Complete Genome Sequence and Methylome Analysis of Micrococcus luteus SA211, a Halophilic, Lithium-Tolerant Actinobacterium from Argentina.

Micrococcus luteus has been found in a wide range of habitats. We report the complete genome sequence and methylome analysis of strain SA211 isolated from a hypersaline, lithium-rich, high-altitude salt flat in Argentina with single-molecule real-time sequencing.

Acanthamoeba in the eye, can the parasite hide even more? Latest developments on the disease.

Acanthamoeba spp. is a free living protozoan in the environment, but can cause serious diseases. Acanthamoeba keratitis (AK), a severe and painful eye infection, must be treated as soon as possible to prevent ulceration of the cornea, loss of visual acuity, and eventually blindness or enucleation. Although the disease affects principally contact lens (CLs) wearers, it is recognized nowadays as a cause of keratitis also in non-CLs wearers. Although the number of infections caused by these amoebae is low, AK is an emerging disease presenting an extended number of cases each year worldwide mostly due to the increasing use of CLs, but also to better diagnostic methods and awareness. There are two principal causes that lead to severe outcomes: misdiagnosis or late diagnosis of the causal agent, and lack of a fully effective therapy due to the existence of a highly resistant cyst stage of Acanthamoeba. Recent studies have reported different genotypes that have not been previously associated with this disease. In addition, Acanthamoeba can act as a reservoir for phylogenetically diverse microorganisms. In this regard, recently giant viruses called Pandoravirus have been found within genotypes producing keratitis. What potential risk this poses is not yet known. This review focuses on an overview of the present status and future prospects of this re-emerging pathology, including features of the parasite, epidemiology, clinical aspects, diagnosis, and treatment.

Tracking novel adenovirus in environmental and human clinical samples: no evidence of endemic human adenovirus type 58 circulation in Córdoba city, Argentina.

In recent years, several types of human adenovirus (HAdV) have arisen from the recombination between two or more previously known HAdV types, but their epidemiology is poorly understood. In this study, we investigated the circulation of HAdV-58, a recently described HAdV isolated from an HIV-positive patient in Córdoba city, Argentina. For this purpose, a 30-month survey was conducted to study the presence of this type of adenovirus in sewage samples collected at the inlet from a wastewater treatment plant in Córdoba city, Argentina. Complementarily, the virus was sought in stools of HIV-positive patients. Although HAdVs were detected in human stool samples and in a high percentage of sewage samples, no evidence of HAdV-58 circulation was detected. We suggest that there is no endemic circulation of HAdV-58 in the geographical local area. The trend is that the number of identified HAdVs increases over time. In this context, understanding the current circulating HAdVs may be biologically relevant.

Evaluation of detachment methods for the enumeration of Bacteroides fragilis in sediments via propidium monoazide quantitative PCR, in comparison with Enterococcus faecalis and Escherichia coli.

AIMS: The aim was to develop an optimized detachment method for separating Bacteroidales from sediments to allow enumeration via PMA-qPCR. The effectiveness of four different detachment treatments in removing Bacteroides fragilis was compared as a function of time as well as in relation to Enterococcus faecalis and Escherichia coli as detected by cultivation and qPCR. METHODS AND RESULTS: Cells were inoculated into four sediments from sea water (SW) and freshwater (FW) beaches. Sediment samples were taken on days 1 and 7 and subjected to four different treatments for separation of micro-organisms. On day 1, the detachment treatments performed equally well in removing intact Bact. fragilis cells. In contrast, 7 days later the detachment treatment with Tween 80 and handshaking (TH) resulted in up to eightfold higher 16S rRNA gene concentrations of intact and total Bact. fragilis cells compared to other detachment treatments. Total Ent. faecalis cells based on the 23S rRNA gene were also preferentially recovered by treatment TH. Cultivable Ent. faecalis or E. coli numbers detached from sediments were similar for all methods in most sediments tested. CONCLUSIONS: Handshaking and 1% Tween 80/NaOH (pH 7·0) eluant was the most efficient technique to recover intact as well as total Bact. fragilis cells in sediment samples with different salinities and after prolonged sediment cell contact time. SIGNIFICANCE AND IMPACT OF THE STUDY: The optimized detachment method enables the application of PMA-qPCR to sediment samples to detect the presence of Bacteroidales cells and their DNA in future microbial source tracking studies.

Analysis of the circulation of hepatitis A virus in Argentina since vaccine introduction.

Hepatitis A virus (HAV) has shown intermediate endemicity in Argentina, but its incidence has decreased since vaccine introduction in 2005. Environmental surveillance was conducted in five rivers from Argentina from 2005 to 2012, complementing clinical information. HAV detection decreased since 2005, although its circulation continues, maintaining viral diversity but not undergoing antigenic drift. Most sequences belonged to subgenotype IA, closely related to Argentinean clinical sequences, but one belonged to proposed subgenotype IC, previously undetected in the country. Environmental surveillance might contribute to monitoring the single-dose vaccination schedule, representing not only strains causing disease but also the circulating population and the viral introductions.

Water quality issues and infant diarrhoea in a South American province.

In the province of Salta, in the Northwest region of Argentina, almost two-thirds of the population live in absolute poverty, and diseases associated with poverty are rampant. Almost 12% of the total population of the province are children below 5 years of age; almost half of these infants are living in situations where the basic necessities are not available. Primitive sanitary conditions, including widespread contamination of available water supplies with pathogens, contribute to a major public health problem. Infant mortality was 17% higher for Salta than for Argentina as a whole in 2001. A major cause of death for these children is infectious disease, especially respiratory and intestinal diseases. In Salta, more than half of the total population of infants is affected by diarrhoea annually. The infectious pathogens are diverse: bacteria (predominantly in spring and summer), viruses (especially in the winter) and parasites (endemic in some situations). This paper evaluates current methods used to test for the presence of pathogens in drinking water; discusses why these methods are less than adequate; documents an episode of contamination in a local water supply source; and suggests appropriate methods that can be used to better address this major public health issue effectively.

Molecular quantitative analysis of human viruses in California stormwater.

Many human pathogenic viruses are transmitted via the oral-fecal route and water is one possible vector, representing a risk for public health. Sixty-one large-volume water samples from storm drains in California were processed by a two-step hollow fiber ultrafiltration procedure followed by molecular analysis for human enterovirus and adenovirus types. Each sample was spiked with a surrogate, the benign bacteriophage PP7. Both surrogate and human viruses were quantified by newly designed TaqMan PCR assays. Equations were developed that account for the main variables in the procedure: recovery of the ultrafiltration, efficiency of nucleic acid extraction, and effect of inhibitors on the amplification of viral targets. Adenovirus 40/41 was detected in one sample at 230 genomes per liter, and no other adenovirus or enterovirus types were found. Samples that resulted in nondetects are reported together with the corresponding sample-specific limit of detection (S(LOD)), a useful tool when estimating the public health risk associated with the contact or ingestion of water. Virus concentrations did not correlate with traditional viable indicator concentrations or any of the physicochemical parameters measured. In contrast, coliform concentrations were correlated with total suspended solids. To our knowledge, this is the first study where all factors known to influence limits of detection have been investigated and integrated into equations that are widely applicable to the quantification of viruses or other microbial targets by PCR.

Detection of Salmonella spp. in water using magnetic capture hybridization combined with PCR or real-time PCR.

The removal of target DNA by magnetic capture hybridization (MCH) from constituents inhibitory to amplification by polymerase chain reaction (PCR) was evaluated using Salmonella as the test pathogen. Hybrids were subjected to both conventional and quantitative real-time PCR (qPCR). When PCR inhibitors commonly found in water were added to the reaction, MCH-PCR increased the detection sensitivity on the order of 8 to 2,000-fold compared with the system using only PCR. To determine the selectivity of MCH for target DNA (Salmonella), different amounts of non-target DNA (Escherichia coli) were added to the qPCR reaction. The highest non-target DNA concentration interfered with the amplification by qPCR alone, while MCH-qPCR was unaffected. Average recovery of Salmonella DNA by MCH-qPCR was 31% using optimized buffers, washing solutions and enzymatic digestion. A recovery function was proposed in order to calculate the real cell number based on the measured value. Preliminary testing confirmed the suitability of this method for analysis of natural waters.

Exocellular hydrolases from Penicillium ulaiense.

Penicillium ulaiense exhibited carboxymethylcellulase, pectinase, protease, amylase and phenolase activities, while no xylanase, cellulase, lipase or ligninase activities were found. Pectinolytic action was studied in liquid medium, showing low levels of pectinesterase and pectinase production. No mycotoxins were detected by thin-layer-chromatography.