Development and application of real-time PCR assays for quantifying total and aerolysin gene-containing aeromonas in source, intermediate, and finished drinking water

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

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

Effects of Dietary Lactic Acid Supplementation on the Activity of Digestive and Antioxidant Enzymes, Gene Expressions, and Bacterial Communities in the Intestine of Common Carp, Cyprinus carpio

The present study investigated the effects of dietary lactic acid (LA) supplementation on the growth performance, intestinal digestive/antioxidant enzymes' activities, gene expression, and bacterial communities in common carp, Cyprinus carpio. Four diets were formulated to contain 0 g/kg LA (control), at 2.5 g/kg LA (2.5LAC), 5 g/kg LA (5LAC), and 10 g/kg LA (10LAC) and offered to the fish over a period of 56 days. The results showed that dietary 5 g/kg LA supplementation improved growth performance and feed efficiency in the fish. All LA treatments exhibited significant elevations in the intestinal trypsin and chymotrypsin activities, whereas the intestinal lipase, amylase, and alkaline phosphatase activities exhibited significant elevations in the 5LAC and 10LAC treatments. All LA treatments exhibited significant elevations in the intestinal heat shock protein 70, tumor necrosis factor-alpha, interleukin-1 beta, and defensin gene expressions, and the highest expression was observed in the 5LAC treatment. Additionally, dietary LA treatment significantly increased the lysozyme expression and Lactobacillus sp. population in the intestine of the fish, and the highest values were observed in the 5LAC and 10LAC treatments. Aeromonas sp. and Vibrio sp. populations decreased in the LA treatments, and the lowest Aeromonas sp. population was observed in the 10LAC treatment. The intestinal mucin2 and mucin5 expressions, and the hepatic reduced glutathione content, significantly increased, whereas hepatic glutathione peroxidase, glutathione reductase, and malondialdehyde significantly decreased in the 5LAC and 10LAC treatments. In conclusion, dietary 5 g/kg LA is recommended for common carp feeding to improve growth rate, antioxidant capacity, and intestinal health.

Controlling pathogenic risks of water treatment biotechnologies at the source by genetic editing means

Antimicrobial-resistant pathogens in the environment and wastewater treatment systems, many of which are also important pollutant degraders and are difficult to control by traditional disinfection approaches, have become an unprecedented treat to ecological security and human health. Here, we propose the adoption of genetic editing techniques as a highly targeted, efficient and simple tool to control the risks of environmental pathogens at the source. An 'all-in-one' plasmid system was constructed in Aeromonas hydrophila to accurately identify and selectively inactivate multiple key virulence factor genes and antibiotic resistance genes via base editing, enabling significantly suppressed bacterial virulence and resistance without impairing their normal phenotype and pollutant-degradation functions. Its safe application for bioaugmented treatment of synthetic textile wastewater was also demonstrated. This genetic-editing technique may offer a promising solution to control the health risks of environmental microorganisms via targeted gene inactivation, thereby facilitating safer application of water treatment biotechnologies.

CRISPRi System as an Efficient, Simple Platform for Rapid Identification of Genes Involved in Pollutant Transformation by Aeromonas hydrophila

Aeromonas species are indigenous in diverse aquatic environments and play important roles in environmental remediation. However, the pollutant transformation mechanisms of these bacteria remain elusive, and their potential in pollution control is largely unexploited so far. In this work, we report an efficient and simple genome regulation tool to edit Aeromonas hydrophila and identify its biomolecular pathways for pollutant transformation. The genome regulation system, which is based on the type II clustered regularly interspaced short palindromic repeat interference (CRISPRi) system from Streptococcus pyogenes, can serve as a reversible and multiplexible platform for gene knockdown in A. hydrophila. A single-plasmid CRISPRi system harboring both dCas9 and the sgRNA was constructed in A. hydrophila and used to silence diverse genes with varied sizes and expression levels. With this system, up to 467-fold repression of gfp expression was achieved, and the function of the essential gene-ftsZ was identified quickly and accurately. Furthermore, simultaneous transcriptional repression of multiple targeted genes was realized. We discovered that the ars operon played an essential role in arsenic detoxification, and the extracellular electron transfer (EET) pathway was involved in methyl orange reduction, but not in vanadium reduction by A. hydrophila. Our method allows better insights and effective genetic manipulation of the pollutant transformation processes in Aeromonas, which might facilitate more efficient utilization of the Aeromonas species and other microbial species for environmental remediation applications.

One-year survey of opportunistic premise plumbing pathogens and free-living amoebae in the tap-water of one northern city of China

In this study, qPCR was used to quantify opportunistic premise plumbing pathogens (OPPPs) and free-living amoebae in 11 tap water samples collected over four seasons from a city in northern China. Results demonstrated that the average numbers of gene copies of Legionella spp. and Mycobacterium spp. were significantly higher than those of Aeromonas spp. (p < 0.05). Legionella spp. and Mycobacterium spp. were 100% (44/44) positively detected while P. aeruginosa and Aeromonas spp. were 79.54% (35/44) and 77.27% (34/44) positively detected. Legionella pneumophila was only detected in 4 samples (4/44), demonstrating its occasional occurrence. No Mycobacterium avium or Naegleria fowleri was detected in any of the samples. The average gene copy numbers of target OPPPs were the highest in summer, suggesting seasonal prevalence of OPPPs. Average gene copy numbers of OPPPs in the taps of low-use-frequency were higher than in taps of high-use-frequency, but the difference was not significant for some OPPPs (p > 0.05). Moderate negative correlations between the chlorine concentration and the gene copy numbers of OPPPs were observed by Spearman analysis (r_s ranged from -0.311 to -0.710, p < 0.05). However, no significant correlations existed between OPPPs and AOC, BDOC, or turbidity. Moderate positive correlations were observed between the target microorganisms, especially for Acanthamoeba spp., through Spearman analysis (p < 0.05). Based on our studies, it is proposed that disinfectant concentration, season, taps with different-use frequency, OPPP species, and potential microbial correlations should be considered for control of OPPPs in tap water.

Effect of sequential UV/free chlorine disinfection on opportunistic pathogens and microbial community structure in simulated drinking water distribution systems

Drinking water distribution systems (DWDS) may be a "Trojan Horse" for some waterborne diseases caused by opportunistic pathogens (OPs). In this study, two simulated DWDS inoculated with groundwater were treated with chlorine (Cl₂) and ultraviolet/chlorine (UV/Cl₂) respectively to compare their effects on the OPs distributed in four different phases (bulk water, biofilms, corrosion products, and loose deposits) of DWDS. 16S rRNA genes sequencing and qPCR were used to profile microbial community and quantify target genes of OPs, respectively. Results showed that UV/Cl₂ was more effective than single Cl₂ to control the regrowth of OPs in the water with the same residual chlorine concentration. However, the OPs inhabiting the biofilms, corrosion products, and loose deposits seemed to be tolerant to UV/Cl₂ and Cl₂, demonstrating that OPs residing in these phases were resistant to the disinfection processes. Some significant microbial correlations between OPs and Acanthamoeba were found by Spearman correlative analysis (p < 0.05), demonstrating that the ecological interactions may exist in the DWDS. 16S rRNA genes sequencing of water samples revealed a significant different microbial community structure between UV/Cl₂ and Cl₂. This study may give some implications for controlling the OPs in the DWDS disinfected with UV/Cl₂.

Occurrence of antibiotic resistance genes and bacterial pathogens in water and sediment in urban recreational water

The emergence and prevalence of antibiotic resistance genes (ARGs) and pathogens in the environment are serious global health concern. However, information about the occurrence of ARGs and pathogens in recreational water is still limited. Accordingly, we investigated the occurrence of six ARGs and human pathogens in three recreational lakes, and the correlations between ARGs and one mobile genetic element (intI1) were analyzed. The quantitative PCR results showed that the concentration of ARGs ranged from 4.58 × 10⁰ to 5.0 × 10⁵ copies/mL in water and from 5.78 × 10³ to 5.89 × 10⁸ copies/g dry weight (dw) in sediment. Sul1 exhibited the highest level among the five quantifiable ARGs. The concentrations of sul1, bla_-TEM, and tetX exhibited significant positive correlations with intI1 (p < 0.05), indicating that intI1 may be involved in their proliferation. The detection frequencies of ARGs ranged from 75%-100%, indicating the prevalence of these risks in this region. The concentration of Escherichia coli, Aeromonas spp., Mycobacterium avium, Pseudomonas aeruginosa, and Salmonella enterica ranged from 10³ to 10⁵ copies/100 mL in water and 10⁴-10⁶ copies/g dw in sediment. In total, 25% of the samples harbored all pathogen genes, indicating the prevalence of these pathogens in recreational lakes. Furthermore, the next-generation sequencing results showed that 68 genera of pathogens were present, among which Aeromonas, Mycobacterium, and Pseudomonas were the dominant ones in this region, posing a considerable potential health risk to public health. Overall, the widespread distribution of ARGs and pathogens underscores the need to better monitor and mitigate their propagation in recreational lakes and the associated risks to human health.

Distribution comparison and risk assessment of free-floating and particle-attached bacterial pathogens in urban recreational water: Implications for water quality management

The risk of pathogen exposure in recreational water is a concern worldwide. Moreover, suspended particles, as ideal shelters for pathogens, in these waters also need attention. However, the risk caused by the pathogen-particle attachment is largely unknown. Accordingly, water samples in three recreational lakes in Beijing were collected and separated into free-floating (FL, 0.22-5μm) and particle-attached (PA, >5μm) fractions. Next-generation sequencing (NGS) was employed to determine the diversity of genera containing pathogens, and quantitative PCR (qPCR) was used to assess the presence of genes from Escherichia coli (uidA), Salmonella enterica (invA), Aeromonas spp. (aerA), Mycobacterium avium (16S) and Pseudomonas aeruginosa (oaa). The NGS results showed stable pathogen genera composition distinctions between the PA and FL fractions. Some genera, such as Aeromonas and Mycobacterium, exhibited higher abundances in the PA fractions. qPCR revealed that most of the gene concentrations were higher within particles than were FL fractions. Some gene levels showed correlations with the particle concentrations and lake nutrient levels. Further quantitative microbial risk assessment (QMRA) of selected strains (S. enterica and M. avium) indicated a higher health risk during secondary contact activities in lakes with more nutrients and particles. We concluded that suspended particles (mainly composed of algae) in urban recreational water might influence the pathogen distribution and could serve as reservoirs for pathogen contamination, with important management implications.

Evaluation of bacterial pathogen diversity, abundance and health risks in urban recreational water by amplicon next-generation sequencing and quantitative PCR

The microbial quality of urban recreational water is of great concern to public health. The monitoring of indicator organisms and several pathogens alone is not sufficient to accurately and comprehensively identify microbial risks. To assess the levels of bacterial pathogens and health risks in urban recreational water, we analyzed pathogen diversity and quantified four pathogens in 46 water samples collected from waterbodies in Beijing Olympic Forest Park in one year. The pathogen diversity revealed by 16S rRNA gene targeted next-generation sequencing (NGS) showed that 16 of 40 genera and 13 of 76 reference species were present. The most abundant species were Acinetobacter johnsonii, Mycobacterium avium and Aeromonas spp. Quantitative polymerase chain reaction (qPCR) of Escherichia coli (uidA), Aeromonas (aerA), M. avium (16S rRNA), Pseudomonas aeruginosa (oaa) and Salmonella (invA) showed that the aerA genes were the most abundant, occurring in all samples with concentrations of 10^4-6 genome copies/100mL, followed by oaa, invA and M. avium. In total, 34.8% of the samples harbored all genes, indicating the prevalence of these pathogens in this recreational waterbody. Based on the qPCR results, a quantitative microbial risk assessment (QMRA) showed that the annual infection risks of Salmonella, M. avium and P. aeruginosa in five activities were mostly greater than the U.S. EPA risk limit for recreational contacts, and children playing with water may be exposed to the greatest infection risk. Our findings provide a comprehensive understanding of bacterial pathogen diversity and pathogen abundance in urban recreational water by applying both NGS and qPCR.

Chironomids' Relationship with Aeromonas Species

Chironomids (Diptera: Chironomidae), also known as non-biting midges, are one of the most abundant groups of insects in aquatic habitats. They undergo a complete metamorphosis of four life stages of which three are aquatic (egg, larva, and pupa), and the adult emerges into the air. Chironomids serve as a natural reservoir of Aeromonas and Vibrio cholerae species. Here, we review existing knowledge about the mutual relations between Aeromonas species and chironomids. Using 454-pyrosequencing of the 16S rRNA gene, we found that the prevalence of Aeromonas species in the insects’ egg masses and larvae was 1.6 and 3.3% of the insects’ endogenous microbiota, respectively. Aeromonas abundance per egg mass remained stable during a 6-month period of bacterial monitoring. Different Aeromonas species were isolated and some demonstrated the ability to degrade the insect’s egg masses and to prevent eggs hatching. Chitinase was identified as the enzyme responsible for the egg mass degradation. Different Aeromonas species isolated from chironomids demonstrated the potential to protect their host from toxic metals. Aeromonas is a causative agent of fish infections. Fish are frequently recorded as feeding on chironomids. Thus, fish might be infected with Aeromonas species via chironomid consumption. Aeromonas strains are also responsible for causing gastroenteritis and wound infections in humans. Different virulence genes were identified in Aeromonas species isolated from chironomids. Chironomids may infest drinking water reservoirs, hence be the source of pathogenic Aeromonas strains in drinking water. Chironomids and Aeromonas species have a complicated mutual relationship.

Development of duplex-PCR for identification of Aeromonas species

INTRODUCTION

The number of reports of intestinal infections caused by Aeromonas spp. has increased significantly in recent years. In most clinical laboratories, identification of these bacteria is carried out by general phenotypic tests that sometimes do not accurately differentiate Aeromonas and Vibrio.

METHODS

A duplex-polymerase chain reaction (PCR) was developed directed to 2 targets identifying Aeromonas spp. pathogenic to humans.

RESULTS

The duplex-PCR results were reproducible and specific for Aeromonas spp. pathogenic to humans.

CONCLUSIONS

This method will allow differentiation between Vibrio and Aeromonas spp. in patients with in cholera-like symptoms and can also be used in water quality monitoring.

Simultaneous detection of six diarrhea-causing bacterial pathogens with an in-house PCR-luminex assay

Diarrhea can be caused by a range of pathogens, including several bacteria. Conventional diagnostic methods, such as culture, biochemical tests, and enzyme-linked immunosorbent assay (ELISA), are laborious. We developed a 7-plex PCR-Luminex assay to simultaneously screen for several of the major diarrhea-causing bacteria directly in fecal specimens, including pathogenic Aeromonas, Campylobacter jejuni, Campylobacter coli, Salmonella, Shigella, enteroinvasive Escherichia coli (EIEC), Vibrio, and Yersinia. We included an extrinsic control to verify extraction and amplification. The assay was first validated with reference strains or isolates and exhibited a limit of detection of 10(3) to 10(5) CFU/g of stool for each pathogen as well as quantitative detection up to 10(9) CFU/g. A total of 205 clinical fecal specimens from individuals with diarrhea, previously cultured for enteric pathogens and tested for Campylobacter by ELISA, were evaluated. Using these predicate methods as standards, sensitivities and specificities of the PCR-Luminex assay were 89% and 94% for Aeromonas, 89% and 93% for Campylobacter, 96% and 95% for Salmonella, 94% and 94% for Shigella, 92% and 97% for Vibrio, and 100% and 100% for Yersinia, respectively. All discrepant results were further examined by singleplex real-time PCR assays targeting different gene regions, which revealed 89% (55/62 results) concordance with the PCR-Luminex assay. The fluorescent signals obtained with this approach exhibited a statistically significant correlation with the cycle threshold (C(T)) values from the cognate real-time PCR assays (P < 0.05). This multiplex PCR-Luminex assay enables sensitive, specific, and quantitative detection of the major bacterial causes of gastroenteritis.

Molecular quantification of virulence gene-containing Aeromonas in water samples collected from different drinking water treatment processes

Pathogenic species of Aeromonas produce a range of virulence factors, including aerolysin, cytotonic enterotoxins, and serine protease, to cause acute gastroenteritis and wound infections in humans and animals. Recognizing that not all Aeromonas strains are pathogenic, in this study, we proposed to evaluate Aeromonas removal effectiveness based on the presence of virulence gene-containing Aeromonas as a proper means to assess microbial risk of Aeromonas. We developed and applied real-time PCR assays to quantify serine protease (ser) gene- and heat-labile cytotonic enterotoxin (alt) gene-containing Aeromonas in water samples. Among 18 Aeromonas isolates from the source water, only three isolates possessed all three genes (aer, ser, and alt). A higher percent of isolates has either ser gene (89%) or alt gene (72%) compared to the percent of isolates containing aer gene (44%). Results of this study suggested that several different conventional and unconventional drinking water treatment processes could effectively remove Aeromonas from source water. As the comprehensive knowledge of the distribution of virulence factors in different Aeromonas species is currently not available, using real-time PCR to quantify various virulence factor genes in water samples and/or isolates can be a practical means for better assessment of microbial risks in water.

Rapid detection of Naegleria fowleri in water distribution pipeline biofilms and drinking water samples

Rapid detection of pathogenic Naegleria fowler in water distribution networks is critical for water utilities. Current detection methods rely on sampling drinking water followed by culturing and molecular identification of purified strains. This culture-based method takes an extended amount of time (days), detects both nonpathogenic and pathogenic species, and does not account for N. fowleri cells associated with pipe wall biofilms. In this study, a total DNA extraction technique coupled with a real-time PCR method using primers specific for N. fowleri was developed and validated. The method readily detected N. fowleri without preculturing with the lowest detection limit for N. fowleri cells spiked in biofilm being one cell (66% detection rate) and five cells (100% detection rate). For drinking water, the detection limit was five cells (66% detection rate) and 10 cells (100% detection rate). By comparison, culture-based methods were less sensitive for detection of cells spiked into both biofilm (66% detection for <10 cells) and drinking water (0% detection for <10 cells). In mixed cultures of N. fowleri and nonpathogenic Naegleria, the method identified N. fowleri in 100% of all replicates, whereastests with the current consensus primers detected N. fowleri in only 5% of all replicates. Application of the new method to drinking water and pipe wall biofilm samples obtained from a distribution network enabled the detection of N. fowleri in under 6 h, versus 3+ daysforthe culture based method. Further, comparison of the real-time PCR data from the field samples and the standard curves enabled an approximation of N. fowleri cells in the biofilm and drinking water. The use of such a method will further aid water utilities in detecting and managing the persistence of N. fowleri in water distribution networks.