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Germe TRM, Bush NG, Baskerville VM, Saman D, Benesch JLP, Maxwell A. Rapid, DNA-induced interface swapping by DNA gyrase. eLife 2024; 12:RP86722. [PMID: 38856655 PMCID: PMC11164529 DOI: 10.7554/elife.86722] [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] [Indexed: 06/11/2024] Open
Abstract
DNA gyrase, a ubiquitous bacterial enzyme, is a type IIA topoisomerase formed by heterotetramerisation of 2 GyrA subunits and 2 GyrB subunits, to form the active complex. DNA gyrase can loop DNA around the C-terminal domains (CTDs) of GyrA and pass one DNA duplex through a transient double-strand break (DSB) established in another duplex. This results in the conversion from a positive (+1) to a negative (-1) supercoil, thereby introducing negative supercoiling into the bacterial genome by steps of 2, an activity essential for DNA replication and transcription. The strong protein interface in the GyrA dimer must be broken to allow passage of the transported DNA segment and it is generally assumed that the interface is usually stable and only opens when DNA is transported, to prevent the introduction of deleterious DSBs in the genome. In this paper, we show that DNA gyrase can exchange its DNA-cleaving interfaces between two active heterotetramers. This so-called interface 'swapping' (IS) can occur within a few minutes in solution. We also show that bending of DNA by gyrase is essential for cleavage but not for DNA binding per se and favors IS. Interface swapping is also favored by DNA wrapping and an excess of GyrB. We suggest that proximity, promoted by GyrB oligomerization and binding and wrapping along a length of DNA, between two heterotetramers favors rapid interface swapping. This swapping does not require ATP, occurs in the presence of fluoroquinolones, and raises the possibility of non-homologous recombination solely through gyrase activity. The ability of gyrase to undergo interface swapping explains how gyrase heterodimers, containing a single active-site tyrosine, can carry out double-strand passage reactions and therefore suggests an alternative explanation to the recently proposed 'swivelling' mechanism for DNA gyrase (Gubaev et al., 2016).
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Affiliation(s)
- Thomas RM Germe
- Department Biochemistry & Metabolism, John Innes Centre, Norwich Research ParkNorwichUnited Kingdom
| | - Natassja G Bush
- Department Biochemistry & Metabolism, John Innes Centre, Norwich Research ParkNorwichUnited Kingdom
| | - Victoria M Baskerville
- Department Biochemistry & Metabolism, John Innes Centre, Norwich Research ParkNorwichUnited Kingdom
| | - Dominik Saman
- Department of Chemistry, Biochemistry Building, University of OxfordOxfordUnited Kingdom
| | - Justin LP Benesch
- Department of Chemistry, Biochemistry Building, University of OxfordOxfordUnited Kingdom
| | - Anthony Maxwell
- Department Biochemistry & Metabolism, John Innes Centre, Norwich Research ParkNorwichUnited Kingdom
- Department of Molecular Microbiology, John Innes Centre, Norwich Research ParkNorwichUnited Kingdom
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2
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Collins J, Osheroff N. Gyrase and Topoisomerase IV: Recycling Old Targets for New Antibacterials to Combat Fluoroquinolone Resistance. ACS Infect Dis 2024; 10:1097-1115. [PMID: 38564341 PMCID: PMC11019561 DOI: 10.1021/acsinfecdis.4c00128] [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: 02/16/2024] [Revised: 03/14/2024] [Accepted: 03/18/2024] [Indexed: 04/04/2024]
Abstract
Beyond their requisite functions in many critical DNA processes, the bacterial type II topoisomerases, gyrase and topoisomerase IV, are the targets of fluoroquinolone antibacterials. These drugs act by stabilizing gyrase/topoisomerase IV-generated DNA strand breaks and by robbing the cell of the catalytic activities of these essential enzymes. Since their clinical approval in the mid-1980s, fluoroquinolones have been used to treat a broad spectrum of infectious diseases and are listed among the five "highest priority" critically important antimicrobial classes by the World Health Organization. Unfortunately, the widespread use of fluoroquinolones has been accompanied by a rise in target-mediated resistance caused by specific mutations in gyrase and topoisomerase IV, which has curtailed the medical efficacy of this drug class. As a result, efforts are underway to identify novel antibacterials that target the bacterial type II topoisomerases. Several new classes of gyrase/topoisomerase IV-targeted antibacterials have emerged, including novel bacterial topoisomerase inhibitors, Mycobacterium tuberculosis gyrase inhibitors, triazaacenaphthylenes, spiropyrimidinetriones, and thiophenes. Phase III clinical trials that utilized two members of these classes, gepotidacin (triazaacenaphthylene) and zoliflodacin (spiropyrimidinetrione), have been completed with positive outcomes, underscoring the potential of these compounds to become the first new classes of antibacterials introduced into the clinic in decades. Because gyrase and topoisomerase IV are validated targets for established and emerging antibacterials, this review will describe the catalytic mechanism and cellular activities of the bacterial type II topoisomerases, their interactions with fluoroquinolones, the mechanism of target-mediated fluoroquinolone resistance, and the actions of novel antibacterials against wild-type and fluoroquinolone-resistant gyrase and topoisomerase IV.
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Affiliation(s)
- Jessica
A. Collins
- Department
of Biochemistry, Vanderbilt University School
of Medicine, Nashville, Tennessee 37232, United States
| | - Neil Osheroff
- Department
of Biochemistry, Vanderbilt University School
of Medicine, Nashville, Tennessee 37232, United States
- Department
of Medicine (Hematology/Oncology), Vanderbilt
University School of Medicine, Nashville, Tennessee 37232, United States
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3
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Gunarathne V, Phillips AJ, Zanoletti A, Rajapaksha AU, Vithanage M, Di Maria F, Pivato A, Korzeniewska E, Bontempi E. Environmental pitfalls and associated human health risks and ecological impacts from landfill leachate contaminants: Current evidence, recommended interventions and future directions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:169026. [PMID: 38056656 DOI: 10.1016/j.scitotenv.2023.169026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 10/17/2023] [Accepted: 11/29/2023] [Indexed: 12/08/2023]
Abstract
The improper management of solid waste, particularly the dumping of untreated municipal solid waste, poses a growing global challenge in both developed and developing nations. The generation of leachate is one of the significant issues that arise from this practice, and it can have harmful impacts on both the environment and public health. This paper presents an overview of the primary waste types that generate landfill leachate and their characteristics. This includes examining the distribution of waste types in landfills globally and how they have changed over time, which can provide valuable insights into potential pollutants in a given area and their trends. With a lack of specific regulations and growing concerns regarding environmental and health impacts, the paper also focuses on emerging contaminants. Furthermore, the environmental and ecological impacts of leachate, along with associated health risks, are analyzed. The potential applications of landfill leachate, suggested interventions and future directions are also discussed in the manuscript. Finally, this work addresses future research directions in landfill leachate studies, with attention, for the first time to the potentialities that artificial intelligence can offer for landfill leachate management, studies, and applications.
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Affiliation(s)
- Viraj Gunarathne
- Ecosphere Resilience Research Centre, Faculty of Applied Sciences, University of Sri Jayewardenepura, Nugegoda, CO 10250, Sri Lanka; University of Wuppertal, School of Architecture and Civil Engineering, Institute of Foundation Engineering, Water- and Waste-Management, Laboratory of Soil- and Groundwater-Management, Pauluskirchstraße 7, 42285 Wuppertal, Germany
| | - Ankur J Phillips
- Department of Microbiology, College of Basic Sciences and Humanities, Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, 263145, Uttarakhand, India
| | - Alessandra Zanoletti
- INSTM and Chemistry for Technologies Laboratory, Department of Mechanical and Industrial Engineering, University of Brescia, Via Branze, 38, 25123 Brescia, Italy
| | - Anushka Upamali Rajapaksha
- Ecosphere Resilience Research Centre, Faculty of Applied Sciences, University of Sri Jayewardenepura, Nugegoda, CO 10250, Sri Lanka; Instrument Center, Faculty of Applied Sciences, University of Sri Jayewardenepura, Nugegoda 10250, Sri Lanka
| | - Meththika Vithanage
- Ecosphere Resilience Research Centre, Faculty of Applied Sciences, University of Sri Jayewardenepura, Nugegoda, CO 10250, Sri Lanka
| | - Francesco Di Maria
- LAR5 Laboratory, Dipartimento di Ingegneria, University of Perugia, via G. Duranti 93, 06125 Perugia, Italy
| | - Alberto Pivato
- DICEA - Department of Civil, Environmental and Architectural Engineering, University of Padova, Via Marzolo 9, 35131 Padova, Italy
| | - Ewa Korzeniewska
- Department of Water Protection Engineering and Environmental Microbiology, The Faculty of Geoengineering, University of Warmia and Mazury in Olsztyn, Prawocheńskiego 1 Str., 10-719 Olsztyn, Poland
| | - Elza Bontempi
- INSTM and Chemistry for Technologies Laboratory, Department of Mechanical and Industrial Engineering, University of Brescia, Via Branze, 38, 25123 Brescia, Italy.
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4
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Yuan M, Huang Z, Malakar PK, Pan Y, Zhao Y, Zhang Z. Antimicrobial resistomes in food chain microbiomes. Crit Rev Food Sci Nutr 2023:1-22. [PMID: 36785889 DOI: 10.1080/10408398.2023.2177607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
The safety and integrity of the global food system is in a constant state of flux with persistent chemical and microbial risks. While chemical risks are being managed systematically, microbial risks pose extra challenges. Antimicrobial resistant microorganism and persistence of related antibiotic resistance genes (ARGs) in the food chain adds an extra dimension to the management of microbial risks. Because the food chain microbiome is a key interface in the global health system, these microbes can affect health in many ways. In this review, we systematically summarize the distribution of ARGs in foods, describe the potential transmission pathway and transfer mechanism of ARGs from farm to fork, and discuss potential food safety problems and challenges. Modulating antimicrobial resistomes in the food chain facilitates a sustainable global food production system.
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Affiliation(s)
- Mengqi Yuan
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Zhenhua Huang
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Pradeep K Malakar
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Yingjie Pan
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
- Laboratory of Quality & Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture and Rural Affairs, Shanghai, China
- Shanghai Engineering Research Center of Aquatic-Product Processing & Preservation, Shanghai Ocean University, Shanghai, China
| | - Yong Zhao
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
- Laboratory of Quality & Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture and Rural Affairs, Shanghai, China
- Shanghai Engineering Research Center of Aquatic-Product Processing & Preservation, Shanghai Ocean University, Shanghai, China
| | - Zhaohuan Zhang
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
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5
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Leinyuy JF, Ali IM, Ousenu K, Tume CB. Molecular characterization of antimicrobial resistance related genes in E. coli, Salmonella and Klebsiella isolates from broilers in the West Region of Cameroon. PLoS One 2023; 18:e0280150. [PMID: 36630464 PMCID: PMC9833522 DOI: 10.1371/journal.pone.0280150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 12/21/2022] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Antibiotic resistance has become an enduring threat to human health. This has prompted extensive research to identify the determinants responsible in a bid to fight the spread of resistance and also develop new antibiotics. However, routine procedures focus on identifying genetic determinants of resistance only on phenotypically resistant isolates. We aimed to characterise plasmid mediated resistance determinants in key Enterobacteriaceae isolates with differential phenotypic susceptibility profiles and evaluated the contribution of resistance genes on phenotypic expression of susceptibility. METHODS The study was carried out on 200 Enterobacteriaceae isolates belonging to the genera E. coli, Salmonella, and Klebsiella; 100 resistant and 100 susceptible to quinolones, aminoglycosides, and ESBL-producing as determined by disk diffusion. Reduced susceptibility in susceptible isolates was determined as an increased MIC by broth microdilution. Plasmid-borne resistance genes were sought in all isolates by endpoint PCR. We performed correlations tests to determine the relationship between the occurrence of resistance genes and increased MIC in susceptible isolates. We then used the notion of penetrance to show adequacy between resistance gene carriage and phenotypic resistance as well as diagnostic odds ratio to evaluate how predictable phenotypic susceptibility profile could determine the presence of resistant genes in the isolates. RESULTS Reduced susceptibility was detected in 30% (9/30) ESBL negative, 50% (20/40) quinolone-susceptible and 53.33% (16/30) aminoglycoside-susceptible isolates. Plasmid-borne resistance genes were detected in 50% (15/30) of ESBL negative, 65% (26/40) quinolone susceptible and 66.67% (20/30) aminoglycoside susceptible isolates. Reduced susceptibility increased the risk of susceptible isolates carrying resistance genes (ORs 4.125, 8.36, and 8.89 respectively for ESBL, quinolone, and aminoglycoside resistance genes). Resistance gene carriage correlated significantly to reduced susceptibility for quinolone and aminoglycoside resistance genes (0.002 and 0.015 at CI95). Gene carriage correlated with phenotypic resistance at an estimated 64.28% for ESBL, 56.90% for quinolone, and 58.33% for aminoglycoside resistance genes. CONCLUSIONS A high carriage of plasmid-mediated genes for ESBL, quinolone, and aminoglycoside resistance was found among the Enterobacteriaceae tested. However, gene carriage was not always correlated with phenotypic expression. This allows us to suggest that assessing genetic determinants of resistance should not be based on AST profile only. Further studies, including assessing the role of chromosomal determinants will shed light on other factors that undermine antimicrobial susceptibility locally.
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Affiliation(s)
- Jude Fonbah Leinyuy
- Research Unit of Microbiology and Antimicrobial Substances, Department of Biochemistry, University of Dschang, Dschang, Cameroon
| | - Innocent Mbulli Ali
- Research Unit of Microbiology and Antimicrobial Substances, Department of Biochemistry, University of Dschang, Dschang, Cameroon
- The Biotechnology Centre, University of Yaoundé 1, Yaoundé, Cameroon
- * E-mail:
| | - Karimo Ousenu
- Research Unit of Microbiology and Antimicrobial Substances, Department of Biochemistry, University of Dschang, Dschang, Cameroon
| | - Christopher B. Tume
- Research Unit of Microbiology and Antimicrobial Substances, Department of Biochemistry, University of Dschang, Dschang, Cameroon
- Department of Biochemistry, Faculty of Science, University of Bamenda, Bamenda, Cameroon
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6
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Wilkinson M, Wilkinson OJ, Feyerherm C, Fletcher EE, Wigley DB, Dillingham MS. Structures of RecBCD in complex with phage-encoded inhibitor proteins reveal distinctive strategies for evasion of a bacterial immunity hub. eLife 2022; 11:e83409. [PMID: 36533901 PMCID: PMC9836394 DOI: 10.7554/elife.83409] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 12/18/2022] [Indexed: 12/23/2022] Open
Abstract
Following infection of bacterial cells, bacteriophage modulate double-stranded DNA break repair pathways to protect themselves from host immunity systems and prioritise their own recombinases. Here, we present biochemical and structural analysis of two phage proteins, gp5.9 and Abc2, which target the DNA break resection complex RecBCD. These exemplify two contrasting mechanisms for control of DNA break repair in which the RecBCD complex is either inhibited or co-opted for the benefit of the invading phage. Gp5.9 completely inhibits RecBCD by preventing it from binding to DNA. The RecBCD-gp5.9 structure shows that gp5.9 acts by substrate mimicry, binding predominantly to the RecB arm domain and competing sterically for the DNA binding site. Gp5.9 adopts a parallel coiled-coil architecture that is unprecedented for a natural DNA mimic protein. In contrast, binding of Abc2 does not substantially affect the biochemical activities of isolated RecBCD. The RecBCD-Abc2 structure shows that Abc2 binds to the Chi-recognition domains of the RecC subunit in a position that might enable it to mediate the loading of phage recombinases onto its single-stranded DNA products.
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Affiliation(s)
- Martin Wilkinson
- Section of Structural Biology, Department of Infectious Disease, Faculty of Medicine, Imperial College LondonLondonUnited Kingdom
| | - Oliver J Wilkinson
- DNA:protein Interactions Unit, School of Biochemistry, University of BristolBristolUnited Kingdom
| | - Connie Feyerherm
- DNA:protein Interactions Unit, School of Biochemistry, University of BristolBristolUnited Kingdom
| | - Emma E Fletcher
- DNA:protein Interactions Unit, School of Biochemistry, University of BristolBristolUnited Kingdom
| | - Dale B Wigley
- Section of Structural Biology, Department of Infectious Disease, Faculty of Medicine, Imperial College LondonLondonUnited Kingdom
| | - Mark S Dillingham
- DNA:protein Interactions Unit, School of Biochemistry, University of BristolBristolUnited Kingdom
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7
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Vasse M, Bonhoeffer S, Frenoy A. Ecological effects of stress drive bacterial evolvability under sub-inhibitory antibiotic treatments. ISME COMMUNICATIONS 2022; 2:80. [PMID: 37938266 PMCID: PMC9723650 DOI: 10.1038/s43705-022-00157-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 07/20/2022] [Accepted: 07/29/2022] [Indexed: 11/09/2023]
Abstract
Stress is thought to increase mutation rate and thus to accelerate evolution. In the context of antibiotic resistance, sub-inhibitory treatments could then lead to enhanced evolvability, thereby fuelling the adaptation of pathogens. Combining wet-lab experiments, stochastic simulations and a meta-analysis of the literature, we found that the increase in mutation rates triggered by antibiotic treatments is often cancelled out by reduced population size, resulting in no overall increase in genetic diversity. A careful analysis of the effect of ecological factors on genetic diversity showed that the potential for regrowth during recovery phase after treatment plays a crucial role in evolvability, being the main factor associated with increased genetic diversity in experimental data.
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Affiliation(s)
- Marie Vasse
- Institute for Integrative Biology, ETH Zürich, Zurich, Switzerland
| | | | - Antoine Frenoy
- Institute for Integrative Biology, ETH Zürich, Zurich, Switzerland.
- Université Grenoble Alpes, CNRS UMR 5525, Grenoble, France.
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8
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Eisenreich W, Rudel T, Heesemann J, Goebel W. Link Between Antibiotic Persistence and Antibiotic Resistance in Bacterial Pathogens. Front Cell Infect Microbiol 2022; 12:900848. [PMID: 35928205 PMCID: PMC9343593 DOI: 10.3389/fcimb.2022.900848] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 06/21/2022] [Indexed: 12/15/2022] Open
Abstract
Both, antibiotic persistence and antibiotic resistance characterize phenotypes of survival in which a bacterial cell becomes insensitive to one (or even) more antibiotic(s). However, the molecular basis for these two antibiotic-tolerant phenotypes is fundamentally different. Whereas antibiotic resistance is genetically determined and hence represents a rather stable phenotype, antibiotic persistence marks a transient physiological state triggered by various stress-inducing conditions that switches back to the original antibiotic sensitive state once the environmental situation improves. The molecular basics of antibiotic resistance are in principle well understood. This is not the case for antibiotic persistence. Under all culture conditions, there is a stochastically formed, subpopulation of persister cells in bacterial populations, the size of which depends on the culture conditions. The proportion of persisters in a bacterial population increases under different stress conditions, including treatment with bactericidal antibiotics (BCAs). Various models have been proposed to explain the formation of persistence in bacteria. We recently hypothesized that all physiological culture conditions leading to persistence converge in the inability of the bacteria to re-initiate a new round of DNA replication caused by an insufficient level of the initiator complex ATP-DnaA and hence by the lack of formation of a functional orisome. Here, we extend this hypothesis by proposing that in this persistence state the bacteria become more susceptible to mutation-based antibiotic resistance provided they are equipped with error-prone DNA repair functions. This is - in our opinion - in particular the case when such bacterial populations are exposed to BCAs.
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Affiliation(s)
- Wolfgang Eisenreich
- Bavarian NMR Center – Structural Membrane Biochemistry, Department of Chemistry, Technische Universität München, Garching, Germany
- *Correspondence: Wolfgang Eisenreich,
| | - Thomas Rudel
- Chair of Microbiology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Jürgen Heesemann
- Max von Pettenkofer-Institute, Ludwig Maximilian University of Munich, München, Germany
| | - Werner Goebel
- Max von Pettenkofer-Institute, Ludwig Maximilian University of Munich, München, Germany
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9
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Patterns of Antibiotic Resistance in Enterobacteriaceae Isolates from Broiler Chicken in the West Region of Cameroon: A Cross-Sectional Study. CANADIAN JOURNAL OF INFECTIOUS DISEASES AND MEDICAL MICROBIOLOGY 2022; 2022:4180336. [PMID: 35722039 PMCID: PMC9203226 DOI: 10.1155/2022/4180336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 05/12/2022] [Accepted: 05/21/2022] [Indexed: 11/18/2022]
Abstract
Background. The emergence of multidrug-resistant food-borne pathogens of animal origin including Enterobacteriaceae is a growing concern. Identifying and monitoring resistance in isolates from human-related environments are of clinical and epidemiological significance in containing antimicrobial resistance. This study aimed to contribute towards the fight against antibiotic resistance and ameliorate the management/treatment of Enterobacteriaceae-linked diseases in Cameroon. Methods. Cloacal swabs from healthy broilers were enriched in buffered-peptone-water and cultured on EMB agar. Antibiotic susceptibility was tested on Mueller-Hinton-Agar by disc diffusion. Plasmid-borne genes for extended-spectrum beta lactamase (ESBL) and resistance to Quinolones (PMQR) and Aminoglycosides were detected by standard endpoint polymerase chain reaction (PCR). Results. A total of 394 isolates were identified belonging to 12 Enterobacteriaceae genera, the most prevalent were Escherichia coli (81/394 = 20.56%), Salmonella spp (74/394 = 18.78%), and Klebsiella spp (39/394 = 9.90%) respectively. Overall, 84/394 (21.32%) were ESBL producers, 164/394 (41.62%) were resistant to quinolones, 66/394 (16.75%) resistant to aminoglycosides with 44.0% (173/394) expressing MDR phenotype. Poor hygiene practice (OR 2.55, 95% CI: 1.67, 3.89,
) and rearing for >45 days, (OR = 7.98, 95% CI: 5.05, 12.6,
) were associated with increased carriage of MDR. Plasmid-borne resistance genes were detected in 76/84 (90.48%) of ESBL-producing isolates, 151/164 (92.07%) quinolone resistant isolates and 59/66 (89.39%) aminoglycoside resistant isolates with co-occurrence of two or more genes per isolate in 58/84 (69.05%) of ESBLs, 132/164 (80.49%) of quinolone resistant isolates and 28/66 (42.42%) of aminoglycoside resistant isolates. Conclusion. This study found high carriage and widespread distribution of Enterobacteriaceae with ESBL and MDR in broiler chicken in the West Region of Cameroon. Most PMQR genes in bacteria were found at levels higher than is seen elsewhere, representing a risk in the wider human community.
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Peraman R, Chinni S, Sure SK, Kutagulla VK, Peraman M, V.N. A, Y. PR. Anti-evolution Drugs: A New Paradigm to Combat Drug Resistance. LETT DRUG DES DISCOV 2022. [DOI: 10.2174/1570180818666210804142612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
:
Drug resistance confronts chemotherapy of neoplasm and microbial infections. A vast
array of molecular mechanisms was implicated in drug resistance, including generation of drug efflux
transporters, mutation of drug targets, and alteration of drug metabolism. With the alarming rate
of increase in drug resistance, pathogens are bolstering in such a way that many new drugs face efficacy
problems within a short span of entry into the market. Evolution is the driving force towards the
development of drug resistance. By adopting the modern genomic and functionomic analytical techniques,
scientists have now identified novel genes and signalling proteins involved in the evolution
of drug resistance in microorganisms. Given the current knowledge of bacterial evolution, antibiotic
drug discovery is ready for a paradigm shift to explore the newer ways to tackle drug resistance. The
article discusses such recent developments and reviews their merits and demerits in an attempt to
envisage the findings in this new domain of medicine.
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Affiliation(s)
- Ramalingam Peraman
- National Institute of Pharmaceutical Education and Research (NIPER)-Hajipur, Bihar, 844102, India
| | - Santhivardhan Chinni
- National Institute of Pharmaceutical Education and Research (NIPER)-Hajipur, Bihar, 844102, India
| | - Sathish Kumar Sure
- National Institute of Pharmaceutical Education and Research (NIPER)-Hajipur, Bihar, 844102, India
| | - Vinay Kumar Kutagulla
- National Institute of Pharmaceutical Education and Research (NIPER)-Hajipur, Bihar, 844102, India
| | | | - Azger V.N.
- ICMR-National
Institute for Research in Tuberculosis, Chennai, TN, 600031, India
| | - Padmanabha Reddy Y.
- National Institute of Pharmaceutical Education and Research (NIPER)-Hajipur, Bihar, 844102, India
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11
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Gu Y, Huang L, Wu C, Huang J, Hao H, Yuan Z, Cheng G. The Evolution of Fluoroquinolone Resistance in Salmonella under Exposure to Sub-Inhibitory Concentration of Enrofloxacin. Int J Mol Sci 2021; 22:ijms222212218. [PMID: 34830098 PMCID: PMC8619427 DOI: 10.3390/ijms222212218] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 10/25/2021] [Accepted: 11/02/2021] [Indexed: 02/04/2023] Open
Abstract
The evolution of resistance in Salmonella to fluoroquinolones (FQs) under a broad range of sub-inhibitory concentrations (sub-MICs) has not been systematically studied. This study investigated the mechanism of resistance development in Salmonella enterica serovar Enteritidis (S. Enteritidis) under sub-MICs of 1/128×MIC to 1/2×MIC of enrofloxacin (ENR), a widely used veterinary FQ. It was shown that the resistance rate and resistance level of S. Enteritidis varied with the increase in ENR concentration and duration of selection. qRT-PCR results demonstrated that the expression of outer membrane porin (OMP) genes, ompC, ompD and ompF, were down-regulated first to rapidly adapt and develop the resistance of 4×MIC, and as the resistance level increased (≥8×MIC), the up-regulated expression of efflux pump genes, acrB, emrB amd mdfA, along with mutations in quinolone resistance-determining region (QRDR) gradually played a decisive role. Cytohubba analysis based on transcriptomic profiles demonstrated that purB, purC, purD, purF, purH, purK, purL, purM, purN and purT were the hub genes for the FQs resistance. The 'de novo' IMP biosynthetic process, purine ribonucleoside monophosphate biosynthetic process and purine ribonucleotide biosynthetic process were the top three biological processes screened by MCODE. This study first described the dynamics of FQ resistance evolution in Salmonella under a long-term selection of sub-MICs of ENR in vitro. In addition, this work offers greater insight into the transcriptome changes of S. Enteritidis under the selection of ENR and provides a framework for FQs resistance of Salmonella for further studies.
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Affiliation(s)
- Yufeng Gu
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (Y.G.); (L.H.); (C.W.); (J.H.); (H.H.); (Z.Y.)
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan 430070, China
| | - Lulu Huang
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (Y.G.); (L.H.); (C.W.); (J.H.); (H.H.); (Z.Y.)
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan 430070, China
| | - Cuirong Wu
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (Y.G.); (L.H.); (C.W.); (J.H.); (H.H.); (Z.Y.)
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan 430070, China
| | - Junhong Huang
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (Y.G.); (L.H.); (C.W.); (J.H.); (H.H.); (Z.Y.)
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan 430070, China
| | - Haihong Hao
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (Y.G.); (L.H.); (C.W.); (J.H.); (H.H.); (Z.Y.)
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan 430070, China
| | - Zonghui Yuan
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (Y.G.); (L.H.); (C.W.); (J.H.); (H.H.); (Z.Y.)
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan 430070, China
| | - Guyue Cheng
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (Y.G.); (L.H.); (C.W.); (J.H.); (H.H.); (Z.Y.)
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan 430070, China
- Correspondence: ; Tel.: +86-027-8728-7165
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12
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Pennycook JH, Scanlan PD. Ecological and Evolutionary responses to Antibiotic Treatment in the Human Gut Microbiota. FEMS Microbiol Rev 2021; 45:fuab018. [PMID: 33822937 PMCID: PMC8498795 DOI: 10.1093/femsre/fuab018] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 03/25/2021] [Indexed: 12/16/2022] Open
Abstract
The potential for antibiotics to affect the ecology and evolution of the human gut microbiota is well recognised and has wide-ranging implications for host health. Here, we review the findings of key studies that surveyed the human gut microbiota during antibiotic treatment. We find several broad patterns including the loss of diversity, disturbance of community composition, suppression of bacteria in the Actinobacteria phylum, amplification of bacteria in the Bacteroidetes phylum, and promotion of antibiotic resistance. Such changes to the microbiota were often, but not always, recovered following the end of treatment. However, many studies reported unique and/or contradictory results, which highlights our inability to meaningfully predict or explain the effects of antibiotic treatment on the human gut microbiome. This problem arises from variation between existing studies in three major categories: differences in dose, class and combinations of antibiotic treatments used; differences in demographics, lifestyles, and locations of subjects; and differences in measurements, analyses and reporting styles used by researchers. To overcome this, we suggest two integrated approaches: (i) a top-down approach focused on building predictive models through large sample sizes, deep metagenomic sequencing, and effective collaboration; and (ii) a bottom-up reductionist approach focused on testing hypotheses using model systems.
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Affiliation(s)
- Joseph Hugh Pennycook
- APC Microbiome Ireland, Biosciences Institute, University College Cork, College Road, Cork, T12 YT20, Ireland
- School of Mirobiology, Food Science & Technology Building, University College Cork, College Road, Cork, T12 K8AF, Ireland
| | - Pauline Deirdre Scanlan
- APC Microbiome Ireland, Biosciences Institute, University College Cork, College Road, Cork, T12 YT20, Ireland
- School of Mirobiology, Food Science & Technology Building, University College Cork, College Road, Cork, T12 K8AF, Ireland
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13
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Chadha J, Khullar L. Subinhibitory concentrations of nalidixic acid alter bacterial physiology and induce anthropogenic resistance in a commensal strain of Escherichia coli in vitro. Lett Appl Microbiol 2021; 73:623-633. [PMID: 34376018 DOI: 10.1111/lam.13550] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 07/29/2021] [Accepted: 08/03/2021] [Indexed: 12/16/2022]
Abstract
The human gut houses a complex group of bacterial genera, including both opportunistic pathogens and commensal micro-organisms. These are regularly exposed to antibiotics, and their subinhibitory concentrations play a pivotal role in shaping the microbial responses. This study was aimed to investigate the effects exerted by sub-MICs of nalidixic acid (NA) on the growth rate, bacterial motility, biofilm formation and expression of outer membrane proteins (OMPs) in a commensal strain of E. coli. The NA-sensitive strain was sequentially passaged under sub-MICs of NA. E-test was used to determine the MIC values of NA. Results indicated significant changes in the growth profile of commensal E. coli upon exposure to NA at sub-MICs. Differential expression of OMPs was observed in cells treated with sub-MICs of NA. Bacterial motility was reduced under 1/2 MIC of NA. Interestingly, successive passaging under 1/2 MIC of NA led to the emergence of resistant E. coli with an increased MIC value of 64 µg ml-1 in just 24 days. The NA-resistant variant was confirmed by comparing its 16S rRNA sequence to that of the sensitive commensal strain. Mutations in the Quinolone Resistance-Determining Regions (QRDRs) of chromosomal gyrA, and Topoisomerase IV-encoding parC genes were detected in NA-resistant E. coli. Our results demonstrate how antibiotics play an important role as signalling molecules or elicitors in driving the pathogenicity of commensal bacteria in vitro.
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Affiliation(s)
- J Chadha
- Department of Microbiology, University of Delhi South Campus, New Delhi, India
| | - L Khullar
- Department of Microbiology, University of Delhi South Campus, New Delhi, India
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14
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Yang X, Hashemi MM, Andini N, Li MM, Kuang S, Carroll KC, Wang TH, Yang S. RNA markers for ultra-rapid molecular antimicrobial susceptibility testing in fluoroquinolone-treated Klebsiella pneumoniae. J Antimicrob Chemother 2021; 75:1747-1755. [PMID: 32191305 DOI: 10.1093/jac/dkaa078] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Revised: 02/06/2020] [Accepted: 02/09/2020] [Indexed: 11/12/2022] Open
Abstract
OBJECTIVES Traditional antimicrobial susceptibility testing (AST) is growth dependent and time-consuming. With rising rates of drug-resistant infections, a novel diagnostic method is critically needed that can rapidly reveal a pathogen's antimicrobial susceptibility to guide appropriate treatment. Recently, RNA sequencing has been identified as a powerful diagnostic tool to explore transcriptional gene expression and improve AST. METHODS RNA sequencing was used to investigate the potential of RNA markers for rapid molecular AST using Klebsiella pneumoniae and ciprofloxacin as a model. Downstream bioinformatic analysis was applied for optimal marker selection. Further validation on 11 more isolates of K. pneumoniae was performed using quantitative real-time PCR. RESULTS From RNA sequencing, we identified RNA signatures that were induced or suppressed following exposure to ciprofloxacin. Significant shifts at the transcript level were observed as early as 10 min after antibiotic exposure. Lastly, we confirmed marker expression profiles with concordant MIC results from traditional culture-based AST and validated across 11 K. pneumoniae isolates. recA, coaA and metN transcripts harbour the most sensitive susceptibility information and were selected as our top markers. CONCLUSIONS Our results suggest that RNA signature is a promising approach to AST development, resulting in faster clinical diagnosis and treatment of infectious disease. This approach is potentially applicable in other models including other pathogens exposed to different classes of antibiotics.
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Affiliation(s)
- Xi Yang
- Department of Emergency Medicine, Stanford University, Stanford, CA, USA
| | - Marjan M Hashemi
- Department of Emergency Medicine, Stanford University, Stanford, CA, USA
| | - Nadya Andini
- Department of Emergency Medicine, Stanford University, Stanford, CA, USA
| | - Michelle M Li
- Department of Mathematical and Computational Science, Stanford University, Stanford, CA, USA
| | - Shuzhen Kuang
- Department of Biological Sciences, Clemson University, Clemson, SC, USA
| | - Karen C Carroll
- Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
| | - Tza-Huei Wang
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Samuel Yang
- Department of Emergency Medicine, Stanford University, Stanford, CA, USA
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15
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Robertson J, McGoverin C, White JR, Vanholsbeeck F, Swift S. Rapid Detection of Escherichia coli Antibiotic Susceptibility Using Live/Dead Spectrometry for Lytic Agents. Microorganisms 2021; 9:924. [PMID: 33925816 PMCID: PMC8147107 DOI: 10.3390/microorganisms9050924] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 04/21/2021] [Accepted: 04/22/2021] [Indexed: 02/06/2023] Open
Abstract
Antibiotic resistance is a serious threat to public health. The empiric use of the wrong antibiotic occurs due to urgency in treatment combined with slow, culture-based diagnostic techniques. Inappropriate antibiotic choice can promote the development of antibiotic resistance. We investigated live/dead spectrometry using a fluorimeter (Optrode) as a rapid alternative to culture-based techniques through application of the LIVE/DEAD® BacLightTM Bacterial Viability Kit. Killing was detected by the Optrode in near real-time when Escherichia coli was treated with lytic antibiotics-ampicillin and polymyxin B-and stained with SYTO 9 and/or propidium iodide. Antibiotic concentration, bacterial growth phase, and treatment time used affected the efficacy of this detection method. Quantification methods of the lethal action and inhibitory action of the non-lytic antibiotics, ciprofloxacin and chloramphenicol, respectively, remain to be elucidated.
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Affiliation(s)
- Julia Robertson
- Department of Molecular Medicine and Pathology, The University of Auckland, Auckland 1023, New Zealand; (J.R.W.); (S.S.)
- The Dodd-Walls Centre for Photonic and Quantum Technologies, Auckland 1010, New Zealand; (C.M.); (F.V.)
| | - Cushla McGoverin
- The Dodd-Walls Centre for Photonic and Quantum Technologies, Auckland 1010, New Zealand; (C.M.); (F.V.)
- Department of Physics, The University of Auckland, Auckland 1010, New Zealand
| | - Joni R. White
- Department of Molecular Medicine and Pathology, The University of Auckland, Auckland 1023, New Zealand; (J.R.W.); (S.S.)
- The Dodd-Walls Centre for Photonic and Quantum Technologies, Auckland 1010, New Zealand; (C.M.); (F.V.)
| | - Frédérique Vanholsbeeck
- The Dodd-Walls Centre for Photonic and Quantum Technologies, Auckland 1010, New Zealand; (C.M.); (F.V.)
- Department of Physics, The University of Auckland, Auckland 1010, New Zealand
| | - Simon Swift
- Department of Molecular Medicine and Pathology, The University of Auckland, Auckland 1023, New Zealand; (J.R.W.); (S.S.)
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16
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Huang M, Liu M, Liu J, Zhu D, Tang Q, Jia R, Chen S, Zhao X, Yang Q, Wu Y, Zhang S, Huang J, Ou X, Mao S, Gao Q, Sun D, Wang M, Cheng A. Functional characterization of Fur in iron metabolism, oxidative stress resistance and virulence of Riemerella anatipestifer. Vet Res 2021; 52:48. [PMID: 33741064 PMCID: PMC7976709 DOI: 10.1186/s13567-021-00919-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 03/01/2021] [Indexed: 12/11/2022] Open
Abstract
Iron is essential for most bacteria to survive, but excessive iron leads to damage by the Fenton reaction. Therefore, the concentration of intracellular free iron must be strictly controlled in bacteria. Riemerella anatipestifer (R. anatipestifer), a Gram-negative bacterium, encodes the iron uptake system. However, the iron homeostasis mechanism remains largely unknown. In this study, it was shown that compared with the wild type R. anatipestifer CH-1, R. anatipestifer CH-1Δfur was more sensitive to streptonigrin, and this effect was alleviated when the bacteria were cultured in iron-depleted medium, suggesting that the fur mutant led to excess iron accumulation inside cells. Similarly, compared with R. anatipestifer CH-1∆recA, R. anatipestifer CH-1∆recAΔfur was more sensitive to H2O2-induced oxidative stress when the bacteria were grown in iron-rich medium rather than iron-depleted medium. Accordingly, it was shown that R. anatipestifer CH-1∆recAΔfur produced more intracellular ROS than R. anatipestifer CH-1∆recA in iron-rich medium. Electrophoretic mobility shift assays showed that R. anatipestifer CH-1 Fur suppressed the transcription of putative iron uptake genes through binding to their promoter regions. Finally, it was shown that compared with the wild type, R. anatipestifer CH-1Δfur was significantly attenuated in ducklings and that the colonization ability of R. anatipestifer CH-1Δfur in various tissues or organs was decreased. All these results suggested that Fur is important for iron homeostasis in R. anatipestifer and its pathogenic mechanism.
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Affiliation(s)
- Mi Huang
- Institute of Preventive Veterinary Medicine, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.,Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, 611130, Sichuan, China
| | - Mafeng Liu
- Institute of Preventive Veterinary Medicine, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.,Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, 611130, Sichuan, China
| | - Jiajun Liu
- Institute of Preventive Veterinary Medicine, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.,Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, 611130, Sichuan, China
| | - Dekang Zhu
- Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, 611130, Sichuan, China
| | - Qianying Tang
- Institute of Preventive Veterinary Medicine, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.,Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, 611130, Sichuan, China
| | - Renyong Jia
- Institute of Preventive Veterinary Medicine, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.,Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, 611130, Sichuan, China
| | - Shun Chen
- Institute of Preventive Veterinary Medicine, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.,Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, 611130, Sichuan, China
| | - Xinxin Zhao
- Institute of Preventive Veterinary Medicine, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.,Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, 611130, Sichuan, China
| | - Qiao Yang
- Institute of Preventive Veterinary Medicine, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.,Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, 611130, Sichuan, China
| | - Ying Wu
- Institute of Preventive Veterinary Medicine, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.,Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, 611130, Sichuan, China
| | - Shaqiu Zhang
- Institute of Preventive Veterinary Medicine, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.,Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, 611130, Sichuan, China
| | - Juan Huang
- Institute of Preventive Veterinary Medicine, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.,Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, 611130, Sichuan, China
| | - Xumin Ou
- Institute of Preventive Veterinary Medicine, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.,Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, 611130, Sichuan, China
| | - Sai Mao
- Institute of Preventive Veterinary Medicine, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.,Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, 611130, Sichuan, China
| | - Qun Gao
- Institute of Preventive Veterinary Medicine, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.,Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, 611130, Sichuan, China
| | - Di Sun
- Institute of Preventive Veterinary Medicine, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.,Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, 611130, Sichuan, China
| | - Mingshu Wang
- Institute of Preventive Veterinary Medicine, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, 611130, Sichuan, China. .,Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, 611130, Sichuan, China. .,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, 611130, Sichuan, China.
| | - Anchun Cheng
- Institute of Preventive Veterinary Medicine, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, 611130, Sichuan, China. .,Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, 611130, Sichuan, China. .,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, 611130, Sichuan, China.
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17
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In Vitro Assessment of Antimicrobial Resistance Dissemination Dynamics during Multidrug-Resistant-Bacterium Invasion Events by Using a Continuous-Culture Device. Appl Environ Microbiol 2021; 87:AEM.02659-20. [PMID: 33361364 DOI: 10.1128/aem.02659-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 12/11/2020] [Indexed: 11/20/2022] Open
Abstract
Antimicrobial-resistant pathogens display significant public health threats by causing difficulties in clinical treatment of bacterial infection. Antimicrobial resistance (AMR) is transmissible between bacteria, significantly increasing the appearance of antimicrobial-resistant pathogens and aggravating the AMR problem. In this work, the dissemination dynamics of AMR from invading multidrug-resistant (MDR) Escherichia coli to a community of pathogenic Salmonella enterica was investigated using a continuous-culture device, and the behaviors of dissemination dynamics under different levels of antibiotic stress were investigated. Three MDR E. coli invasion events were analyzed in this work: MDR E. coli-S. enterica cocolonization, MDR E. coli invasion after antibiotic treatment of S. enterica, and MDR E. coli invasion before antibiotic treatment of S. enterica It was found that both horizontal gene transfer (HGT) and vertical gene transfer (VGT) play significant roles in AMR dissemination, although different processes contribute differently under different circumstances, that environmental levels of antibiotics promote AMR dissemination by enhancing HGT rather than leading to selective advantage for resistant bacteria, and that early invasion of MDR E. coli completely and quickly sabotages the effectiveness of antibiotic treatment. These findings contribute to understanding the drivers of AMR dissemination under different antibiotic stresses, the detrimental impact of environmental tetracycline contamination, and the danger of nosocomial presence and dissemination of MDR nonpathogens.IMPORTANCE Antimicrobial resistance poses a grave threat to public health and reduces the effectiveness of antimicrobial drugs in treating bacterial infections. Antimicrobial resistance is transmissible, either by horizontal gene transfer between bacteria or by vertical gene transfer following inheritance of genetic traits. The dissemination dynamics and behaviors of this threat, however, have not been rigorously investigated. In this work, with a continuous-culture device, we studied antimicrobial resistance dissemination processes by simulating antimicrobial-resistant Escherichia coli invasion to a pathogenic Salmonella enterica community. Using this novel tool, we provide evidence on the drivers of antimicrobial resistance dissemination, on the detrimental impact of environmental antibiotic contamination, and on the danger of antimicrobial resistance in hospitals, even if what harbors the antimicrobial resistance is not a pathogen. This work furthers our understanding of antimicrobial resistance and its dissemination between bacteria and of antibiotic therapy, our most powerful tool against bacterial infection.
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18
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Bacterial phenotypic heterogeneity in DNA repair and mutagenesis. Biochem Soc Trans 2021; 48:451-462. [PMID: 32196548 PMCID: PMC7200632 DOI: 10.1042/bst20190364] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 02/26/2020] [Accepted: 02/28/2020] [Indexed: 02/06/2023]
Abstract
Genetically identical cells frequently exhibit striking heterogeneity in various phenotypic traits such as their morphology, growth rate, or gene expression. Such non-genetic diversity can help clonal bacterial populations overcome transient environmental challenges without compromising genome stability, while genetic change is required for long-term heritable adaptation. At the heart of the balance between genome stability and plasticity are the DNA repair pathways that shield DNA from lesions and reverse errors arising from the imperfect DNA replication machinery. In principle, phenotypic heterogeneity in the expression and activity of DNA repair pathways can modulate mutation rates in single cells and thus be a source of heritable genetic diversity, effectively reversing the genotype-to-phenotype dogma. Long-standing evidence for mutation rate heterogeneity comes from genetics experiments on cell populations, which are now complemented by direct measurements on individual living cells. These measurements are increasingly performed using fluorescence microscopy with a temporal and spatial resolution that enables localising, tracking, and counting proteins with single-molecule sensitivity. In this review, we discuss which molecular processes lead to phenotypic heterogeneity in DNA repair and consider the potential consequences on genome stability and dynamics in bacteria. We further inspect these concepts in the context of DNA damage and mutation induced by antibiotics.
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19
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Bush NG, Diez-Santos I, Abbott LR, Maxwell A. Quinolones: Mechanism, Lethality and Their Contributions to Antibiotic Resistance. Molecules 2020; 25:E5662. [PMID: 33271787 PMCID: PMC7730664 DOI: 10.3390/molecules25235662] [Citation(s) in RCA: 123] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/27/2020] [Accepted: 11/28/2020] [Indexed: 12/05/2022] Open
Abstract
Fluoroquinolones (FQs) are arguably among the most successful antibiotics of recent times. They have enjoyed over 30 years of clinical usage and become essential tools in the armoury of clinical treatments. FQs target the bacterial enzymes DNA gyrase and DNA topoisomerase IV, where they stabilise a covalent enzyme-DNA complex in which the DNA is cleaved in both strands. This leads to cell death and turns out to be a very effective way of killing bacteria. However, resistance to FQs is increasingly problematic, and alternative compounds are urgently needed. Here, we review the mechanisms of action of FQs and discuss the potential pathways leading to cell death. We also discuss quinolone resistance and how quinolone treatment can lead to resistance to non-quinolone antibiotics.
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Affiliation(s)
| | | | | | - Anthony Maxwell
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK; (N.G.B.); (I.D.-S.); (L.R.A.)
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20
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Revitt-Mills SA, Robinson A. Antibiotic-Induced Mutagenesis: Under the Microscope. Front Microbiol 2020; 11:585175. [PMID: 33193230 PMCID: PMC7642495 DOI: 10.3389/fmicb.2020.585175] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 09/28/2020] [Indexed: 11/24/2022] Open
Abstract
The development of antibiotic resistance poses an increasing threat to global health. Understanding how resistance develops in bacteria is critical for the advancement of new strategies to combat antibiotic resistance. In the 1980s, it was discovered that certain antibiotics induce elevated rates of mutation in bacteria. From this, an “increased evolvability” hypothesis was proposed: antibiotic-induced mutagenesis increases the genetic diversity of bacterial populations, thereby increasing the rate at which bacteria develop antibiotic resistance. However, antibiotic-induced mutagenesis is one of multiple competing factors that act on bacterial populations exposed to antibiotics. Its relative importance in shaping evolutionary outcomes, including the development of antibiotic resistance, is likely to depend strongly on the conditions. Presently, there is no quantitative model that describes the relative contribution of antibiotic-induced mutagenesis to bacterial evolution. A far more complete understanding could be reached if we had access to technology that enabled us to study antibiotic-induced mutagenesis at the molecular-, cellular-, and population-levels simultaneously. Direct observations would, in principle, allow us to directly link molecular-level events with outcomes in individual cells and cell populations. In this review, we highlight microscopy studies which have allowed various aspects of antibiotic-induced mutagenesis to be directly visualized in individual cells for the first time. These studies have revealed new links between error-prone DNA polymerases and recombinational DNA repair, evidence of spatial regulation occurring during the SOS response, and enabled real-time readouts of mismatch and mutation rates. Further, we summarize the recent discovery of stochastic population fluctuations in cultures exposed to sub-inhibitory concentrations of bactericidal antibiotics and discuss the implications of this finding for the study of antibiotic-induced mutagenesis. The studies featured here demonstrate the potential of microscopy to provide direct observation of phenomena relevant to evolution under antibiotic-induced mutagenesis.
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Affiliation(s)
- Sarah A Revitt-Mills
- Molecular Horizons Institute and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia.,Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia
| | - Andrew Robinson
- Molecular Horizons Institute and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia.,Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia
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21
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Rodríguez-Rosado AI, Valencia EY, Rodríguez-Rojas A, Costas C, Galhardo RS, Rodríguez-Beltrán J, Blázquez J. N-acetylcysteine blocks SOS induction and mutagenesis produced by fluoroquinolones in Escherichia coli. J Antimicrob Chemother 2020; 74:2188-2196. [PMID: 31102529 DOI: 10.1093/jac/dkz210] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 04/15/2019] [Accepted: 04/17/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Fluoroquinolones such as ciprofloxacin induce the mutagenic SOS response and increase the levels of intracellular reactive oxygen species (ROS). Both the SOS response and ROS increase bacterial mutagenesis, fuelling the emergence of resistant mutants during antibiotic treatment. Recently, there has been growing interest in developing new drugs able to diminish the mutagenic effect of antibiotics by modulating ROS production and the SOS response. OBJECTIVES To test whether physiological concentrations of N-acetylcysteine, a clinically safe antioxidant drug currently used in human therapy, is able to reduce ROS production, SOS induction and mutagenesis in ciprofloxacin-treated bacteria without affecting antibiotic activity. METHODS The Escherichia coli strain IBDS1 and its isogenic mutant deprived of SOS mutagenesis (TLS-) were treated with different concentrations of ciprofloxacin, N-acetylcysteine or both drugs in combination. Relevant parameters such as MICs, growth rates, ROS production, SOS induction, filamentation and antibiotic-induced mutation rates were evaluated. RESULTS Treatment with N-acetylcysteine reduced intracellular ROS levels (by ∼40%), as well as SOS induction (by up to 75%) and bacterial filamentation caused by subinhibitory concentrations of ciprofloxacin, without affecting ciprofloxacin antibacterial activity. Remarkably, N-acetylcysteine completely abolished SOS-mediated mutagenesis. CONCLUSIONS Collectively, our data strongly support the notion that ROS are a key factor in antibiotic-induced SOS mutagenesis and open the possibility of using N-acetylcysteine in combination with antibiotic therapy to hinder the development of antibiotic resistance.
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Affiliation(s)
| | - Estela Ynés Valencia
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | | | - Coloma Costas
- Instituto de Biomedicina de Sevilla (IBiS), Seville, Spain
| | - Rodrigo S Galhardo
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | | | - Jesús Blázquez
- Centro Nacional de Biotecnología (CNB), Madrid, Spain.,Clinical Unit of Infectious Diseases, Microbiology and Preventive Medicine, University Hospital Virgen del Rocio, Seville, Spain
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22
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Gudda FO, Waigi MG, Odinga ES, Yang B, Carter L, Gao Y. Antibiotic-contaminated wastewater irrigated vegetables pose resistance selection risks to the gut microbiome. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 264:114752. [PMID: 32417582 DOI: 10.1016/j.envpol.2020.114752] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 05/03/2020] [Accepted: 05/05/2020] [Indexed: 06/11/2023]
Abstract
Wastewater reuse in food crop irrigation has led to agroecosystem pollution concerns and human health risks. However, there is limited attention on the relationship of sub-lethal antibiotic levels in vegetables and resistance selection. Most risk assessment studies show non-significant toxicity, but overlook the link between antibiotics in crops and propagation of gut microbiome resistance selection. The review highlights the risk of antibiotics in treated water used for irrigation, uptake, and accumulation in edible vegetable parts. Moreover, it elucidates the risks to the adaptive resistance selection of the gut microbiome from sub-lethal antibiotic levels, as a result of dietary contaminated vegetables. Experiments have reported that bacterial resistance selection is possible at concentrations that are several hundred-folds lower than lethal effect levels on susceptible cells. Consequently, mutants selected at low antibiotic levels, such as those from vegetables, are fitter and more resistant compared to those selected at high concentrations. Necessary standardization, such as the development of minimum acceptable antibiotic limits allowable in food crop irrigation water, with a focus on minimum selection concentration, and not only toxicity, has been proposed. Wastewater irrigation offers environmental benefits and can contribute to food security, but it has non-addressed risks. Research gaps, future perspectives, and frameworks of mitigating the potential risks are discussed.
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Affiliation(s)
- Fredrick Owino Gudda
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China; Faculty of Environment and Resource Development, Department of Environmental Sciences, Egerton University, Box 536, Egerton, 20115, Kenya
| | - Michael Gatheru Waigi
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Emmanuel Stephen Odinga
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Bing Yang
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Laura Carter
- School of Geography, University of Leeds, Leeds, LS2 9JT, UK
| | - Yanzheng Gao
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China.
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23
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Goneau LW, Delport J, Langlois L, Poutanen SM, Razvi H, Reid G, Burton JP. Issues beyond resistance: inadequate antibiotic therapy and bacterial hypervirulence. FEMS MICROBES 2020; 1:xtaa004. [PMID: 37333955 PMCID: PMC10117437 DOI: 10.1093/femsmc/xtaa004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 10/15/2020] [Indexed: 10/15/2023] Open
Abstract
The administration of antibiotics while critical for treatment, can be accompanied by potentially severe complications. These include toxicities associated with the drugs themselves, the selection of resistant organisms and depletion of endogenous host microbiota. In addition, antibiotics may be associated with less well-recognized complications arising through changes in the pathogens themselves. Growing evidence suggests that organisms exposed to antibiotics can respond by altering the expression of toxins, invasins and adhesins, as well as biofilm, resistance and persistence factors. The clinical significance of these changes continues to be explored; however, it is possible that treatment with antibiotics may inadvertently precipitate a worsening of the clinical course of disease. Efforts are needed to adjust or augment antibiotic therapy to prevent the transition of pathogens to hypervirulent states. Better understanding the role of antibiotic-microbe interactions and how these can influence disease course is critical given the implications on prescription guidelines and antimicrobial stewardship policies.
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Affiliation(s)
- Lee W Goneau
- Department of Microbiology and Immunology, Western University, London, Ontario, Canada
- Lawson Health Research Institute, 268 Grosvenor St, London, Ontario, N6A 4V2 Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto,1 King's College Cir, Toronto, ON M5S 1A8 Ontario, Canada
| | - Johannes Delport
- Department of Pathology, London Health Sciences Center - Victoria Hospital, 800 Commissioners Rd E, London, Ontario, Canada N6A 5W9
| | - Luana Langlois
- Department of Microbiology and Immunology, Western University, London, Ontario, Canada
| | - Susan M Poutanen
- Department of Laboratory Medicine and Pathobiology, University of Toronto,1 King's College Cir, Toronto, ON M5S 1A8 Ontario, Canada
- Department of Medicine, University of Toronto, 1 King's College Cir, Toronto, ON M5S 1A8 Toronto, Ontario, Canada
- Department of Microbiology, University Health Network and Sinai Health, 190 Elizabeth St. Toronto, ON M5G 2C4, Ontario, Canada
| | - Hassan Razvi
- Lawson Health Research Institute, 268 Grosvenor St, London, Ontario, N6A 4V2 Canada
- Division of Urology, Department of Surgery, Western University, 1151 Richmond St, London, Ontario, N6A 3K7 Canada
| | - Gregor Reid
- Department of Microbiology and Immunology, Western University, London, Ontario, Canada
- Lawson Health Research Institute, 268 Grosvenor St, London, Ontario, N6A 4V2 Canada
- Division of Urology, Department of Surgery, Western University, 1151 Richmond St, London, Ontario, N6A 3K7 Canada
| | - Jeremy P Burton
- Department of Microbiology and Immunology, Western University, London, Ontario, Canada
- Lawson Health Research Institute, 268 Grosvenor St, London, Ontario, N6A 4V2 Canada
- Division of Urology, Department of Surgery, Western University, 1151 Richmond St, London, Ontario, N6A 3K7 Canada
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24
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Cheng D, Hao Ngo H, Guo W, Wang Chang S, Duc Nguyen D, Liu Y, Zhang X, Shan X, Liu Y. Contribution of antibiotics to the fate of antibiotic resistance genes in anaerobic treatment processes of swine wastewater: A review. BIORESOURCE TECHNOLOGY 2020; 299:122654. [PMID: 31917094 DOI: 10.1016/j.biortech.2019.122654] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 12/16/2019] [Accepted: 12/18/2019] [Indexed: 06/10/2023]
Abstract
Antibiotic resistance genes (ARGs) in water environment have become a global health concern. Swine wastewater is widely considered to be one of the major contributors for promoting the proliferation of ARGs in water environments. This paper comprehensively reviews and discusses the occurrence and removal of ARGs in anaerobic treatment of swine wastewater, and contributions of antibiotics to the fate of ARGs. The results reveal that ARGs' removal is unstable during anaerobic processes, which negatively associated with the presence of antibiotics. The abundance of bacteria carrying ARGs increases with the addition of antibiotics and results in the spread of ARGs. The positive relationship was found between antibiotics and the abundance and transfer of ARGs in this review. However, it is necessary to understand the correlation among antibiotics, ARGs and microbial communities, and obtain more knowledge about controlling the dissemination of ARGs in the environment.
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Affiliation(s)
- Dongle Cheng
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Sydney, NWS 2007, Australia
| | - Huu Hao Ngo
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Sydney, NWS 2007, Australia; Joint Research Centre for Protective Infrastructure Technology and Environmental Green Bioprocess, Department of Environmental and Municipal Engineering, Tianjin Chengjian University, Tianjin 300384, China; Department of Environmental Energy Engineering, Kyonggi University, 442-760, Republic of Korea.
| | - Wenshan Guo
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Sydney, NWS 2007, Australia; Joint Research Centre for Protective Infrastructure Technology and Environmental Green Bioprocess, Department of Environmental and Municipal Engineering, Tianjin Chengjian University, Tianjin 300384, China
| | - Soon Wang Chang
- Department of Environmental Energy Engineering, Kyonggi University, 442-760, Republic of Korea
| | - Dinh Duc Nguyen
- Department of Environmental Energy Engineering, Kyonggi University, 442-760, Republic of Korea; Institution of Research and Development, Duy Tan University, Da Nang, Viet Nam; NTT Institute of Hi-Technology, Nguyen Tat Thanh University, Ho Chi Minh City, Viet Nam
| | - Yiwen Liu
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Sydney, NWS 2007, Australia
| | - Xinbo Zhang
- Joint Research Centre for Protective Infrastructure Technology and Environmental Green Bioprocess, Department of Environmental and Municipal Engineering, Tianjin Chengjian University, Tianjin 300384, China
| | - Xue Shan
- Joint Research Centre for Protective Infrastructure Technology and Environmental Green Bioprocess, Department of Environmental and Municipal Engineering, Tianjin Chengjian University, Tianjin 300384, China
| | - Yi Liu
- Department of Environmental Science and Engineering, Fudan University, 2205 Songhu Road, Shanghai 200438, PR China
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25
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Ribeiro ÁCDS, Martins WMBDS, Silva AAD, Gales AC, Rando DGG, Minarini LADR. Exposure to sub-inhibitory ciprofloxacin and nitrofurantoin concentrations increases recA gene expression in uropathogenic Escherichia coli: The role of RecA protein as a drug target. Eur J Pharm Sci 2020; 146:105268. [PMID: 32081832 DOI: 10.1016/j.ejps.2020.105268] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 02/03/2020] [Accepted: 02/15/2020] [Indexed: 01/01/2023]
Abstract
Sub-inhibitory concentrations (sub-MIC) of antimicrobial agents can lead to genetic changes in bacteria, modulating the expression of genes related to bacterial stress and leading to drug resistance. Herein we describe the impact of sub-MIC of ciprofloxacin and nitrofurantoin on three uropathogenic Escherichia coli strains. Disk-diffusion assays with different antimicrobial agents were tested to detect phenotype alterations, and quantitative real-time PCR (qRT-PCR) was performed to analyze the expression of ompF and recA genes. Significant reduction on the susceptibility to ciprofloxacin and nitrofurantoin was detected on disk diffusion test. The qRT-PCR results revealed a 1.2-4.7 increase in recA expression in all E. coli studied, while the ompF expression varied. Because RecA was pointed as an important component to the development of drug resistance, molecular docking studies were performed with three experimentally known inhibitors of this enzyme. These studies aimed to understand the inhibitory binding mode of such compounds. The results confirmed the ADP/ATP binding site as a potential site of inhibitor recognition and a binding mode based on π-stacking interactions with Tyr103 and hydrogen bonds with Tyr264. These findings can be useful for guiding the search and design of new antimicrobial agents, mainly concerning the treatment of infections with resistant bacterial strains.
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Affiliation(s)
- Ághata Cardoso da Silva Ribeiro
- Universidade Federal de São Paulo - UNIFESP, Instituto de Ciências Ambientais, Químicas e Farmacêuticas, Laboratório Multidisciplinar em Saúde e Meio Ambiente, Departamento de Ciências Farmacêuticas, Rua São Nicolau, 210 Diadema, SP, Brazil
| | - Willames Marcos Brasileiro da Silva Martins
- Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina/Universidade Federal de São Paulo - UNIFESP, Rua Pedro de Toledo, 781 São Paulom, SP, Brazil
| | - Adilson Aderito da Silva
- Universidade Presbiteriana Mackenzie, Centro de Ciências Sociais e Aplicadas, Rua da Consolação, 930, São Paulo, SP, Brazil
| | - Ana Cristina Gales
- Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina/Universidade Federal de São Paulo - UNIFESP, Rua Pedro de Toledo, 781 São Paulom, SP, Brazil
| | - Daniela Gonçales Galasse Rando
- Universidade Federal de São Paulo - UNIFESP, Instituto de Ciências Ambientais, Químicas e Farmacêuticas, Grupo de Pesquisas Químico-Farmacêuticas da UNIFESP, Departamento de Ciências Farmacêuticas, Rua São Nicolau, 210, Diadema, SP, Brazil
| | - Luciene Andrade da Rocha Minarini
- Universidade Federal de São Paulo - UNIFESP, Instituto de Ciências Ambientais, Químicas e Farmacêuticas, Laboratório Multidisciplinar em Saúde e Meio Ambiente, Departamento de Ciências Farmacêuticas, Rua São Nicolau, 210 Diadema, SP, Brazil.
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26
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Lim CSQ, Ha KP, Clarke RS, Gavin LA, Cook DT, Hutton JA, Sutherell CL, Edwards AM, Evans LE, Tate EW, Lanyon-Hogg T. Identification of a potent small-molecule inhibitor of bacterial DNA repair that potentiates quinolone antibiotic activity in methicillin-resistant Staphylococcus aureus. Bioorg Med Chem 2019; 27:114962. [PMID: 31307763 PMCID: PMC6892255 DOI: 10.1016/j.bmc.2019.06.025] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 06/12/2019] [Accepted: 06/13/2019] [Indexed: 11/03/2022]
Abstract
The global emergence of antibiotic resistance is one of the most serious challenges facing modern medicine. There is an urgent need for validation of new drug targets and the development of small molecules with novel mechanisms of action. We therefore sought to inhibit bacterial DNA repair mediated by the AddAB/RecBCD protein complexes as a means to sensitize bacteria to DNA damage caused by the host immune system or quinolone antibiotics. A rational, hypothesis-driven compound optimization identified IMP-1700 as a cell-active, nanomolar potency compound. IMP-1700 sensitized multidrug-resistant Staphylococcus aureus to the fluoroquinolone antibiotic ciprofloxacin, where resistance results from a point mutation in the fluoroquinolone target, DNA gyrase. Cellular reporter assays indicated IMP-1700 inhibited the bacterial SOS-response to DNA damage, and compound-functionalized Sepharose successfully pulled-down the AddAB repair complex. This work provides validation of bacterial DNA repair as a novel therapeutic target and delivers IMP-1700 as a tool molecule and starting point for therapeutic development to address the pressing challenge of antibiotic resistance.
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Affiliation(s)
- Carine S Q Lim
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
| | - Kam Pou Ha
- MRC Centre for Molecular Bacteriology and Infection, Department of Medicine, Imperial College London, London SW7 2AZ, UK
| | - Rebecca S Clarke
- MRC Centre for Molecular Bacteriology and Infection, Department of Medicine, Imperial College London, London SW7 2AZ, UK
| | - Leigh-Anne Gavin
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
| | - Declan T Cook
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
| | - Jennie A Hutton
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
| | - Charlotte L Sutherell
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
| | - Andrew M Edwards
- MRC Centre for Molecular Bacteriology and Infection, Department of Medicine, Imperial College London, London SW7 2AZ, UK
| | - Lindsay E Evans
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK; MRC Centre for Molecular Bacteriology and Infection, Department of Medicine, Imperial College London, London SW7 2AZ, UK.
| | - Edward W Tate
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK.
| | - Thomas Lanyon-Hogg
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK.
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27
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Xie X, Lv R, Yang C, Song Y, Yan Y, Cui Y, Yang R. Soft sweep development of resistance in Escherichia coli under fluoroquinolone stress. J Microbiol 2019; 57:1056-1064. [PMID: 31555989 DOI: 10.1007/s12275-019-9177-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 08/05/2019] [Accepted: 08/13/2019] [Indexed: 11/30/2022]
Abstract
We employed a stepwise selection model for investigating the dynamics of antibiotic-resistant variants in Escherichia coli K-12 treated with increasing concentrations of ciprofloxacin (CIP). Firstly, we used Sanger sequencing to screen the variations in the fluoquinolone target genes, then, employed Illumina NGS sequencing for amplicons targeted regions with variations. The results demonstrated that variations G81C in gyrA and K276N and K277L in parC are standing resistance variations (SRVs), while S83A and S83L in gyrA and G78C in parC were emerging resistance variations (ERVs). The variants containing SRVs and/or ERVs were selected successively based on their sensitivities to CIP. Variant strain 1, containing substitution G81C in gyrA, was immediately selected following ciprofloxacin exposure, with obvious increases in the parC SRV, and parC and gyrA ERV allele frequencies. Variant strain 2, containing the SRVs, then dominated the population following a 20× increase in ciprofloxacin concentration, with other associated allele frequencies also elevated. Variant strains 3 and 4, containing ERVs in gyrA and parC, respectively, were then selected at 40× and 160× antibiotic concentrations. Two variants, strains 5 and 6, generated in the selection procedure, were lost because of higher fitness costs or a lower level of resistance compared with variants 3 and 4. For the second induction, all variations/indels were already present as SRVs and selected out step by step at different passages. Whatever the first induction or second induction, our results confirmed the soft selective sweep hypothesis and provided critical information for guiding clinical treatment of pathogens containing SRVs.
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Affiliation(s)
- Xianxing Xie
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P. R. China
| | - Ruichen Lv
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P. R. China.,Huadong Research Institute for Medicine and Biotechnics, Nanjing, P. R. China
| | - Chao Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P. R. China
| | - Yajun Song
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P. R. China
| | - Yanfeng Yan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P. R. China
| | - Yujun Cui
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P. R. China
| | - Ruifu Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P. R. China.
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28
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Blázquez J, Rodríguez-Beltrán J, Matic I. Antibiotic-Induced Genetic Variation: How It Arises and How It Can Be Prevented. Annu Rev Microbiol 2019; 72:209-230. [PMID: 30200850 DOI: 10.1146/annurev-micro-090817-062139] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
By targeting essential cellular processes, antibiotics provoke metabolic perturbations and induce stress responses and genetic variation in bacteria. Here we review current knowledge of the mechanisms by which these molecules generate genetic instability. They include production of reactive oxygen species, as well as induction of the stress response regulons, which lead to enhancement of mutation and recombination rates and modulation of horizontal gene transfer. All these phenomena influence the evolution and spread of antibiotic resistance. The use of strategies to stop or decrease the generation of resistant variants is also discussed.
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Affiliation(s)
- Jesús Blázquez
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), 28049 Madrid, Spain; .,Unidad de Enfermedades Infecciosas, Microbiologia y Medicina Preventiva, Hospital Universitario Virgen del Rocio, 41013 Seville, Spain.,Red Española de Investigacion en Patologia Infecciosa, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | | | - Ivan Matic
- Faculté de Médecine Paris Descartes, INSERM 1001, CNRS, Université Paris-Descartes-Sorbonne Paris Cité, 75014 Paris, France;
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29
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Recombination of the Phase-Variable spnIII Locus Is Independent of All Known Pneumococcal Site-Specific Recombinases. J Bacteriol 2019; 201:JB.00233-19. [PMID: 31085693 PMCID: PMC6620402 DOI: 10.1128/jb.00233-19] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 05/03/2019] [Indexed: 02/03/2023] Open
Abstract
Streptococcus pneumoniae is a leading cause of pneumonia, septicemia, and meningitis. The discovery that genetic rearrangements in a type I restriction-modification locus can impact gene regulation and colony morphology led to a new understanding of how this pathogen switches from harmless colonizer to invasive pathogen. These rearrangements, which alter the DNA specificity of the type I restriction-modification enzyme, occur across many different pneumococcal serotypes and sequence types and in the absence of all known pneumococcal site-specific recombinases. This finding suggests that this is a truly global mechanism of pneumococcal gene regulation and the need for further investigation of mechanisms of site-specific recombination. Streptococcus pneumoniae is one of the world’s leading bacterial pathogens, causing pneumonia, septicemia, and meningitis. In recent years, it has been shown that genetic rearrangements in a type I restriction-modification system (SpnIII) can impact colony morphology and gene expression. By generating a large panel of mutant strains, we have confirmed a previously reported result that the CreX (also known as IvrR and PsrA) recombinase found within the locus is not essential for hsdS inversions. In addition, mutants of homologous recombination pathways also undergo hsdS inversions. In this work, we have shown that these genetic rearrangements, which result in different patterns of genome methylation, occur across a wide variety of serotypes and sequence types, including two strains (a 19F and a 6B strain) naturally lacking CreX. Our gene expression analysis, by transcriptome sequencing (RNAseq), confirms that the level of creX expression is impacted by these genomic rearrangements. In addition, we have shown that the frequency of hsdS recombination is temperature dependent. Most importantly, we have demonstrated that the other known pneumococcal site-specific recombinases XerD, XerS, and SPD_0921 are not involved in spnIII recombination, suggesting that a currently unknown mechanism is responsible for the recombination of these phase-variable type I systems. IMPORTANCEStreptococcus pneumoniae is a leading cause of pneumonia, septicemia, and meningitis. The discovery that genetic rearrangements in a type I restriction-modification locus can impact gene regulation and colony morphology led to a new understanding of how this pathogen switches from harmless colonizer to invasive pathogen. These rearrangements, which alter the DNA specificity of the type I restriction-modification enzyme, occur across many different pneumococcal serotypes and sequence types and in the absence of all known pneumococcal site-specific recombinases. This finding suggests that this is a truly global mechanism of pneumococcal gene regulation and the need for further investigation of mechanisms of site-specific recombination.
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30
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Morgan RN, Saleh SE, Farrag HA, Aboulwafa MM. Prevalence and pathologic effects of colibactin and cytotoxic necrotizing factor-1 (Cnf 1) in Escherichia coli: experimental and bioinformatics analyses. Gut Pathog 2019; 11:22. [PMID: 31139264 PMCID: PMC6525971 DOI: 10.1186/s13099-019-0304-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 05/02/2019] [Indexed: 12/29/2022] Open
Abstract
Background The colibactin and cytotoxic necrotizing factor 1 (Cnf 1) are toxins with cell cycle modulating effects that contribute to tumorgenesis and hyperproliferation. This study aimed to investigate the prevalence and pathologic effects of Cnf 1 and colibactin among hemolytic uropathogenic Escherichia coli (UPEC). The bioinformatics approach incorporated in this study aimed to expand the domain of the in vitro study and explore the prevalence of both toxins among other bacterial species. A total of 125 E. coli isolates were recovered from UTIs patients. The isolates were tested for their hemolytic activity, subjected to tissue culture and PCR assays to detect the phenotypic and genotypic features of both toxins. A rat ascending UTI in vivo model was conducted using isolates expressing or non-expressing Cnf 1 and colibactin (ClbA and ClbQ). The bioinformatics analyses were inferred by Maximum likelihood method and the evolutionary relatedness was deduced by MEGA X. Results Only 21 (16.8%) out of 125 isolates were hemolytic and 10 of these (47.62%) harbored the toxins encoding genes (cnf 1+, clbA+ and clbQ+). The phenotypic features of both toxins were exhibited by only 7 of the (cnf 1+clbA+clbQ+) harboring isolates. The severest infections, hyperplastic and genotoxic changes in kidneys and bladders were observed in rats infected with the cnf 1+clbA+clbQ+ isolates. Conclusion Only 33.3% of the hemolytic UPEC isolates exhibited the phenotypic and genotypic features of Cnf 1 and Colibactin. The in vivo animal model results gives an evidence of active Cnf 1 and Colibactin expression and indicates the risks associated with recurrent and chronic UTIs caused by UPEC. The bioinformatics analyses confirmed the predominance of colibactin pks island among Enterobacteriaceae family (92.86%), with the highest occurrence among Escherichia species (53.57%), followed by Klebsiella (28.57%), Citrobacter (7.14%), and Enterobacter species (3.57%). The Cnf 1 is predominant among Escherichia coli (94.05%) and sporadically found among Shigella species (1.08%), Salmonella enterica (0.54%), Yersinia pseudotuberculosis (1.08%), Photobacterium (1.08%), Moritella viscosa (0.54%), and Carnobacterium maltaromaticum (0.54%). A close relatedness was observed between the 54-kb pks island of Escherichia coli, the probiotic Escherichia coli Nissle 1917, Klebsiella aerogenes, Klebsiella pneumoniae and Citrobacter koseri. Electronic supplementary material The online version of this article (10.1186/s13099-019-0304-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Radwa N Morgan
- 1Drug Radiation Research Department, National Centre for Radiation Research and Technology (NCRRT), Egyptian Atomic Energy Authority (EAEA), 3 Ahmed El-Zomor Street, Nasr City, Cairo, 11787 Egypt
| | - Sarra E Saleh
- 2Microbiology and Immunology Department, Faculty of Pharmacy, Ain Shams University, African Union Organization Street, Abbassia, Cairo, 11566 Egypt
| | - Hala A Farrag
- 1Drug Radiation Research Department, National Centre for Radiation Research and Technology (NCRRT), Egyptian Atomic Energy Authority (EAEA), 3 Ahmed El-Zomor Street, Nasr City, Cairo, 11787 Egypt
| | - Mohammad M Aboulwafa
- 2Microbiology and Immunology Department, Faculty of Pharmacy, Ain Shams University, African Union Organization Street, Abbassia, Cairo, 11566 Egypt
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31
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Khan FA, Söderquist B, Jass J. Prevalence and Diversity of Antibiotic Resistance Genes in Swedish Aquatic Environments Impacted by Household and Hospital Wastewater. Front Microbiol 2019; 10:688. [PMID: 31019498 PMCID: PMC6458280 DOI: 10.3389/fmicb.2019.00688] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Accepted: 03/19/2019] [Indexed: 12/16/2022] Open
Abstract
Antibiotic-resistant Enterobacteriaceae and non-lactose fermenting Gram-negative bacteria are a major cause of nosocomial infections. Antibiotic misuse has fueled the worldwide spread of resistant bacteria and the genes responsible for antibiotic resistance (ARGs). There is evidence that ARGs are ubiquitous in non-clinical environments, especially those affected by anthropogenic activity. However, the emergence and primary sources of ARGs in the environment of countries with strict regulations for antibiotics usage are not fully explored. The aim of the present study was to evaluate the repertoire of ARGs of culturable Gram-negative bacteria from directionally connected sites from the hospital to the wastewater treatment plant (WWTP), and downstream aquatic environments in central Sweden. The ARGs were detected from genomic DNA isolated from a population of selectively cultured coliform and Gram-negative bacteria using qPCR. The results show that hospital wastewater was a reservoir of several class B β-lactamase genes such as bla IMP-1 , bla IMP-2, and bla OXA-23, however, most of these genes were not observed in downstream locations. Moreover, β-lactamase genes such as bla OXA-48, bla CTX-M-8, and bla SFC-1, bla V IM-1, and bla V IM-13 were detected in downstream river water but not in the WWTP. The results indicate that the WWTP and hospital wastewaters were reservoirs of most ARGs and contribute to the diversity of ARGs in associated natural environments. However, this study suggests that other factors may also have minor contributions to the prevalence and diversity of ARGs in natural environments.
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Affiliation(s)
- Faisal Ahmad Khan
- The Life Science Centre – Biology, School of Science and Technology, Örebro University, Örebro, Sweden
| | - Bo Söderquist
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Jana Jass
- The Life Science Centre – Biology, School of Science and Technology, Örebro University, Örebro, Sweden
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Bacterial Cytological Profiling as a Tool To Study Mechanisms of Action of Antibiotics That Are Active against Acinetobacter baumannii. Antimicrob Agents Chemother 2019; 63:AAC.02310-18. [PMID: 30745382 DOI: 10.1128/aac.02310-18] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 01/30/2019] [Indexed: 01/09/2023] Open
Abstract
An increasing number of multidrug-resistant Acinetobacter baumannii (MDR-AB) infections have been reported worldwide, posing a threat to public health. The establishment of methods to elucidate the mechanism of action (MOA) of A. baumannii-specific antibiotics is needed to develop novel antimicrobial therapeutics with activity against MDR-AB We previously developed bacterial cytological profiling (BCP) to understand the MOA of compounds in Escherichia coli and Bacillus subtilis Given how distantly related A. baumannii is to these species, it was unclear to what extent it could be applied. Here, we implemented BCP as an antibiotic MOA discovery platform for A. baumannii We found that the BCP platform can distinguish among six major antibiotic classes and can also subclassify antibiotics that inhibit the same cellular pathway but have different molecular targets. We used BCP to show that the compound NSC145612 inhibits the growth of A. baumannii via targeting RNA transcription. We confirmed this result by isolating and characterizing resistant mutants with mutations in the rpoB gene. Altogether, we conclude that BCP provides a useful tool for MOA studies of antibacterial compounds that are active against A. baumannii.
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33
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Rehman A, Patrick WM, Lamont IL. Mechanisms of ciprofloxacin resistance in Pseudomonas aeruginosa: new approaches to an old problem. J Med Microbiol 2019; 68:1-10. [DOI: 10.1099/jmm.0.000873] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Affiliation(s)
- Attika Rehman
- 1Department of Biochemistry, University of Otago, New Zealand
| | - Wayne M. Patrick
- 1Department of Biochemistry, University of Otago, New Zealand
- 2School of Biological Sciences, Victoria University of Wellington, New Zealand
| | - Iain L. Lamont
- 1Department of Biochemistry, University of Otago, New Zealand
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Akkaya Ö, Nikel PI, Pérez-Pantoja D, de Lorenzo V. Evolving metabolism of 2,4-dinitrotoluene triggers SOS-independent diversification of host cells. Environ Microbiol 2018; 21:314-326. [DOI: 10.1111/1462-2920.14459] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 10/12/2018] [Accepted: 10/21/2018] [Indexed: 01/09/2023]
Affiliation(s)
- Özlem Akkaya
- Department of Molecular Biology and Genetics; Gebze Technical University; Kocaeli Turkey
- Centro Nacional de Biotecnología-CSIC; Campus de Cantoblanco; Madrid 28049 Spain
| | - Pablo I. Nikel
- The Novo Nordisk Foundation Center for Biosustainability; Technical University of Denmark; 2800 Kgs Lyngby Denmark
| | - Danilo Pérez-Pantoja
- Programa Institucional de Fomento a la Investigación, Desarrollo e Innovación; Universidad Tecnológica Metropolitana; Ignacio Valdivieso 2409, San Joaquín, Santiago Chile
| | - Víctor de Lorenzo
- Centro Nacional de Biotecnología-CSIC; Campus de Cantoblanco; Madrid 28049 Spain
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35
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Peterson E, Kaur P. Antibiotic Resistance Mechanisms in Bacteria: Relationships Between Resistance Determinants of Antibiotic Producers, Environmental Bacteria, and Clinical Pathogens. Front Microbiol 2018; 9:2928. [PMID: 30555448 PMCID: PMC6283892 DOI: 10.3389/fmicb.2018.02928] [Citation(s) in RCA: 418] [Impact Index Per Article: 69.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 11/14/2018] [Indexed: 11/13/2022] Open
Abstract
Emergence of antibiotic resistant pathogenic bacteria poses a serious public health challenge worldwide. However, antibiotic resistance genes are not confined to the clinic; instead they are widely prevalent in different bacterial populations in the environment. Therefore, to understand development of antibiotic resistance in pathogens, we need to consider important reservoirs of resistance genes, which may include determinants that confer self-resistance in antibiotic producing soil bacteria and genes encoding intrinsic resistance mechanisms present in all or most non-producer environmental bacteria. While the presence of resistance determinants in soil and environmental bacteria does not pose a threat to human health, their mobilization to new hosts and their expression under different contexts, for example their transfer to plasmids and integrons in pathogenic bacteria, can translate into a problem of huge proportions, as discussed in this review. Selective pressure brought about by human activities further results in enrichment of such determinants in bacterial populations. Thus, there is an urgent need to understand distribution of resistance determinants in bacterial populations, elucidate resistance mechanisms, and determine environmental factors that promote their dissemination. This comprehensive review describes the major known self-resistance mechanisms found in producer soil bacteria of the genus Streptomyces and explores the relationships between resistance determinants found in producer soil bacteria, non-producer environmental bacteria, and clinical isolates. Specific examples highlighting potential pathways by which pathogenic clinical isolates might acquire these resistance determinants from soil and environmental bacteria are also discussed. Overall, this article provides a conceptual framework for understanding the complexity of the problem of emergence of antibiotic resistance in the clinic. Availability of such knowledge will allow researchers to build models for dissemination of resistance genes and for developing interventions to prevent recruitment of additional or novel genes into pathogens.
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Affiliation(s)
- Elizabeth Peterson
- Department of Biology, Georgia State University, Atlanta, GA, United States
| | - Parjit Kaur
- Department of Biology, Georgia State University, Atlanta, GA, United States
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36
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Contributions of RecA and RecBCD DNA repair pathways to the oxidative stress response and sensitivity of Acinetobacter baumannii to antibiotics. Int J Antimicrob Agents 2018; 52:629-636. [DOI: 10.1016/j.ijantimicag.2018.07.022] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 07/08/2018] [Accepted: 07/29/2018] [Indexed: 01/24/2023]
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37
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Ghaly TM, Gillings MR. Mobile DNAs as Ecologically and Evolutionarily Independent Units of Life. Trends Microbiol 2018; 26:904-912. [DOI: 10.1016/j.tim.2018.05.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 05/16/2018] [Accepted: 05/17/2018] [Indexed: 10/14/2022]
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Abstract
Ever since antibiotics were introduced into human and veterinary medicine to treat and prevent bacterial infections there has been a steady selection and increase in the frequency of antibiotic resistant bacteria. To be able to reduce the rate of resistance evolution, we need to understand how various biotic and abiotic factors interact to drive the complex processes of resistance emergence and transmission. We describe several of the fundamental factors that underlay resistance evolution, including rates and niches of emergence and persistence of resistant bacteria, time- and space-gradients of various selective agents, and rates and routes of transmission of resistant bacteria between humans, animals and other environments. Furthermore, we discuss the options available to reduce the rate of resistance evolution and/ or transmission and their advantages and disadvantages.
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Jutkina J, Marathe NP, Flach CF, Larsson DGJ. Antibiotics and common antibacterial biocides stimulate horizontal transfer of resistance at low concentrations. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 616-617:172-178. [PMID: 29112840 DOI: 10.1016/j.scitotenv.2017.10.312] [Citation(s) in RCA: 176] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 10/28/2017] [Accepted: 10/30/2017] [Indexed: 05/08/2023]
Abstract
There is a rising concern that antibiotics, and possibly other antimicrobial agents, can promote horizontal transfer of antibiotic resistance genes. For most types of antimicrobials their ability to induce conjugation below minimal inhibitory concentrations (MICs) is still unknown. Our aim was therefore to explore the potential of commonly used antibiotics and antibacterial biocides to induce horizontal transfer of antibiotic resistance. Effects of a wide range of sub-MIC concentrations of the antibiotics cefotaxime, ciprofloxacin, gentamicin, erythromycin, sulfamethoxazole, trimethoprim and the antibacterial biocides chlorhexidine digluconate, hexadecyltrimethylammoniumchloride and triclosan were investigated using a previously optimized culture-based assay with a complex bacterial community as a donor of mobile resistance elements and a traceable Escherichia coli strain as a recipient. Chlorhexidine (24.4μg/L), triclosan (0.1mg/L), gentamicin (0.1mg/L) and sulfamethoxazole (1mg/L) significantly increased the frequencies of transfer of antibiotic resistance whereas similar effects were not observed for any other tested antimicrobial compounds. This corresponds to 200 times below the MIC of the recipient for chlorhexidine, 1/20 of the MIC for triclosan, 1/16 of the MIC for sulfamethoxazole and right below the MIC for gentamicin. To our best knowledge, this is the first study showing that triclosan and chlorhexidine could stimulate the horizontal transfer of antibiotic resistance. Together with recent research showing that tetracycline is a potent inducer of conjugation, our results indicate that several antimicrobials including both common antibiotics and antibacterial biocides at low concentrations could contribute to antibiotic resistance development by facilitating the spread of antibiotic resistance between bacteria.
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Affiliation(s)
- J Jutkina
- Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Sweden; Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy at University of Gothenburg, Sweden
| | - N P Marathe
- Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Sweden; Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy at University of Gothenburg, Sweden
| | - C-F Flach
- Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Sweden; Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy at University of Gothenburg, Sweden
| | - D G J Larsson
- Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Sweden; Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy at University of Gothenburg, Sweden.
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40
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Range Expansion and the Origin of USA300 North American Epidemic Methicillin-Resistant Staphylococcus aureus. mBio 2018; 9:mBio.02016-17. [PMID: 29295910 PMCID: PMC5750399 DOI: 10.1128/mbio.02016-17] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The USA300 North American epidemic (USA300-NAE) clone of methicillin-resistant Staphylococcus aureus has caused a wave of severe skin and soft tissue infections in the United States since it emerged in the early 2000s, but its geographic origin is obscure. Here we use the population genomic signatures expected from the serial founder effects of a geographic range expansion to infer the origin of USA300-NAE and identify polymorphisms associated with its spread. Genome sequences from 357 isolates from 22 U.S. states and territories and seven other countries are compared. We observe two significant signatures of range expansion, including decreases in genetic diversity and increases in derived allele frequency with geographic distance from the Pennsylvania region. These signatures account for approximately half of the core nucleotide variation of this clone, occur genome wide, and are robust to heterogeneity in temporal sampling of isolates, human population density, and recombination detection methods. The potential for positive selection of a gyrA fluoroquinolone resistance allele and several intergenic regions, along with a 2.4 times higher recombination rate in a resistant subclade, is noted. These results are the first to show a pattern of genetic variation that is consistent with a range expansion of an epidemic bacterial clone, and they highlight a rarely considered but potentially common mechanism by which genetic drift may profoundly influence bacterial genetic variation. The process of geographic spread of an origin population by a series of smaller populations can result in distinctive patterns of genetic variation. We detect these patterns for the first time with an epidemic bacterial clone and use them to uncover the clone’s geographic origin and variants associated with its spread. We study the USA300 clone of methicillin-resistant Staphylococcus aureus, which was first noticed in the early 2000s and subsequently became the leading cause of skin and soft tissue infections in the United States. The eastern United States is the most likely origin of epidemic USA300. Relatively few variants, which include an antibiotic resistance mutation, have persisted during this clone’s spread. Our study suggests that an early chapter in the genetic history of this epidemic bacterial clone was greatly influenced by random subsampling of isolates during the clone’s geographic spread.
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41
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Bengtsson-Palme J, Kristiansson E, Larsson DGJ. Environmental factors influencing the development and spread of antibiotic resistance. FEMS Microbiol Rev 2018; 42:4563583. [PMID: 29069382 PMCID: PMC5812547 DOI: 10.1093/femsre/fux053] [Citation(s) in RCA: 472] [Impact Index Per Article: 78.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 10/19/2017] [Indexed: 11/25/2022] Open
Abstract
Antibiotic resistance and its wider implications present us with a growing healthcare crisis. Recent research points to the environment as an important component for the transmission of resistant bacteria and in the emergence of resistant pathogens. However, a deeper understanding of the evolutionary and ecological processes that lead to clinical appearance of resistance genes is still lacking, as is knowledge of environmental dispersal barriers. This calls for better models of how resistance genes evolve, are mobilized, transferred and disseminated in the environment. Here, we attempt to define the ecological and evolutionary environmental factors that contribute to resistance development and transmission. Although mobilization of resistance genes likely occurs continuously, the great majority of such genetic events do not lead to the establishment of novel resistance factors in bacterial populations, unless there is a selection pressure for maintaining them or their fitness costs are negligible. To enable preventative measures it is therefore critical to investigate under what conditions and to what extent environmental selection for resistance takes place. In addition, understanding dispersal barriers is not only key to evaluate risks, but also to prevent resistant pathogens, as well as novel resistance genes, from reaching humans.
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Affiliation(s)
- Johan Bengtsson-Palme
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Box 440, SE-40530, Gothenburg, Sweden
- Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Guldhedsgatan 10, SE-413 46, Gothenburg, Sweden
| | - Erik Kristiansson
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Box 440, SE-40530, Gothenburg, Sweden
- Department of Mathematical Sciences, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
| | - D G Joakim Larsson
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Box 440, SE-40530, Gothenburg, Sweden
- Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Guldhedsgatan 10, SE-413 46, Gothenburg, Sweden
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42
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Peterson E, Kaur P. Antibiotic Resistance Mechanisms in Bacteria: Relationships Between Resistance Determinants of Antibiotic Producers, Environmental Bacteria, and Clinical Pathogens. Front Microbiol 2018; 9:2928. [PMID: 30555448 DOI: 10.3389/fmicb.2018.02928/bibtex] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 11/14/2018] [Indexed: 05/20/2023] Open
Abstract
Emergence of antibiotic resistant pathogenic bacteria poses a serious public health challenge worldwide. However, antibiotic resistance genes are not confined to the clinic; instead they are widely prevalent in different bacterial populations in the environment. Therefore, to understand development of antibiotic resistance in pathogens, we need to consider important reservoirs of resistance genes, which may include determinants that confer self-resistance in antibiotic producing soil bacteria and genes encoding intrinsic resistance mechanisms present in all or most non-producer environmental bacteria. While the presence of resistance determinants in soil and environmental bacteria does not pose a threat to human health, their mobilization to new hosts and their expression under different contexts, for example their transfer to plasmids and integrons in pathogenic bacteria, can translate into a problem of huge proportions, as discussed in this review. Selective pressure brought about by human activities further results in enrichment of such determinants in bacterial populations. Thus, there is an urgent need to understand distribution of resistance determinants in bacterial populations, elucidate resistance mechanisms, and determine environmental factors that promote their dissemination. This comprehensive review describes the major known self-resistance mechanisms found in producer soil bacteria of the genus Streptomyces and explores the relationships between resistance determinants found in producer soil bacteria, non-producer environmental bacteria, and clinical isolates. Specific examples highlighting potential pathways by which pathogenic clinical isolates might acquire these resistance determinants from soil and environmental bacteria are also discussed. Overall, this article provides a conceptual framework for understanding the complexity of the problem of emergence of antibiotic resistance in the clinic. Availability of such knowledge will allow researchers to build models for dissemination of resistance genes and for developing interventions to prevent recruitment of additional or novel genes into pathogens.
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Affiliation(s)
- Elizabeth Peterson
- Department of Biology, Georgia State University, Atlanta, GA, United States
| | - Parjit Kaur
- Department of Biology, Georgia State University, Atlanta, GA, United States
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43
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Single-molecule live-cell imaging of bacterial DNA repair and damage tolerance. Biochem Soc Trans 2017; 46:23-35. [PMID: 29196610 DOI: 10.1042/bst20170055] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 10/30/2017] [Accepted: 11/01/2017] [Indexed: 01/19/2023]
Abstract
Genomic DNA is constantly under threat from intracellular and environmental factors that damage its chemical structure. Uncorrected DNA damage may impede cellular propagation or even result in cell death, making it critical to restore genomic integrity. Decades of research have revealed a wide range of mechanisms through which repair factors recognize damage and co-ordinate repair processes. In recent years, single-molecule live-cell imaging methods have further enriched our understanding of how repair factors operate in the crowded intracellular environment. The ability to follow individual biochemical events, as they occur in live cells, makes single-molecule techniques tremendously powerful to uncover the spatial organization and temporal regulation of repair factors during DNA-repair reactions. In this review, we will cover practical aspects of single-molecule live-cell imaging and highlight recent advances accomplished by the application of these experimental approaches to the study of DNA-repair processes in prokaryotes.
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44
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Li J, Xie S, Ahmed S, Wang F, Gu Y, Zhang C, Chai X, Wu Y, Cai J, Cheng G. Antimicrobial Activity and Resistance: Influencing Factors. Front Pharmacol 2017; 8:364. [PMID: 28659799 PMCID: PMC5468421 DOI: 10.3389/fphar.2017.00364] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 05/26/2017] [Indexed: 01/09/2023] Open
Abstract
Rational use of antibiotic is the key approach to improve the antibiotic performance and tackling of the antimicrobial resistance. The efficacy of antimicrobials are influenced by many factors: (1) bacterial status (susceptibility and resistance, tolerance, persistence, biofilm) and inoculum size; (2) antimicrobial concentrations [mutant selection window (MSW) and sub-inhibitory concentration]; (3) host factors (serum effect and impact on gut micro-biota). Additional understandings regarding the linkage between antimicrobial usages, bacterial status and host response offers us new insights and encourage the struggle for the designing of antimicrobial treatment regimens that reaching better clinical outcome and minimizing the emergence of resistance at the same time.
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Affiliation(s)
- Jun Li
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural UniversityWuhan, China.,National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA Key Laboratory for The Detection of Veterinary Drug Residues in Foods, Huazhong Agricultural UniversityWuhan, China
| | - Shuyu Xie
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural UniversityWuhan, China.,National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA Key Laboratory for The Detection of Veterinary Drug Residues in Foods, Huazhong Agricultural UniversityWuhan, China
| | - Saeed Ahmed
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural UniversityWuhan, China.,National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA Key Laboratory for The Detection of Veterinary Drug Residues in Foods, Huazhong Agricultural UniversityWuhan, China
| | - Funan Wang
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural UniversityWuhan, China.,National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA Key Laboratory for The Detection of Veterinary Drug Residues in Foods, Huazhong Agricultural UniversityWuhan, China
| | - Yufeng Gu
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural UniversityWuhan, China.,National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA Key Laboratory for The Detection of Veterinary Drug Residues in Foods, Huazhong Agricultural UniversityWuhan, China
| | - Chaonan Zhang
- Basic Veterinary Medicine, College of Veterinary Medicine, Huazhong Agricultural UniversityWuhan, China
| | - Ximan Chai
- Basic Veterinary Medicine, College of Veterinary Medicine, Huazhong Agricultural UniversityWuhan, China
| | - Yalan Wu
- Basic Veterinary Medicine, College of Veterinary Medicine, Huazhong Agricultural UniversityWuhan, China
| | - Jinxia Cai
- Basic Veterinary Medicine, College of Veterinary Medicine, Huazhong Agricultural UniversityWuhan, China
| | - Guyue Cheng
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural UniversityWuhan, China.,National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA Key Laboratory for The Detection of Veterinary Drug Residues in Foods, Huazhong Agricultural UniversityWuhan, China.,Basic Veterinary Medicine, College of Veterinary Medicine, Huazhong Agricultural UniversityWuhan, China
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45
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Khan S, Beattie TK, Knapp CW. The use of minimum selectable concentrations (MSCs) for determining the selection of antimicrobial resistant bacteria. ECOTOXICOLOGY (LONDON, ENGLAND) 2017; 26:283-292. [PMID: 28155034 PMCID: PMC5318476 DOI: 10.1007/s10646-017-1762-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 01/11/2017] [Indexed: 05/25/2023]
Abstract
The use of antimicrobial compounds is indispensable in many industries, especially drinking water production, to eradicate microorganisms. However, bacterial growth is not unusual in the presence of disinfectant concentrations that would be typically lethal, as bacterial populations can develop resistance. The common metric of population resistance has been based on the Minimum Inhibitory Concentration (MIC), which is based on bacteria lethality. However, sub-lethal concentrations may also select for resistant bacteria due to the differences in bacterial growth rates. This study determined the Minimal Selective Concentrations (MSCs) of bacterial populations exposed to free chlorine and monochloramine, representing a metric that possibly better reflects the selective pressures occurring at lower disinfectant levels than MIC. Pairs of phylogenetically similar bacteria were challenged to a range of concentrations of disinfectants. The MSCs of free chlorine and monochloramine were found to range between 0.021 and 0.39 mg L-1, which were concentrations 1/250 to 1/5 than the MICs of susceptible bacteria (MIC susc ). This study indicates that sub-lethal concentrations of disinfectants could result in the selection of resistant bacterial populations, and MSCs would be a more sensitive indicator of selective pressure, especially in environmental systems.
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Affiliation(s)
- Sadia Khan
- Department of Civil and Environmental Engineering, University of Strathclyde, James Weir Building, 75 Montrose Street, Glasgow, Scotland, G1 1XJ, UK.
- Department of Environmental Engineering, NED University of Engineering and Technology, University Road, Karachi, 75270, Pakistan.
| | - Tara K Beattie
- Department of Civil and Environmental Engineering, University of Strathclyde, James Weir Building, 75 Montrose Street, Glasgow, Scotland, G1 1XJ, UK
| | - Charles W Knapp
- Department of Civil and Environmental Engineering, University of Strathclyde, James Weir Building, 75 Montrose Street, Glasgow, Scotland, G1 1XJ, UK
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46
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Abstract
Antibiotics have been widely used for a number of decades for human therapy and farming production. Since a high percentage of antibiotics are discharged from the human or animal body without degradation, this means that different habitats, from the human body to river water or soils, are polluted with antibiotics. In this situation, it is expected that the variable concentration of this type of microbial inhibitor present in different ecosystems may affect the structure and the productivity of the microbiota colonizing such habitats. This effect can occur at different levels, including changes in the overall structure of the population, selection of resistant organisms, or alterations in bacterial physiology. In this review, I discuss the available information on how the presence of antibiotics may alter the microbiota and the consequences of such alterations for human health and for the activity of microbiota from different habitats.
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Affiliation(s)
- José Luis Martínez
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Calle Darwin, Madrid, Spain
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47
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Wilkinson M, Troman LA, Wan Nur Ismah WAK, Chaban Y, Avison MB, Dillingham MS, Wigley DB. Structural basis for the inhibition of RecBCD by Gam and its synergistic antibacterial effect with quinolones. eLife 2016; 5:e22963. [PMID: 28009252 PMCID: PMC5218532 DOI: 10.7554/elife.22963] [Citation(s) in RCA: 34] [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: 11/11/2016] [Accepted: 12/22/2016] [Indexed: 12/11/2022] Open
Abstract
Our previous paper (Wilkinson et al, 2016) used high-resolution cryo-electron microscopy to solve the structure of the Escherichia coli RecBCD complex, which acts in both the repair of double-stranded DNA breaks and the degradation of bacteriophage DNA. To counteract the latter activity, bacteriophage λ encodes a small protein inhibitor called Gam that binds to RecBCD and inactivates the complex. Here, we show that Gam inhibits RecBCD by competing at the DNA-binding site. The interaction surface is extensive and involves molecular mimicry of the DNA substrate. We also show that expression of Gam in E. coli or Klebsiella pneumoniae increases sensitivity to fluoroquinolones; antibacterials that kill cells by inhibiting topoisomerases and inducing double-stranded DNA breaks. Furthermore, fluoroquinolone-resistance in K. pneumoniae clinical isolates is reversed by expression of Gam. Together, our data explain the synthetic lethality observed between topoisomerase-induced DNA breaks and the RecBCD gene products, suggesting a new co-antibacterial strategy.
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Affiliation(s)
- Martin Wilkinson
- Department of Medicine, Section of Structural Biology, Imperial College London, London, United Kingdom
| | - Luca A Troman
- School of Biochemistry, University of Bristol, Bristol, United Kingdom
| | - Wan AK Wan Nur Ismah
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | - Yuriy Chaban
- Department of Medicine, Section of Structural Biology, Imperial College London, London, United Kingdom
| | - Matthew B Avison
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | - Mark S Dillingham
- School of Biochemistry, University of Bristol, Bristol, United Kingdom
| | - Dale B Wigley
- Department of Medicine, Section of Structural Biology, Imperial College London, London, United Kingdom
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Mutational Consequences of Ciprofloxacin in Escherichia coli. Antimicrob Agents Chemother 2016; 60:6165-72. [PMID: 27480851 DOI: 10.1128/aac.01415-16] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 07/26/2016] [Indexed: 11/20/2022] Open
Abstract
We examined the mutagenic specificity of the widely used antibiotic ciprofloxacin (CPR), which displays weak to moderate mutagenic activity in several bacteria and generates short in-frame deletions in rpoB in Staphylococcus aureus To determine the spectrum of mutations in a system where any gene knockout would result in a recovered mutant, including frameshifts and both short and long deletions, we examined CPR-induced mutations in the thymidylate synthase-encoding thyA gene. Here, any mutation resulting in loss of thymidylate synthase activity generates trimethoprim (Trm) resistance. We found that deletions and insertions in all three reading frames predominated in the spectrum. They tend to be short deletions and cluster in two regions, one being a GC-rich region with potential extensive secondary structures. We also exploited the well-characterized rpoB-Rif(r) system in Escherichia coli to determine that cells grown in the presence of sublethal doses of CPR not only induced short in-frame deletions in rpoB, but also generated base substitution mutations resulting from induction of the SOS system. Some of the specific point mutations prominent in the spectrum of a strain that overproduces the dinB-encoded Pol IV were also present after growth in CPR. However, these mutations disappeared in CPR-treated dinB mutants, whereas the deletions remained. Moreover, CPR-induced deletions also occurred in a strain lacking all three SOS-induced polymerases. We discuss the implications of these findings for the consequences of overuse of CPR and other antibiotics.
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49
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Urinary Tract Physiological Conditions Promote Ciprofloxacin Resistance in Low-Level-Quinolone-Resistant Escherichia coli. Antimicrob Agents Chemother 2016; 60:4252-8. [PMID: 27139482 DOI: 10.1128/aac.00602-16] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 04/27/2016] [Indexed: 11/20/2022] Open
Abstract
Escherichia coli isolates carrying chromosomally encoded low-level-quinolone-resistant (LLQR) determinants are frequently found in urinary tract infections (UTIs). LLQR mutations are considered the first step in the evolutionary pathway producing high-level fluoroquinolone resistance. Therefore, their evolution and dissemination might influence the outcome of fluoroquinolone treatments of UTI. Previous studies support the notion that low urine pH decreases susceptibility to ciprofloxacin (CIP) in E. coli However, the effect of the urinary tract physiological parameters on the activity of ciprofloxacin against LLQR E. coli strains has received little attention. We have studied the activity of ciprofloxacin under physiological urinary tract conditions against a set of well-characterized isogenic E. coli derivatives carrying the most prevalent chromosomal mutations (ΔmarR, gyrA-S83L, gyrA-D87N, and parC-S80R and some combinations). The results presented here demonstrate that all the LLQR strains studied became resistant to ciprofloxacin (according to CLSI guidelines) under physiological conditions whereas the control strain lacking LLQR mutations did not. Moreover, the survival of some LLQR E. coli variants increased up to 100-fold after challenge with a high concentration of ciprofloxacin under UTI conditions compared to the results seen with Mueller-Hinton broth. These selective conditions could explain the high prevalence of LLQR mutations in E. coli Furthermore, our data strongly suggest that recommended methods for MIC determination produce poor estimations of CIP activity against LLQR E. coli in UTIs.
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50
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Antibiotic treatment enhances the genome-wide mutation rate of target cells. Proc Natl Acad Sci U S A 2016; 113:E2498-505. [PMID: 27091991 DOI: 10.1073/pnas.1601208113] [Citation(s) in RCA: 122] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Although it is well known that microbial populations can respond adaptively to challenges from antibiotics, empirical difficulties in distinguishing the roles of de novo mutation and natural selection have left several issues unresolved. Here, we explore the mutational properties of Escherichia coli exposed to long-term sublethal levels of the antibiotic norfloxacin, using a mutation accumulation design combined with whole-genome sequencing of replicate lines. The genome-wide mutation rate significantly increases with norfloxacin concentration. This response is associated with enhanced expression of error-prone DNA polymerases and may also involve indirect effects of norfloxacin on DNA mismatch and oxidative-damage repair. Moreover, we find that acquisition of antibiotic resistance can be enhanced solely by accelerated mutagenesis, i.e., without direct involvement of selection. Our results suggest that antibiotics may generally enhance the mutation rates of target cells, thereby accelerating the rate of adaptation not only to the antibiotic itself but to additional challenges faced by invasive pathogens.
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