Background: Tuberculosis is a serious infectious disease affecting millions of people. In spite of efforts to reduce the disease, increasing antibiotic resistance has contributed to persist in the top 10 causes of death worldwide. In fact, the increased cases of multi (MDR) and extreme drug resistance (XDR) worldwide remains the main challenge for tuberculosis control. Whole genome sequencing is a powerful tool for predicting drug resistance-related variants, studying lineages, tracking transmission, and defining outbreaks. This study presents the identification and characterization of resistant clinical isolates of Mycobacterium tuberculosis including a phylogenetic and molecular resistance profile study by sequencing the complete genome of 24 strains from different provinces of Ecuador. Results: Genomic sequencing was used to identify the variants causing resistance. A total of 15/21 isolates were identified as MDR, 4/21 as pre-XDR and 2/21 as XDR, with three isolates discarded due to low quality; the main sub-lineage was LAM (61.9%) and Haarlem (19%) but clades X, T and S were identified. Of the six pre-XDR and XDR strains, it is noteworthy that five come from females; four come from the LAM sub-lineage and two correspond to the X-class sub-lineage. A core genome of 3,750 genes, distributed in 295 subsystems, was determined. Among these, 64 proteins related to virulence and implicated in the pathogenicity of M. tuberculosis and 66 possible pharmacological targets stand out. Most variants result in nonsynonymous amino acid changes and the most frequent genotypes were identified as conferring resistance to rifampicin, isoniazid, ethambutol, para-aminosalicylic acid and streptomycin. However, an increase in the resistance to fluoroquinolones was detected. Conclusion: This work shows for the first time the variability of circulating resistant strains between men and women in Ecuador, highlighting the usefulness of genomic sequencing for the identification of emerging resistance. In this regard, we found an increase in fluoroquinolone resistance. Further sampling effort is needed to determine the total variability and associations with the metadata obtained to generate better health policies.

Introduction: Tuberculosis (TB) is among the deadliest diseases worldwide, and its impact is mainly due to the continuous emergence of resistant isolates during treatment due to the laborious process of resistance diagnosis, nonadherence to treatment and circulation of previously resistant isolates of Mycobacterium tuberculosis. In this study, we evaluated the performance and functionalities of web-based tools, including Mykrobe, TB-profiler, PhyResSE, KvarQ, and SAM-TB, for detecting resistance in 88 Ecuadorian isolates of Mycobacterium tuberculosis drug susceptibility tested previously. Statistical analysis was used to determine the correlation between genomic and phenotypic analysis. Our results showed that with the exception of KvarQ, all tools had the highest correlation with the conventional drug susceptibility test (DST) for global resistance detection (98% agreement and 0.941 Cohen’s kappa), while SAM-TB, PhyResSE, TB-profiler and Mykrobe had better correlations with DST for first-line drug analysis individually. We also identified that in our study, only 50% of mutations characterized by the web-based tools in the rpoB, katG, embB, pncA, gyrA and rrs regions were canonical and included in the World Health Organization (WHO) catalogue. Our findings suggest that SAM-TB, PhyResSE, TB-profiler and Mykrobe were efficient in determining canonical resistance-related mutations, but more analysis is needed to improve second-line detection. Improving surveillance programs using whole-genome sequencing tools for first-line drugs, MDR-TB and XDR-TB is essential to understand the molecular epidemiology of TB in Ecuador. Importance: Tuberculosis, an infectious disease caused by Mycobacterium tuberculosis, most commonly affects the lungs and is often spread through the air when infected people cough, sneeze, or spit. However, despite the existence of effective drug treatment, patient adherence, long duration of treatment, and late diagnosis have reduced the effectiveness of therapy and increased drug resistance. The increase in resistant cases, added to the impact of the COVID-19 pandemic, has highlighted the importance of implementing efficient and timely diagnostic methodologies worldwide. The significance of our research is in evaluating and identifying a more efficient and user-friendly web-based tool to characterize resistance in Mycobacterium tuberculosis by whole-genome sequencing, which will allow more routine application to improve TB strain surveillance programs locally.

Tuberculosis is a global public health concern, and understanding Mycobacterium tuberculosis transmission routes and genetic diversity of M. tuberculosis is crucial for outbreak control. This study aimed to explore the genomic epidemiology and genetic diversity of M. tuberculosis in Ecuador by analyzing 88 local isolates and 415 public genomes from 19 countries within the Euro-American lineage (L4). Our results revealed significant genomic diversity among the isolates, particularly in the genes related to protein processing, carbohydrate metabolism, lipid metabolism, and xenobiotic biodegradation and metabolism. The population structure analysis showed that sub-lineages 4.3.2/3 (35.4%), 4.1.2.1 (22.7%), 4.4.1 (12.7%), and 4.1.1. (10.7%) were the most prevalent. Phylogenetic and transmission network analyses suggest that these isolates circulating within Ecuador share genetic ties with isolates from other continents, implying historical and ongoing intercontinental transmission events. Our findings underscore the importance of integrating genomic data into public health strategies for tuberculosis control and suggest that enhanced genomic surveillance is essential for understanding and mitigating the global spread of M. tuberculosis. This study provides a comprehensive genomic framework for future epidemiological investigations and control measures targeting M. tuberculosis L4 in Ecuador.

The sunblotch disease is one of the diseases that affects avocado (Persea americana Mill) crops in particular, causing serious crop losses. The causal agent is the avocado sunblotch viroid (ASBVd), a circular RNA-based pathogen built of 247 nucleotides, which causes stem discoloration, bleaching, variegation, and distortion on the leaves and sunken yellow or red blotches on the fruits. In this study, a novel SYBR green-based real-time RT-PCR (RT-qPCR) assay specific for ASB viroid was developed. The assay was followed by a standard curve and a melting curve analysis for the detection, identification, and quantification of the full-length ASB viroid. The assay’s lower limit of detection in the samples of avocado leaves was 8.8 copies/μl. The RT-qPCR was 100 times more sensitive to ASBVd than the conventional RT-PCR. The melting curve analysis showed a variation in the specific melting temperature (Tm) between positive samples, probably due to the alteration in the nucleotide sequences of viroids. In conclusion, the use of RT-qPCR assays established in this study, as a routine diagnostic method in breeding programs, could decrease the viroid incidence in avocado crops and its further accumulation in plants.

Con el objetivo de caracterizar la calidad seminal de hombres en un centro de reproducción asistida de la ciudad Guayaquil (Ecuador), se colectaron 204 muestras de semen de pacientes con problemas de fertilidad de entre 20 y 57 años, atendidos entre mayo de 2017 y septiembre de 2018. Se realizó un espermograma básico a cada muestra, siguiendo las recomendaciones del manual para la examinación y procesamiento de semen humano. El 27,4% de las muestras presentó normozoospermia. Dentro de las alteraciones la teratozoospermia fue de 27,9%, oligoteratozoospermia del 8,8%, evidenciándose mayor número en pacientes de 30 a 39 años. Un alto porcentaje de pacientes presentan una calidad del semen y morfología espermática por debajo los limites de referencia establecidos por la Organización Mundial de la Salud.

Las infecciones oportunistas son una de las principales causas de hospitalización y morbilidad de pacientes VIH/SIDA. En Latinoamérica, toxoplasmosis cerebral, candidiasis y tuberculosis pulmonar han sido reportadas como las más recurrentes en este grupo de pacientes de riesgo. El conocimiento del comportamiento de las infecciones oportunistas en pacientes VIH/SIDA dentro de cada país es importante, permitiendo aplicar estrategias oportunas de control y tratamiento, por tal motivo se realizó un trabajo para conocer la frecuencia de infecciones oportunistas en pacientes VIH atendidos en el Hospital de Infectología, Guayaquil, Ecuador, durante el año 2017. Se desarrolló un estudio observacional, descriptivo, retrospectivo a partir de 143 registro de pacientes que ingresaron al Hospital de Infectología. La información se analizó en el programa SPSS, frecuencias y porcentajes para las variables categóricas, y la media y desviación estándar para las variables cuantitativas, fueron empleadas para la estadística descriptiva. Se obtuvo como resultado que la Histoplasmosis fue la principal infección oportunista presente en el 55,7% de los casos, seguido por tuberculosis pulmonar (15,6%) como segunda causa. A pesar de los grandes avances en el tratamiento del VIH/SIDA, un número considerable de pacientes aún son afectados por infecciones oportunistas en el país, por lo cual una detección oportuna del agente causal es necesaria.