The first wave of the COVID-19 epidemic in Spain was associated with early introductions and fast spread of a dominating genetic variant.

The coronavirus disease 2019 (COVID-19) pandemic has affected the world radically since 2020. Spain was one of the European countries with the highest incidence during the first wave. As a part of a consortium to monitor and study the evolution of the epidemic, we sequenced 2,170 samples, diagnosed mostly before lockdown measures. Here, we identified at least 500 introductions from multiple international sources and documented the early rise of two dominant Spanish epidemic clades (SECs), probably amplified by superspreading events. Both SECs were related closely to the initial Asian variants of SARS-CoV-2 and spread widely across Spain. We inferred a substantial reduction in the effective reproductive number of both SECs due to public-health interventions (Re < 1), also reflected in the replacement of SECs by a new variant over the summer of 2020. In summary, we reveal a notable difference in the initial genetic makeup of SARS-CoV-2 in Spain compared with other European countries and show evidence to support the effectiveness of lockdown measures in controlling virus spread, even for the most successful genetic variants.

Skin manifestations during the COVID-19 pandemic in the pediatric emergency department.

BACKGROUND: The role of SARS-CoV-2 as the cause of chilblains in children remains a matter of debate but it is important to elucidate it for patient isolation and contact tracing. We sought to define the etiology, clinical presentation, time course, and outcomes of children presenting to the emergency department (ED) with cutaneous manifestations shortly after the first pandemic peak of COVID-19 in Spain. METHODS: A prospective, observational study in children <15 years of age evaluated for skin lesions in the EDs of three pediatric hospitals. Children underwent a comprehensive work-up including tests for SARS-CoV-2 antibodies and polymerase chain reaction (PCR), and serology and PCR tests for other viruses and bacteria. A 1 month follow-up visit was conducted. RESULTS: From April 14 through May 8, 2020, we enrolled 62 children. Of those, 34 had acro-ischemic skin lesions and 28 had a variety of skin rashes. Overall, 40% of children had mild systemic symptoms. Children with chilblains were older, had pain more frequently and a more prolonged duration of skin lesions, while those with non-specific rashes had fever more frequently. Lesions were resolved in 75% of children at follow up. Five patients demonstrated SARS-CoV-2 antibodies, and none tested positive with PCR. Three additional patients tested positive with PCR for rhinovirus, Mycoplasma pneumoniae and Chlamydia pneumoniae. CONCLUSIONS: The number of ED visits for chilblains, which are rare in pediatrics, was high soon after the first peak of COVID-19 in Spain. The disease course was self-limited, outcomes were favorable, and the possibility of viral transmission was negligible as all patients tested negative for SARS-CoV-2 by PCR.

[Microbiological diagnosis of urinary tract infections]. / Diagnóstico microbiológico de las infecciones urinarias.

Urinary tract infections (UTI) are the most common infectious diseases observed in primary care; up to one-third of women will have at least one symptomatic UTI by age 24, and more than one-half of women will be affected by the end of life. In addition, UTIs represent 40% of nosocomial infections, and being usually associated with urinary catheters. Although urine cultures would not be indicated in all cases, these samples are the most abundant in the laboratories of clinical microbiology. Thus, the working protocols applied to these samples have an important impact in the performance of the laboratory. The samples are collected by mid stream urine, and 60-70% of them are negative culture. At present, several commercial systems have been introduced in order to simplify and automate this process. A urine culture with ≥ 10(5) CFU/ml has classically been considered as positive, although lower counts are valued in certain clinical settings. Factors related to this count e.g. methods to obtain urine, conservation of the sample or use of chemical preservatives as well as low counts are critical points to be discussed in detail. The development of antimicrobial resistance logically affects uropathogens, mainly Escherichia coli, which remains the most frequently isolated in urine cultures. The aim of this paper is to review the most innovating aspects influencing the microbiological diagnosis of UTI.

Use of MALDI-TOF MS for Identification of Nontuberculous Mycobacterium Species Isolated from Clinical Specimens.

The aim of this study was to compare the results obtained for identification by MALDI-TOF of nontuberculous mycobacteria (NTM) isolated in clinical samples with those obtained by GenoType Mycobacterium CM/AS (common mycobacteria/additional species). A total of 66 Mycobacterium isolates from various clinical specimens (mainly respiratory) were tested in this study. They were identified using MALDI-TOF Bruker from strains isolated in Lowenstein, following the recommended protocol of heat inactivation and extraction, and were simultaneously analyzed through hybridization by GenoType Mycobacterium from liquid culture MGIT. Our results showed that identification by MALDI-TOF was correct in 98.4% (65/66) of NTM isolated in our clinical practice (M. avium, M. intracellulare, M. abscessus, M. chelonae, M. fortuitum, M. mucogenicum, M. kansasii, and M. scrofulaceum). MALDI-TOF was found to be an accurate, rapid, and cost-effective system for identification of mycobacteria species.

[Serum C-reactive protein as a marker of outcome and infection in critical care patients]. / Valor de la determinación de la proteína C reactiva como marcador pronóstico y de infección en pacientes críticos.

BACKGROUND AND OBJECTIVE: C-reactive protein (CRP) has been considered a marker for infection and an aid for diagnosing sepsis. We analyze the relation of CRP to infection and outcome in intensive care units (ICU) patients. PATIENTS AND METHOD: Prospective study on 77 ventilated patients. Expected short ICU stay or (suspected or confirmed) infection at admission were excluding criteria. 55 admissions after elective surgery were the controls. CRP measurement the first (CRP-1), third (CRP-3) and sixth (CRP-6) day of stay. APACHE II (Acute Physiology Score and Chronic Health Evaluation), SOFA (Sepsis-related Organ Failure Assessment), shock, respiratory or renal failure, leucocytes, platelets and albumin were registered. Follow-up until day 9 for infection and ICU discharge for outcome. RESULTS: CRP-1 in controls was 5.3 (3.9) mg/l and cases 67.8 (77.4) (p < 0.001). Shock on admission was related to CRP-1: patients in shock had higher CRP-1 levels (118.6 [82.8] vs 62.8 [75.6]; p = 0.06). 40.25% of cases developed infection, and CRP-1 levels were higher in this patients (88.8 [93.9] vs 53.8 [60.9]; p < 0.05). ROC area under curve was 0.6 with a sensibility of 23% and a specificity of 89% for a level of CRP-1 > 100. Mortality was 23.4% in cases and 1.8% in controls. Age, shock, APACHE II and SOFA were related to mortality, but CRP-1 did not. ROC area under curve for CRP-1 as mortality predictor in all patients was 0.62 (0.76 for APACHE II and 0.77 for SOFA) but only in cases was of 0.49 (0.69 for APACHE II and 0.67 for SOFA). CONCLUSIONS: CRP level on admission is an useful marker for early infection but not for outcome in critically ill patients admited to the ICU.