scholarly journals Molecular detection of Mycobacterium tuberculosis from buccal swabs among adult in Peru

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Annelies W. Mesman ◽  
Roger I. Calderon ◽  
Nira R. Pollock ◽  
Martín Soto ◽  
Milagros Mendoza ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Sputum Sample ◽  
Patient Characteristics ◽  
Sputum Smear ◽  
Buccal Swab ◽  
Sample Type ◽  
Sample Collection ◽  
Safe Alternative ◽  
Fta Cards ◽  
Cavitary Disease

AbstractTuberculosis (TB) diagnosis relies on a sputum sample, which cannot be easily obtained from all symptomatic patients. Mycobacterium tuberculosis DNA can be detected from oral swabs, a noninvasive, safe alternative sample type; however, reported sensitivities have been variable and likely depend on sample collection, processing procedures and host characteristics. We analyzed three buccal swab samples from 123 adults with culture-confirmed TB in Lima, Peru. We compared the sensitivity and specificity of two sample collection devices (OmniSwab and EasiCollect FTA cards) and examined factors associated with detection. DNA was extracted with a commercially available kit and detected via real-time PCR IS6110 amplification. Overall sensitivity for buccal samples was 51% (95% Confidence Interval [CI] 42–60%). Specificity from a single sample among healthy controls was 96.7% (95% CI 83–99.9%). Positive sputum smear and cavitary disease, correlates of disease burden, were associated with detection via buccal swab. Although we observed higher sensitivities with the Omniswab samples, this appeared to be due primarily to differences in patient characteristics (e.g., cavitary disease). Overall, our findings support the potential for a buccal sample-based TB assay. Future work should focus on assay optimization and streamlining the assay workflow.

scholarly journals Detection of Mycobacterium tuberculosis in pediatric stool samples using TruTip technology

2019 ◽  
Author(s):  
AW Mesman ◽  
M Soto ◽  
J Coit ◽  
R Calderon ◽  
J Aliaga ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Sputum Sample ◽  
Multi Drug Resistance ◽  
Sample Type ◽  
Extraction Technology ◽  
Assay Sensitivity ◽  
Positive Stool ◽  
Cavitary Disease ◽  
Amplification System ◽  
Stool Samples

AbstractBackgroundRapid and accurate diagnosis of childhood tuberculosis (TB) is challenging because children are often unable to produce the sputum sample required for conventional tests. Stool is an alternative sample type that is easy to collect from children, and studies investigating the use of stool for molecular detection of Mycobacterium tuberculosis (Mtb) have led to promising results. However, tests performed thus far are not able to examine multi-drug resistance. The TruTip workstation (Akonni Biosystems) is an automated lysis and extraction platform that can be integrated with a closed amplification system to detect both Mtb and resistance-associated mutations. Our objective here was to evaluate the use of TruTip extraction technology for Mtb detection in stool.MethodsWe tested stool samples of 259 children with TB symptoms, ages 0-14 years old, in Lima, Peru. We used the TruTip workstation for sample processing and extraction, followed by IS6110 real-time PCR to detect the presence of Mtb DNA. We calculated assay sensitivity in two groups: (1) children with culture confirmed TB (N=22); and (2) children with unconfirmed, clinically diagnosed TB (N=84). We calculated specificity among children in whom TB was ruled out (N=153). Among children with TB, we examined factors associated with a positive stool test.ResultsOverall assay sensitivity was 59% (95% confidence interval 39%-80%) and 1.2% (0.0%-6.5%) in children with culture-confirmed and clinically-diagnosed TB, respectively, and specificity was 97% (93%-99%). The assay detected Mtb in stool of 7/7 children with smear-positive TB [100% sensitivity; (59%-100%)], and in 6/15 [40% (16%-68%)] of children with smear-negative, culture-confirmed TB. Older age, smear positivity, culture positivity and cavitary disease were associated with a positive stool result.ConclusionFor molecular Mtb detection from stool, the TruTip workstation, in combination with IS6110 amplification, led to sensitivity and specificity estimates comparable to other tests such as Xpert. Future optimization is required to also diagnose TB disease in children who now received an unconfirmed diagnosis.

scholarly journals Porcine reproductive and respiratory syndrome virus RNA detection in different matrices under typical storage conditions in the UK

2019 ◽  
Vol 185 (1) ◽  
pp. 21-21 ◽  
Author(s):  
Jinghui Fan ◽  
Priscilla F Gerber ◽  
Ana Cubas Atienzar ◽  
Lysan Eppink ◽  
Chong Wang ◽  
...  
Keyword(s):  
Storage Condition ◽  
Early Morning ◽  
Respiratory Syndrome Virus ◽  
Blood Collection ◽  
Practical Reasons ◽  
Sample Type ◽  
Sample Collection ◽  
Blood Samples ◽  
Fta Cards ◽  
The Uk

In the UK, approximately 40 per cent of the pig breeding herds are outdoors. To monitor their porcine reproductive and respiratory syndrome virus (PRRSV) status, blood is collected commonly from piglets around weaning. Sample collection in British outdoor pigs often occurs during the early morning hours when the piglets tend to accumulate inside sheltered areas. For practical reasons, dry cotton swabs are occasionally used for blood collection and stored at room temperature until arrival in the laboratory. Detection of PRRSV RNA is a function of viral concentration, sample type and storage condition. To evaluate a possible impact of the sampling protocol on PRRSV1 detection, experimentally spiked blood samples using three dilutions of a representative PRRSV1 strain were prepared. In addition, blood samples from pigs naturally infected with PRRSV were obtained from a PRRSV-positive British herd. Spiked blood and blood from infected pigs were used to obtain sera, dry or wet (immersed in saline) polyester or cotton swabs and FTA cards. The different samples were stored for 24 hours, 48 hours or 7 days at 4°C or 20°C and tested by a real-time reverse transcriptase PRRSV PCR assay. Under the study conditions, the best matrix was serum (96.7 per cent), followed by wet swabs (78 per cent), dry swabs (61.3 per cent) and FTA cards (51 per cent). Polyester swabs (76 per cent) showed a better performance than cotton swabs (63.3 per cent). The reduction in sensitivity obtained for swabs and FTA cards was particularly high at low viral concentrations. The results indicate that wet polyester swabs should be used whenever possible.

scholarly journals Validation of self-collected buccal swab and saliva as a diagnostic tool for COVID-19

2020 ◽  
Author(s):  
Chee Wai Ku ◽  
Durai Shivani ◽  
Jacqueline Q T Kwan ◽  
See Ling Loy ◽  
Christina Erwin ◽  
...  
Keyword(s):  
Large Scale ◽  
Buccal Swab ◽  
Nasopharyngeal Swab ◽  
Sample Collection ◽  
Safe Alternative ◽  
Cross Sectional ◽  
Percent Agreement ◽  
Buccal Swabs ◽  
Single Centre Study ◽  
Saliva Test

ABSTRACTBackgroundEffective management of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) requires large-scale testing. Collection of nasopharyngeal swab (NPS) by healthcare workers (HCW) is currently used to diagnose SARS-CoV-2, which increases the risk of transmission to HCWs. Self-administered saliva and buccal swabs are convenient, painless and safe alternative sample collection methods.MethodsA cross-sectional single centre study was conducted on 42 participants who were tested positive for SARS-CoV-2 via NPS within the past 7 days. A self-collected saliva and buccal swab and a HCW-collected NPS were obtained. Real-time polymerase chain reaction (RT-PCR) was performed and cycle threshold (CT) values were obtained. Positive percent agreement (PPA), negative percent agreement (NPA) and overall agreement (OA) were calculated for saliva and buccal swabs, as compared with NPS.ResultsAmong the 42 participants, 73.8% (31/42) tested positive via any one of the 3 tests. With reference to NPS, the saliva test had PPA 66.7%, NPA 91.7% and OA 69.0%. The buccal swab had PPA 56.7%, NPA 100% and OA 73.8%. Presence of symptoms improved diagnostic accuracy. There was no statistically significant association between CT values and duration of symptom onset within the first 12 days of symptoms for all three modalities.ConclusionSelf-collected saliva tests and buccal swabs have only moderate agreement with HCW-collected NPS swabs. Primary screening for SARS-CoV-2 may be performed with a saliva test or buccal swab, with a negative test warranting a confirmatory NPS to avoid false negatives. This combined strategy minimizes discomfort and reduces the risk of spread to the community and HCWs.

Tuberculosis and Other Mycobacterial Infections

2019 ◽  
Author(s):  
Simon Tiberi
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Sputum Sample ◽  
Interferon Γ ◽  
Sputum Smear ◽  
Rapid Progression ◽  
Course Of Illness ◽  
Mycolic Acids ◽  
Latent Tb Infection ◽  
The Uk ◽  
Factor Α

Mycobacterium tuberculosis (MTB) is a thin, aerobic, non-spore forming, slow-growing (doubling time twelve hours) non-motile rod-shaped bacteria, belonging to the family Mycobacteriaceae. Mycobacterium tuberculosis complex is made up of several species, including M. tuberculosis, M. bovis, Bacillus Calmette-Guerin (BCG), M. africanum, M. canetii, M.caprae, M. microti, and others. Transmission is via inhalation of aerosolized respiratory secretions. After inhalation, majority of bacilli are captured in the upper respiratory tract by mucus and removed through a process called clearance, although bacteria in small droplets can reach the alveoli where the bacilli are ingested by macrophages. If clearance is not effective infection may result. With the involvement of CD4 lymphocytes, interferon-γ and tumour necrosis factor-α, a granuloma is formed, and bacilli may be destroyed. In many cases, the bacilli are not destroyed and can spread into lymphatics or via blood to other sites (any organs) where it can lie dormant for years. This asymptomatic situation is called latent TB infection (LTBI). It may reactivate in 10% of people throughout their lifetime; this increases with immunosuppression and HIV infection. The course of illness is chronic and indolent. However, rapid progression to fulminant disease may result if the host is immunocompromised. Pulmonary TB is the most common and important form of TB because it is the infectious form of the disease. In areas where reactivation predominates (like the UK), there is a higher proportion of extrapulmonary TB. Tuberculosis bacilli resist destaining with acid alcohol treatment hence the term. This retention is due to complexing of the carbolfuschin Ziehl-Neelsen stain with mycolic acids present in the waxy cell wall, including lipoarabinomannan (which facilitates survival in macrophages). Microscopy will diagnose TB in 80% of smear-positive patients with a first sputum sample, a further 15% with the second, and 5% with a third. In endemic areas finding acid-fast bacilli in sputum has a 98% specificity, but this is not the case in the UK, a low-prevalence setting, where atypical mycobacteria can have a similar prevalence. In the best settings only 60% of culture-positive patients are also sputum smear-positive as liquid culture, the gold standard, and most sensitive test.

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

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.

scholarly journals Assessment of Plasmodium antigens and CRP in dried blood spots with multiplex malaria array

2021 ◽  
Author(s):  
Ihn Kyung Jang ◽  
Sara Aranda ◽  
Rebecca Barney ◽  
Andrew Rashid ◽  
Muhammad Helwany ◽  
...  
Keyword(s):  
Thermal Stability ◽  
Whole Blood ◽  
Dried Blood Spots ◽  
Careful Consideration ◽  
Clinical Samples ◽  
Sample Type ◽  
Sample Collection ◽  
Malaria Surveillance ◽  
Inflammatory Biomarker ◽  
Blood Spots

AbstractDried blood spots (DBS) typically prepared on filter papers are an ideal sample type for malaria surveillance by offering easy and cost-effective methods in terms of sample collection, storage, and transport. The objective of this study was to evaluate the applicability of DBS with a commercial multiplex malaria assay, developed to concurrently measure Plasmodium antigens, histidine-rich protein 2 (HRP2), Plasmodium lactate dehydrogenase (pLDH), and a host inflammatory biomarker, C-reactive protein (CRP), in whole blood. The assay conditions were optimized for DBS, and thermal stability for measurement of Plasmodium antigens and CRP in dried blood were determined. Performance of the multiplex assay on matched DBS and whole blood pellet samples was also evaluated using the clinical samples. The results indicate the acceptable performance in multiplex antigen detection using DBS samples. At cutoff levels for DBS, with a diagnostic specificity with a lower 95% confidence bound > 92%, diagnostic sensitivities against polymerase chain reaction (PCR)–confirmed malaria for HRP2, Pf LDH, Pv LDH, and Pan LDH were 93.5%, 80.4%, 21.3%, and 55.6%, respectively. The half-life of pLDH was significantly less than that of HRP2 in thermal stability studies. Results with DBS samples collected from Peru indicate that the uncontrolled storage conditions of DBS can result in inaccurate reporting for infection with P. falciparum parasites with hrp2/3 deletions. With careful consideration that minimizing the unfavorable DBS storage environment is essential for ensuring integrity of heat-labile Plasmodium antigens, DBS samples can be used as an alternative to liquid whole blood to detect P. falciparum with hrp2/3 deletions in malaria surveillance.

scholarly journals Environmental reservoirs of Mycobacterium bovis and Mycobacterium tuberculosis in the Ruaha region, Tanzania

2019 ◽  
Author(s):  
Emma R. Travis ◽  
Yujiun Hung ◽  
David Porter ◽  
Goodluck Paul ◽  
Robert James ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Mycobacterium Bovis ◽  
Bacterial Species ◽  
Sample Type ◽  
Household Dust ◽  
Non Invasive ◽  
Temporal Correlations ◽  
Invasive Test ◽  
Cattle Faeces ◽  
Ruaha National Park

ABSTRACTThis study was designed to investigate the prevalence of members of the Mycobacterium tuberculosis complex (MTBC) in the environment of pastoralists and villagers in the Iringa district, adjacent to the Ruaha National Park in Tanzania. Utilising specific qPCR assays, both Mycobacterium bovis and Mycobacterium tuberculosis were detected in cattle faeces, boma soil, water and household dust. M. bovis was also found in goat faeces and goat boma soil. This is the first report of faecal shedding of M. bovis in goats and the first molecular survey of faecal shedding in cattle. The prevalence of both bacterial species varied by village, area, season and sample type. Geographical and temporal correlations across sample types were suggestive of cross species transmission. This non-invasive test has previously been rigorously validated for screening other mammals; in this study it has successfully been applied to detect M. bovis and M. tuberculosis in livestock faeces and the environment.

scholarly journals Endobronchial tuberculosis: histopathological subsets and microbiological results

2012 ◽  
Vol 7 ◽  
Author(s):  
Sevket Ozkaya ◽  
Salih Bilgin ◽  
Serhat Findik ◽  
Hayriye Çete Kök ◽  
Canan Yuksel ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Lavage Fluid ◽  
Tracheobronchial Tree ◽  
Sputum Smear ◽  
Tuberculous Infection ◽  
Bronchial Lavage ◽  
Culture Positivity ◽  
Endobronchial Tuberculosis ◽  
Smear Negative ◽  
Histopathological Evidence

Background: Endobronchial tuberculosis (EBTB) is defined as a tuberculous infection of the tracheobronchial tree with microbial and histopathological evidence, with or without parenchymal involvement. Bronchoscopic appearances of EBTB have been divided into seven subtypes: actively caseating, edematous-hyperemic, fibrostenotic, tumorous, granular, ulcerative, and nonspecific bronchitic. However, information for establishing a definite microbiological diagnosis in each of these categories is lacking. We aimed to present bronchoscopic appearances and percentages for the EBTB subtypes and to compare bronchoscopic appearances with microbiological positivity in bronchial lavage fluid. Methods: From 2003 to 2009, 23 biopsy-proven EBTB patients were enrolled in the study. Diagnosis of EBTB was histopathologically confirmed in all patients. Results: The commonest subtype was the edematous-hyperemic type (34.7%); other subtypes in order of occurrence were: tumorous (21.7%), granular (17.3%), actively caseating (17.3%), fibrostenotic (4.3%), and nonspecific bronchitic (4.3%). Although all patients were sputum-smear-negative for acid-fast bacilli (AFB), 26% of patients were smear-positive for AFB in the bronchial lavage fluid. The bronchial lavage fluid grew Mycobacterium tuberculosis in 39.1% of all patients. The bronchial lavage smear positivity for AFB in the bronchial lavage fluid was 75%, 25%, 20%, 12.5%, 0%, and 0% for the granular, actively caseating, tumorous, edematous-hyperemic, fibrostenotic, and nonspecific bronchitic subtypes of EBTB, respectively. Culture positivity for Mycobacterium tuberculosis in bronchial lavage fluid was 75%, 50%, 40%, 25%, 0%, and 0%, respectively. Conclusion: The commonest subtype of EBTB was the edematous-hyperemic subtype. The granular type had the highest smear positivity and culture positivity for Mycobacterium tuberculosis in bronchial lavage fluid. Bronchoscopy should be performed in all patients suspected to have EBTB.

scholarly journals Annotated Sequence of Mycobacterium tuberculosis MTBR3/09 Isolated from a Sputum Sample in Malaysia

2016 ◽  
Vol 4 (3) ◽  
Author(s):  
Rahizan Issa ◽  
Valentinus H. Seradja ◽  
Mohd Khairul Hafizi Abdullah ◽  
Hatijah Abdul
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Genome Sequence ◽  
Sputum Sample

This is a report of the annotated genome sequence of Mycobacterium tuberculosis MTBR3/09. The organism was isolated from a sputum sample in Malaysia.

scholarly journals GeneXpert MTB/RIF Assay for Rapid Identification of Mycobacterium Tuberculosis and Rifampicin Resistance Directly from Sputum Sample

2017 ◽  
Vol 7 (2) ◽  
pp. 86-89 ◽  
Author(s):  
Nourjahan Laskar ◽  
Md Akram Hossain ◽  
Jannatul Fardows ◽  
Mominur Rahman
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Sputum Sample ◽  
Rapid Identification ◽  
Rapid Diagnosis ◽  
World Health ◽  
Multi Drug Resistance ◽  
Drug Resistant ◽  
Resistant Tuberculosis ◽  
The World ◽  
Health Organization

Background: The World Health Organization has endorsed the use of molecular methods for the detection of tuberculosis (TB) and drug resistant TB as a rapid method. In Bangladesh, the Xpert MTB/RIF assay has been implemented into reference laboratories for diagnosis of TB and also MDR TB.Objective: Drug resistant tuberculosis has long been a common problem prevailing in our country. The present study focused on the rapid identification of Mycobacterium tuberculosis as well as drug resistance.Materials and Methods: Sputum samples from a total of 107 cases, assumed as multi-drug resistance tuberculosis, were studied through GeneXpert assay.Results: Out of 107 cases, 91 (85.05%) were detected having M. tuberculosis ? 64 (59.81%) were rifampicin sensitive and 27 (25.23%) were rifampicin resistant. The sensitivity and specificity of the GeneXpert are 87.64% and 75% respectively.Conclusion: GeneXpert assay can be considered for the rapid diagnosis of drug resistant tuberculosis.J Enam Med Col 2017; 7(2): 86-89

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