Transmission Dynamics of a Mycobacterium tuberculosis Complex Outbreak in an Indigenous Population in the Colombian Amazon Region.

Whole genome sequencing (WGS) has become the main tool for studying the transmission of Mycobacterium tuberculosis complex (MTBC) strains; however, the clonal expansion of one strain often limits its application in local MTBC outbreaks. The use of an alternative reference genome and the inclusion of repetitive regions in the analysis could potentially increase the resolution, but the added value has not yet been defined. Here, we leveraged short and long WGS read data of a previously reported MTBC outbreak in the Colombian Amazon Region to analyze possible transmission chains among 74 patients in the indigenous setting of Puerto Nariño (March to October 2016). In total, 90.5% (67/74) of the patients were infected with one distinct MTBC strain belonging to lineage 4.3.3. Employing a reference genome from an outbreak strain and highly confident single nucleotide polymorphisms (SNPs) in repetitive genomic regions, e.g., the proline-glutamic acid/proline-proline-glutamic-acid (PE/PPE) gene family, increased the phylogenetic resolution compared to a classical H37Rv reference mapping approach. Specifically, the number of differentiating SNPs increased from 890 to 1,094, which resulted in a more granular transmission network as judged by an increasing number of individual nodes in a maximum parsimony tree, i.e., 5 versus 9 nodes. We also found in 29.9% (20/67) of the outbreak isolates, heterogenous alleles at phylogenetically informative sites, suggesting that these patients are infected with more than one clone. In conclusion, customized SNP calling thresholds and employment of a local reference genome for a mapping approach can improve the phylogenetic resolution in highly clonal MTBC populations and help elucidate within-host MTBC diversity. IMPORTANCE The Colombian Amazon around Puerto Nariño has a high tuberculosis burden with a prevalence of 1,267/100,000 people in 2016. Recently, an outbreak of Mycobacterium tuberculosis complex (MTBC) bacteria among the indigenous populations was identified with classical MTBC genotyping methods. Here, we employed a whole-genome sequencing-based outbreak investigation in order to improve the phylogenetic resolution and gain new insights into the transmission dynamics in this remote Colombian Amazon Region. The inclusion of well-supported single nucleotide polymorphisms in repetitive regions and a de novo-assembled local reference genome provided a more granular picture of the circulating outbreak strain and revealed new transmission chains. Multiple patients from different settlements were possibly infected with at least two different clones in this high-incidence setting. Thus, our results have the potential to improve molecular surveillance studies in other high-burden settings, especially regions with few clonal multidrug-resistant (MDR) MTBC lineages/clades.

[Prevalence and risk factors associated to tuberculosis and non-tuberculous mycobacterial infections in HIV-positive patients in Bogotá].

INTRODUCTION: Tuberculosis is one of the most widely distributed infectious diseases worldwide. It is the most common cause of mortality among AIDS patients. In Colombia, 12,918 tuberculosis cases were notified, and 926 deaths were reported in 2015. OBJECTIVE: To determine the prevalence and risk factors associated to mycobacterial infections in HIVpositive patients in two public hospitals from Bogotá. MATERIALS AND METHODS: A prospective and descriptive study was carried out by an active search for tuberculosis cases and non-tuberculous mycobacterial infections in HIV-positive patients. We considered demographic, social, clinical, and personal habits as variables. Statistical analyses were done using Stata 13™ software. RESULTS: Three hundred and fifty six patients were included, 81.2% were men and 18.8% were women; the mean age was 36.5 years. Tuberculosis infection had a frequency of 19.9% (95% CI: 15.9-24.5%) and non-tuberculous mycobacterial infection had a 3.9% frequency (95% CI: 2.16-6.5%). Bivariate analysis showed a statistically significant association between tuberculosis infection and CD4+ T cell counts (p=0.003), viral load (p=0.008), antiretroviral therapy (p=0.014), and body mass index (BMI) <18 kg/m2 (p=0.000). In non-tuberculous mycobacterial infections there was a statistically significantassociation with BMI (p=0.027) and CD4+ T cell counts (p=0.045). CONCLUSION: Factors associated with an impaired immune system caused by HIV infection are an important risk factor for developing tuberculosis. The lack of antiretroviral therapy and the BMI were also important risk factors for tuberculosis.

Prevalencia y factores asociados a la tuberculosis y las micobacteriosis en pacientes positivos para HIV en Bogotá / Prevalence and risk factors associated to tuberculosis and non-tuberculous mycobacterial infections in HIV-positive patients in Bogotá

Resumen Introducción. La tuberculosis es una de las enfermedades infecciosas de más amplia distribución en el mundo y constituye una de las primeras causas de muerte en pacientes con sida. En Colombia, en el 2015, se notificaron 12.918 casos de tuberculosis y 926 muertes. Objetivo. Determinar la prevalencia y los factores asociados a infecciones micobacterianas en pacientes infectados con el virus de inmunodeficiencia humana (HIV) en dos hospitales públicos de Bogotá. Materiales y métodos. Se hizo un estudio descriptivo de corte transversal con búsqueda activa de casos de tuberculosis y micobacteriosis en pacientes positivos para HIV. Se estudiaron variables demográficas, sociales, clínicas y de hábitos personales. Los análisis estadísticos se hicieron con el programa Stata 13TM. Resultados. Se incluyeron en el estudio 356 pacientes: 81,2 % hombres y 18,8 %, mujeres, con una media de edad de 36,5 años. La frecuencia de la tuberculosis fue de 19,9 % (IC95% 15,9-24,5 %) y la de infecciones por micobacterias no tuberculosas, de 3,9 % (IC95% 2,16-6,5 %). El análisis bivariado evidenció una asociación estadísticamente significativa entre la tuberculosis y el conteo de linfocitos TCD4+ (p=0,003), la carga viral (p=0,0008), el tratamiento antirretroviral (p=0,017) y un índice de masa corporal (IMC) menor de 18 kg/m2 (p=0,000). En las micobacteriosis solamente se presentó asociación estadísticamente significativa con el IMC (p=0,017) y con el conteo de linfocitos TCD4+ (p=0,045). Conclusión. Los factores asociados al deterioro del sistema inmunitario causados por el HIV, así como el no administrar el tratamiento antirretroviral de gran actividad y el IMC, constituyeron factores de riesgo para desarrollar la tuberculosis.

Abstract Introduction. Tuberculosis is one of the most widely distributed infectious diseases worldwide. It is the most common cause of mortality among AIDS patients. In Colombia, 12,918 tuberculosis cases were notified, and 926 deaths were reported in 2015. Objective. To determine the prevalence and risk factors associated to mycobacterial infections in HIV-positive patients in two public hospitals from Bogotá. Materials and methods. A prospective and descriptive study was carried out by an active search for tuberculosis cases and non-tuberculous mycobacterial infections in HIV-positive patients. We considered demographic, social, clinical, and personal habits as variables. Statistical analyses were done using Stata 13TM software. Results. Three hundred and fifty six patients were included, 81.2% were men and 18.8% were women; the mean age was 36.5 years. Tuberculosis infection had a frequency of 19.9% (95% CI: 15.9-24.5%) and non-tuberculous mycobacterial infection had a 3.9% frequency (95% CI: 2.16-6.5%). Bivariate analysis showed a statistically significant association between tuberculosis infection and CD4+ T cell counts (p=0.003), viral load (p=0.008), antiretroviral therapy (p=0.014), and body mass index (BMI) <18 kg/m2 (p=0.000). In non-tuberculous mycobacterial infections there was a statistically significant association with BMI (p=0.027) and CD4+ T cell counts (p=0.045). Conclusion. Factors associated with an impaired immune system caused by HIV infection are an important risk factor for developing tuberculosis. The lack of antiretroviral therapy and the BMI were also important risk factors for tuberculosis.

Development of a genetic tool for functional screening of anti-malarial bioactive extracts in metagenomic libraries.

BACKGROUND: The chemical treatment of Plasmodium falciparum for human infections is losing efficacy each year due to the rise of resistance. One possible strategy to find novel anti-malarial drugs is to access the largest reservoir of genomic biodiversity source on earth present in metagenomes of environmental microbial communities. METHODS: A bioluminescent P. falciparum parasite was used to quickly detect shifts in viability of microcultures grown in 96-well plates. A synthetic gene encoding the Dermaseptin 4 peptide was designed and cloned under tight transcriptional control in a large metagenomic insert context (30 kb) to serve as proof-of-principle for the screening platform. RESULTS: Decrease in parasite viability consistently correlated with bioluminescence emitted from parasite microcultures, after their exposure to bacterial extracts containing a plasmid or fosmid engineered to encode the Dermaseptin 4 anti-malarial peptide. CONCLUSIONS: Here, a new technical platform to access the anti-malarial potential in microbial environmental metagenomes has been developed.

Identificación de sujetos a riesgo de deficiencia de hierro mediante el indice receptor soluble de transferrina-log ferritina sérica en hombres afrodescendientes residentes en San Basilio de Palenque, Cartagena de Indias, DTyC., Bolívar, Colombia / Identification of iron deficiency risk by index soluble transferrin receptor-log ferritin in African descent men living at San Basilio de Palenque, Cartagena de Indias, DT and C., Bolivar, Colombia

En el ámbito mundial, sin distingo de raza, edad, género ni procedencia geográfica, la anemia de mayor prevalencia es la anemia ferropénica. De la misma forma, son insuficientes los reportes nacionales e internacionales sobre la prevalencia de los estados subclínicos de hierro, especialmente en comunidad afrodescendiente. El objetivo de la investigación fue caracterizar una población masculina afrodescendiente de 73 hombres sanos con edades comprendidas entre los 16 y 30 años mediante el comportamiento del índice (sTfR- Log F.S.), residentes en San Basilio de Palenque y en Cartagena de Indias DTyC. Se determinaron los índices primarios eritroides: hemoglobina (Hb), hematocrito (Hto), estudio de sangre periférica (E.S.P.); el receptor soluble de transferrina (sTfR), la ferritina sérica (F.S.) y el índice receptor soluble de transferrina – Logaritmo de la ferritina sérica (sTfR-Log F.S.) El análisis estadístico se realizó mediante el software de SPSS versión 17,0. En la población de San Basilio de Palenque el hallazgo hematológico por el algoritmo de mayor frecuencia se asoció a la enfermedad crónica acompañada de deficiencia de hierro en el 41.6%, seguido de deficiencia subclínica de hierro estadio II con un 33.3%. En Cartagena el hallazgo de mayor frecuencia fue la enfermedad crónica con deficiencia de hierro en 49%, seguido de deficiencia subclínica de hierro estadio II 20.41%. Las dos poblaciones evidenciaron un comportamiento hematológico similar en las diferentes variables, constituyéndose estos resultados en pioneros para futuras investigaciones de los estadios subclínicos que anteceden la deficiencia de hierro en afrodescendientes colombianos.