Evaluation of a new culture medium for isolation of nontuberculous mycobacteria from environmental water samples

T, Tomioka N, Ebie Y, Syutsubo K. Quantitative detection and reduction of potentially pathogenic bacterial groups of Aeromonas, Arcobacter, Klebsiella pneumoniae species complex, and Mycobacterium in wastewater treatment facilities

Water quality parameters influence the abundance of pathogenic bacteria. The genera Aeromonas, Arcobacter, Klebsiella, and Mycobacterium are among the representative pathogenic bacteria identified in wastewater. However, information on the correlations between water quality and the abundance of these bacteria, as well as their reduction rate in existing wastewater treatment facilities (WTFs), is lacking. Hence, this study aimed to determine the abundance and reduction rates of these bacterial groups in WTFs. Sixty-eight samples (34 influent and 34 non-disinfected, treated, effluent samples) were collected from nine WTFs in Japan and Thailand. 16S rRNA gene amplicon sequencing analysis revealed the presence of Aeromonas, Arcobacter, and Mycobacterium in all influent wastewater and treated effluent samples. Quantitative real-time polymerase chain reaction (qPCR) was used to quantify the abundance of Aeromonas, Arcobacter, Klebsiella pneumoniae species complex (KpSC), and Mycobacterium. The geometric mean abundances of Aeromonas, Arcobacter, KpSC, and Mycobacterium in the influent wastewater were 1.2 × 104-2.4 × 105, 1.0 × 105-4.5 × 106, 3.6 × 102-4.3 × 104, and 6.9 × 103-5.5 × 104 cells mL-1, respectively, and their average log reduction values were 0.77-2.57, 1.00-3.06, 1.35-3.11, and -0.67-1.57, respectively. Spearman's rank correlation coefficients indicated significant positive or negative correlations between the abundances of the potentially pathogenic bacterial groups and Escherichia coli as well as water quality parameters, namely, chemical/biochemical oxygen demand, total nitrogen, nitrate-nitrogen, nitrite-nitrogen, ammonium-nitrogen, suspended solids, volatile suspended solids, and oxidation-reduction potential. This study provides valuable information on the development and appropriate management of WTFs to produce safe, hygienic water.

Environmental risk of nontuberculous mycobacterial infection: Strategies for advancing methodology

The National Institute of Allergy and Infectious Diseases organized a symposium in June 2022, to facilitate discussion of the environmental risks for nontuberculous mycobacteria exposure and disease. The expert researchers presented recent studies and identified numerous research gaps. This report summarizes the discussion and identifies six major areas of future research related to culture-based and culture independent laboratory methods, alternate culture media and culturing conditions, frameworks for standardized laboratory methods, improved environmental sampling strategies, validation of exposure measures, and availability of high-quality spatiotemporal data.

Mycobacterium biofilms

The genus Mycobacterium includes some of the deadliest pathogens of History (Mycobacterium tuberculosis, Mycobacterium leprae), but most of the species within the genus are environmental microorganisms. Because some of these nontuberculous mycobacteria (NTM) species can be human pathogens, the study of these mycobacterial biofilms has increased during the last decades, and the interest in this issue increased as well as the growing number of patients with diseases caused by NTM. Different molecular mechanisms have been described, being especially well known the importance of glycopeptidolipids. Moreover, the knowledge of the extracellular matrix has shown important differences with other microorganisms, especially because of the presence of lipidic molecules as a key component of this structure. The clinical importance of mycobacterial biofilms has been described for many chronic diseases, especially lung diseases and implant-related ones, both in vitro and in vivo, and even in patients. Moreover, the biofilm-producing capacity has been proven also in M. tuberculosis, while its importance is not well understood. Biofilm studies have also shown the increasing resistance of mycobacteria in sessile form, and the importance of this resistance in the management of the patients is beyond doubt, being surgery necessary in some cases to cure the patients. Diagnosis of mycobacterial diseases is still based on culture-based techniques designed for the detection of M. tuberculosis. Molecular biology-based methods are also broadly used but again designed for tuberculosis diagnosis. Antimicrobial susceptibility testing is also well developed for tuberculosis, but only some species of NTM have standardized techniques for this purpose. New tools or approaches are necessary to treat these patients, whose importance is increasing, as the number of potential hosts is also increasing throughout the world.

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 New Culture Method for the Detection of Non-Tuberculous Mycobacteria in Water Samples from Heater-Cooler Units and Extracorporeal Membrane Oxygenation Machines

The isolation of non-tuberculous mycobacteria (NTM) from cultures is particularly laborious due to the potential overgrowth of coexisting non-acid fast bacilli. To reduce the overgrowth of these non-mycobacterial organisms, a decontamination step with NaOH or cetylpyridinium chloride is highly recommended before plating the samples on the culture medium. However, due to their toxicity, decontamination solutions tend to decrease NTM recovery from clinical and environmental samples. Here, we tested an alternative method for NTM recovery based on the use of NTM Elite agar, a selective medium that does not require a decontamination step. Using NTM Elite agar, we were able to detect non-tuberculous mycobacteria in 27.7% (30/108) of water samples analyzed. The average time to NTM detection was 18 days, but some strains required longer to grow, perhaps due to the stressful environmental conditions (periodical disinfection of devices). NTM Elite agar's effectiveness in inhibiting background flora was proven by the isolation of NTM from samples with and without background flora, showing no statistically significant differences in detection rates for different total viable counts of background flora (p = 0.4989). In conclusion, our findings indicate that effective NTM recovery from HCU- and ECMO-derived water samples can be achieved via filtration and direct culture of the filters on NTM Elite agar. This simple procedure can speed up laboratory work and provide an improved method, successfully resulting in low contamination and high detection rate, in addition to being less time-consuming. Its sensitivity and lack of a decontamination step make this protocol particularly useful for monitoring the effectiveness of device disinfection in hospital settings, even in the presence of low NTM loads. Reading timeframes should probably be extended to 7 weeks (i.e., well beyond the standard 4 weeks advised by the manufacturer), in order to isolate even the slow-growing mycobacteria. However, an extended incubation period is not necessary for exclusion of M. chimaera contamination of the devices, as M. chimaera isolation times do not generally exceed 3 weeks.

A Comparison of Three Culture Media for the Detection of Rapid-Growing Nontuberculous Mycobacteria in Environmental Samples

Nontuberculous mycobacteria (NTM) are common in the environment and certain species can cause serious infections. Improved environmental surveillance methods are needed to combat the increased incidence of NTM disease. Recently, two methods were developed to improve NTM detection. The MYChrOme™ Culture Plate (patent-pending, Phigenics, LLC, Reno, NV, USA) is the first chromogenic medium for rapid-growing NTM detection in water samples. NTM Elite agar (Biomerieux, Marcy-l’Étoile, France), was developed for rapid-growing NTM detection in clinical samples. Fifty water samples (25 potable and 25 non-potable) with three technical replicates were analyzed by each method and Middlebrook 7H11 selective medium (7H11S) (ASTM E2563-07 method modified for water). The MYChrOme method was overall equivalent to or better than 7H11S medium and NTM Elite agar for the detection of rapid-growing NTM in potable water. All three methods detected similar amounts of NTM in non-potable water samples. The chromogenic property of MYChrOme allowed NTM colonies to be quickly identified and differentiated from other bacteria. Additional analysis is required for colony confirmation on 7H11S medium and NTM Elite agar. The use of innovative environmental NTM diagnostics, in addition to proper water management, can greatly reduce the risk of NTM disease.

Recovery of Mycobacteria from Heavily Contaminated Environmental Matrices

For epidemiology studies, a decontamination method using a solution containing 4.0% NaOH and 0.5% tetradecyltrimethylammonium bromide (TDAB) represents a relatively simple and universal procedure for processing heavily microbially contaminated matrices together with increase of mycobacteria yield and elimination of gross contamination. A contamination rate only averaging 7.3% (2.4% in Cluster S; 6.9% in Cluster R and 12.6% in Cluster E) was found in 787 examined environmental samples. Mycobacteria were cultured from 28.5% of 274 soil and water sediments samples (Cluster S), 60.2% of 251 samples of raw and processed peat and other horticultural substrates (Cluster R), and 29.4% of 262 faecal samples along with other samples of animal origin (Cluster E). A total of 38 species of slow and rapidly growing mycobacteria were isolated. M. avium ssp. hominissuis, M. fortuitum and M. malmoense were the species most often isolated. The parameters for the quantitative detection of mycobacteria by PCR can be significantly refined by treating the sample suspension before DNA isolation with PMA (propidium monoazide) solution. This effectively eliminates DNA residue from both dead mycobacterial cells and potentially interfering DNA segments present from other microbial flora. In terms of human exposure risk assessment, the potential exposure to live non-tuberculous mycobacteria can be more accurately determined.