Dynamics of the MRSA Population in A Chilean Hospital: A Phylogenomic Analysis (2000-2016).

The global dissemination of methicillin-resistant Staphylococcus aureus (MRSA) is associated with the emergence and establishment of clones in specific geographic areas. The Chilean-Cordobes clone (ChC) (ST5-SCC mec I) has been the predominant MRSA clone in Chile since its first description in 1998, despite the report of other emerging MRSA clones in the last years. Here, we characterize the evolutionary history of MRSA from 2000 to 2016 in a Chilean tertiary healthcare center using phylogenomic analyses. We sequenced 469 MRSA isolates collected between 2000-2016 in a tertiary healthcare center in Chile. We evaluated the temporal trends of the circulating clones and performed a phylogenomic reconstruction to characterize the clonal dynamics. We found a significant increase in the diversity and richness of sequence types (STs; Spearman r=0.8748, p<0.0001) with a Shannon diversity index increasing from 0.221 in the year 2000 to 1.33 in 2016. The temporal trend analysis revealed that in the period 2000-2003 most of the isolates (94.2%; n=98) belonged to the ChC clone. However, since then, the frequency of the ChC clone has decreased over time, accounting for 52% of the collection in the 2013-2016 period. This decline was accompanied by the rise of two emerging MRSA lineages, ST105-SCC mec II and ST72-SCC mec VI. In conclusion, the ChC clone remains the most frequent MRSA lineage in Chile. However, this lineage is gradually being replaced by several emerging clones, the most important of which is clone ST105-SCC mec II. To the best of our knowledge, this is the largest study of MRSA clonal dynamics performed in South America. Importance: Methicillin-resistant Staphylococcus aureus (MRSA) is a major public health pathogen that disseminates through the emergence of successful dominant clones in specific geographic regions. Knowledge of the dissemination and molecular epidemiology of MRSA in Latin America is scarce and is largely based on small studies or classical typing techniques with several limitations to depict an accurate description of their genomic landscape. We used whole-genome sequencing to study 469 MRSA isolates collected between 2000-2016 in Chile to provide the largest and most detailed study of clonal dynamics of MRSA carried out in South America to date. We found a significant increase in the diversity of MRSA clones circulating over the 17-year study period. Additionally, we describe the emergence of two novel clones (ST105-SCCmecII and ST72-SCCmecVI), which have been gradually increasing their frequency over time. Our results drastically improve our understanding of the dissemination and update our knowledge about MRSA in Latin America.

Conocimiento y conductas asociadas al uso comunitario de antimicrobianos en adultos en Santiago de Chile

Introducción: El uso de antimicrobianos se asocia a efectos laterales como alergias, reacciones adversas específicas y emergencia de resistencia antimicrobiana. Resulta fundamental una comunicación de riesgo efectiva a la población general sobre su utilidad y potenciales problemas. Experiencias internacionales revelan un bajo grado de conocimiento en la comunidad en países sin políticas educativas dirigidas, lo que mejora tras su implementación; a nivel regional y nacional existen escasas publicaciones al respecto. Objetivo: Describir el grado de conocimiento y conductas sobre el uso de antimicrobianos en adultos de Santiago de Chile. Métodos: Estudio transversal realizado mediante una encuesta a adultos en Santiago de Chile, evaluando cuatro aspectos sobre antimicrobianos: conocimiento, uso reciente, conductas sobre su uso y nociones sobre resistencia antimicrobiana. Resultados: Se encuestaron 300 personas entre 18 y 81 años (tres fueron descartadas posteriormente), siendo 75% de ellas menores de 45 años. Un 65% de los encuestados cree que los antibióticos antimicrobianos son activos frente a virus, 51% cree que sirven para tratar el resfrío común y 32% los ha utilizado sin receta. Un 51% ha escuchado el término resistencia antimicrobiana y 33% conoce su definición correcta. Conclusión: El conocimiento sobre la utilidad y problemas de los antimicrobianos en población chilena es deficiente, lo que podría favorecer su uso inapropiado.

Background: Antimicrobials use is associated with diverse secondary effects, as allergies, specific adverse drug reactions and emergence of antimicrobial resistance. Effective risk communication to the general public about their uses and potential issues is critical. International experience reveals deficient knowledge in countries without educational policies regarding this issue, but their implementation can reverse such deficit. There are scarce publications at regional and national level about these topics. Aim: To describe the knowledge and behaviors regarding antimicrobial use in adults in Santiago de Chile. Methods: We conducted a cross-sectional study through a survey in 300 people in Santiago de Chile, evaluating 4 areas about antimicrobials: knowledge, use, behaviors, and antimicrobial resistance knowledge. Results: 297 people were surveyed with ages between 18 and 81 years old. Seventy-five percent of them were younger than 45 years old. 65% of the surveyed thinks antimicrobials works against viruses, 51% believes they work against the common cold and 32% of the population has used them without a prescription. Fifty-one percent of the sample has heard about antimicrobial resistance and 33% knows its correct definition. Conclusions: The Chilean population has an important deficit in antimicrobial knowledge and use.

Effectiveness and duration of a second COVID-19 vaccine booster

Using a prospective national cohort of 3.75 million individuals aged 20 or older, we evaluated the effectiveness against COVID-19 related ICU admissions and death of mRNA-based second vaccine boosters for four different three-dose background regimes: BNT162b2 primary series plus a homologous booster, and CoronaVac primary series plus an mRNA booster, a homologous booster, and a ChAdOx-1 booster. We estimated the vaccine effectiveness weekly from February 14 to August 15, 2022, by estimating hazard ratios of immunization over non-vaccination, accounting for relevant confounders. The overall adjusted effectiveness of a second mRNA booster shot was 88.2% (95%CI, 86.2-89.9) and 90.5% (95%CI 89.4-91.4) against ICU admissions and death, respectively. Vaccine effectiveness showed a mild decrease for all regimens and outcomes, probably associated with the introduction of BA.4 and BA.5 Omicron sub-lineages and immunity waning. The duration of effectiveness suggests that no additional boosters are needed six months following a second booster shot.

Tool for estimating the probability of having COVID-19 with one or more negative RT-PCR results

Early case detection and isolation of infected individuals are critical to controlling COVID-19. RT-PCR is considered the diagnosis gold standard, but false-negatives occur. Based on previous work, we built a user-friendly online tool to estimate the probability of having COVID-19 with negative RT-PCR results and thus avoid preventable SARS-CoV-2 transmission.

Rapid SARS-CoV-2 antigen detection by immunofluorescence - a new tool to detect infectivity

The evaluated SARS-CoV-2 antigen rapid fluorescence immunoassays reliably identified patients within the first 5 days of symptom onset, when respiratory secretions carried high viral loads. This high performance suggests that these tests might play an important role for future PCR-independent strategies to detect early or infective cases.

Clinical and Epidemiological Characteristics of the First Month of the Covid-19 Pandemic in Chile

IntroductionUnderstanding the clinical course and outcomes of patients with Covid-19 in underrepresented populations like Latin America is paramount. In this study, we report the clinical characteristics of Covid-19 in Chile, with a focus on subjects requiring hospitalization during the initial phases of the SARS-CoV-2 pandemic. MethodsThis is a single center study including all consecutive patients diagnosed with Covid-19 during the first month of the pandemic. Demographics, clinical characteristics and laboratory data were collected within 24 hours of admission. The primary outcome was a composite of ICU admission or all-cause, in-hospital mortality. ResultsDuring the first month of the pandemic, 381 patients were confirmed as positive for SARS-CoV-2 by molecular testing; 88 (23.1%) of them eventually required hospitalization. Median age of the cohort was 39 years (IQR 31-49). Overall mortality was 0.7% and 18 (3.7%) out of the 88 subjects who required hospitalization either died and/or required ICU. Increased body mass index (BMI), C-reactive protein levels (CRP) and the SaTO2/FiO2 index on admission were independently associated with a higher risk of ICU care or death. DiscussionThe lower mortality observed in our prospective cohort during the first month of SARS-Cov-2 pandemic was lower than previously reported. This finding could be due to a lower threshold for admission, a healthcare system not yet overburdened and a younger population, among other factors. BMI, CRP on admission were strong predictors for ICU care or all-cause, in-hospital mortality. Our data provide important information regarding the clinical course of Covid-19 in Latin America.

Head-to-head comparison of four antigen-based rapid detection tests for the diagnosis of SARS-CoV-2 in respiratory samples

In the context of the Covid-19 pandemic, the development and validation of rapid and easy-to-perform diagnostic methods are of high priority. We compared the performance of four rapid antigen detection tests for SARS-CoV-2 in respiratory samples. Immunochromatographic SARS-CoV-2 assays from RapiGEN, Liming bio, Savant, and Bioeasy were evaluated using universal transport medium containing naso-oropharyngeal swabs from suspected Covid-19 cases. The diagnostic accuracy was determined in comparison to SARS-CoV-2 RT-PCR. A total of 111 samples were included; 80 were RT-PCR positive. Median patients age was 40 years, 55% were female, and 88% presented within the first week after symptom onset. The evaluation of the Liming bio assay was discontinued due to insufficient performance. The overall sensitivity values of RapiGEN, Liming bio, and Bioeasy tests were 62.0% (CI95% 51.0-71.9), 16.7% (CI95% 10.0-26.5), and 85.0% (CI95% 75.6-91.2), respectively, with specificities of 100%. Sensitivity was significantly higher in samples with high viral loads (RapiGEN, 84.9%; Bioeasy, 100%). The study highlighted the significant heterogeneity of test performance among evaluated assays, which might have been influenced by the use of a non-validated sample material. The high sensitivity of some tests demonstrated that rapid antigen detection has the potential to serve as an alternative diagnostic method, especially in patients presenting with high viral loads in early phases of infection. This is particularly important in situations with limited access to RT-PCR or prolonged turnaround time. Further comparative evaluations are necessary to select products with high performance among the growing market of diagnostic tests for SARS-CoV-2.