Information on the clinical, epidemiological and molecular characterization of human metapneumovirus in critically ill adult patients with severe community-acquired pneumonia (CAP) and the role of biomarkers identifying bacterial coinfection is scarce. This is a retrospective epidemiological study of adult patients with hMPV severe CAP admitted to ICU during a ten-year period with admission PSI score ≥ 3. The 92.8% of the 28 patients with severe CAP due to human metapneumovirus were detected during the first half of the year. Median age was 62 years and 60.7% were male. The genotyping of isolated human metapneumovirus showed group B predominance (60.7%). All patients had acute respiratory failure. Median APACHE II and SOFA score were 13 and 6.55, respectively. The 25% were coinfected with Streptococcus pneumoniae. 60.7% of the patients had shock at admission and 50% underwent mechanical ventilation. Seven patients developed ARDS, three of them younger than 60 years and without comorbidities. Mortality in ICU was 14.3%. Among survivors, ICU and hospital stay were 6.5 and 14 days, respectively. Plasma levels of procalcitonin were higher in patients with bacterial coinfection (18.2 vs 0.54; p < 0.05). The levels of C-reactive protein, however, were similar. Human metapneumovirus was associated with severe CAP requiring ICU admission among elderly patients or patients with comorbidities, but also in healthy young subjects. These patients often underwent mechanical ventilation with elevated health resource consumption. While one out of four patients showed pneumococcal coinfection, plasma procalcitonin helped to implement antimicrobial stewardship.

Strains 335427^T and 234509^T, isolated from two 76-year-old patients with chronic pulmonary diseases, were the subject of polyphasic taxonomic studies and comparative genomic analyses for virulence factors. The 16 rRNA gene sequence similarity between strains 335427^T and 234509^T and their closest phylogenetic neighbors Nocardia asiatica NBRC 100129^T and Nocardia abscessus NBRC 100374^T were 99.5% and 100%, respectively. Digital DNA–DNA hybridization values between the aforementioned studied strains were well below the 70% threshold for assigning prokaryotic strains to a novel species. Strains 335427^T and 234509^T have genome sizes of 8.49 Mpb and 8.07 Mpb, respectively, with G + C content of 68.5%. Isolate 335427^T has C_16:0, C_18:1 ω₉c, C_18:0 and C_18:0 10 methyl as major fatty acids (>15%) and mycolic acids formed of 52–54 carbon atoms. However, only C_18:1 ω₉c was detected for isolate 234509^T, which had mycolic acids with 44–56 carbon. Based on phenotypic and genetic data, strains 335427^T (DSM 109819^T = CECT 9924^T) and 234509^T (DSM 111366^T = CECT 30129^T) merit recognition as novel species, which are named Nocardia barduliensis sp. nov. and Nocardia gipuzkoensis sp. nov., respectively. All the strains studied had homologous VF-associated genes to those described in M. tuberculosis, including experimentally verified virulence genes in humans related to tuberculosis. The narGHIJ (nitrate reduction pathway) and gvpAFGOJLMK (gas vesicles) genetic maps of strains 335427^T, 234509^T, NBRC 100129^T and NBRC 100374^T showed the same syntenic block and raise the question of whether their functions are interlinked during the infection of the human host. However, further research is required to decipher the role of the gas vesicle in the pathogenicity mechanism of Nocardia spp.

Background: Pertussis has re-emerged in many countries despite the wide use of vaccines for over 60 years. During 2023, we observed an increase in the incidence of pertussis in Gipuzkoa, north of Spain (with a population of 657,140 inhabitants), mainly affecting children between 11 and 15 years of age. Methods: This study included all confirmed cases diagnosed by PCR in nasopharyngeal swab samples. The genome of seven isolates collected in 2023 was sequenced. Results: Between 2018 and 2023, 884 cases of whooping cough were diagnosed. Pertussis incidence (in cases per 100,000 inhabitants) decreased from 36.7 in 2018 to no cases in 2021, increasing again to 56.8 in 2023. In 2023, the age group of 11–15 years old had the highest incidence rate of 409.3. Only 2 of the 56 children < 6 years old required hospitalization, and there were no deaths. The seven isolates collected in 2023 showed the same BPagST-4 (ptxA1/ptxP3/prn2/fim2-1/fim3-1 allelic combination), with all of them expressing the pertactin antigen. Conclusions: Immunity waning after the last dose of vaccination at 6 years old, together with the lack of circulation of Bordetella pertussis during the COVID-19 pandemic, were probably the main reasons for the high increase in the incidence of pertussis in Gipuzkoa in 2023.

Gordonia species differentiation is a tedious task. Herein, Gordonia identification was performed according to the standard Bruker score system and a recently proposed score for Gram positive rods identification (≥ 1.5 genus level and ≥ 1.7 species level). New scores significantly improved the identification at genus and species level.