Exploring the Complexities of Intestinal and Pulmonary Microbiota in Cystic Fibrosis: A Multi-Omics Approach.

Background: We aimed to elucidate the cystic fibrosis (CF) microbiota composition (shotgun metagenomics) and functionality (short-chain fatty acids, SCFAs).

Methods: Fecal and sputum samples were recruited from 39 clinically stable CF subjects.

Results: Bacillota and Pseudomonadota were dominant in both gut and lung compartments, whereas Ascomycota were the most abundant fungi in feces, and Basidiomycota, especially Malassezia globosa, in sputum.

Randomized controlled diagnostic trial to assess dRAST time to result and its utility for antimicrobial stewardship recommendation in bacteremic patients.

Unlabelled: Bloodstream infections cause great mortality and morbidity. Real-time microbiological information has been shown to have an impact on prognosis when combined with an antimicrobial stewardship (AMS) program. dRAST is a rapid commercial antimicrobial susceptibility testing (AST) system based on real-time microscopy.

ICU environment as a reservoir of KPC-ST307-Klebsiella pneumoniae high-risk clone resistant to ceftazidime-avibactam.

We characterized all ceftazidime-avibactam-resistant KPC-producing K. pneumoniae (KPC-Kp) isolates recovered from both patients and environmental samples at the ICU of our hospital in 2020, during the COVID-19 pandemic initiation. Antimicrobial susceptibility testing (Sensititre-EUMDROXF; disk-diffusion) and WGS analysis (Illumina-Novaseq/Miseq; Oxford Nanopore-MinION) were performed.

Plasma calprotectin as a severity biomarker in pediatric invasive Streptococcus pyogenes infections: insights from a multicenter immune profiling study during an outbreak.

Purpose: To characterize the immune signature of pediatric invasive Streptococcus pyogenes infections (iGAS) and identify host biomarkers associated with disease severity.

Methods: Plasma samples (n = 32) were collected during an iGAS outbreak from a multicentric Spanish pediatric cohort, including patients with iGAS (n = 19), S. pyogenes acute tonsillitis (n = 3), and healthy children/controls (n = 10).

Spanish nationwide survey of Pseudomonas aeruginosa cefiderocol susceptibility and resistance mechanisms.

Objective: Cefiderocol is a new siderophore-cephalosporin showing potent activity against Pseudomonas aeruginosa, including isolates showing extensively drug-resistant (XDR) or difficult-to-treat resistant (DTR) phenotypes. However, there is still a limited understanding of the potential resistance mechanisms. The objective of this study was to analyse the activity of cefiderocol in a nationwide Spanish survey, determine its stability against most relevant resistance mechanisms, and analyse potential drivers of resistance through whole-genome sequencing.

Urinary tract infection in adults: gaps in current guidelines - opinions from an international multidisciplinary panel and relevance to clinical practice.

Purpose: Although urinary tract infections (UTIs) are one of the most common infections encountered in clinical practice, many challenges remain with respect to classification and management. The purpose of this report is to discuss key issues in the management of UTIs and identify gaps in current knowledge and guidelines, as well as future research needs.

Design: A multidisciplinary panel of 13 experts from 6 European countries and the United States met on April 27, 2024.

A European survey on anaerobes from paediatric blood cultures: a comparative analysis with adults.

Infections caused by anaerobes are common in children. However, limited data are available on bloodstream infections caused by these bacteria in Europe. A multicentre retrospective observational study was conducted over a 4-year period (2020-2023) across 44 European hospitals to analyze all anaerobes isolated from blood cultures.

Bronchopulmonary colonization patterns in Spanish people with cystic fibrosis: Results of a national multicentre study.

Background: We investigate bronchopulmonary colonization patterns in Spanish people with CF (pwCF), gathering clinical, demographic, and microbiological data to supplement nine years of registry information, comparing 2021 findings with a similar multicenter study conducted in 2013.

Methods: Sixteen CF units from 14 hospitals across Spain participated, each randomly recruiting around 20 patients. Patients provided sputum samples for culture.

Management of multidrug-resistant gram-negative bacilli infections in adult solid organ transplant recipients: GESITRA-IC/SEIMC, CIBERINFEC, and SET recommendations update.

Multidrug-resistant (MDR) Gram-negative bacilli (GNB) infections in solid organ transplant (SOT) recipients continue to pose a significant threat despite advances in diagnostics and treatments. The last international consensus guidelines of the Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC) on the management of MDR GNB in adult solid organ transplant (SOT) recipients were published in 2018, underscoring the need for an update to incorporate recent advances, particularly the availability of new drugs that may improve the current standard of care. A working group consisting of members from the Study Group of Infection in Transplantation and Immunocompromised Hosts (GESITRA-IC) of SEIMC, the Center for Biomedical Research Network in Infectious Diseases (CIBERINFEC) and the Spanish Society of Transplantation (SET) developed consensus-based recommendations for managing MDR GNB infections during the transplant procedure.

Effect of oxygen on antimicrobial resistance genes from a one health perspective.

Bacteria must face and adapt to a variety of physicochemical conditions in the environment and during infection. A key condition is the concentration of dissolved oxygen, proportional to the partial pressure of oxygen (PO), which is extremely variable among environmental biogeographical areas and also compartments of the human and animal body. Here, we sought to understand if the phenotype of resistance determinants commonly found in Enterobacterales can be influenced by oxygen pressure.

Whole Genome Sequencing Analysis of Isolates from Health Care-Associated Bacteremia of Urinary Origin in Spain: Findings from the Multicenter ITUBRAS-2 Cohort Study.

Background: The objective of this study was to assess the microbiological and clinical features of health care-associated bacteremia of urinary origin (HCA-BUO) in Spain, with a focus on third-generation cephalosporin-(3GCR-Kp) and carbapenem-resistant (CR-Kp) isolates.

Methods: A total of 96 (21.4%, 96/449) blood isolates were prospectively collected from patients with HCA-BUO (n = 443) from 12 tertiary care hospitals in Spain (2017-2019).

Invasive pneumococcal disease in a tertiary hospital in Madrid: are we using pneumococcal vaccine correctly?

Introduction: Invasive pneumococcal disease (IPD) is of concern. We describe the epidemiology and assess the vaccination schedule adequacy of IPD episodes (2019-2021) in northern Madrid.

Methods: Clinical, laboratory and vaccination data were collected from clinical/epidemiological records.

Diagnostic and epidemiological landscape of anaerobic bacteria in Europe, 2020-2023 (ANAEuROBE).

Introduction: Despite being implicated in a wide spectrum of community- and healthcare-acquired infections, anaerobes have not yet been incorporated into systematic surveillance programs in Europe.

Methods: We conducted a multicentre retrospective observational study analysing all anaerobic strains isolated from blood cultures in 44 European Hospital Centres over a 4-y period (2020-2023). Diagnostic approach, epidemiology, and antimicrobial susceptibility according to EUCAST v.

Cefepime-enmetazobactam: first approved cefepime-β- lactamase inhibitor combination for multi-drug resistant Enterobacterales.

Cefepime-enmetazobactam is a β-lactam/β-lactamase inhibitor (BL/BLI) combination that has demonstrated potent activity against extended spectrum beta-lactamase (ESBL)-producing Enterobacterales, recently approved by the US FDA for the treatment of complicated urinary tract infections (cUTI) and by the European Medicines Agency and the UK Healthcare products Regulatory Agency for the treatment of cUTI, hospital-acquired pneumonia including ventilator-associated pneumonia and bacteremia in adults. Cefepime is a 4th generation cephalosporin with a broad spectrum bactericidal activity and enhanced stability to degradation by chromosomal and plasmid-mediated AmpC cephalosporinases as well as carbapenemase OXA-48 like enzymes. Enmetazobactam is a novel penicillanic acid sulfone β-lactamase inhibitor structurally similar to tazobactam with activity against CTX-M, TEM, and SHV ESBL, and other class A β-lactamases, that restores cefepime activity in vitro and in vivo against ESBLs-producing Enterobacterales.

Phenotypic Ultra-Rapid Antimicrobial Susceptibility Testing for Ceftazidime-Avibactam: In Support of Antimicrobial Stewardship.

Ceftazidime-avibactam (CZA) is a potent broad-spectrum drug combination covering extended-spectrum β-lactamases, AmpC, and carbapenemases of class A and D, OXA-48-type producers. Rapid antimicrobial susceptibility testing is crucial for the timely de-escalation/escalation of therapy. We evaluate CZA susceptibility using the CE-IVD FASTgramneg kit (FASTinov), a ground-breaking 2 h assay, based on flow cytometry technology for antimicrobial susceptibility testing.

Burden of bacterial antimicrobial resistance among hospitalised patients in Spain: findings from three nationwide prospective studies.

Background: Assessing the burden of antimicrobial resistance is essential to determine the magnitude of this problem and to set its priority. We aimed to estimate the burden of disease caused by multidrug-resistant microorganisms (MDRO) in hospitalised patients in Spain.

Methods: Three prospective nationwide studies were conducted in 2018, 2019 and 2023.

CRISPR-associated Plasmonic Colorimeter Method (Ca-PCM): A real-time RGB detection system for gold nanoparticles-based nucleic acid biosensors.

Background: The detection of genetic sequences represents the gold standard procedure for species discrimination, genetic characterisation of tumours, and identification of pathogens. The development of new molecular detection methods, accessible and cost effective, is of great relevance. Biosensors based on plasmonic nanoparticles, such as gold nanoparticles (AuNPs), provide a powerful and versatile platform for highly sensitive, economic, user-friendly and label-free sensing.

Cefiderocol AST in a real-life Klebsiella pneumoniae collection: challenges in the ATU range.

Objectives: FDC susceptibility testing is challenging as none of the commercial tests have been proven to accurately determine the susceptibility in the area of technical uncertainty (ATU). Here, we evaluated the performance of different FDC testing methods on Klebsiella pneumoniae isolates around this range.

Methods: A challenging collection of 104 K.

The role of rapid multiplex molecular syndromic panels in the clinical management of infections in critically ill patients: an experts-opinion document.

Rapid multiplex molecular syndromic panels (RMMSP) (3 or more pathogens and time-to-results < 6 h) allow simultaneous detection of multiple pathogens and genotypic resistance markers. Their implementation has revolutionized the clinical landscape by significantly enhancing diagnostic accuracy and reducing time-to-results in different critical conditions. The current revision is a comprehensive but not systematic review of the literature.

Unravelling the mechanisms causing murepavadin resistance in : lipopolysaccharide alterations and its consequences.

Introduction: Murepavadin is an antimicrobial peptide (AMP) in clinical development that selectively targets LptD and whose resistance profile remains unknown. We aimed to explore genomic modifications and consequences underlying murepavadin and/or colistin susceptibility.

Methods: To define genomic mechanisms underlying resistance, we performed two approaches: 1) a genome-wide association study (GWAS) in a clinical collection (n=496), considering >0.

Genomic characterization of MRSA recovered from people with cystic fibrosis during two Spanish multicentre studies (2013 and 2021).

Background: Chronic bronchopulmonary infection due to MRSA in people with cystic fibrosis (pwCF) has been associated with accelerated decline in lung function, increased hospitalizations and increased mortality.

Material And Methods: We studied microbiological and genomic characteristics of MRSA isolates recovered from pwCF in two Spanish multicentre studies (2013, 2021). Antimicrobial susceptibility was performed.

Monitoring of Pseudomonas aeruginosa mutational resistome dynamics using an enrichment panel for direct sequencing of clinical samples.

Background: Pseudomonas aeruginosa is a major cause of hospital-acquired and chronic infections, characterised by an extraordinary capacity to develop antimicrobial resistance through the selection of chromosomal mutations, leading to treatment failure. Here, we designed and tested a hybridisation-based capture system for the enrichment of genes of interest before sequencing to monitor resistant populations genomics directly from clinical samples.

Methods: A panel for enrichment before sequencing of close to 200 genes related to P.