Dispersal history of SARS-CoV-2 in Galicia, Spain.

The dynamics of SARS-CoV-2 transmission are influenced by a variety of factors, including social restrictions and the emergence of distinct variants. In this study, we delve into the origins and dissemination of the Alpha, Delta, and Omicron variants of concern in Galicia, northwest Spain. For this, we leveraged genomic data collected by the EPICOVIGAL Consortium and from the GISAID database, along with mobility information from other Spanish regions and foreign countries. Our analysis indicates that initial introductions during the Alpha phase were predominantly from other Spanish regions and France. However, as the pandemic progressed, introductions from Portugal and the USA became increasingly significant. Notably, Galicia's major coastal cities emerged as critical hubs for viral transmission, highlighting their role in sustaining and spreading the virus. This research emphasizes the critical role of regional connectivity in the spread of SARS-CoV-2 and offers essential insights for enhancing public health strategies and surveillance measures.

The Modification of the Illumina® CovidSeq™ Workflow for RSV Genomic Surveillance: The Genetic Variability of RSV during the 2022-2023 Season in Northwest Spain.

There is growing interest in the molecular surveillance of the Respiratory Syncytial Virus and the monitorization of emerging mutations that could impair the efficacy of antiviral prophylaxis and treatments. A simple, scalable protocol for viral nucleic acid enrichment could improve the surveillance of RSV. We developed a protocol for RSV-A and B amplification based on the Illumina CovidSeq workflow using an RSV primer panel. A total of 135 viral genomes were sequenced from nasopharyngeal samples through the optimization steps of this panel, while an additional 15 samples were used to test the final version. Full coverage of the G gene and over 95% of the coverage of the F gene, the target of the available RSV antivirals or monoclonal antibodies, were obtained. The F:K68N mutation, associated with decreased nirsevimab activity, was detected in our facility. Additionally, phylogenetic analysis showed several sublineages in the 2022-2023 influenza season in Europe. Our protocol allows for a simple and scalable simultaneous amplification of the RSV-A and B whole genome, increasing the yield of RSV sequencing and reducing costs. Its application would allow the world to be ready for the detection of arising mutations in relation to the widespread use of nirsevimab for RSV prevention.

Influence of perinatal and childhood exposure to tobacco and mercury in children's gut microbiota.

Background: Early life determinants of the development of gut microbiome composition in infants have been widely investigated; however, if early life pollutant exposures, such as tobacco or mercury, have a persistent influence on the gut microbial community, its stabilization at later childhood remains largely unknown. Objective: In this exposome-wide study, we aimed at identifying the contribution of exposure to tobacco and mercury from the prenatal period to childhood, to individual differences in the fecal microbiome composition of 7-year-old children, considering co-exposure to a width of established lifestyle and clinical determinants. Methods: Gut microbiome was studied by 16S rRNA amplicon sequencing in 151 children at the genus level. Exposure to tobacco was quantified during pregnancy through questionnaire (active tobacco consumption, second-hand smoking -SHS) and biomonitoring (urinary cotinine) at 4 years (urinary cotinine, SHS) and 7 years (SHS). Exposure to mercury was quantified during pregnancy (cord blood) and at 4 years (hair). Forty nine other potential environmental determinants (12 at pregnancy/birth/infancy, 15 at 4 years and 22 at 7 years, such as diet, demographics, quality of living/social environment, and clinical records) were registered. We used multiple models to determine microbiome associations with pollutants including multi-determinant multivariate analysis of variance and linear correlations (wUnifrac, Bray-Curtis and Aitchison ß-diversity distances), single-pollutant permutational multivariate analysis of variance adjusting for co-variates (Aitchison), and multivariable association model with single taxa (MaAsLin2; genus). Sensitivity analysis was performed including genetic data in a subset of 107 children. Results: Active smoking in pregnancy was systematically associated with microbiome composition and ß-diversity (R2 2-4%, p < 0.05, Aitchison), independently of other co-determinants. However, in the adjusted single pollutant models (PERMANOVA), we did not find any significant association. An increased relative abundance of Dorea and decreased relative abundance of Akkermansia were associated with smoking during pregnancy (q < 0.05). Discussion: Our findings suggest a long-term sustainable effect of prenatal tobacco exposure on the children's gut microbiota. This effect was not found for mercury exposure or tobacco exposure during childhood. Assessing the role of these exposures on the children's microbiota, considering multiple environmental factors, should be further investigated.

In vivo monitoring of Lactiplantibacillus plantarum in the nasal and vaginal mucosa using infrared fluorescence.

Lactic acid bacteria (LAB) of the genus Lactiplantibacillus have been explored as potential mucosal vaccine vectors due to their ability to elicit an immune response against expressed foreign antigens and to their safety. However, tools for monitoring LAB distribution and persistence at the mucosal surfaces are needed. Here, we characterize Lactiplantibacillus plantarum bacteria expressing the infrared fluorescent protein IRFP713 for exploring their in vivo distribution in the mucosa and potential use as a mucosal vaccine vector. This bacterial species is commonly used as a vaginal probiotic and was recently found to have a niche in the human nose. Three different fluorescent L. plantarum strains were obtained using the nisin-inducible pNZRK-IRFP713 plasmid which contains the nisRK genes, showing stable and constitutive expression of IRFP713 in vitro. One of these strains was further monitored in BALB/c mice using near-infrared fluorescence, indicating successful colonization of the nasal and vaginal mucosae for up to 72 h. This study thus provides a tool for the in vivo spatiotemporal monitoring of lactiplantibacilli, allowing non-invasive bacterial detection in these mucosal sites. KEY POINTS: • Stable and constitutive expression of the IRFP713 protein was obtained in different L. plantarum strains. • IRFP713+ L. plantarum 3.12.1 was monitored in vivo using near-infrared fluorescence. • Residence times observed after intranasal and vaginal inoculation were 24-72 h.

Efficacy and Safety of Lithium Treatment in SARS-CoV-2 Infected Patients.

At the beginning of the pandemic, we observed that lithium carbonate had a positive effect on the recovery of severely ill patients with COVID-19. Lithium is able to inhibit the replication of several types of viruses, some of which are similar to the SARS-CoV-2 virus, increase the immune response and reduce inflammation by preventing or reducing the cytokine storm. Previously, we published an article with data from six patients with severe COVID-19 infection, where we proposed that lithium carbonate could be used as a potential treatment for COVID-19. Now, we set out to conduct a randomized clinical trial number EudraCT 2020-002008-37 to evaluate the efficacy and safety of lithium treatment in patients infected with severe SARS-CoV-2. We showed that lithium was able to reduce the number of days of hospital and intensive care unit admission as well as the risk of death, reduces inflammatory cytokine levels by preventing cytokine storms, and also reduced the long COVID syndromes. We propose that lithium carbonate can be used to reduce the severity of COVID-19.

Limited genomic reconstruction of SARS-CoV-2 transmission history within local epidemiological clusters.

A detailed understanding of how and when severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission occurs is crucial for designing effective prevention measures. Other than contact tracing, genome sequencing provides information to help infer who infected whom. However, the effectiveness of the genomic approach in this context depends on both (high enough) mutation and (low enough) transmission rates. Today, the level of resolution that we can obtain when describing SARS-CoV-2 outbreaks using just genomic information alone remains unclear. In order to answer this question, we sequenced forty-nine SARS-CoV-2 patient samples from ten local clusters in NW Spain for which partial epidemiological information was available and inferred transmission history using genomic variants. Importantly, we obtained high-quality genomic data, sequencing each sample twice and using unique barcodes to exclude cross-sample contamination. Phylogenetic and cluster analyses showed that consensus genomes were generally sufficient to discriminate among independent transmission clusters. However, levels of intrahost variation were low, which prevented in most cases the unambiguous identification of direct transmission events. After filtering out recurrent variants across clusters, the genomic data were generally compatible with the epidemiological information but did not support specific transmission events over possible alternatives. We estimated the effective transmission bottleneck size to be one to two viral particles for sample pairs whose donor-recipient relationship was likely. Our analyses suggest that intrahost genomic variation in SARS-CoV-2 might be generally limited and that homoplasy and recurrent errors complicate identifying shared intrahost variants. Reliable reconstruction of direct SARS-CoV-2 transmission based solely on genomic data seems hindered by a slow mutation rate, potential convergent events, and technical artifacts. Detailed contact tracing seems essential in most cases to study SARS-CoV-2 transmission at high resolution.

In vitro neutralizing activity of BNT162b2 mRNA-induced antibodies against full B.1.351 SARS-CoV-2 variant.

SARS-CoV-2 variation represents a serious challenge to current COVID-19 vaccines. Recent reports suggest that B.1.351 and other variants may escape the neutralization activity of the antibodies generated by current vaccines. Ninety-nine healthcare workers undertaking BNT162b2 mRNA vaccination were sampled at baseline, on the day of the second dose, and 14 days after the latter. Neutralization activity against SARS-CoV-2 B.1, B.1.1.7 and B.1.351 was investigated using a Vero-E6 model. Eleven of the study participants had prior infection with SARS-CoV-2. Neutralization titers against the B.1 and the B.1.1.7 variants were not statistically different and were significantly higher than titers against the B.1.351 variant across pre-exposed and non-pre-exposed vaccinated individuals (p < .01). While all vaccinated individuals presented neutralizing antibodies against B.1 and B 1.1.7 after the second dose, 14% were negative against B.1.351 and 76% had low titers (1/201/80). Pre-exposed vaccinated individuals showed higher titers than non-pre-exposed after the first (median titers of 1/387 versus 1/28, respectively) and the second doses (1/995 versus 1/703, respectively). As high as 72% of the pre-exposed vaccines presented titers >1/80 after a single dose, while only 11% of non-exposed vaccinated individuals had titers >1/80. BNT162b2 mRNA-induced antibodies show a lower in vitro neutralizing activity against B.1.351 variant compared to neutralization against B.1.1.7 or B.1 variants. Interestingly, for individuals pre-exposed to SARS-CoV-2, one dose of BNT162b2 mRNA may be adequate to produce neutralizing antibodies against B.1.1.7 and B.1, while two doses of BNT162b2 mRNA provide optimal neutralizing antibody response against B.1.351 too.

The fate of SARS-COV-2 in WWTPS points out the sludge line as a suitable spot for detection of COVID-19.

SARS-CoV-2 genetic material is detectable in the faeces of a considerable part of COVID-19 cases and hence, in municipal wastewater. This fact was confirmed early during the spread of the COVID-19 pandemic and prompted several studies that proposed monitoring its incidence by wastewater. This paper studies the fate of SARS-CoV-2 genetic material in wastewater treatment plants using RT-qPCR with a two-fold goal: i) to check its presence in the water effluent and in the produced sludge and ii) based on the understanding of the virus particles fate, to identify the most suitable spots for detecting the incidence of COVID-19 and monitor its evolution. On the grounds of the affinity of enveloped virus towards biosolids, we hypothesized that the sludge line acts as a concentrator of SARS-CoV-2 genetic material. Sampling several spots in primary, secondary and sludge treatment at the Ourense (Spain) WWTP in 5 different days showed that, in effect, most of SARS-CoV-2 particles cannot be detected in the water effluent as they are retained by the sludge line. We identified the sludge thickener as a suitable spot for detecting SARS-CoV-2 particles thanks to its higher solids concentration (more virus particles) and longer residence time (less sensitive to dilution caused by precipitation). These findings could be useful to develop a suitable strategy for early warning of COVID-19 incidence based on WWTP monitoring.

The role of the gut microbiota in schizophrenia: Current and future perspectives.

OBJECTIVES: Schizophrenia is a poorly understood chronic disease. Its pathophysiology is complex, dynamic, and linked to epigenetic mechanisms and microbiota involvement. Nowadays, correlating schizophrenia with the environment makes sense owing to its multidimensional implications: temporal and spatial variability. Microbiota involvement and epigenetic mechanisms are factors that are currently being considered to better understand another dimension of schizophrenia. METHODS: This review summarises and discusses currently available information, focussing on the microbiota, epigenetic mechanisms, technological approaches aimed at performing exhaustive analyses of the microbiota, and psychotherapies, to establish future perspectives. RESULTS: The connection between the microbiota, epigenetic mechanisms and technological developments allows for formulating new approaches objectively oriented towards the development of alternative psychotherapies that may help treat schizophrenia. CONCLUSIONS: In this review, the gut microbiota and epigenetic mechanisms were considered as key regulators, revealing a potential new aetiology of schizophrenia. Likewise, continuous technological advances (e.g. culturomics), aimed at the microbiota-gut-brain axis generate new evidence on this concept.

[Historical perspective of mass spectrometry in microbiology]. / Perspectiva histórica de la espectrometría de masas en microbiología.

La espectrometría de masas (EM) es una técnica de análisis que permite caracterizar muestras midiendo las masas (estrictamente las razones masa-carga) de las moléculas componentes. Cuenta con más de un siglo de historia y evolución tecnológica y a lo largo de los años ha ampliado su alcance desde los isótopos a moléculas pequeñas, moléculas orgánicas más complejas y, en las últimas décadas, macromoléculas (ácidos nucleicos y proteínas). La EM MALDI-TOF (matrix-assisted laser desorption ionization time-of-flight) es una variante que permite el análisis de mezclas complejas de proteínas y que se ha aplicado recientemente a la identificación de microorganismos en cultivo, convirtiéndose en una herramienta rápida y eficaz para el diagnóstico microbiológico que ha conseguido entrar en poco tiempo en la rutina de muchos servicios de microbiología clínica. El gran impacto que ha tenido está impulsando el desarrollo de nuevas aplicaciones en el campo de la microbiología clínica.

Perspectiva histórica de la espectrometría de masas en microbiología / Historical perspective of mass spectrometry in microbiology

La espectrometría de masas (EM) es una técnica de análisis que permite caracterizar muestras midiendo las masas (estrictamente las razones masa-carga) de las moléculas componentes. Cuenta con más de un siglo de historia y evolución tecnológica y a lo largo de los años ha ampliado su alcance desde los isótopos a moléculas pequeñas, moléculas orgánicas más complejas y, en las últimas décadas, macromoléculas (ácidos nucleicos y proteínas). La EM MALDI-TOF (matrix-assisted laser desorption ionization time-of-flight) es una variante que permite el análisis de mezclas complejas de proteínas y que se ha aplicado recientemente a la identificación de microorganismos en cultivo, convirtiéndose en una herramienta rápida y eficaz para el diagnóstico microbiológico que ha conseguido entrar en poco tiempo en la rutina de muchos servicios de microbiología clínica. El gran impacto que ha tenido está impulsando el desarrollo de nuevas aplicaciones en el campo de la microbiología clínica

Mass spectrometry (MS) is an analytical technique that allows samples to be characterized by measuring the masses (strictly speaking their mass-to-charge ratio) of the component molecules. This technique has been used for more than one hundred years and technological development throughout this time has broadened its scope from isotopes to small molecules, more complex organic molecules, and in the last few decades, macromolecules (nucleic acids and proteins). MALDI-TOF (matrix-assisted laser desorption ionization time-of-flight) MS is a variant that allows analysis of complex mixtures of proteins and has recently been applied to the identification of cultured microorganisms, making it a rapid and effective tool for microbiological diagnosis. In a short time, MALDI-TOF MS has become a routinely used technique in many clinical microbiology services and its strong impact is prompting the development of new applications in the field of clinical microbiology

Relation of Skin Flora of Hands with Glove Perforation and Contamination in Cardiac Surgery.

BACKGROUND AND OBJECTIVES: Surgical scrub reduces the number of microorganisms, but fails to sterilize hands, and therefore the use of sterile gloves is recommended. Glove perforation allows bacteria passage from the surgeons´ hands to the patient´s tissues. We analyze the relationship between skin flora of hands, glove perforation and contamination. METHODS: A prospective study comprising 139 patients undergoing open heart surgery through a median sternotomy was conducted. Surgeons´hands were studied. Gloved and ungloved fingertips were placed on culture plates after scrubbing and before sternal closure. Removed gloves were evaluated for perforations. Samples from the surgical wound were taken for culture. Identification of isolated microorganisms was performed by conventional biochemical tests. RESULTS: Culture of fingertips after scrubbing resulted positive in 29.13% of the samples and increased to 34.53% at the end of the procedure. Culture of gloved fingertips before closing the sternum demonstrated contamination of the outer surface in 11.87% of samples. Gloves removed before sternal closure showed perforations in 23.02% of samples. Holes were observed in 33% of contaminated gloves. No relationship between perforation and contamination of gloves was observed. The culture of the sternal wound resulted positive in 7.91% of cases. A significant relationship between the presence of microorganisms in the wound and glove contamination was demonstrated. (P<0,001). CONCLUSIONS: Perforation does not cause significant contamination of the outer surface of surgical gloves. The statistical correlation between glove contamination and surgical wound colonization could be explained by the presence of other sources of contaminating microorganisms.

[Plasmid-mediated AMPc producing Proteus mirabilis in the Health Care Area of Santiago de Compostela: molecular and epidemiological analysis by rep-PCR and MALDI-TOF]. / Proteus mirabilis productor de AmpC plasmídica en el Área Sanitaria de Santiago de Compostela: prevalencia y caracterización molecular por rep-PCR y MALDI-TOF MS.

INTRODUCTION: Proteus mirabilis is an important pathogen isolated from both community-acquired and health-care associated infections. Acquired AmpC-type beta-lactamases represent an important mechanism of resistance to extended-spectrum cephalosporins and are emerging in several European countries. The objective of this work was to know the prevalence of acquired AmpC beta-lactamase producing P. mirabilis over the last three years and eight months and their clonal relationships comparing MALDI-TOF and automated rep-PCR results. METHODS: P. mirabilis isolates (n= 1,396) were obtained from routine cultures at the University Hospital Complex of Santiago de Compostela from January 2006 to August 2009. Identification to the species level and antimicrobial susceptibility testing were achieved with Vitek 2. The isolates showing intermediate or total resistance to amoxicillin-clavulanic and cefoxitin, cefotaxime or ceftazidime were selected for AmpC phenotypic detection by double-disk synergy test, and molecular confirmation by multiplex PCR. Molecular typing of the isolates was performed by automated rep-PCR and MALDI-TOF. RESULTS: For the last three years and eight months, the prevalence of AmpC-producing P. mirabilis increased from 0.17% to 4.5%, mainly associated with urinary tract infection in elderly outpatients. In all cases, plasmidic AmpC belonging to LAT/CMY lineage were detected. A high genetic variability was seen with both, rep-PCR and MALDI-TOF MS. CONCLUSIONS: AmpC-producing P. mirabilis is an emergent pathogen. The high genetic variability detected suggests that the spread of the resistance mechanism is more probable than a clone dispersion. Automated rep-PCR and MALDI-TOF MS show as fast and decisive methods for bacterial strain typing in clinical microbiology laboratories.

Proteus mirabilis productor de AmpC plasmídica en el Área Sanitaria de Santiago de Compostela: prevalencia y caracterización molecular por rep-PCR y MALDI-TOF MS / Plasmid-mediated AMPc producing Proteus mirabilis in the Health Care Area of Santiago de Compostela: molecular and epidemiological analysis by rep-PCR and MALDI-TOF

Introducción: Proteus mirabilis es un patógeno de importancia creciente tanto en las infecciones nosocomiales como en las comunitarias. La producción de AmpC plasmídica es un mecanismo de resistencia frente a cefalosporinas de espectro extendido emergente en esta bacteria por lo que se consideró de gran interés estudiar su prevalencia en nuestro Área Sanitaria así como su variabilidad genética, comparando dos métodos recientemente incorporados al mercado: MALDI-TOF y rep-PCR automatizada. Métodos: Entre enero de 2006 y agosto de 2009 se recuperaron 1.396 aislamientos de P. mirabilis a partir de los cultivos de rutina realizados en Complejo Hospitalario Universitario de Santiago de Compostela. La identificación y el antibiograma se hicieron por Vitek 2. Aquellos aislamientos con sensibilidad reducida a amoxicilina-clavulánico y a cefoxitina, cefotaxima o ceftazidima fueron seleccionados para la detección fenotípica y genotípica de AmpC plasmídica mediante sinergia con doble disco y PCR múltiple, respectivamente. La tipificación molecular se llevó a cabo, comparativamente, mediante rep-PCR automatizada y MALDI-TOF. Resultados: A lo largo de tres años y ocho meses, la prevalencia de P. mirabilis productor de AmpC pasó del 0,17% al 4,5%, mayoritariamente asociado a infección urinaria en pacientes ancianos no hospitalizados. En todos los casos, AmpC plasmídica perteneció a la familia LAT/CMY. Se observó una gran variabilidad genética entre los aislamientos tanto por rep-PCR (DiversiLab) como por MALDI-TOF MS. Conclusión: P. mirabilis productor de AmpC adquirida es un patógeno emergente. La variabilidad genética de las cepas estudiadas apunta a una dispersión de este mecanismo de resistencia más que a una diseminación clonal. Rep-PCR automatizada y MALDI-TOF se muestran como métodos rápidos y resolutivos para la tipificación molecular en los laboratorios de microbiología clínica(AU)

Introduction: Proteus mirabilis is an important pathogen isolated from both community-acquired and health-care associated infections. Acquired AmpC-type beta-lactamases represent an important mechanism of resistance to extended-spectrum cephalosporins and are emerging in several European countries. The objective of this work was to know the prevalence of acquired AmpC beta-lactamase producing P. mirabilis over the last three years and eight months and their clonal relationships comparing MALDI-TOF and automated rep-PCR results. Methods: P. mirabilis isolates (n= 1,396) were obtained from routine cultures at the University Hospital Complex of Santiago de Compostela from January 2006 to August 2009. Identification to the species level and antimicrobial susceptibility testing were achieved with Vitek 2. The isolates showing intermediate or total resistance to amoxicillin-clavulanic and cefoxitin, cefotaxime or ceftazidime were selected for AmpC phenotypic detection by double-disk synergy test, and molecular confirmation by multiplex PCR. Molecular typing of the isolates was performed by automated rep-PCR and MALDI-TOF. Results: For the last three years and eight months, the prevalence of AmpC-producing P. mirabilis increased from 0.17% to 4.5%, mainly associated with urinary tract infection in elderly outpatients. In all cases, plasmidic AmpC belonging to LAT/CMY lineage were detected. A high genetic variability was seen with both, rep-PCR and MALDI-TOF MS. Conclusions: AmpC-producing P. mirabilis is an emergent pathogen. The high genetic variability detected suggests that the spread of the resistance mechanism is more probable than a clone dispersion. Automated rep-PCR and MALDI-TOF MS show as fast and decisive methods for bacterial strain typing in clinical microbiology laboratories(AU)

Susceptibility trends of Bacteroides fragilis group and characterisation of carbapenemase-producing strains by automated REP-PCR and MALDI TOF.

Susceptibility testing of clinical isolates of anaerobic bacteria is not considered, often, mandatory in routine clinical practice and the treatments are empirically established. Thus, periodic monitoring of the susceptibility patterns of anaerobic bacteria is advisable. The aim of this study was to update on resistance of Bacteroides fragilis group in our Institution with special attention to carbapenems reporting metallo-beta-lactamase producing strains for the first time in Spain, and to compare fingerprinting analysis results obtained by using automated rep-PCR (DiversiLab System) and MALDI-TOF MS. A total of 830 non-duplicated clinical isolates of the B. fragilis group recovered from the years 2006 to 2010 were studied. B. fragilis was the most prevalent species (59.5%). The total susceptibility of B. fragilis group isolates were: penicillin, 13.3%; amoxicillin/clavulanic, 89.6%; piperacillin-tazobactam, 91.8%; cefoxitin, 65.8%; ertapenem, 95.9%; imipenem, 98.2%; clindamycin, 53.4% and metronidazole, 96.4%. The percentage of sensitive isolates did not change significantly over time for amoxicillin/clavulanic, cefoxitin, clindamycin and metronidazole. A slight increase in the rate of resistance to ertapenem and imipenem was observed. Imipenem resistance and carbapenemase production were detected for the first time in our laboratory in the year 2007. No other report of carbapenemase-producing B. fragilis in our country has been previously published. Six imipenem-resistant isolates were MBL-producing and PCR positive for cfiA gene. Four of them were PCR positive for IS-like immediately upstream cfiA gene and two of them were negative. Both, automated rep-PCR (DiversiLab) and MALDI-TOF MS, revealed a great genetic diversity among carbapenem-producing strains suggesting the acquisition of novel resistance genes more than clonal dissemination of them. Both methods seem to be useful tools for fast and accurate identification and strain typing of B. fragilis group in the daily laboratory routine. Because of the relevant increase observed in Bacteroides species isolated from blood cultures and the appearance of carbapenemase-producing strains in our Institution, we recommend to test the antimicrobial susceptibility of the isolates, at least in the most severe patients.

Espectrometría de masas matrix-assisted laser desorption ionization time-of-flight vs. metodología convencional en la identificación de Candida no-albicans / Matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry vs conventional methods in the identification of Candida non-albicans

Introducción La infección por Candida se ha convertido en un importante problema de salud en todo el mundo. La epidemiología de la candidemia se ha modificado considerablemente por la emergencia de las especies de Candida no-albicans. Esta variación tiene especial importancia en la elección de la profilaxis y tratamiento empírico. Los métodos bioquímicos y los basados en biología molecular presentan limitaciones para la identificación correcta de las especies de Candida. El objetivo de este estudio es demostrar la capacidad del sistema de espectrometría de masas MALDI-TOF para la identificación de estas especies y compararlo con la tecnología utilizada en la actualidad. Métodos Se incluyeron todos los aislados recogidos durante dos años (n=73) de Candida no-albicans procedentes de muestras invasivas. La identificación se realizó mediante los sistemas Vitek-2 YST y API CAUX. Las identificaciones del MALDI-TOF se hicieron con el sistema Axima Confidence (Shimadzu Corporation), utilizando el software Shimadzu Launchpad y la base de datos SARAMIS (AnagnosTec GmbH). Las discrepancias se resolvieron mediante PCR multiplex LightCycler SeptiFast, PCR específica de C. glabrata y digestión enzimática con BanI del fragmento SADH en los aislados de C. parapsilosis. Resultados De los 73 aislados de Candida no-albicans, los métodos bioquímicos identificaron de forma concluyente 67 a nivel de especie y 6 a nivel de género. El sistema MALDI-TOF obtuvo identificaciones a nivel de especie en todas ellas. La correlación en la especie de todos los aislados estudiados fue del 85,07%, llegando al 94,52% si se estudia la correlación entre la identificación obtenida mediante métodos bioquímicos junto con los métodos empleados para el análisis de las discrepancias. En los aislados de C. parapsilosis, el sistema MALDI-TOF obtuvo una identificación de C. orthopsilosis en tres de ellos, confirmándose por digestión con BanI del fragmento SADH (..) (AU)

Introduction: Candida infection has become a major health problem worldwide. The epidemiology of Candidaemia has substantially changed by the emergence of the species Candida non-albicans. This variation is particularly important in the choice of prophylaxis and empirical treatment. The methods based on biochemical and molecular biology have limitations for the correct identification of Candida species. The aim of this study is to demonstrate the ability of the MALDI-TOF mass spectrometry for the identification of these species and compare it with the technology used today. Methods: We included all isolates collected over 2 years (n=73) of Candida non-albicans from non-invasive samples. The identification was carried out by Vitek-2 systems YST and API CAUX. The MALDI-TO Fidentifications were made with Confidence Axima system (Shimadzu Corporation) using the Shimadzu Launchpad software and database SARAMIS (AnagnosTec GmbH). Discrepancies were resolved by Septi-Fast Light Cycler multiplex PCR, specific PCR C. glabrata and enzymatic digestion with BanI SADH fragment in isolates of C. parapsilosis. Results: Of the 73 isolates of Candida non-albicans, the biochemical methods conclusively identified 67 to species level and 6 at the genus level. The MALDI-TOF system obtained identifications at the species level in all cases. The correlation in the species of all isolates studied was 85.07%, reaching 94.52% when the correlation was made between the identification obtained by biochemical methods and the methods for the analysis of the discrepancies. In isolates of C. parapsilosis, MALDI-TOF system obtained an identification (..) (AU)

[Matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry vs conventional methods in the identification of Candida non-albicans]. / Espectrometría de masas matrix-assisted laser desorption ionization time-of-flight vs. metodología convencional en la identificación de Candida no-albicans.

INTRODUCTION: Candida infection has become a major health problem worldwide. The epidemiology of Candidaemia has substantially changed by the emergence of the species Candida non-albicans. This variation is particularly important in the choice of prophylaxis and empirical treatment. The methods based on biochemical and molecular biology have limitations for the correct identification of Candida species. The aim of this study is to demonstrate the ability of the MALDI-TOF mass spectrometry for the identification of these species and compare it with the technology used today. METHODS: We included all isolates collected over 2 years (n=73) of Candida non-albicans from non-invasive samples. The identification was carried out by Vitek-2 systems YST and API CAUX. The MALDI-TOF identifications were made with Confidence Axima system (Shimadzu Corporation) using the Shimadzu Launchpad software and database SARAMIS (AnagnosTec GmbH). Discrepancies were resolved by SeptiFast LightCycler multiplex PCR, specific PCR C. glabrata and enzymatic digestion with BanI SADH fragment in isolates of C. parapsilosis. RESULTS: Of the 73 isolates of Candida non-albicans, the biochemical methods conclusively identified 67 to species level and 6 at the genus level. The MALDI-TOF system obtained identifications at the species level in all cases. The correlation in the species of all isolates studied was 85.07%, reaching 94.52% when the correlation was made between the identification obtained by biochemical methods and the methods for the analysis of the discrepancies. In isolates of C. parapsilosis, MALDI-TOF system obtained an identification of C. orthopsilosis. In 3 of them it was confirmed by digestion with BanI SADH fragment. CONCLUSION: This study has demonstrated the use of mass spectrometry (MALDI-TOF system) to provide the microbiology laboratory with greater efficiency and reliability to identify isolates of Candida non-albicans to species level. It also shows its potential usefulness in identifying related species, such as C. parapsilosis, metapsilosis and orthopsilosis.

Molecular and epidemiological analysis of nosocomial carbapenem-resistant Klebsiella spp. using repetitive extragenic palindromic-polymerase chain reaction and matrix-assisted laser desorption/ionization-time of flight.

INTRODUCTION: Infections with carbapenem-resistant enterobacteria are an emerging threat. This study reports the microbiologic, clinical, and epidemiologic features and the therapeutic outcomes of the infections caused by carbapenem- and pandrug-resistant Klebsiella emerged in our hospital. Fingerprinting analyses by automated repetitive extragenic palindromic-polymerase chain reaction (rep-PCR) and matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry are also compared. MATERIALS AND METHODS: Carbapenem-resistant Klebsiella spp. affecting 13 patients were investigated using automated rep-PCR (DiversiLab System) and MALDI-TOF. Species identification was performed by Vitek 2 System and MALDI-TOF. Antimicrobial susceptibility testing was made using Vitek 2 System and Etest. Screening for extended spectrum beta-lactamase (ESBL) and carbapenemase production was made by double disk synergy and Hodge tests, respectively. Synergy studies were performed using Etest. DNA array was used for detection of KPC and ESBLs. bla(VIM-1) gene was amplified by PCR and sequencing. Use of carbapenems in the hospital was studied. RESULTS: A total of 13 patients were found to be colonized/infected with carbapenem-resistant Klebsiella. All patients were previously submitted to surgery and/or presented with severe underlying disease. After carbapenem-resistant Klebsiella isolation, the majority of the patients were treated with amikacin plus carbapenem, tigecycline, or fosfomycin. All Klebsiella isolates (n = 14), except two, had the bla(VIM-1) gene and all Klebsiella pneumoniae also had bla(SHV) gene associated with ESBL production. DiversiLab system showed higher discriminatory power than MALDI-TOF for strain typing. CONCLUSIONS: The risk of a rapid dissemination and the persistence of these multidrug-resistant strains through the time determine the need to implement routine procedures for metallo-beta-lactamase detection and measures for prevention of the spread of these microorganisms. The combined use of MALDI-TOF for species identification and DiversiLab System for clonal strain typing may be a useful tool for fast and accurate management of nosocomial outbreaks. The potential clinical utility of fosfomycin in this matter should be considered in future studies.

[Variability in HIV viral tropism determination using different genotypic algorithms in patients infected with B versus non-B HIV-1 subtypes]. / Variabilidad en la determinación del tropismo viral del VIH utilizando diferentes algoritmos genotípicos de interpretación en pacientes VIH-1 infectados con subtipos B versus no-B.

BACKGROUND: Genotypic tools based on the analysis of the V3 region are seen as an alternative to phenotypic assays for viral tropism determination before prescribing maraviroc. The concordance between different genotypic algorithms has been evaluated in HIV+ patients infected with B versus non-B subtypes. METHODS: HIV-infected patients on regular follow up at Hospital Universitario de Santiago de Compostela (Spain) were selected. The env-V3 region was sequenced from plasma samples and viral tropism was estimated using 8 different genotypic algorithms. Concordance among predictors was statistically evaluated by the calculation of the kappa index. Phylogenetic analyses were performed to determine the genetic subtype. RESULTS: A total of 92 HIV-infected patients were selected, 72 B and 20 non-B subtypes. Regarding the B subtype group, significant kappa values were obtained among all 28 possible combinations between the genotypic predictors evaluated. The best concordance among non-related predictors was observed for webPSSM(SINSI)/Wetcat(PART) (k: 0.771) and webPSSM(SINSI)/geno2pheno (k: 0.574). Conversely, among non-B subtypes, a significative kappa index was only obtained for 13 combinations. Among non-B subtypes, the best concordance values were obtained for webPSSM(X4R5)/Wetcat(PART) (k: 0.600) and webPSSM(SINSI)/Charge rule (k: 0.590). CONCLUSION: A high concordance was observed between different genotypic algorithms to determine viral tropism among HIV-1 B subtypes infected patients, especially between webPSSM(SINSI) and geno2pheno or Wetcat. Conversely, the overall concordance among non-B subtypes was lower. This heterogeneity could be justified by the low prevalence of non B subtypes in the datasets in which the genotypic tropism predictors were trained.