Environmental mycobacteria from alpine and subalpine habitats

Environmental sphagnum-associated fungi target thiol homeostasis to compete with Mycobacterium tuberculosis

Mycobacterial species in nature are found in abundance in sphagnum peat bogs where they compete for nutrients with a variety of microorganisms including fungi. We screened a collection of fungi isolated from sphagnum bogs by co-culture with Mycobacterium tuberculosis ( Mtb ) to look for inducible expression of antitubercular agents and identified five fungi that produced cidal antitubercular agents upon exposure to live Mtb . Whole genome sequencing of these fungi followed by fungal RNAseq after Mtb exposure allowed us to identify biosynthetic gene clusters induced by co-culture. Three of these fungi induced expression of patulin, one induced citrinin expression and one induced the production of nidulalin A. The biosynthetic gene clusters for patulin and citrinin have been previously described but the genes involved in nidulalin A production have not been described before. All three of these potent electrophiles react with thiols and treatment of Mtb cells with these agents followed by Mtb RNAseq showed that these natural products all induce profound thiol stress suggesting a rapid depletion of mycothiol. The induction of thiol-reactive mycotoxins through three different systems in response to exposure to Mtb suggests that fungi have identified this as a highly vulnerable target in a similar microenvironment to that of the caseous human lesion.

Clinical spectrum and relevance of Mycobacterium malmoense: Systematic review and meta-analysis of 859 patients

INTRODUCTION

The clinical relevance of Mycobacterium malmoense isolation from pulmonary specimens has been considered high compared with other non-tuberculous mycobacteria. In this study, we aimed to analyse all published clinical data of patients with M. malmoense isolation to investigate the clinical spectrum, relevance, and outcomes of infections with this uncommon mycobacterium.

METHODS

A systematic review of PubMed, Web of Science, Embase, and Scopus was performed to identify all clinical data about M. malmoense. Random effects meta-analyses of proportions were calculated for clinical relevance, treatment success, and mortality, as well as for other clinical characteristics. A logistic regression analysis, investigating predictors of mortality, as well as Kaplan-Meier survival analyses, were performed.

RESULTS

One hundred and eighty eight patients with individual data from 112 articles and 671 patients with pooled data from 12 articles were included in the meta-analyses. Of patients with individual data, pulmonary infection was the most common manifestation (n = 106/188, 56.4%). One third (n = 61/188, 32.4%) suffered from isolated extra-pulmonary and 21/188 (11.2%) from disseminated disease. In 288 patients with pooled data and pulmonary affection, clinical relevance was high with 68% (95% CI 44-85%) of patients fulfilling criteria for clinical disease. Macrolide and rifamycin-containing regimens were associated with improved survival (adjusted OR 0.12, 95% CI 0.03-0.42, p = 0.002, and 0.23, 95% CI 0.04-0.86, p = 0.03, for lethal events, respectively).

CONCLUSION

In this study, we provide a detailed clinical description of M. malmoense infections. The pathogen is of high clinical relevance for the individual patient with more than 2 out of 3 patients having relevant disease and >40% of manifestations being extra-pulmonary or disseminated. Macrolide and rifamycin-containing regimens are associated with improved survival.

The risk of pulmonary NTM infections and water-quality constituents among persons with cystic fibrosis in the United States, 2010-2019

Rationale

The prevalence of nontuberculous mycobacterial (NTM) pulmonary disease varies geographically in the United States. Previous studies indicate that the presence of certain water-quality constituents in source water increases NTM infection risk.

Objective

To identify water-quality constituents that influence the risk of NTM pulmonary infection in persons with cystic fibrosis in the United States.

Methods

We conducted a population-based case-control study using NTM incidence data collected from the Cystic Fibrosis Foundation Patient Registry during 2010-2019. We linked patient zip code to the county and associated patient county of residence with surface water data extracted from the Water Quality Portal. We used logistic regression models to estimate the odds of NTM infection as a function of water-quality constituents. We modeled two outcomes: pulmonary infection due to Mycobacterium avium complex (MAC) and Mycobacterium abscessus species.

Results

We identified 484 MAC cases, 222 M. abscessus cases and 2816 NTM-negative cystic fibrosis controls resident in 11 states. In multivariable models, we found that for every 1-standardized unit increase in the log concentration of sulfate and vanadium in surface water at the county level, the odds of infection increased by 39% and 21%, respectively, among persons with cystic fibrosis with MAC compared with cystic fibrosis-NTM-negative controls. When modeling M. abscessus as the dependent variable, every 1-standardized unit increase in the log concentration of molybdenum increased the odds of infection by 36%.

Conclusions

These findings suggest that naturally occurring and anthropogenic water-quality constituents may influence the NTM abundance in water sources that supply municipal water systems, thereby increasing MAC and M. abscessus infection risk.

Methods of isolation and identification of nontuberculous mycobacteria from environmental samples: A scoping review

Nontuberculous mycobacteria (NTM) are ubiquitous in the environment. Some species of NTM are pathogenic and cause lung disease in susceptible persons. Epidemiologic studies of environmental NTM infection risk rely on both culture-dependent and culture-independent techniques for NTM isolation and identification. In this review, we summarized current methods used to isolate and identify NTM from the environment. We searched PubMed, Embase, Scopus, Web of Science: Core Collection, and Global Health (CAB Direct) for peer-reviewed studies from the last 12 years. We identified 1685 unique citations and 110 studies met our inclusion and exclusion criteria. Approximately half (55%) of the studies identified in this review used a combination of culture-independent and culture-dependent methods. The most common environmental substrate analyzed was water (n = 90). Identification of current, common methods for the isolation and identification of NTM from environmental samples may contribute to the development of standard methodological practices in the future. The choice of isolation method is based on the research question, environment, and species. A summary of common methods may contribute to the development of standard practices for isolation and identification of NTM from environmental samples, which may lead to more robust and comparable results.

A Comprehensive Review and Update on Epidemiology, Symptomatology and Management of Nontuberculous Mycobacteria (NTM)

Nontuberculous mycobacteria (NTM) are free-living organisms ubiquitously present in the environment. In recent times, NTM gained much importance due to the increase in incidence globally. They are potential agents in causing both pulmonary and extrapulmonary infections in both immunocompromised and immunocompetent individuals. The problem arises when the possible NTM cases are misdiagnosed as drug-resistant tuberculosis (DR-TB). Hence, it is essential to correctly identify the NTMs causing disease due to two major reasons. One is to prevent clinicians from starting anti-tuberculous drugs and the other is that treatment regimen differs for certain NTM from tuberculosis. Apart from conventional methods like smear microscopy, culture, in the current era newer diagnostic modalities like matrix-assisted laser desorption of ionization-time of flight mass spectrometry (MALDI TOF MS), line probe assay, genomic sequencing, are used in referral laboratories which allows identification and speciation of the organism. A thorough literature search was done in PubMed, Google Scholar, Cochrane Library, Embase, Scopus on nontuberculous mycobacteria. The search keywords include nontuberculous mycobacteria, atypical mycobacteria, case reports, and original articles on NTM. In this review, we have summarised the current knowledge on epidemiology, pathogenesis, clinical features, and treatment of NTM.

Ecology of Nontuberculous Mycobacteria

Nontuberculous mycobacteria (NTM) are opportunistic human pathogens that are widespread in the human environment. In fact, NTM surround humans. The basis for their widespread presence in soils and natural and human-engineered waters lies primarily in their disinfectant resistance, biofilm formation, and adaptability to fluctuating environmental conditions. As NTM in drinking water surround humans, a major route of infection is through aerosols. The characteristics of NTM, including resistance to disinfection, adherence to surfaces and biofilm formation, present challenges to contemporary water treatment processes developed for control of Escherichia coli and fecal coliforms.

A Cluster of Nontuberculous Mycobacterial Tenosynovitis Following Hurricane Relief Efforts

BACKGROUND

Nontuberculous mycobacteria (NTM) are a rare cause of infectious tenosynovitis of the upper extremity. Using molecular methods, clinical microbiology laboratories are increasingly reporting identification down to the species level. Improved methods for speciation are revealing new insights into the clinical and epidemiologic features of rare NTM infections.

METHODS

We encountered 3 cases of epidemiologically linked upper extremity NTM tenosynovitis associated with exposure to hurricane-damaged wood. We conducted whole-genome sequencing to assess isolate relatedness followed by a literature review of NTM infections that involved the upper extremity.

RESULTS

Despite shared epidemiologic risk, the cases were caused by 3 distinct organisms. Two cases were rare infections caused by closely related but distinct species within the Mycobacterium terrae complex that could not be differentiated by traditional methods. The third case was caused by Mycobacterium intracellulare. An updated literature review that focused on research that used modern molecular speciation methods found that several species within the M. terrae complex are increasingly reported as a cause of upper extremity tenosynovitis, often in association with environmental exposures.

CONCLUSIONS

These cases illustrate the importance of molecular methods for speciating phenotypically similar NTM, as well as the limitations of laboratory-based surveillance in detecting point-source outbreaks when the source is environmental and may involve multiple organisms.

Lower Recovery of Nontuberculous Mycobacteria from Outdoor Hawai'i Environmental Water Biofilms Compared to Indoor Samples

Nontuberculous mycobacteria (NTM) are environmental organisms that can cause opportunistic pulmonary disease with species diversity showing significant regional variation. In the United States, Hawai'i shows the highest rate of NTM pulmonary disease. The need for improved understanding of NTM reservoirs led us to identify NTM from patient respiratory specimens and compare NTM diversity between outdoor and indoor locations in Hawai'i. A total of 545 water biofilm samples were collected from 357 unique locations across Kaua'i (n = 51), O'ahu (n = 202), Maui (n = 159), and Hawai'i Island (n = 133) and divided into outdoor (n = 179) or indoor (n = 366) categories. rpoB sequence analysis was used to determine NTM species and predictive modeling applied to develop NTM risk maps based on geographic characteristics between environments. M. chimaera was frequently identified from respiratory and environmental samples followed by M. chelonae and M. abscessus; yet significantly less NTM were consistently recovered from outdoor compared to indoor biofilms, as exemplified by showerhead biofilm samples. While the frequency of M. chimaera recovery was comparable between outdoor and indoor showerhead biofilms, phylogenetic analyses demonstrate similar rpoB gene sequences between all showerhead and respiratory M. chimaera isolates, supporting outdoor and indoor environments as possible sources for pulmonary M. chimaera infections.

Non-Tuberculous Mycobacteria: Molecular and Physiological Bases of Virulence and Adaptation to Ecological Niches

Non-tuberculous mycobacteria (NTM) are paradigmatic colonizers of the total environment, circulating at the interfaces of the atmosphere, lithosphere, hydrosphere, biosphere, and anthroposphere. Their striking adaptive ecology on the interconnection of multiple spheres results from the combination of several biological features related to their exclusive hydrophobic and lipid-rich impermeable cell wall, transcriptional regulation signatures, biofilm phenotype, and symbiosis with protozoa. This unique blend of traits is reviewed in this work, with highlights to the prodigious plasticity and persistence hallmarks of NTM in a wide diversity of environments, from extreme natural milieus to microniches in the human body. Knowledge on the taxonomy, evolution, and functional diversity of NTM is updated, as well as the molecular and physiological bases for environmental adaptation, tolerance to xenobiotics, and infection biology in the human and non-human host. The complex interplay between individual, species-specific and ecological niche traits contributing to NTM resilience across ecosystems are also explored. This work hinges current understandings of NTM, approaching their biology and heterogeneity from several angles and reinforcing the complexity of these microorganisms often associated with a multiplicity of diseases, including pulmonary, soft-tissue, or milliary. In addition to emphasizing the cornerstones of knowledge involving these bacteria, we identify research gaps that need to be addressed, stressing out the need for decision-makers to recognize NTM infection as a public health issue that has to be tackled, especially when considering an increasingly susceptible elderly and immunocompromised population in developed countries, as well as in low- or middle-income countries, where NTM infections are still highly misdiagnosed and neglected.

Nontuberculous Mycobacterial Disease and Molybdenum in Colorado Watersheds

Nontuberculous mycobacteria (NTM) are environmental bacteria that may cause chronic lung disease. Environmental factors that favor NTM growth likely increase the risk of NTM exposure within specific environments. We aimed to identify water-quality constituents (Al, As, Cd, Ca, Cu, Fe, Pb, Mg, Mn, Mo, Ni, K, Se, Na, Zn, and pH) associated with NTM disease across Colorado watersheds. We conducted a geospatial, ecological study, associating data from patients with NTM disease treated at National Jewish Health and water-quality data from the Water Quality Portal. Water-quality constituents associated with disease risk were identified using generalized linear models with Poisson-distributed discrete responses. We observed a highly robust association between molybdenum (Mo) in the source water and disease risk. For every 1- unit increase in the log concentration of molybdenum in the source water, disease risk increased by 17.0%. We also observed a statistically significant association between calcium (Ca) in the source water and disease risk. The risk of NTM varied by watershed and was associated with watershed-specific water-quality constituents. These findings may inform mitigation strategies to decrease the overall risk of exposure.

A Global Survey of Mycobacterial Diversity in Soil

Mycobacteria are a diverse bacterial group ubiquitous in many soil and aquatic environments. Members of this group have been associated with human and other animal diseases, including the nontuberculous mycobacteria (NTM), which are of growing relevance to public health worldwide. Although soils are often considered an important source of environmentally acquired NTM infections, the biodiversity and ecological preferences of soil mycobacteria remain largely unexplored across contrasting climates and ecosystem types. Using a culture-independent approach by combining 16S rRNA marker gene sequencing with mycobacterium-specific hsp65 gene sequencing, we analyzed the diversity, distributions, and environmental preferences of soil-dwelling mycobacteria in 143 soil samples collected from a broad range of ecosystem types. The surveyed soils harbored highly diverse mycobacterial communities that span the full extent of the known mycobacterial phylogeny, with most soil mycobacteria (97% of mycobacterial clades) belonging to previously undescribed lineages. While mycobacteria tended to have higher relative abundances in cool, wet, and acidic soil environments, several individual mycobacterial clades had contrasting environmental preferences. We identified the environmental preferences of many mycobacterial clades, including the clinically relevant Mycobacterium avium complex that was more commonly detected in wet and acidic soils. However, most of the soil mycobacteria detected were not closely related to known pathogens, calling into question previous assumptions about the general importance of soil as a source of NTM infections. Together, this work provides novel insights into the diversity, distributions, and ecological preferences of soil mycobacteria and lays the foundation for future efforts to link mycobacterial phenotypes to their distributions.IMPORTANCE Mycobacteria are common inhabitants of soil, and while most members of this bacterial group are innocuous, some mycobacteria can cause environmentally acquired infections of humans and other animals. Human infections from nontuberculous mycobacteria (NTM) are increasingly prevalent worldwide, and some areas appear to be "hotspots" for NTM disease. While exposure to soil is frequently implicated as an important mode of NTM transmission, the diversity, distributions, and ecological preferences of soil mycobacteria remain poorly understood. We analyzed 143 soils from a range of ecosystems and found that mycobacteria and lineages within the group often exhibited predictable preferences for specific environmental conditions. Soils harbor large amounts of previously undescribed mycobacterial diversity, and lineages that include known pathogens were rarely detected in soil. Together, these findings suggest that soil is an unlikely source of many mycobacterial infections. The biogeographical patterns we documented lend insight into the ecology of this important group of soil-dwelling bacteria.

Micobacterias no tuberculosas de sitios arqueológicos de México

Se examinaron varios edificios de nueve sitios arqueológicos en México para detectar la presencia de micobacterias y se pudieron aislar 45 cepas no tuberculosas. Se obtuvieron a partir de biopelículas usando medios selectivos con antibióticos y colorantes. Las cepas aisladas se determinaron como micobacterias mediante una PCR específica, posteriormente se identificaron con tres marcadores moleculares: genes rrs (16S rRNA), hsp65 y rpoB. Además se relacionaron los datos fisiográficos de las zonas arqueológicas estudiadas con el número de bacterias ácido alcohol resistentes mediante un análisis univariado de varianza. De las 45 cepas de micobacterias aisladas 21 correspondieron a Mycobacteroides chelonae; siete, M. abscessus; cinco, Mycolicibacterium flavescens; cuatro, Mycobacterium alvei; dos, M. fortuitum; y seis quedaron como Mycobacterium sp. La mayoría de las micobacteriasno tuberculosas(MNT) fueron aisladas de dos de las zonas arqueológicas: 25 de Guachimontones (Jalisco) y 13 de Atetelco (Estado de México). El análisis estadístico mostró que los factores ambientales como clima y la interacción temperatura-humedad-precipitación tuvieron una gran influencia en la presencia de este grupo bacteriano en las zonas arqueológicas.

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.

Environmental reservoirs of pathogenic mycobacteria across the Ethiopian biogeographical landscape

The Mycobacterium genus comprises over one-hundred-and-fifty recognised species, the majority of which reside in the environment and many of which can be pathogenic to mammals. Some species of environmental mycobacteria may interfere with BCG vaccination efficacy and in tuberculin test interpretation. Examining biogeographic trends in the distribution of members of the mycobacteria across a number of physicochemical and spatial gradients in soil and water environments across Ethiopia using oligotyping identified differential distributions of pathogenic and significant species. The tuberculosis complex was identified in more than 90% of water samples and taxonomic groups implicated in lower BCG vaccine efficiency were core in both soil and water Mycobacterium communities. A reservoir of Mycobacterium bovis was identified in water, with up to 7.3×102 genome equivalents per ml. Elevation, temperature, habitat and vegetation type were important predictors of both soil and water Mycobacterium communities. These results represent the first step in understanding the potential risk of exposure to environmental mycobacteria that may undermine efforts to reduce disease incidence.

Non-tuberculous mycobacterial infections of veterinary relevance

Mycobacteria play an important role in human and animal health fields. We here examine the place of non tuberculous mycobacteria (NTM) infections in the veterinary context. Relevant aspects of a reference laboratory experience and a literature review are presented in this article. Importance is given both to productivity and to economic losses due to misdiagnosis with bovine tuberculosis and paratuberculosis. The impact NTM may have is relative to geographical location, ecology, husbandry, extent of surveillance programs and bovine tuberculosis and paratuberculosis prevalence. The role of the most relevant NTM in animal disease is summarized with a special focus on Mycobacterium avium subsp. paratuberculosis, given its role as causative agent of paratuberculosis, a disease with huge economic consequences for ruminant livestock.

Prospecting environmental mycobacteria: combined molecular approaches reveal unprecedented diversity

Background

Environmental mycobacteria (EM) include species commonly found in various terrestrial and aquatic environments, encompassing animal and human pathogens in addition to saprophytes. Approximately 150 EM species can be separated into fast and slow growers based on sequence and copy number differences of their 16S rRNA genes. Cultivation methods are not appropriate for diversity studies; few studies have investigated EM diversity in soil despite their importance as potential reservoirs of pathogens and their hypothesized role in masking or blocking M. bovis BCG vaccine.

Methods

We report here the development, optimization and validation of molecular assays targeting the 16S rRNA gene to assess diversity and prevalence of fast and slow growing EM in representative soils from semi tropical and temperate areas. New primer sets were designed also to target uniquely slow growing mycobacteria and used with PCR-DGGE, tag-encoded Titanium amplicon pyrosequencing and quantitative PCR.

Results

PCR-DGGE and pyrosequencing provided a consensus of EM diversity; for example, a high abundance of pyrosequencing reads and DGGE bands corresponded to M. moriokaense, M. colombiense and M. riyadhense. As expected pyrosequencing provided more comprehensive information; additional prevalent species included M. chlorophenolicum, M. neglectum, M. gordonae, M. aemonae. Prevalence of the total Mycobacterium genus in the soil samples ranged from 2.3×10⁷ to 2.7×10⁸ gene targets g⁻¹; slow growers prevalence from 2.9×10⁵ to 1.2×10⁷ cells g⁻¹.

Conclusions

This combined molecular approach enabled an unprecedented qualitative and quantitative assessment of EM across soil samples. Good concordance was found between methods and the bioinformatics analysis was validated by random resampling. Sequences from most pathogenic groups associated with slow growth were identified in extenso in all soils tested with a specific assay, allowing to unmask them from the Mycobacterium whole genus, in which, as minority members, they would have remained undetected.

Evaluation of a method to detect Mycobacterium bovis in air samples from infected Eurasian badgers (Meles meles) and their setts

Environmental air sampling was evaluated as a method to detect the presence of M. bovis in the vicinity of infected badgers and their setts. Airborne particles were collected on gelatine filters using a commercially available air sampling instrument and tested for the presence of M. bovis using bacteriological culture and real-time PCR. The sensitivity of bacteriological culture was broadly similar to that of real-time PCR when testing samples artificially spiked with M. bovis. Sampling was undertaken from directly under the muzzles of badgers which had been experimentally infected with M. bovis (37 samples), within enclosures housing the experimentally infected animals (50 samples), and in the vicinity of setts with resident infected wild badgers (52 samples). The methods employed did not detect M. bovis from either infected badgers or artificial or natural setts known to contain infected animals. However, samples taken at four of the six natural setts were positive for Mycobacterium gordonae.

Clinical and laboratory aspects of the diagnosis and management of cutaneous and subcutaneous infections caused by rapidly growing mycobacteria

Rapidly growing mycobacteria (RGM) are known to cause pulmonary, extra-pulmonary, systemic/disseminated, and cutaneous and subcutaneous infections. The erroneous detection of RGM that is based solely on microscopy, solid and liquid cultures, Bactec systems, and species-specific polymerase chain reaction (PCR) may produce misleading results. Thus, inappropriate therapeutic measures may be used in dermatologic settings, leading to increased numbers of skin deformity cases or recurrent infections. Molecular tools such as the sequence analyses of 16S rRNA, rpoB and hsp65 or PCR restriction enzyme analyses, and the alternate gene sequencing of the superoxide dismutase (SOD) gene, dnaJ, the 16S-23S rRNA internal transcribed spacers (ITS), secA, recA1, dnaK, and the 32-kDa protein gene have shown promising results in the detection of RGM species. PCR restriction enzyme analyses (PRA) work better than conventional methods at identifying species that are closely related. Recently introduced molecular tools such as matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), pyrosequencing, DNA chip technology, and Beacon probes-combined PCR probes have shown comparable results in the detection of various species of RGM. Closely related RGM species (e.g., Mycobacterium fortuitum, M. chelonae, and M. abscessus) must be clearly differentiated using accurate molecular techniques because their therapeutic responses are species-specific. Hence, this paper reviews the following aspects of RGM: (i) its sources, predisposing factors, clinical manifestations, and concomitant fungal infections; (ii) the risks of misdiagnoses in the management of RGM infections in dermatological settings; (iii) the diagnoses and outcomes of treatment responses in common and uncommon infections in immunocompromised and immunocompetent patients; (iv) conventional versus current molecular methods for the detection of RGM; (v) the basic principles of a promising MALDI-TOF MS, sampling protocol for cutaneous or subcutaneous lesions and its potential for the precise differentiation of M. fortuitum, M. chelonae, and M. abscessus; and (vi) improvements in RGM infection management as described in the recent 2011 Clinical and Laboratory Standards Institute (CLSI) guidelines, including interpretation criteria of molecular methods and antimicrobial drug panels and their break points [minimum inhibitory concentrations (MICs)], which have been highlighted for the initiation of antimicrobial therapy.