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

Sources, transmission and hospital-associated outbreaks of nontuberculous mycobacteria: a review

Nontuberculous mycobacteria (NTM) are widespread environmental organisms found in both natural and man-made settings, such as building plumbing, water distribution networks and hospital water systems. Their ubiquitous presence increases the risk of transmission, leading to a wide range of human infections, particularly in immunocompromised individuals. NTM primarily spreads through environmental exposures, such as inhaling aerosolized particles, ingesting contaminated food and introducing it into wounds. Hospital-associated outbreaks have been linked to contaminated medical devices and water systems. Furthermore, the rising global incidence, prevalence and isolation rates highlight the urgency of addressing NTM infections. Gaining a thorough insight into the sources and epidemiology of NTM infection is crucial for devising novel strategies to prevent and manage NTM transmission and infections.

Toward Characterizing Environmental Sources of Non-tuberculous Mycobacteria (NTM) at the Species Level: A Tutorial Review of NTM Phylogeny and Phylogenetic Classification

Nontuberculous mycobacteria (NTM) are any mycobacteria that do not cause tuberculosis or leprosy. While the majority of NTM are harmless and some of them are considered probiotic, a growing number of people are being diagnosed with NTM infections. Therefore, their detection in the environment is of interest to clinicians, environmental microbiologists, and water quality researchers alike. This review provides a tutorial on the foundational approaches for taxonomic classifications, with a focus on the phylogenetic relationships among NTM revealed by the 16S rRNA gene, rpoB gene, and hsp65 gene, and by genome-based approaches. Recent updates on the Mycobacterium genus taxonomy are also provided. A synthesis on the habitats of 189 mycobacterial species in a genome-based taxonomy framework was performed, with attention paid to environmental sources (e.g., drinking water, aquatic environments, and soil). The 16S rRNA gene-based classification accuracy for various regions was evaluated (V3, V3-V4, V3-V5, V4, V4-V5, and V1-V9), revealing overall excellent genus-level classification (up to 100% accuracy) yet only modest performance (up to 63.5% accuracy) at the species level. Future research quantifying NTM species in water systems, determining the effects of water treatment and plumbing conditions on their variations, developing high throughput species-level characterization tools for use in the environment, and incorporating the characterization of functions in a phylogenetic framework will likely fill critical knowledge gaps. We believe this tutorial will be useful for researchers new to the field of molecular or genome-based taxonomic profiling of environmental microbiomes. Experts may also find this review useful in terms of the selected key findings of the past 30 years, recent updates on phylogenomic analyses, as well as a synthesis of the ecology of NTM in a phylogenetic framework.

Quantitative Microbial Risk Assessment Framework Incorporating Water Ages with Legionella pneumophila Growth Rates

Water age in drinking water systems is often used as a proxy for water quality but is rarely used as a direct input in assessing microbial risk. This study directly linked water ages in a premise plumbing system to concentrations of Legionella pneumophila via a growth model. In turn, the L. pneumophila concentrations were used for a quantitative microbial risk assessment to calculate the associated probabilities of infection (Pinf) and clinically severe illness (Pcsi) due to showering. Risk reductions achieved by purging devices, which reduce water age, were also quantified. The median annual Pinf exceeded the commonly used 1 in 10,000 (10-4) risk benchmark in all scenarios, but the median annual Pcsi was always 1-3 orders of magnitude below 10-4. The median annual Pcsi was lower in homes with two occupants (4.7 × 10-7) than with one occupant (7.5 × 10-7) due to more frequent use of water fixtures, which reduced water ages. The median annual Pcsi for homes with one occupant was reduced by 39-43% with scheduled purging 1-2 times per day. Smart purging devices, which purge only after a certain period of nonuse, maintained these lower annual Pcsi values while reducing additional water consumption by 45-62%.

Responses of drinking water bulk and biofilm microbiota to elevated water age in bench-scale simulated distribution systems

Reductions in nonresidential water demand during the COVID-19 pandemic highlighted the importance of understanding how water age impacts drinking water quality and microbiota in piped distribution systems. Using benchtop model distribution systems, we aimed to characterize the impacts of elevated water age on microbiota in bulk water and pipe wall biofilms. Five replicate constant-flow reactors were fed with municipal chloraminated tap water for 6 months prior to building closures and 7 months after. After building closures, chloramine levels entering the reactors dropped; in the reactor bulk water and biofilms the mean cell counts and ATP concentrations increased over an order of magnitude while the detection of opportunistic pathogens remained low. Water age, and the corresponding physicochemical changes, strongly influenced microbial abundance and community composition. Differential initial microbial colonization also had a lasting influence on microbial communities in each reactor (i.e., historical contingency).

Deciphering the diversity and assemblage mechanisms of nontuberculous mycobacteria community in four drinking water distribution systems with different disinfectants

Nontuberculous mycobacteria (NTM) represent an emerging health concern due to their escalating infections worldwide. Although drinking water distribution systems (DWDSs) have been considered as NTM reservoirs and a potential infection route, NTM community at the species level remain largely elusive in DWDSs. This study employed high-throughput sequencing coupled with qPCR to profile NTM community and estimate their abundances at the species level in water and biofilm samples in four DWDSs using three different disinfectants (i.e. free chlorine, chloramine and chlorine dioxide). Results demonstrated the dominance of Mycobacterium paragordonae and Mycobacterium mucogenicum in both biofilm and water across four DWDSs, whereas Mycobacterium abscessus and Mycobacterium chelonae, the two clinically significant species, exhibited low abundance but high prevalence. Comparable NTM community was observed in biofilm across these four DWDSs. Distinct separation of NTM community between SH-chloramine DWDSs water and other DWDSs highlighted the selective pressure of chloramine on NTM community. Furthermore, the research revealed that biofilm and water exhibited distinct NTM community structures, with biofilm harboring more diverse NTM community. Certain NTM species displayed a preference for biofilm, such as Mycobacterium gordonae, while others, like Mycobacterium mucogenicum, were more abundant in water samples (P < 0.05). In terms of NTM community assembly, stochastic processes dominated biofilm, while comparable role of stochastic and deterministic processes was observed in water. In conclusion, this study offers a pioneering and comprehensive insight into the dynamics and assembly mechanisms of NTM community within four DWDSs treated with three distinct disinfectants. These findings serve as a critical foundation for assessing NTM exposure risks and devising effective management strategies within DWDSs.

How clean is your ice machine? Revealing microbial amplification and presence of opportunistic pathogens in hospital ice-water machines

BACKGROUND

Ice machines in healthcare facilities have been suspected and even linked to outbreaks and pseudo-outbreaks. Guidelines exist for maintenance of these devices but there is no clear independent infection control standard, and little is known about their microbial contamination.

AIM

To evaluate the microbial contamination, amplification, and presence of opportunistic pathogens in ice-water machines in a healthcare facility.

METHODS

Concentrations of general microbial indicators (heterotrophic plate counts (HPC), total and intact cells), faecal indicators (enterococci) and opportunistic pathogens (Pseudomonas aeruginosa, non-tuberculous mycobacteria (NTM), Candida spp.) were measured in 36 ice-water machines on patient wards of a 772-bed hospital. Profile sampling was performed on five ice-water machines and adjacent faucets to identify sites of microbial proliferation.

FINDINGS

Candida spp. were found in half of ice-water samples while enterococci and P. aeruginosa were present in six and 11 drain inlets respectively. NTM were measured in all ice-water samples and 35 out of 36 biofilms. Pre-filters and ice machines are sites for additional amplification: NTM densities were on average 1.3 log10 higher in water of ice machine flushed 5 min compared to flushed adjacent tap water.

CONCLUSION

Ice machine design needs to be adapted to reduce microbial proliferation. The absence of correlation between HPC densities (current microbial indicators) and NTM concentrations suggests a need for cleaning efficiency indicators better correlated with opportunistic pathogens. Cleaning and disinfection guidelines of ice machines in healthcare facilities need to be improved, especially when ice is given to the most vulnerable patients, and NTM may be an efficiency indicator.

Impact of fixture purging on water age and excess water usage, considering stochastic water demands

Higher water ages are linked with water quality decline as chlorine dissipates, temperatures become more favorable for microbial growth, and metals and organic matter leach from the pipes. Water fixtures with automated purging devices can limit water age in premise plumbing systems, but also increase water use. To develop purging strategies that lower age while also minimizing water use, the stochastic nature of water demands must be considered. In this research, a hydraulic plumbing network model, with stochastic demands at fixtures, was used to compare water age and water use for five purging conditions: purging at regular intervals, "smart" purging (considering the time of last use), purging with different volumes of water, purging at different fixtures, and the purging with different levels of home occupancy. Higher purging frequency and volume resulted in lower water ages, but higher water use. Purging greatly reduced the variability in water ages, avoiding extreme ages entirely. Water age was minimized by scheduling the purging around occupancy behavior, such as before the occupants wake up or return from work. Scheduled purging used more water than smart purging. Purging after 12 h of nonuse used only 55% of the additional water required for purging every 12 h. Purging after 24 h of nonuse at the kitchen tap and shower used only 38% of the additional water required for purging every 24 h, while maintaining lower water ages and removing the variability in water ages. While larger purging volumes had a greater impact on water age, there were diminishing returns. Purging has a larger impact on low-occupancy homes because fixtures have less frequent use. Overall, this research provides a methodology to compare purging strategies that minimize both water age and water use. While the numerical results presented here are only valid for the specific layout and usage habits, they provide insights and trends applicable to other cases.

A Critical Review on the Factors that Influence Opportunistic Premise Plumbing Pathogens: From Building Entry to Fixtures in Residences

Residential buildings provide unique conditions for opportunistic premise plumbing pathogen (OPPP) exposure via aerosolized water droplets produced by showerheads, faucets, and tubs. The objective of this review was to critically evaluate the existing literature that assessed the impact of potentially enhancing conditions to OPPP occurrence associated with residential plumbing and to point out knowledge gaps. Comprehensive studies on the topic were found to be lacking. Major knowledge gaps identified include the assessment of OPPP growth in the residential plumbing, from building entry to fixtures, and evaluation of the extent of the impact of typical residential plumbing design (e.g., trunk and branch and manifold), components (e.g., valves and fixtures), water heater types and temperature setting of operation, and common pipe materials (copper, PEX, and PVC/CPVC). In addition, impacts of the current plumbing code requirements on OPPP responses have not been assessed by any study and a lack of guidelines for OPPP risk management in residences was identified. Finally, the research required to expand knowledge on OPPP amplification in residences was discussed.

Shower water contributes viable nontuberculous mycobacteria to indoor air

Nontuberculous mycobacteria (NTM) are frequently present in municipal drinking water and building plumbing, and some are believed to cause respiratory tract infections through inhalation of NTM-containing aerosols generated during showering. However, the present understanding of NTM transfer from water to air is insufficient to develop NTM risk mitigation strategies. This study aimed to characterize the contribution of shower water to the abundance of viable NTM in indoor air. Shower water and indoor air samples were collected, and 16S rRNA and rpoB genes were sequenced. The sequencing results showed that running the shower impacted the bacterial community structure and NTM species composition in indoor air by transferring certain bacteria from water to air. A mass balance model combined with NTM quantification results revealed that on average 1/132 and 1/254 of NTM cells in water were transferred to air during 1 hour of showering using a rain and massage showerhead, respectively. A large fraction of the bacteria transferred from water to air were membrane-damaged, i.e. they had compromised membranes based on analysis by live/dead staining and flow cytometry. However, the damaged NTM in air were recoverable as shown by growth in a culture medium mimicking the respiratory secretions of people with cystic fibrosis, implying a potential infection risk by NTM introduced to indoor air during shower running. Among the recovered NTM, Mycobacterium mucogenicum was the dominant species as determined by rpoB gene sequencing. Overall, this study lays the groundwork for future pathogen risk management and public health protection in the built environment.

New design of multilocus sequence analysis of rpoB, ssrA, tuf, atpE, ku, and dnaK for identification of Mycobacterium species

BACKGROUND

Differentiating Mycobacterium tuberculosis (MTB) from nontuberculous mycobacteria (NTM) is very important in the treatment process of patients. According to the American Thoracic Society guideline (ATS), NTM clinical isolates should be identified at the species level proper treatment and patient management. This study aimed to identify NTM clinical isolates by evaluationg rpoB, ssrA, tuf, atpE, ku, and dnaK genes, and use multilocus sequence analysis (MLSA) to concatenate the six genes.

METHODS

Ninety-six Mycobacterium isolates, including 86 NTM and 10 MTB isolates, from all the patients referred to the certain TB Reference Centres were included. All isolates were evaluated by PCR amplification of rpoB, ssrA, tuf, ku, atpE, and dnaK genes and MLSA.

RESULTS

Out of 96 isolates, 91 (94.8%), 87 (90.6%), 72 (75%), 84 (87.5%) and 79 (82.3%) were differentiated to the species level by rpoB, tuf, ssrA, dnaK and atpE genes, respectively. The ku gene was able to identify 69 (80.2%) isolates of the 86 NTM isolates to the species level. We could identify 100% of the isolates to the species level by MLSA.

CONCLUSIONS

None of the PCR targets used in this study were able to completely differentiate all species. The MLSA technique used to concatenate the six genes could increase the identification of clinical Mycobacterium isolates and all 16 species were well-differentiated.

The role of pipe biofilms on dissemination of viral pathogens and virulence factor genes in a full-scale drinking water supply system

Water is an important medium for virus transmission and viral pathogens are increasingly appreciated as a significant water safety issue. However, the effect of pipe biofilms on viral pathogens remains unclear. This research aimed to investigate the dissemination of viruses in a full-scale drinking water supply system (DWSS) and the effect of pipe biofilms on viral pathogens in bulking water. Viral pathogens, pathogenic viral hosts, and viral virulence factors (VFs) were found to disseminate from source water to tap water. The proportion of virus and viral VFs in the biofilm was far less than that in water. The contribution of biofilms in pipe wall to viruses and viral VFs in bulking water was less than 4%, and viruses in the biofilm had no obvious effect on pathogenic viruses in water. Dominant viruses carrying VFs changed from Cyanobacteria virus to Mycobacterium virus after advanced water treatment. Mycobacterium and organics were identified as the key factors influencing composition and abundance of viral VFs, which could explain 41.1% of the variation in viral virulence in the water supply system. Host bacteria and organics may be used as the key targets to control the risk of viruses in DWSSs.

The Presence of Opportunistic Premise Plumbing Pathogens in Residential Buildings: A Literature Review

Opportunistic premise plumbing pathogens (OPPP) are microorganisms that are native to the plumbing environment and that present an emerging infectious disease problem. They share characteristics, such as disinfectant resistance, thermal tolerance, and biofilm formation. The colonisation of domestic water systems presents an elevated health risk for immune-compromised individuals who receive healthcare at home. The literature that has identified the previously described OPPPs (Aeromonas spp., Acinetobacter spp., Helicobacter spp., Legionella spp., Methylobacterium spp., Mycobacteria spp., Pseudomonas spp., and Stenotrophomonas spp.) in residential drinking water systems were systematically reviewed. By applying the Preferred reporting items for systematic reviews and meta-analyses guidelines, 214 studies were identified from the Scopus and Web of Science databases, which included 30 clinical case investigations. Tap components and showerheads were the most frequently identified sources of OPPPs. Sixty-four of these studies detected additional clinically relevant pathogens that are not classified as OPPPs in these reservoirs. There was considerable variation in the detection methods, which included traditional culturing and molecular approaches. These identified studies demonstrate that the current drinking water treatment methods are ineffective against many waterborne pathogens. It is critical that, as at-home healthcare services continue to be promoted, we understand the emergent risks that are posed by OPPPs in residential drinking water. Future research is needed in order to provide consistent data on the prevalence of OPPPs in residential water, and on the incidence of waterborne homecare-associated infections. This will enable the identification of the contributing risk factors, and the development of effective controls.

Dynamics of the Microbial Community and Opportunistic Pathogens after Water Stagnation in the Premise Plumbing of a Building

In premise plumbing, microbial water quality may deteriorate under certain conditions, such as stagnation. Stagnation results in a loss of disinfectant residual, which may lead to the regrowth of microorganisms, including opportunistic pathogens. In the present study, microbial regrowth was investigated at eight faucets in a building over four seasons in one year. Water samples were obtained before and after 24 h of stagnation. In the first 100‍ ‍mL after stagnation, total cell counts measured by flow cytometry increased 14- to 220-fold with a simultaneous decrease in free chlorine from 0.17–0.36‍ ‍mg L^–1 to <0.02‍ ‍mg L^–1. After stagnation, total cell counts were not significantly different among seasons; however, the composition of the microbial community varied seasonally. The relative abundance of Pseudomonas spp. was dominant in winter, whereas Sphingomonas spp. were dominant in most faucets after stagnation in other seasons. Opportunistic pathogens, such as Legionella pneumophila, Mycobacterium avium, Pseudomonas aeruginosa, and Acanthamoeba spp., were below the quantification limit for real-time quantitative PCR in all samples. However, sequences related to other opportunistic pathogens, including L. feeleii, L. maceachernii, L. micdadei, M. paragordonae, M. gordonae, and M. haemophilum, were detected. These results indicate that health risks may increase after stagnation due to the regrowth of opportunistic pathogens.

Tenets of a holistic approach to drinking water-associated pathogen research, management, and communication

In recent years, drinking water-associated pathogens that can cause infections in immunocompromised or otherwise susceptible individuals (henceforth referred to as DWPI), sometimes referred to as opportunistic pathogens or opportunistic premise plumbing pathogens, have received considerable attention. DWPI research has largely been conducted by experts focusing on specific microorganisms or within silos of expertise. The resulting mitigation approaches optimized for a single microorganism may have unintended consequences and trade-offs for other DWPI or other interests (e.g., energy costs and conservation). For example, the ecological and epidemiological issues characteristic of Legionella pneumophila diverge from those relevant for Mycobacterium avium and other nontuberculous mycobacteria. Recent advances in understanding DWPI as part of a complex microbial ecosystem inhabiting drinking water systems continues to reveal additional challenges: namely, how can all microorganisms of concern be managed simultaneously? In order to protect public health, we must take a more holistic approach in all aspects of the field, including basic research, monitoring methods, risk-based mitigation techniques, and policy. A holistic approach will (i) target multiple microorganisms simultaneously, (ii) involve experts across several disciplines, and (iii) communicate results across disciplines and more broadly, proactively addressing source water-to-customer system management.

Recovery of microbiological quality of long-term stagnant tap water in university buildings during the COVID-19 pandemic

Stagnant water can cause water quality deterioration and, in particular, microbiological contaminations, posing potential health risks to occupants. University buildings were unoccupied with little water usage during the COVID-19 pandemic. It's an opportunity to study microbiological quality of long-term stagnant water (LTSW) in university buildings. The tap water samples were collected for three months from four types of campus buildings to monitor water quality and microbial risks after long-term stagnation. Specifically, the residual chlorine, turbidity, and iron/zinc were disqualified, and the heterotrophic plate counts (HPC) exceeded the Chinese national standard above 100 times. It took 4-54 days for these parameters to recover to the routine levels. Six species of pathogens were detected with high frequency and levels (10¹-10⁵ copies/100 mL). Remarkably, L. pneumophilia occurred in 91% of samples with turbidity > 1 NTU. The absence of the culturable cells for these bacteria possibly implied their occurrence in a viable but non-culturable (VBNC) status. The bacterial community of the stagnant tap water differed significantly and reached a steady state in more than 50 days. Furthermore, a high concentration of endotoxin (>10 EU/mL) was found in LTSW, which was in accordance with the high proportion of dead bacteria. The results suggested that the increased microbiological risks require more attention and the countermeasures before the building reopens should be taken.

The Pathway towards Photoelectrocatalytic Water Disinfection: Review and Prospects of a Powerful Sustainable Tool

Photoelectrocatalysis is a hybrid photon/electron-driven process that benefits from the synergistic effects of both processes to enhance and stabilize the generation of disinfecting oxidants. Photoelectrocatalysis is an easy to operate technology that can be scaled-up or scaled-down for various water treatment applications as low-cost decentralized systems. This review article describes the fundamentals of photoelectrocatalysis, applied to water disinfection to ensure access to clean water for all as a sustainable development goal. Advances in reactor engineering design that integrate light-delivery and electrochemical system requirements are presented, with a description of photo-electrode material advances, including doping, nano-decoration, and nanostructure control. Disinfection and cell inactivation are described using different model microorganisms such as E. coli, Mycobacteria, Legionella, etc., as well the fungus Candida parapsilosis, with relevant figures of merit. The key advances in the elucidation of bacterial inactivation mechanisms by photoelectrocatalytic treatments are presented and knowledge gaps identified. Finally, prospects and further research needs are outlined, to define the pathway towards the future of photoelectrocatalytic disinfection technologies.

Microbial diversity in full-scale water supply systems through sequencing technology: a review

The prevalence of microorganisms in full-scale water supply systems raises concerns about their pathogenicity and threats to public health. Clean tap water is essential for public health safety. The conditions of the water treatment process from the source water to tap water, including source water quality, water treatment processes, the drinking water distribution system (DWDS), and building water supply systems (BWSSs) in buildings, greatly influence the bacterial community in tap water. Given the importance of drinking water biosafety, the study of microbial diversity from source water to tap water is essential. With the development of molecular biology methods and bioinformatics in recent years, sequencing technology has been applied to study bacterial communities in full-scale water supply systems. In this paper, changes in the bacterial community and the influence of each treatment stage on microbial diversity in full-scale water supply systems are classified and analyzed. Microbial traceability analysis and control are discussed, and suggestions for future drinking water biosafety research and its prospects are proposed.

Microbial abundance and community composition in biofilms on in-pipe sensors in a drinking water distribution system

Collecting biofilm samples from drinking water distribution systems (DWDSs) is challenging due to limited access to the pipes during regular operations. We report here the analysis of microbial communities in biofilm and water samples collected from sensors installed in a DWDS where monochloramine is used as a residual disinfectant. A total of 52 biofilm samples and 14 bulk water samples were collected from 17 pipe sections representing different water ages. Prokaryotic genome copies (bacterial and archaeal 16S rRNA genes, Mycobacterium spp., ammonia-oxidizing bacteria (AOB), and cyanobacteria) were quantified with droplet digital PCR, which revealed the abundance of these genes in both biofilm and water samples. Prokaryotic 16S rRNA gene sequencing analysis was carried out for a subset of the samples (12 samples from four sites). Mycobacterium and AOB species were dominant in the DWDS sections with low water age and sufficient residual monochloramine, whereas Nitrospira species (nitrite-oxidizing bacteria) dominated in the sections with higher water age and depleted monochloramine level, suggesting the occurrence of nitrification in the studied DWDS. The present study provides novel information on the abundance and identity of prokaryotes in biofilms and water in a full-scale operational DWDS.

Next generation sequencing approaches to evaluate water and wastewater quality

The emergence of next generation sequencing (NGS) is revolutionizing the potential to address complex microbiological challenges in the water industry. NGS technologies can provide holistic insight into microbial communities and their functional capacities in water and wastewater systems, thus eliminating the need to develop a new assay for each target organism or gene. However, several barriers have hampered wide-scale adoption of NGS by the water industry, including cost, need for specialized expertise and equipment, challenges with data analysis and interpretation, lack of standardized methods, and the rapid pace of development of new technologies. In this critical review, we provide an overview of the current state of the science of NGS technologies as they apply to water, wastewater, and recycled water. In addition, a systematic literature review was conducted in which we identified over 600 peer-reviewed journal articles on this topic and summarized their contributions to six key areas relevant to the water and wastewater fields: taxonomic classification and pathogen detection, functional and catabolic gene characterization, antimicrobial resistance (AMR) profiling, bacterial toxicity characterization, Cyanobacteria and harmful algal bloom identification, and virus characterization. For each application, we have presented key trends, noteworthy advancements, and proposed future directions. Finally, key needs to advance NGS technologies for broader application in water and wastewater fields are assessed.

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

Nontuberculous mycobacteria (NTM) are waterborne pathogens commonly found in building water systems where they are a primary concern to vulnerable patient populations and can cause severe disease. The recovery of NTM from environmental samples can be a laborious undertaking and current pre-treatment methods and selective media lack sensitivity. We explored the use of the highly selective Rapidly Growing Mycobacteria (RGM) medium for culturing NTM from environmental water samples compared to existing methods. In total, 223 environmental water samples, including potable and non-potable water, were cultured for NTM using three culture media. In addition to direct culture on RGM medium, each sample was cultured on Middlebrook 7H10 medium and Mitchison 7H11 medium after pre-treatment with 0.2M KCl-HCl. Additionally, 33 distinct species of NTM were inoculated onto RGM medium and 7H10 medium in parallel to directly compare their growth. The use of RGM medium alone without pre-treatment provided a sensitivity (91%) comparable to that offered by culture on both 7H10 and 7H11 with acid pretreatment (combined sensitivity; 86%) with significantly less overgrowth and interference from other organisms on RGM medium. The average concentration of NTM observed on RGM medium alone was comparable to or greater than the NTM concentration on either medium alone or combined. Thirty-three species were examined in parallel and all tested strains of 27 of these species successfully grew on RGM medium, including 19 of 21 from the CDC’s healthcare-associated infections species list. RGM medium was successful at recovering environmental NTM without a pre-treatment, greatly reducing labor and materials required to process samples. Simplification of culture processing for environmental NTM will allow for a better assessment of their presence in building water systems and the potential for reduced exposure of susceptible populations.

Metagenomic Quantification of Genes with Internal Standards

qPCR and metagenomics are central molecular techniques that have offered insights into biological processes for decades, from monitoring spatial and temporal gene dynamics to tracking ARGs or pathogens. Still needed is a tool that can quantify thousands of relevant genes in a sample as gene copies per sample mass or volume.

We demonstrate that an assembly-independent and spike-in facilitated metagenomic quantification approach can be used to screen and quantify over 2,000 genes simultaneously, while delivering absolute gene concentrations comparable to those for quantitative PCR (qPCR). DNA extracted from dairy manure slurry, digestate, and compost was spiked with genomic DNA from a marine bacterium and sequenced using the Illumina HiSeq4000. We compared gene copy concentrations, in gene copies per mass of sample, of five antimicrobial resistance genes (ARGs) generated with (i) our quantitative metagenomic approach, (ii) targeted qPCR, and (iii) a hybrid quantification approach involving metagenomics and qPCR-based 16S rRNA gene quantification. Although qPCR achieved lower quantification limits, the metagenomic method avoided biases caused by primer specificity inherent to qPCR-based methods and was able to detect orders of magnitude more genes than is possible with qPCR assays. We used the approach to simultaneously quantify ARGs in the Comprehensive Antimicrobial Resistance Database (CARD). We observed that the total abundance of tetracycline resistance genes was consistent across different stages of manure treatment on three farms, but different samples were dominated by different tetracycline resistance gene families.

Flushing of Stagnant Premise Water Systems after the COVID-19 Shutdown Can Reduce Infection Risk by Legionella and Mycobacterium spp

There is concern about potential exposure to opportunistic pathogens when reopening buildings closed due to the COVID-19 pandemic. In this study, water samples were collected before, during, and after flushing showers in five unoccupied (i.e., for ∼2 months) university buildings with quantification of opportunists via a cultivation-based assay (Legionella pneumophila only) and quantitative PCR. L. pneumophila were not detected by either method; Legionella spp., nontuberculous mycobacteria (NTM), and Mycobacterium avium complex (MAC), however, were widespread. Using quantitative microbial risk assessment (QMRA), the estimated risks of illness from exposure to L. pneumophila and MAC via showering were generally low (i.e., less than a 10^-7 daily risk threshold), with the exception of systemic infection risk from MAC exposure in some buildings. Flushing rapidly restored the total chlorine (as chloramine) residual and decreased bacterial gene targets to building inlet concentrations within 30 min. During the postflush stagnation period, the residual chlorine dissipated within a few days and bacteria rebounded, approaching preflush concentrations after 6-7 days. These results suggest that flushing can quickly improve water quality in unoccupied buildings, but the improvement may only last a few days.

Critical Review: Propensity of Premise Plumbing Pipe Materials to Enhance or Diminish Growth of Legionella and Other Opportunistic Pathogens

Growth of Legionella pneumophila and other opportunistic pathogens (OPs) in drinking water premise plumbing poses an increasing public health concern. Premise plumbing is constructed of a variety of materials, creating complex environments that vary chemically, microbiologically, spatially, and temporally in a manner likely to influence survival and growth of OPs. Here we systematically review the literature to critically examine the varied effects of common metallic (copper, iron) and plastic (PVC, cross-linked polyethylene (PEX)) pipe materials on factors influencing OP growth in drinking water, including nutrient availability, disinfectant levels, and the composition of the broader microbiome. Plastic pipes can leach organic carbon, but demonstrate a lower disinfectant demand and fewer water chemistry interactions. Iron pipes may provide OPs with nutrients directly or indirectly, exhibiting a high disinfectant demand and potential to form scales with high surface areas suitable for biofilm colonization. While copper pipes are known for their antimicrobial properties, evidence of their efficacy for OP control is inconsistent. Under some circumstances, copper's interactions with premise plumbing water chemistry and resident microbes can encourage growth of OPs. Plumbing design, configuration, and operation can be manipulated to control such interactions and health outcomes. Influences of pipe materials on OP physiology should also be considered, including the possibility of influencing virulence and antibiotic resistance. In conclusion, all known pipe materials have a potential to either stimulate or inhibit OP growth, depending on the circumstances. This review delineates some of these circumstances and informs future research and guidance towards effective deployment of pipe materials for control of OPs.

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.

Isolation, identification and associated risk factors of non-tuberculous mycobacteria infection in humans and dromedary camels in Samburu County, Kenya

Non-tuberculous mycobacteria are of public health significance, and zoonotic infection is attributed to the sociocultural practice of consumption of raw milk and the close human-livestock contact in pastoral communities. This study aimed at isolation, identification of mycobacteria from human sputum and camel milk and risk factors assessment in Samburu East, Kenya. Six hundred and twelve camels and 48 people presumed to have tuberculosis (TB) from 86 households in Wamba and Waso regions were screened. Camels were categorized into Somali, Turkana and Rendile breeds. Single intradermal comparative tuberculin test (SICTT) was used as a herd-screening test on lactating camels and a milk sample collected from reactive camels. Sputum samples were collected from eligible members of participating households. A standard questionnaire on possible risk factors for both humans and camels was administered to respective household heads or their representatives. Total camel skin test reactors were 238/612 (38.9%). Milk and sputum samples were analysed at KEMRI/TB research laboratory for microscopy, GeneXpert^® , culture and identification. Isolates were identified using 16S rRNA gene sequencing at Inqaba biotec in South Africa. Sixty-four isolates were acid-fast bacilli (AFB) positive of which M. fortuitum (3), M. szulgai (20), M. monacense (5), M. lehmanni (4), M. litorale (4), M. elephantis (3), M. duvalii (3), M. brasiliensis (1), M. arcueilense (1) and M. lentiflavum (1) were from milk; M. fortuitum (1), M. szulgai (2) and M. litorale (1) were from humans. Risk factors included the following: Turkana breed (OR = 3.4; 95% CI: 1.2-9.3), replacements from outside the County (OR = 2.1; 95% CI: 0.3-12.3), presence of other domestic species (small stock; OR = 4.6) and replacement from within the herd (OR = 3.2; 95% CI: 0.7-14.7). Zoonotic risk practices included raw milk consumption, shared housing and handling camels. Monitoring of zoonotic NTM through surveillance and notification systems is required.

Feeding the Building Plumbing Microbiome: The Importance of Synthetic Polymeric Materials for Biofilm Formation and Management

The environmental conditions in building plumbing systems differ considerably from the larger distribution system and, as a consequence, uncontrolled changes in the drinking water microbiome through selective growth can occur. In this regard, synthetic polymeric plumbing materials are of particular relevance, since they leach assimilable organic carbon that can be utilized for bacterial growth. Here, we discuss the complexity of building plumbing in relation to microbial ecology, especially in the context of low-quality synthetic polymeric materials (i.e., plastics) and highlight the major knowledge gaps in the field. We furthermore show how knowledge on the interaction between material properties (e.g., carbon migration) and microbiology (e.g., growth rate) allows for the quantification of initial biofilm development in buildings. Hence, research towards a comprehensive understanding of these processes and interactions will enable the implementation of knowledge-based management strategies. We argue that the exclusive use of high-quality materials in new building plumbing systems poses a straightforward strategy towards managing the building plumbing microbiome. This can be achieved through comprehensive material testing and knowledge sharing between all stakeholders including architects, planners, plumbers, material producers, home owners, and scientists.

A comparative analysis of drinking water employing metagenomics

The microbiological content of drinking water traditionally is determined by employing culture-dependent methods that are unable to detect all microorganisms, especially those that are not culturable. High-throughput sequencing now makes it possible to determine the microbiome of drinking water. Thus, the natural microbiota of water and water distribution systems can now be determined more accurately and analyzed in significantly greater detail, providing comprehensive understanding of the microbial community of drinking water applicable to public health. In this study, shotgun metagenomic analysis was performed to determine the microbiological content of drinking water and to provide a preliminary assessment of tap, drinking fountain, sparkling natural mineral, and non-mineral bottled water. Predominant bacterial species detected were members of the phyla Actinobacteria and Proteobacteria, notably the genera Alishewanella, Salmonella, and Propionibacterium in non-carbonated non-mineral bottled water, Methyloversatilis and Methylibium in sparkling natural mineral water, and Mycobacterium and Afipia in tap and drinking fountain water. Fecal indicator bacteria, i.e., Escherichia coli or enterococci, were not detected in any samples examined in this study. Bacteriophages and DNA encoding a few virulence-associated factors were detected but determined to be present only at low abundance. Antibiotic resistance markers were detected only at abundance values below our threshold of confidence. DNA of opportunistic plant and animal pathogens was identified in some samples and these included bacteria (Mycobacterium spp.), protozoa (Acanthamoeba mauritaniensis and Acanthamoeba palestinensis), and fungi (Melampsora pinitorqua and Chryosporium queenslandicum). Archaeal DNA (Candidatus Nitrosoarchaeum) was detected only in sparkling natural mineral water. This preliminary study reports the complete microbiome (bacteria, viruses, fungi, and protists) of selected types of drinking water employing whole-genome high-throughput sequencing and bioinformatics. Investigation into activity and function of the organisms detected is in progress.

Membrane-sensitive bacterial DNA extractions and absolute quantitation of recovery efficiencies

Absolute quantification of waterborne pathogens is mandatory for microbiological risk assessment (MRA). Determination of the DNA recovery efficiency is an essential step before the quantitative molecular measurements, which has been largely ignored. In this study, we compared the DNA recovery efficiency and quality of five extraction methods, including two modified phenol-chloroform-based extractions with mechanical shearing and three commercial kits for the extraction of DNA from indigenous mixed-bacteria culture of river water. All of the methods gave relatively satisfying results from the pelleted sample through centrifugation. However, the commercial kits provided surprisingly low DNA yields for membrane-filtered samples because of DNA trapping and/or absorption on the membrane. Integrating with enzymatic lysis, bath sonication, phenol extraction, and alcohol precipitation achieved highest DNA yields and an acceptable DNA integrity for quantitative PCR. A plasmid containing the human GADPH gene fragment was demonstrated to be a suitable spiking control for determining the absolute DNA recovery efficiency. The unexpectedly low efficiencies of commercial kit extractions imply the significant underestimation of pathogenic bacteria in previous studies, which should gain enough concern in the area of pathogen monitoring in the future.

Diversity of Mycobacteriaceae from aquatic environment at the São Paulo Zoological Park Foundation in Brazil

We investigated the species diversity of Mycobacteriaceae in surface water samples from six environments at the zoological park in São Paulo, Brazil. Three hundred and eighty isolates were cultivated and identified by phenotypic characteristics (growth rate and pigmentation) and sequencing of hsp65, rpoB and 16S rRNA genes. The results revealed that almost 48% of the isolates could be identified at the species level; about 50% were classified at the genus level, and only less than 2% of the isolates showed an inconclusive identification. The isolates classified at the genus level and not identified were then evaluated by phylogenetic analyses using the same three concatenated target genes. The results allowed us to identify at the genus level some isolates that previously had inconclusive identification, and they also suggested the presence of putative candidate species within the sample, demonstrating that this zoological park is an important source of diversity.

Characterizing species interactions that contribute to biofilm formation in a multispecies model of a potable water bacterial community

Microbial biofilms are ubiquitous in drinking water systems, yet our understanding of drinking water biofilms lags behind our understanding of those in other environments. Here, a six-member model bacterial community was used to identify the interactions and individual contributions of each species to community biofilm formation. These bacteria were isolated from the International Space Station potable water system and include Cupriavidus metallidurans, Chryseobacterium gleum, Ralstonia insidiosa, Ralstonia pickettii, Methylorubrum (Methylobacterium) populi and Sphingomonas paucimobilis, but all six species are common members of terrestrial potable water systems. Using reconstituted assemblages, from pairs to all 6 members, community biofilm formation was observed to be robust to the absence of any single species and only removal of the C. gleum/S. paucimobilis pair, out of all 15 possible 2-species subtractions, led to loss of community biofilm formation. In conjunction with these findings, dual-species biofilm formation assays supported the view that the contribution of C. gleum to community biofilm formation was dependent on synergistic biofilm formation with either R. insidiosa or C. metallidurans. These data support a model of multiple, partially redundant species interactions to generate robustness in biofilm formation. A bacteriophage and multiple predatory bacteria were used to test the resilience of the community to the removal of individual members in situ, but the combination of precise and substantial depletion of a single target species was not achievable. We propose that this assemblage can be used as a tractable model to understand the molecular bases of the interactions described here and to decipher other functions of drinking water biofilms.

Linking Microbial Community Composition in Treated Wastewater with Water Quality in Distribution Systems and Subsequent Health Effects

The increases in per capita water consumption, coupled in part with global climate change have resulted in increased demands on available freshwater resources. Therefore, the availability of safe, pathogen-free drinking water is vital to public health. This need has resulted in global initiatives to develop sustainable urban water infrastructure for the treatment of wastewater for different purposes such as reuse water for irrigation, and advanced waste water purification systems for domestic water supply. In developed countries, most of the water goes through primary, secondary, and tertiary treatments combined with disinfectant, microfiltration (MF), reverse osmosis (RO), etc. to produce potable water. During this process the total bacterial load of the water at different stages of the treatment will decrease significantly from the source water. Microbial diversity and load may decrease by several orders of magnitude after microfiltration and reverse osmosis treatment and falling to almost non-detectable levels in some of the most managed wastewater treatment facilities. However, one thing in common with the different end users is that the water goes through massive distribution systems, and the pipes in the distribution lines may be contaminated with diverse microbes that inhabit these systems. In the main distribution lines, microbes survive within biofilms which may contain opportunistic pathogens. This review highlights the role of microbial community composition in the final effluent treated wastewater, biofilms formation in the distribution systems as the treated water goes through, and the subsequent health effects from potential pathogens associated with poorly treated water. We conclude by pointing out some basic steps that may be taken to reduce the accumulation of biofilms in the water distribution systems.

Revisiting John Snow to Meet the Challenge of Nontuberculous Mycobacterial Lung Disease

Nontuberculous mycobacteria (NTM) are ubiquitous components of the soil and surface water microbiome. Disparities by sex, age, and geography demonstrate that both host and environmental factors are key determinants of NTM disease in populations, which predominates in the form of chronic pulmonary disease. As the incidence of NTM pulmonary disease rises across the United States, it becomes increasingly evident that addressing this emerging human health issue requires a bold, multi-disciplinary research framework that incorporates host risk factors for NTM pulmonary disease alongside the determinants of NTM residence in the environment. Such a framework should include the assessment of environmental characteristics promoting NTM growth in soil and surface water, detailed evaluations of water distribution systems, direct sampling of water sources for NTM contamination and species diversity, and studies of host and bacterial factors involved in NTM pathogenesis. This comprehensive approach can identify intervention points to interrupt the transmission of pathogenic NTM species from the environment to the susceptible host and to reduce NTM pulmonary disease incidence.

Nontuberculous Mycobacteria in Two Drinking Water Distribution Systems and the Role of Residual Disinfection

Nontuberculous mycobacteria (NTM) are frequently found in chloraminated drinking water distribution systems (DWDSs) due to their chloramine tolerance. NTM were investigated in the water-main biofilms and drinking water of a chloraminated DWDS in the United States (initial chloramine residual = 3.8 ± 0.1 mg L^-1) and a DWDS in Norway with minimal residual disinfectant (0.08 ± 0.01 mg L^-1). Total mycobacteria and Mycobacterium avium complex (MAC) were quantified by qPCR targeting, respectively, atpE genes and the internal transcribed spacer region. Mycobacteria concentrations in drinking water did not differ between the two systems (P = 0.09; up to 6 × 10⁴ copies L^-1) but were higher in the biofilms from the chloraminated DWDS (P = 5 × 10^-9; up to 5 × 10⁶ copies cm^-2). MAC were not detected in either system. Sequencing of mycobacterial hsp65 genes indicated that the chloraminated DWDS lacked diversity and consisted almost exclusively of M. gordonae. In contrast, there were various novel mycobacteria in the no-residual DWDS. Finally, Mycobacterium- and Methylobacterium-like 16S rRNA genes were often detected simultaneously, though without correlation as previously observed. We conclude that, though residual chloramine may increase mycobacterial biomass in a DWDS, it may also decrease mycobacterial diversity.

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.

mSphere of Influence: Engineering Microbes

Patrick J. McNamara works in the field of environmental engineering. In this mSphere of Influence article, he reflects on how the papers “Bacterial community structure in the drinking water microbiome is governed by filtration processes” (A. J. Pinto, C. Xi, and L.

Patrick J. McNamara works in the field of environmental engineering. In this mSphere of Influence article, he reflects on how the papers “Bacterial community structure in the drinking water microbiome is governed by filtration processes” (A. J. Pinto, C. Xi, and L. Raskin, Environ Sci Technol 46:8851–8859, 2012, https://doi.org/10.1021/es302042t) and “Differential resistance of drinking water bacterial populations to monochloramine disinfection” (T. Chiao, T. M. Clancy, A. Pinto, C. Xi, and L. Raskin, Environ Sci Technol 48:4038–4047, 2014, https://doi.org/10.1021/es4055725) by Lutgarde Raskin and colleagues made an impact on him by providing a foundation for the study of microbial ecology in engineering drinking water treatment plants and drinking water distribution systems.

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.

Antibiotic Resistome Alteration by Different Disinfection Strategies in a Full-Scale Drinking Water Treatment Plant Deciphered by Metagenomic Assembly

Disinfection regimes are considered the most solid strategy to reduce microbial risks in drinking water, but their roles in shaping the antibiotic resistome are poorly understood. This study revealed the alteration of antibiotic resistance genes (ARGs) profiles, their co-occurrence with mobile genetic elements (MGEs), and potential hosts during drinking water disinfection based on metagenomic assembly. We found the ozone/chlorine (O₃/Cl₂) coupled disinfection significantly increased the relative abundance of ARGs and MGE-carrying antibiotic resistance contigs (ARCs) through the enrichment of ARGs within the resistance-nodulation-cell division and ATP-binding cassette antibiotic efflux families that are primarily carried by Pseudomonas, Acinetobacter, Mycobacterium, and Methylocystis, whereas the antimicrobial resin/chlorine coupled disinfection posed unremarkable changes to the ARG and MGE abundances. Moreover, the co-occurrence patterns of antibiotic efflux and beta-lactam ARGs and MGEs were widely identified, and ARCs carrying the recR and mexH genes were detected in all the samples, with the highest abundance of 2.25 × 10^-2 copies per cell after O₃/Cl₂ disinfection. Sequence-independent binning analysis successfully retrieved two draft ARG-carrying genomes of Acidovorax sp. MR-S7 and Hydrogenophaga sp. IBVHS2, further revealing the host-ARG relationship during O₃/Cl₂ disinfection. Overall, this study provides novel insights into the antibiotic resistome alteration during drinking water disinfection.

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.

Shotgun Metagenomics Reveals Taxonomic and Functional Shifts in Hot Water Microbiome Due to Temperature Setting and Stagnation

Hot water premise plumbing has emerged as a critical nexus of energy, water, and public health. The composition of hot water microbiomes is of special interest given daily human exposure to resident flora, especially opportunistic pathogens (OPs), which rely on complex microbial ecological interactions for their proliferation. Here, we applied shotgun metagenomic sequencing to characterize taxonomic and functional shifts in microbiomes as a function of water heater temperature setting, stagnation in distal pipes, and associated shifts in water chemistry. A cross-section of samples from controlled, replicated, pilot-scale hot water plumbing rigs representing different temperature settings (39, 42, and 51°C), stagnation periods (8 h vs. 7 days), and time-points, were analyzed. Temperature setting exhibited an overarching impact on taxonomic and functional gene composition. Further, distinct taxa were selectively enriched by specific temperature settings (e.g., Legionella at 39°C vs. Deinococcus at 51°C), while relative abundances of genes encoding corresponding cellular functions were highly consistent with expectations based on the taxa driving these shifts. Stagnation in distal taps diminished taxonomic and functional differences induced by heating the cold influent water to hot water in recirculating line. In distal taps relative to recirculating hot water, reads annotated as being involved in metabolism and growth decreased, while annotations corresponding to stress response (e.g., virulence disease and defense, and specifically antibiotic resistance) increased. Reads corresponding to OPs were readily identified by metagenomic analysis, with L. pneumophila reads in particular correlating remarkably well with gene copy numbers measured by quantitative polymerase chain reaction. Positive correlations between L. pneumophila reads and those of known protozoan hosts were also identified. Elevated proportions of genes encoding metal resistance and hydrogen metabolism were noted, which was consistent with elevated corrosion-induced metal concentrations and hydrogen generation. This study provided new insights into real-world factors influencing taxonomic and functional compositions of hot water microbiomes. Here metagenomics is demonstrated as an effective tool for screening for potential presence, and even quantities, of pathogens, while also providing diagnostic capabilities for assessing functional responses of microbiomes to various operational conditions. These findings can aid in informing future monitoring and intentional control of hot water microbiomes.