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Patel L, Ailloud F, Suerbaum S, Josenhans C. Single-base resolution quantitative genome methylation analysis in the model bacterium Helicobacter pylori by enzymatic methyl sequencing (EM-Seq) reveals influence of strain, growth phase, and methyl homeostasis. BMC Biol 2024; 22:125. [PMID: 38807090 PMCID: PMC11134628 DOI: 10.1186/s12915-024-01921-1] [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: 01/14/2024] [Accepted: 05/16/2024] [Indexed: 05/30/2024] Open
Abstract
BACKGROUND Bacterial epigenetics is a rapidly expanding research field. DNA methylation by diverse bacterial methyltransferases (MTases) contributes to genomic integrity and replication, and many recent studies extended MTase function also to global transcript regulation and phenotypic variation. Helicobacter pylori is currently one of those bacterial species which possess the highest number and the most variably expressed set of DNA MTases. Next-generation sequencing technologies can directly detect DNA base methylation. However, they still have limitations in their quantitative and qualitative performance, in particular for cytosine methylation. RESULTS As a complementing approach, we used enzymatic methyl sequencing (EM-Seq), a technology recently established that has not yet been fully evaluated for bacteria. Thereby, we assessed quantitatively, at single-base resolution, whole genome cytosine methylation for all methylated cytosine motifs in two different H. pylori strains and isogenic MTase mutants. EM-Seq reliably detected both m5C and m4C methylation. We demonstrated that three different active cytosine MTases in H. pylori provide considerably different levels of average genome-wide single-base methylation, in contrast to isogenic mutants which completely lost specific motif methylation. We found that strain identity and changed environmental conditions, such as growth phase and interference with methyl donor homeostasis, significantly influenced quantitative global and local genome-wide methylation in H. pylori at specific motifs. We also identified significantly hyper- or hypo-methylated cytosines, partially linked to overlapping MTase target motifs. Notably, we revealed differentially methylated cytosines in genome-wide coding regions under conditions of methionine depletion, which can be linked to transcript regulation. CONCLUSIONS This study offers new knowledge on H. pylori global and local genome-wide methylation and establishes EM-Seq for quantitative single-site resolution analyses of bacterial cytosine methylation.
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Affiliation(s)
- Lubna Patel
- Max von Pettenkofer Institute, Chair for Medical Microbiology, Faculty of Medicine, LMU Munich, Pettenkoferstr. 9a, 80336, Munich, Germany
| | - Florent Ailloud
- Max von Pettenkofer Institute, Chair for Medical Microbiology, Faculty of Medicine, LMU Munich, Pettenkoferstr. 9a, 80336, Munich, Germany
| | - Sebastian Suerbaum
- Max von Pettenkofer Institute, Chair for Medical Microbiology, Faculty of Medicine, LMU Munich, Pettenkoferstr. 9a, 80336, Munich, Germany
| | - Christine Josenhans
- Max von Pettenkofer Institute, Chair for Medical Microbiology, Faculty of Medicine, LMU Munich, Pettenkoferstr. 9a, 80336, Munich, Germany.
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2
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Shepherd MJ, Fu T, Harrington NE, Kottara A, Cagney K, Chalmers JD, Paterson S, Fothergill JL, Brockhurst MA. Ecological and evolutionary mechanisms driving within-patient emergence of antimicrobial resistance. Nat Rev Microbiol 2024:10.1038/s41579-024-01041-1. [PMID: 38689039 DOI: 10.1038/s41579-024-01041-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/13/2024] [Indexed: 05/02/2024]
Abstract
The ecological and evolutionary mechanisms of antimicrobial resistance (AMR) emergence within patients and how these vary across bacterial infections are poorly understood. Increasingly widespread use of pathogen genome sequencing in the clinic enables a deeper understanding of these processes. In this Review, we explore the clinical evidence to support four major mechanisms of within-patient AMR emergence in bacteria: spontaneous resistance mutations; in situ horizontal gene transfer of resistance genes; selection of pre-existing resistance; and immigration of resistant lineages. Within-patient AMR emergence occurs across a wide range of host niches and bacterial species, but the importance of each mechanism varies between bacterial species and infection sites within the body. We identify potential drivers of such differences and discuss how ecological and evolutionary analysis could be embedded within clinical trials of antimicrobials, which are powerful but underused tools for understanding why these mechanisms vary between pathogens, infections and individuals. Ultimately, improving understanding of how host niche, bacterial species and antibiotic mode of action combine to govern the ecological and evolutionary mechanism of AMR emergence in patients will enable more predictive and personalized diagnosis and antimicrobial therapies.
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Affiliation(s)
- Matthew J Shepherd
- Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester, UK.
| | - Taoran Fu
- Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester, UK
| | - Niamh E Harrington
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Anastasia Kottara
- Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester, UK
| | - Kendall Cagney
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - James D Chalmers
- Division of Molecular and Clinical Medicine, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - Steve Paterson
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Joanne L Fothergill
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Michael A Brockhurst
- Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester, UK.
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3
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Zimmerman EH, Ramsey EL, Hunter KE, Villadelgado SM, Phillips CM, Shipman RT, Forsyth MH. The Helicobacter pylori methylome is acid-responsive due to regulation by the two-component system ArsRS and the type I DNA methyltransferase HsdM1 (HP0463). J Bacteriol 2024; 206:e0030923. [PMID: 38179929 PMCID: PMC10810217 DOI: 10.1128/jb.00309-23] [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: 09/23/2023] [Accepted: 12/14/2023] [Indexed: 01/06/2024] Open
Abstract
In addition to its role in genome protection, DNA methylation can regulate gene expression. In this study, we characterized the impact of acidity, phase variation, and the ArsRS TCS on the expression of the Type I m6A DNA methyltransferase HsdM1 (HP0463) of Helicobacter pylori 26695 and their subsequent effects on the methylome. Transcription of hsdM1 increases at least fourfold in the absence of the sensory histidine kinase ArsS, the major acid-sensing protein of H. pylori. hsdM1 exists in the phase-variable operon hsdR1-hsdM1. Phase-locking hsdR1 (HP0464), the restriction endonuclease gene, has significant impacts on the transcription of hsdM1. To determine the impacts of methyltransferase transcription patterns on the methylome, we conducted methylome sequencing on samples cultured at pH 7 or pH 5. We found differentially methylated motifs between these growth conditions and that deletions of arsS and/or hsdM1 interfere with the epigenetic acid response. Deletion of arsS leads to altered activity of HsdM1 and multiple other methyltransferases under both pH conditions indicating that the ArsRS TCS, in addition to direct effects on regulon transcription during acid acclimation, may also indirectly impact gene expression via regulation of the methylome. We determined the target motif of HsdM1 (HP0463) to be the complementary bipartite sequence pair 5'-TCAm6AVN6TGY-3' and 3'-AGTN6GAm6ACA-5'. This complex regulation of DNA methyltransferases, and thus differential methylation patterns, may have implications for the decades-long persistent infection by H. pylori. IMPORTANCE This study expands the possibilities for complex, epigenomic regulation in Helicobacter pylori. We demonstrate that the H. pylori methylome is plastic and acid sensitive via the two-component system ArsRS and the DNA methyltransferase HsdM1. The control of a methyltransferase by ArsRS may allow for a layered response to changing acidity. Likely, an early response whereby ArsR~P affects regulon expression, including the methyltransferase hsdM1. Then, a somewhat later effect as the altered methylome, due to altered HsdM1 expression, subsequently alters the expression of other genes involved in acclimation. The intermediate methylation of certain motifs supports the hypothesis that methyltransferases play a regulatory role. Untangling this additional web of regulation could play a key role in understanding H. pylori colonization and persistence.
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Affiliation(s)
| | - Erin L. Ramsey
- Department of Biology, William & Mary, Williamsburg, Virginia, USA
| | | | | | | | - Ryan T. Shipman
- Department of Biology, William & Mary, Williamsburg, Virginia, USA
| | - Mark H. Forsyth
- Department of Biology, William & Mary, Williamsburg, Virginia, USA
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4
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Ailloud F, Gottschall W, Suerbaum S. Methylome evolution suggests lineage-dependent selection in the gastric pathogen Helicobacter pylori. Commun Biol 2023; 6:839. [PMID: 37573385 PMCID: PMC10423294 DOI: 10.1038/s42003-023-05218-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 08/04/2023] [Indexed: 08/14/2023] Open
Abstract
The bacterial pathogen Helicobacter pylori, the leading cause of gastric cancer, is genetically highly diverse and harbours a large and variable portfolio of restriction-modification systems. Our understanding of the evolution and function of DNA methylation in bacteria is limited. Here, we performed a comprehensive analysis of the methylome diversity in H. pylori, using a dataset of 541 genomes that included all known phylogeographic populations. The frequency of 96 methyltransferases and the abundance of their cognate recognition sequences were strongly influenced by phylogeographic structure and were inter-correlated, positively or negatively, for 20% of type II methyltransferases. Low density motifs were more likely to be affected by natural selection, as reflected by higher genomic instability and compositional bias. Importantly, direct correlation implied that methylation patterns can be actively enriched by positive selection and suggests that specific sites have important functions in methylation-dependent phenotypes. Finally, we identified lineage-specific selective pressures modulating the contraction and expansion of the motif ACGT, revealing that the genetic load of methylation could be dependent on local ecological factors. Taken together, natural selection may shape both the abundance and distribution of methyltransferases and their specific recognition sequences, likely permitting a fine-tuning of genome-encoded functions not achievable by genetic variation alone.
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Affiliation(s)
- Florent Ailloud
- Medical Microbiology and Hospital Epidemiology, Max von Pettenkofer Institute, Faculty of Medicine, LMU Munich, Munich, Germany.
- German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany.
| | - Wilhelm Gottschall
- Medical Microbiology and Hospital Epidemiology, Max von Pettenkofer Institute, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Sebastian Suerbaum
- Medical Microbiology and Hospital Epidemiology, Max von Pettenkofer Institute, Faculty of Medicine, LMU Munich, Munich, Germany.
- German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany.
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5
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Suerbaum S, Ailloud F. Genome and population dynamics during chronic infection with Helicobacter pylori. Curr Opin Immunol 2023; 82:102304. [PMID: 36958230 DOI: 10.1016/j.coi.2023.102304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 02/21/2023] [Accepted: 02/22/2023] [Indexed: 03/25/2023]
Abstract
Helicobacter pylori is responsible for one of the most prevalent bacterial infections worldwide. Chronic infection typically leads to chronic active gastritis. Clinical sequelae, including peptic ulcers, mucosa-associated lymphoid tissue lymphoma or, most importantly, gastric adenocarcinoma develop in 10-15% of cases. H. pylori is characterized by extensive inter-strain diversity which is the result of a high mutation rate, recombination, and a large repertoire of restriction-modification systems. This diversity is thought to be a major contributor to H. pylori's persistence and exceptional aptitude to adapt to the gastric environment and evade the immune system. This review covers efforts in the last decade to characterize and understand the multiple layers of H. pylori's diversity in different biological contexts.
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Affiliation(s)
- Sebastian Suerbaum
- Max von Pettenkofer Institute for Hygiene and Medical Microbiology, Medical Faculty, LMU Munich, Pettenkoferstr. 9a, 80336 Munich, Germany; DZIF German Centre for Infection Research, Munich Partner Site, Pettenkoferstr. 9a, 80336 Munich, Germany; German National Reference Centre for Helicobacter pylori, Pettenkoferstr. 9a, 80336 Munich, Germany.
| | - Florent Ailloud
- Max von Pettenkofer Institute for Hygiene and Medical Microbiology, Medical Faculty, LMU Munich, Pettenkoferstr. 9a, 80336 Munich, Germany; DZIF German Centre for Infection Research, Munich Partner Site, Pettenkoferstr. 9a, 80336 Munich, Germany
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6
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Yamaoka Y, Saruuljavkhlan B, Alfaray RI, Linz B. Pathogenomics of Helicobacter pylori. Curr Top Microbiol Immunol 2023; 444:117-155. [PMID: 38231217 DOI: 10.1007/978-3-031-47331-9_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2024]
Abstract
The human stomach bacterium Helicobacter pylori, the causative agent of gastritis, ulcers and adenocarcinoma, possesses very high genetic diversity. H. pylori has been associated with anatomically modern humans since their origins over 100,000 years ago and has co-evolved with its human host ever since. Predominantly intrafamilial and local transmission, along with genetic isolation, genetic drift, and selection have facilitated the development of distinct bacterial populations that are characteristic for large geographical areas. H. pylori utilizes a large arsenal of virulence and colonization factors to mediate the interaction with its host. Those include various adhesins, the vacuolating cytotoxin VacA, urease, serine protease HtrA, the cytotoxin-associated genes pathogenicity island (cagPAI)-encoded type-IV secretion system and its effector protein CagA, all of which contribute to disease development. While many pathogenicity-related factors are present in all strains, some belong to the auxiliary genome and are associated with specific phylogeographic populations. H. pylori is naturally competent for DNA uptake and recombination, and its genome evolution is driven by extraordinarily high recombination and mutation rates that are by far exceeding those in other bacteria. Comparative genome analyses revealed that adaptation of H. pylori to individual hosts is associated with strong selection for particular protein variants that facilitate immune evasion, especially in surface-exposed and in secreted virulence factors. Recent studies identified single-nucleotide polymorphisms (SNPs) in H. pylori that are associated with the development of severe gastric disease, including gastric cancer. Here, we review the current knowledge about the pathogenomics of H. pylori.
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Affiliation(s)
- Yoshio Yamaoka
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, 1-1, Idaigaoka, Hasama-machi, Yufu Oita, 879-5593, Japan
- Department of Medicine, Gastroenterology and Hepatology Section, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Batsaikhan Saruuljavkhlan
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, 1-1, Idaigaoka, Hasama-machi, Yufu Oita, 879-5593, Japan
| | - Ricky Indra Alfaray
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, 1-1, Idaigaoka, Hasama-machi, Yufu Oita, 879-5593, Japan
- Helicobacter pylori and Microbiota Study Group, Universitas Airlangga, Surabaya, 60286, East Java, Indonesia
| | - Bodo Linz
- Division of Microbiology, Department Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Staudtstr. 5, 91058, Erlangen, Germany.
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7
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Xiao W, Ma ZS. Influences of Helicobacter pylori infection on diversity, heterogeneity, and composition of human gastric microbiomes across stages of gastric cancer development. Helicobacter 2022; 27:e12899. [PMID: 35678078 DOI: 10.1111/hel.12899] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 04/09/2022] [Accepted: 04/21/2022] [Indexed: 12/15/2022]
Abstract
BACKGROUND About a half of the world's population is infected with Helicobacter pylori (H. pylori), but only 1%-3% of them develop gastric cancer. As a primary risk factor for gastric cancer, the relationship between H. pylori infection and gastric microbiome has been a focus in recent years. MATERIALS AND METHODS We reanalyze 11 human gastric microbiome datasets with or without H. pylori, covering the healthy control (HC) and four disease stages (chronic gastritis (CG), atrophic gastritis (AG), intestinal metaplasia (IM), and gastric cancer (GC)) of gastric cancer development to quantitatively compare the influences of the H. pylori infection and disease stages on the diversity, heterogeneity, and composition of gastric microbiome. Four medical ecology approaches including (i) diversity analysis with Hill numbers, (ii) heterogeneity analysis with Taylor's power law extensions (TPLE), (iii) diversity scaling analysis with diversity-area relationship (DAR) model, and (iv) shared species analysis were applied to fulfill the data reanalysis. RESULTS (i) The influences of H. pylori infection on the species diversity, spatial heterogeneity, and potential diversity of gastric microbiome seem to be more prevalent than the influences of disease stages during gastric cancer development. (ii) The influences of H. pyloriinfection on diversity, heterogeneity, and composition of gastric microbiomes in HC, CG, IM, and GC stages appear more prevalent than those in AG stage. CONCLUSION Our study confirmed the impact of H. pylori infection on human gastric microbiomes: The influences of H. pylori infection on the diversity, heterogeneity, and composition of gastric microbiomes appear to be disease-stage dependent.
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Affiliation(s)
- Wanmeng Xiao
- Computational Biology and Medical Ecology Lab, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Sciences, University of Chinese Academy of Sciences, Kunming, China
| | - Zhanshan Sam Ma
- Computational Biology and Medical Ecology Lab, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Sciences, University of Chinese Academy of Sciences, Kunming, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
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8
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Loh JT, Shuman JHB, Lin AS, Favret N, Piazuelo MB, Mallal S, Chopra A, McClain MS, Cover TL. Positive Selection of Mutations in the Helicobacter pylori katA 5' Untranslated Region in a Mongolian Gerbil Model of Gastric Disease. Infect Immun 2022; 90:e0000422. [PMID: 35652648 PMCID: PMC9302185 DOI: 10.1128/iai.00004-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 05/11/2022] [Indexed: 01/18/2023] Open
Abstract
To evaluate potential effects of gastric inflammation on Helicobacter pylori diversification and evolution within the stomach, we experimentally infected Mongolian gerbils with an H. pylori strain in which Cag type IV secretion system (T4SS) activity is controlled by a TetR/tetO system. Gerbils infected with H. pylori under conditions in which Cag T4SS activity was derepressed had significantly higher levels of gastric inflammation than gerbils infected under conditions with repressed Cag T4SS activity. Mutations in the 5' untranslated region (UTR) of katA (encoding catalase) were detected in strains cultured from 8 of the 17 gerbils infected with Cag T4SS-active H. pylori and none of the strains from 17 gerbils infected with Cag T4SS-inactive H. pylori. Catalase enzymatic activity, steady-state katA transcript levels, and katA transcript stability were increased in strains with these single nucleotide polymorphisms (SNPs) compared to strains in which these SNPs were absent. Moreover, strains harboring these SNPs exhibited increased resistance to bactericidal effects of hydrogen peroxide, compared to control strains. Experimental introduction of the SNPs into the wild-type katA 5' UTR resulted in increased katA transcript stability, increased katA steady-state levels, and increased catalase enzymatic activity. Based on site-directed mutagenesis and modeling of RNA structure, increased katA transcript levels were correlated with higher predicted thermal stability of the katA 5' UTR secondary structure. These data suggest that high levels of gastric inflammation positively select for H. pylori strains producing increased levels of catalase, which may confer survival advantages to the bacteria in an inflammatory gastric environment.
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Affiliation(s)
- John T. Loh
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Jennifer H. B. Shuman
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Aung Soe Lin
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Natalie Favret
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - M. Blanca Piazuelo
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Simon Mallal
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Australia
| | - Abha Chopra
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Australia
| | - Mark S. McClain
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennesse, USA
| | - Timothy L. Cover
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennesse, USA
- Veterans Affairs Tennessee Valley Healthcare System, Nashville, Tennessee, USA
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9
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Hu X, Zhou X, Yin T, Chen K, Hu Y, Zhu B, Mi K. The Mycobacterial DNA Methyltransferase HsdM Decreases Intrinsic Isoniazid Susceptibility. Antibiotics (Basel) 2021; 10:antibiotics10111323. [PMID: 34827261 PMCID: PMC8614780 DOI: 10.3390/antibiotics10111323] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 10/26/2021] [Accepted: 10/26/2021] [Indexed: 02/02/2023] Open
Abstract
Tuberculosis, caused by the pathogen Mycobacterium tuberculosis, is a serious infectious disease worldwide. Multidrug-resistant TB (MDR-TB) remains a global problem, and the understanding of this resistance is incomplete. Studies suggested that DNA methylation promotes bacterial adaptability to antibiotic treatment, but the role of mycobacterial HsdM in drug susceptibility has not been explored. Here, we constructed an inactivated Mycobacterium bovis (BCG) strain, ΔhsdM. ΔhsdM shows growth advantages over wild-type BCG under isoniazid treatment and hypoxia-induced stress. Using high-precision PacBio single-molecule real-time sequencing to compare the ΔhsdM and BCG methylomes, we identified 219 methylated HsdM substrates. Bioinformatics analysis showed that most HsdM-modified genes were enriched in respiration- and energy-related pathways. qPCR showed that HsdM-modified genes directly affected their own transcription, indicating an altered redox regulation. The use of the latent Wayne model revealed that ΔhsdM had growth advantages over wild-type BCG and that HsdM regulated trcR mRNA levels, which may be crucial in regulating transition from latency to reactivation. We found that HsdM regulated corresponding transcription levels via gene methylation; thus, altering the mycobacterial redox status and decreasing the bacterial susceptibility to isoniazid, which is closely correlated with the redox status. Our results provide valuable insight into DNA methylation on drug susceptibility.
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Affiliation(s)
- Xinling Hu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (X.H.); (X.Z.); (T.Y.); (K.C.); (B.Z.)
| | - Xintong Zhou
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (X.H.); (X.Z.); (T.Y.); (K.C.); (B.Z.)
| | - Tong Yin
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (X.H.); (X.Z.); (T.Y.); (K.C.); (B.Z.)
| | - Keyu Chen
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (X.H.); (X.Z.); (T.Y.); (K.C.); (B.Z.)
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 101408, China
| | - Yongfei Hu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China;
| | - Baoli Zhu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (X.H.); (X.Z.); (T.Y.); (K.C.); (B.Z.)
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 101408, China
| | - Kaixia Mi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (X.H.); (X.Z.); (T.Y.); (K.C.); (B.Z.)
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 101408, China
- Correspondence: ; Tel.: +86-01-64806082
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10
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Harvey ML, Lin AS, Sun L, Koyama T, Shuman JHB, Loh JT, Algood HMS, Scholz MB, McClain MS, Cover TL. Enhanced Fitness of a Helicobacter pylori babA Mutant in a Murine Model. Infect Immun 2021; 89:e0072520. [PMID: 34310886 PMCID: PMC8445181 DOI: 10.1128/iai.00725-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 07/05/2021] [Indexed: 11/20/2022] Open
Abstract
Helicobacter pylori genomes encode over 60 predicted outer membrane proteins (OMPs). Several OMPs in the Hop family act as adhesins, but the functions of most Hop proteins are unknown. To identify hop mutant strains exhibiting differential fitness in vivo compared to in vitro, we used a genetic barcoding method that allowed us to track changes in the proportional abundance of H. pylori strains within a mixed population. We generated a library of hop mutant strains, each containing a unique nucleotide barcode, as well as a library of control strains, each containing a nucleotide barcode in an intergenic region predicted to be a neutral locus unrelated to bacterial fitness. We orogastrically inoculated each of the libraries into mice and analyzed compositional changes in the populations over time in vivo compared to changes detected in the populations during library passage in vitro. The control library proliferated as a relatively stable community in vitro, but there was a reduction in the population diversity of this library in vivo and marked variation in the dominant strains recovered from individual animals, consistent with the existence of a nonselective bottleneck in vivo. We did not identify any OMP mutants exhibiting fitness defects exclusively in vivo without corresponding fitness defects in vitro. Conversely, a babA mutant exhibited a strong fitness advantage in vivo but not in vitro. These findings, when taken together with results of other studies, suggest that production of BabA may have differential effects on H. pylori fitness depending on the environmental conditions.
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Affiliation(s)
- M. Lorena Harvey
- Department of Pathology, Microbiology and Immunology, Vanderbilt University, Nashville, Tennessee, USA
- Vanderbilt Institute for Infection, Immunology and Inflammation, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Aung Soe Lin
- Department of Pathology, Microbiology and Immunology, Vanderbilt University, Nashville, Tennessee, USA
- Vanderbilt Institute for Infection, Immunology and Inflammation, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Lili Sun
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Tatsuki Koyama
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Jennifer H. B. Shuman
- Department of Pathology, Microbiology and Immunology, Vanderbilt University, Nashville, Tennessee, USA
- Vanderbilt Institute for Infection, Immunology and Inflammation, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - John T. Loh
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Holly M. Scott Algood
- Department of Pathology, Microbiology and Immunology, Vanderbilt University, Nashville, Tennessee, USA
- Vanderbilt Institute for Infection, Immunology and Inflammation, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
- Veterans Affairs Tennessee Valley Healthcare System, Nashville, Tennessee, USA
| | - Matthew B. Scholz
- Vanderbilt Technologies for Advanced Genetics (VANTAGE), Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Mark S. McClain
- Vanderbilt Institute for Infection, Immunology and Inflammation, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Timothy L. Cover
- Department of Pathology, Microbiology and Immunology, Vanderbilt University, Nashville, Tennessee, USA
- Vanderbilt Institute for Infection, Immunology and Inflammation, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
- Veterans Affairs Tennessee Valley Healthcare System, Nashville, Tennessee, USA
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Ailloud F, Estibariz I, Suerbaum S. Evolved to vary: genome and epigenome variation in the human pathogen Helicobacter pylori. FEMS Microbiol Rev 2021; 45:5900976. [PMID: 32880636 DOI: 10.1093/femsre/fuaa042] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 08/31/2020] [Indexed: 12/24/2022] Open
Abstract
Helicobacter pylori is a Gram-negative, spiral shaped bacterium that selectively and chronically infects the gastric mucosa of humans. The clinical course of this infection can range from lifelong asymptomatic infection to severe disease, including peptic ulcers or gastric cancer. The high mutation rate and natural competence typical of this species are responsible for massive inter-strain genetic variation exceeding that observed in all other bacterial human pathogens. The adaptive value of such a plastic genome is thought to derive from a rapid exploration of the fitness landscape resulting in fast adaptation to the changing conditions of the gastric environment. Nevertheless, diversity is also lost through recurrent bottlenecks and H. pylori's lifestyle is thus a perpetual race to maintain an appropriate pool of standing genetic variation able to withstand selection events. Another aspect of H. pylori's diversity is a large and variable repertoire of restriction-modification systems. While not yet completely understood, methylome evolution could generate enough transcriptomic variation to provide another intricate layer of adaptive potential. This review provides an up to date synopsis of this rapidly emerging area of H. pylori research that has been enabled by the ever-increasing throughput of Omics technologies and a multitude of other technological advances.
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Affiliation(s)
- Florent Ailloud
- Max von Pettenkofer Institute, Faculty of Medicine, LMU München, Pettenkoferstr. 9a, 80336 München, Germany
| | - Iratxe Estibariz
- Max von Pettenkofer Institute, Faculty of Medicine, LMU München, Pettenkoferstr. 9a, 80336 München, Germany
| | - Sebastian Suerbaum
- Max von Pettenkofer Institute, Faculty of Medicine, LMU München, Pettenkoferstr. 9a, 80336 München, Germany.,DZIF Deutsches Zentrum für Infektionsforschung, Partner Site Munich, Pettenkoferstr. 9a, 80336 München, Germany.,National Reference Center for Helicobacter pylori, Pettenkoferstr. 9a, 80336 München, Germany
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Mannion A, Dzink-Fox J, Shen Z, Piazuelo MB, Wilson KT, Correa P, Peek RM, Camargo MC, Fox JG. Helicobacter pylori Antimicrobial Resistance and Gene Variants in High- and Low-Gastric-Cancer-Risk Populations. J Clin Microbiol 2021; 59:e03203-20. [PMID: 33692136 PMCID: PMC8091839 DOI: 10.1128/jcm.03203-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 02/28/2021] [Indexed: 02/07/2023] Open
Abstract
Colombia, South America has one of the world's highest burdens of Helicobacter pylori infection and gastric cancer. While multidrug antibiotic regimens can effectively eradicate H. pylori, treatment efficacy is being jeopardized by the emergence of antibiotic-resistant H. pylori strains. Moreover, the spectrum of and genetic mechanisms for antibiotic resistance in Colombia is underreported. In this study, 28 H. pylori strains isolated from gastric biopsy specimens from a high-gastric-cancer-risk (HGCR) population living in the Andes Mountains in Túquerres, Colombia and 31 strains from a low-gastric-cancer-risk (LGCR) population residing on the Pacific coast in Tumaco, Colombia were subjected to antibiotic susceptibility testing for amoxicillin, clarithromycin, levofloxacin, metronidazole, rifampin, and tetracycline. Resistance-associated genes were amplified by PCR for all isolates, and 29 isolates were whole-genome sequenced (WGS). No strains were resistant to amoxicillin, clarithromycin, or rifampin. One strain was resistant to tetracycline and had an A926G mutation in its 16S rRNA gene. Levofloxacin resistance was observed in 12/59 isolates and was significantly associated with N87I/K and/or D91G/Y mutations in gyrA Most isolates were resistant to metronidazole; this resistance was significantly higher in the LGCR (31/31) group compared to the HGCR (24/28) group. Truncations in rdxA and frxA were present in nearly all metronidazole-resistant strains. There was no association between phylogenetic relationship and resistance profiles based on WGS analysis. Our results indicate H. pylori isolates from Colombians exhibit multidrug antibiotic resistance. Continued surveillance of H. pylori antibiotic resistance in Colombia is warranted in order to establish appropriate eradication treatment regimens for this population.
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Affiliation(s)
- Anthony Mannion
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - JoAnn Dzink-Fox
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Zeli Shen
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | | | | | | | | | - M Constanza Camargo
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, USA
| | - James G Fox
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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