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Funding Information: Collaborators of the CIMBA-LT study: Hospital Vila Franca de Xira: André Oliveira; João Gonçalves-Pereira; Joaquim Lima. Centro Hospitalar de Médio Tejo (Abrantes): Rui Assis; Joana Monteiro. Hospital Nélio Mendonça (Funchal): André Simões; Catarina Lume. Centro Hospitalar de Trás-os-Montes e Alto Douro (Vila Real): Maria João Pinto. Centro Hospitalar de Vila Nova de Gaia: Sara Pipa. Hospital de Braga: Laura Costa. Hospital de Bragança: Cristina Nunes. Hospital do Divino Espírito Santo (S. Miguel): Manuela Henriques; Luís Tavares. Hospital de Leiria: Filipa Sequeira. Centro Hospitalar Universitário de S.João (Porto): José-Artur Paiva; Tatiana Santos Vieira; Núria Jorge. Centro Hospital Universitário de Lisboa Norte (Lisboa): Ana Bento Rodrigues; Susana Fernandes; João Ribeiro. Hospital S.Francisco Xavier (Lisboa): Rui Morais; Pedro Póvoa; Luís Coelho. Centro Hospitalar Universitário de Coimbra: Ana Martinho; Iolanda Santos. Hospital Egas Moniz (Lisboa): Gabriela Almeida. Hospital de Beja: Alexandra Paula; Filipe Morais de Almeida. Centro Hospitalar Universitário do Algarve (Faro): Sofia Ribeiro. Publisher Copyright: © 2023, The Author(s). Background: The past years have witnessed dramatic changes in the population admitted to the intensive care unit (ICU). Older and sicker patients are now commonly treated in this setting due to the newly available sophisticated life support. However, the short- and long-term benefit of this strategy is scarcely studied. Methods: The Critically Ill patients’ mortality by age: Long-Term follow-up (CIMbA-LT) was a multicentric, nationwide, retrospective, observational study addressing short- and long-term prognosis of patients admitted to Portuguese multipurpose ICUs, during 4 years, according to their age and disease severity. Patients were followed for two years after ICU admission. The standardized hospital mortality ratio (SMR) was calculated according to the Simplified Acute Physiology Score (SAPS) II and the follow-up risk, for patients discharged alive from the hospital, according to official demographic national data for age and gender. Survival curves were plotted according to age group. Results: We included 37.118 patients, including 15.8% over 80 years old. The mean SAPS II score was 42.8 ± 19.4. The ICU all-cause mortality was 16.1% and 76% of all patients survive until hospital discharge. The SAPS II score overestimated hospital mortality [SMR at hospital discharge 0.7; 95% confidence interval (CI) 0.63–0.76] but accurately predicted one-year all-cause mortality [1-year SMR 1.01; (95% CI 0.98–1.08)]. Survival curves showed a peak in mortality, during the first 30 days, followed by a much slower survival decline thereafter. Older patients had higher short- and long-term mortality and their hospital SMR was also slightly higher (0.76 vs. 0.69). Patients discharged alive from the hospital had a 1-year relative mortality risk of 6.3; [95% CI 5.8–6.7]. This increased risk was higher for younger patients [21.1; (95% CI 15.1–39.6) vs. 2.4; (95% CI 2.2–2.7) for older patients]. Conclusions: Critically ill patients’ mortality peaked in the first 30 days after ICU admission. Older critically ill patients had higher all-cause mortality, including a higher hospital SMR. A long-term increased relative mortality risk was noted in patients discharged alive from the hospital, but this was more noticeable in younger patients. publishersversion published

Poultry meat has been a vehicle of antibiotic resistant bacteria and genes. Yet, the diversity of selective pressures associated with their maintenance in the poultry-production chain remains poorly explored. We evaluated the susceptibility of Enterococcus spp. from chicken meat collected 20 years apart to antibiotics, metals, acidic pH and peracetic acid-PAA. Contemporary chicken-meat samples (n = 53 batches, each including a pool of neck skin from 10 single carcasses) were collected in a slaughterhouse facility using PAA as disinfectant (March-August 2018, North of Portugal). Broilers were raised in intensive farms (n = 29) using CuSO4 and organic acids as feed additives. Data were compared with that of 67 samples recovered in the same region during 1999-2001. All 2018 samples had multidrug resistant-MDR isolates, with >45 % carrying Enterococcus faecalis, Enterococcus faecium or Enterococcus gallinarum resistant to tetracycline, erythromycin, ampicillin, quinupristin-dalfopristin, ciprofloxa-cin, chloramphenicol or aminoglycosides. Resistance rates were similar (P > 0.05) to those of 1999-2001 samples for all but five antibiotics. The decrease of samples carrying vancomycin-resistant isolates from 46 % to % between 1999-2001 and 2018 was the most striking difference. Isolates from both periods were similarly susceptible to acid pH [minimum-growth pH (4.5-5.0), minimum-survival pH (3.0-4.0)] and to PAA (MIC90 = 100-120 mg/L/MBC90 = 140-160 mg/L; below concentrations used in slaughterhouse). Copper tolerance genes (tcrB and/or cueO) were respectively detected in 21 % and 4 % of 2018 and 1999-2001 samples. The tcrB gene was only detected in E. faecalis (MICCuSO4 > 12 mM), and their genomes were compared with other international ones of chicken origin (PATRIC database), revealing a polyclonal population and a plasmid or chromosomal location for tcrB. The tcrB plasmids shared diverse genetic modules, including multiple antimicrobial resistance genes (e.g. to tetracyclines, chloramphenicol, macrolide-lincosamide-streptogramin B-MLSB, aminoglycosides, bacitracin, coccidiostats). When in chromosome, the tcrB gene was co-located closely to merA (mercury) genes. Chicken meat remains an important vehicle of MDR Enterococcus spp. able to survive under diverse stresses (e.g. copper, acid) potentially contributing to these bacteria maintenance and flux among animal-environment -humans.

The present document describes the HUG project data management plan (DMP), which is neededto specify what data is being processed and to manage how that data will be handled, stored and shared. Funded by the Portuguese Foundation for Science and Technology (PTDC/GES-OUT/1662/2020), this project is expected to generate evidence on the health consequences of the neighbourhood social changes caused by the housing crisis to inform the design and planning of healthier neighbourhoods and housing conditions. More information about the project can be found at:https://www.hug-project.com/ Funding statement:This project is financed by national funds through FCT- Fundação para a Ciência e a Tecnologia, I.P., under the project “HUG: The health impacts of inner-city gentrification, displacement and housing insecurity: a quasi-experimental multi-cohort study (PTDC/GES-OUT/1662/2020)” and the projects UIDB/04750/2020 and LA/P/0064/2020.Ana Isabel Ribeiro, the project's principal investigator, is supported by National Funds through FCT, under the ‘Stimulus of Scientific Employment–Individual Support’ programme within the contract CEECIND/02386/2018.

Background: Antimicrobial resistance (AMR) is one of the main threats to global health. The dissemination of mobile colistin resistance genes (mcr) is a major concern affecting humans, animals and environment. Food-producing animals are considered the main reservoir of mcr genes, however the role of wild animals and pets is less studied. Here, we investigate the mcr occurrence among wild animals, wild birds, food-producing animals and pets. Material & Methods: Between 2019-2021, faecal samples obtained from wild animals (boars, N=39; deer, N=62; other, N=6), wild birds (N=98), food-producing animals (cattle, N=40; pigs, N=56) and pets (cats and dogs, N=199). Isolation was performed in selective and non-selective medium, followed by identification of virulence genes of E. coli by PCR, and Salmonella serotyping. The mcr 1-5 genes were screened by PCR in all E. coli and Salmonella isolates recovered. Whole-genome sequencing was used to investigate the presence of AMR genes, multilocus sequence type and phylogeny of all pathogenic isolates, as well as mcr-carrying isolates. Results: The overall occurrence rate of E.coli and Salmonella was 77.8% (389/500) and 2.8% (14/500), respectively. Pathogenic E.coli was detected in 46.7% (50/107) of wild animals, 2.0% (2/98) of wild birds, 11.4% (11/96) of food-producing animals and 19.1% (38/199) of pets, while Salmonella was identified in 2.8% of wild animals (3/107), 3.1% (3/98) of wild birds, and 7.3% (7/96) of food-producing animals. The mcr-1 gene was detected in 1.8% (7/389) of the E. coli positive samples, all of them in isolates recovered from pigs (13.7%; 7/51). All this mcr-1-positive showed additional resistance phenotypes, including MDR, and several virulence genes. No cases of mcr genes were identified in Salmonella isolates. Conclusions: Pathogenic E. coli was significantly more frequent than Salmonella spp in the studied animals. Besides the general low prevalence of the resistance to colistin mediated by mcr genes, the only cases were identified in E. coli food-producing isolates, namely in pigs. Our results highlight the importance of a continuous surveillance of antimicrobial resistance in an OneHealth approach. Funding: This work has received funding from the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No 773830) OHEJP Discover.

Aim:This study aimed to estimate the prevalence, to characterize, and to evaluate antimicrobial susceptibility of pathogenic E. coli and Salmonella spp.in stray cats and dogs. Methods:Between November 2019 and October 2020, 199 faecal samples were obtained from 102 cats and 97 dogs rescued by a kennel in Lisboa. Isolation was performed in selective and non-selective medium, followed by identification of virulence genes of E. coli by PCR, and Salmonella serotyping. Antimicrobial susceptibility testing (AST) was performed according to EUCAST. mcr-1-5 genes were detected by PCR. All pathogenic isolates were further characterized by WGS. Results:The overall rate of E.coli and Salmonella was 73.9% (147/199) and 0.5% (1/199), respectively. Pathogenic E. coli were detected in 19.6% dogs and 18.6% cats. No cases of STEC were found. AST revealed that 13.0% of the isolates were resistant (16.2% dogs vs. 10.0% cats). Resistance to ampicillin, tetracycline, sulfamethoxazole, and/or trimethoprimwere the most frequent. MDR was observed in four ETEC isolated from dogs, which have the same ST155 and blaTEM-1B, sul1, sul2, dfrA1, and tet(A) resistance genes. All commensal E. coli were susceptible to antimicrobials. Salmonella (S.4,5:i:-) was identified in a cat. Belongs to ST3478 and presents ac(6')-Iaa, blaTEM-1B, and sul2 resistance genes. None isolate was ESBL or harboured mcr genes. Conclusions:Some of the isolates have relevant antimicrobial resistance. Due to the close contact with humans and to the potential release of pathogenic and resistant enteric bacteria in the environment, it is important to monitor stray cats and dogs health status following a One Health approach. Funding:This work is part of DiSCoVeR project (JRP24-R2-FBZ2-DiSCoVeR), funded by the European Union’s Horizon 2020 Research and Innovation programme under grant agreement No. 773830.