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Zahid A, Wilson JC, Grice ID, Peak IR. Otitis media: recent advances in otitis media vaccine development and model systems. Front Microbiol 2024; 15:1345027. [PMID: 38328427 PMCID: PMC10847372 DOI: 10.3389/fmicb.2024.1345027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 01/08/2024] [Indexed: 02/09/2024] Open
Abstract
Otitis media is an inflammatory disorder of the middle ear caused by airways-associated bacterial or viral infections. It is one of the most common childhood infections as globally more than 80% of children are diagnosed with acute otitis media by 3 years of age and it is a common reason for doctor's visits, antibiotics prescriptions, and surgery among children. Otitis media is a multifactorial disease with various genetic, immunologic, infectious, and environmental factors predisposing children to develop ear infections. Streptococcus pneumoniae, Haemophilus influenzae, and Moraxella catarrhalis are the most common culprits responsible for acute otitis media. Despite the massive global disease burden, the pathogenesis of otitis media is still unclear and requires extensive future research. Antibiotics are the preferred treatment to cure middle ear infections, however, the antimicrobial resistance rate of common middle ear pathogens has increased considerably over the years. At present, pneumococcal and influenza vaccines are administered as a preventive measure against otitis media, nevertheless, these vaccines are only beneficial in preventing carriage and/or disease caused by vaccine serotypes. Otitis media caused by non-vaccine serotype pneumococci, non-typeable H. influenza, and M. catarrhalis remain an important healthcare burden. The development of multi-species vaccines is an arduous process but is required to reduce the global burden of this disease. Many novel vaccines against S. pneumoniae, non-typeable H. influenza, and M. catarrhalis are in preclinical trials. It is anticipated that these vaccines will lower the disease burden and provide better protection against otitis media. To study disease pathology the rat, mouse, and chinchilla are commonly used to induce experimental acute otitis media to test new therapeutics, including antibiotics and vaccines. Each of these models has its advantages and disadvantages, yet there is still a need to develop an improved animal model providing a better correlated mechanistic understanding of human middle ear infections, thereby underpinning the development of more effective otitis media therapeutics. This review provides an updated summary of current vaccines against otitis media, various animal models of otitis media, their limitations, and some future insights in this field providing a springboard in the development of new animal models and novel vaccines for otitis media.
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Affiliation(s)
- Ayesha Zahid
- Institute for Glycomics, Griffith University, Gold Coast, QLD, Australia
| | - Jennifer C. Wilson
- School of Pharmacy and Medical Science, Griffith University, Gold Coast, QLD, Australia
| | - I. Darren Grice
- Institute for Glycomics, Griffith University, Gold Coast, QLD, Australia
- School of Pharmacy and Medical Science, Griffith University, Gold Coast, QLD, Australia
| | - Ian R. Peak
- Institute for Glycomics, Griffith University, Gold Coast, QLD, Australia
- School of Pharmacy and Medical Science, Griffith University, Gold Coast, QLD, Australia
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Tram G, Jen FEC, Phillips ZN, Lancashire JF, Timms J, Poole J, Jennings MP, Atack JM. Phasevarions in Haemophilus influenzae biogroup aegyptius control expression of multiple proteins. Microbiol Spectr 2024; 12:e0260123. [PMID: 38054719 PMCID: PMC10783040 DOI: 10.1128/spectrum.02601-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 10/31/2023] [Indexed: 12/07/2023] Open
Abstract
IMPORTANCE Haemophilus influenzae biogroup aegyptius is a human-adapted pathogen and the causative agent of Brazilian purpuric fever (BPF), an invasive disease with high mortality, that sporadically manifests in children previously suffering conjunctivitis. Phase variation is a rapid and reversible switching of gene expression found in many bacterial species, and typically associated with outer-membrane proteins. Phase variation of cytoplasmic DNA methyltransferases has been shown to play important roles in bacterial gene regulation and can act as epigenetic switches, regulating the expression of multiple genes as part of systems called phasevarions (phase-variable regulons). This study characterized two alleles of the ModA phasevarion present in H. influenzae biogroup aegyptius, ModA13, found in non-BPF causing strains and ModA16, unique to BPF causing isolates. Phase variation of ModA13 and ModA16 led to genome-wide changes to DNA methylation resulting in altered protein expression. These changes did not affect serum resistance in H. influenzae biogroup aegyptius strains.
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Affiliation(s)
- Greg Tram
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, Australia
| | - Freda E.-C. Jen
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, Australia
| | - Zachary N. Phillips
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, Australia
| | - John F. Lancashire
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, Australia
| | - Jamie Timms
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, Australia
| | - Jessica Poole
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, Australia
| | - Michael P. Jennings
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, Australia
| | - John M. Atack
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, Australia
- School of Environment and Science, Griffith University, Gold Coast, Queensland, Australia
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Tamir SO, Bialasiewicz S, Brennan-Jones CG, Der C, Kariv L, Macharia I, Marsh RL, Seguya A, Thornton R. ISOM 2023 research Panel 4 - Diagnostics and microbiology of otitis media. Int J Pediatr Otorhinolaryngol 2023; 174:111741. [PMID: 37788516 DOI: 10.1016/j.ijporl.2023.111741] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 09/17/2023] [Accepted: 09/19/2023] [Indexed: 10/05/2023]
Abstract
OBJECTIVES To identify and review key research advances from the literature published between 2019 and 2023 on the diagnosis and microbiology of otitis media (OM) including acute otitis media (AOM), recurrent AOM (rAOM), otitis media with effusion (OME), chronic suppurative otitis media (CSOM) and AOM complications (mastoiditis). DATA SOURCES PubMed database of the National Library of Medicine. REVIEW METHODS All relevant original articles published in Medline in English between July 2019 and February 2023 were identified. Studies that were reviews, case studies, relating to OM complications (other than mastoiditis), and studies focusing on guideline adherence, and consensus statements were excluded. Members of the panel drafted the report based on these search results. MAIN FINDINGS For the diagnosis section, 2294 unique records screened, 55 were eligible for inclusion. For the microbiology section 705 unique records were screened and 137 articles were eligible for inclusion. The main themes that arose in OM diagnosis were the need to incorporate multiple modalities including video-otoscopy, tympanometry, telemedicine and artificial intelligence for accurate diagnoses in all diagnostic settings. Further to this, was the use of new, cheap, readily available tools which may improve access in rural and lowmiddle income (LMIC) settings. For OM aetiology, PCR remains the most sensitive method for detecting middle ear pathogens with microbiome analysis still largely restricted to research use. The global pandemic response reduced rates of OM in children, but post-pandemic shifts should be monitored. IMPLICATION FOR PRACTICE AND FUTURE RESEARCH Cheap, easy to use multi-technique assessments combined with artificial intelligence and/or telemedicine should be integrated into future practice to improve diagnosis and treatment pathways in OM diagnosis. Longitudinal studies investigating the in-vivo process of OM development, timings and in-depth interactions between the triad of bacteria, viruses and the host immune response are still required. Standardized methods of collection and analysis for microbiome studies to enable inter-study comparisons are required. There is a need to target underlying biofilms if going to effectively prevent rAOM and OME and possibly enhance ventilation tube retention.
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Affiliation(s)
- Sharon Ovnat Tamir
- Department of Otolaryngology-Head and Neck Surgery, Sasmon Assuta Ashdod University Hospital, Faculty of Health Sciences, Ben Gurion University of the Negev, Israel.
| | - Seweryn Bialasiewicz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Christopher G Brennan-Jones
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, The University of Western Australia, Perth, Western Australia, Australia; Faculty of Health Sciences, Curtin University, Perth, Western Australia, Australia
| | - Carolina Der
- Facultad de Medicina, Universidad Del Desarrollo, Dr Luis Calvo Mackenna Hospital, Santiago, Chile
| | - Liron Kariv
- Hearing, Speech and Language Institute, Sasmon Assuta Ashdod University Hospital, Israel
| | - Ian Macharia
- Kenyatta University Teaching, Referral & Research Hospital, Kenya
| | - Robyn L Marsh
- Menzies School of Health Research, Darwin, Australia; School of Health Sciences, University of Tasmania, Launceston, Australia
| | - Amina Seguya
- Department of Otolaryngology - Head and Neck Surgery, Mulago National Referral Hospital, Kampala, Uganda
| | - Ruth Thornton
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, The University of Western Australia, Perth, Western Australia, Australia; Centre for Child Health Research, University of Western Australia, Perth, Australia
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Wang X, Yu D, Chen L. Antimicrobial resistance and mechanisms of epigenetic regulation. Front Cell Infect Microbiol 2023; 13:1199646. [PMID: 37389209 PMCID: PMC10306973 DOI: 10.3389/fcimb.2023.1199646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 05/26/2023] [Indexed: 07/01/2023] Open
Abstract
The rampant use of antibiotics in animal husbandry, farming and clinical disease treatment has led to a significant issue with pathogen resistance worldwide over the past decades. The classical mechanisms of resistance typically investigate antimicrobial resistance resulting from natural resistance, mutation, gene transfer and other processes. However, the emergence and development of bacterial resistance cannot be fully explained from a genetic and biochemical standpoint. Evolution necessitates phenotypic variation, selection, and inheritance. There are indications that epigenetic modifications also play a role in antimicrobial resistance. This review will specifically focus on the effects of DNA modification, histone modification, rRNA methylation and the regulation of non-coding RNAs expression on antimicrobial resistance. In particular, we highlight critical work that how DNA methyltransferases and non-coding RNAs act as transcriptional regulators that allow bacteria to rapidly adapt to environmental changes and control their gene expressions to resist antibiotic stress. Additionally, it will delve into how Nucleolar-associated proteins in bacteria perform histone functions akin to eukaryotes. Epigenetics, a non-classical regulatory mechanism of bacterial resistance, may offer new avenues for antibiotic target selection and the development of novel antibiotics.
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Affiliation(s)
- Xinrui Wang
- Medical Research Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, Fuzhou, Fujian, China
- National Health Commission Key Laboratory of Technical Evaluation of Fertility Regulation for Non-Human Primate, Fujian Maternity and Child Health Hospital, Fuzhou, Fujian, China
| | - Donghong Yu
- Medical Research Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, Fuzhou, Fujian, China
- National Health Commission Key Laboratory of Technical Evaluation of Fertility Regulation for Non-Human Primate, Fujian Maternity and Child Health Hospital, Fuzhou, Fujian, China
| | - Lu Chen
- Medical Research Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, Fuzhou, Fujian, China
- National Health Commission Key Laboratory of Technical Evaluation of Fertility Regulation for Non-Human Primate, Fujian Maternity and Child Health Hospital, Fuzhou, Fujian, China
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Nahar N, Tram G, Jen FEC, Phillips ZN, Weinert L, Bossé J, Jabbari J, Gouil Q, Du MM, Ritchie M, Bowden R, Langford P, Tucker A, Jennings M, Turni C, Blackall P, Atack J. Actinobacillus pleuropneumoniae encodes multiple phase-variable DNA methyltransferases that control distinct phasevarions. Nucleic Acids Res 2023; 51:3240-3260. [PMID: 36840716 PMCID: PMC10123105 DOI: 10.1093/nar/gkad091] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 01/31/2023] [Accepted: 02/03/2023] [Indexed: 02/26/2023] Open
Abstract
Actinobacillus pleuropneumoniae is the cause of porcine pleuropneumonia, a severe respiratory tract infection that is responsible for major economic losses to the swine industry. Many host-adapted bacterial pathogens encode systems known as phasevarions (phase-variable regulons). Phasevarions result from variable expression of cytoplasmic DNA methyltransferases. Variable expression results in genome-wide methylation differences within a bacterial population, leading to altered expression of multiple genes via epigenetic mechanisms. Our examination of a diverse population of A. pleuropneumoniae strains determined that Type I and Type III DNA methyltransferases with the hallmarks of phase variation were present in this species. We demonstrate that phase variation is occurring in these methyltransferases, and show associations between particular Type III methyltransferase alleles and serovar. Using Pacific BioSciences Single-Molecule, Real-Time (SMRT) sequencing and Oxford Nanopore sequencing, we demonstrate the presence of the first ever characterised phase-variable, cytosine-specific Type III DNA methyltransferase. Phase variation of distinct Type III DNA methyltransferase in A. pleuropneumoniae results in the regulation of distinct phasevarions, and in multiple phenotypic differences relevant to pathobiology. Our characterisation of these newly described phasevarions in A. pleuropneumoniae will aid in the selection of stably expressed antigens, and direct and inform development of a rationally designed subunit vaccine against this major veterinary pathogen.
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Affiliation(s)
- Nusrat Nahar
- Institute for Glycomics, Griffith University, Gold Coast, Queensland 4222, Australia
| | - Greg Tram
- Institute for Glycomics, Griffith University, Gold Coast, Queensland 4222, Australia
| | - Freda E-C Jen
- Institute for Glycomics, Griffith University, Gold Coast, Queensland 4222, Australia
| | - Zachary N Phillips
- Institute for Glycomics, Griffith University, Gold Coast, Queensland 4222, Australia
| | - Lucy A Weinert
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK
| | - Janine T Bossé
- Section of Paediatric Infectious Disease, Imperial College London, St Mary's Campus, London W2 1PG, UK
| | - Jafar S Jabbari
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville 3010, Australia
| | - Quentin Gouil
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville 3010, Australia
| | - Mei R M Du
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
| | - Matthew E Ritchie
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville 3010, Australia
| | - Rory Bowden
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville 3010, Australia
| | - Paul R Langford
- Section of Paediatric Infectious Disease, Imperial College London, St Mary's Campus, London W2 1PG, UK
| | - Alexander W Tucker
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK
| | - Michael P Jennings
- Institute for Glycomics, Griffith University, Gold Coast, Queensland 4222, Australia
| | - Conny Turni
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Patrick J Blackall
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - John M Atack
- Institute for Glycomics, Griffith University, Gold Coast, Queensland 4222, Australia
- School of Environment and Science, Griffith University, Gold Coast, Queensland 4222, Australia
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6
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Adamczyk-Poplawska M, Bacal P, Mrozek A, Matczynska N, Piekarowicz A, Kwiatek A. Phase-variable Type I methyltransferase M.NgoAV from Neisseria gonorrhoeae FA1090 regulates phasevarion expression and gonococcal phenotype. Front Microbiol 2022; 13:917639. [PMID: 36267167 PMCID: PMC9577141 DOI: 10.3389/fmicb.2022.917639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 09/02/2022] [Indexed: 11/13/2022] Open
Abstract
The restriction-modification (RM) systems are compared to a primitive, innate, prokaryotic immune system, controlling the invasion by foreign DNA, composed of methyltransferase (MTase) and restriction endonuclease. The biological significance of RM systems extends beyond their defensive function, but the data on the regulatory role of Type I MTases are limited. We have previously characterized molecularly a non-canonical Type I RM system, NgoAV, with phase-variable specificity, encoded by Neisseria gonorrhoeae FA1090. In the current work, we have investigated the impact of methyltransferase NgoAV (M.NgoAV) activity on gonococcal phenotype and on epigenetic control of gene expression. For this purpose, we have constructed and studied genetic variants (concerning activity and specificity) within M.NgoAV locus. Deletion of M.NgoAV or switch of its specificity had an impact on phenotype of N. gonorrhoeae. Biofilm formation and planktonic growth, the resistance to antibiotics, which target bacterial peptidoglycan or other antimicrobials, and invasion of human epithelial host cells were affected. The expression of genes was deregulated in gonococcal cells with knockout M.NgoAV gene and the variant with new specificity. For the first time, the existence of a phasevarion (phase-variable regulon), directed by phase-variable Type I MTase, is demonstrated.
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Affiliation(s)
- Monika Adamczyk-Poplawska
- Department of Molecular Virology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
- *Correspondence: Monika Adamczyk-Poplawska,
| | - Pawel Bacal
- Institute of Paleobiology, Polish Academy of Sciences, Warsaw, Poland
| | - Agnieszka Mrozek
- Department of Molecular Virology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Natalia Matczynska
- Department of Molecular Virology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Andrzej Piekarowicz
- Department of Molecular Virology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Agnieszka Kwiatek
- Department of Molecular Virology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
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7
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Pneumococcal Phasevarions Control Multiple Virulence Traits, Including Vaccine Candidate Expression. Microbiol Spectr 2022; 10:e0091622. [PMID: 35536022 PMCID: PMC9241608 DOI: 10.1128/spectrum.00916-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Streptococcus pneumoniae is the most common cause of bacterial illness worldwide. Current vaccines based on the polysaccharide capsule are only effective against a limited number of the >100 capsular serotypes. A universal vaccine based on conserved protein antigens requires a thorough understanding of gene expression in S. pneumoniae. All S. pneumoniae strains encode the SpnIII Restriction-Modification system. This system contains a phase-variable methyltransferase that switches specificity, and controls expression of multiple genes—a phasevarion. We examined the role of this phasevarion during pneumococcal pathobiology, and determined if phase variation resulted in differences in expression of currently investigated conserved protein antigens. Using locked strains that express a single methyltransferase specificity, we found differences in clinically relevant traits, including survival in blood, and adherence to and invasion of human cells. We also observed differences in expression of numerous proteinaceous vaccine candidates, which complicates selection of antigens for inclusion in a universal protein-based pneumococcal vaccine. This study will inform vaccine design against S. pneumoniae by ensuring only stably expressed candidates are included in a rationally designed vaccine. IMPORTANCES. pneumoniae is the world’s foremost bacterial pathogen. S. pneumoniae encodes a phasevarion (phase-variable regulon), that results in differential expression of multiple genes. Previous work demonstrated that the pneumococcal SpnIII phasevarion switches between six different expression states, generating six unique phenotypic variants in a pneumococcal population. Here, we show that this phasevarion generates multiple phenotypic differences relevant to pathobiology. Importantly, expression of conserved protein antigens varies with phasevarion switching. As capsule expression, a major pneumococcal virulence factor, is also controlled by the phasevarion, our work will inform the selection of the best candidates to include in a rationally designed, universal pneumococcal vaccine.
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Kim SK, Hong SJ, Yoo DM, Min C, Choi HG. Association between asthma or chronic obstructive pulmonary disease and chronic otitis media. Sci Rep 2022; 12:4228. [PMID: 35273329 PMCID: PMC8913729 DOI: 10.1038/s41598-022-08287-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 02/11/2022] [Indexed: 11/09/2022] Open
Abstract
We hypothesized that asthma/chronic obstructive pulmonary disease (COPD) might increase the risk of chronic otitis media (COM), as asthma or COPD affects other diseases. The aim of this research was to investigate whether the incidence of COM is affected by a diagnosis of asthma or COPD in patients compared to matched controls from the national health screening cohort. A COM group (n = 11,587) and a control group that was 1:4 matched for age, sex, income, and residence area (n = 46,348) were selected. The control group included participants who never received treatment for COM from Korean National Health Insurance Service-Health Screening Cohort from 2002 to 2015. The crude and adjusted odds ratios (ORs) of previous asthma/COPD before the index date for COM were analyzed using conditional logistic regression. The analyses were stratified by age, sex, income, and region of residence. The period prevalence of asthma (17.5% vs. 14.3%, p < 0.001) and COPD (6.6% vs. 5.0%, p < 0.001) were significantly higher in the COM group than in the control group. In addition, the odds of asthma and COPD were significantly higher in the COM group than in the control group. Both asthma (adjusted OR 1.23, 95% confidence interval [CI] 1.16-1.31, p < 0.001) and COPD (adjusted OR 1.23, 95% CI 1.13-1.35, p < 0.001) increased the ORs for COM. This positive association between asthma/COPD and COM indicates that asthma/COPD might increase the incidence of COM.
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Affiliation(s)
- Sung Kyun Kim
- Department of Otorhinolaryngology-Head and Neck Surgery, Hallym University College of Medicine, Dongtan, Korea.,Laboratory of Brain & Cognitive Sciences for Convergence Medicine, Hallym University College of Medicine, Anyang, Korea
| | - Seok Jin Hong
- Department of Otorhinolaryngology-Head and Neck Surgery, Hallym University College of Medicine, Dongtan, Korea
| | - Dae Myoung Yoo
- Hallym Data Science Laboratory, Hallym University College of Medicine, Anyang, Korea
| | - Chanyang Min
- Hallym Data Science Laboratory, Hallym University College of Medicine, Anyang, Korea.,Graduate School of Public Health, Seoul National University, Seoul, Korea
| | - Hyo Geun Choi
- Hallym Data Science Laboratory, Hallym University College of Medicine, Anyang, Korea. .,Department of Otorhinolaryngology-Head and Neck Surgery, Hallym University College of Medicine, Hallym University Sacred Heart Hospital, 22, Gwanpyeong-ro 170, Anyang, Gyeonggi, 14068, Republic of Korea.
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9
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Janoušková M, Straw ML, Su YC, Riesbeck K. Gene Expression Regulation in Airway Pathogens: Importance for Otitis Media. Front Cell Infect Microbiol 2022; 12:826018. [PMID: 35252035 PMCID: PMC8895709 DOI: 10.3389/fcimb.2022.826018] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 01/19/2022] [Indexed: 11/13/2022] Open
Abstract
Otitis media (OM) is an inflammatory disorder in the middle ear. It is mainly caused by viruses or bacteria associated with the airways. Streptococcus pneumoniae, Haemophilus influenzae and Moraxella catarrhalis are the three main pathogens in infection-related OM, especially in younger children. In this review, we will focus upon the multifaceted gene regulation mechanisms that are well-orchestrated in S. pneumoniae, H. influenzae, and M. catarrhalis during the course of infection in the middle ear either in experimental OM or in clinical settings. The sophisticated findings from the past 10 years on how the othopathogens govern their virulence phenotypes for survival and host adaptation via phase variation- and quorum sensing-dependent gene regulation, will be systematically discussed. Comprehensive understanding of gene expression regulation mechanisms employed by pathogens during the onset of OM may provide new insights for the design of a new generation of antimicrobial agents in the fight against bacterial pathogens while combating the serious emergence of antimicrobial resistance.
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10
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Mehershahi KS, Chen SL. DNA methylation by three Type I restriction modification systems of Escherichia coli does not influence gene regulation of the host bacterium. Nucleic Acids Res 2021; 49:7375-7388. [PMID: 34181709 PMCID: PMC8287963 DOI: 10.1093/nar/gkab530] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 06/01/2021] [Accepted: 06/22/2021] [Indexed: 12/13/2022] Open
Abstract
DNA methylation is a common epigenetic mark that influences transcriptional regulation, and therefore cellular phenotype, across all domains of life. In particular, both orphan methyltransferases and those from phasevariable restriction modification systems (RMSs) have been co-opted to regulate virulence epigenetically in many bacteria. We now show that three distinct non-phasevariable Type I RMSs in Escherichia coli have no measurable impact on gene expression, in vivo virulence, or any of 1190 in vitro growth phenotypes. We demonstrated this using both Type I RMS knockout mutants as well as heterologous installation of Type I RMSs into two E. coli strains. These data provide three clear and currently rare examples of restriction modification systems that have no impact on their host organism’s gene regulation. This leads to the possibility that other such nonregulatory methylation systems may exist, broadening our view of the potential role that RMSs may play in bacterial evolution.
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Affiliation(s)
- Kurosh S Mehershahi
- NUHS Infectious Diseases Translational Research Programme, Department of Medicine, Division of Infectious Diseases, Yong Loo Lin School of Medicine, Singapore 119228
| | - Swaine L Chen
- NUHS Infectious Diseases Translational Research Programme, Department of Medicine, Division of Infectious Diseases, Yong Loo Lin School of Medicine, Singapore 119228.,Laboratory of Bacterial Genomics, Genome Institute of Singapore, Singapore 138672
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11
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Payelleville A, Brillard J. Novel Identification of Bacterial Epigenetic Regulations Would Benefit From a Better Exploitation of Methylomic Data. Front Microbiol 2021; 12:685670. [PMID: 34054792 PMCID: PMC8160106 DOI: 10.3389/fmicb.2021.685670] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 04/22/2021] [Indexed: 12/21/2022] Open
Abstract
DNA methylation can be part of epigenetic mechanisms, leading to cellular subpopulations with heterogeneous phenotypes. While prokaryotic phenotypic heterogeneity is of critical importance for a successful infection by several major pathogens, the exact mechanisms involved in this phenomenon remain unknown in many cases. Powerful sequencing tools have been developed to allow the detection of the DNA methylated bases at the genome level, and they have recently been extensively applied on numerous bacterial species. Some of these tools are increasingly used for metagenomics analysis but only a limited amount of the available methylomic data is currently being exploited. Because newly developed tools now allow the detection of subpopulations differing in their genome methylation patterns, it is time to emphasize future strategies based on a more extensive use of methylomic data. This will ultimately help to discover new epigenetic gene regulations involved in bacterial phenotypic heterogeneity, including during host-pathogen interactions.
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Affiliation(s)
- Amaury Payelleville
- DGIMI, INRAE, Univ. Montpellier, Montpellier, France.,Cellular and Molecular Microbiology, Faculté des Sciences, Université Libre de Bruxelles, Gosselies, Belgium
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12
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Seib KL, Srikhanta YN, Atack JM, Jennings MP. Epigenetic Regulation of Virulence and Immunoevasion by Phase-Variable Restriction-Modification Systems in Bacterial Pathogens. Annu Rev Microbiol 2020; 74:655-671. [PMID: 32689914 DOI: 10.1146/annurev-micro-090817-062346] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Human-adapted bacterial pathogens use a mechanism called phase variation to randomly switch the expression of individual genes to generate a phenotypically diverse population to adapt to challenges within and between human hosts. There are increasing reports of restriction-modification systems that exhibit phase-variable expression. The outcome of phase variation of these systems is global changes in DNA methylation. Analysis of phase-variable Type I and Type III restriction-modification systems in multiple human-adapted bacterial pathogens has demonstrated that global changes in methylation regulate the expression of multiple genes. These systems are called phasevarions (phase-variable regulons). Phasevarion switching alters virulence phenotypes and facilitates evasion of host immune responses. This review describes the characteristics of phasevarions and implications for pathogenesis and immune evasion. We present and discuss examples of phasevarion systems in the major human pathogens Haemophilus influenzae, Neisseria meningitidis, Neisseria gonorrhoeae, Helicobacter pylori, Moraxella catarrhalis, and Streptococcus pneumoniae.
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Affiliation(s)
- Kate L Seib
- Institute for Glycomics, Griffith University, Gold Coast, Queensland 4222, Australia; ,
| | - Yogitha N Srikhanta
- Monash Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia
| | - John M Atack
- Institute for Glycomics, Griffith University, Gold Coast, Queensland 4222, Australia; ,
| | - Michael P Jennings
- Institute for Glycomics, Griffith University, Gold Coast, Queensland 4222, Australia; ,
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Moraxella catarrhalis phase-variable loci show differences in expression during conditions relevant to disease. PLoS One 2020; 15:e0234306. [PMID: 32555615 PMCID: PMC7302503 DOI: 10.1371/journal.pone.0234306] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Accepted: 05/22/2020] [Indexed: 11/29/2022] Open
Abstract
Moraxella catarrhalis is a human-adapted, opportunistic bacterial pathogen of the respiratory mucosa. Although asymptomatic colonization of the nasopharynx is common, M. catarrhalis can ascend into the middle ear, where it is a prevalent causative agent of otitis media in children, or enter the lower respiratory tract, where it is associated with acute exacerbations of chronic obstructive pulmonary disease in adults. Phase variation is the high frequency, random, reversible switching of gene expression that allows bacteria to adapt to different host microenvironments and evade host defences, and is most commonly mediated by simple DNA sequence repeats. Bioinformatic analysis of five closed M. catarrhalis genomes identified 17 unique simple DNA sequence repeat tracts that were variable between strains, indicating the potential to mediate phase variable expression of the associated genes. Assays designed to assess simple sequence repeat variation under conditions mimicking host infection demonstrated that phase variation of uspA1 (ubiquitous surface protein A1) from high to low expression occurs over 72 hours of biofilm passage, while phase variation of uspA2 (ubiquitous surface protein A2) to high expression variants occurs during repeated exposure to human serum, as measured by mRNA levels. We also identify and confirm the variable expression of two novel phase variable genes encoding a Type III DNA methyltransferase (modO), and a conserved hypothetical permease (MC25239_RS00020). These data reveal the repertoire of phase variable genes mediated by simple sequence repeats in M. catarrhalis and demonstrate that modulation of expression under conditions mimicking human infection is attributed to changes in simple sequence repeat length.
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Transcriptome RNA Sequencing Data Set of Gene Expression in Moraxella catarrhalis On- and Off-Phase Variants of the Type III DNA Methyltransferase ModM3. Microbiol Resour Announc 2020; 9:9/14/e01559-19. [PMID: 32241868 PMCID: PMC7118194 DOI: 10.1128/mra.01559-19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Moraxella catarrhalis
is a leading bacterial cause of otitis media and exacerbations of chronic obstructive pulmonary disease. Here, we announce a transcriptome RNA sequencing data set detailing global gene expression in two
M. catarrhalis
CCRI-195ME variants with expression of the DNA methyltransferase ModM3 phase varied either on or off.
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