SciCombinator

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Concept: Sputum

27

The aim of this study was to characterize Mycobacterium tuberculosis isolates circulating in the Amhara Region of Ethiopia. Sputum samples were collected from new pulmonary tuberculosis (TB) patients in the Region. Genotyping of mycobacterial DNA was performed by spoligotyping and isolates were assigned to families using the SpolDB4 and the model-based program ‘Spotclust’. A high level of diversity was found among the 237 isolates. Sixty-five different spoligopatterns were obtained. The T (30.8%), Central Asian (CAS; 21.1%) and U (17.7%) families were the predominant isolates comprising 69.6% of the total strains. Eighty-five per cent of the U lineage belonged to Spoligo-International-Type (SIT) 910 and SIT 1729. Only a few of these strains are included in SpolDB4 to date. Of the total strains, 41 (17.3%) were unique and have not been described in SpolDB4 to date. This study indicated that the TB epidemic in Amhara Region, Ethiopia, is characterized by the circulation of numerous M. tuberculosis strain families. The high proportion of SIT 910 and SIT 1729 strains may indicate an increase in the importance of these lineages in the transmission of TB in the study region.

Concepts: Amhara people, Tubercle, Ethiopia, Robert Koch, Sputum, Mycobacterium, Mycobacterium tuberculosis, Tuberculosis

26

Early detection of Mycobacterium tuberculosis complex (MTBC) and markers conveying drug resistance can have a beneficial impact on preventive public-health actions. We describe a new molecular point-of-care (POC) system - Genedrive®- based on a simple sample preparation combined with PCR to provide detection of MTBC and a simultaneous detection of mutation markers in the rpoB gene directly from raw sputa. Hybridization probes were used to report the presence of the key mutations in codons 516, 526, and 531 of the rpoB gene. Sensitivity MTBC and rpoB detection from sputa was assessed using model sputa spiked with known numbers of bacteria prepared from liquid cultures of Mycobacterium tuberculosis. The overall sensitivity was 90.8% (95% CI: 81, 96.5) for MTBC detection and 72.3% (95% CI: 59.8, 82.7) for rpoB detection. For samples ≥1,000 CFU/mL sensitivity was 100% for MTBC and 85.7% for rpoB detection while for samples containing ≤100 CFU/mL was 86.4% and 65.9% for MTBC and rpoB detections, respectively. Specificity was shown to be 100% (95% CI: 83.2, 100) for both MTBC and rpoB. Clinical sputum samples were processed using the same protocol and showed good concordance with data generated from the model. Tuberculosis infected subjects with smear samples assessed as scanty or negative were detectable by the Genedrive®. In these paubacillary patients, the performance of Genedrive® was comparable to GeneXpert®. The characteristics of Genedrive® platform make it particularly useful for MTBC detection and rifampicin resistance in low resource setting and reduce the burden of tuberculosis disease.

Concepts: 175, Bacteria, Rifampicin, Antibiotic resistance, Mycobacterium tuberculosis, Sputum, Mycobacterium, Tuberculosis

23

The Community-Acquired Pneumonia Immunization Trial in Adults (CAPiTA) assessed vaccine-type community-acquired pneumonia (VT-CAP) and vaccine-type invasive pneumococcal disease (VT-IPD) prevention with 13-valent pneumococcal conjugate vaccine (PCV13) in adults aged ⩾65years. We report vaccine efficacy (VE) of PCV13 for the remaining 23 exploratory endpoints and serotype distributions for pneumococcal CAP and IPD.

Concepts: Sputum, Haemophilus influenzae, Vaccine, Pneumococcal vaccine, Pneumococcal polysaccharide vaccine, Pneumococcal conjugate vaccine, Streptococcus pneumoniae, Pneumonia

10

Pneumonia and pneumococcal disease cause a large disease burden in resource-constrained settings. We pursue an extended cost-effectiveness analysis (ECEA) of two fully publicly financed interventions in Ethiopia: pneumococcal vaccination for newborns and pneumonia treatment for under-five children in Ethiopia.

Concepts: Sputum, Haemophilus influenzae, Cost-effectiveness analysis, Pneumococcal polysaccharide vaccine, Public health, Pneumonia, Streptococcus pneumoniae, Health economics

8

Pneumococcal pneumonia causes significant morbidity and mortality among adults. Given limitations of diagnostic tests for non-bacteremic pneumococcal pneumonia, most studies report the incidence of bacteremic or invasive pneumococcal disease (IPD), and thus, grossly underestimate the pneumococcal pneumonia burden. We aimed to develop a conceptual and quantitative strategy to estimate the non-bacteremic disease burden among adults with community-acquired pneumonia (CAP) using systematic study methods and the availability of a urine antigen assay.

Concepts: Pneumococcal infection, Microbiology, Sputum, Haemophilus influenzae, Epidemiology, Pneumococcal polysaccharide vaccine, Streptococcus pneumoniae, Pneumonia

6

Bacteria of the genus Legionella cause water-based infections resulting in severe pneumonia. Here we analyze and compare the bacterial microbiome of sputum samples from pneumonia patients in relation to the presence and abundance of the genus Legionella. The prevalence of Legionella species was determined by culture, PCR, and Next Generation Sequencing (NGS). Nine sputum samples out of the 133 analyzed were PCR-positive using Legionella genus-specific primers. Only one sample was positive by culture. Illumina MiSeq 16S rRNA gene sequencing analyses of Legionella-positive and Legionella-negative sputum samples, confirmed that indeed, Legionella was present in the PCR-positive sputum samples. This approach allowed the identification of the sputum microbiome at the genus level, and for Legionella genus at the species and sub-species level. 42% of the sputum samples were dominated by Streptococcus. Legionella was never the dominating genus and was always accompanied by other respiratory pathogens. Interestingly, sputum samples that were Legionella positive were inhabited by aquatic bacteria that have been observed in an association with amoeba, indicating that amoeba might have transferred Legionella from the drinking water together with its microbiome. This is the first study that demonstrates the sputum major bacterial commensals and pathogens profiles with regard to Legionella presence.

Concepts: Organism, DNA, Pathogen, Ribosomal RNA, Sputum, Pneumonia, 16S ribosomal RNA, Bacteria

6

New treatment options are needed to maintain and improve therapy for tuberculosis, which caused the death of 1.5 million people in 2013 despite potential for an 86 % treatment success rate. A greater understanding of Mycobacterium tuberculosis (M.tb) bacilli that persist through drug therapy will aid drug development programs. Predictive biomarkers for treatment efficacy are also a research priority.

Concepts: Therapy, Sputum, Robert Koch, Pharmacology, Efficacy, Mycobacterium, Mycobacterium tuberculosis, Tuberculosis

6

Undetected and untreated, low-levels of drug resistant (DR) subpopulations in clinical Mycobacterium tuberculosis (Mtb) infections may lead to development of DR-tuberculosis, potentially resulting in treatment failure. Current phenotypic DR susceptibility testing has a theoretical potential for 1% sensitivity, is not quantitative, and requires several weeks to complete. The use of “single molecule-overlapping reads” (SMOR) analysis with next generation DNA sequencing for determination of ultra-rare target alleles in complex mixtures provides increased sensitivity over standard DNA sequencing. Ligation free amplicon sequencing with SMOR analysis enables the detection of resistant allele subpopulations at ≥0.1% of the total Mtb population in near real-time analysis. We describe the method using standardized mixtures of DNA from resistant and susceptible Mtb isolates and the assay’s performance for detecting ultra-rare DR subpopulations in DNA extracted directly from clinical sputum samples. SMOR analysis enables rapid near real-time detection and tracking of previously undetectable DR sub-populations in clinical samples allowing for the evaluation of the clinical relevance of low-level DR subpopulations. This will provide insights into interventions aimed at suppressing minor DR subpopulations before they become clinically significant.

Concepts: Sputum, Mycobacterium, Tuberculosis, Pharmacology, Mycobacterium tuberculosis, Genotype, Gene, Antibiotic resistance

5

Tuberculosis relapse is a barrier to shorter treatment. It is thought that lipid rich cells, phenotypically resistant to antibiotics, may play a major role. Most studies investigating relapse use sputum samples although tissue bacteria may play an important role. We developed a non-destructive, label-free technique combining wavelength modulated Raman (WMR) spectroscopy and fluorescence detection (Nile Red staining) to interrogate Mycobacterium tuberculosis cell state. This approach could differentiate single “dormant” (lipid rich, LR) and “non-dormant” (lipid poor, LP) cells with high sensitivity and specificity. We applied this to experimentally infected guinea pig lung sections and were able to distinguish both cell types showing that the LR phenotype dominates in infected tissue. Both in-vitro and ex-vivo spectra correlated well, showing for the first time that Mycobacterium tuberculosis, likely to be phenotypically resistant to antibiotics, are present in large numbers in tissue. This is an important step in understanding the pathology of relapse supporting the idea that they may be caused by M. tuberculosis cells with lipid inclusions.

Concepts: Mycobacterium, Gene, Sputum, Sensitivity and specificity, Bacteria, Tuberculosis, Mycobacterium tuberculosis

3

African pouched rats sniffing sputum samples provided by local clinics have significantly increased tuberculosis case findings in Tanzania and Mozambique. The objective of this study was to determine the reproducibility of rat results.

Concepts: Rat, Giant pouched rat, Sputum, Mycobacterium, Tuberculosis, Mycobacterium tuberculosis