Apoptosis, Toll-like, RIG-I-like and NOD-like Receptors Are Pathways Jointly Induced by Diverse Respiratory Bacterial and Viral Pathogens.

Lower respiratory tract infections are among the top five leading causes of human death. Fighting these infections is therefore a world health priority. Searching for induced alterations in host gene expression shared by several relevant respiratory pathogens represents an alternative to identify new targets for wide-range host-oriented therapeutics.

Molecular diagnosis of bloodstream infections in onco-haematology patients with PCR/ESI-MS technology.

Objectives: Onco-haematological patients are prone to develop infections, and antibiotic prophylaxis may lead to negative blood cultures. Thus, the microbiological diagnosis and subsequent administration of a targeted antimicrobial therapy is often difficult. The goal of this study was to evaluate the usefulness of IRIDICA (PCR/ESI-MS technology) for the molecular diagnosis of bloodstream infections in this patient group.

Identification of hepatitis C virus genotype 3 by a commercial assay challenged by natural polymorphisms detected in Spain from patients with diverse origins.

Background: Hepatitis C virus (HCV) genotyping is crucial in clinical practise for determining the type and duration of antiviral therapy. Between 2009 and 2014, 24 (7.95%) of all HCV genotype 3 (HCV-3) cases obtained indeterminate results via the RealTime HCV Genotype II assay (Abbott) at a tertiary care center in Spain.

Evaluation of the SediMax automated microscopy sediment analyzer and the Sysmex UF-1000i flow cytometer as screening tools to rule out negative urinary tract infections.

Urinary tract infections (UTI) are highly prevalent in nosocomial and community settings, and their diagnosis is costly and time-consuming. Screening methods represent an important advance towards the final UTI diagnosis, diminishing inappropriate treatment or clinical complications. Automated analyzers have been developed and commercialized to screen and rule out negative urine samples.

Direct Identification of Urinary Tract Pathogens from Urine Samples, Combining Urine Screening Methods and Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry.

Early diagnosis of urinary tract infections (UTIs) is essential to avoid inadequate or unnecessary empirical antibiotic therapy. Microbiological confirmation takes 24 to 48 h. The use of screening methods, such as cytometry and automated microscopic analysis of urine sediment, allows the rapid prediction of negative samples.

Usefulness of a novel multiplex real-time PCR assay for the diagnosis of sexually-transmitted infections.

Introduction: Sexually transmitted infections (STI) are currently on the increase worldwide. New molecular tools have been developed in the past few years in order to improve their diagnosis. An evaluation was carried out using a new commercially available real-time PCR assay, Anyplex™ II STI-7 (Seegene, Seoul, Korea), which detects seven major pathogens in a single reaction - Chlamydia trachomatis, Neisseria gonorrhoeae, Trichomonas vaginalis, Mycoplasma hominis, Mycoplasma genitalium, Ureaplasma urealyticum, and Ureaplasma parvum - and compared with conventional methods performed in our laboratory.

Evaluation of the Broad-Range PCR/ESI-MS Technology in Blood Specimens for the Molecular Diagnosis of Bloodstream Infections.

Background: Rapid identification of the etiological agent in bloodstream infections is of vital importance for the early administration of the most appropriate antibiotic therapy. Molecular methods may offer an advantage to current culture-based microbiological diagnosis. The goal of this study was to evaluate the performance of IRIDICA, a platform based on universal genetic amplification followed by mass spectrometry (PCR/ESI-MS) for the molecular diagnosis of sepsis-related pathogens directly from the patient's blood.

Pyrosequencing for rapid detection of Mycobacterium tuberculosis second-line drugs and ethambutol resistance.

The aim of this work was to study the diagnostic accuracy of pyrosequencing to detect resistance to fluoroquinolones, kanamycin, amikacin, capreomycin, and ethambutol (EMB) in Mycobacterium tuberculosis clinical strains. One hundred four clinical isolates previously characterized by BACTEC 460TB/MGIT 960 were included. Specific mutations were targeted in gyrA, rrs, eis promoter, and embB.

Bactibilia and Antibiotic Resistance in Elective Cholecysctectomy: An Updated Ecologic Survey.

Background: The role of bactibilia as a risk factor for an unfavorable outcome during biliary disease or surgical procedures remains obscure. Our aim was to identify possible risk factors for bactibilia and their possible relations to complications after elective cholecystectomy. As secondary aims, composition and antibiotic resistance patterns were studied.

Immunogenicity of 60 novel latency-related antigens of Mycobacterium tuberculosis.

The aim of our work here was to evaluate the immunogenicity of 60 mycobacterial antigens, some of which have not been previously assessed, notably a novel series of in vivo-expressed Mycobacterium tuberculosis (IVE-TB) antigens. We enrolled 505 subjects and separated them in individuals with and without latent tuberculosis infection (LTBI) vs. patients with active tuberculosis (TB).

Improving the diagnosis of bloodstream infections: PCR coupled with mass spectrometry.

The reference method for the diagnosis of bloodstream infections is blood culture followed by biochemical identification and antibiotic susceptibility testing of the isolated pathogen. This process requires 48 to 72 hours. The rapid administration of the most appropriate antimicrobial treatment is crucial for the survival of septic patients; therefore, a rapid method that enables diagnosis directly from analysis of a blood sample without culture is needed.

Tools for the diagnosis of hepatitis C virus infection and hepatic fibrosis staging.

Hepatitis C virus (HCV) infection represents a major public health issue. Hepatitis C can be cured by therapy, but many infected individuals are unaware of their status. Effective HCV screening, fast diagnosis and characterization, and hepatic fibrosis staging are highly relevant for controlling transmission, treating infected patients and, consequently, avoiding end-stage liver disease.

Correlation of inflammatory and cardiovascular biomarkers with pneumonia severity scores.

Purpose: To assess the correlation of procalcitonin (PCT), C-reactive protein (CRP), neopterin, mid-regional pro-atrial natriuretic peptide (MR-proANP), and mid-regional pro-adrenomedullin (MR-proADM) with severity risk scores: severe CAP (SCAP) and SMART-COP in patients with community-acquired pneumonia (CAP), as well as short term prognosis and to determine the correlation with mortality risk scores.

Methods: Eighty-five patients with a final diagnosis of pneumonia were consecutively included during a two month period. Epidemiological, clinical, microbiological, and radiological data were recorded.

Relevance of baseline viral genetic heterogeneity and host factors for treatment outcome prediction in hepatitis C virus 1b-infected patients.

Background: Only about 50% of patients chronically infected with HCV genotype 1 (HCV-1) respond to treatment with pegylated interferon-alfa and ribavirin (dual therapy), and protease inhibitors have to be administered together with these drugs increasing costs and side-effects. We aimed to develop a predictive model of treatment response based on a combination of baseline clinical and viral parameters.

Methodology: Seventy-four patients chronically infected with HCV-1b and treated with dual therapy were studied (53 retrospectively -training group-, and 21 prospectively -validation group-).

Construction, characterization and preclinical evaluation of MTBVAC, the first live-attenuated M. tuberculosis-based vaccine to enter clinical trials.

The development of a new tuberculosis vaccine is an urgent need due to the failure of the current vaccine, BCG, to protect against the respiratory form of the disease. MTBVAC is an attenuated Mycobacterium tuberculosis vaccine candidate genetically engineered to fulfil the Geneva consensus requirements to enter human clinical trials. We selected a M.

Rapid diagnosis of bloodstream infections with PCR followed by mass spectrometry.

Achieving a rapid microbiological diagnosis is crucial for decreasing morbidity and mortality of patients with a bloodstream infection, as it leads to the administration of an appropriate empiric antimicrobial therapy. Molecular methods may offer a rapid alternative to conventional microbiological diagnosis involving blood culture. In this study, the performance of a new technology that uses broad-spectrum PCR coupled with mass spectrometry (PCR/ESI-MS) was evaluated for the detection of microorganisms directly from whole blood.

Hepatitis C virus transmission during colonoscopy evidenced by phylogenetic analysis.

Background: Nosocomial transmission events still play an important role in hepatitis C virus (HCV) spreading. Among most reported medical procedures involved in nosocomial transmission, endoscopy procedures remain controversial and might be underestimated.

Objective: The aim of the study was to investigate a case of nosocomial person-to-person transmission of HCV in an endoscopy unit.

Evolutionary dynamics of the E1-E2 viral populations during combination therapy in non-responder patients chronically infected with hepatitis C virus subtype 1b.

Half of the patients chronically infected with hepatitis C virus (HCV) genotype 1 fail to respond to pegylated interferon alpha (PEG-IFN) and ribavirin (RBV) therapy. This study assesses the effects of treatment on the evolution of the E1-E2 viral region in non-responder patients infected with HCV-1b. Twenty-three HCV-1b chronically infected patients were studied retrospectively, including 19 non-responders to PEG-IFN/RBV therapy (11 null-responders and 8 relapsers) in the study group, and 4 untreated patients in the control group.

Validation of a polymerase chain reaction-oligochromatography test for detection of influenza A (H1N1) 2009 virus.

The outbreak of pandemic influenza A (H1N1) 2009 virus caused the first influenza pandemic disease of the 21st century. In August 2010, the pandemic moved into the post-pandemic period. However, localized outbreaks of various magnitudes continued with a higher rate of disease severity.

Comparison between two human papillomavirus genotyping assays targeting the L1 or E6/E7 region in cervical cancer biopsies.

Introduction: Human papillomavirus (HPV) testing is increasingly used in cervical cancer prevention strategies, and a variety of HPV genotyping assays have been developed. We aimed to compare the performance of two HPV genotyping techniques in formalin-fixed paraffin-embedded (FFPE) tissue specimens from a series of invasive squamous cell carcinoma (SCC) cases.

Methods: Archival FFPE tissue blocks from 78 SCC cases were initially considered.

Comparison of 2 molecular assays and a serologic test in diagnosing Mycoplasma pneumoniae infection in paediatrics patients.

Two commercial polymerase chain reaction (PCR) assays (a real-time PCR [Cepheid] and an oligochromatographic test [Speed-oligo]) and 1 serology test (Serodia-Myco II) for detecting Mycoplasma pneumoniae in nasopharyngeal aspirates and serum samples were studied. Among the 145 samples, 32 serum pairs were serologically positive for M. pneumoniae.

Specific Mycobacterium tuberculosis T cell responses to RD1-selected peptides for the monitoring of anti-tuberculosis therapy.

Background: Recently, a selection of HLA class II-restricted epitopes of ESAT-6 and CFP-10 Mycobacterium tuberculosis proteins from the region of difference (RD) 1 have been described. We have evaluated the host interferon-gamma (IFN-γ) T cell response to these RD1 selected peptides at the beginning and during anti-tuberculosis therapy.

Methods: We studied 29 pulmonary TB patients enrolled at the beginning of treatment and 24 enrolled during treatment.

Value of procalcitonin, C-reactive protein, and neopterin in exacerbations of chronic obstructive pulmonary disease.

Objective: The identification of biological markers in order to assess different aspects of COPD is an area of growing interest. The objective of this study was to investigate whether levels of procalcitonin (PCT), C-reactive protein (CRP), and neopterin in COPD patients could be useful in identifying the etiological origin of the exacerbation and assessing its prognosis.

Methods: We included 318 consecutive COPD patients: 46 in a stable phase, 217 undergoing an exacerbation, and 55 with pneumonia.

Hepatitis C virus sequences from different patients confirm the existence and transmissibility of subtype 2q, a rare subtype circulating in the metropolitan area of Barcelona, Spain.

The hepatitis C virus (HCV) has been classified into six genotypes and more than 70 subtypes with distinct geographical and epidemiological distributions. While 18 genotype 2 subtypes have been proposed, only 5 have had their complete sequence determined. The aim of this study was to characterize HCV isolates from three patients from the Barcelona metropolitan area of Spain for whom commercial genotyping methods provided discordant results.

Baseline prediction of combination therapy outcome in hepatitis C virus 1b infected patients by discriminant analysis using viral and host factors.

Background: Current treatment of chronic hepatitis C virus (HCV) infection has limited efficacy -especially among genotype 1 infected patients-, is costly, and involves severe side effects. Thus, predicting non-response is of major interest for both patient wellbeing and health care expense. At present, treatment cannot be individualized on the basis of any baseline predictor of response.