Modern lineages of Mycobacterium tuberculosis were recently introduced in western India and demonstrate increased transmissibility

Background: Mycobacterium tuberculosis (Mtb) transmissibility may vary between lineages (or variants) and this may contribute to the slow decline of tuberculosis (TB) incidence. The objective of our study was to compare transmissibility across four major lineages (L1-4) of Mtb among participants from two cohort studies in Pune, India. Methods: We performed whole-genome sequencing (WGS) of Mtb sputum culture-positive isolates from participants in two prospective cohort studies of adults with pulmonary TB seeking care at public treatment centers in Pune, Maharashtra. We performed genotypic susceptibility prediction for both first- and second-line drugs using a previously validated random forest model. We used single nucleotide substitutions (SNS) and maximum likelihood estimation to build isolate phylogenies by lineage. We used Bayesian molecular dating to estimate ancestral node ages and compared tree characteristics using a two-sample Kolmogorov-Smirnov (KS) test. Results: Of the 642 isolates from distinct study participants that underwent WGS, 612 met sequence quality criteria. The median age of the 612 participants was 31 years (IQR 24.4-44.2), the majority were male (64.7%) and sputum smear-positive (83.3%), and 6.7% had co-infection with HIV. Most isolates belonged to L3 (44.6%). The majority (61.1%) of multidrug-resistant isolates (MDR, resistant to isoniazid and rifampin) belonged to L2 (P < 0.001 [Fisher's Exact]). There was no significant difference in host characteristics between participants infected with the four major lineages. In phylogenetic analysis, we measured shorter terminal branch lengths in the L2 tree compared to L1 and L3 trees indicating less time elapsing between transmission and sampling and higher transmissibility (median branch lengths: L2 - 3.3, L3 - 7.8, p <0.001). Branching times for L2 and L4 were more recent than L1 and L3 indicating recent introduction into the region (p < 0.01 [KS test]). Conclusion: Modern Mtb lineages (L2 and L4) were more recently introduced in western India, compared to older lineages (L1 and L3). L2 shows a higher frequency of drug-resistance and higher transmissibility. Our findings highlight the need for contact tracing around cases of TB due to L2, and heightened surveillance of TB antibiotic resistance in India.

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1397. Modern Lineages of Mycobacterium tuberculosis Were Recently Introduced in Western India and Demonstrate Increased Transmissibility

Open Forum Infectious Diseases ◽

10.1093/ofid/ofab466.1589 ◽

2021 ◽

Vol 8 (Supplement_1) ◽

pp. S783-S784

Author(s):

Avika Dixit ◽

Anju Kagal ◽

Yasha Ektefaie ◽

Luca Freschi ◽

Rahul Lokhande ◽

...

Keyword(s):

Single Nucleotide Polymorphism ◽

Mycobacterium Tuberculosis ◽

Molecular Dating ◽

Western India ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Branch Lengths ◽

Kolmogorov Smirnov ◽

Study Participants ◽

Ks Test

Abstract Background Mycobacterium tuberculosis (Mtb) transmissibility may vary between lineages (or variants) and this may contribute to the slow decline of tuberculosis incidence. The objective of our study was to compare transmissibility across four major lineages (L1-4) of Mtb in Pune, India. Methods We performed whole-genome sequencing (WGS) of Mtb isolated from sputum culture of adult patients with pulmonary TB. We performed genotypic susceptibility testing for both first- and second-line drugs using a previously validated random forest predictor. We identified single nucleotide polymorphisms and generated a multiple sequence alignment excluding drug resistance conferring mutations to avoid skewing the phylogeny due to convergent evolution in these regions. We used Bayesian molecular dating to generate phylogenies and compared tree characteristics using a two-sample Kolmogorov-Smirnov (KS) test. Results Of the 642 isolates from distinct study participants that underwent WGS, 612 met quality criteria. The median age of participants was 31 years (range 18-74), the majority were male (64.7%) and sputum smear-positive (83.3%), and 6.7% had co-infection with HIV (Table 1). There was no significant difference in baseline characteristics between lineages. The majority of isolates belonged to L3 (44.6%). The majority (61.1%) of multidrug-resistant (MDR, resistant to isoniazid and rifampin) isolates belonged to L2. In phylogenetic analysis, we found evidence of higher transmissibility of L2 as indicated by shorter branch lengths (i.e., less time had elapsed between transmission and sampling) and more genetic similarity (smaller pairwise single nucleotide polymorphism [SNP] distances) among L2 isolates as compared to other lineages (Figure 1). Branching times for L2 and L4 were smaller than L1 and L3 indicating recent introduction into the region (p < 0.001 [KS test]). Figure 1: Lineage-wise distribution of A) phylogenetic tree branch lengths (log) and B) pairwise single nucleotide polymorphism (SNP) distance, using 612 tuberculosis isolates from Pune, India. P values calculated using two-sample Kolmogorov-Smirnov test. Table 1: Demographic characteristics of study participants included in the study, by lineage. Conclusion Modern Mtb lineages (L2 and L4) were relatively recently introduced in western India, as compared to older lineages (L1 and L3), with the more drug-resistant L2 showing higher transmissibility. These findings highlight the need for early detection and treatment initiation to interrupt transmission with important implications for antimicrobial stewardship and heightened surveillance of TB resistance rates. Disclosures All Authors: No reported disclosures

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Population structure, biogeography and transmissibility of Mycobacterium tuberculosis

Nature Communications ◽

10.1038/s41467-021-26248-1 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Luca Freschi ◽

Roger Vargas ◽

Ashaque Husain ◽

S. M. Mostofa Kamal ◽

Alena Skrahina ◽

...

Keyword(s):

Mycobacterium Tuberculosis ◽

Population Structure ◽

Global Scale ◽

Rapid Identification ◽

Genomic Diversity ◽

Terminal Branch ◽

Nucleotide Substitutions ◽

Central Asian ◽

Depth Analysis ◽

Branch Lengths

AbstractMycobacterium tuberculosis is a clonal pathogen proposed to have co-evolved with its human host for millennia, yet our understanding of its genomic diversity and biogeography remains incomplete. Here we use a combination of phylogenetics and dimensionality reduction to reevaluate the population structure of M. tuberculosis, providing an in-depth analysis of the ancient Indo-Oceanic Lineage 1 and the modern Central Asian Lineage 3, and expanding our understanding of Lineages 2 and 4. We assess sub-lineages using genomic sequences from 4939 pan-susceptible strains, and find 30 new genetically distinct clades that we validate in a dataset of 4645 independent isolates. We find a consistent geographically restricted or unrestricted pattern for 20 groups, including three groups of Lineage 1. The distribution of terminal branch lengths across the M. tuberculosis phylogeny supports the hypothesis of a higher transmissibility of Lineages 2 and 4, in comparison with Lineages 3 and 1, on a global scale. We define an expanded barcode of 95 single nucleotide substitutions that allows rapid identification of 69 M. tuberculosis sub-lineages and 26 additional internal groups. Our results paint a higher resolution picture of the M. tuberculosis phylogeny and biogeography.

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

10.1101/2022.01.03.474767 ◽

2022 ◽

Author(s):

Fabrizio Menardo

Keyword(s):

Mycobacterium Tuberculosis ◽

Transmission Rate ◽

Basic Reproductive Number ◽

Infectious Period ◽

Reproductive Number ◽

Data Sets ◽

Terminal Branch ◽

Branch Lengths ◽

Disease Epidemics ◽

Epidemiological Characteristics

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 difference 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, and molecular clock), and found that all these factors, except the length of the infectious period and R0, 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. 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.

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Determination some Immunological Aspects in Pulmonary Tuberculosis Patients in Qadisiyah Province

International Journal of Pharmaceutical Quality Assurance ◽

10.25258/ijpqa.v9i2.13632 ◽

2018 ◽

Vol 9 (2) ◽

Author(s):

Syoof Khowman Alramahy ◽

Akram Hadi Hamza

Keyword(s):

Mycobacterium Tuberculosis ◽

Pulmonary Tuberculosis ◽

Statistical Difference ◽

Positive Culture ◽

Control Group ◽

Tuberculosis Patients ◽

Significant Difference ◽

Lowenstein Jensen ◽

The Mean ◽

Igg Level

This study was carried out to study of some immunological aspects among the pulmonary Tuberculosis patients infected with causative agent, Mycobacterium tuberculosis. A Total of 200 sputum samples were collected from patients attending the consultant Clinic for Chest and Respiratory disease center, Diwaniya. Control group (No=15) also included. According to acid fast stain of sputum, the patients were classified as positive (No=91,45.5%) and negative (No=109,54.5, Lowenstein Jensen medium used for the cultivation of samples, on which 70% of sputum samples where positive culture for this microorganism. The grown microorganism were identified as M. tuberculosis, based on positive A.F.B, Niacin producers ,negative for catlase at 68c. The mean IgG level was l184.053±76.684 mg/100 ml in tuberculosis group compared with 1016.533 ± 44.882 mg/100ml in control group, rendering the statistical difference significant. For IgA and IgM levels, they were at mean of 315.880±38.552 mg/100 ml and 119.527±8.464 mg/100 ml in control group compared with 396.358±38.776 mg/100 ml and 134.207±11.696 mg/100 ml in patients group respectively with significant difference

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Efficacy of electronic cigarettes for tobacco smoking cessation: An adapted systematic review

European Journal of Public Health ◽

10.1093/eurpub/ckaa166.1167 ◽

2020 ◽

Vol 30 (Supplement_5) ◽

Author(s):

T O'Dowd

Keyword(s):

Smoking Cessation ◽

Cohort Studies ◽

Randomised Controlled Trials ◽

Electronic Cigarettes ◽

Controlled Trials ◽

Significant Heterogeneity ◽

Smoking Reduction ◽

Significant Difference ◽

Randomised Controlled

Abstract Background Worldwide smoking remains the leading cause of preventable morbidity and mortality. Electronic cigarettes (ECs) are increasingly used by tobacco smokers as an aid to smoking cessation; however, their efficacy remains uncertain. Methods Electronic databases, clinical trial registries and grey literature sources were searched. The aim was to examine randomised controlled trials or prospective cohort studies, published since the 2016 Cochrane review on this topic, that assessed the efficacy of ECs in achieving smoking cessation among current smokers. Results Two RCTs and five cohort studies, including a total of 16,460 participants, were eligible for inclusion. One RCT found sustained 1-year abstinence of 18.0% in the EC group versus 9.9% in the nicotine replacement therapy group (RR: 1.83; 95% CI 1.30 to 2.58; P < 0.001). The second RCT did not find a statistically significant difference in abstinence rates between EC users and non-users (RR 0.71). Of the five included cohort studies, four reported statistically significant RRs. Two found a positive association (RRs of 1.45 and 1.84) between EC use and smoking cessation but two studies showed EC use was associated with reduced smoking cessation (RRs of 0.25 and 0.35). Due to significant heterogeneity between the studies the data were deemed unsuitable for pooling into a meta-analysis. All trials assessing smoking reduction reported higher rates of reduction among EC users. No serious adverse events were reported with EC use. Follow-up periods of included trials ranged from one to four years, with an average of 1.6 years. Conclusions There is limited, low-quality evidence that ECs are an effective intervention for smoking cessation and smoking reduction. The overall quality of evidence is low as it is based on a small number of studies with inconsistent and imprecise results. Due to the short follow-up periods of the included trials, the long-term safety of ECs is unclear from this review. Key messages Limited evidence that electronic cigarettes are an effective smoking cessation intervention. Further well-designed randomised controlled trials are required to investigate the efficacy of ECs for smoking cessation.

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Tuberculosis contact investigation results among paediatric contacts in low-incidence settings in Finland

European Journal of Pediatrics ◽

10.1007/s00431-021-04000-7 ◽

2021 ◽

Author(s):

Antti Kontturi ◽

Satu Kekomäki ◽

Eeva Ruotsalainen ◽

Eeva Salo

Keyword(s):

Early Diagnosis ◽

Young Children ◽

Large Scale ◽

Index Case ◽

Contact Tracing ◽

Sputum Smear ◽

Endemic Country ◽

Household Contacts ◽

Contact Investigation ◽

Positive Index

AbstractTuberculosis (TB) risk is highest immediately after primary infection, and young children are vulnerable to rapid and severe TB disease. Contact tracing should identify infected children rapidly and simultaneously target resources effectively. We conducted a retrospective review of the paediatric TB contact tracing results in the Hospital District of Helsinki and Uusimaa from 2012 to 2016 and identified risk factors for TB disease or infection. Altogether, 121 index cases had 526 paediatric contacts of whom 34 were diagnosed with TB disease or infection. The maximum delay until first contact investigation visit among the household contacts under 5 years of age with either TB disease or infection was 7 days. The yield for TB disease or infection was 4.6% and 12.8% for household contacts, 0.5% and 0% for contacts exposed in a congregate setting and 1.4% and 5.0% for other contacts, respectively. Contacts born in a TB endemic country (aOR 3.07, 95% CI 1.10–8.57), with household exposure (aOR 2.96, 95% CI 1.33–6.58) or a sputum smear positive index case (aOR 3.96, 95% CI 1.20–13.03) were more likely to have TB disease or infection.Conclusions: Prompt TB investigations and early diagnosis can be achieved with a well-organised contact tracing structure. The risk for TB infection or disease was higher among contacts with household exposure, a sputum smear positive index case or born in a TB endemic country. Large-scale investigations among children exposed in congregate settings can result in a very low yield and should be cautiously targeted. What is Known:• Vulnerable young children are a high priority in contact tracing and should be evaluated as soon as possible after TB exposure What is New:• Prompt investigations for paediatric TB contacts and early diagnosis of infected children can be achieved with a well-organised contact tracing structure• Large-scale investigations among children exposed in congregate settings can result in a very low yield and should be cautiously targeted

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Characterization of Drug-Resistant Lipid-Dependent Differentially Detectable Mycobacterium tuberculosis

Journal of Clinical Medicine ◽

10.3390/jcm10153249 ◽

2021 ◽

Vol 10 (15) ◽

pp. 3249

Author(s):

Annelies W. Mesman ◽

Seung-Hun Baek ◽

Chuan-Chin Huang ◽

Young-Mi Kim ◽

Sang-Nae Cho ◽

...

Keyword(s):

Mycobacterium Tuberculosis ◽

Culture Media ◽

Multidrug Resistant ◽

Culture Conditions ◽

Sputum Smear ◽

Smear Microscopy ◽

Solid Culture ◽

Lowenstein Jensen ◽

Genetic Mechanisms ◽

Lipid Resuscitation

An estimated 15–20% of patients who are treated for pulmonary tuberculosis (TB) are culture-negative at the time of diagnosis. Recent work has focused on the existence of differentially detectable Mycobacterium tuberculosis (Mtb) bacilli that do not grow under routine solid culture conditions without the addition of supplementary stimuli. We identified a cohort of TB patients in Lima, Peru, in whom acid-fast bacilli could be detected by sputum smear microscopy, but from whom Mtb could not be grown in standard solid culture media. When we attempted to re-grow Mtb from the frozen sputum samples of these patients, we found that 10 out of 15 could be grown in a glycerol-poor/lipid-rich medium. These fell into the following two groups: a subset that could be regrown in glycerol after “lipid-resuscitation”, and a group that displayed a heritable glycerol-sensitive phenotype that were unable to grow in the presence of this carbon source. Notably, all of the glycerol-sensitive strains were found to be multidrug resistant. Although whole-genome sequencing of the lipid-resuscitated strains identified 20 unique mutations compared to closely related strains, no single genetic lesion could be associated with this phenotype. In summary, we found that lipid-based media effectively fostered the growth of Mtb from a series of sputum smear-positive samples that were not culturable in glycerol-based Lowenstein–Jensen or 7H9 media, which is consistent with Mtb’s known preference for non-glycolytic sources during infection. Analysis of the recovered strains demonstrated that both genetic and non-genetic mechanisms contribute to the observed differential capturability, and suggested that this phenotype may be associated with drug resistance.

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Comparison of In Vitro Activity and MIC Distributions between the Novel Oxazolidinone Delpazolid and Linezolid against Multidrug-Resistant and Extensively Drug-Resistant Mycobacterium tuberculosis in China

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00165-18 ◽

2018 ◽

Vol 62 (8) ◽

Cited By ~ 18

Author(s):

Zhaojing Zong ◽

Wei Jing ◽

Jin Shi ◽

Shu'an Wen ◽

Tingting Zhang ◽

...

Keyword(s):

Mycobacterium Tuberculosis ◽

Novel Mutation ◽

Multidrug Resistant ◽

23S Rrna ◽

Drug Resistant ◽

Content Type ◽

Extensively Drug Resistant ◽

Significant Difference ◽

Mdr Tb

ABSTRACT Oxazolidinones are efficacious in treating mycobacterial infections, including tuberculosis (TB) caused by drug-resistant Mycobacterium tuberculosis. In this study, we compared the in vitro activities and MIC distributions of delpazolid, a novel oxazolidinone, and linezolid against multidrug-resistant TB (MDR-TB) and extensively drug-resistant TB (XDR-TB) in China. Additionally, genetic mutations in 23S rRNA, rplC, and rplD genes were analyzed to reveal potential mechanisms underlying the observed oxazolidinone resistance. A total of 240 M. tuberculosis isolates were included in this study, including 120 MDR-TB isolates and 120 XDR-TB isolates. Overall, linezolid and delpazolid MIC90 values for M. tuberculosis isolates were 0.25 mg/liter and 0.5 mg/liter, respectively. Based on visual inspection, we tentatively set epidemiological cutoff (ECOFF) values for MIC determinations for linezolid and delpazolid at 1.0 mg/liter and 2.0 mg/liter, respectively. Although no significant difference in resistance rates was observed between linezolid and delpazolid among XDR-TB isolates (P > 0.05), statistical analysis revealed a significantly greater proportion of linezolid-resistant isolates than delpazolid-resistant isolates within the MDR-TB group (P = 0.036). Seven (53.85%) of 13 linezolid-resistant isolates were found to harbor mutations within the three target genes. Additionally, 1 isolate exhibited an amino acid substitution (Arg126His) within the protein encoded by rplD that contributed to high-level resistance to linezolid (MIC of >16 mg/liter), compared to a delpazolid MIC of 0.25. In conclusion, in vitro susceptibility testing revealed that delpazolid antibacterial activity was comparable to that of linezolid. A novel mutation within rplD that endowed M. tuberculosis with linezolid, but not delpazolid, resistance was identified.

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KORELASI ANTARA HASIL TES MIKROSKOPIS DENGAN TES CEPAT MOLEKULER PADA PASIEN TUBERCULOSIS DAN MULTIDRUG RESISTEN TUBERCULOSIS DI RSUD Dr. H CHASAN BOESOIRIE TERNATE

Kieraha Medical Journal ◽

10.33387/kmj.v2i1.2324 ◽

2020 ◽

Vol 2 (1) ◽

Author(s):

Andi Sitti Nur Afiah ◽

Fera The

Keyword(s):

Mycobacterium Tuberculosis ◽

Pulmonary Disease ◽

Program Analysis ◽

Rifampicin Resistance ◽

Test Results ◽

Chi Square ◽

Significant Difference ◽

Mdr Tb ◽

Chi Square Test ◽

Analytical Research

Tuberculosis (TB) is a pulmonary disease caused by Mycobacterium tuberculosis. Globally in 2018 theestimated number of people affected by TB was estimated at 10.0 million population and 484,000 cases ofmultidrug-resistant TB (MDR-TB). This study aims to determine the correlation between microscopic testresults with RMT on TB and MDR-TB patients at RSUD Dr. H Chasan Boesoirie Ternate. This type of researchis analytical research using a retrospective approach. The sample in this study were patients with suspected TBand MDR-TB who had performed microscopic tests and TCM in February – April at 2020 in the ClinicalPathology Laboratory of RSUD Dr. H Chasan Boesoirie Ternate, who met the inclusion and exclusion criteria.Data were analyzed using the SPSS program analysis was carried out in stages, namely by univariate andbivariate using chi-square test. From 100 samples, the results of RMT examination with TB suspects were 30rifampicin sensitive samples with 2 rifampicin resistance and 5 rifampin sensitive samples for TB MDR-TBsuspects RMT examination results. Chi-square test results obtained the value of p = 000 (p <0.05). There is stilla significant difference between the microscopic test results with RMT in TB and MDR-TB suspect patients atRSUD Dr. H Chasan Boesoirie Ternate.

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The efficacy of remdesivir in coronavirus disease 2019 (COVID-19): a systematic review

Iranian Journal of Microbiology ◽

10.18502/ijm.v12i5.4597 ◽

2020 ◽

Author(s):

Amirhossein Roshanshad ◽

Alireza Kamalipour ◽

Mohammad Ali Ashraf ◽

Romina Roshanshad ◽

Sirous Jafari ◽

...

Keyword(s):

Systematic Review ◽

Adverse Event ◽

Cohort Studies ◽

Clinical Improvement ◽

Day Treatment ◽

Mortality Rates ◽

Severe Adverse Event ◽

Adverse Event Rate ◽

Significant Difference ◽

Event Rates

Background and Objectives: Researchers all around the world are working hard to find an effective treatment for the new coronavirus 2019. We performed a comprehensive systematic review to investigate the latest clinical evidence on the efficacy and safety of treatment with Remdesivir in hospitalized patients with COVID-19. Materials and Methods: We performed a systematic search in Pubmed, Embase, Web of Science, Google scholar and MedRxiv for relevant observational and interventional studies. The outcomes measures were mortality rates, improvement rates, time to clinical improvement, all adverse event rates and severe adverse event rates. Results: Three randomized controlled trials and 2 cohort studies were included in our study. In the 2 cohort studies, patients received Remdesivir for 10 days. 2 RCTs evaluated 10-day efficacy of treatment with Remdesivir versus placebo group and the other RCT compared its 5-day regimen versus 10-day regimen. Visual inspection of the forest plots revealed that the efficacy of Remdesivir was not much different in reducing 28-day mortality versus 14-day mortality rates. Besides, 10-day treatment regimen overpowered 5-day treatment and placebo in decreasing time to clinical improvement. All adverse event rates did not have a significant difference; however, severe adverse event rate was lower in the 5-day Remdesivir group compared to the 10-day and placebo groups. Conclusion: 5-day course of Remdesivir therapy in COVID-19 patients is probably efficacious and safe, and patients without invasive mechanical ventilation benefit the most. Treatment can be extended to 10 days if satisfactory improvement is not seen by day 5. Most benefits from Remdesivir therapy take place in the first 14 days of the start of the treatment.

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