Role of IP-10 to Predict Clinical Progression and Response to IL-6 Blockade With Sarilumab in Early COVID-19 Pneumonia. A Subanalysis of the SARICOR Clinical Trial.

Background: The Clinical Trial of Sarilumab in Adults With COVID-19 (SARICOR) showed that patients with coronavirus disease 2019 (COVID-19) pneumonia and increased levels of interleukin (IL)-6 might benefit from blockade of the IL-6 pathway. However, the benefit from this intervention might not be uniform. In this subanalysis, we sought to determine if other immunoactivation markers, besides IL-6, could identify which subgroup of patients benefit most from this intervention. Methods: The SARICOR trial was a phase II, open-label, multicenter, controlled trial (July 2020-March 2021) in which patients were randomized to receive usual care (UC; control group), UC plus a single dose of sarilumab 200 mg (sarilumab-200 group), or UC plus a single dose of sarilumab 400 mg (sarilumab-400 group). Patients who had baseline serum samples for cytokine determination (IL-8, IL-10, monocyte chemoattractant protein-1, interferon-inducible protein [IP]-10) were included in this secondary analysis. Progression to acute respiratory distress syndrome (ARDS) according to cytokine levels and treatment received was evaluated. Results: One hundred one (88%) of 115 patients enrolled in the SARICOR trial had serum samples (control group: n = 33; sarilumab-200: n = 33; sarilumab-400: n = 35). Among all evaluated biomarkers, IP-10 showed the strongest association with treatment outcome. Patients with IP-10 ≥2500 pg/mL treated with sarilumab-400 had a lower probability of progression (13%) compared with the control group (58%; hazard ratio, 0.19; 95% CI, 0.04-0.90; P = .04). Conversely, patients with IP-10 <2500 pg/mL did not show these differences. Conclusions: IP-10 may predict progression to ARDS in patients with COVID-19 pneumonia and IL-6 levels >40 pg/mL. Importantly, IP-10 value <2500 pg/mL might discriminate those individuals who might not benefit from sarilumab therapy among those with high IL-6 levels.

Detection of High Level of Co-Infection and the Emergence of Novel SARS CoV-2 Delta-Omicron and Omicron-Omicron Recombinants in the Epidemiological Surveillance of Andalusia.

Recombination is an evolutionary strategy to quickly acquire new viral properties inherited from the parental lineages. The systematic survey of the SARS-CoV-2 genome sequences of the Andalusian genomic surveillance strategy has allowed the detection of an unexpectedly high number of co-infections, which constitute the ideal scenario for the emergence of new recombinants. Whole genome sequence of SARS-CoV-2 has been carried out as part of the genomic surveillance programme. Sample sources included the main hospitals in the Andalusia region. In addition to the increase of co-infections and known recombinants, three novel SARS-CoV-2 delta-omicron and omicron-omicron recombinant variants with two break points have been detected. Our observations document an epidemiological scenario in which co-infection and recombination are detected more frequently. Finally, we describe a family case in which co-infection is followed by the detection of a recombinant made from the two co-infecting variants. This increased number of recombinants raises the risk of emergence of recombinant variants with increased transmissibility and pathogenicity.

Sample pooling for SARS-CoV-2 RT-PCR screening.

OBJECTIVE: To evaluate the efficacy of sample pooling compared to the individual analysis for the diagnosis of coronavirus disease 2019 (COVID-19) by using different commercial platforms for nucleic acid extraction and amplification. METHODS: A total of 3519 nasopharyngeal samples received at nine Spanish clinical microbiology laboratories were processed individually and in pools (342 pools of ten samples and 11 pools of nine samples) according to the existing methodology in place at each centre. RESULTS: We found that 253 pools (2519 samples) were negative and 99 pools (990 samples) were positive; with 241 positive samples (6.85%), our pooling strategy would have saved 2167 PCR tests. For 29 pools (made out of 290 samples), we found discordant results when compared to their correspondent individual samples, as follows: in 22 of 29 pools (28 samples), minor discordances were found; for seven pools (7 samples), we found major discordances. Sensitivity, specificity and positive and negative predictive values for pooling were 97.10% (95% confidence interval (CI), 94.11-98.82), 100%, 100% and 99.79% (95% CI, 99.56-99.90) respectively; accuracy was 99.80% (95% CI, 99.59-99.92), and the kappa concordant coefficient was 0.984. The dilution of samples in our pooling strategy resulted in a median loss of 2.87 (95% CI, 2.46-3.28) cycle threshold (Ct) for E gene, 3.36 (95% CI, 2.89-3.85) Ct for the RdRP gene and 2.99 (95% CI, 2.56-3.43) Ct for the N gene. CONCLUSIONS: We found a high efficiency of pooling strategies for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA testing across different RNA extraction and amplification platforms, with excellent performance in terms of sensitivity, specificity and positive and negative predictive values.

Analytical performance of the Alere(TM) i Influenza A&B assay for the rapid detection of influenza viruses / Evaluación del sistema Alere(TM) i Influenza A&B para la detección rápida de virus de la gripe

The analytical performance of the new Alere(TM) i Influenza A&B kit (AL-Flu) assay, based on isothermal nucleic acids amplification, was evaluated and compared with an antigen detection method, SD Bioline Influenza Virus Antigen Test (SDB), and an automated real-time RT-PCR, Simplexa(TM) Flu A/B & VRS Direct assay (SPX), for detection of influenza viruses. An ‘in-house’ RT-PCR was used as the reference method. Sensitivity of AL-Flu, SDB, and SPX was 71.7%, 34.8%, and 100%, respectively. Specificity was 100% for all techniques. The turnaround time was 13min for AL-Flu, 15min for SDB, and 75min for SPX. The Alere(TM) i Influenza A&B assay is an optimal point-of-care assay for influenza diagnosis in clinical emergency settings, and is more sensitive and specific than antigen detection methods (AU)

Se evaluó el nuevo ensayo Alere(TM) i Influenza A&B kit (AL-Flu), basado en la amplificación isotérmica de ácidos nucleicos, y se comparó con un método de detección de antígeno, SD Bioline Influenza Virus Antigen Test (SDB), y con una RT-PCR en tiempo real automática, Simplexa(TM) Flu A/B & VRS Direct assay (SPX), para la detección de virus de la gripe. Se utilizó una RT-PCR en tiempo real casera como método de referencia. La sensibilidad de AL-Flu, SDB y SPX fue del 71,7%, del 34,8% y del 100%, respectivamente. Se obtuvo una especificidad del 100% con todos los métodos. El tiempo de realización fue de 13min para AL-Flu, de 15min para SDB y de 75min para SPX. El ensayo Alere(TM) i Influenza A&B es óptimo para el diagnóstico de gripe en unidades de urgencias, al ser más sensible y específico que las técnicas de detección de antígeno (AU)

Optimization of genotypic and biochemical methods to profile P. acnes isolates from a patient population.

Propionibacterium acnes is a key factor in the pathogenesis of acne vulgaris, although currently it is also being associated with medical-device infections. The aim of this work was to validate a safe and quick identification and typing of 24 clinical isolates of Propionibacterium acnes, applying a range of biochemical as well as genetic methods, and investigating the pathogenic potential to associate the different types with human health. RAPD-PCRs revealed the existence of two discernible clusters in correspondence with the phylogroups I and II, according to the PAtig gene polymorphism, leading them to be assigned as P. acnes subsp. acnes subsp. nov. Biotyping according to the pattern of sugar fermentation evidenced that all the isolates from acne and the majority from opportunistic infections fit the biotype I-B3. Consistent with the multiplex touchdown analysis, nearly all the isolates included in this biotype belonged to the subgroups IA1 (the exception being four strains classified as IB). The remaining ones were assigned to phylogroup II, considered to be part of the normal cutaneous microbiota. The susceptibility to three antibiotics was also investigated to explore the relations with the virulence, although no clear trend was identified.

First report of NDM-1-producing clinical isolate of Leclercia adecarboxylata in Spain.

We describe the case of NDM-1-producing Leclercia adecarboxylata recovered from the clinical sample of a patient hospitalized for a trauma-related injury to his foot. The isolate was resistant to all beta-lactams, quinolones, trimetroprim-sulfametoxazol, gentamicin and tobramicyn. The blaNDM-1 gene was located in a conjugative plasmid that also contained the blaSHV-12 gene and was preceded by a disrupted insertion sequence of ISAba125. The plasmid belongs to the incompatibility group X3, which is known to be an important vector for NDM-1 dissemination in China. This is the first reported case of NDM-1L. adecarboxylata in our country and evidences that species of uncertain clinical relevance can act as hidden sources of clinically important resistance determinants.

Analytical performance of the Alere™ i Influenza A&B assay for the rapid detection of influenza viruses.

The analytical performance of the new Alere™ i Influenza A&B kit (AL-Flu) assay, based on isothermal nucleic acids amplification, was evaluated and compared with an antigen detection method, SD Bioline Influenza Virus Antigen Test (SDB), and an automated real-time RT-PCR, Simplexa™ Flu A/B & VRS Direct assay (SPX), for detection of influenza viruses. An "in-house" RT-PCR was used as the reference method. Sensitivity of AL-Flu, SDB, and SPX was 71.7%, 34.8%, and 100%, respectively. Specificity was 100% for all techniques. The turnaround time was 13min for AL-Flu, 15min for SDB, and 75min for SPX. The Alere™ i Influenza A&B assay is an optimal point-of-care assay for influenza diagnosis in clinical emergency settings, and is more sensitive and specific than antigen detection methods.

[Sensitivity of three inmunocromathographic tests in faeces samples for Campylobacter and Salmonella detection in comparison to culture]. / Sensibilidad de tres test inmunocromatográficos para detección de Campylobacter y Salmonella en heces en comparación con el cultivo.

UNLABELLED: Introduction: Campylobacter sp. and Salmonella enterica are two of the main organisms causing gastroenteritis in our environment. Immunochromatographic tests for antigen detection performed directly on stool samples for its simplicity and rapid results may make them useful diagnostic elements in the context of primary care. METHOD: During October 2012 we selected all feces in which enteropathogenic bacteria are isolated from those received for stool culture in the laboratory of Microbiology of the University Hospital Virgen de las Nieves of Granada. After standard management of faeces samples and isolation of any enteropathogen, the commercial kits: Campy Leti, Ridaquick Campylobacterscreen and Salmonella Leti were tested for simultaneous research of Campylobacter and Salmonella antigens. Sensitivity and specificity were determined. RESULTS: Two hundred and thirty five stool samples were received in which 8 Salmonella enterica (7 B serogroup and 1 D serogroup), 7 Campylobacter jejuni, 4 Aeromonas hydrophila and 1 Yersinia enterocolitica were isolated. Campy Leti, Ridaquick Campylobacterscreen and Salmonella Leti presented a sensitivity of 100%, 100% and 75%, respectively. Specificities corresponded to 46%, 69% and 100%, respectively. CONCLUSION: Immunocromatographic tests can be useful for a first screening of enteropathogen in primary care.

Sensibilidad de tres test inmunocromatográficos para detección de Campylobacter y Salmonella en heces en comparación con el cultivo / Sensitivity of three inmunocromathographic tests in faeces samples for Campylobacter and Salmonella detection in comparison to culture

Introducción. Campylobacter sp. y Salmonella enterica son dos de los principales microorganismos causantes de gastroenteritis en nuestro medio. Las pruebas inmunocromatográficas de detección de antígeno realizadas directamente sobre muestras de heces por su sencillez y rapidez de obtención de resultados pueden hacer de ellas elementos de diagnóstico útiles en el contexto de la atención primaria. Material y métodos. Durante octubre de 2012 se seleccionaron todas las heces en las que se aisló una bacteria enteropatógena de entre las recibidas en el laboratorio de Microbiología del Hospital Universitario Virgen de las Nieves de Granada para coprocultivo. Dichas muestras fueron estudiadas mediante procedimientos estandarizados y en aquellas en las que se aisló un enteropatógeno se investigó simultáneamente la presencia de antígenos de Campylobacter (Campy Leti® y Ridaquick Campylobacter®) y Salmonella (Salmonella Leti®) para determinar su sensibilidad y especificidad. Resultados. Se recibieron 235 muestras de las que se aislaron 8 Salmonella enterica (7 del serogrupo B y 1 del serogrupo D), 7 Campylobacter jejuni, 4 Aeromonas hydrophila y 1 Yersinia enterocolítica. La sensibilidad y especificidad de Campy Leti, Ridaquick Campylobacterscreen y Salmonella Leti fueron respectivamente: 100% y 46%; 100% y 69%; y 75% y 100%. La concordancia entre los test para detección de Campylobacter fue 77, 8%. Conclusiones. En atención primaria las pruebas rápidas inmunocromatográficas pueden ser útiles para el cribado de enteropatógenos en heces (AU)

Introduction. Campylobacter sp. and Salmonella enterica are two of the main organisms causing gastroenteritis in our environment. Immunochromatographic tests for antigen detection performed directly on stool samples for its simplicity and rapid results may make them useful diagnostic elements in the context of primary care. Method. During October 2012 we selected all feces in which enteropathogenic bacteria are isolated from those received for stool culture in the laboratory of Microbiology of the University Hospital Virgen de las Nieves of Granada. After standard management of faeces samples and isolation of any enteropathogen, the commercial kits: Campy Leti, Ridaquick Campylobacterscreen and Salmonella Leti were tested for simultaneous research of Campylobacter and Salmonella antigens. Sensitivity and specificity were determined. Results. Two hundred and thirty five stool samples were received in which 8 Salmonella enterica (7 B serogroup and 1 D serogroup), 7 Campylobacter jejuni, 4 Aeromonas hydrophila and 1 Yersinia enterocolitica were isolated. Campy Leti, Ridaquick Campylobacterscreen and Salmonella Leti presented a sensitivity of 100%, 100% and 75%, respectively. Specificities corresponded to 46%, 69% and 100%, respectively. Conclusion. Immunocromatographic tests can be useful for a first screening of enteropathogen in primary care (AU)

Sysmex UF-1000i performance for screening yeasts in urine.

We tested the capacity of the Sysmex UF-1000i system to detect yeasts in urine by screening a total of 22 132 urine samples received for culture in our microbiology laboratory during 1 year. We also analyzed different dilutions of previously filtered urine inoculated with a strain of Candida albicans. With clinical samples, a single cut-off point of 50 yeast-like cells (YLCs)/µL detected candiduria ≥10 000 colony forming units (CFU)/mL and >100 000 CFU/mL with a sensitivity of 87.3%/95.4%, a specificity of 97%, a negative predictive value of 95.9%, and a positive predictive value of 9.3%/5.7%. With the simulated samples, a linear relationship was observed between the dilution factor and the number of cells detected by UF-1000i. This instrument appears to be able to reliably rule out candiduria of a magnitude of at least 10 000 CFU/mL and facilitate urine sample screening, thereby providing fast results. The Sysmex UF1000i system can be adapted for candiduria screening by the use of an appropriate YLCs/µL cut-off point that takes account of the prevalence of candiduria in the population.

Molecular study on three morphotypes of Demodex mites (Acarina: Demodicidae) from dogs.

Canine demodicosis is a severe and highly prevalent dermatologic disease in dogs. Pet dogs can be affected by three recognized Demodex species that can produce clinical effects. In this paper, three morphological types of Demodex mites have been isolated from Spanish dogs. A complete morphobiometrical study of each one has been carried out. Morphological and biometrical studies revealed three closely related populations with some distinctive characteristics and could be identified as Demodex canis, Demodex injai, and Demodex sp. "cornei." Furthermore, one population of D. canis from China, different populations of Demodex folliculorum from human skin (Spain and China), D. folliculorum from human eyelashes (Spain), and Demodex brevis from human skin (China) were considered to find out the level of variation between different species and geographical origin. The aim of the present study is to assess the usefulness of mitochondrial DNA molecular markers in establishing phylogenetic relationships and resolve taxonomic questions in Demodex mites. Molecular studies based on the amplification and sequencing of the 16S rDNA and cytochrome oxidase I mitochondrial genes did not show clear differences between the three morphotypes considered. Furthermore, phylogenetic relationships in Demodex mites were analyzed. The resulting phylogenetic trees show that Demodex species from dogs were gathered together, and populations of D. folliculorum from humans appear together in a different branch; however, D. brevis from humans seemed to be more distant. Our results show that cytochrome oxidase I region is a useful tool to solve different taxonomic questions at the species and population level and to infer phylogenetic relationships in Demodex species. However, 16S mitochondrial rDNA seems a good marker for comparisons at an interspecies level, but not at a population level in this group of mites. Furthermore, from genetic distance and divergence data, we would suggest that D. canis, D. injai, and Demodex sp. cornei are polymorphisms of the same species.

Morphobiometrical and molecular study of two populations of Demodex folliculorum from humans.

A morphobiometrical and molecular study of two populations of Demodex folliculorum from humans isolated from different habitats, skin and eyelashes follicles, were carried out. Morphological and biometrical studies revealed two closely related populations with any distinctive characteristics. For molecular study, a 436-bp region of the 16S rDNA gene and a 453-bp region of the cytochrome oxidase I (COI) gene from individual mites of each population considered were sequenced. Intraindividual and interindividual sequence variation was studied in both populations. Our data show that 16S rDNA is not a useful marker to discriminate between populations; however, COI gene sequences can help to identify the two populations considered, which are morphologically very close and difficult to separate by classic methods. These results are in agreement with the morphological and biometrical differences detected between D. folliculorum from eyelashes and human skin. This study appeals for the revision of the taxonomic status of the D. folliculorum populations, as well as for the species included within genus Demodex.