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Macrolide antibiotics are recommended for the treatment of pneumococcal pneumonia and invasive pneumococcal disease (IPD). Prior to 2000, â¼10% of Streptococcus pneumoniae strains isolated from IPD cases in Latin American countries were resistant to macrolides. The mechanism of resistance to macrolides was associated mainly with the efflux pump known as the macrolide efflux genetic assembly, since most pneumococcal strains carried the mef(A/E) gene, whereas <6% strains carried both the methylase gene ermB and mef(A/E). In the first decade of this century, a significant increase in the prevalence of macrolide resistance was observed in pneumococcal strains in both Mexico and Peru. Approximately 30% of S. pneumoniae strains in these countries were already resistant to erythromycin, while the prevalence in Colombia, Argentina, and Brazil remained below 10%. During the last decade, we have been experiencing a worrisome increase in pneumococcal strains carrying resistance to macrolides, with a prevalence of up to 80% for resistance to erythromycin. The mechanism for disseminating macrolide resistance has evolved. Currently, more than 55% of invasive S. pneumoniae macrolide-resistant strains carry both the ermB and the mef(A/E)/mel genes. Lessons learned from the current macrolide resistance crisis in Latin America can inform interventions in other regions.
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Antibacterianos , Farmacorresistencia Bacteriana , Macrólidos , Infecciones Neumocócicas , Streptococcus pneumoniae , Humanos , Antibacterianos/farmacología , Antibacterianos/uso terapéutico , Farmacorresistencia Bacteriana/genética , América Latina/epidemiología , Macrólidos/farmacología , Macrólidos/uso terapéutico , Pruebas de Sensibilidad Microbiana , Infecciones Neumocócicas/microbiología , Infecciones Neumocócicas/epidemiología , Infecciones Neumocócicas/tratamiento farmacológico , Streptococcus pneumoniae/efectos de los fármacos , Streptococcus pneumoniae/genéticaRESUMEN
Worldwide, the COVID-19 pandemic caused by SARS-CoV-2 has enormously impacted healthcare systems, especially in low and middle-income countries. Coinfections with respiratory pathogens in COVID-19 patients may contribute to worse outcomes. This study identified the presence of 12 viral coinfections and pneumococcal carriers among individuals with SARS-CoV-2 infection in outpatient and community settings in Ecuador. From January 2020 to November 2021, 215 nasopharyngeal and nasal swabs were taken from individuals who reported symptoms of COVID-19 or had known exposure to someone with confirmed or suspected COVID-19. One hundred fifty-eight tested positive for SARS-CoV-2 by RT-qPCR and coinfections were detected in 12% (19/158) of SARS-CoV-2-positive patients; the most frequent coinfection was with influenza A virus at 4.4% (7/158; 95% CI: 1.2-7.6), followed by respiratory syncytial virus with 3.1% (5/158; 95% CI: 0.4-5.8), and finally rhinovirus and human coronavirus NL63 with 1.2% (2/158). Pneumococcal carriage was detected in 3.7% (6/158; 95% CI: 0.76-6.64) of SARS-CoV-2 cases. Influenza B, adenovirus, human metapneumovirus (HMPV), parainfluenza virus types 1, 2, and 3, and human coronavirus HKU1 were undetected. To our knowledge, this is the first study of coinfection of SARS-CoV-2 and respiratory pathogens performed on outpatients in Latin America. The high proportion of outpatients with viral coinfections reported in our cohort allows us to suggest that testing for SARS-CoV-2 and other common respiratory pathogens should be carried out to ensure accurate diagnoses, prompt patient treatment, and appropriate isolation.
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COVID-19 , Coinfección , Humanos , SARS-CoV-2 , COVID-19/epidemiología , Pacientes Ambulatorios , Coinfección/epidemiología , Pandemias , Ecuador/epidemiologíaAsunto(s)
COVID-19 , SARS-CoV-2 , Humanos , Ecuador , Poblaciones Vulnerables , Pandemias , Reacción en Cadena de la Polimerasa , Prueba de COVID-19Asunto(s)
COVID-19 , Humanos , COVID-19/diagnóstico , SARS-CoV-2 , Pruebas Inmunológicas , Bebidas , Sensibilidad y EspecificidadRESUMEN
INTRODUCTION: During the first months of the COVID-19 pandemic in Latin America, countries like Ecuador, Peru and Colombia experienced chaotic scenarios with public health systems collapsing and lack of testing capacity to control the spread of the virus. In main cities like Guayaquil in Ecuador, dramatic situations such as corpses in the streets were internationally broadcasted. METHODS: While the COVID-19 pandemic was devastating South America, SARS-CoV-2 transmission was successfully managed in the Galapagos Islands due to the implementation of a massive screening strategy including hospitalized and community-dwelling populations, and travel restrictions facilitated by its geographical location (972 km from the Ecuadorian continental territory). Floreana Island was one of the few locations in the world that remained COVID-19 free during 2020. RESULTS: In this study, we retrospectively analyzed the data related to SARS-CoV-2 massive testing campaigns from April to September 2020 in the Galapagos Islands, and found this territory to have the lowest positivity rate in South America (4.8-6.7%) and the highest testing ratio among Ecuadorian provinces (9.87% of the population, which is 2480 out of 25 124 inhabitants) during the first wave of the COVID-19 pandemic. CONCLUSION: This story of success was possible because of the interinstitutional collaboration between the regional government of Galapagos Islands (Consejo de Gobierno), the local authorities (Gobiernos Autonomos Descentralizados de Santa Cruz, San Cristobal and Isabela), the regional authorities from Ecuadorian Ministry of Health, the Agencia de Regulación y Control de la Bioseguridad y Cuarentena para Galápagos and Universidad de Las Américas.
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COVID-19 , SARS-CoV-2 , Humanos , Ecuador/epidemiología , COVID-19/epidemiología , Pandemias , Estudios Retrospectivos , América del SurRESUMEN
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an emerging virus that, since March 2020, has been responsible for a global and ongoing pandemic. Its rapid spread over the past nearly 3 years has caused novel variants to arise. To monitor the circulation and emergence of SARS-CoV-2 variants, surveillance systems based on nucleotide mutations are required. In this regard, we searched in the spike, ORF8, and nucleocapsid genes to detect variable sites among SARS-CoV-2 variants. We describe polymorphic genetic regions that enable us to differentiate between the Alpha, Beta, Gamma, Delta, and Omicron variants of concern (VoCs). We found 21 relevant mutations, 13 of which are unique for Omicron lineages BA.1/BA.1.1, BA.2, BA.3, BA.4, and BA.5. This genetic profile enables the discrimination between VoCs using only four reverse transcription PCR fragments and Sanger sequencing, offering a cheaper and faster alternative to whole-genome sequencing for SARS-CoV-2 surveillance. IMPORTANCE Our work describes a new (Sanger sequencing-based) screening methodology for SARS-CoV-2, performing PCR amplifications of a few target regions to detect diagnostic mutations between virus variants. Using the methodology developed in this work, we were able to discriminate between the following VoCs: Alpha, Beta, Gamma, Delta, and Omicron (BA.1/BA.1.1, BA.2, BA.3, BA.4, and BA.5). This becomes important, especially in low-income countries where current methodologies like next-generation sequencing have prohibitive costs. Furthermore, rapid detection would allow sanitary authorities to take rapid measures to limit the spread of the virus and therefore reduce the probability of new virus dispersion. With this methodological approach, 13 previously unreported diagnostic mutations among several Omicron lineages were found.
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Background: The SARS-CoV-2 gold standard detection method is an RT-qPCR with a previous step of viral RNA extraction from the patient sample either by using commercial automatized or manual extraction kits. This RNA extraction step is expensive and time demanding. Objective: The aim of our study was to evaluate the clinical performance of a simple SARS-CoV-2 detection protocol based on a fast and intense sample homogenization followed by direct RT-qPCR. Results: 388 nasopharyngeal swabs were analyzed in this study. 222 of them tested positive for SARS-CoV-2 by the gold standard RNA extraction and RT-qPCR method, while 166 tested negative. 197 of those 222 positive samples were also positive for the homogenization protocol, yielding a sensitivity of 88.74% (95% IC; 83.83 - 92.58). 166 of those negative samples were also negative for the homogenization protocol, so the specificity obtained was 97% (95% IC; 93.11 - 99.01). For Ct values below 30, meaning a viral load of 103 copies/uL, only 4 SARS-CoV-2 positive samples failed for the RNA extraction free method; for that limit of detection, the homogenizer-based method had a sensitivity of 97.92% (95% CI; 96.01 - 99.83). Conclusions: Our results show that this fast and cheap homogenization method for the SARS-CoV-2 detection by RT-qPCR is a reliable alternative of high sensitivity for potentially infectious SARS-CoV-2 positive patients. This RNA extraction free protocol would help to reduce diagnosis time and cost, and to overcome the RNA extraction kits shortage experienced during COVID-19 pandemic.
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COVID-19 , SARS-CoV-2 , Humanos , SARS-CoV-2/genética , COVID-19/diagnóstico , Prueba de COVID-19 , Pandemias , ARN Viral/genética , Sensibilidad y EspecificidadRESUMEN
Background: Neglected indigenous groups and underserved rural populations in Latin America are highly vulnerable to COVID-19 due to poor health infrastructure and limited access to SARS-CoV-2 diagnosis. The Andean region in Ecuador includes a large number of isolated rural mestizo and indigenous communities living under poverty conditions. Objective: We herein present a retrospective analysis of the surveillance SARS-CoV-2 testing in community-dwelling populations from four provinces in the Ecuadorian Andes, carried out during the first weeks after the national lockdown was lifted in June 2020. Results: A total number of 1,021 people were tested for SARS-CoV-2 by RT-qPCR, resulting in an overall high infection rate of 26.2% (268/1,021, 95% CI: 23.6-29%), which was over 50% in several communities. Interestingly, community-dwelling super spreaders with viral loads over 108 copies/mL represented 7.46% (20/268, 95% CI: 4.8-11.1%) of the SARS-CoV-2 infected population. Conclusion: These results support that COVID-19 community transmission in rural communities from the Andean region was happening at the early stages of the COVID-19 pandemic in Ecuador and point out the weakness of the COVID-19 control program. Community-dwelling individuals in neglected rural and indigenous communities should be considered for a successful control and surveillance program in future pandemics in low- and middle-income countries.
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Aim: The COVID-19 outbreak has already caused more than 6.5 million deaths, overwhelming health systems worldwide. The unusual demand for funeral home services could make these workers a potential risk group for occupational exposure to SARS-CoV-2 associated with corpses management for COVID-19 patients. Methodology: This is a cross-sectional study aimed to describe the infection rate of SARS-CoV-2 in funeral home staff by testing them with RT-qPCR in Quito, Ecuador. A total of 232 funeral home workers, representing more than 40% of funeral home personnel in Quito, were included in the study, in June 2020, immediately after the population lockdown was lifted in Ecuador. Results: A total of 48 individuals tested positive for SARS-CoV-2, yielding an infection rate of 20.7%. The SARS-CoV-2 infection rate was 18.1 and 20.0% among personnel managing corpses or not managing corpses, respectively. Among the SARS-CoV-2 positive patients, 81.3% reported no symptoms related to COVID-19, and 3 individuals had high viral loads over 108 copies/ml. Conclusion: The high SARS-CoV-2 infection rate in funeral home staff suggested a potential occupational risk for COVID-19 but not related to corpses management. Public health guidelines for safe corpses management for COVID-19 victims and safe funeral services should be reinforced.
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COVID-19 , Funerarias , Humanos , COVID-19/epidemiología , Estudios Transversales , Ecuador/epidemiología , SARS-CoV-2 , Control de Enfermedades Transmisibles , CadáverRESUMEN
SARS-CoV-2 has spread throughout the world, including areas located at high or very high altitudes. There is a debate about the role of high altitude hypoxia on viral transmission, incidence, and COVID-19 related mortality. This is the first comparison of SARS-CoV-2 viral load across elevations ranging from 0 to 4300 m. To describe the SARS-CoV-2 viral load across samples coming from 62 cities located at low, moderate, high, and very high altitudes in Ecuador. An observational analysis of viral loads among nasopharyngeal swap samples coming from a cohort of 4929 patients with a RT-qPCR test positive for SARS-CoV-2. The relationship between high and low altitude only considering our sample of 4929 persons is equal in both cases and not significative (p-value 0.19). In the case of low altitude, adding the sex variable to the analysis, it was possible to find a significative difference between men and women (p-value < 0.05). Considering initially sex and then altitude, it was possible to find a significative difference between high and low altitude for men (p-value 0.05). There is not enough evidence to state that viral load is affected directly by altitude range but adding a new variable as sex in the analysis shows that the presence of new variables influences the relationship of altitude range and viral load. There is no evidence that viral loads (Ct and copies/ml) differ at low or high altitude. Using sex as a co-factor, we found that men have higher viral loads than women at low and moderate altitude locations, while living at high altitude, no differences were found. When Ct values were aggregated by low, moderate, and high viral load, we found no significant differences when sex was excluded from the analysis. We conclude that viral load is not directly affected by altitude, but COVID-19 incidence and mortality are rather affected by socio-demographic and idiosyncratic dynamics.
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COVID-19 , SARS-CoV-2 , Altitud , Femenino , Humanos , Masculino , Nasofaringe , Carga ViralAsunto(s)
COVID-19 , SARS-CoV-2 , Humanos , Prueba de COVID-19 , América Latina , España , Ecuador/epidemiología , Carga ViralRESUMEN
Background: Neglected ethnic minorities from underserved rural populations in Latin America are highly vulnerable to coronavirus disease 2019 (COVID-19) due to poor health infrastructure and limited access to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) diagnosis. Esmeraldas is a mainly rural province of the Coastal Region of Ecuador characterized by a high presence of Afro-Ecuadorian population living under poverty conditions. Objective: We herein present a retrospective analysis of the surveillance SARS-CoV-2 testing in community-dwelling population from Esmeraldas carried out by our university laboratory in collaboration with regional health authorities during the first week of October 2020, in a region where no public SARS-CoV-2 detection laboratory was available at that time. Results: A total number of 1,259 people were tested for SARS-CoV-2 by Reverse Transcription quantitative Polimerasa Chain Reaction (RT-qPCR), resulting in an overall infection rate of 7.7% (97/1259, 95% CI: [6.32-9.35%]) for SARS-CoV-2, up to 12.1% in some communities. Interestingly, community-dwelling super spreaders with viral loads over 108 copies/ml represented 6.2% of the SARS-CoV-2-infected population. Furthermore, anti-SARS-CoV-2 IgG serological tests were applied to the same study group, yielding an overall seroprevalence of 11.68% (95% CI: [9.98-13.62%]) but as high as 24.47% at some communities. Conclusion: These results support active COVID-19 community transmission in Esmeraldas province during the first semester of the COVID-19 pandemic as it has been shown for other rural communities in the Ecuadorian Coastal Region.
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During the second year of the COVID-19 pandemic, the use of Rapid Diagnosis Antigen Tests (RDAgTs) for SARS-CoV-2 detection has substantially increased as some of the brands available in the market were certified for clinical use by international regulatory agencies. RDAgTs are a fast and cheap tool for SARS-CoV-2 surveillance with great potential to improve testing capacities in middle- and low-income countries compared to the gold standard RT-qPCR. However, as the clinical performance of RDAgTs has been shown to vary greatly between the commercial brands available, evaluation studies are necessary. Moreover, the available evaluation has been done in high-income countries while SARS-CoV-2 transmission is also actively happening in developing countries, many of which are located in tropical latitudes where cross-reactivity with other infectious agents is highly prevalent, which could compromise RDAgT specificity. Moreover, unreported mutations and/or new SARS-CoV-2 variants may compromise RDAgT sensitivity as genomic surveillance is limited in these settings. Here we describe a multicenter and manufacturer-independent evaluation of the clinical performance and analytical sensitivity of three different RDAgTs brands available in South America from three companies, Rapigen (South Korea), SD-Biosensor (South Korea), and Certest (Spain), compared to the gold standard RT-qPCR. A total number of 1,646 nasopharyngeal swabs from community-dwelling individuals were included in the study, and 379 of them were SARS-CoV-2 positive by RT-qPCR. The overall sensitivity for each RDAgT was 79% (IC95%: 72 - 86.2), 64.2% (IC95%: 56.7 - 71.6), and 45.8% (IC95%: 35.8 - 55.8) for SD-Biosensor, Certest, and Rapigen, respectively. The overall specificity for each RDAgT was 100%, 97.7% (IC95%: 96.8 - 98.6), and 100% for SD-Biosensor, Certest, and Rapigen, respectively. However, the limit of detection (LoD) to achieve a sensitivity over 90% was substantially lower for Certest RDAgT (102 copies/uL) compared to SD-Biosensor (103 copies/uL) or Rapigen (106 copies/uL) RDAgTs, considering that the gold standard RT-qPCR method used in this study has a high sensitivity of 97.7% and low LoD of 5 copies/uL. Additionally, the Certest RDAgT also showed an improved sensitivity up to 79.7% (IC95%: 70.2 - 89.2) for symptomatic individuals. Finally, the slight reduction in specificity for Certest RDAgTs was only associated with one of the laboratories performing this study, pointing out the need for locally assessed evaluation for RDAgTs like this one carried out in Ecuador. In conclusion, two of the three the RDAgTs tested in this study are a fast, cheap, and point of care tool for SARS-CoV-2 surveillance and reliable enough to detect SARS-CoV-2 infectious individuals.
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COVID-19 , SARS-CoV-2 , COVID-19/diagnóstico , Humanos , Vida Independiente , Pandemias , SARS-CoV-2/genética , Sensibilidad y EspecificidadRESUMEN
BACKGROUND: Dozens of commercial RT-qPCR kits for SARS-CoV-2 detection are available with or without Emergency Use Authorization (EUA) by FDA or other regulatory agencies. OBJECTIVE: We evaluated the clinical performance of two SARS-CoV-2 RT-PCR kits designed and produced in South America, "COVID-19 RT-PCR Real TM FAST (CY5)" (ATGen, Uruguay) and "ECUGEN SARS-CoV-2 RT-qPCR" (UDLA-STARNEWCORP, Ecuador), for RT-qPCR SARS-CoV2 detection using "TaqMan 2019-nCoV Assay Kit v1" (Thermofisher, USA) as a gold standard technique. RESULTS: We report a great clinical performance and analytical sensitivity for the two South American kits with sensitivity values of 96.4 and 100%, specificity of 100% and limit of detection in the range of 10 copies/uL of RNA extraction. CONCLUSIONS: "COVID-19 RT-PCR Real TM FAST (CY5)" and "ECUGEN SARS-CoV-2 RT-qPCR" kits are reliable SARS-CoV-2 tests made in South America that have been extensively used in Uruguay, Argentina, Brazil, Bolivia and Ecuador. These locally produced SARS-CoV-2 tests have contributed to overcome supply shortages and reduce diagnosis cost, while maintaining the high quality standards of FDA EUA commercially available kits. This approach could be extended for other diagnostic products to improve infectious diseases surveillance at middle and low income countries beyond COVID-19 pandemic.
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COVID-19 , SARS-CoV-2 , Brasil , COVID-19/diagnóstico , Carbocianinas , Ecuador/epidemiología , Humanos , Pandemias , ARN Viral/análisis , ARN Viral/genética , Reacción en Cadena de la Polimerasa de Transcriptasa Inversa , SARS-CoV-2/genética , Sensibilidad y Especificidad , UruguayRESUMEN
Neglected rural communities in Latin America are highly vulnerable to COVID-19 due to a poor health infrastructure and limited access to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) diagnosis. Manabí is a province of the Coastal Region of Ecuador characterized by a high prevalence of rural population living under poverty conditions. In the current study, we present the retrospective analysis of the results of a massive SARS-CoV-2 testing operation in nonhospitalized populations from Manabí carried out from August to September 2020. A total of 4,003 people from 15 cantons were tested for SARS-CoV-2 by reverse-transcriptase quantitative polymerase chain reaction, resulting in an overall infection rate of 16.13% for SARS-CoV-2, with several communities > 30%. Moreover, 29 SARS-CoV-2 super-spreader community-dwelling individuals with viral loads above 108 copies/mL were found. These results support that uncontrolled COVID-19 community transmission was happening in Manabí during the first semester of COVID-19 pandemic. This report endorses the utility of massive SARS-CoV-2 testing among asymptomatic population for control and surveillance of COVID-19.
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Prueba de COVID-19/estadística & datos numéricos , COVID-19/epidemiología , COVID-19/transmisión , Población Rural , SARS-CoV-2/genética , Adolescente , Adulto , Anciano , Anciano de 80 o más Años , COVID-19/diagnóstico , Prueba de Ácido Nucleico para COVID-19/estadística & datos numéricos , Niño , Preescolar , Ecuador/epidemiología , Femenino , Humanos , Lactante , Masculino , Persona de Mediana Edad , Nasofaringe/virología , ARN Viral/aislamiento & purificación , Estudios Retrospectivos , Adulto JovenRESUMEN
BACKGROUND: One of the constraints in containing the impact of the COVID-19 pandemic in Ecuador is limited testing capacity, especially in high-risk populations such as people living in humanitarian shelters. OBJECTIVES: The "United Nations High Commissioner for Refugees" office in Ecuador in collaboration with "Universidad de Las Américas" performed surveillance screening at shelters for women victims of gender-based violence. They had been granted access to RT-qPCR tests for SARS-CoV-2 diagnosis since July 2020, a few weeks after the general population lockdown was lifted. RESULTS: From 411 people tested, 52 tests were SARS-CoV-2 positive, yielding an overall high attack rate of 12.65%. Moreover, COVID-19 outbreaks were found in nine of 11 shelters that were included in the study. While attacks rates varied among shelters, no association was found with occupancy. CONCLUSION: This study is key to clarifying the epidemiological situation in this highly vulnerable population in Latin America. It highlights the importance of mass testing beyond the symptomatic population to prevent the spread of COVID-19.
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COVID-19 , Violencia de Género , Prueba de COVID-19 , Control de Enfermedades Transmisibles , Brotes de Enfermedades , Ecuador/epidemiología , Femenino , Humanos , Pandemias , SARS-CoV-2RESUMEN
COVID-19 pandemic has challenged public health systems worldwide, particularly affecting developing countries in Latin America like Ecuador. In this report, we exposed the fundamental role of the Ecuadorian universities to improve COVID-19 surveillance in the country, with an overall contribution over 15% of the total SARS-CoV-2 RT-PCR tests done. We highlight the role of our university during the first semester of the COVID-19 pandemic, contributing to a massive free SARS-CoV-2 testing up to almost 10% of the total diagnosis completed in the country, mainly focus on underserved urban, rural and indigenous communities. Finally, we described our contribution to a high quality and low-cost SARS-CoV-2 RT-PCR diagnostic in Ecuador.
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Background: At the beginning of the COVID-19 pandemic, health workers and first-responders, such as police officers, were in charge of trying to contain a disease that was unknown at that time. The lack of information and the tremendous need to contain new outbreaks put police officers at higher risk. Methodology: A cross-sectional study was conducted to describe SARS-CoV-2 infection rates among Police Special Forces Officers in Quito, Ecuador. In this study, 163 community-dwelling police officers from elite divisions voluntarily participated in our SARS-CoV-2 detection program using reverse transcription quantitative real-time PCR (RT-qPCR). Results: A total of 20 out of 163 police officers tested positive for SARS-CoV-2, yielding an infection rate of 12.3%. Within this cohort, 10% (2/20) of SARS-CoV-2 positive individuals were potentially super spreaders with viral loads over 108 copies/ul. About 85% of the SARS-CoV-2 positive individuals were asymptomatic and 15% reported mild symptoms related to COVID-19. Conclusions: We found a high SARS-CoV-2 infection rate within the special forces police officers that, beyond a high health risk for themselves, their families, and coworkers. Our results point out the need for permanent SARS-CoV-2 testing among asymptomatic essential workers and first-responders to avoid local outbreaks and to prevent work-place absenteeism among police special units.