Diagnostic accuracy of adenosine deaminase for pleural tuberculosis in a low prevalence setting: A machine learning approach within a 7-year prospective multi-center study.

OBJECTIVE: To analyze the performance of adenosine deaminase in pleural fluid combined with other parameters routinely measured in clinical practice and assisted by machine learning algorithms for the diagnosis of pleural tuberculosis in a low prevalence setting, and secondly, to identify effusions that are non-tuberculous and most likely malignant. PATIENTS AND METHODS: We prospectively analyzed 230 consecutive patients diagnosed with lymphocytic exudative pleural effusion from March 2013 to June 2020. Diagnosis according to the composite reference standard was achieved in all cases. Pre-test probability of pleural tuberculosis was 3.8% throughout the study period. Parameters included were: levels of adenosine deaminase, pH, glucose, proteins, and lactate dehydrogenase, red and white cell counts and lymphocyte percentage in pleural fluid, as well as age. We tested six different machine learning-based classifiers to categorize the patients. Two different classifications were performed: a) tuberculous/non-tuberculous and b) tuberculous/malignant/other. RESULTS: Out of a total of 230 patients with pleural effusion included in the study, 124 were diagnosed with malignant effusion and 44 with pleural tuberculosis, while 62 were given other diagnoses. In the tuberculous/non-tuberculous classification, and taking into account the validation predictions, the support vector machine yielded the best result: an AUC of 0.98, accuracy of 97%, sensitivity of 91%, and specificity of 98%, whilst in the tuberculous/malignant/other classification, this type of classifier yielded an overall accuracy of 80%. With this three-class classifier, the same sensitivity and specificity was achieved in the tuberculous/other classification, but it also allowed the correct classification of 90% of malignant cases. CONCLUSION: The level of adenosine deaminase in pleural fluid together with cell count, other routine biochemical parameters and age, combined with a machine-learning approach, is suitable for the diagnosis of pleural tuberculosis in a low prevalence scenario. Secondly, non-tuberculous effusions that are suspected to be malignant may also be identified with adequate accuracy.

Recommendations of the Spanish Antibiogram Committee (COESANT) for selecting antimicrobial agents and concentrations for in vitro susceptibility studies using automated systems.

Automated antimicrobial susceptibility testing devices are widely implemented in clinical microbiology laboratories in Spain, mainly using EUCAST (European Committee on Antimicrobial Susceptibility Testing) breakpoints. In 2007, a group of experts published recommendations for including antimicrobial agents and selecting concentrations in these systems. Under the patronage of the Spanish Antibiogram Committee (Comité Español del Antibiograma, COESANT) and the Study Group on Mechanisms of Action and Resistance to Antimicrobial Agents (GEMARA) from the Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), and aligned with the Spanish National Plan against Antimicrobial Resistance (PRAN), a group of experts have updated this document. The main modifications from the previous version comprise the inclusion of new antimicrobial agents, adaptation of the ranges of concentrations to cover the EUCAST breakpoints and epidemiological cut-off values (ECOFFs), and the inference of new resistance mechanisms. This proposal should be considered by different manufacturers and users when designing new panels or cards. In addition, recommendations for selective reporting are also included. With this approach, the implementation of EUCAST breakpoints will be easier, increasing the quality of antimicrobial susceptibility testing data and their microbiological interpretation. It will also benefit epidemiological surveillance studies as well as the clinical use of antimicrobials aligned with antimicrobial stewardship programs.

The burden of PCV13 serotypes in hospitalized pneumococcal pneumonia in Spain using a novel urinary antigen detection test. CAPA study.

BACKGROUND: Streptococcus pneumoniae serotypes distribution in community-acquired pneumonia (CAP) requiring hospitalization in adults after introduction of PCV13 in children is not well known. Our aim was to evaluate the distribution of serotypes in pneumococcal pneumonia according to risk factors and comorbidity conditions after the introduction of PCV13 in children in 2010. METHODS: A prospective study from 2011 to 2014 was performed in immunocompetent adults hospitalized with CAP in 3 Spanish hospitals. Microbiological confirmation was obtained using a serotype specific urinary antigen detection test (UAD test), Binax Now and conventional cultures. RESULTS: 1258 adults were enrolled and pneumococcal pneumonia (invasive disease in 17.7%) was confirmed in 368 (29.3%) and 17.6% of the any-cause CAP were caused by PVC13 serotypes (3.5% PCV7 serotypes). Around 60% of pneumococcal CAP were caused by PCV13 serotypes (74.6% in invasive episodes vs 57.4% in non-invasive ones). The most prevalent serotypes in invasive disease were 1, 3, 7F, 19A and 14. No significant differences were observed in the distribution of PCV13 serotypes across the study periods. Regarding comorbidity, the rate of PCV13 serotypes was similar among them, and it was slightly higher in those with no underlying conditions. CONCLUSIONS: Serotypes included in PCV13 caused a significant proportion of CAP in adults with underlying conditions and in healthy adults, with no significant changes in cases due to PCV7 or PCV13 from 2011 to 2014, suggesting an insufficient indirect protection from childhood vaccination. Strategies for implementing pneumococcal vaccination of adults are encouraged to reduce the incidence of pneumococcal episodes.

Decrease of invasive pneumococcal disease (IPD) in adults after introduction of pneumococcal 13-valent conjugate vaccine in Spain.

A prospective laboratory-based multicenter study that collected all adult invasive pneumococcal disease (IPD) episodes from 6 Spanish hospitals before (2008-2009) and after (2012-2013). The 13-valent pneumococcal conjugate vaccine (PCV13) licensure was conducted in order to analyze the impact of PCV13 introduction for children on adult IPD. A total of 1558 IPD episodes were detected. The incidence of IPD decreased significantly in the second period by -33.9% (95% CI, -40.3% to -26.8%). IPD due to PCV7 serotypes (-52.7%; 95% CI, -64.2% to -37.5%) and to PCV13 additional serotypes (-55.0% 95% CI, -62.0% to -46.7%) significantly decreased whereas IPD due to non-PCV13 serotypes remained stable (1.0% 95% CI, -12.9% to 17.2%). IPD due to all PCV13 additional serotypes significantly declined with the exception of serotype 3 (-11.3%; 95%CI -35.0% to 21.1%). IPD due to two non-PCV13 serotypes varied: serotype 6C that rose (301.6%; 95%CI, 92.7% to 733.3%, p<0.001), related to the expansion of ST3866C, and serotype 8 that decreased (-34.9%, 95%CI, -57.1 to -1.2, p = 0.049), related to a decline of the ST638. The recombinant clone ST652111A (variant of ST1569V) increased in frequency. The decrease of serotype 19A IPD was linked to a fall in those antibiotic susceptible clones. In the last period, rates of penicillin- and cefotaxime-resistance remained under 10% and 4%, respectively. Adult IPD decreased after the PCV13 introduction in Spain due to herd protection. The spread of multidrug resistant clones (ST3866C, ST652111A) related to non-PCV13 serotypes needs further surveillance.

Clarithromycin resistance in Helicobacter pylori and its molecular determinants in Northern Spain, 2013-2015.

OBJECTIVES: Clarithromycin resistance (CLR-R) is the main reason for failure of Helicobacter pylori infection treatment, which is frequently empirically prescribed due to the erroneous belief that culture for susceptibility testing is difficult. The aim of this study was to determine CLR-R in a region of southern Europe and to evaluate the utility of a PCR sequencing assay applied on gastroduodenal biopsies in detecting H. pylori and clarithromycin (CLR) susceptibility. METHODS: The susceptibility of all H. pylori isolates obtained by culture during 2013-2015 was determined by Etest. During 2014-2015, H. pylori detection and CLR susceptibility were also studied by PCR followed by sequencing performed on gastroduodenal biopsies. Point mutations in the 23S rRNA gene were studied in all CLR-resistant isolates in 2014. RESULTS: Of 1986 H. pylori isolates obtained by culture (63 from children and 1923 from adults), 349 (17.6%) were CLR-resistant [21/63 (33.3%) in children and 328/1923 (17.1%) in adults; P<0.001], of which 31.5% were also resistant to levofloxacin. The main mutations detected were A2147G (79.8%), A2146G (17.2%) and A2146C (2%). Concordance between the PCR sequencing assay on biopsies and CLR susceptibility by Etest after culture was 89.8%. CONCLUSIONS: CLR-R was high in Gipuzkoa, northern Spain. The molecular PCR method performed directly on biopsies was a good alternative to the traditional Etest susceptibility method and was an aid when culture was non-viable.

Biomarker Tools to Design Clinical Vaccines Determined from a Study of Annual Listeriosis Incidence in Northern Spain.

Two regions of northern Spain, Gipuzkoa, and Cantabria present high annual incidence of listeriosis (1.86 and 1.71 cases per 100,000 inhabitants, respectively). We report that the high annual incidences are a consequence of infection with highly virulent Listeria monocytogenes isolates linked to fatal outcomes in elderly patients with cancer. In addition, listeriosis patients with cancer present low IL-17A/IL-6 ratios and significantly reduced levels of anti-GAPDH1-22 antibodies, identified as two novel biomarkers of poor prognosis. Analysis of these biomarkers may aid in reducing the incidence of listeriosis. Moreover, GAPDH1-22-activated monocyte-derived dendritic cells of listeriosis patients with cancer seem useful tools to prepare clinical vaccines as they produce mainly Th1 cytokines.

Single-Step Multiplex PCR Assay for Determining 92 Pneumococcal Serotypes.

For pneumococcal disease surveillance, simple and cost-effective methods capable of determining all serotypes are needed. Combining a single-tube multiplex PCR with fluorescently labeled primers followed by amplicon analysis using automated fluorescent capillary electrophoresis, each serotype of 92 reference isolates and 297 recently collected clinical isolates was successfully determined.

Prevalence of Chlamydia trachomatis infection in parturient women in Gipuzkoa, Northern Spain.

The prevalence of Chlamydia trachomatis infection in Southern Europe is poorly understood and its identification is essential for the design of appropriate prevention policies. The prevalence of C. trachomatis in 2011-2014 was determined through polymerase chain reaction in urine samples from 11,687 unselected parturient women from the Basque Country, Spain (San Sebastián area). The overall age-adjusted prevalence was 1.0 % (95 % CI 0.8-1.2). The prevalence of infection in women younger than 25 years was 6.4 % and decreased substantially with increasing age: 2.0 % in 25-29 year-olds and 0.5 % in older women (P < 0.001). The prevalence was higher in parturient of foreign origin (1.9 %, 95 % CI 1.3-2.5) than in Spanish parturients (0.8 %, 95 % CI 0.6-1.0), (P < 0.001). The results of this study support the need to screen young women as part of antenatal care in Spain.

IV Spanish Consensus Conference on Helicobacter pylori infection treatment. / IV Conferencia Española de Consenso sobre el tratamiento de la infección por Helicobacter pylori.

Helicobacter pylori approximately infect 50% of Spanish population and causes chronic gastritis, peptic ulcer and gastric cancer. Until now, three consensus meetings on H.pylori infection had been performed in Spain (the last in 2012). The changes in the treatment schemes, and the increasing available evidence, have justified organizing the IVSpanish Consensus Conference (March 2016), focused on the treatment of this infection. Nineteen experts participated, who performed a systematic review of the scientific evidence and developed a series of recommendation that were subjected to an anonymous Delphi process of iterative voting. Scientific evidence and the strength of the recommendation were classified using GRADE guidelines. As starting point, this consensus increased the minimum acceptable efficacy of recommended treatments that should reach, or preferably surpass, the 90% cure rate when prescribed empirically. Therefore, only quadruple therapies (with or without bismuth), and generally lasting 14 days, are recommended both for first and second line treatments. Non-bismuth quadruple concomitant regimen, including a proton pump inhibitor, clarithromycin, amoxicillin and metronidazole, is recommended as first line. In the present consensus, other first line alternatives and rescue treatments are also reviewed and recommended.

Streptococcus pyogenes Pneumonia in Adults: Clinical Presentation and Molecular Characterization of Isolates 2006-2015.

INTRODUCTION: In the preantibiotic era Streptococcus pyogenes was a common cause of severe pneumonia but currently, except for postinfluenza complications, it is not considered a common cause of community-acquired pneumonia in adults. AIM AND MATERIAL AND METHODS: This study aimed to identify current clinical episodes of S. pyogenes pneumonia, its relationship with influenza virus circulation and the genotypes of the involved isolates during a decade in a Southern European region (Gipuzkoa, northern Spain). Molecular analysis of isolates included emm, multilocus-sequence typing, and superantigen profile determination. RESULTS: Forty episodes were detected (annual incidence 1.1 x 100,000 inhabitants, range 0.29-2.29). Thirty-seven episodes were community-acquired, 21 involved an invasive infection and 10 developed STSS. The associated mortality rate was 20%, with half of the patients dying within 24 hours after admission. Influenza coinfection was confirmed in four patients and suspected in another. The 52.5% of episodes occurred outside the influenza seasonal epidemic. The 67.5% of affected persons were elderly individuals and adults with severe comorbidities, although 13 patients had no comorbidities, 2 of them had a fatal outcome. Eleven clones were identified, the most prevalent being emm1/ST28 (43.6%) causing the most severe cases. CONCLUSIONS: S. pyogenes pneumonia had a continuous presence frequently unrelated to influenza infection, being rapidly fatal even in previously healthy individuals.

Long-Term Epidemiology of Streptococcus pneumoniae Serogroup 6 in a Region of Southern Europe with Special Reference to Serotype 6E.

Streptococcus pneumoniae serotype 6E has recently been described, but its long-term epidemiology is not well known. From 1981-2013, 704 serogroup 6 clinical isolates were obtained in Gipuzkoa, Basque Country, Spain. All invasive and one in four non-invasive isolates were included. Overall, 75, 97, 51 and 45 serotypes 6A, 6B, 6C and 6E isolates, respectively, were detected. No serotype 6D isolates were identified. The prevalence of serotypes 6E and 6B, but not that of serotypes 6A and 6C, declined after the introduction of pneumococcal conjugate vaccines. Serotype 6E isolates showed the highest resistance rate. Most serotype 6E isolates were ST90.

Nocardia donostiensis sp. nov., isolated from human respiratory specimens.

Three human clinical isolates (X1654, X1655, and W9944) were recovered from the sputum and bronchial washings of two patients with pulmonary infections. The 16S rRNA gene sequence analysis of the isolates showed that they share 100 % sequence similarity with each other and belong to the genus Nocardia. Close phylogenetic neighbours are Nocardia brevicatena ATCC 15333(T) (98.6 %) and Nocardia paucivorans ATCC BAA-278T (98.4 %). The in silico DNA-DNA relatedness between the isolates ranges from 96.8 to 100 % suggesting that they belong to the same genomic species. The DNA-DNA relatedness between X1654 and N. brevicatena ATCC 15333(T) is 13.3 ± 2.3 % and N. paucivorans ATCC BAA-278T is 18.95 ± 1.1 % suggesting that they do not belong to the same genomic species. Believed to represent a novel species, these isolates were further characterised to establish their taxonomic standing within the genus. Chemotaxonomic data for isolate X1654 are consistent with those described for the genus Nocardia: this isolate produced saturated and unsaturated fatty acids, tuberculostearic acid (15.9 %), the major menaquinone was MK-8 (H4cyclic), mycolic acid chain lengths ranged from 38 to 58 carbons, produced meso-diaminopimelic acid with arabinose, glucose, and galactose as the whole cell sugars. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, and phosphatidylinositol mannosides. The DNA G+C content is 66.7 mol  %. Based on the combination of phenotypic, chemotaxonomic, and genotypic data for X1654, X1655, and W9944, we conclude that these isolates represent a novel species within the genus Nocardia for which we propose the name Nocardia donostiensis sp. nov. with X1654(T) (=DSM 46814(T) = CECT 8839(T)) as the type strain.

Autochthonous Nocardia cerradoensis Infection in Humans, Spain, 2011 and 2014.

Nocardia cerradoensis was first isolated in 2003 in the El Cerrado region of Brazil; since then, only 2 human infections, in France and Spain, have been reported. We describe 3 autochthonous cases in residents of Spain during 2011 and 2014. Together these cases support the idea of an emerging global pathogenic microorganism.

Detection of bacteria and viruses in the pleural effusion of children and adults with community-acquired pneumonia.

AIM: To study the etiology and the utility of new molecular methods in the diagnosis of complicated pneumonia with empyema. MATERIALS & METHODS: Bacteria and viruses detection was performed by several traditional and molecular methods in the pleural fluid (PF) of 60 patients (38 children) with community-acquired pneumonia (CAP). RESULTS: Despite prior antimicrobial therapy in 49 (81.7%) CAP patients, an etiological diagnosis could be established in 41 (68.3%), 35 being (58.3%) Streptococcus pneumoniae. PF culture was positive in only 6 patients but each molecular test detected more than 82% of cases. CONCLUSION: Traditional culture methods have poor diagnostic sensitivity in PF because most CAP patients are under antimicrobial therapy when it is obtained. S. pneumoniae detection by molecular methods highly improves diagnosis.

Helicobacter pylori Infection in Children. Antimicrobial Resistance and Treatment Response.

BACKGROUND: The aim of this study was to determine the appropriateness of the recent recommendations for managing Helicobacter pylori infection in children in a university hospital in Southern Europe. Antimicrobial resistance and response to eradication therapy were also determined. MATERIALS AND METHODS: The presence of H. pylori was studied in 143 children: by gastric biopsy culture (GBC), (13)C-urea breath test (UBT) and stool antigen immunochromatography test (SAIT) in 56 children; by GBC and UBT in 20, by GBC and SAIT in 18, and by GBC alone in 49. Antimicrobial susceptibility was determined by E-test. Infection was defined as a positive culture or positivity in both UBT and SAIT. Disease progression was studied in 118 patients. First evaluation of symptoms was carried out at 3-6 months after diagnosis and/or after treatment of the infection. RESULTS: H. pylori was detected in 74 from the 143 children analyzed (100% GBC positive, 98.1% UBT positive, and 58.1% SAIT positive). The main symptom was chronic abdominal pain (n = 121). Macroscopic antral nodularity was observed in 29.7% of infected patients and in 5.8% of uninfected patients, respectively. Resistance to clarithromycin and metronidazole was found in 34.7 and 16.7%, respectively. Eradication when susceptible antimicrobials were used occurred in 78.7% (48/61) versus 37.5% (3/8) when the treatment included a drug with resistance (p = .024). In patients with recurrent abdominal pain, symptoms resolved in 92.9% (39/42) patients with HP eradication versus 42.9% (6/14) without HP eradication (p < .001). CONCLUSION: Treated patients often failed to meet the criteria established in the guidelines for H. pylori diagnostic screening and treatment because most of them had only recurrent abdominal pain, but remission of their symptoms was associated with H. pylori eradication.

Progressive decrease in the potential usefulness of meningococcal serogroup B vaccine (4CMenB, Bexsero®) in Gipuzkoa, Northern Spain.

The effectiveness of a vaccine is determined not only by the immunogenicity of its components, but especially by how widely it covers the disease-causing strains circulating in a given region. Because vaccine coverage varies over time, this study aimed to detect possible changes that could affect vaccine protection during a specific period in a southern European region. The 4CMenB vaccine is licensed for use in Europe, Canada, and Australia and is mainly directed against Neisseria meningitidis serogroup B. This vaccine contains four main immunogenic components: three recombinant proteins, FHbp, Nhba and NadA, and an outer membrane vesicle [PorA P1.4]. The allelic distribution of FHbp, Nhba, NadA, and PorA antigens in 82 invasive isolates (B and non-B serogroups) isolated from January 2008 to December 2013 were analyzed. 4CMenB was likely protective against 61.8% and 50% of serogroup B and non-B meningococci, respectively, in the entire period, but between 2012 and 2013, the predicted protection fell below 45% (42.1% for serogroup B isolates).The observed decreasing trend in the predicted protection during the 6 years of the study (Χ2 for trend  = 4.68, p = 0.03) coincided with a progressive decrease of several clonal complexes (e.g., cc11, cc32 and cc41/44), which had one or more antigens against which the vaccine would offer protection.

Two outbreaks of Listeria monocytogenes infection, Northern Spain.

In the province of Gipuzkoa, Spain (≈700,000 inhabitants), 7-12 episodes of human listeriosis were recorded annually during 2009-2012. However, during January 2013-February 2014, 27 episodes were detected, including 11 pregnancy-associated cases. Fifteen cases in 2 epidemiologically unrelated outbreaks were caused by a rare type of Listeria monocytogenes, sequence type 87 serotype 1/2b.

Spread of Streptococcus pneumoniae serotype 8-ST63 multidrug-resistant recombinant Clone, Spain.

Since 2004, a total of 131 isolates of Streptococcus pneumoniae multidrug-resistant invasive serotype 8 have been detected in Spain. These isolates showed resistance to erythromycin, clindamycin, tetracycline, and ciprofloxacin. All isolates were obtained from adult patients and shared a common genotype (sequence type [ST]63; penicillin-binding protein 1a [pbp1a], pbp2b, and pbp2x gene profiles; ermB and tetM genes; and a ParC-S79F change). Sixty-eight isolates that required a ciprofloxacin MIC ≥16 µg/mL had additional gyrA gene changes. Serotype 8-ST63 pbp2x sequences were identical with those of antimicrobial drug-susceptible serotype 8-ST53 isolates. Serotype 8-ST63 pbp2b sequences were identical with those of the multidrug-resistant Sweden 15A-ST63 clone. Recombination between the capsular locus and flanking regions of an ST53 isolate (donor) and an ST63 pneumococcus (recipient) generated the novel 15A-ST63 clone. One recombination point was upstream of pbp2x and another was within pbp1a. A serotype 8-ST63 clone was identified as a cause of invasive disease in Spain.