Prevalence and Species Distribution of Candida Clinical Isolates in a Tertiary Care Hospital in Ecuador Tested from January 2019 to February 2020.

The incidence of candidemia in healthcare centers is associated with high morbidity and mortality. Frequency varies significantly among regions, with some species being more prevalent than others in Latin America. In this study, 191 clinical Candida isolates were collected from a major hospital in Ecuador from January 2019 to February 2020 aiming to assess their prevalence and distribution. After data processing, 168 isolates characterized by the VITEK 2 system were subsequently identified by ITS sequencing. Results showed diverse Candida species distributions, with C. albicans and C. tropicalis being the most prevalent across different clinical sources. In hospitalized individuals, C. tropicalis (38%) and C. albicans (37%) were the most prevalent, followed by, C. parapsilosis (16%), C. glabrata (5%), and other non-Candida albicans (NCA) species (6%). Conversely, C. parapsilosis (48%), C. albicans (20%), and C. glabrata (14%), associated with candidemia, were the most common in blood and CSF. Additionally, uncommon NCA species such as C. haemulonii, C. kefyr, and C. pelliculosa were identified in Ecuador for the first time. Discrepancies in species identification were observed between the VITEK 2 system and ITS sequencing, coinciding at 85%. This highlights the need for ongoing surveillance and identification efforts in Ecuador's clinical and epidemiological settings.

A precision overview of genomic resistance screening in Ecuadorian isolates of Mycobacterium tuberculosis using web-based bioinformatics tools.

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.

Comparative genomics of drug-resistant strains of Mycobacterium tuberculosis in Ecuador.

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.

Impact of biosecurity measures, social pressure and bullying on attitudes, perceptions, and job satisfaction levels among healthcare workers during the COVID-19 pandemic: a cross-sectional survey.

INTRODUCTION: The extent and nature of social pressure and bullying towards healthcare workers (HCWs) during the COVID-19 remains unclear. The following study identifies the effect of social pressure and bullying directed towards HCWs when using biosecurity measures during the COVID-19 pandemic; further, the impact on perceptions, attitudes and job satisfaction level is also explored. METHODOLOGY: We conducted a cross-sectional survey-based study among 684 Ecuadorian HCWs. The survey consisted of 38 questions related to the frequency, attitudes, and perceptions of biosecurity measures during the COVID-19 pandemic. Exploratory factor analysis was performed to assess the validity of the questionnaire. Associations between variables were analysed using χ2 and Fisher's exact test. Using SPSS V.25, qualitative and quantitative data were analysed. RESULTS: Of the 684 participants, 175 (25.59%) experienced or felt bullying or social pressure during the COVID-19 pandemic associated with the use of biosecurity measures. Of these, 40.6% believed it was due to an imbalance of power in the workplace. The perception that HCWs wearing personal protective equipment resulting in bullying was noted in 12% of the respondents. Job satisfaction was positive among 73% of the respondents. Gender (female) and type of institution (public) were noted to contribute towards job satisfaction and bullying experiences. CONCLUSION: Exposure to social bullying and pressure due to the use of biosecurity measures during the COVID-19 pandemic may result in reduced job satisfaction and thoughts about quitting work.

Omicron Sub-Lineages (BA.1.1.529 + BA.*) Current Status in Ecuador.

The Omicron variant of SARS-CoV-2 is the latest pandemic lineage causing COVID-19. Despite having a vaccination rate ≥85%, Ecuador recorded a high incidence of Omicron from December 2021 to March 2022. Since Omicron emerged, it has evolved into multiple sub-lineages with distinct prevalence in different regions. In this work, we use all Omicron sequences from Ecuador available at GISAID until March 2022 and the software Nextclade and Pangolin to identify which lineages circulate in this country. We detected 12 different sub-lineages (BA.1, BA.1.1, BA.1.1.1, BA.1.1.14, BA.1.1.2, BA.1.14, BA.1.15, BA.1.16, BA.1.17, BA.1.6, BA.2, BA.2.3), which have been reported in Africa, America, Europe, and Asia, suggesting multiple introduction events. Sub-lineages BA.1 and BA.1.1 were the most prevalent. Genomic surveillance must continue to evaluate the dynamics of current sub-lineages, the early introduction of new ones and vaccine efficacy against evolving SARS-CoV-2.

Adverse reactions following COVID-19 vaccination: An Ecuadorian experience.

BACKGROUND: Limited large-scale studies have been conducted to investigate the adverse effects of COVID-19 vaccine in Latin America, particularly among the healthcare worker (HCW) population in Ecuador. The objective of this study was to assess a cohort of Ecuadorian healthcare workers for adverse reactions following vaccination with the Pfizer-BioNTech vaccine. METHODS: We conducted an observational cross-sectional study to assess the potential adverse reactions to the Pfizer-BioNTech COVID-19 vaccine among a sample of healthcare workers (HCWs) in the city of Guayaquil, Ecuador, from March to May 2021. RESULTS: The sample comprised 1291 patients, with a mean age of 39.3 years (SD, 13.5). In general, 79% (N = 1020) of participants presented an adverse effect of any type at first dose, while 75.1% (N = 969) did so at the second dose. Pain at the puncture site was the most common adverse effect overall after either the first (68.4%) and second (55.6%) dose. Regarding anaphylaxis, no participant developed the condition after the first dose, and only 0.2% (N = 2) developing it at the second dose. No fatalities were reported. CONCLUSION: Our findings suggest that adverse reactions following COVID-19 vaccination with the Pfizer-BioNTech vaccine are relatively common, albeit often mild and self-limited. Consistent with the literature there were few cases of anaphylaxis, and no deaths that could be attributed to the inoculation with the vaccine. We hope our findings can help to reassure the public that benefits of vaccination highly outweigh the risks and contribute to the effort of reducing vaccine hesitancy among those who are concerned about the safety and potential side effects.

Genomic epidemiology of SARS-CoV-2 transmission lineages in Ecuador.

Characterisation of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) genetic diversity through space and time can reveal trends in virus importation and domestic circulation and permit the exploration of questions regarding the early transmission dynamics. Here, we present a detailed description of SARS-CoV-2 genomic epidemiology in Ecuador, one of the hardest hit countries during the early stages of the coronavirus-19 pandemic. We generated and analysed 160 whole genome sequences sampled from all provinces of Ecuador in 2020. Molecular clock and phylogeographic analysis of these sequences in the context of global SARS-CoV-2 diversity enable us to identify and characterise individual transmission lineages within Ecuador, explore their spatiotemporal distributions, and consider their introduction and domestic circulation. Our results reveal a pattern of multiple international importations across the country, with apparent differences between key provinces. Transmission lineages were mostly introduced before the implementation of non-pharmaceutical interventions, with differential degrees of persistence and national dissemination.

Genomic epidemiology of SARS-CoV-2 transmission lineages in Ecuador.

Characterisation of SARS-CoV-2 genetic diversity through space and time can reveal trends in virus importation and domestic circulation, and permit the exploration of questions regarding the early transmission dynamics. Here we present a detailed description of SARS-CoV-2 genomic epidemiology in Ecuador, one of the hardest hit countries during the early stages of the COVID-19 pandemic. We generate and analyse 160 whole genome sequences sampled from all provinces of Ecuador in 2020. Molecular clock and phylgeographic analysis of these sequences in the context of global SARS-CoV-2 diversity enable us to identify and characterise individual transmission lineages within Ecuador, explore their spatiotemporal distributions, and consider their introduction and domestic circulation. Our results reveal a pattern of multiple international importations across the country, with apparent differences between key provinces. Transmission lineages were mostly introduced before the implementation of non-pharmaceutical interventions (NPIs), with differential degrees of persistence and national dissemination.

Assessment of depression, anxiety and stress levels in the Ecuadorian general population during social isolation due to the COVID-19 outbreak: a cross-sectional study.

BACKGROUND: Coronavirus disease 2019 (COVID-19) has become a global pandemic with serious consequences that have led to the implementation of unprecedented social isolation measures. At the early stages of the pandemic, Ecuador was one of the most affected countries in Latin America. The objective of this study was to assess the levels of depression, anxiety and stress in the Ecuadorian general population during the social isolation period due to COVID-19. METHODS: A web-based survey consisting of 31 short-answer and multiple-choice questions was administered to the general population from April 22-May 3, 2020. Mental health status was assessed through the Depression, Anxiety and Stress Scale-21 Items (DASS-21) questionnaire. Ordinal logistic analyses were used to identify potential risk factors associated with the severity of mental health issues. RESULTS: A total of 626 individuals were included. Most of them were females (60.5%), and their mean age was 29.6 ± 11.7 years. Approximately 17.7% of the respondents had moderate to very severe levels of depression, 30.7% had similar levels of anxiety, and 14.2% experienced stress. Female sex, younger age, student status, and having a relative diagnosed with COVID-19 were associated with significantly higher levels of depression, anxiety and stress. Ordinal regression models showed that being a student was a risk factor for having more severe levels of depression (OR = 3.67; 95% CI = 2.56-5.26, p: 0.0001), anxiety (OR= 1.86; 95% CI= 1.35-2.55, p: 0.0001), and stress (OR = 2.17; 95% CI= 1.47-3.19, p: 0.0001). Having a relative with COVID-19 was also found to be a risk factor only for depression (OR= 1.70; 95% CI= 1.03-2.80, p: 0.036) and anxiety (OR = 2.17; 95% CI= 1.35-3.47, p: 0.001). Additionally, male sex,  older age, and having more children were found to be protective factors for the three conditions. CONCLUSIONS: Our findings suggest that social isolation due to the COVID-19 outbreak has impacted the mental health of the general population in Ecuador. We identified potential risk and protective factors that could serve as a foundation from which to develop psychological strategies to safeguard the mental health of our population during the current pandemic.

SARS-CoV-2 genome sequencing from COVID-19 in Ecuadorian patients: a whole country analysis.

SARS-CoV-2, the etiological agent of COVID-19, was first described in Wuhan, China in December 2019 and has now spread globally. Ecuador was the second country in South America to confirm cases and Guayaquil was one of the first cities in the world to experience high mortality due to COVID-19. The aim of this study was to describe the lineages circulating throughout the country and to compare the mutations in local variants, to the reference strain. In this work we used the MinION platform (Oxford Nanopore Technologies) to sequence the whole SARS-CoV-2 genomes of 119 patients from all provinces of Ecuador, using the ARTIC network protocols. Our data from lineage assignment of the one hundred and nineteen whole genomes revealed twenty different lineages. All genomes presented differences in the S gene compared to the Wuhan reference strain, being the D614G amino acid replacement the most common change. The B.1.1.119 lineage was the most frequent and was found in several locations in the Coast and Andean region. Three sequences were assigned to the new B.1.1.7 lineage. Our work is an important contribution to the understanding of the epidemiology of SARS-CoV-2 in Ecuador and South America.