Fatal Psychrobacter sp. infection in a pediatric patient with meningitis identified by metagenomic next-generation sequencing in cerebrospinal fluid.

The genus Psychrobacter contains environmental, psychrophilic and halotolerant gram-negative bacteria considered rare opportunistic pathogens in humans. Metagenomics was performed on the cerebrospinal fluid (CSF) of a pediatric patient with meningitis. Nucleic acids were extracted, randomly amplified, and sequenced with the 454 GS FLX Titanium next-generation sequencing (NGS) system. Sequencing reads were assembled, and potential virulence genes were predicted. Phylogenomic and phylogenetic studies were performed. Psychrobacter sp. 310 was identified, and several virulence genes characteristic of pathogenic bacteria were found. The phylogenomic study and 16S rRNA gene phylogenetic analysis showed that the closest relative of Psychrobacter sp. 310 was Psychrobacter sanguinis. To our knowledge, this is the first report of a meningitis case associated with Psychrobacter sp. identified by NGS metagenomics in CSF from a pediatric patient. The metagenomic strategy based on NGS was a powerful tool to identify a rare unknown pathogen in a clinical case.

Is ultra-violet radiation the main force shaping molecular evolution of varicella-zoster virus?

BACKGROUND: Varicella (chickenpox) exhibits a characteristic epidemiological pattern which is associated with climate. In general, primary infections in tropical regions are comparatively less frequent among children than in temperate regions. This peculiarity regarding varicella-zoster virus (VZV) infection among certain age groups in tropical regions results in increased susceptibility during adulthood in these regions. Moreover, this disease shows a cyclic behavior in which the number of cases increases significantly during winter and spring. This observation further supports the participation of environmental factors in global epidemiology of chickenpox. However, the underlying mechanisms responsible for this distinctive disease behavior are not understood completely. In a recent publication, Philip S. Rice has put forward an interesting hypothesis suggesting that ultra-violet (UV) radiation is the major environmental factor driving the molecular evolution of VZV. DISCUSSION: While we welcomed the attempt to explain the mechanisms controlling VZV transmission and distribution, we argue that Rice's hypothesis takes lightly the circulation of the so called "temperate VZV genotypes" in tropical regions and, to certain degree, overlooks the predominance of such lineages in certain non-temperate areas. Here, we further discuss and present new information about the overwhelming dominance of temperate VZV genotypes in Mexico regardless of geographical location and climate. SUMMARY: UV radiation does not satisfactorily explain the distribution of VZV genotypes in different tropical and temperate regions of Mexico. Additionally, the cyclic behavior of varicella does not shown significant differences between regions with different climates in the country. More studies should be conducted to identify the factors directly involved in viral spreading. A better understanding of the modes of transmissions exploited by VZV and their effect on viral fitness is likely to facilitate the implementation of preventive measures for disease control.

Simultaneous cocirculation of both European varicella-zoster virus genotypes (E1 and E2) in Mexico city.

Full-length genome analysis of varicella-zoster virus (VZV) has shown that viral strains can be classified into seven different genotypes: European (E), Mosaic (M), and Japanese (J), and the E and M genotypes can be further subclassified into E1, E2, and M1 through 4, respectively. The distribution of the main VZV genotypes in Mexico was described earlier, demonstrating the predominance of E genotype, although other genotypes (M1 and M4) were also identified. However, no information regarding the circulation of either E genotype in the country is available. In the present study, we confirm the presence of both E1 and E2 genotypes in the country and explore the possibility of coinfection as the triggering factor for increased virulence among severe cases. A total of 61 different European VZV isolates collected in the Mexico City metropolitan area from 2005 to 2006 were typed by using a PCR method based on genotype-specific primer amplification. Fifty isolates belonged to the E1 genotype, and the eleven remaining samples were classified as E2 genotypes. No coinfection with both E genotypes was identified among these specimens. We provide here new information on the distribution of VZV genotypes circulating in Mexico City.

Monoarthritis of the knee with unusual lesions in adults associated with varicella-zoster virus infection.

Varicella-zoster virus-associated arthritis has not been well documented in adults. We present the case of a 27-year-old female patient with monoarthritis of the knee associated with clinical symptoms typical of varicella. Arthroscopic examination showed unusual oval and circular lesions in cartilage, some of which measured 5 +/- 3 mm in diameter in weight-supporting zones. Such lesions have not been described previously and were type III-A lesions on the Noyes scale or grade IV on the Outerbridge scale. On microscopic observation, synovial fluid cultures and hemocultures were negative for the presence of bacteria. A biopsy sample and synovial liquid from the affected knee produced a positive polymerase chain reaction for varicella-zoster virus, genotype E. These findings suggest a strong relation between clinical varicella infection and important lesion invasion in the knee articulation of such a young adult, probably related to the virus. However, it remains necessary to corroborate this relation between cartilage destruction and clinical symptoms of varicella associated with monoarthritis of an adult knee. Nevertheless, it is advisable to initiate the appropriate antiviral treatment in adults with varicella-related gonalgia because the lesions produce the most severe effects on exposure to the knee bone.

Analysis of human rotavirus G1P[8] strains by RFLP reveals higher genetic drift in the VP7 than the VP4 gene during a 4-year period in Mexico.

Several studies have demonstrated that rotaviruses of the G1P[8] genotype are among the most important worldwide. Sequence analysis of G1P[8] strains has revealed high genetic variability of VP4 and VP7 genes. The aim of this study was to investigate by restriction fragment length polymorphism (RFLP) analysis the genetic variability of the VP7 and VP4 genes within rotaviruses of the G1P[8] genotype. A total of 60 rotavirus-positive fecal samples genotyped as G1P[8], were collected from children with acute diarrhea under 5 years of age, between October 1995 and October 1998. The VP7 and VP4 genes were amplified by RT/PCR, using the Beg9/End9 primer pair and the Con3 and Con2 primers, respectively. VP7 amplicons were digested with three restriction enzymes Hae III, Taq I and Rsa I in separate reactions and VP4 amplicons were digested similarly with endonucleases Hinf I, Sau96 I and Rsa I. Analysis of the digested VP7 and VP4 amplicons showed a higher genetic drift for the VP7 gene (18 RFLPs) compared to the VP4 gene (9 RFLPs). The combination of profiles for both VP7 and VP4 amplicons, showed 27 different patterns, none of them similar to the Wa-1 strain. Furthermore, RFLP analysis of these G1P[8] strains, clearly differentiated the viruses into two main clusters, both of them sharing the same restriction pattern for the VP4 gene, and a different one for the VP7 gene.

Full-Genome Sequence of a Novel Varicella-Zoster Virus Clade Isolated in Mexico.

Varicella-zoster virus (VZV) is a member of the Herpesviridae family, which causes varicella (chicken pox) and herpes zoster (shingles) in humans. Here, we report the complete genome sequence of varicella-zoster virus, isolated from a vesicular fluid sample, revealing the circulation of VZV clade VIII in Mexico.

Genetic variation of Varicella-Zoster Virus strains circulating in Mexico City.

BACKGROUND: Different studies regarding VZV genotype distribution worldwide have demonstrated that genetic diversity and epidemiology of infection significantly vary from region to region. In Mexico, VZV genotype distribution is largely unknown mostly due to the lack of a surveillance system that monitors accurately the presence of viral strains circulating in the country. OBJECTIVE: To identify the main VZV genotypes circulating in the metropolitan area of Mexico City. STUDY DESIGN: In this study, 127 different VZV isolates, obtained from residents of the Mexico City Metropolitan area from 2005 to 2008, were identified and genotyped. Viral detection and preliminary genotyping was performed by amplification of the VZV ORF-38 and -54 and RFLP analysis using PstI and BglI endonuclease restriction patterns, respectively. Genotype was confirmed by nucleotide sequence variation along the ORF-22. RESULTS: RFLP analysis classified 121 viral strains as European and 6 as mosaic genotype. Genotyping scheme based on the ORF-22 sequence variation identified 120 viral strains belonging to the E genotype, 6 M1 and 1 M4 genotype strains. CONCLUSIONS: VZV European genotype appears to predominate in Mexico City. This is the first study addressing VZV genotype distribution in Mexico. The information reported in this paper may be useful for future epidemiological studies conducted in the country and also contributes to understand better the molecular epidemiology of VZV in the Americas.