DNA microarrays to identify etiological agents, as sensors of environmental wellbeing.

Background: The epidemiologic transition in Mexico has generated a change of paradigm in public health. Morbidity is characterized by infectious diseases and the mortality is due to chronic degenerative diseases. The three most important infectious diseases in the country are: respiratory infections, diarrhea, and urinary tract infections. Method: The objective of this work was to build a tool to monitor the presence of health risks in the environment in a timely manner and to demonstrate its application in different sicknesses, especially those that are water related. In this study, we analyzed water samples from five cenotes with high tourist flow in the State of Yucatan. We developed a DNA microarray for the adequate and prompt detection of viruses, bacteria, fungi, and parasites. This microarray could be used in samples of different origin including air, water (fresh, brackish and saltwater), food, inert surfaces or wounds. Clinically, it would allow prompt and precise detection of etiological agents of infectious diseases to prevent outbreaks. It would also be useful for the identification of those agents that cannot be detected in our laboratories with the traditional methods. It includes 38,000 probes that detect 252 etiological agents of diseases in humans and antimicrobial resistance genes. Results from DNA samples can be obtained in 24 h, which would be difficult or impossible using other technologies. Results: The results are readily available within 24 h. Samples from five cenotes (sinkholes) with high flow of people, were analyzed with the microarray. The water samples analyzed detected 228 different bacteria, viruses, fungi, and protozoa. They are amongst the most important etiological agents for infectious diseases in Mexico. Conclusions: The microarray provides the opportunity for precise and early detection of various infectious agents in individuals, hospitals and natural environments. This could help reduce the global burden of diseases, the severity of outbreaks, and reduce antibiotic resistance.

Influence of bacterial biopolymers on physical properties of experimental limestone blocks.

This article describes the consolidation effects of bacterial biopolymers synthesized by biofilm bacteria colonizing Mayan limestone buildings on the surface properties of limestone blocks, including disaggregation, hardness, and total color change at the laboratory level. The biopolymers evaluated, produced by bacterial isolates TM1B-488, TM1B-489, TM1B-349, and TM1B-464, influenced surface properties at different levels. 16S rRNA gene sequences analysis showed that isolate TM1B-349 was related with Psychrobacter sp. strain Marseille P-5312, TM1B-464 was related with Agrococcus terreus strain BT116, and isolates TM1B-488 and TM1B-489 were related with Xanthomonas citri pv. mangiferaeindicae strain XC01. Biopolymer A reduced the surface disaggregation of the material (26%) compared to the untreated control, as revealed by the peeling test, followed by biopolymer B (10%), while the remaining biopolymers had a negligible effect. The cactus biopolymer reduced disaggregation at higher levels (37%). On the other hand, there was a similar concomitant increase in surface hardness of limestone samples coated with biopolymer A (34%) and biopolymer B (32%), higher than biopolymers C (10%) and D (19%). Total color change for all treatments was below the threshold value of 5, indicating a non-significant color alteration. Partial chemical characterization of best-performing biopolymer (A) suggests its probable glycoprotein nature, whose constitutive acidic monosaccharides probably contributed to higher adherence to the limestone surfaces, contributing to surface stabilization, hardening the surface, and decreasing surface decohesion. These preliminary findings suggest its potential application in bioconsolidants, but further studies are required.

Genotypic variability analysis of DENV-1 in Mexico reveals the presence of a novel Mexican lineage.

Here, we report for the first time the circulation of dengue virus type 1 (DENV-1) belonging to the lineage IV of genotype V (African American genotype) based on phylogenetic analysis of nucleotide sequences from 10 DENV-1-positive samples obtained in Mexico between 2012 and 2014. Our data revealed that the lineages III and IV of DENV-1 genotype V were found circulating during the same period, probably explaining the rise in the number of cases of severe dengue during that period.

Genome Sequence of a Rabies Virus Isolated from a Dog in Chiapas, Mexico, 2013.

Rabies virus (RABV), a member of the genus Lyssavirus, causes encephalitis that is almost always fatal following the onset of clinical signs. Here, we report the complete codifying sequence of an RABV isolated from a dog in Mexico. Molecular data showed that this strain belongs to the Chiapas lineage.

Complete Genome Sequence of Hepatitis B Virus Genotype E, the First Molecular Characterization from an Imported Case in Mexico.

Hepatitis B virus infection is currently a global public health problem. Here, we present the first characterization and complete genome sequence of a strain belonging to genotype E in Mexico, obtained from a foreign carrier with chronic infection.

Biochemical and full genome sequence analyses of clinical Vibrio cholerae isolates in Mexico reveals the presence of novel V. cholerae strains.

The first week of September 2013, the National Epidemiological Surveillance System identified two cases of cholera in Mexico City. The cultures of both samples were confirmed as Vibrio cholerae serogroup O1, serotype Ogawa, biotype El Tor. Initial analyses by PFGE and by PCR-amplification of the virulence genes, suggested that both strains were similar, but different from those previously reported in Mexico. The following week, four more cases were identified in a community in the state of Hidalgo, located 121 km northeast of Mexico City. Thereafter a cholera outbreak started in the region of La Huasteca. Genomic analyses of the four strains obtained in this study confirmed the presence of Pathogenicity Islands VPI-1 and -2, VSP-1 and -2, and of the integrative element SXT. The genomic structure of the 4 isolates was similar to that of V. cholerae strain 2010 EL-1786, identified during the epidemic in Haiti in 2010.

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.

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.