Opportunistic pathogens and large microbial diversity detected in source-to-distribution drinking water of three remote communities in Northern Australia

Metagenomic insight into the pathogenic-related characteristics and resistome profiles within microbiome residing on the Angkor sandstone monuments in Cambodia

To reveal the characteristics of indigenous microbiome including the pathogenic-related ones on Angkor monuments in Cambodia and the distribution pattern of resistome at different locations, several sites, namely Angkor Wat, Bayon of Angkor Thom, and Prasat Preah Vihear with different exposure levels to tourists were selected to conduct the metagenomic analysis in this study. The general characteristics of the microbiome on these monuments were revealed, and the association between the environmental geo-ecological feature and the indigenous microbiome was delineated. The most common microbial groups included 6 phyla, namely Acidobacteria, Actinobacteria, Gemmatimonadetes, Nitrospirae, Proteobacteria and Verrucomicrobia on the monuments, but Firmicutes and Chlamydiae were the most dominant phyla found in bats droppings. The taxonomic family of Chitinophagaceae could serve as a signature microbial group for Preah Vihear, the less visited site. More importantly, the pathogenic-related characteristics of the microbiome residing on Angkor monuments were uncovered. A set of specific antibiotic resistance genes (ARGs) with cross-niches dispersal capacity (between the environmental microbiome and the microbiome within warm blood fauna) was identified to be high by the source tracking analysis based on ARGs profile varies in this study. Among the 10 ARG-types detected in this study, 6 of them are confined to resistance mechanism of antibiotic efflux-pump. The findings of this study provide new a new direction on public health management and implication globally at archaeological sites for tourism.

Burkholderia pseudomallei and melioidosis

Burkholderia pseudomallei, the causative agent of melioidosis, is found in soil and water of tropical and subtropical regions globally. Modelled estimates of the global burden predict that melioidosis remains vastly under-reported, and a call has been made for it to be recognized as a neglected tropical disease by the World Health Organization. Severe weather events and environmental disturbance are associated with increased case numbers, and it is anticipated that, in some regions, cases will increase in association with climate change. Genomic epidemiological investigations have confirmed B. pseudomallei endemicity in newly recognized regions, including the southern United States. Melioidosis follows environmental exposure to B. pseudomallei and is associated with comorbidities that affect the immune response, such as diabetes, and with socioeconomic disadvantage. Several vaccine candidates are ready for phase I clinical trials. In this Review, we explore the global burden, epidemiology and pathophysiology of B. pseudomallei as well as current diagnostics, treatment recommendations and preventive measures, highlighting research needs and priorities.

Red mark syndrome: Is the aquaculture water microbiome a keystone for understanding the disease aetiology?

Aquaculture significantly contributes to the growing demand for food worldwide. However, diseases associated with intensive aquaculture conditions, especially the skin related syndromes, may have significant implications on fish health and industry. In farmed rainbow trout, red mark syndrome (RMS), which consists of multiple skin lesions, currently lacks recognized aetiological agents, and increased efforts are needed to elucidate the onset of these conditions. Most of the past studies were focused on analyzing skin lesions, but no study focused on water, a medium constantly interacting with fish. Indeed, water tanks are environmental niches colonized by microbial communities, which may be implicated in the onset of the disease. Here, we present the results of water and sediment microbiome analyses performed in an RMS-affected aquaculture facility, bringing new knowledge about the environmental microbiomes harbored under these conditions. On the whole, no significant differences in the bacterial community structure were reported in RMS-affected tanks compared to the RMS-free ones. However, we highlighted significant differences in microbiome composition when analyzing different samples source (i.e., water and sediments). Looking at the finer scale, we measured significant changes in the relative abundances of specific taxa in RMS-affected tanks, especially when analyzing water samples. Our results provide worthwhile insight into a mostly uncharacterized ecological scenario, aiding future studies on the aquaculture built environment for disease prevention and monitoring.

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.

The lung microbiota in Korean patients with non-tuberculous mycobacterial pulmonary disease

Background

The microbiota of the lower respiratory tract in patients with non-tuberculous mycobacterial pulmonary disease (NTM-PD) has not been fully evaluated. We explored the role of the lung microbiota in NTM-PD by analyzing protected specimen brushing (PSB) and bronchial washing samples from patients with NTM-PD obtained using a flexible bronchoscope.

Results

Bronchial washing and PSB samples from the NTM-PD group tended to have fewer OTUs and lower Chao1 richness values compared with those from the control group. In both bronchial washing and PSB samples, beta diversity was significantly lower in the NTM-PD group than in the control group (P = 2.25E-6 and P = 4.13E-4, respectively). Principal component analysis showed that the PSBs and bronchial washings exhibited similar patterns within each group but differed between the two groups. The volcano plots indicated differences in several phyla and genera between the two groups.

Conclusions

The lower respiratory tract of patients with NTM-PD has a unique microbiota distribution that is low in richness/diversity.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-021-02141-1.

Assessment of heavy metals contamination and water quality characterization in the Nanming River, Guizhou Province

The analysis to assess the water quality and potential ecological risks in sediments was carried out by means of the distribution characteristics of nutrient properties and heavy metals in water, and heavy metals in sediments from the Nanming River. The results from nutrient properties demonstrated that the majority of TN and TP exceeded the permissible limit and concentrated within the study area. The concentrations of heavy metal in water were lower than the permissible limits but may pose potential threat to aquatic ecosystems. Based on the potential ecological risk results of heavy metals in sediments, Cd posed risk to ecological environment, and the serious contaminations mainly existed in the center of Guiyang City. The multivariate statistical analyses were used to support the idea that the Upstream Area and Midstream Area were significantly dominated by NH₄⁺, TP, TN and COD_Mn in water. Furthermore, landscape characteristics and hydrology condition better explained the certain trend of water quality. Finally, identifying relationship between nutrient properties and heavy metals that are key ecological components of ecosystem can potentially aid the advances for restoration of geochemical transformations and give rise to river restoration efforts.

Characterisation of Microbial Community Associated with Different Disinfection Treatments in Hospital hot Water Networks

Many disinfection treatments can be adopted for controlling opportunistic pathogens in hospital water networks in order to reduce infection risk for immunocompromised patients. Each method has limits and strengths and it could determine modifications on bacterial community. The aim of our investigation was to study under real-life conditions the microbial community associated with different chemical (monochloramine, hydrogen peroxide, chlorine dioxide) and non-chemical (hyperthermia) treatments, continuously applied since many years in four hot water networks of the same hospital. Municipal cold water, untreated secondary, and treated hot water were analysed for microbiome characterization by 16S amplicon sequencing. Cold waters had a common microbial profile at genera level. The hot water bacterial profiles differed according to treatment. Our results confirm the effectiveness of disinfection strategies in our hospital for controlling potential pathogens such as Legionella, as the investigated genera containing opportunistic pathogens were absent or had relative abundances ≤1%, except for non-tuberculous mycobacteria, Sphingomonas, Ochrobactrum and Brevundimonas. Monitoring the microbial complexity of healthcare water networks through 16S amplicon sequencing is an innovative and effective approach useful for Public Health purpose in order to verify possible modifications of microbiota associated with disinfection treatments.