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Introduction: Infections acquired in hospitals are the cause of high morbidity and mortality and with the emergence of resistant bacteria, the problem is greater. The aim of this work was to determine the genetic characteristics and timeline of Klebsiella pneumoniae blaNDM-1 carrying a class 1 integron involved in an intrahospital outbreak. Methodology: Investigation was made from the first detection of K. pneumoniae blaNDM-1, strain “466”, and the last clone “423”. 16S rRNA gene analysis showed that 466 strain and clones were related to K. pneumoniae. Extended-spectrum β-lactamases (ESBL) was detected according to the Clinical and Laboratory Standards Institute (CLSI) and real time-PCR. Typing of K. pneumoniae blaNDM-1 strains was carried by ERIC-PCR and sequencing the variable region of the integrons were performed. Results: A cluster of six resistant isolates of K. pneumoniae blaNDM-1 was detected in intensive care unit (ICU), internal medicine (IM) and orthopedics (OT). Timeline revealed that the first bacterial identification was in ICU and the last clone in OT service. The array genetic of variable region was “IntI/aadA5-drfA17/qacEΔ1-Sul1”. Conclusions: The evidences highlight the importance of the epidemiological surveillance of Extended-spectrum β-lactamases (ESBL) strains, as well as the need for molecular epidemiological studies to identify the routes of transmission and the contamination sources within health personnel.

In 2014, the chikungunya virus (CHIKV) was detected for the first time in Mexico, the identified strain was the one corresponding to the Asian genotype which was phylogenetically grouped with the strains that circulated in the British Virgin Islands outbreak and was later classified with lineages of Caribbean strains. In three years, 13,569 cases of chikungunya were registered in Mexico. Although the transmission and spread of the virus are now considered a moderate risk, the danger that the virus reemerges is not ruled out due to the infestation of Aedes mosquitoes. In this study, we reviewed the chikungunya fever (CHIKF) cases reported between 2014 and 2016 to reanalyze the data. Seventeen cases were selected from different states where the circulation of the virus had been reported. Statistical data were analyzed and a retrospective analysis was carried out. Nucleic acid sequences were determined of these 17 samples. 2015 was the year with the highest number of cases (92.8%) and they were detected in 28 states of the country. There is a predominance of females, and the most affected age group was between 25 and 44 years. In 2016, CHIKV genotypes were not known, in this study the presence of the Asian genotype of Caribbean lineage was confirmed. The presence of the West African and ECSA genotypes was phylogenetically ruled out. The sequences obtained were deposited in GeneBank.

Cases of acute haemorrhagic conjunctivitis (AHC) caused by a coxsackie virus A24 variant (CV-A24v) in Mexico have been reported since 1987; however, no molecular data on the causative strains have been available. Here, we report the identification of the etiological agent responsible for the most recent AHC outbreak in southeastern Mexico (at the end of 2017) as well as the complete genome sequences of seven isolates, using next-generation sequencing (NGS). Phylogenomic analysis of the CV-A24v sequences reported here showed similarity to contemporary strains causing AHC outbreaks in French Guiana and Uganda, forming a novel clade related to genotype IV. Moreover, a specific mutational pattern in the non-structural proteins was identified in the 2017 isolates. This is the first report of genetic characterization of CV-A24v isolates obtained in Mexico.

Class D β-lactamases OXA-232 and OXA-48 hydrolyze penicillin, cephalosporins and carbapenems, limiting the pharmacological therapeutics in bacteraemia. OXA producer microorganisms are considered a great emergent threat, especially in nosocomial environments. To determine the resistance profile and genomic characterization of two isolates initially identified as potential carbapenemase-producer Klebsiella oxytoca in a third level hospital. Automated platform BD Phoenix-100 System was used to identify and to biochemically characterize both isolates. Furthermore, the resistance profile was determined through CLSI methods and the whole genome sequences were obtained using Next-Generation Sequencing. Resistance genes were analyzed, and the virtual fingerprinting was determined to corroborate the similarity with related bacteria. Both strains correspond to Raoultella ornithinolytica carrying OXA 232 and OXA-48 genes, confirming the class D β-lactamases assay results. Here, we present the genetic and phenotypic analysis of multidrug resistance R. ornithinolytica, representing the first report in Mexico.

The Papillomaviridae family is probably the most diverse group of viruses that affect vertebrates. The study of the relationship between infection by certain types of human papillomavirus (HPV) and the development of neoplastic epithelial lesions is of particular interest because of the high prevalence of HPV-related carcinomas in populations of developing countries. To understand the mechanisms of infection and their association with different clinical manifestations, molecular tools play an important role in the description of new types of HPV, the characterization of effector properties of the viral factors, the specific diagnosis and monitoring of HPV types, and the alteration patterns at genetic level in the host. Technological advances in the field of DNA sequencing have led to the development of different next-generation sequencing systems, allowing obtaining a large amount of data and broadening the applications to study viral diseases. In this review, we summarize the main approaches and their perspectives where the use of massively parallel sequencing has been proved as a useful tool in the research of the HPV infection.

Human papillomavirus genotype 16 (HPV16) is the most frequent high-risk HPV (HR-HPV) identified in cervical precursor lesions and cervical cancer (CC) worldwide. The oncogenic potential of HPV16 is partly dependent on the lineage involved in the infection and the presence of clinically relevant mutations. In this report, we present the distribution of HR-HPV and the mutational profile and intra-host variability of HPV16 lineages, based on analysis of the long control region (LCR) and the E6 gene in samples with normal cytology (n = 39), squamous intraepithelial lesions (n = 25), and CC (n = 39). HR-HPV genotyping was performed using multiplex real-time PCR. HPV16 lineage assignments and mutation frequencies were determined by conventional PCR and Sanger DNA sequencing, and intra-patient viral populations were analyzed using next-generation sequencing (NGS). The most frequent HR-HPV type was HPV16, followed by HPV31 and HPV18. The frequency of HPV16 sublineages was A1/A2 > D2 > D3 and B1. Moreover, the most frequent mutations, both in samples from this study and in the available sequences from Mexican isolates in the GenBank database were LCR-G7518A, which is involved in carcinogenesis, and E6-T350G (producing L83V), associated with persistence of infection. Otherwise, deep sequencing revealed high conservation of viral lineages and mutations, independently of the stages studied. In conclusion, the high frequency and stability of these molecular markers, as well as the circulating viral lineages, could be related to the incidence of CC associated with HPV16. Hence, they deserve a broader analysis to determine the risk of specific populations for progression of the disease.

Introduccion: La reemergencia de las infecciones por Enterovirus D68 (EV-D68) se reporto en los EE.UU. desde agosto-octubre de 2014 (691 casos). En Mexico, un brote se reporto en el Instituto Nacional de Enfermedades Respiratorias (24 casos). Se presentan los resultados de la vigilancia epidemiologica en un hospital pediatrico nacional de tercer nivel para Enterovirus sp. (EV) y otros virus respiratorios. Metodo: Tras la alerta emitida por la reemergencia del EV-D68 en 2014, la vigilancia epidemiologica -que solo detectaba virus respiratorios mediante PCR en pacientes con enfermedad tipo influenza mediante toma de hisopados nasofaringeos- se expandio para incluir ninos con exacerbacion de asma o dificultad respiratoria aguda. Las muestras positivas para EV fueron confirmadas y tipificadas por secuenciacion. Posteriormente, se utilizo secuenciacion de siguiente generacion para obtener el genoma viral completo. Resultados: De 1705 muestras, 13 fueron positivas para EV. Los pacientes con EV presentaron la siguiente comorbilidad: enfermedad pulmonar cronica (7.7%), enfermedad neoplasica (15.4%), asma/rinitis alergica (23%), neumonias de repeticion (23%), y otras (23%). De las 13 muestras positivas para EV, tres resultaron positivas para EV-D68. Dichos casos requirieron ventilacion mecanica invasiva, no tuvieron afectacion neurologica y sobrevivieron. Conclusiones: La afectacion por EV-D68 de la poblacion estudiada fue menor que lo reportado en Mexico durante el mismo periodo. Los casos de infeccion por EV-D68 presentan diversa comorbilidad, aunque escasas enfermedades pulmonares, lo cual pudiera explicar la baja tasa de ataque. La presencia del sistema de vigilancia epidemiologica establecido y la prevencion de infecciones pudieron haber contenido el brote

Background Human enterovirus D68 (EV‐D68) recently caused an increase in mild‐to‐severe pediatric respiratory cases in North America and some European countries. Even though few of these children presented with acute paralytic disease, direct causal relationship cannot yet be assumed. Objectives The purposes of this report were to describe the clinical findings of an outbreak of EV‐D68 infection in Mexico City and identify the genetic relationship with previously reported strains. Patients/Methods Between September and December 2014, 126 nasopharyngeal samples (NPS) of hospitalized children

Hepatitis B virus genotype F (HBV/F) is endemic in Central and South America with a minor proportion in Mexico and North America. HBV/F is divided into subgenotypes and subtypes with particular geographic circulation patterns. Here, we report the complete genome sequence and molecular characterization of HBV/F from three isolates. Phylogenetic analysis with all available HBV/F sequences showed that our sequences belonged to the F1b subtype and, in addition, the absence of the previously reported F1a subtype in Mexican isolates. Our findings suggest the circulation of HBV/F1b, the first phylogenomic study of HBV/F in Mexico.

To the Editor: Zika virus is an emerging arbovirus spread by Aedes aegypti mosquitoes and belongs to the genus Flavivirus of the Spondweni serocomplex (1,2). Most often, signs and symptoms of infection are maculopapular rash, fever, arthralgia, myalgia, headache, and conjunctivitis; edema, sore throat, cough, and vomiting occur less frequently. Zika virus is an RNA virus containing 10,794 nt, and diagnostic tests include PCRs on acute-phase serum samples to detect viral RNA (1). The genome contains 5′ and 3′ untranslated regions flanking a single open reading frame (ORF) that encodes a polyprotein that is cleaved into the structural proteins capsid (C), premembrane/membrane (prM), and envelope (E), and 8 non-structural proteins (NS1, NS2A, NS2B, NS3, NS4A, 2K, NS4B, and NS5) (3). Genetic studies in which nucleotide sequences derived from the NS5 gene were used indicated 3 Zika virus lineages: East African, West African, and Asian (4,5). In Brazil, the first identified cases of dengue-like syndrome with subsequent Zika virus confirmation were documented in the early months of 2015 in the state of Rio Grande do Norte (6). Later that year, autochthonous transmission was reported in Colombia and Suriname during October–November (5) and Puerto Rico in December (6,7). During the same period, imported cases in the United States and Mexico were reported (6). By December 2015, we had already identified at least 15 autochthonous and 1 imported Zika cases in Mexico, initially detected by real-time reverse transcription PCR (RT-PCR). Here, we report on the documentation of a case of Zika virus infection in a male traveler returning to Mexico from Colombia in October 2015. On October 21, 2015, we identified an imported case of Zika virus infection in the central state of Queretaro, Mexico. The patient, a 26-year-old man, had visited Santa Martha, Colombia, during the previous 12 days. Symptoms including fever, muscle pain, mild to moderate arthralgia, arthritis, back pain, chills, and conjunctivitis began on October 19, two days after his return to Mexico. A sample was collected at a primary healthcare clinic. Initial molecular testing for dengue virus at the Queretaro Public Health Laboratory was negative; to test for Zika virus, the sample was sent to the National Reference Laboratory (InDRE), where viral RNA was extracted from it by using the QIAamp Viral RNA Mini Kit (QIAGEN, Hilden, Germany). We used real-time RT-PCR for diagnosis, using the Superscript III system (Invitrogen, Carlsbad, CA, USA) and primers and probes previously reported (8). Using Zika virus nucleotide sequence data in the Primer3Plus web interface (8), we amplified a 760-bp fragment with the following primers for partial characterization of viral NS5 coding gene: ZikV9113Fwd TTYGAAGCCCTTGGATTCTT and ZikV9872Rev CYCGGCCAATCAGTTCATC. We used the QIAGEN One-Step RT-PCR Kit as follows: reverse transcription at 50°C for 30 min, followed by an activation step at 95°C for 15 min and 35 cycles of 94°C for 30 sec, 55°C for 30 sec, and 72°C for 1 min, and a final extension step at 72°C for 10 min. We sequenced amplicons in the ABI PRISM 3130xl Genetic Analyzer instrument using the BigDye Terminator v3.1 Cycle Sequencing kit (Applied Biosystems, Foster City, CA). The partial sequence of the identified strain ((MEX/InDRE/14/2015) was deposited in GenBank under accession no. {"type":"entrez-nucleotide","attrs":{"text":"KU556802","term_id":"984943318","term_text":"KU556802"}}KU556802. We performed phylogenetic analysis to compare the extracted sequences with a database of 39 available nucleotide sequences from GenBank (Figure). Sequences from NS5 data were aligned, the dataset was adjusted to a common size of 531 pb, and a phylogenetic tree was constructed in MEGA6 (http://www.megasoftware.net) from aligned nucleotide sequences. The maximum-likelihood statistical algorithm and the Tamura-Nei substitution model with 1,000 replicates for bootstrap were used. Phylogenetic analyses showed that the partially sequenced strain MEX/InDRE/14/2015 belongs to the Zika virus Asian lineage and is closely related to those reported from Brazil and Suriname in 2015 (Figure). The phylogeny does show some genetic distance with respect to strains causing outbreaks in 2014 in the Americas, suggesting acquired genetic changes probably caused by adaptations during the spread of the virus, similar to those observed for chikungunya virus (9). Figure Phylogenetic analysis of nonsegmented protein 5 partial sequences of Zika virus isolated from a traveler returning from Colombia to Mexico (MEX/InDRE/14/2015; black dot), October 2015, showing close relationship Zika virus strains reported from Brazil ... We conducted a nonsynonymous mutation analysis using the NS5 protein from the Zika virus isolated in French Polynesia in 2013 (903 aa; GenBank accession no. {"type":"entrez-nucleotide","attrs":{"text":"KJ776791.1","term_id":"631250742","term_text":"KJ776791.1"}}KJ776791.1) as a reference. The strain MEX/InDRE/14/2015bears the mutation markers K546R, K642R, and E561K, which cause the differentiation of the Asian lineage from the clades representing the African lineage (Figure). In addition, we observed that markers A527I, G588K, K531R, R648N, and S704D were acquired during the virus dispersion from Southeast Asia to the Pacific region and the Americas. In summary, we identified Zika virus in a traveler who returned from Colombia to Mexico in October 2015. A partial sequence of the NS5 gene showed that the isolate from this patient was closely related to those described elsewhere in the Western Hemisphere belonging to the Asian lineage, particularly to 2 strains identified in Brazil and Suriname during 2015.

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.

OBJECTIVE: The present study aimed to identify Mollicutes infection in the reproductive system. We also examined the microbiological, biochemical, and antimicrobial profiles of Mollicutes infection, which are potentially associated with clinical reproductive abnormalities causing infertility in couples. METHODS: Thirty-seven couples who were attending an infertility clinic were enrolled. Detection of genital mycoplasmas was performed in cervicovaginal samples or male urethral swabs. Microbiological culture and biochemical and antimicrobial profiles were characterized using a Mycoplasma kit. The results were associated with reproductive abnormalities, as assessed by medical specialists from the infertility clinic. RESULTS: Up to 28.3% of all biological samples (n = 74) showed positive cultures. Bacterial isolates were Ureaplasma urealyticum (71.4%), Mycoplasma hominis (9.5%), or coinfections (19%). Most Mollicutes showed significant resistance to fluoroquinolones, macrolides, and tetracycline; and showed susceptibility to doxycycline, josamycin, and pristinamycin. The presence of resistant strains to any antibiotic was significantly associated with genital abnormalities (χ2 test, relative risk = 11.38 [95% confidence interval: 5.8-22.9]), particularly in women. The highest statistical association was found for macrolide-resistant strains. CONCLUSION: The microbiological antibiotic resistance profile is epidemiologically associated with abnormalities of the reproductive system in couples attending an infertility clinic.

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.

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.

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.