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1.
Commun Earth Environ ; 5(1): 597, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-39430423

RESUMO

Atmospheric turbulence, irregular fluctuations of the fluid state, is studied on Mars. Universality of the turbulence spectrum underpins atmospheric models where computational requirements preclude full fidelity simulations of the smallest scales. However, there are discrepancies among reports on the existence and spectral location of universal scaling in Martian atmospheric data. Here, results indicate the smallest resolvable structures from Martian wind speed data are still associated with the energetic regime, which may ultimately explain why multiple reports have not found a consistent Kolmogorov-like spectral regime on Mars. Universal spectral scaling of wind data from Perseverance's Mars Environmental Dynamics Analyzer is used to estimate the thresholds that separate three turbulence regimes: energetic, inertial, and molecular dissipation. Wind measurements at 2-Hz, the fastest sampling rate for direct wind sensor measurements on Mars, resolves turbulence in the energetic regime and approaches the inertial regime, which is consistent with reported Martian dust devil sizes.

2.
Pediatr Infect Dis J ; 2024 Oct 14.
Artigo em Inglês | MEDLINE | ID: mdl-39417786

RESUMO

This study conducted in Madrid (Spain) between 2018 and 2023 shows a significant decrease in the pediatric bacterial community-acquired pneumonia cases during the COVID-19 pandemic, followed by a notable postpandemic increase surpassing prepandemic incidence. Streptococcus pneumoniae remains predominant, with an increasing prevalence of serotype 3, while Streptococcus pyogenes was the second most common pathogen.

3.
Pediatr Infect Dis J ; 2024 Oct 09.
Artigo em Inglês | MEDLINE | ID: mdl-39348498

RESUMO

BACKGROUND: Klebsiella michiganensis , a member of the Klebsiella oxytoca complex, is an emerging nosocomial pathogen known to frequently carry plasmids with antibiotic-resistance genes, including carbapenemases. Using genomics, this study redefined an outbreak alert of K. michiganensis carrying a blaVIM carbapenemase in a pediatric ward in a Spanish hospital. METHODS: A total of 31 isolates of Verona integron-encoded metallo-ß-lactamase (VIM)-carbapenemase K. oxytoca from suspected outbreak cases and unrelated controls from 2015 to 2022 were analyzed. Whole-genome sequencing (both short and long reads) was applied to determine phylogenetic relationships based on single-nucleotide polymorphisms (SNPs) and identify plasmids and antimicrobial resistance genes. RESULTS: The sequences from 12 isolates identified in 2021 showed pairwise SNP distances ranging from 0 to 16 SNPs, confirming the outbreak. Examination of isolates before and after the study period revealed 7 additional cases, 2 in 2020 and 5 in 2022. The outbreak comprised 18 isolates from 17 patients in 3 different pediatric wards, together with 1 environmental sample. In all outbreak isolates, the blaVIM-1 gene was located within a gene cassette carried by a class 1 integron on an IncFIB(pQil) plasmid. A genomic network based on SNPs revealed 5 unsampled intermediate nodes, suggesting additional subclones that may have involved healthcare staff, patient relatives or environmental reservoirs. Blood and rectal isolates obtained from the same patient were positioned on separate branches of the network, making a direct evolutionary pathway between them unlikely. CONCLUSIONS: Our study redefined the full extent of this K. michiganensis -VIM outbreak and highlights the critical importance of genomic analysis in accurately understanding outbreaks in healthcare settings.

5.
Front Cell Infect Microbiol ; 13: 1237500, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-37780848

RESUMO

Introduction: Clostridioides difficile infection (CDI) is the main cause of nosocomial diarrhoea in developed countries. Recurrent CDI (R-CDI), which affects 20%-30% of patients and significantly increases hospital stay and associated costs, is a key challenge. The main objective of this study was to explore the role of the microbiome and calprotectin levels as predictive biomarkers of R-CDI. Methods: We prospectively (2019-2021) included patients with a primary episode of CDI. Clinical data and faecal samples were collected. The microbiome was analysed by sequencing the hypervariable V4 region of the 16S rRNA gene on an Illumina Miseq platform. Results: We enrolled 200 patients with primary CDI, of whom 54 developed R-CDI and 146 did not. We analysed 200 primary samples and found that Fusobacterium increased in abundance, while Collinsella, Senegalimassilia, Prevotella and Ruminococcus decreased in patients with recurrent versus non-recurrent disease. Elevated calprotectin levels correlated significantly with R-CDI (p=0.01). We built a risk index for R-CDI, including as prognostic factors age, sex, immunosuppression, toxin B amplification cycle, creatinine levels and faecal calprotectin levels (overall accuracy of 79%). Discussion: Calprotectin levels and abundance of microbial genera such as Fusobacterium and Prevotella in primary episodes could be useful as early markers of R-CDI. We propose a readily available model for prediction of R-CDI that can be applied at the initial CDI episode. The use of this tool could help to better tailor treatments according to the risk of R-CDI.


Assuntos
Clostridioides difficile , Infecções por Clostridium , Microbiota , Humanos , Complexo Antígeno L1 Leucocitário , RNA Ribossômico 16S/genética , Clostridioides difficile/genética , Infecções por Clostridium/microbiologia
6.
PLoS One ; 18(9): e0290998, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-37682961

RESUMO

BACKGROUND: Prosthetic valve endocarditis (PVE) is a serious infection associated with high mortality that often requires surgical treatment. METHODS: Study on clinical characteristics and prognosis of a large contemporary prospective cohort of prosthetic valve endocarditis (PVE) that included patients diagnosed between January 2008 and December 2020. Univariate and multivariate analysis of factors associated with in-hospital mortality was performed. RESULTS: The study included 1354 cases of PVE. The median age was 71 years with an interquartile range of 62-77 years and 66.9% of the cases were male. Patients diagnosed during the first year after valve implantation (early onset) were characterized by a higher proportion of cases due to coagulase-negative staphylococci and Candida and more perivalvular complications than patients detected after the first year (late onset). In-hospital mortality of PVE in this series was 32.6%; specifically, it was 35.4% in the period 2008-2013 and 29.9% in 2014-2020 (p = 0.031). Variables associated with in-hospital mortality were: Age-adjusted Charlson comorbidity index (OR: 1.15, 95% CI: 1.08-1.23), intracardiac abscess (OR:1.78, 95% CI:1.30-2.44), acute heart failure related to PVE (OR: 3. 11, 95% CI: 2.31-4.19), acute renal failure (OR: 3.11, 95% CI:1.14-2.09), septic shock (OR: 5.56, 95% CI:3.55-8.71), persistent bacteremia (OR: 1.85, 95% CI: 1.21-2.83) and surgery indicated but not performed (OR: 2.08, 95% CI: 1.49-2.89). In-hospital mortality in patients with surgical indication according to guidelines was 31.3% in operated patients and 51.3% in non-operated patients (p<0.001). In the latter group, there were more cases of advanced age, comorbidity, hospital acquired PVE, PVE due to Staphylococcus aureus, septic shock, and stroke. CONCLUSIONS: Not performing cardiac surgery in patients with PVE and surgical indication, according to guidelines, has a significant negative effect on in-hospital mortality. Strategies to better discriminate patients who can benefit most from surgery would be desirable.


Assuntos
Endocardite Bacteriana , Endocardite , Próteses Valvulares Cardíacas , Choque Séptico , Humanos , Masculino , Pessoa de Meia-Idade , Idoso , Feminino , Prognóstico , Endocardite Bacteriana/cirurgia , Próteses Valvulares Cardíacas/efeitos adversos , Endocardite/cirurgia , Sistema de Registros
7.
J Antimicrob Chemother ; 78(8): 1948-1954, 2023 08 02.
Artigo em Inglês | MEDLINE | ID: mdl-37325878

RESUMO

OBJECTIVES: To evaluate the impact of time to results (TTR) on the outcome of patients with carbapenemase-producing Enterobacterales bloodstream infections (CPE-BSI). METHODS: Times-series study conducted from January 2014 to December 2021, selecting patients with first CPE-BSI episodes. Periods of intervention were defined according to implementation of diagnostic bundle tests in the microbiology laboratory: pre-intervention (January 2014-December 2017) and post-intervention (January 2018-December 2021). TTR was defined as time elapsed from positivity time of the blood culture bottles to physicians' notification of CPE-BSI episodes, and was evaluated in patients who received inappropriate empirical and switched to appropriate targeted treatment (switch group). Analysis of a composite unfavourable outcome (mortality at Day 30 and/or persistent and/or recurrent bacteraemia) was performed for the total episodes and in the switch group. RESULTS: One hundred and nine episodes were analysed: 66 pre-intervention and 43 post-intervention. Compared with pre-intervention, patients in the post-intervention period were younger (68 versus 63 years, P = 0.04), had INCREMENT score > 7 (31.8% versus 53.5%, P = 0.02) and unfavourable outcome (37.9% versus 20.9%, P = 0.04). Proportion of TTR > 30 h was more frequent pre-intervention than post-intervention (61.7% versus 35.5%, P = 0.02). In multivariate analysis of the 109 episodes, source other than urinary or biliary (OR 2.76, 95% CI 1.11-6.86) was associated with unfavourable outcome, while targeted appropriate treatment trended to being protective (OR 0.17, 95% CI 0.03-1.00). Considering the switch group (n = 78), source other than urinary or biliary (OR 14.9, 95% CI 3.25-69.05) and TTR > 30 h (OR 4.72, 95% CI 1.29-17.22) were associated with unfavourable outcome. CONCLUSIONS: Decreased TTR in the post-intervention period was associated with the outcome in patients with CPE-BSI episodes.


Assuntos
Infecções por Enterobacteriaceae , Gammaproteobacteria , Sepse , Humanos , Antibacterianos/uso terapêutico , Estudos Retrospectivos , beta-Lactamases , Proteínas de Bactérias , Sepse/tratamento farmacológico , Infecções por Enterobacteriaceae/diagnóstico , Infecções por Enterobacteriaceae/tratamento farmacológico , Infecções por Enterobacteriaceae/microbiologia
8.
Front Cell Infect Microbiol ; 13: 1130701, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-37124040

RESUMO

Introduction: Clostridioides difficile infection (CDI) is the main cause of nosocomial diarrhea in developed countries. A key challenge in CDI is the lack of objective methods to ensure more accurate diagnosis, especially when differentiating between true infection and colonization/diarrhea of other causes. The main objective of this study was to explore the role of the microbiome as a predictive biomarker of CDI. Methods: Between 2018 and 2021, we prospectively included patients with CDI, recurrent CDI (R-CDI), non-CDI diarrhea (NO-CDI), colonization by C. difficile, and healthy individuals. Clinical data and fecal samples were collected. The microbiome was analyzed by sequencing the hypervariable V4 region of the 16S rRNA gene on an Illumina Miseq platform. The mothur bioinformatic pipeline was followed for pre-processing of raw data, and mothur and R were used for data analysis. Results: During the study period, 753 samples from 657 patients were analyzed. Of these, 247 were from patients with CDI, 43 were from patients colonized with C. difficile, 63 were from healthy individuals, 324 were from NOCDI, and 76 were from R-CDI. We found significant differences across the groups in alpha and beta diversity and in taxonomic abundance. We identified various genera as the most significant biomarkers for CDI (Bacteroides, Proteus, Paraprevotella, Robinsoniella), R-CDI (Veillonella, Fusobacterium, Lactobacillus, Clostridium sensu stricto I), and colonization by C. difficile (Parabacteroides, Faecalicoccus, Flavonifractor, Clostridium XVIII). Discussion: We observed differences in microbiome patterns between healthy individuals, colonized patients, CDI, R-CDI, and NOCDI diarrhea. We identified possible microbiome biomarkers that could prove useful in the diagnosis of true CDI infections. Further studies are warranted.


Assuntos
Clostridioides difficile , Infecções por Clostridium , Microbioma Gastrointestinal , Humanos , RNA Ribossômico 16S/genética , Clostridioides difficile/genética , Infecções por Clostridium/diagnóstico , Infecções por Clostridium/microbiologia , Fezes/microbiologia , Diarreia/microbiologia
9.
J Fungi (Basel) ; 9(4)2023 Mar 28.
Artigo em Inglês | MEDLINE | ID: mdl-37108869

RESUMO

Pneumocystis jirovecii pneumonia (PJP) in immunocompromised patients entails high mortality and requires adequate laboratory diagnosis. We compared the performance of a real time-PCR assay against the immunofluorescence assay (IFA) in the routine of a large microbiology laboratory. Different respiratory samples from HIV and non-HIV-infected patients were included. The retrospective analysis used data from September 2015 to April 2018, which included all samples for which a P. jirovecii test was requested. A total of 299 respiratory samples were tested (bronchoalveolar lavage fluid (n = 181), tracheal aspirate (n = 53) and sputum (n = 65)). Forty-eight (16.1%) patients fulfilled the criteria for PJP. Five positive samples (10%) had only colonization. The PCR test was found to have a sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of 96%, 98%, 90% and 99%, compared to 27%, 100%, 100% and 87%, for the IFA, respectively. PJ-PCR sensitivity and specificity were >80% and >90% for all tested respiratory samples. Median cycle threshold values in definite PJP cases were 30 versus 37 in colonized cases (p < 0.05). Thus, the PCR assay is a robust and reliable test for the diagnosis PJP in all respiratory sample types. Ct values of ≥36 could help to exclude PJP diagnosis.

10.
Open Forum Infect Dis ; 10(2): ofad028, 2023 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-36776780

RESUMO

Background: We aimed to describe the frequency of use and effectiveness of bezlotoxumab (BZX) and fecal microbiota transplantation (FMT) in patients with Clostridioides difficile infection (CDI) in real-world practice. Methods: This was a retrospective study conducted in a university hospital in which adult patients treated with BZX or FMT from January 2018 to April 2021 were included. The primary objective was to evaluate the effectiveness of BZX and FMT in preventing early (within 8 weeks) and late (within 1 year) CDI recurrences (rCDI). A multivariate analysis of risk factors for early recurrence was performed. Results: Of 1377 consecutive CDI episodes, 117 (8.5%) received BZX or FMT, with full information available for 100 of the episodes: 51 received BZX, and 49 received FMT. BZX was used mostly in immunosuppressed patients (66.7%) and in first episodes or first recurrences in 70.6% of the cases. FMT was prescribed only in CDI recurrences. Despite the different conditions of the patients, there were no significant differences between BZX and FMT in preventing early rCDI (19.6% vs 24.5%; P = .55) or late rCDI (9.8% vs 18.4%; P = .31). In the multivariate analysis, risk factors for recurrence were presence of ≥2 previous rCDI episodes (odds ratio [OR], 2.90; 95% CI, 1.03-8.63) and use of non-CDI antibiotics (OR, 3.45; 95% CI, 1.24-9.57). Conclusions: BZX and FMT were infrequently used in real-world practice. Both treatments had similar effectiveness in preventing CDI recurrence despite their application to different populations.

12.
Microb Biotechnol ; 16(4): 778-783, 2023 04.
Artigo em Inglês | MEDLINE | ID: mdl-36541026

RESUMO

Identification of Nocardia and Mycobacterium species by matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) is still a challenging task that requires both suitable protein extraction procedures and extensive databases. This study aimed to evaluate the VITEK MS Plus system coupled with updated RUO (v4.17) and IVD (v3.2) databases for the identification of Nocardia spp. and Mycobacterium spp. clinical isolates. Sample preparation was carried out using the VITEK MS Mycobacterium/Nocardia kit for protein extraction. From 90 Nocardia spp. isolates analysed, 86 (95.6%) were correctly identified at species or complex level using IVD and 78 (86.7%) using RUO. Only two strains were misidentified as other species pertaining to the same complex. Among the 106 non-tuberculous Mycobacterium clinical isolates tested from a liquid culture medium, VITEK MS identified correctly at species or complex level 96 (90.6%) isolates in the IVD mode and 89 (84.0%) isolates in the RUO mode. No misidentifications were detected. Although the IVD mode was unable to differentiate members of the M. fortuitum complex, the RUO mode correctly discriminated M. peregrinum and M. septicum. The robustness and accuracy showed by this system allow its implementation for routine identification of these microorganisms in clinical laboratories.


Assuntos
Mycobacterium , Nocardia , Nocardia/química , Espectrometria de Massas por Ionização e Dessorção a Laser Assistida por Matriz/métodos , Mycobacterium/química , Meios de Cultura , Micobactérias não Tuberculosas
13.
Front Biosci (Elite Ed) ; 14(3): 23, 2022 08 18.
Artigo em Inglês | MEDLINE | ID: mdl-36137991

RESUMO

BACKGROUND: Abiotrophia spp. and Granulicatella spp. are Gram-positive cocci, formerly known as nutritionally variant or deficient Streptococcus. Their role as causative agents of infective endocarditis (IE) is numerically uncertain, as well as diagnostic and clinical management of this infection. The aim of our study is to describe the clinical, microbiological, therapeutic, and prognosis of patients with IE caused by these microorganisms in a large microbiology department. METHODS: Retrospective analysis of all the patients with Abiotrophia spp. and Granulicatella spp. IE registered in our centre in the period 2004-2021. RESULTS: Of the 822 IE in the study period, 10 (1.2%) were caused by Abiotrophia spp. (7) or Granulicatella spp. (3). The species involved were A.defectiva (7), G.adiacens (2) and G.elegans (1). Eight patients were male, their mean age was 46 years and four were younger than 21 years. The most frequent comorbidities were congenital heart disease (4; 40%) and the presence of intracardiac prosthetic material (5; 50%). IE occurred on 5 native valves and 5 prosthetic valve or material. Blood cultures were positive in 8/10 patients, within a mean incubation period of 18.07 hours. In the other two patients, a positive 16SPCR from valve or prosthetic material provided the diagnosis. Surgery for IE was performed in seven patients (70%) and in all cases positive 16S rRNA PCR and sequencing from valve or prosthetic material was demonstrated. Valves and/or prosthetic removed material cultures were positive in four patients. Nine patients received ceftriaxone (4 in monotherapy and 5 in combination with other antibiotics). The mean length of treatment was 6 weeks and IE-associated mortality was 20% at one year follow-up. CONCLUSIONS: Abiotrophia spp. or Granulicatella spp. IE were infrequent but not exceptional in our environment and particularly affected patients with congenital heart disease or prosthetic material. Blood cultures and molecular methods allowed the diagnosis. Most of them required surgery and the associated mortality, in spite of a mean age of 46 years, was high.


Assuntos
Abiotrophia , Carnobacteriaceae , Endocardite Bacteriana , Endocardite , Abiotrophia/genética , Antibacterianos , Carnobacteriaceae/genética , Ceftriaxona , Endocardite/diagnóstico , Endocardite Bacteriana/diagnóstico , Endocardite Bacteriana/tratamento farmacológico , Endocardite Bacteriana/epidemiologia , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , RNA Ribossômico 16S/genética , Estudos Retrospectivos , Streptococcus/genética
14.
Front Med (Lausanne) ; 9: 953724, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-36072952

RESUMO

Information on Clostridioides difficile infection (CDI) in patients with COVID-19 is scarce and points to an overall decrease of episodes during the pandemic. This situation results paradoxical, as COVID-19 patients had long periods of hospital stay and high use of antibiotics. We conducted a retrospective study from January 1st 2019 to December 31st 2020 comparing the incidence of hospital-acquired episodes of CDI (HA-CDI) among patients with and without COVID-19 admitted to our institution. During the study period, there were 47,048 patient admissions in 2019, 35,662 admissions of patients without COVID-19 in 2020 and 6,763 of COVID-19 patients. There were 68 episodes of HA-CDI in COVID-19 patients (14.75/10,000 days), 159 in 2020-non-COVID-19 patients (5.54/10,000 days) and 238 in 2019 (6.80/10,000 days). Comparison of HA-CDI in COVID-19 and non-COVID-19 patients indicates it occurs more frequently, in terms of CDI disease severity, COVID-19 does not seem to have a negative impact.

15.
J Plast Reconstr Aesthet Surg ; 75(9): 3085-3093, 2022 09.
Artigo em Inglês | MEDLINE | ID: mdl-35872019

RESUMO

The most frequent complications of post-mastectomy reconstructions are breast implant (BI) infection and capsular contracture (CC). The diagnosis of BI colonization is based on cultures from the sonicated BI and from the capsule tissue. Therefore, we first aimed to assess the yield of conventional culture and molecular techniques in periprosthetic fluid, in addition to BI and capsular tissue. Moreover, we compare colonization and biofilm production between patients with and without CC. During 19 months, we prospectively included patients whose BIs had been removed and divided them into two groups: A (CC, Baker III-IV) and B (no CC). Samples were obtained for conventional culture, 16 s rRNA PCR, and MALDI-TOF. Biofilm production was also evaluated. We included 81 BIs from 69 patients with CC (22) and without CC (53). Forty-three (53.1%) of the 81 BIs had ≥1 positive culture. The culture was positive in 57.1% and 50.9% in groups A and B, respectively (p = 0.645). The highest 16 s rRNA PCR positivity rate was detected in capsular tissue (40.5%). MALDI-TOF was unable to detect colonization in any of the samples. High biofilm production was the following: high biomass: A, 29.8%; B, 39.7% (p = 0.293); high metabolic activity: A, 36.2%; B, 34.5% (p = 0.857). We confirm that cultures from different sites are mandatory to ensure a proper diagnosis of BI colonization. Our study is the first to demonstrate that CC was not associated with BI colonization or high biofilm production. The application of molecular techniques in BI samples was not substantially useful for predicting colonization.


Assuntos
Implante Mamário , Implantes de Mama , Neoplasias da Mama , Contratura , Biofilmes , Implante Mamário/efeitos adversos , Implante Mamário/métodos , Implantes de Mama/efeitos adversos , Implantes de Mama/microbiologia , Neoplasias da Mama/cirurgia , Contratura/cirurgia , Feminino , Humanos , Contratura Capsular em Implantes/microbiologia , Mastectomia
16.
Diagnostics (Basel) ; 12(2)2022 Jan 27.
Artigo em Inglês | MEDLINE | ID: mdl-35204419

RESUMO

Vancomycin-resistant Enterococcus faecium represents a health threat due to its ability to spread and cause outbreaks. MALDI-TOF MS has demonstrated its usefulness for E. faecium identification, but its implementation for antimicrobial resistance detection is still under evaluation. This study assesses the repeatability of MALDI-TOF MS for peak analysis and its performance in the discrimination of vancomycin-susceptible (VSE) from vancomycin-resistant isolates (VRE). The study was carried out on protein spectra from 178 E. faecium unique clinical isolates-92 VSE, 31 VanA VRE, 55 VanB VRE-, processed with Clover MS Data Analysis software. Technical and biological repeatability were assayed. Unsupervised (principal component analysis, (PCA)) and supervised algorithms (support vector machine (SVM), random forest (RF) and partial least squares-discriminant analysis (PLS-DA)) were applied. The repeatability assay was performed with 18 peaks common to VSE and VRE with intensities above 1.0% of the maximum peak intensity. It showed lower variability for normalized data and for the peaks within the 3000-9000 m/z range. It was found that 80.9%, 79.2% and 77.5% VSE vs. VRE discrimination was achieved by applying SVM, RF and PLS-DA, respectively. Correct internal differentiation of VanA from VanB VRE isolates was obtained by SVM in 86.6% cases. The implementation of MALDI-TOF MS and peak analysis could represent a rapid and effective tool for VRE screening. However, further improvements are needed to increase the accuracy of this approach.

17.
Diagn Microbiol Infect Dis ; 101(2): 115426, 2021 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-34217111

RESUMO

OBJECTIVES: To quantify the workload and cost overload that the COVID-19 pandemic has meant for a Clinical Microbiology laboratory in a real-life scenario. METHODS: We compared the number of samples received, their distribution, the human resources, and the budget of a Microbiology laboratory in the COVID pandemic (March-December 2020) with the same months of the previous year. RESULTS: the total number of samples processed in the Clinical Microbiology laboratory in March to December 2020 increased 96.70% with respect to 2019 (from 246,060 to 483,993 samples), reflecting an increment of 127.50% when expressed as samples/1000 admissions (from 6057 to 13,780). The increase in workload was mainly at the expense of the virology (+2058%) and serology (+86%) areas. Despite additional personnel hiring, the samples processed per technician increased 12.5%. The extra cost attributed to Microbiology amounts to 6,616,511 euros (114.8%). CONCLUSIONS: This is the first study to provide quantitative figures about workload and cost increase caused by the COVID-19 in a Microbiology laboratory.


Assuntos
COVID-19/epidemiologia , Laboratórios Hospitalares/estatística & dados numéricos , COVID-19/diagnóstico , COVID-19/economia , Teste para COVID-19/economia , Teste para COVID-19/estatística & dados numéricos , Serviços de Laboratório Clínico/economia , Serviços de Laboratório Clínico/estatística & dados numéricos , Custos e Análise de Custo , Hospitalização/estatística & dados numéricos , Humanos , Laboratórios Hospitalares/economia , Pessoal de Laboratório Médico/economia , Pessoal de Laboratório Médico/estatística & dados numéricos , SARS-CoV-2/isolamento & purificação , Espanha/epidemiologia , Centros de Atenção Terciária , Carga de Trabalho/estatística & dados numéricos
18.
Front Cell Infect Microbiol ; 11: 521014, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-33968791

RESUMO

Because of the special culture requirements of anaerobic bacteria, their low growth-rate and the difficulties to isolate them, MALDI-TOF MS has become a reliable identification tool for these microorganisms due to the little amount of bacteria required and the accuracy of MALDI-TOF MS identifications. In this study, the performance of MALDI-TOF MS for the identification of anaerobic isolates during a 4-year period is described. Biomass from colonies grown on Brucella agar was directly smeared onto the MALDI-TOF target plate and submitted to on-plate protein extraction with 1µl of 100% formic acid. Sequencing analysis of the 16S rRNA gene was used as a reference method for the identification of isolates unreliably or not identified by MALDI-TOF MS. Overall, 95.7% of the isolates were identified to the species level using the updated V6 database vs 93.8% with previous databases lacking some anaerobic species; 68.5% of the total were reliably identified with high-confidence score values (≥2.0) and 95.0% with low-confidence values (score value ≥1.7). Besides, no differences between Gram-positive and Gram-negative isolates were detected beyond a slight decrease of correct species assignment for gram positive cocci (94.1% vs 95.7% globally). MALDI-TOF MS has demonstrated its usefulness for the identification of anaerobes, with high correlation with phenotypic and conventional methods. Over the study period, only 2.1% of the isolates could not be reliably identified and required molecular methods for a final identification. Therefore, MALDI-TOF MS provided reliable identification of anaerobic isolates, allowing clinicians to streamline the most appropriate antibiotic therapy and manage patients accordingly.


Assuntos
Bactérias Anaeróbias , Bactérias , Bactérias Anaeróbias/genética , Humanos , RNA Ribossômico 16S/genética , Espectrometria de Massas por Ionização e Dessorção a Laser Assistida por Matriz
19.
Diagn Microbiol Infect Dis ; 100(1): 115330, 2021 May.
Artigo em Inglês | MEDLINE | ID: mdl-33571860

RESUMO

SARS-CoV-2 pandemic shows the importance of having efficient virus diagnosis, especially in groups of particular relevance such as health care professionals, without involving a large economic expense. This is a prevalence study carried out in 7400 health care professionals in a 1350-bed hospital in Madrid, Spain. Pools of 10 samples were performed, using the Xpert® Xpress SARS-CoV-2 test for the diagnosis from clinical samples of nasopharyngeal exudate. A previous study was performed to evaluate the effect of the dilution in terms of sensitivity. The estimated sensitivity was over 95%. A total of 740 pools were performed, with a final result of 218 health care professionals being positive. Using the pooling system, the reagent cost reduction to the institution was 75.3%. It can be concluded that the described sample pooling system is a useful and efficient tool in the diagnosis of SARS-CoV-2 in certain groups, assuming a cost reduction without reducing the sensitivity.


Assuntos
Teste de Ácido Nucleico para COVID-19/métodos , Recursos Humanos em Hospital/estatística & dados numéricos , Reação em Cadeia da Polimerase/métodos , COVID-19/epidemiologia , Reações Falso-Positivas , Humanos , Nasofaringe/virologia , Prevalência , Reprodutibilidade dos Testes , Sensibilidade e Especificidade , Espanha/epidemiologia , Manejo de Espécimes/métodos
20.
Front Pediatr ; 9: 810718, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-35155320

RESUMO

Toxoplasma gondii infection is a severe complication of hematopoietic stem-cell transplantation (HSCT) recipients that can remain unnoticed without a high clinical suspicion. We present the case of a 6-year-old patient with acute lymphoblastic leukemia and HSCT recipient who was admitted to the Pediatric Intensive Care Unit (PICU) on post-transplantation day +39 with fever, hypotension, severe respiratory distress and appearance of a lumbar subcutaneous node. She developed severe Acute Respiratory Distress Syndrome (ARDS) and underwent endotracheal intubation and early mechanical ventilation. Subsequently, she required prone ventilation, inhaled nitric oxide therapy and high-frequency oscillatory ventilation (HFOV). An etiologic study was performed, being blood, urine, bronchoalveolar lavage and biopsy of the subcutaneous node positive for Toxoplasma gondii by Polymerase Chain Reaction (PCR). Diagnosis of disseminated toxoplasmosis was established and treatment with pyrimethamine, sulfadiazine and folinic acid started. The patient showed clinical improvement, allowing weaning of mechanical ventilation and transfer to the hospitalization ward after 40 days in the PICU. It is important to consider toxoplasmosis infection in immunocompromised patients with sepsis and, in cases of severe respiratory distress, early mechanical ventilation should be started using the open lung approach. In Toxoplasma IgG positive patients, close monitoring and appropriate anti-infectious prophylaxis is needed after HSCT.

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