1
|
Nduba V, Njagi LN, Murithi W, Mwongera Z, Byers J, Logioia G, Peterson G, Segnitz RM, Fennelly K, Hawn TR, Horne DJ. Mycobacterium tuberculosis cough aerosol culture status associates with host characteristics and inflammatory profiles. Nat Commun 2024; 15:7604. [PMID: 39217183 PMCID: PMC11365933 DOI: 10.1038/s41467-024-52122-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 08/27/2024] [Indexed: 09/04/2024] Open
Abstract
Interrupting transmission events is critical to tuberculosis control. Cough-generated aerosol cultures predict tuberculosis transmission better than microbiological or clinical markers. We hypothesize that highly infectious individuals with pulmonary tuberculosis (positive for cough aerosol cultures) have elevated inflammatory markers and unique transcriptional profiles compared to less infectious individuals. We performed a prospective, longitudinal study using cough aerosol sampling system. We enrolled 142 participants with treatment-naïve pulmonary tuberculosis in Kenya and assessed the association of clinical, microbiologic, and immunologic characteristics with Mycobacterium tuberculosis aerosolization and transmission in 129 household members. Contacts of the forty-three aerosol culture-positive participants (30%) are more likely to have a positive interferon-gamma release assay (85% vs 53%, P = 0.006) and higher median IFNγ level (P < 0.001, 4.28 IU/ml (1.77-5.91) vs. 0.71 (0.01-3.56)) compared to aerosol culture-negative individuals. We find that higher bacillary burden, younger age, larger mean upper arm circumference, and host inflammatory profiles, including elevated serum C-reactive protein and lower plasma TNF levels, associate with positive cough aerosol cultures. Notably, we find pre-treatment whole blood transcriptional profiles associate with aerosol culture status, independent of bacillary load. These findings suggest that tuberculosis infectiousness is associated with epidemiologic characteristics and inflammatory signatures and that these features may identify highly infectious persons.
Collapse
Affiliation(s)
- Videlis Nduba
- Centre for Respiratory Diseases Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Lilian N Njagi
- Centre for Respiratory Diseases Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Wilfred Murithi
- Centre for Respiratory Diseases Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Zipporah Mwongera
- Centre for Respiratory Diseases Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Jodi Byers
- Department of Global Health, University of Washington, Seattle, WA, USA
| | - Gisella Logioia
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Glenna Peterson
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - R Max Segnitz
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Kevin Fennelly
- Division of Intramural Research, National Heart, Lung and Blood Institute (NHLBI), National Institutes of Health, Bethesda, MD, USA
| | - Thomas R Hawn
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - David J Horne
- Department of Global Health, University of Washington, Seattle, WA, USA.
- Department of Medicine, University of Washington, Seattle, WA, USA.
| |
Collapse
|
2
|
Horne D, Nduba V, Njagi L, Murithi W, Mwongera Z, Logioia G, Peterson G, Segnitz RM, Fennelly K, Hawn T. Tuberculosis Infectiousness is Associated with Distinct Clinical and Inflammatory Profiles. RESEARCH SQUARE 2024:rs.3.rs-3722244. [PMID: 38328225 PMCID: PMC10849670 DOI: 10.21203/rs.3.rs-3722244/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Interrupting transmission events to prevent new acquisition of infection and disease is a critical part of tuberculosis (TB) control efforts. However, knowledge gaps in understanding the biology and determinants of TB transmission, including poor estimates of individual infectiousness and the lack of accurate and convenient biomarkers, undermine efforts to develop interventions. Cough-generated aerosol cultures have been found to predict TB transmission better than any microbiological or clinical markers in cohorts from Uganda and Brazil. We hypothesized that highly infectious individuals with pulmonary TB (defined as positive for cough aerosol cultures) have elevated inflammatory markers and unique transcriptional profiles compared to less infectious individuals (negative for cough aerosol cultures). We performed a prospective, longitudinal study using a cough aerosol sampling system as in other studies. We enrolled 142 participants with treatment-naïve pulmonary TB in Nairobi, Kenya, and assessed the association of clinical, microbiologic, and immunologic characteristics with Mtb aerosolization and transmission in 143 household members. Contacts of the forty-three aerosol culture-positive participants (30%) were more likely to have a positive IGRA (85% vs 53%, P = 0.005) and a higher median IGRA IFNγ level (P < 0.001, median 4.25 IU/ml (0.90-5.91) vs. 0.71 (0.01-3.56)) compared to aerosol culture-negative individuals. We found that higher bacillary burden, younger age, and larger mean upper arm circumference were associated with positive aerosol cultures. In addition, novel host inflammatory profiles, including elevated serum C-reactive protein and sputum cytokines, were associated with aerosol culture status. Notably, we found pre-treatment whole blood transcriptional profiles associated with aerosol culture status, independent of bacillary load. Together, these findings suggest that TB infectiousness is associated with epidemiologic characteristics and inflammatory signatures and that these features may be used to identify highly infectious persons. These results provide new public health tools and insights into TB pathogenesis.
Collapse
Affiliation(s)
| | - Videlis Nduba
- Centre for Respiratory Diseases Research, Kenya Medical Research Institute
| | - Lilian Njagi
- Centre for Respiratory Diseases Research, Kenya Medical Research Institute
| | - Wilfred Murithi
- Centre for Respiratory Diseases Research, Kenya Medical Research Institute
| | - Zipporah Mwongera
- Centre for Respiratory Diseases Research, Kenya Medical Research Institute
| | | | | | | | - Kevin Fennelly
- National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH)
| | | |
Collapse
|
3
|
Warren JL, Chitwood MH, Sobkowiak B, Colijn C, Cohen T. Spatial modeling of Mycobacterium tuberculosis transmission with dyadic genetic relatedness data. Biometrics 2023; 79:3650-3663. [PMID: 36745619 PMCID: PMC10404301 DOI: 10.1111/biom.13836] [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: 08/23/2022] [Accepted: 01/31/2023] [Indexed: 02/07/2023]
Abstract
Understanding factors that contribute to the increased likelihood of pathogen transmission between two individuals is important for infection control. However, analyzing measures of pathogen relatedness to estimate these associations is complicated due to correlation arising from the presence of the same individual across multiple dyadic outcomes, potential spatial correlation caused by unmeasured transmission dynamics, and the distinctive distributional characteristics of some of the outcomes. We develop two novel hierarchical Bayesian spatial methods for analyzing dyadic pathogen genetic relatedness data, in the form of patristic distances and transmission probabilities, that simultaneously address each of these complications. Using individual-level spatially correlated random effect parameters, we account for multiple sources of correlation between the outcomes as well as other important features of their distribution. Through simulation, we show the limitations of existing approaches in terms of estimating key associations of interest, and the ability of the new methodology to correct for these issues across datasets with different levels of correlation. All methods are applied to Mycobacterium tuberculosis data from the Republic of Moldova, where we identify previously unknown factors associated with disease transmission and, through analysis of the random effect parameters, key individuals, and areas with increased transmission activity. Model comparisons show the importance of the new methodology in this setting. The methods are implemented in the R package GenePair.
Collapse
Affiliation(s)
| | - Melanie H. Chitwood
- Department of Epidemiology of Microbial Diseases, Yale University, Connecticut, USA
| | | | - Caroline Colijn
- Department of Mathematics, Simon Fraser University, Burnaby, Canada
| | - Ted Cohen
- Department of Epidemiology of Microbial Diseases, Yale University, Connecticut, USA
| |
Collapse
|
4
|
Plumlee CR, Barrett HW, Shao DE, Lien KA, Cross LM, Cohen SB, Edlefsen PT, Urdahl KB. Assessing vaccine-mediated protection in an ultra-low dose Mycobacterium tuberculosis murine model. PLoS Pathog 2023; 19:e1011825. [PMID: 38011264 PMCID: PMC10703413 DOI: 10.1371/journal.ppat.1011825] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 12/07/2023] [Accepted: 11/14/2023] [Indexed: 11/29/2023] Open
Abstract
Despite widespread immunization with Bacille-Calmette-Guérin (BCG), the only currently licensed tuberculosis (TB) vaccine, TB remains a leading cause of mortality globally. There are many TB vaccine candidates in the developmental pipeline, but the lack of a robust animal model to assess vaccine efficacy has hindered our ability to prioritize candidates for human clinical trials. Here we use a murine ultra-low dose (ULD) Mycobacterium tuberculosis (Mtb) challenge model to assess protection conferred by BCG vaccination. We show that BCG confers a reduction in lung bacterial burdens that is more durable than that observed after conventional dose challenge, curbs Mtb dissemination to the contralateral lung, and, in a small percentage of mice, prevents detectable infection. These findings are consistent with the ability of human BCG vaccination to mediate protection, particularly against disseminated disease, in specific human populations and clinical settings. Overall, our findings demonstrate that the ultra-low dose Mtb infection model can measure distinct parameters of immune protection that cannot be assessed in conventional dose murine infection models and could provide an improved platform for TB vaccine testing.
Collapse
Affiliation(s)
- Courtney R. Plumlee
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, United States of America
| | - Holly W. Barrett
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, United States of America
- University of Washington, Dept. of Global Health, Seattle, Washington, United States of America
| | - Danica E. Shao
- Vaccine and Infectious Disease Division, Fred Hutch Cancer Center, Seattle, Washington, United States of America
| | - Katie A. Lien
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, United States of America
| | - Lauren M. Cross
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, United States of America
| | - Sara B. Cohen
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, United States of America
| | - Paul T. Edlefsen
- Vaccine and Infectious Disease Division, Fred Hutch Cancer Center, Seattle, Washington, United States of America
| | - Kevin B. Urdahl
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, United States of America
- University of Washington, Dept. of Immunology, Seattle, Washington, United States of America
- University of Washington, Dept. of Pediatrics, Seattle, Washington, United States of America
| |
Collapse
|
5
|
Anderson TL, Nande A, Merenstein C, Raynor B, Oommen A, Kelly BJ, Levy MZ, Hill AL. Quantifying individual-level heterogeneity in infectiousness and susceptibility through household studies. Epidemics 2023; 44:100710. [PMID: 37556994 PMCID: PMC10594662 DOI: 10.1016/j.epidem.2023.100710] [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: 12/01/2022] [Revised: 03/17/2023] [Accepted: 07/18/2023] [Indexed: 08/11/2023] Open
Abstract
The spread of SARS-CoV-2, like that of many other pathogens, is governed by heterogeneity. "Superspreading," or "over-dispersion," is an important factor in transmission, yet it is hard to quantify. Estimates from contact tracing data are prone to potential biases due to the increased likelihood of detecting large clusters of cases, and may reflect variation in contact behavior more than biological heterogeneity. In contrast, the average number of secondary infections per contact is routinely estimated from household surveys, and these studies can minimize biases by testing all members of a household. However, the models used to analyze household transmission data typically assume that infectiousness and susceptibility are the same for all individuals or vary only with predetermined traits such as age. Here we develop and apply a combined forward simulation and inference method to quantify the degree of inter-individual variation in both infectiousness and susceptibility from observations of the distribution of infections in household surveys. First, analyzing simulated data, we show our method can reliably ascertain the presence, type, and amount of these heterogeneities given data from a sufficiently large sample of households. We then analyze a collection of household studies of COVID-19 from diverse settings around the world, and find strong evidence for large heterogeneity in both the infectiousness and susceptibility of individuals. Our results also provide a framework to improve the design of studies to evaluate household interventions in the presence of realistic heterogeneity between individuals.
Collapse
Affiliation(s)
- Thayer L Anderson
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD 21218, United States of America
| | - Anjalika Nande
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD 21218, United States of America
| | - Carter Merenstein
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States of America
| | - Brinkley Raynor
- Department of Biostatistics, Epidemiology, & Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States of America
| | - Anisha Oommen
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD 21218, United States of America; Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, United States of America
| | - Brendan J Kelly
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States of America; Department of Biostatistics, Epidemiology, & Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States of America; Division of Infectious Diseases, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States of America
| | - Michael Z Levy
- Department of Biostatistics, Epidemiology, & Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States of America
| | - Alison L Hill
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD 21218, United States of America; Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, United States of America.
| |
Collapse
|
6
|
Smith JP, Cohen T, Dowdy D, Shrestha S, Gandhi NR, Hill AN. Quantifying Mycobacterium tuberculosis Transmission Dynamics Across Global Settings: A Systematic Analysis. Am J Epidemiol 2023; 192:133-145. [PMID: 36227246 PMCID: PMC10144641 DOI: 10.1093/aje/kwac181] [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: 03/15/2022] [Revised: 07/23/2022] [Accepted: 10/10/2022] [Indexed: 01/11/2023] Open
Abstract
The degree to which individual heterogeneity in the production of secondary cases ("superspreading") affects tuberculosis (TB) transmission has not been systematically studied. We searched for population-based or surveillance studies in which whole genome sequencing was used to estimate TB transmission and in which the size distributions of putative TB transmission clusters were enumerated. We fitted cluster-size-distribution data to a negative binomial branching process model to jointly infer the transmission parameters $R$ (the reproduction number) and the dispersion parameter, $k$, which quantifies the propensity of superspreading in a population (generally, lower values of $k$ ($<1.0$) suggest increased heterogeneity). Of 4,796 citations identified in our initial search, 9 studies from 8 global settings met the inclusion criteria (n = 5 studies of all TB; n = 4 studies of drug-resistant TB). Estimated $R$ values (range, 0.10-0.73) were below 1.0, consistent with declining epidemics in the included settings; estimated $k$ values were well below 1.0 (range, 0.02-0.48), indicating the presence of substantial individual-level heterogeneity in transmission across all settings. We estimated that a minority of cases (range, 2%-31%) drive the majority (80%) of ongoing TB transmission at the population level. Identifying sources of heterogeneity and accounting for them in TB control may have a considerable impact on mitigating TB transmission.
Collapse
Affiliation(s)
- Jonathan P Smith
- Correspondence to Dr. Jonathan Smith, Yale School of Public Health, Yale University, 60 College Street, New Haven, CT 06510 (e-mail: )
| | | | | | | | | | | |
Collapse
|
7
|
Árnason E, Koskela J, Halldórsdóttir K, Eldon B. Sweepstakes reproductive success via pervasive and recurrent selective sweeps. eLife 2023; 12:80781. [PMID: 36806325 PMCID: PMC9940914 DOI: 10.7554/elife.80781] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 12/28/2022] [Indexed: 02/22/2023] Open
Abstract
Highly fecund natural populations characterized by high early mortality abound, yet our knowledge about their recruitment dynamics is somewhat rudimentary. This knowledge gap has implications for our understanding of genetic variation, population connectivity, local adaptation, and the resilience of highly fecund populations. The concept of sweepstakes reproductive success, which posits a considerable variance and skew in individual reproductive output, is key to understanding the distribution of individual reproductive success. However, it still needs to be determined whether highly fecund organisms reproduce through sweepstakes and, if they do, the relative roles of neutral and selective sweepstakes. Here, we use coalescent-based statistical analysis of population genomic data to show that selective sweepstakes likely explain recruitment dynamics in the highly fecund Atlantic cod. We show that the Kingman coalescent (modelling no sweepstakes) and the Xi-Beta coalescent (modelling random sweepstakes), including complex demography and background selection, do not provide an adequate fit for the data. The Durrett-Schweinsberg coalescent, in which selective sweepstakes result from recurrent and pervasive selective sweeps of new mutations, offers greater explanatory power. Our results show that models of sweepstakes reproduction and multiple-merger coalescents are relevant and necessary for understanding genetic diversity in highly fecund natural populations. These findings have fundamental implications for understanding the recruitment variation of fish stocks and general evolutionary genomics of high-fecundity organisms.
Collapse
Affiliation(s)
- Einar Árnason
- Institute of Life- and environmental Sciences, University of IcelandReykjavikIceland,Department of Organismal and Evolutionary Biology, Harvard UniversityCambridgeUnited States
| | - Jere Koskela
- Department of Statistics, University of WarwickCoventryUnited Kingdom
| | - Katrín Halldórsdóttir
- Institute of Life- and environmental Sciences, University of IcelandReykjavikIceland
| | - Bjarki Eldon
- Leibniz Institute for Evolution and Biodiversity Science, Museum für NaturkundeBerlinGermany
| |
Collapse
|
8
|
Anderson TL, Nande A, Merenstein C, Raynor B, Oommen A, Kelly BJ, Levy MZ, Hill AL. Quantifying individual-level heterogeneity in infectiousness and susceptibility through household studies. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2022:2022.12.02.22281853. [PMID: 36523404 PMCID: PMC9753792 DOI: 10.1101/2022.12.02.22281853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
The spread of SARS-CoV-2, like that of many other pathogens, is governed by heterogeneity. "Superspreading," or "over-dispersion," is an important factor in transmission, yet it is hard to quantify. Estimates from contact tracing data are prone to potential biases due to the increased likelihood of detecting large clusters of cases, and may reflect variation in contact behavior more than biological heterogeneity. In contrast, the average number of secondary infections per contact is routinely estimated from household surveys, and these studies can minimize biases by testing all members of a household. However, the models used to analyze household transmission data typically assume that infectiousness and susceptibility are the same for all individuals or vary only with predetermined traits such as age. Here we develop and apply a combined forward simulation and inference method to quantify the degree of inter-individual variation in both infectiousness and susceptibility from observations of the distribution of infections in household surveys. First, analyzing simulated data, we show our method can reliably ascertain the presence, type, and amount of these heterogeneities with data from a sufficiently large sample of households. We then analyze a collection of household studies of COVID-19 from diverse settings around the world, and find strong evidence for large heterogeneity in both the infectiousness and susceptibility of individuals. Our results also provide a framework to improve the design of studies to evaluate household interventions in the presence of realistic heterogeneity between individuals.
Collapse
Affiliation(s)
- Thayer L Anderson
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD 21218
| | - Anjalika Nande
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD 21218
| | - Carter Merenstein
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Brinkley Raynor
- Department of Biostatistics, Epidemiology, & Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Anisha Oommen
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD 21218
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218
| | - Brendan J Kelly
- Division of Infectious Diseases, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Michael Z Levy
- Department of Biostatistics, Epidemiology, & Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Alison L Hill
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD 21218
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218
| |
Collapse
|
9
|
Shrestha S, Winglee K, Hill AN, Shaw T, Smith JP, Kammerer JS, Silk BJ, Marks SM, Dowdy D. Model-based Analysis of Tuberculosis Genotype Clusters in the United States Reveals High Degree of Heterogeneity in Transmission and State-level Differences Across California, Florida, New York, and Texas. Clin Infect Dis 2022; 75:1433-1441. [PMID: 35143641 PMCID: PMC9412192 DOI: 10.1093/cid/ciac121] [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: 10/01/2021] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Reductions in tuberculosis (TB) transmission have been instrumental in lowering TB incidence in the United States. Sustaining and augmenting these reductions are key public health priorities. METHODS We fit mechanistic transmission models to distributions of genotype clusters of TB cases reported to the Centers for Disease Control and Prevention during 2012-2016 in the United States and separately in California, Florida, New York, and Texas. We estimated the mean number of secondary cases generated per infectious case (R0) and individual-level heterogeneity in R0 at state and national levels and assessed how different definitions of clustering affected these estimates. RESULTS In clusters of genotypically linked TB cases that occurred within a state over a 5-year period (reference scenario), the estimated R0 was 0.29 (95% confidence interval [CI], .28-.31) in the United States. Transmission was highly heterogeneous; 0.24% of simulated cases with individual R0 >10 generated 19% of all recent secondary transmissions. R0 estimate was 0.16 (95% CI, .15-.17) when a cluster was defined as cases occurring within the same county over a 3-year period. Transmission varied across states: estimated R0s were 0.34 (95% CI, .3-.4) in California, 0.28 (95% CI, .24-.36) in Florida, 0.19 (95% CI, .15-.27) in New York, and 0.38 (95% CI, .33-.46) in Texas. CONCLUSIONS TB transmission in the United States is characterized by pronounced heterogeneity at the individual and state levels. Improving detection of transmission clusters through incorporation of whole-genome sequencing and identifying the drivers of this heterogeneity will be essential to reducing TB transmission.
Collapse
Affiliation(s)
- Sourya Shrestha
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Kathryn Winglee
- Division of Tuberculosis Elimination, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Andrew N Hill
- Division of Tuberculosis Elimination, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Tambi Shaw
- California Department of Public Health, Richmond, California, USA
| | - Jonathan P Smith
- Department of Policy and Administration, Yale University, New Haven, Connecticut, USA
| | - J Steve Kammerer
- Division of Tuberculosis Elimination, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Benjamin J Silk
- Division of Tuberculosis Elimination, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Suzanne M Marks
- Division of Tuberculosis Elimination, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - David Dowdy
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| |
Collapse
|
10
|
Smith JP, Oeltmann JE, Hill AN, Tobias JL, Boyd R, Click ES, Finlay A, Mondongo C, Zetola NM, Moonan PK. Characterizing tuberculosis transmission dynamics in high-burden urban and rural settings. Sci Rep 2022; 12:6780. [PMID: 35474076 PMCID: PMC9042872 DOI: 10.1038/s41598-022-10488-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 04/06/2022] [Indexed: 12/23/2022] Open
Abstract
Mycobacterium tuberculosis transmission dynamics in high-burden settings are poorly understood. Growing evidence suggests transmission may be characterized by extensive individual heterogeneity in secondary cases (i.e., superspreading), yet the degree and influence of such heterogeneity is largely unknown and unmeasured in high burden-settings. We conducted a prospective, population-based molecular epidemiology study of TB transmission in both an urban and rural setting of Botswana, one of the highest TB burden countries in the world. We used these empirical data to fit two mathematical models (urban and rural) that jointly quantified both the effective reproductive number, [Formula: see text], and the propensity for superspreading in each population. We found both urban and rural populations were characterized by a high degree of individual heterogeneity, however such heterogeneity disproportionately impacted the rural population: 99% of secondary transmission was attributed to only 19% of infectious cases in the rural population compared to 60% in the urban population and the median number of incident cases until the first outbreak of 30 cases was only 32 for the rural model compared to 791 in the urban model. These findings suggest individual heterogeneity plays a critical role shaping local TB epidemiology within subpopulations.
Collapse
Affiliation(s)
- Jonathan P Smith
- Department of Health Policy and Management, Yale School of Public Health, 60 College Street, New Haven, CT, 06510, USA.
- Peraton, 2800 Century Pkwy NE, Atlanta, GA, USA.
| | - John E Oeltmann
- Division of Global HIV and Tuberculosis, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Andrew N Hill
- Division of Tuberculosis Elimination, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | - Rosanna Boyd
- Division of Tuberculosis Elimination, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Eleanor S Click
- Division of Global HIV and Tuberculosis, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Alyssa Finlay
- Division of Global HIV and Tuberculosis, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Chawangwa Mondongo
- Botswana-UPenn Partnership, University of Pennsylvania, Philadelphia, USA
| | - Nicola M Zetola
- Botswana-UPenn Partnership, University of Pennsylvania, Philadelphia, USA
| | - Patrick K Moonan
- Division of Global HIV and Tuberculosis, Centers for Disease Control and Prevention, Atlanta, GA, USA
| |
Collapse
|
11
|
Smith JP, Gandhi NR, Silk BJ, Cohen T, Lopman B, Raz K, Winglee K, Kammerer S, Benkeser D, Kramer MR, Hill AN. A Cluster-based Method to Quantify Individual Heterogeneity in Tuberculosis Transmission. Epidemiology 2022; 33:217-227. [PMID: 34907974 PMCID: PMC8886690 DOI: 10.1097/ede.0000000000001452] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND Recent evidence suggests transmission of Mycobacterium tuberculosis (Mtb) may be characterized by extreme individual heterogeneity in secondary cases (i.e., few cases account for the majority of transmission). Such heterogeneity implies outbreaks are rarer but more extensive and has profound implications in infectious disease control. However, discrete person-to-person transmission events in tuberculosis (TB) are often unobserved, precluding our ability to directly quantify individual heterogeneity in TB epidemiology. METHODS We used a modified negative binomial branching process model to quantify the extent of individual heterogeneity using only observed transmission cluster size distribution data (i.e., the simple sum of all cases in a transmission chain) without knowledge of individual-level transmission events. The negative binomial parameter k quantifies the extent of individual heterogeneity (generally, indicates extensive heterogeneity, and as transmission becomes more homogenous). We validated the robustness of the inference procedure considering common limitations affecting cluster size data. Finally, we demonstrate the epidemiologic utility of this method by applying it to aggregate US molecular surveillance data from the US Centers for Disease Control and Prevention. RESULTS The cluster-based method reliably inferred k using TB transmission cluster data despite a high degree of bias introduced into the model. We found that the TB transmission in the United States was characterized by a high propensity for extensive outbreaks (; 95% confidence interval = 0.09, 0.10). CONCLUSIONS The proposed method can accurately quantify critical parameters that govern TB transmission using simple, more easily obtainable cluster data to improve our understanding of TB epidemiology.
Collapse
Affiliation(s)
- Jonathan P. Smith
- Emory University Rollins School of Public Health, Atlanta, GA
- Yale University School of Public Health, New Haven, CT
| | - Neel R. Gandhi
- Emory University Rollins School of Public Health, Atlanta, GA
| | - Benjamin J. Silk
- United States Centers for Disease Control and Prevention, Atlanta, GA
| | - Ted Cohen
- Yale University School of Public Health, New Haven, CT
| | - Benjamin Lopman
- Emory University Rollins School of Public Health, Atlanta, GA
| | - Kala Raz
- United States Centers for Disease Control and Prevention, Atlanta, GA
| | - Kathryn Winglee
- United States Centers for Disease Control and Prevention, Atlanta, GA
| | - Steve Kammerer
- United States Centers for Disease Control and Prevention, Atlanta, GA
| | - David Benkeser
- Emory University Rollins School of Public Health, Atlanta, GA
| | | | - Andrew N. Hill
- United States Centers for Disease Control and Prevention, Atlanta, GA
| |
Collapse
|
12
|
Early alveolar macrophage response and IL-1R-dependent T cell priming determine transmissibility of Mycobacterium tuberculosis strains. Nat Commun 2022; 13:884. [PMID: 35173157 PMCID: PMC8850437 DOI: 10.1038/s41467-022-28506-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 01/28/2022] [Indexed: 12/15/2022] Open
Abstract
Mechanisms underlying variability in transmission of Mycobacterium tuberculosis strains remain undefined. By characterizing high and low transmission strains of M.tuberculosis in mice, we show here that high transmission M.tuberculosis strain induce rapid IL-1R-dependent alveolar macrophage migration from the alveolar space into the interstitium and that this action is key to subsequent temporal events of early dissemination of bacteria to the lymph nodes, Th1 priming, granulomatous response and bacterial control. In contrast, IL-1R-dependent alveolar macrophage migration and early dissemination of bacteria to lymph nodes is significantly impeded in infection with low transmission M.tuberculosis strain; these events promote the development of Th17 immunity, fostering neutrophilic inflammation and increased bacterial replication. Our results suggest that by inducing granulomas with the potential to develop into cavitary lesions that aids bacterial escape into the airways, high transmission M.tuberculosis strain is poised for greater transmissibility. These findings implicate bacterial heterogeneity as an important modifier of TB disease manifestations and transmission.
Collapse
|
13
|
Menardo F, Gagneux S, Freund F. Multiple Merger Genealogies in Outbreaks of Mycobacterium tuberculosis. Mol Biol Evol 2021; 38:290-306. [PMID: 32667991 PMCID: PMC8480183 DOI: 10.1093/molbev/msaa179] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The Kingman coalescent and its developments are often considered among the most important advances in population genetics of the last decades. Demographic inference based on coalescent theory has been used to reconstruct the population dynamics and evolutionary history of several species, including Mycobacterium tuberculosis (MTB), an important human pathogen causing tuberculosis. One key assumption of the Kingman coalescent is that the number of descendants of different individuals does not vary strongly, and violating this assumption could lead to severe biases caused by model misspecification. Individual lineages of MTB are expected to vary strongly in reproductive success because 1) MTB is potentially under constant selection due to the pressure of the host immune system and of antibiotic treatment, 2) MTB undergoes repeated population bottlenecks when it transmits from one host to the next, and 3) some hosts show much higher transmission rates compared with the average (superspreaders). Here, we used an approximate Bayesian computation approach to test whether multiple-merger coalescents (MMC), a class of models that allow for large variation in reproductive success among lineages, are more appropriate models to study MTB populations. We considered 11 publicly available whole-genome sequence data sets sampled from local MTB populations and outbreaks and found that MMC had a better fit compared with the Kingman coalescent for 10 of the 11 data sets. These results indicate that the null model for analyzing MTB outbreaks should be reassessed and that past findings based on the Kingman coalescent need to be revisited.
Collapse
Affiliation(s)
- Fabrizio Menardo
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Sébastien Gagneux
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Fabian Freund
- Department of Plant Biodiversity and Breeding Informatics, Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, Stuttgart, Germany
| |
Collapse
|
14
|
Plumlee CR, Duffy FJ, Gern BH, Delahaye JL, Cohen SB, Stoltzfus CR, Rustad TR, Hansen SG, Axthelm MK, Picker LJ, Aitchison JD, Sherman DR, Ganusov VV, Gerner MY, Zak DE, Urdahl KB. Ultra-low Dose Aerosol Infection of Mice with Mycobacterium tuberculosis More Closely Models Human Tuberculosis. Cell Host Microbe 2021; 29:68-82.e5. [PMID: 33142108 PMCID: PMC7854984 DOI: 10.1016/j.chom.2020.10.003] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 07/21/2020] [Accepted: 09/25/2020] [Indexed: 02/02/2023]
Abstract
Tuberculosis (TB) is a heterogeneous disease manifesting in a subset of individuals infected with aerosolized Mycobacterium tuberculosis (Mtb). Unlike human TB, murine infection results in uniformly high lung bacterial burdens and poorly organized granulomas. To develop a TB model that more closely resembles human disease, we infected mice with an ultra-low dose (ULD) of between 1-3 founding bacteria, reflecting a physiologic inoculum. ULD-infected mice exhibited highly heterogeneous bacterial burdens, well-circumscribed granulomas that shared features with human granulomas, and prolonged Mtb containment with unilateral pulmonary infection in some mice. We identified blood RNA signatures in mice infected with an ULD or a conventional Mtb dose (50-100 CFU) that correlated with lung bacterial burdens and predicted Mtb infection outcomes across species, including risk of progression to active TB in humans. Overall, these findings highlight the potential of the murine TB model and show that ULD infection recapitulates key features of human TB.
Collapse
Affiliation(s)
- Courtney R Plumlee
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA
| | - Fergal J Duffy
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA
| | - Benjamin H Gern
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA; Department of Pediatrics, University of Washington, Seattle, WA 98109, USA
| | - Jared L Delahaye
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA; Department of Immunology, University of Washington, Seattle, WA 98109, USA
| | - Sara B Cohen
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA
| | - Caleb R Stoltzfus
- Department of Immunology, University of Washington, Seattle, WA 98109, USA
| | - Tige R Rustad
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA
| | - Scott G Hansen
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Michael K Axthelm
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Louis J Picker
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - John D Aitchison
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA
| | - David R Sherman
- Department of Microbiology, University of Washington, Seattle, WA 98109, USA
| | - Vitaly V Ganusov
- Department of Microbiology, University of Tennessee, Knoxville, TN 37996, USA
| | - Michael Y Gerner
- Department of Immunology, University of Washington, Seattle, WA 98109, USA
| | - Daniel E Zak
- Center for Infectious Disease Research, Seattle, WA 98109, USA
| | - Kevin B Urdahl
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA; Department of Pediatrics, University of Washington, Seattle, WA 98109, USA; Department of Immunology, University of Washington, Seattle, WA 98109, USA.
| |
Collapse
|
15
|
Genotyping indicates marked heterogeneity of tuberculosis transmission in the United States, 2009–2018. Epidemiol Infect 2021. [PMCID: PMC8506451 DOI: 10.1017/s0950268821002041] [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: 11/07/2022] Open
Abstract
Heterogeneity in the number of secondary tuberculosis (TB) cases per source case, the effective reproductive number, R, is important in modelling prevention strategies' impact on incidence. We estimated mean R (Rm) and calculate the dispersion parameter of this distribution, k, using surveillance and genotyping data for U.S. cases during 2009–2018. We modelled transmission assuming cases in a cluster have matching genotypes and share characteristics related to geography, temporal proximity (i.e. serial interval) and time since U.S. arrival among non-U.S.-born persons. Complete data were available for 55 330/85 958 cases. Varying the serial interval and geographic proximity used to derive clusters, we consistently estimated Rm<1.0 and k < 0.08; the low value of k indicates a small number of source cases produce a disproportionate number of secondary cases. U.S. TB reproductive number has a highly skewed distribution, indicating a minority of source cases disproportionately contribute to transmission.
Collapse
|
16
|
Theron G, Limberis J, Venter R, Smith L, Pietersen E, Esmail A, Calligaro G, Te Riele J, de Kock M, van Helden P, Gumbo T, Clark TG, Fennelly K, Warren R, Dheda K. Bacterial and host determinants of cough aerosol culture positivity in patients with drug-resistant versus drug-susceptible tuberculosis. Nat Med 2020; 26:1435-1443. [PMID: 32601338 PMCID: PMC8353872 DOI: 10.1038/s41591-020-0940-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 05/13/2020] [Indexed: 12/27/2022]
Abstract
A burgeoning epidemic of drug-resistant tuberculosis (TB) threatens to derail global control efforts. Although the mechanisms remain poorly clarified, drug-resistant strains are widely believed to be less infectious than drug-susceptible strains. Consequently, we hypothesized that lower proportions of patients with drug-resistant TB would have culturable Mycobacterium tuberculosis from respirable, cough-generated aerosols compared to patients with drug-susceptible TB, and that multiple factors, including mycobacterial genomic variation, would predict culturable cough aerosol production. We enumerated the colony forming units in aerosols (≤10 µm) from 452 patients with TB (227 with drug resistance), compared clinical characteristics, and performed mycobacterial whole-genome sequencing, dormancy phenotyping and drug-susceptibility analyses on M. tuberculosis from sputum. After considering treatment duration, we found that almost half of the patients with drug-resistant TB were cough aerosol culture-positive. Surprisingly, neither mycobacterial genomic variants, lineage, nor dormancy status predicted cough aerosol culture positivity. However, mycobacterial sputum bacillary load and clinical characteristics, including a lower symptom score and stronger cough, were strongly predictive, thereby supporting targeted transmission-limiting interventions. Effective treatment largely abrogated cough aerosol culture positivity; however, this was not always rapid. These data question current paradigms, inform public health strategies and suggest the need to redirect TB transmission-associated research efforts toward host-pathogen interactions.
Collapse
Affiliation(s)
- Grant Theron
- Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine and UCT Lung Institute & South African MRC/UCT Centre for the Study of Antimicrobial Resistance, University of Cape Town, Cape Town, South Africa
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research and South African Medical Research Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Jason Limberis
- Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine and UCT Lung Institute & South African MRC/UCT Centre for the Study of Antimicrobial Resistance, University of Cape Town, Cape Town, South Africa
| | - Rouxjeane Venter
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research and South African Medical Research Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Liezel Smith
- Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine and UCT Lung Institute & South African MRC/UCT Centre for the Study of Antimicrobial Resistance, University of Cape Town, Cape Town, South Africa
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research and South African Medical Research Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Elize Pietersen
- Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine and UCT Lung Institute & South African MRC/UCT Centre for the Study of Antimicrobial Resistance, University of Cape Town, Cape Town, South Africa
| | - Aliasgar Esmail
- Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine and UCT Lung Institute & South African MRC/UCT Centre for the Study of Antimicrobial Resistance, University of Cape Town, Cape Town, South Africa
| | - Greg Calligaro
- Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine and UCT Lung Institute & South African MRC/UCT Centre for the Study of Antimicrobial Resistance, University of Cape Town, Cape Town, South Africa
| | | | - Marianna de Kock
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research and South African Medical Research Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Paul van Helden
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research and South African Medical Research Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Tawanda Gumbo
- Center for Infectious Diseases Research and Experimental Therapeutics, Baylor University Medical Center, Dallas, TX, USA
| | - Taane G Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
- Faculty of Epidemiology and Public Health, London School of Hygiene & Tropical Medicine, London, UK
| | - Kevin Fennelly
- Pulmonary Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Robin Warren
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research and South African Medical Research Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Keertan Dheda
- Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine and UCT Lung Institute & South African MRC/UCT Centre for the Study of Antimicrobial Resistance, University of Cape Town, Cape Town, South Africa.
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK.
| |
Collapse
|
17
|
Trauer JM, Dodd PJ, Gomes MGM, Gomez GB, Houben RMGJ, McBryde ES, Melsew YA, Menzies NA, Arinaminpathy N, Shrestha S, Dowdy DW. The Importance of Heterogeneity to the Epidemiology of Tuberculosis. Clin Infect Dis 2020; 69:159-166. [PMID: 30383204 PMCID: PMC6579955 DOI: 10.1093/cid/ciy938] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 10/31/2018] [Indexed: 12/23/2022] Open
Abstract
Although less well-recognized than for other infectious diseases, heterogeneity is a defining feature of tuberculosis (TB) epidemiology. To advance toward TB elimination, this heterogeneity must be better understood and addressed. Drivers of heterogeneity in TB epidemiology act at the level of the infectious host, organism, susceptible host, environment, and distal determinants. These effects may be amplified by social mixing patterns, while the variable latent period between infection and disease may mask heterogeneity in transmission. Reliance on notified cases may lead to misidentification of the most affected groups, as case detection is often poorest where prevalence is highest. Assuming that average rates apply across diverse groups and ignoring the effects of cohort selection may result in misunderstanding of the epidemic and the anticipated effects of control measures. Given this substantial heterogeneity, interventions targeting high-risk groups based on location, social determinants, or comorbidities could improve efficiency, but raise ethical and equity considerations.
Collapse
Affiliation(s)
- James M Trauer
- School of Public Health and Preventive Medicine, Monash University, Melbourne, Victoria, Australia
| | - Peter J Dodd
- Health Economic and Decision Science, University of Sheffield, United Kingdom
| | - M Gabriela M Gomes
- Liverpool School of Tropical Medicine, United Kingdom.,CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Portugal
| | - Gabriela B Gomez
- Department of Global Health and Development, London School of Hygiene and Tropical Medicine, United Kingdom
| | - Rein M G J Houben
- Tuberculosis Centre, London School of Hygiene and Tropical Medicine, United Kingdom.,Infectious Disease Epidemiology Department, London School of Hygiene and Tropical Medicine, United Kingdom
| | - Emma S McBryde
- Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, Queensland
| | - Yayehirad A Melsew
- School of Public Health and Preventive Medicine, Monash University, Melbourne, Victoria, Australia
| | - Nicolas A Menzies
- Department of Global Health and Population, Harvard T. H. Chan School of Public Health, Boston, Massachusetts
| | - Nimalan Arinaminpathy
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, United Kingdom
| | - Sourya Shrestha
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - David W Dowdy
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| |
Collapse
|
18
|
Brooks-Pollock E, Danon L, Korthals Altes H, Davidson JA, Pollock AMT, van Soolingen D, Campbell C, Lalor MK. A model of tuberculosis clustering in low incidence countries reveals more transmission in the United Kingdom than the Netherlands between 2010 and 2015. PLoS Comput Biol 2020; 16:e1007687. [PMID: 32218567 PMCID: PMC7141699 DOI: 10.1371/journal.pcbi.1007687] [Citation(s) in RCA: 4] [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: 07/17/2019] [Revised: 04/08/2020] [Accepted: 01/16/2020] [Indexed: 11/18/2022] Open
Abstract
Tuberculosis (TB) remains a public health threat in low TB incidence countries, through a combination of reactivated disease and onward transmission. Using surveillance data from the United Kingdom (UK) and the Netherlands (NL), we demonstrate a simple and predictable relationship between the probability of observing a cluster and its size (the number of cases with a single genotype). We demonstrate that the full range of observed cluster sizes can be described using a modified branching process model with the individual reproduction number following a Poisson lognormal distribution. We estimate that, on average, between 2010 and 2015, a TB case generated 0.41 (95% CrI 0.30,0.60) secondary cases in the UK, and 0.24 (0.14,0.48) secondary cases in the NL. A majority of cases did not generate any secondary cases. Recent transmission accounted for 39% (26%,60%) of UK cases and 23%(13%,37%) of NL cases. We predict that reducing UK transmission rates to those observed in the NL would result in 538(266,818) fewer cases annually in the UK. In conclusion, while TB in low incidence countries is strongly associated with reactivated infections, we demonstrate that recent transmission remains sufficient to warrant policies aimed at limiting local TB spread.
Collapse
Affiliation(s)
- Ellen Brooks-Pollock
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
- Bristol Veterinary School, University of Bristol, Bristol, United Kingdom
- * E-mail:
| | - Leon Danon
- College of Engineering and Mathematical Sciences, University of Exeter, Exeter, United Kingdom
- The Alan Turing Institute, London, United Kingdom
| | - Hester Korthals Altes
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | | | | | - Dick van Soolingen
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
- Departments of Clinical Microbiology and Pulmonary Diseases, Radboud University Nijmegen Medical Center, Nijmegen, The Netherlands
| | - Colin Campbell
- TB Section, Public Health England, London, United Kingdom
| | - Maeve K. Lalor
- TB Section, Public Health England, London, United Kingdom
- Institute for Global Health, University College London, London, United Kingdom
| |
Collapse
|
19
|
Skuce R, Breadon E, Allen A, Milne G, McCormick C, Hughes C, Rutherford D, Smith G, Thompson S, Graham J, Harwood R, Byrne A. Longitudinal dynamics of herd-level Mycobacterium bovis MLVA type surveillance in cattle in Northern Ireland 2003-2016. INFECTION GENETICS AND EVOLUTION 2019; 79:104131. [PMID: 31786341 DOI: 10.1016/j.meegid.2019.104131] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 10/28/2019] [Accepted: 11/27/2019] [Indexed: 02/02/2023]
Abstract
Investigating genetically-structured diversity in pathogen populations over time is important to better understand disease maintenance and spread. Herd-level surveillance of Mycobacterium bovis genotypes (multi-locus VNTR analysis types, MLVA types) from all culture-confirmed bovine tuberculosis (TB) herd cases was undertaken in Northern Ireland (NI), generating an unparalleled, longitudinal, population-level 14-year survey for this pathogen. Across this population, 295 genetically-distinct M. bovis MLVA types were identified in the 19,717 M. bovis isolates surveyed. Of these, the most frequent was MLVA type 002 (23.0%); 151 MLVA types were represented more than once, in groups ranging from 2 to 4438 isolates. Only 23 MLVA types were isolated in all 14 years. Investigating inter-annual frequency of M. bovis MLVA types, examples of statistically-significant expansions (MLVA types 002, 004, 006, 009 and 027), contractions (MLVA types 001, 007 and 011) and maintenance (MLVA types 003 and 005) were disclosed, during a period of fluctuating bovine TB herd-level incidence at the NI scale. The fixed period frequency distribution of MLVA types remained highly right-skewed. Novel VNTR copy number variant MLVA types (N = 242; an average of 17 per annum) were identified throughout the survey. The MLVA type distribution in the landscape was not random; MLVA types showed statistically-significant geographical localization and strong spatial associations with Divisional Veterinary Office (DVO) regions. There was also evidence of differential risk of particular MLVA types across breeds (Holstein/Friesian vs. other), age-class, and sex and some evidence of an association between the number of animals testing positive for bovine TB during the disclosing test and particular MLVA types, although there was substantial variation.
Collapse
Affiliation(s)
- R Skuce
- Veterinary Sciences Division, Agri-food and Biosciences Institute (AFBI), Stoney Road, Stormont, Belfast BT4 3SD, UK; School of Biological Sciences, Queen's University Belfast, Belfast BT7 1NN, UK.
| | - E Breadon
- Veterinary Sciences Division, Agri-food and Biosciences Institute (AFBI), Stoney Road, Stormont, Belfast BT4 3SD, UK
| | - A Allen
- Veterinary Sciences Division, Agri-food and Biosciences Institute (AFBI), Stoney Road, Stormont, Belfast BT4 3SD, UK
| | - G Milne
- Veterinary Sciences Division, Agri-food and Biosciences Institute (AFBI), Stoney Road, Stormont, Belfast BT4 3SD, UK
| | - C McCormick
- Veterinary Sciences Division, Agri-food and Biosciences Institute (AFBI), Stoney Road, Stormont, Belfast BT4 3SD, UK; Veterinary Service and Animal Health Group, Department of Agriculture, Environment and Rural Affairs, Dundonald House, Stormont, Belfast BT4 3SB, UK
| | - C Hughes
- Veterinary Sciences Division, Agri-food and Biosciences Institute (AFBI), Stoney Road, Stormont, Belfast BT4 3SD, UK
| | - D Rutherford
- Veterinary Sciences Division, Agri-food and Biosciences Institute (AFBI), Stoney Road, Stormont, Belfast BT4 3SD, UK; Faculty of Electrical Engineering, Czech Technical University, Prague, Czech Republic (⁎)current address
| | - G Smith
- Veterinary Sciences Division, Agri-food and Biosciences Institute (AFBI), Stoney Road, Stormont, Belfast BT4 3SD, UK
| | - S Thompson
- Veterinary Sciences Division, Agri-food and Biosciences Institute (AFBI), Stoney Road, Stormont, Belfast BT4 3SD, UK
| | - J Graham
- Veterinary Sciences Division, Agri-food and Biosciences Institute (AFBI), Stoney Road, Stormont, Belfast BT4 3SD, UK
| | - R Harwood
- Veterinary Service and Animal Health Group, Department of Agriculture, Environment and Rural Affairs, Dundonald House, Stormont, Belfast BT4 3SB, UK
| | - A Byrne
- Veterinary Sciences Division, Agri-food and Biosciences Institute (AFBI), Stoney Road, Stormont, Belfast BT4 3SD, UK; School of Biological Sciences, Queen's University Belfast, Belfast BT7 1NN, UK; One-Health Unit, Surveillance, Animal By-Products and TSEs (SAT), Division Department of Agriculture, Food and Marine (DAFM), Agriculture House, Dublin 2, Ireland
| |
Collapse
|
20
|
Heterogeneous infectiousness in mathematical models of tuberculosis: A systematic review. Epidemics 2019; 30:100374. [PMID: 31685416 DOI: 10.1016/j.epidem.2019.100374] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 10/09/2019] [Accepted: 10/13/2019] [Indexed: 11/20/2022] Open
Abstract
TB mathematical models employ various assumptions and approaches in dealing with the heterogeneous infectiousness of persons with active TB. We reviewed existing approaches and considered the relationship between them and existing epidemiological evidence. We searched the following electronic bibliographic databases from inception to 9 October 2018: MEDLINE, EMBASE, Biosis, Global Health and Scopus. Two investigators extracted data using a standardised data extraction tool. We included in the review any transmission dynamic model of M. tuberculosis transmission explicitly simulating heterogeneous infectiousness of person with active TB. We extracted information including: study objective, model structure, number of active TB compartments, factors used to stratify the active TB compartment, relative infectiousness of each active TB compartment and any intervention evaluated in the model. Our search returned 1899 unique references, of which the full text of 454 records were assessed for eligibility, and 99 studies met the inclusion criteria. Of these, 89 used compartmental models implemented with ordinary differential equations, while the most common approach to stratification of the active TB compartment was to incorporate two levels of infectiousness. However, various clinical characteristics were used to stratify the active TB compartments, and models differed as to whether they permitted transition between these states. Thirty-four models stratified the infectious compartment according to sputum smear status or pulmonary involvement, while 18 models stratified based on health care-related factors. Variation in infectiousness associated with drug-resistant M. tuberculosis was the rationale for stratifying active TB in 33 models, with these models consistently assuming that drug-resistant active TB cases were less infectious. Given the evidence of extensive heterogeneity in infectiousness of individuals with active TB, an argument exists for incorporating heterogeneous infectiousness, although this should be considered in light of the objectives of the study and the research question. PROSPERO Registration: CRD42019111936.
Collapse
|
21
|
Karmakar M, Trauer JM, Ascher DB, Denholm JT. Hyper transmission of Beijing lineage Mycobacterium tuberculosis: Systematic review and meta-analysis. J Infect 2019; 79:572-581. [PMID: 31585190 DOI: 10.1016/j.jinf.2019.09.016] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 08/30/2019] [Accepted: 09/27/2019] [Indexed: 12/12/2022]
Abstract
OBJECTIVES The globally distributed "Beijing" lineage of Mycobacterium tuberculosis has been associated with outbreaks worldwide. Laboratory based studies have suggested that Beijing lineage may have increased fitness; however, it has not been established whether these differences are of epidemiological significance with regards to transmission. Therefore, we undertook a systematic review of epidemiological studies of tuberculosis clustering to compare the transmission dynamics of Beijing lineages versus the non-Beijing lineages. METHODS We systematically searched Embase and MEDLINE before 31st December 2018, for studies which provided information on the transmission dynamics of the different M. tuberculosis lineages. We included articles that conducted population-based cross-sectional or longitudinal molecular epidemiological studies reporting information about extent of transmission of different lineages. The protocol for this systematic review was prospectively registered with PROSPERO (CDR42018088579). RESULTS Of 2855 records identified by the search, 46 were included in the review, containing 42,700 patients from 27 countries. Beijing lineage was the most prevalent and highly clustered strain in 72.4% of the studies and had a higher likelihood of transmission than non-Beijing lineages (OR 1·81 [95% 1·28-2·57], I2 = 94·0%, τ2 = 0·59, p < 0·01). CONCLUSIONS Despite considerable heterogeneity across epidemiological contexts, Beijing lineage appears to be more transmissible than other lineages.
Collapse
Affiliation(s)
- Malancha Karmakar
- Victorian Tuberculosis Program, Melbourne Health, 792 Elizabeth Street, Melbourne, Victorian 3000 Australia; Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Melbourne, Victoria 3010, Australia; Department of Microbiology and Immunology, at the Doherty Institute of Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia; Structural Biology and Bioinformatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - James M Trauer
- Victorian Tuberculosis Program, Melbourne Health, 792 Elizabeth Street, Melbourne, Victorian 3000 Australia; School of Public Health and Preventive Medicine, Monash University, Melbourne, Australia
| | - David B Ascher
- Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Melbourne, Victoria 3010, Australia; Structural Biology and Bioinformatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia; Department of Biochemistry, University of Cambridge, CB2 1GA, UK
| | - Justin T Denholm
- Victorian Tuberculosis Program, Melbourne Health, 792 Elizabeth Street, Melbourne, Victorian 3000 Australia; Department of Microbiology and Immunology, at the Doherty Institute of Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia.
| |
Collapse
|
22
|
Mekonnen D, Derbie A, Chanie A, Shumet A, Biadglegne F, Kassahun Y, Bobosha K, Mihret A, Wassie L, Munshea A, Nibret E, Yimer SA, Tønjum T, Aseffa A. Molecular epidemiology of M. tuberculosis in Ethiopia: A systematic review and meta-analysis. Tuberculosis (Edinb) 2019; 118:101858. [PMID: 31430694 PMCID: PMC6817397 DOI: 10.1016/j.tube.2019.101858] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 06/12/2019] [Accepted: 08/05/2019] [Indexed: 10/26/2022]
Abstract
The molecular epidemiology of Mycobacterium tuberculosis (M. tuberculosis, Mtb) is poorly documented in Ethiopia. The data that exists has not yet been collected in an overview metadata form. Thus, this review summarizes available literature on the genomic diversity, geospatial distribution and transmission patterns of Mtb lineages (L) and sublineages in Ethiopia. Spoligotyping and Mycobacterial Interspersed Repetitive Units-Variable Number Tandem Repeats (MIRU-VNTR) based articles were identified from MEDLINE via PubMed and Scopus. The last date of article search was done on 12th February 2019. Articles were selected following the PRISMA flow diagram. The proportion of (sub)lineages was summarized at national level and further disaggregated by region. Clustering and recent transmission index (RTI) were determined using metan command and random effect meta-analysis model. The meta-analysis was computed using Stata 14 (Stata Corp. College Station, TX, USA). Among 4371 clinical isolates, 99.5% were Mtb and 0.5% were M. bovis. Proportionally, L4, L3, L1 and L7 made up 62.3%, 21.7%, 7.9% and 3.4% of the total isolates, respectively. Among sublineages, L4.2. ETH/SIT149, L4.10/SIT53, L3. ETH1/SIT25 and L4.6/SIT37 were the leading clustered isolates accounting for 14.4%, 9.7%, 7.2% and 5.5%, respectively. Based on MIRU-VNTR, the rate of clustering was 41% and the secondary case rate from a single source case was estimated at 29%. Clustering and recent transmission index was higher in eastern and southwestern Ethiopia compared with the northwestern part of the country. High level of genetic diversity with a high rate of clustering was noted which collectively mirrored the phenomena of micro-epidemics and super-spreading. The largest set of clustered strains deserves special attention and further characterization using whole genome sequencing (WGS) to better understand the evolution, genomic diversity and transmission dynamics of Mtb.
Collapse
Affiliation(s)
- Daniel Mekonnen
- Department of Medical Microbiology, College of Medicine and Health Sciences, Bahir Dar University, Bahir Dar, Ethiopia; Biotechnology Research Institute, Bahir Dar University, Bahir Dar, Ethiopia.
| | - Awoke Derbie
- Department of Medical Microbiology, College of Medicine and Health Sciences, Bahir Dar University, Bahir Dar, Ethiopia; The Centre for Innovative Drug Development and Therapeutic Trials for Africa (CDT-Africa), Addis Ababa University, Addis Ababa, Ethiopia.
| | - Asmamaw Chanie
- Institute of Land Administration, Bahir Dar University, Bahir Dar, Ethiopia.
| | - Abebe Shumet
- Felege Hiwot Referral Hospital, Bahir Dar, Ethiopia.
| | - Fantahun Biadglegne
- Department of Medical Microbiology, College of Medicine and Health Sciences, Bahir Dar University, Bahir Dar, Ethiopia.
| | - Yonas Kassahun
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia.
| | - Kidist Bobosha
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia.
| | - Adane Mihret
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia; Department of Medical Microbiology, Immunology and Parasitology, College of Medicine and Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia.
| | - Liya Wassie
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia.
| | - Abaineh Munshea
- Biotechnology Research Institute, Bahir Dar University, Bahir Dar, Ethiopia; Department of Biology, Bahir Dar University, Bahir Dar, Ethiopia.
| | - Endalkachew Nibret
- Biotechnology Research Institute, Bahir Dar University, Bahir Dar, Ethiopia; Department of Biology, Bahir Dar University, Bahir Dar, Ethiopia.
| | - Solomon Abebe Yimer
- Department of Microbiology, University of Oslo, PO Box 4950, Nydalen, NO-0424, Oslo, Norway; Coalition for Epidemic Preparedness Innovations, CEPI, P.O. Box 123, Torshov 0412, Oslo, Norway.
| | - Tone Tønjum
- Department of Microbiology, University of Oslo, PO Box 4950, Nydalen, NO-0424, Oslo, Norway.
| | - Abraham Aseffa
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia.
| |
Collapse
|
23
|
Melsew YA, Gambhir M, Cheng AC, McBryde ES, Denholm JT, Tay EL, Trauer JM. The role of super-spreading events in Mycobacterium tuberculosis transmission: evidence from contact tracing. BMC Infect Dis 2019; 19:244. [PMID: 30866840 PMCID: PMC6417041 DOI: 10.1186/s12879-019-3870-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2017] [Accepted: 03/04/2019] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND In current epidemiology of tuberculosis (TB), heterogeneity in infectiousness among TB patients is a challenge, which is not well studied. We aimed to quantify this heterogeneity and the presence of "super-spreading" events that can assist in designing optimal public health interventions. METHODS TB epidemiologic investigation data notified between 1 January 2005 and 31 December 2015 from Victoria, Australia were used to quantify TB patients' heterogeneity in infectiousness and super-spreading events. We fitted a negative binomial offspring distribution (NBD) for the number of secondary infections and secondary active TB disease each TB patient produced. The dispersion parameter, k, of the NBD measures the level of heterogeneity, where low values of k (e.g. k < 1) indicate over-dispersion. Super-spreading was defined as patients causing as many or more secondary infections as the 99th centile of an equivalent homogeneous distribution. Contact infection was determined based on a tuberculin skin test (TST) result of ≥10 mm. A NBD model was fitted to identify index characteristics that were associated with the number of contacts infected and risk ratios (RRs) were used to quantify the strength of this association. RESULTS There were 4190 (2312 pulmonary and 1878 extrapulmonary) index TB patients and 18,030 contacts. A total of 15,522 contacts were tested with TST, of whom 3213 had a result of ≥10 mm. The dispersion parameter, k for secondary infections was estimated at 0.16 (95%CI 0.14-0.17) and there were 414 (9.9%) super-spreading events. From the 3213 secondary infections, 2415 (75.2%) were due to super-spreading events. There were 226 contacts who developed active TB disease and a higher level of heterogeneity was found for this outcome than for secondary infection, with k estimated at 0.036 (95%CI 0.025-0.046). In regression analyses, we found that infectiousness was greater among index patients found by clinical presentation and those with bacteriological confirmation. CONCLUSION TB transmission is highly over dispersed and super-spreading events are responsible for a substantial majority of secondary infections. Heterogeneity of transmission and super-spreading are critical issues to consider in the design of interventions and models of TB transmission dynamics.
Collapse
Affiliation(s)
- Yayehirad A. Melsew
- Department of Epidemiology and Preventive Medicine, School of Public Health and Preventive Medicine, Monash University, Melbourne, Victoria Australia
- Department of Epidemiology and Biostatistics, Institute of Public Health, University of Gondar, Gondar, Ethiopia
| | - Manoj Gambhir
- Department of Epidemiology and Preventive Medicine, School of Public Health and Preventive Medicine, Monash University, Melbourne, Victoria Australia
| | - Allen C. Cheng
- Department of Epidemiology and Preventive Medicine, School of Public Health and Preventive Medicine, Monash University, Melbourne, Victoria Australia
| | - Emma S. McBryde
- Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, Queensland Australia
- Department of Medicine at Royal Melbourne Hospital, University of Melbourne, Melbourne, Victoria Australia
| | - Justin T. Denholm
- The Victorian Tuberculosis Program at the Peter Doherty Institute, Melbourne, Victoria Australia
- Department of Microbiology and Immunology, University of Melbourne, Melbourne, Victoria Australia
| | - Ee Laine Tay
- Department of Health and Human Services, Health Protection branch, Melbourne, Victoria Australia
| | - James M. Trauer
- Department of Epidemiology and Preventive Medicine, School of Public Health and Preventive Medicine, Monash University, Melbourne, Victoria Australia
- The Victorian Tuberculosis Program at the Peter Doherty Institute, Melbourne, Victoria Australia
| |
Collapse
|
24
|
Vo LNQ, Vu TN, Nguyen HT, Truong TT, Khuu CM, Pham PQ, Nguyen LH, Le GT, Creswell J. Optimizing community screening for tuberculosis: Spatial analysis of localized case finding from door-to-door screening for TB in an urban district of Ho Chi Minh City, Viet Nam. PLoS One 2018; 13:e0209290. [PMID: 30562401 PMCID: PMC6298730 DOI: 10.1371/journal.pone.0209290] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 12/03/2018] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Tuberculosis (TB) is the deadliest infectious disease globally. Current case finding approaches may miss many people with TB or detect them too late. DATA AND METHODS This study was a retrospective, spatial analysis of routine TB surveillance and cadastral data in Go Vap district, Ho Chi Minh City. We geocoded TB notifications from 2011 to 2015 and calculated theoretical yields of simulated door-to-door screening in three concentric catchment areas (50m, 100m, 200m) and three notification window scenarios (one, two and four quarters) for each index case. We calculated average yields, compared them to published reference values and fit a GEE (Generalized Estimating Equation) linear regression model onto the data. RESULTS The sample included 3,046 TB patients. Adjusted theoretical yields in 50m, 100m and 200m catchment areas were 0.32% (95%CI: 0.27,0.37), 0.21% (95%CI: 0.14,0.29) and 0.17% (95%CI: 0.09,0.25), respectively, in the baseline notification window scenario. Theoretical yields in the 50m-catchment area for all notification window scenarios were significantly higher than a reference yield from literature. Yield was positively associated with treatment failure index cases (beta = 0.12, p = 0.001) and short-term inter-province migrants (beta = 0.06, p = 0.022), while greater distance to the DTU (beta = -0.02, p<0.001) was associated with lower yield. CONCLUSIONS This study is an example of inter-departmental collaboration and application of repurposed cadastral data to progress towards the end TB objectives. The results from Go Vap showed that the use of spatial analysis may be able to identify areas where targeted active case finding in Vietnam can help improve TB case detection.
Collapse
Affiliation(s)
| | - Thanh Nguyen Vu
- Ho Chi Minh City Public Health Association, Ho Chi Minh City, Viet Nam
| | - Hoa Trung Nguyen
- Go Vap District Preventive Health Center, Ho Chi Minh City, Viet Nam
| | - Tung Thanh Truong
- Ho Chi Minh City Department of Science & Technology, Center for Applied Geographic Information Systems (HCMGIS), Ho Chi Minh City, Viet Nam
| | - Canh Minh Khuu
- Ho Chi Minh City Department of Science & Technology, Center for Applied Geographic Information Systems (HCMGIS), Ho Chi Minh City, Viet Nam
| | - Phuong Quoc Pham
- Ho Chi Minh City Department of Science & Technology, Center for Applied Geographic Information Systems (HCMGIS), Ho Chi Minh City, Viet Nam
| | | | - Giang Truong Le
- Ho Chi Minh City Public Health Association, Ho Chi Minh City, Viet Nam
| | | |
Collapse
|
25
|
Tsairidou S, Allen A, Banos G, Coffey M, Anacleto O, Byrne AW, Skuce RA, Glass EJ, Woolliams JA, Doeschl-Wilson AB. Can We Breed Cattle for Lower Bovine TB Infectivity? Front Vet Sci 2018; 5:310. [PMID: 30581821 PMCID: PMC6292866 DOI: 10.3389/fvets.2018.00310] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 11/22/2018] [Indexed: 11/13/2022] Open
Abstract
Host resistance and infectivity are genetic traits affecting infectious disease transmission. This Perspective discusses the potential exploitation of genetic variation in cattle infectivity, in addition to resistance, to reduce the risk, and prevalence of bovine tuberculosis (bTB). In bTB, variability in M. bovis shedding has been previously reported in cattle and wildlife hosts (badgers and wild boars), but the observed differences were attributed to dose and route of infection, rather than host genetics. This article addresses the extent to which cattle infectivity may play a role in bTB transmission, and discusses the feasibility, and potential benefits from incorporating infectivity into breeding programmes. The underlying hypothesis is that bTB infectivity, like resistance, is partly controlled by genetics. Identifying and reducing the number of cattle with high genetic infectivity, could reduce further a major risk factor for herds exposed to bTB. We outline evidence in support of this hypothesis and describe methodologies for detecting and estimating genetic parameters for infectivity. Using genetic-epidemiological prediction models we discuss the potential benefits of selection for reduced infectivity and increased resistance in terms of practical field measures of epidemic risk and severity. Simulations predict that adding infectivity to the breeding programme could enhance and accelerate the reduction in breakdown risk compared to selection on resistance alone. Therefore, given the recent launch of genetic evaluations for bTB resistance and the UK government's goal to eradicate bTB, it is timely to consider the potential of integrating infectivity into breeding schemes.
Collapse
Affiliation(s)
- Smaragda Tsairidou
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | - Adrian Allen
- Agri-Food and Biosciences Institute, Belfast, United Kingdom
| | - Georgios Banos
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
- Scotland's Rural College, Midlothian, United Kingdom
| | - Mike Coffey
- Scotland's Rural College, Midlothian, United Kingdom
| | - Osvaldo Anacleto
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
- Institute of Mathematical and Computer Sciences, University of São Paulo, São Paulo, Brazil
| | - Andrew W. Byrne
- Agri-Food and Biosciences Institute, Belfast, United Kingdom
| | - Robin A. Skuce
- Agri-Food and Biosciences Institute, Belfast, United Kingdom
| | - Elizabeth J. Glass
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | - John A. Woolliams
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | - Andrea B. Doeschl-Wilson
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| |
Collapse
|
26
|
van der Heijden YF, Abdullah F, Andrade BB, Andrews JR, Christopher DJ, Croda J, Ewing H, Haas DW, Hatherill M, Horsburgh CR, Mave V, Nakaya HI, Rolla V, Srinivasan S, Sugiyono RI, Ugarte-Gil C, Hamilton C. Building capacity for advances in tuberculosis research; proceedings of the third RePORT international meeting. Tuberculosis (Edinb) 2018; 113:153-162. [PMID: 30514497 PMCID: PMC6349374 DOI: 10.1016/j.tube.2018.09.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 09/26/2018] [Accepted: 09/27/2018] [Indexed: 10/28/2022]
Abstract
RePORT International is a global network of research sites in India, Brazil, Indonesia, South Africa, China, and the Philippines dedicated to collaborative tuberculosis research in the context of HIV. A standardized research protocol (the Common Protocol) guides the enrollment of participants with active pulmonary tuberculosis and contacts into observational cohorts. The establishment of harmonized clinical data and bio-repositories will allow cutting-edge, large-scale advances in the understanding of tuberculosis, including identification of novel biomarkers for progression to active tuberculosis and relapse after treatment. The RePORT International infrastructure aims to support research capacity development through enabling globally-diverse collaborations. To that end, representatives from the RePORT International network sites, funding agencies, and other stakeholders gathered together in Brazil in September 2017 to present updates on relevant research findings and discuss ideas for collaboration. Presenters emphasized research involving biomarker identification for incipient tuberculosis, host immunity and pharmacogenomics, co-morbidities such as HIV and type 2 diabetes mellitus, and tuberculosis transmission in vulnerable and high-risk populations. Currently, 962 active TB participants and 670 household contacts have contributed blood, sputum, urine and microbes to in-country biorepositories. Cross-consortium collaborations have begun sharing data and specimens to analyze molecular and cytokine predictive patterns.
Collapse
Affiliation(s)
- Yuri F van der Heijden
- Vanderbilt Tuberculosis Center, Vanderbilt University School of Medicine, Nashville, TN, USA; Division of Infectious Diseases, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA.
| | - Fareed Abdullah
- Office of AIDS and TB Research, South African Medical Research Council, Pretoria, South Africa.
| | - Bruno B Andrade
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, Bahia, 40296-710, Brazil; Multinational Organization Network Sponsoring Translational and Epidemiological Research (MONSTER) Initiative, José Silveira Foundation, Salvador, 45204-040, Brazil; Wellcome Centre for Infectious Disease Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, 7925, South Africa; Division of Infectious Diseases, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA; Universidade Salvador (UNIFACS), Laureate University, Salvador, Bahia, 41720-200, Brazil; Escola Bahiana de Medicina e Saúde Pública, Salvador, Bahia, 40290-000, Brazil.
| | - Jason R Andrews
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
| | | | - Julio Croda
- School of Medicine, Federal University of Mato Grosso do Sul, Campo Grande, Brazil, Oswaldo Cruz Foundation, Campo Grande, Brazil.
| | - Heather Ewing
- Vanderbilt University School of Medicine, Nashville, TN, USA.
| | - David W Haas
- Departments of Medicine, Pharmacology, Pathology, Microbiology & Immunology, Vanderbilt University School of Medicine, Nashville, TN, USA; Department of Internal Medicine, Meharry Medical College, Nashville, TN, USA.
| | - Mark Hatherill
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease & Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, South Africa.
| | - C Robert Horsburgh
- Department of Epidemiology, Boston University School of Public Health, Boston, MA, USA; Section of Infectious Diseases, Department of Medicine, Boston University School of Medicine, Boston, MA, USA.
| | - Vidya Mave
- Byramjee-Jeejeebhoy Government Medical College-Johns Hopkins University Clinical Research Site, Pune, India; Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Helder I Nakaya
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil.
| | - Valeria Rolla
- Clinical Research Laboratory on Mycobacteria, National Institute of Infectious Diseases Evandro Chagas, Fiocruz, Brazil.
| | - Sudha Srinivasan
- Division of AIDS, National Institute of Allergy and Infectious Diseases at the National Institutes of Health, Bethesda, MD, USA.
| | - Retna Indah Sugiyono
- INA-RESPOND, National Institute of Health Research and Development, Ministry of Health, Indonesia.
| | - Cesar Ugarte-Gil
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru; School of Medicine, Universidad Peruana Cayetano Heredia, Lima, Peru; TB Centre, London School of Hygiene and Tropical Medicina, London, UK; Department of International Health, Johns Hopkins Bloomberg School of Public Health, Maryland, USA.
| | | |
Collapse
|
27
|
Yamamoto K, Takeuchi S, Seto J, Shimouchi A, Komukai J, Hase A, Nakamura H, Umeda K, Hirai Y, Matsumoto K, Ogasawara J, Wada T, Yamamoto T. Longitudinal genotyping surveillance of Mycobacterium tuberculosis in an area with high tuberculosis incidence shows high transmission rate of the modern Beijing subfamily in Japan. INFECTION GENETICS AND EVOLUTION 2018; 72:25-30. [PMID: 30261265 DOI: 10.1016/j.meegid.2018.09.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 09/14/2018] [Accepted: 09/16/2018] [Indexed: 11/26/2022]
Abstract
Tuberculosis (TB) is a severe and wide-spread infectious disease worldwide. The modern Beijing subfamily, one lineage of M. tuberculosis, reportedly has high pathogenicity and transmissibility. This study used a molecular epidemiological approach to investigate the transmissibility of the modern Beijing subfamily in the Airin area of Osaka City, Japan. During 2006-2016, we collected 596 M. tuberculosis clinical isolates in the Airin area, Osaka city, Japan. We analyzed the 24-locus variable number of tandem repeats typing optimized for the Beijing family of isolates, M. tuberculosis lineage, and patient epidemiological data. The proportion of the modern Beijing subfamily was significantly higher not only than previously obtained data for the Airin area: it was also higher than the nationwide in Japan. The rate of recent clusters, defined as a variable number of tandem repeats profile identified within two years, of the modern Beijing subfamily was significantly higher than that the rate of recent clusters of the ancient Beijing subfamily. Results suggest that TB control measures formulated with attention to the modern Beijing subfamily might be an important benchmark to understanding recent TB transmission in the area.
Collapse
Affiliation(s)
- Kaori Yamamoto
- Graduate School of Biomedical Sciences, Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan; Division of Microbiology, Osaka Institute of Public Health, 8-34 Tojo-cho, Tennoji-ku, Osaka 543-0026, Japan
| | - Shouhei Takeuchi
- Department of Nutrition Science, Faculty of Nursing and Nutrition, University of Nagasaki, 1-1-1 Manabino, Nagayo, Nishisonogi, Nagasaki 851-2195, Japan
| | - Junji Seto
- Department of Microbiology, Yamagata Prefectural Institute of Public Health, 1-6-6 Toka-machi, Yamagata-shi, Yamagata 990-0031, Japan
| | - Akira Shimouchi
- Nishinari Ward Office, 1-15-17 Taishi-cho, Nishinari-ku, Osaka 557-0002, Japan
| | - Jun Komukai
- Osaka City Public Health Center, 1-27-1000 Asahimachi, Abeno-ku, Osaka 545-0051, Japan
| | - Atsushi Hase
- Division of Microbiology, Osaka Institute of Public Health, 8-34 Tojo-cho, Tennoji-ku, Osaka 543-0026, Japan
| | - Hiromi Nakamura
- Division of Microbiology, Osaka Institute of Public Health, 8-34 Tojo-cho, Tennoji-ku, Osaka 543-0026, Japan
| | - Kaoru Umeda
- Division of Microbiology, Osaka Institute of Public Health, 8-34 Tojo-cho, Tennoji-ku, Osaka 543-0026, Japan
| | - Yuki Hirai
- Division of Microbiology, Osaka Institute of Public Health, 8-34 Tojo-cho, Tennoji-ku, Osaka 543-0026, Japan
| | - Kenji Matsumoto
- Osaka City Public Health Center, 1-27-1000 Asahimachi, Abeno-ku, Osaka 545-0051, Japan
| | - Jun Ogasawara
- Division of Microbiology, Osaka Institute of Public Health, 8-34 Tojo-cho, Tennoji-ku, Osaka 543-0026, Japan
| | - Takayuki Wada
- Department of International Health, Institute of Tropical Medicine, Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan; School of Tropical Medicine and Global Health, Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan.
| | - Taro Yamamoto
- Graduate School of Biomedical Sciences, Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan; Department of International Health, Institute of Tropical Medicine, Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan
| |
Collapse
|
28
|
Quantifying TB transmission: a systematic review of reproduction number and serial interval estimates for tuberculosis. Epidemiol Infect 2018; 146:1478-1494. [PMID: 29970199 PMCID: PMC6092233 DOI: 10.1017/s0950268818001760] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Tuberculosis (TB) is the leading global infectious cause of death. Understanding TB transmission is critical to creating policies and monitoring the disease with the end goal of TB elimination. To our knowledge, there has been no systematic review of key transmission parameters for TB. We carried out a systematic review of the published literature to identify studies estimating either of the two key TB transmission parameters: the serial interval (SI) and the reproductive number. We identified five publications that estimated the SI and 56 publications that estimated the reproductive number. The SI estimates from four studies were: 0.57, 1.42, 1.44 and 1.65 years; the fifth paper presented age-specific estimates ranging from 20 to 30 years (for infants <1 year old) to <5 years (for adults). The reproductive number estimates ranged from 0.24 in the Netherlands (during 1933-2007) to 4.3 in China in 2012. We found a limited number of publications and many high TB burden settings were not represented. Certain features of TB dynamics, such as slow transmission, complicated parameter estimation, require novel methods. Additional efforts to estimate these parameters for TB are needed so that we can monitor and evaluate interventions designed to achieve TB elimination.
Collapse
|
29
|
Proaño A, Bui DP, López JW, Vu NM, Bravard MA, Lee GO, Tracey BH, Xu Z, Comina G, Ticona E, Mollura DJ, Friedland JS, Moore DAJ, Evans CA, Caligiuri P, Gilman RH. Cough Frequency During Treatment Associated With Baseline Cavitary Volume and Proximity to the Airway in Pulmonary TB. Chest 2018; 153:1358-1367. [PMID: 29559307 PMCID: PMC6026292 DOI: 10.1016/j.chest.2018.03.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2017] [Revised: 02/14/2018] [Accepted: 03/01/2018] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Cough frequency, and its duration, is a biomarker that can be used in low-resource settings without the need of laboratory culture and has been associated with transmission and treatment response. Radiologic characteristics associated with increased cough frequency may be important in understanding transmission. The relationship between cough frequency and cavitary lung disease has not been studied. METHODS We analyzed data in 41 adults who were HIV negative and had culture-confirmed, drug-susceptible pulmonary TB throughout treatment. Cough recordings were based on the Cayetano Cough Monitor, and sputum samples were evaluated using microscopic observation drug susceptibility broth culture; among culture-positive samples, bacillary burden was assessed by means of time to positivity. CT scans were analyzed by a US-board-certified radiologist and a computer-automated algorithm. The algorithm evaluated cavity volume and cavitary proximity to the airway. CT scans were obtained within 1 month of treatment initiation. We compared small cavities (≤ 7 mL) and large cavities (> 7 mL) and cavities located closer to (≤ 10 mm) and farther from (> 10 mm) the airway to cough frequency and cough cessation until treatment day 60. RESULTS Cough frequency during treatment was twofold higher in participants with large cavity volumes (rate ratio [RR], 1.98; P = .01) and cavities located closer to the airway (RR, 2.44; P = .001). Comparably, cough ceased three times faster in participants with smaller cavities (adjusted hazard ratio [HR], 2.89; P = .06) and those farther from the airway (adjusted HR, 3.61;, P = .02). Similar results were found for bacillary burden and culture conversion during treatment. CONCLUSIONS Cough frequency during treatment is greater and lasts longer in patients with larger cavities, especially those closer to the airway.
Collapse
Affiliation(s)
- Alvaro Proaño
- Laboratorio de Investigación en Enfermedades Infecciosas, Laboratorio de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru.
| | - David P Bui
- Department of Epidemiology and Biostatistics, Mel and Enid Zuckerman College of Public Health, University of Arizona, Tucson, AZ
| | - José W López
- Laboratorio de Bioinformática y Biología Molecular, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru; Instituto Nacional de Salud del Niño San Borja, Lima, Peru
| | - Nancy M Vu
- Department of Internal Medicine, Cleveland Clinic, Cleveland, OH
| | - Marjory A Bravard
- Innovation for Health and Development, Laboratory of Research and Development, Universidad Peruana Cayetano Heredia, Lima, Peru; Asociación Benéfica PRISMA, Lima, Peru; Department of General Internal Medicine, Massachusetts General Hospital, Boston, MA
| | - Gwenyth O Lee
- Department of Global Community Health and Behavioral Sciences, Tulane University, New Orleans, LA
| | - Brian H Tracey
- Department of Electrical and Computer Engineering, Tufts University, Medford, MA
| | - Ziyue Xu
- Center for Infectious Disease Imaging, Radiology and Imaging Sciences, National Institutes of Health, Bethesda, MD
| | - Germán Comina
- Escuela Profesional de Ingeniería Física, Facultad de Ciencias, Universidad Nacional de Ingeniería, Lima, Peru; Department of Global Community Health and Behavioral Sciences, Tulane University, New Orleans, LA
| | - Eduardo Ticona
- Facultad de Medicina, Universidad Nacional Mayor de San Marcos, Lima, Peru; Servicio de Enfermedades Infecciosas y Tropicales, Hospital Nacional Dos de Mayo, Lima, Peru
| | - Daniel J Mollura
- Center for Infectious Disease Imaging, Radiology and Imaging Sciences, National Institutes of Health, Bethesda, MD
| | - Jon S Friedland
- Section of Infectious Diseases & Immunity and Wellcome Trust Imperial College Centre for Global Health Research, Imperial College London, London, England
| | - David A J Moore
- Laboratorio de Investigación en Enfermedades Infecciosas, Laboratorio de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru; Asociación Benéfica PRISMA, Lima, Peru; TB Centre, London School of Hygiene and Tropical Medicine, London, England
| | - Carlton A Evans
- Innovation for Health and Development, Laboratory of Research and Development, Universidad Peruana Cayetano Heredia, Lima, Peru; Asociación Benéfica PRISMA, Lima, Peru; Section of Infectious Diseases & Immunity and Wellcome Trust Imperial College Centre for Global Health Research, Imperial College London, London, England
| | - Philip Caligiuri
- Department of Radiology & Imaging Sciences, University of Utah School of Medicine, Salt Lake City, UT
| | - Robert H Gilman
- Laboratorio de Investigación en Enfermedades Infecciosas, Laboratorio de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru; Asociación Benéfica PRISMA, Lima, Peru; Program in Global Disease Epidemiology and Control, Department of International Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD
| |
Collapse
|
30
|
Variation in Wolbachia effects on Aedes mosquitoes as a determinant of invasiveness and vectorial capacity. Nat Commun 2018; 9:1483. [PMID: 29662096 PMCID: PMC5902584 DOI: 10.1038/s41467-018-03981-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 03/27/2018] [Indexed: 12/26/2022] Open
Abstract
Wolbachia has been introduced into Aedes aegypti mosquitoes to control the spread of arboviruses, such as dengue, chikungunya and Zika. Studies showed that certain Wolbachia strains (such as wMel) reduce replication of dengue viruses in the laboratory, prompting the release of mosquitoes carrying the bacterium into the field, where vectorial capacity can be realistically assessed in relation to native non-carriers. Here we apply a new analysis to two published datasets, and show that wMel increases the mean and the variance in Ae. aegypti susceptibility to dengue infection when introgressed into Brazil and Vietnam genetic backgrounds. In the absence of other processes, higher mean susceptibility should lead to enhanced viral transmission. The increase in variance, however, widens the basis for selection imposed by unexplored natural forces, retaining the potential for reducing transmission overall. Wolbachia infection in mosquitoes reduces dengue virus spread under specific lab conditions, prompting its use in disease control. Here, King et al. show that Wolbachia increases mean and variance in mosquito susceptibility and explain how this affects Wolbachia invasion and dengue transmission.
Collapse
|
31
|
McCreesh N, White RG. An explanation for the low proportion of tuberculosis that results from transmission between household and known social contacts. Sci Rep 2018; 8:5382. [PMID: 29599463 PMCID: PMC5876383 DOI: 10.1038/s41598-018-23797-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 03/14/2018] [Indexed: 02/05/2023] Open
Abstract
We currently have little idea where Mycobacterium tuberculosis (Mtb) transmission occurs in high incidence settings. Molecular studies suggest that only around 8-19% of transmission to adults occurs within-household, or between known social-contacts. This contrasts with findings from social-contact studies, which show that substantial proportions of contact time occur in households, workplaces and schools. A mathematical model of social-contact behaviour and Mtb transmission was developed, incorporating variation in susceptibility and infectiousness. Three types of contact were simulated: household, repeated (individuals outside household contacted repeatedly with daily-monthly frequency) and non-repeated. The model was parameterised using data from Cape Town, South Africa, on mean and variance in contact numbers and contact durations, by contact type, and fitted to an estimate of overdispersion in numbers of secondary cases ('superspreading') in Cape Town. Household, repeated, and non-repeated contacts contributed 36%, 13%, and 51% of contact time, and 13%, 8%, and 79% of disease, respectively. Results suggest contact saturation, exacerbated by long disease durations and superspreading, cause the high proportion of transmission between non-repeated contacts. Household and social-contact tracing is therefore unlikely to reach most tuberculosis cases. A better understanding of transmission locations, and methods to identify superspreaders, are urgently required to improve tuberculosis prevention strategies.
Collapse
Affiliation(s)
- Nicky McCreesh
- London School of Hygiene and Tropical Medicine, London, UK.
| | | |
Collapse
|
32
|
Trewby H, Wright DM, Skuce RA, McCormick C, Mallon TR, Presho EL, Kao RR, Haydon DT, Biek R. Relative abundance of Mycobacterium bovis molecular types in cattle: a simulation study of potential epidemiological drivers. BMC Vet Res 2017; 13:268. [PMID: 28830547 PMCID: PMC5567634 DOI: 10.1186/s12917-017-1190-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 08/11/2017] [Indexed: 11/10/2022] Open
Abstract
Background The patterns of relative species abundance are commonly studied in ecology and epidemiology to provide insights into underlying dynamical processes. Molecular types (MVLA-types) of Mycobacterium bovis, the causal agent of bovine tuberculosis, are now routinely recorded in culture-confirmed bovine tuberculosis cases in Northern Ireland. In this study, we use ecological approaches and simulation modelling to investigate the distribution of relative abundances of MVLA-types and its potential drivers. We explore four biologically plausible hypotheses regarding the processes driving molecular type relative abundances: sampling and speciation; structuring of the pathogen population; historical changes in population size; and transmission heterogeneity (superspreading). Results Northern Irish herd-level MVLA-type surveillance shows a right-skewed distribution of MVLA-types, with a small number of types present at very high frequencies and the majority of types very rare. We demonstrate that this skew is too extreme to be accounted for by simple neutral ecological processes. Simulation results indicate that the process of MVLA-type speciation and the manner in which the MVLA-typing loci were chosen in Northern Ireland cannot account for the observed skew. Similarly, we find that pathogen population structure, assuming for example a reservoir of infection in a separate host, would drive the relative abundance distribution in the opposite direction to that observed, generating more even abundances of molecular types. However, we find that historical increases in bovine tuberculosis prevalence and/or transmission heterogeneity (superspreading) are both capable of generating the skewed MVLA-type distribution, consistent with findings of previous work examining the distribution of molecular types in human tuberculosis. Conclusion Although the distribution of MVLA-type abundances does not fit classical neutral predictions, our simulations show that increases in pathogen population size and/or superspreading are consistent with the pattern observed, even in the absence of selective pressures acting on the system. Electronic supplementary material The online version of this article (doi:10.1186/s12917-017-1190-5) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Hannah Trewby
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity and Animal Health, University of Glasgow, Glasgow, UK.
| | - David M Wright
- School of Medicine, Dentistry, and Biomedical Sciences, Queen's University Belfast, Belfast, UK
| | - Robin A Skuce
- Veterinary Sciences Division, Agri-Food and Biosciences Institute, Stormont, Belfast, UK.,School of Biological Sciences, Queen's University Belfast, Belfast, UK
| | - Carl McCormick
- Veterinary Sciences Division, Agri-Food and Biosciences Institute, Stormont, Belfast, UK
| | - Thomas R Mallon
- Veterinary Sciences Division, Agri-Food and Biosciences Institute, Stormont, Belfast, UK
| | - Eleanor L Presho
- Veterinary Sciences Division, Agri-Food and Biosciences Institute, Stormont, Belfast, UK
| | - Rowland R Kao
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity and Animal Health, University of Glasgow, Glasgow, UK
| | - Daniel T Haydon
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity and Animal Health, University of Glasgow, Glasgow, UK
| | - Roman Biek
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity and Animal Health, University of Glasgow, Glasgow, UK
| |
Collapse
|
33
|
Lee RS, Proulx JF, Menzies D, Behr MA. Progression to tuberculosis disease increases with multiple exposures. Eur Respir J 2016; 48:1682-1689. [PMID: 27824599 DOI: 10.1183/13993003.00893-2016] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 08/02/2016] [Indexed: 11/05/2022]
Abstract
During a single year, a Canadian village had 34 individuals with microbiologically confirmed tuberculosis (TB) among 169 people with a new infection (20%). A contact investigation revealed multiple exposures for each person. We investigated whether the intensity of exposure might contribute to this extraordinary risk of disease.We carried out a case-control study using a public health database. Among those with a new infection, 34 had culture-confirmed TB (cases) and 118 did not progress to disease (controls). 17 patients with probable disease were excluded. Contact investigation data were utilised to tabulate the number of potential sources (total exposures). Generalised estimating equations with a logit link were used to identify associations between exposures and progression, and to investigate other potential risk factors.The median (interquartile range) number of total exposures was 15 (3-23) for cases and 3 (2-12) for controls (p=0.001). The adjusted OR for disease was 1.11 (95% CI 1.06-1.16) per additional exposure, corresponding to an OR of 3.4 for disease when comparing the medians of 15 versus 3 total exposures. This association increased when restricting to tuberculin skin test conversions.Increased exposure could be a marker of greater risk of progression to TB disease. Therefore, this risk may not be transportable across epidemiologic settings with variable exposure intensities.
Collapse
Affiliation(s)
- Robyn S Lee
- Dept of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC, Canada.,McGill International TB Centre, Montreal, QC, Canada.,The Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | | | - Dick Menzies
- McGill International TB Centre, Montreal, QC, Canada.,The Research Institute of the McGill University Health Centre, Montreal, QC, Canada.,Respiratory Epidemiology and Clinical Research Unit, Montreal Chest Institute, Montreal, QC, Canada
| | - Marcel A Behr
- Dept of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC, Canada .,McGill International TB Centre, Montreal, QC, Canada.,The Research Institute of the McGill University Health Centre, Montreal, QC, Canada.,Dept of Medicine, McGill University, Montreal, QC, Canada
| |
Collapse
|
34
|
Yates TA, Tanser F, Abubakar I. Plan Beta for tuberculosis: it's time to think seriously about poorly ventilated congregate settings. Int J Tuberc Lung Dis 2016; 20:5-10. [PMID: 26688524 PMCID: PMC4677622 DOI: 10.5588/ijtld.15.0494] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Globally, the rates of decline in tuberculosis (TB) incidence are disappointing, but in line with model predictions regarding the likely impact of the DOTS strategy. Here, we review evidence from basic epidemiology, molecular epidemiology and modelling, all of which suggest that, in high-burden settings, the majority of Mycobacterium tuberculosis transmission may occur in indoor congregate settings. We argue that mass environmental modifications in these places might have a significant impact on TB control and suggest a research agenda that might inform interventions of this nature. The necessary technology exists and, critically, implementation would not be dependent on health care workers who are in short supply in the communities worst affected by TB.
Collapse
Affiliation(s)
- T A Yates
- Centre for Infectious Disease Epidemiology, Research Department of Infection and Population Health, University College London, London, UK; Wellcome Trust Africa Centre for Population Health, University of KwaZulu-Natal, Mtubatuba, South Africa
| | - F Tanser
- Wellcome Trust Africa Centre for Population Health, University of KwaZulu-Natal, Mtubatuba, South Africa; School of Nursing and Public Health, University of KwaZulu-Natal, Durban, South Africa
| | - I Abubakar
- Centre for Infectious Disease Epidemiology, Research Department of Infection and Population Health, University College London, London, UK; Medical Research Council Clinical Trials Unit, University College London, London, UK
| |
Collapse
|
35
|
Cao K, Yang K, Wang C, Guo J, Tao L, Liu Q, Gehendra M, Zhang Y, Guo X. Spatial-Temporal Epidemiology of Tuberculosis in Mainland China: An Analysis Based on Bayesian Theory. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2016; 13:E469. [PMID: 27164117 PMCID: PMC4881094 DOI: 10.3390/ijerph13050469] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2016] [Revised: 04/06/2016] [Accepted: 04/27/2016] [Indexed: 01/12/2023]
Abstract
OBJECTIVE To explore the spatial-temporal interaction effect within a Bayesian framework and to probe the ecological influential factors for tuberculosis. METHODS Six different statistical models containing parameters of time, space, spatial-temporal interaction and their combination were constructed based on a Bayesian framework. The optimum model was selected according to the deviance information criterion (DIC) value. Coefficients of climate variables were then estimated using the best fitting model. RESULTS The model containing spatial-temporal interaction parameter was the best fitting one, with the smallest DIC value (-4,508,660). Ecological analysis results showed the relative risks (RRs) of average temperature, rainfall, wind speed, humidity, and air pressure were 1.00324 (95% CI, 1.00150-1.00550), 1.01010 (95% CI, 1.01007-1.01013), 0.83518 (95% CI, 0.93732-0.96138), 0.97496 (95% CI, 0.97181-1.01386), and 1.01007 (95% CI, 1.01003-1.01011), respectively. CONCLUSIONS The spatial-temporal interaction was statistically meaningful and the prevalence of tuberculosis was influenced by the time and space interaction effect. Average temperature, rainfall, wind speed, and air pressure influenced tuberculosis. Average humidity had no influence on tuberculosis.
Collapse
Affiliation(s)
- Kai Cao
- School of Public Health, Capital Medical University, No. 10 Xitoutiao, You'anmen Wai, Fengtai District, Beijing 100069, China.
- Beijing Municipal Key Laboratory of Clinical Epidemiology, Beijing 100069, China.
- Beijing Ophthalmology & Visual Science Key Lab., Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, China.
| | - Kun Yang
- School of Public Health, Capital Medical University, No. 10 Xitoutiao, You'anmen Wai, Fengtai District, Beijing 100069, China.
- Beijing Municipal Key Laboratory of Clinical Epidemiology, Beijing 100069, China.
| | - Chao Wang
- School of Public Health, Capital Medical University, No. 10 Xitoutiao, You'anmen Wai, Fengtai District, Beijing 100069, China.
- Beijing Municipal Key Laboratory of Clinical Epidemiology, Beijing 100069, China.
- Department of Statistics and Information, Beijing Centers for Disease Control and Prevention, No 16, Hepingli Middle Street, Dongcheng District, Beijing 100013, China.
| | - Jin Guo
- School of Public Health, Capital Medical University, No. 10 Xitoutiao, You'anmen Wai, Fengtai District, Beijing 100069, China.
- Beijing Municipal Key Laboratory of Clinical Epidemiology, Beijing 100069, China.
| | - Lixin Tao
- School of Public Health, Capital Medical University, No. 10 Xitoutiao, You'anmen Wai, Fengtai District, Beijing 100069, China.
- Beijing Municipal Key Laboratory of Clinical Epidemiology, Beijing 100069, China.
| | - Qingrong Liu
- School of Public Health, Capital Medical University, No. 10 Xitoutiao, You'anmen Wai, Fengtai District, Beijing 100069, China.
- Beijing Municipal Key Laboratory of Clinical Epidemiology, Beijing 100069, China.
| | - Mahara Gehendra
- School of Public Health, Capital Medical University, No. 10 Xitoutiao, You'anmen Wai, Fengtai District, Beijing 100069, China.
- Beijing Municipal Key Laboratory of Clinical Epidemiology, Beijing 100069, China.
| | - Yingjie Zhang
- Chinese Center for Disease Control and Prevention, Beijing 102206, China.
| | - Xiuhua Guo
- School of Public Health, Capital Medical University, No. 10 Xitoutiao, You'anmen Wai, Fengtai District, Beijing 100069, China.
- Beijing Municipal Key Laboratory of Clinical Epidemiology, Beijing 100069, China.
| |
Collapse
|
36
|
Jones-López EC, Acuña-Villaorduña C, Ssebidandi M, Gaeddert M, Kubiak RW, Ayakaka I, White LF, Joloba M, Okwera A, Fennelly KP. Cough Aerosols of Mycobacterium tuberculosis in the Prediction of Incident Tuberculosis Disease in Household Contacts. Clin Infect Dis 2016; 63:10-20. [PMID: 27025837 DOI: 10.1093/cid/ciw199] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 03/18/2016] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Tuberculosis disease develops in only 5%-10% of humans infected with Mycobacterium tuberculosis The mechanisms underlying this variability remain poorly understood. We recently demonstrated that colony-forming units of M. tuberculosis in cough-generated aerosols are a better predictor of infection than the standard sputum acid-fast bacilli smear. We hypothesized that cough aerosol cultures may also predict progression to tuberculosis disease in contacts. METHODS We conducted a retrospective cohort study of 85 patients with smear-positive tuberculosis and their 369 household contacts in Kampala, Uganda. Index case patients underwent a standard evaluation, and we cultured M. tuberculosis from cough aerosols. Contacts underwent a standard evaluation at enrollment, and they were later traced to determine their tuberculosis status. RESULTS During a median follow-up of 3.9 years, 8 (2%) of the contacts developed tuberculosis disease. In unadjusted and adjusted analyses, incident tuberculosis disease in contacts was associated with sputum Mycobacterial Growth Indicator Tube culture (odds ratio, 8.2; 95% confidence interval, 1.1-59.2; P = .04), exposure to a high-aerosol tuberculosis case patient (6.0, 1.4-25.2; P = .01), and marginally, human immunodeficiency virus in the contact (6.11; 0.89-41.7; P = .07). We present data demonstrating that sputum and aerosol specimens measure 2 related but different phenomena. CONCLUSIONS We found an increased risk of tuberculosis progression among contacts of high-aerosol case patients. The hypothesis that a larger infectious inoculum, represented by high aerosol production, determines the risk of disease progression deserves evaluation in future prospective studies.
Collapse
Affiliation(s)
- Edward C Jones-López
- Section of Infectious Diseases, Department of Medicine, Boston Medical Center and Boston University School of Medicine Makerere University-Boston Medical Center Research Collaboration
| | - Carlos Acuña-Villaorduña
- Section of Infectious Diseases, Department of Medicine, Boston Medical Center and Boston University School of Medicine
| | | | - Mary Gaeddert
- Section of Infectious Diseases, Department of Medicine, Boston Medical Center and Boston University School of Medicine
| | - Rachel W Kubiak
- Section of Infectious Diseases, Department of Medicine, Boston Medical Center and Boston University School of Medicine
| | - Irene Ayakaka
- Makerere University-Boston Medical Center Research Collaboration
| | - Laura F White
- Department of Biostatistics, Boston University School of Public Health, Massachusetts
| | - Moses Joloba
- Department of Microbiology, Makerere University College of Health Sciences
| | - Alphonse Okwera
- Makerere University-Boston Medical Center Research Collaboration Mulago Hospital Tuberculosis Clinic, Mulago Hospital, Kampala, Uganda
| | - Kevin P Fennelly
- Pulmonary Clinical Medicine Section, Cardiovascular and Pulmonary Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| |
Collapse
|
37
|
Gomes MGM, Barreto ML, Glaziou P, Medley GF, Rodrigues LC, Wallinga J, Squire SB. End TB strategy: the need to reduce risk inequalities. BMC Infect Dis 2016; 16:132. [PMID: 27001766 PMCID: PMC4802713 DOI: 10.1186/s12879-016-1464-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 03/10/2016] [Indexed: 12/19/2022] Open
Abstract
Background Diseases occur in populations whose individuals differ in essential characteristics, such as exposure to the causative agent, susceptibility given exposure, and infectiousness upon infection in the case of infectious diseases. Discussion Concepts developed in demography more than 30 years ago assert that variability between individuals affects substantially the estimation of overall population risk from disease incidence data. Methods that ignore individual heterogeneity tend to underestimate overall risk and lead to overoptimistic expectations for control. Concerned that this phenomenon is frequently overlooked in epidemiology, here we feature its significance for interpreting global data on human tuberculosis and predicting the impact of control measures. Summary We show that population-wide interventions have the greatest impact in populations where all individuals face an equal risk. Lowering variability in risk has great potential to increase the impact of interventions. Reducing inequality, therefore, empowers health interventions, which in turn improves health, further reducing inequality, in a virtuous circle. Electronic supplementary material The online version of this article (doi:10.1186/s12879-016-1464-8) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- M Gabriela M Gomes
- Liverpool School of Tropical Medicine, Liverpool, UK. .,CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vila do Conde, Portugal. .,Instituto de Matemática e Estatística, Universidade de São Paulo, São Paulo, Brazil.
| | - Maurício L Barreto
- Centro de Pesquisas Gonçalo Moniz, FIOCRUZ, Salvador, Brazil.,Instituto de Saúde Coletiva, Universidade Federal da Bahia, Salvador, Brazil
| | | | | | | | - Jacco Wallinga
- Department of Infectious Diseases Epidemiology, National Institute of Public Health and the Environment, PO Box 1, 3720 BA, Bilthoven, The Netherlands.,Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, PO Box 9600, 2300 RC, Leiden, The Netherlands
| | | |
Collapse
|
38
|
Gomes MGM, Gjini E, Lopes JS, Souto-Maior C, Rebelo C. A theoretical framework to identify invariant thresholds in infectious disease epidemiology. J Theor Biol 2016; 395:97-102. [PMID: 26869215 DOI: 10.1016/j.jtbi.2016.01.029] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Revised: 01/17/2016] [Accepted: 01/20/2016] [Indexed: 10/22/2022]
Abstract
Setting global strategies and targets for disease prevention and control often involves mathematical models. Model structure is typically subject to intense scrutiny, such as confrontation with empirical data and alternative formulations, while a less frequently challenged aspect is the widely adopted reduction of parameters to their average values. Focusing on endemic diseases, we use a general transmission model to explain how mean field approximations decrease the estimated R0 from prevalence data, while threshold phenomena - such as the epidemic and reinfection thresholds - remain invariant. This results in an underestimation of the effort required to control disease, which may be particularly severe when the approximation inappropriately places transmission estimates below important thresholds. These concepts are widely applicable across endemic pathogen systems.
Collapse
Affiliation(s)
- M Gabriela M Gomes
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Portugal; Instituto de Matemática e Estatística, Universidade de São Paulo, Brazil; Liverpool School of Tropical Medicine, United Kingdom.
| | - Erida Gjini
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Joao S Lopes
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | | | - Carlota Rebelo
- Departamento de Matemática e Centro de Matemática, Aplicações Fundamentais e Investigação Operacional, Universidade de Lisboa, Portugal
| |
Collapse
|
39
|
Yates TA, Khan PY, Knight GM, Taylor JG, McHugh TD, Lipman M, White RG, Cohen T, Cobelens FG, Wood R, Moore DAJ, Abubakar I. The transmission of Mycobacterium tuberculosis in high burden settings. THE LANCET. INFECTIOUS DISEASES 2016; 16:227-38. [PMID: 26867464 DOI: 10.1016/s1473-3099(15)00499-5] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Revised: 11/03/2015] [Accepted: 11/26/2015] [Indexed: 01/06/2023]
Abstract
Unacceptable levels of Mycobacterium tuberculosis transmission are noted in high burden settings and a renewed focus on reducing person-to-person transmission in these communities is needed. We review recent developments in the understanding of airborne transmission. We outline approaches to measure transmission in populations and trials and describe the Wells-Riley equation, which is used to estimate transmission risk in indoor spaces. Present research priorities include the identification of effective strategies for tuberculosis infection control, improved understanding of where transmission occurs and the transmissibility of drug-resistant strains, and estimates of the effect of HIV and antiretroviral therapy on transmission dynamics. When research is planned and interventions are designed to interrupt transmission, resource constraints that are common in high burden settings-including shortages of health-care workers-must be considered.
Collapse
Affiliation(s)
- Tom A Yates
- Centre for Infectious Disease Epidemiology, Research Department of Infection and Population Health, University College London, London, UK; Wellcome Trust Africa Centre for Population Health, Mtubatuba, South Africa, London School of Hygiene & Tropical Medicine, London, UK.
| | - Palwasha Y Khan
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK; Tuberculosis Centre, London School of Hygiene & Tropical Medicine, London, UK; Karonga Prevention Study, Chilumba, Malawi
| | - Gwenan M Knight
- Tuberculosis Centre, London School of Hygiene & Tropical Medicine, London, UK; Tuberculosis Modelling Group, London School of Hygiene & Tropical Medicine, London, UK; National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infection and Antimicrobial Resistance, Imperial College London, London, UK
| | - Jonathon G Taylor
- UCL Institute for Environmental Design and Engineering, Bartlett School of Environment, Energy and Resources, University College London, London, UK
| | - Timothy D McHugh
- Centre for Clinical Microbiology, University College London, London, UK
| | - Marc Lipman
- Division of Medicine, University College London, London, UK
| | - Richard G White
- Tuberculosis Centre, London School of Hygiene & Tropical Medicine, London, UK; Tuberculosis Modelling Group, London School of Hygiene & Tropical Medicine, London, UK
| | - Ted Cohen
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Frank G Cobelens
- Department of Global Health, Academic Medical Center, Amsterdam, Netherlands; KNCV Tuberculosis Foundation, The Hague, Netherlands
| | - Robin Wood
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK; Tuberculosis Centre, London School of Hygiene & Tropical Medicine, London, UK; The Desmond Tutu HIV Centre, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - David A J Moore
- Tuberculosis Centre, London School of Hygiene & Tropical Medicine, London, UK; Department of Clinical Research, London School of Hygiene & Tropical Medicine, London, UK
| | - Ibrahim Abubakar
- Centre for Infectious Disease Epidemiology, Research Department of Infection and Population Health, University College London, London, UK; MRC Clinical Trials Unit at University College London, University College London, London, UK
| |
Collapse
|
40
|
Pathogen Epidemiology. ENCYCLOPEDIA OF EVOLUTIONARY BIOLOGY 2016. [PMCID: PMC7148661 DOI: 10.1016/b978-0-12-800049-6.00228-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
41
|
Zelner JL, Murray MB, Becerra MC, Galea J, Lecca L, Calderon R, Yataco R, Contreras C, Zhang Z, Manjourides J, Grenfell BT, Cohen T. Identifying Hotspots of Multidrug-Resistant Tuberculosis Transmission Using Spatial and Molecular Genetic Data. J Infect Dis 2015; 213:287-94. [PMID: 26175455 DOI: 10.1093/infdis/jiv387] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 07/08/2015] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND We aimed to identify and determine the etiology of "hotspots" of concentrated multidrug-resistant tuberculosis (MDR-tuberculosis) risk in Lima, Peru. METHODS From 2009 to 2012, we conducted a prospective cohort study among households of tuberculosis cases from 106 health center (HC) areas in Lima, Peru. All notified tuberculosis cases and their household contacts were followed for 1 year. Symptomatic individuals were screened by microscopy and culture; positive cultures were tested for drug susceptibility (DST) and genotyped by 24-loci mycobacterial interspersed repetitive units-variable-number tandem repeats (MIRU-VNTR). RESULTS 3286 individuals with culture-confirmed disease, DST, and 24-loci MIRU-VNTR were included in our analysis. Our analysis reveals: (1) heterogeneity in annual per-capita incidence of tuberculosis and MDR-tuberculosis by HC, with a rate of MDR-tuberculosis 89 times greater (95% confidence interval [CI], 54,185) in the most-affected versus the least-affected HC; (2) high risk for MDR-tuberculosis in a region spanning several HCs (odds ratio = 3.19, 95% CI, 2.33, 4.36); and (3) spatial aggregation of MDR-tuberculosis genotypes, suggesting localized transmission. CONCLUSIONS These findings reveal that localized transmission is an important driver of the epidemic of MDR-tuberculosis in Lima. Efforts to interrupt transmission may be most effective if targeted to this area of the city.
Collapse
Affiliation(s)
- Jonathan L Zelner
- Robert Wood Johnson Foundation Health and Society Scholars Program, Interdisciplinary Center for Innovative Theory and Empirics (INCITE) & Mailman School of Public Health, Columbia University, New York, New York
| | - Megan B Murray
- Department of Global Health and Social Medicine, Harvard Medical School, Department of Epidemiology, Harvard School of Public Health
| | - Mercedes C Becerra
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, Massachusetts
| | | | | | | | | | | | - Zibiao Zhang
- Division of Global Health Equity, Brigham and Women's Hospital
| | - Justin Manjourides
- Department of Health Sciences, Bouvé College of Health Sciences, Northeastern University, Boston, Massachusetts
| | - Bryan T Grenfell
- Department of Ecology and Evolutionary Biology, Princeton University, New Jersey Fogarty International Center, National Institutes of Health, Bethesda, Maryland
| | - Ted Cohen
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut
| |
Collapse
|
42
|
Mathematical Modelling and Tuberculosis: Advances in Diagnostics and Novel Therapies. Adv Med 2015; 2015:907267. [PMID: 26556559 PMCID: PMC4590968 DOI: 10.1155/2015/907267] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 02/18/2015] [Accepted: 02/26/2015] [Indexed: 11/18/2022] Open
Abstract
As novel diagnostics, therapies, and algorithms are developed to improve case finding, diagnosis, and clinical management of patients with TB, policymakers must make difficult decisions and choose among multiple new technologies while operating under heavy resource constrained settings. Mathematical modelling can provide helpful insight by describing the types of interventions likely to maximize impact on the population level and highlighting those gaps in our current knowledge that are most important for making such assessments. This review discusses the major contributions of TB transmission models in general, namely, the ability to improve our understanding of the epidemiology of TB. We focus particularly on those elements that are important to appropriately understand the role of TB diagnosis and treatment (i.e., what elements of better diagnosis or treatment are likely to have greatest population-level impact) and yet remain poorly understood at present. It is essential for modellers, decision-makers, and epidemiologists alike to recognize these outstanding gaps in knowledge and understand their potential influence on model projections that may guide critical policy choices (e.g., investment and scale-up decisions).
Collapse
|
43
|
Ren J, Ning Z, Kirkness CS, Asche CV, Wang H. Risk of using logistic regression to illustrate exposure-response relationship of infectious diseases. BMC Infect Dis 2014; 14:540. [PMID: 25282153 PMCID: PMC4287313 DOI: 10.1186/1471-2334-14-540] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Accepted: 09/25/2014] [Indexed: 01/23/2023] Open
Abstract
Background In most biological experiments, especially infectious disease, the exposure-response relationship is interrelated by a multitude of factors rather than many independent factors. Little is known about the suitability of ordinary, categorical exposures, and logarithmic transformation which have been presented in logistic regression models to assess the likelihood of an infectious disease as a function of a risk or exposure. This study aims to examine and compare the current approaches. Methods A simulated human immunodeficiency virus (HIV) population, dynamic infection data for 100,000 individuals with 1% initial prevalence and 2% infectivity, was created. Using the Monte Carlo method (computational algorithm) to repeat random sampling to obtain numerical results, linearity between log odds and exposure, and suitability in practice were examined in the three model approaches. Results Despite diverse population prevalence, the linearity was not satisfied between log odds and raw exposures. Logarithmic transformation of exposures improved the linearity to a certain extent, and categorical exposures satisfied the linear assumption (which was important for modelling). When the population prevalence was low (assumed < 10%), performances of the three models were significantly different. Comparing to ordinary logistic regression, the logarithmic transformation approach demonstrated better accuracy of estimation except that at the two inflection points: likelihood of infection increased from slowly to sharply, then slowly again. The approach using categorical exposures had better estimations around the real values, but the measurement was coarse due to categorization. Conclusions It is not suitable to directly use ordinary logistic regression to explore the exposure-response relationship of HIV as an infectious disease. This study provides some recommendations for practical implementations including: 1) utilize categorical exposure if a large sample size and low population prevalence are provided; 2) utilize a logarithmic transformed exposure if the sample size is insufficient or the population prevalence is too high (such as 30%). Electronic supplementary material The online version of this article (doi:10.1186/1471-2334-14-540) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Jinma Ren
- Center for Outcomes Research, University of Illinois College of Medicine at Peoria, One Illini Drive, Box 1649, Peoria, IL 61656, USA.
| | | | | | | | | |
Collapse
|
44
|
Shrestha S, Knight GM, Fofana M, Cohen T, White RG, Cobelens F, Dowdy DW. Drivers and trajectories of resistance to new first-line drug regimens for tuberculosis. Open Forum Infect Dis 2014; 1:ofu073. [PMID: 25734143 PMCID: PMC4281792 DOI: 10.1093/ofid/ofu073] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Accepted: 08/04/2014] [Indexed: 11/24/2022] Open
Abstract
Background New first-line drug regimens for treatment of tuberculosis (TB) are in clinical trials: emergence of resistance is a key concern. Because population-level data on resistance cannot be collected in advance, epidemiological models are important tools for understanding the drivers and dynamics of resistance before novel drug regimens are launched. Methods We developed a transmission model of TB after launch of a new drug regimen, defining drug-resistant TB (DR-TB) as resistance to the new regimen. The model is characterized by (1) the probability of acquiring resistance during treatment, (2) the transmission fitness of DR-TB relative to drug-susceptible TB (DS-TB), and (3) the probability of treatment success for DR-TB versus DS-TB. We evaluate the effect of each factor on future DR-TB prevalence, defined as the proportion of incident TB that is drug-resistant. Results Probability of acquired resistance was the strongest predictor of the DR-TB proportion in the first 5 years after the launch of a new drug regimen. Over a longer term, however, the DR-TB proportion was driven by the resistant population's transmission fitness and treatment success rates. Regardless of uncertainty in acquisition probability and transmission fitness, high levels (>10%) of drug resistance were unlikely to emerge within 50 years if, among all cases of TB that were detected, 85% of those with DR-TB could be appropriately diagnosed as such and then successfully treated. Conclusions Short-term surveillance cannot predict long-term drug resistance trends after launch of novel first-line TB regimens. Ensuring high treatment success of drug-resistant TB through early diagnosis and appropriate second-line therapy can mitigate many epidemiological uncertainties and may substantially slow the emergence of drug-resistant TB.
Collapse
Affiliation(s)
- Sourya Shrestha
- Department of Epidemiology , Johns Hopkins School of Public Health , Baltimore, Maryland
| | - Gwenan M Knight
- TB Modelling Group, Department of Infectious Disease Epidemiology , London School of Hygiene and Tropical Medicine , United Kingdom
| | - Mariam Fofana
- Department of Epidemiology , Johns Hopkins School of Public Health , Baltimore, Maryland
| | - Ted Cohen
- Division of Global Health Equity , Brigham and Women's Hospital , Boston, Massachusetts
| | - Richard G White
- TB Modelling Group, Department of Infectious Disease Epidemiology , London School of Hygiene and Tropical Medicine , United Kingdom
| | - Frank Cobelens
- Amsterdam Institute for Global Health and Development , The Netherlands
| | - David W Dowdy
- Department of Epidemiology , Johns Hopkins School of Public Health , Baltimore, Maryland
| |
Collapse
|
45
|
Dowdy DW, Azman AS, Kendall EA, Mathema B. Transforming the fight against tuberculosis: targeting catalysts of transmission. Clin Infect Dis 2014; 59:1123-9. [PMID: 24982034 DOI: 10.1093/cid/ciu506] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The global tuberculosis control community has committed itself to ambitious 10-year targets. To meet these targets, biomedical advances alone will be insufficient; a more targeted public health tuberculosis strategy is also needed. We highlight the role of "tuberculosis transmission catalysts," defined as variabilities in human behavior, bacillary properties, and host physiology that fuel the propagation of active tuberculosis at the local level. These catalysts can be categorized as factors that increase contact rates, infectiousness, or host susceptibility. Different catalysts predominate in different epidemiological and sociopolitical settings, and public health approaches are likely to succeed only if they are tailored to target the major catalysts driving transmission in the corresponding community. We argue that global tuberculosis policy should move from a country-level focus to a strategy that prioritizes collection of data on key transmission catalysts at the local level followed by deployment of "catalyst-targeted" interventions, supported by strengthened health systems.
Collapse
Affiliation(s)
- David W Dowdy
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health
| | - Andrew S Azman
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health
| | - Emily A Kendall
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Barun Mathema
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York
| |
Collapse
|
46
|
Vadivelu S, Effendi S, Starke JR, Luerssen TG, Jea A. A review of the neurological and neurosurgical implications of tuberculosis in children. Clin Pediatr (Phila) 2013; 52:1135-43. [PMID: 23847176 DOI: 10.1177/0009922813493833] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Tuberculous involvement of the central nervous system (CNS) and vertebral column is the most lethal and disabling form of tuberculosis (TB). Several factors contribute to poor outcome, including cerebrovascular involvement with ischemia, hydrocephalus, direct parenchymal injury and formation of abscess and inflammation in the brain and spinal cord, hyponatremia, seizures, and delayed diagnosis. Spinal spondylitis from TB and associated spinal deformity is the leading cause of paraplegia in developing countries. The evidence for supportive treatment of TB infection of the CNS is limited, leading to substantial differences in management protocols. Many of the treatment approaches used in TB infection of the CNS have been extrapolated from treatment of other acute neurological disorders such as bacterial meningitis and traumatic brain injury. We review data from the available literature and highlight questions relating to the neurological and neurosurgical care of children with TB infection of the CNS and vertebral column.
Collapse
|