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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.
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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.
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Vírus da Dengue/genética , Genótipo , Filogenia , RNA Viral/genética , Dengue Grave/epidemiologia , Adolescente , Adulto , Criança , Vírus da Dengue/classificação , Vírus da Dengue/isolamento & purificação , Evolução Molecular , Feminino , Efeito Fundador , Variação Genética , Humanos , Masculino , México/epidemiologia , Pessoa de Meia-Idade , Epidemiologia Molecular , Filogeografia , Dengue Grave/diagnóstico , Dengue Grave/patologia , Dengue Grave/virologiaRESUMO
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.
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Rabies is an infectious viral disease that is practically always fatal following the onset of clinical signs. In Mexico, the last case of human rabies transmitted by dogs was reported in 2006 and canine rabies has declined significantly due to vaccination campaigns implemented in the country. Here we report on the molecular characterization of six rabies virus strains found in Yucatan and Chiapas, remarkably, four of them showed an atypical reaction pattern when antigenic characterization with a reduced panel of eight monoclonal antibodies was performed. Phylogenetic analyses on the RNA sequences unveiled that the three atypical strains from Yucatan are associated with skunks. Analysis using the virus entire genome showed that they belong to a different lineage distinct from the variants described for this animal species in Mexico. The Chiapas atypical strain was grouped in a lineage that was considered extinct, while the others are clustered within classic dog variants.
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Doenças do Cão/epidemiologia , Doenças do Cão/virologia , Genótipo , Vírus da Raiva/classificação , Vírus da Raiva/genética , Raiva/veterinária , Animais , Análise por Conglomerados , Transmissão de Doença Infecciosa , Vetores de Doenças , Doenças do Cão/transmissão , Cães , Humanos , Mephitidae/virologia , México/epidemiologia , Epidemiologia Molecular , Filogenia , RNA Viral/genética , Raiva/epidemiologia , Raiva/transmissão , Raiva/virologia , Vírus da Raiva/isolamento & purificação , Análise de Sequência de DNARESUMO
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.
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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.
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Técnicas de Tipagem Bacteriana , Cólera/microbiologia , DNA Bacteriano/química , Genoma Bacteriano , Análise de Sequência de DNA , Vibrio cholerae O1/classificação , Vibrio cholerae O1/isolamento & purificação , Adolescente , Adulto , Idoso , Idoso de 80 Anos ou mais , Criança , Pré-Escolar , Cólera/epidemiologia , DNA Bacteriano/genética , Surtos de Doenças , Feminino , Ordem dos Genes , Humanos , Masculino , México/epidemiologia , Pessoa de Meia-Idade , Sintenia , Vibrio cholerae O1/genética , Vibrio cholerae O1/fisiologia , Adulto JovemRESUMO
We identified 25 autochthonous chikungunya virus cases in Mexico, initially detected by RT-PCR targeting the E1 gene and propagated in C6/36 Aedes albopictus cells, in 2014. To determine the type of virus found, in a previous report, the genomes of 2 CHIKV strains were fully sequenced. Genome sequence analysis revealed that these isolates from Mexico belonged to the Asian genotype, and a phylogenetic association with the circulating strain in the British Virgin Islands was also established in the same year. This was further supported by changes in specific amino acids, E2-V368A and 6K-L20M. For these reasons, it can be inferred that the route of virus entry to Mexico was held across the countries in the Caribbean and Central America. The presence of E1-A226V mutation associated with more efficient replication in the salivary gland of the A. albopictus mosquito was not observed. Interestingly, a newly acquired NSP4-S399C mutation was observed; however, the significance of changes in amino acid found in non-structural proteins in autochthonous strains remains to be elucidated.
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Febre de Chikungunya/virologia , Vírus Chikungunya/genética , Vírus Chikungunya/isolamento & purificação , Genoma Viral , Sequência de Aminoácidos , Ásia , Genótipo , México , Dados de Sequência Molecular , Especificidade da EspécieRESUMO
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.
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Líquido Cefalorraquidiano/microbiologia , Meningite/microbiologia , Metagenômica , Infecções por Moraxellaceae/microbiologia , Psychrobacter/genética , Adolescente , Sequência de Bases , Evolução Fatal , Genoma Bacteriano/genética , Humanos , Masculino , Meningite/líquido cefalorraquidiano , México , Dados de Sequência Molecular , Infecções por Moraxellaceae/líquido cefalorraquidiano , Filogenia , Psychrobacter/classificação , Psychrobacter/isolamento & purificação , RNA Ribossômico 16S/genética , Fatores de Virulência/genéticaRESUMO
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.
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The mosquito-borne chikungunya virus, an alphavirus of the Togaviridae family, is responsible for acute polyarthralgia epidemics. Here, we report the complete genome sequences of two chikungunya virus strains, InDRE04 and InDRE51, identified in the Mexican states of Jalisco and Chiapas in 2014. Phylogenetic analysis showed that both strains belong to the Asian genotype.