Rapid and improved identification of drinking water bacteria using the Drinking Water Library, a dedicated MALDI-TOF MS database

Dyadobacter helix sp. nov. and Dyadobacter linearis sp. nov., from drinking water

The purpose of this study is to better characterize and complete the classification of two bacterial strains, CECT 9275T and CECT 9623T, isolated from drinking water systems and affiliated to the genus Dyadobacter by partial 16S rRNA gene sequence comparison. Hence, we report here the phenotypic, genomic and phylogenetic characterization performed on these strains. Both strains grow on R2A agar forming mucous, bright yellow colonies, developing at 26 °C in 48 h. They produce flexirubin and are oxidase and catalase positive, mesophilic and non-halophilic. The cells of strain CECT 9275T are curved rods mainly associated in pairs, forming nearly closed rings or resembling the shape of the number three, to long spirals resembling a corkscrew. Its draft genome has an estimated size of 7.23 Mbp (G+C content 45.4%). Strain CECT 9623T appeared on wet mounts as straight rods, mostly in pairs, sometimes forming long filaments (up to 20 µm). Its draft genome is shorter, with an estimated size of 6.45 Mbp (G+C content is 46.1%). Overall genome relatedness indexes clearly define them as separate organisms, so based on all the data collected, we propose the species Dyadobacter helix sp. nov. with type strain AB1T (=CECT 9275T=LMG 32341T) and Dyadobacter linearis sp. nov. with type strain AB67T (=CECT 9623T=LMG 32342T).

Microbial drinking water monitoring now and in the future

Over time, humanity has addressed microbial water contamination in various ways. Historically, individuals resorted to producing beer to combat the issue. Fast forward to the 19th century, and we witnessed a scientific approach by Robert Koch. His groundbreaking gelatine plating method aimed to identify and quantify bacteria, with a proposed limit of 100 colony-forming units per millilitre (CFU/mL) to avoid Cholera outbreaks. Despite considerable advancements in plating techniques through experimentation with media compositions and growth temperatures, the reliance on a century-old method for water safety remains the state-of-the-art. Even though most countries succeed in producing qualitative water at the end of the production centres, it is difficult to control, and guarantee, the same quality during distribution. Rather than focusing solely on specific sampling points, we propose a holistic examination of the entire water network to ensure comprehensive safety. Current practices leave room for uncertainties, especially given the low concentrations of pathogens. Innovative methods like flow cytometry and flow cytometric fingerprinting offer the ability to detect changes in the microbiome of drinking water. Additionally, molecular techniques and emerging sequencing technologies, such as third-generation sequencing (MinION), mark a significant leap forward, enhancing detection limits and emphasizing the identification of unwanted genes rather than the unwanted bacteria/microorganisms itself. Over the last decades, there has been the realization that the drinking water distribution networks are complex ecosystems that, beside bacteria, comprise of viruses, protozoans and even isopods. Sequencing techniques to find eukaryotic DNA are necessary to monitor the entire microbiome of the drinking water distribution network. Or will artificial intelligence, big data and machine learning prove to be the way to go for (microbial) drinking water monitoring? In essence, it is time to transcend century-old practices and embrace modern technologies to ensure the safety of our drinking water from production to consumption.

Comparison of MALDI-TOF mass spectrometry and 16S rDNA sequencing for identification of environmental bacteria: a case study of cave mussel-associated culturable microorganisms

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is routinely used as a rapid and cost-effective method for pathogen identification in clinical settings. In comparison, its performance in other microbiological fields, such as environmental microbiology, is still being tested, although isolates of environmental microbes are essential for in-depth in vivo studies of their biology, including biotechnological applications. We investigated the applicability of MALDI-TOF MS for the identification of bacterial isolates from a highly oligotrophic environment - Dinaric Karst caves, which likely harbor specific microorganisms. We cultured bacteria from the shell surface of the endemic mussel Congeria jalzici, one of the three known cave mussels in the world that lives in the Dinaric karst underground. The bacterial isolates were obtained by swabbing the shell surface of mussels living in microhabitats with different amounts of water: 10 air-exposed mussels, 10 submerged mussels, and 10 mussels in the hygropetric zone. A collection of 87 pure culture isolates was obtained, mostly belonging to the phylum Bacillota (72%), followed by Pseudomonadota (16%), Actinomycetota (11%), and Bacteroidota (1%). We compared the results of MALDI-TOF MS identification (Bruker databases DB-5989 and version 11, v11) with the results of 16S rDNA-based phylogenetic analysis, a standard procedure for bacterial identification. Identification to the genus level based on 16S rDNA was possible for all isolates and clearly outperformed the results from MALDI-TOF MS, although the updated MALDI-TOF MS database v11 gave better results than the DB-5989 version (85% versus 62%). However, identification to the species-level by 16S rDNA sequencing was achieved for only 17% of isolates, compared with 14% and 40% for the MALDI-TOF MS databases DB-5989 and v11 database, respectively. In conclusion, our results suggest that continued enrichment of MALDI-TOF MS libraries will result with this method soon becoming a rapid, accurate, and efficient tool for assessing the diversity of culturable bacteria from different environmental niches.

A cohort study of wastewater treatment plant workers: Association between levels of biomarkers of systemic inflammation and exposure to bacteria and fungi, and endotoxin as measured using two methods

Work in wastewater treatment plants (WWTPs) can be associated with exposure to airborne microorganisms and endotoxin from the working environment. The aim of this study was to obtain knowledge about whether serum levels of the markers of systemic inflammation, C-reactive protein (CRP) and serum amyloid A (SAA), are associated with personal exposure to endotoxin, measured using the Limulus (endotoxin_Limulus) and the rFC (endotoxin_rFC) assays, as well as bacteria and fungi in a cohort of WWTP workers. Exposure and blood samples were collected for 11 workers over one year. Exposure to endotoxin_Limulus-day and endotoxin_rFC-day correlated significantly (r = 0.80, p<0.0001, n = 104), but endotoxin_Limulus-day was 4.4 (Geometric mean (GM) value) times higher than endotoxin_rFC-day (p<0.0001). The endotoxin_Limulus-day, endotoxin_rFC-day, bacteria, and fungal exposure as well as serum levels of CRP_-day (GM=1.4 mg/l) and SAA_-day (GM=12 mg/l) differed between workers. Serum levels of SAA_day correlated significantly with CRP_day (r = 0.30, p = 0.0068). The serum levels of CRP_day were associated significantly with exposure to endotoxin_Limulus-day. Exposure, SAA and CRP data were also analyzed as av. of each season, and SAA_season was associated positively and significantly with endotoxin_{Limulus-season} and endotoxin_rFC-season and negatively with fungal_season exposure. In conclusion, CRP_day was associated with the endotoxin_Limulus-day and SAA_season with endotoxin_{Limulus-season} and endotoxin_rFC-season exposure. Thus, we hereby document that WWTP workers are exposed to airborne endotoxin which seems to have a negative impact on their health.

Culture and molecular methods as complementary tools for water quality management

Bacterial communities in a full-scale drinking water treatment plant (DWTP) were characterized using matrix-assisted laser desorption/ionization time of flight mass-spectrometry (MALDI-TOF MS) to identify HPC isolates and the obtained results were compared to 16S rRNA (V4) metabarcoding data acquired in a previous study. Sixty-three samples were collected at nine stages of the potabilization process: river water and groundwater intake, decantation, sand filtration, ozonization, carbon filtration, reverse osmosis, the mixing chamber and post-chlorination drinking water. In total, 1807 bacterial colonies were isolated, 32 % of which were successfully identified to at least the genus level by MALDI-TOF MS using our previously developed Drinking Water Library. Trends in diversity were similar by both approaches, but differences were observed in the detection of taxa, especially at lower hierarchy levels. High bacterial diversity was observed in river and groundwater, where Proteobacteria predominated. The diversity decreased significantly after the chlorination step, where Bacillus sp. (Firmicutes) and an unknown genus of Obscuribacteraceae (Cyanobacteria) were the most prevalent genera according to MALDI-TOF MS and metabarcoding, respectively. The two approaches gave similar results for the decantation, sand filtration and mixing chamber steps, where the most abundant taxon was Flavobacterium. The combined use of these culture-based and culture-independent methods to characterize microbial populations may help to better understand the role of bacteria in water treatment and quality, which will be of value for DWTP management.

Plasmid-Mediated Fluoroquinolone Resistance Genes in Quinolone-Susceptible Aeromonas spp. Phenotypes Isolated From Recreational Surface Freshwater Reservoir

Aeromonas spp. are recognized as opportunistic pathogens causing diseases. Infections in humans can result mainly in gastrointestinal and wound diseases with or without progression to septicemia. Although Aeromonas spp. are not known uropathogens and they rarely cause urinary tract infection, we hypothesize that the presence of these bacteria in the water and the contact during, e.g., recreational and bathing activity can create the conditions for the colonization of the human body and may result to diseases in various locations, including the urinary tract. Our study presents the occurrence of aeromonad fluoroquinolone-susceptible phenotypes with the presence of plasmid-mediated fluoroquinolone resistance (PMQR) genes in a natural freshwater reservoir occasionally used for recreational activities. Sixty-nine isolates collected during the bathing period were identified by mass spectrometry and screened for the presence of fluoroquinolone-resistant phenotypes and genotypes. Fluoroquinolone susceptibility was determined as minimal inhibitory concentration values. PMQR qnr genes were detected by PCR. Isolates comprising eight species, namely, mainly Aeromonas veronii (50.7% isolates) and Aeromonas media (24.6% isolates) and rarely Aeromonas eucrenophila, Aeromonas caviae, Aeromonas bestiarum, Aeromonas ichthiosmia, and Aeromonas hydrophila, were selected. All isolates were phenotypically susceptible either to ciprofloxacin or levofloxacin. Unexpectedly, at least one to three of the PMQR genes were detected in 42.0% of the fluoroquinolone-susceptible Aeromonas spp. phenotypes. Mainly the qnrS (34.8% isolates) and qnrA (14.5% isolates) determinants were detected. In conclusion, the freshwater reservoir occasionally used for bathing was tainted with aeromonads, with a high occurrence of opportunistic pathogens such as A. veronii and A. media. MALDI‐TOF MS is a powerful technique for aeromonad identification. Our data reveals the mismatch phenomenon between fluoroquinolone-susceptible aeromonad phenotypes and the presence of plasmid-mediated qnr resistance genes. It suggests that phenotypically susceptible bacteria might be a potential source for the storage and transmission of these genes. The exposure during, e.g., a recreational activity may create the potential risk for causing infections, both diagnostically and therapeutically difficult, after expressing the resistance genes and quinolone-resistant strain selection.

Rapid Antibiotic Resistance Serial Prediction in Staphylococcus aureus Based on Large-Scale MALDI-TOF Data by Applying XGBoost in Multi-Label Learning

Multidrug resistance has become a phenotype that commonly exists among Staphylococcus aureus and is a serious concern for infection treatment. Nowadays, to detect the antibiotic susceptibility, antibiotic testing is generated based on the level of genomic for cure decision consuming huge of time and labor, while matrix-assisted laser desorption-ionization (MALDI) time-of-flight mass spectrometry (TOF/MS) shows its possibility in high-speed and effective detection on the level of proteomic. In this study, on the basis of MALDI-TOF spectra data of discovery cohort with 26,852 samples and replication cohort with 4,963 samples from Taiwan area and their corresponding susceptibilities to oxacillin and clindamycin, a multi-label prediction model against double resistance using Lowest Power set ensemble with XGBoost is constructed for rapid susceptibility prediction. With the output of serial susceptibility prediction, the model performance can realize 77% of accuracy for the serial prediction, the area under the receiver characteristic curve of 0.93 for oxacillin susceptibility prediction, and the area under the receiver characteristic curve of 0.89 for clindamycin susceptibility prediction. The generated multi-label prediction model provides serial antibiotic resistance, such as the susceptibilities of oxacillin and clindamycin in this study, for S. aureus-infected patients based on MALDI-TOF, which will provide guidance in antibiotic usage during the treatment taking the advantage of speed and efficiency.

An Efficient Method for Testing the Quality of Drinking-Water Filters Used for Home Necessities

This paper presents research conducted in the direction of analyzing the efficiency of filters used for drinking water intended for domestic consumption, with effects on the water quality gained from the public distribution network. A basic method that uses accessible techniques, such as optical microscopy and tests that involve the use of existing products on the consumer market, was developed regarding the filtration capacities of the main filters existing on the market—a method that has advantages, such as speed and ease of application, a unitary character in obtaining samples, low costs, and high efficiency. The technique approached is that of microscopy, and the samples used were taken from the laboratory tests made on the mentioned filters, using a specific experimental stand designed to support laboratory tests by using chosen filter cartridges. The research results obtained were analyzed to make a classification from the perspective of filtration efficiency, in terms of using statistical analysis tools (mathematical models and methods processed in MATLAB software). Moreover, by using a certain type of application based on specific mathematical algorithms, which takes into account some influential factors with a decisive role on household consumers, it was aimed to identify the optimal filter element for acquisition and use in its own regime. The aim of the study was to identify the optimal filter cartridge from the perspective of quality–price ratio.

Application of MALDI-TOF MS for identification of environmental bacteria: A review

Bacteria play a variety of roles in the environment. They maintain the balance in the ecosystem and provide different ecosystem services such as in biogeochemical cycling of nutrients, biodegradation of toxic pollutants, and others. Therefore, isolation and identification of different environmental bacteria are important to most environmental research. Due to the high cost and time associated with the conventional molecular techniques, matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has gained considerable attention for routine identification of bacteria. This review aims to provide an overview of the application of MALDI-TOF MS in various environmental studies through bibliometric analysis and literature review. The bibliometric analysis helped to understand the time-variable application of MALDI-TOF MS in various environmental studies. The categorical literature review covers various environmental studies comprising areas like ecology, food microbiology, environmental biotechnology, agriculture, and plant sciences, which show the application of the technique for identification and characterization of pollutant-degrading, plant-associated, disease-causing, soil-beneficial, and other environmental bacteria. Further research should focus on bridging the gap between the phylogenetic identity of bacteria and their specific environmental functions or metabolic traits that can help in rapid advancements in environmental research, thereby, improving time and cost savings.