Public transportation and tuberculosis transmission in a high incidence setting.
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ABSTRACT:
SUBMITTER: Zamudio C
PROVIDER: S-EPMC4338233 | biostudies-other | 2015
REPOSITORIES: biostudies-other
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Project description:BackgroundGenotyping Mycobacterium tuberculosis isolates allows study of dynamics of tuberculosis transmission, while geoprocessing allows spatial analysis of clinical and epidemiological data. Here, genotyping data and spatial analysis were combined to characterize tuberculosis transmission in Vitória, Brazil, to identify distinct neighborhoods and risk factors associated with recent tuberculosis transmission.MethodsFrom 2003 to 2007, 503 isolates were genotyped by IS6110 restriction fragment length polymorphism (RFLP) and spoligotyping. The analysis included kernel density estimation, K-function analysis, and a t test distance analysis. Mycobacterium tuberculosis isolates belonging to identical RFLP patterns (clusters) were considered to represent recent tuberculosis infection (cases).ResultsOf 503 genotyped isolates, 242 (48%) were categorized into 70 distinct clusters belonging to 12 RFLP families. The proportion of recent transmission was 34.2%. Kernel density maps indicated 3 areas of intense concentration of cases. K-function analysis of the largest RFLP clusters and families showed they co-localized in space. The distance analysis confirmed these results and demonstrated that unique strain patterns (controls) randomly distributed in space. A logit model identified young age, positive smear test, and lower Index of Quality of Urban Municipality as risk factors for recent transmission. The predicted probabilities for each neighborhood were mapped and identified neighborhoods with high risk for recent transmission.ConclusionsSpatial and genotypic clustering of M. tuberculosis isolates revealed ongoing active transmission of tuberculosis caused by a small subset of strains in specific neighborhoods of the city. Such information provides an opportunity to target tuberculosis transmission control, such as through rigorous and more focused contact investigation programs.
| S-EPMC4626752 | biostudies-literature
Project description:To compare epidemiological data between recurrent cases after cure (RC), distinguishing relapse from reinfection, after dropout (RD) and new cases (NC) in an ambulatory setting in a TB-endemic country.Records of patients who started treatment for pulmonary TB between 2004 and 2010 in a TB clinic were reviewed. Epidemiological data were analyzed. Spoligotyping and MIRU patterns were used to determine relapse or reinfection in 13 RC available.Of the eligible group (1449), 1060 were NC (73.2%), among the recurrent cases, 203 (14%) were RC and 186 (12.8%) were RD. Of RC, 171 (84.2%) occurred later than 6 months after a previous episode, 13 had available DNA, in 4 (30.7%) the disease was attributed to reinfection and in 9 (69.3%), to relapse. Comparing RC to NC, HIV (p?<?0.0001) was independent risk factor for RC. When RC and RD were compared, alcohol abuse (p?=?0.001) and treatment noncompliance (p?=?0.006) were more frequent in RD.HIV is the sole more important associated factor for RC. This finding points the need to improve the approach to manage TB in order to decrease the chance for exposure especially in vulnerable people with increased risk of developing disease and to improve DOTS strategy to deal with factors associated to treatment noncompliance.
| S-EPMC4215011 | biostudies-literature
Project description:In East Greenland, a dramatic increase of tuberculosis (TB) incidence has been observed in recent years. Classical genotyping suggests a genetically similar Mycobacterium tuberculosis (Mtb) strain population as cause, however, precise transmission patterns are unclear. We performed whole genome sequencing (WGS) of Mtb isolates from 98% of culture-positive TB cases through 21?years (n?=?182) which revealed four genomic clusters of the Euro-American lineage (mainly sub-lineage 4.8 (n?=?134)). The time to the most recent common ancestor of lineage 4.8 strains was found to be 100?years. This sub-lineage further diversified in the 1970s, and massively expanded in the 1990s, a period of lowered TB awareness in Greenland. Despite the low genetic strain diversity, WGS data revealed several recent short-term transmission events in line with the increasing incidence in the region. Thus, the isolated setting and the uniformity of circulating Mtb strains indicated that the majority of East Greenlandic TB cases originated from one or few strains introduced within the last century. Thereby, the study shows the consequences of even short interruptions in TB control efforts in previously TB high incidence areas and demonstrates the potential role of WGS in detecting ongoing micro epidemics, thus guiding public health efforts in the future.
| S-EPMC5018808 | biostudies-literature
Project description:BackgroundRegionality is often a significant factor in tuberculosis (TB) management and outcomes worldwide. A wide range of context-specific factors may influence these differences and change over time. We compared TB treatment in regional and metropolitan areas, considering demographic and temporal trends affecting TB diagnosis and outcomes.MethodsRetrospective analyses of data for patients notified with TB in Victoria, Australia, were conducted. The study outcomes were treatment delays and treatment outcomes. Multivariable Cox proportional hazard model analyses were performed to investigate the effect of regionality in the management of TB. Six hundred and eleven (7%) TB patients were notified in regional and 8,163 (93%) in metropolitan areas between 1995 and 2019. Of the 611 cases in the regional cohort, 401 (66%) were overseas-born. Fifty-one percent of the overseas-born patients in regional Victoria developed TB disease within five years of arrival in Australia. Four cases of multidrug-resistant tuberculosis were reported in regional areas, compared to 97 cases in metropolitan areas. A total of 3,238 patients notified from 2012 to 2019 were included in the survival analysis. The time follow-up for patient delay started at symptom onset date, and the event was the presentation to the healthcare centre. For healthcare system delay, follow-up time began at the presentation to the healthcare centre, and the event was commenced on TB treatment. Cases with extrapulmonary TB in regional areas have a non-significantly longer healthcare system delay than patients in metropolitan (median 64 days versus 54 days, AHR = 0.8, 95% CI 0.6-1.0, P = 0.094).ConclusionTuberculosis in regional Victoria is common among the overseas-born population, and patients with extrapulmonary TB in regional areas experienced a non-significant minor delay in treatment commencement with no apparent detriment to treatment outcomes. Improving access to LTBI management in regional areas may reduce the burden of TB.
| S-EPMC10030020 | biostudies-literature
Project description:BackgroundExposure to pathogens in public transport systems is a common means of spreading infection, mainly by inhaling aerosol or droplets from infected individuals. Such particles also contaminate surfaces, creating a potential surface-transmission pathway.MethodsA fast acoustic biosensor with an antifouling nano-coating was introduced to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on exposed surfaces in the Prague Public Transport System. Samples were measured directly without pre-treatment. Results with the sensor gave excellent agreement with parallel quantitative reverse-transcription polymerase chain reaction (qRT-PCR) measurements on 482 surface samples taken from actively used trams, buses, metro trains and platforms between 7 and 9 April 2021, in the middle of the lineage Alpha SARS-CoV-2 epidemic wave when 1 in 240 people were COVID-19 positive in Prague.ResultsOnly ten of the 482 surface swabs produced positive results and none of them contained virus particles capable of replication, indicating that positive samples contained inactive virus particles and/or fragments. Measurements of the rate of decay of SARS-CoV-2 on frequently touched surface materials showed that the virus did not remain viable longer than 1-4 h. The rate of inactivation was the fastest on rubber handrails in metro escalators and the slowest on hard-plastic seats, window glasses and stainless-steel grab rails. As a result of this study, Prague Public Transport Systems revised their cleaning protocols and the lengths of parking times during the pandemic.ConclusionsOur findings suggest that surface transmission played no or negligible role in spreading SARS-CoV-2 in Prague. The results also demonstrate the potential of the new biosensor to serve as a complementary screening tool in epidemic monitoring and prognosis.
| S-EPMC10481417 | biostudies-literature
Project description:Throughout a phase IIIb/IV efficacy study of repeated treatment with four artemisinin-based combination therapies, significant heterogeneity was found in the number of clinical episodes experienced by individuals during the 2-year follow-up. Several factors, including host, parasite, and environmental factors, may contribute to the differential malaria incidence. We aimed to identify risk factors of malaria incidence in the context of a longitudinal study of the efficacy of different artemisinin-based combination therapy regimens in Bougoula-Hameau, a high-transmission setting in Mali. Risk factors including age, residence, and treatment regimen were compared among individuals experiencing eight or more clinical episodes of malaria ("high-incidence group") and individuals experiencing up to three clinical episodes ("low-incidence group"). Consistent with the known association between age and malaria risk in high-transmission settings, individuals in the high incidence group were significantly younger than individuals in the low-risk group (mean age, 7.0 years versus 10.6 years, respectively; t-test, P < 0.0001). Compared with individuals receiving artemether-lumefantrine, those receiving artesunate-amodiaquine had greater odds of being in the high-incidence group (odds ratio [OR], 2.24; 95% CI, 1.03 - 4.83, P = 0.041), while individuals receiving dihydroartemisinin-piperaquine had a lower odds of being in high incidence group (OR: 0.30, 95% CI, 0.11-0.85; P = 0.024). Individuals residing in the forested areas of Sokourani and Karamogobougou had significantly greater odds of being in the high-incidence group compared with individuals residing in the semi-urban area of Bougoula-Hameau 1 (Karamogobougou: OR, 3.68; 95% CI, 1.46-9.31; P = 0.0059; Sokourani: OR, 11.46; 95% CI, 4.49-29.2; P < 0.0001). This study highlights the importance of fine-mapping malaria risks even at sub-district levels for targeted and customized interventions.
| S-EPMC8991365 | biostudies-literature
Project description:BACKGROUND:Transmission patterns in high tuberculosis incidence areas in England are poorly understood but need elucidating to focus contact tracing. We study transmission within and between age, ethnic and immigrant groups using molecular data from the high incidence West Midlands region. METHODS:Isolates from culture-confirmed tuberculosis cases during 2007-2011 were typed using 24-locus Mycobacterial Interspersed Repetitive Unit-Variable Number Tandem Repeats (MIRU-VNTR). We estimated the proportion of disease attributable to recent transmission, calculated the proportion of isolates matching those from the two preceding years ("retrospectively clustered"), and identified risk factors for retrospective clustering using multivariate analyses. We calculated the ratio (RCR) between the observed and expected proportion clustered retrospectively within or between age, ethnic and immigrant groups. RESULTS:Of the 2159 available genotypes (79% of culture-confirmed cases), 34% were attributed to recent transmission. The percentage retrospectively clustered decreased from 50 to 24% for 0-14 and???65?year olds respectively (p =?0.01) and was significantly lower for immigrants than the UK-born. Higher than expected clustering occurred within 15-24?year olds (RCR: 1.4 (95% CI: 1.1-1.8)), several ethnic groups, and between UK-born or long-term immigrants with the UK-born (RCR: 1.8 (95% CI: 1.1-2.4) and 1.6 (95% CI: 1.2-1.9) respectively). CONCLUSIONS:This study is the first to consider "who clusters with whom" in a high incidence area in England, laying the foundation for future whole-genome sequencing work. The higher than expected clustering seen here suggests that preferential mixing between some age, ethnic and immigrant groups occurs; prioritising contact tracing to groups with which cases are most likely to cluster retrospectively could improve TB control.
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Project description:BACKGROUND:In high-incidence settings, recurrent disease among previously treated individuals contributes substantially to the burden of incident and prevalent tuberculosis. The extent to which interventions targeted to this high-risk group can improve tuberculosis control has not been established. We aimed to project the population-level effect of control interventions targeted to individuals with a history of previous tuberculosis treatment in a high-incidence setting. METHODS:We developed a transmission-dynamic model of tuberculosis and HIV in a high-incidence setting with a population of roughly 40?000 people in suburban Cape Town, South Africa. The model was calibrated to data describing local demography, TB and HIV prevalence, TB case notifications and treatment outcomes using a Bayesian calibration approach. We projected the effect of annual targeted active case finding in all individuals who had previously completed tuberculosis treatment and targeted active case finding combined with lifelong secondary isoniazid preventive therapy. We estimated the effect of these targeted interventions on local tuberculosis incidence, prevalence, and mortality over a 10 year period (2016-25). FINDINGS:We projected that, under current control efforts in this setting, the tuberculosis epidemic will remain in slow decline for at least the next decade. Additional interventions targeted to previously treated people could greatly accelerate these declines. We projected that annual targeted active case finding combined with secondary isoniazid preventive therapy in those who previously completed tuberculosis treatment would avert 40% (95% uncertainty interval [UI] 21-56) of incident tuberculosis cases and 41% (16-55) of tuberculosis deaths occurring between 2016 and 2025. INTERPRETATION:In this high-incidence setting, the use of targeted active case finding in combination with secondary isoniazid preventive therapy in previously treated individuals could accelerate decreases in tuberculosis morbidity and mortality. Studies to measure cost and resource implications are needed to establish the feasibility of this type of targeted approach for improving tuberculosis control in settings with high tuberculosis and HIV prevalence. FUNDING:National Institutes of Health, German Research Foundation.
| S-EPMC5849574 | biostudies-literature
Project description:As the outbreak of novel coronavirus disease (COVID-19) continues to spread throughout the world, steps are being taken to limit the impact on public health. In the realm of infectious diseases like COVID-19, social distancing is one of the effective measures to avoid exposure to the virus and reduce its spread. Traveling on public transport can meaningfully facilitate the propagation of the transmission of infectious diseases. Accordingly, responsive actions taken by public transit agencies against risk factors can effectively limit the risk and make transit systems safe. Among the multitude of risk factors that can affect infection spread on public transport, the likelihood of exposure is a major factor that depends on the number of people riding the public transport and can be reduced by socially distanced settings. Considering that many individuals may not act in the socially optimal manner, the necessity of public transit agencies to implement measures and restrictions is vital. In this study, we present a novel web-based application, T-Ridership, based on a hybrid optimized dynamic programming inspired by neural networks algorithm to optimize public transit for safety with respect to COVID-19. Two main steps are taken in the analysis through Metropolitan Transportation Authority (MTA): detecting high-density stations by input data normalization, and then, using these results, the T-Ridership tool automatically determines optimal station order to avoid overcrowded transit vehicles. Effectively our proposed web tool helps public transit to be safe to ride under risk of infections by reducing the density of riders on public transit vehicles as well as trip duration. These results can be used in expanding on and improving policy in public transit, to better plan the scheduled time of trains and buses in a way that prevents high-volume human contact, increases social distance, and reduces the possibility of disease transmission (available at:http://t-ridership.com and GitHub at: https://github.com/Imani-Saba/TRidership).
| S-EPMC9995304 | biostudies-literature
Project description:Whole genome sequencing (WGS) can elucidate Mycobacterium tuberculosis (Mtb) transmission patterns but more data is needed to guide its use in high-burden settings. In a household-based TB transmissibility study in Peru, we identified a large MIRU-VNTR Mtb cluster (148 isolates) with a range of resistance phenotypes, and studied host and bacterial factors contributing to its spread. WGS was performed on 61 of the 148 isolates. We compared transmission link inference using epidemiological or genomic data and estimated the dates of emergence of the cluster and antimicrobial drug resistance (DR) acquisition events by generating a time-calibrated phylogeny. Using a set of 12,032 public Mtb genomes, we determined bacterial factors characterizing this cluster and under positive selection in other Mtb lineages. Four of the 61 isolates were distantly related and the remaining 57 isolates diverged ca. 1968 (95%HPD: 1945-1985). Isoniazid resistance arose once and rifampin resistance emerged subsequently at least three times. Emergence of other DR types occurred as recently as within the last year of sampling. We identified five cluster-defining SNPs potentially contributing to transmissibility. In conclusion, clusters (as defined by MIRU-VNTR typing) may be circulating for decades in a high-burden setting. WGS allows for an enhanced understanding of transmission, drug resistance, and bacterial fitness factors.
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