Species identification of mycobacteria by PCR-restriction fragment length polymorphism of the rpoB gene

Clinical Characteristics and Treatment Outcomes of Pulmonary Diseases Caused by Coinfections With Multiple Nontuberculous Mycobacterial Species

BACKGROUND

Coinfections with multiple nontuberculous mycobacterial (NTM) species have not been widely studied. We aimed to evaluate the clinical characteristics and treatment outcomes in patients with NTM-pulmonary disease (PD) caused by coinfection with multiple NTM species.

METHODS

We retrospectively reviewed patients with NTM-PD at a tertiary referral hospital in Korea between March 2012 and December 2018. Coinfection was defined as two or more species of NTM pathogens isolated from the same respiratory specimen or different specimens within three months.

RESULTS

Among 1,009 patients with NTM-PD, 147 (14.6%) NTM coinfections were observed (average age 64.7 years, 69.4% women). NTM species were identified more frequently (median 6 vs. 3 times, P < 0.001) in the coinfection group than in the single species group, and follow-up duration was also longer in the coinfection group (median 44.9 vs. 27.1 months, P < 0.001). Mycobacterium avium complex (MAC) and M. abscessus and M. massiliense (MAB) were the dominant combinations (n = 71, 48.3%). For patients treated for over six months in the MAC plus MAB group (n = 31), sputum culture conversion and microbiological cure were achieved in 67.7% and 41.9% of patients, respectively. We divided the MAC plus MAB coinfection group into three subgroups according to the target mycobacteria; however, no statistical differences were found in the treatment outcomes.

CONCLUSION

In NTM-PD cases, a significant number of multiple NTM species coinfections occurred. Proper identification of all cultured NTM species through follow-up is necessary to detect multispecies coinfections. Further research is needed to understand the nature of NTM-PD in such cases.

Rapid and accurate identification and differentiation of Mycobacterium tuberculosis and non-tuberculous mycobacteria using PCR kits available in a high-burden setting

Infections caused by mycobacteria, including Mycobacterium tuberculosis complex (MTBC) and non-tuberculous mycobacteria (NTM), are a major public health issue worldwide. An accurate diagnosis of mycobacterial species is a challenge for surveillance and treatment, particularly in high-burden settings usually associated with low- and middle-income countries. In this study, we analyzed the clinical performance of two commercial PCR kits designed for the identification and differentiation of MTBC and NTM, available in a high-burden setting such as Ecuador. A total of 109 mycobacteria isolates were included in the study, 59 of which were previously characterized as M. tuberculosis and the other 59 as NTM. Both kits displayed great clinical performance for the identification of M. tuberculosis, with 100% sensitivity. On the other hand, for NTM, one of the kits displayed a good clinical performance with a sensitivity of 94.9% (CI 95%: 89-100%), while the second kit had a reduced sensitivity of 77.1% (CI 95%: 65-89%). In conclusion, one of the kits is a fast and reliable tool for the identification and discrimination of MTBC and NTM from clinical isolates.

The Re-Identification of Previously Unidentifiable Clinical Non-Tuberculous Mycobacterial Isolates Shows Great Species Diversity and the Presence of Other Acid-Fast Genera

Non-tuberculous mycobacteria that cannot be identified at the species level represent a challenge for clinical laboratories, as proper species assignment is key to implementing successful treatments or epidemiological studies. We re-identified forty-eight isolates of Ziehl-Neelsen (ZN)-staining-positive "acid-fast bacilli" (AFB), which were isolated in a clinical laboratory and previously identified as Mycobacterium species but were unidentifiable at the species level with the hsp65 PCR restriction fragment length polymorphism analysis (PRA). As most isolates also could not be identified confidently via 16S, hsp65, or rpoB DNA sequencing and a nBLAST search analysis, we employed a phylogenetic method for their identification using the sequences of the 16S rDNA, which resulted in the identification of most AFB and a Mycobacterium species diversity not found before in our laboratory. Most were rare species with only a few clinical reports. Moreover, although selected with the ZN staining as AFB, not all isolates belonged to the genus Mycobacterium, and we report for the first time in Latin America the isolation of Nocardia puris, Tsukamurella pulmosis, and Gordonia sputi from sputum samples of symptomatic patients. We conclude that ZN staining does not differentiate between the genus Mycobacterium and other genera of AFB. Moreover, there is a need for a simple and more accurate tree-based identification method for mycobacterial species. For this purpose, and in development in our lab, is a web-based identification system using a phylogenetic analysis (including all AFB genera) based on 16S rDNA sequences (and in the future multigene datasets) and the closest relatives.

The Higher Incidence of COVID-19 in Patients With Non-Tuberculous Mycobacterial Pulmonary Disease: A Single Center Experience in Korea

The aim of our study was to investigate the incidence of and risk factors for coronavirus disease 2019 (COVID-19) in patients with non-tuberculous mycobacterial-pulmonary disease (NTM-PD). A total of 3,866 patients with NTM-PD were retrospectively identified from a single center. Compared to the general population of Korea, patients with NTM-PD had a substantially increased age-standardized incidence of COVID-19 from January 2020 to February 2021 (2.1% vs. 0.2%). The odds of being infected with COVID-19 was particularly higher in patients who received treatment for NTM-PD than in those who did not receive treatment for NTM-PD (adjusted odd ratio = 1.99, 95% confidence interval = 1.09-3.64, P = 0.026). Patients with NTM-PD might be regarded as a high-risk group for COVID-19 and may need a more proactive preventive strategy for COVID-19 and other pandemics in the future.

Comparative study of in vitro activity of tedizolid and linezolid against Mycobacterium avium complex

OBJECTIVES

The aim of this study is to compare the in vitro activity and minimal inhibitory concentration (MIC) distributions of tedizolid and linezolid against Mycobacterium avium complex (MAC) strains using a reference broth microdilution assay and a macrodilution assay with the Bactec-MGIT-960.

METHODS

A total of 37 clinical isolates of MAC were included in the study. Reference broth microdilution was performed according to CLSI guidelines in a range of concentrations from 64 to 0.064 mg/L. Macrodilution was performed with the Bactec-MGIT-960 system. The cut-off points defined by CLSI for linezolid (resistant: > 16 mg/L, intermediate: 16 mg/L, susceptible: <16 mg/L) were used to define clinical categories of this drug. Essential agreement for both linezolid and tedizolid and categorical agreement for linezolid were defined following FDA criteria.

RESULTS

The MIC₅₀ (16mg/L) and MIC₉₀ (32mg/L) values for linezolid were identical with both methods. However, the MIC₅₀ and MIC₉₀ of tedizolid by microdilution (4 mg/L and 8 mg/L, respectively) were one twofold dilution higher than by macrodilution (2 mg/L and 4 mg/L, respectively). Ninety-four percent and 2.7% of the strains had MICs of tedizolid ≤4 mg/L and ≤ 0.5 mg/L, respectively, by the reference method. The linezolid macrodilution assay showed a categorical agreement of 40.5%, a minor error rate of 56.7% and a major error rate of 2.7% with respect to the reference method.

CONCLUSIONS

Tedizolid showed higher in vitro activity than linezolid against the tested MAC isolates. Macrodilution using the BD Bactec-MGIT-960 system is a practical approach to determine the susceptibility of MAC strains to tedizolid.

Mycolicibacter acidiphilus sp. nov., an extremely acid-tolerant member of the genus Mycolicibacter

A nonmotile, facultatively anaerobic and rod-shaped bacterial strain, designated M1T was isolated from a bioreactor being operated at pH ~2 at Brisbane, Australia. Colonies appeared to be convex and white. Phylogenetic analysis of its genome revealed an affiliation with the genus Mycolicibacter and its closest species based on 16S rRNA gene analysis were Mycolicibacter algericus DSM 45454T (98.8 % similarity) and Mycolicibacter terrae CIP 104321T (98.8 %) with which strain M1T shared average nucleotide identity of 81.2 % and digital DNA–DNA hybridization similarity of 23.8 %. Strain M1T grew optimally at 0 % NaCl, at pH 6 and at between 30–33 °C. The polar lipid profile of strain M1T consisted of diphosphatidylglycerol, aminophosphoglycolipid, phosphatidylcholine, phospholipid, aminolipid, phosphoglyolipid, phosphatidylglycerol, two unidentified glycolipids and four unidentified lipids. The dominant cellular fatty acids (>10 %) were C16 : 0 and C18 : 1  ω9c and summed feature 7 (C19 : 1  ω7c and/or C19 : 1  ω6c). The DNA G+C content of strain M1T was 69.1 mol%. Based on in silico phylogenomic analysis coupled with physiological and chemotaxonomic characterizations, we classify strain M1T as representing a novel species within the genus Mycolicibacter , for which the name Mycolicibacter acidiphilus nov. is proposed. The type strain is M1T (=MCCC 1H00416T=KCTC 49392T).

Identification of nontuberculous mycobacteria isolated from household showerheads of patients with nontuberculous mycobacteria

This study aimed to examine whether nontuberculous mycobacteria (NTM) inside household showerheads are identical to those in patients with NTM-pulmonary disease (PD) since household water is one of the potential NTM sources. Samples were obtained from 32 household showerheads of patients with NTM-PD recruited through the Pulmonary Outpatient Department at the Severance Hospital between October 2018 and October 2019. All isolates from patients with NTM-PD were diagnosed using a reverse-hybridization line probe assay based on the ropB gene. To determine the mycobacterial compositions, the washing fluids were collected and investigated using multiplex polymerase chain reaction assay and NTM culture; suspected microbial isolates in these fluids and culture were identified using sequencing analysis of 16S rRNA gene. NTM species causing the PD in the patients were Mycobacterium avium, M. intracellulare, M. abscessus, M. massiliense, and M. fortuitum complex. The mycobacteria isolated from the showerhead were M. lentiflavum, M. gordonae, M. triplex, M. phocaicum, M. mucogenicum, M. florentinum, M. gilvum, M. llatzerense, and M. peregrinum. However, the species identified in the showerheads did not match those of the patients. Despite NTM species in the showerheads, clinical implications in the main pathogenesis associated with the disease in the patients studied were not elucidated.

Global prevalence of Mycobacterium bovis infections among human tuberculosis cases: Systematic review and meta-analysis

Tuberculosis (TB) is a chronic communicable bacterial disease caused by Mycobacterium tuberculosis complex (MTBC) species. M. tuberculosis is the main causative agent of human TB, and cattle are the primary host of Mycobacterium bovis; due to close interaction between cattle and humans, M. bovis poses a zoonotic risk. This review summarizes and estimates the prevalence of M. bovis infection among human cases. Studies reporting TB prevalence data that were published in English during 10 years from 20 April 2009 to 17 April 2019 were identified through search of PubMed and other sources. Quality of studies and risk of bias were assessed using standard tools for prevalence study reports. Characteristics of included studies and their main findings were summarized in tables and discussed with narrative syntheses. Meta-analysis was performed on 19 included studies, with a total of 7,185 MTBC isolates identified; 702 (9.7%) of them were characterized as of subspecies M. bovis, but there was a large prevalence difference between the studies, ranging from 0.4% to 76.7%. The genotyping-based studies reported significantly lower prevalence of zoonotic TB than did the studies based on older techniques. The overall pooled prevalence of M. bovis aggregated from all included studies was 12.1% of the total MTBC isolates, while the corresponding pooled figure from the 14 genotyping-based studies was only 1.4%. Generally, human M. bovis cases reported from different countries of the world suggest that the impact of zoonotic TB is still important in all regions. However, it was difficult to understand the true picture of the disease prevalence because of methodological differences. Future investigations on zoonotic TB should carefully consider these differences when evaluating prevalence results.

Early detection of MDR Mycobacterium tuberculosis mutations in Pakistan

The result of improper treatment has led to the rise of Multidrug-resistant (MDR) strains. This concern still exists in Pakistan. In order to save energy, time and resources an early detection of resistant cases is imperative. Thus, a treated group of 100 isolates and a control group of 56 untreated isolates were studied. PCR and gene sequencing showed mutations at codon 531 and 513 in the rpoB gene. 12% of cases showed a double mutation in the rpoB gene. katG gene showed mutations at codon 315 and 299. 28.6% of the control group cases were positive for MDR whereas 100% of the treated group were positive for MDR. This study explores the significantly increasing ratio of MDR-TB among Pakistani population. This study provides prevalent MDR mutations among Pakistanis and suggests developing such molecular assays that are time and cost effective. Importance: Pakistan is a developing country and has fourth highest incidence rate of MDR-TB. The treatment of MDR-TB is the use of second line drugs that has severe side effects as well as it requires long time span. One of the strategies to control the spread of MDR-TB is to decipher the aberrations at molecular level in order to formulate potent drugs that can treat the patients within short span of time. Determining the mutation profile of MDR in Pakistani populations will open new horizons for the improvement of drug treatment regimens to make it more effective or for the development of novel potent drugs and vaccines to better treat the drug-resistant TB. Moreover, this study will be help in disease control program.

Impact of Susceptibility to Injectable Antibiotics on the Treatment Outcomes of Mycobacterium abscessus Pulmonary Disease

Background

Current guidelines recommend a susceptibility-based regimen for Mycobacterium abscessus subspecies abscessus pulmonary disease (MAB-PD), but the evidence is weak. We aimed to investigate the association between treatment outcomes and in vitro drug susceptibility to injectable antibiotics in MAB-PD patients.

Methods

We enrolled MAB-PD patients treated with intravenous amikacin and beta-lactams for ≥4 weeks at 4 referral hospitals in Seoul, South Korea. Culture conversion and microbiological cure at 1 year were evaluated based on susceptibility to injectable antibiotics among patients treated with those antibiotics for ≥2 weeks.

Results

A total of 82 patients were analyzed. The mean age was 58.7 years, and 65.9% were women. Sputum culture conversion and microbiological cure were achieved in 52.4% and 41.5% of patients, respectively. Amikacin was the most common agent to which the M. abscessus subspecies abscessus isolates were susceptible (81.7%); 9.8% and 24.0% of the isolates were resistant to cefoxitin and imipenem, respectively. The clarithromycin-inducible resistance (IR) group (n = 65) had a lower microbiological cure rate than the clarithromycin-susceptible group (35.4% vs 64.7%). The treatment outcomes appeared to be similar regardless of in vitro susceptibility results with regard to intravenous amikacin, cefoxitin, imipenem, and moxifloxacin. In the subgroup analysis of the clarithromycin-IR group, the treatment outcomes did not differ according to antibiotic susceptibility.

Conclusions

We did not find evidence supporting the use of susceptibility-based treatment with intravenous amikacin and beta-lactams in patients with MAB-PD. Further research is required.

Redevelopment after spontaneous sputum conversion in noncavitary nodular bronchiectatic Mycobacterium avium complex lung disease

BACKGROUND

Although spontaneous sputum conversion can occur in noncavitary nodular bronchiectatic (NC-NB) Mycobacterium avium complex lung disease (MAC-LD), little is known about redevelopment after spontaneous conversion. We investigated the redevelopment phenomenon after spontaneous sputum conversion in patients with NC-NB MAC-LD.

MATERIAL AND METHODS

Among patients diagnosed with NC-NB MAC-LD between 2000 and 2013, 140 patients who experienced spontaneous sputum conversion, and whose follow-up duration after conversion was ≥6 months, were enrolled at a tertiary referral center in South Korea. Their medical records were retrospectively reviewed.

RESULTS

Of the 140 patients, 34 (24.3%) underwent redevelopment during the median follow-up period of 71.0 months (interquartile range [IQR], 58.8-87.5). Redevelopment occurred at a median interval of 25.0 months (IQR, 11.5-41.8) after spontaneous sputum conversion. The mean age of the 34 patients with redevelopment was 63.6 years, and 73.5% were women. No statistically significant differences in clinical characteristics were noted between the 34 patients with redevelopment and those with persistent conversion. Among the 34 patients with redevelopment, 6 received treatment at a median interval of 8 months (IQR, 1.5-16.8) after redevelopment. No significant differences in clinical characteristics were noted between the six treated and 28 untreated patients.

CONCLUSION

At least approximately 24% of patients with spontaneous sputum conversion in NC-NB MAC-LD had redevelopment, and a portion of them required treatment. These findings suggest that long-term follow-up is necessary for patients with NC-NB MAC-LD, even those who experience spontaneous sputum conversion.

Cavity formation and its predictors in noncavitary nodular bronchiectatic Mycobacterium avium complex pulmonary disease

INTRODUCTION

The temporal dynamics of cavity formation in patients with the noncavitary nodular bronchiectatic (NC-NB) form of Mycobacterium avium complex pulmonary disease (MAC-PD) have not yet been well described. We aimed to investigate the development of new cavities in the NC-NB form of MAC-PD.

METHODS

Of the patients diagnosed with NC-NB-type MAC-PD between 2002 and 2013 and followed-up until July 2018 at a tertiary referral center in South Korea, we identified 589 patients who underwent follow-up chest computed tomography at least once after the diagnosis and retrospectively analysed their medical records.

RESULTS

The patients' mean age was 62.0 years, 64.7% were women. During the median follow-up of 3.8 years (interquartile range [IQR] 1.7-5.9), new cavity formation was noted in 51 (8.7%) patients. The median interval between the diagnosis of NC-NB MAC-PD and cavity formation was 3.7 years (IQR 1.8-5.4), with a constant occurrence over time. The Cox regression analysis showed that a history of pulmonary tuberculosis (adjusted hazard ratio [HR] 1.85; 95% confidence interval [CI] 1.06-3.23; P = 0.030) and M. intracellulare as the causative organism (adjusted HR 2.03; 95% CI 1.15-3.59; P = 0.014) were independently associated with new cavity formation.

CONCLUSIONS

New cavity formation was noted in 8.7% of the patients with NC-NB MAC-PD in approximately 4 years after diagnosis, particular in those infected with M. intracellulare and those with a previous history of tuberculosis.

Age- and sex-related characteristics of the increasing trend of nontuberculous mycobacteria pulmonary disease in a tertiary hospital in South Korea from 2006 to 2016

BACKGROUND/AIMS

The incidence rate of nontuberculous mycobacterial pulmonary disease (NTM-PD) is increasing worldwide. However, data regarding the age- and sex-specific epidemiology of NTM-PD are limited. This study aimed to investigate the long-term epidemiologic trends of NTM-PD within the recent 11- year period in a tertiary referral hospital in Korea.

METHODS

We retrospectively reviewed the medical records of the patients diagnosed with NTM-PD between January 2006 and December 2016 at Severance Hospital, South Korea.

RESULTS

There were 1,017 incident cases with NTM-PD during the study period. The mean age was 62.7 years, and 41.2% were men. Women were younger than men (59.9 years vs. 66.7 years, p < 0.001) and a higher proportion of women had bronchiectasis (88.6% vs. 77.1%, p < 0.001). The incidence rates of NTM-PD annually increased by 14% (95% confidence interval, 10% to 19%) from 1.2 in 2006 to 4.8 in 2016 (per 100,000 patients-year). The peak incidence rate was in the 50s for women and in the 70s for men, except for those aged ≥ 80 years. Mycobacterium avium complex was the most common causative species of NTM-PD (63.6%).

CONCLUSION

The incidence rate of NTM-PD in a tertiary referral hospital in South Korea continued to increase from 2006 to 2016. Furthermore, there were age- and sex-related differences in the clinical characteristics, which might contribute to understanding the nature of the disease and inherited and acquired host factors.

Association Between Duration of Aminoglycoside Treatment and Outcome of Cavitary Mycobacterium avium Complex Lung Disease

BACKGROUND

Although aminoglycosides are recommended for cavitary Mycobacterium avium complex lung disease (MAC-LD), the optimal duration of treatment is unclear. We investigated the association between duration of aminoglycoside treatment and outcomes in cavitary MAC-LD.

METHODS

Among patients diagnosed with macrolide-susceptible cavitary MAC-LD between 2000 and 2013, 101 who received treatment up to August 2017 with a regimen containing aminoglycosides were enrolled at a tertiary referral center in South Korea. Their medical records were retrospectively reviewed. The duration of aminoglycoside treatment was at the discretion of the attending physician.

RESULTS

A total of 75 patients (74.3%) were administered aminoglycosides for ≥3 months (median 164 days), whereas the remaining 26 patients (25.7%) received treatment for <3 months (median 59 days). The overall treatment success rate was 63.4% (64/101). Patients treated with aminoglycosides for ≥3 months had a significantly higher success rate than those treated for <3 months (69.3% vs 46.2%; P = .035). Multivariate analysis revealed that aminoglycoside treatment for ≥3 months was a significant factor for treatment success (adjusted odds ratio, 3.602; 95% confidence interval, 1.249-10.390; P = .018). Recurrence occurred in 8 (22.9%) of 35 patients who were followed up for at least 3 years after the end of treatment; all 8 patients received aminoglycosides for ≥3 months.

CONCLUSIONS

Patients with cavitary MAC-LD treated with aminoglycosides for ≥3 months showed higher treatment success rate than those treated for <3 months. However, treatment for ≥3 months was not associated with the development of recurrence.

Identification of Nontuberculous Mycobacteria from Clinical Isolates and Specimens using AdvanSure Mycobacteria GenoBlot Assay

The aim of this study was to evaluate the clinical performance of AdvanSure GenoBlot assay using nontuberculous mycobacteria (NTM) isolates and clinical specimens. A total of 136 NTM isolates and 176 clinical specimens were used in this study. AdvanSure Mycobacteria GenoBlot assay was performed according to the manufacturer's instructions. We compared the results with those of 16S rRNA and rpoB genes sequencing. Out of the 136 NTM isolates, 111 (81.6%) were correctly identified to the species level using the GenoBlot assay. The final concordance rate was 89.7% (122/136), including 11 Mycobacterium genus positive control (GPC) results for uncommon NTM. The most common NTM, M. avium, M. fortuitum, M. gordonae, M. intracellulare, M. chelonae, M. abscessus, and M. kansasii, were correctly identified using the GenoBlot assay. For 176 organisms in clinical specimens, 117 were identified to the species level, including single species for 111 specimens and two species for 6 specimens. The final detection and identification rates for clinical specimens were 94.9% and 66.5%, respectively. The AdvanSure GenoBlot assay performs well in identifying the most common NTM, and would be useful in a clinical laboratory.

Outcome of shorter treatment duration in non-cavitary nodular bronchiectatic Mycobacterium avium complex lung disease

Background

The recommended treatment duration for non-cavitary nodular bronchiectatic (NC-NB) Mycobacterium avium complex (MAC) lung disease (LD) is at least 12 months after culture conversion, but evidence supporting this is limited. This study investigated whether treatment for less than 12 months after culture conversion is acceptable in terms of recurrence rate.

Methods

The study enrolled the patients diagnosed with NC-NB MAC LD between 2001 and 2014 at a tertiary referral center in South Korea who received the standard treatment for at least 9 months after culture conversion up to October 2018. The patients were divided into a shorter treatment group (9-11 months after culture conversion) and a standard treatment group (≥12 months).

Results

Of the 228 patients enrolled, 59 (25.9%) were treated for 9-11 months after culture conversion and 169 (74.1%) for ≥12 months. The mean treatment durations after culture conversion in the shorter and standard treatment groups were 11.1 and 13.8 months, respectively (P<0.001). During median follow-up durations after the completion of treatment of 56.5 and 55.9 months, respectively, the recurrence rates in the two groups were similar, at 39.0% (23/59) and 36.7% (62/169). There were also no significant differences between the groups in the 1-year and 3-year recurrence rates.

Conclusions

Post-conversion treatment shorter than the recommended duration may be adequate in terms of recurrence rate for patients with NC-NB MAC LD who receive the standard treatment for at least 9 months after culture conversion.

Nontuberculous mycobacteria in drinking water systems - the challenges of characterization and risk mitigation

Nontuberculous mycobacteria (NTM) pulmonary infections are a growing concern worldwide, with a disproportionate incidence in persons with pre-existing health conditions. NTM have frequently been found in municipally-treated drinking water and building plumbing, leading to the hypothesis that an important source of NTM exposure is drinking water. The identification and quantification of NTM in environmental samples are complicated by genetic variability among NTM species, making it challenging to determine if clinically relevant NTM are present. Additionally, their unique cellular features and lifestyles make NTM and their nucleic acids difficult to recover. This review highlights a recent work focused on quantification and characterization of NTM and on understanding the influence of source water, treatment plants, distribution systems, and building plumbing on the abundance of NTM in drinking water.

The natural history of non-cavitary nodular bronchiectatic Mycobacterium avium complex lung disease

PURPOSE

We aimed to investigate the natural history of non-cavitary nodular bronchiectatic (NC-NB) Mycobacterium avium complex (MAC) lung disease (LD).

METHODS

Among all patients diagnosed with NC-NB MAC LD between March 2000 and December 2013, 551 patients who were followed until December 2017 were enrolled at a tertiary referral center in South Korea. Patients were subdivided into progressive and stationary groups, depending on whether treatment was initiated within 3 years after diagnosis. We investigated the proportion of patients not receiving anti-MAC treatment within 3 years after the diagnosis. The rate for spontaneous sputum conversion in the untreated group was also calculated.

RESULTS

The mean age of 551 patients was 61.1 years. During the median 5.8 years of follow-up, 323 (58.6%) patients received treatment within 3 years (progressive group), whereas the remaining 228 (41.4%) patients did not (stationary group). Multivariate analysis revealed that age ≤ 60 years, a positive sputum smear, the presence of systemic symptoms, body mass index >18.5 kg/m², and the involvement of ≥ 4 lobes were predictors of receiving treatment. Additionally, during the median of 5.0 years follow-up, spontaneous sputum conversion occurred in 52.2% of patients who did not receive treatment.

CONCLUSIONS

Among patients diagnosed with NC-NB MAC LD, approximately 40% did not receive antibiotic treatment within 3 years of diagnosis. Moreover, about 50% of untreated patients experienced spontaneous sputum conversion.

Mycobacterial species and their contribution to cholesterol degradation in wastewater treatment plants

Mycobacterium often presents as an abundant bacterial genus in activated sludge in many wastewater treatment plants (WWTPs), but the species-level taxonomy and functions remain poorly understood. In this study, we profiled the mycobacterial communities in eleven WWTPs from five countries by pyrosequencing the rpoB amplicons and searching against a customized database of mycobacterial rpoB sequences. Results indicated that major mycobacterial species were related to M. brumae, M. crocinum, M. sphagni, etc., most of which belong to poorly characterized rapidly-growing group. A few opportunistic pathogenic species were detected, suggesting the potential risk of mycobacteria in WWTPs. Genomic analysis of four isolates from activated sludge indicated these genomes contained genes of degradations of alkane, aromatics, steroids and a variety of cytochrome P450 families. Additionally, a few key genes responsible for cholesterol degradation were detected in a full-scale activated sludge metatranscriptomic dataset reported previously and taxonomically assigned to mycobacteria. Evidence showed that all isolates can degrade cholesterol, a major composition of sewage. Relative abundance of mycobacteria in activated sludge was enriched by 4.7 folds after adding cholesterol into the influent for one week. Our results provided the insights into mycobacterial species and functions in WWTPs.

In Vitro MIC Values of Rifampin and Ethambutol and Treatment Outcome in Mycobacterium avium Complex Lung Disease

Although it is known that the in vitro MICs of rifampin and ethambutol are poorly correlated with the clinical response in Mycobacterium avium complex (MAC) lung disease (MAC-LD), evidence for this is limited. This study investigated the association between treatment outcome and the in vitro MICs of rifampin and ethambutol in patients with MAC-LD. Among patients diagnosed with macrolide-susceptible MAC-LD between January 2008 and December 2013, 274 patients who were treated with a standard regimen for ≥12 months until August 2017 and whose in vitro MIC results were available were enrolled at a tertiary referral center in South Korea. The MICs of antimicrobial agents were determined using the broth microdilution method. The mean age of the included patients was 60.4 years. The overall treatment success rate was 79.6% (218/274 patients) and tended to decrease with increasing MICs of rifampin and ethambutol, particularly at MICs of ≥8 μg/ml. Treatment success rate was significantly different between MAC isolates with MICs of ≥8 μg/ml for rifampin and ethambutol and those with MICs of <8 μg/ml for rifampin and/or ethambutol (64.9% versus 85.3%, P < 0.001). Multivariate analysis showed that an MIC of ≥8 μg/ml for both drugs and initial sputum acid-fast bacillus (AFB) smear positivity were independent risk factors for an unfavorable response (adjusted odds ratio [OR] = 3.154, 95% confidence interval [CI] = 1.641 to 6.063, and P = 0.001 for an MIC of ≥8 μg/ml; adjusted OR = 2.769, 95% CI = 1.420 to 5.399, and P = 0.003 for initial sputum AFB smear positivity). These findings suggest that the in vitro MICs of rifampin and ethambutol may be related to treatment outcome in MAC-LD.

Six species of nontuberculous mycobacteria carry non-identical 16S rRNA gene copies

Nontuberculous mycobacteria (NTM) can carry two or more 16S rRNA gene copies that are, in some instances, non-identical. In this study, we used a combined cloning and sequencing approach to analyze 16S rRNA gene sequences of six NTM species, Mycobacterium cosmeticum, M. pallens, M. hodleri, M. crocinum, M. flavescens, and M. xenopi. Our approach facilitated the identification of two distinct gene copies in each species. The two M. cosmeticum genes had a single nucleotide difference, whereas two nucleotide polymorphisms were identified in M. hodleri, M. flavescens, and M. xenopi. M. pallens had a difference in four nucleotides and M. crocinum - in 23 nucleotides. Thus, we showed that the six NTM species possess at least two non-identical 16S rRNA gene copies. The full-length sequences of the intraspecies 16S rRNA variants will facilitate NTM identification and sequence analysis of specimens or other samples.

A High-Throughput Approach for Identification of Nontuberculous Mycobacteria in Drinking Water Reveals Relationship between Water Age and Mycobacterium avium

Nontuberculous mycobacteria (NTM) frequently detected in drinking water (DW) include species associated with human infections, as well as species rarely linked to disease. Methods for improved the recovery of NTM DNA and high-throughput identification of NTM are needed for risk assessment of NTM infection through DW exposure. In this study, different methods of recovering bacterial DNA from DW were compared, revealing that a phenol-chloroform DNA extraction method yielded two to four times as much total DNA and eight times as much NTM DNA as two commercial DNA extraction kits. This method, combined with high-throughput, single-molecule real-time sequencing of NTM rpoB genes, allowed the identification of NTM to the species, subspecies, and (in some cases) strain levels. This approach was applied to DW samples collected from 15 households serviced by a chloraminated distribution system, with homes located in areas representing short (<24 h) and long (>24 h) distribution system residence times. Multivariate statistical analysis revealed that greater water age (i.e., combined distribution system residence time and home plumbing stagnation time) was associated with a greater relative abundance of Mycobacterium avium subsp. avium, one of the most prevalent NTM causing infections in humans. DW from homes closer to the treatment plant (with a shorter water age) contained more diverse NTM species, including Mycobacterium abscessus and Mycobacterium chelonae. Overall, our approach allows NTM identification to the species and subspecies levels and can be used in future studies to assess the risk of waterborne infection by providing insight into the similarity between environmental and infection-associated NTM.

An extraction method for improved recovery of DNA from nontuberculous mycobacteria (NTM), combined with single-molecule real-time sequencing (PacBio) of NTM rpoB genes, was used for high-throughput characterization of NTM species and in some cases strains in drinking water (DW). The extraction procedure recovered, on average, eight times as much NTM DNA and three times as much total DNA from DW as two widely used commercial DNA extraction kits. The combined DNA extraction and sequencing approach allowed high-throughput screening of DW samples to identify NTM, revealing that the relative abundance of Mycobacterium avium subsp. avium increased with water age. Furthermore, the two-step barcoding approach developed as part of the PacBio sequencing method makes this procedure highly adaptable, allowing it to be used for other target genes and species.

Identification of nontuberculous mycobacteria isolated from hospital water by sequence analysis of the hsp65 and 16S rRNA genes

Nontuberculous mycobacteria (NTM) have emerged as an important cause of opportunistic nosocomial infections. NTM has frequently been isolated from hospital water distribution systems. The aim of this study was to survey the risk of NTM infections and determine the prevalence of NTM species in the hospital water distribution systems in Tabriz, Iran. One hundred and twenty samples of water from different sources of Tabriz hospitals were collected. The samples were filtered through 0.45-µm pore size membranes and decontaminated with 0.01% cetylpyridinium chloride. The sediment was inoculated onto Lowenstein-Jensen medium and incubated for 8 weeks. For identification to the species level, partial sequence analysis of the hsp65 and 16S rRNA genes were used. NTM were detected in 76 (63.3%) of 120 samples. Potentially pathogenic mycobacteria and saprophytic mycobacteria were isolated. Mycobacterium gordonae was the only single species that was present in all types of water. The prevalence of NTM in Tabriz hospitals' water compared with many investigations on hospital waters was high. This indicates that the immunocompromised patients and transplant recipients are at risk of contamination which necessitates considering decontamination of water sources to prevent such potential hazards.

Performance of the Quantamatrix Multiplexed Assay Platform system for the differentiation and identification of Mycobacterium species

PURPOSE

The purpose of this study was to evaluate the usefulness of a new diagnostic multiplexed bead-based bioassay (Quantamatrix Multiplexed Assay Platform; QMAP) system with shape-encoded silica microparticles for the rapid and accurate detection and identification of 23 mycobacterial species/groups, including Mycobacterium tuberculosis complex (MTBC).

METHODOLOGY

A total of 295 mycobacterial clinical isolates cultured from respiratory specimens were used for identification of MTBC and non-tuberculous mycobacteria (NTM) using the QMAP system and the results were confirmed with PCR-restriction fragment length polymorphism (RFLP) analysis of the rpoB gene, rpoB sequence analysis and PCR-reverse blot hybridization assay (REBA).Results/Key findings. The Mycobacterium genus-specific probe of the QMAP system was positive for all 46 Mycobacterium reference strains and negative for 59 non-Mycobacterium strains. Based on 295 liquid culture-positive samples, both the culture-based conventional identification method and the QMAP system identified each 212 and 81 isolates as MTB and NTM species. The concordance rates for the identification of NTM species between the QMAP system and molecular assays were 92.8 % (77/83), 97.6 % (81/83) and 100 % (83/83) for PCR-RFLP, the rpoB sequence analysis and PCR-REBA, respectively.

CONCLUSION

The QMAP system yielded rapid, highly sensitive and specific results for the identification of MTBC and NTM and accurately discriminated between NTM species within 3 h.

Evaluation of the Quantamatrix Multiplexed Assay Platform system for simultaneous detection of Mycobacterium tuberculosis and the rifampicin resistance gene using cultured mycobacteria

BACKGROUND

The differentiation of Mycobacterium tuberculosis complex (MTBC) from non-tuberculous mycobacteria (NTM) is of primary importance for infection control and the selection of anti-tuberculosis drugs. Up to date data on rifampicin (RIF)-resistant tuberculosis (TB) is essential for the early management of multidrug-resistant TB. The aim of this study was to evaluate the usefulness of a newly developed multiplexed, bead-based bioassay (Quantamatrix Multiplexed Assay Platform, QMAP) for the rapid differentiation of 23 Mycobacterium species including MTBC and RIF-resistant strains.

METHODS

A total of 314 clinical Mycobacterium isolates cultured from respiratory specimens were used in this study.

RESULTS

The sensitivity and specificity of the QMAP system for Mycobacterium species were 100% (95% CI 99.15-100%, p<0.0001) and 97.8% (95% CI 91.86-99.87%, p<0.0001), respectively. The results of conventional drug susceptibility testing and the QMAP Dual-ID assay were completely concordant for all clinical isolates (100%, 95% CI 98.56-100%). Out of 223 M. tuberculosis (MTB) isolates, 196 were pan-susceptible and 27 were resistant to RIF according to QMAP results. All of the mutations in the RIF resistance-determining region detected by the QMAP system were confirmed by rpoB sequence analysis and a REBA MTB-Rifa reverse blot hybridization assay. The majority of the mutations (n=26, 96.3%), including those missing wild-type probe signals, were located in three codons (529-534, 524-529, and 514-520), and 17 (65.4%) of these mutations were detected by three mutation probes (531TTG, 526TAC, and 516GTC).

CONCLUSIONS

The entire QMAP system assay takes about 3h to complete, while results from the culture-based conventional method can take up to 48-72h. Although improvements to the QMAP system are needed for direct respiratory specimens, it may be useful for rapid screening, not only to identify and accurately discriminate MTBC from NTM, but also to identify RIF-resistant MTB strains in positive culture samples.

Isolation and identification of multiple drug resistant nontuberculous mycobacteria from organs of cattle produced typical granuloma lesions

Nontuberculosis mycobacteria are widespread in the environment and some are zoonotic. 320 tissue samples with visible lesions were obtained from dairy cows and examined by histopathology. Eleven samples showed typical granulomatous lesions and a total of 8 strains were cultured. Three genes (16S rRNA, hsp65 and rpoB) were sequenced for species identification. All mycobacterial isolates were tested for rifampicin, isoniazid, ethambutol, streptomycin, capreomycin, kanamycin, para-aminosalicylic acid susceptibility. Six strains were identified as M. fortuitum, 1 was M. avium, 1 was M. conceptionense, isolated from cattle for the first time. Seven of the 8 isolated strains showed multiple drug resistance.

Natural history of Mycobacterium avium complex lung disease in untreated patients with stable course

Little is known about the long-term natural history of Mycobacterium avium complex lung disease (MAC-LD) in untreated patients with stable course.The aim of this study was to investigate the natural course of untreated stable MAC-LD, with a focus on factors associated with clinical deterioration, spontaneous sputum conversion and prognosis.Of 488 patients diagnosed with MAC-LD between 1998 and 2011, 305 patients (62.5%) showed progressive MAC-LD resulting in treatment initiation within 3 years of diagnosis and 115 patients (23.6%) exhibited stable MAC-LD for at least 3 years with a median follow-up duration of 5.6 years. Patients with stable MAC-LD were more likely to have higher body mass index and less systemic symptoms at initial diagnosis compared with patients with progressive MAC-LD, while positive sputum acid-fast bacilli smear, fibrocavitary type and more extensive disease in radiological findings were more associated with progressive MAC-LD. Of the untreated patients with stable MAC-LD, 51.6% underwent spontaneous sputum conversion, with younger age, higher body mass index and negative sputum acid-fast bacilli smear at initial diagnosis found to be predictors of this occurrence.Advanced age, fibrocavitary type and abnormal pulmonary function were negative prognostic factors for survival in patients with stable MAC-LD.

Identification of Species of Nontuberculous Mycobacteria Clinical Isolates from 8 Provinces of China

Pulmonary diseases caused by nontuberculous mycobacteria (NTM) are increasing in incidence and prevalence worldwide. In this study, we identified NTM species of the clinical isolates from 8 provinces in China, in order to preliminarily provide some basic scientific data in the different species and distribution of NTM related to pulmonary disease in China. A total of 523 clinical isolates from patients with tuberculosis (TB) diagnosed clinically from 2005 to 2012 were identified to the species using conventional and molecular methods, including multilocus PCR, rpoB and hsp65 PCR-PRA, hsp65, rpoB, and 16S-23S internal transcribed spacer region sequencing. The isolates were identified into 3 bacterium genera, including NTM, Gordonia bronchialis, and Nocardia farcinica, and, for the 488 NTM isolates, 27 species were identified. For all the 27 species of NTM which were found to cause pulmonary infections in humans, the most prevalent species was M. intracellulare, followed by M. avium and M. abscessus. And seven other species were for the first time identified in patients with TB in China. NTM species identification is very important for distinguishing between tuberculosis and NTM pulmonary diseases, and the species diversity drives the creation of diverse and integrated identification methods with higher accuracy and efficacy.

Mycobacterium haemophilum infection in a juvenile leatherback sea turtle (Dermochelys coriacea)

Mycobacteriosis is infrequently reported in free-ranging sea turtles. Nontuberculous Mycobacterium haemophilum was identified as the causative agent of disseminated mycobacteriosis in a juvenile leatherback turtle (Dermochelys coriacea) that was found stranded on the Atlantic coast of Florida. Disseminated granulomatous inflammation was identified histologically, most notably affecting the nervous system. Identification of mycobacterial infection was based on cytologic, molecular, histologic, and microbiologic methods. Among stranded sea turtles received for diagnostic evaluation from the Atlantic and Gulf of Mexico coasts of the United States between 2004 and 2015, the diagnosis of mycobacteriosis was overrepresented in stranded oceanic-phase juveniles compared with larger size classes, which suggests potential differences in susceptibility or exposure among different life phases in this region. We describe M. haemophilum in a sea turtle, which contributes to the knowledge of diseases of small juvenile sea turtles, an especially cryptic life phase of the leatherback turtle.

Changes in cholesterol level correlate with the course of pulmonary nontuberculous mycobacterial disease

BACKGROUND

Nutritional assessment is important in patients with pulmonary nontuberculous mycobacterial (PNTM) disease. The therapeutic effect of a cholesterol-rich diet in tuberculosis (TB) patients has been demonstrated, but the role of cholesterol in PNTM disease is unclear. This study evaluated the sequential changes in nutritional markers, including cholesterol, total lymphocyte count and visceral fat volume, according to the PNTM disease course.

METHODS

This was an age-, sex- and number of comorbid diseases-matched case-control analysis of 89 patients with PNTM disease and 356 controls, who were participants in a Korean national survey.

RESULTS

The median body mass index (BMI) and cholesterol level in the PNTM group [BMI =19.7 kg/m²; interquartile range (IQR): 17.8-21.6; cholesterol: 159 mg/dL; IQR, 135-185] were lower than those in controls (BMI: 23.1 kg/m²; IQR, 21.3-25.3; cholesterol: 188 mg/dL; IQR, 164-217; both P<0.001). In a multivariate analysis, Age more than 70 years (OR =3.38; 95% CI: 1.13-10.15, P=0.029), BMI <19.5 kg/m² (OR =5.09; 95% CI: 1.67-15.48; P=0.004) and cavitary lesions (OR: 3.86; 95% CI: 1.30-11.47; P=0.015) were independently associated with extensive pulmonary lesions involving more than four lobes. The total cholesterol level, total lymphocyte count showed a tendency to decrease in PNTM patients with disease progression (both, P value <0.05), but not in those with a stable disease course. A decrease in cholesterol concentration of >20 mg/dL and a decrease in lymphocyte count more than 200/µL were predictive factors for disease progression (cholesterol: OR =10.50, 95% CI: 2.51-43.98, P=0.001; lymphocyte count: OR =5.32, 95% CI: 1.46-19.35, P=0.011).

CONCLUSIONS

These findings suggest that the change in cholesterol level may be a marker of disease progression in patients with PNTM disease.

Multiple Cavitary Pulmonary Nodules Caused by Mycobacterium intracellulare

Nontuberculous mycobacteria (NTM) have been increasingly recognized as an important cause of chronic pulmonary infections. The Mycobacterium avium complex (MAC), which is composed of two species, Mycobacterium avium and Mycobacterium intracelluare, is the most commonly encountered pathogen associated with NTM lung disease. MAC pulmonary infection typically presents in a fibrocavitary form or a nodular bronchiectatic form. However, there have been atypical presentations of MAC pulmonary infections, including solitary pulmonary nodules (SPN). There have been several previous reports of SPN due to MAC infection in the United States, Japan, and Korea. In 2009, Sekine and colleagues reported a case of MAC pulmonary infection presenting with multiple nodules. To date, however, there have been no cases of NTM lung infection with multiple cavitary pulmonary nodules, and neither a fibrotic change nor nodular bronchiectasis. The present case showed a multiple cavitating nodular lung infection due to MAC, which is very rare and different from the typical presentation of MAC pulmonary infections. We also showed that percutaneous transthoracic needle aspiration can be a useful diagnostic tool to evaluate a case of multiple cavitary nodules.

Nontuberculous mycobacterial pulmonary disease mimicking lung cancer: Clinicoradiologic features and diagnostic implications

To describe the features and clinical implications of computed tomography (CT), positron emission tomography (PET), and percutaneous needle aspiration biopsy (PCNB) in pulmonary nontuberculous mycobacterial (NTM) disease manifesting as a solitary nodule, mass, or mass-like consolidation mimicking malignancy.Among a cohort of 388 patients with NTM pulmonary disease, 14 patients with clinically and radiologically suspected lung cancer were included in our study. Two chest radiologists evaluated CT features, including lesion type (nodule, mass, or mass-like consolidation), morphologic features (margin, degree of enhancement, calcification), and presence of accompanying findings suggestive of NTM pulmonary disease (bronchiectasis with clustered centrilobular nodules or upper-lobe cavitary lesions) by consensus. Diagnostic procedures for microbiologic diagnosis of NTM disease and clinical outcome were reviewed.Incidence of NTM pulmonary disease presenting as solitary nodule/mass (n = 8) or mass-like consolidation (n = 6) was 3.6% (14 of 388). Most lesions were detected incidentally during routine health check-up or evaluation of other disease (11 of 14, 79%). Lesions typically showed poor contrast-enhancement (9 of 12) and internal calcification (6 of 14). No lesions had CT features suggestive of NTM pulmonary disease. All 4 lesions for which PET/CT imaging was performed showed strong fluorodeoxyglucose uptake simulating malignant lesions (mean, 4.9; range, 3.6-7.8). PCNB revealed mycobacterial histology in 6 of 11 specimens and positive culture results were obtained for 7 of 7 specimens.NTM pulmonary disease may present as a solitary nodule, mass, or mass-like consolidation mimicking malignancy. CT features and PCNB are important to diagnose NTM disease mimicking lung cancer to avoid unnecessary surgery.

Phylogenetic Analysis of Prevalent Tuberculosis and Non-Tuberculosis Mycobacteria in Isfahan, Iran, Based on a 360 bp Sequence of the rpoB Gene

Background

Taxonomic and phylogenetic studies of Mycobacterium species have been based around the 16sRNA gene for many years. However, due to the high strain similarity between species in the Mycobacterium genus (94.3% - 100%), defining a valid phylogenetic tree is difficult; consequently, its use in estimating the boundaries between species is limited. The sequence of the rpoB gene makes it an appropriate gene for phylogenetic analysis, especially in bacteria with limited variation.

Objectives

In the present study, a 360bp sequence of rpoB was used for precise classification of Mycobacterium strains isolated in Isfahan, Iran.

Materials and Methods

From February to October 2013, 57 clinical and environmental isolates were collected, subcultured, and identified by phenotypic methods. After DNA extraction, a 360bp fragment was PCR-amplified and sequenced. The phylogenetic tree was constructed based on consensus sequence data, using MEGA5 software.

Results

Slow and fast-growing groups of the Mycobacterium strains were clearly differentiated based on the constructed tree of 56 common Mycobacterium isolates. Each species with a unique title in the tree was identified; in total, 13 nods with a bootstrap value of over 50% were supported. Among the slow-growing group was Mycobacterium kansasii, with M. tuberculosis in a cluster with a bootstrap value of 98% and M. gordonae in another cluster with a bootstrap value of 90%. In the fast-growing group, one cluster with a bootstrap value of 89% was defined, including all fast-growing members present in this study.

Conclusions

The results suggest that only the application of the rpoB gene sequence is sufficient for taxonomic categorization and definition of a new Mycobacterium species, due to its high resolution power and proper variation in its sequence (85% - 100%); the resulting tree has high validity.

Elevated serum CA 19-9 levels in patients with pulmonary nontuberculous mycobacterial disease

Increased serum CA 19-9 levels in patients with nonmalignant diseases have been investigated in previous reports. This study evaluates the clinical significance of serum CA 19-9 elevation in pulmonary nontuberculous mycobacterial disease and pulmonary tuberculosis. The median CA 19-9 level was higher in patients with pulmonary nontuberculous mycobacterial disease than in patients with pulmonary tuberculosis (pulmonary nontuberculous mycobacterial disease: 13.80, tuberculosis: 5.85, p < 0.001). A multivariate logistic regression analysis performed in this study showed that Mycobacterium abscessus (OR 9.97, 95% CI: 1.58, 62.80; p = 0.014) and active phase of pulmonary nontuberculous mycobacterial disease (OR 12.18, 95% CI: 1.07, 138.36, p = 0.044) were found to be risk factors for serum CA 19-9 elevation in pulmonary nontuberculous mycobacterial disease. The serum CA 19-9 levels showed a tendency to decrease during successful treatment of pulmonary nontuberculous mycobacterial disease but not in pulmonary tuberculosis. These findings suggest that CA 19-9 may be a useful marker for monitoring therapeutic responses in pulmonary nontuberculous mycobacterial disease, although it is not pulmonary nontuberculous mycobacterial disease-specific marker.

Direct identification of mycobacteria from liquid media using a triplex real-time PCR coupled with pyrosequencing method

Culture in enriched broth, as well as on a solid medium, is recommended for primary isolation of mycobacteria. With the introduction of liquid mycobacterial culture methods, a substantial workload regarding the identification of culture-recovered mycobacterial species, particularly Mycobacterium tuberculosis complex (MTC), has been imposed on our laboratory. We thus developed a triplex, real-time PCR coupled with pyrosequencing assay that can directly identify mycobacterial species from liquid media, which can reduce the workload. In this assay, real-time PCR simultaneously detects MTC and Mycobacterium xenopi, and amplifies the region of 16S rRNA gene containing hypervariable region A for pyrosequencing analysis; subsequent, pyrosequencing identifies many other nontuberculous mycobacteria. The assay was evaluated using 333 DNA samples directly prepared from liquid media, including 24 reference strains and 309 clinical isolates. Three hundred and twenty-eight (98.5%) of the 333 samples were correctly identified. The remaining five were determined as indeterminate. In conclusion, this coupled assay would be an alternative method for rapid identification of mycobacteria directly from liquid media in a clinical laboratory with a high workload in regions where tuberculosis is endemic.

Molecular analysis of clinical isolates previously diagnosed as Mycobacterium intracellulare reveals incidental findings of "Mycobacterium indicus pranii" genotypes in human lung infection

Background

Mycobacterium intracellulare is a major cause of Mycobacterium avium complex lung disease in many countries. Molecular studies have revealed several new Mycobacteria species that are closely related to M. intracellulare. The aim of this study was to re-identify and characterize clinical isolates from patients previously diagnosed with M. intracellulare lung disease at the molecular level.

Methods

Mycobacterial isolates from 77 patients, initially diagnosed with M. intracellulare lung disease were re-analyzed by multi-locus sequencing and pattern of insertion sequences.

Results

Among the 77 isolates, 74 (96 %) isolates were designated as M. intracellulare based on multigene sequence-based analysis. Interestingly, the three remaining strains (4 %) were re-identified as “Mycobacterium indicus pranii” according to distinct molecular phylogenetic positions in rpoB and hsp65 sequence-based typing. In hsp65 sequevar analysis, code 13 was found in the majority of cases and three unreported codes were identified. In 16S–23S rRNA internal transcribed spacer (ITS) sequevar analysis, all isolates of both species were classified within the Min-A ITS sequevar. Interestingly, four of the M. intracellulare isolates harbored IS1311, a M. avium-specific element. Two of three patients infected with “M. indicus pranii” had persistent positive sputum cultures after antibiotic therapy, indicating the clinical relevance of this study.

Conclusions

This analysis highlights the importance of precise identification of clinical isolates genetically close to Mycobacterium species, and suggests that greater attention should be paid to nontuberculous mycobacteria lung disease caused by “M. indicus pranii”.

Molecular typing of Iranian mycobacteria isolates by polymerase chain reaction-restriction fragment length polymorphism analysis of 360-bp rpoB gene

Background:

Diagnosis and typing of Mycobacterium genus provides basic tools for investigating the epidemiology and pathogenesis of this group of bacteria. Polymerase chain reaction (PCR)-restriction fragment length polymorphism analysis (PRA) is an accurate method providing diagnosis and typing of species of mycobacteria. The present study is conducted by the purpose of determining restriction fragment profiles of common types of mycobacteria by PRA method of rpoB gene in this geographical region.

Materials and Methods:

Totally 60 clinical and environmental isolates from February to October, 2013 were collected and subcultured and identified by phenotypic methods. A 360 bp fragment of the rpoB gene amplified by PCR and products were digested by MspI and HaeIII enzymes.

Results:

In the present study, of all mycobacteria isolates identified by PRA method, 13 isolates (21.66%) were Mycobacterium tuberculosis, 34 isolates (56.66%) were rapidly growing Nontuberculosis Mycobacteria (NTM) that including 26 clinical isolates (43.33%) and 8 environmental isolates (13.33%), 11 isolates (18.33%) were clinical slowly growing NTM. among the clinical NTM isolates, Mycobacterium fortuitum Type I with the frequency of 57.77% was the most prevalent type isolates. Furthermore, an unrecorded of the PRA pattern of Mycobacterium conceptionense (HeaIII: 120/90/80, MspI: 120/105/80) was found. This study demonstrated that the PRA method was high discriminatory power for identification and typing of mycobacteria species and was able to identify 96.6% of all isolates.

Conclusion:

Based on the result of this study, rpoB gene could be a potentially useful tool for identification and investigation of molecular epidemiology of mycobacterial species.

Two-Year Monitoring of Water Samples from Dam of Iskar and the Black Sea, Bulgaria, by Molecular Analysis: Focus on Mycobacterium spp

The coast of the Bulgarian Black Sea is a popular summer holiday destination. The Dam of Iskar is the largest artificial dam in Bulgaria, with a capacity of 675 million m³. It is the main source of tap water for the capital Sofia and for irrigating the surrounding valley. There is a close relationship between the quality of aquatic ecosystems and human health as many infections are waterborne. Rapid molecular methods for the analysis of highly pathogenic bacteria have been developed for monitoring quality. Mycobacterial species can be isolated from waste, surface, recreational, ground and tap waters and human pathogenicity of nontuberculose mycobacteria (NTM) is well recognized. The objective of our study was to perform molecular analysis for key-pathogens, with a focus on mycobacteria, in water samples collected from the Black Sea and the Dam of Iskar. In a two year period, 38 water samples were collected—24 from the Dam of Iskar and 14 from the Black Sea coastal zone. Fifty liter water samples were concentrated by ultrafiltration. Molecular analysis for 15 pathogens, including all species of genus Mycobacterium was performed. Our results showed presence of Vibrio spp. in the Black Sea. Rotavirus A was also identified in four samples from the Dam of Iskar. Toxigenic Escherichia coli was present in both locations, based on markers for stx1 and stx2 genes. No detectable amounts of Cryptosporidium were detected in either location using immunomagnetic separation and fluorescence microscopy. Furthermore, mass spectrometry analyses did not detect key cyanobacterial toxins. On the basis of the results obtained we can conclude that for the period 2012–2014 no Mycobacterium species were present in the water samples. During the study period no cases of waterborne infections were reported.

Direct identification of mycobacteria from clinical specimens by multiplex real-time PCR

AIMS

To directly identify clinically relevant mycobacteria from clinical specimens, we have developed a multiplex real-time PCR assay with hydrolysis probes that can identify 20 mycobacterial species.

METHODS AND RESULTS

The assay was initially evaluated using 248 strains, including both reference strains and clinical isolates. Then, the assay was implemented according to a scheme in our laboratory. The scheme based on the clinical differences between the Mycobacterium tuberculosis complex (MTC) and nontuberculous mycobacteria (NTM) consisted of three stepwise PCRs. MTC and NTM were differentially detected in the step 1 PCR, and the NTM species were identified in the step 2 and step 3 PCRs. During a 2·5-year period, 1877 isolates of MTC (1142 directly recovered from clinical specimens) and 596 isolates of NTM (143 directly recovered from clinical specimens) were detected, and the species of 590 (99·0%) of the 596 NTM isolates were identified.

CONCLUSIONS

Our experience shows that this is a new paradigm for rapidly and accurately identifying clinically relevant mycobacteria, in which a multiplex real-time PCR assay is directly applied to clinical specimens in a stepwise fashion.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study is the first report of a multiplex real-time PCR assay for identifying clinically important mycobacterial species directly from clinical specimens and its application in a clinical microbiology laboratory.

Performance of a real-time PCR assay for the rapid identification of Mycobacterium species

Mycobacteria cause a variety of illnesses that differ in severity and public health implications. The differentiation of Mycobacterium tuberculosis (MTB) from nontuberculous mycobacteria (NTM) is of primary importance for infection control and choice of antimicrobial therapy. The diagnosis of diseases caused by NTM is difficult because NTM species are prevalent in the environment and because they have fastidious properties. In the present study, we evaluated 279 clinical isolates grown in liquid culture provided by The Catholic University of Korea, St. Vincent's Hospital using real-time PCR based on mycobacterial rpoB gene sequences. The positive rate of real-time PCR assay accurately discriminated 100% (195/195) and 100% (84/84) between MTB and NTM species. Comparison of isolates identified using the MolecuTech REBA Myco-ID(®) and Real Myco-ID® were completely concordant except for two samples. Two cases that were identified as mixed infection (M. intracellulare-M. massiliense and M. avium-M. massiliense co-infection) by PCRREBA assay were only detected using M. abscessus-specific probes by Real Myco-ID(®). Among a total of 84 cases, the most frequently identified NTM species were M. intracellulare (n=38, 45.2%), M. avium (n=18, 23.7%), M. massiliense (n=10, 13.2%), M. fortuitum (n=5, 6%), M. abscessus (n=3, 3.9%), M. gordonae (n=3, 3.9%), M. kansasii (n=2, 2.4%), M. mucogenicum (n=2, 2.4%), and M. chelonae (n= 1, 1.2%). Real Myco-ID(®) is an efficient tool for the rapid detection of NTM species as well as MTB and sensitive and specific and comparable to conventional methods.

The Recombinant BCG ΔureC::hly Vaccine Targets the AIM2 Inflammasome to Induce Autophagy and Inflammation

BACKGROUND

The recombinant BCG ΔureC::hly (rBCG) vaccine candidate induces improved protection against tuberculosis over parental BCG (pBCG) in preclinical studies and has successfully completed a phase 2a clinical trial. However, the mechanisms responsible for the superior vaccine efficacy of rBCG are still incompletely understood. Here, we investigated the underlying biological mechanisms elicited by the rBCG vaccine candidate relevant to its protective efficacy.

METHODS

THP-1 macrophages were infected with pBCG or rBCG, and inflammasome activation and autophagy were evaluated. In addition, mice were vaccinated with pBCG or rBCG, and gene expression in the draining lymph nodes was analyzed by microarray at day 1 after vaccination.

RESULTS

BCG-derived DNA was detected in the cytosol of rBCG-infected macrophages. rBCG infection was associated with enhanced absent in melanoma 2 (AIM2) inflammasome activation, increased activation of caspases and production of interleukin (IL)-1β and IL-18, as well as induction of AIM2-dependent and stimulator of interferon genes (STING)-dependent autophagy. Similarly, mice vaccinated with rBCG showed early increased expression of Il-1β, Il-18, and Tmem173 (transmembrane protein 173; also known as STING).

CONCLUSIONS

rBCG stimulates AIM2 inflammasome activation and autophagy, suggesting that these cell-autonomous functions should be exploited for improved vaccine design.

Occurrence of nontuberculous mycobacteria in aquatic sources of Sri Lanka

Nontuberculous mycobacteria (NTM) have been reported to cause opportunistic infections with increasing frequency, especially in immunocompromised patients. Water plays a major role in the epidemiology of nontuberculous mycobacterial infection in humans, as it is one of the natural sources for transmission of this group of organisms. The current study focused on determining the occurrence of NTM in different aquatic sources of Sri Lanka by using phenotypic tests and polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis of the rpoβ gene. Of 290 water samples, 45 (15%) were positive for NTM on culture. The percentage of mycobacteria identified at species level by phenotypic tests and PCR-RFLP analysis were 44% (20/45) and 73% (33/45), respectively. The frequency of isolation of mycobacteria from aquarium water, surface water, ground water and chlorinated water were 29% (20/70), 26% (20/76), 5% (4/76) and 1% (1/68), respectively. Eleven different NTM species were identified by PCR-RFLP analysis. M. fortuitum type I was the most frequently isolated species from all the four water sources. The current study suggests that water is an environmental source harboring NTM, a potential public health hazard especially for those with immunodeficiency.

A shorter treatment duration may be sufficient for patients with Mycobacterium massiliense lung disease than with Mycobacterium abscessus lung disease

BACKGROUND

Mycobacterium abscessus complex is the second most common organism isolated from patients with nontuberculous mycobacterial (NTM) lung disease in South Korea. This study aimed to compare clinical features and treatment outcomes of M. abscessus and Mycobacterium massiliense lung disease.

METHODS

We retrospectively identified stored clinical isolates of M. abscessus complex as either M. abscessus or M. massiliense and reviewed medical records to compare clinical characteristics and treatment responses. All patients were treated empirically over several months with multidrug regimens, including a macrolide and one or more parenteral agents.

RESULTS

Of the 249 patient isolates tested, 128 (59 with M. abscessus and 69 with M. massiliense) met the American Thoracic Society diagnostic criteria for NTM pulmonary disease, and treatment outcomes were analyzed in 48 patients (26 with M. abscessus and 22 with M. massiliense). The clinical and radiologic findings were similar between the two groups. Although the durations of parenteral and total treatment were significantly shorter in patients with M. massiliense than in those with M. abscessus (4.7 months vs 7.4 months, P = .006, and 12.1 months vs 16.3 months, P = .043), the treatment success rate was significantly higher in patients with M. massiliense (95.5%) than in M. abscessus cases (42.3%, P < .001).

CONCLUSION

Patients with M. massiliense pulmonary infection responded better to this antibiotic strategy than those with M. abscessus infection. A shortened duration of treatment may be sufficient for M. massiliense pulmonary infection.

Chronic mycobacterial meningitis due to Mycobacterium chelonae: a case report

We report a case of chronic meningitis due to Mycobacterium chelonae. This organism is a rapidly growing Mycobacterium (RGM) and can be found worldwide in environmental sources such as soil, dust, and water. M. chelonae is an uncommon cause of meningitis; the majority of infections caused by this organism are localized cutaneous or soft tissue infections, and rarely lung infections. The organism is indistinguishable phenotypically, so we applied PCR based on the rpoB gene sequence followed by restriction fragment length polymorphism (RFLP) for molecular identification. The subsequent sequencing of RFLP products revealed 99.7% similarity with M. chelonae.

Mycobacterial diseases developed during anti-tumour necrosis factor-α therapy

Nontuberculous mycobacterial (NTM) disease and tuberculosis (TB) develop during anti-tumour necrosis factor (TNF)-α therapy. We compared clinical characteristics and outcomes between the two diseases. A total of 1165 patients were screened for TB and treated with TNF-α antagonists from July 2004 to July 2013 for the following conditions: inflammatory bowel disease (n = 422), rheumatoid arthritis (n = 320), and ankylosing spondylitis (n = 389). TB and NTM disease were diagnosed at baseline screening in four and three patients, respectively, and developed during anti-TNF-α therapy in 19 and six patients, respectively. The incidence rate of TB and NTM disease was 747.7 per 100 000 and 238.2 per 100 000 person-years, respectively. Patients with NTM disease were older, with a greater proportion of females. All cases of NTM disease involved the lung, with rheumatoid arthritis (83.3%) being the most frequent underlying disease. The most common radiological feature was consolidation in NTM disease, and honeycombing was present in two rheumatoid arthritis patients with NTM disease. The most common pathogen was Mycobacterium intracellulare (n = 3) followed by Mycobacterium avium (n = 2). Both the NTM and TB group showed favourable outcomes. The clinical characteristics differed between NTM disease and TB that developed on anti-TNF-α agents, but clinical outcomes were favourable in both diseases.

Factors associated with quality of life measured by EQ-5D in patients with nontuberculous mycobacterial pulmonary disease

PURPOSE

The impact of pulmonary nontuberculous mycobacterial (pNTM) disease on health-related quality of life (HRQoL) has not received significant attention in the literature. In this study, we compared the HRQoL in patients with pNTM disease and healthy subjects and identified influencing factors using EuroQol 5D (EQ-5D) data.

METHODS

The present study used an age- and sex-matched case-control analysis from a cohort of 85 pNTM patients and 340 participants from a national survey. Baseline EQ-5D utility scores and EQ-5D visual analog scale (VAS) scores were measured in both groups. In patients with pNTM disease, the factors affecting EQ-5D were identified using multiple linear regression analysis.

RESULTS

While the median EQ-5D VAS scores were lower in pNTM patients than in the control subjects (pNTM, 70; control, 80; P < 0.001), the median EQ-5D utility scores were similar in two groups (both, 1.000, P = 0.878). Interestingly, the percentage of subjects reporting problems on the anxiety/depression dimension was higher for patients with pNTM disease (18.8 %) compared with the control subjects (11.5 %, P = 0.07). In multivariate analysis, increasing severity of forced expired volume in one second (FEV1) decline was associated with a significant decrease in EQ-5D scores of pNTM patients.

CONCLUSIONS

This study suggested the EQ-5D may not be useful instrument in pNTM patients due to ceiling effect of EQ-5D and mild disease activity. Patients with pNTM disease tended to report more reduced health status and more problems with anxiety/depression than the healthy controls. Lung function, measured by FEV1, was independently associated with EQ-5D scores in patients with pNTM disease.