Distribution of non-tuberculosis mycobacteria strains from suspected tuberculosis patients by heat shock protein 65 PCR-RFLP

Screening and Drug Resistance Analysis of Non-Tuberculous Mycobacteria in Patients with Suspected Pulmonary Tuberculosis on the Hainan Island, China

Background

China has seen a drastic increase in the incidence of non-tuberculous mycobacteria (NTM) infection, which is a notable public health issue. Due to a lack of reliable epidemiological surveillance information, there is a need to gather accurate epidemiological and surveillance data, which can help clinicians effectively treat NTM patients. Moreover, drug susceptibility testing for NTM is not frequently performed in China. This retrospective study, therefore, determined the prevalence and resistance characteristics of NTM to provide a reference to control the NTM epidemic.

Methods

Sputum, alveolar lavage fluid, and other respiratory specimens were collected from 3025 patients with suspected pulmonary tuberculosis attending The Second Affiliated Hospital of Hainan Medical University from January 2014 to December 2021. Strain identification and species distribution of NTM were performed by DNA chip technology and gene sequencing, and the drug resistance of NTM isolates was evaluated by calculating the minimum inhibitory concentration through antimicrobial susceptibility testing for NTM.

Results

From 2014 to 2021, 373 strains of NTM were isolated and identified from respiratory specimens of 3025 suspected tuberculosis patients. Except in 2014, NTM-infected patients accounted for more than 10% of suspected tuberculosis patients in other years. The median age of patients with NTM infection was 62.0 years (53.0, 71.0), and the male-to-female ratio among these patients was 0.79:1. Among culture-positive strains, 12.3% (373/3040; 95% CI 11.1-13.4%) were identified as NTM comprising forty species of NTM. The forty species of NTM included 23 slow-growing mycobacteria (SGM) and 17 rapidly-growing mycobacteria (RGM). Among the NTM isolates, 58.7% (219/373; 95% CI 53.7-63.7%) were SGM and 41.3% (154/373; 95% CI 36.3-46.3%) were RGM. M.avium complex(MAC)(41.3%; 95% CI 36.3-46.3%) and M.abscessus complex (MABC)(33.2%; 95% CI 28.4-38.0%) were the most frequently detected species, followed by M.simiae Complex (11.8%; 95% CI 8.5-15.1%), M.fortuitum group (5.1%; 95% CI 2.9-7.3%), and others. Drug sensitivity test results showed that most of the NTM isolates were susceptible to amikacin and clarithromycin with a drug resistance rate of less than 10%. However, clarithromycin could induce drug resistance, followed by linezolid and moxifloxacin, and their drug resistance rate was less than 50%.

Conclusion

During 2014-2021, the number of NTM isolates detected in the respiratory specimens of the study patients in The Second Affiliated Hospital of Hainan Medical University increased year by year. M. intracellulare is the most common pathogenic NTM species, and there is a high incidence of NTM infection on Hainan Island. Our findings might be of great importance for diagnosing and treating this patient population in Hainan.

Isolation of nontuberculous mycobacteria species from different water sources: a study of six hospitals in Tehran, Iran

Purpose

Nontuberculous mycobacteria (NTM) are ubiquitous bacteria that are naturally resistant to disinfectants and antibiotics and can colonize systems for supplying drinking water. Therefore, this study aimed to evaluate the prevalence of NTM in the drinking water of six hospitals in Tehran, Iran.

Methods

Totally, 198 water samples were collected. Each water sample was filtered via a membrane filter with a pore size of 0.45 µm and then decontaminated by 0.005% cetylpyridinium chloride. The membrane filters were incubated on two Lowenstein-Jensen media at 25 °C and 37 °C for 8 weeks. The positive cultures were identified with phenotypic tests, and then NTM species were detected according to the hsp65, rpoB, and 16S rDNA genes. Drug susceptibility testing (DST) was also carried out.

Results

Overall, 76 (40.4%) of the isolates were slowly growing mycobacteria (SGM) and 112 (59.6%) of the ones were rapidly growing mycobacteria (RGM). The most common NTM were Mycobacterium aurum, M. gordonae, M. phocaicum, M. mucogenicum, M. kansasii, M. simiae, M. gadium, M. lentiflavum, M. fortuitum, and M. porcinum. Among these 188 samples, NTM ranged from 1 to > 300 colony-forming unit (CFU) /500 mL, with a median of 182 CFU/500 mL. In the infectious department of all hospitals, the amount of CFU was higher than in other parts of the hospitals. The DST findings in this study indicated the diversity of resistance to different drugs. Among RGM, M. mucogenicum was the most susceptible isolate; however, M. fortuitum showed a different resistance pattern. Also, among SGM isolates, M. kansasii and M. simiae, the diversity of DST indicated.

Conclusions

The current study showed NTM strains could be an important component of hospital water supplies and a possible source of nosocomial infections according to the CFU reported in this study. The obtained findings also help clarify the dynamics of NTM variety and distribution in the water systems of hospitals in the research area.

Surgical Treatment of Nontuberculous Mycobacterial Pulmonary Disease and a Combination of Nontuberculous Mycobacterium Pulmonary Disease and Pulmonary Tuberculosis

OBJECTIVES

Nontuberculous mycobacterial pulmonary disease (NTMPD) is an important health system problem worldwide. Surgical treatment experience is limited, and the safety of such operations is still unclarified. Therefore, improving our knowledge of NTMPD is important.

DESIGN

In this retrospective observational study, we analyzed the medical records of 2,432 patients operated on from January 2011 through December 2017 in our hospital. There were 20 patients with NTMPD in group 1 and 23 patients with combined NTMPD and pulmonary tuberculosis in group 2. Patients received antibiotic treatment before and after surgery as per Russian Federal clinical guidelines and individual drug susceptibility.

RESULTS

Postoperative complications occurred in 2 (10%) cases in group 1 and 4 (17.4%) in group 2, and intraoperative complications occurred in 2 (8.7%) cases in group 2. There was no 30-day mortality in both groups. After 1 year, all 40 traced patients had neither bacterial excretion nor cavities in the lungs. After 3 years and 5 years, the efficacy among 32 and 13 traced patients was 100%, respectively.

CONCLUSIONS

Modern surgery for small NTMPD forms is safe - helping improve outcomes for ineffective antibiotic treatment. Combined surgery and antibiotic treatment are acceptable in both the short and long term.

Investigation of species distribution of nontuberculosis mycobacteria isolated from sputum samples in patients with suspected pulmonary tuberculosis

Aims

Rapid and accurate identification of mycobacteria is important for the species-specific treatment of the disease. The aim of this study was the identification at the species level of 34 nontuberculous mycobacteria strains isolated from respiratory tract samples and 14 reference strains as by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method.

Materials and Methods

Isolates derived from clinical specimens were subcultured in the Lowenstein-Jensen medium. Deoxyribonucleic acid isolation was carried out using the boiling method. PCR amplification was performed using primers specific to the hsp65 gene region. The PCR products were digested BstEII and HaEIII enzymes. All samples were studied comparatively by two different centers.

Results

In our study, the most common species were found to be Mycobacterium intracellulare in 23.52% (8/34). The performance of the PCR-RFLP method in detecting mycobacteria was found to be 82.35%.

Conclusions

The PCR-RFLP method is a rapid, cheap, and practical method for the identification of mycobacteria.

Nontuberculous Mycobacterial Resistance to Antibiotics and Disinfectants: Challenges Still Ahead

The mortality incidence from nontuberculous mycobacteria (NTM) infections has been steadily developing globally. These bacterial agents were once thought to be innocent environmental saprophytic that are only dangerous to patients with defective lungs or the immunosuppressed. Nevertheless, the emergence of highly resistant NTM to different antibiotics and disinfectants increased the importance of these agents in the health system. Currently, NTM frequently infect seemingly immunocompetent individuals at rising rates. This is of concern as the resistant NTM are difficult to control and treat. The details behind this NTM development are only beginning to be clarified. The current study will provide an overview of the most important NTM resistance mechanisms to not only antibiotics but also the most commonly used disinfectants. Such evaluations can open new doors to improving control strategies and reducing the risk of NTM infection. Moreover, further studies are crucial to uncover this association.

Evaluation of a new assay for nontuberculous mycobacteria species identification in diagnostic material and cultures

The purpose of the present study was to evaluate a real-time PCR system for 12 nontuberculous mycobacteria (NTM) species identification developed by Central Tuberculosis Research Institute (CTRI; Moscow, Russia) in cooperation with Syntol LLC (Moscow, Russia). NTM cultures (210 strains, 19 species), Mycobacterium tuberculosis complex (MTBC) cultures (21 strains, 2 species), non-mycobacterial microorganisms (18 strains, 13 species) were used for the first stage of the assay evaluation. Clinical samples (sputum, N = 973) positive for smear microscopy and MTBC/NTM DNA by a PCR-based screening assay collected from 819 patients were used for specificity and sensitivity evaluation. Sensitivity for determining the NTM species directly from diagnostic material was 99.71%, with the specificity of 100%. The sensitivity and specificity for NTM species identification in cultures was 99.67% and 100%, respectively. Both sensitivity and specificity for determining MTBC in cultures was 100%.

Identification of Nontuberculous Mycobacteria in Patients with Pulmonary Diseases in Gyeongnam, Korea, Using Multiplex PCR and Multigene Sequence-Based Analysis

Background

Nontuberculous mycobacteria (NTM) are widely present in environments, such as soil and water, and have recently been recognized as important pathogenic bacteria. The incidence of NTM-related infections is steadily increasing. As the diagnosis and treatment of NTM infection should be distinguished from tuberculosis, and the treatment should be specific to the species of NTM acquired, accurate species identification is required.

Methods

In this study, two-step multiplex PCR (mPCR) and multigene sequence-based analysis were used to accurately identify NTM species in 320 clinical isolates from Gyeongsang National University Hospital (GNUH). In particular, major mycobacterial strains with a high isolation frequency as well as coinfections with multiple species were diagnosed through two-step mPCR. Multigene sequencing was performed to accurately identify other NTM species not detected by mPCR. Variable regions of the genes 16S rRNA, rpoB, hsp65, and 16S-23S rRNA internal transcribed spacer were included in the analysis.

Results

Two-step mPCR identified 234 (73.1%) cases of M. intracellulare, 26 (8.1%) cases of M. avium subsp. avium, and 13 (4.1%) cases of M. avium subsp. hominissuis infection. Additionally, 9 (2.8%) M. fortuitum, 9 (2.8%) M. massiliense, 2 (0.6%) M. abscessus, and 4 (1.2%) M. kansasii isolates were identified. Coinfection was identified in 7 (2.2%) samples. The sixteen samples not classified by two-step mPCR included 6 (1.9%) cases of M. chimaera, 4 (1.3%) M. gordonae, 1 (0.3%) M. colombiense, 1 (0.3%) M. mageritense, and 1 (0.3%) M. persicum identified by sequence analysis.

Conclusions

The results of this study suggest a strategy for rapid detection and accurate identification of species using two-step mPCR and multigene sequence-based analysis. To the best of our knowledge, this study is the first to report the identification of NTM species isolated from patients in Gyeongnam/Korea.

A case report of wrist synovial infection due to Mycobacterium jacuzzii, Iran

Background

Mycobacterium jacuzzii (M. jacuzzii) was first isolated in 2003 by insertion of breast implants in Tel Aviv, Israel. In this case report, we describe our experience in detection of M. jacuzzii using phenotypic and genotypic test of wrist synovial sample.

Case presentation

A 73-year-old woman complained of pain and swelling in the right wrist for 4 months. Her body temperature was 37–38 °C, and symptoms, such as pain, swelling, and some movement limitation, were reported. Clinical laboratory parameters showed an elevated C-reactive protein (CRP) level, erythrocyte sedimentation rate (ESR), and white blood cells (WBC) count. The sequences of hsp65, rpoB, 16S rDNA, and sodA genes indicated very high homology to M. jacuzzii.

Conclusion

We report a case of synovial infection caused by M. jacuzzii in a patient with severe wrist pain in Iran, who was treated with amikacin, levofloxacin, and ethambutol. The outcomes of treatment after 8 months were positive, and no recurrence of infection was reported in the patient.

Molecular analysis of edible bird's nest and rapid authentication of Aerodramus fuciphagus from its subspecies by PCR-RFLP based on the cytb gene

Edible bird's nest (EBN), for its great nutritional value, is widely used around the world, especially in China and Singapore. EBNs of different origins and types may vary in price and quality. Nowadays, birds' nests are difficult to identify morphologically, except for some whole bird's nests of which origins can be roughly identified. In this study, forty-two samples were collected from different regions for sequencing analysis and phylogenetic classification to initially determine their origins. Two stable enzyme digestion sites were found in the analysis of restriction maps of the species. Then, a quick and specific PCR-RFLP method was established to identify the EBN samples' origins. The genetic identification results indicated that the forty-two samples were from five origins. With the Af/g-486bp-F/R primer and restriction enzyme Taq I, Aerodramus fuciphagus (A. fuciphagus) was efficiently differentiated from the other species. Furthermore, the cytb-592bp-F/R primer and the BamH I enzyme were found to be useful in distinguishing Aerodramus fuciphagus (A. fuciphagus) from its subspecies (Aerodramus germani, A. germani). The PCR-RFLP method provides a potential tool for the rapid discrimination of A. fuciphagus at the species and even the subspecies levels to ensure the quality of the EBN products.

Nontuberculous mycobacteria in patients with suspected tuberculosis and the genetic diversity of Mycobacterium avium in the extreme south of Brazil

Objective:

Nontuberculous mycobacteria (NTM) are a heterogeneous group of bacteria that are widely distributed in nature and associated with opportunistic infections in humans. The aims of this study were to identify NTM in patients with suspected tuberculosis who presented positive cultures and to evaluate the genetic diversity of strains identified as Mycobacterium avium.

Methods:

We studied pulmonary and extrapulmonary samples obtained from 1,248 patients. The samples that tested positive on culture and negative for the M. tuberculosis complex by molecular identification techniques were evaluated by detection of the hsp65 and rpoB genes and sequencing of conserved fragments of these genes. All strains identified as M. avium were genotyped using the eight-locus mycobacterial interspersed repetitive unit-variable-number tandem-repeat method.

Results:

We found that NTM accounted for 25 (7.5%) of the 332 mycobacteria isolated. Of those 25, 18 (72%) were M. avium, 5 (20%) were M. abscessus, 1 (4%) was M. gastri, and 1 (4%) was M. kansasii. The 18 M. avium strains showed high diversity, only two strains being genetically related.

Conclusions:

These results highlight the need to consider the investigation of NTM in patients with suspected active tuberculosis who present with positive cultures, as well as to evaluate the genetic diversity of M. avium strains.

First detection of the invasive Haplosporidian and Mycobacteria parasites hosting the endangered bivalve Pinna nobilis in Thermaikos Gulf, North Greece

Mycobacterium sp. and Haplosporidium pinnae constitute invasive parasite species of bivalves, reported for the first time in the present study in the Aegean Sea and Thermaikos Gulf, respectively. During the last years, the endangered fan mussel (Pinna nobilis) experienced several mortality events in the Mediterranean Sea that caused deaths to 90% or more of their populations and have been attributed to infections by these pathogens. In Greece, two mass mortality events have been recently reported, namely in the Gulf of Kalloni and in Limnos island. In the present study we investigated the presence of both pathogens in P. nobilis from these marine areas as well as from Thermaikos Gulf using both histopathological microscopy and molecular markers. The detected parasite DNA was further quantified in the three populations utilizing a real time qPCR. Histopathological results indicated the presence of a Mycobacterium species alongside with the existence of the Haplosporidian parasite, which was identified in all mortality events in the Mediterranean Sea. The parasite was present in different phases mostly on the digestive gland epithelium. Phylogenetic analysis confirmed the taxonomy of the Haplosporidian parasite as the recently described Haplosporidium pinnae, whereas it failed to identify the Mycobacteria parasite at species level. While Mycobacterium sp. was detected in all examined specimens, H. pinnae was not detected in all diseased fan mussels. Interestingly, monitoring of P. nobilis population from Thermaikos Gulf, an estuary of extremely high importance for bivalve production, revealed the presence of both pathogens in a few specimens in higher quantity but with no symptoms of the disease. Besides, all the specimens from Thermaikos Gulf had inflammatory responses similarly to moribund specimens from mortality events.

Cas12a/Guide RNA-Based Platform for Rapid and Accurate Identification of Major Mycobacterium Species

Mycobacterium tuberculosis infection and nontuberculous mycobacteria (NTM) infections exhibit similar clinical symptoms; however, the therapies for these two types of infections are different. Therefore, the rapid and accurate identification of M. tuberculosis and NTM species is very important for the control of tuberculosis and NTM infections. In the present study, a Cas12a/guide RNA (gRNA)-based platform was developed to identify M. tuberculosis and most NTM species. By designing species-specific gRNA probes targeting the rpoB sequence, a Cas12a/gRNA-based platform successfully identified M. tuberculosis and six major NTM species (Mycobacterium abscessus, Mycobacterium intracellulare, Mycobacterium avium, Mycobacterium kansasii, Mycobacterium gordonae, and Mycobacterium fortuitum) without cross-reactivity. In a blind assessment, a total of 72 out of 73 clinical Mycobacterium isolates were correctly identified, which is consistent with previous rpoB sequencing results. These results suggest that the Cas12a/gRNA-based platform is a promising tool for the rapid, accurate, and cost-effective identification of both M. tuberculosis and NTM species.

Detection of non-tuberculous mycobacterial species using PCR-RFLP analysis in trans-tracheal washes in cattle and buffaloes with respiratory distress

BACKGROUND

Bovine tuberculosis (bTB) is a chronic disease of cattle with high economic importance in livestock farming caused by Mycobacterium bovis and bears a zoonotic potential. There are some non-tuberculous mycobacteria (NTM) which cause disease similar to bTB and interfere with diagnosis of bTB. Non-tuberculous mycobacteria are saprophytic in nature but some of them may cause pulmonary infections, mastitis, lesions in respiratory tract and lymph nodes of cattle, due to which they are being recognized worldwide and interfere with the diagnosis of bTB.

AIMS

The aim of the study was to detect NTM species from cattle and buffaloes with respiratory distress using biochemical test and polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis (PRA).

METHODS

A total of 50 trans-tracheal washes were collected from cattle (n=41) and buffaloes (n=9) with respiratory distress. The samples were inoculated on Middlebrook 7H10 media after proper decontamination with 4% NaOH. The isolate obtained was identified by biochemical testing. Extracted DNA from samples and isolate was subjected to PRA which involved hsp65 gene amplification (439 bp) and RFLP analysis of amplified product.

RESULTS

Out of 50 trans-tracheal washes only one isolate of Mycobacterium kansasii (n=1) (2%) was obtained which was confirmed by biochemical testing and PRA. Mycobacterium kansasii (n=4) (8%), Mycobacterium intracellulare (n=1) (2%), and Mycobacterium vaccae (n=1) (2%) were identified by PRA.

CONCLUSION

The study emphasizes the importance of NTM in animals. Polymerase chain reaction-restriction fragment length polymorphism analysis is a more reliable and rapid method for identification of NTM than conventional methods.

Evaluating the clinical significance of nontuberculous mycobacteria isolated from respiratory samples in Iran: an often overlooked disease

Purpose

Nontuberculous mycobacteria (NTM) infection is an increasing problem worldwide whose clinical significance is still largely unknown. The aim of this study was to investigate the epidemiology of NTM infection from respiratory samples and to determine their clinical significance.

Patients and methods

This cross-sectional study was performed on 7,825 clinical samples from December 2015 to December 2017. Detection was conducted using phenotypic and genotypic (hsp65 PCR-RFLP, rpoB, and 16S rRNA genes sequencing) methods. All clinical information including symptoms and radiological findings was extracted from patients’ records.

Results

A total of 478 were confirmed to have respiratory samples which were culture positive for mycobacteria, with the prevalence of NTM infection obtained as 53 (11.1%). Overall, Mycobacterium (M.) fortuitum was the most frequent NTM isolate, followed by M. simiae, M. kansasii, M. gordonae, and M. conceptionense. There was a relationship between NTM isolates and gender (P=0.039), symptoms (P=0.048), and radiographic findings (P=0.013). Bronchiectasis, infiltration, and cavitary lesion were the most frequent radiological findings in M. fortuitum, M. simiae, and M. kansasii, respectively, with cough being the most frequent symptom.

Conclusion

We reported five different NTM isolates in respiratory samples with a high frequency of M. fortuitum. NTM infections may play an important role in causing pulmonary disease and in tuberculosis management in endemic settings. Nevertheless, more studies are required to further examine the clinical significance of NTM isolates.

Mycobacterium simiae pulmonary disease in Iran: systematic review and meta-analysis

Mycobacterium simiae is one of the most common nontuberculous mycobacteria (NTM) microorganisms causing lung disease in many countries in the world. A reliable estimate of the extent of M. simiae pulmonary disease has not been well investigated in Iran. We systematically searched multiple databases to identify relative studies. Studies were excluded if they did not use the American Thoracic Society (ATS) and Infectious Diseases Society of America (IDSA) diagnostic criteria for NTM diseases. Data were extracted independently and in duplicate. We assessed pooled estimate by using a random model effect, and sources of heterogeneity were assessed by using Cochran's Q and the I 2 statistic. The potential for publication bias was explored by using Begg's and Egger's tests. All analyses were conducted with Stata 14.0 (StataCorp, College Station, TX, USA). Of 172 articles identified, seven met the inclusion criteria. Of 355 patients who were culture positive for NTM, 82 had M. simiae pulmonary disease according to the ATS/IDSA diagnostic criteria. The pooled frequency of M. simiae pulmonary disease among patients with NTM was 25.0% (95% confidence interval, 16.8-33.2). No evidence of publication bias was observed among the included studies (p >0.05 for Begg's and Egger's tests). Clinical isolates of M. simiae are increasingly being recognized as a cause of pulmonary disease in Iran and need further attention by health authorities.

High rates of Mycobacterium fortuitum isolation in respiratory samples from Iranian patients with suspected tuberculosis: is it clinically important?

PURPOSE

Although Mycobacterium fortuitum (M. fortuitum) is not an organism rarely isolated from respiratory samples, its clinical importance is still not fully understood, which therefore prompted our current study.

METHODOLOGY

We evaluated respiratory samples from 6800 patients with suspected tuberculosis from May 2014 to May 2016, for the detection of M. fortuitum using phenotypic and genotyping methods.Results/Key findings. Of the 40 patients with M. fortuitum lung disease, 35 had two or more positive culture results. The mean age of these 35 patients was 50.7±18.4 years, and 20 (57.1 %) were men. Sputum (68.6 %), haemoptysis (51.4 %), cough (45.7 %) and gastroesophageal disease (22.9 %) were the major presenting symptoms. Cystic fibrosis, other bacterial lung diseases and lung cancer were the main underlying pulmonary diseases. Five patients (12.5 %) were human immunodeficiency virus (HIV) positive. The most common chest X-ray findings were reticulonodular opacities (53.3 %). Multivariate logistic regression analysis revealed that cigarette smoking history (OR 0.334, 95 % CI 0.125-0.843, P=0.048) and underlying lung disease (OR 0.393, 95 % CI 0.216-0.588, P=0.023) were significant predictors for positive M. fortuitum infection.

CONCLUSION

These results demonstrated the high frequency of M. fortuitum in respiratory samples and that this bacterium causes transient infection or colonization in patients with underlying pulmonary conditions, such as cystic fibrosis and cigarette smoking-induced. Additionally, it appears that infection with M. fortuitum is particularly common and may be important in patients with HIV.