Whole Sequencing and Detailed Analysis of SARS-CoV-2 Genomes in Southeast Spain: Identification of Recurrent Mutations in the 20E (EU1) Variant with Some Clinical Implications.

During the COVID-19 pandemic caused by SARS-CoV-2, new waves have been associated with new variants and have the potential to escape vaccinations. Therefore, it is useful to conduct retrospective genomic surveillance research. Herein, we present a detailed analysis of 88 SARS-CoV-2 genomes belonging to samples taken from COVID-19 patients from October 2020 to April 2021 at the "Reina Sofía" Hospital (Murcia, Spain) focused to variant appeared later. The results at the mentioned stage show the turning point since the 20E (EU1) variant was still prevalent (71.6%), but Alpha was bursting to 14.8%. Concern mutations have been found in 5 genomes classified as 20E (EU1), which were not characteristic of this still little evolved variant. Most of those mutations are found in the spike protein, namely Δ69-70, E484K, Q675H and P681H. However, a relevant deletion in ORF1a at positions 3675-3677 was also identified. These mutations have been reported in many later SARS-CoV-2 lineages, including Omicron. Taken together, our data suggest that preferential emergence mutations could already be present in the early converging evolution. Aside from this, the molecular information has been contrasted with clinical data. Statistical analyses suggest that the correlation between age and severity criteria is significantly higher in the viral samples with more accumulated changes.

Atypical Kaposi's sarcoma in young inmunocompetent patient.

Kaposi´s sarcoma is a rare tumor associated with human herpes virus 8 (HHV-8) infection. Four main clinical subtypes have been described. This study reports on a form of KS in an HIV negative and immunocompetent middle-aged man. The only remarkable factor is that he has sex with other men. This form of Kaposi´s sarcoma is rare. It occurs more in younger patients than in the classic form, is limited to the skin, and is associated with a good prognosis. The means of transmission of the virus is through saliva in oroanal or orogenital sexual practices. Mechanisms of tumor development are still not well known. Given the possible increased number of this variant, it would be interesting to extend this study.

High prevalence and diversity of HIV-1 non-B genetic forms due to immigration in southern Spain: A phylogeographic approach.

Phylogenetic studies are a valuable tool to understand viral transmission patterns and the role of immigration in HIV-1 spread. We analyzed the spatio-temporal relationship of different HIV-1 non-B subtype variants over time using phylogenetic analysis techniques. We collected 693 pol (PR+RT) sequences that were sampled from 2005 to 2012 from naïve patients in different hospitals in southern Spain. We used REGA v3.0 to classify them into subtypes and recombinant forms, which were confirmed by phylogenetic analysis through maximum likelihood (ML) using RAxML. For the main HIV-1 non-B variants, publicly available, genetically similar sequences were sought using HIV-BLAST. The presence of HIV-1 lineages circulating in our study population was established using ML and Bayesian inference (BEAST v1.7.5) and transmission networks were identified. We detected 165 (23.4%) patients infected with HIV-1 non-B variants: 104 (63%) with recombinant viruses in pol: CRF02_AG (71, 43%), CRF14_BG (8, 4.8%), CRF06_cpx (5, 3%) and nine other recombinant forms (11, 6.7%) and unique recombinants (9, 5.5%). The rest (61, 37%) were infected with non-recombinant subtypes: A1 (30, 18.2%), C (7, [4.2%]), D (3, [1.8%]), F1 (9, 5.5%) and G (12, 7.3%). Most patients infected with HIV-1 non-B variants were men (63%, p < 0.001) aged over 35 (73.5%, p < 0.001), heterosexuals (92.2%, p < 0.001), from Africa (59.5%, p < 0.001) and living in the El Ejido area (62.4%, p<0.001). We found lineages of epidemiological relevance (mainly within Subtype A1), imported primarily through female sex workers from East Europe. We detected 11 transmission clusters of HIV-1 non-B Subtypes, which included patients born in Spain in half of them. We present the phylogenetic profiles of the HIV-1 non-B variants detected in southern Spain, and explore their putative geographical origins. Our data reveals a high HIV-1 genetic diversity likely due to the import of viral lineages that circulate in other countries. The highly immigrated El Ejido area acts as a gateway through which different subtypes are introduced into other regions, hence the importance of setting up epidemiological control measures to prevent future outbreaks.

Actividad comparativa de tedizolid frente a Staphylococcus coagulasa negativos resistentes a linezolid y Staphylococcus aureus resistentes a meticilina / Comparative activity of tedizolid against clinical isolates of linezolid-resistant coagulase-negative staphylococci and methicillin-resistant Staphylococcus aureus

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Atypical Kaposi's sarcoma in young inmunocompetent patient

Abstract: Kaposi´s sarcoma is a rare tumor associated with human herpes virus 8 (HHV-8) infection. Four main clinical subtypes have been described. This study reports on a form of KS in an HIV negative and immunocompetent middle-aged man. The only remarkable factor is that he has sex with other men. This form of Kaposi´s sarcoma is rare. It occurs more in younger patients than in the classic form, is limited to the skin, and is associated with a good prognosis. The means of transmission of the virus is through saliva in oroanal or orogenital sexual practices. Mechanisms of tumor development are still not well known. Given the possible increased number of this variant, it would be interesting to extend this study.

Phylodynamic and Phylogeographic Profiles of Subtype B HIV-1 Epidemics in South Spain.

BACKGROUND: Since 1982, HIV-1 epidemics have evolved to different scenarios in terms of transmission routes, subtype distribution and characteristics of transmission clusters. We investigated the evolutionary history of HIV-1 subtype B in south Spain. PATIENTS & METHODS: We studied all newly diagnosed HIV-1 subtype B patients in East Andalusia during the 2005-2012 period. For the analysis, we used the reverse transcriptase and protease sequences from baseline resistance, and the Trugene® HIV Genotyping kit (Siemens, Barcelona, Spain). Subtyping was done with REGA v3.0. The maximum likelihood trees constructed with RAxML were used to study HIV-1 clustering. Phylogeographic and phylodynamic profiles were studied by Bayesian inference methods with BEAST v1.7.5 and SPREAD v1.0.6. RESULTS: Of the 493 patients infected with HIV-1 subtype B, 234 grouped into 55 clusters, most of which were small (44 clusters ≤ 5 patients, 31 with 2 patients, 13 with 3). The rest (133/234) were grouped into 11 clusters with ≥ 5 patients, and most (82%, 109/133) were men who have sex with men (MSM) grouped into 8 clusters. The association with clusters was more frequent in Spanish (p = 0.02) men (p< 0.001), MSM (p<0.001) younger than 35 years (p = 0.001) and with a CD4+ T-cell count above 350 cells/ul (p<0.001). We estimated the date of HIV-1 subtype B regional epidemic diversification around 1970 (95% CI: 1965-1987), with an evolutionary rate of 2.4 (95%CI: 1.7-3.1) x 10-3 substitutions/site/year. Most clusters originated in the 1990s in MSMs. We observed exponential subtype B HIV-1 growth in 1980-1990 and 2005-2008. The most significant migration routes for subtype B went from inland cities to seaside locations. CONCLUSIONS: We provide the first data on the phylodynamic and phylogeographic profiles of HIV-1 subtype B in south Spain. Our findings of transmission clustering among MSMs should alert healthcare managers to enhance preventive measures in this risk group in order to prevent future outbreaks.

[Letal endocarditis due to Corynebacterium pseudodiphtheriticum]. / Endocarditis infecciosa fatal por Corynebacterium pseudodiphtheriticum.

We present a case report of a infective endocarditis by Corynebacterium pseudodiphtheriticum in a young patient eight years old with bicuspid aortic valve that led to a severe neurological embolism and death. Corynebacterium pseudodiphtheriticum is part of the nasopharyngeal and skin flora. However, there are cases reported of endocarditis usually associated with immunocompromised patients that mostly presented a poor clinical outcome.

Endocarditis infecciosa fatal por Corynebacterium pseudodiphtheriticum / Letal endocarditis due to Corynebacterium pseudodiphtheriticum

We present a case report of a infective endocarditis by Corynebacterium pseudodiphtheriticum in a young patient eight years old with bicuspid aortic valve that led to a severe neurological embolism and death. Corynebacterium pseudodiphtheriticum is part of the nasopharyngeal and skin flora. However, there are cases reported of endocarditis usually associated with immunocompromised patients that mostly presented a poor clinical outcome.

Se presenta el caso clínico de una endocarditis infecciosa por Corynebacterium pseudodiphtheriticum en un niño de 8 años, portador de una valvulopatía aórtica bicúspide, que falleció por una embolia cerebral grave. Corynebacterium pseudodiphtheriticum forma parte de la microbiota de la piel y nasofaringe. Sin embargo, se han descrito casos de endocarditis en pacientes inmunocomprometidos, asociados, en su mayoría, a una mala evolución clínica.

Los estudios de resistencias a antirretrovirales como herramienta para el análisis de los clusters de transmisión del virus de la inmunodeficiencia humana / Study of human immunodeficiency virus transmission chains in Andalusia: Analysis from baseline antiretroviral resistance sequences

INTRODUCCIÓN Y OBJETIVO: Las secuencias de proteasa y transcriptasa reversa del VIH-1 aportan una información muy valiosa para el manejo de la infección por VIH, más allá de la información de resistencias a los antirretrovirales. En nuestro estudio la hemos utilizado para evaluar las cadenas de transmisión, la transmisión de resistencias entre ellos, y para conocer la distribución espacial de los diferentes subtipos utilizando técnicas de georreferenciación. MÉTODOS: Hemos estudiado 693 pacientes diagnosticados de VIH-1 durante el periodo 2005-2012, todos ellos residentes en Andalucía Oriental. La secuencia del gen pol (transcriptasa reversa y proteasa) se generó utilizando Trugene® HIV Genotyping Kit (Siemens, NAD). La historia evolutiva fue inferida a través de MEGA 5.2 mediante el método de Neighbor-Joining. Para la filogeografía y el estudio de resistencias utilizamos ArcGIS y REGA. RESULTADOS: Doscientos noventa y ocho pacientes se asociaron en 77 clusters diferentes. La mayoría de los cluster estaban formados por parejas (n = 49), de hombres que practican sexo con hombres (n = 26), de nacionalidad española (n = 37), con una edad menor a 45 años (73,5%). Las áreas de mayor heterogeneidad de subtipos fueron el área metropolitana de Granada y las zonas de costa de Almería y Granada. Hemos encontrado 5 cluster con más de 10 individuos. En 15 cluster detectamos mutaciones de resistencia. CONCLUSIONES: Presentamos datos que demuestran que el estudio epidemiológico de los diferentes clusters de transmisión de VIH mediante análisis filogenético se presenta como una herramienta potente y de gran utilidad para la vigilancia y control epidemiológico de la propagación del VIH, que puede ayudar a diseñar actuaciones eficaces para prevenir la diseminación del VIH

INTRODUCTION AND OBJECTIVE: Protease and reverse transcriptase HIV-1 sequences provide useful information for patient clinical management, as well as information on resistance to antiretrovirals. The aim of this study is to evaluate transmission events, transmitted drug resistance, and to georeference subtypes among newly diagnosed patients referred to our center. METHODS: A study was conducted on 693 patients diagnosed between 2005 and 2012 in Southern Spain. Protease and reverse transcriptase sequences were obtained for resistance to cART analysis with Trugene® HIV Genotyping Kit (Siemens, NAD). MEGA 5.2, Neighbor-Joining, ArcGIS and REGA were used for subsequent analysis. RESULTS: The results showed 298 patients clustered into 77 different transmission events. Most of the clusters were formed by pairs (n = 49), of men having sex with men (n = 26), Spanish (n = 37), and below 45 years of age (73.5%). Urban areas from Granada, and the coastal areas of Almeria and Granada showed the greatest subtype heterogeneity. Five clusters were formed by more than 10 patients, and 15 clusters had transmitted drug resistance. CONCLUSIONS: The study data demonstrate how the phylogenetic characterization of transmission clusters is a powerful tool to monitor the spread of HIV, and may contribute to design correct preventive measures to minimize it

Sensibilidad in vitro a ceftarolina de Staphylococcus aureus / In vitro sensitivity to ceftaroline of Staphylococcus aureus

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[Study of human immunodeficiency virus transmission chains in Andalusia: analysis from baseline antiretroviral resistance sequences]. / Los estudios de resistencias a antirretrovirales como herramienta para el análisis de los clusters de transmisión del virus de la inmunodeficiencia humana.

INTRODUCTION AND OBJECTIVE: Protease and reverse transcriptase HIV-1 sequences provide useful information for patient clinical management, as well as information on resistance to antiretrovirals. The aim of this study is to evaluate transmission events, transmitted drug resistance, and to georeference subtypes among newly diagnosed patients referred to our center. METHODS: A study was conducted on 693 patients diagnosed between 2005 and 2012 in Southern Spain. Protease and reverse transcriptase sequences were obtained for resistance to cART analysis with Trugene(®) HIV Genotyping Kit (Siemens, NAD). MEGA 5.2, Neighbor-Joining, ArcGIS and REGA were used for subsequent analysis. RESULTS: The results showed 298 patients clustered into 77 different transmission events. Most of the clusters were formed by pairs (n=49), of men having sex with men (n=26), Spanish (n=37), and below 45 years of age (73.5%). Urban areas from Granada, and the coastal areas of Almeria and Granada showed the greatest subtype heterogeneity. Five clusters were formed by more than 10 patients, and 15 clusters had transmitted drug resistance. CONCLUSIONS: The study data demonstrate how the phylogenetic characterization of transmission clusters is a powerful tool to monitor the spread of HIV, and may contribute to design correct preventive measures to minimize it.

Case for diagnosis.

Majocchi's granuloma is a persistent supurative folliculitis, associated with a deep granulomatous reaction induced by dermatophytes. There are two clinical forms of Majocchi's granuloma: the superficial form that appears in healthy individuals after localized trauma; and the nodular form, which occurs in inmunocompromised patients. We present a case of nodular Majocchi's granuloma on the forearm of an immunocompetent patient. Microbiological culture and examination of a deep aspiration sample identified Trichophyton rubrum. Collecting a deep sample of tissue is essential in achieving a good diagnostic performance.

Case for diagnosis

Majocchi's granuloma is a persistent supurative folliculitis, associated with a deep granulomatous reaction induced by dermatophytes. There are two clinical forms of Majocchi's granuloma: the superficial form that appears in healthy individuals after localized trauma; and the nodular form, which occurs in inmunocompromised patients. We present a case of nodular Majocchi's granuloma on the forearm of an immunocompetent patient. Microbiological culture and examination of a deep aspiration sample identified Trichophyton rubrum. Collecting a deep sample of tissue is essential in achieving a good diagnostic performance.