Resistance phenotype and virulence potential of Leclercia adecarboxylata strains isolated from different sources.

Introduction. Leclercia adecarboxylata is a member of Enterobacterales, often considered an opportunistic pathogen. Recent reports have highlighted L. adecarboxylata as an emerging pathogen harbouring virulence and resistance determinants.Gap statement. Little information exists on virulence and resistance determinants in L. adecarboxylata strains isolated from environmental, food, and clinical samples.Aim. To determine the presence of resistance and virulence determinants and plasmid features in L. adecarboxylata strains isolated from environmental, food, and clinical samples, as well as their phylogenetic relationship.Results. All strains tested showed resistance to ß-lactams and quinolones but were sensitive to aminoglycosides and nitrofurans. However, even though fosfomycin resistance is considered a characteristic trait of L. adecarboxylata, the resistance phenotype was only observed in 50 % of the strains; bla TEM was the most prevalent BLEE gene (70 %), while the quinolone qnrB gene was observed in 60 % of the strains. Virulence genes were differentially observed in the strains, with adhesion-related genes being the most abundant, followed by toxin genes. Finally, all strains carried one to seven plasmid bands ranging from 7 to 125 kbps and harboured several plasmid addiction systems, such as ParDE, VagCD, and CcdAB in 80 % of the strains.Conclusions. L. adecarboxylata is an important emerging pathogen that may harbour resistance and virulence genes. Additionally, it has mobilizable genetic elements that may contribute to the dissemination of genetic determinants to other bacterial genera.

Genomic insights of Leclercia adecarboxylata strains linked to an outbreak in public hospitals in Mexico.

BACKGROUND: Leclercia adecarboxylata is a bacteria closely related to Escherichia coli according to its biochemical characteristics and is commonly considered non-pathogenic although a growing number of publications classify it as an emerging pathogen. Fosfomycin resistance is a common trait for L. adecarboxylata encoded by fosALA gene. OBJECTIVE: To analyze genomic traits of sixteen L. adecarboxylata strains isolated from blood culture and a bottle of total parenteral nutrition. METHODS: Twenty-eight L. adecarboxylata strains isolated from blood culture and a bottle of total parenteral nutrition were identified biochemically with a Vitek ® automated system. The strains were phenotyped by their growth on Eosin Methylene Blue agar or MacConkey agar plates. Additionally, Pulsed field gel electrophoresis (PFGE) was performed to establish the clonal relationship. The genomic DNA of sixteen strains was obtained using a Qubit ® dsDNA HS Assay Kit and sequenced on an Illumina ® MiSeq instrument. Draft genomes were assembled using PROKKA and Rast. Assemblies were submitted to Resfinder and PathogenFinder from the Center for Genomic Epidemiology in order to find resistance genes and pathogenic potential. IslandViewer4 was also used to find Pathogenicity and Phage Islands. For identification of the fosA gene, manual curation and Clustal analysis was performed. A novel FosA variant was identified. Finally, phylogenetic analysis was performed using VAMPhyRE software and Mega X. RESULTS: In this paper, we report the genomes of sixteen strains of Leclercia adecarboxylata causing an outbreak associated with parenteral nutrition in public hospitals in Mexico. The genomes were analyzed for genetic determinants of virulence and resistance. A high pathogenic potential (pathogenicity index 0.82) as well as multiple resistance genes including carbapenemics, colistin and efflux pumps were determined. Based on sequence analysis, a new variant of the fosALA gene was described. Finally, the outbreak was confirmed by establishing the clonal relationship among the sixteen genomes obtained. CONCLUSIONS: Commensal strains of L. adecarboxylata may acquire genetic determinants that provide mechanisms of host damage and go unnoticed in clinical diagnosis. L. adecarboxylata can evolve in a variety of ways including the acquisition of resistance and virulence genes representing a therapeutic challenge in patient care.

Genetic diversity and spatiotemporal dynamics of DENV-1 and DENV-2 infections during the 2012-2013 outbreak in Mexico.

Dengue fever is caused by four related dengue virus serotypes, DENV-1 to DENV-4, where each serotype comprises distinct genotypes and lineages. The last major outbreak in Mexico occurred during 2012 and 2013, when 112,698 confirmed cases were reported (DENV-1 and DENV-2 were predominant). Following partial E, NS2A and NS5 gene sequencing, based on the virus genome variability, we analyzed 396 DENV-1 and 248 DENV-2 gene sequences from serum samples from dengue acute clinical cases from 13 Mexican states, Mutations were identified, and their genetic variability estimated, along with their evolutionary relationship with DENV sequences sampled globally. DENV-1 genotype V and DENV-2 Asian-American genotype V were the only genotypes circulating during the outbreak. Mutations in NS2A and NS5 proteins were widely disseminated and suggested local emergence of new lineages. Phylogeographic analysis suggested viral spread occurred from coastal regions, and tourist destinations, such as Yucatan and Quintana Roo, which played important roles in disseminating these lineages.

Pregnant Women Infected with Zika Virus Show Higher Viral Load and Immunoregulatory Cytokines Profile with CXCL10 Increase.

BACKGROUND: Zika virus (ZIKV) infection during pregnancy usually shows only mild symptoms and is frequently subclinical. However, it can be vertically transmitted to the fetus, causing microcephaly and other congenital defects. During pregnancy, the immune environment modifications can alter the response to viruses in general and ZIKV in particular. OBJECTIVE: To describe the role of pregnancy in the systemic pro- and anti-inflammatory response during symptomatic ZIKV infection. MATERIALS AND METHODS: A multiplex assay was used to measure 25 cytokines, chemokines, and receptors in 110 serum samples from pregnant and nonpregnant women with and without ZIKV infection with and without symptoms. Samples were collected through an epidemiological surveillance system. RESULTS: Samples from pregnant women with ZIKV infection showed a higher viral load but had similar profiles of inflammatory markers as compared with nonpregnant infected women, except for CXCL10 that was higher in infected pregnant women. Notably, the presence of ZIKV in pregnancy favored a regulatory profile by significantly increasing anti-inflammatory cytokines such as interleukin (IL)-10, receptors IL-1RA, and IL-2R, but only those pro-inflammatory cytokines such as IL-6, interferon (IFN)-α, IFN-γ and IL-17 that are essential for the antiviral response. Interestingly, there were no differences between symptomatic and weakly symptomatic ZIKV-infected groups. CONCLUSION: Our results revealed a systemic anti-inflammatory cytokine and chemokine profile that could participate in the control of the virus. The anti-inflammatory response in pregnant women infected with ZIKA was characterized by high CXCL10, a cytokine that has been correlated with congenital malformations.

Genetic Diversity and Spatiotemporal Dynamics of Chikungunya Infections in Mexico during the Outbreak of 2014-2016.

Chikungunya virus (CHIKV) is an alphavirus transmitted by Aedes mosquitoes, which causes Chikungunya fever. Three CHIKV genotypes have been identified: West African, East-Central-South African and Asian. In 2014, CHIKV was detected for the first time in Mexico, accumulating 13,569 confirmed cases in the following three years. Studies on the molecular diversification of CHIKV in Mexico focused on limited geographic regions or investigated only one structural gene of the virus. To describe the dynamics of this outbreak, we analyzed 309 serum samples from CHIKV acute clinical cases from 15 Mexican states. Partial NSP3, E1, and E2 genes were sequenced, mutations were identified, and their genetic variability was estimated. The evolutionary relationship with CHIKV sequences sampled globally were analyzed. Our sequences grouped with the Asian genotype within the Caribbean lineage, suggesting that the Asian was the only circulating genotype during the outbreak. Three non-synonymous mutations (E2 S248F and NSP3 A437T and L451F) were present in our sequences, which were also identified in sequences of the Caribbean lineage and in one Philippine sequence. Based on the phylogeographic analysis, the viral spread was reconstructed, suggesting that after the introduction through the Mexican southern border (Chiapas), CHIKV dispersed to neighboring states before reaching the center and north of the country through the Pacific Ocean states and Quintana Roo. This is the first viral phylogeographic reconstruction in Mexico characterizing the CHIKV outbreak across the country.

Antiviral resistance markers in influenza virus sequences in Mexico, 2000-2017.

BACKGROUND: Influenza causes high rates of morbidity and mortality. Genetic variability of influenza viruses generates resistance to antivirals, which are of two types, since they act on two different viral targets: adamantanes, which block the M2 ion channel, and the neuraminidase (NA) inhibitors. METHODS: In Mexico, the available studies on the antiviral resistance of circulating influenza strains are scarce, so this work undertook an analysis of the Mexican sequences reported in public gene banks to perform a systematic analysis of the antiviral resistance markers on both M2 and NA. In all, 284 M2 sequences and 423 NA sequences were retrieved from three genetic databases (sequences from 2000 to 2017 were considered). RESULTS: The resistance markers to M2 blockers were present in 100% of H1N1 pdm2009, 83.6% of H3N2, and 5.8% of seasonal H1N1 sequences. Two resistance markers conferring resistance to NA inhibitors were present in seasonal H1N1 sequences, H275Y (50.0%) and N70S (33.3%). None of these viruses had both resistance markers, which are associated with oseltamivir resistance. The more frequent resistance marker in H1N1 pdm2009 NA sequences was H275Y, present in 3.6%, while S247N was present in 0.30%. Only one of the resistance-associated markers (Q136K) in NA (1.5%) was present in the analyzed H3N2 sequences, while sequences of influenza B virus did not present resistance markers to NA inhibitors. Some influenza A H1N1 pdm2009 sequences (1.8%) presented resistance markers to both M2 and NA. CONCLUSION: Based on the present analysis, 7.1% of the all serotypes of influenza virus A sequences analyzed in Mexico from 2000 to 2017 have mutations conferring resistance to NA inhibitors. Because of this, and the limited availability of influenza drugs, it is necessary to increase the epidemiological surveillance, including molecular analysis, which will provide data such as the presence of changes associated with antiviral resistance.

Genomic Epidemiology Reconstructs the Introduction and Spread of Zika Virus in Central America and Mexico.

The Zika virus (ZIKV) epidemic in the Americas established ZIKV as a major public health threat and uncovered its association with severe diseases, including microcephaly. However, genetic epidemiology in some at-risk regions, particularly Central America and Mexico, remains limited. We report 61 ZIKV genomes from this region, generated using metagenomic sequencing with ZIKV-specific enrichment, and combine phylogenetic, epidemiological, and environmental data to reconstruct ZIKV transmission. These analyses revealed multiple independent ZIKV introductions to Central America and Mexico. One introduction, likely from Brazil via Honduras, led to most infections and the undetected spread of ZIKV through the region from late 2014. Multiple lines of evidence indicate biannual peaks of ZIKV transmission in the region, likely driven by varying local environmental conditions for mosquito vectors and herd immunity. The spatial and temporal heterogeneity of ZIKV transmission in Central America and Mexico challenges arbovirus surveillance and disease control measures.

Differential Detection of Enterovirus and Herpes Simplex Virus in Cerebrospinal Fluid by Real-Time RT-PCR.

BACKGROUND: Enterovirus (EV) and herpes simplex virus 1 and 2 (HSV1 and HSV2) are the main etiologic agents of central nervous system infections. Early laboratory confirmation of these infections is performed by viral culture of the cerebrospinal fluid (CSF), or the detection of specific antibodies in serum (e.g., HSV). The sensitivity of viral culture ranges from 65 to 75%, with a recovery time varying from 3 to 10 days. Serological tests are faster and easy to carry out, but they exhibit cross-reactivity between HSV1 and HSV2. Although molecular techniques are more sensitive (sensitivity >95%), they are more expensive and highly susceptible to cross-contamination. METHODS: A real-time RT-PCR for the detection of EV, HSV1, and HSV2 was compared with end-point nested PCR. RESULTS: We tested 87 CSF samples of patients with a clinical diagnosis of viral meningitis or encephalitis. Fourteen samples were found to be positive by RT-PCR, but only 8 were positive by end-point PCR. The RT-PCR showed a specificity range of 94-100%, the negative predictive value was 100%, and the positive predictive value was 62, 100, and 28% for HSV1, HSV2, and EV, respectively. CONCLUSION: Real-time RT-PCR detected EV, HSV1, and HSV2 with a higher sensitivity and specificity than end-point nested RT-PCR.

Epidemiological characterization of a fourth wave of pandemic A/H1N1 influenza in Mexico, winter 2011-2012: age shift and severity.

BACKGROUND AND AIMS: A substantial recrudescent wave of pandemic influenza A/H1N1 affected the Mexican population from December 1, 2011-March 20, 2012 following a 2-year period of sporadic transmission. METHODS: We analyzed demographic and geographic data on all hospitalizations with severe acute respiratory infection (SARI) and laboratory-confirmed A/H1N1 influenza, and inpatient deaths, from a large prospective surveillance system maintained by a Mexican social security medical system during April 1, 2009-March 20, 2012. We also estimated the reproduction number (R) based on the growth rate of the daily case incidence by date of symptoms onset. RESULTS: A total of 7569 SARI hospitalizations and 443 in-patient deaths (5.9%) were reported between December 1, 2011, and March 20, 2012 (1115 A/H1N1-positive inpatients and 154 A/H1N1-positive deaths). The proportion of laboratory-confirmed A/H1N1 hospitalizations and deaths was higher among subjects ≥60 years of age (χ(2) test, p <0.0001) and lower among younger age groups (χ(2) test, p <0.04) for the 2011-2012 pandemic wave compared to the earlier waves in 2009. The reproduction number of the winter 2011-2012 wave in central Mexico was estimated at 1.2-1.3, similar to that reported for the fall 2009 wave, but lower than that of spring 2009. CONCLUSIONS: We documented a substantial increase in the number of SARI hospitalizations during the period December 2011-March 2012 and an older age distribution of laboratory-confirmed A/H1N1 influenza hospitalizations and deaths relative to 2009 A/H1N1 pandemic patterns. The gradual change in the age distribution of A/H1N1 infections in the post-pandemic period is consistent with a build-up of immunity among younger populations.

Genetic rearrangement MLL/AF4 is most frequent in children with acute lymphoblastic leukemias in Mexico City.

One of the highest incidences of acute lymphoblastic leukemia (ALL) in the world has been reported in Mexico City. In the current study (26 cases), the frequencies of the most frequent genetic rearrangements TEL-AML1, MLL/AF4, BCR-ABL (major and minor) in ALL in children from Mexico City were determined. For the ALL, the frequency of MLL/AF4 was 65.4%, for TEL-AML1 and that of BCR/ABL was 3.8%. Only 6 of the 17 children with the MLL/AF4 rearrangement were less than 26 months old. The frequency reported for MLL/AF4 in Mexican children with ALL is one of the highest worldwide. These findings could potentially explain the higher frequency of ALL with poor prognosis for children in Mexico City.

Prevalence and risk factors of hepatitis C virus, hepatitis B virus, and human immunodeficiency virus in multiply transfused recipients in Mexico.

BACKGROUND: Transfusion-transmitted viral infection (TTI) is a major problem in patients receiving blood products. Monitoring high-risk patients is essential for assessing the epidemiology of blood-borne infections. STUDY DESIGN AND METHODS: A 1-year, cross-sectional seroprevalence study in patients with a history of multiple transfusions was conducted. Peripheral blood samples were titered to detect serologic markers of human immunodeficiency virus (HIV), hepatitis B virus (HBV), and hepatitis C virus (HCV). The presence of these viruses and demographic, behavioral, and medical traits were assessed. RESULTS: A total of 300 male and female multiply transfused patients with a mean age of 30.7 (+/-17.5) years were studied. The prevalence was 13.7% for HCV, 7% for HBV, and 1.7% for HIV. Patients with hemophilia had the highest prevalence for HCV and HIV infections, and hemodialyzed patients, for HBV infection. The risk factors related to acquired HCV were hemophilia (odds ratio [OR], 5.6; 95% confidence interval [CI], 2.5-12.6), more than five hospitalizations (OR, 3.8; 95% CI, 1.6-8.9), and having received a transfusion before mandatory screening in 1993 (OR, 8.4; 95% CI, 2.0-34.6), and for HIV, having received a transfusion before 1987 (OR, 19.0; 95% CI, 2.0-177.7). The main risk factors for HBV were having end-stage renal disease and being treated with hemodialysis (OR, 3.7; 95% CI, 1.4-9.9) and transplantation (OR, 4.2; 95% CI, 1.4-12.1). CONCLUSIONS: This study showed that HCV infection was more frequently identified than HBV and HIV infections in multiply transfused Mexican patients. Additionally, several risk factors are associated with TTI such as mandatory screenings before 1987 and 1993, which were the most important for HIV and HCV infections but not for HBV.

[Association between cardiovascular disease and anti-Chlamydia pneumoniae antibodies]. / Asociación entre enfermedad cardiovascular y anticuerpos contra Chlamydia pneumoniae.

OBJECTIVE: To evaluate the association between cardiovascular disease (CVD) and antibodies against Chlamydia in Mexican population. MATERIAL AND METHODS: A cross-sectional study was conducted from August 1988 to April 2000, at the Immunology and Infectology Research Unit of Hospital de Infectología, Centro Médico Nacional La Raza (CMNR)--and at the Cardiovascular Surgery and Circulatory Care, Hospital General CMNR, Instituto Mexicano del Seguro Social (IMSS). Study subjects were 70 CVD hospitalized patients, older than 30 years, from both genders. Serum IgG and IgM antibodies against C. psitaccii, C. trachomatis and C. pneumoniae were determined by microimmunofluorescence in study subjects and compared with those from 140 healthy individuals, matched by age and sex. Simple random sampling was used, for an expected prevalence of 50% and a 99% confidence level; the sample size was 110 subjects. The chi-squared test and odds ratios were used to compare proportions. RESULTS: IgG antibodies against C. pneumoniae were found in 94.3% (66/70) patients, as compared to only 37% (52/140) of healthy individuals (p < 0.001). CONCLUSIONS: An association between IgG antibodies against C. pneumoniae and CVD was found. This finding warrants further studies to evaluate the role of C. pneumoniae as a predictor of CVD. The English version of this paper is available at: http://www.insp.mx/salud/index.html.

Asociación entre enfermedad cardiovascular y anticuerpos contra Chlamydia pneumoniae / Association between cardiovascular disease and antibodies against Chlamydia pneumoniae

Objetivo. Precisar si existe asociación entre enfermedad cardiovascular (ECV) y anticuerpos contra Chlamydia en población mexicana. Material y métodos. Estudio transversal, realizado en la Unidad de Investigación en Inmunología e Infectología -Hospital de Infectología del Centro Médico Nacional La Raza (CMNR)- y en el Servicio de Cirugía Cardiovascular y Asistencia Circulatoria, del Hospital General del CMNR, Instituto Mexicano del Seguro Social (IMSS), de agosto de 1998 a abril de 2000. Se determinaron anticuerpos IgG e IgM contra C. psittaci, C. trachomatis y C. pneumoniae mediante microinmunofluorescencia, en suero de 70 pacientes con ECV hospitalizados en el CMNR, mayores de 30 años, de uno u otro sexo, y se compararon con 140 sanos, pareados por edad y sexo. Se utilizaron muestras aleatorias simples, con un tamaño poblacional de 110, una prevalencia de 50 por ciento y un nivel de confianza de 99 por ciento. Para establecer la diferencia entre las proporciones de los títulos se utilizó ji cuadrada y se calculó la razón de momios. Resultados. El 94.3 por ciento (66/70) de los pacientes presentó IgG en contra de C. pneumoniae vs 37 por ciento (52/140) de los individuos sanos (p<0.001). Conclusiones. Existe una fuerte asociación entre anticuerpos IgG hacia C. pneumoniae y ECV.

Objective. To evaluate the association between cardiovascular disease (CVD) and antibodies against Chlamydia in Mexican population. Material and Methods. A cross-sectional study was conducted from August 1988 to April 2000, at the Immunology and Infectology Research Unit of Hospital de Infectología, Centro Médico Nacional La Raza (CMNR)- and at the Cardiovascular Surgery and Circulatory Care, Hospital General CMNR, Instituto Mexicano del Seguro Social (IMSS). Study subjects were 70 CVD hospitalized patients, older than 30 years, from both genders. Serum IgG and IgM antibodies against C. psitaccii, C. trachomatis and C. pneumoniae were determined by microimmunofluorescence in study subjects and compared with those from 140 healthy individuals, matched by age and sex. Simple random sampling was used, for an expected prevalence of 50 percent and a 99 percent confidence level; the sample size was 110 subjects. The chi-squared test and odds ratios were used to compare proportions. Results. IgG antibodies against C. pneumoniae were found in 94.3 percent (66/70) patients, as compared to only 37 percent (52/140) of healthy individuals (p<0.001). Conclusions. An association between IgG antibodies against C. pneumoniae and CVD was found. This finding warrants further studies to evaluate the role of C. pneumoniae as a predictor of CVD.

Patogenia de la infección por el virus de la inmunodeficiencia humana tipo 1 / Pathogenesis of human immunodeficiency virus type 1 infection

El virus de la inmunodeficiencia humana (VIH), que pertenece a la familia de los lentivirus, es el agente causal del síndrome de inmunodeficiencia adquirida (SIDA). Existen dos tipos de VIH: el tipo 1 (VIH-1) se encuentra diseminado en todo el mundo y es responsable de la mayor parte de casos de SIDA, y el tipo 2 (VIH-2) que está relativamente restringido a África. Este artículo revisa la patogenia de la infección por el VIH.