Integrated genomic epidemiology and phenotypic profiling of Clostridium difficile across intra-hospital and community populations in Colombia.

Clostridium difficile, the causal agent of antibiotic-associated diarrhea, has a complex epidemiology poorly studied in Latin America. We performed a robust genomic and phenotypic profiling of 53 C. difficile clinical isolates established from diarrheal samples from either intrahospital (IH) or community (CO) populations in central Colombia. In vitro tests were conducted to evaluate the cytopathic effect, the minimum inhibitory concentration of ten antimicrobial agents, the sporulation efficiency and the colony forming ability. Eleven different sequence types (STs) were found, the majority present individually in each sample, however in three samples two different STs were isolated. Interestingly, CO patients were infected with STs associated with hypervirulent strains (ST-1 in Clade-2). Three coexistence events (two STs simultaneously detected in the same sample) were observed always involving ST-8 from Clade-1. A total of 2,502 genes were present in 99% of the isolates with 95% of identity or more, it represents a core genome of 28.6% of the 8,735 total genes identified in the set of genomes. A high cytopathic effect was observed for the isolates positive for the two main toxins but negative for binary toxin (TcdA+/TcdB+/CDT- toxin production type), found only in Clade-1. Molecular markers conferring resistance to fluoroquinolones (cdeA and gyrA) and to sulfonamides (folP) were the most frequent in the analyzed genomes. In addition, 15 other markers were found mostly in Clade-2 isolates. These results highlight the regional differences that C. difficile isolates display, being in this case the CO isolates the ones having a greater number of accessory genes and virulence-associated factors.

Predicción espacio-temporal probabilista de la epidemia de dengue total y grave en Colombia / Probabilistic spatial-temporal prediction of total and severe epidemic of dengue in Colombia / Previsão probabilística espaço-temporal da epidemia de dengue total e grave na Colômbia

RESUMEN Objetivo Establecer una nueva metodología predictiva de la proporción de dengue grave respecto al total anual de infectados de dengue por departamento con base en la teoría de la probabilidad. Métodos Con base en los datos anuales de número de infectados por departamentos en el periodo 2005 -2010, se calculó la proporción entre casos de dengue grave respecto al total para cada año, y se construyeron espacios de probabilidad que evalúan estos eventos en rangos de 0,5 y 0,3. Se determinaron conjuntos de rangos y se calculó probabilidad, desviación media cuadrática y la diferencia entre ellas. Se realizó una predicción del rango de infectados para el 2011 con el promedio aritmético de los valores de los últimos dos años. Resultados Se predijo correctamente el rango en el que se encuentra incluida la proporción de número de infectados de dengue grave sobre el total en cada departamento con una efectividad del 93,3% para el rango de 0,5 y de 86,7% para el de 0,3. Conclusión Se evidenció una autoorganización matemática espacio temporal en la proporción de dengue grave respecto al total que permite establecer predicciones de utilidad para la toma de decisiones de salud pública.(AU)

ABSTRACT Objective To establish a new predictive methodology to determine the proportion of severe dengue with respect to the annual total of dengue infections per department based on the probability theory. Materials and Methods Based on annual data on the number of infected persons by department in the period 2005-2010, the proportion of cases of severe dengue was calculated with respect to the total for each year. Probability spaces were constructed to evaluate these events in the ranges 0.5 and 0.3. Sets of ranges were determined and probability, mean square deviation and the difference between them were estimated. A prediction of the range of infected people for 2011 was made using the arithmetic average of the values of the last two years. Results The range in which the proportion of the number of people infected with severe dengue is included with respect to the total amount in each department was correctly predicted, with an effectiveness of 93.3% for the 0.5 range and 86.7% for the 0.3 range. Conclusion A mathematical spatial-temporal self-organization was found in the proportion of severe dengue with respect to the total, which allows establishing useful predictions for decision-making in public health.(AU)

RESUMO Objetivo Estabelecer uma nova metodologia preditiva para a proporção de dengue grave em relação ao dengue total anual infectado por departamento com base na teoria da probabilidade. Métodos Com base nos dados anuais do número de infectados por departamentos no período 2005-2010, a proporção entre os casos de dengue grave em relação ao total foi calculada para cada ano, e foram construídos espaços de probabilidade que avaliam esses eventos em intervalos de 0, 5 e 0,3. Conjuntos de intervalos foram determinados e a probabilidade, o desvio médio quadrático e a diferença entre eles foram calculados. A previsão da faixa de infectados para 2011 foi feita com a média aritmética dos valores dos últimos dois anos. Resultados A faixa na qual a proporção do número de infectados por dengue grave sobre o total está incluída em cada departamento foi corretamente prevista com uma eficácia de 93,3% para a faixa de 0,5 e 86,7% para aquela de 0,3. Conclusão Evidenciou-se uma auto-organização matemática espaço-temporal na proporção de dengue grave em relação ao total, o que permite estabelecer previsões úteis para a tomada de decisões em saúde pública.(AU)

New Insights into Clostridium difficile (CD) Infection in Latin America: Novel Description of Toxigenic Profiles of Diarrhea-Associated to CD in Bogotá, Colombia.

Clostridium difficile (CD) produces antibiotic associated diarrhea and leads to a broad range of diseases. The source of CD infection (CDI) acquisition and toxigenic profile are factors determining the impact of CD. This study aimed at detecting healthcare facility onset- (HCFO) and community-onset (CO) CDI and describing their toxigenic profiles in Bogotá, Colombia. A total of 217 fecal samples from patients suffering diarrhea were simultaneously submitted to two CDI detection strategies: (i) in vitro culture using selective chromogenic medium (SCM; chromID, bioMérieux), followed verification by colony screening (VCS), and (ii) molecular detection targeting constitutive genes, using two conventional PCR tests (conv.PCR) (conv.16S y conv.gdh) and a quantitative test (qPCR.16s). The CD toxigenic profile identified by any molecular test was described using 6 tests independently for describing PaLoc and CdtLoc organization. High overall CDI frequencies were found by both SCM (52.1%) and conv.PCR (45.6% for conv.16S and 42.4% for conv.gdh), compared to reductions of up to half the frequency by VCS (27.2%) or qPCR.16S (22.6%). Infection frequencies were higher for SCM and conv.16S regarding HCFO but greater for CO concerning conv.gdh, such differences being statistically significant. Heterogeneous toxigenic profiles were found, including amplification with lok1/3 primers simultaneously with other PaLoc markers (tcdA, tcdB or tcdC). These findings correspond the first report regarding the differential detection of CDI using in vitro culture and molecular detection tests in Colombia, the circulation of CD having heterogeneous toxigenic profiles and molecular arrays which could affect the impact of CDI epidemiology.

[Probabilistic spatial-temporal prediction of total and severe epidemic of dengue in Colombia]. / Predicción espacio-temporal probabilista de la epidemia de dengue total y grave en Colombia.

OBJECTIVE: To establish a new predictive methodology to determine the proportion of severe dengue with respect to the annual total of dengue infections per department based on the probability theory. MATERIALS AND METHODS: Based on annual data on the number of infected persons by department in the period 2005-2010, the proportion of cases of severe dengue was calculated with respect to the total for each year. Probability spaces were constructed to evaluate these events in the ranges 0.5 and 0.3. Sets of ranges were determined and probability, mean square deviation and the difference between them were estimated. A prediction of the range of infected people for 2011 was made using the arithmetic average of the values of the last two years. RESULTS: The range in which the proportion of the number of people infected with severe dengue is included with respect to the total amount in each department was correctly predicted, with an effectiveness of 93.3% for the 0.5 range and 86.7% for the 0.3 range. CONCLUSION: A mathematical spatial-temporal self-organization was found in the proportion of severe dengue with respect to the total, which allows establishing useful predictions for decision-making in public health.

OBJETIVO: Establecer una nueva metodología predictiva de la proporción de dengue grave respecto al total anual de infectados de dengue por departamento con base en la teoría de la probabilidad. MÉTODOS: Con base en los datos anuales de número de infectados por departamentos en el periodo 2005 -2010, se calculó la proporción entre casos de dengue grave respecto al total para cada año, y se construyeron espacios de probabilidad que evalúan estos eventos en rangos de 0,5 y 0,3. Se determinaron conjuntos de rangos y se calculó probabilidad, desviación media cuadrática y la diferencia entre ellas. Se realizó una predicción del rango de infectados para el 2011 con el promedio aritmético de los valores de los últimos dos años. RESULTADOS: Se predijo correctamente el rango en el que se encuentra incluida la proporción de número de infectados de dengue grave sobre el total en cada departamento con una efectividad del 93,3% para el rango de 0,5 y de 86,7% para el de 0,3. CONCLUSIÓN: Se evidenció una autoorganización matemática espacio temporal en la proporción de dengue grave respecto al total que permite establecer predicciones de utilidad para la toma de decisiones de salud pública.