Variability of Staphylococcus Aureus Carriers on a Medicine Student’s Population

Para evaluar en estudiantes de medicina la variación del estado de portador de Staphylococcus aureus y su resistencia antimicrobiana, antes y después de la práctica clínica, se realizó un estudio longitudinal en una cohorte de 159 estudiantes de cuarto y noveno semestre universitario. Se tomaron muestras de las zonas periamigdalianas y/o pared posterior de orofaringe, de las fosas nasales y las manos, se cultivaron en agar sangre de cordero al 5% y se incubaron en aerobiosis a 37°C, durante 48 horas. La identificación de Staphylococcus aureus se realizó según las características macroscópicas y pruebas bioquímicas. La susceptibilidad a los antimicrobianos se evaluó mediante el método de difusión de disco, por la técnica de Kirby-Bauer, siguiendo las normas internacionales del Clinical and Laboratory Standards Institute (CLSI), con los siguientes antimicrobianos: ciprofloxacina, vancomicina, oxacilina, cefalotina,clindamicina y rifampicina. La edad promedio de los alumnos de cuarto semestre fue 19,1±1,2 años y el género femenino fue 2/1 más frecuente que el masculino. Se analizaron la presencia de antecedentes como: infecciones, alergias, estado de fumador, otras patologías no infecciosas, uso de antibióticos en los últimos tres meses y procedimientos quirúrgicos u hospitalizaciones seis meses previos a la toma de las muestras. No hubo relación significativa entre la incidencia del estado de portador y los antecedentes estudiados. Se observó un aumento significativo del 15,1%, con respecto al grupo de estudiantes de cuarto semestre, en el estado de portador de S. aureus en el grupo de estudiantes de noveno semestre, después de haber estado expuestos durante tres años al ambiente hospitalario, (p=0,001 Test exacto de Mc Nemar). De los portadores, el 16,4% presentó la bacteria en manos (p<0,001), el 13,8% en fosas nasales (p=0,0015) y el 3,2% en faringe. Por otra parte,el 35,8% de los portadores presentó persistencia, de los cuales el 25,2% fue en fosas nasales; el 4,4%, en faringe y el 3,8% en manos. En cuanto a la resistencia a los antimicrobianos, el 1,9% de las cepas aisladas de los estudiantes de cuarto semestre presentó resistencia: una a ciprofloxacina y dos a clindamicina (tres estudiantes). Por su parte, el 2,5% de las cepas aisladas de estudiantes de noveno semestre fue resistente: una a cefalotina, ciprofloxacina, oxacilina y clindamicina, una a cefalotina y oxacilina y dos a clindamicina (cuatro estudiantes). En el 1,3% del grupo estudiado se aislaron cepas de Staphylococcus aureus Resistentes a la Meticilina (MRSA, por sus siglas en inglés). Estos resultados no muestran diferencias significativas (p=1.000). This is a longitudinal study performed in a 159 medicine student’s cohort, of fourth and ninth study semester, in order to evaluate the variation of Staphylococcus aureus carriers and its antimicrobial susceptibility on students, before and after clinical practice. Clinical samples were taken with a swab from the tonsils, pharynx posterior wall, nasal fosses and hands and were cultured in 5% sheep blood and incubated at 37oC in aerobic conditions during 48 hours. The identification of Sthaphylococcus aureus was performed according to the phenotypic and biochemical test. The antimicrobial susceptibility was evaluated by the diffusion disc method using the Kirby-Bauer technique, according to Clinical and Laboratory Standards Institute (CLSI), with the following antibiotics: Ciprofloxacyn, Vancomycin, Oxacyclin, Cephalotine, Clyndamycin, and Ryphampycin. The average age of the fourth semester students was 19.1± 1,2 years and the female gender was 2/1 more frequent than the male. The history of infections, allergy, smoke habit, non infectious diseases, surgeries, antibiotic use during the last three months and hospitalizations six months before sampling was analyzed. There was no significant relationship between previous history analysis and the carrier state incidence (p=0.001 Mc Nemar exact Test). A significant increase of 15,1% for S. aureus carrier state was observed after three years of exposure to hospital environment on ninth semester students, compared to fourth semester students (p=0.001 Test Mc Nemar); from which 16.4% (p<0.001) was founded in hands, 13.8% in nasal fosses (p=0.0015) and 3.2% in pharynx. 35.8% of S. aureus carrier was persistent: 25.2% in nasal fosses, 4.4% in pharynx and 3.8% in hands. Antimicrobial resistance was observed in 1.9% of the bacterial strains isolated from fourth semester students: One to Ciprofloxacyn and two to Clyndamycin. Besides was observed 2.5% of bacterial strains isolated from ninth semester students: one to Ciprofloxacyn, Oxacyclin, Cephalotine and Clyndamycin, one to Cephalotine and Oxacyclin and two to Clyndamycin. Finally, Methycylin Resistant Sthaphylococcus Aureus (MRSA) strains were isolated from 1.3% of the studied group. This results didn’t show significant differences b(p=1.000)

On the contribution of Angola to the initial spread of HIV-1

Licenced under CC-BY-NC-NDAngola borders and has long-term links with Democratic Republic of Congo (DRC) as well as high levels of Human Immunodeficiency Virus (HIV) genetic diversity, indicating a potential role in the initial spread of the HIV-1 pandemic. Herein, we analyze 564 C2V3 and 354 pol publicly available sequences from DRC, Republic of Congo (RC) and Angola to better understand the initial spread of the virus in this region. Phylogeographic analyses were performed with the BEAST software. While our results pinpoint the origin of the pandemic to Kinshasa (DRC) around 1906, the introduction of HIV-1 to Angola could have occurred early between the 1910s and 1940s. Furthermore, most of the HIV-1 migrations out of Kinshasa were directed not only to Lubumbashi and Mbuji-Mayi (DRC), but also to Luanda and Brazzaville. Kinshasa census records corroborate these findings, indicating that the early exportation of the virus to Angola might be related to the high number of Angolans in Kinshasa at that time, originated mostly from the North of Angola. In summary, our results place Angola at the epicenter of the early HIV dissemination, together with DRC and RC.info:eu-repo/semantics/publishedVersio

Reconstruction of the origin and dispersal of the worldwide dominant Hepatitis B Virus subgenotype D1

Funding Information: N.S.T. and P.L. were supported by the European Union Seventh Framework Programme [FP7/2007-2013] under Grant Agreement number 278433-PREDEMICS. The research leading to these results has received funding from the European Research Council under the European Union's Horizon 2020 research and innovation programme (grant agreement no. 725422 - ReservoirDOCS). MT is a PhD fellow at the Research Foundation Flanders (FWO, Belgium, grant number 1S47118N). A.-C.P.-P. was supported by European Funds through grant 'Bio-Molecular and Epidemiological Surveillance of HIV Transmitted Drug Resistance, Hepatitis Co- Infections and Ongoing Transmission Patterns in Europe' (BEST HOPE) (project funded through HIVERA: Harmonizing Integrating Vitalizing European Research on HIV/Aids, grant 249697); by Fundação para a Cieñcia e Tecnologia for funds to GHTMUID/ Multi/04413/2013; by the Migrant HIV project (financed by FCT: PTDC/DTP-EPI/7066/2014; and by Gilead Ǵenese HIVLatePresenters. B.V. was supported by a postdoctoral grant (12U7121N) of the FWO (Fonds Wetenschappelijk Onderzoek - Vlaanderen). G.B. acknowledges support from the Interne Fondsen KU Leuven/ Internal Funds KU Leuven under grant agreement C14/18/094 and the Research Foundation - Flanders ('Fonds voor Wetenschappelijk Onderzoek - Vlaanderen', G0E1420N, G098321N). This work was supported by the Bijzonder Onderzoeksfonds KU Leuven (BOF) No. OT/14/115. This work was supported by public grants. The funders had no role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. Publisher Copyright: © 2022 The Author(s).Hepatitis B is a potentially life-threatening liver infection caused by the hepatitis B virus (HBV). HBV-D1 is the dominant subgenotype in the Mediterranean basin, Eastern Europe, and Asia. However, little is currently known about its evolutionary history and spatio-temporal dynamics. We use Bayesian phylodynamic inference to investigate the temporal history of HBV-D1, for which we calibrate the molecular clock using ancient sequences, and reconstruct the viral global spatial dynamics based, for the first time, on full-length publicly available HBV-D1 genomes from a wide range of sampling dates. We pinpoint the origin of HBV subgenotype D1 before the current era (BCE) in Turkey/Anatolia. The spatial reconstructions reveal global viral transmission with a high degree of mixing. By combining modern-day and ancient sequences, we ensure sufficient temporal signal in HBV-D1 data to enable Bayesian phylodynamic inference using a molecular clock for time calibration. Our results shed light on the worldwide HBV-D1 epidemics and suggest that this originally Middle Eastern virus significantly affects more distant countries, such as those in mainland Europe.publishersversionpublishe

Sub-epidemics explain localized high prevalence of reduced susceptibility to Rilpivirine in treatment-naive HIV-1-infected patients: subtype and geographic compartmentalization of baseline resistance mutations

This Open Access article is distributed under the terms of the Creative Commons Attribution Noncommercial License (http://creativecommons.org/licenses/by-nc/4.0/) which permits any noncommercial use, distribution, and reproduction in any medium, provided the original author(s) and the source are credited."Objective: The latest nonnucleoside reverse transcriptase inhibitor (NNRTI) rilpivirine (RPV) is indicated for human immunodeficiency virus type-1 (HIV-1) patients initiating antiretroviral treatment, but the extent of genotypic RPV resistance in treatment-naive patients outside clinical trials is poorly defined. Study Design: This retrospective observational study of clinical data from Belgium and Portugal evaluates genotypic information from HIV-1 drug-naive patients obtained for the purpose of drug resistance testing. Rilpivirine resistance-associated mutations (RPV-RAMs) were defined based on clinical trials, phenotypic studies, and expert-based resistance algorithms. Viral susceptibility to RPV alone and to the single-tablet regimen was estimated using expert-based resistance algorithms. Results: In 4,631 HIV-1 treatment-naive patients infected with diverse HIV-1 subtypes, major RPV-RAMs were detected in 4.6%, while complete viral susceptibility to RPV was estimated in 95% of patients. Subtype C- and F1-infected patients displayed the highest levels of reduced viral susceptibility at baseline, respectively 13.2% and 9.3%, mainly due to subtype- and geographic-dependent occurrence of RPV-RAMs E138A and A98G as natural polymorphisms. Strikingly, a founder effect in Portugal resulted in a 138A prevalence of 13.2% in local subtype C-infected treatment-naive patients. The presence of transmitted drug resistance did not impact our estimates. Conclusion: RPV is the first HIV-1 inhibitor for which, in the absence of transmitted drug resistance, intermediate or high-level genotypic resistance can be detected in treatment-naive patients. The extent of RPV susceptibility in treatment-naive patients differs depending on the HIV-1 subtype and dynamics of local compartmentalized epidemics. The highest prevalence of reduced susceptibility was found to be 15.7% in Portuguese subtype C-infected treatment-naive patients. In this context, even in the absence of transmitted HIV-1 drug resistance (TDR), drug resistance testing at baseline should be considered extremely important before starting treatment with this NNRTI.

Trends and predictors of transmitted drug resistance (TDR) and clusters with TDR in a local Belgian HIV-1 epidemic

We aimed to study epidemic trends and predictors for transmitted drug resistance (TDR) in our region, its clinical impact and its association with transmission clusters. We included 778 patients from the AIDS Reference Center in Leuven (Belgium) diagnosed from 1998 to 2012. Resistance testing was performed using population-based sequencing and TDR was estimated using the WHO-2009 surveillance list. Phylogenetic analysis was performed using maximum likelihood and Bayesian techniques. The cohort was predominantly Belgian (58.4%), men who have sex with men (MSM) (42.8%), and chronically infected (86.5%). The overall TDR prevalence was 9.6% (95% confidence interval (CI): 7.7-11.9), 6.5% (CI: 5.0-8.5) for nucleoside reverse transcriptase inhibitors (NRTI), 2.2% (CI: 1.4-3.5) for non-NRTI (NNRTI), and 2.2% (CI: 1.4-3.5) for protease inhibitors. A significant parabolic trend of NNRTI-TDR was found (p = 0.019). Factors significantly associated with TDR in univariate analysis were male gender, Belgian origin, MSM, recent infection, transmission clusters and subtype B, while multivariate and Bayesian network analysis singled out subtype B as the most predictive factor of TDR. Subtype B was related with transmission clusters with TDR that included 42.6% of the TDR patients. Thanks to resistance testing, 83% of the patients with TDR who started therapy had undetectable viral load whereas half of the patients would likely have received a suboptimal therapy without this test. In conclusion, TDR remained stable and a NNRTI up-and-down trend was observed. While the presence of clusters with TDR is worrying, we could not identify an independent, non-sequence based predictor for TDR or transmission clusters with TDR that could help with guidelines or public health measures

HIV-1 Infection in Cyprus, the Eastern Mediterranean European Frontier: A Densely Sampled Transmission Dynamics Analysis from 1986 to 2012

Since HIV-1 treatment is increasingly considered an effective preventionstrategy, it is important to study local HIV-1 epidemics to formulate tailored preventionpolicies. The prevalence of HIV-1 in Cyprus was historically low until 2005. To investigatethe shift in epidemiological trends, we studied the transmission dynamics of HIV-1 in Cyprususing a densely sampled Cypriot HIV-1 transmission cohort that included 85 percent ofHIV-1-infected individuals linked to clinical care between 1986 and 2012 based on detailedclinical, epidemiological, behavioral and HIV-1 genetic information. Subtyping andtransmission cluster reconstruction were performed using maximum likelihood and Bayesianmethods, and the transmission chain network was linked to the clinical, epidemiological andbehavioral data. The results reveal that for the main HIV-1 subtype A1 and B sub-epidemics,young and drug-naïve HIV-1-infected individuals in Cyprus are driving the dynamics of thelocal HIV-1 epidemic. The results of this study provide a better understanding of thedynamics of the HIV-1 infection in Cyprus, which may impact the development of preventionstrategies. Furthermore, this methodology for analyzing densely sampled transmissiondynamics is applicable to other geographic regions to implement effective HIV-1 preventionstrategies in local settings

The dynamics of local hiv-1 epidemics: the colombian and belgian cohorts

We aimed to characterize the HIV-1 epidemic of the Belgian and Colombian cohorts using an integrated approach that includes socio-demographic information, clinical data, and viral sequences, analyzed with statistical and phylogenetic approaches.Andrea-Clemencia Pineda-Peña was supported by a Doctoral Research Training Program ‘‘Francisco Jose de Caldas’’ by the Departamento Administrativo de Ciencia, Tecnología e Innovación, COLCIENCIAS, Republic of Colombia and ERACOL academic exchange in medicine and the health sciences, between Europe and Latin America. The research was supported in part by the European Community’s Seventh Framework Programme (FP7/2007–2013) under the project ‘‘Collaborative HIV and Anti-HIV Drug Resistance Network (CHAIN)’’ grant agreement n° 223131 and ERC grant agreement no. 260864; by the Fonds voor Wetenschappelijk Onderzoek – Flanders (FWO) grant G.0611.09 and grant G069214N; by the AIDS Reference Laboratory of Leuven that receives support from the Belgian Ministry of Social Affairs through a fund within the Health Insurance System; by the University of Leuven (Program Financing no. PF/10/018. The computational resources and services used in this work were provided by the Hercules Foundation and the Flemish Government – department EWI-FWO Krediet aan Navorsers (Theys, KAN2012 1.5.249.12). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscripts.We aimed to characterize the HIV-1 epidemic of the Belgian and Colombian cohorts using an integrated approach that includes socio-demographic information, clinical data, and viral sequences, analyzed with statistical and phylogenetic approaches

O impacto da imigração sobre a tuberculose e a carga de HIV entre Colômbia e Venezuela e nas regiões de fronteira

Historically, human migrations have determined the spread of many infectious diseases by promoting the emergence of temporal outbreaks between populations. We aimed to analyze health indicators, expenditure, and disability caused by tuberculosis (TB) and HIV/AIDS burden under the Colombian-Venezuelan migration flow focusing on the Northeastern border. A retrospective study was conducted using TB and HIV/AIDS data since 2009. We consolidated a database using official reports from the Colombian Surveillance System, World Health Organization, Indexmundi, the Global Health Observatory, IHME HIV atlas, and Joint United Nations Programme on HIV/AIDS (UNAIDS). Disability metrics regarding DALYs (disability adjusted life years) and YLDs (years lived with disability), were compared between countries. Mapping was performed on ArcGIS using official migration data of Venezuelan citizens. Our results indicate that TB profiles from Colombia and Venezuela are identical in terms of disease burden, except for an increase in TB incidence in the Colombian-Venezuelan border departments in recent years, concomitantly with the massive Venezuelan immigration since 2005. We identified a four-fold underfunding for the TB program in Venezuela, which might explain the low-testing rates for cases of multidrug-resistant TB (67%) and HIV/AIDS (60%), as well as extended hospital stays (150 days). We found a significant increase in DALYs of HIV/AIDS patients in Venezuela, specifically, 362.35 compared to 265.37 observed in Colombia during 2017. This study suggests that the Venezuelan massive migration and program underfunding might exacerbate the dual burden of TB and HIV in Colombia, especially towards the Colombian‐Venezuelan border.Históricamente, las migraciones humanas han determinado la expansión de muchas enfermedades infecciosas, promoviendo el surgimiento de brotes temporales en la población. Nuestro objetivo fue analizar indicadores de salud, gastos, así como la discapacidad causada por la tuberculosis (TB) y la carga del VIH/SIDA ante el flujo migratorio entre Colombia-Venezuela, centrándose en los departamentos fronterizos del nordeste. Se realizó un estudio retrospectivo usando datos sobre TB y VIH/SIDA desde 2009. Consolidamos una base de datos usando informes oficiales del Sistema de Vigilancia Colombiano, Organización Mundial de la Salud, Indexmundi, Observatorio Global de la Salud, IHME HIV atlas, y Programa Conjunto de las Naciones Unidas sobre el VIH/SIDA (ONUSIDA). Se midió la discapacidad en términos del DALYs (incapacidad ajustada por años de vida) y YLDs (años vividos con discapacidad) y se compararon entre ambos países. El mapeo se realizó en ArcGIS, usando datos oficiales de migración de ciudadanos venezolanos. Nuestros resultados indican que los perfiles de TB de Colombia y Venezuela son idénticos, en lo que se refiere a la carga de la enfermedad, excepto por el incremento en la incidencia de TB en los departamentos fronterizos de la frontera entre Colombia y Venezuela en años recientes, concomitantemente con la inmigración masiva venezolana desde 2005. Identificamos una cuadruplicación de la subfinanciación para el programa de TB en Venezuela, que podría explicar las bajas tasas de test para los casos multirresistentes a medicamentos contra la TB (67%) y VIH/SIDA (60%), al igual que las estancias prolongadas en el hospital (150 días). Hallamos un incremento significativo en DALYs de pacientes con VIH/SIDA en Venezuela, específicamente, 362,35 comparados con los 265,37 observados en Colombia durante 2017. Este estudio sugiere que la migración venezolana masiva y la subfinanciación del programa podrían haber exacerbado la doble carga de la TB y el VIH en Colombia, especialmente a través de la frontera entre Colombia y VenezuelHistoricamente, as migrações humanas determinaram a propagação de muitas doenças infecciosas ao facilitar surtos temporais entre populações. O estudo buscou analisar os indicadores sanitários e os gastos e taxas de incapacidade relacionados à tuberculose (TB) e à carga de HIV/aids no fluxo migratório entre Colômbia e Venezuela, com destaque para os departamentos (estados) da fronteira nordeste. Foi realizado um estudo retrospectivo de dados sobre TB e HIV/aids desde 2009. Consolidamos uma base de dados a partir de relatórios do Sistema de Vigilância da Colômbia, Organização Mundial da Saúde, Indexmundi, Observatório de Saúde Global, IHME HIV Atlas e Programa Conjunto das Nações Unidas sobre HIV/AIDS (UNAIDS). As métricas de incapacidade em termos de AVAIs (anos de vida ajustados para incapacidade) e AVIs (anos vividos com incapacidade) foram comparadas entre os dois países. O mapeamento foi realizado no ArcGIS, com dados oficiais sobre migração de cidadãos venezuelanos. Nossos resultados indicam que os perfis de TB da Colômbia e da Venezuela são idênticos em termos de carga de doença, exceto por um aumento da incidência de TB nos departamentos na fronteira entre os dois países em anos recentes, concomitantemente com a imigração venezuelana maciça desde 2005. Identificamos um subfinanciamento (por um fator de quatro) no programa de tuberculose da Venezuela, o que pode explicar as baixas taxas de testagem para casos de TB multirresistente (67%) e HIV/aids (60%), além das internações hospitalares prolongadas (150 dias). Encontramos um aumento significativo de AVAIs em pacientes de HIV/aids na Venezuela, especificamente 362,35 comparado com 265,37 na Colômbia em 2017. O estudo sugere que a migração maciça venezuelana e o subfinanciamento podem exacerbar a carga dupla de TB e HIV na Colômbia, principalmente na fronteira com a Venezuela.Incluye referencias bibliográfica

The impact of HIV-1 within-host evolution on transmission dynamics

"The adaptive potential of HIV-1 is a vital mechanism to evade host immune responses and antiviral treatment. However, high evolutionary rates during persistent infection can impair transmission efficiency and alter disease progression in the new host, resulting in a delicate trade-off between within-host virulence and between-host infectiousness. This trade-off is visible in the disparity in evolutionary rates at within-host and between-host levels, and preferential transmission of ancestral donor viruses. Understanding the impact of within-host evolution for epidemiological studies is essential for the design of preventive and therapeutic measures. Herein, we review recent theoretical and experimental work that generated new insights into the complex link between within-host evolution and between-host fitness, revealing temporal and selective processes underlying the structure and dynamics of HIV-1 transmission. © 2017 Elsevier B.V.