Rapid identification of the causative agent of hospital-acquired pneumonia (HAP) will allow an earlier administration of a more appropriate antibiotic and could improve the outcome of these patients. The aim of this study was to develop a rapid protocol to identify the main microorganisms involved in HAP by loop-mediated isothermal amplification (LAMP) directly from respiratory samples. First of all, a rapid procedure (<30 min) to extract the DNA from bronchoalveolar lavage (BAL), endotracheal aspirate (EA) or bronchoaspirate (BAS) was set up. A specific LAMP for Staphylococcus aureus, Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, Stenotrophomonas maltophilia and Acinetobacter baumannii was performed with the extracted solution at 65 °C for 30–40 min. Overall, 58 positive BAL and 83 EA/BAS samples were tested. The limits of detection varied according to the microorganism detected. Validation of the LAMP assay with BAL samples showed that the assay was 100% specific and 86.3% sensitive (positive predictive value of 100% and a negative predictive value of 50%) compared with culture. Meanwhile for BAS/EA samples, the assay rendered the following statistical parameters: 100% specificity, 94.6% sensitivity, 100% positive predictive value and 69.2% negative predictive value. The turnaround time including sample preparation and LAMP was circa 1 h. LAMP method may be used to detect the most frequent bacteria causing HAP. It is a simple, cheap, sensitive, specific and rapid assay.

Animal and human studies indicate that exposure to air pollution and natural environments might modulate the gut microbiota, but epidemiological evidence is very scarce. To assess the potential impact of pre- and postnatal exposure to air pollution and green spaces on infant gut microbiota assembly and trajectories during the first year of life. MAMI ("MAternal MIcrobes") birth cohort (Valencia, Spain, N=162) was used to study the impact of environmental exposure (acute and chronic) on infant gut microbiota during the first year of life (amplicon-based 16S rRNA sequencing). At 7 days and at 1, 6 and 12 months, residential pre- and postnatal exposure to air pollutants (NO₂, black carbon -BC-, PM_2.5 and O₃) and green spaces indicators (NDVI and area of green spaces at 300, 500 and 1000 m buffers) were obtained. For the association between exposures and alpha diversity indicators linear regression models (cross-sectional analyses) and mixed models, including individual as a random effect (longitudinal analyses), were applied. For the differential taxon analysis, the ANCOM-BC package with a log count transformation and multiple-testing corrections were used. Acute exposure in the first week of life and chronic postnatal exposure to NO₂ were associated with a reduction in microbial alpha diversity, while the effects of green space exposure were not evident. Acute and chronic (prenatal or postnatal) exposure to NO₂ resulted in increased abundance of Haemophilus, Akkermansia, Alistipes, Eggerthella, and Tyzerella populations, while increasing green space exposure associated with increased Negativicoccus, Senegalimassilia and Anaerococcus and decreased Tyzzerella and Lachnoclostridium populations. We observed a decrease in the diversity of the gut microbiota and signs of alteration in its composition among infants exposed to higher levels of NO₂. Increasing green space exposure was also associated with changes in gut microbial composition. Further research is needed to confirm these findings.

Antimicrobial resistance data for Neisseria gonorrhoeae is globally sparse and resistant strains are emerging in Catalonia. We aim to describe epidemiological and antimicrobial resistance in all patients infected with N. gonorrhoeae during the period from 2016 to 2019, using available antimicrobial susceptibility data. We retrospectively analysed confirmed N. gonorrhoeae cases notified to Catalonia’s microbiological reporting system. Antibiotic susceptibility testing (azithromycin, cefixime, ceftriaxone, ciprofloxacin, penicillin, spectinomycin, and tetracycline) was assessed using clinical breakpoints published by the European Committee on Antimicrobial Susceptibility Testing. Incidence rates were calculated and proportions were compared using the χ² test or Fisher’s exact test, and analysed using the Statistical Package for Social Sciences (SPSS 18.0). A total of 14,251 confirmed cases of N. gonorrhoeae were notified. Incidence increased from 30.7 cases/100,000 person-years (p < 0.001) in 2016 to 64.7 in 2019. Culture was available in 6,292 isolates (44.2%), of which 5,377 (85.5%) were resistant to at least one of the antibiotics tested. Azithromycin resistance rose from 6.1% in 2016 to 16% in 2019 (p < 0.001). Only 1.0% (45 cases) were resistant to ceftriaxone. Multidrug-resistant N. gonorrhoeae increased from 0.25% in 2016 to 0.42% in 2019 (p = 0.521). One case presented extensively drug-resistant N. gonorrhoeae. In Catalonia, 10% of the N. gonorrhoeae isolates were resistant to azithromycin in the 2016–2019 period. According to World Health Organization guidelines, resistance above 5% indicates an alert to review treatment guidelines. Antimicrobial susceptibility testing in clinical practice followed by surveillance and interventions are essential to monitor trends and prevent the spread of antimicrobial resistance.

This study assessed the impact of a topical phytocomplex on the acne skin microbiota, encompassing bacterial, fungal, and phage communities. Skin samples obtained from participants exhibiting a positive response to the treatment were analyzed using high-throughput sequencing and bioinformatic approaches including taxonomic profiling, metagenome assembly, functional annotation, and phage identification. Results showed that after treatment, microbial diversity increased, reflecting a more balanced microbial composition. Cutibacterium acnes levels were reduced, particularly virulent IA1/IA2 phylotypes, whereas non-pathogenic or unclassified strains increased. Opportunistic pathogens such as Klebsiella pneumoniae were no longer detected, and beneficial genera including Psychrobacter and Dermabacter were enriched. Functional analysis showed reduced virulence- and biofilm-related pathways, alongside enhanced tryptophan metabolism, SCFA production, lipid synthesis, and riboflavin and folate biosynthesis. Fungal populations, dominated by Malassezia, became more evenly distributed, with notable post-treatment reductions in M. arunalokei, Exophiala spinifera, and Wickerhamomyces anomalus. Phage populations mirrored bacterial changes, with enrichment of Cutibacterium-associated phages post-treatment. These findings demonstrate that the phytocomplex promotes functional rebalancing of the skin microbiota by reducing pathogenic features while maintaining ecosystem stability. The inhibition of quorum sensing, potentially mediated by N-acyl-homoserine lactone acetylation, emerged from metabolic pathway annotation as a hypothetic key mechanism impairing bacterial communication and virulence associated with acne vulgaris.

Background: Early-life gut microbiota development is shaped by environmental exposures, yet the impact of the urban exposome remains poorly understood. Here, we comprehensively examined whether the urban exposome influences gut microbiota diversity, composition, functional potential, and metabolic activity during early childhood.Methods: We conducted a prospective longitudinal analysis within the population-based Barcelona Life Study Cohort. Urban-related exposures, including air pollution, green spaces, surrounding greenness, and socioeconomic status were assessed from conception to 18 months. During the 6-month and 18-month follow-up visits, 1,076 faecal samples were collected, generating shotgun metagenomic and liquid chromatography-tandem mass spectrometry-based short-chain fatty acid (SCFA) data for 631 children. These data enabled longitudinal characterisation of microbial diversity, taxonomic composition, functional potential, and metabolic activity across the developmental and transitional stages of gut microbiota maturation. Associations were evaluated using a sequential multivariate framework combining PERMANOVA, distance-based redundancy analysis, linear regression, and mixed-effects models, incorporating inverse probability weighting, extensive confounder adjustment, and multiple-testing correction.Findings: The urban exposome explained a proportion of gut microbiota variation, with more consistent associations at 18 than at 6 months, although its contribution remained substantially smaller than that of proximal determinants (i.e., diet, delivery-related factors, recent antibiotic use, gastrointestinal infections). Green-space exposures were consistently associated with taxa linked to microbiota maturation, whereas air pollution was associated with shifts toward oral-associated taxa and reduced abundance of Bifidobacterium species. Associations with functional pathways and SCFAs were weaker and less consistent.Interpretation: The urban exposome, particularly green spaces and air pollution, was associated with gut microbiota composition, especially during the transitional phase of microbiome maturation. Associations were mainly observed at the taxonomic compositional level, with comparatively more limited evidence for functional potential or downstream metabolic alterations. These findings suggest that the transitional microbiome may be particularly environmentally responsive to the urban exposome and highlight the potential role of the urban environments in shaping gut microbiota development during early childhood.