Biodiversity of amoebae and amoeba-associated bacteria in water treatment plants

Amoebae as training grounds for microbial pathogens

Grazing of amoebae on microorganisms represents one of the oldest predator-prey dynamic relationships in nature. It represents a genetic "melting pot" for an ancient and continuous multi-directional inter- and intra-kingdom horizontal gene transfer between amoebae and its preys, intracellular microbial residents, endosymbionts, and giant viruses, which has shaped the evolution, selection, and adaptation of microbes that evade degradation by predatory amoeba. Unicellular phagocytic amoebae are thought to be the ancient ancestors of macrophages with highly conserved eukaryotic processes. Selection and evolution of microbes within amoeba through their evolution to target highly conserved eukaryotic processes have facilitated the expansion of their host range to mammals, causing various infectious diseases. Legionella and environmental Chlamydia harbor an immense number of eukaryotic-like proteins that are involved in ubiquitin-related processes or are tandem repeats-containing proteins involved in protein-protein and protein-chromatin interactions. Some of these eukaryotic-like proteins exhibit novel domain architecture and novel enzymatic functions absent in mammalian cells, such as ubiquitin ligases, likely acquired from amoebae. Mammalian cells and amoebae may respond similarly to microbial factors that target highly conserved eukaryotic processes, but mammalian cells may undergo an accidental response to amoeba-adapted microbial factors. We discuss specific examples of microbes that have evolved to evade amoeba predation, including the bacterial pathogens- Legionella, Chlamydia, Coxiella, Rickettssia, Francisella, Mycobacteria, Salmonella, Bartonella, Rhodococcus, Pseudomonas, Vibrio, Helicobacter, Campylobacter, and Aliarcobacter. We also discuss the fungi Cryptococcus, and Asperigillus, as well as amoebae mimiviruses/giant viruses. We propose that amoeba-microbe interactions will continue to be a major "training ground" for the evolution, selection, adaptation, and emergence of microbial pathogens equipped with unique pathogenic tools to infect mammalian hosts. However, our progress will continue to be highly dependent on additional genomic, biochemical, and cellular data of unicellular eukaryotes.

Protozoan-Priming and Magnesium Conditioning Enhance Legionella pneumophila Dissemination and Monochloramine Resistance

Opportunistic pathogens (OPs) are of concern in drinking water distribution systems because they persist despite disinfectant residuals. While many OPs garner protection from disinfectants via a biofilm lifestyle, Legionella pneumophila (Lp) also gains disinfection resistance by being harbored within free-living amoebae (FLA). It has been long established, but poorly understood, that Lp grown within FLA show increased infectivity toward subsequent FLA or human cells (i.e., macrophage), via a process we previously coined "protozoan-priming". The objectives of this study are (i) to identify in Lp a key genetic determinant of how protozoan-priming increases its infectivity, (ii) to determine the chemical stimulus within FLA to which Lp responds during protozoan-priming, and (iii) to determine if more infectious forms of Lp also exhibit enhanced disinfectant resistance. Using Acanthamoeba castellanii as a FLA host, the priming effect was isolated to Lp's sidGV locus, which is activated upon sensing elevated magnesium concentrations. Supplementing growth medium with 8 mM magnesium is sufficient to produce Lp grown in vitro with an infectivity equivalent to that of Lp grown via the protozoan-primed route. Both Lp forms with increased infectivity (FLA-grown and Mg2+-supplemented) exhibit greater monochloramine resistance than Lp grown in standard media, indicating that passage through FLA not only increases Lp's infectivity but also enhances its monochloramine resistance. Therefore, laboratory-based testing of disinfection strategies should employ conditions that simulate or replicate intracellular growth to accurately assess disinfectant resistance.

Variation in the Structure and Composition of Bacterial Communities within Drinking Water Fountains in Melbourne, Australia

Modern drinking water distributions systems (DWDSs) have been designed to transport treated or untreated water safely to the consumer. DWDSs are complex environments where microorganisms are able to create their own niches within water, biofilm or sediment. This study was conducted on twelve drinking fountains (of three different types, namely types A, B and C) within the Melbourne (Australia) city area with the aim to (i) characterize the water quality and viable and total counts at each fountain, (ii) compare the differences in the structure and diversity of the bacterial community between bulk water and biofilm and (iii) determine differences between the bacterial communities based on fountain type. Samples of water and biofilm were assessed using both culture-dependent and culture-independent techniques. Heterotrophic plate counts of water samples ranged from 0.5 to 107.5 CFU mL−1, and as expected, total cell counts (cells mL−1) were, on average, 2.9 orders of magnitude higher. Based on the mean relative abundance of operational taxonomic units (OTUs), ANOSIM showed that the structure of the bacterial communities in drinking water and biofilm varied significantly (R = 0.58, p = 0.001). Additionally, ANOSIM showed that across fountain types (in water), the bacterial community was more diverse in fountain type C compared to type A (p < 0.001) and type B (p < 0.001). 16S rRNA next-generation sequencing revealed that the bacterial communities in both water and biofilm were dominated by only seven phyla, with Proteobacteria accounting for 71.3% of reads in water and 68.9% in biofilm. The next most abundant phylum was Actinobacteria (10.4% water; 11.7% biofilm). In water, the genus with the highest overall mean relative abundance was Sphingomonas (24.2%), while Methylobacterium had the highest mean relative abundance in biofilm samples (54.7%). At the level of genus and higher, significant differences in dominance were found across fountain types. In water, Solirubrobacterales (order) were present in type C fountains at a relative abundance of 17%, while the mean relative abundance of Sphingomonas sp. in type C fountains was less than half that in types A (25%) and B (43%). In biofilm, the relative abundance of Sphingomonas sp. was more than double in type A (10%) fountains compared to types B (4%) and C (5%), and Sandarakinorhabdus sp. were high in type A fountains (6%) and low in types B and C (1%). Overall this research showed that there were significant differences in the composition of bacterial communities in water and biofilm from the same site. Furthermore, significant variation exists between microbial communities present in the fountain types, which may be related to age. Long-established environments may lead to a greater chance of certain bacteria gaining abilities such as increased disinfection resistance. Variations between the structure of the bacterial community residing in water and biofilm and differences between fountain types show that it is essential to regularly test samples from individual locations to determine microbial quality.

Legionella and other opportunistic pathogens in full-scale chloraminated municipal drinking water distribution systems

Water-based opportunistic pathogens (OPs) are a leading cause of drinking-water-related disease outbreaks, especially in developed countries such as the United States (US). Physicochemical water quality parameters, especially disinfectant residuals, control the (re)growth, presence, colonization, and concentrations of OPs in drinking water distribution systems (DWDSs), while the relationship between OPs and those parameters remain unclear. This study aimed to quantify how physicochemical parameters, mainly monochloramine residual concentration, hydraulic residence time (HRT), and seasonality, affected the occurrence and concentrations of four common OPs (Legionella, Mycobacterium, Pseudomonas, and Vermamoeba vermiformis) in four full-scale DWDSs in the US. Legionella as a dominant OP occurred in 93.8% of the 64 sampling events and had a mean density of 4.27 × 105 genome copies per liter. Legionella positively correlated with Mycobacterium, Pseudomonas, and total bacteria. Multiple regression with data from the four DWDSs showed that Legionella had significant correlations with total chlorine residual level, free ammonia concentration, and trihalomethane concentration. Therefore, Legionella is a promising indicator of water-based OPs, reflecting microbial water quality in chloraminated DWDSs. The OP concentrations had strong seasonal variations and peaked in winter and/or spring possibly because of reduced water usage (i.e., increased water stagnation or HRT) during cold seasons. The OP concentrations generally increased with HRT presumably because of disinfectant residual decay, indicating the importance of well-maintaining disinfectant residuals in DWDSs for OP control. The concentrations of Mycobacterium, Pseudomonas, and V. vermiformis were significantly associated with total chlorine residual concentration, free ammonia concentration, and pH and trihalomethane concentration, respectively. Overall, this study demonstrates how the significant spatiotemporal variations of OP concentrations in chloraminated DWDSs correlated with critical physicochemical water quality parameters such as disinfectant residual levels. This work also indicates that Legionella is a promising indicator of OPs and microbial water quality in chloraminated DWDSs.

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.

Enzyme-Loaded Flower-Shaped Nanomaterials: A Versatile Platform with Biosensing, Biocatalytic, and Environmental Promise

As a result of their unique structural and multifunctional characteristics, organic-inorganic hybrid nanoflowers (hNFs), a newly developed class of flower-like, well-structured and well-oriented materials has gained significant attention. The structural attributes along with the surface-engineered functional entities of hNFs, e.g., their size, shape, surface orientation, structural integrity, stability under reactive environments, enzyme stabilizing capability, and organic-inorganic ratio, all significantly contribute to and determine their applications. Although hNFs are still in their infancy and in the early stage of robust development, the recent hike in biotechnology at large and nanotechnology in particular is making hNFs a versatile platform for constructing enzyme-loaded/immobilized structures for different applications. For instance, detection- and sensing-based applications, environmental- and sustainability-based applications, and biocatalytic and biotransformation applications are of supreme interest. Considering the above points, herein we reviewed current advances in multifunctional hNFs, with particular emphasis on (1) critical factors, (2) different metal/non-metal-based synthesizing processes (i.e., (i) copper-based hNFs, (ii) calcium-based hNFs, (iii) manganese-based hNFs, (iv) zinc-based hNFs, (v) cobalt-based hNFs, (vi) iron-based hNFs, (vii) multi-metal-based hNFs, and (viii) non-metal-based hNFs), and (3) their applications. Moreover, the interfacial mechanism involved in hNF development is also discussed considering the following three critical points: (1) the combination of metal ions and organic matter, (2) petal formation, and (3) the generation of hNFs. In summary, the literature given herein could be used to engineer hNFs for multipurpose applications in the biosensing, biocatalysis, and other environmental sectors.

Role of amoebae for survival and recovery of 'non-culturable' Helicobacter pylori cells in aquatic environments

Helicobacter pylori is a fastidious Gram-negative bacterium that infects over half of the world's population, causing chronic gastritis and is a risk factor for stomach cancer. In developing and rural regions where prevalence rate exceeds 60%, persistence and waterborne transmission are often linked to poor sanitation conditions. Here we demonstrate that H. pylori not only survives but also replicates within acidified free-living amoebal phagosomes. Bacterial counts of the clinical isolate H. pylori G27 increased over 50-fold after three days in co-culture with amoebae. In contrast, a H. pylori mutant deficient in a cagPAI gene (cagE) showed little growth within amoebae, demonstrating the likely importance of a type IV secretion system in H. pylori for amoebal infection. We also demonstrate that H. pylori can be packaged by amoebae and released in extracellular vesicles. Furthermore, and for the first time, we successfully demonstrate the ability of two free-living amoebae to revert and recover viable but non-cultivable coccoid (VBNC)-H. pylori to a culturable state. Our studies provide evidence to support the hypothesis that amoebae and perhaps other free-living protozoa contribute to the replication and persistence of human-pathogenic H. pylori by providing a protected intracellular microenvironment for this pathogen to persist in natural aquatic environments and engineered water systems, thereby H. pylori potentially uses amoeba as a carrier and a vector of transmission.

A Systematic Review of Intracellular Microorganisms within Acanthamoeba to Understand Potential Impact for Infection

Acanthamoeba, an opportunistic pathogen is known to cause an infection of the cornea, central nervous system, and skin. Acanthamoeba feeds different microorganisms, including potentially pathogenic prokaryotes; some of microbes have developed ways of surviving intracellularly and this may mean that Acanthamoeba acts as incubator of important pathogens. A systematic review of the literature was performed in order to capture a comprehensive picture of the variety of microbial species identified within Acanthamoeba following the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) guidelines. Forty-three studies met the inclusion criteria, 26 studies (60.5%) examined environmental samples, eight (18.6%) studies examined clinical specimens, and another nine (20.9%) studies analysed both types of samples. Polymerase chain reaction (PCR) followed by gene sequencing was the most common technique used to identify the intracellular microorganisms. Important pathogenic bacteria, such as E. coli, Mycobacterium spp. and P. aeruginosa, were observed in clinical isolates of Acanthamoeba, whereas Legionella, adenovirus, mimivirus, and unidentified bacteria (Candidatus) were often identified in environmental Acanthamoeba. Increasing resistance of Acanthamoeba associated intracellular pathogens to antimicrobials is an increased risk to public health. Molecular-based future studies are needed in order to assess the microbiome residing in Acanthamoeba, as a research on the hypotheses that intracellular microbes can affect the pathogenicity of Acanthamoeba infections.

Nested Species Distribution Models of Chlamydiales in Ixodes ricinus (Tick) Hosts in Switzerland

The tick Ixodes ricinus is the vector of various pathogens, including Chlamydiales bacteria, which potentially cause respiratory infections. In this study, we modeled the spatial distribution of I. ricinus and associated Chlamydiales over Switzerland from 2009 to 2019. We used a total of 2,293 ticks and 186 Chlamydiales occurrences provided by a Swiss Army field campaign, a collaborative smartphone application, and a prospective campaign. For each tick location, we retrieved from Swiss federal data sets the environmental factors reflecting the topography, climate, and land cover. We then used the Maxent modeling technique to estimate the suitability of particular areas for I. ricinus and to subsequently build the nested niche of Chlamydiales bacteria. Results indicate that I. ricinus habitat suitability is determined by higher temperature and normalized difference vegetation index (NDVI) values, lower temperature during the driest months, and a higher percentage of artificial and forest areas. The performance of the model was improved when extracting the environmental variables for a 100-m radius buffer around the sampling points and when considering the climatic conditions of the 2 years previous to the sampling date. Chlamydiales bacteria were favored by a lower percentage of artificial surfaces, drier conditions, high precipitation during the coldest months, and short distances to wetlands. From 2009 to 2018, we observed an extension of areas suitable to ticks and Chlamydiales, associated with a shift toward higher altitude. The importance of considering spatiotemporal variations in the environmental conditions for obtaining better prediction was also demonstrated.IMPORTANCEIxodes ricinus is the vector of pathogens including the agent of Lyme disease, the tick-borne encephalitis virus, and the less well-known Chlamydiales bacteria, which are responsible for certain respiratory infections. In this study, we identified the environmental factors influencing the presence of I. ricinus and Chlamydiales in Switzerland and generated maps of their distribution from 2009 to 2018. We found an important expansion of suitable areas for both the tick and the bacteria during the last decade. Results also provided the environmental factors that determine the presence of Chlamydiales within ticks. Distribution maps as generated here are expected to bring valuable information for decision makers in controlling tick-borne diseases in Switzerland and establishing prevention campaigns. The methodological framework presented could be used to predict the distribution and spread of other host-pathogen pairs to identify environmental factors driving their distribution and to develop control or prevention strategies accordingly.

The use of epilithic biofilms as bioaccumulators of pesticides and pharmaceuticals in aquatic environments

Biofilms are a consortium of communities of organisms that live in syntrophic relationships and present a higher organization level than that of individual cells. Biofilms dominate microbial life in streams and rivers, enable crucial ecosystem processes, contribute to global biogeochemical flows and represent the main active bacterial life form. Epilithic biofilms are the main biomass found in rivers; their exposure to contaminants can lead to changes in their structure and composition. The composition of these communities is influenced by physicochemical factors, temperature, light and prior exposure to pollutants, among other factors, and it can be used for water quality monitoring purposes. The heterogenous composition of biofilms enables them to accumulate compounds in an integrative manner. Moreover, the availability of several sorption sites and their likely saturation can contribute to bioaccumulation. In aquatic environments, biofilms are also susceptible to the acquisition of antibiotic resistance genes and participate in their dissemination. Anthropic pressure intensification processes continuously expose water resources and, consequently, biofilm communities to different contamination sources. Therefore, the use of biofilms to indicate environmental pollution is reinforced by the progress of studies on the subject. Biofilm communities' response to pollutants in aquatic environments can be mainly influenced by the presence of different organisms, which may change due to community development or age. The current research aims to review studies about biofilm contamination and highlight the importance of biofilm use to better evaluate and maintain the quality of water bodies.

Species Monitoring Using Unmanned Aerial Vehicle to Reveal the Ecological Role of Plateau Pika in Maintaining Vegetation Diversity on the Northeastern Qinghai-Tibetan Plateau

Plateau pika (Ochotona curzoniae, hereafter pika) is considered to exert a profound impact on vegetation species diversity of alpine grasslands. Great efforts have been made at mound or quadrat scales; nevertheless, there is still controversy about the effect of pika. It is vital to monitor vegetation species composition in natural heterogeneous ecosystems at a large scale to accurately evaluate the real role of pika. In this study, we performed field survey at 55 alpine grassland sites across the Shule River Basin using combined methods of aerial photographing using an unmanned aerial vehicle (UAV) and traditional ground measurement. Based on our UAV operation system, Fragmentation Monitoring and Analysis with aerial Photography (FragMAP), aerial images were acquired. Plot-scale vegetation species were visually identified, and total pika burrow exits were automatically retrieved using the self-developed image processing software. We found that there were significant linear relationships between the vegetation species diversity indexes obtained by these two methods. Additionally, the total number of identified species by the UAV method was 71, which was higher than the Quadrat method recognition, with the quantity of 63. Our results indicate that the UAV was suitable for long-term repeated monitoring vegetation species composition of multiple alpine grasslands at plot scale. With the merits of UAV, it confirmed that pika’s disturbance belonged to the medium level, with the density ranging from 30.17 to 65.53 ha−1. Under this density level, pika had a positive effect on vegetation species diversity, particularly for the species richness of sedge and forb. These findings conclude that the UAV was an efficient and economic tool for species monitoring to reveal the role of pika in the alpine grasslands.

Presence and interaction of free-living amoebae and amoeba-resisting bacteria in water from drinking water treatment plants

Free-living amoebae (FLA) are ubiquitous and many isolates have been shown to be infected with amoeba-resisting bacteria, as the example of Acanthamoeba and Legionella interaction. Due to the high environmental prevalence of Acanthamoeba. in the Castilian Plateau (Spain), the aims of this work were to investigate the occurrence of Acanthamoeba and other FLA in water from several sampling points from four Drinking Water Treatment Plants (DWTP) and to investigate the presence of Legionella spp. and other amoeba-resisting bacteria in biofilms in raw and finished water, taking into account that no legislation exists for this protozoa control. Acanthamoeba was detected at different sampling points, and sand filters seemed to contribute to amoebic enrichment. After ozonation, a temporary decrease in viable amoebae was observed. The genotypes detected were T3, T4, and T5, revealing the first report of genotype T5 in waters from this region. Moreover, Balamuthia mandrillaris, Vermamoeba vermiformis and Paravahlkampfia sp. were detected. Regarding Legionella, PCR detection in raw and finished water was higher than by agar culture, but even higher after Acanthamoeba co-culture. Also, Legionella's presence was higher in raw water than in finished water. The decrease of free Legionella observed from raw (27.5%, by PCR) to finished water (3.4% by PCR) contrasted with the increase of Legionella-infected FLA from raw (30.7%) to finished water (52%). At biofilm, free Legionella was not detected, and the percentage of infected FLA was low (3.8%). Legionella species identified in these samples were L. drozanskii, L. donaldsonii and L. feeleii. Additionally, Acanthamoeba co-culture led to the isolation of Pseudomonas aeruginosa, P. stutzeri, P. fluorecens, Achromobacter xylosoxidans and Stenotrophomonas maltophilia. The highly disseminated presence of Acanthamoeba and the detection of amoeba-resisting bacteria inside amoebae highlight the importance of developing methods for controlling FLA in order to limit human pathogenic amoeba-resisting bacteria survival to the water purification processes.

Limited presence of Waddlia chondrophila in drinking water systems in the Netherlands

Waddlia chondrophila is an emerging pathogen belonging to the order of Chlamydiales. This obligate intracellular bacterium was initially isolated from an aborted bovine fetus and is associated with adverse pregnancy outcomes in women. The ability of W. chondrophila to reside and replicate within a range of free-living amoebae implies a possible widespread environmental presence. Potential hosts of W. chondrophila are present in Dutch drinking water. This study therefore investigated the presence of W. chondrophila DNA in drinking water by analysing 59 samples from ten drinking water systems throughout the Netherlands. Samples were taken at three distances from the treatment plant, during both summer and winter. Twelve of the samples were positive, originating from two of the treatment plants, of which three samples were quantifiable.

The core microbiome of sessile ciliate Stentor coeruleus is not shaped by the environment

Microbiomes of multicellular organisms are one of the hottest topics in microbiology and physiology, while only few studies addressed bacterial communities associated with protists. Protists are widespread in all environments and can be colonized by plethora of different bacteria, including also human pathogens. The aim of this study was to characterize the prokaryotic community associated with the sessile ciliate Stentor coeruleus. 16S rRNA gene metabarcoding was performed on single cells of S. coeruleus and on their environment, water from the sewage stream. Our results showed that the prokaryotic community composition differed significantly between Stentor cells and their environment. The core microbiome common for all ciliate specimens analyzed could be defined, and it was composed mainly by representatives of bacterial genera which include also potential human pathogens and commensals, such as Neisseria, Streptococcus, Capnocytophaga, Porphyromonas. Numerous 16S rRNA gene contigs belonged to endosymbiont “Candidatus Megaira polyxenophila”. Our data suggest that each ciliate cell can be considered as an ecological microniche harboring diverse prokaryotic organisms. Possible benefits for persistence and transmission in nature for bacteria associated with protists are discussed. Our results support the hypothesis that ciliates attract potentially pathogenic bacteria and play the role of natural reservoirs for them.

The cooling tower water microbiota: Seasonal dynamics and co-occurrence of bacterial and protist phylotypes

Cooling towers for heating, ventilation and air conditioning are ubiquitous in the built environment. Often located on rooftops, their semi-open water basins provide a suitable environment for microbial growth. They are recognized as a potential source of bacterial pathogens and have been associated with disease outbreaks such as Legionnaires' disease. While measures to minimize public health risks are in place, the general microbial and protist community structure and dynamics in these systems remain largely elusive. In this study, we analysed the microbiome of the bulk water from the basins of three cooling towers by 16S and 18S rRNA gene amplicon sequencing over the course of one year. Bacterial diversity in all three towers was broadly comparable to other freshwater systems, yet less diverse than natural environments; the most abundant taxa are also frequently found in freshwater or drinking water. While each cooling tower had a pronounced site-specific microbial community, taxa shared among all locations mainly included groups generally associated with biofilm formation. We also detected several groups related to known opportunistic pathogens, such as Legionella, Mycobacterium, and Pseudomonas species, albeit at generally low abundance. Although cooling towers represent a rather stable environment, microbial community composition was highly dynamic and subject to seasonal change. Protists are important members of the cooling tower water microbiome and known reservoirs for bacterial pathogens. Co-occurrence analysis of bacteria and protist taxa successfully captured known interactions between amoeba-associated bacteria and their hosts, and predicted a large number of additional relationships involving ciliates and other protists. Together, this study provides an unbiased and comprehensive overview of microbial diversity of cooling tower water basins, establishing a framework for investigating and assessing public health risks associated with these man-made freshwater environments.

Active eukaryotes in drinking water distribution systems of ground and surface waterworks

BACKGROUND

Eukaryotes are ubiquitous in natural environments such as soil and freshwater. Little is known of their presence in drinking water distribution systems (DWDSs) or of the environmental conditions that affect their activity and survival.

METHODS

Eukaryotes were characterized by Illumina high-throughput sequencing targeting 18S rRNA gene (DNA) that estimates the total community and the 18S rRNA gene transcript (RNA) that is more representative of the active part of the community. DWDS cold water (N = 124), hot water (N = 40), and biofilm (N = 16) samples were collected from four cities in Finland. The sampled DWDSs were from two waterworks A-B with non-disinfected, recharged groundwater as source water and from three waterworks utilizing chlorinated water (two DWDSs of surface waterworks C-D and one of ground waterworks E). In each DWDS, samples were collected from three locations during four seasons of 1 year.

RESULTS

A beta-diversity analysis revealed that the main driver shaping the eukaryotic communities was the DWDS (A-E) (R = 0.73, P < 0.001, ANOSIM). The kingdoms Chloroplastida (green plants and algae), Metazoa (animals: rotifers, nematodes), Fungi (e.g., Cryptomycota), Alveolata (ciliates, dinoflagellates), and Stramenopiles (algae Ochrophyta) were well represented and active-judging based on the rRNA gene transcripts-depending on the surrounding conditions. The unchlorinated cold water of systems (A-B) contained a higher estimated total number of taxa (Chao1, average 380-480) than chlorinated cold water in systems C-E (Chao1 ≤ 210). Within each DWDS, unique eukaryotic communities were identified at different locations as was the case also for cold water, hot water, and biofilms. A season did not have a consistent impact on the eukaryotic community among DWDSs.

CONCLUSIONS

This study comprehensively characterized the eukaryotic community members within the DWDS of well-maintained ground and surface waterworks providing good quality water. The study gives an indication that each DWDS houses a unique eukaryotic community, mainly dependent on the raw water source and water treatment processes in place at the corresponding waterworks. In particular, disinfection as well as hot water temperature seemed to represent a strong selection pressure that controlled the number of active eukaryotic species.

Symbiont-Mediated Defense against Legionella pneumophila in Amoebae

Bacterial pathogens are generally investigated in the context of disease. To prevent outbreaks, it is essential to understand their lifestyle and interactions with other microbes in their natural environment. Legionella pneumophila is an important human respiratory pathogen that survives and multiplies in biofilms or intracellularly within protists, such as amoebae. Importantly, transmission to humans occurs from these environmental sources. Legionella infection generally leads to rapid host cell lysis. It was therefore surprising to observe that amoebae, including fresh environmental isolates, were well protected during Legionella infection when the bacterial symbiont Protochlamydia amoebophila was also present. Legionella was not prevented from invading amoebae but was impeded in its ability to develop fully virulent progeny and were ultimately cleared in the presence of the symbiont. This study highlights how ecology and virulence of an important human pathogen is affected by a defensive amoeba symbiont, with possibly major consequences for public health.

Legionella pneumophila is an important opportunistic pathogen for which environmental reservoirs are crucial for the infection of humans. In the environment, free-living amoebae represent key hosts providing nutrients and shelter for highly efficient intracellular proliferation of L. pneumophila, which eventually leads to lysis of the protist. However, the significance of other bacterial players for L. pneumophila ecology is poorly understood. In this study, we used a ubiquitous amoeba and bacterial endosymbiont to investigate the impact of this common association on L. pneumophila infection. We demonstrate that L. pneumophila proliferation was severely suppressed in Acanthamoeba castellanii harboring the chlamydial symbiont Protochlamydia amoebophila. The amoebae survived the infection and were able to resume growth. Different environmental amoeba isolates containing the symbiont were equally well protected as different L. pneumophila isolates were diminished, suggesting ecological relevance of this symbiont-mediated defense. Furthermore, protection was not mediated by impaired L. pneumophila uptake. Instead, we observed reduced virulence of L. pneumophila released from symbiont-containing amoebae. Pronounced gene expression changes in the presence of the symbiont indicate that interference with the transition to the transmissive phase impedes the L. pneumophila infection. Finally, our data show that the defensive response of amoebae harboring P. amoebophila leaves the amoebae with superior fitness reminiscent of immunological memory. Given that mutualistic associations between bacteria and amoebae are widely distributed, P. amoebophila and potentially other amoeba endosymbionts could be key in shaping environmental survival, abundance, and virulence of this important pathogen, thereby affecting the frequency of human infection.

Chlorine and Monochloramine Disinfection of Legionella pneumophila Colonizing Copper and Polyvinyl Chloride Drinking Water Biofilms

Building water systems promote the regrowth and survival of opportunistic pathogens, such as Legionella pneumophila, especially within biofilms, where most drinking water microbes reside. However, compared to their planktonic form, disinfection efficacy for the biofilm-associated forms of water-based pathogens is unclear. The aim of this study was to determine the effectiveness of free chlorine and monochloramine in the inactivation of biofilm-associated L. pneumophila strain Philadelphia-1 serogroup 1 (LpP1s1). Mature (1.5- to 2-year-old) drinking water biofilms were developed on copper (Cu) and polyvinyl chloride (PVC) slides within biofilm annular reactors, then colonized with LpP1s1 at approximately 4 log₁₀ CFU cm^-2 and exposed to 2 mg liter^-1 of free chlorine or monochloramine. Ct (disinfectant concentration × time, expressed as mg min liter^-1) inactivation values for 2-, 3-, and 4-log₁₀ reductions of planktonic and biofilm LpP1s1 were determined. For planktonic LpP1s1, free chlorine was more effective at inactivation than was monochloramine treatment, and for biofilm-associated LpP1s1, monochloramine was more effective on Cu biofilms while free chlorine was more effective on PVC biofilms. In contrast to monochloramine, free chlorine treatment of Cu and PVC biofilms, negatively impacted LpP1s1 16S rRNA gene transcript levels and may act synergistically with Cu surfaces to further reduce transcript levels. Moreover, LpP1s1 cells shed from biofilms into the bulk water were more resistant to disinfection than were prepared planktonic LpP1s1 cells. Results from this study indicate that biofilm association, disinfectant type, and substratum play an important role in the survival of Legionella pneumophila in building water systems.IMPORTANCE Microbial regrowth within building water systems are promoted by water stagnation, low disinfectant residual, high surface-to-volume ratio, amenable growth temperatures, and colonization of drinking water biofilms. Moreover, biofilms provide protection from environmental stresses, access to higher levels of nutrients, and opportunities for symbiotic interactions with other microbes. Disinfectant efficacy information is historically based on inactivation of pathogens in their planktonic, free-floating forms. However, due to the ecological importance of drinking water biofilms for pathogen survival, this study evaluated the efficacy of two common disinfectants, free chlorine and monochloramine, on Legionella pneumophila colonizing mature, drinking water biofilms established on copper and PVC surfaces. Results showed that inactivation was dependent on the disinfectant type and biofilm substratum. Overall, this, and other related research, will provide a better understanding of Legionella ecological stability and survival and aid policy makers in the management of exposure risks to water-based pathogens within building water systems.

Removal Efficacy of Opportunistic Pathogens and Bacterial Community Dynamics in Two Drinking Water Treatment Trains

Drinking water treatment processes (DWTPs) impact pathogen colonization and microbial communities in finished water; however, their efficacies against opportunistic pathogens are not fully understood. In this study, the effects of treatment steps on the removal of Legionella spp., Legionella pneumophila, nontuberculous mycobacteria, Mycobacterium avium, and two amoeba hosts (Vermamoeba vermiformis, Acanthamoeba) are evaluated in two parallel trains of DWTPs equipped with different pretreatment units. Quantitative polymerase chain reaction analysis demonstrates significantly reduced numbers of total bacteria, Legionella, and mycobacteria during ozonation, followed by a rebound in granular activated carbon (GAC) filtration, whereas sand filtration exerts an overarching effect in removing microorganisms in both treatment trains. V. vermiformis is more prevalent in biofilm (34%) than water samples (7.7%), while Acanthamoeba is not found in the two trains of DWTPs. Illumina sequencing of bacterial 16S rRNA genes reveals significant community shifts at different treatment steps, as well as distinct bacterial community structures in water and biofilm samples in parallel units (e.g., ozonation, GAC, sand filtration) between the two trains (analysis of similarities (ANOSIM), p < 0.05), implying the potential influence of different pretreatment steps in shaping the downstream microbiome. Overall, the results provide insights to mitigation of opportunistic pathogens and engineer approaches for managing bacterial communities in DWTPs.

The Influence of Acanthamoeba-Legionella Interaction in the Virulence of Two Different Legionella Species

The genus Legionella comprises more than 60 species, and about half are associated with infection. Legionella pneumophila is the most commonly associated with these infections and by far the most studied, but L. non-pneumophila species, such as L. feeleii, L. anisa, etc., may also present clinical importance. Free-living amoebae are their preferred environmental host, where these bacteria not only survive but also succeed in multiplying, and this relationship can lead to an increase in bacterial virulence. The goal of this study was to evaluate the alterations of Legionella pathogenicity due to its interaction with Acanthamoeba. For this, the expression of protein effectors SdhA, LegK2, and SidK were evaluated in L. pneumophila and L. feeleii, before and after infecting Acanthamoeba. Additionally, the host response was evaluated by measuring the production of IL-6, IL-8, and IFN-γ in infected macrophages. Regarding the virulence factors, an increase in SdhA expression was observed after these bacteria infected Acanthamoeba, with a higher increase in the macrophage cultures infected with L. feeleii. Also, an increase in the expression of LegK2 was observed after infecting Acanthamoeba, but it was more intense in the cultures infected with L. pneumophila. With regard to SidK, it was increased in L. feeleii after infecting Acanthamoeba, however the same effect was not observed for L. pneumophila. In cytokine production, the effect on IL-6 and IL-8 was similar for both cytokines, increasing their concentration, but higher production was observed in the cultures infected with L. feeleii, even though it demonstrated slightly lower production with the inoculum obtained from Acanthamoeba. Concerning IFN-γ, induction was observed in both species but higher in the infection by L. pneumophila. Nevertheless, it is not known if this induction is enough to promote an efficient immune response against either L. pneumophila or L. feeleii. Altogether, these alterations seem to increase L. feeleii virulence after infecting Acanthamoeba. However, this increase does not seem to turn L. feeleii as virulent as L. pneumophila. More studies are necessary to understand the aspects influenced in these bacteria by their interaction with Acanthamoeba and, thus, identify targets to be used in future therapeutic approaches.

How to: identify non-tuberculous Mycobacterium species using MALDI-TOF mass spectrometry

BACKGROUND

The implementation of MALDI-TOF MS for microorganism identification has changed the routine of the microbiology laboratories as we knew it. Most microorganisms can now be reliably identified within minutes using this inexpensive, user-friendly methodology. However, its application in the identification of mycobacteria isolates has been hampered by the structure of their cell wall. Improvements in the sample processing method and in the available database have proved key factors for the rapid and reliable identification of non-tuberculous mycobacteria isolates using MALDI-TOF MS.

AIMS

The main objective is to provide information about the proceedings for the identification of non-tuberculous isolates using MALDI-TOF MS and to review different sample processing methods, available databases, and the interpretation of the results.

SOURCES

Results from relevant studies on the use of the available MALDI-TOF MS instruments, the implementation of innovative sample processing methods, or the implementation of improved databases are discussed.

CONTENT

Insight about the methodology required for reliable identification of non-tuberculous mycobacteria and its implementation in the microbiology laboratory routine is provided.

IMPLICATIONS

Microbiology laboratories where MALDI-TOF MS is available can benefit from its capacity to identify most clinically interesting non-tuberculous mycobacteria in a rapid, reliable, and inexpensive manner.

Occurrence of Infected Free-Living Amoebae in Cooling Towers of Southern Brazil

This study determined the occurrence of potentially pathogenic free-living amoebae (FLA) and bacteria associated with amoebae in air-conditioning cooling towers in southern Brazil. Water samples were collected from 36 cooling systems from air-conditioning in the state of Rio Grande do Sul, Brazil. The organisms were identified using polymerase chain reaction (PCR) and sequencing automated. The results showed that these aquatic environments, with variable temperature, are potential "hot spots" for emerging human pathogens like free-living amoebae and bacteria associated. In total, 92% of the cooling-tower samples analyzed were positive for FLA, and Acanthamoeba was the dominant genus by culture and PCR. Amoebal isolates revealed intracellular bacteria in 39.3% of them and all were confirmed as members of the genus Pseudomonas. The results obtained show the important role of cooling towers as a source of amoebae-associated pathogens.

Effect of temperature and colonization of Legionella pneumophila and Vermamoeba vermiformis on bacterial community composition of copper drinking water biofilms

It is unclear how the water-based pathogen, Legionella pneumophila (Lp), and associated free-living amoeba (FLA) hosts change or are changed by the microbial composition of drinking water (DW) biofilm communities. Thus, this study characterized the bacterial community structure over a 7-month period within mature (> 600-day-old) copper DW biofilms in reactors simulating premise plumbing and assessed the impact of temperature and introduction of Lp and its FLA host, Vermamoeba vermiformis (Vv), co-cultures (LpVv). Sequence and quantitative PCR (qPCR) analyses indicated a correlation between LpVv introduction and increases in Legionella spp. levels at room temperature (RT), while at 37°C, Lp became the dominant Legionella spp. qPCR analysis suggested Vv presence may not be directly associated with Lp biofilm growth at RT and 37°C, but may contribute to or be associated with non-Lp legionellae persistence at RT. Two-way PERMANOVA and PCoA revealed that temperature was a major driver of microbiome diversity. Biofilm community composition also changed over the seven-month period and could be associated with significant shifts in dissolved oxygen, alkalinity and various metals in the influent DW. Hence, temperature, biofilm age, DW quality and transient intrusions/amplification of pathogens and FLA hosts may significantly impact biofilm microbiomes and modulate pathogen levels over extended periods.

Enhanced survival but not amplification of Francisella spp. in the presence of free-living amoebae

Transmission of Francisella tularensis, the etiologic agent of tularemia, has been associated with various water sources. Survival of many waterborne pathogens within free-living amoeba (FLA) is well documented; however, the role of amoebae in the environmental persistence of F. tularensis is unclear. In this study, axenic FLA cultures of Acanthamoeba castellanii, Acanthamoeba polyphaga, and Vermamoeba vermiformis were each inoculated with virulent strains of F. tularensis (Types A and B), the attenuated live vaccine strain, and Francisella novicida. Experimental parameters included low and high multiplicity of infection and incubation temperatures of 25 and 30 °C for 0-10 days. Francisella spp. survival was enhanced by the presence of FLA; however, bacterial growth and protozoa infectivity were not observed. In contrast, co-infections of A. polyphaga and Legionella pneumophila, used as an amoeba pathogen control, resulted in bacterial proliferation, cytopathic effects, and amoebal lysis. Collectively, even though short-term incubation with FLA was beneficial, the long-term effects on Francisella survival are unknown, especially given the expenditure of available amoebal derived nutrients and the fastidious nature of Francisella spp. These factors have clear implications for the role of FLA in Francisella environmental persistence.

Prevalence and diversity of Chlamydiales and other amoeba-resisting bacteria in domestic drinking water systems

A growing number of human infections incriminate environmental bacteria that have evolved virulent mechanisms to resist amoebae and use them as a replicative niche. These bacteria are designated amoeba-resisting bacteria (ARB). Despite the isolation of these ARB in various human clinical samples, the possible source of infection remains undetermined in most cases. However, it is known that the ARB Legionella pneumophila, for instance, causes a respiratory infection in susceptible hosts after inhalation of contaminated water aerosols from various sources. The Chlamydiales order contains many ARB, such as Parachlamydia acanthamoebae or Simkania negevensis, previously implicated in human respiratory infections with no identified contamination sources. We thus investigated whether domestic water systems are a potential source of transmission of these Chlamydiales to humans by using amoebal culture and molecular methods. Other important ARB such as mycobacteria and Legionella were also investigated, as were their possible amoebal hosts. This work reports for the first time a very high prevalence and diversity of Chlamydiales in drinking water, being detected in 35 (72.9%) of 48 investigated domestic water systems, with members of the Parachlamydiaceae family being dominantly detected. Furthermore, various Legionella and mycobacteria species were also recovered, some species of which are known to be causal agents of human infections.

Molecular identification of bacterial endosymbionts of Sappinia strains

The genus Sappinia comprises free-living amoebae occurring worldwide in a variety of habitats such as soils, plant matter and freshwater ponds, but also animal faeces, and includes at present three species, S. pedata, S. diploidea and S. platani. The genus is potentially pathogenic, as indicated by the identification of S. pedata in a case of human amoebic encephalitis. Electron microscopy studies on some strains already revealed intracellular bacteria in Sappinia. In the current study, we performed 16S ribosomal RNA gene (rDNA) analysis of these bacterial endosymbionts. We first inferred relationships among Sappinia strains on the basis of 18S rDNA, demonstrating that S. pedata emerged as sister to a larger clade including S. diploidea, S. platani and a few 'S. diploidea-like' strains. Thus, bacterial 16S rDNA was searched for in representative strains of each Sappinia species/subgroup. We found that Sappinia strains were associated to distinct species of Flavobacterium or Pedobacter (phylum Bacteroidetes). These appear to be distributed following the amoebal host subgroups, and are not directly related to other Bacteroidetes species known as interacting with free-living amoebae. While all the endosymbionts' close relatives are known to grow on agar, bacteriological media inoculated with amoebal extracts remained negative. Overall, results indicate that the recovered bacteria are likely specific obligate endosymbionts of Sappinia species. Further studies, including additional amoebal strains and deep morphological and molecular analyses, will be necessary to confirm this hypothesis.

Neglected waterborne parasitic protozoa and their detection in water

Outbreak incidents raise the question of whether the less frequent aetiological agents of outbreaks are really less frequent in water. Alternatively, waterborne transmission could be relevant, but the lack of attention and rapid, sensitive methods to recover and detect the exogenous stages in water may keep them under-recognized. High quality information on the prevalence and detection of less frequent waterborne protozoa, such as Cyclospora cayetanensis, Toxoplasma gondii, Isospora belli, Balantidium coli, Blastocystis hominis, Entamoeba histolytica and other free-living amoebae (FLA), are not available. This present paper discusses the detection tools applied for the water surveillance of the neglected waterborne protozoa mentioned above and provides future perspectives.

Chlamydial seasonal dynamics and isolation of 'Candidatus Neptunochlamydia vexilliferae' from a Tyrrhenian coastal lake

The Chlamydiae are a phylum of obligate intracellular bacteria comprising important human and animal pathogens, yet their occurrence in the environment, their phylogenetic diversity and their host range has been largely underestimated. We investigated the seasonality of environmental chlamydiae in a Tyrrhenian coastal lake. By catalysed reporter deposition fluorescence in situ hybridization, we quantified the small planktonic cells and detected a peak in the abundance of environmental chlamydiae in early autumn with up to 5.9 × 10(4) cells ml(-1) . Super-resolution microscopy improved the visualization and quantification of these bacteria and enabled the detection of pleomorphic chlamydial cells in their protist host directly in an environmental sample. To isolate environmental chlamydiae together with their host, we applied a high-throughput limited dilution approach and successfully recovered a Vexillifera sp., strain harbouring chlamydiae (93% 16S rRNA sequence identity to Simkania negevensis), tentatively named 'Candidatus Neptunochlamydia vexilliferae'. Transmission electron microscopy in combination with fluorescence in situ hybridization was used to prove the intracellular location of these bacteria representing the first strain of marine chlamydiae stably maintained alongside with their host in a laboratory culture. Taken together, this study contributes to a better understanding of the distribution and diversity of environmental chlamydiae in previously neglected marine environments.

Waddlia: An emerging pathogen and a model organism to study the biology of chlamydiae

Waddlia chondrophila is an emerging pathogen associated with abortion in cattle. In humans, a growing body of evidence supports its pathogenic role in miscarriage and in respiratory tract infection. The human pathogenicity of W. chondrophila is further supported by the presence of several virulence factors including a catalase, a functional T3SS and several adhesins. Despite this medical importance, no commercial tests are available and diagnostic of this strict intracellular bacterium mainly relies on serology, PCR and immunohistochemistry. So far, the epidemiology of W. chondrophila remains largely unexplored and zoonotic, waterborne or interhuman transmission has been considered. Apart from its pathogenic role, chlamydiologists are also interested in W. chondrophila in order to better understand biological mechanisms conserved and shared with Chlamydia spp. Indeed, W. chondrophila proved to be a useful model organism to study the pathobiology of chlamydiae thanks to its rapid replication, its large size allowing precise subcellular protein localization, as well as its growth in Dictyostelium amoebae.

Marine amoebae with cytoplasmic and perinuclear symbionts deeply branching in the Gammaproteobacteria

Amoebae play an important ecological role as predators in microbial communities. They also serve as niche for bacterial replication, harbor endosymbiotic bacteria and have contributed to the evolution of major human pathogens. Despite their high diversity, marine amoebae and their association with bacteria are poorly understood. Here we describe the isolation and characterization of two novel marine amoebae together with their bacterial endosymbionts, tentatively named ‘Candidatus Occultobacter vannellae’ and ‘Candidatus Nucleophilum amoebae’. While one amoeba strain is related to Vannella, a genus common in marine habitats, the other represents a novel lineage in the Amoebozoa. The endosymbionts showed only low similarity to known bacteria (85–88% 16S rRNA sequence similarity) but together with other uncultured marine bacteria form a sister clade to the Coxiellaceae. Using fluorescence in situ hybridization and transmission electron microscopy, identity and intracellular location of both symbionts were confirmed; one was replicating in host-derived vacuoles, whereas the other was located in the perinuclear space of its amoeba host. This study sheds for the first time light on a so far neglected group of protists and their bacterial symbionts. The newly isolated strains represent easily maintainable model systems and pave the way for further studies on marine associations between amoebae and bacterial symbionts.

Current and past strategies for bacterial culture in clinical microbiology

A pure bacterial culture remains essential for the study of its virulence, its antibiotic susceptibility, and its genome sequence in order to facilitate the understanding and treatment of caused diseases. The first culture conditions empirically varied incubation time, nutrients, atmosphere, and temperature; culture was then gradually abandoned in favor of molecular methods. The rebirth of culture in clinical microbiology was prompted by microbiologists specializing in intracellular bacteria. The shell vial procedure allowed the culture of new species of Rickettsia. The design of axenic media for growing fastidious bacteria such as Tropheryma whipplei and Coxiella burnetii and the ability of amoebal coculture to discover new bacteria constituted major advances. Strong efforts associating optimized culture media, detection methods, and a microaerophilic atmosphere allowed a dramatic decrease of the time of Mycobacterium tuberculosis culture. The use of a new versatile medium allowed an extension of the repertoire of archaea. Finally, to optimize the culture of anaerobes in routine bacteriology laboratories, the addition of antioxidants in culture media under an aerobic atmosphere allowed the growth of strictly anaerobic species. Nevertheless, among usual bacterial pathogens, the development of axenic media for the culture of Treponema pallidum or Mycobacterium leprae remains an important challenge that the patience and innovations of cultivators will enable them to overcome.

Confirmed and Potential Sources of Legionella Reviewed

Legionella bacteria are ubiquitous in natural matrices and man-made systems. However, it is not always clear if these reservoirs can act as source of infection resulting in cases of Legionnaires' disease. This review provides an overview of reservoirs of Legionella reported in the literature, other than drinking water distribution systems. Levels of evidence were developed to discriminate between potential and confirmed sources of Legionella. A total of 17 systems and matrices could be classified as confirmed sources of Legionella. Many other man-made systems or natural matrices were not classified as a confirmed source, since either no patients were linked to these reservoirs or the supporting evidence was weak. However, these systems or matrices could play an important role in the transmission of infectious Legionella bacteria; they might not yet be considered in source investigations, resulting in an underestimation of their importance. To optimize source investigations it is important to have knowledge about all the (potential) sources of Legionella. Further research is needed to unravel what the contribution is of each confirmed source, and possibly also potential sources, to the LD disease burden.

Detection of novel Chlamydiae and Legionellales from human nasal samples of healthy volunteers

Chlamydiae are intracellular bacterial parasites of eukaryotes, ranging from amoebae to humans. They comprise many novel members and are investigated as emerging pathogens. Environmental studies highlighted similarities between the ecologies of chlamydiae and legionellae, both groups being important agents of respiratory infections. Herein, we analyzed nasal samples from healthy persons, searching for the presence of amoebae, chlamydiae and legionellae. From a total of 25 samples, we recovered by PCR eight samples positive to chlamydiae and six samples positive to legionellae. Among these samples, four were positive to both organisms. The sequencing of 16S rDNAs allowed to identify (i) among Chlamydiae: Parachlamydia acanthamoebae, Chlamydophila psittaci, Chlamydophila felis, and members of Rhabdochlamydiaceae, Simkaniaceae and E6 lineage and (ii) among Legionellaceae: Legionella longbeachae, Legionella bozemanii and Legionella impletisoli. Unexpectedly, we also recovered Diplorickettsia sp. Amoebae collected from nasal mucosae, Acanthamoeba and Vermamoeba, were endosymbiont-free, and chlamydiae revealed refractory to amoeba coculture. This study shows common exposure to chlamydiae and legionellae and suggests open air activities like gardening as a probable additional source of infection.

Molecular characterization of viable Legionella spp. in cooling tower water samples by combined use of ethidium monoazide and PCR

Viable Legionella spp. in environmental water samples were characterized phylogenetically by a clone library analysis combining the use of ethidium monoazide and quantitative PCR. To examine the diversity of Legionella spp., six cooling tower water samples and three bath water samples were collected and analyzed. A total of 617 clones were analyzed for their 16S rRNA gene sequences and classified into 99 operational taxonomic units (OTUs). The majority of OTUs were not clustered with currently described Legionella spp., suggesting the wide diversity of not-yet-cultured Legionella groups harbored in cooling tower water environments.

Importance of amoebae as a tool to isolate amoeba-resisting microorganisms and for their ecology and evolution: the Chlamydia paradigm

Free-living amoebae are distributed worldwide and are frequently in contact with humans and animals. As cysts, they can survive in very harsh conditions and resist biocides and most disinfection procedures. Several microorganisms, called amoeba-resisting microorganisms (ARMs), have evolved to survive and multiply within these protozoa. Among them are many important pathogens, such as Legionella and Mycobacteria, and also several newly discovered Chlamydia-related bacteria, such as Parachlamydia acanthamoebae, Estrella lausannensis, Simkania negevensis or Waddlia chondrophila whose pathogenic role towards human or animal is strongly suspected. Amoebae represent an evolutionary crib for their resistant microorganisms since they can exchange genetic material with other ARMs and develop virulence traits that will be further used to infect other professional phagocytes. Moreover, amoebae constitute an ideal tool to isolate strict intracellular microorganisms from complex microbiota, since they will feed on other fast-growing bacteria, such as coliforms potentially present in the investigated samples. The paradigm that ARMs are likely resistant to macrophages, another phagocytic cell, and that they are likely virulent towards humans and animals is only partially true. Indeed, we provide examples of the Chlamydiales order that challenge this assumption and suggest that the ability to multiply in protozoa does not strictly correlate with pathogenicity and that we should rather use the ability to replicate in multiple and diverse eukaryotic cells as an indirect marker of virulence towards mammals. Thus, cell-culture-based microbial culturomics should be used in the future to try to discover new pathogenic bacterial species.

Impact of drinking water conditions and copper materials on downstream biofilm microbial communities and Legionella pneumophila colonization

AIMS

This study examined the impact of pipe materials and introduced Legionella pneumophila on downstream Leg. pneumophila colonization and microbial community structures under conditions of low flow and low chlorine residual.

METHODS AND RESULTS

CDC biofilm(™) reactors containing either unplasticized polyvinylchloride (uPVC) or copper (Cu) coupons were used to develop mature biofilms on Norprene(™) tubing effluent lines to simulate possible in-premise biofilm conditions. The microbial communities were characterized through 16S and 18S rRNA gene clone libraries and Leg. pneumophila colonization was determined via specific qPCR assays. The Cu significantly decreased downstream microbial diversity, approximately halved bacterial and eukaryotic abundance, with some groups only detected in uPVC-reactor tubing biofilms. However, some probable amoeba-resisting bacteria (ARB) like Mycobacterium spp. and Rhodobacteraceae were significantly more abundant in the Cu than uPVC-reactor tubing biofilms. In particular, Leg. pneumophila only persisted (postinoculation) within the Cu-reactor tubing biofilms, and the controlled low chlorine residue and water flow conditions led to a general high abundance of possible free-living protozoa in all tubing biofilms. The higher relative abundance of ARB-like sequences from Cu-coupons vs uPVC may have been promoted by amoebal selection and subsequent ARB protection from Cu inhibitory effects.

CONCLUSIONS

Copper pipe and low flow conditions had significant impact on downstream biofilm microbial structures (on plastic pipe) and the ability for Leg. pneumophila colonization post an introduction event.

SIGNIFICANCE AND IMPACT OF THE STUDY

This is the first report that compares the effects of copper and uPVC materials on downstream biofilm communities grown on a third (Norprene(™)) surface material. The downstream biofilms contained a high abundance of free-living amoebae and ARB, which may have been driven by a lack of residual disinfectant and periodic stagnant conditions. Given the prevalence of Cu-piping in buildings, there may be increased risk from drinking water exposures to ARB following growth on pipe/fixture biofilms within premise drinking water systems.

Microbial diversities (16S and 18S rRNA gene pyrosequencing) and environmental pathogens within drinking water biofilms grown on the common premise plumbing materials unplasticized polyvinylchloride and copper

Drinking water (DW) biofilm communities influence the survival of opportunistic pathogens, yet knowledge about the microbial composition of DW biofilms developed on common in-premise plumbing material is limited. Utilizing 16S and 18S rRNA gene pyrosequencing, this study characterized the microbial community structure within DW biofilms established on unplasticized polyvinyl chloride (uPVC) and copper (Cu) surfaces and the impact of introducing Legionella pneumophila (Lp) and Acanthamoeba polyphaga. Mature (> 1 year old) biofilms were developed before inoculation with sterilized DW (control, Con), Lp, or Lp and A. polyphaga (LpAp). Comparison of uPVC and Cu biofilms indicated significant differences between bacterial (P = 0.001) and eukaryotic (P < 0.01) members attributable to the unique presence of several family taxa: Burkholderiaceae, Characeae, Epistylidae, Goniomonadaceae, Paramoebidae, Plasmodiophoridae, Plectidae, Sphenomonadidae, and Toxariaceae within uPVC biofilms; and Enterobacteriaceae, Erythrobacteraceae, Methylophilaceae, Acanthamoebidae, and Chlamydomonadaceae within Cu biofilms. Introduction of Lp alone or with A. polyphaga had no effect on bacterial community profiles (P > 0.05) but did affect eukaryotic members (uPVC, P < 0.01; Cu, P = 0.001). Thus, established DW biofilms host complex communities that may vary based on substratum matrix and maintain consistent bacterial communities despite introduction of Lp, an environmental pathogen.

A year long study of the presence of free living amoeba in Spain

Free-living amoeba such as Acanthamoeba and Balamuthia mandrillaris can act as opportunistic parasites on a wide range of vertebrates and they are becoming a serious threat to human health due to the resistance of their cysts to harsh environmental conditions, disinfectants, some water treatment practices and their ubiquitous distribution. This work was carried out in order to study the presence of these free-living amoebae (FLA) and their possible seasonality in a continental-Mediterranean climate in different types of water. For this purpose, a total of 223 water samples were collected during one year from four drinking water treatment plants (DWTP), seven wastewater treatment plants (WWTP) and six locations of influence (LI) on four river basins from Spain. Water samples were concentrated using the IDEXX Filta-Max(®) system and analyzed by a triplex real time PCR that detects Acanthamoeba, B. mandrillaris and Naegleria fowleri. Agar plates were also seeded for Acanthamoeba culture. From the three FLA studied, N. fowleri was not detected in any sample while B. mandrillaris was found at the entrance of a DWTP; this being, to our knowledge, the first report of these protozoa in water worldwide. On the other hand, the presence of Acanthamoeba observed was higher, 94.6% of the studied points were positive by real time PCR and 85.2% by culture, resulting in 99.1% positive for Acanthamoeba with both methods. All genetically analyzed Acanthamoeba were genotype T4 but nine different T4/DF3 sequences were observed, three of them being described for the first time, assigning new codes. No seasonal distribution of Acanthamoeba was found. These facts should serve as a warning to contact lens wearers of the risk of a poor hygiene when handling their contact lenses. It should also serve as a signal to physicians to consider FLA as a possible causative agent of nervous system infections as well as Acanthamoeba keratitis due to their high environmental presence shown in this study.

Discovery of new intracellular pathogens by amoebal coculture and amoebal enrichment approaches

Intracellular pathogens such as legionella, mycobacteria and Chlamydia-like organisms are difficult to isolate because they often grow poorly or not at all on selective media that are usually used to cultivate bacteria. For this reason, many of these pathogens were discovered only recently or following important outbreaks. These pathogens are often associated with amoebae, which serve as host-cell and allow the survival and growth of the bacteria. We intend here to provide a demonstration of two techniques that allow isolation and characterization of intracellular pathogens present in clinical or environmental samples: the amoebal coculture and the amoebal enrichment. Amoebal coculture allows recovery of intracellular bacteria by inoculating the investigated sample onto an amoebal lawn that can be infected and lysed by the intracellular bacteria present in the sample. Amoebal enrichment allows recovery of amoebae present in a clinical or environmental sample. This can lead to discovery of new amoebal species but also of new intracellular bacteria growing specifically in these amoebae. Together, these two techniques help to discover new intracellular bacteria able to grow in amoebae. Because of their ability to infect amoebae and resist phagocytosis, these intracellular bacteria might also escape phagocytosis by macrophages and thus, be pathogenic for higher eukaryotes.

Eukaryotic diversity in premise drinking water using 18S rDNA sequencing: implications for health risks

The goal of this study was to characterize microbial eukaryotes over a 12-month period to provide insight into the occurrence of potential bacterial predators and hosts in premise plumbing. Nearly 6,300 partial 18S rRNA gene sequences from 24 hot (36.9-39.0 °C) and cold (6.8-29.1 °C) drinking water samples were analyzed and classified into major eukaryotic groups. Each major group, consisting of free-living amoebae (FLA)/protozoa, algae, copepods, dinoflagellates, fungi, nematodes, and unique uncultured eukaryotic sequences, showed limited diversity dominated by a few distinct populations, which may be characteristic of oligotrophic environments. Changes in the relative abundance of predators such as nematodes, copepods, and FLA appear to be related to temperature and seasonal changes in water quality. Sequences nearly identical to FLA such as Hartmannella vermiformis, Echinamoeba thermarmum, Pseudoparamoeba pagei, Protacanthamoeba bohemica, Platyamoeba sp., and Vannella sp. were obtained. In addition to FLA, various copepods, rotifers, and nematodes have been reported to internalize viral and bacterial pathogens within drinking water systems thus potentially serving as transport hosts; implications of which are discussed further. Increasing the knowledge of eukaryotic occurrence and their relationship with potential pathogens should aid in assessing microbial risk associated with various eukaryotic organisms in drinking water.

Integrating metagenomic and amplicon databases to resolve the phylogenetic and ecological diversity of the Chlamydiae

In the era of metagenomics and amplicon sequencing, comprehensive analyses of available sequence data remain a challenge. Here we describe an approach exploiting metagenomic and amplicon data sets from public databases to elucidate phylogenetic diversity of defined microbial taxa. We investigated the phylum Chlamydiae whose known members are obligate intracellular bacteria that represent important pathogens of humans and animals, as well as symbionts of protists. Despite their medical relevance, our knowledge about chlamydial diversity is still scarce. Most of the nine known families are represented by only a few isolates, while previous clone library-based surveys suggested the existence of yet uncharacterized members of this phylum. Here we identified more than 22,000 high quality, non-redundant chlamydial 16S rRNA gene sequences in diverse databases, as well as 1900 putative chlamydial protein-encoding genes. Even when applying the most conservative approach, clustering of chlamydial 16S rRNA gene sequences into operational taxonomic units revealed an unexpectedly high species, genus and family-level diversity within the Chlamydiae, including 181 putative families. These in silico findings were verified experimentally in one Antarctic sample, which contained a high diversity of novel Chlamydiae. In our analysis, the Rhabdochlamydiaceae, whose known members infect arthropods, represents the most diverse and species-rich chlamydial family, followed by the protist-associated Parachlamydiaceae, and a putative new family (PCF8) with unknown host specificity. Available information on the origin of metagenomic samples indicated that marine environments contain the majority of the newly discovered chlamydial lineages, highlighting this environment as an important chlamydial reservoir.

Isolation and identification of free-living amoebae from tap water in Sivas, Turkey

The present work focuses on a local survey of free-living amoebae (FLA) that cause opportunistic and nonopportunistic infections in humans. Determining the prevalence of FLA in water sources can shine a light on the need to prevent FLA related illnesses. A total of 150 samples of tap water were collected from six districts of Sivas province. The samples were filtered and seeded on nonnutrient agar containing Escherichia coli spread. Thirty-three (22%) out of 150 samples were found to be positive for FLA. The FLA were identified by morphology and by PCR using 18S rDNA gene. The morphological analysis and partial sequencing of the 18S rDNA gene revealed the presence of three different species, Acanthamoeba castellanii, Acanthamoeba polyphaga, and Hartmannella vermiformis. Naegleria fowleri, Balamuthia mandrillaris, or Sappinia sp. was not isolated during the study. All A. castellanii and A. polyphaga sequence types were found to be genotype T4 that contains most of the pathogenic Acanthamoeba strains. The results indicated the occurrence and distribution of FLA species in tap water in these localities of Sivas, Turkey. Furthermore, the presence of temperature tolerant Acanthamoeba genotype T4 in tap water in the region must be taken into account for health risks.

Sensitivity of free-living amoeba trophozoites and cysts to water disinfectants

Free-living amoebae are naturally present in water. These protozoa could be pathogenic and could also shelter pathogenic bacteria. Thus, they are described as a potential hazard for health. Also, free-living amoebae have been described to be resistant to biocides, especially under their cyst resistant form. There are several studies on amoeba treatments but none of them compare sensitivity of trophozoites and cysts from different genus to various water disinfectants. In our study, we tested chlorine, monochloramine and chlorine dioxide on both cysts and trophozoites from three strains, belonging to the three main genera of free-living amoebae. The results show that, comparing cysts to trophozoites inactivation, only the Acanthamoeba cysts were highly more resistant to treatment than trophozoites. Comparison of the disinfectant efficiency led to conclude that chlorine dioxide was the most efficient treatment in our conditions and was particularly efficient against cysts. In conclusion, our results would help to adapt water treatments in order to target free-living amoebae in water networks.