-
BMC Microbiology Mar 2021The microbiota of the lower respiratory tract in patients with non-tuberculous mycobacterial pulmonary disease (NTM-PD) has not been fully evaluated. We explored the...
BACKGROUND
The microbiota of the lower respiratory tract in patients with non-tuberculous mycobacterial pulmonary disease (NTM-PD) has not been fully evaluated. We explored the role of the lung microbiota in NTM-PD by analyzing protected specimen brushing (PSB) and bronchial washing samples from patients with NTM-PD obtained using a flexible bronchoscope.
RESULTS
Bronchial washing and PSB samples from the NTM-PD group tended to have fewer OTUs and lower Chao1 richness values compared with those from the control group. In both bronchial washing and PSB samples, beta diversity was significantly lower in the NTM-PD group than in the control group (P = 2.25E-6 and P = 4.13E-4, respectively). Principal component analysis showed that the PSBs and bronchial washings exhibited similar patterns within each group but differed between the two groups. The volcano plots indicated differences in several phyla and genera between the two groups.
CONCLUSIONS
The lower respiratory tract of patients with NTM-PD has a unique microbiota distribution that is low in richness/diversity.
Topics: Adult; Aged; Biodiversity; Female; Humans; Male; Middle Aged; Mycobacterium Infections, Nontuberculous; Nontuberculous Mycobacteria; Republic of Korea; Young Adult
PubMed: 33736609
DOI: 10.1186/s12866-021-02141-1 -
Pathogens and Global Health Feb 2023There are limited studies on the antibiotic resistance patterns of slowly growing mycobacteria (SGM) species and their related gene mutations in Iran. This study aimed...
Drug resistance profiles and related gene mutations in slow-growing non-tuberculous mycobacteria isolated in regional tuberculosis reference laboratories of Iran: a three year cross-sectional study.
There are limited studies on the antibiotic resistance patterns of slowly growing mycobacteria (SGM) species and their related gene mutations in Iran. This study aimed to elucidate the antibiotic susceptibility profiles and the mutations in some genes that are associated with the antibiotic resistance among SGM isolates from Iran. The SGM strains were isolated from sputum samples of suspected tuberculosis (TB) patients. SGM species were identified by standard phenotypic tests and were assigned to species level by amplification and sequencing of the gene. The minimum inhibitory concentration (MIC) of eight antibiotics was determined using broth microdilution method. The mutations in , and genes were investigated in clarithromycin, rifampin, and moxifloxacin resistant isolates using sequencing method. A total of 77 SGM isolates including 46 (59.7%) , 21 (27.3%) , and 10 (13%) (MAC) were detected. The amikacin and linezolid with the susceptibility rates of 97.4% and 1.3% were the most and the least effective antibiotics, respectively. All MAC and isolates, and 32 (69.6%) strains had multiple-drug resistance (MDR) profiles. The , and genes showed various mutations in resistant isolates. Although the current study showed an association among resistance to the clarithromycin, rifampin, and moxifloxacin with mutations in the relevant genes, further research using the whole-genome sequencing is needed to provide a clearer insight into the molecular origins of drug resistance in SGM isolates.
Topics: Humans; Anti-Bacterial Agents; Clarithromycin; Cross-Sectional Studies; Iran; Microbial Sensitivity Tests; Moxifloxacin; Mutation; Mycobacterium Infections, Nontuberculous; Nontuberculous Mycobacteria; Rifampin; Tuberculosis; Drug Resistance, Multiple, Bacterial
PubMed: 35261334
DOI: 10.1080/20477724.2022.2049029 -
Microbiology Spectrum Jun 2024Tuberculosis (TB) and infectious diseases caused by non-tuberculous mycobacteria (NTM) are global concerns. The development of a rapid and accurate diagnostic method,...
Tuberculosis (TB) and infectious diseases caused by non-tuberculous mycobacteria (NTM) are global concerns. The development of a rapid and accurate diagnostic method, capable of detecting and identifying different mycobacteria species, is crucial. We propose a molecular approach, the BiDz-TB/NTM, based on the use of binary deoxyribozyme (BiDz) sensors for the detection of (Mtb) and NTM of clinical interest. A panel of DNA samples was used to evaluate Mtb-BiDz, /-BiDz, -BiDz, /-BiDz, and -BiDz sensors in terms of specificity, sensitivity, accuracy, and limit of detection. The BiDz sensors were designed to hybridize specifically with the genetic signatures of the target species. To obtain the BiDz sensor targets, amplification of a fragment containing the hypervariable region 2 of the 16S rRNA was performed, under asymmetric PCR conditions using the reverse primer designed based on linear-after-the-exponential principles. The BiDz-TB/NTM was able to correctly identify 99.6% of the samples, with 100% sensitivity and 0.99 accuracy. The individual values of specificity, sensitivity, and accuracy, obtained for each BiDz sensor, satisfied the recommendations for new diagnostic methods, with sensitivity of 100%, specificity and accuracy ranging from 98% to 100% and from 0.98 to 1.0, respectively. The limit of detection of BiDz sensors ranged from 12 genome copies (Mtb-BiDz) to 2,110 genome copies (Mkan-BiDz). The BiDz-TB/NTM platform would be able to generate results rapidly, allowing the implementation of the appropriate therapeutic regimen and, consequently, the reduction of morbidity and mortality of patients.IMPORTANCEThis article describes the development and evaluation of a new molecular platform for accurate, sensitive, and specific detection and identification of and other mycobacteria of clinical importance. Based on BiDz sensor technology, this assay prototype is amenable to implementation at the point of care. Our data demonstrate the feasibility of combining the species specificity of BiDz sensors with the sensitivity afforded by asymmetric PCR amplification of target sequences. Preclinical validation of this assay on a large panel of clinical samples supports the further development of this diagnostic tool for the molecular detection of pathogenic mycobacteria.
Topics: Humans; Mycobacterium tuberculosis; Polymerase Chain Reaction; Mycobacterium Infections, Nontuberculous; Nontuberculous Mycobacteria; Sensitivity and Specificity; RNA, Ribosomal, 16S; Tuberculosis; DNA, Bacterial; Biosensing Techniques
PubMed: 38651877
DOI: 10.1128/spectrum.03506-23 -
Indian Journal of Medical Microbiology 2020Non-tuberculous mycobacteria, although identified as pathogenic to humans long time ago, are emerging as the new threat in the past two decades. Even in tuberculosis... (Observational Study)
Observational Study
INTRODUCTION
Non-tuberculous mycobacteria, although identified as pathogenic to humans long time ago, are emerging as the new threat in the past two decades. Even in tuberculosis endemic country such as India, they are being isolated from the clinical specimens more often than previously. This change in trend is of concern, because they are often misdiagnosed as Mycobacterium tuberculosis or even as drug-resistant tuberculosis.
OBJECTIVES
A prospective, observational study was planned to identify the frequency and risk factors associated with pulmonary and extrapulmonary non-tuberculous mycobacterial (NTM) infections. Agreement between two commercially available molecular systems, namely GenoType Mycobacteria CM assay and matrix-assisted laser desorption/ionisation time of flight mass spectrometry (MALDI TOF MS) used in the identification of mycobacterial species is also analysed.
MATERIALS AND METHODS
NTM isolated from pulmonary and extrapulmonary clinical specimens over a period of 1½ year was included in the study. Patient demographics were collected, and the risk factors associated with NTM infections were analyzed. NTM grown on culture was speciated using GenoType Mycobacteria CM assay (HAIN Life Sciences, Germany) and MALDI TOF MS (bioMerieux, France). Drug-susceptibility tests were done for rapid-growing NTM using E-test (bioMerieux, France).
RESULTS
Eight hundred and fifty-four mycobacteria were isolated from 5009 specimens processed during the study period. Out of the mycobacteria grown, 74 (8.7%) were NTM and 780 (91.3%) were Mycobacterium tuberculosis complex. The NTM isolated from pulmonary specimens were 46 (62.16%) and from extrapulmonary sources were 28 (37.84%). The most common species isolated from pulmonary specimens was Mycobacterium intracellulare and from extrapulmonary specimens was Mycobacterium abscessus. Concordance between the two commercial assays used for the identification was 96.49%. The most common risk factor associated with pulmonary NTM was previous lung pathology, while with extrapulmonary NTM infection was previous surgical intervention. Drug-susceptibility tests for rapid growers showed amikacin and clarithromycin as the most active drugs in vitro.
CONCLUSIONS
NTM plays a significant role in causing pulmonary and extrapulmonary infections even in our part of the country with high endemicity of tuberculosis. NTM has emerged as important pathogens even in the immunocompetent patients. There is a need for rapid diagnosis and susceptibility testing of NTM to aid physicians administer timely and appropriate treatment to the patients.
Topics: Anti-Bacterial Agents; Endemic Diseases; Humans; India; Lung; Lung Diseases; Microbial Sensitivity Tests; Mycobacterium Infections, Nontuberculous; Nontuberculous Mycobacteria; Prospective Studies; Risk Factors; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; Tuberculosis
PubMed: 32883930
DOI: 10.4103/ijmm.IJMM_20_274 -
European Journal of Internal Medicine May 2015Multidrug resistant tuberculosis (MDR-TB) presents a great challenge to public health, especially for developing countries. Some nontuberculous mycobacteria (NTM) cause...
INTRODUCTION
Multidrug resistant tuberculosis (MDR-TB) presents a great challenge to public health, especially for developing countries. Some nontuberculous mycobacteria (NTM) cause the similar clinical and radiological characteristics with tuberculosis. We aimed to identify the frequency of NTM infections among subjects who were suspected to have MDR-TB due to lack of response to anti-TB treatment.
METHODS
This retrospective study evaluated patients with suspected MDR-TB due to lack of sputum conversion after 2-3 month therapy with first line anti-TB treatment from 2009 through 2014. Cultures for mycobacteria were performed and identification was done to species level by phenotypic and molecular tests. The outcome of the patients with NTM disease and related risk factors for poor outcome were evaluated.
RESULTS
Out of 117 consecutive strains isolated from suspected MDR-TB subjects, 35 (30%) strains were identified as NTM by using conventional and molecular approaches. Of these patients with positive NTM cultures, 32 (27%) patients met ATS/IDSA diagnostic criteria. Out of 32, 29 (90%) individuals with confirmed NTM diseases had underlying disorders including 8 subjects with malignancy, 5 with organ transplantations, and 4 with the human immunodeficiency virus. No known underlying disorder was found in 3 (9%) subjects. Treatment outcomes were available for 27 subjects, 17 (63%) of whom were cured and 10 (37%) had poor outcome including 6 (60%) who failed and 4 (40%) who died during treatment.
CONCLUSION
The high costs to the patient and society should lead health care providers to consider NTM in all patients suspected of having TB.
Topics: Adult; Aged; Diagnosis, Differential; Female; Humans; Male; Middle Aged; Mycobacterium Infections, Nontuberculous; Nontuberculous Mycobacteria; Retrospective Studies; Risk Factors; Sputum; Treatment Outcome; Tuberculosis, Multidrug-Resistant
PubMed: 25784643
DOI: 10.1016/j.ejim.2015.03.001 -
Brazilian Journal of Microbiology :... 2014Milk is widely consumed in Brazil and can be the vehicle of agent transmission. In this study, was evaluated the occurrence of Mycobacterium bovis and non-tuberculous...
Milk is widely consumed in Brazil and can be the vehicle of agent transmission. In this study, was evaluated the occurrence of Mycobacterium bovis and non-tuberculous mycobacteria (NTM) in raw and pasteurized milk consumed in the northwestern region of Paraná, Brazil. Fifty-two milk samples (20 pasteurized and 32 raw) from dairy farms near the municipality of Maringa, Parana State, Brazil were collected. Milk samples were decontaminated using 5% oxalic acid method and cultured on Lowenstein-Jensen and Stonebrink media at 35 °C and 30 °C, with and without 5-10% CO2. Mycobacteria isolates were identified by morphological features, PCR-Restriction Fragment Length Polymorphism Analysis (PCR-PRA) and Mycolic acids analysis. Thirteen (25%) raw and 2 (4%) pasteurized milk samples were positive for acid fast bacilli growth. Nine different species of NTM were isolated (M. nonchromogenicum, M. peregrinum, M. smegmatis, M. neoaurum, M. fortuitum, M. chelonae, M. flavescens, M. kansasii and M. scrofulaceum). M. bovis was not detected. Raw and pasteurized milk may be considered one source for NTM human infection. The paper reinforces the need for intensification of measures in order to avoid the milk contamination and consequently prevent diseases in the south of Brazil.
Topics: Animals; Bacteriological Techniques; Brazil; Milk; Mycobacterium bovis; Nontuberculous Mycobacteria; Pasteurization; Raw Foods
PubMed: 25242962
DOI: 10.1590/s1517-83822014000200046 -
The European Respiratory Journal Oct 2018Aspiration is associated with nontuberculous mycobacterial (NTM) pulmonary disease and airway dysbiosis is associated with increased inflammation. We examined whether... (Observational Study)
Observational Study
Aspiration is associated with nontuberculous mycobacterial (NTM) pulmonary disease and airway dysbiosis is associated with increased inflammation. We examined whether NTM disease was associated with a distinct airway microbiota and immune profile.297 oral wash and induced sputum samples were collected from 106 participants with respiratory symptoms and imaging abnormalities compatible with NTM. Lower airway samples were obtained in 20 participants undergoing bronchoscopy. 16S rRNA gene and nested mycobacteriome sequencing approaches characterised microbiota composition. In addition, inflammatory profiles of lower airway samples were examined.The prevalence of NTM cultures was 58%. Few changes were noted in microbiota characteristics or composition in oral wash and sputum samples among groups. Among NTM samples, 27% of the lower airway samples were enriched with A mycobacteriome approach identified in a greater percentage of samples, including some nonpathogenic strains. In NTM lower airway samples, taxa identified as oral commensals were associated with increased inflammatory biomarkers.The 16S rRNA gene sequencing approach is not sensitive in identifying NTM among airway samples that are culture-positive. However, associations between lower airway inflammation and microbiota signatures suggest a potential role for these microbes in the inflammatory process in NTM disease.
Topics: Aged; Bronchoalveolar Lavage Fluid; Female; Humans; Male; Microbiota; Middle Aged; Mycobacterium Infections, Nontuberculous; Nontuberculous Mycobacteria; Prospective Studies; RNA, Ribosomal, 16S; Respiratory System; Sputum
PubMed: 30093571
DOI: 10.1183/13993003.00810-2018 -
Emerging Infectious Diseases Nov 2017In Ontario, Canada, during 1998-2010, nontuberculous mycobacteria (NTM) from pulmonary sites comprised 96% of species/patient combinations isolated; annual rates of...
In Ontario, Canada, during 1998-2010, nontuberculous mycobacteria (NTM) from pulmonary sites comprised 96% of species/patient combinations isolated; annual rates of isolation and cases increased steadily. NTM isolates from nonpulmonary sites comprised 4% of species/patient combinations; annual rates and cases were temporally stable. NTM increases were driven exclusively by pulmonary isolates and disease.
Topics: Humans; Lung; Mycobacterium Infections, Nontuberculous; Nontuberculous Mycobacteria; Ontario; Prevalence; Retrospective Studies
PubMed: 29048292
DOI: 10.3201/eid2311.170959 -
Scientific Reports Oct 2018In low-income countries of the Horn of Africa, pulmonary infections are usually considered as tuberculosis, which diagnosis relies on clinical data and positive...
In low-income countries of the Horn of Africa, pulmonary infections are usually considered as tuberculosis, which diagnosis relies on clinical data and positive microscopic observation. This strategy allows non-tuberculous mycobacteria to escape detection, facilitating their emergence in populations. A non-tuberculous mycobacterium strain FB-527 was unexpectedly cultured from the sputum of a Djiboutian patient otherwise diagnosed with multi-drug resistant (MDR) tuberculosis. The sequencing of the rpoB and 16S rRNA genes showed that the isolate was identical to strain FI-09026 previously named "Mycobacterium simulans" and reported only once from a Somali patient. Strain FB-527 mimicked Mycobacterium tuberculosis colonies and enzymatic profile using API ZYM strip and was in vitro resistant to rifampicin and isoniazid. Isolation of two MDR mycobacteria complicated the diagnosis and therapeutic management of the patient. We here report on the complete description of strain FB-527 and strain FI-09026 including genome sequencing, finalizing the description of the proposed new species "Mycobacterium simulans".
Topics: Adult; Africa; Antitubercular Agents; Bacterial Proteins; Drug Resistance, Multiple, Bacterial; Humans; Isoniazid; Male; Microbial Sensitivity Tests; Mycobacterium tuberculosis; Nontuberculous Mycobacteria; Phenotype; Phylogeny; RNA, Ribosomal, 16S; Rifampin; Sputum; Tuberculosis, Multidrug-Resistant
PubMed: 30367075
DOI: 10.1038/s41598-018-33737-9 -
Indian Journal of Medical Microbiology 2016Non-tuberculous mycobacteria (NTM) are emerging as important pathogens. Their treatment also differs from that of Mycobacterium tuberculosis. In India, any datum on them...
BACKGROUND
Non-tuberculous mycobacteria (NTM) are emerging as important pathogens. Their treatment also differs from that of Mycobacterium tuberculosis. In India, any datum on them is scarce as species identification and drug susceptibility are not performed in most laboratories. Susceptibility also differs from one geographic area to another, and in our country, there are no data even to guide the clinicians to start treatment empirically.
METHODOLOGY
The present study endeavours to generate drug susceptibility data on NTM isolated from sputum samples collected and stored from 6445 symptomatics for pulmonary tuberculosis during a prevalence survey and from specimens received from the hospital. Isolates were not necessarily associated with the disease. Species were identified and antibiotic susceptibility was performed using micro-broth dilution technique as per the standard Clinical and Laboratory Standards Institute guidelines.
RESULTS
A total of 65 NTM with 11 species were identified, of which 27 belonged to Mycobacterium fortuitum complex, 14 Mycobacterium gordonae, 9 Mycobacterium avium, 7 Mycobacterium flavescens, 4 Mycobacterium scrofulaceum and one each of others. Sensitivity to amikacin for M. fortuitum was 95.22% (20 out of 21), followed by ciprofloxacin (76.19%) and clarithromycin (71.42%). All the 9 M. avium isolates, 11 of M. gordonae (78.57%), 5 of M. flavescens and 2 of M. scrofulaceum were sensitive to clarithromycin. All NTM were resistant to first-line antitubercular drugs except 8, which were sensitive to streptomycin.
CONCLUSIONS
Drug sensitivity of NTM varies from species to species. While amikacin was the best for rapidly growing mycobacteria, clarithromycin was the most active drug against M. avium and other slow growers.
Topics: Anti-Bacterial Agents; Humans; India; Microbial Sensitivity Tests; Mycobacterium Infections, Nontuberculous; Nontuberculous Mycobacteria; Sputum; Tuberculosis, Pulmonary
PubMed: 27934821
DOI: 10.4103/0255-0857.195375