1
|
Antony BS, Nagarajan C, Devaraj DV, Subbaraj GK. A Systemic Review and Meta-analysis on Natural Resistance-associated Macrophage Protein 1 (3'-Untranslated Region) and Nucleotide-binding Oligomerization Domain-2 (rs8057341) Polymorphisms and Leprosy Susceptibility in Asian and Caucasian Populations. Int J Mycobacteriol 2024; 13:115-125. [PMID: 38916380 DOI: 10.4103/ijmy.ijmy_43_24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Accepted: 05/15/2024] [Indexed: 06/26/2024] Open
Abstract
The current meta-analysis aims to explore the potential correlation between natural resistance-associated macrophage protein 1 (NRAMP1) (3'-Untranslated region [3'-UTR]) and nucleotide-binding oligomerization domain-2 (NOD2 [rs8057341]) gene polymorphisms and their association with leprosy susceptibility in both Asian and Caucasian populations. Datas were retrieved from case control studies with NOD 2 and NRAMP 1 gene polymorphism associated with leprosy disease. Leprosy emerges as a particularly distinctive ailment among women on a global scale. The NRAMP1 (3'-UTR) and NOD2 (rs8057341) genetic variations play a crucial role in the progression of leprosy. A systematic review of relevant case-control studies was conducted across several databases, including ScienceDirect, PubMed, Google Scholar, and Embase. Utilizing MetaGenyo and Review Manager 5.4 Version, statistical analyses were carried out. Nine case-control studies totaling 3281 controls and 3062 leprosy patients are included in the research, with the objective of examining the potential association between NRAMP1 (3'-UTR) and NOD2 (rs8057341) gene polymorphisms and leprosy risk. The review methodology was registered in PROSPERO (ID520883). The findings reveal a robust association between NRAMP1 (3'-UTR) and NOD2 (rs8057341) gene polymorphisms and leprosy risk across various genetic models. Although the funnel plot analysis did not identify publication bias, bolstering these findings and elucidating potential gene-gene and gene-environment interactions require further comprehensive epidemiological research. This study identified a strong correlation between polymorphisms in the NOD2 (rs8057341) genes and susceptibility to leprosy across two genetic models. Further comprehensive epidemiological investigations are warranted to validate these findings and explore potential interactions between these genes and environmental factors.
Collapse
Affiliation(s)
- Bibin Savio Antony
- Department of Medical Genetics, Faculty of Allied Health Science, Chettinad Hospital and Research Institute, Chettinad Academy of Research and Education, Kelambakkam, Tamil Nadu, India
| | - Chitra Nagarajan
- Department of Microbiology, Sri Venkateswara Dental College and Hospital, Chennai, Tamil Nadu, India
| | - Danis Vijay Devaraj
- Department of Microbiology, Karpaga Vinayaga Institute of Medical Sciences and Research Centre, Chengalpattu, Tamil Nadu, India
| | - Gowtham Kumar Subbaraj
- Department of Medical Genetics, Faculty of Allied Health Science, Chettinad Hospital and Research Institute, Chettinad Academy of Research and Education, Kelambakkam, Tamil Nadu, India
| |
Collapse
|
2
|
Salamaikina S, Korchagin V, Kulabukhova E, Mironov K, Zimina V, Kravtchenko A, Akimkin V. Association of Toll-Like Receptor Gene Polymorphisms with Tuberculosis in HIV-Positive Participants. EPIGENOMES 2023; 7:15. [PMID: 37606452 PMCID: PMC10443360 DOI: 10.3390/epigenomes7030015] [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: 06/07/2023] [Revised: 07/20/2023] [Accepted: 07/21/2023] [Indexed: 08/23/2023] Open
Abstract
Genetic factors in the HIV-background may play a significant role in the susceptibility to secondary diseases, like tuberculosis, which is the leading cause in mortality of HIV-positive people. Toll-like receptors (TLRs) are considered to be receptors for adaptive immunity, and polymorphisms in TLR genes can influence the activity of the immune response to infection. We conducted a case-control study of the association of TLR gene polymorphisms with the risk of tuberculosis coinfection in a multi-country sample of HIV-positive participants. Our study revealed certain associations between TLR4 and TLR6 polymorphisms and HIV-tuberculosis coinfection. We also found that the analyzed TLR1 and TLR4 polymorphisms were linked with the decline in CD4+ cell count, which is a predictor of disease progression in HIV-infected individuals. Our findings confirm that TLR gene polymorphisms are factors that may contribute to development of HIV-tuberculosis coinfection. However, the essence of the observed associations remains unclear, since it can also include both environmental factors and epigenetic mechanisms of gene expression regulation.
Collapse
Affiliation(s)
- Svetlana Salamaikina
- Central Research Institute of Epidemiology Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing Russian Federation, Novogireevskaya Str. 3a, 111123 Moscow, Russia
| | - Vitaly Korchagin
- Central Research Institute of Epidemiology Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing Russian Federation, Novogireevskaya Str. 3a, 111123 Moscow, Russia
| | - Ekaterina Kulabukhova
- Central Research Institute of Epidemiology Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing Russian Federation, Novogireevskaya Str. 3a, 111123 Moscow, Russia
- Medical Institute, The Peoples’ Friendship University of Russia (RUDN University), Miklukho-Maklaya Str. 6, 117198 Moscow, Russia
| | - Konstantin Mironov
- Central Research Institute of Epidemiology Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing Russian Federation, Novogireevskaya Str. 3a, 111123 Moscow, Russia
| | - Vera Zimina
- Medical Institute, The Peoples’ Friendship University of Russia (RUDN University), Miklukho-Maklaya Str. 6, 117198 Moscow, Russia
| | - Alexey Kravtchenko
- Central Research Institute of Epidemiology Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing Russian Federation, Novogireevskaya Str. 3a, 111123 Moscow, Russia
| | - Vasily Akimkin
- Central Research Institute of Epidemiology Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing Russian Federation, Novogireevskaya Str. 3a, 111123 Moscow, Russia
| |
Collapse
|
3
|
Prieto MD, Jang J, Franciosi AN, Av-Gay Y, Bach H, Tebbutt SJ, Quon BS. Whole blood RNA-seq demonstrates an increased host immune response in individuals with cystic fibrosis who develop nontuberculous mycobacterial pulmonary disease. PLoS One 2022; 17:e0278296. [PMID: 36480571 PMCID: PMC9731410 DOI: 10.1371/journal.pone.0278296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 11/14/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Individuals with cystic fibrosis have an elevated lifetime risk of colonization, infection, and disease caused by nontuberculous mycobacteria. A prior study involving non-cystic fibrosis individuals reported a gene expression signature associated with susceptibility to nontuberculous mycobacteria pulmonary disease (NTM-PD). In this study, we determined whether people living with cystic fibrosis who progress to NTM-PD have a gene expression pattern similar to the one seen in the non-cystic fibrosis population. METHODS We evaluated whole blood transcriptomics using bulk RNA-seq in a cohort of cystic fibrosis patients with samples collected closest in timing to the first isolation of nontuberculous mycobacteria. The study population included patients who did (n = 12) and did not (n = 30) develop NTM-PD following the first mycobacterial growth. Progression to NTM-PD was defined by a consensus of two expert clinicians based on reviewing clinical, microbiological, and radiological information. Differential gene expression was determined by DESeq2. RESULTS No differences in demographics or composition of white blood cell populations between groups were identified at baseline. Out of 213 genes associated with NTM-PD in the non-CF population, only two were significantly different in our cystic fibrosis NTM-PD cohort. Gene set enrichment analysis of the differential expression results showed that CF individuals who developed NTM-PD had higher expression levels of genes involved in the interferon (α and γ), tumor necrosis factor, and IL6-STAT3-JAK pathways. CONCLUSION In contrast to the non-cystic fibrosis population, the gene expression signature of patients with cystic fibrosis who develop NTM-PD is characterized by increased innate immune responses.
Collapse
Affiliation(s)
- Miguel Dario Prieto
- Department of Medicine, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- Centre for Heart Lung Innovation, University of British Columbia and St Paul’s Hospital, Vancouver, British Columbia, Canada
| | - Jiah Jang
- Centre for Heart Lung Innovation, University of British Columbia and St Paul’s Hospital, Vancouver, British Columbia, Canada
| | - Alessandro N. Franciosi
- Department of Medicine, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- Centre for Heart Lung Innovation, University of British Columbia and St Paul’s Hospital, Vancouver, British Columbia, Canada
| | - Yossef Av-Gay
- Division of Infectious Diseases, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Horacio Bach
- Division of Infectious Diseases, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Scott J. Tebbutt
- Department of Medicine, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- Centre for Heart Lung Innovation, University of British Columbia and St Paul’s Hospital, Vancouver, British Columbia, Canada
- Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, British Columbia, Canada
| | - Bradley S. Quon
- Department of Medicine, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- Centre for Heart Lung Innovation, University of British Columbia and St Paul’s Hospital, Vancouver, British Columbia, Canada
- * E-mail:
| |
Collapse
|
4
|
Cruz-Aguilar M, Castillo-Rodal AI, Arredondo-Hernández R, López-Vidal Y. Non-tuberculous mycobacteria immunopathogenesis: Closer than they appear. a prime of innate immunity trade-off and NTM ways into virulence. Scand J Immunol 2021; 94:e13035. [PMID: 33655533 PMCID: PMC9285547 DOI: 10.1111/sji.13035] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 01/16/2021] [Accepted: 02/26/2021] [Indexed: 12/14/2022]
Abstract
Introduction The growing incidence of non‐tuberculous mycobacteria (NTM) and changes in epidemiological factors have indicated that immune dysregulation may be associated with the emergence of NTM. Minireview entails to acknowledge complex interaction and new ways NTM are evolving around diverse immune status. Methods In order to perform this review, we selected peer reviewed, NLM database articles under the terms NTM, mycobacterium complex ‘AND’ ‐Host‐ immune response, immunity regulation, Disease, Single Nucleotide Polymorphism (SNP´s), and ‐pathogen‐ followed by a snow ball rolling basis search on immune components and NTM related with diseases distribution. Results The universal exposure and diversity of NTM are well‐documented; however, hospitals seldom establish vigilant control of water quality or immunodeficiencies for patients with NTM infections. Depending on the chemical structures and immune mechanisms presented by various NTM varieties, they can trigger different effects in dendritic and natural killer cells, which release interleukin (IL)‐17, tumour necrosis factor‐α (TNF‐α), interferon‐γ (IFN‐γ) and rIL‐1B. The T helper (Th)2‐acquired immune response is responsible for autoimmune responses in patients with NTM infections, and, quite disturbingly, immunocompetent patients have been reported to suffer from NTM infections. Conclusion New technologies and a comprehensive view has taught us; to acknowledge metabolic/immune determinants and trade‐offs along transit through mutualism‐parasite continuous.
Collapse
Affiliation(s)
- Marisa Cruz-Aguilar
- Programa de Inmunología Molecular Microbiana, Departamento de Microbiología y Parasitología, Facultad de Medicina, UNAM, Mexico City, Mexico
| | - Antonia I Castillo-Rodal
- Programa de Inmunología Molecular Microbiana, Departamento de Microbiología y Parasitología, Facultad de Medicina, UNAM, Mexico City, Mexico
| | - René Arredondo-Hernández
- Laboratorio de Microbioma, Division de Investigación, Facultad de Medicina, UNAM, Mexico City, Mexico
| | - Yolanda López-Vidal
- Programa de Inmunología Molecular Microbiana, Departamento de Microbiología y Parasitología, Facultad de Medicina, UNAM, Mexico City, Mexico
| |
Collapse
|
5
|
Glickman C, Kammlade SM, Hasan NA, Epperson LE, Davidson RM, Strong M. Characterization of integrated prophages within diverse species of clinical nontuberculous mycobacteria. Virol J 2020; 17:124. [PMID: 32807206 PMCID: PMC7433156 DOI: 10.1186/s12985-020-01394-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 08/03/2020] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Nontuberculous mycobacterial (NTM) infections are increasing in prevalence, with current estimates suggesting that over 100,000 people in the United States are affected each year. It is unclear how certain species of mycobacteria transition from environmental bacteria to clinical pathogens, or what genetic elements influence the differences in virulence among strains of the same species. A potential mechanism of genetic evolution and diversity within mycobacteria is the presence of integrated viruses called prophages in the host genome. Prophages may act as carriers of bacterial genes, with the potential of altering bacterial fitness through horizontal gene transfer. In this study, we quantify the frequency and composition of prophages within mycobacteria isolated from clinical samples and compare them against the composition of PhagesDB, an environmental mycobacteriophage database. METHODS Prophages were predicted by agreement between two discovery tools, VirSorter and Phaster, and the frequencies of integrated prophages were compared by growth rate. Prophages were assigned to PhagesDB lettered clusters. Bacterial virulence gene frequency was calculated using a combination of the Virulence Factor Database (VFDB) and the Pathosystems Resource Integration Center virulence database (Patric-VF) within the gene annotation software Prokka. CRISPR elements were discovered using CRT. ARAGORN was used to quantify tRNAs. RESULTS Rapidly growing mycobacteria (RGM) were more likely to contain prophage than slowly growing mycobacteria (SGM). CRISPR elements were not associated with prophage abundance in mycobacteria. The abundance of tRNAs was enriched in SGM compared to RGM. We compared the abundance of bacterial virulence genes within prophage genomes from clinical isolates to mycobacteriophages from PhagesDB. Our data suggests that prophages from clinical mycobacteria are enriched for bacterial virulence genes relative to environmental mycobacteriophage from PhagesDB. CONCLUSION Prophages are present in clinical NTM isolates. Prophages are more likely to be present in RGM compared to SGM genomes. The mechanism and selective advantage of this enrichment by growth rate remain unclear. In addition, the frequency of bacterial virulence genes in prophages from clinical NTM is enriched relative to the PhagesDB environmental proxy. This suggests prophages may act as a reservoir of genetic elements bacteria could use to thrive within a clinical environment.
Collapse
Affiliation(s)
- Cody Glickman
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA.
- Computational Bioscience Program, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA.
| | - Sara M Kammlade
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA
| | - Nabeeh A Hasan
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA
| | - L Elaine Epperson
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA
| | - Rebecca M Davidson
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA
| | - Michael Strong
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA
- Computational Bioscience Program, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
| |
Collapse
|
6
|
Epperson LE, Strong M. A scalable, efficient, and safe method to prepare high quality DNA from mycobacteria and other challenging cells. J Clin Tuberc Other Mycobact Dis 2020; 19:100150. [PMID: 32154387 PMCID: PMC7052505 DOI: 10.1016/j.jctube.2020.100150] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The rapid development in sequencing technology is creating an increase in demand for largely intact DNA as starting material as very long strands of DNA are sequenced directly to generate reads that are thousands of bases long. Organisms with thick cell walls are difficult to lyse, often impacting both DNA recovery and quality. Consequently, most mycobacterial DNA extraction methods require bead-beating steps or toxic chemicals. Here we present an updated method that yields abundant, high quality genomic DNA from M. tuberculosis and diverse nontuberculous mycobacterial (NTM) species, in addition to complex biological communities from a variety of sources. This method eliminates the time-consuming phenol and chloroform extraction and ethanol precipitation steps, and high quality DNA from up to 96 samples can be extracted in about 2-3 h of hands-on time. This DNA is suitable for long and short read sequencing technologies as well as PCR and qPCR amplification.
Collapse
Affiliation(s)
- L Elaine Epperson
- Center for Genes, Environment, and Health, National Jewish Health, 1400 Jackson Street, Denver, Colorado 80206, USA
| | - Michael Strong
- Center for Genes, Environment, and Health, National Jewish Health, 1400 Jackson Street, Denver, Colorado 80206, USA
| |
Collapse
|
7
|
Duffy AR, O'Connell JR, Pavlovich M, Ryan KA, Lowry CA, Daue M, Raheja UK, Brenner LA, Markon AO, Punzalan CM, Dagdag A, Hill DE, Pollin TI, Seyfang A, Groer MW, Mitchell BD, Postolache TT. Toxoplasma gondii Serointensity and Seropositivity: Heritability and Household-Related Associations in the Old Order Amish. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2019; 16:E3732. [PMID: 31623376 PMCID: PMC6801611 DOI: 10.3390/ijerph16193732] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 09/27/2019] [Accepted: 09/30/2019] [Indexed: 01/29/2023]
Abstract
Toxoplasma gondii (T. gondii) is an intracellular parasite infecting one third of the world's population. Latent T. gondii infection has been associated with mental illness, including schizophrenia and suicidal behavior. T. gondii IgG antibody titers were measured via ELISA. The heritability of T. gondii IgG was estimated using a mixed model that included fixed effects for age and sex and random kinship effect. Of 2017 Old Order Amish participants, 1098 had positive titers (54.4%). The heritability for T. gondii serointensity was estimated to be 0.22 (p = 1.7 × 10-8 and for seropositivity, it was estimated to be 0.28 (p = 1.9 × 10-5). Shared household environmental effects (i.e., household effects) were also determined. Household effects, modeled as a random variable, were assessed as the phenotypic covariance between any two individuals who had the same current address (i.e., contemporaneous household), and nuclear household (i.e., the phenotypic covariance between parents and children only, not other siblings or spouses). Household effects did not account for a significant proportion of variance in either T. gondii serointensity or T. gondii seropositivity. Our results suggest a significant familial aggregation of T. gondii serointensity and seropositivity with significant heritability. The shared household does not contribute significantly to family aggregation with T. gondii, suggesting that there are possible unmeasured non-household shared and non-shared environmental factors that may play a significant role. Furthermore, the small but significant heritability effects justify the exploration of genetic vulnerability to T. gondii exposure, infection, virulence, and neurotropism.
Collapse
Affiliation(s)
- Allyson R Duffy
- Mood and Anxiety Program, University of Maryland School of Medicine, Baltimore, MD 20201, USA.
- College of Nursing, University of South Florida, Tampa, FL 33612, USA.
| | - Jeffrey R O'Connell
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
- Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
| | - Mary Pavlovich
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
- Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
| | - Kathleen A Ryan
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
- Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
| | - Christopher A Lowry
- Veterans Health Administration, Rocky Mountain Mental Illness Research Education and Clinical Center (MIRECC), Rocky Mountain Regional Veterans Affairs Medical Center (RMRVAMC), Aurora, CO 80045, USA.
- Department of Physical Medicine and Rehabilitation, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
- Military and Veteran Microbiome: Consortium for Research and Education (MVM-CoRE), Aurora, CO 80045, USA.
- Department of Integrative Physiology and Center for Neuroscience, University of Colorado Boulder, Boulder, CO 80309, USA.
- Center for Neuroscience, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
| | - Melanie Daue
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
- Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
| | - Uttam K Raheja
- Mood and Anxiety Program, University of Maryland School of Medicine, Baltimore, MD 20201, USA.
| | - Lisa A Brenner
- Veterans Health Administration, Rocky Mountain Mental Illness Research Education and Clinical Center (MIRECC), Rocky Mountain Regional Veterans Affairs Medical Center (RMRVAMC), Aurora, CO 80045, USA.
- Department of Physical Medicine and Rehabilitation, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
- Military and Veteran Microbiome: Consortium for Research and Education (MVM-CoRE), Aurora, CO 80045, USA.
| | - André O Markon
- US Food and Drug Administration, College Park, MD 20740, USA.
| | | | - Aline Dagdag
- Mood and Anxiety Program, University of Maryland School of Medicine, Baltimore, MD 20201, USA.
| | - Dolores E Hill
- US Department of Agriculture, Agricultural Research Service, Beltsville Agricultural Research Center, Animal Parasitic Diseases Laboratory, Beltsville, MD 20705, USA.
| | - Toni I Pollin
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
- Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
| | - Andreas Seyfang
- College of Medicine, University of South Florida, Tampa, FL 33612, USA.
| | - Maureen W Groer
- College of Nursing, University of South Florida, Tampa, FL 33612, USA.
| | - Braxton D Mitchell
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
- Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
- Geriatrics Research Education and Clinical Center (GRECC), Baltimore, MD 21201, USA.
| | - Teodor T Postolache
- Mood and Anxiety Program, University of Maryland School of Medicine, Baltimore, MD 20201, USA.
- Veterans Health Administration, Rocky Mountain Mental Illness Research Education and Clinical Center (MIRECC), Rocky Mountain Regional Veterans Affairs Medical Center (RMRVAMC), Aurora, CO 80045, USA.
- Military and Veteran Microbiome: Consortium for Research and Education (MVM-CoRE), Aurora, CO 80045, USA.
- Mental Illness Research, Education, and Clinical Center (MIRECC), Veterans Integrated Service Network (VISN 5), VA Capitol Health Care Network, Baltimore, MD 21201, USA.
| |
Collapse
|
8
|
Ricotta EE, Olivier KN, Lai YL, Prevots DR, Adjemian J. Hospital-based antibiotic use in patients with Mycobacterium avium complex. ERJ Open Res 2018; 4:00109-2018. [PMID: 30402451 PMCID: PMC6213287 DOI: 10.1183/23120541.00109-2018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 09/02/2018] [Indexed: 11/17/2022] Open
Abstract
Treatment guidelines exist for pulmonary Mycobacterium avium complex (MAC) infection, although studies suggest poor concordance in clinician practice. Using a national database including hospital encounters of laboratory-confirmed MAC patients, we sought to characterise US treatment practices. We assessed patients in the Premier Healthcare Database from 2009 to 2013 with two or more MAC-positive cultures or one MAC-positive culture and the International Classification of Diseases (9th revision) code for pulmonary nontuberculous mycobacteria (PNTM). Treatment was characterised by patient-, provider- and facility-level factors; significant differences were assessed (p<0.05). Multilevel Poisson regression estimated adjusted relative risks (aRR) of receiving guidelines-based or macrolide resistance-promoting regimens. Of 1326 MAC patients, 645 (49%) received treatment: 10% received guidelines-based treatment and 18% resistance-associated therapy. Patients were more likely to receive guidelines-based therapy if they had multiple hospital encounters (aRR 1.5), codes for PNTM (aRR 5.7) or tuberculosis (aRR 4.5) or radiological procedures (aRR 10.9); multiple hospital encounters (aRR 0.8) or a tuberculosis code (aRR 0.1) were less likely to be associated with receiving resistance-promoting regimens. In hospital-based MAC patients, half received antibiotics active against MAC, a low proportion received therapy based on MAC guidelines and many received antibiotics that promote macrolide resistance. Improved implementation of guidelines-based treatment is needed to decrease use of regimens associated with macrolide resistance. Few MAC patients receive recommended therapy and improved treatment is needed to prevent resistancehttp://ow.ly/4F0S30lIihn
Collapse
Affiliation(s)
- Emily E Ricotta
- Epidemiology Unit, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Kenneth N Olivier
- Pulmonary Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Yi Ling Lai
- Epidemiology Unit, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - D Rebecca Prevots
- Epidemiology Unit, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Jennifer Adjemian
- Epidemiology Unit, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.,United States Public Health Service, Commissioned Corps, Rockville, MD, USA
| |
Collapse
|
9
|
Profiling non-tuberculous mycobacteria in an Asian setting: characteristics and clinical outcomes of hospitalized patients in Singapore. BMC Pulm Med 2018; 18:85. [PMID: 29788943 PMCID: PMC5964916 DOI: 10.1186/s12890-018-0637-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 04/25/2018] [Indexed: 01/15/2023] Open
Abstract
Background Non-tuberculous mycobacteria (NTM) infection is an increasing problem worldwide. The epidemiology of NTM in most Asian countries is unknown. This study investigated the epidemiology, and clinical profile of inpatients in whom NTM was isolated from various anatomical sites in a Singaporean population attending a major tertiary referral centre. Methods Demographic profile, clinical data, and characteristics of patients hospitalized with NTM isolates at a major tertiary hospital over two-year period were prospectively assessed (2011–2012). Data collected included patient demographics, ethnicity, smoking status, co-morbidities, NTM species, intensive care unit (ICU) treatment, and mortality. Results A total of 485 patients (62.1% male) with 560 hospital admissions were analysed. The median patient age was 70 years. Thirteen different NTM species were isolated from this cohort. Mycobacterium abscessus (M. abscessus) (38.4%) was most frequently isolated followed by Mycobacterium fortuitum (M. fortuitum) (16.6%), Mycobacterium avium complex (MAC) (16.3%), Mycobacterium kansasii (M. kansasii) (15.4%), and Mycobacterium gordonae (M. gordonae) (6.8%). Most (91%) NTM was isolated from the respiratory tract. The three most common non-pulmonary sites were; blood (2.7%), skin wounds and abscesses (2.1%), and gastric aspirates (1.1%). A third (34.4%) of the study population had prior pulmonary tuberculosis (PTB). There was a significant association between isolated NTM species, and patient age (p = 0.0002). Eleven (2.2%) patients received intensive care unit (ICU) treatment during the study period and all cause mortality within 1 year of the study was 16.9% (n = 82). Of these, 72 (87.8%) patients died of pulmonary causes. Conclusions The profile of NTM species in Singapore is unique. M. abscessus is the commonest NTM isolated, with a higher prevalence in males, and in the elderly. High NTM prevalence is associated with high rates of prior PTB in our cohort.
Collapse
|
10
|
Tulu B, Ameni G. Spoligotyping based genetic diversity of Mycobacterium tuberculosis in Ethiopia: a systematic review. BMC Infect Dis 2018; 18:140. [PMID: 29587640 PMCID: PMC5870191 DOI: 10.1186/s12879-018-3046-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 03/16/2018] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Understanding the types of strains and lineages of Mycobacterium tuberculosis (M. tuberculosis) circulating in a country is of paramount importance for tuberculosis (TB) control program of that country. The main aim of this study was to review and compile the results of studies conducted on strains and lineages of M. tuberculosis in Ethiopia. METHODS A systematic search and review of articles published on M. tuberculosis strains and lineages in Ethiopia were made. PubMed and Google Scholar databases were considered for the search while the keywords used were M. tuberculosis, molecular epidemiology, molecular typing spoligotyping and Ethiopia. RESULT Twenty-one studies were considered in this review and a total of 3071 M. tuberculosis isolates and 3067 strains were included. These studies used spoligotyping and identified five lineages including Indo-Ocean, East Asian/Beijing, East African-Indian, Euro-American and Ethiopian in a proportion of 7.1%, 0.2%, 23.0%, 64.8%, and 4.1%, respectively. Thus, Euro-American was the most frequently (64.8%) occurring Lineage while East Asian was the least (0.2%) frequently occurring Lineage in the country. Surprisingly, the Ethiopian Lineage seemed to be localized to northeastern Ethiopia. In addition, the top five clades identified by this review were T, CAS, H, Manu and Ethiopian comprising of 48.0%, 23.0%, 11.0%, 6.0% and 4.1% of the strains, respectively. Furthermore, predominant shared types (spoligotype patterns) identified were SIT149, SIT53, SIT25, SIT37, and SIT21, each consisting of 420, 343, 266, 162 and 102 isolates, respectively, while, on the other hand, 15% of the strains were orphan. CONCLUSION According to the summary of the results of this review, diversified strains and lineages of M. tuberculosis were found in Ethiopia, and the frequencies of occurrence of these strains and lineages were variable in different regions of the country. This systematic review is registered in the PRISMA with the registration number of 42017059263.
Collapse
Affiliation(s)
- Begna Tulu
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, P. O. Box 1176, Addis Ababa, Ethiopia. .,Department of Microbiology, Immunology and Parasitology, Bahir Dar University, P. O. Box 79, Bahir Dar, Ethiopia.
| | - Gobena Ameni
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, P. O. Box 1176, Addis Ababa, Ethiopia
| |
Collapse
|
11
|
Chen F, Szymanski EP, Olivier KN, Liu X, Tettelin H, Holland SM, Duggal P. Whole-Exome Sequencing Identifies the 6q12-q16 Linkage Region and a Candidate Gene, TTK, for Pulmonary Nontuberculous Mycobacterial Disease. Am J Respir Crit Care Med 2017; 196:1599-1604. [PMID: 28777004 DOI: 10.1164/rccm.201612-2479oc] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
RATIONALE Pulmonary nontuberculous mycobacterial disease (PNTM) often affects white postmenopausal women, with a tall and lean body habitus and higher rates of scoliosis, pectus excavatum, mitral valve prolapse, and mutations in the CFTR gene. These clinical features and the familial clustering of the disease suggest an underlying genetic mechanism. OBJECTIVES To map the genes associated with PNTM, whole-exome sequencing was conducted in 12 PNTM families and 57 sporadic cases recruited at the National Institutes of Health Clinical Center during 2001-2013. METHODS We performed a variant-level and a gene-level parametric linkage analysis on nine PNTM families (16 affected and 20 unaffected) as well as a gene-level association analysis on nine PNTM families and 55 sporadic cases. MEASUREMENTS AND MAIN RESULTS The genome-wide variant-level linkage analysis using 4,328 independent common variants identified a 20-cM region on chromosome 6q12-6q16 (heterogeneity logarithm of odds score = 3.9), under a recessive disease model with 100% penetrance and a risk allele frequency of 5%. All genes on chromosome 6 were then tested in the gene-level linkage analysis, using the collapsed haplotype pattern method. The TTK protein kinase gene (TTK) on chromosome 6q14.1 was the most significant (heterogeneity logarithm of odds score = 3.38). In addition, the genes MAP2K4, RCOR3, KRT83, IFNLR1, and SLC29A1 were associated with PNTM in our gene-level association analysis. CONCLUSIONS The TTK gene encodes a protein kinase that is essential for mitotic checkpoints and the DNA damage response. TTK and other genetic loci identified in our study may contribute to the increased susceptibility to NTM infection and its progression to pulmonary disease.
Collapse
Affiliation(s)
- Fei Chen
- 1 Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Eva P Szymanski
- 2 Laboratory of Clinical Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Bethesda, Maryland
| | - Kenneth N Olivier
- 3 Cardiovascular and Pulmonary Branch, National Heart, Lung, and Blood Institute, NIH, Bethesda, Maryland; and
| | - Xinyue Liu
- 4 Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland
| | - Hervé Tettelin
- 4 Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland
| | - Steven M Holland
- 2 Laboratory of Clinical Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Bethesda, Maryland
| | - Priya Duggal
- 1 Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| |
Collapse
|
12
|
In silico search for modifier genes associated with pancreatic and liver disease in Cystic Fibrosis. PLoS One 2017; 12:e0173822. [PMID: 28339466 PMCID: PMC5365109 DOI: 10.1371/journal.pone.0173822] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 02/27/2017] [Indexed: 12/15/2022] Open
Abstract
Cystic Fibrosis is the most common lethal autosomal recessive disorder in the white population, affecting among other organs, the lung, the pancreas and the liver. Whereas Cystic Fibrosis is a monogenic disease, many studies reveal a very complex relationship between genotype and clinical phenotype. Indeed, the broad phenotypic spectrum observed in Cystic Fibrosis is far from being explained by obvious genotype-phenotype correlations and it is admitted that Cystic Fibrosis disease is the result of multiple factors, including effects of the environment as well as modifier genes. Our objective was to highlight new modifier genes with potential implications in the lung, pancreatic and liver outcomes of the disease. For this purpose we performed a system biology approach which combined, database mining, literature mining, gene expression study and network analysis as well as pathway enrichment analysis and protein-protein interactions. We found that IFI16, CCNE2 and IGFBP2 are potential modifiers in the altered lung function in Cystic Fibrosis. We also found that EPHX1, HLA-DQA1, HLA-DQB1, DSP and SLC33A1, GPNMB, NCF2, RASGRP1, LGALS3 and PTPN13, are potential modifiers in pancreas and liver, respectively. Associated pathways indicate that immune system is likely involved and that Ubiquitin C is probably a central node, linking Cystic Fibrosis to liver and pancreatic disease. We highlight here new modifier genes with potential implications in Cystic Fibrosis. Nevertheless, our in silico analysis requires functional analysis to give our results a physiological relevance.
Collapse
|