51
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Bikel S, López-Leal G, Cornejo-Granados F, Gallardo-Becerra L, García-López R, Sánchez F, Equihua-Medina E, Ochoa-Romo JP, López-Contreras BE, Canizales-Quinteros S, Hernández-Reyna A, Mendoza-Vargas A, Ochoa-Leyva A. Gut dsDNA virome shows diversity and richness alterations associated with childhood obesity and metabolic syndrome. iScience 2021; 24:102900. [PMID: 34409269 PMCID: PMC8361208 DOI: 10.1016/j.isci.2021.102900] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 05/01/2021] [Accepted: 07/21/2021] [Indexed: 01/19/2023] Open
Abstract
Changes in the human gut microbiome are associated with obesity and metabolic syndrome, but the role of the gut virome in both diseases remains largely unknown. We characterized the gut dsDNA virome of 28 school-aged children with healthy normal-weight (NW, n = 10), obesity (O, n = 10), and obesity with metabolic syndrome (OMS, n = 8), using metagenomic sequencing of virus-like particles (VLPs) from fecal samples. The virome classification confirmed the bacteriophages' dominance, mainly composed of Caudovirales. Notably, phage richness and diversity of individuals with O and OMS tended to increase, while the VLP abundance remained the same among all groups. Of the 4,611 phage contigs composing the phageome, 48 contigs were highly prevalent in ≥80% of individuals, suggesting high inter-individual phage diversity. The abundance of several contigs correlated with gut bacterial taxa; and with anthropometric and biochemical parameters altered in O and OMS. To our knowledge, this gut phageome represents one of the largest datasets and suggests disease-specific phage alterations.
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Affiliation(s)
- Shirley Bikel
- Departamento de Microbiologia Molecular, Instituto de Biotecnologia, Universidad Nacional Autonoma de Mexico, Avenida Universidad 2001, Cuernavaca, Morelos 62210, Mexico
| | - Gamaliel López-Leal
- Departamento de Microbiologia Molecular, Instituto de Biotecnologia, Universidad Nacional Autonoma de Mexico, Avenida Universidad 2001, Cuernavaca, Morelos 62210, Mexico
| | - Fernanda Cornejo-Granados
- Departamento de Microbiologia Molecular, Instituto de Biotecnologia, Universidad Nacional Autonoma de Mexico, Avenida Universidad 2001, Cuernavaca, Morelos 62210, Mexico
| | - Luigui Gallardo-Becerra
- Departamento de Microbiologia Molecular, Instituto de Biotecnologia, Universidad Nacional Autonoma de Mexico, Avenida Universidad 2001, Cuernavaca, Morelos 62210, Mexico
| | - Rodrigo García-López
- Departamento de Microbiologia Molecular, Instituto de Biotecnologia, Universidad Nacional Autonoma de Mexico, Avenida Universidad 2001, Cuernavaca, Morelos 62210, Mexico
| | - Filiberto Sánchez
- Departamento de Microbiologia Molecular, Instituto de Biotecnologia, Universidad Nacional Autonoma de Mexico, Avenida Universidad 2001, Cuernavaca, Morelos 62210, Mexico
| | - Edgar Equihua-Medina
- Departamento de Microbiologia Molecular, Instituto de Biotecnologia, Universidad Nacional Autonoma de Mexico, Avenida Universidad 2001, Cuernavaca, Morelos 62210, Mexico
| | - Juan Pablo Ochoa-Romo
- Departamento de Microbiologia Molecular, Instituto de Biotecnologia, Universidad Nacional Autonoma de Mexico, Avenida Universidad 2001, Cuernavaca, Morelos 62210, Mexico
| | - Blanca Estela López-Contreras
- Unidad de Genomica de Poblaciones Aplicada a la Salud, Facultad de Quimica, UNAM/Instituto Nacional de Medicina Genomica (INMEGEN), Mexico City, Mexico
| | - Samuel Canizales-Quinteros
- Unidad de Genomica de Poblaciones Aplicada a la Salud, Facultad de Quimica, UNAM/Instituto Nacional de Medicina Genomica (INMEGEN), Mexico City, Mexico
| | - Abigail Hernández-Reyna
- Departamento de Microbiologia Molecular, Instituto de Biotecnologia, Universidad Nacional Autonoma de Mexico, Avenida Universidad 2001, Cuernavaca, Morelos 62210, Mexico
| | | | - Adrian Ochoa-Leyva
- Departamento de Microbiologia Molecular, Instituto de Biotecnologia, Universidad Nacional Autonoma de Mexico, Avenida Universidad 2001, Cuernavaca, Morelos 62210, Mexico
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Abstract
Bacteriophages represent the main microbiological threat for the manufacture of fermented foods. The dairy industry is the most affected by this problem, as phages are naturally present in raw milk, surfaces, vats, tanks, floors, and distributed by air displacements. Cheese whey may also contain high phage concentrations. Prophages harbored by lysogenic strains could be induced, generating new lytic phages. In this context, where phages cannot be eradicated from dairies, methods of phage monitoring are mandatory. These are mainly based in microbiological features, like classical methods, that are the most used, economic and simple to carry out. Phage DNA detection and quantification by PCR and qPCR, more complex and expensive, are faster, although not able to discern between viable and non-viable virions. Electron microscopy allows direct visualization and characterization of phage morphology, but the apparatus is expensive. Alternative methods based in other phage traits also exist, though less studied and not applicable on a daily basis. Recognition of contamination sources and correct phage monitoring in dairy factories allow a correct application of control measures. These include general measures such as proper factory design, efficient programs of sanitization, good treatment of raw materials, especially milk, and careful handling of by-products. Additionally, the use of starts cultures should be adequate, with application of rotation schemes when possible. Finally, the selection of bacteriophage insensitive mutants (BIM) is essential, and can be achieved simply and empirically, though the study of CRISPR-Cas and other newly discovered mechanisms provide a more rational basis to obtain BIMs with optimized features.
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53
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RexAB promotes the survival of Staphylococcus aureus exposed to multiple classes of antibiotics. Antimicrob Agents Chemother 2021; 65:e0059421. [PMID: 34310219 PMCID: PMC8448105 DOI: 10.1128/aac.00594-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Antibiotics inhibit essential bacterial processes, resulting in arrest of growth and, in some cases, cell death. Many antibiotics are also reported to trigger endogenous production of reactive oxygen species (ROS), which damage DNA, leading to induction of the mutagenic SOS response associated with the emergence of drug resistance. However, the type of DNA damage that arises and how this triggers the SOS response are largely unclear. We found that several different classes of antibiotic triggered dose-dependent induction of the SOS response in Staphylococcus aureus, indicative of DNA damage, including some bacteriostatic drugs. The SOS response was heterogenous and varied in magnitude between strains and antibiotics. However, in many cases, full induction of the SOS response was dependent upon the RexAB helicase/nuclease complex, which processes DNA double-strand breaks to produce single-stranded DNA and facilitate RecA nucleoprotein filament formation. The importance of RexAB in repair of DNA was confirmed by measuring bacterial survival during antibiotic exposure, with most drugs having significantly greater bactericidal activity against rexB mutants than against wild-type strains. For some, but not all, antibiotics there was no difference in bactericidal activity between wild type and rexB mutant under anaerobic conditions, indicative of a role for reactive oxygen species in mediating DNA damage. Taken together, this work confirms previous observations that several classes of antibiotics cause DNA damage in S. aureus and extends them by showing that processing of DNA double-strand breaks by RexAB is a major trigger of the mutagenic SOS response and promotes bacterial survival.
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54
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Su M, Davis MH, Peterson J, Solis-Lemus C, Satola SW, Read TD. Effect of genetic background on the evolution of Vancomycin-Intermediate Staphylococcus aureus (VISA). PeerJ 2021; 9:e11764. [PMID: 34306830 PMCID: PMC8284308 DOI: 10.7717/peerj.11764] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 06/22/2021] [Indexed: 11/20/2022] Open
Abstract
Vancomycin-intermediate Staphylococcus aureus (VISA) typically arises through accumulation of chromosomal mutations that alter cell-wall thickness and global regulatory pathways. Genome-based prediction of VISA requires understanding whether strain background influences patterns of mutation that lead to resistance. We used an iterative method to experimentally evolve three important methicillin-resistant S. aureus (MRSA) strain backgrounds-(CC1, CC5 and CC8 (USA300)) to generate a library of 120 laboratory selected VISA isolates. At the endpoint, isolates had vancomycin MICs ranging from 4 to 10 μg/mL. We detected mutations in more than 150 genes, but only six genes (already known to be associated with VISA from prior studies) were mutated in all three background strains (walK, prs, rpoB, rpoC, vraS, yvqF). We found evidence of interactions between loci (e.g., vraS and yvqF mutants were significantly negatively correlated) and rpoB, rpoC, vraS and yvqF were more frequently mutated in one of the backgrounds. Increasing vancomycin resistance was correlated with lower maximal growth rates (a proxy for fitness) regardless of background. However, CC5 VISA isolates had higher MICs with fewer rounds of selection and had lower fitness costs than the CC8 VISA isolates. Using multivariable regression, we found that genes differed in their contribution to overall MIC depending on the background. Overall, these results demonstrated that VISA evolved through mutations in a similar set of loci in all backgrounds, but the effect of mutation in common genes differed with regard to fitness and contribution to resistance in different strains.
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Affiliation(s)
- Michelle Su
- Division of Infectious Diseases, Department of Medicine, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - Michelle H Davis
- Division of Infectious Diseases, Department of Medicine, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - Jessica Peterson
- Division of Infectious Diseases, Department of Medicine, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - Claudia Solis-Lemus
- Wisconsin Institute for Discovery and Department of Plant Pathology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Sarah W Satola
- Division of Infectious Diseases, Department of Medicine, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - Timothy D Read
- Division of Infectious Diseases, Department of Medicine, School of Medicine, Emory University, Atlanta, Georgia, USA.,Department of Dermatology, School of Medicine, Emory University, Atlanta, Georgia, USA
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55
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Lauman P, Dennis JJ. Advances in Phage Therapy: Targeting the Burkholderia cepacia Complex. Viruses 2021; 13:1331. [PMID: 34372537 PMCID: PMC8310193 DOI: 10.3390/v13071331] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 06/29/2021] [Accepted: 07/06/2021] [Indexed: 01/16/2023] Open
Abstract
The increasing prevalence and worldwide distribution of multidrug-resistant bacterial pathogens is an imminent danger to public health and threatens virtually all aspects of modern medicine. Particularly concerning, yet insufficiently addressed, are the members of the Burkholderia cepacia complex (Bcc), a group of at least twenty opportunistic, hospital-transmitted, and notoriously drug-resistant species, which infect and cause morbidity in patients who are immunocompromised and those afflicted with chronic illnesses, including cystic fibrosis (CF) and chronic granulomatous disease (CGD). One potential solution to the antimicrobial resistance crisis is phage therapy-the use of phages for the treatment of bacterial infections. Although phage therapy has a long and somewhat checkered history, an impressive volume of modern research has been amassed in the past decades to show that when applied through specific, scientifically supported treatment strategies, phage therapy is highly efficacious and is a promising avenue against drug-resistant and difficult-to-treat pathogens, such as the Bcc. In this review, we discuss the clinical significance of the Bcc, the advantages of phage therapy, and the theoretical and clinical advancements made in phage therapy in general over the past decades, and apply these concepts specifically to the nascent, but growing and rapidly developing, field of Bcc phage therapy.
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Affiliation(s)
| | - Jonathan J. Dennis
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada;
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56
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Tomlinson BR, Malof ME, Shaw LN. A global transcriptomic analysis of Staphylococcus aureus biofilm formation across diverse clonal lineages. Microb Genom 2021; 7. [PMID: 34227933 PMCID: PMC8477394 DOI: 10.1099/mgen.0.000598] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
A key characteristic of Staphylococcus aureus infections, and one that also varies phenotypically between clones, is that of biofilm formation, which aids in bacterial persistence through increased adherence and immune evasion. Though there is a general understanding of the process of biofilm formation - adhesion, proliferation, maturation and dispersal - the tightly orchestrated molecular events behind each stage, and what drives variation between S. aureus strains, has yet to be unravelled. Herein we measure biofilm progression and dispersal in real-time across the five major S. aureus CDC-types (USA100-USA500) revealing adherence patterns that differ markedly amongst strains. To gain insight into this, we performed transcriptomic profiling on these isolates at multiple timepoints, compared to planktonically growing counterparts. Our findings support a model in which eDNA release, followed by increased positive surface charge, perhaps drives initial abiotic attachment. This is seemingly followed by cooperative repression of autolysis and activation of poly-N-acetylglucosamine (PNAG) production, which may indicate a developmental shift in structuring the biofilm matrix. As biofilms mature, diminished translational capacity was apparent, with 53 % of all ribosomal proteins downregulated, followed by upregulation of anaerobic respiration enzymes. These findings are noteworthy because reduced cellular activity and an altered metabolic state have been previously shown to contribute to higher antibiotic tolerance and bacterial persistence. In sum, this work is, to our knowledge, the first study to investigate transcriptional regulation during the early, establishing phase of biofilm formation, and to compare global transcriptional regulation both temporally and across multiple clonal lineages.
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Affiliation(s)
- Brooke R Tomlinson
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, 4202 East Fowler Avenue, ISA 2015, Tampa, FL, USA
| | - Morgan E Malof
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, 4202 East Fowler Avenue, ISA 2015, Tampa, FL, USA
| | - Lindsey N Shaw
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, 4202 East Fowler Avenue, ISA 2015, Tampa, FL, USA
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57
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Dörr T. Understanding tolerance to cell wall-active antibiotics. Ann N Y Acad Sci 2021; 1496:35-58. [PMID: 33274447 PMCID: PMC8359209 DOI: 10.1111/nyas.14541] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 11/02/2020] [Accepted: 11/04/2020] [Indexed: 12/19/2022]
Abstract
Antibiotic tolerance-the ability of bacteria to survive for an extended time in the presence of bactericidal antibiotics-is an understudied contributor to antibiotic treatment failure. Herein, I review the manifestations, mechanisms, and clinical relevance of tolerance to cell wall-active (CWA) antibiotics, one of the most important groups of antibiotics at the forefront of clinical use. I discuss definitions of tolerance and assays for tolerance detection, comprehensively discuss the mechanism of action of β-lactams and other CWA antibiotics, and then provide an overview of how cells mitigate the potentially lethal effects of CWA antibiotic-induced cell damage to become tolerant. Lastly, I discuss evidence for a role of CWA antibiotic tolerance in clinical antibiotic treatment failure.
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Affiliation(s)
- Tobias Dörr
- Weill Institute for Cell and Molecular Biology, Department of Microbiology, and Cornell Institute of Host–Pathogen Interactions and DiseaseCornell UniversityIthacaNew York
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58
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Tomlinson BR, Malof ME, Shaw LN. A global transcriptomic analysis of Staphylococcus aureus biofilm formation across diverse clonal lineages. Microb Genom 2021. [PMID: 34227933 DOI: 10.1099/mgen0000598] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023] Open
Abstract
A key characteristic of Staphylococcus aureus infections, and one that also varies phenotypically between clones, is that of biofilm formation, which aids in bacterial persistence through increased adherence and immune evasion. Though there is a general understanding of the process of biofilm formation - adhesion, proliferation, maturation and dispersal - the tightly orchestrated molecular events behind each stage, and what drives variation between S. aureus strains, has yet to be unravelled. Herein we measure biofilm progression and dispersal in real-time across the five major S. aureus CDC-types (USA100-USA500) revealing adherence patterns that differ markedly amongst strains. To gain insight into this, we performed transcriptomic profiling on these isolates at multiple timepoints, compared to planktonically growing counterparts. Our findings support a model in which eDNA release, followed by increased positive surface charge, perhaps drives initial abiotic attachment. This is seemingly followed by cooperative repression of autolysis and activation of poly-N-acetylglucosamine (PNAG) production, which may indicate a developmental shift in structuring the biofilm matrix. As biofilms mature, diminished translational capacity was apparent, with 53 % of all ribosomal proteins downregulated, followed by upregulation of anaerobic respiration enzymes. These findings are noteworthy because reduced cellular activity and an altered metabolic state have been previously shown to contribute to higher antibiotic tolerance and bacterial persistence. In sum, this work is, to our knowledge, the first study to investigate transcriptional regulation during the early, establishing phase of biofilm formation, and to compare global transcriptional regulation both temporally and across multiple clonal lineages.
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Affiliation(s)
- Brooke R Tomlinson
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, 4202 East Fowler Avenue, ISA 2015, Tampa, FL, USA
| | - Morgan E Malof
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, 4202 East Fowler Avenue, ISA 2015, Tampa, FL, USA
| | - Lindsey N Shaw
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, 4202 East Fowler Avenue, ISA 2015, Tampa, FL, USA
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59
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Role of the SOS Response in the Generation of Antibiotic Resistance In Vivo. Antimicrob Agents Chemother 2021; 65:e0001321. [PMID: 33875437 DOI: 10.1128/aac.00013-21] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The SOS response to DNA damage is a conserved stress response in Gram-negative and Gram-positive bacteria. Although this pathway has been studied for years, its relevance is still not familiar to many working in the fields of clinical antibiotic resistance and stewardship. Under some conditions, the SOS response favors DNA repair and preserves the genetic integrity of the organism. On the other hand, the SOS response also includes induction of error-prone DNA polymerases, which can increase the rate of mutation, called the mutator phenotype or "hypermutation." As a result, mutations can occur in genes conferring antibiotic resistance, increasing the acquisition of resistance to antibiotics. Almost all of the work on the SOS response has been on bacteria exposed to stressors in vitro. In this study, we sought to quantitate the effects of SOS-inducing drugs in vivo, in comparison with the same drugs in vitro. We used a rabbit model of intestinal infection with enteropathogenic Escherichia coli strain E22. SOS-inducing drugs triggered the mutator phenotype response in vivo as well as in vitro. Exposure of E. coli strain E22 to ciprofloxacin or zidovudine, both of which induce the SOS response in vitro, resulted in increased antibiotic resistance to 3 antibiotics: rifampin, minocycline, and fosfomycin. Zinc was able to inhibit the SOS-induced emergence of antibiotic resistance in vivo, as previously observed in vitro. Our findings may have relevance in reducing the emergence of resistance to new antimicrobial drugs.
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60
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Chatterjee S, Bose D, Seth R. Host gut microbiome and potential therapeutics in Gulf War Illness: A short review. Life Sci 2021; 280:119717. [PMID: 34139232 DOI: 10.1016/j.lfs.2021.119717] [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: 01/08/2021] [Revised: 05/22/2021] [Accepted: 06/07/2021] [Indexed: 02/07/2023]
Abstract
AIMS Since our troops had returned from the first Persian Gulf War in 1990-91, the veterans have reported chronic multisymptomatic illness widely referred to as Gulf War Illness (GWI). We aim to review the current directions of GWI pathology research in the context of chronic multisymptomatic illness and its possible gut microbiome targeted therapies. The veterans of Gulf War show symptoms of chronic fatigue, cognitive deficits, and a subsection report of gastrointestinal complications. METHOD Efforts of finding a suitable treatment regimen and clinical management remain a challenge. More recently, we have shown that the pathology is connected to alterations in the gut microbiome, and efforts of finding a suitable regimen for gut-directed therapeutics are underway. We discuss the various clinical interventions and summarize the possible effectiveness of gut-directed therapies such as the use of short-chain fatty acids (SCFA), phenolic compounds, and their metabolites, use of probiotics, and fecal microbiota transfer. SIGNIFICANCE The short review will be helpful to GWI researchers to expand their studies to the gut and find an effective treatment strategy for chronic multisymptomatic illness.
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Affiliation(s)
- Saurabh Chatterjee
- Environmental Health and Disease Laboratory, Department of Environmental Health Sciences, University of South Carolina, Columbia, SC 29208, USA; Columbia VA Medical Center, Columbia, SC 29205, USA.
| | - Dipro Bose
- Environmental Health and Disease Laboratory, Department of Environmental Health Sciences, University of South Carolina, Columbia, SC 29208, USA; Columbia VA Medical Center, Columbia, SC 29205, USA
| | - Ratanesh Seth
- Environmental Health and Disease Laboratory, Department of Environmental Health Sciences, University of South Carolina, Columbia, SC 29208, USA; Columbia VA Medical Center, Columbia, SC 29205, USA
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61
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Townsend EM, Kelly L, Muscatt G, Box JD, Hargraves N, Lilley D, Jameson E. The Human Gut Phageome: Origins and Roles in the Human Gut Microbiome. Front Cell Infect Microbiol 2021; 11:643214. [PMID: 34150671 PMCID: PMC8213399 DOI: 10.3389/fcimb.2021.643214] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 05/19/2021] [Indexed: 12/14/2022] Open
Abstract
The investigation of the microbial populations of the human body, known as the microbiome, has led to a revolutionary field of science, and understanding of its impacts on human development and health. The majority of microbiome research to date has focussed on bacteria and other kingdoms of life, such as fungi. Trailing behind these is the interrogation of the gut viruses, specifically the phageome. Bacteriophages, viruses that infect bacterial hosts, are known to dictate the dynamics and diversity of bacterial populations in a number of ecosystems. However, the phageome of the human gut, while of apparent importance, remains an area of many unknowns. In this paper we discuss the role of bacteriophages within the human gut microbiome. We examine the methods used to study bacteriophage populations, how this evolved over time and what we now understand about the phageome. We review the phageome development in infancy, and factors that may influence phage populations in adult life. The role and action of the phageome is then discussed at both a biological-level, and in the broader context of human health and disease.
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Affiliation(s)
- Eleanor M Townsend
- School of Life Sciences, The University of Warwick, Coventry, United Kingdom
| | - Lucy Kelly
- School of Life Sciences, The University of Warwick, Coventry, United Kingdom
| | - George Muscatt
- School of Life Sciences, The University of Warwick, Coventry, United Kingdom
| | - Joshua D Box
- School of Life Sciences, The University of Warwick, Coventry, United Kingdom
| | - Nicole Hargraves
- School of Life Sciences, The University of Warwick, Coventry, United Kingdom
| | - Daniel Lilley
- Warwick Medical School, The University of Warwick, Coventry, United Kingdom
| | - Eleanor Jameson
- School of Life Sciences, The University of Warwick, Coventry, United Kingdom
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62
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Jancheva M, Böttcher T. A Metabolite of Pseudomonas Triggers Prophage-Selective Lysogenic to Lytic Conversion in Staphylococcus aureus. J Am Chem Soc 2021; 143:8344-8351. [PMID: 33978401 PMCID: PMC8193634 DOI: 10.1021/jacs.1c01275] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
![]()
Bacteriophages have
major impact on their microbial hosts and shape
entire microbial communities. The majority of these phages are latent
and reside as prophages integrated in the genomes of their microbial
hosts. A variety of intricate regulatory systems determine the switch
from a lysogenic to lytic life style, but so far strategies are lacking
to selectively control prophage induction by small molecules. Here
we show that Pseudomonas aeruginosa deploys a trigger
factor to hijack the lysogenic to lytic switch of a polylysogenic Staphylococcus aureus strain causing the selective production
of only one of its prophages. Fractionating extracts of P. aeruginosa identified the phenazine pyocyanin
as a highly potent prophage inducer of S. aureus that, in contrast to mitomycin C, displayed prophage
selectivity. Mutagenesis and biochemical investigations confirm the
existence of a noncanonical mechanism beyond SOS-response that is
controlled by the intracellular oxidation level and is prophage-selective.
Our results demonstrate that human pathogens can produce metabolites
triggering lysogenic to lytic conversion in a prophage-selective manner.
We anticipate our discovery to be the starting point of unveiling
metabolite-mediated microbe–prophage interactions and laying
the foundations for a selective small molecule controlled manipulation
of prophage activity. These could be for example applied to control
microbial communities by their built-in destruction mechanism in a
novel form of phage therapy or for the construction of small molecule-inducible
switches in synthetic biology.
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Affiliation(s)
- Magdalena Jancheva
- Department of Chemistry, Konstanz Research School Chemical Biology, Zukunftskolleg, University of Konstanz, 78457 Konstanz, Germany
| | - Thomas Böttcher
- Department of Chemistry, Konstanz Research School Chemical Biology, Zukunftskolleg, University of Konstanz, 78457 Konstanz, Germany.,Faculty of Chemistry, Department of Biological Chemistry & Centre for Microbiology and Environmental Systems Science, University of Vienna, 1090 Vienna, Austria
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63
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Temperate phage-antibiotic synergy eradicates bacteria through depletion of lysogens. Cell Rep 2021; 35:109172. [PMID: 34038739 DOI: 10.1016/j.celrep.2021.109172] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 03/13/2021] [Accepted: 05/04/2021] [Indexed: 01/02/2023] Open
Abstract
There is renewed interest in bacterial viruses (phages) as alternatives to antibiotics. All phage treatments to date have used virulent phages rather than temperate ones, as these can integrate into the genome of the bacterial host and lie dormant. However, temperate phages are abundant and easier to isolate. To make use of these entities, we leverage stressors known to awaken these dormant, integrated phages. Co-administration of the temperate phage HK97 with sub-inhibitory concentrations of the antibiotic ciprofloxacin results in bacterial eradication (≥8 log reduction) in vitro. This synergy is mechanistically distinct from phage-antibiotic-synergy described for virulent phages. Instead, the antibiotic specifically selects against bacteria in which the phage has integrated. As the interaction between temperate phages and stressors such as ciprofloxacin are known to be widespread, this approach may be broadly applicable and enable the use of temperate phages to combat bacterial infections.
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64
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Rodríguez-Rubio L, Haarmann N, Schwidder M, Muniesa M, Schmidt H. Bacteriophages of Shiga Toxin-Producing Escherichia coli and Their Contribution to Pathogenicity. Pathogens 2021; 10:404. [PMID: 33805526 PMCID: PMC8065619 DOI: 10.3390/pathogens10040404] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 03/18/2021] [Accepted: 03/24/2021] [Indexed: 12/25/2022] Open
Abstract
Shiga toxins (Stx) of Shiga toxin-producing Escherichia coli (STEC) are generally encoded in the genome of lambdoid bacteriophages, which spend the most time of their life cycle integrated as prophages in specific sites of the bacterial chromosome. Upon spontaneous induction or induction by chemical or physical stimuli, the stx genes are co-transcribed together with the late phase genes of the prophages. After being assembled in the cytoplasm, and after host cell lysis, mature bacteriophage particles are released into the environment, together with Stx. As members of the group of lambdoid phages, Stx phages share many genetic features with the archetypical temperate phage Lambda, but are heterogeneous in their DNA sequences due to frequent recombination events. In addition to Stx phages, the genome of pathogenic STEC bacteria may contain numerous prophages, which are either cryptic or functional. These prophages may carry foreign genes, some of them related to virulence, besides those necessary for the phage life cycle. Since the production of one or more Stx is considered the major pathogenicity factor of STEC, we aim to highlight the new insights on the contribution of Stx phages and other STEC phages to pathogenicity.
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Affiliation(s)
- Lorena Rodríguez-Rubio
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Diagonal 643, 08028 Barcelona, Spain; (L.R.-R.); (M.M.)
| | - Nadja Haarmann
- Department of Food Microbiology and Hygiene, Institute of Food Science and Biotechnology, University of Hohenheim, 70599 Stuttgart, Germany; (N.H.); (M.S.)
| | - Maike Schwidder
- Department of Food Microbiology and Hygiene, Institute of Food Science and Biotechnology, University of Hohenheim, 70599 Stuttgart, Germany; (N.H.); (M.S.)
| | - Maite Muniesa
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Diagonal 643, 08028 Barcelona, Spain; (L.R.-R.); (M.M.)
| | - Herbert Schmidt
- Department of Food Microbiology and Hygiene, Institute of Food Science and Biotechnology, University of Hohenheim, 70599 Stuttgart, Germany; (N.H.); (M.S.)
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Sutcliffe SG, Shamash M, Hynes AP, Maurice CF. Common Oral Medications Lead to Prophage Induction in Bacterial Isolates from the Human Gut. Viruses 2021; 13:v13030455. [PMID: 33799646 PMCID: PMC8000485 DOI: 10.3390/v13030455] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 03/04/2021] [Accepted: 03/09/2021] [Indexed: 01/22/2023] Open
Abstract
Many bacteria carry bacteriophages (bacterial viruses) integrated in their genomes in the form of prophages, which replicate passively alongside their bacterial host. Environmental conditions can lead to prophage induction; the switching from prophage replication to lytic replication, that results in new bacteriophage progeny and the lysis of the bacterial host. Despite their abundance in the gut, little is known about what could be inducing these prophages. We show that several medications, at concentrations predicted in the gut, lead to prophage induction of bacterial isolates from the human gut. We tested five medication classes (non-steroidal anti-inflammatory, chemotherapy, mild analgesic, cardiac, and antibiotic) for antimicrobial activity against eight prophage-carrying human gut bacterial representative isolates in vitro. Seven out of eight bacteria showed signs of growth inhibition in response to at least one medication. All medications led to growth inhibition of at least one bacterial isolate. Prophage induction was confirmed in half of the treatments showing antimicrobial activity. Unlike antibiotics, host-targeted medications led to a species-specific induction of Clostridium beijerinckii, Bacteroides caccae, and to a lesser extent Bacteroides eggerthii. These results show how common medication consumption can lead to phage-mediated effects, which in turn would alter the human gut microbiome through increased prophage induction.
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Affiliation(s)
- Steven G. Sutcliffe
- Department of Microbiology and Immunology, McGill University, Montreal, QC H3A2B4, Canada; (S.G.S.); (M.S.)
| | - Michael Shamash
- Department of Microbiology and Immunology, McGill University, Montreal, QC H3A2B4, Canada; (S.G.S.); (M.S.)
| | - Alexander P. Hynes
- Department of Medicine, McMaster University, Hamilton, ON L8S4L8, Canada;
| | - Corinne F. Maurice
- Department of Microbiology and Immunology, McGill University, Montreal, QC H3A2B4, Canada; (S.G.S.); (M.S.)
- Correspondence:
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66
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Amaro F, Morón Á, Díaz S, Martín-González A, Gutiérrez JC. Metallic Nanoparticles-Friends or Foes in the Battle against Antibiotic-Resistant Bacteria? Microorganisms 2021; 9:364. [PMID: 33673231 PMCID: PMC7917771 DOI: 10.3390/microorganisms9020364] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 02/08/2021] [Accepted: 02/10/2021] [Indexed: 12/15/2022] Open
Abstract
The rapid spread of antibiotic resistances among bacteria demands novel strategies for infection control, and metallic nanoparticles appear as promising tools because of their unique size and tunable properties that allow their antibacterial effects to be maximized. Furthermore, their diverse mechanisms of action towards multiple cell components have suggested that bacteria could not easily develop resistance against nanoparticles. However, research published over the last decade has proven that bacteria can indeed evolve stable resistance mechanisms upon continuous exposure to metallic nanoparticles. In this review, we summarize the currently known individual and collective strategies employed by bacteria to cope with metallic nanoparticles. Importantly, we also discuss the adverse side effects that bacterial exposure to nanoparticles may have on antibiotic resistance dissemination and that might constitute a challenge for the implementation of nanoparticles as antibacterial agents. Overall, studies discussed in this review point out that careful management of these very promising antimicrobials is necessary to preserve their efficacy for infection control.
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Affiliation(s)
- Francisco Amaro
- Department of Genetics, Physiology and Microbiology, Faculty of Biology, Complutense University of Madrid, 28040 Madrid, Spain; (Á.M.); (S.D.); (A.M.-G.); (J.C.G.)
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67
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Li X, Liu Y, Wang Y, Lin Z, Wang D, Sun H. Resistance risk induced by quorum sensing inhibitors and their combined use with antibiotics: Mechanism and its relationship with toxicity. CHEMOSPHERE 2021; 265:129153. [PMID: 33302207 DOI: 10.1016/j.chemosphere.2020.129153] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 11/22/2020] [Accepted: 11/27/2020] [Indexed: 06/12/2023]
Abstract
The abuse of antibiotics has brought out serious bacterial resistance, which threatens the ecological environment and human health. Quorum sensing inhibitors (QSIs), as a new kind of potential antibiotic substitutes that are theoretically difficult to trigger bacterial resistance, are recommended to individually use or jointly use with traditional antibiotics. However, there are few studies on the resistance risk in the use of QSIs. In this study, the influence of QSIs alone or in combination with sulfonamides (SAs) on conjugative transfer and mutation of Escherichia coli (E. coli) was investigated to explore whether QSIs have the potential to induce bacterial resistance. The results show that QSIs may facilitate plasmid RP4 conjugative transfer by binding with SdiA protein to regulate pilus expression, and interact with LsrR protein to increase SOS gene expression, inducing gene mutation. The QSIs-SAs mixtures could promote plasmid RP4 conjugative transfer and mutation in E. coli, and the main joint effects are synergism and antagonism. Furthermore, there is a good correlation among conjugative transfer, mutation, and growth inhibition of QSIs-SAs to E. coli. It could be speculated that bacteria may delay cell division to provide sufficient energy and time for regulating conjugative transfer and mutation under the stress of QSIs and their combined exposure with antibiotics, which is essentially a balance between bacterial resistance and toxicity. This study provides a reference for the resistance risk assessment of QSIs and benefits the clinical application of QSIs.
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Affiliation(s)
- Xufei Li
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, China
| | - Yingying Liu
- State Key Laboratory of Earth Surface Processes and Resource Ecology, Beijing Normal University, Beijing, 100875, China
| | - Yajuan Wang
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, China
| | - Zhifen Lin
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, China; Shanghai Key Lab of Chemical Assessment and Sustainability, Shanghai, China
| | - Dali Wang
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou, 511443, China
| | - Haoyu Sun
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, China; Shanghai Key Lab of Chemical Assessment and Sustainability, Shanghai, China; Post-doctoral Research Station, College of Civil Engineering, Tongji University, Shanghai, 200092, China.
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68
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Wendling CC, Refardt D, Hall AR. Fitness benefits to bacteria of carrying prophages and prophage-encoded antibiotic-resistance genes peak in different environments. Evolution 2021; 75:515-528. [PMID: 33347602 PMCID: PMC7986917 DOI: 10.1111/evo.14153] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 11/12/2020] [Accepted: 12/09/2020] [Indexed: 12/14/2022]
Abstract
Understanding the role of horizontal gene transfer (HGT) in adaptation is a key challenge in evolutionary biology. In microbes, an important mechanism of HGT is prophage acquisition (phage genomes integrated into bacterial chromosomes). Prophages can influence bacterial fitness via the transfer of beneficial genes (including antibiotic‐resistance genes, ARGs), protection from superinfecting phages, or switching to a lytic lifecycle that releases free phages infectious to competitors. We expect these effects to depend on environmental conditions because of, for example, environment‐dependent induction of the lytic lifecycle. However, it remains unclear how costs/benefits of prophages vary across environments. Here, studying prophages with/without ARGs in Escherichia coli, we disentangled the effects of prophages alone and adaptive genes they carry. In competition with prophage‐free strains, benefits from prophages and ARGs peaked in different environments. Prophages were most beneficial when induction of the lytic lifecycle was common, whereas ARGs were more beneficial upon antibiotic exposure and with reduced prophage induction. Acquisition of prophage‐encoded ARGs by competing strains was most common when prophage induction, and therefore free phages, were common. Thus, selection on prophages and adaptive genes they carry varies independently across environments, which is important for predicting the spread of mobile/integrating genetic elements and their role in evolution.
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Affiliation(s)
- Carolin C Wendling
- ETH Zürich, Institute of Integrative Biology, Universitätstrasse 16, Zürich, Switzerland
| | - Dominik Refardt
- Institute of Natural Resource Sciences, Zürich University of Applied Sciences, Campus Grüental, Wädenswil, Switzerland
| | - Alex R Hall
- ETH Zürich, Institute of Integrative Biology, Universitätstrasse 16, Zürich, Switzerland
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69
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Remmington A, Haywood S, Edgar J, Green LR, de Silva T, Turner CE. Cryptic prophages within a Streptococcus pyogenes genotype emm4 lineage. Microb Genom 2021; 7:mgen000482. [PMID: 33245690 PMCID: PMC8115907 DOI: 10.1099/mgen.0.000482] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 11/04/2020] [Indexed: 01/27/2023] Open
Abstract
The major human pathogen Streptococcus pyogenes shares an intimate evolutionary history with mobile genetic elements, which in many cases carry genes encoding bacterial virulence factors. During recent whole-genome sequencing of a longitudinal sample of S. pyogenes isolates in England, we identified a lineage within emm4 that clustered with the reference genome MEW427. Like MEW427, this lineage was characterized by substantial gene loss within all three prophage regions, compared to MGAS10750 and isolates outside of the MEW427-like lineage. Gene loss primarily affected lysogeny, replicative and regulatory modules, and to a lesser and more variable extent, structural genes. Importantly, prophage-encoded superantigen and DNase genes were retained in all isolates. In isolates where the prophage elements were complete, like MGAS10750, they could be induced experimentally, but not in MEW427-like isolates with degraded prophages. We also found gene loss within the chromosomal island SpyCIM4 of MEW427-like isolates, although surprisingly, the SpyCIM4 element could not be experimentally induced in either MGAS10750-like or MEW427-like isolates. This did not, however, appear to abolish expression of the mismatch repair operon, within which this element resides. The inclusion of further emm4 genomes in our analyses ratified our observations and revealed an international emm4 lineage characterized by prophage degradation. Intriguingly, the USA population of emm4 S. pyogenes appeared to constitute predominantly MEW427-like isolates, whereas the UK population comprised both MEW427-like and MGAS10750-like isolates. The degraded and cryptic nature of these elements may have important phenotypic and fitness ramifications for emm4 S. pyogenes, and the geographical distribution of this lineage raises interesting questions on the population dynamics of the genotype.
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Affiliation(s)
- Alex Remmington
- Department of Molecular Biology and Biotechnology, Florey Institute, University of Sheffield, Sheffield, UK
| | - Samuel Haywood
- Department of Molecular Biology and Biotechnology, Florey Institute, University of Sheffield, Sheffield, UK
| | - Julia Edgar
- Department of Molecular Biology and Biotechnology, Florey Institute, University of Sheffield, Sheffield, UK
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Luke R. Green
- Department of Infection, Immunity and Cardiovascular Disease, Florey Institute, University of Sheffield, Sheffield, UK
| | - Thushan de Silva
- Department of Infection, Immunity and Cardiovascular Disease, Florey Institute, University of Sheffield, Sheffield, UK
| | - Claire E. Turner
- Department of Molecular Biology and Biotechnology, Florey Institute, University of Sheffield, Sheffield, UK
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70
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Verma T, Annappa H, Singh S, Umapathy S, Nandi D. Profiling antibiotic resistance in Escherichia coli strains displaying differential antibiotic susceptibilities using Raman spectroscopy. JOURNAL OF BIOPHOTONICS 2021; 14:e202000231. [PMID: 32981183 DOI: 10.1002/jbio.202000231] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 08/22/2020] [Accepted: 09/25/2020] [Indexed: 06/11/2023]
Abstract
The rapid identification of antibiotic resistant bacteria is important for public health. In the environment, bacteria are exposed to sub-inhibitory antibiotic concentrations which has implications in the generation of multi-drug resistant strains. To better understand these issues, Raman spectroscopy was employed coupled with partial least squares-discriminant analysis to profile Escherichia coli strains treated with sub-inhibitory concentrations of antibiotics. Clear differences were observed between cells treated with bacteriostatic (tetracycline and rifampicin) and bactericidal (ampicillin, ciprofloxacin, and ceftriaxone) antibiotics for 6 hr: First, atomic force microscopy revealed that bactericidal antibiotics cause extensive cell elongation whereas short filaments are observed with bacteriostatic antibiotics. Second, Raman spectral analysis revealed that bactericidal antibiotics lower nucleic acid to protein (I812 /I830 ) and nucleic acid to lipid ratios (I1483 /I1452 ) whereas the opposite is seen with bacteriostatic antibiotics. Third, the protein to lipid ratio (I2936 /I2885 and I2936 /I2850 ) is a Raman stress signature common to both the classes. These signatures were validated using two mutants, Δlon and ΔacrB, that exhibit relatively high and low resistance towards antibiotics, respectively. In addition, these spectral markers correlated with the emergence of phenotypic antibiotic resistance. Overall, this study demonstrates the efficacy of Raman spectroscopy to identify resistance in bacteria to sub-lethal concentrations of antibiotics.
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Affiliation(s)
- Taru Verma
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, India
| | - Harshitha Annappa
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Saumya Singh
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore, India
| | - Siva Umapathy
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, India
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore, India
| | - Dipankar Nandi
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, India
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
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71
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Pishchany G, Kolter R. On the possible ecological roles of antimicrobials. Mol Microbiol 2020; 113:580-587. [PMID: 31975454 DOI: 10.1111/mmi.14471] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 01/13/2020] [Accepted: 01/17/2020] [Indexed: 12/29/2022]
Abstract
The Introduction of antibiotics into the clinical use in the middle of the 20th century had a profound impact on modern medicine and human wellbeing. The contribution of these wonder molecules to public health and science is hard to overestimate. Much research has informed our understanding of antibiotic mechanisms of action and resistance at inhibitory concentrations in the lab and in the clinic. Antibiotics, however, are not a human invention as most of them are either natural products produced by soil microorganisms or semisynthetic derivatives of natural products. Because we use antibiotics to inhibit the bacterial growth, it is generally assumed that growth inhibition is also their primary ecological function in the environment. Nevertheless, multiple studies point to diverse nonlethal effects that are exhibited at lower levels of antibiotics. Here we review accumulating evidence of antibiosis and of alternative functions of antibiotics exhibited at subinhibitory concentrations. We also speculate on how these effects might alter phenotypes, fitness, and community composition of microbes in the context of the environment and suggest directions for future research.
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Affiliation(s)
- Gleb Pishchany
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Roberto Kolter
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
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72
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Draper LA, Ryan FJ, Dalmasso M, Casey PG, McCann A, Velayudhan V, Ross RP, Hill C. Autochthonous faecal viral transfer (FVT) impacts the murine microbiome after antibiotic perturbation. BMC Biol 2020; 18:173. [PMID: 33218339 PMCID: PMC7679995 DOI: 10.1186/s12915-020-00906-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 10/20/2020] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND It has become increasingly accepted that establishing and maintaining a complex and diverse gut microbiota is fundamental to human health. There are growing efforts to identify means of modulating and influencing the microbiota, especially in individuals who have experienced a disruption in their native microbiota. Faecal microbiota transplantation (FMT) is one method that restores diversity to the microbiota of an individual by introducing microbes from a healthy donor. FMT introduces the total microbial load into the recipient, including the bacteria, archaea, yeasts, protists and viruses. In this study, we investigated whether an autochthonous faecal viral transfer (FVT), in the form of a sterile faecal filtrate, could impact the recovery of a bacteriome disrupted by antibiotic treatment. RESULTS Following antibiotic disruption of the bacteriome, test mice received an FVT harvested prior to antibiotic treatment, while control mice received a heat- and nuclease-treated FVT. In both groups of mice, the perturbed microbiome reverted over time to one more similar to the pre-treatment one. However, the bacteriomes of mice that received an FVT, in which bacteriophages predominate, separated from those of the control mice as determined by principal co-ordinate analysis (PCoA). Moreover, analysis of the differentially abundant taxa indicated a closer resemblance to the pre-treatment bacteriome in the test mice that had received an FVT. Similarly, metagenomic sequencing of the virome confirmed that faecal bacteriophages of FVT and control mice differed over time in both abundance and diversity, with the phages constituting the FVT persisting in mice that received them. CONCLUSIONS An autochthonous virome transfer reshaped the bacteriomes of mice post-antibiotic treatment such that they more closely resembled the pre-antibiotic microbiota profile compared to mice that received non-viable phages. Thus, FVT may have a role in addressing antibiotic-associated microbiota alterations and potentially prevent the establishment of post-antibiotic infection. Given that bacteriophages are biologically inert in the absence of their host bacteria, they could form a safe and effective alternative to whole microbiota transplants that could be delivered during/following perturbation of the gut flora.
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Affiliation(s)
- Lorraine A Draper
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Feargal J Ryan
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
- Present Address: SAHMRI, North Terrace Adelaide, 5000, South Australia
| | - Marion Dalmasso
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
- Present Address: Normandie Univ, UNICAEN, ABTE, 14000, Caen, France
| | - Pat G Casey
- School of Microbiology, University College Cork, Cork, Ireland
| | - Angela McCann
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Vimalkumar Velayudhan
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - R Paul Ross
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Colin Hill
- APC Microbiome Ireland, University College Cork, Cork, Ireland.
- School of Microbiology, University College Cork, Cork, Ireland.
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73
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Memar MY, Yekani M, Celenza G, Poortahmasebi V, Naghili B, Bellio P, Baghi HB. The central role of the SOS DNA repair system in antibiotics resistance: A new target for a new infectious treatment strategy. Life Sci 2020; 262:118562. [PMID: 33038378 DOI: 10.1016/j.lfs.2020.118562] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 09/15/2020] [Accepted: 10/01/2020] [Indexed: 01/19/2023]
Abstract
Bacteria have a considerable ability and potential to acquire resistance against antimicrobial agents by acting diverse mechanisms such as target modification or overexpression, multidrug transporter systems, and acquisition of drug hydrolyzing enzymes. Studying the mechanisms of bacterial cell physiology is mandatory for the development of novel strategies to control the antimicrobial resistance phenomenon, as well as for the control of infections in clinics. The SOS response is a cellular DNA repair mechanism that has an essential role in the bacterial biologic process involved in resistance to antibiotics. The activation of the SOS network increases the resistance and tolerance of bacteria to stress and, as a consequence, to antimicrobial agents. Therefore, SOS can be an applicable target for the discovery of new antimicrobial drugs. In the present review, we focus on the central role of SOS response in bacterial resistance mechanisms and its potential as a new target for control of resistant pathogens.
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Affiliation(s)
- Mohammad Yousef Memar
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Students' Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mina Yekani
- Department of Microbiology, Faculty of Medicine, Kashan University of Medical Sciences, Kashan, Iran; Student Research Committee, Kashan University of Medical Sciences, Kashan, Iran
| | - Giuseppe Celenza
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy.
| | - Vahdat Poortahmasebi
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Microbiology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran; Research Center for Clinical Virology, Tehran University of Medical Sciences, Tehran, Iran
| | - Behrooz Naghili
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Pierangelo Bellio
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | - Hossein Bannazadeh Baghi
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Microbiology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
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74
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Jebri S, Rahmani F, Hmaied F. Bacteriophages as antibiotic resistance genes carriers in agro-food systems. J Appl Microbiol 2020; 130:688-698. [PMID: 32916015 DOI: 10.1111/jam.14851] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 09/04/2020] [Indexed: 12/14/2022]
Abstract
Antibiotic resistance genes (ARGs) are a global health concern. Antibiotic resistance occurs naturally, but misuse of antibiotics in humans and animals is accelerating the process of antibiotic resistance emergency, which has been aggravated by exposure to molecules of antibiotics present in clinical and agricultural settings and the engagement of many countries in water reuse especially in Middle East and North Africa region. Bacteriophages have the potential to be significant actors in ARGs transmission through the transduction process. These viruses have been detected along with ARGs in non impacted habitats and in anthropogenic impacted environments like wastewater, reclaimed water and manure amended soil as well as minimally processed food and ready to eat vegetables. The ubiquity of bacteriophages and their persistence in the environment raises concern about their involvement in ARGs transmission among different biomes and the generation of pathogenic-resistant bacteria that pose a great threat to human health. The aim of this review is to give an overview of the potential role of bacteriophages in the dissemination and the transfer of ARGs to pathogens in food production and processing and the consequent contribution to antibiotic resistance transmission through faecal oral route carrying ARGs to our dishes.
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Affiliation(s)
- S Jebri
- Laboratoire de Biotechnologies et Technologie Nucléaire (LR16CNSTN01), Centre National des Sciences et Technologie Nucléaire, Sidi Thabet, Tunisia
| | - F Rahmani
- Laboratoire de Biotechnologies et Technologie Nucléaire (LR16CNSTN01), Centre National des Sciences et Technologie Nucléaire, Sidi Thabet, Tunisia
| | - F Hmaied
- Laboratoire de Biotechnologies et Technologie Nucléaire (LR16CNSTN01), Centre National des Sciences et Technologie Nucléaire, Sidi Thabet, Tunisia
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75
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Characteristics of microbial community of soil subjected to industrial production of antibiotics. Folia Microbiol (Praha) 2020; 65:1061-1072. [PMID: 32901430 DOI: 10.1007/s12223-020-00819-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 08/30/2020] [Indexed: 10/23/2022]
Abstract
Ecosystems worldwide are exposed to pollutants connected to the industrial production of pharmaceuticals. The objective of this study was to study the composition and characteristics of the soil microbial communities that had been exposed to long-term selection pressure caused by the industrial production of penicillin G. Soil samples from four sites among the penicillin G production plant were analysed using 16S rRNA profiling via Illumina MiSeq platform and were compared with the control samples from four sites outside the plant. Total metagenomic DNA from the impacted soil was also used for the preparation of E. coli T1R-based fosmid library which was consequently qualitatively tested for the presence of penicillin G acylase (PGA)-encoding genes using the method of sequence homology. Analyses of alpha diversity revealed that the long-term antibiotic presence in the soil significantly increased the microbial diversity and richness in terms of Shannon diversity index (p = 0.002) and Chao estimates (p = 0.004). Principal component analysis showed that the two types of communities (on-site and control) could be separated at the phylum, class and genus level. The on-site soil was enriched in Betaproteobacteria, Deltaproteobacteria, Gemmatimonadetes, Acidobacteria and Planctomycetia, while a significant decrease in Actinobacteria was observed. Metagenomic fosmid library revealed high hit rates in identifying PGAs (14 different genes identified) and confirmed the biotechnological potential of soils impacted by anthropogenic activity. This study offers new insights into the changes in microbial communities of soils exposed to anthropogenic activity as well as indicates that those soils may represent a hotspot for biotechnologically interesting targets.
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76
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Gudda FO, Waigi MG, Odinga ES, Yang B, Carter L, Gao Y. Antibiotic-contaminated wastewater irrigated vegetables pose resistance selection risks to the gut microbiome. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 264:114752. [PMID: 32417582 DOI: 10.1016/j.envpol.2020.114752] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 05/03/2020] [Accepted: 05/05/2020] [Indexed: 06/11/2023]
Abstract
Wastewater reuse in food crop irrigation has led to agroecosystem pollution concerns and human health risks. However, there is limited attention on the relationship of sub-lethal antibiotic levels in vegetables and resistance selection. Most risk assessment studies show non-significant toxicity, but overlook the link between antibiotics in crops and propagation of gut microbiome resistance selection. The review highlights the risk of antibiotics in treated water used for irrigation, uptake, and accumulation in edible vegetable parts. Moreover, it elucidates the risks to the adaptive resistance selection of the gut microbiome from sub-lethal antibiotic levels, as a result of dietary contaminated vegetables. Experiments have reported that bacterial resistance selection is possible at concentrations that are several hundred-folds lower than lethal effect levels on susceptible cells. Consequently, mutants selected at low antibiotic levels, such as those from vegetables, are fitter and more resistant compared to those selected at high concentrations. Necessary standardization, such as the development of minimum acceptable antibiotic limits allowable in food crop irrigation water, with a focus on minimum selection concentration, and not only toxicity, has been proposed. Wastewater irrigation offers environmental benefits and can contribute to food security, but it has non-addressed risks. Research gaps, future perspectives, and frameworks of mitigating the potential risks are discussed.
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Affiliation(s)
- Fredrick Owino Gudda
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China; Faculty of Environment and Resource Development, Department of Environmental Sciences, Egerton University, Box 536, Egerton, 20115, Kenya
| | - Michael Gatheru Waigi
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Emmanuel Stephen Odinga
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Bing Yang
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Laura Carter
- School of Geography, University of Leeds, Leeds, LS2 9JT, UK
| | - Yanzheng Gao
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China.
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77
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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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78
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Regulation of virulence and antibiotic resistance in Gram-positive microbes in response to cell wall-active antibiotics. Curr Opin Infect Dis 2020; 32:217-222. [PMID: 31021953 DOI: 10.1097/qco.0000000000000542] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
PURPOSE OF REVIEW Antibiotic stress can evoke considerable genotypic and phenotypic changes in Gram-positive bacteria. Here, we review recent studies describing altered virulence expression in response to cell wall-acting antibiotics and discuss mechanisms that coordinate regulation of the antibiotic response. RECENT FINDINGS Pleiotropic effects induced by antibiotic exposure include alterations to bacterial metabolism, cell wall structure and antibiotic resistance. In addition, subinhibitory concentrations of cell wall-active (CWA) antibiotics have increasingly been shown to induce the production of exotoxins and biofilm formation that may influence virulence. Remarkably, phenotypes associated with comparable antibiotic stresses can vary considerably, emphasizing the need to better understand the response to CWA antibiotics. Recent studies support both direct antibiotic recognition and recognition of antibiotic-induced stress to the bacterial cell wall. Specifically, bacterial two-component systems, penicillin-binding protein and serine/threonine kinase-associated kinases and conserved oxidative-stress sensors each contribute to modulating the antibiotic stress response. SUMMARY Bacterial sensory systems and global regulators coordinate signaling in response to CWA antibiotics. Regulation of the antibiotic response is complex and involves integration of signals from multiple response pathways. A better definition of the antibiotic stress response among Gram-positive pathogens may yield novel therapeutic targets to counter antibiotic resistance and virulence factor expression.
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79
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Abstract
The human gut is home to a myriad of organisms. While some are harmless commensals, others are transient, pathogenic flora. The gut microbiome is composed of diverse bacterial flora, and apart from playing a major role in protecting from various infectious and non-infectious diseases, it plays an important role in resistance to antimicrobials. The collection of genes or genetic material that confers antimicrobial resistance constitutes the gut resistome, and it may involve the pathogens or commensals of the intestinal tract. The diversity of this gut resistome is influenced by various environmental factors including the diet and antibiotic exposure. This review highlights the recent concepts pertaining to the human gut resistome, factors affecting it, how it impacts human health and diseases, methods to study the resistome and potential therapeutic approaches.
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Affiliation(s)
- Shreya Singh
- Department of Medical Microbiology, Postgraduate Institute of Medical Education & Research, Chandigarh, India
| | - Nipun Verma
- Department of Hepatology, Postgraduate Institute of Medical Education & Research, Chandigarh, India
| | - Neelam Taneja
- Department of Medical Microbiology, Postgraduate Institute of Medical Education & Research, Chandigarh, India
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80
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Bajaj JS, Khoruts A. Microbiota changes and intestinal microbiota transplantation in liver diseases and cirrhosis. J Hepatol 2020; 72:1003-1027. [PMID: 32004593 DOI: 10.1016/j.jhep.2020.01.017] [Citation(s) in RCA: 95] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 01/07/2020] [Accepted: 01/20/2020] [Indexed: 02/08/2023]
Abstract
Patients with chronic liver disease and cirrhosis demonstrate a global mucosal immune impairment, which is associated with altered gut microbiota composition and functionality. These changes progress along with the advancing degree of cirrhosis and can be linked with hepatic encephalopathy, infections and even prognostication independent of clinical biomarkers. Along with compositional changes, functional alterations to the microbiota, related to short-chain fatty acids, bioenergetics and bile acid metabolism, are also associated with cirrhosis progression and outcomes. Altering the functional and structural profile of the microbiota is partly achieved by medications used in patients with cirrhosis such as rifaximin, lactulose, proton pump inhibitors and other antibiotics. However, the role of faecal or intestinal microbiota transplantation is increasingly being recognised. Herein, we review the challenges, opportunities and road ahead for the appropriate and safe use of intestinal microbiota transplantation in liver disease.
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Affiliation(s)
- Jasmohan S Bajaj
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, Virginia, USA.
| | - Alexander Khoruts
- Division of Gastroenterology Hepatology and Nutrition, University of Minnesota, Minneapolis, Minnesota, USA
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81
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Lu J, Wang Y, Jin M, Yuan Z, Bond P, Guo J. Both silver ions and silver nanoparticles facilitate the horizontal transfer of plasmid-mediated antibiotic resistance genes. WATER RESEARCH 2020; 169:115229. [PMID: 31783256 DOI: 10.1016/j.watres.2019.115229] [Citation(s) in RCA: 156] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 08/04/2019] [Accepted: 10/24/2019] [Indexed: 05/21/2023]
Abstract
Antibiotic resistance in bacteria is a growing threat to global human health. Horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs) is recognized as the primary contributor to antibiotic resistance dissemination. Silver nanoparticles (AgNPs) are widely used in personal care products as antimicrobial agents. While heavy metals are known to induce antibiotic resistance in bacteria, it is not known whether AgNPs in the environment can stimulate the HGT of ARGs. Here, we report that both AgNPs and ionic silver Ag+, at environmentally relevant and sub-lethal concentrations, facilitate the conjugative transfer of plasmid-borne ARGs across bacterial genera (from the donor Escherichia coli K-12 LE392 to the recipient Pseudomonas putida KT2440). The underlying mechanisms of the Ag+- or AgNPs-promoted HGT were unveiled by detecting oxidative stress and cell membrane permeability, combined with genome-wide RNA sequencing and proteomic analyses. It was found that both Ag+ and AgNPs exposure induced various bacterial responses that included reactive oxygen species (ROS) generation, membrane damage and the SOS response. This study exposes the potential ecological risks of environmental levels of AgNPs and Ag+ for promoting the spread of ARGs and highlights concerns regarding the management of nanoparticles and heavy metals.
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Affiliation(s)
- Ji Lu
- Advanced Water Management Centre (AWMC), The University of Queensland, St Lucia, Brisbane, QLD, 4072, Australia
| | - Yue Wang
- Advanced Water Management Centre (AWMC), The University of Queensland, St Lucia, Brisbane, QLD, 4072, Australia
| | - Min Jin
- Advanced Water Management Centre (AWMC), The University of Queensland, St Lucia, Brisbane, QLD, 4072, Australia
| | - Zhiguo Yuan
- Advanced Water Management Centre (AWMC), The University of Queensland, St Lucia, Brisbane, QLD, 4072, Australia
| | - Philip Bond
- Advanced Water Management Centre (AWMC), The University of Queensland, St Lucia, Brisbane, QLD, 4072, Australia
| | - Jianhua Guo
- Advanced Water Management Centre (AWMC), The University of Queensland, St Lucia, Brisbane, QLD, 4072, Australia.
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82
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Tracking microbial evolution in the human gut using Hi-C reveals extensive horizontal gene transfer, persistence and adaptation. Nat Microbiol 2019; 5:343-353. [PMID: 31873203 PMCID: PMC6992475 DOI: 10.1038/s41564-019-0625-0] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 10/30/2019] [Indexed: 12/15/2022]
Abstract
Despite the importance of horizontal gene transfer for rapid bacterial evolution, reliable assignment of mobile genetic elements to their microbial hosts in natural communities such as the human gut microbiota is lacking. We used high-throughput chromosomal conformation capture coupled with probabilistic modelling of experimental noise to resolve 88 strain-level metagenome-assembled genomes of distal gut bacteria from two participants, including 12,251 accessory elements. Comparisons of two samples collected 10 years apart for each of the participants revealed extensive in situ exchange of accessory elements as well as evidence of adaptive evolution in core genomes. Accessory elements were predominantly promiscuous and prevalent in the distal gut metagenomes of 218 adult individuals. This research provides a foundation and approach for studying microbial evolution in natural environments.
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83
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Environmental Prevalence of Carbapenem Resistance Enterobacteriaceae (CRE) in a Tropical Ecosystem in India: Human Health Perspectives and Future Directives. Pathogens 2019; 8:pathogens8040174. [PMID: 31581701 PMCID: PMC6963203 DOI: 10.3390/pathogens8040174] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 09/29/2019] [Accepted: 09/29/2019] [Indexed: 01/21/2023] Open
Abstract
In the past few decades, infectious diseases have become increasingly challenging to treat, which is explained by the growing number of antibiotic-resistant bacteria. Notably, carbapenem-resistant Enterobacteriaceae (CRE) infections at global level attribute a vast, dangerous clinical threat. In most cases, there are enormous difficulties for CRE infection except a few last resort toxic drugs such as tigecycline and colistin (polymyxin E). Due to this, CRE has now been categorized as one among the three most dangerous multidrug resistance (MDR) pathogens by the US Centres for Disease Control and Prevention (CDC). Considering this, the study of the frequency of CRE infections and the characterization of CRE is an important area of research in clinical settings. However, MDR bacteria are not only present in hospitals but are spreading more and more into the environment, thereby increasing the risk of infection with resistant bacteria outside the hospital. In this context, developing countries are a global concern where environmental regulations are often insufficient. It seems likely that overcrowding, poor sanitation, socioeconomic status, and limited infrastructures contribute to the rapid spread of MDR bacteria, becoming their reservoirs in the environment. Thus, in this review, we present the occurrence of CRE and their resistance determinants in different environmental compartments in India.
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84
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Ingmer H, Gerlach D, Wolz C. Temperate Phages of Staphylococcus aureus. Microbiol Spectr 2019; 7:10.1128/microbiolspec.gpp3-0058-2018. [PMID: 31562736 PMCID: PMC10921950 DOI: 10.1128/microbiolspec.gpp3-0058-2018] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Indexed: 12/22/2022] Open
Abstract
Most Staphylococcus aureus isolates carry multiple bacteriophages in their genome, which provide the pathogen with traits important for niche adaptation. Such temperate S. aureus phages often encode a variety of accessory factors that influence virulence, immune evasion and host preference of the bacterial lysogen. Moreover, transducing phages are primary vehicles for horizontal gene transfer. Wall teichoic acid (WTA) acts as a common phage receptor for staphylococcal phages and structural variations of WTA govern phage-host specificity thereby shaping gene transfer across clonal lineages and even species. Thus, bacteriophages are central for the success of S. aureus as a human pathogen.
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Affiliation(s)
- Hanne Ingmer
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - David Gerlach
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Christiane Wolz
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
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85
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Blázquez J, Rodríguez-Beltrán J, Matic I. Antibiotic-Induced Genetic Variation: How It Arises and How It Can Be Prevented. Annu Rev Microbiol 2019; 72:209-230. [PMID: 30200850 DOI: 10.1146/annurev-micro-090817-062139] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
By targeting essential cellular processes, antibiotics provoke metabolic perturbations and induce stress responses and genetic variation in bacteria. Here we review current knowledge of the mechanisms by which these molecules generate genetic instability. They include production of reactive oxygen species, as well as induction of the stress response regulons, which lead to enhancement of mutation and recombination rates and modulation of horizontal gene transfer. All these phenomena influence the evolution and spread of antibiotic resistance. The use of strategies to stop or decrease the generation of resistant variants is also discussed.
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Affiliation(s)
- Jesús Blázquez
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), 28049 Madrid, Spain; .,Unidad de Enfermedades Infecciosas, Microbiologia y Medicina Preventiva, Hospital Universitario Virgen del Rocio, 41013 Seville, Spain.,Red Española de Investigacion en Patologia Infecciosa, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | | | - Ivan Matic
- Faculté de Médecine Paris Descartes, INSERM 1001, CNRS, Université Paris-Descartes-Sorbonne Paris Cité, 75014 Paris, France;
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86
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Leclerc QJ, Lindsay JA, Knight GM. Mathematical modelling to study the horizontal transfer of antimicrobial resistance genes in bacteria: current state of the field and recommendations. J R Soc Interface 2019; 16:20190260. [PMID: 31409239 DOI: 10.1098/rsif.2019.0260] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Antimicrobial resistance (AMR) is one of the greatest public health challenges we are currently facing. To develop effective interventions against this, it is essential to understand the processes behind the spread of AMR. These are partly dependent on the dynamics of horizontal transfer of resistance genes between bacteria, which can occur by conjugation (direct contact), transformation (uptake from the environment) or transduction (mediated by bacteriophages). Mathematical modelling is a powerful tool to investigate the dynamics of AMR; however, the extent of its use to study the horizontal transfer of AMR genes is currently unclear. In this systematic review, we searched for mathematical modelling studies that focused on horizontal transfer of AMR genes. We compared their aims and methods using a list of predetermined criteria and used our results to assess the current state of this research field. Of the 43 studies we identified, most focused on the transfer of single genes by conjugation in Escherichia coli in culture and its impact on the bacterial evolutionary dynamics. Our findings highlight the existence of an important research gap in the dynamics of transformation and transduction and the overall public health implications of horizontal transfer of AMR genes. To further develop this field and improve our ability to control AMR, it is essential that we clarify the structural complexity required to study the dynamics of horizontal gene transfer, which will require cooperation between microbiologists and modellers.
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Affiliation(s)
- Quentin J Leclerc
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Jodi A Lindsay
- Institute for Infection and Immunity, St George's University of London, London, UK
| | - Gwenan M Knight
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, London, UK
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87
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Claessen D, Errington J. Cell Wall Deficiency as a Coping Strategy for Stress. Trends Microbiol 2019; 27:1025-1033. [PMID: 31420127 DOI: 10.1016/j.tim.2019.07.008] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 07/02/2019] [Accepted: 07/23/2019] [Indexed: 12/22/2022]
Abstract
The cell wall is a surface layer located outside the cell membrane of almost all bacteria; it protects cells from environmental stresses and gives them their typical shape. The cell wall is highly conserved in bacteria and is the target for some of our best antibiotics. Surprisingly, some bacteria are able to shed their wall under the influence of stress, yielding cells that are cell-wall-deficient. Notably, wall-deficient cells are flexible and are able to maneuver through narrow spaces, insensitive to wall-targeting antibiotics, and capable of taking up and exchanging DNA. Moreover, given that wall-associated epitopes are often recognized by host defense systems, wall deficiency provides a plausible explanation for how some bacteria may hide in their host. In this review we focus on this paradoxical stress response, which provides cells with unique opportunities that are unavailable to walled cells.
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Affiliation(s)
- Dennis Claessen
- Institute of Biology, Leiden University, Sylviusweg 72, 2333, BE, Leiden, The Netherlands.
| | - Jeff Errington
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle-upon-Tyne, NE2 4AX, UK.
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88
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Zuo T, Lu XJ, Zhang Y, Cheung CP, Lam S, Zhang F, Tang W, Ching JYL, Zhao R, Chan PKS, Sung JJY, Yu J, Chan FKL, Cao Q, Sheng JQ, Ng SC. Gut mucosal virome alterations in ulcerative colitis. Gut 2019; 68:1169-1179. [PMID: 30842211 PMCID: PMC6582748 DOI: 10.1136/gutjnl-2018-318131] [Citation(s) in RCA: 235] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 02/04/2019] [Accepted: 02/15/2019] [Indexed: 12/17/2022]
Abstract
OBJECTIVE The pathogenesis of UC relates to gut microbiota dysbiosis. We postulate that alterations in the viral community populating the intestinal mucosa play an important role in UC pathogenesis. This study aims to characterise the mucosal virome and their functions in health and UC. DESIGN Deep metagenomics sequencing of virus-like particle preparations and bacterial 16S rRNA sequencing were performed on the rectal mucosa of 167 subjects from three different geographical regions in China (UC=91; healthy controls=76). Virome and bacteriome alterations in UC mucosa were assessed and correlated with patient metadata. We applied partition around medoids clustering algorithm and classified mucosa viral communities into two clusters, referred to as mucosal virome metacommunities 1 and 2. RESULTS In UC, there was an expansion of mucosa viruses, particularly Caudovirales bacteriophages, and a decrease in mucosa Caudovirales diversity, richness and evenness compared with healthy controls. Altered mucosal virome correlated with intestinal inflammation. Interindividual dissimilarity between mucosal viromes was higher in UC than controls. Escherichia phage and Enterobacteria phage were more abundant in the mucosa of UC than controls. Compared with metacommunity 1, metacommunity 2 was predominated by UC subjects and displayed a significant loss of various viral species. Patients with UC showed substantial abrogation of diverse viral functions, whereas multiple viral functions, particularly functions of bacteriophages associated with host bacteria fitness and pathogenicity, were markedly enriched in UC mucosa. Intensive transkingdom correlations between mucosa viruses and bacteria were significantly depleted in UC. CONCLUSION We demonstrated for the first time that UC is characterised by substantial alterations of the mucosa virobiota with functional distortion. Enrichment of Caudovirales bacteriophages, increased phage/bacteria virulence functions and loss of viral-bacterial correlations in the UC mucosa highlight that mucosal virome may play an important role in UC pathogenesis.
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Affiliation(s)
- Tao Zuo
- Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China,State Key Laboratory for digestive disease, Institute of Digestive Disease, Li Ka Shing Institute of Health Science, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China,Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese Univetsity of Hong Kong, Shatin, Hong Kong, China
| | - Xiao-Juan Lu
- Department of Gastroenterology, The General Hospital of the People’s Liberation Army, Beijing, China
| | - Yu Zhang
- Faculty of Medicine, Zhejiang University, Hangzhou, China
| | - Chun Pan Cheung
- State Key Laboratory for digestive disease, Institute of Digestive Disease, Li Ka Shing Institute of Health Science, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China,Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese Univetsity of Hong Kong, Shatin, Hong Kong, China
| | - Siu Lam
- State Key Laboratory for digestive disease, Institute of Digestive Disease, Li Ka Shing Institute of Health Science, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China,Department of Microbiology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Fen Zhang
- State Key Laboratory for digestive disease, Institute of Digestive Disease, Li Ka Shing Institute of Health Science, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China,Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese Univetsity of Hong Kong, Shatin, Hong Kong, China
| | - Whitney Tang
- Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese Univetsity of Hong Kong, Shatin, Hong Kong, China
| | - Jessica Y L Ching
- Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese Univetsity of Hong Kong, Shatin, Hong Kong, China
| | - Risheng Zhao
- State Key Laboratory for digestive disease, Institute of Digestive Disease, Li Ka Shing Institute of Health Science, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China,Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese Univetsity of Hong Kong, Shatin, Hong Kong, China
| | - Paul K S Chan
- Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China,Department of Microbiology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Joseph J Y Sung
- State Key Laboratory for digestive disease, Institute of Digestive Disease, Li Ka Shing Institute of Health Science, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China,Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese Univetsity of Hong Kong, Shatin, Hong Kong, China
| | - Jun Yu
- State Key Laboratory for digestive disease, Institute of Digestive Disease, Li Ka Shing Institute of Health Science, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China,Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese Univetsity of Hong Kong, Shatin, Hong Kong, China
| | - Francis K L Chan
- Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Qian Cao
- Faculty of Medicine, Zhejiang University, Hangzhou, China,Department of Gastroenterology, School of Medicine, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China
| | - Jian-Qiu Sheng
- Department of Gastroenterology, The General Hospital of the People’s Liberation Army, Beijing, China
| | - Siew C Ng
- Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China,State Key Laboratory for digestive disease, Institute of Digestive Disease, Li Ka Shing Institute of Health Science, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China,Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese Univetsity of Hong Kong, Shatin, Hong Kong, China
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89
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Ram Y, Hadany L. Evolution of Stress-Induced Mutagenesis in the Presence of Horizontal Gene Transfer. Am Nat 2019; 194:73-89. [PMID: 31251650 DOI: 10.1086/703457] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Stress-induced mutagenesis has been observed in multiple species of bacteria and yeast. It has been suggested that in asexual populations, a mutator allele that increases the mutation rate during stress can sweep to fixation with the beneficial mutations it generates. However, even asexual microbes can undergo horizontal gene transfer and rare recombination, which typically interfere with the spread of mutator alleles. Here we examine the effect of horizontal gene transfer on the evolutionary advantage of stress-induced mutator alleles. Our results demonstrate that stress-induced mutator alleles are favored by selection even in the presence of horizontal gene transfer and more so when the mutator alleles also increase the rate of horizontal gene transfer. We suggest that when regulated by stress, mutation and horizontal gene transfer can be complementary rather than competing adaptive strategies and that stress-induced mutagenesis has important implications for evolutionary biology, ecology, and epidemiology, even in the presence of horizontal gene transfer and rare recombination.
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90
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Kraemer SA, Ramachandran A, Perron GG. Antibiotic Pollution in the Environment: From Microbial Ecology to Public Policy. Microorganisms 2019; 7:E180. [PMID: 31234491 PMCID: PMC6616856 DOI: 10.3390/microorganisms7060180] [Citation(s) in RCA: 356] [Impact Index Per Article: 71.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 06/06/2019] [Accepted: 06/10/2019] [Indexed: 01/06/2023] Open
Abstract
The ability to fight bacterial infections with antibiotics has been a longstanding cornerstone of modern medicine. However, wide-spread overuse and misuse of antibiotics has led to unintended consequences, which in turn require large-scale changes of policy for mitigation. In this review, we address two broad classes of corollaries of antibiotics overuse and misuse. Firstly, we discuss the spread of antibiotic resistance from hotspots of resistance evolution to the environment, with special concerns given to potential vectors of resistance transmission. Secondly, we outline the effects of antibiotic pollution independent of resistance evolution on natural microbial populations, as well as invertebrates and vertebrates. We close with an overview of current regional policies tasked with curbing the effects of antibiotics pollution and outline areas in which such policies are still under development.
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Affiliation(s)
- Susanne A Kraemer
- Department of Biology, Concordia University, 7141 Sherbrooke Street W, Montreal, QC H4B1R6, Canada.
| | - Arthi Ramachandran
- Department of Biology, Concordia University, 7141 Sherbrooke Street W, Montreal, QC H4B1R6, Canada.
| | - Gabriel G Perron
- Department of Biology, Reem-Kayden Center for Sciences and Computation, Bard College, 31 Campus Road, Annandale-On-Hudson, NY 12504, USA.
- Center for the Study of Land, Water, and Air, Bard College, Annandale-On-Hudson, NY 12504, USA.
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91
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Segall AM, Roach DR, Strathdee SA. Stronger together? Perspectives on phage-antibiotic synergy in clinical applications of phage therapy. Curr Opin Microbiol 2019; 51:46-50. [PMID: 31226502 DOI: 10.1016/j.mib.2019.03.005] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 03/11/2019] [Accepted: 03/12/2019] [Indexed: 01/21/2023]
Abstract
Increasingly, clinical infections are becoming recalcitrant or completely resistant to antibiotics treatment and multidrug resistance is rising alarmingly. Patients suffering from infections that used to be treated successfully by antibiotic regimens are running out of the treatment options. Bacteriophage (phage) therapy, long practiced in parts of Eastern Europe and the states of the former Soviet Union, is now being reevaluated as a treatment option complementary to and synergistic with antibiotic treatments. We discuss some current studies that have addressed synergistic killing activity between phages and antibiotics, the issues of treatment order and antibiotic class, and point to considerations that will have to be addressed by future studies. Overall, co-treatments with phages and antibiotics promise to extend the utility of antibiotics in current use. Nevertheless, a lot of work, both basic and clinical, remains to be done before such co-treatments become routine options in the hospital setting.
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Affiliation(s)
- Anca M Segall
- Department of Biology and the Viral Information Institute, San Diego State University, San Diego, CA 92182-4614, United States.
| | - Dwayne R Roach
- Department of Biology and the Viral Information Institute, San Diego State University, San Diego, CA 92182-4614, United States
| | - Steffanie A Strathdee
- Division of Infectious Diseases and Global Health, Department of Medicine, University of California San Diego, United States.
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92
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Zhou R, Zeng S, Hou D, Liu J, Weng S, He J, Huang Z. Occurrence of human pathogenic bacteria carrying antibiotic resistance genes revealed by metagenomic approach: A case study from an aquatic environment. J Environ Sci (China) 2019; 80:248-256. [PMID: 30952342 DOI: 10.1016/j.jes.2019.01.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 01/04/2019] [Accepted: 01/04/2019] [Indexed: 06/09/2023]
Abstract
Antibiotic resistance genes (ARGs), human pathogenic bacteria (HPB), and HPB carrying ARGs are public issues that pose a high risk to aquatic environments and public health. Their diversity and abundance in water, intestine, and sediments of shrimp culture pond were investigated using metagenomic approach. A total of 19 classes of ARGs, 52 HPB species, and 7 species of HPB carrying ARGs were found. Additionally, 157, 104, and 86 subtypes of ARGs were detected in shrimp intestine, pond water, and sediment samples, respectively. In all the samples, multidrug resistance genes were the highest abundant class of ARGs. The dominant HPB was Enterococcus faecalis in shrimp intestine, Vibrio parahaemolyticus in sediments, and Mycobacterium yongonense in water, respectively. Moreover, E. faecalis (contig Intestine_364647) and Enterococcus faecium (contig Intestine_80272) carrying efrA, efrB and ANT(6)-Ia were found in shrimp intestine, Desulfosaricina cetonica (contig Sediment_825143) and Escherichia coli (contig Sediment_188430) carrying mexB and APH(3')-IIa were found in sediments, and Laribacter hongkongensis (contig Water_478168 and Water_369477), Shigella sonnei (contig Water_880246), and Acinetobacter baumannii (contig Water_525520) carrying sul1, sul2, ereA, qacH, OXA-21, and mphD were found in pond water. Mobile genetic elements (MGEs) analysis indicated that horizontal gene transfer (HGT) of integrons, insertion sequences, and plasmids existed in shrimp intestine, sediment, and water samples, and the abundance of integrons was higher than that of other two MGEs. The results suggested that HPB carrying ARGs potentially existed in aquatic environments, and that these contributed to the environment and public health risk evaluation.
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Affiliation(s)
- Renjun Zhou
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Shenzheng Zeng
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Dongwei Hou
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Jian Liu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Shaoping Weng
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Jianguo He
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-sen University, Guangzhou 510275, China; School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Zhijian Huang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-sen University, Guangzhou 510275, China.
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93
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Hoikkala V, Almeida GMF, Laanto E, Sundberg LR. Aquaculture as a source of empirical evidence for coevolution between CRISPR-Cas and phage. Philos Trans R Soc Lond B Biol Sci 2019; 374:20180100. [PMID: 30905289 PMCID: PMC6452259 DOI: 10.1098/rstb.2018.0100] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/11/2018] [Indexed: 12/20/2022] Open
Abstract
So far, studies on the bacterial immune system CRISPR-Cas and its ecological and evolutionary effects have been largely limited to laboratory conditions. While providing crucial information on the constituents of CRISPR-Cas, such studies may overlook fundamental components that affect bacterial immunity in natural habitats. Translating laboratory-derived predictions to nature is not a trivial task, owing partly to the instability of natural communities and difficulties in repeated sampling. To this end, we review how aquaculture, the farming of fishes and other aquatic species, may provide suitable semi-natural laboratories for examining the role of CRISPR-Cas in phage/bacterium coevolution. Existing data from disease surveillance conducted in aquaculture, coupled with growing interest towards phage therapy, may have already resulted in large collections of bacterium and phage isolates. These data, combined with premeditated efforts, can provide empirical evidence on phage-bacterium dynamics such as the bacteriophage adherence to mucus hypothesis, phage life cycles and their relationship with CRISPR-Cas and other immune defences. Typing of CRISPR spacer content in pathogenic bacteria can also provide practical information on diversity and origin of isolates during outbreaks. In addition to providing information of CRISPR functionality and phage-bacterium dynamics, aquaculture systems can significantly impact perspectives on design of phage-based disease treatment at the current era of increasing antibiotic resistance. This article is part of a discussion meeting issue 'The ecology and evolution of prokaryotic CRISPR-Cas adaptive immune systems'.
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Affiliation(s)
| | | | | | - Lotta-Riina Sundberg
- Centre of Excellence in Biological Interactions, Department of Biological and Environmental Science and Nanoscience Center, University of Jyvaskyla, PO Box 35, 40014 Jyvaskyla, Finland
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94
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Park H, Laffin MR, Jovel J, Millan B, Hyun JE, Hotte N, Kao D, Madsen KL. The success of fecal microbial transplantation in Clostridium difficile infection correlates with bacteriophage relative abundance in the donor: a retrospective cohort study. Gut Microbes 2019; 10:676-687. [PMID: 30866714 PMCID: PMC6867182 DOI: 10.1080/19490976.2019.1586037] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Background: Fecal microbial transplantation (FMT) is used in the treatment of relapsing Clostridium difficile infection (rCDI). Failure rate for FMT is as high as 10% but the mechanisms contributing to a failed FMT are not understood. We utilized metagenomic data to identify the role of bacteria and bacteriophages on FMT success.Results: Subjects with rCDI (n = 19) received FMT from volunteer donors (n = 7) via colonoscopy. Twelve patients fully recovered after a single FMT, while seven patients required a subsequent FMT. DNA was extracted from patient and donor stool samples for shotgun metagenomic analysis. Metagenomics libraries were analyzed focusing on bacterial taxonomy and bacteriophage sequences. Gammaproteobacteria were dominant in rCDI patients prior to FMT largely due to elevated levels of Klebsiella and Escherichia. A successful FMT led to increased levels of Clostridia and Bacteroidia and a reduction in Gammaproteobacteria. In contrast, a failed FMT led to no significant changes in bacterial composition. Bacteriophages were classified during whole metagenomic analysis of each sample and were markedly different between rCDI patients, donors, and a healthy control cohort (n = 96). Bacteriophage sequence reads were increased in CDI patients compared with donors and healthy controls. Successful FMT donors had higher bacteriophage α-diversity and lower relative abundance compared to the donors of a failed initial FMT.Conclusions: In this retrospective analysis, FMTs with increased bacteriophage α-diversity were more likely to successfully treat rCDI. In addition, the relative number of bacteriophage reads was lower in donations leading to a successful FMT. These results suggest that bacteriophage abundance may have some role in determining the relative success of FMT.
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Affiliation(s)
- Heekuk Park
- Division of Gastroenterology, Department of Medicine, University of Alberta, Edmonton, AB, Canada,Center of Excellence for Gastrointestinal Inflammation and Immunity Research, Edmonton, AB, Canada
| | | | - Juan Jovel
- Division of Gastroenterology, Department of Medicine, University of Alberta, Edmonton, AB, Canada,Center of Excellence for Gastrointestinal Inflammation and Immunity Research, Edmonton, AB, Canada
| | - Braden Millan
- Division of Gastroenterology, Department of Medicine, University of Alberta, Edmonton, AB, Canada,Center of Excellence for Gastrointestinal Inflammation and Immunity Research, Edmonton, AB, Canada
| | - Jae E. Hyun
- Division of Gastroenterology, Department of Medicine, University of Alberta, Edmonton, AB, Canada,Center of Excellence for Gastrointestinal Inflammation and Immunity Research, Edmonton, AB, Canada
| | - Naomi Hotte
- Division of Gastroenterology, Department of Medicine, University of Alberta, Edmonton, AB, Canada,Center of Excellence for Gastrointestinal Inflammation and Immunity Research, Edmonton, AB, Canada
| | - Dina Kao
- Division of Gastroenterology, Department of Medicine, University of Alberta, Edmonton, AB, Canada,Center of Excellence for Gastrointestinal Inflammation and Immunity Research, Edmonton, AB, Canada
| | - Karen L. Madsen
- Division of Gastroenterology, Department of Medicine, University of Alberta, Edmonton, AB, Canada,Center of Excellence for Gastrointestinal Inflammation and Immunity Research, Edmonton, AB, Canada,CONTACT Karen L. Madsen Division of Gastroenterology, Department of Medicine, University of Alberta, 7-142 Katz Group Center, Edmonton, AB, Canada
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95
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Copin R, Sause WE, Fulmer Y, Balasubramanian D, Dyzenhaus S, Ahmed JM, Kumar K, Lees J, Stachel A, Fisher JC, Drlica K, Phillips M, Weiser JN, Planet PJ, Uhlemann AC, Altman DR, Sebra R, van Bakel H, Lighter J, Torres VJ, Shopsin B. Sequential evolution of virulence and resistance during clonal spread of community-acquired methicillin-resistant Staphylococcus aureus. Proc Natl Acad Sci U S A 2019; 116:1745-1754. [PMID: 30635416 PMCID: PMC6358666 DOI: 10.1073/pnas.1814265116] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The past two decades have witnessed an alarming expansion of staphylococcal disease caused by community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA). The factors underlying the epidemic expansion of CA-MRSA lineages such as USA300, the predominant CA-MRSA clone in the United States, are largely unknown. Previously described virulence and antimicrobial resistance genes that promote the dissemination of CA-MRSA are carried by mobile genetic elements, including phages and plasmids. Here, we used high-resolution genomics and experimental infections to characterize the evolution of a USA300 variant plaguing a patient population at increased risk of infection to understand the mechanisms underlying the emergence of genetic elements that facilitate clonal spread of the pathogen. Genetic analyses provided conclusive evidence that fitness (manifest as emergence of a dominant clone) changed coincidently with the stepwise emergence of (i) a unique prophage and mutation of the regulator of the pyrimidine nucleotide biosynthetic operon that promoted abscess formation and colonization, respectively, thereby priming the clone for success; and (ii) a unique plasmid that conferred resistance to two topical microbiocides, mupirocin and chlorhexidine, frequently used for decolonization and infection prevention. The resistance plasmid evolved through successive incorporation of DNA elements from non-S. aureus spp. into an indigenous cryptic plasmid, suggesting a mechanism for interspecies genetic exchange that promotes antimicrobial resistance. Collectively, the data suggest that clonal spread in a vulnerable population resulted from extensive clinical intervention and intense selection pressure toward a pathogen lifestyle that involved the evolution of consequential mutations and mobile genetic elements.
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Affiliation(s)
- Richard Copin
- Division of Infectious Diseases and Immunology, Department of Medicine, New York University School of Medicine, New York, NY 10016
| | - William E Sause
- Department of Microbiology, New York University School of Medicine, New York, NY 10016
| | - Yi Fulmer
- Division of Infectious Diseases and Immunology, Department of Medicine, New York University School of Medicine, New York, NY 10016
| | - Divya Balasubramanian
- Department of Microbiology, New York University School of Medicine, New York, NY 10016
| | - Sophie Dyzenhaus
- Department of Microbiology, New York University School of Medicine, New York, NY 10016
| | - Jamil M Ahmed
- Division of Infectious Diseases and Immunology, Department of Medicine, New York University School of Medicine, New York, NY 10016
| | - Krishan Kumar
- Division of Infectious Diseases and Immunology, Department of Medicine, New York University School of Medicine, New York, NY 10016
| | - John Lees
- Department of Microbiology, New York University School of Medicine, New York, NY 10016
| | - Anna Stachel
- Division of Infectious Diseases and Immunology, Department of Medicine, New York University School of Medicine, New York, NY 10016
| | - Jason C Fisher
- Division of Pediatric Surgery, Department of Surgery, New York University School of Medicine, New York, NY 10016
| | - Karl Drlica
- Public Health Research Institute, New Jersey Medical School, Rutgers Biomedical and Health Sciences, Rutgers University, Newark, NJ 07103
- Department of Microbiology, Biochemistry, and Molecular Genetics, New Jersey Medical School, Rutgers Biomedical and Health Sciences, Rutgers University, Newark, NJ 07103
| | - Michael Phillips
- Division of Infectious Diseases and Immunology, Department of Medicine, New York University School of Medicine, New York, NY 10016
| | - Jeffrey N Weiser
- Department of Microbiology, New York University School of Medicine, New York, NY 10016
| | - Paul J Planet
- Department of Pediatric Infectious Disease, Children's Hospital of Philadelphia, Philadelphia, PA 19104
| | - Anne-Catrin Uhlemann
- Division of Infectious Diseases, Department of Medicine, Columbia University Medical Center, New York, NY 10032
| | - Deena R Altman
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York City, NY 10029
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Robert Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Harm van Bakel
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Jennifer Lighter
- Division of Pediatric Infectious Diseases, Department of Pediatrics, New York University School of Medicine, New York, NY 10016
| | - Victor J Torres
- Department of Microbiology, New York University School of Medicine, New York, NY 10016;
| | - Bo Shopsin
- Division of Infectious Diseases and Immunology, Department of Medicine, New York University School of Medicine, New York, NY 10016;
- Department of Microbiology, New York University School of Medicine, New York, NY 10016
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96
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Hoeksema M, Jonker MJ, Bel K, Brul S, Ter Kuile BH. Genome rearrangements in Escherichia coli during de novo acquisition of resistance to a single antibiotic or two antibiotics successively. BMC Genomics 2018; 19:973. [PMID: 30591014 PMCID: PMC6307192 DOI: 10.1186/s12864-018-5353-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 12/07/2018] [Indexed: 11/25/2022] Open
Abstract
Background The ability of bacteria to acquire resistance to antibiotics relies to a large extent on their capacity for genome modification. Prokaryotic genomes are highly plastic and can utilize horizontal gene transfer, point mutations, and gene deletions or amplifications to realize genome expansion and rearrangements. The contribution of point mutations to de novo acquisition of antibiotic resistance is well-established. In this study, the internal genome rearrangement of Escherichia coli during to de novo acquisition of antibiotic resistance was investigated using whole-genome sequencing. Results Cells were made resistant to one of the four antibiotics and subsequently to one of the three remaining. This way the initial genetic rearrangements could be documented together with the effects of an altered genetic background on subsequent development of resistance. A DNA fragment including ampC was amplified by a factor sometimes exceeding 100 as a result of exposure to amoxicillin. Excision of prophage e14 was observed in many samples with a double exposure history, but not in cells exposed to a single antibiotic, indicating that the activation of the SOS stress response alone, normally the trigger for excision, was not sufficient to cause excision of prophage e14. Partial deletion of clpS and clpA occurred in strains exposed to enrofloxacin and tetracycline. Other deletions were observed in some strains, but not in replicates with the exact same exposure history. Various insertion sequence transpositions correlated with exposure to specific antibiotics. Conclusions Many of the genome rearrangements have not been reported before to occur during resistance development. The observed correlation between genome rearrangements and specific antibiotic pressure, as well as their presence in independent replicates indicates that these events do not occur randomly. Taken together, the observed genome rearrangements illustrate the plasticity of the E. coli genome when exposed to antibiotic stress. Electronic supplementary material The online version of this article (10.1186/s12864-018-5353-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Marloes Hoeksema
- Laboratory for Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Martijs J Jonker
- RNA Biology & Applied Bioinformatics, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Keshia Bel
- Laboratory for Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Stanley Brul
- Laboratory for Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Benno H Ter Kuile
- Laboratory for Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands. .,Netherlands Food and Consumer Product Safety Authority, Office for Risk Assessment, Utrecht, The Netherlands.
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97
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Rendueles O, de Sousa JAM, Bernheim A, Touchon M, Rocha EPC. Genetic exchanges are more frequent in bacteria encoding capsules. PLoS Genet 2018; 14:e1007862. [PMID: 30576310 PMCID: PMC6322790 DOI: 10.1371/journal.pgen.1007862] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 01/07/2019] [Accepted: 11/29/2018] [Indexed: 12/12/2022] Open
Abstract
Capsules allow bacteria to colonize novel environments, to withstand numerous stresses, and to resist antibiotics. Yet, even though genetic exchanges with other cells should be adaptive under such circumstances, it has been suggested that capsules lower the rates of homologous recombination and horizontal gene transfer. We analysed over one hundred pan-genomes and thousands of bacterial genomes for the evidence of an association between genetic exchanges (or lack thereof) and the presence of a capsule system. We found that bacteria encoding capsules have larger pan-genomes, higher rates of horizontal gene transfer, and higher rates of homologous recombination in their core genomes. Accordingly, genomes encoding capsules have more plasmids, conjugative elements, transposases, prophages, and integrons. Furthermore, capsular loci are frequent in plasmids, and can be found in prophages. These results are valid for Bacteria, independently of their ability to be naturally transformable. Since we have shown previously that capsules are commonly present in nosocomial pathogens, we analysed their co-occurrence with antibiotic resistance genes. Genomes encoding capsules have more antibiotic resistance genes, especially those encoding efflux pumps, and they constitute the majority of the most worrisome nosocomial bacteria. We conclude that bacteria with capsule systems are more genetically diverse and have fast-evolving gene repertoires, which may further contribute to their success in colonizing novel niches such as humans under antibiotic therapy. Previous works showed that bacteria encoding capsules are better colonizers and are dominant in most environments suggesting a positive role for capsules in the genetic diversification of bacteria. Yet, it has been repeatedly suggested, based almost exclusively studies in few model species, that such bacteria are less diverse and engage in fewer genetic exchanges. Here, we reverse the current paradigm and show that bacteria encoding capsules have larger and more diverse gene repertoires, which change faster by horizontal gene transfer and recombination. Our study alters the traditional view of the capsule as a barrier to gene flow and raises novel questions about the role of capsules in bacterial adaptation.
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Affiliation(s)
- Olaya Rendueles
- Microbial Evolutionary Genomics, Institut Pasteur, Paris, France
- UMR 3525, CNRS, Paris, France
- * E-mail:
| | - Jorge A. Moura de Sousa
- Microbial Evolutionary Genomics, Institut Pasteur, Paris, France
- UMR 3525, CNRS, Paris, France
| | - Aude Bernheim
- Microbial Evolutionary Genomics, Institut Pasteur, Paris, France
- UMR 3525, CNRS, Paris, France
| | - Marie Touchon
- Microbial Evolutionary Genomics, Institut Pasteur, Paris, France
- UMR 3525, CNRS, Paris, France
| | - Eduardo P. C. Rocha
- Microbial Evolutionary Genomics, Institut Pasteur, Paris, France
- UMR 3525, CNRS, Paris, France
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98
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Lu J, Wang Y, Li J, Mao L, Nguyen SH, Duarte T, Coin L, Bond P, Yuan Z, Guo J. Triclosan at environmentally relevant concentrations promotes horizontal transfer of multidrug resistance genes within and across bacterial genera. ENVIRONMENT INTERNATIONAL 2018; 121:1217-1226. [PMID: 30389380 DOI: 10.1016/j.envint.2018.10.040] [Citation(s) in RCA: 156] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 10/18/2018] [Accepted: 10/20/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Antibiotic resistance poses an increasing threat to public health. Horizontal gene transfer (HGT) promoted by antibiotics is recognized as a significant pathway to disseminate antibiotic resistance genes (ARGs). However, it is unclear whether non-antibiotic, anti-microbial (NAAM) chemicals can directly promote HGT of ARGs in the environment. OBJECTIVES We aimed to investigate whether triclosan (TCS), a widely-used NAAM chemical in personal care products, is able to stimulate the conjugative transfer of antibiotic multi-resistance genes carried by plasmid within and across bacterial genera. METHODS We established two model mating systems, to investigate intra-genera transfer and inter-genera transfer. Escherichia coli K-12 LE392 carrying IncP-α plasmid RP4 was used as the donor, and E. coli K-12 MG1655 or Pseudomonas putida KT2440 were the intra- and inter-genera recipients, respectively. The mechanisms of the HGT promoted by TCS were unveiled by detecting oxidative stress and cell membrane permeability, in combination with Nanopore sequencing, genome-wide RNA sequencing and proteomic analyses. RESULTS Exposure of the bacteria to environmentally relevant concentrations of TCS (from 0.02 μg/L to 20 μg/L) significantly stimulated the conjugative transfer of plasmid-encoded multi-resistance genes within and across genera. The TCS exposure promoted ROS generation and damaged bacterial membrane, and caused increased expression of the SOS response regulatory genes umuC, dinB and dinD in the donor. In addition, higher expression levels of ATP synthesis encoding genes in E. coli and P. putida were found with increased TCS dosage. CONCLUSIONS TCS could enhance the conjugative ARGs transfer between bacteria by triggering ROS overproduction at environmentally relevant concentrations. These findings improve our awareness of the hidden risks of NAAM chemicals on the spread of antibiotic resistance.
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Affiliation(s)
- Ji Lu
- Advanced Water Management Centre (AWMC), The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia
| | - Yue Wang
- Advanced Water Management Centre (AWMC), The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia
| | - Jie Li
- Advanced Water Management Centre (AWMC), The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia
| | - Likai Mao
- Advanced Water Management Centre (AWMC), The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia
| | - Son Hoang Nguyen
- Institute for Molecular Bioscience, University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - Tania Duarte
- Institute for Molecular Bioscience, University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - Lachlan Coin
- Institute for Molecular Bioscience, University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - Philip Bond
- Advanced Water Management Centre (AWMC), The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia
| | - Zhiguo Yuan
- Advanced Water Management Centre (AWMC), The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia
| | - Jianhua Guo
- Advanced Water Management Centre (AWMC), The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia.
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99
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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: 424] [Impact Index Per Article: 70.7] [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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100
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Crane JK, Cheema MB, Olyer MA, Sutton MD. Zinc Blockade of SOS Response Inhibits Horizontal Transfer of Antibiotic Resistance Genes in Enteric Bacteria. Front Cell Infect Microbiol 2018; 8:410. [PMID: 30519543 PMCID: PMC6258817 DOI: 10.3389/fcimb.2018.00410] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 11/05/2018] [Indexed: 11/30/2022] Open
Abstract
The SOS response is a conserved response to DNA damage that is found in Gram-negative and Gram-positive bacteria. When DNA damage is sustained and severe, activation of error-prone DNA polymerases can induce a higher mutation rate than is normally observed, which is called the SOS mutator phenotype or hypermutation. We previously showed that zinc blocked the hypermutation response induced by quinolone antibiotics and mitomycin C in Escherichia coli and Klebsiella pneumoniae. In this study, we demonstrate that zinc blocks the SOS-induced development of chloramphenicol resistance in Enterobacter cloacae. Zinc also blocked the transfer of an extended spectrum beta-lactamase (ESBL) gene from Enterobacter to a susceptible E. coli strain. A zinc ionophore, zinc pyrithione, was ~100-fold more potent than zinc salts in inhibition of ciprofloxacin-induced hypermutation in E. cloacae. Other divalent metals, such as iron and manganese, failed to inhibit these responses. Electrophoretic mobility shift assays (EMSAs) revealed that zinc, but not iron or manganese, blocked the ability of the E. coli RecA protein to bind to single-stranded DNA, an important early step in the recognition of DNA damage in enteric bacteria. This suggests a mechanism for zinc's inhibitory effects on bacterial SOS responses, including hypermutation.
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Affiliation(s)
- John K Crane
- Division of Infectious Diseases, Department of Medicine, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, United States
| | - Muhammad B Cheema
- Division of Infectious Diseases, Department of Medicine, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, United States
| | - Michael A Olyer
- Division of Infectious Diseases, Department of Medicine, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, United States
| | - Mark D Sutton
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, United States
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