Genomic epidemiological analysis identifies high relapse among individuals with recurring tuberculosis and provides evidence of recent household-related transmission of tuberculosis in Ghana

Characterizing the Etiology of Recurrent Tuberculosis Using Whole Genome Sequencing: Alaska, 2008-2020

BACKGROUND

Understanding the etiology of recurrent tuberculosis (rTB) is important for effective tuberculosis control. Prior to the advent of whole genome sequencing (WGS), attributing rTB to relapse or reinfection using genetic information was complicated by the limited resolution of conventional genotyping methods.

METHODS

We applied a systematic method of evaluating whole genome single-nucleotide polymorphism (wgSNP) distances and results of phylogenetic analyses to characterize the etiology of rTB in American Indian and Alaska Native (AIAN) persons in Alaska during 2008 to 2020. We contextualized our findings through descriptive analyses of surveillance data and results of a literature search for investigations that characterized rTB etiology using WGS.

RESULTS

The percentage of tuberculosis cases in AIAN persons in Alaska classified as recurrent episodes (11.8%) was 3 times the national percentage (3.9%). Of 38 recurrent episodes included in genetic analyses, we attributed 25 (65.8%) to reinfection based on wgSNP distances and phylogenetic analyses; this proportion was the highest among 16 published point estimates identified through the literature search. By comparison, we attributed 11 (28.9%) and 6 (15.8%) recurrent episodes to reinfection based on wgSNP distances alone and on conventional genotyping methods, respectively.

CONCLUSIONS

WGS and attribution criteria involving genetic distances and patterns of relatedness can provide an effective means of elucidating rTB etiology. Our findings indicate that rTB occurs at high proportions among AIAN persons in Alaska and is frequently attributable to reinfection, reinforcing the importance of active surveillance and control measures to limit the spread of tuberculosis disease in Alaskan AIAN communities.

Global dynamics of a tuberculosis model with age-dependent latency and time delays in treatment

Since there exists heterogeneity in incubation periods of tuberculosis and a time lag between treatment and recovery. In this study, we develop a tuberculosis model that takes into account age-dependent latency and time delays in treatment to describe the transmission of tuberculosis. We first show that the solution semi-flow of the model is well-posed and has a global attractor [Formula: see text] within an infinite dimensional space [Formula: see text]. Then we define the basic reproduction number [Formula: see text] and prove that it determines the global dynamics of the model. If [Formula: see text], the global attractor [Formula: see text] reduces to the disease-free equilibrium state, indicating that the disease-free equilibrium state is globally asymptotically stable. When [Formula: see text], the semi-flow generated by the model is uniformly persistent, and there exists an interior global attractor [Formula: see text] for this uniformly persistent model. By constructing a suitable Lyapunov function and applying LaSalle's Invariance Principle, we show that the global attractor [Formula: see text] is reduced to the endemic equilibrium state, which means that the endemic equilibrium state is globally asymptotically stable. Based on the tuberculosis data in China from 2007 to 2020, we simulate the parameters and initial values of the proposed model. Furthermore, we calculate the sensitivity of [Formula: see text] to the parameters and find the most sensitive parameters to [Formula: see text]. Finally, we present an improved strategy to achieve the WHO's goal of reducing the incidence of tuberculosis by 90% by 2035 compared to 2015.

The Relevance of Genomic Epidemiology for Control of Tuberculosis in West Africa

Tuberculosis (TB), an airborne infectious disease caused by Mycobacterium tuberculosis complex (MTBC), remains a global health problem. West Africa has a unique epidemiology of TB that is characterized by medium- to high-prevalence. Moreover, the geographical restriction of M. africanum to the sub-region makes West Africa have an extra burden to deal with a two-in-one pathogen. The region is also burdened with low case detection, late reporting, poor treatment adherence leading to development of drug resistance and relapse. Sporadic studies conducted within the subregion report higher burden of drug resistant TB (DRTB) than previously thought. The need for more sensitive and robust tools for routine surveillance as well as to understand the mechanisms of DRTB and transmission dynamics for the design of effective control tools, cannot be overemphasized. The advancement in molecular biology tools including traditional fingerprinting and next generation sequencing (NGS) technologies offer reliable tools for genomic epidemiology. Genomic epidemiology provides in-depth insight of the nature of pathogens, circulating strains and their spread as well as prompt detection of the emergence of new strains. It also offers the opportunity to monitor treatment and evaluate interventions. Furthermore, genomic epidemiology can be used to understand potential emergence and spread of drug resistant strains and resistance mechanisms allowing the design of simple but rapid tools. In this review, we will describe the local epidemiology of MTBC, highlight past and current investigations toward understanding their biology and spread as well as discuss the relevance of genomic epidemiology studies to TB control in West Africa.