Bacteriophages pass through candle-shaped porous ceramic filters: Application for the collection of viruses in soil water

Despite the ubiquity of viruses in soils, their diversity in soil water has not been explored, mainly due to the difficulty of collecting them. In hydrology, soil water is usually collected using porous candles. This study proposes using these porous candles as a new tool for sampling viruses in soil water to analyze their passage through the ceramic part of the candles. The recovery of the viruses was determined after filtration under laboratory conditions using three model bacteriophages (MS2, ΦX174, and Φ6) and Escherichia coli, at neutral and acidic pH. Then, a field experiment was carried out where soil water filtration and viral identification by metagenomic shotgun were performed. At neutral pH, all bacteriophages tested successfully passed through the porous candles during the filtration process, with reductions of 0.02 log, 0.16 log, and 0.55 log for MS2 ΦX174 and Φ6, respectively. At pH 4.4, the passage of MS2 was not affected while ΦX174 underwent a slight reduction in recovery, probably caused by adsorption onto the filter material. Regarding the application of the porous candles in the field, the results obtained allowed the successful recovery of viruses, exposing porous candles as a new method suitable for the collection of viruses from soil water in the context of the study of viral communities

Investigating the host specificity of Campylobacter jejuni and Campylobacter coli by sequencing gyrase subunit A

Abstract This research evaluated the association between socio demographic characteristics and housing satisfaction of Iranian immigrant’s homeowners in Kuala Lumpur, Malaysia. Data was collected from 325 participants through self-administered questionnaire.  Pearson’s correlation analysis revealed  monthly income of first income earner, total earned income earner, price of residential unit, number of bed room, time owners have been in Malaysia,  had positive significant relationship with housing satisfaction of Iranian immigrants homeowners  in  the study region. Nevertheless, there was no significant association between age, number of bath room, number of dining room, number of living room, length of residence in current house, monthly income of second income earner, number of income earner, number of children, and size of household and housing satisfaction of the immigrant owners’ households. Analysis of variance (ANOVA) indicated that housing satisfaction differed between level of education, level of income, and level of price of residential unit. Independent t-test shown that there was significant difference between gender and housing satisfaction of the participants. These associations indicate that those who are females, higher income, higher education, higher residential unit with more room are more satisfied. It is recommended planners and policy makers should prominence on development of housing conditions of immigrant’s households to increase their housing satisfaction. Keywords:background characteristic, housing satisfaction, housing, immigrant’s homeowner’s household

Investigation of MALDI-TOF Mass Spectrometry for Assessing the Molecular Diversity of Campylobacter jejuni and Comparison with MLST and cgMLST: A Luxembourg One-Health Study

There is a need for active molecular surveillance of human and veterinary Campylobacter infections. However, sequencing of all isolates is associated with high costs and a considerable workload. Thus, there is a need for a straightforward complementary tool to prioritize isolates to sequence. In this study, we proposed to investigate the ability of MALDI-TOF MS to pre-screen C. jejuni genetic diversity in comparison to MLST and cgMLST. A panel of 126 isolates, with 10 clonal complexes (CC), 21 sequence types (ST) and 42 different complex types (CT) determined by the SeqSphere+ cgMLST, were analysed by a MALDI Biotyper, resulting into one average spectra per isolate. Concordance and discriminating ability were evaluated based on protein profiles and different cut-offs. A random forest algorithm was trained to predict STs. With a 94% similarity cut-off, an AWC of 1.000, 0.933 and 0.851 was obtained for MLSTCC, MLSTST and cgMLST profile, respectively. The random forest classifier showed a sensitivity and specificity up to 97.5% to predict four different STs. Protein profiles allowed to predict C. jejuni CCs, STs and CTs at 100%, 93% and 85%, respectively. Machine learning and MALDI-TOF MS could be a fast and inexpensive complementary tool to give an early signal of recurrent C. jejuni on a routine basis

Combination of MALDI-TOF Mass Spectrometry and Machine Learning for Rapid Antimicrobial Resistance Screening: The Case of Campylobacter spp.

While MALDI-TOF mass spectrometry (MS) is widely considered as the reference method for the rapid and inexpensive identification of microorganisms in routine laboratories, less attention has been addressed to its ability for detection of antimicrobial resistance (AMR). Recently, some studies assessed its potential application together with machine learning for the detection of AMR in clinical pathogens. The scope of this study was to investigate MALDI-TOF MS protein mass spectra combined with a prediction approach as an AMR screening tool for relevant foodborne pathogens, such as Campylobacter coli and Campylobacter jejuni. A One-Health panel of 224 C. jejuni and 116 C. coli strains was phenotypically tested for seven antimicrobial resistances, i.e., ciprofloxacin, erythromycin, tetracycline, gentamycin, kanamycin, streptomycin, and ampicillin, independently, and were submitted, after an on- and off-plate protein extraction, to MALDI Biotyper analysis, which yielded one average spectra per isolate and type of extraction. Overall, high performance was observed for classifiers detecting susceptible as well as ciprofloxacin- and tetracycline-resistant isolates. A maximum sensitivity and a precision of 92.3 and 81.2%, respectively, were reached. No significant prediction performance differences were observed between on and off-plate types of protein extractions. Finally, three putative AMR biomarkers for fluoroquinolones, tetracyclines, and aminoglycosides were identified during the current study. Combination of MALDI-TOF MS and machine learning could be an efficient and inexpensive tool to swiftly screen certain AMR in foodborne pathogens, which may enable a rapid initiation of a precise, targeted antibiotic treatment

Chemical contamination in fish species from rivers in the North of Luxembourg: Potential impact on the Eurasian otter (Lutra lutra).

Contamination levels of PCBs, and of the heavy metals cadmium (Cd), lead (Pb) and mercury (Hg) were analyzed in four fish species from seven rivers in the North of Luxembourg. During August and September 2007, 85 samples of fish were collected belonging to four species: the stone loach (Barbatula barbatula, n = 12 pools), the chub (Squalius cephalus, n = 36), the barbel (Barbus barbus, n = 23) and eel (Anguilla anguilla, n = 14). The concentration of seven indicator PCBs (P7PCBs) reached a mean of 39 ng g 1 and varied between 4.0 and 346.2 ng g 1 (wet wt) depending on the site and species. Fish collected at Wal- lendorf on the Our River and sites on the Wiltz and the Clerve rivers showed the highest concentrations for PCBs. In comparison with 1994, PCB levels in fish decreased strongly during the last decade in these rivers. Lead was detected at low levels (0–181.4 ng g 1 wet wt). Mercury concentrations ranged between 10.3 and 534.5ngg 1 (wet wt) exceeding maximum tolerable levels for human consumption of 500 ng g 1 in two fish out of 85. Chubs and eels from the Sûre River were the most contaminated by mer- cury. Cadmium levels varied between 4.0 and 103.9 ng g 1 (wet wt). In addition to mercury in fish, cad- mium was the most problematic pollutant on the Our, the Wiltz, the Clerve and the Troine Rivers, because values found in 20% of fish exceeded the threshold of about 10–50 ng g 1 (wet wt) recommended for human health. The total PCB level predicted to accumulate in livers from otter potentially feeding on these fish based on a previously published mathematical model is 37.7 lg g 1 (lipid wt), which is between a proposed ‘‘safe level” and a ‘‘critical level” for otters. Rivers in the North of Luxembourg are thus to some extent polluted, and the establishment of otter populations could be affected by current levels of contamination.Peer reviewe

The ecological role of ponds in a changing world

The fifth conference of the European Pond Conservation Network (Luxembourg, June 2012) brought together researchers, environmental managers, and other stakeholders with the aim to share stateof-the-art knowledge on the ecology, management, and conservation of ponds in the context of the many challenges facing the wider water environment. Although well-known ecological patterns apply to most ponds in Europe and elsewhere, recent data highlight that part of the environmental variables governing pond biodiversity remain specific to climatic/ biogeographic regions and to elevation ranges, suggesting that, in addition to common practice, management plans should include range-specific measures. Beyond the contribution of individual ponds to the aquatic and terrestrial life, connected networks of ponds are vital in the provision of new climate space as a response to global climate change, by allowing the observed northward and/or upward movements of species. In terms of services, ponds offer sustainable solutions to key issues of water management and climate change such as nutrient retention, rainfall interception, or carbon sequestration. While the ecological role of ponds is now well established, authoritative research-based advice remains needed to inform future direction in the conservation of small water bodies and to further bridge the gap between science and practice

The ecological role of ponds in a changing world

The fifth conference of the European Pond Conservation Network (Luxembourg, June 2012) brought together researchers, environmental managers, and other stakeholders with the aim to share stateof-the-art knowledge on the ecology, management, and conservation of ponds in the context of the many challenges facing the wider water environment. Although well-known ecological patterns apply to most ponds in Europe and elsewhere, recent data highlight that part of the environmental variables governing pond biodiversity remain specific to climatic/ biogeographic regions and to elevation ranges, suggesting that, in addition to common practice, management plans should include range-specific measures. Beyond the contribution of individual ponds to the aquatic and terrestrial life, connected networks of ponds are vital in the provision of new climate space as a response to global climate change, by allowing the observed northward and/or upward movements of species. In terms of services, ponds offer sustainable solutions to key issues of water management and climate change such as nutrient retention, rainfall interception, or carbon sequestration. While the ecological role of ponds is now well established, authoritative research-based advice remains needed to inform future direction in the conservation of small water bodies and to further bridge the gap between science and practice

A Virological Perspective on the Use of Bacteriophages as Hydrological Tracers

Hydrological tracers, commonly used for characterizing water flow paths and sources, do not often meet all the requirements of an ideal tracer. Trans-disciplinary approaches are advocated as the way forward to enlarge the number of tracers available for investigating hydrological processes. Since the 19th century, hydrological tracers have been increasingly used, particularly in underground areas. The tracer toolbox at hand includes a large variety of options, including fluorescent dyes, isotopes, salts or bacteriophages, with each tracer offering specific qualities and complementarities. While their potential for hydrological studies has been studied in karstic environments since the 1960s, bacteriophages remain insufficiently understood. According to the selection methodology used in this review, more than thirty experiments have been listed, involving in total around seventeen different bacteriophages. These have facilitated the investigation of groundwater, surface water (i.e., river, lake and marine water), wetland and wastewater hydrological processes. The tracing experiments have also highlighted the possible interaction between bacteriophages and the surrounding environments. Bacteriophages have successfully helped researchers to understand the water flow within watersheds. Certain advantages, such as the sensitivity of detection, the ease of producing high concentrations of bacteriophages to be injected, their specificity for a host and their non-pathogenicity for human and animal cells, make bacteriophages appreciable tracer candidates for tracing experiments. However, the adsorption process or environmental factors such as temperature, pH and UV light considerably impact the fate of bacteriophages, thereby leading to an attenuation of the phage signal. Considering both the flaws and the qualities of bacteriophages, their use as hydrological tracers requires new insight and further discussions regarding experimental tracing conditions

Contribution of hydrological data to the understanding of the spatio-temporal dynamics of F-specific RNA bacteriophages in river water during rainfall-runoff events

International audienceHeavy rainfall events were previously reported to bring large amounts of microorganisms in surface water, including viruses. However, little information is available on the origin and transport of viral particles in water during such rain events. In this study, an integrative approach combining microbiological and hydrological measurements was investigated to appreciate the dynamics and origins of F-specific RNA bacteriophage fluxes during two distinct rainfall-runoff events. A high frequency sampling (automatic sampler) was set up to monitor the F-specific RNA bacteriophages fluxes at a fine temporal scale during the whole course of the rainfall-runoff events. A total of 276 rainfall-runoff samples were collected and analysed using both infectivity and RT-qPCR assays. The results highlight an increase of 2.5 log(10) and 1.8 log(10) of infectious F-specific RNA bacteriophage fluxes in parallel of an increase of the water flow levels for both events. Faecal pollution was characterised as being mainly from anthropic origin with a significant flux of phage particles belonging to the genogroup II. At the temporal scale, two successive distinct waves of phage pollution were established and identified through the hydrological measurements. The first arrival of phages in the water column was likely to be linked to the resuspension of riverbed sediments that was responsible for a high input of genogroup II. Surface runoff contributed further to the second input of phages, and more particularly of genogroup I. In addition, an important contribution of infectious phage particles has been highlighted. These findings imply the existence of a close relationship between the risk for human health and the viral contamination of flood water. (C) 2016 Luxembourg institute of Science and Technology