om as , F e r na n d o G on zález Candelas, SeqCOVID-SPAIN consortium, Tanja Stadler & Richard A. NeherThis is a PDF file of a peer-reviewed paper that has been accepted for publication. Although unedited, the content has been subjected to preliminary formatting. Nature is providing this early version of the typeset paper as a service to our authors and readers. The text and figures will undergo copyediting and a proof review before the paper is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers apply.

a total of 622 cases of SARS-CoV-2 infection compatible with the Omicron variant (BA.1/B.1.1.529) (1) were studied by the Contact Tracing Programe in Cantabria, Spain. A total of 1,420 close contacts (household, social, and occupational) were identified; 455 secondary cases were identified. We report the main epidemiologic characteristics of these cases, such as secondary attack rate (SAR), transmission period, incubation period, and serial interval, and compared these characteristics with those for Delta variant cases.

The coronavirus disease 2019 (COVID-19) pandemic has affected the world radically since 2020. Spain was one of the European countries with the highest incidence during the first wave. As a part of a consortium to monitor and study the evolution of the epidemic, we sequenced 2,170 samples, diagnosed mostly before lockdown measures. Here, we identified at least 500 introductions from multiple international sources and documented the early rise of two dominant Spanish epidemic clades (SECs), probably amplified by superspreading events. Both SECs were related closely to the initial Asian variants of SARS-CoV-2 and spread widely across Spain. We inferred a substantial reduction in the effective reproductive number of both SECs due to public-health interventions ( R e < 1), also reflected in the replacement of SECs by a new variant over the summer of 2020. In summary, we reveal a notable difference in the initial genetic makeup of SARS-CoV-2 in Spain compared with other European countries and show evidence to support the effectiveness of lockdown measures in controlling virus spread, even for the most successful genetic variants.

Objectives To analyse the epidemiology, the resistome and the virulome of ceftolozane/tazobactam-susceptible or -resistant Pseudomonas aeruginosa clinical isolates recovered from surveillance studies in Portugal (STEP, 2017–18) and Spain (SUPERIOR, 2016–17). Methods P. aeruginosa isolates were recovered from intra-abdominal, urinary tract and lower respiratory tract infections in ICU patients admitted to 11 Portuguese and 8 Spanish hospitals. MICs were determined (ISO-standard broth microdilution, EUCAST 2020 breakpoints). A subset of 28 ceftolozane/tazobactam-resistant P. aeruginosa isolates were analysed and compared with 28 ceftolozane/tazobactam-susceptible P. aeruginosa strains by WGS. Results Clonal complex (CC) 235 (27%) and CC175 (18%) were the most frequent, followed by CC244 (13%), CC348 (9%), CC253 (5%) and CC309 (5%). Inter-hospital clonal dissemination was observed, limited to a geographical region (CC235, CC244, CC348 and CC253 in Portugal and CC175 and CC309 in Spain). Carbapenemases were detected in 25 isolates (45%): GES-13 (13/25); VIM type (10/25) [VIM-2 (4/10), VIM-20 (3/10), VIM-1 (2/10) and VIM-36 (1/10)]; and KPC-3 (2/25). GES-13-CC235 (13/15) and VIM type-CC175 (5/10) associations were observed. Interestingly, KPC-3 and VIM-36 producers showed ceftolozane/tazobactam-susceptible phenotypes. However, ceftolozane/tazobactam resistance was significantly associated with GES-13 and VIM-type carbapenemase production. Six non-carbapenemase producers also displayed ceftolozane/tazobactam resistance, three of them showing known ceftolozane/tazobactam resistance-associated mutations in the PBP3 gene, ftsI (R504C and F533L). Overall, an extensive virulome was identified in all P. aeruginosa isolates, particularly in carbapenemase-producing strains. Conclusions GES-13-CC235 and VIM type-CC175 were the most frequent MDR/XDR P. aeruginosa clones causing infections in Portuguese and Spanish ICU patients, respectively. Ceftolozane/tazobactam resistance was mainly due to carbapenemase production, although mutations in PBP-encoding genes may additionally be involved.

The decreased incidence of infectious diseases in developed countries may make their diagnosis difficult. Cutaneous tuberculosis is an example of this fact. A 44-year-old man presented with two painful abscesses on his lower extremities, which developed into chronic ulcers. A cutaneous biopsy revealed necrotizing granulomas in the dermis. Ziehl-Neelsen and periodic acid-Schiff stain were negative. Mantoux test was positive. Tc-99m scintigraphy showed increased uptake in the bone tissue of the left ankle and right tibiae, without direct relation to cutaneous lesions. Chest X-ray showed micronodular, apical, bilateral infiltrates, reduced volume of the right lung, and cavitation of the right superior lobe. Mycobacterium tuberculosis was grown from sputum and skin biopsy samples. Isoniazid, rifampin and pyrazinamide treatment for 2 months, followed by isoniazid and rifampin for 12 months, resulted in complete resolution. The clinical features of cutaneous tuberculosis in our patient were characteristic of tuberculous abscesses. Some uncommon findings, such as the low number of lesions, negative acid-fast resistant stains in cutaneous biopsy samples and his preserved general state of health, may be explained by a higher competence of the immune system than is usual in this clinical subset of disseminated tuberculosis. Cutaneous tuberculosis should be included in the differential diagnosis of cutaneous abscesses in immunocompetent patients.