Impact of industrial structure and soil exposure on the regional variations in pulmonary nontuberculous mycobacterial disease prevalence

A practical guide to the diagnosis and management of suspected Non-tuberculous Mycobacterial Pulmonary Disease (NTM-PD) in the United Kingdom

Non-tuberculous Mycobacterial Pulmonary Disease (NTM-PD) is a chronic disease characterised by progressive inflammatory lung damage due to infection by non-tuberculous mycobacteria (NTM). Global prevalence of NTM-PD is generally low but is rising, likely due to a combination of increased surveillance, increasing multimorbidity and improved diagnostic techniques. Most disease is caused by Mycobacterium avium complex species. NTM-PD can be challenging to both diagnose and manage but given the risk of untreated disease and the challenges around drug treatments, it is vital that all healthcare professionals involved in primary care consider NTM-PD at the earliest opportunity. In particular, NTM-PD should be considered where there are respiratory symptoms in the setting of pre-existing chronic lung disease such as chronic obstructive pulmonary disease (COPD) and bronchiectasis. Early suspicion should lead to appropriate primary screening measures. This article discusses the relevance of NTM-PD today, risk factors for developing disease, pathways from clinical presentation to referral to specialist care, and discusses management and drug treatments. A flow diagram of a screening process is presented as a guideline for best practice from a United Kingdom perspective.

Isolation and identification of nontuberculous mycobacteria from raw milk and traditional cheese based on the 16S rRNA and hsp65 genes, Tehran, Iran

As an important source of human food, milk can be a carrier of human pathogenic bacteria, including tuberculous and nontuberculous mycobacteria (NTM), in its raw and unpasteurized state. In this research, 175 raw milk samples and 175 traditional cheese samples were collected from traditional dairy stores in 22 regions of Tehran in a 9- month period from August 2019 to May 2020. Samples were prepared and transferred to a specialized laboratory, where they were inoculated in Lowenstein-Jensen (LJ) medium containing glycerol or sodium pyruvate, as well as Herrold's egg-yolk with and without Mycobactin J. to determine the sample's identity of samples. The recommended 16S rRNA (1436 bp) and hsp65 (644 bp) gene fragments from the positive isolates identified in Ziehl-Neelsen (Z-N) staining were amplified and sequenced using PCR and compared with the sequences of the gene fragments of reference strains available in the global GenBank database. No mycobacterial species were isolated from traditional cheese samples in microbial culture. In case of raw milk samples, a total of four bacteria were collected, all of which were found in the genetic differential testing to be NTM, including n = 1 Mycobacterium heraklionense, n = 2 Mycolicibacterium fortuitum, and n = 1 Mycobacterium thermoresistibile. The analysis of the results obtained by isolate sequencing using the 16S rRNA gene showed higher discriminatory power and percentage similarities in the identification of the isolates than the hsp65 gene.

Long-range transport of airborne bacteria over East Asia: Asian dust events carry potentially nontuberculous Mycobacterium populations

The nontuberculous mycobacterial pulmonary disease (NTM-PD) caused by Mycobacterium species has increased in prevalence all over the world. The distributions of NTM-PD are possibly determined by the westerly wind traveling at high altitudes over East Asia. However, the long-range transport of Mycobacterium species has not been demonstrated by analyzing the bacterial communities in aerosols such as desert mineral particles and anthropogenic pollutants transported by the westerly wind. Here, airborne bacterial compositions were investigated including Mycobacterium species in high-elevation aerosols, which were captured in the snow cover at 2,450 m altitude on Mt. Tateyama. This was further compared to the ground-level or high-altitude aerosols collected at six sampling sites distributed from Asian-dust source region (Tsogt-Ovoo) to downwind areas in East Asia (Asian continental cities; Erenhot, Beijing, Yongin, Japanese cities; Yonago, Suzu, Noto Peninsula). The cell concentrations and taxonomic diversities of airborne bacteria decreased from the Asian continent to the Japan area. Terrestrial bacterial populations belonging to Firmicutes and Actinobacteria showed higher relative abundance at high-elevation and Japanese cities. Additionally, Mycobacterium species captured in the snow cover on Mt. Tateyama increased in relative abundance in correspondence to the increase of black carbon concentrations. The relative abundance of Mycobacterium sequences was higher in the aerosol samples of Asian continental cities and Japanese cities than in the desert area. Presumably, anthropogenic pollution over East Asia carries potential Mycobacterium species, which induce NTM-PD, thereby impacting upon the public health.

Soil Properties and Moisture Synergistically Influence Nontuberculous Mycobacterial Prevalence in Natural Environments of Hawai'i

Nontuberculous mycobacteria (NTM) are opportunistic pathogens that cause chronic pulmonary disease (PD). NTM infections are thought to be acquired from the environment; however, the basal environmental factors that drive and sustain NTM prevalence are not well understood. The highest prevalence of NTM PD cases in the United States is reported from Hawai'i, which is unique in its climate and soil composition, providing an opportunity to investigate the environmental drivers of NTM prevalence. We used microbiological sampling and spatial logistic regression complemented with fine-scale soil mineralogy to model the probability of NTM presence across the natural landscape of Hawai'i. Over 7 years, we collected and microbiologically cultured 771 samples from 422 geographic sites in natural areas across the Hawaiian Islands for the presence of NTM. NTM were detected in 210 of these samples (27%), with Mycobacterium abscessus being the most frequently isolated species. The probability of NTM presence was highest in expansive soils (those that swell with water) with a high water balance (>1-m difference between rainfall and evapotranspiration) and rich in Fe-oxides/hydroxides. We observed a positive association between NTM presence and iron in wet soils, supporting past studies, but no such association in dry soils. High soil-water balance may facilitate underground movement of NTM into the aquifer system, potentially compounded by expansive capabilities allowing crack formation under drought conditions, representing further possible avenues for aquifer infiltration. These results suggest both precipitation and soil properties are mechanisms by which surface NTM may reach the human water supply. IMPORTANCE Nontuberculous mycobacteria (NTM) are ubiquitous in the environment, being found commonly in soils and natural bodies of freshwater. However, little is known about the environmental niches of NTM and how they relate to NTM prevalence in homes and other human-dominated areas. To characterize NTM environmental associations, we collected and cultured 771 samples from 422 geographic sites in natural areas across Hawai'i, the U.S. state with the highest prevalence of NTM pulmonary disease. We show that the environmental niches of NTM are most associated with highly expansive, moist soils containing high levels of iron oxides/hydroxides. Understanding the factors associated with NTM presence in the natural environment will be crucial for identifying potential mechanisms and risk factors associated with NTM infiltration into water supplies, which are ultimately piped into homes where most exposure risk is thought to occur.

Pulmonary nontuberculous mycobacterial infections and environmental factors: A review of the literature

BACKGROUND

Pulmonary nontuberculous mycobacterial (pNTM) infection is mainly acquired through the inhalation of bioaerosols. Nevertheless, behavioural restrictions are rarely given by clinicians to susceptible populations, in part because the available guidelines for pNTM management emphasize more diagnosis and treatment than prevention. Aim of this review is to clarify if pNTM prevention should routinely include recommendations about risk reducing behaviors.

METHODS

We used PubMed as biomedical database. We limited our search to the publication period 2000 to 2020 with selected keyword combinations including "nontuberculous mycobacteria", "water", "soil", and "exposure". Titles and abstract of selected articles were systematically screened. Articles were included in the analysis if they were published under free access through the digital library of the University of Brescia (Italy), and provided full text either in English, French, German or Italian. Articles were excluded if the topic was beyond the aim of our study. Finally, we selected 20 articles.

RESULTS

Studies disagree in identifying the type of aerosol posing the highest risk for the development of pNTM infection. In the retrieved publications the colonization of household niches has been associated with a higher risk of pNTM disease, such as in the exposure to shower aerosols. Considering the non-household settings, the exposure to aerosols in indoor swimming and the higher soil exposure (>2 h/week) seem to correlate with a higher risk to develop pNTM disease. According to our findings, randomized behavioural intervention studies are missing.

CONCLUSIONS

Stringent scientific evidence is missing to formulate recommendations on behavioural risk reduction for pNTM.

Genome-wide identification of essential genes in Mycobacterium intracellulare by transposon sequencing - Implication for metabolic remodeling

The global incidence of the human nontuberculous mycobacteria (NTM) disease is rapidly increasing. However, knowledge of gene essentiality under optimal growth conditions and conditions relevant to the natural ecology of NTM, such as hypoxia, is lacking. In this study, we utilized transposon sequencing to comprehensively identify genes essential for growth in Mycobacterium intracellulare. Of 5126 genes of M. intracellulare ATCC13950, 506 genes were identified as essential genes, of which 280 and 158 genes were shared with essential genes of M. tuberculosis and M. marinum, respectively. The shared genes included target genes of existing antituberculous drugs including SQ109, which targets the trehalose monomycolate transporter MmpL3. From 175 genes showing decreased fitness as conditionally essential under hypoxia, preferential carbohydrate metabolism including gluconeogenesis, glyoxylate cycle and succinate production was suggested under hypoxia. Virulence-associated genes including proteasome system and mycothiol redox system were also identified as conditionally essential under hypoxia, which was further supported by the higher effective suppression of bacterial growth under hypoxia compared to aerobic conditions in the presence of these inhibitors. This study has comprehensively identified functions essential for growth of M. intracellulare under conditions relevant to the host environment. These findings provide critical functional genomic information for drug discovery.

Changing epidemiology of nontuberculous mycobacterial lung disease over the last two decades in a region of the Basque country

Recent studies suggest an increasing prevalence of nontuberculous mycobacteria (NTM) lung disease. The aim of the present study was to describe incidence rates of NTM lung disease and trends therein in our area over a 20-year period. This was a retrospective study of all cases of NTM lung disease between 1997 and 2016 that met the 2007 American Thoracic Society criteria. We analysed the annual incidence rates, species of mycobacteria isolated, trends over time and annual mortality in 327 patients. Mycobacterium kansasii was the most common mycobacterium isolated (84%), followed by Mycobacterium avium complex (MAC) (13%). We compared two periods: 1997-2006 (257 cases, 79%) and 2007-2016 (70 cases, 21%). The incidence rates tended to decrease across these years, with a peak of incidence in 2000 with 10.6 cases per 100 000. There was a clearly decreasing trend in M. kansasii infection, not only in the first period (incident rate ratio (IRR) 0.915, 95% CI 0.88-0.90; p<0.0001) but also in the second (IRR 0.869, 95% CI 0.780-1.014; p=0.080), reaching 1.8 per 100 000 in 2016. In contrast, MAC infection tended to increase across the two periods (IRR 1.251, 95% CI 1.081-1.447; p=0.003). In our region, the incidence of NTM lung disease has notably decreased in recent years. M. kansasii had high incidence rates in the first decade but clearly decreased in the second decade.

Non-tuberculous mycobacterial pulmonary disease

Nontuberculous mycobacterial pulmonary disease (NTM-PD) is a challenging infection which is becoming increasingly prevalent, particularly in the elderly, for reasons which are unknown. While underlying lung disease is a well-established risk factor for NTM-PD, it may also occur in apparently healthy individuals. No single common genetic or immunological defect has been identified in this group, and it is likely that multiple pathways contribute towards host susceptibility to NTM-PD which further interact with environmental and microbiological factors leading to the development of disease.The diagnosis of NTM-PD relies on the integration of clinical, radiological and microbiological results. The clinical course of NTM-PD is heterogeneous, with some patients remaining stable without the need for treatment and others developing refractory disease associated with considerable mortality and morbidity. Treatment regimens are based on the identity of the isolated species, drug sensitivity testing (for some agents) and the severity of disease. Multiple antibiotics are typically required for prolonged periods of time and treatment is frequently poorly tolerated. Surgery may be beneficial in selected cases. In some circumstances cure may not be attainable and there is a pressing need for better regimens to treat refractory and drug-resistant NTM-PD.This review summarises current knowledge on the epidemiology, aetiology and diagnosis of NTM-PD and discusses the treatment of two of the most clinically significant species, the M. avium and M. abscessus complexes, with a focus on refractory disease and novel therapies.

Retrospective Analysis of Nontuberculous Mycobacterial Infection and Monochloramine Disinfection of Municipal Drinking Water in Michigan

Infections by nontuberculous mycobacteria (NTM) result in significant morbidity, mortality, and health care costs. NTM are primarily acquired from environmental sources, including exposure to municipally treated drinking water. Higher levels of NTM have been reported in drinking water disinfected with monochloramine than in drinking water disinfected with chlorine. Our results suggest that municipal drinking water disinfection with monochloramine compared to chlorine is not associated with higher risk of NTM infection. This is important given that regulations that limit drinking water concentrations of disinfection by-products, which are formed primarily when chlorine disinfection is used, incentivize drinking water utilities to change from chlorine disinfection to monochloramine disinfection.

Infections by nontuberculous mycobacteria (NTM) are primarily acquired from environmental sources, including exposure to municipally treated drinking water. Higher levels of NTM have been reported in drinking water disinfected with monochloramine than in that disinfected with chlorine. However, the relationships between water treatment practices and NTM infection are unclear. The objective of this study was to examine a possible relationship between residual disinfectant used for municipal drinking water treatment (monochloramine or chlorine) and NTM infection. We retrospectively reviewed NTM diagnostic tests performed at a single health care center during a 15-year period. Information on municipal water treatment practices, including disinfectant and primary source water type, was obtained for 140 cities. Based on a logistic regression model, municipal drinking water disinfection with monochloramine compared to chlorine was not associated with NTM infection (P = 0.24). An additional model variable examining water source showed that the likelihood of having an NTM infection was 1.46 times higher for patients residing in cities with drinking water derived from surface water than for those residing in cities with drinking water derived from groundwater (odds ratio [OR], 1.46; 95% confidence interval [CI], 1.03 to 2.08; P = 0.04). In an inverse propensity score weighted regression, monochloramine disinfection was also not associated with NTM infection. A moderate effect on NTM infection rates was observed in the weighted regression for municipal drinking water derived from surface water, though the results were not statistically significant (OR, 1.24; 95% CI, 0.92 to 1.69; P = 0.17).

IMPORTANCE Infections by nontuberculous mycobacteria (NTM) result in significant morbidity, mortality, and health care costs. NTM are primarily acquired from environmental sources, including exposure to municipally treated drinking water. Higher levels of NTM have been reported in drinking water disinfected with monochloramine than in drinking water disinfected with chlorine. Our results suggest that municipal drinking water disinfection with monochloramine compared to chlorine is not associated with higher risk of NTM infection. This is important given that regulations that limit drinking water concentrations of disinfection by-products, which are formed primarily when chlorine disinfection is used, incentivize drinking water utilities to change from chlorine disinfection to monochloramine disinfection.

The Incidence of Non-Tuberculous Mycobacteria in Infants in Kenya

There is inadequate understanding of the epidemiology of Non-Tuberculous Mycobacteria (NTM) among infants in high tuberculosis burden countries. The objective of this study was to document the incidence and diversity of NTM disease or colonisation in sputum specimens from infants with presumptive TB, the risk factors, and clinical characteristics, in a high TB and HIV burden setting in Western Kenya. A cohort of 2900 newborns was followed for 1–2 years to assess TB incidence. TB investigations included collection of induced sputa and gastric aspirates for culture and speciation by HAIN®, Tuberculin Skin Testing (TST), HIV testing, and chest radiography. The American Thoracic Society Criteria (ATS) were applied to identify NTM disease. Among 927 (32% of 2900) with presumptive TB, 742 (80%) were investigated. NTM were isolated from 19/742 (2.6%) infants. M. fortuitum was most frequently speciated (32%). Total person-time was 3330 years. NTM incidence was 5.7/1,000 person-years, 95% CI (3.5, 8.7). Infants diagnosed with TB were more likely to have NTM isolation (odds ratio 11.5; 95% CI 3.25, 41.0). None of the infants with NTM isolated met the criteria for NTM disease. The incidence of NTM isolation was comparable to similar studies in Africa. NTM isolation did not meet ATS criteria for disease and could represent colonisation. TB disease appears to be structural lung disease predisposing to NTM colonisation.

Global Environmental Nontuberculous Mycobacteria and Their Contemporaneous Man-Made and Natural Niches

Seminal microbiological work of environmental nontuberculous mycobacteria (NTM) includes the discovery that NTM inhabit water distribution systems and soil, and that the species of NTM found are geographically diverse. It is likely that patients acquire their infections from repeated exposures to their environments, based on the well-accepted paradigm that water and soil bioaerosols - enriched for NTM - can be inhaled into the lungs. Support comes from reports demonstrating NTM isolated from the lungs of patients are genetically identical to NTM found in their environment. Well documented sources of NTM include peat-rich soils, natural waters, drinking water, hot water heaters, refrigerator taps, catheters, and environmental amoeba. However, NTM have also been recovered in biofilms from ice machines, heated nebulizers, and heater-cooler units, as well as seat dust from theaters, vacuum cleaners, and cobwebs. New studies on the horizon aim to significantly expand the current knowledge of environmental NTM niches in order to improve our current understanding of the specific ecological factors driving the emergence of NTM lung disease. Specifically, the Hawaiian Island environment is currently being studied as a model to identify other point sources of exposure as it is the U.S. state with the highest number of NTM lung disease cases. Because of its geographic isolation and unique ecosystem, the Hawaiian environment is being probed for correlative factors that may promote environmental NTM colonization.

Diagnosis and Management of Children With Mycobacterium abscessus Infections in the Head and Neck

PURPOSE

Controversy exists regarding the most appropriate treatment strategy for children with nontuberculous mycobacterial (NTM) cervical lymphadenitis. Mycobacterium abscessus (MAB) is an uncommon cause of NTM cervical lymphadenitis. The purpose of the present study was to evaluate diagnosis, management, and treatment outcomes in children with MAB-associated cervical lymphadenitis resulting from a pulpotomy.

MATERIALS AND METHODS

This was a retrospective chart review of children with NTM lymphadenitis of the head and neck caused by MAB treated at Children's Healthcare of Atlanta hospitals (Atlanta, GA). The predictor variables were patient demographics, dental history, clinical presentation, imaging characteristics, laboratory findings, histopathologic examination, treatment, and complications. The outcome variable was disease resolution or persistence.

RESULTS

Twenty-two patients (mean age, 6.5 yr) met the inclusion criteria. All patients had pulpotomy at 1 dental practice. The mean time from dental procedure to symptom onset was 43.1 days (range, 3 to 180 days). Children presented with cervical or submandibular swelling, facial swelling, gingival erythema, and skin erythema. Radiographic findings were submandibular or cervical lymphadenitis, maxillary or mandibular osteolysis, subcutaneous abscess, and pulmonary nodules. All children had confirmed or probable MAB infection diagnosed on the pathologic specimen. There were 2 distinct patient presentations that guided surgical management: isolated noninflammatory cervical lymphadenitis, which was partly or completely excised (n = 11), and adjacent extension or disseminated infection requiring subtotal lymph node excision, bone debridement, and postoperative antibiotics (n = 11). Most children required multiple surgical interventions to remove infected tissues. All achieved clinical resolution.

CONCLUSION

In this cohort, treatment of NTM lymphadenitis caused by MAB depended on extent of disease and virulence of bacteria. When complete surgical excision was possible, disease resolution was achieved. However, in cases with adjacent extension or dissemination infection, postoperative antibiotics were necessary.

Isolation of nontuberculous mycobacteria from soil using Middlebrook 7H10 agar with increased malachite green concentration

Environmental exposure is considered to be responsible for nontuberculous mycobacterial infections in humans. To facilitate the isolation of mycobacteria from soil, Middlebrook 7H10 agar was optimized as an enhanced selective medium by increasing the concentration of malachite green. A series of modified Middlebrook 7H10 agar media with malachite green concentrations ranging from 2.5 to 2500 mg/L was evaluated using 20 soil samples decontaminated with 3% sodium dodecyl sulfate plus 2% NaOH for 30 min. Among these modified Middlebrook 7H10 media, the medium with malachite green at a concentration of 250 mg/L, i.e., at the same concentration as in Löwenstein–Jensen medium, was the most effective in terms of the number of plates with mycobacterial growth. This medium was further evaluated with 116 soil samples. The results showed that 87.1% (101/116) of the samples produced mycobacterial growth, and 15 samples (12.9%) produced no mycobacterial growth. Of the plates inoculated with the soil samples, each in duplicate, 5.2% (12/232) showed late contamination. In total, 19 mycobacterial species were isolated, including seven (36.8%) rapidly growing mycobacteria and 12 (63.2%) slowly growing mycobacteria. Our results demonstrate that the modified Middlebrook 7H10 agar with 250 mg/L malachite green is useful for the primary isolation of nontuberculous mycobacteria from soil.

Septicemia and pneumonia due to Mycobacterium fortuitum infection in a patient with extronodal NK/T-cell lymphoma, nasal type: A case report

RATIONALE

Mycobacterium fortuitum (M.fortuitum) is one of the rapidly growing nontuberculous mycobacterium (NTM) that is widespread in the environment. M.fortuitum can cause different types of disease including pulmonary disease, lymphadenitis, cutaneous disease, and disseminated disease. However, the infection presenting as septicemia is exceedingly rare.

PATIENT CONCERNS

A 48-year-old immunocompromised male with extranodal NK/T-cell lymphoma, nasal type was admitted to the hospital because of high fever for 10 days.

DIAGNOSES

The pathogen identified twice in the hemoculture was M.fortuitum, but not in the sputum culture. The chest computed tomographic (CT) scan showed a chronic inflammatory infection.

INTERVENTIONS

The patient was treated with sulfamethoxazole and levofloxacin.

OUTCOMES

The symptom of patient disappeared after the treatment for one week, and near-total absorption of the consolidation in CT after the treatment for one month. He continued the treatment for one year until the last negative hemoculture.

LESSONS

Although the M.fortuitum infection presenting as septicemia is rare, a high suspicion of M.fortuitum is required, particularly in the immunosuppressive patients. Timely and adequate treatment is necessary.

Infection Sources of a Common Non-tuberculous Mycobacterial Pathogen, Mycobacterium avium Complex

Numerous studies have revealed a continuous increase in the worldwide incidence and prevalence of non-tuberculous mycobacteria (NTM) diseases, especially pulmonary Mycobacterium avium complex (MAC) diseases. Although it is not clear why NTM diseases have been increasing, one possibility is an increase of mycobacterial infection sources in the environment. Thus, in this review, we focused on the infection sources of pathogenic NTM, especially MAC. The environmental niches for MAC include water, soil, and dust. The formation of aerosols containing NTM arising from shower water, soil, and pool water implies that these niches can be infection sources. Furthermore, genotyping has shown that clinical isolates are identical to environmental ones from household tap water, bathrooms, potting soil, and garden soil. Therefore, to prevent and treat MAC diseases, it is essential to identify the infection sources for these organisms, because patients with these diseases often suffer from reinfections and recurrent infections with them. In the environmental sources, MAC and other NTM organisms can form biofilms, survive within amoebae, and exist in a free-living state. Mycobacterial communities are also likely to occur in these infection sources in households. Water distribution systems are a transmission route from natural water reservoirs to household tap water. Other infection sources include areas with frequent human contact, such as soil and bathrooms, indicating that individuals may carry NTM organisms that concomitantly attach to their household belongings. To explore the mechanisms associated with the global spread of infection and MAC transmission routes, an epidemiological population-wide genotyping survey would be very useful. A good example of the power of genotyping comes from M. avium subsp. hominissuis, where close genetic relatedness was found between isolates of it from European patients and pigs in Japan and Europe, implying global transmission of this bacterium. It is anticipated that whole genome sequencing technologies will improve NTM surveys so that the mechanisms for the global spread of MAC disease will become clearer in the near future. Better understanding of the niches exploited by MAC and its ecology is essential for preventing MAC infections and developing new methods for its effective treatment and elimination.