The Association between Dengue Virus Infection and Liver and Kidney Function among Cambodian Children

Severe liver and kidney dysfunction are prevalent in 10%-30% of the Southeast Asian population. Dengue virus infection has been reported as a modifiable risk factor for liver and kidney dysfunction, especially among children in Southeast Asia. Epidemiologic studies assessing this relationship are sparse, often failed to include children, and did not adjust for important covariates. Therefore, we evaluated the relationship between dengue virus infection and liver and kidney dysfunction among hospitalized children in Cambodia (n=551). Participants with a serologically confirmed dengue virus infection were categorized according to increasing severity of infection (i.e. dengue fever, dengue hemorrhagic fever, or dengue shock syndrome) using clinical assessment. Laboratory assays were used to assess liver (i.e. albumin, alanine aminotransferase (ALT), aspartate aminotransferase (AST), and total protein) and kidney protein levels (i.e. creatinine and urea). Descriptive statistics were used to assess the impact of severity of dengue virus infection on kidney dysfunction. Additionally, descriptive statistics and linear mixed modeling were used to assess the impact of severity of dengue virus infection on liver dysfunction while adjusting for important risk factors. Approximately 75% of all participants had abnormal liver or kidney protein level(s) over the first four days of follow-up. Overall, a negative association was observed between increasing dengue disease severity and albumin (ßadj = -0.08, 95% CI = -0.45 to 0.29), ALT (ßadj = -18.02, 95% CI = -51.59 to 15.55), and AST (ßadj = -7.18, 95% CI = -49.57 to 35.21) protein levels. A positive association was observed between increasing dengue disease severity and total protein levels (ßadj = 7.14, 95% CI = 1.15 to 13.13). While abnormal liver function (increases in ALT and/or AST levels and decreases in albumin and/or total protein levels) is a common clinical finding in dengue infections, we did not find evidence for a significant association with more severe forms of dengue virus infection (i.e. dengue hemorrhagic fever or dengue shock syndrome) and greater liver dysfunction as compared to patients with dengue fever in pediatric populations in Cambodia

Bacteriophages of Lactobacillus

In this review, we are listing Lactobacillus phages that have been reported in peer-reviewed articles published since 1960. Putative phages that are defective or have not been shown to be infectious, such as phage-like particles, are not discussed. Our literature searches led to the identification of 231 Lactobacillus phages, 186 of which have been observed by electron microscopy, with 109 belonging to the Siphoviridae family, 76 to the Myoviridae family, and 1 to the Podoviridae family. Model phages infecting Lb delbrueckii, casei, rhamnosus, plantarum, and gasseri are highlighted, as well as prophages of Lactobacillus hosts. To date, nine complete Lactobacillus phage genomes are available for comparisons and evolution studies. Features such as phage receptors and endolysins are also reviewed, as well as phage-derived genetic tools. Lactobacillus phage research has progressed significantly over the past decade but a thorough understanding of their biology is still lacking. Because of the risks they represent and the knowledge gaps that need to be filled, the outlook for research on Lactobacillus phages is bright

CRISPR-Cas : an efficient tool for genome engineering of virulent bacteriophages

Bacteriophages are now widely recognized as major players in a wide variety of ecosystems. Novel genes are often identified in newly isolated phages as well as in environmental metavirome studies. Most of these novel viral genes have unknown functions but appear to be coding for small, non-structural proteins. To understand their biological role, very efficient genetic tools are required to modify them, especially in the genome of virulent phages. We first show that specific point mutations and large deletions can be engineered in the genome of the virulent phage 2972 using the Streptococcus thermophilus CRISPR-Cas Type II-A system as a selective pressure to increase recombination efficiencies. Of significance, all the plaques tested contained recombinant phages with the desired mutation. Furthermore, we show that the CRISPR-Cas engineering system can be used to efficiently introduce a functional methyltransferase gene into a virulent phage genome. Finally, synthetic CRISPR bacteriophage insensitive mutants were constructed by cloning a spacer-repeat unit in a low-copy vector illustrating the possibility to target multiple regions of the phage genome. Taken together, this data shows that the CRISPR-Cas system is an efficient and adaptable tool for editing the otherwise intractable genomes of virulent phages and to better understand phage-host interactions

Mutational analysis of the antitoxin in the Lactococcal type III toxin-antitoxin system AbiQ

The lactococcal abortive phage infection mechanism AbiQ recently was classified as a type III toxin-antitoxin system in which the toxic protein (ABIQ) is regulated following cleavage of its repeated noncoding RNA antitoxin (antiQ). In this study, we investigated the role of the antitoxin in antiphage activity. The cleavage of antiQ by ABIQ was characterized using 5' rapid amplification of cDNA ends PCR and was located in an adenine-rich region of antiQ. We next generated a series of derivatives with point mutations within antiQ or with various numbers of antiQ repetitions. These modifications were analyzed for their effect on the antiphage activity (efficiency of plaquing) and on the endoribonuclease activity (Northern hybridization). We observed that increasing or reducing the number of antiQ repeats significantly decreased the antiphage activity of the system. Several point mutations had a similar effect on the antiphage activity and were associated with changes in the digestion profile of antiQ. Interestingly, a point mutation in the putative pseudoknot structure of antiQ mutants led to an increased AbiQ antiphage activity, thereby offering a novel way to increase the activity of an abortive infection mechanism

Characterization of a novel panton-valentine leukocidin (PVL) - encoding staphylococcal phage and its naturally PVL-lacking variant

A new siphophage (LH1) was isolated from raw milk using a Staphylococcus aureus ST352 host. Its genome (46,048 bp, 57 open reading frames) includes the two genes encoding Panton-Valentine leukocidin (PVL), a virulence factor usually harbored by S. aureus prophages. Nine structural proteins were identified, including a tail protein generated through a 1 frameshift. A phage lytic mutant was isolated, and its analysis revealed the deletion of genes coding for the PVL and an integrase. The deletion likely occurred through recombination between direct repeats

Bacteriophages of lactic acid bacteria and their impact on milk fermentations

Every biotechnology process that relies on the use of bacteria to make a product or to overproduce a molecule may, at some time, struggle with the presence of virulent phages. For example, phages are the primary cause of fermentation failure in the milk transformation industry. This review focuses on the recent scientific advances in the field of lactic acid bacteria phage research. Three specific topics, namely, the sources of contamination, the detection methods and the control procedures will be discussed

Evolution of Lactococcus lactis phages within a cheese factory

We have sequenced the double-stranded DNA genomes of six lactococcal phages (SL4, CB13, CB14, CB19, CB20, and GR7) from the 936 group that were isolated over a 9-year period from whey samples obtained from a Canadian cheese factory. These six phages infected the same two industrial Lactococcus lactis strains out of 30 tested. The CB14 and GR7 genomes were found to be 100% identical even though they were isolated 14 months apart, indicating that a phage can survive in a cheese plant for more than a year. The other four genomes were related but notably different. The length of the genomes varied from 28,144 to 32,182 bp, and they coded for 51 to 55 open reading frames. All five genomes possessed a 3 overhang cos site that was 11 nucleotides long. Several structural proteins were also identified by nano-high-performance liquid chromatography–tandem mass spectrometry, confirming bioinformatic analyses. Comparative analyses suggested that the most recently isolated phages (CB19 and CB20) were derived, in part, from older phage isolates (CB13 and CB14/GR7). The organization of the five distinct genomes was similar to the previously sequenced lactococcal phage genomes of the 936 group, and from these sequences, a core genome was determined for lactococcal phages of the 936 group

Programming native CRISPR arrays for the generation of targeted immunity

ABSTRACT : The adaptive immune system of prokaryotes, called CRISPR-Cas (clustered regularly interspaced short palindromic repeats and CRISPR-associated genes), results in specific cleavage of invading nucleic acid sequences recognized by the cell’s “memory” of past encounters. Here, we exploited the properties of native CRISPR-Cas systems to program the natural “memorization” process, efficiently generating immunity not only to a bacteriophage or plasmid but to any specifically chosen DNA sequence. IMPORTANCE : CRISPR-Cas systems have entered the public consciousness as genome editing tools due to their readily programmable nature. In industrial settings, natural CRISPR-Cas immunity is already exploited to generate strains resistant to potentially disruptive viruses. However, the natural process by which bacteria acquire new target specificities (adaptation) is difficult to study and manipulate. The target against which immunity is conferred is selected stochastically. By biasing the immunization process, we offer a means to generate customized immunity, as well as provide a new tool to study adaptation