Molecular epidemiology of tuberculosis in Cambodian children

Distribution and origins of Mycobacterium tuberculosis L4 in Southeast Asia

Molecular and genomic studies have revealed that Mycobacterium tuberculosis Lineage 4 (L4, Euro-American lineage) emerged in Europe before becoming distributed around the globe by trade routes, colonial migration and other historical connections. Although L4 accounts for tens or hundreds of thousands of tuberculosis (TB) cases in multiple Southeast Asian countries, phylogeographical studies have either focused on a single country or just included Southeast Asia as part of a global analysis. Therefore, we interrogated public genomic data to investigate the historical patterns underlying the distribution of L4 in Southeast Asia and surrounding countries. We downloaded 6037 genomes associated with 29 published studies, focusing on global analyses of L4 and Asian studies of M. tuberculosis. We identified 2256 L4 genomes including 968 from Asia. We show that 81 % of L4 in Thailand, 51 % of L4 in Vietnam and 9 % of L4 in Indonesia belong to sub-lineages of L4 that are rarely seen outside East and Southeast Asia (L4.2.2, L4.4.2 and L4.5). These sub-lineages have spread between East and Southeast Asian countries, with no recent European ancestor. Although there is considerable uncertainty about the exact direction and order of intra-Asian M. tuberculosis dispersal, due to differing sampling frames between countries, our analysis suggests that China may be the intermediate location between Europe and Southeast Asia for two of the three predominantly East and Southeast Asian L4 sub-lineages (L4.2.2 and L4.5). This new perspective on L4 in Southeast Asia raises the possibility of investigating host population-specific evolution and highlights the need for more structured sampling from Southeast Asian countries to provide more certainty of the historical and current routes of dispersal.

Understanding drivers of phylogenetic clustering and terminal branch lengths distribution in epidemics of Mycobacterium tuberculosis

Detecting factors associated with transmission is important to understand disease epidemics, and to design effective public health measures. Clustering and terminal branch lengths (TBL) analyses are commonly applied to genomic data sets of Mycobacterium tuberculosis (MTB) to identify sub-populations with increased transmission. Here, I used a simulation-based approach to investigate what epidemiological processes influence the results of clustering and TBL analyses, and whether differences in transmission can be detected with these methods. I simulated MTB epidemics with different dynamics (latency, infectious period, transmission rate, basic reproductive number R0, sampling proportion, sampling period, and molecular clock), and found that all considered factors, except for the length of the infectious period, affect the results of clustering and TBL distributions. I show that standard interpretations of this type of analyses ignore two main caveats: (1) clustering results and TBL depend on many factors that have nothing to do with transmission, (2) clustering results and TBL do not tell anything about whether the epidemic is stable, growing, or shrinking, unless all the additional parameters that influence these metrics are known, or assumed identical between sub-populations. An important consequence is that the optimal SNP threshold for clustering depends on the epidemiological conditions, and that sub-populations with different epidemiological characteristics should not be analyzed with the same threshold. Finally, these results suggest that different clustering rates and TBL distributions, that are found consistently between different MTB lineages, are probably due to intrinsic bacterial factors, and do not indicate necessarily differences in transmission or evolutionary success.

Tuberculosis management continues to utilize a large amount of hospital resources in the United States

BACKGROUND AND AIMS

The objective of this study is to examine longitudinal trends in hospital admissions attributed to tuberculosis and resulting hospitalization outcomes in the United States for the years 2000-2010.

METHODS

We used the Nationwide Inpatient Sample, which is the largest all-payer and nationally representative in-hospital dataset in the United States. All hospitalizations that had a primary diagnosis for tuberculosis were selected for analysis. Patient characteristics and outcomes including discharge status following hospitalization, length of stay in hospital and hospitalization charges were examined.

RESULTS

During the study period, a total of 96 431 hospitalizations occurred due to tuberculosis. The mean age of hospitalizations was 48.6 years. Males comprised 64.2% of all hospitalizations; 24.8% were Whites, 25.5% Blacks, 26.5% Hispanics, 14.3% Asians/Pacific Islanders, 1% Native Americans, and 7.9% other/mixed races. Following hospitalization, 72.1% were discharged routinely, 3.4% were transferred to another acute-care hospital, 10.7% to long-term care facilities including skilled nursing facilities, 7.6% to home health care, and 2.1% were discharged against medical advice. There were 3815 patients who died (4% of hospitalizations). The total hospitalization charge for this cohort of patients admitted due to tuberculosis across the United States was $6.96 billion and the total hospitalization days over study period was 1 419 605 days.

CONCLUSION

High-risk cohorts who are likely to be hospitalized due to tuberculosis included Blacks and Hispanics. Majority of hospitalization comprised of males. Even though the annual number of hospitalizations reduced over the study period, substantial amounts of resources are used in hospital settings to manage tuberculosis.