Characterization of 'faecal streptococci' as indicators of faecal pollution and distribution in the environment

Metagenomics-Based Microbial Ecological Community Threshold and Indicators of Anthropogenic Disturbances in Estuarine Sediments

Assessing the impacts of cumulative anthropogenic disturbances on estuarine ecosystem health is challenging. Using spatially distributed sediments from the Pearl River Estuary (PRE) in southern China, which are significantly influenced by anthropogenic activities, we demonstrated that metagenomics-based surveillance of benthic microbial communities is a robust approach to assess anthropogenic impacts on estuarine benthic ecosystems. Correlational and threshold analyses between microbial compositions and environmental conditions indicated that anthropogenic disturbances in the PRE sediments drove the taxonomic and functional variations in the benthic microbial communities. An ecological community threshold of anthropogenic disturbances was identified, which delineated the PRE sediments into two groups (H and L) with distinct taxa and functional traits. Group H, located nearshore and subjected to a higher level of anthropogenic disturbances, was enriched with pollutant degraders, putative human pathogens, fecal pollution indicators, and functional traits related to stress tolerance. In contrast, Group L, located offshore and subjected to a lower level of anthropogenic disturbances, was enriched with halotolerant and oligotrophic taxa and functional traits related to growth and resource acquisition. The machine learning random forest model identified a number of taxonomic and functional indicators that could differentiate PRE sediments between Groups H and L. The identified ecological community threshold and microbial indicators highlight the utility of metagenomics-based microbial surveillance in assessing the adverse impacts of anthropogenic disturbances in estuarine sediments, which can assist environmental management to better protect ecosystem health.

Effect of Sonication on Microwave Inactivation Kinetics of Enterococcus faecalis in Dairy Effluent

The aim of this study is to inactivate Enterococcus faecalis ATCC 29212 present in dairy wastewater effluent using microwave (MW) waves and/or ultrasound waves (US). The ultrasonic bath treatment (35 kHz) had no significant effect on the reduction of the survival rate (predominant declumping effect). At 650 W of microwave treatment, the total destruction was completed at 75 s, while at 350 W a 3 log reduction was achieved. The Weibull model was fitted to the survival curves to describe the inactivation kinetics, and the effect of the combined microwave-ultrasound treatments was evaluated. The scaling parameter α that was estimated from the inactivation kinetics for the microwaves combined with the ultrasound waves in pre-treatment was found to be lower than the scaling parameters obtained in post-treatment, which were in turn lower than those estimated for microwaves or ultrasound waves alone. The use of the ultrasound waves in pre-treatment was more effective than in post-treatment; a total reduction was achieved using a combination of US (30 min) followed by MW (650 W) with α = 28.3 s, while 4.0 log was obtained by reversing all processes with α = 34.5 s. The results from the protein assays indicate that the bacterial wall was damaged and that holes were formed from which protein leakage occurred.

Assessment of listing and categorisation of animal diseases within the framework of the Animal Health Law (Regulation (EU) No 2016/429): antimicrobial-resistant Enterococcus faecalis in poultry

Enterococcus faecalis (E. faecalis) was identified among the most relevant antimicrobial-resistant (AMR) bacteria in the EU for poultry in a previous scientific opinion. Thus, it has been assessed according to the criteria of the Animal Health Law (AHL), in particular criteria of Article 7 on disease profile and impacts, Article 5 on its eligibility to be listed, Annex IV for its categorisation according to disease prevention and control rules as in Article 9 and Article 8 for listing animal species related to the bacterium. The assessment has been performed following a methodology previously published. The outcome is the median of the probability ranges provided by the experts, which indicates whether each criterion is fulfilled (lower bound ≥ 66%) or not (upper bound ≤ 33%), or whether there is uncertainty about fulfilment. Reasoning points are reported for criteria with uncertain outcome. According to the assessment here performed, it is uncertain whether AMR E. faecalis can be considered eligible to be listed for Union intervention according to Article 5 of the AHL (33-66% probability). According to the criteria in Annex IV, for the purpose of categorisation related to the level of prevention and control as in Article 9 of the AHL, the AHAW Panel concluded that the bacterium does not meet the criteria in Sections 1, 2 and 4 (Categories A, B and D; 0-5%, 5-10% and 1-10% probability of meeting the criteria, respectively) and the AHAW Panel is uncertain whether it meets the criteria in Sections 3 and 5 (Categories C and E, 33-66% and 33-66% probability of meeting the criteria, respectively). The animal species to be listed for AMR E. faecalis according to Article 8 criteria are mostly birds of the orders Galliformes and Anseriformes, but also mammals and reptiles can serve as reservoirs.

Epidemiology of antimicrobial resistance (AMR) on California dairies: descriptive and cluster analyses of AMR phenotype of fecal commensal bacteria isolated from adult cows

Background

This study describes the occurrence of antimicrobial resistance (AMR) in commensal Escherichia coli and Enterococcus/Streptococcus spp. (ES) isolated from fecal samples of dairy cows and assesses the variation of AMR profiles across regions and seasons following the implementation of the Food and Agricultural Code (FAC) Sections 14400–14408 (formerly known as Senate Bill, SB 27) in California (CA).

Methods

The study was conducted on ten dairies distributed across CA’s three milk sheds: Northern California (NCA), Northern San Joaquin Valley (NSJV), and the Greater Southern California (GSCA). On each study dairy, individual fecal samples were collected from two cohorts of lactating dairy cows during the fall/winter 2018 and spring/summer 2019 seasons. Each cohort comprised of 12 cows per dairy. The fecal samples were collected at enrollment before calving (close-up stage) and then monthly thereafter for four consecutive time points up to 120 days in milk. A total of 2,171 E. coli and 2,158 ES isolates were tested for antimicrobial susceptibility using the broth microdilution method against a select panel of antimicrobials.

Results

The E. coli isolates showed high resistance to florfenicol (83.31% ± 0.80) and sulphadimethoxine (32.45%), while resistance to ampicillin (1.10% ± 0.21), ceftiofur (1.93% ± 0.29), danofloxacin (4.01% ± 0.42), enrofloxacin (3.31% ± 0.38), gentamicin (0.32% ± 0.12) and neomycin (1.61% ± 0.27) had low resistance proportions. The ES isolates were highly resistant to tildipirosin (50.18% ± 1.10), tilmicosin (48% ± 1.10), tiamulin (42%) and florfenicol (46% ± 1.10), but were minimally resistant to ampicillin (0.23%) and penicillin (0.20%). Multidrug resistance (MDR) (resistance to at least 1 drug in ≥3 antimicrobial classes) was observed in 14.14% of E. coli isolates and 39% of ES isolates. Escherichia coli isolates recovered during winter showed higher MDR prevalence compared to summer isolates (20.33% vs. 8.04%). A higher prevalence of MDR was observed in NSJV (17.29%) and GSCA (15.34%) compared with NCA (10.10%).

Conclusions

Our findings showed high rates of AMR to several drugs that are not labeled for use in lactating dairy cattle 20 months of age or older. Conversely, very low resistance was observed for drugs labeled for use in adult dairy cows, such as cephalosporins and penicillin. Overall, our findings identified important differences in AMR by antimicrobial class, region and season.

Streptococcus gordonii: Pathogenesis and Host Response to Its Cell Wall Components

Streptococcus gordonii, a Gram-positive bacterium, is a commensal bacterium that is commonly found in the skin, oral cavity, and intestine. It is also known as an opportunistic pathogen that can cause local or systemic diseases, such as apical periodontitis and infective endocarditis. S. gordonii, an early colonizer, easily attaches to host tissues, including tooth surfaces and heart valves, forming biofilms. S. gordonii penetrates into root canals and blood streams, subsequently interacting with various host immune and non-immune cells. The cell wall components of S. gordonii, which include lipoteichoic acids, lipoproteins, serine-rich repeat adhesins, peptidoglycans, and cell wall proteins, are recognizable by individual host receptors. They are involved in virulence and immunoregulatory processes causing host inflammatory responses. Therefore, S.gordonii cell wall components act as virulence factors that often progressively develop diseases through overwhelming host responses. This review provides an overview of S. gordonii, and how its cell wall components could contribute to the pathogenesis and development of therapeutic strategies.

Diversity and antimicrobial resistance of Enterococcus from the Upper Oconee Watershed, Georgia

AIM

It is well-known that enterococci are abundant in the environment; however, the role of surface water as a reservoir of antimicrobial-resistant enterococci remains largely undefined. In this study, surface water samples were collected over a 2-year period from the Upper Oconee watershed, Athens, GA to examine enterococci and their antimicrobial resistance.

METHODS AND RESULTS

Approximately 97% (445/458) of the samples were positive for enterococci and a total of 637 enterococci were isolated. The predominant species were Enterococcus casseliflavus (33·6%) followed by Enterococcus faecalis (26·5%) and Enterococcus hirae (13·2%). Regardless of species, the highest levels of resistance were to lincomycin (88·5%) and tetracycline (13%); isolates also exhibited resistance to newer antimicrobials, daptomycin (8·9%) and tigecycline (6·4%). Multidrug resistance (resistance ≥3 antimicrobial classes) was observed to as many as five classes of antimicrobials. Resistant enterococci appeared to be randomly dispersed over the seasons rather than clustered by species or antimicrobial resistance.

CONCLUSIONS

This study demonstrated that surface waters contain a large population of diverse species of antimicrobial-resistant enterococci, including resistance to new antimicrobials.

SIGNIFICANCE AND IMPACT OF THE STUDY

These results may indicate the potential of human intestinal illness and/or colonization of the human gut with resistant enterococci as enterococci correlate with increased disease risk to humans during recreational exposure to water.

Resazurin assay for assessment of antimicrobial properties of electrospun nanofiber filtration membranes

We developed a simple and fast microplate assay for evaluation of the antimicrobial activity of electrospun nanofiber filtration membranes or similar porous materials for water treatment technologies. Resazurin (alamarBlue®) was used as an indicator of the amount of viable experimental microorganisms Gram-negative Escherichia coli, Gram-positive Enterococcus faecalis, and natural wastewater treatment plant effluent bacteria. A bacterial inoculum of concentration 1-3 × 105 CFU mL-1 was pipetted onto the surface of assessed both functionalized and respective control membranes and incubated in 12-well plates for 4 h at 37 °C. Kinetics of resazurin metabolization, i.e. its reduction to fluorescent resorufin, was evaluated fluorimetrically (λex520/λem590 nm). A number of viable bacteria on the membranes expressed as CFU mL-1 was calculated from the kinetic curves by using calibration curves that were constructed for both experimental bacterial species. Antimicrobial activities of the membranes were evaluated by either resazurin assay or modified ISO 20743 plate count assay. Results of both assays showed the significant antimicrobial activity of membranes functionalized with silver nanoparticles for both bacterial species and wastewater treatment plant effluent bacteria as well (log CFU reduction compared to control membrane > 4), while membranes containing specific quaternary ammonium salts were inefficient (log CFU reduction < 1). The suitability of resazurin microplate assay for testing nanofiber filtration membranes and analogous matrices has proven to be a faster and less demanding alternative to the traditionally used approach providing comparable results.

The Impact of Winter Relocation and Depuration on Norovirus Concentrations in Pacific Oysters Harvested from a Commercial Production Site

Oysters contaminated with norovirus present a significant public health risk when consumed raw. In this study, norovirus genome copy concentrations were determined in Pacific oysters (Magallana gigas) harvested from a sewage-impacted production site and then subjected to site-specific management procedures. These procedures consisted of relocation of oysters to an alternative production area during the norovirus high-risk winter periods (November to March) followed by an extended depuration (self-purification) under controlled temperature conditions. Significant differences in norovirus RNA concentrations were demonstrated at each point in the management process. Thirty-one percent of oyster samples from the main harvest area (Site 1) contained norovirus concentrations > 500 genome copies/g and 29% contained norovirus concentrations < 100 genome copies/g. By contrast, no oyster sample from the alternative harvest area (Site 2) or following depuration contained norovirus concentrations > 500 genome copies/g. In addition, 60 and 88% of oysters samples contained norovirus concentrations < 100 genome copies/g in oysters sampled from Site 2 and following depuration, respectively. These data demonstrate that site-specific management processes, supported by norovirus monitoring, can be an effective strategy to reduce, but not eliminate, consumer exposure to norovirus genome copies.

Spatial distribution of sewage pollution on a Hawaiian coral reef

While sewage pollution is contributing to the global decline of coral reefs, its offshore extent and direct reef impacts from water column mixing and benthic seeps are poorly documented. We addressed this knowledge gap on a Hawaiian coral reef using sewage indicator and benthic cover measurements, macroalgal bioassays, and a pollution scoring tool. Fecal indicator bacteria (FIB) and nutrient concentrations were spatially variable in surface and benthic waters, with shoreline values being highest. Shoreline macroalgae δ¹⁵N and %N indicated high nitrogen loads containing sewage, while offshore surface and benthic values suggested lower nitrogen loads from environmental sources. Coral cover was negatively correlated with FIB, macroalgal δ¹⁵N, and nutrient concentrations. Benthic salinity and temperature measurements detected daily tidal groundwater pulses which may explain these associations. While pollution scores revealed that sewage was largely concentrated along the shoreline, results showed some reached the reef and may be contributing to its declining condition.

A multi-indicator approach for identifying shoreline sewage pollution hotspots adjacent to coral reefs

Sewage pollution is contributing to the global decline of coral reefs. Identifying locations where it is entering waters near reefs is therefore a management priority. Our study documented shoreline sewage pollution hotspots in a coastal community with a fringing coral reef (Puakō, Hawai'i) using dye tracer studies, sewage indicator measurements, and a pollution scoring tool. Sewage reached shoreline waters within 9 h to 3 d. Fecal indicator bacteria concentrations were high and variable, and δ¹⁵N macroalgal values were indicative of sewage at many stations. Shoreline nutrient concentrations were two times higher than those in upland groundwater. Pollution hotspots were identified with a scoring tool using three sewage indicators. It confirmed known locations of sewage pollution from dye tracer studies. Our study highlights the need for a multi-indicator approach and scoring tool to identify sewage pollution hotspots. This approach will be useful for other coastal communities grappling with sewage pollution.

Ugly ducklings-the dark side of plastic materials in contact with potable water

Bath toys pose an interesting link between flexible plastic materials, potable water, external microbial and nutrient contamination, and potentially vulnerable end-users. Here, we characterized biofilm communities inside 19 bath toys used under real conditions. In addition, some determinants for biofilm formation were assessed, using six identical bath toys under controlled conditions with either clean water prior to bathing or dirty water after bathing. All examined bath toys revealed notable biofilms on their inner surface, with average total bacterial numbers of 5.5 × 10⁶ cells/cm² (clean water controls), 9.5 × 10⁶ cells/cm² (real bath toys), and 7.3 × 10⁷ cells/cm² (dirty water controls). Bacterial community compositions were diverse, showing many rare taxa in real bath toys and rather distinct communities in control bath toys, with a noticeable difference between clean and dirty water control biofilms. Fungi were identified in 58% of all real bath toys and in all dirty water control toys. Based on the comparison of clean water and dirty water control bath toys, we argue that bath toy biofilms are influenced by (1) the organic carbon leaching from the flexible plastic material, (2) the chemical and biological tap water quality, (3) additional nutrients from care products and human body fluids in the bath water, as well as, (4) additional bacteria from dirt and/or the end-users’ microbiome. The present study gives a detailed characterization of bath toy biofilms and a better understanding of determinants for biofilm formation and development in systems comprising plastic materials in contact with potable water.

While bathing typically means good hygiene, bath toys can serve as incubators for microbial growth. Microbes colonize nearly every natural and human-made surface, sometimes living within complex communities called biofilms. A team led by Frederik Hammes at the Swiss Federal Institute of Aquatic Science and Technology found that tap water bacteria and fungi readily formed biofilms inside bath toys, suggesting that bathing provides food for microbes. These nutrients may come from bath toys’ polymeric material, from care products like soap and from human secretions like sweat. While 16S rRNA sequence analysis found that some of the microbes were related to disease-causing strains, future work is needed to assess the disease risk from these bath toy-associated biofilms. This work sheds light on how microbes are spread by our routine activities and that we are bathed in microbes, literally.

Assessing the impact of water treatment on bacterial biofilms in drinking water distribution systems using high-throughput DNA sequencing

Biofilm control in drinking water distribution systems (DWDSs) is crucial, as biofilms are known to reduce flow efficiency, impair taste and quality of drinking water and have been implicated in the transmission of harmful pathogens. Microorganisms within biofilm communities are more resistant to disinfection compared to planktonic microorganisms, making them difficult to manage in DWDSs. This study evaluates the impact of four unique drinking water treatments on biofilm community structure using metagenomic DNA sequencing. Four experimental DWDSs were subjected to the following treatments: (1) conventional coagulation, (2) magnetic ion exchange contact (MIEX) plus conventional coagulation, (3) MIEX plus conventional coagulation plus granular activated carbon, and (4) membrane filtration (MF). Bacterial biofilms located inside the pipes of each system were sampled under sterile conditions both (a) immediately after treatment application ('inlet') and (b) at a 1 km distance from the treatment application ('outlet'). Bacterial 16S rRNA gene sequencing revealed that the outlet biofilms were more diverse than those sampled at the inlet for all treatments. The lowest number of unique operational taxonomic units (OTUs) and lowest diversity was observed in the MF inlet. However, the MF system revealed the greatest increase in diversity and OTU count from inlet to outlet. Further, the biofilm communities at the outlet of each system were more similar to one another than to their respective inlet, suggesting that biofilm communities converge towards a common established equilibrium as distance from treatment application increases. Based on the results, MF treatment is most effective at inhibiting biofilm growth, but a highly efficient post-treatment disinfection regime is also critical in order to prevent the high rates of post-treatment regrowth.

Identification and antimicrobial resistance of Enterococcus spp. isolated from the river and coastal waters in northern Iran

As fecal streptococci commonly inhabit the intestinal tract of humans and warm blooded animals, and daily detection of all pathogenic bacteria in coastal water is not practical, thus these bacteria are used to detect the fecal contamination of water. The present study examined the presence and the antibiotic resistance patterns of Enterococcus spp. isolated from the Babolrud River in Babol and coastal waters in Babolsar. Seventy samples of water were collected in various regions of the Babolrud and coastal waters. Isolated bacteria were identified to the species level using standard biochemical tests and PCR technique. In total, 70 Enterococcus spp. were isolated from the Babolrud River and coastal waters of Babolsar. Enterococcus faecalis (68.6%) and Enterococcus faecium (20%) were the most prevalent species. Resistance to chloramphenicol, ciprofloxacin, and tetracyclin was prevalent. The presence of resistant Enterococcus spp. in coastal waters may transmit resistant genes to other bacteria; therefore, swimming in such environments is not suitable.

Performance and specificity of the covalently linked immunomagnetic separation-ATP method for rapid detection and enumeration of enterococci in coastal environments

The performance and specificity of the covalently linked immunomagnetic separation-ATP (Cov-IMS/ATP) method for the detection and enumeration of enterococci was evaluated in recreational waters. Cov-IMS/ATP performance was compared with standard methods: defined substrate technology (Enterolert; IDEXX Laboratories), membrane filtration (EPA Method 1600), and an Enterococcus-specific quantitative PCR (qPCR) assay (EPA Method A). We extend previous studies by (i) analyzing the stability of the relationship between the Cov-IMS/ATP method and culture-based methods at different field sites, (ii) evaluating specificity of the assay for seven ATCC Enterococcus species, (iii) identifying cross-reacting organisms binding the antibody-bead complexes with 16S rRNA gene sequencing and evaluating specificity of the assay to five nonenterococcus species, and (iv) conducting preliminary tests of preabsorption as a means of improving the assay. Cov-IMS/ATP was found to perform consistently and with strong agreement rates (based on exceedance/compliance with regulatory limits) of between 83% and 100% compared to the culture-based Enterolert method at a variety of sites with complex inputs. The Cov-IMS/ATP method is specific to five of seven different Enterococcus spp. tested. However, there is potential for nontarget bacteria to bind the antibody, which may be reduced by purification of the IgG serum with preabsorption at problematic sites. The findings of this study help to validate the Cov-IMS/ATP method, suggesting a predictable relationship between the Cov-IMS/ATP method and traditional culture-based methods, which will allow for more widespread application of this rapid and field-portable method for coastal water quality assessment.

Speciation and antimicrobial resistance of Enterococci isolated from recreational beaches in Malaysia

We report the first study on the occurrence of antibiotic-resistant enterococci in coastal bathing waters in Malaysia. One hundred and sixty-five enterococci isolates recovered from two popular recreational beaches in Malaysia were speciated and screened for antibiotic resistance to a total of eight antibiotics. Prevalence of Enterococcus faecalis and Enterococcus faecium was highest in both beaches. E. faecalis/E. faecium ratio was 0.384:1 and 0.375:1, respectively, for isolates from Port Dickson (PD) and Bagan Lalang (BL). Analysis of Fisher's exact test showed that association of prevalence of E. faecalis and E. faecium with considered locations was not statistically significant (p < 0.05). Chi-square test revealed significant differences (χ(2) = 82.630, df = 20, p < 0.001) in the frequency of occurrence of enterococci isolates from the considered sites. Resistance was highest to nalidixic acid (94.84 %) and least for chloramphenicol (8.38 %). One-way ANOVA using Tukey-Kramer multiple comparison test showed that resistance to ampicillin was higher in PD beach isolates than BL isolates and the difference was extremely statistically significant (p < 0.0001). Frequency of occurrence of multiple antibiotic resistance (MAR) isolates were higher for PD beach water (64.29 %) as compared to BL beach water (13.51 %), while MAR indices ranged between 0.198 and 0.48. The results suggest that samples from Port Dickson may contain MAR bacteria and that this could be due to high-risk faecal contamination from sewage discharge pipes that drain into the sea water.

Comparative analysis of classical and molecular microbiology methods for the detection of Escherichia coli and Enterococcus spp. in well water

The microbiological quality of 165 1 litre well water samples collected in the Québec City region was assessed by culture-based methods (mFC agar, Chromocult coliform agar, Colilert(®), MI agar, Chromocult enterococci, Enterolert™, and mEI agar) and by a molecular microbiology strategy, dubbed CRENAME-rtPCR, developed for the detection of Escherichia coli, Enterococcus spp., Enterococcus faecalis/faecium, and Bacillus atrophaeus subsp. globigii. In these drinking water samples, approved culture-based methods detected E. coli at rates varying from 1.8 to 3.6% and Enterococcus spp. at rates varying from 3.0 to 11.5%, while the molecular microbiology approach for E. coli was found to be as efficient, detecting contamination in 3.0% of samples. In contrast, CRENAME-rtPCR detected Enterococcus spp. in 27.9% of samples while the E. faecalis/faecium molecular assay did not uncover a single contaminated sample, thereby revealing a discrepancy in the coverage of waterborne enterococcal species detected by classical and molecular microbiology methods. The validation of the CRENAME-E. coli rtPCR test as a new tool to assess the quality of drinking water will require larger scale studies elaborated to demonstrate its equivalence to approved methods.

Escherichia coli and Enterococcus spp. in rainwater tank samples: comparison of culture-based methods and 23S rRNA gene quantitative PCR assays

In this study, culture-based methods and quantitative PCR (qPCR) assays were compared with each other for the measurement of Escherichia coli and Enterococcus spp. in water samples collected from rainwater tanks in Southeast Queensland, Australia. Among the 50 rainwater tank samples tested, 26 (52%) and 46 (92%) samples yielded E. coli numbers as measured by EPA Method 1603 and E. coli 23S rRNA gene qPCR assay, respectively. Similarly, 49 (98%) and 47 (94%) samples yielded Enterococcus spp. numbers as measured by EPA Method 1600 and Enterococcus spp. 23S rRNA gene qPCR assay, respectively. The mean E. coli (2.49 ± 0.85) log(10) and Enterococcus spp. (2.72 ± 0.32) log(10) numbers as measured by qPCR assays were significantly (P < 0001) different than E. coli (0.91 ± 0.80) log(10) and Enterococcus spp. (1.86 ± 0.60) log(10) numbers as measured by culture-based method. Weak but significant correlations were observed between both EPA Method 1603 and the E. coli qPCR assay (r = 0.47, P = 0.0009), and EPA Method 1600 and the Enterococcus spp. qPCR assay (r = 0.42, P = 0.002). Good qualitative agreement was found between the culture-based method and the Enterococcus spp. qPCR assay in terms of detecting fecal pollution in water samples from the studied rainwater tanks. More research studies, however, are needed to shed some light on the discrepancies associated with the culture-based methods and qPCR assays for measuring fecal indicator bacteria.

Speciation and frequency of virulence genes of Enterococcus spp. isolated from rainwater tank samples in Southeast Queensland, Australia

In this study, 212 Enterococcus isolates from 23 rainwater tank samples in Southeast Queensland (SEQ), Australia were identified to the species level. The isolates were also tested for the presence of 6 virulence genes associated with Enterococcus related infections. Among the 23 rainwater tank samples, 20 (90%), 10 (44%), 7 (30%), 5 (22%), 4 (17%), 2 (9%), and 1 (4%) samples yielded E. faecalis, E. mundtii, E. casseliflavus, E. faecium, E. hirae, E. avium, and E. durans, respectively. Among the 6 virulence genes tested, gelE and efaA were most prevalent, detected in 19 (83%) and 18 (78%) of 23 rainwater tank samples, respectively. Virulence gene ace was also detected in 14 (61%) rainwater tank samples followed by AS, esp (E. faecalis variant), and cylA genes which were detected in 3 (13%), 2 (9%), and 1 (4%) samples, respectively. In all, 120 (57%) Enterococcus isolates from 20 rainwater tank samples harbored virulence genes. Among these tank water samples, Enterococcus spp. from 5 (25%) samples harbored a single virulence gene and 15 (75%) samples were harboring two or more virulence genes. The significance of these strains in terms of health implications remains to be assessed. The potential sources of these strains need to be identified for the improved management of captured rainwater quality. Finally, it is recommended that Enterococcus spp. should be used as an additional fecal indicator bacterium in conjunction with E. coli for the microbiological assessment of rainwater tanks.

Application of PFGE to source tracking of faecal pollution in coastal recreation area: a case study in Aoshima Beach, Japan

AIMS

The development of a microbial source tracking (MST) method is strongly desired to ensure public health and bacteriological safety in coastal recreation areas. We try to specify the source of faecal pollution by applying pulsed-field gel electrophoresis (PFGE) to the study of the aquatic environment on Aoshima Beach, Japan.

METHODS AND RESULTS

Enterococcus faecium, an enterococcus, was used as a faecal indicator bacterium in this study. Enterococcus faecium strains were isolated and identified from each water sample collected from Aoshima Beach and five rivers (Oyodo, Kiyotake, Kaeda, Chifuku and Tsukunami Rivers) that might be potential sources of faecal pollution. Enterococcus faecium strains collected from water samples were analysed using PFGE. The similarities of all the PFGE types of the Ent. faecium strains were compared using dendrogram analysis. The PFGE types of the strains isolated from Aoshima Beach showed a high similarity to those of the strains isolated from the Oyodo River at a 0·9 similarity level. It was suggested that the Oyodo River is the source of faecal pollution on Aoshima Beach.

CONCLUSIONS

The PFGE analysis using enterococci is a potential tool for the MST of faecal indicator bacteria that can be applied to the study of the coastal environment.

SIGNIFICANCE AND IMPACT OF THE STUDY

This is one of the studies that PFGE was applied to the coastal environment. The approach using PFGE could estimate the river that is source of faecal pollution in Aoshima Beach. By applying PFGE as a tool of MST method, detailed information of faecal pollution in coastal area can be provided.

The importance of sediment and submerged aquatic vegetation as potential habitats for persistent strains of enterococci in a subtropical watershed

Recent evidence of extended survival of fecal indicator bacteria in sediments and submerged aquatic vegetation (SAV) has raised concerns about using indicator bacteria to reliably detect fecal contamination. We monitored enterococci densities and population structure in water, sediment and SAV simultaneously at sites across a subtropical watershed (Tampa Bay, FL, USA) over one year to determine the extent to which each matrix serves as a potential reservoir of enterococci. SAV harbored significantly higher mean densities of enterococci than sediments, which harbored higher densities than water. Mean enterococci densities were also greater at sites located further upstream in the watershed. The population structure assessed by BOX-PCR genotyping was relatively dissimilar in each sample, although some similarities among samples suggested grouping by location. Strain diversity ranged from very high to negligible, with lowest overall diversity in lake samples taken during the summer. Several strains were highly abundant and cosmopolitan (found across sites, seasons, and matrices) and were identified by 16S rRNA gene sequencing as the Enterococcus species casseliflavus, faecalis, faecium, hirae, and mundtii. The proportional dominance of certain strains suggests the existence of persistent and possibly naturalized indicator bacteria populations that are not directly related to pollution events.

Water microbiology. Bacterial pathogens and water

Water is essential to life, but many people do not have access to clean and safe drinking water and many die of waterborne bacterial infections. In this review a general characterization of the most important bacterial diseases transmitted through water—cholera, typhoid fever and bacillary dysentery—is presented, focusing on the biology and ecology of the causal agents and on the diseases’ characteristics and their life cycles in the environment. The importance of pathogenic Escherichia coli strains and emerging pathogens in drinking water-transmitted diseases is also briefly discussed. Microbiological water analysis is mainly based on the concept of fecal indicator bacteria. The main bacteria present in human and animal feces (focusing on their behavior in their hosts and in the environment) and the most important fecal indicator bacteria are presented and discussed (focusing on the advantages and limitations of their use as markers). Important sources of bacterial fecal pollution of environmental waters are also briefly indicated. In the last topic it is discussed which indicators of fecal pollution should be used in current drinking water microbiological analysis. It was concluded that safe drinking water for all is one of the major challenges of the 21st century and that microbiological control of drinking water should be the norm everywhere. Routine basic microbiological analysis of drinking water should be carried out by assaying the presence of Escherichia coli by culture methods. Whenever financial resources are available, fecal coliform determinations should be complemented with the quantification of enterococci. More studies are needed in order to check if ammonia is reliable for a preliminary screening for emergency fecal pollution outbreaks. Financial resources should be devoted to a better understanding of the ecology and behavior of human and animal fecal bacteria in environmental waters.

Rapid QPCR-based assay for fecal Bacteroides spp. as a tool for assessing fecal contamination in recreational waters

Concentrations of fecal indicator bacteria (FIB; e.g. Escherichia coli, and Enterococcus sp.) can only be used in limited ways for determining the source of fecal contamination in recreational waters because they cannot distinguish human from non-human fecal contamination. Several Bacteroides spp. have been suggested as potential alternative indicators. We have developed a rapid, culture-independent method for quantifying fecal Bacteroides spp. using quantitative PCR (QPCR) targeting the 16S rRNA gene. The assay specifically targets and quantifies the most common human Bacteroides spp. The details of the method are presented, including analyses of a wide range of fecal samples from different organisms. Specificity and performance of the QPCR assay were also tested via a laboratory experiment where human sewage and gull guano were inoculated into a range of environmental water samples. Concentrations of fecal Bacteroides spp., total Enterococcus sp., Enterococcus faecium, Enterococcus faecalis, and Enterococcus casseliflavus were measured using QPCR, and total Enterococcus sp. and E. coli were quantified by membrane filtration (MF). Samples spiked with gull guano were highly concentrated with total Enterococcus sp., E. coli, E. faecalis, and E. casseliflavus, demonstrating that these indicators are prominent in animal feces. On the other hand, fecal Bacteroides spp. concentrations were high in samples containing sewage and were relatively low in samples spiked with gull guano. Sensitivity and specificity results suggest that the rapid fecal Bacteroides spp. QPCR assay may be a useful tool to effectively predict the presence and concentration of human-specific fecal pollution.

Species distribution and antimicrobial resistance of enterococci isolated from surface and ocean water

AIMS

The species identification and antimicrobial resistance profiles were determined for enterococci isolated from Southern California surface and ocean waters.

METHODS AND RESULTS

Species identification was determined for 1413 presumptive Enterococcus isolates from urban runoff, bay, ocean and sewage water samples. The most frequently isolated species were Enterococcus faecalis, Enterococcus faecium, Enterococcus hirae, Enterococcus casseliflavus and Enterococcus mundtii. All five of these species were isolated from ocean and bay water with a frequency ranging from 7% to 36%. Enterococcus casseliflavus was the most frequently isolated species in urban runoff making up 36-65% of isolates while E. faecium was the most frequently isolated species in sewage making up 53-78% of isolates. The similar distribution of species in urban runoff and receiving water suggests that urban runoff may be the source of Enterococcus. No vancomycin or high level gentamycin resistance was detected in E. faecalis and E. faecium isolates.

CONCLUSIONS

Enterococcus faecalis, E. faecium, E. casseliflavus and E. mundtii are the most commonly isolated Enterococcus species from urban runoff and receiving waters in Southern California.

SIGNIFICANCE AND IMPACT OF THE STUDY

Determination of the Enterococcus species isolated from receiving waters and potential pollution sources may assist in determining the sources of pollution.

Antimicrobial resistance and species composition of Enterococcus spp. isolated from waters and sands of marine recreational beaches in Southeastern Brazil

Density, species composition and antimicrobial resistance in bacteria of the Enterococcus genus were evaluated in seawater and sands from 2 marine recreational beaches with different levels of pollution. The 2 beaches showed predominance of Enterococcus faecalis and Enterococcus faecium, in the water and the sand. Dry sand presented higher densities of Enterococcus sp. and higher frequency of resistant strains than wet sand and seawater. The beach with a higher degree of pollution presented higher percentages of resistant strains (66.7% and 61.5%, in sand and in water, respectively) and resistance to a larger number of antimicrobials compared with the less polluted beach, Ilha Porchat (35.7% and 31.25% of resistant strains in sand and water, respectively). In water samples, the highest frequencies of resistance were obtained against streptomycin (38.5%) and erythromycin (25%), whilst in sand, the highest frequencies were observed in relation to erythromycin and tetracycline (38.1% and 14.3%, respectively). These results show that water and sands from beaches with high indexes of faecal contamination of human origin may be potential sources of contamination by pathogens and contribute to the dissemination of bacterial resistance.

Development of a fluorescent antibody method for the detection of Enterococcus faecium and its potential for coastal aquatic environment monitoring

A direct, microscopic fluorescent antibody method was developed to detect the occurrence of Enterococcus faecium in coastal aquatic environments and was compared with the conventional membrane filtering method. The "in situ" application of the antibody-based protocol in the analysis of water samples collected from coastal polyhaline habitats demonstrated good sensitivity and ease of implementation. Data obtained with the microscopic technique were in agreement with those obtained from culture counts. The fluorescent antibody method proved to be a rapid and reliable technique for the detection of E. faecium. The advantages and limitations intrinsic to the method are discussed, highlighting the potential of this new technique for monitoring coastal aquatic environments.

[Annual distribution of bacterial indicators generated by the domestic wastes from the landfill of Etueffont (France)]

We assessed over 15 months the distribution of total coliforms concentrations of Escherichia coli, Enterococci, Pseudomonas aeruginosa, Salmonella and Staphylococcus aureus in three monitoring points in the Etueffont landfill (Belfort, France). We selected the piezometer (PZ30) which is located downstream from the dump and two leachate collectors from the old dump and the new casing. The results showed that the leachate was free from both Salmonella and Staphylococcus aureus. The absence of Salmonella was most likely due to the small occupation of the landfill environment by vertebrates, especially rodents, birds and reptiles, which are known to be principal vectors of Salmonella. S. aureu, is generally hosted on skins and mucus of animals. The mean densities of E. coli and Enterococcus in the leachates were low. In contrast, P. aeruginosa abundance was high and closely related to precipitations. Coliform bacteria concentrations in the leachate averaged UFC.100 CFU x ml(-1). In the contaminated groundwaters, the coliforms, E. coli and Enterococci were always present at concentrations 10 to 100 fold higher than those reported from septic tank effluents. P. aeruginosa concentrations were low (mean: 11 CFU.100 ml(-1)) and inferior to those quoted in the leachate. This may be explained by the anoxic conditions which prevailed in the shistous aquifer. The absence of Salmonella in groundwaters may be due to its sensitivity to disinfectants and that of S. aureus linked to the fact that it is not a common host of the human intestine. Finally, our study clearly indicates the role played by E. coli and Enterococci as biomarkers of recent faecal contamination.

Microbiological quality of indoor and outdoor swimming pools in Greece: investigation of the antibiotic resistance of the bacterial isolates

During 1997-2005, the microbiological quality and susceptibility of bacterial isolates of swimming pool waters were investigated. A total of 462 water samples were collected from three indoor swimming pools (a teaching pool, a competition public pool, a hydrotherapy pool) and two outdoor swimming pools (a hotel semi-public and a residential private pool) in Northwestern Greece. All water samples were analyzed for the presence of bacteria, protozoa and fungi and susceptibility tests were performed for the bacterial isolates. Sixty-seven percent of the examined water samples conformed to the microbiological standards and 32.9% exceeded at least one of the indicated limits. Out of 107 bacterial isolates, 38 (35.5%) resistant strains were detected. Multi-resistant Pseudomonas alcaligenes, Leuconostoc, and Staphylococcus aureus (isolated from the teaching pool), Staphylococcus wernerii, Chryseobacterium indologenes and Ochrobactrum anthropi (isolated from the competition pool), Pseudomonas aeruginosa, P. fluorescens, Aeromonas hydrophila, Enterobacter cloacae, Klebsiella pneumoniae and S. aureus (isolated from the hydrotherapy pool) and A. hydrophila (isolated from the hotel pool) were detected. The swimming pool with the poorest microbiological quality (THC 500 cfu/ml in 12.1% of the samples, P. aeruginosa counts 1500 cfu/100 ml in 6% of the samples) and the highest prevalence of multi-resistant isolates (73.6%) was the hydrotherapy pool. No Cryptosporidium or Giardia cysts and no Legionella, Mycobacteria and Salmonella were detected, but there were isolations of Candida albicans, Aspergillus spp., Mucor spp., Alternaria spp., Rhizopus spp., Trichophyton spp., and Penicillium spp.

Identification and antagonistic activity of lactic acid bacteria occurring in porcine blood from industrial slaughterhouses—a preliminary study

Ninety-seven lactic acid bacteria (LAB) were isolated from slaughterhouse porcine blood in order to select autochthonous LAB strains for use as biopreservatives of this by-product. They were identified by 16S rDNA sequencing; and their inhibition capacity was determined against four bacterial species frequently found in contaminated blood, i.e. Staphylococcus aureus, Escherichia coli, Pseudomonas fluorescens and Bacillus spp. The taxonomic study showed an unexpected low diversity of LAB in blood, i.e. only 8 different species were found, from which just 4, i.e. Enterococcus raffinosus, Lactobacillus murinus, Lactobacillus reuteri and Lactococcus garvieae, amounted to more than 90% of all isolates. Inhibition tests in solid culture media proved that S. aureus and Bacillus spp. were inhibited by most LAB strains obtained from porcine blood. E. coli was the indicator less affected by the isolated LAB species. Several isolates efficiently inhibited the growth of all tested indicators.

Survival of enterococcal species in aquatic environments

Analysis of the survival ability of faecal streptococci/enterococci in the environment has almost invariably been conducted using the standard culture method (CFU counts) despite the demonstration that these microorganisms are capable of entering a viable but nonculturable (VBNC) state. In this study we evaluated the fate, in terms of culturability and viability, of different enterococcal species under laboratory stress conditions mimicking those of the aquatic environment. The results indicate that enterococcal species may activate two different survival strategies, namely starvation and the VBNC state, depending on the specific environmental condition. Moreover, the different enterococcal species can be divided into three groups on the basis of the time needed to activate the VBNC state and the resuscitation capability. The differences in activation of the two survival strategies and the different kinetics observed among the enterococcal species reaching the VBNC state should be taken into consideration when the microbiological quality of waters has to be evaluated and because of their role as faecal contamination indicators.

Enumeration and speciation of enterococci found in marine and intertidal sediments and coastal water in southern California

AIMS

To determine the levels and species distribution of enterococci in intertidal and marine sediments and coastal waters at two beaches frequently in violation of bacterial water standards.

METHODS AND RESULTS

Faecal indicator bacteria were extracted from sediment and enumerated using membrane filtration. High levels of enterococci were detected in intertidal sediments in a seasonal river and near a storm drain outlet. Low levels were found in marine sediments at 10 m depths and in surf zone sand. Bacterial isolates presumptively identified as Enterococcus on mEI media were speciated. The predominant species found in both water and sediment included Enterococcus faecalis, Enterococcus faecium, Enterococcus hirae, Enterococcus casseliflavus and Enterococcus mundtii. A number of isolates (11-26%) from regulatory water samples presumptively identified as enterococci on mEI media were subsequently identified as species other than Enterococcus. At both study sites, the distribution of species present in water was comparable with those in sediments and the distribution of species was similar in water samples passing and exceeding bacterial indicator standards.

CONCLUSIONS

High levels of Enterococcus in intertidal sediments indicate retention and possible regrowth in this environment.

SIGNIFICANCE AND IMPACT OF THE STUDY

Resuspension of enterococci that are persistent in sediments may cause beach water quality failures and calls into question the specificity of this indicator for determining recent faecal contamination.

Occurrence of antibiotic-resistant enterobacteria in agricultural foodstuffs

Antibiotic-resistant bacteria or their corresponding resistance determinants are known to spread from animals to humans via the food chain. We screened 20 vegetable foods for antibiotic-resistant coliform bacteria and enterococci. Isolates were directly selected on antibiotic-containing selective agar (color detection). Thirteen "common vegetables" (tomato, mushrooms, salad) possessed 10(4)-10(7) cfu/g vegetable of coliform bacteria including only few antibiotic-resistant variants (0-10(5) cfu/g). All seven sprout samples showed a some orders of magnitude higher contamination with coliform bacteria (10(7)-10(9) cfu/g) including a remarkable amount of resistant isolates (up to 10(7) cfu/g). Multiple resistances (up to 9) in single isolates were more common in sprout isolates. Resistant bacteria did not originate from sprout seeds. The most common genera among 92 isolates were: 25 Enterobacter spp. (19 E. cloacae), 22 Citrobacter spp. (8 C. freundii), and 21 Klebsiella spp. (9 K. pneumoniae). Most common resistance phenotypes were: tetracycline (43%), streptomycin (37%), kanamycin (26%), chloramphenicol (29%), co-trimoxazol (9%), and gentamicin (4%). The four gentamicin-resistant isolates were investigated in molecular details. Only three (chloramphenicol) resistant, typical plant-associated enterococci were isolated from overnight enrichment cultures. In conclusion, a contribution of sprouts contaminated with multiresistant, Gram-negative enterobacteria to a common gene pool among human commensal and pathogenic bacteria cannot be excluded.

Antibiotic resistance and genotypic characterization by PFGE of clinical and environmental isolates of enterococci

Fifty-four Enterococcus faecalis and 20 Enterococcus faecium isolates from clinical and non-human sources in Rome, Italy, were characterized by antibiotic resistance and pulsed field gel electrophoresis (PFGE). Resistance to vancomycin, teicoplanin, ampicillin, and ciprofloxacin was more frequent in E. faecium than in E. faecalis, whereas high-level resistance to aminoglycoside was found primarily in E. faecalis. Multi-resistance was found primarily among clinical isolates, but was also observed among environmental isolates. Common genotypes shared among clinical and environmental isolates were observed, however, the majority of isolates occurred as unique, source-specific clones. Several PFGE types were associated with shared features in their antibiotic resistance patterns; evidences of clonal spread between and within wards were also noted. This is the first report indicating clonal relatedness between human and environmental enterococci isolated in Italy.

Differentiation of Enterococcus spp. by cell membrane fatty acid methyl ester profiling, biotyping and ribotyping

AIMS

Gas chromatographic analysis of cell membrane fatty acid methyl esters (FAME), biochemical profiling (biotyping) and EcoRI restriction endonuclease profiling of DNA containing ribosomal RNA sequences (ribotyping) were compared for differentiation of Enterococcus spp.

METHODS AND RESULTS

FAME profiling, biotype profiling and ribotyping of 41 strains from retail Swiss-type cheeses and five strains from culture collections resulted in 17, 25 and 26 groups, respectively, with only two pairs of strains having the same FAME group, biotype profile and ribogroup.

CONCLUSION

Substantial overlap occurred in groupings assigned by the three methods.

SIGNIFICANCE AND IMPACT OF THE STUDY

Differentiation of Enterococcus spp. strains increases if multiple methods are used.

Identification and antibiotic resistance of faecal enterococci isolated from water samples

We have isolated 47 strains of presumptive faecal streptococci from different water samples. Identification was made by the method of Facklam et al. (1989). Antibiotic resistance was studied on Mueller-Hinton Agar. Twelve antibiotics were tested. High-level aminoglycoside resistance (HLAR) and resistance to glycopeptides were studied. Biochemical identification of presumptive faecal streptococci isolates gave the following results: 19 Enterococcus faecalis, 12 E. faecium, 8 E. hirae, 4 E. durans and 4 E. mundtii. E. mundtii is not included among faecal enterococci. None of the strains were resistant to glycopeptides (vancomycin and teicoplanin). Three strains of Enterococci showed HLAR. Two of them were isolated from coastal bathing waters and the other from wastewater. This suggests that water could contribute to spread of HLAR enterococci and it should be a matter of concern for public health authorities.