The within-host evolution of antimicrobial resistance in Mycobacterium tuberculosis

Tuberculosis (TB) has been responsible for the greatest number of human deaths due to an infectious disease in general, and due to antimicrobial resistance (AMR) in particular. The etiological agents of human TB are a closely-related group of human-adapted bacteria that belong to the Mycobacterium tuberculosis complex (MTBC). Understanding how MTBC populations evolve within-host may allow for improved TB treatment and control strategies. In this Review, we highlight recent works that have shed light on how AMR evolves in MTBC populations within individual patients. We discuss the role of heteroresistance in AMR evolution, and review the bacterial, patient, and environmental factors that likely modulate the magnitude of heteroresistance within-host. We further highlight recent works on the dynamics of MTBC genetic diversity within-host, and discuss how spatial substructures in patients' lungs, spatiotemporal heterogeneity in antimicrobial concentrations, and phenotypic drug tolerance likely modulates the dynamics of MTBC genetic diversity in patients during treatment. We note the general characteristics that are shared between how the MTBC and other bacterial pathogens evolve in humans, and highlight the characteristics unique to the MTBC

Monitoring and characterization of bacterial populations of two biological air filters during the start up phase

[Abstract] This study aimed to monitor and characterize bacterial populations of two biological air filters during their start up phase (four months). The main objective of this work was to assess the potentiality of a microbiological approach to better understand the evolution of the bacterial populations within biofilters and therefore help to select biomass carrier media. The two biological filters were operated at full-scale (480 m3), filled with organic materials and dedicated to the removal of ammonia and Volatile Organic Compounds (VOCs). The first step of the work consisted in developing an extraction method for the biomass fixed on the solid supports. The second step investigated biofilters’ microbial ecology using molecular tools: DAPI (4,6-DiAmino-2- PhenylIndole), TVC (Total Viable Counts), FISH (Fluorescent In Situ Hybridization) and SSCP (Single Strand Conformation Polymorphism). The findings of the experiments did not show a significant evolution of total bacterial concentrations in biofilms of both biological filters during their start up phase. However, SSCP data analysis underlined important variations in the composition of bacterial populations. Finally, examination of the results highlighted the interest to inoculate organic media in order to reduce the acclimation time of microbial populations

Developing customized stepwise MIRU-VNTR typing for tuberculosis surveillance in Georgia

INTRODUCTION: Mycobacterial Interspersed Repetitive Units-Variable Tandem Repeats (MIRU-VNTR) typing has been widely used for molecular epidemiological studies of tuberculosis (TB). However, genotyping tools for Mycobacterium tuberculosis (Mtb) may be limiting in some settings due to high cost and workload. In this study developed a customized stepwise MIRU-VNTR typing that prioritizes high discriminatory loci and validated this method using penitentiary system cohort in the country of Georgia. METHODS: We used a previously generated MIRU-VNTR dataset from recurrent TB cases (32 cases) in Georgia and a new dataset of TB cases from the penitentiary system (102 cases) recruited from 2014 to 2015. A Hunter-Gaston Discriminatory Index (HGDI) was calculated utilizing a 24 standard loci panel, to select high discriminatory power loci, subsequently defined as the customized Georgia-specific set of loci for initial typing. The remaining loci were scored and hierarchically grouped for second and third step typing of the cohort. We then compared the processing time and costs of the customized stepwise method to the standard 24-loci method. RESULTS: For the customized Georgia-specific set that was used for initial typing, 10 loci were selected with a minimum value of 0.32 to the highest HGDI score locus. Customized 10 loci (step 1) typing of 102 Mtb patient isolates revealed 35.7% clustered cases. This proportion was reduced to 19.5% after hierarchical application of 2nd and 3rd step typing with the corresponding groups of loci. Our customized stepwise MIRU-VNTR genotyping approach reduced the quantity of samples to be typed and therefore overall processing time and costs by 42.6% each. CONCLUSION: Our study shows that our customized stepwise MIRU-VNTR typing approach is a valid alternative of standard MIRI-VNTR typing panels for molecular epidemiological investigation in Georgia that saves time, workload and costs. Similar approaches could be developed for other settings

Comparison of Verbal Episodic Memory Measures: Consortium to Establish a Registry for Alzheimer's Disease—Neuropsychological Assessment Battery (CERAD-NAB) versus California Verbal Learning Test (CVLT)

Episodic memory is affected early in the course of dementia. Two well-established tests to assess verbal episodic memory functioning are the Word List task from the Consortium to Establish a Registry for Alzheimer's disease Neuropsychological Assessment Battery (CERAD-NAB) and the California Verbal Learning Test (CVLT). In clinical and/or research settings, patients are typically administered either one or the other test, making statistical comparisons difficult. This study aimed to (i) compare the z-scores of these two tests in patients with MCI and different types of dementia and (ii) establish formulae to transform CERAD-NAB scores into CVLT scores and vice versa. Sixty-five patients completed both tests for the first time and within 10 days of each other. Pearson correlation coefficients indicated that the two tests assess similar aspects of episodic memory and that the CVLT is more sensitive to subtle episodic memory impairments. Finally, conversion formulae are provided and their implementation illustrate

Necessary Optimality Conditions for a Dead Oil Isotherm Optimal Control Problem

We study a system of nonlinear partial differential equations resulting from the traditional modelling of oil engineering within the framework of the mechanics of a continuous medium. Recent results on the problem provide existence, uniqueness and regularity of the optimal solution. Here we obtain the first necessary optimality conditions.Comment: 9 page

Mycobacterium tuberculosis genetic diversity and drug resistance conferring mutations in the Democratic Republic of the Congo

Background: The Democratic Republic of the Congo (DRC) belongs to the 22 tuberculosis (TB) high-burden countries and to the 27 high-burden multidrug-resistant (MDR)-TB countries. To date, there are no data on the genetic diversity of Mycobacterium tuberculosis in the DRC.Objective: To describe the genetic diversity and the distribution of drug resistance conferring mutations of clinical M. tuberculosis isolates from the DRC.Design: We analysed consecutive M. tuberculosis single patient isolates cultured in 2010 at the laboratory of the National TB Control Programme in Kinshasa.Setting: National TB Control Programme in Kinshasa, DRC.Results: Isolates from 50 patients with pulmonary TB were analysed, including 45 patients (90%) who failed treatment. All isolates belonged to the Euro-American lineage (main phylogenetic Lineage 4). Six different spoligotype families were observed within this lineage, including LAM (20 patients, 40%), T (15 patients; 30%), U (4 patients; 8%), S (3 patients; 6%), Haarlem (2 patients; 4%), and X (1 patient; 2%). No M. africanum strains were observed. The most frequently detected drug  resistance-conferring mutations were rpoB S531L and katG S315T1. Various other mutations, including previously unreported mutations, were detected.Conclusions: The Euro-American lineage dominates in the DRC, with substantial variation in spoligotype families. This study fills an important gap on the molecular map of M. tuberculosis in sub-Saharan Africa

First insights into the phylogenetic diversity of Mycobacterium tuberculosis in Nepal

BACKGROUND: Tuberculosis (TB) is a major public health problem in Nepal. Strain variation in Mycobacterium tuberculosis may influence the outcome of TB infection and disease. To date, the phylogenetic diversity of M. tuberculosis in Nepal is unknown. METHODS AND FINDINGS: We analyzed 261 M. tuberculosis isolates recovered from pulmonary TB patients recruited between August 2009 and August 2010 in Nepal. M. tuberculosis lineages were determined by single nucleotide polymorphisms (SNP) typing and spoligotyping. Drug resistance was determined by sequencing the hot spot regions of the relevant target genes. Overall, 164 (62.8%) TB patients were new, and 97 (37.2%) were previously treated. Any drug resistance was detected in 50 (19.2%) isolates, and 16 (6.1%) were multidrug-resistant. The most frequent M. tuberculosis lineage was Lineage 3 (CAS/Delhi) with 106 isolates (40.6%), followed by Lineage 2 (East-Asian lineage, includes Beijing genotype) with 84 isolates (32.2%), Lineage 4 (Euro-American lineage) with 41 (15.7%) isolates, and Lineage 1 (Indo-Oceanic lineage) with 30 isolates (11.5%). Based on spoligotyping, we found 45 different spoligotyping patterns that were previously described. The Beijing (83 isolates, 31.8%) and CAS spoligotype (52, 19.9%) were the dominant spoligotypes. A total of 36 (13.8%) isolates could not be assigned to any known spoligotyping pattern. Lineage 2 was associated with female sex (adjusted odds ratio [aOR] 2.58, 95% confidence interval [95% CI] 1.42-4.67, p = 0.002), and any drug resistance (aOR 2.79; 95% CI 1.43-5.45; p = 0.002). We found no evidence for an association of Lineage 2 with age or BCG vaccination status. CONCLUSIONS: We found a large genetic diversity of M. tuberculosis in Nepal with representation of all four major lineages. Lineages 3 and 2 were dominating. Lineage 2 was associated with clinical characteristics. This study fills an important gap on the map of the M. tuberculosis genetic diversity in the Asian reg

Genome-wide mutational biases fuel transcriptional diversity in the Mycobacterium tuberculosis complex

Abstract: The Mycobacterium tuberculosis complex (MTBC) members display different host-specificities and virulence phenotypes. Here, we have performed a comprehensive RNAseq and methylome analysis of the main clades of the MTBC and discovered unique transcriptional profiles. The majority of genes differentially expressed between the clades encode proteins involved in host interaction and metabolic functions. A significant fraction of changes in gene expression can be explained by positive selection on single mutations that either create or disrupt transcriptional start sites (TSS). Furthermore, we show that clinical strains have different methyltransferases inactivated and thus different methylation patterns. Under the tested conditions, differential methylation has a minor direct role on transcriptomic differences between strains. However, disruption of a methyltransferase in one clinical strain revealed important expression differences suggesting indirect mechanisms of expression regulation. Our study demonstrates that variation in transcriptional profiles are mainly due to TSS mutations and have likely evolved due to differences in host characteristics

The Past and Future of Tuberculosis Research

Renewed efforts in tuberculosis (TB) research have led to important new insights into the biology and epidemiology of this devastating disease. Yet, in the face of the modern epidemics of HIV/AIDS, diabetes, and multidrug resistance—all of which contribute to susceptibility to TB—global control of the disease will remain a formidable challenge for years to come. New high-throughput genomics technologies are already contributing to studies of TB's epidemiology, comparative genomics, evolution, and host–pathogen interaction. We argue here, however, that new multidisciplinary approaches—especially the integration of epidemiology with systems biology in what we call “systems epidemiology”—will be required to eliminate TB