Nontuberculous mycobacterial disease managed within UK primary care, 2006-2016

Global Epidemiology of Nontuberculous Mycobacterial Pulmonary Disease: A Review

Nontuberculous mycobacterial (NTM) isolation and pulmonary disease (NTM-PD) have continued to increase in most regions of the world, driven mainly by Mycobacterium avium. Single-center studies also support increasing trends as well as a persistent burden of undiagnosed NTM among persons suspected of having tuberculosis (TB), in countries with moderate-to-high TB prevalence. Cumulative exposure to water and soil presents an increased risk to susceptible hosts, and trace metals in water supply are recently recognized risk factors. Establishing standard case definitions for subnational and national surveillance systems with mandatory notification of NTM-PD are needed to allow comparisons within and across countries and regions.

Whole genome sequencing and prediction of antimicrobial susceptibilities in non-tuberculous mycobacteria

Non-tuberculous mycobacteria (NTM) are opportunistic pathogens commonly causing chronic, pulmonary disease which is notoriously hard to treat. Current treatment for NTM infections involves at least three active drugs (including one macrolide: clarithromycin or azithromycin) over 12 months or longer. At present there are limited phenotypic in vitro drug susceptibility testing options for NTM which are standardised globally. As seen with tuberculosis, whole genome sequencing has the potential to transform drug susceptibility testing in NTM, by utilising a genotypic approach. The Comprehensive Resistance Prediction for Tuberculosis is a database used to predict Mycobacterium tuberculosis resistance: at present there are no similar databases available to accurately predict NTM resistance. Recent studies have shown concordance between phenotypic and genotypic NTM resistance results. To benefit from the advantages of whole genome sequencing, further advances in resistance prediction need to take place, as well as there being better information on novel drug mutations and an understanding of the impact of whole genome sequencing on NTM treatment outcomes.

The epidemiology of nontuberculous mycobacterial pulmonary disease in the Netherlands

Background

Nontuberculous mycobacteria (NTM) are emerging opportunistic pathogens of humans. Because NTM pulmonary disease (PD) is not a notifiable disease in Europe, the epidemiology of NTM-PD is not well known. However, the prevalence of NTM-PD is thought to be increasing, particularly in countries where tuberculosis rates have decreased. Here we aim to determine the prevalence of NTM-PD in the Netherlands.

Methods

Annual prevalence estimates of NTM-PD in the Netherlands (2012-2019) were derived from four separate databases, including two drug dispensing databases, an ICD-10 code database and a hospitalisation database. Databases covered a fraction of the Dutch population and were extrapolated. In addition, annual NTM-PD prevalence was also estimated by means of a pulmonologist survey.

Results

The estimated annual prevalence of NTM-PD using databases is between 2.3 and 5.9 patients per 100 000 inhabitants. Prevalence estimates derived from the drug dispensing databases, the hospitalisation database and the claims database were 2.3, 5.9, 3.5 and 4.5 per 100 000 inhabitants, respectively. The annual prevalence estimated in the pulmonologist survey was between 6.2 and 9.9 per 100 000 inhabitants. The annual prevalence remained stable over the included period.

Conclusion

The estimated annual prevalence of NTM-PD using databases was between 2.3 and 5.9 patients per 100 000 inhabitants. Due to the possible presence of tuberculosis patients and low coverage in one dispensing database, we believe an annual prevalence of between 2.3 and 4.5 patients per 100 000 inhabitants is more probable, which still renders NTM-PD a serious health threat. This estimate is lower than the estimate from the pulmonologist survey, indicating physicians likely overestimate prevalence.

Mycobacterial biofilms as players in human infections: a review

The role of biofilms in pathogenicity and treatment strategies is often neglected in mycobacterial infections. In recent years, the emergence of nontuberculous mycobacterial infections has necessitated the development of novel prophylactic strategies and elucidation of the mechanisms underlying the establishment of chronic infections. More importantly, the question arises whether members of the Mycobacterium tuberculosis complex can form biofilms and contribute to latent tuberculosis and drug resistance because of the long-lasting and recalcitrant nature of its infections. This review discusses some of the molecular mechanisms by which biofilms could play a role in infection or pathological events in humans.

Predictive modeling of nontuberculous mycobacterial pulmonary disease epidemiology using German health claims data

OBJECTIVES

Administrative claims data are prone to underestimate the burden of non-tuberculous mycobacterial pulmonary disease (NTM-PD).

METHODS

We developed machine learning-based algorithms using historical claims data from cases with NTM-PD to predict patients with a high probability of having previously undiagnosed NTM-PD and to assess actual prevalence and incidence. Adults with incident NTM-PD were classified from a representative 5% sample of the German population covered by statutory health insurance during 2011-2016 by the International Classification of Diseases, 10th revision code A31.0. Pre-diagnosis characteristics (patient demographics, comorbidities, diagnostic and therapeutic procedures, and medications) were extracted and compared to that of a control group without NTM-PD to identify risk factors.

RESULTS

Applying a random forest model (area under the curve 0.847; total error 19.4%) and a risk threshold of >99%, prevalence and incidence rates in 2016 increased 5-fold and 9-fold to 19 and 15 cases/100,000 population, respectively, for both coded and non-coded vs. coded cases alone.

CONCLUSIONS

The use of a machine learning-based algorithm applied to German statutory health insurance claims data predicted a considerable number of previously unreported NTM-PD cases with high probabilty.

Identification of potentially undiagnosed patients with nontuberculous mycobacterial lung disease using machine learning applied to primary care data in the UK

Nontuberculous mycobacterial lung disease (NTMLD) is a rare lung disease often missed due to a low index of suspicion and unspecific clinical presentation. This retrospective study was designed to characterise the prediagnosis features of NTMLD patients in primary care and to assess the feasibility of using machine learning to identify undiagnosed NTMLD patients.IQVIA Medical Research Data (incorporating THIN, a Cegedim Database), a UK electronic medical records primary care database was used. NTMLD patients were identified between 2003 and 2017 by diagnosis in primary or secondary care or record of NTMLD treatment regimen. Risk factors and treatments were extracted in the prediagnosis period, guided by literature and expert clinical opinion. The control population was enriched to have at least one of these features.741 NTMLD and 112 784 control patients were selected. Annual prevalence rates of NTMLD from 2006 to 2016 increased from 2.7 to 5.1 per 100 000. The most common pre-existing diagnoses and treatments for NTMLD patients were COPD and asthma and penicillin, macrolides and inhaled corticosteroids. Compared to random testing, machine learning improved detection of patients with NTMLD by almost a thousand-fold with AUC of 0.94. The total prevalence of diagnosed and undiagnosed cases of NTMLD in 2016 was estimated to range between 9 and 16 per 100 000.This study supports the feasibility of machine learning applied to primary care data to screen for undiagnosed NTMLD patients, with results indicating that there may be a substantial number of undiagnosed cases of NTMLD in the UK.

Epidemiology of nontuberculous mycobacterial pulmonary disease in Europe and Japan by Delphi estimation

BACKGROUND

Nontuberculous mycobacterial pulmonary disease (NTM-PD) is an emerging opportunistic infection, but basic epidemiological data are lacking in most regions. We have investigated epidemiology and diagnostic and treatment practices in five EU countries (United Kingdom, Spain, Italy, France, Germany; EU5) and Japan.

STUDY DESIGN

and methods: Annual prevalence in each country was established using a 2-round Delphi method in combination with a regional prevalence-estimation model that incorporated data obtained from a blinded physician screening survey (3154 physicians) and a real-world NTM-PD treating-physician/patient-chart observational study (619 physicians - 1429 patient charts).

RESULTS

The annual prevalence of NTM-PD was estimated at 6.2/100,000 in the EU5 and 24.9/100,000 in Japan. Overall prevalence between the EU5 was comparable, while differences in regional prevalence were found to be pronounced in France and The United Kingdom. Regional differences were also found in Japan, with the majority of cases in Chubu and Kanto regions.

CONCLUSION

This new methodology for obtaining often missing regional-level epidemiological data reveals dramatic variations in NTM-PD annual prevalence and helps pinpoint areas that may merit special preventative and treatment focus.

Physical Measures to Reduce Exposure to Tap Water-Associated Nontuberculous Mycobacteria

Nontuberculous mycobacteria (NTM) that cause human disease can be isolated from household tap water. Easy-to-use physical methods to reduce NTM from this potential source of exposure are needed. Filters and UV disinfection have been evaluated for their ability to reduce numbers of waterborne non-NTM organisms from drinking water, but their efficacy in reducing NTM counts are not well-established. Thus, five commercially available disinfection methods were evaluated for their potential as practical, efficient, and low-cost methods to reduce NTM from tap water. First, suspensions of tap water–adapted Mycobacterium smegmatis were passed through either a point-of-use, disposable, 7-day or 14-day Pall-Aquasafe filter. The 7-day filter prevented passage of M. smegmatis in effluent water for 13 days, and the 14-day filter prevented the passage of M. smegmatis for 25 days. Second, a granular activated carbon filter system failed to significantly reduce Mycobacterium abscessus and Mycobacterium avium numbers. Third, suspensions of tap water–adapted M. abscessus, M. avium, and M. chimaera (“MycoCocktail”) were passed through the “LifeStraw GO” hollow-fiber, two-stage membrane filtration system. LifeStraw GO prevented passage of the MycoCocktail suspension for the entire 68-day evaluation period. Finally, two different water bottle UV sterilization systems, “Mountop” and “SteriPEN,” were evaluated for their capacity to reduce NTM numbers from tap water. Specifically, MycoCocktail suspensions were dispensed into Mountop and SteriPEN water bottles and UV treated as per the manufacturer instructions once daily for 7 days, followed by a once weekly treatment for up to 56 days. After 4 days of daily UV treatment, both systems achieved a >4 log reduction in MycoCocktail CFU. After the 56-day evaluation period, suspension and biofilm-associated CFU were measured, and a >4 log reduction in CFU was maintained in both systems. Taken together, physical disinfection methods significantly reduced NTM numbers from tap water and may be easy-to-use, accessible applications to reduce environmental NTM exposures from drinking water.

Potential therapeutic effect of ninjinyoeito for the treatment of pulmonary nontuberculous mycobacterial infections: A case report

A 40-year-old man presented with refractory pulmonary Mycobacterium avium complex infection, despite administration of antituberculous drugs for 2 years. We administered ninjinyoeito (NYT) to the patient, who experienced weight gain and demonstrated marked reduction in the lung cavity lesions. Thus, the traditional Japanese medicine, NYT could serve as an adjunct to the conventional pharmacotherapy for pulmonary Mycobacterium avium complex infection.

Incidence, comorbidities, and treatment patterns of nontuberculous mycobacterial infection in South Korea

Nontuberculous mycobacteria (NTM) are important pathogens in humans, and hospital-based studies have shown an increased incidence of NTM infection. However, little is known about the treatment pattern of NTM infection with respect to the number of cases per population in South Korea. This study evaluated the trends in the incidence of NTM infection, respiratory comorbidities, and treatment patterns in South Korea.National claims data from the Health Insurance Review and Assessment service database for the years 2009 to 2015 were reviewed, and codes related to NTM infection, respiratory comorbidities occurring from one year before NTM infection and associated treatments were identified.In total, 52,551 patients were included in the study and the average annual incidence per 100,000 person-years was 12.8. The annual incidence was found to have increased from 6.6 to 26.6 per 100,000 persons. Accompanied comorbidities were tuberculosis (33.7%), followed by bronchial asthma (33.2%), chronic obstructive pulmonary disease (25.6%), and lung cancer (5.8%). A total of 76.6% of patients did not receive any combination treatment within one year after the diagnosis of NTM infection. Macrolide-based treatment was administered to 18.8% of patients.A dramatic increase in the incidence of NTM infection was noted in the population of South Korea. Approximately three-fourth of the patients with NTM infection were clinically observed without treatment for at least 1 year after the identification of NTM infection and most patients who treated NTM infection received macrolide-based combination therapy.

Prevalence, incidence, and mortality of nontuberculous mycobacterial infection in Korea: a nationwide population-based study

BACKGROUND

Epidemiologic characteristics of nontuberculous mycobacterial (NTM) disease remain largely unknown. The objective of this study was to evaluate incidence, prevalence, and mortality of NTM infection in a large nationwide population-based cohort in Korea.

METHODS

Data of the National Health Insurance Service database, an extensive health-related database including most Korean residents, were used. Adults with a primary diagnosis of NTM as determined by International Classification of Disease-Tenth Revision coding (A31) were identified between 2003 and 2016. Incidence, prevalence, and mortality of NTM infection were analyzed.

RESULTS

A total of 46,194 individuals had a primary diagnosis of NTM infection. Their mean age was 55.8 years. Of these subjects, 61.1% were females. Annual age-adjusted incidence and prevalence of NTM infection tended to increase rapidly from 2003 to 2016. Age-adjusted incidence and prevalence was 17.9 and 33.3 per 100,000 population in 2016. The incidence and prevalence were higher in females and the elderly. The 5-year mortality rate in the population with NTM infection was 17.8%. The standardized mortality ratio of patients with NTM infection to the general population was 2.16 (95% confidence interval: 2.10 to 2.22).

CONCLUSIONS

This large population-based study showed that the incidence and prevalence of NTM infection in Korea increased rapidly from 2003 to 2016. They were higher in women and the elderly. The mortality rate in the population with NTM infection was higher than that in the general population.

Diversity of Nontuberculous Mycobacteria in Kuwait: Rapid Identification and Differentiation of Mycobacterium Species by Multiplex PCR, INNO-LiPA Mycobacteria v2 Assay and PCR Sequencing of rDNA

OBJECTIVE

Nontuberculous mycobacteria (NTM) often cause disease that is clinically indistinguishable from tuberculosis. Specific identification is important as treatment varies according to Mycobacterium species causing the infection. This study used multiplex PCR (mPCR) assay for rapid differentiation of mycobacterial growth indicator tube 960 system (MGIT) cultures as Mycobacterium tuberculosis (MTB) or NTM together with INNO LiPA Mycobacteria v2 assay (LiPA) and/or PCR sequencing of rDNA for species-specific identification of selected MTB and all NTM isolates in Kuwait.

MATERIALS AND METHODS

DNA was extracted from MGIT cultures (n = 1,033) grown from 664 pulmonary and 369 extrapulmonary specimens from 1,033 suspected tuberculosis patients. mPCR was performed to differentiate MTB from NTM. LiPA was performed and results were interpreted according to kit instructions. rDNA was amplified and sequenced by using panmycobacterial primers.

RESULTS

mPCR identified 979 isolates as MTB, 53 as NTM and 1 isolate as mixed culture. LiPA and/or PCR sequencing confirmed 112 of 979 selected isolates as MTB. Mixed culture contained M. tuberculosis and M. fortuitum. LiPA yielded 12 patterns and identified 10 species/species complexes among 47 NTM, M. kansasii + M. scrofulaceum in one culture and 5 isolates only at genus level. PCR sequencing yielded more specific identification for 22 isolates at the species/subspecies level.

CONCLUSIONS

mPCR rapidly differentiated MTB from NTM. LiPA identified 44 of 52 NTM isolates at the species/species complex level and 2 mixed cultures. PCR sequencing yielded more specific identification at the species/subspecies level. Rapid differentiation as MTB or NTM by mPCR, followed by species-specific NTM identification by LiPA/PCR sequencing is suitable for the proper management of mycobacterial infections in Kuwait.

Risk factors and secondary care utilisation in a primary care population with non-tuberculous mycobacterial disease in the UK

Prior research has identified risk factors associated with developing non-tuberculous mycobacterial disease (NTMD); we identified risk factors and secondary care utilisation of NTMD patients in the UK. This was a matched case-control study using electronic healthcare records from Clinical Practice Research Datalink from 2006 to 2016. NTMD was defined using prescription data and Read codes, based on international guidelines. Risk factors for NTMD were investigated using conditional logistic regression within a representative general population. All-cause secondary care utilisation (combined inpatient, outpatient, emergency visits) was investigated for participants with linked Hospital Episode Statistics (HES), using incidence rate ratio (IRR) from 2007 to 2015. We identified 1225 individuals with NTMD. A subset of individuals (426 patients) were eligible for linkage with HES. In the adjusted model, risk factors most strongly associated with an increased likelihood of NTMD included previous tuberculosis (OR 69.0; 47.7-99.8); bronchiectasis (OR 23.3; 12.4-43.9); lung cancer (OR 14.9; 3.98-55.7); oral corticosteroids (OCS; OR 7.28; 4.94-10.7); immunosuppressive (excluding corticosteroids) medication (OR 3.05; 1.15-8.10); being underweight (odds ratio (OR) 2.92; 95% CI 1.95, 4.36); and rheumatoid arthritis (OR 2.12; 1.05-4.27). NTMD patients had significantly higher rates of all-cause secondary care utilisation than non-NTMD patients (IRR 5.80; 5.14-6.46). Using a representative adult population, we identified prior TB, bronchiectasis, lung cancer, immunosuppressive medication, and OCS as the risk factors associated with the highest odds of developing NTMD in the UK. Patients with NTMD experienced nearly six times more all-cause secondary care events following their NTMD diagnosis than patients without NTMD.