methylene blue) or oxidative stress induced by aPDI employing a structurally different photosensitizer, i.e., zinc phthalocyanine, indicating a lack of cross resistance. The results indicate that S. agalactiae may develop stable aPDI tolerance but not resistance when subjected to multiple sublethal phototreatments, and this risk should be considered significant when defining efficient anti-S. agalactiae aPDI protocols.
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Affiliation(s)
- Michal Pieranski
- Intercollegiate Faculty of Biotechnology, Laboratory of Molecular Diagnostics, University of Gdansk and Medical University of Gdansk, Abrahama 58, 80-307, Gdansk, Poland
| | - Izabela Sitkiewicz
- Department of Drug Biotechnology and Bioinformatics, National Medicines Institute, Chelmska 30/34, 00-725, Warszawa, Poland
| | - Mariusz Grinholc
- Intercollegiate Faculty of Biotechnology, Laboratory of Molecular Diagnostics, University of Gdansk and Medical University of Gdansk, Abrahama 58, 80-307, Gdansk, Poland.
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13
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Yu T, Jiang G, Gao R, Chen G, Ren Y, Liu J, van der Mei HC, Busscher HJ. Circumventing antimicrobial-resistance and preventing its development in novel, bacterial infection-control strategies. Expert Opin Drug Deliv 2020; 17:1151-1164. [PMID: 32510243 DOI: 10.1080/17425247.2020.1779697] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
INTRODUCTION Development of new antimicrobials with ever 'better' bacterial killing has long been considered the appropriate response to the growing threat of antimicrobial-resistant infections. However, the time-period between the introduction of a new antibiotic and the appearance of resistance amongst bacterial pathogens is getting shorter and shorter. This suggests that alternative pathways than making ever 'better' antimicrobials should be taken. AREAS COVERED This review aims to answer the questions (1) whether we have means to circumvent existing antibiotic-resistance mechanisms, (2) whether we can revert existing antibiotic-resistance, (3) how we can prevent the development of antimicrobial-resistance against novel infection-control strategies, including nano-antimicrobials. EXPERT OPINION Relying on relieving antibiotic-pressure and natural outcompeting of antimicrobial-resistant bacteria seems an uncertain way out of the antibiotic-crisis facing us. Novel, non-antibiotic, nanotechnology-based infection control-strategies are promising. At the same time, rapid development of new resistance mechanisms once novel strategies is taken into global clinical use, may not be ruled out and must be closely monitored. This suggests focusing research and development on designing suitable combinations of existing antibiotics with new nano-antimicrobials in a way that induction of new antimicrobial-resistance mechanisms is avoided. The latter suggestion, however, requires a change of focus in research and development.
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Affiliation(s)
- Tianrong Yu
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Collaborative Innovation Center of Suzhou Nano Science and Technology, Soochow University , Jiangsu, P. R. China.,Department of Biomedical Engineering, University of Groningen and University Medical Center , Groningen, The Netherlands
| | - Guimei Jiang
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Collaborative Innovation Center of Suzhou Nano Science and Technology, Soochow University , Jiangsu, P. R. China.,Department of Biomedical Engineering, University of Groningen and University Medical Center , Groningen, The Netherlands
| | - Ruifang Gao
- Department of Biomedical Engineering, University of Groningen and University Medical Center , Groningen, The Netherlands.,College of Chemistry, Chemical Engineering and Materials Science, Soochow University , Suzhou, P.R. China
| | - Gaojian Chen
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University , Suzhou, P.R. China
| | - Yijin Ren
- Department of Orthodontics, University of Groningen and University Medical Center of Groningen , Groningen, The Netherlands
| | - Jian Liu
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Collaborative Innovation Center of Suzhou Nano Science and Technology, Soochow University , Jiangsu, P. R. China
| | - Henny C van der Mei
- Department of Biomedical Engineering, University of Groningen and University Medical Center , Groningen, The Netherlands
| | - Henk J Busscher
- Department of Biomedical Engineering, University of Groningen and University Medical Center , Groningen, The Netherlands
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14
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Cushnie TPT, Cushnie B, Echeverría J, Fowsantear W, Thammawat S, Dodgson JLA, Law S, Clow SM. Bioprospecting for Antibacterial Drugs: a Multidisciplinary Perspective on Natural Product Source Material, Bioassay Selection and Avoidable Pitfalls. Pharm Res 2020; 37:125. [PMID: 32529587 DOI: 10.1007/s11095-020-02849-1] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 05/30/2020] [Indexed: 12/12/2022]
Abstract
Bioprospecting is the exploration, extraction and screening of biological material and sometimes indigenous knowledge to discover and develop new drugs and other products. Most antibiotics in current clinical use (eg. β-lactams, aminoglycosides, tetracyclines, macrolides) were discovered using this approach, and there are strong arguments to reprioritize bioprospecting over other strategies in the search for new antibacterial drugs. Academic institutions should be well positioned to lead the early stages of these efforts given their many thousands of locations globally and because they are not constrained by the same commercial considerations as industry. University groups can lack the full complement of knowledge and skills needed though (eg. how to tailor screening strategy to biological source material). In this article, we review three key aspects of the bioprospecting literature (source material and in vitro antibacterial and toxicity testing) and present an integrated multidisciplinary perspective on (a) source material selection, (b) legal, taxonomic and other issues related to source material, (c) cultivation methods, (d) bioassay selection, (e) technical standards available, (f) extract/compound dissolution, (g) use of minimum inhibitory concentration and selectivity index values to identify progressible extracts and compounds, and (h) avoidable pitfalls. The review closes with recommendations for future study design and information on subsequent steps in the bioprospecting process.
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Affiliation(s)
- T P Tim Cushnie
- Faculty of Medicine, Mahasarakham University, 269 Nakornsawan Road, Mahasarakham, 44000, Thailand.
| | - Benjamart Cushnie
- Faculty of Pharmacy, Mahasarakham University, Kantarawichai, Thailand
| | - Javier Echeverría
- Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Winita Fowsantear
- Faculty of Medicine, Mahasarakham University, 269 Nakornsawan Road, Mahasarakham, 44000, Thailand
| | - Sutthiwan Thammawat
- Faculty of Medicine, Mahasarakham University, 269 Nakornsawan Road, Mahasarakham, 44000, Thailand
| | | | - Samantha Law
- National Collection of Industrial, Food and Marine Bacteria (NCIMB) Ltd, Aberdeen, UK
| | - Simon M Clow
- PMI BioPharma Solutions LLC, Nashville, Tennessee, USA
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15
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Hayes AJ, Satiaputra J, Sternicki LM, Paparella AS, Feng Z, Lee KJ, Blanco-Rodriguez B, Tieu W, Eijkelkamp BA, Shearwin KE, Pukala TL, Abell AD, Booker GW, Polyak SW. Advanced Resistance Studies Identify Two Discrete Mechanisms in Staphylococcus aureus to Overcome Antibacterial Compounds that Target Biotin Protein Ligase. Antibiotics (Basel) 2020; 9:antibiotics9040165. [PMID: 32268615 PMCID: PMC7235819 DOI: 10.3390/antibiotics9040165] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 04/03/2020] [Accepted: 04/04/2020] [Indexed: 11/16/2022] Open
Abstract
Biotin protein ligase (BPL) inhibitors are a novel class of antibacterial that target clinically important methicillin-resistant Staphylococcus aureus (S. aureus). In S. aureus, BPL is a bifunctional protein responsible for enzymatic biotinylation of two biotin-dependent enzymes, as well as serving as a transcriptional repressor that controls biotin synthesis and import. In this report, we investigate the mechanisms of action and resistance for a potent anti-BPL, an antibacterial compound, biotinyl-acylsulfamide adenosine (BASA). We show that BASA acts by both inhibiting the enzymatic activity of BPL in vitro, as well as functioning as a transcription co-repressor. A low spontaneous resistance rate was measured for the compound (<10−9) and whole-genome sequencing of strains evolved during serial passaging in the presence of BASA identified two discrete resistance mechanisms. In the first, deletion of the biotin-dependent enzyme pyruvate carboxylase is proposed to prioritize the utilization of bioavailable biotin for the essential enzyme acetyl-CoA carboxylase. In the second, a D200E missense mutation in BPL reduced DNA binding in vitro and transcriptional repression in vivo. We propose that this second resistance mechanism promotes bioavailability of biotin by derepressing its synthesis and import, such that free biotin may outcompete the inhibitor for binding BPL. This study provides new insights into the molecular mechanisms governing antibacterial activity and resistance of BPL inhibitors in S. aureus.
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Affiliation(s)
- Andrew J. Hayes
- School of Biological Sciences, University of Adelaide, South Australia 5005, Australia; (A.J.H.); (J.S.); (L.M.S.); (A.S.P.); (Z.F.); (B.A.E.); (K.E.S.); (G.W.B.)
| | - Jiulia Satiaputra
- School of Biological Sciences, University of Adelaide, South Australia 5005, Australia; (A.J.H.); (J.S.); (L.M.S.); (A.S.P.); (Z.F.); (B.A.E.); (K.E.S.); (G.W.B.)
| | - Louise M. Sternicki
- School of Biological Sciences, University of Adelaide, South Australia 5005, Australia; (A.J.H.); (J.S.); (L.M.S.); (A.S.P.); (Z.F.); (B.A.E.); (K.E.S.); (G.W.B.)
| | - Ashleigh S. Paparella
- School of Biological Sciences, University of Adelaide, South Australia 5005, Australia; (A.J.H.); (J.S.); (L.M.S.); (A.S.P.); (Z.F.); (B.A.E.); (K.E.S.); (G.W.B.)
| | - Zikai Feng
- School of Biological Sciences, University of Adelaide, South Australia 5005, Australia; (A.J.H.); (J.S.); (L.M.S.); (A.S.P.); (Z.F.); (B.A.E.); (K.E.S.); (G.W.B.)
| | - Kwang J. Lee
- School of Physical Sciences, University of Adelaide, South Australia 5005, Australia; (K.J.L.); (B.B.-R.); (W.T.); (T.L.P.); (A.D.A.)
| | - Beatriz Blanco-Rodriguez
- School of Physical Sciences, University of Adelaide, South Australia 5005, Australia; (K.J.L.); (B.B.-R.); (W.T.); (T.L.P.); (A.D.A.)
| | - William Tieu
- School of Physical Sciences, University of Adelaide, South Australia 5005, Australia; (K.J.L.); (B.B.-R.); (W.T.); (T.L.P.); (A.D.A.)
| | - Bart A. Eijkelkamp
- School of Biological Sciences, University of Adelaide, South Australia 5005, Australia; (A.J.H.); (J.S.); (L.M.S.); (A.S.P.); (Z.F.); (B.A.E.); (K.E.S.); (G.W.B.)
| | - Keith E. Shearwin
- School of Biological Sciences, University of Adelaide, South Australia 5005, Australia; (A.J.H.); (J.S.); (L.M.S.); (A.S.P.); (Z.F.); (B.A.E.); (K.E.S.); (G.W.B.)
| | - Tara L. Pukala
- School of Physical Sciences, University of Adelaide, South Australia 5005, Australia; (K.J.L.); (B.B.-R.); (W.T.); (T.L.P.); (A.D.A.)
| | - Andrew D. Abell
- School of Physical Sciences, University of Adelaide, South Australia 5005, Australia; (K.J.L.); (B.B.-R.); (W.T.); (T.L.P.); (A.D.A.)
- Centre for Nanoscale BioPhotonics (CNBP), University of Adelaide, Adelaide, SA 5005, Australia
- Institute of Photonics and Advanced Sensing (IPAS), School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Grant W. Booker
- School of Biological Sciences, University of Adelaide, South Australia 5005, Australia; (A.J.H.); (J.S.); (L.M.S.); (A.S.P.); (Z.F.); (B.A.E.); (K.E.S.); (G.W.B.)
| | - Steven W. Polyak
- School of Biological Sciences, University of Adelaide, South Australia 5005, Australia; (A.J.H.); (J.S.); (L.M.S.); (A.S.P.); (Z.F.); (B.A.E.); (K.E.S.); (G.W.B.)
- Correspondence: ; Tel.: +61883021603
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16
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Overexpression of RamA, Which Regulates Production of the Multidrug Resistance Efflux Pump AcrAB-TolC, Increases Mutation Rate and Influences Drug Resistance Phenotype. Antimicrob Agents Chemother 2020; 64:AAC.02460-19. [PMID: 31988103 DOI: 10.1128/aac.02460-19] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 01/15/2020] [Indexed: 01/29/2023] Open
Abstract
In Enterobacteriales, the AcrAB-TolC efflux pump exports substrates, including antimicrobials, from the cell. Overexpression of AcrAB-TolC can occur after exposure to fluoroquinolones, leading to multidrug resistance. The expression of AcrAB-TolC in Salmonella is primarily regulated by the transcriptional activator RamA. However, other transcriptional activators, such as MarA, SoxRS, and Rob, can influence AcrAB-TolC expression. This study determined whether the overproduction or absence of RamA influences the mutation rate or the phenotype of mutants selected in Salmonella enterica serovar Typhimurium SL1344 after ciprofloxacin exposure. The absence of RamA (SL1344 ramA::aph) resulted in mutation frequencies/rates similar to those of wild-type Salmonella Typhimurium SL1344. However, the overproduction of RamA (SL1344 ramR::aph) and, consequently, AcrB resulted in a significantly higher mutation frequency and rate than for wild-type Salmonella Typhimurium SL1344. Whole-genome sequencing revealed that in addition to selecting gyrA mutants resistant to quinolones, SL1344 and SL1344 ramA::aph also produced multidrug-resistant (MDR) mutants, associated with mutations in soxR Conversely, mutations in SL1344 ramR::aph occurred in gyrA only. Although transcriptional regulators such as SoxRS are believed to play a minor role in AcrAB-TolC regulation under antibiotic selective pressure, we show that soxR mutants can be selected after exposure to ciprofloxacin, including when RamA is absent. This demonstrates that under selective pressure, Salmonella can respond to increased efflux pump expression by mutating other AcrAB-TolC regulatory genes, allowing for the evolution of MDR. Understanding how Salmonella responds to antibiotic pressure in the absence/overproduction of RamA is important if targeting transcriptional regulators to alter efflux is to be considered an avenue for future drug discovery.
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17
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Mei L, Zhu S, Yin W, Chen C, Nie G, Gu Z, Zhao Y. Two-dimensional nanomaterials beyond graphene for antibacterial applications: current progress and future perspectives. Theranostics 2020; 10:757-781. [PMID: 31903149 PMCID: PMC6929992 DOI: 10.7150/thno.39701] [Citation(s) in RCA: 99] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 09/21/2019] [Indexed: 12/12/2022] Open
Abstract
The marked augment of drug-resistance to traditional antibiotics underlines the crying need for novel replaceable antibacterials. Research advances have revealed the considerable sterilization potential of two-dimension graphene-based nanomaterials. Subsequently, two-dimensional nanomaterials beyond graphene (2D NBG) as novel antibacterials have also demonstrated their power for disinfection due to their unique physicochemical properties and good biocompatibility. Therefore, the exploration of antibacterial mechanisms of 2D NBG is vital to manipulate antibacterials for future applications. Herein, we summarize the recent research progress of 2D NBG-based antibacterial agents, starting with a detailed introduction of the relevant antibacterial mechanisms, including direct contact destruction, oxidative stress, photo-induced antibacterial, control drug/metallic ions releasing, and the multi-mode synergistic antibacterial. Then, the effect of the physicochemical properties of 2D NBG on their antibacterial activities is also discussed. Additionally, a summary of the different kinds of 2D NBG is given, such as transition-metal dichalcogenides/oxides, metal-based compounds, nitride-based nanomaterials, black phosphorus, transition metal carbides, and nitrides. Finally, we rationally analyze the current challenges and new perspectives for future study of more effective antibacterial agents. This review not only can help researchers grasp the current status of 2D NBG antibacterials, but also may catalyze breakthroughs in this fast-growing field.
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Affiliation(s)
- Linqiang Mei
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China
- College of Materials Science and Optoelectronic Technology, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuang Zhu
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China
| | - Wenyan Yin
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China
| | - Chunying Chen
- CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Chinese Academy of Sciences, Beijing 100190, China
| | - Guangjun Nie
- CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Chinese Academy of Sciences, Beijing 100190, China
| | - Zhanjun Gu
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China
- College of Materials Science and Optoelectronic Technology, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuliang Zhao
- CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Chinese Academy of Sciences, Beijing 100190, China
- College of Materials Science and Optoelectronic Technology, University of Chinese Academy of Sciences, Beijing 100049, China
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18
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Mutation rate and efflux response of bacteria exposed to a novel antimicrobial iodo-thiocyanate complex. J Glob Antimicrob Resist 2019; 22:13-17. [PMID: 31857249 DOI: 10.1016/j.jgar.2019.12.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 12/04/2019] [Accepted: 12/05/2019] [Indexed: 12/11/2022] Open
Abstract
OBJECTIVES Antimicrobials, at sub-lethal concentrations, can act as selectors and promoters of resistance by increasing mutation rates. We measured the rate of Escherichia coli mutation from levofloxacin (LVX) sensitivity to resistance when it was grown under the near-lethal challenge of the novel biocidal iodo-thiocyanate complex (ITC). Another relevant factor affecting the emergence of antimicrobial resistance is the role of efflux pumps. Consequently, we evaluated whether ITC could potentially be a substrate for efflux pumps, and thus that efflux-mediated resistance could arise towards ITC. METHODS The mutation rate was measured by fluctuation analysis, when multiple parallel E. coli cultures were grown in the absence and presence of ITC. Then the mutational events, which occurred independently in each culture, were scored by plating the fraction of the culture in LVX-selective solid media and compared with the total cell number. To detect if ITC is a substrate for efflux pumps, minimum inhibitory concentrations (MICs) were determined against Pseudomonas aeruginosa in the absence and presence of the efflux pump inhibitor (EPI). RESULTS We have found that the E. coli exposed to the near-lethal level of ITC had a slight, but not significant, increase in mutation rate compared with unexposed cultures. Furthermore, the presence of EPI decreased the MIC of ITC by a modest 2-fold, showing that ITC was not a target for efflux pumps. CONCLUSIONS ITC usage most likely will not promote resistance development via increased mutation rates, and efflux-mediated resistance emergence to it is less likely than for some other antimicrobials.
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Card KJ, LaBar T, Gomez JB, Lenski RE. Historical contingency in the evolution of antibiotic resistance after decades of relaxed selection. PLoS Biol 2019; 17:e3000397. [PMID: 31644535 PMCID: PMC6827916 DOI: 10.1371/journal.pbio.3000397] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 11/04/2019] [Accepted: 10/10/2019] [Indexed: 12/21/2022] Open
Abstract
Populations often encounter changed environments that remove selection for the maintenance of particular phenotypic traits. The resulting genetic decay of those traits under relaxed selection reduces an organism's fitness in its prior environment. However, whether and how such decay alters the subsequent evolvability of a population upon restoration of selection for a previously diminished trait is not well understood. We addressed this question using Escherichia coli strains from the long-term evolution experiment (LTEE) that independently evolved for multiple decades in the absence of antibiotics. We first confirmed that these derived strains are typically more sensitive to various antibiotics than their common ancestor. We then subjected the ancestral and derived strains to various concentrations of these drugs to examine their potential to evolve increased resistance. We found that evolvability was idiosyncratic with respect to initial genotype; that is, the derived strains did not generally compensate for their greater susceptibility by "catching up" to the resistance level of the ancestor. Instead, the capacity to evolve increased resistance was constrained in some backgrounds, implying that evolvability depended upon prior mutations in a historically contingent fashion. We further subjected a time series of clones from one LTEE population to tetracycline and determined that an evolutionary constraint arose early in that population, corroborating the role of contingency. In summary, relaxed selection not only can drive populations to increased antibiotic susceptibility, but it can also affect the subsequent evolvability of antibiotic resistance in an unpredictable manner. This conclusion has potential implications for public health, and it underscores the need to consider the genetic context of pathogens when designing drug-treatment strategies.
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Affiliation(s)
- Kyle J. Card
- BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, Michigan, United States of America
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, United States of America
- Program in Ecology, Evolutionary Biology, and Behavior, Michigan State University, East Lansing, Michigan, United States of America
| | - Thomas LaBar
- BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, Michigan, United States of America
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Jasper B. Gomez
- BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, Michigan, United States of America
- Biomedical Laboratory Diagnostics Program, Michigan State University, East Lansing, Michigan, United States of America
| | - Richard E. Lenski
- BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, Michigan, United States of America
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, United States of America
- Program in Ecology, Evolutionary Biology, and Behavior, Michigan State University, East Lansing, Michigan, United States of America
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20
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Rapacka-Zdonczyk A, Wozniak A, Pieranski M, Woziwodzka A, Bielawski KP, Grinholc M. Development of Staphylococcus aureus tolerance to antimicrobial photodynamic inactivation and antimicrobial blue light upon sub-lethal treatment. Sci Rep 2019; 9:9423. [PMID: 31263139 PMCID: PMC6603016 DOI: 10.1038/s41598-019-45962-x] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 06/18/2019] [Indexed: 12/31/2022] Open
Abstract
Antimicrobial photodynamic inactivation (aPDI) and antimicrobial blue light (aBL) are considered low-risk treatments for the development of bacterial resistance and/or tolerance due to their multitargeted modes of action. In this study, we assessed the development of Staphylococcus aureus tolerance to these phototreatments. Reference S. aureus USA300 JE2 was subjected to 15 cycles of both sub-lethal aPDI (employing an exogenously administered photosensitizer (PS), i.e., rose Bengal (RB)) and sub-lethal aBL (employing endogenously produced photosensitizing compounds, i.e., porphyrins). We demonstrate substantial aPDI/aBL tolerance development and tolerance stability after 5 cycles of subculturing without aPDI/aBL exposure (the development of aPDI/aBL tolerance was also confirmed with the employment of clinical MRSA and MSSA strain as well as other representatives of Gram-positive microbes, i.e. Enterococcus faecium and Streptococcus agalactiae). In addition, a rifampicin-resistant (RIFR) mutant selection assay showed an increased mutation rate in S. aureus upon sub-lethal phototreatments, indicating that the increased aPDI/aBL tolerance may result from accumulated mutations. Moreover, qRT-PCR analysis following sub-lethal phototreatments demonstrated increased expression of umuC, which encodes stress-responsive error-prone DNA polymerase V, an enzyme that increases the rate of mutation. Employment of recA and umuC transposon S. aureus mutants confirmed SOS-induction dependence of the tolerance development. Interestingly, aPDI/aBL-tolerant S. aureus exhibited increased susceptibility to gentamicin (GEN) and doxycycline (DOX), supporting the hypothesis of genetic alterations induced by sub-lethal phototreatments. The obtained results indicate that S. aureus may develop stable tolerance to studied phototreatments upon sub-lethal aPDI/aBL exposure; thus, the risk of tolerance development should be considered significant when designing aPDI/aBL protocols for infection treatments in vitro and in clinical settings.
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Affiliation(s)
- Aleksandra Rapacka-Zdonczyk
- Laboratory of Molecular Diagnostics, Department of Biotechnology, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, Poland
| | - Agata Wozniak
- Laboratory of Molecular Diagnostics, Department of Biotechnology, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, Poland
| | - Michal Pieranski
- Laboratory of Molecular Diagnostics, Department of Biotechnology, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, Poland
| | - Anna Woziwodzka
- Laboratory of Biophysics, Department of Molecular and Cellular Biology, Intercollegiate Faculty of Biotechnology University of Gdansk and Medical University of Gdansk, Gdansk, Poland
| | - Krzysztof P Bielawski
- Laboratory of Molecular Diagnostics, Department of Biotechnology, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, Poland
| | - Mariusz Grinholc
- Laboratory of Molecular Diagnostics, Department of Biotechnology, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, Poland.
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21
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Hajian B, Scocchera E, Shoen C, Krucinska J, Viswanathan K, G-Dayanandan N, Erlandsen H, Estrada A, Mikušová K, Korduláková J, Cynamon M, Wright D. Drugging the Folate Pathway in Mycobacterium tuberculosis: The Role of Multi-targeting Agents. Cell Chem Biol 2019; 26:781-791.e6. [PMID: 30930162 DOI: 10.1016/j.chembiol.2019.02.013] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 01/22/2019] [Accepted: 02/24/2019] [Indexed: 01/19/2023]
Abstract
The folate biosynthetic pathway offers many druggable targets that have yet to be exploited in tuberculosis therapy. Herein, we have identified a series of small molecules that interrupt Mycobacterium tuberculosis (Mtb) folate metabolism by dual targeting of dihydrofolate reductase (DHFR), a key enzyme in the folate pathway, and its functional analog, Rv2671. We have also compared the antifolate activity of these compounds with that of para-aminosalicylic acid (PAS). We found that the bioactive metabolite of PAS, in addition to previously reported activity against DHFR, inhibits flavin-dependent thymidylate synthase in Mtb, suggesting a multi-targeted mechanism of action for this drug. Finally, we have shown that antifolate treatment in Mtb decreases the production of mycolic acids, most likely due to perturbation of the activated methyl cycle. We conclude that multi-targeting of the folate pathway in Mtb is associated with highly potent anti-mycobacterial activity.
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Affiliation(s)
- Behnoush Hajian
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT 06269, USA
| | - Eric Scocchera
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT 06269, USA
| | | | - Jolanta Krucinska
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT 06269, USA
| | - Kishore Viswanathan
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT 06269, USA
| | | | - Heidi Erlandsen
- Center for Open Research Resources and Equipment, University of Connecticut, Storrs, CT 06269, USA
| | - Alexavier Estrada
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT 06269, USA
| | - Katarína Mikušová
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Mlynská Dolina CH-1, Ilkovičova 6, 842 15, Bratislava, Slovakia
| | - Jana Korduláková
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Mlynská Dolina CH-1, Ilkovičova 6, 842 15, Bratislava, Slovakia
| | | | - Dennis Wright
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT 06269, USA.
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22
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Brockhurst MA, Harrison F, Veening JW, Harrison E, Blackwell G, Iqbal Z, Maclean C. Assessing evolutionary risks of resistance for new antimicrobial therapies. Nat Ecol Evol 2019; 3:515-517. [DOI: 10.1038/s41559-019-0854-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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23
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Nyinoh IW. Spontaneous mutations conferring antibiotic resistance to antitubercular drugs at a range of concentrations in Mycobacterium smegmatis. Drug Dev Res 2018; 80:147-154. [PMID: 30511362 DOI: 10.1002/ddr.21497] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Revised: 11/07/2018] [Accepted: 11/09/2018] [Indexed: 11/06/2022]
Abstract
Mycobacteria populations can undergo mutations in their DNA sequence during replication, which if not repaired would be transferred to future generations. Earlier studies have tackled the estimation of mutation rate in mycobacteria at fixed concentrations. However, in this study, in vitro spontaneous mutations in Mycobacterium smegmatis (Msm) mc2 155 (Msm) that confers resistance to some of the most important antitubercular drugs; isoniazid (INHr ), rifampicin (RIFr ), kanamycin (KANr ) and streptomycin (STRr ) were first determined at several highly lethal concentrations, a few of which have not been previously investigated, in a fluctuation assay. Thereafter, mutation rate was estimated using the most commonly adopted Po method, and estimates were then compared concurrently with the Lea-Coulson method of the median and Ma-Sandri-Sarkar Maximum Likelihood Estimator method available on the Fluctuation AnaLysis CalculatOR (FALCOR). The mutation rates of RIFr ranged from 9.24 × 10-8 to 2.18 × 10-10 , INHr 1.2 × 10-7 -1.20 × 10-9 , STRr 2.77 × 10-8 -5.31 × 10-8 and KANr 1.7 × 10-8 mutations per cell division. Data obtained in this study provide mutation rate estimates to key antitubercular drugs at a range of concentrations while also validating a number of the frequent approaches for estimating mutation rates.
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Affiliation(s)
- Iveren Winifred Nyinoh
- Department of Biological Sciences, Benue State University, Makurdi, Benue State, Nigeria
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24
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Johnston T, Van Tyne D, Chen RF, Fawzi NL, Kwon B, Kelso MJ, Gilmore MS, Mylonakis E. Propyl-5-hydroxy-3-methyl-1-phenyl-1H-pyrazole-4-carbodithioate (HMPC): a new bacteriostatic agent against methicillin-resistant Staphylococcus aureus. Sci Rep 2018; 8:7062. [PMID: 29728636 PMCID: PMC5935714 DOI: 10.1038/s41598-018-25571-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 04/20/2018] [Indexed: 01/03/2023] Open
Abstract
The emergence of Staphylococcus aureus strains resistant to ‘last resort’ antibiotics compels the development of new antimicrobials against this important human pathogen. We found that propyl 5-hydroxy-3-methyl-1-phenyl-1H-pyrazole-4-carbodithioate (HMPC) shows bacteriostatic activity against S. aureus (MIC = 4 μg/ml) and rescues Caenorhabditis elegans from S. aureus infection. Whole-genome sequencing of S. aureus mutants resistant to the compound, along with screening of a S. aureus promoter-lux reporter array, were used to explore possible mechanisms of action. All mutants resistant to HMPC acquired missense mutations at distinct codon positions in the global transcriptional regulator mgrA, followed by secondary mutations in the phosphatidylglycerol lysyltransferase fmtC/mprF. The S. aureus promoter-lux array treated with HMPC displayed a luminescence profile that was unique but showed similarity to DNA-damaging agents and/or DNA replication inhibitors. Overall, HMPC is a new anti-staphylococcal compound that appears to act via an unknown mechanism linked to the global transcriptional regulator MgrA.
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Affiliation(s)
- Tatiana Johnston
- Department of Infectious Disease, Rhode Island Hospital, Alpert Medical School of Brown University, Providence, Rhode Island, USA
| | - Daria Van Tyne
- Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts, USA.,Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Roy F Chen
- Department of Infectious Disease, Rhode Island Hospital, Alpert Medical School of Brown University, Providence, Rhode Island, USA
| | - Nicolas L Fawzi
- Department of Molecular Pharmacology, Physiology, and Biotechnology, Brown University, Providence, Rhode Island, USA
| | - Bumsup Kwon
- Department of Neurology, Rhode Island Hospital, Warren Alpert Medical School of Brown University, Providence, RI, 02903, USA
| | - Michael J Kelso
- School of Chemistry and Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Michael S Gilmore
- Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts, USA.,Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Eleftherios Mylonakis
- Department of Infectious Disease, Rhode Island Hospital, Alpert Medical School of Brown University, Providence, Rhode Island, USA.
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25
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Kunrath-Lima M, Repolês BM, Alves CL, Furtado C, Rajão MA, Macedo AM, Franco GR, Pena SDJ, Valenzuela L, Wisnovsky S, Kelley SO, Galanti N, Cabrera G, Machado CR. Characterization of Trypanosoma cruzi MutY DNA glycosylase ortholog and its role in oxidative stress response. INFECTION GENETICS AND EVOLUTION 2017; 55:332-342. [PMID: 28970112 DOI: 10.1016/j.meegid.2017.09.030] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 09/25/2017] [Accepted: 09/26/2017] [Indexed: 12/11/2022]
Abstract
Trypanosoma cruzi is a protozoan parasite and the causative agent of Chagas disease. Like most living organisms, it is susceptible to oxidative stress, and must adapt to distinct environments. Hence, DNA repair is essential for its survival and the persistence of infection. Therefore, we studied whether T. cruzi has a homolog counterpart of the MutY enzyme (TcMYH), important in the DNA Base Excision Repair (BER) mechanism. Analysis of T. cruzi genome database showed that this parasite has a putative MutY DNA glycosylase sequence. We performed heterologous complementation assays using this genomic sequence. TcMYH complemented the Escherichia coli MutY- strain, reducing the mutation rate to a level similar to wild type. In in vitro assays, TcMYH was able to remove an adenine that was opposite to 8-oxoguanine. We have also constructed a T. cruzi lineage that overexpresses MYH. Although in standard conditions this lineage has similar growth to control cells, the overexpressor is more sensitive to hydrogen peroxide and glucose oxidase than the control, probably due to accumulation of AP sites in its DNA. Localization experiments with GFP-fused TcMYH showed this enzyme is present in both nucleus and mitochondrion. QPCR and MtOX results reinforce the presence and function of TcMYH in these two organelles. Our data suggest T. cruzi has a functional MYH DNA glycosylase, which participates in nuclear and mitochondrial DNA Base Excision Repair.
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Affiliation(s)
- Marianna Kunrath-Lima
- Departamento de Bioquímica e Imunologia, ICB, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Caixa Postal 486, Belo Horizonte 30161-970, MG, Brazil
| | - Bruno Marçal Repolês
- Departamento de Bioquímica e Imunologia, ICB, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Caixa Postal 486, Belo Horizonte 30161-970, MG, Brazil
| | - Ceres Luciana Alves
- Departamento de Bioquímica e Imunologia, ICB, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Caixa Postal 486, Belo Horizonte 30161-970, MG, Brazil
| | - Carolina Furtado
- Departamento de Bioquímica e Imunologia, ICB, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Caixa Postal 486, Belo Horizonte 30161-970, MG, Brazil
| | - Matheus Andrade Rajão
- Departamento de Bioquímica e Imunologia, ICB, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Caixa Postal 486, Belo Horizonte 30161-970, MG, Brazil
| | - Andrea Mara Macedo
- Departamento de Bioquímica e Imunologia, ICB, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Caixa Postal 486, Belo Horizonte 30161-970, MG, Brazil
| | - Glória Regina Franco
- Departamento de Bioquímica e Imunologia, ICB, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Caixa Postal 486, Belo Horizonte 30161-970, MG, Brazil.
| | - Sérgio Danilo Junho Pena
- Departamento de Bioquímica e Imunologia, ICB, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Caixa Postal 486, Belo Horizonte 30161-970, MG, Brazil.
| | - Lucía Valenzuela
- Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Simon Wisnovsky
- Department of Biochemistry, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Shana O Kelley
- Department of Biochemistry, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada.
| | - Norbel Galanti
- Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile.
| | - Gonzalo Cabrera
- Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile.
| | - Carlos Renato Machado
- Departamento de Bioquímica e Imunologia, ICB, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Caixa Postal 486, Belo Horizonte 30161-970, MG, Brazil.
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26
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Engineering a riboswitch-based genetic platform for the self-directed evolution of acid-tolerant phenotypes. Nat Commun 2017; 8:411. [PMID: 28871084 PMCID: PMC5583362 DOI: 10.1038/s41467-017-00511-w] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 07/05/2017] [Indexed: 12/12/2022] Open
Abstract
Environmental pH is a fundamental signal continuously directing the metabolism and behavior of living cells. Programming the precise cellular response toward environmental pH is, therefore, crucial for engineering cells for increasingly sophisticated functions. Herein, we engineer a set of riboswitch-based pH-sensing genetic devices to enable the control of gene expression according to differential environmental pH. We next develop a digital pH-sensing system to utilize the analogue-sensing behavior of these devices for high-resolution recording of host cell exposure to discrete external pH levels. The application of this digital pH-sensing system is demonstrated in a genetic program that autonomously regulated the evolutionary engineering of host cells for improved tolerance to a broad spectrum of organic acids, a valuable phenotype for metabolic engineering and bioremediation applications. Cells are exposed to shifts in environmental pH, which direct their metabolism and behavior. Here the authors design pH-sensing riboswitches to create a gene expression program, digitalize the system to respond to a narrow pH range and apply it to evolve host cells with improved tolerance to a variety of organic acids.
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27
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Hirmondo R, Lopata A, Suranyi EV, Vertessy BG, Toth J. Differential control of dNTP biosynthesis and genome integrity maintenance by the dUTPase superfamily enzymes. Sci Rep 2017; 7:6043. [PMID: 28729658 PMCID: PMC5519681 DOI: 10.1038/s41598-017-06206-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 06/12/2017] [Indexed: 01/22/2023] Open
Abstract
dUTPase superfamily enzymes generate dUMP, the obligate precursor for de novo dTTP biosynthesis, from either dUTP (monofunctional dUTPase, Dut) or dCTP (bifunctional dCTP deaminase/dUTPase, Dcd:dut). In addition, the elimination of dUTP by these enzymes prevents harmful uracil incorporation into DNA. These two beneficial outcomes have been thought to be related. Here we determined the relationship between dTTP biosynthesis (dTTP/dCTP balance) and the prevention of DNA uracilation in a mycobacterial model that encodes both the Dut and Dcd:dut enzymes, and has no other ways to produce dUMP. We show that, in dut mutant mycobacteria, the dTTP/dCTP balance remained unchanged, but the uracil content of DNA increased in parallel with the in vitro activity-loss of Dut accompanied with a considerable increase in the mutation rate. Conversely, dcd:dut inactivation resulted in perturbed dTTP/dCTP balance and two-fold increased mutation rate, but did not increase the uracil content of DNA. Thus, unexpectedly, the regulation of dNTP balance and the prevention of DNA uracilation are decoupled and separately brought about by the Dcd:dut and Dut enzymes, respectively. Available evidence suggests that the discovered functional separation is conserved in humans and other organisms.
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Affiliation(s)
- Rita Hirmondo
- Institute of Enzymology, RCNS, Hungarian Academy of Sciences, Budapest, Hungary
| | - Anna Lopata
- Institute of Enzymology, RCNS, Hungarian Academy of Sciences, Budapest, Hungary
| | - Eva Viola Suranyi
- Institute of Enzymology, RCNS, Hungarian Academy of Sciences, Budapest, Hungary
- Department of Applied Biotechnology, Budapest University of Technology and Economics, Budapest, Hungary
| | - Beata G Vertessy
- Institute of Enzymology, RCNS, Hungarian Academy of Sciences, Budapest, Hungary
- Department of Applied Biotechnology, Budapest University of Technology and Economics, Budapest, Hungary
| | - Judit Toth
- Institute of Enzymology, RCNS, Hungarian Academy of Sciences, Budapest, Hungary.
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28
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Mazoyer A, Ycart B, Veziris N. Correction: Unbiased Estimation of Mutation Rates under Fluctuating Final Counts. PLoS One 2017; 12:e0173143. [PMID: 28288161 PMCID: PMC5347993 DOI: 10.1371/journal.pone.0173143] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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29
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Pompilio A, Crocetta V, Ghosh D, Chakrabarti M, Gherardi G, Vitali LA, Fiscarelli E, Di Bonaventura G. Stenotrophomonas maltophilia Phenotypic and Genotypic Diversity during a 10-year Colonization in the Lungs of a Cystic Fibrosis Patient. Front Microbiol 2016; 7:1551. [PMID: 27746770 PMCID: PMC5044509 DOI: 10.3389/fmicb.2016.01551] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 09/15/2016] [Indexed: 11/25/2022] Open
Abstract
The present study was carried out to understand the adaptive strategies developed by Stenotrophomonas maltophilia for chronic colonization of the cystic fibrosis (CF) lung. For this purpose, 13 temporally isolated strains from a single CF patient chronically infected over a 10-year period were systematically characterized for growth rate, biofilm formation, motility, mutation frequencies, antibiotic resistance, and pathogenicity. Pulsed-field gel electrophoresis (PFGE) showed over time the presence of two distinct groups, each consisting of two different pulsotypes. The pattern of evolution followed by S. maltophilia was dependent on pulsotype considered, with strains belonging to pulsotype 1.1 resulting to be the most adapted, being significantly changed in all traits considered. Generally, S. maltophilia adaptation to CF lung leads to increased growth rate and antibiotic resistance, whereas both in vivo and in vitro pathogenicity as well as biofilm formation were decreased. Overall, our results show for the first time that S. maltophilia can successfully adapt to a highly stressful environment such as CF lung by paying a “biological cost,” as suggested by the presence of relevant genotypic and phenotypic heterogeneity within bacterial population. S. maltophilia populations are, therefore, significantly complex and dynamic being able to fluctuate rapidly under changing selective pressures.
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Affiliation(s)
- Arianna Pompilio
- Department of Medical, Oral, and Biotechnological Sciences, "G. d'Annunzio" University of Chieti-PescaraChieti, Italy; Center of Excellence on Aging and Translational Medicine (CeSI-MeT), "G. d'Annunzio" University of Chieti-PescaraChieti, Italy
| | - Valentina Crocetta
- Department of Medical, Oral, and Biotechnological Sciences, "G. d'Annunzio" University of Chieti-PescaraChieti, Italy; Center of Excellence on Aging and Translational Medicine (CeSI-MeT), "G. d'Annunzio" University of Chieti-PescaraChieti, Italy
| | - Dipankar Ghosh
- Special Center for Molecular Medicine, Jawaharlal Nehru University New Delhi, India
| | - Malabika Chakrabarti
- Special Center for Molecular Medicine, Jawaharlal Nehru University New Delhi, India
| | | | | | | | - Giovanni Di Bonaventura
- Department of Medical, Oral, and Biotechnological Sciences, "G. d'Annunzio" University of Chieti-PescaraChieti, Italy; Center of Excellence on Aging and Translational Medicine (CeSI-MeT), "G. d'Annunzio" University of Chieti-PescaraChieti, Italy
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30
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Satta G, Witney AA, Shorten RJ, Karlikowska M, Lipman M, McHugh TD. Genetic variation in Mycobacterium tuberculosis isolates from a London outbreak associated with isoniazid resistance. BMC Med 2016; 14:117. [PMID: 27530812 PMCID: PMC4988016 DOI: 10.1186/s12916-016-0659-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 07/26/2016] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND The largest outbreak of isoniazid-resistant (INH-R) Mycobacterium tuberculosis in Western Europe is centred in North London, with over 400 cases diagnosed since 1995. In the current study, we evaluated the genetic variation in a subset of clinical samples from the outbreak with the hypothesis that these isolates have unique biological characteristics that have served to prolong the outbreak. METHODS Fitness assays, mutation rate estimation, and whole-genome sequencing were performed to test for selective advantage and compensatory mutations. RESULTS This detailed analysis of the genetic variation of these INH-R samples suggests that this outbreak consists of successful, closely related, circulating strains with heterogeneous resistance profiles and little or no associated fitness cost or impact on their mutation rate. CONCLUSIONS Specific deletions and SNPs could be a peculiar feature of these INH-R M. tuberculosis isolates, and could potentially explain their persistence over the years.
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Affiliation(s)
- Giovanni Satta
- Department of Infection, Centre for Clinical Microbiology, University College London, London, UK. .,Imperial College Healthcare NHS Trust, London, UK.
| | - Adam A Witney
- Institute of Infection and Immunity, St George's, University of London, London, UK
| | - Robert J Shorten
- Department of Infection, Centre for Clinical Microbiology, University College London, London, UK.,Public Health Laboratory Manchester, Manchester Royal Infirmary, Manchester, UK
| | - Magdalena Karlikowska
- Department of Infection, Centre for Clinical Microbiology, University College London, London, UK
| | - Marc Lipman
- Royal Free London NHS Foundation Trust, London, UK.,UCL Respiratory, Division of Medicine, University College London, London, UK
| | - Timothy D McHugh
- Department of Infection, Centre for Clinical Microbiology, University College London, London, UK
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31
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Couce A, Alonso-Rodriguez N, Costas C, Oliver A, Blázquez J. Intrapopulation variability in mutator prevalence among urinary tract infection isolates of Escherichia coli. Clin Microbiol Infect 2016; 22:566.e1-7. [DOI: 10.1016/j.cmi.2016.03.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 03/09/2016] [Accepted: 03/11/2016] [Indexed: 11/29/2022]
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32
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Determinants of Genetic Diversity of Spontaneous Drug Resistance in Bacteria. Genetics 2016; 203:1369-80. [PMID: 27182949 DOI: 10.1534/genetics.115.185355] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 05/04/2016] [Indexed: 01/05/2023] Open
Abstract
Any pathogen population sufficiently large is expected to harbor spontaneous drug-resistant mutants, often responsible for disease relapse after antibiotic therapy. It is seldom appreciated, however, that while larger populations harbor more mutants, the abundance distribution of these mutants is expected to be markedly uneven. This is because a larger population size allows early mutants to expand for longer, exacerbating their predominance in the final mutant subpopulation. Here, we investigate the extent to which this reduction in evenness can constrain the genetic diversity of spontaneous drug resistance in bacteria. Combining theory and experiments, we show that even small variations in growth rate between resistant mutants and the wild type result in orders-of-magnitude differences in genetic diversity. Indeed, only a slight fitness advantage for the mutant is enough to keep diversity low and independent of population size. These results have important clinical implications. Genetic diversity at antibiotic resistance loci can determine a population's capacity to cope with future challenges (i.e., second-line therapy). We thus revealed an unanticipated way in which the fitness effects of antibiotic resistance can affect the evolvability of pathogens surviving a drug-induced bottleneck. This insight will assist in the fight against multidrug-resistant microbes, as well as contribute to theories aimed at predicting cancer evolution.
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Kaushik KS, Ratnayeke N, Katira P, Gordon VD. The spatial profiles and metabolic capabilities of microbial populations impact the growth of antibiotic-resistant mutants. J R Soc Interface 2016; 12:rsif.2015.0018. [PMID: 25972434 DOI: 10.1098/rsif.2015.0018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Antibiotic resistance adversely affects clinical and public health on a global scale. Using the opportunistic human pathogen Pseudomonas aeruginosa, we show that increasing the number density of bacteria, on agar containing aminoglycoside antibiotics, can non-monotonically impact the survival of antibiotic-resistant mutants. Notably, at high cell densities, mutant survival is inhibited. A wide range of bacterial species can inhibit antibiotic-resistant mutants. Inhibition results from the metabolic breakdown of amino acids, which results in alkaline by-products. The consequent increase in pH acts in conjunction with aminoglycosides to mediate inhibition. Our work raises the possibility that the manipulation of microbial population structure and nutrient environment in conjunction with existing antibiotics could provide therapeutic approaches to combat antibiotic resistance.
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Affiliation(s)
- Karishma S Kaushik
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA Center for Nonlinear Dynamics and Department of Physics, University of Texas, Austin, TX 78712, USA
| | - Nalin Ratnayeke
- Center for Nonlinear Dynamics and Department of Physics, University of Texas, Austin, TX 78712, USA
| | - Parag Katira
- Center for Nonlinear Dynamics and Department of Physics, University of Texas, Austin, TX 78712, USA
| | - Vernita D Gordon
- Center for Nonlinear Dynamics and Department of Physics, University of Texas, Austin, TX 78712, USA Institute of Cellular and Molecular Biology, University of Texas, Austin, TX 78712, USA
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Wang D, Lin Z, Ding X, Hu J, Liu Y. The Comparison of the Combined Toxicity between Gram-negative and Gram-positive Bacteria: a Case Study of Antibiotics and Quorum-sensing Inhibitors. Mol Inform 2015; 35:54-61. [DOI: 10.1002/minf.201500061] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2015] [Accepted: 10/01/2015] [Indexed: 11/10/2022]
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Zheng Q. A new practical guide to the Luria-Delbrück protocol. Mutat Res 2015; 781:7-13. [PMID: 26366669 DOI: 10.1016/j.mrfmmm.2015.08.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Revised: 07/25/2015] [Accepted: 08/23/2015] [Indexed: 06/05/2023]
Abstract
Since 2000 several review papers have been published about the analysis of experimental data obtained using the Luria-Delbrück protocol. These timely papers cleared much of the confusion surrounding various methods for estimating or comparing mutation rates. As a result, today the fluctuation test is more widely applied with much improved accuracy. The present paper provides guidelines on a few remaining problems that continue to baffle mutation researchers. Among the issues addressed are incomplete plating, relative fitness, and comparison of experiments where average final cell population sizes differ. It also offers a fresh view on the estimation methods that are based on the sample median.
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Affiliation(s)
- Qi Zheng
- Department of Epidemiology and Biostatistics, Texas A&M School of Public Health, College Station, TX 77843, United States.
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36
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Grinnage-Pulley T, Zhang Q. Genetic Basis and Functional Consequences of Differential Expression of the CmeABC Efflux Pump in Campylobacter jejuni Isolates. PLoS One 2015; 10:e0131534. [PMID: 26132196 PMCID: PMC4488513 DOI: 10.1371/journal.pone.0131534] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 06/03/2015] [Indexed: 11/18/2022] Open
Abstract
The CmeABC multidrug efflux transporter of Campylobacter jejuni plays a key role in antimicrobial resistance and is suppressed by CmeR, a transcriptional regulator of the TetR family. Overexpression of CmeABC has been observed in laboratory-generated mutants, but it is unknown if this phenotype occurs naturally in C. jejuni isolates and if it has any functional consequences. To answer these questions, expression of cmeABC in natural isolates obtained from broiler chickens, turkeys and humans was examined, and the genetic mechanisms and role of cmeABC differential expression in antimicrobial resistance was determined. Among the 64 C. jejuni isolates examined in this study, 43 and 21 were phenotypically identified as overexpression (OEL) and wild-type expression (WEL) levels. Representative mutations of the cmeABC promoter and/or CmeR-coding sequence were analyzed using electrophoretic mobility shift assays and transcriptional fusion assays. Reduced CmeR binding to the mutated cmeABC promoter sequences or decreased CmeR levels increased cmeABC expression. Several examined amino acid substitutions in CmeR did not affect its binding to the cmeABC promoter, but a mutation that led to C-terminal truncation of CmeR abolished its DNA-binding activity. Interestingly, some OEL isolates harbored no mutations in known regulatory elements, suggesting that cmeABC is also regulated by unidentified mechanisms. Overexpression of cmeABC did not affect the susceptibility of C. jejuni to most tested antimicrobials except for chloramphenicol, but promoted the emergence of ciprofloxacin-resistant mutants under antibiotic selection. These results link CmeABC overexpression in natural C. jejuni isolates to various mutations and indicate that this phenotypic change promotes the emergence of antibiotic-resistant mutants under selection pressure. Thus, differential expression of CmeABC may facilitate Campylobacter adaptation to antibiotic treatments.
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Affiliation(s)
- Tara Grinnage-Pulley
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, United States of America
| | - Qijing Zhang
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, United States of America
- * E-mail:
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Karve SM, Daniel S, Chavhan YD, Anand A, Kharola SS, Dey S. Escherichia coli populations in unpredictably fluctuating environments evolve to face novel stresses through enhanced efflux activity. J Evol Biol 2015; 28:1131-43. [PMID: 25865653 DOI: 10.1111/jeb.12640] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Accepted: 04/07/2015] [Indexed: 12/12/2022]
Abstract
There is considerable understanding about how laboratory populations respond to predictable (constant or deteriorating environment) selection for single environmental variables such as temperature or pH. However, such insights may not apply when selection environments comprise multiple variables that fluctuate unpredictably, as is common in nature. To address this issue, we grew replicate laboratory populations of Escherichia coli in nutrient broth whose pH and concentrations of salt (NaCl) and hydrogen peroxide (H2 O2 ) were randomly changed daily. After ~170 generations, the fitness of the selected populations had not increased in any of the three selection environments. However, these selected populations had significantly greater fitness in four novel environments which have no known fitness-correlation with tolerance to pH, NaCl or H2 O2 . Interestingly, contrary to expectations, hypermutators did not evolve. Instead, the selected populations evolved an increased ability for energy-dependent efflux activity that might enable them to throw out toxins, including antibiotics, from the cell at a faster rate. This provides an alternate mechanism for how evolvability can evolve in bacteria and potentially lead to broad-spectrum antibiotic resistance, even in the absence of prior antibiotic exposure. Given that environmental variability is increasing in nature, this might have serious consequences for public health.
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Affiliation(s)
- S M Karve
- Population Biology Laboratory, Biology Division, Indian Institute of Science Education and Research, Pune, Maharashtra, India
| | - S Daniel
- Population Biology Laboratory, Biology Division, Indian Institute of Science Education and Research, Pune, Maharashtra, India
| | - Y D Chavhan
- Population Biology Laboratory, Biology Division, Indian Institute of Science Education and Research, Pune, Maharashtra, India
| | - A Anand
- Population Biology Laboratory, Biology Division, Indian Institute of Science Education and Research, Pune, Maharashtra, India.,Indian Institute of Science Education and Research-Kolkata, Mohanpur, West Bengal, India
| | - S S Kharola
- Population Biology Laboratory, Biology Division, Indian Institute of Science Education and Research, Pune, Maharashtra, India
| | - S Dey
- Population Biology Laboratory, Biology Division, Indian Institute of Science Education and Research, Pune, Maharashtra, India
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38
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Oide S, Gunji W, Moteki Y, Yamamoto S, Suda M, Jojima T, Yukawa H, Inui M. Thermal and solvent stress cross-tolerance conferred to Corynebacterium glutamicum by adaptive laboratory evolution. Appl Environ Microbiol 2015; 81:2284-98. [PMID: 25595768 PMCID: PMC4357955 DOI: 10.1128/aem.03973-14] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 01/12/2015] [Indexed: 11/20/2022] Open
Abstract
Reinforcing microbial thermotolerance is a strategy to enable fermentation with flexible temperature settings and thereby to save cooling costs. Here, we report on adaptive laboratory evolution (ALE) of the amino acid-producing bacterium Corynebacterium glutamicum under thermal stress. After 65 days of serial passage of the transgenic strain GLY3, in which the glycolytic pathway is optimized for alanine production under oxygen deprivation, three strains adapted to supraoptimal temperatures were isolated, and all the mutations they acquired were identified by whole-genome resequencing. Of the 21 mutations common to the three strains, one large deletion and two missense mutations were found to promote growth of the parental strain under thermal stress. Additive effects on thermotolerance were observed among these mutations, and the combination of the deletion with the missense mutation on otsA, encoding a trehalose-6-phosphate synthase, allowed the parental strain to overcome the upper limit of growth temperature. Surprisingly, the three evolved strains acquired cross-tolerance for isobutanol, which turned out to be partly attributable to the genomic deletion associated with the enhanced thermotolerance. The deletion involved loss of two transgenes, pfk and pyk, encoding the glycolytic enzymes, in addition to six native genes, and elimination of the transgenes, but not the native genes, was shown to account for the positive effects on thermal and solvent stress tolerance, implying a link between energy-producing metabolism and bacterial stress tolerance. Overall, the present study provides evidence that ALE can be a powerful tool to refine the phenotype of C. glutamicum and to investigate the molecular bases of stress tolerance.
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Affiliation(s)
- Shinichi Oide
- Research Institute of Innovative Technology for the Earth, Kizugawa, Kyoto, Japan
| | - Wataru Gunji
- Research Institute of Innovative Technology for the Earth, Kizugawa, Kyoto, Japan
| | - Yasuhiro Moteki
- Research Institute of Innovative Technology for the Earth, Kizugawa, Kyoto, Japan
| | - Shogo Yamamoto
- Research Institute of Innovative Technology for the Earth, Kizugawa, Kyoto, Japan
| | - Masako Suda
- Research Institute of Innovative Technology for the Earth, Kizugawa, Kyoto, Japan
| | - Toru Jojima
- Research Institute of Innovative Technology for the Earth, Kizugawa, Kyoto, Japan
| | - Hideaki Yukawa
- Research Institute of Innovative Technology for the Earth, Kizugawa, Kyoto, Japan
| | - Masayuki Inui
- Research Institute of Innovative Technology for the Earth, Kizugawa, Kyoto, Japan Graduate School of Biological Sciences, Nara Institute of Science and Technology, Takayama, Ikoma, Nara, Japan
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39
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Ycart B, Veziris N. Unbiased estimation of mutation rates under fluctuating final counts. PLoS One 2014; 9:e101434. [PMID: 24988217 PMCID: PMC4079557 DOI: 10.1371/journal.pone.0101434] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Accepted: 06/06/2014] [Indexed: 11/18/2022] Open
Abstract
Estimation methods for mutation rates (or probabilities) in Luria-Delbrück fluctuation analysis usually assume that the final number of cells remains constant from one culture to another. We show that this leads to systematically underestimate the mutation rate. Two levels of information on final numbers are considered: either the coefficient of variation has been independently estimated, or the final number of cells in each culture is known. In both cases, unbiased estimation methods are proposed. Their statistical properties are assessed both theoretically and through Monte-Carlo simulation. As an application, the data from two well known fluctuation analysis studies on Mycobacterium tuberculosis are reexamined.
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Affiliation(s)
- Bernard Ycart
- Laboratoire Jean Kuntzmann, Univ. Grenoble Alpes, Grenoble, France
- Laboratoire d'Excellence “TOUCAN” (Toulouse Cancer), Toulouse, France
| | - Nicolas Veziris
- Sorbonne Universités, UPMC Univ. Paris 06, CR7, Centre d'Immunologie et des Maladies Infectieuses, CIMI, Team E13 (Bacteriology), Paris, France
- INSERM, U1135, Centre d'Immunologie et des Maladies Infectieuses, CIMI, Team E13 (Bacteriology), Paris, France
- AP-HP, Hôpital Pitié-Salpêtrière, Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux, Laboratoire de Bactériologie-Hygiène, Paris, France
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
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40
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Rapa RA, Islam A, Monahan LG, Mutreja A, Thomson N, Charles IG, Stokes HW, Labbate M. A genomic island integrated into recA of Vibrio cholerae contains a divergent recA and provides multi-pathway protection from DNA damage. Environ Microbiol 2014; 17:1090-102. [PMID: 24889424 PMCID: PMC4405046 DOI: 10.1111/1462-2920.12512] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 05/13/2014] [Indexed: 11/28/2022]
Abstract
Lateral gene transfer (LGT) has been crucial in the evolution of the cholera pathogen, Vibrio cholerae. The two major virulence factors are present on two different mobile genetic elements, a bacteriophage containing the cholera toxin genes and a genomic island (GI) containing the intestinal adhesin genes. Non-toxigenic V. cholerae in the aquatic environment are a major source of novel DNA that allows the pathogen to morph via LGT. In this study, we report a novel GI from a non-toxigenic V. cholerae strain containing multiple genes involved in DNA repair including the recombination repair gene recA that is 23% divergent from the indigenous recA and genes involved in the translesion synthesis pathway. This is the first report of a GI containing the critical gene recA and the first report of a GI that targets insertion into a specific site within recA. We show that possession of the island in Escherichia coli is protective against DNA damage induced by UV-irradiation and DNA targeting antibiotics. This study highlights the importance of genetic elements such as GIs in the evolution of V. cholerae and emphasizes the importance of environmental strains as a source of novel DNA that can influence the pathogenicity of toxigenic strains.
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Affiliation(s)
- Rita A Rapa
- ithree Institute, University of Technology, PO Box 123 Broadway, Sydney, NSW, 2007, Australia; Department of Medical and Molecular Biosciences, University of Technology, Sydney, NSW, Australia
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41
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McGrath M, Gey van Pittius NC, van Helden PD, Warren RM, Warner DF. Mutation rate and the emergence of drug resistance in Mycobacterium tuberculosis. J Antimicrob Chemother 2013; 69:292-302. [DOI: 10.1093/jac/dkt364] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
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Osburne MS, Holmbeck BM, Coe A, Chisholm SW. The spontaneous mutation frequencies of Prochlorococcus strains are commensurate with those of other bacteria. ENVIRONMENTAL MICROBIOLOGY REPORTS 2011; 3:744-749. [PMID: 23761365 DOI: 10.1111/j.1758-2229.2011.00293.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The marine cyanobacterium Prochlorococcus, the smallest and most abundant oxygenic phototroph, has an extremely streamlined genome and a high rate of protein evolution. High-light adapted strains of Prochlorococcus in particular have seemingly inadequate DNA repair systems, raising the possibility that inadequate repair may lead to high mutation rates. Prochlorococcus mutation rates have been difficult to determine, in part because traditional methods involving quantifying colonies on solid selective media are not straightforward for this organism. Here we used a liquid dilution method to measure the approximate number of antibiotic-resistant mutants in liquid cultures of Prochlorococcus strains previously unexposed to antibiotic selection. Several antibiotics for which resistance in other bacteria is known to result from a single base pair change were used. The resulting frequencies of antibiotic resistance in Prochlorococcus cultures allowed us to then estimate maximum spontaneous mutation rates, which were similar to those in organisms such as E. coli (∼5.4 × 10(-7) per gene per generation). Therefore, despite the lack of some DNA repair genes, it appears unlikely that the Prochlorcoccus genomes studied here are currently being shaped by unusually high mutation rates.
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Affiliation(s)
- Marcia S Osburne
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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43
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Couce A, Blázquez J. Estimating mutation rates in low-replication experiments. Mutat Res 2011; 714:26-32. [PMID: 21736881 DOI: 10.1016/j.mrfmmm.2011.06.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2011] [Revised: 05/24/2011] [Accepted: 06/21/2011] [Indexed: 11/25/2022]
Abstract
Since mutation rate is a key biological parameter, its proper estimation has received great attention for decades. However, instead of the mutation rate, many authors opt for reporting the average mutant frequency, a less meaningful quantity. This is because the standard methods to estimate the mutation rate, derived from the Luria and Delbrück's fluctuation analysis, ideally require high-replication experiments to be applied; a requirement often unattainable due to constraints of time, budget or sample availability. But the main problem with mutant frequency, apart from being less informative, is its poor reproducibility; an especially marked defect when the chosen average is the arithmetic mean. Several authors tried to avoid this by employing other averages (such as the median or the geometric mean) or discarding outliers, though as far as we know nobody has evaluated which method performs best under low-replication settings. Here we use computer simulations to compare the performance of different methods used in low-replication experiments (≤4 cultures). Besides the customary averages of mutant frequency, we also tested two well-known fluctuation methods. Contrary to common practice, our results support that fluctuation methods should be applied in such circumstances, as they perform as well as or better than any average of mutant frequency. In particular, experimentalists will benefit from using MSS maximum likelihood in low-replication experiments because it: (i) provides more reproducible results, (ii) allows for direct estimation of mutation rate and (iii) allows for the application of conventional statistics.
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Affiliation(s)
- Alejandro Couce
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, 28049 Madrid, Spain.
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44
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Russell MS, March JC. Bootstrap estimation of confidence intervals on mutation rate ratios. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2011; 52:385-396. [PMID: 21630358 DOI: 10.1002/em.20636] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2010] [Revised: 09/15/2010] [Accepted: 09/15/2010] [Indexed: 05/30/2023]
Abstract
The fluctuation test is a useful tool for estimating the mutation rate of cells. However, statistical methods for comparing mutation rate estimates between different strains or conditions have not yet been fully developed. Methods exist for placing confidence intervals on estimates of the number of mutational events in cultures for a given strain and set of conditions, but placing confidence intervals on mutation rate is complicated by differences in the final number of cells in culture between parallel cultures. Additionally, confidence intervals on individual mutation rate estimates are not always the most useful statistical tool when comparing two or more different strains or conditions. We present a bootstrap method for estimating confidence intervals on the quotient of two mutation rates determined from two fluctuation test experiments using experimental and control strains or conditions. We use Monte Carlo simulations to validate this method over a wide range of mutation rates and for empirically measured variation in the estimates of final number of cells in culture. Furthermore, we provide the computational tools to implement the bootstrap method described here on experimental fluctuation test data and to evaluate this method for experimental parameters other than those considered herein.
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Affiliation(s)
- Matthew S Russell
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, New York 14853, USA
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45
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Lee JY, Song JH, Ko KS. Recombination rates of Streptococcus pneumoniae isolates with both erm(B) and mef(A) genes. FEMS Microbiol Lett 2010; 309:163-9. [PMID: 20618866 DOI: 10.1111/j.1574-6968.2010.02032.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Erythromycin-resistant Streptococcus pneumoniae isolates containing both erm(B) and mef(A) genes have a higher rate of multidrug resistance (MDR). We investigated the relationships between the presence of erythromycin resistance determinants and the recombination rate. We determined the mutation and recombination frequencies of 46 S. pneumoniae isolates, which included 19 with both erm(B) and mef(A), nine with only erm(B), six with only mef(A), and 11 erythromycin-susceptible isolates. Mutation frequency values were estimated as the number of rifampin-resistant colonies as a proportion of total viable count. Genotypes and serotypes of isolates with the hyper-recombination phenotype were determined. Twelve S. pneumoniae isolates were hypermutable and four isolates were determined to have hyper-recombination frequency. Streptococcus pneumoniae isolates with both erm(B) and mef(A) genes did not show a high mutation frequency. In contrast, all isolates with a hyper-recombination phenotype contained both erm(B) and mef(A) genes. In addition, the recombination rate of isolates with both erm(B) and mef(A) genes was statistically higher than the rate of other isolates. The dual presence of erm(B) and mef(A) genes in some pneumococcal isolates may be associated with high recombination frequency. This may be one of the reasons for the frequent emergence of MDR in certain pneumococcal isolates.
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Affiliation(s)
- Ji-Young Lee
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, Korea
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46
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Stoebel DM, Dorman CJ. The effect of mobile element IS10 on experimental regulatory evolution in Escherichia coli. Mol Biol Evol 2010; 27:2105-12. [PMID: 20400481 PMCID: PMC2922620 DOI: 10.1093/molbev/msq101] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Mobile genetic elements are widespread in bacteria, where they cause several kinds of mutations. Although their effects are on the whole negative, rare beneficial mutations caused by insertion sequence elements are frequently selected in some experimental evolution systems. For example, in earlier work, we found that strains of Escherichia coli that lack the sigma factor RpoS adapt to a high-osmolarity environment by the insertion of element IS10 into the promoter of the otsBA operon, rewiring expression from RpoS dependent to RpoS independent. We wished to determine how the presence of IS10 in the genome of this strain shaped the evolutionary outcome. IS10 could influence the outcome by causing mutations that confer adaptive phenotypes that cannot be achieved by strains without the element. Alternatively, IS10 could influence evolution by increasing the rate of appearance of certain classes of beneficial mutations even if they are no better than those that could be achieved by a strain without the element. We found that populations evolved from an IS10-free strain did not upregulate otsBA. An otsBA-lacZY fusion facilitated the recovery of a number of mutations that upregulate otsB without involving IS10 and found that two caused greater fitness increases than IS10 insertion, implying that evolution could have upregulated otsBA in the IS10-free strain. Finally, we demonstrate that there is epistasis between the IS10 insertion into the otsBA promoter and the other adaptive mutations, implying that introduction of IS10 into the otsBA promoter may alter the trajectory of adaptive evolution. We conclude that IS10 exerts its effect not by creating adaptive phenotypes that could not otherwise occur but by increasing the rate of appearance of certain adaptive mutations.
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Affiliation(s)
- Daniel M Stoebel
- Department of Microbiology, Moyne Institute of Preventive Medicine, School of Genetics and Microbiology, Trinity College Dublin, Dublin, Ireland
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47
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Abstract
The environment encountered by Mycobacterium tuberculosis during infection is genotoxic. Most bacteria tolerate DNA damage by engaging specialized DNA polymerases that catalyze translesion synthesis (TLS) across sites of damage. M. tuberculosis possesses two putative members of the DinB class of Y-family DNA polymerases, DinB1 (Rv1537) and DinB2 (Rv3056); however, their role in damage tolerance, mutagenesis, and survival is unknown. Here, both dinB1 and dinB2 are shown to be expressed in vitro in a growth phase-dependent manner, with dinB2 levels 12- to 40-fold higher than those of dinB1. Yeast two-hybrid analyses revealed that DinB1, but not DinB2, interacts with the beta-clamp, consistent with its canonical C-terminal beta-binding motif. However, knockout of dinB1, dinB2, or both had no effect on the susceptibility of M. tuberculosis to compounds that form N(2)-dG adducts and alkylating agents. Similarly, deletion of these genes individually or in combination did not affect the rate of spontaneous mutation to rifampin resistance or the spectrum of resistance-conferring rpoB mutations and had no impact on growth or survival in human or mouse macrophages or in mice. Moreover, neither gene conferred a mutator phenotype when expressed ectopically in Mycobacterium smegmatis. The lack of the effect of altering the complements or expression levels of dinB1 and/or dinB2 under conditions predicted to be phenotypically revealing suggests that the DinB homologs from M. tuberculosis do not behave like their counterparts from other organisms.
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Liaqat I, Sabri AN. Isolation and characterization of biocides resistant bacteria from dental unit water line biofilms. J Basic Microbiol 2009; 49:275-84. [DOI: 10.1002/jobm.200800212] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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49
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Sun S, Negrea A, Rhen M, Andersson DI. Genetic analysis of colistin resistance in Salmonella enterica serovar Typhimurium. Antimicrob Agents Chemother 2009; 53:2298-305. [PMID: 19332669 PMCID: PMC2687247 DOI: 10.1128/aac.01016-08] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2008] [Revised: 09/29/2008] [Accepted: 03/23/2009] [Indexed: 11/20/2022] Open
Abstract
Colistin is a cyclic cationic peptide that kills gram-negative bacteria by interacting with and disrupting the outer membrane. We isolated 44 independent mutants in Salmonella enterica serovar Typhimurium with reduced susceptibility to colistin and identified 27 different missense mutations located in the pmrA and pmrB genes (encoding the regulator and sensor of a two-component regulatory system) that conferred increased resistance. By comparison of the two homologous sensor kinases, PmrB and EnvZ, the 22 missense mutations identified in pmrB were shown to be located in four different structural domains of the protein. All five pmrA mutations were located in the phosphate receiver domain of the regulator protein. The mutants appeared at a mutation rate of 0.6 x 10(-6) per cell per generation. The MICs of colistin for the mutants increased 2- to 35-fold, and the extent of killing was reduced several orders of magnitude compared to the susceptible strain. The growth rates of the mutants were slightly reduced in both rich medium and M9-glycerol minimal medium, whereas growth in mice appeared unaffected by the pmrA and pmrB mutations. The low fitness costs and the high mutation rate suggest that mutants with reduced susceptibility to colistin could emerge in clinical settings.
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Affiliation(s)
- Song Sun
- Department of Medical Biochemistry and Microbiology, Uppsala University, S-751 23 Uppsala, Sweden
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50
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Abstract
In previous work by M. E. Jones and colleagues, it was shown that mutation rate estimates can be improved and corresponding confidence intervals tightened by following a very easy modification of the standard fluctuation assay: cultures are grown to a larger-than-usual final density, and mutants are screened for in only a fraction of the culture. Surprisingly, this very promising development has received limited attention, perhaps because there has been no efficient way to generate the predicted mutant distribution to obtain non-moment-based estimates of the mutation rate. Here, the improved fluctuation assay discovered by Jones and colleagues is made amenable to quantile-based, likelihood, and other Bayesian methods by a simple recursion formula that efficiently generates the entire mutant distribution after growth and dilution. This formula makes possible a further protocol improvement: grow cultures as large as is experimentally possible and severely dilute before plating to obtain easily countable numbers of mutants. A preliminary look at likelihood surfaces suggests that this easy protocol adjustment gives markedly improved mutation rate estimates and confidence intervals.
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