Abundance and distribution of bacteria carrying sltII gene in natural river water

Evaluation of recreational risks due to exposure of antibiotic-resistance bacteria from environmental water: A proposed framework

This research provides a framework for the human health risk assessment due to exposure of AR (antibiotic resistance) E. coli from recreational water (swimming activity). Literature-based epidemiological studies were used for f-value formulation (i.e., AR E. coli/total number of E. coli isolates) and the theoretical calculation of AR and non-AR E. coli concentrations. Risk was estimated using calculated values by considering four different dose-response (D-R) scenarios with known characteristics due to current lack of availability of D-R for AR bacteria. f-values ranged between 0.14 and 0.59 and the order of calculated theoretical values of maximum AR E. coli are as follows: ampicillin or amoxicillin (38 CFU/dip) > co-trimoxazole (19 CFU/dip) ~ tetracycline (18 CFU/dip) > ceftriaxone or cefotaxime or ceftazidime (10 CFU/dip) ~ ciprofloxacin or ofloxacin (9 CFU/dip). The risk of infection was considerably high for theoretical calculated concentration values regardless of the chosen D-R model (annual risk of infection (95th percentile) = 1, Spearman's rank correlation coefficient = -0.06 to 0.94), under the conditions studied. Further, AR levels of human gastrointestinal-tract were determined using literature-reported data in stool samples and indicated that the resistance level was very high in healthy human (range: 3.7 × 10⁷-8.4 × 10⁷ CFU/g of wet lumen content). The maximum allowable concentration values for AR E. coli and non-ARB (0.0075 CFU/dip and 2.56 CFU/dip) were found to be smaller than the USEPA recreational water quality guidelines (≤126 CFU/100 mL), which can help the USEPA and other regulatory bodies in revisiting the current guidelines. So based on the noted results, we can conclude that the maintenance of inventory of actual measured concentration of ARB in the recreational water sites is needed to prevent unwanted complication related to the treatment of infectious sustained by resistant microbes.

Visualization and direct counting of individual denitrifying bacterial cells in soil by nirK-targeted direct in situ PCR

The abundance of denitrifying bacteria in soil has been determined primarily by the conventional most probable number (MPN) method. We have developed a single-cell identification technique that is culture-independent, direct in situ PCR, to enumerate denitrifying bacteria in soils. The specificity of this method was evaluated with six species of denitrifying bacteria using nirK as the target gene; Escherichia coli was used as a negative control. Almost all (97.3%-100%) of the nirK-type denitrifying bacteria (Agromonas oligotrophica, Alcaligenes faecalis, Achromobacter denitrificans, Bradyrhizobium japonicum, and Pseudomonas chlororaphis) were detected by direct in situ PCR, whereas no E. coli cells and only a few cells (2.4%) of nirS-type denitrifying bacteria (Pseudomonas aeruginosa) were detected. Numbers of denitrifying bacteria in upland and paddy soil samples quantified by this method were 3.3 × 10(8) to 2.6 × 10(9) cells g(-1) dry soil. These values are approximately 1,000 to 300,000 times higher than those estimated by the MPN method. These results suggest that direct in situ PCR is a better tool for quantifying denitrifying bacteria in soil than the conventional MPN method.

Shiga toxin: expression, distribution, and its role in the environment

In this review, we highlight recent work that has increased our understanding of the production and distribution of Shiga toxin in the environment. Specifically, we review studies that offer an expanded view of environmental reservoirs for Shiga toxin producing microbes in terrestrial and aquatic ecosystems. We then relate the abundance of Shiga toxin in the environment to work that demonstrates that the genetic mechanisms underlying the production of Shiga toxin genes are modified and embellished beyond the classical microbial gene regulatory paradigms in a manner that apparently "fine tunes" the trigger to modulate the amount of toxin produced. Last, we highlight several recent studies examining microbe/protist interactions that postulate an answer to the outstanding question of why microbes might harbor and express Shiga toxin genes in the environment.

Rapid, semiautomated quantification of bacterial cells in freshwater by using a microfluidic device for on-chip staining and counting

A microfluidic device-based system for the rapid and semiautomated counting of bacteria in freshwater was fabricated and examined. Bacteria in groundwater and in potable water, as well as starved Escherichia coli O157:H7 spiked in pond water, were able to be on-chip stained and enumerated within 1 h using this system.

Gene and antigen markers of shiga-toxin producing E. coli from Michigan and Indiana river water: occurrence and relation to recreational water quality criteria

The relation of bacterial pathogen occurrence to fecal indicator bacteria (FIB) concentrations used for recreational water quality criteria (RWQC) is poorly understood. This study determined the occurrence of Shiga-toxin producing Escherichia coli (STEC) markers and their relation to FIB concentrations in Michigan and Indiana river water. Using 67 fecal coliform (FC) bacteria cultures from 41 river sites in multiple watersheds, we evaluated the occurrence of five STEC markers: the Escherichia coli (EC) O157 antigen and gene, and the STEC virulence genes eaeA, stx1, and stx2. Simple isolations from selected FC cultures yielded viable EC O157. By both antigen and gene assays, EC O157 was detected in a greater proportion of samples exceeding rather than meeting FC RWQC (P < 0.05), but was unrelated to EC and enterococci RWQC. The occurrence of all other STEC markers was unrelated to any FIB RWQC. The eaeA, stx2, and stx1 genes were found in 93.3, 13.3, and in 46.7% of samples meeting FC RWQC and in 91.7, 0.0, and 37.5% of samples meeting the EC RWQC. Although not statistically significant, the percentage of samples positive for each STEC marker except stx1 was lower in samples that met, as opposed to exceeded, FIB RWQC. Viable STEC were common members of the FC communities in river water throughout southern Michigan and northern Indiana, regardless of FIB RWQC. Our study indicates that further information on the occurrence of pathogens in recreational waters, and research on alternative indicators of their occurrence, may help inform water-resource management and public health decision-making.

Gene transfer events and their occurrence in selected environments

Genes encoding virulence determinants are transferred between species in many different environments. In this review we describe gene transfer events to and from different species of bacteria, from bacteria to plants, and from plants to bacteria. Examples of the setting for these transfer events include: the GI tract, the rumen, the oral cavity, and in food matrixes. As a case study, the flux of virulence factors from E.coli O157:H7 is described as an example of gene flow in the environment.

Occurrence of Escherichia coli O157:H7 and other enterohemorrhagic Escherichia coli in the environment

Enterohemorrhagic Escherichia coli (EHEC) (O157 and other serotypes) are zoonotic pathogens linked with severe human illnesses. The main virulence factors of EHEC are the Shiga toxins, among others. Most of the genes coding for these toxins are bacteriophage-encoded. Although ruminants are recognized as their main natural reservoir, water has also been documented as a way of transmission of EHEC. E. coli O157:H7 and other EHEC may contaminate waters (recreational, drinking or irrigation waters) through feces from humans and other animals. Indeed, the occurrence of EHEC carrying the stx2 gene in raw municipal sewage and animal wastewater from several origins has been widely documented. However, the evaluation of the persistence of naturally occurring EHEC in the environment is still difficult due to methodological problems. Methods proposed for the detection and isolation of stx-encoding bacteria, ranging from the classic culture-based methods to molecular approaches, and their application in the environment, are discussed here. Most virulence factors associated with these strains are linked to either plasmids or phages, and consequently they are likely to be subject to horizontal gene transfer between species or serotypes. Moreover, the presence of infectious stx-phages isolated as free particles in the environment and their high persistence in water systems suggest that they may contribute to the spread of stx genes, as they are directly involved in the emergence of new pathogenic strains, which might have important health consequences.

Quantitative determination of free-DNA uptake in river bacteria at the single-cell level by in situ rolling-circle amplification

Detection of plasmid DNA uptake in river bacteria at the single-cell level was carried out by rolling-circle amplification (RCA). Uptake of a plasmid containing the green fluorescent protein gene (gfp) by indigenous bacteria from two rivers in Osaka, Japan, was monitored for 506 h using this in situ gene amplification technique with optimized cell permeabilization conditions. Plasmid uptake determined by in situ RCA was compared to direct counts of cells expressing gfp under fluorescence microscopy to examine differences in detection sensitivities between the two methods. Detection of DNA uptake as monitored by in situ RCA was 20 times higher at maximum than that by direct counting of gfp-expressing cells. In situ RCA could detect bacteria taking up the plasmid in several samples in which no gfp-expressing cells were apparent, indicating that in situ gene amplification techniques can be used to determine accurate rates of extracellular DNA uptake by indigenous bacteria in aquatic environments.

Recognition of individual genes in diverse microorganisms by cycling primed in situ amplification

Cycling primed in situ amplification-fluorescent in situ hybridization (CPRINS-FISH) was developed to recognize individual genes in a single bacterial cell. In CPRINS, the amplicon was long single-stranded DNA and thus retained within the permeabilized microbial cells. FISH with a multiply labeled fluorescent probe set enabled significant reduction in nonspecific background while maintaining high fluorescence signals of target bacteria. The ampicillin resistance gene in Escherichia coli, chloramphenicol acetyltransferase gene in different gram-negative strains, and RNA polymerase sigma factor (rpoD) gene in Aeromonas spp. could be detected under identical permeabilization conditions. After concentration of environmental freshwater samples onto polycarbonate filters and subsequent coating of filters in gelatin, no decrease in bacterial cell numbers was observed with extensive permeabilization. The detection rates of bacterioplankton in river and pond water samples by CPRINS-FISH with a universal 16S rRNA gene primer and probe set ranged from 65 to 76% of total cell counts (mean, 71%). The concentrations of cells detected by CPRINS-FISH targeting of the rpoD genes of Aeromonas sobria and A. hydrophila in the water samples varied between 2.1 x 10(3) and 9.0 x 10(3) cells ml(-1) and between undetectable and 5.1 x 10(2) cells ml(-1), respectively. These results demonstrate that CPRINS-FISH provides a high sensitivity for microscopic detection of bacteria carrying a specific gene in natural aquatic samples.

rRNA sequence-based scanning electron microscopic detection of bacteria

A new scanning electron microscopic method was developed for gaining both phylogenetic and morphological information about target microbes using in situ hybridization with rRNA-targeted oligonucleotide probes (SEM-ISH). Target cells were hybridized with oligonucleotide probes after gold labeling. Gold enhancement was used for amplification of probe signals from hybridized cells. The hybridized cells released a strong backscatter electron signal due to accumulation of gold atoms inside cells. SEM-ISH was applied to analyze bacterial community composition in freshwater samples, and bacterial cell counts determined by SEM-ISH with rRNA-targeted probes for major phyla within the domain Bacteria were highly correlated to those by fluorescent in situ hybridization (FISH). The bacterial composition on surface of river sediment particles before and after cell dispersion treatment by sonication was successfully revealed by SEM-ISH. Direct enumeration of bacterial cells on the surface of sonicated sediment particles by SEM-ISH demonstrated that members of Cytophaga-Flavobacterium existed tightly on the surface of particles. SEM-ISH allows defining the number and distribution of phylogenetically defined cells adherent to material surfaces, which is difficult in FISH, and it gives new insight into electron microscopic studies of microorganisms in their natural environment.

Multicolour digital image analysis system for identification of bacteria and concurrent assessment of their respiratory activity

AIMS

To develop a rapid and simple multicolour digital image analysis system for simultaneous identification of bacteria and assessment of their metabolic activity.

METHODS AND RESULTS

We developed an image analyser capable of distinguishing triple-stained bacterial cells. Bacteria were stained with a nucleic acid stain, a fluorescent antibody and a fluorescent metabolic indicator for enumeration, species identification and assessment of metabolic activity. This multicolour image analyser was used to simultaneously identify Escherichia coli O157:H7 in milk samples and assess their respiratory activity. The images of the triple-stained bacteria were captured using a combination of blue light and u.v. excitation and an epifluorescence microscope and were processed by our image analyser. We found a good correlation between the counts of actively respiring (r = 0.93) and total (r = 0.94) E. coli O157:H7 measured by digital image analysis and visual observation.

CONCLUSION

The multicolour digital image analysis system described here was able to quantify active pathogenic micro-organisms within 2 h.

SIGNIFICANCE AND IMPACT OF THE STUDY

This multicolour image analysis allows the rapid and simultaneous quantification of bacteria, identification of species and assessment of metabolic activity.

Prevalence of the stx 2 Gene in Coliform Populations from Aquatic Environments

Shiga toxin-producing Escherichia coli strains are human pathogens linked to hemorrhagic colitis and hemolytic uremic syndrome. The major virulence factors of these strains are Shiga toxins Stx1 and Stx2. The majority of the genes coding for these toxins are borne by bacteriophages. Free Stx2-encoding bacteriophages have been found in aquatic environments, but there is limited information about the lysogenic strains and bacteria present in the environment that are susceptible to phage infection. The aim of this work was to study the prevalence and the distribution of the stx 2 gene in coliform bacteria in sewage samples of different origins. The presence of the stx 2 gene was monitored every 2 weeks over a 1-year period in a municipal sewage treatment plant. A mean value of 10 2 genes/ml was observed without significant variation during the study period. This concentration was of the same order of magnitude in raw municipal sewage of various origins and in animal wastewater from several slaughterhouses. A total of 138 strains carrying the stx 2 gene were isolated by colony hybridization. This procedure detected approximately 1 gene-carrying colony per 1,000 fecal coliform colonies in municipal sewage and around 1 gene-carrying colony per 100 fecal coliform colonies in animal wastewaters. Most of the isolates belonged to E. coli serotypes other than E. coli O157, suggesting a low prevalence of strains of this serotype carrying the stx 2 gene in the wastewater studied.

Development of multicolour digital image analysis system to enumerate actively respiring bacteria in natural river water

AIMS

To develop a rapid and simple method for the assessment of metabolic activity of bacteria in natural environment.

METHODS AND RESULTS

A rapid and simple multicolour digital image analysis system for enumerating viable bacteria based on active fluorescent staining has been developed. This system can accurately differentiate actively respiring bacteria and non-respiring bacteria by distinctive colour information in the digital image captured by an epifluorescence microscope equipped with low magnification objective lens. An algorithm to distinguish bacteria from considerable detritus, which produced bright fluorescence in different colours, by colour segmentation has also been developed. This system was applied to river water samples, and the total and respiratory active bacterial counts by digital image analysis were highly related to those by epifluorescence microscopy (r2 = 0.96 and 0.93, respectively).

CONCLUSION

This system allowed the rapid and simple differentiation of bacteria from detritus and concurrent assessment of their metabolic activity, with results being available within 1 h.

SIGNIFICANCE AND IMPACT OF THE STUDY

The low magnification image analysis allows more rapid and simple quantification of bacteria and could considerably decrease image data amount and acquisition time. This system could be easily applied to the rapid analysis of microbes in various environments.

Detection of bacteria carrying the stx2 gene by in situ loop-mediated isothermal amplification

A new in situ DNA amplification technique for microscopic detection of bacteria carrying a specific gene is described. Loop-mediated isothermal amplification (LAMP) was used to detect stxA(2) in Escherichia coli O157:H7 cells. The mild permeabilization conditions and low isothermal temperature used in the in situ LAMP method caused less cell damage than in situ PCR. It allowed use of fluorescent antibody labeling in the bacterial mixture after the DNA amplification for identification of E. coli O157:H7 cells with an stxA(2) gene. Higher-contrast images were obtained with this method than with in situ PCR.

Rapid detection of respiring Escherichia coli O157:H7 in apple juice, milk, and ground beef by flow cytometry

BACKGROUND

Rapid and simple methods to detect viable pathogenic microbes in foods and drinks are required. Flow cytometry was used for the rapid detection of respiring Escherichia coli O157:H7 cells in apple juice, milk, and ground beef.

METHODS

CTC (5-cyano-2,3-ditolyl tetrazolium chloride) was used to estimate the respiratory activity of bacteria. Fluorescein isothiocyanate (FITC)-labeled anti-E. coli O157:H7 direct antibody (FA) was used for the specific detection of target cells. Food samples were inoculated with starved E. coli O157:H7 and E. coli K-12 cells, and analyzed by both fluorescent microscopy and flow cytometry after double staining with FA and CTC.

RESULTS

Respiring E. coli O157:H7 cells in food samples showed strong fluorescence of both FA (green) and CTC (red); thus, they could be clearly and specifically distinguished from respiring E. coli K-12 or inactive cells. A good correlation was achieved in flow cytometric analysis between the numbers of inoculated viable E. coli O157:H7 and those detected in milk and apple juice. The detection threshold for this flow cytometry for E. coli O157:H7 in milk, apple juice, and ground beef was 10(3) cells/ml (milk and apple juice) or 10(3) cells/g (ground beef) of sample when the total bacterial number in the sample was 10(6) cells/ml.

CONCLUSIONS

Respiring E. coli O157:H7 in food samples can be detected specifically within a few hours. Flow cytometry with FA-CTC double staining can be used to examine food contamination with various pathogenic microbes demonstrating physiologic activity through the use of a suitable fluorescent antibody.

Monitoring of Ralstonia eutropha KT1 in groundwater in an experimental bioaugmentation field by in situ PCR

Ralstonia eutropha KT1, which degrades trichloroethylene, was injected into the aquifer after activation with toluene, and then the number of bacteria was monitored by in situ PCR targeting the phenol hydroxylase gene and by fluorescent in situ hybridization (FISH) targeting 16S rRNA. Before injection of the bacterial suspension, the total concentration of bacteria in the groundwater was approximately 3 x 10(5) cells/ml and the amount of Ralstonia and bacteria carrying the phenol hydroxylase gene as a percentage of total bacterial cells was less than 0.1%. The concentration of bacteria carrying the phenol hydroxylase gene detected by in situ PCR was approximately 3 x 10(7) cells/ml 1 h after injection, and the concentration of Ralstonia detected by FISH was similar. The number of bacteria detected by in situ PCR was similar to that detected by FISH 4 days after the start of the extraction of groundwater. On and after day 7, however, the number of bacterial cells detected by FISH was less than that detected by in situ PCR.

In situ reverse transcription to detect the cbbL gene and visualize RuBisCO in chemoautotrophic nitrifying bacteria

AIMS

In situ methodologies targeting the cbbL gene were used to visualize cells of nitrifying bacteria. Both procaryotic in situ PCR (IS-PCR) and in situ reverse transcription (ISRT) protocols were employed to determine gene presence and expression, respectively.

METHODS AND RESULTS

Aged-oligotropic seawater samples were inoculated with microbial assemblages containing a mixture of actively growing nitrifying bacteria, starved nitrifying bacteria, and heterotrophic bacteria without cbbL. After the molecular manipulations, we found that while all the nitrifiers (healthy or starved) with the cbbL gene were detected by IS-PCR, only the actively growing autotrophic nitrifiers with detectable levels of carbon fixation and nitrification activity were detected by ISRT analysis.

CONCLUSION

These results show how IS-PCR and ISRT supplement each other, and their potential for the analysis of heterogeneous populations where an assortment of healthy and starved/dormant cells are expected.

Nucleic acid-based fluorescent probes in microbial ecology: application of flow cytometry

Microorganisms in natural environments have often been treated as 'black box' systems. Researchers have measured the inputs and outputs of the box, and have made bulk measurements on cell behaviour. However, unravelling the details of the diversity and interactions that exist within these microbial populations has proven exceptionally difficult. The information gained from the black box approach has been invaluable, and has allowed models of global foodwebs to be generated and tested. However, there is still little information about the interactions of individual microbial cells within natural populations. Such studies are essential to fully understand the integrated functioning of ecosystems. To achieve this goal, researchers need to be able to identify individual cells within a population, enumerate them, estimate both viability and activity, and monitor changes in response to relevant parameters. Due to the diversity, heterogeneity and numbers of cells that make up these populations, these measurements require automation and speed. At present, the use of flow cytometry in conjunction with nucleic acid probes provides an excellent method with which to pursue such studies.

Flow cytometric detection of specific gene expression in prokaryotic cells using in situ RT-PCR

Prokaryotic in situ RT-PCR was coupled with flow cytometry to detect mRNA transcripts of the toluene dioxygenase (todC1) gene in intact cells of the bacterium Pseudomonas putida F1. Recovery efficiency of fixed cells over the course of the entire in situ detection procedure was approximately 81% for both P. putida F1 and AC10R cells. It appeared that lysozyme treatment and PCR thermal cycling were the steps responsible for most of observed cell loss. Bacterial cells expressing the todC1 gene could be discriminated from negative control cells of the same size based on flow cytometrically-measured fluorescence and forward angle light scatter. According to flow cytometric analysis, the fluorescence intensity of positive cells was 4-5 times brighter than that of negative cells. The combination of flow cytometry and a prokaryotic in situ reverse transcription-PCR (RT-PCR) approach make possible the rapid detection and enumeration of functional (based on mRNA) populations of microbial cells.