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DOE OSTI2014

Optimal deployment of thermal energy storage under diverse economic and climate conditions

This paper presents an investigation of the economic benefit of thermal energy storage (TES) for cooling, across a range of economic and climate conditions. Chilled water TES systems are simulated for a large office building in four distinct locations, Miami in the U.S.; Lisbon, Portugal; Shanghai, China; and Mumbai, India. Optimal system size and operating schedules are determined using the optimization model DER-CAM, such that total cost, including electricity and amortized capital costs are minimized. The economic impacts of each optimized TES system is then compared to systems sized using a simple heuristic method, which bases system size as fraction (50percent and 100percent) of total on-peak summer cooling loads. Results indicate that TES systems of all sizes can be effective in reducing annual electricity costs (5percent-15percent) and peak electricity consumption (13percent-33percent). The investigation also indentifies a number of criteria which drive TES investment, including low capital costs, electricity tariffs with high power demand charges and prolonged cooling seasons. In locations where these drivers clearly exist, the heuristically sized systems capture much of the value of optimally sized systems; between 60percent and 100percent in terms of net present value. However, in instances where these drivers are less pronounced, the heuristic tends to oversize systems, and optimization becomes crucial to ensure economically beneficial deployment of TES, increasing the net present value of heuristically sized systems by as much as 10 times in some instances.

25 ENERGY STORAGE↗

DOE OSTI2023

Microwave radiometer, sun-photometer and GNSS multi-comparison of integrated water vapor in Southwestern Europe

This work presents a comparison of integrated water vapor (IWV) data recorded from microwave radiometer (MWR) and sun-photometer (SP) using global navigation satellite system (GNSS) IWV as reference in five mid-latitude sites of Portugal and Spain (2003–2021). A very high correlation is obtained for both instruments (R2 between 0.94 and 0.98), although, while MWR shows a wet bias, SP exhibits a dry one. In addition, a dependence of mean bias error (MBE) and standard deviation (SD) on IWV has been observed, increasing (larger discrepancies) both indices as IWV increases. The solar zenith angle (SZA) dependence is also studied, finding slightly larger discrepancies for the MWR than for SP in comparison with GNSS for very high values of SZA. Finally, a marked seasonal dependence is observed for SP-GNSS differences, modulated by the IWV dependence explained above. In contrast, the seasonal dependence for MWR is quite weaker than it is for SP. Therefore, in spite of the excellent agreement found among the different instruments, it is recommended that: i) the dependence with IWV be studied and corrected to further increase the performance of the instruments, and ii) metadata be used to filter out situations in which the instrument cannot operate properly.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2015

No evidence of a threshold in traffic volume affecting road-kill mortality at a large spatio-temporal scale

Previous studies have found that the relationship between wildlife road mortality and traffic volume follows a threshold effect on low traffic volume roads. We aimed at evaluating the response of several species to increasing traffic intensity on highways over a large geographic area and temporal period. We used data of four terrestrial vertebrate species with different biological and ecological features known by their high road-kill rates: the barn owl (Tyto alba), hedgehog (Erinaceus europaeus), red fox (Vulpes vulpes) and European rabbit (Oryctolagus cuniculus). Additionally, we checked whether road-kill likelihood varies when traffic patterns depart from the average. We used annual average daily traffic (AADT) and road-kill records observed along 1000 km of highways in Portugal over seven consecutive years (2003–2009). We fitted candidate models using Generalized Linear Models with a binomial distribution through a sample unit of 1 km segments to describe the effect of traffic on the probability of finding at least one victim in each segment during the study. We also assigned for each road-kill record the traffic of that day and the AADT on that year to test for differences using Paired Student's t-test. Mortality risk declined significantly with traffic volume but varied among species: the probability of finding road-killed red foxes and rabbits occurs up to moderate traffic volumes (< 20,000 AADT) whereas barn owls and hedgehogs occurred up to higher traffic volumes (40,000 AADT). Perception of risk may explain differences in responses towards high traffic highway segments. Road-kill rates did not vary significantly when traffic intensity departed from the average. In summary, we did not find evidence of traffic thresholds for the analysed species and traffic intensities. We suggest mitigation measures to reduce mortality be applied in particular on low traffic roads (< 5000 AADT) while additional measures to reduce barrier effects should take into account species-specific behavioural traits. - Highlights: • Traffic and road-kills were analysed along 1000 km of highways over seven years. • Mortality risk declined significantly with traffic volume. • Perception of risk may explain different responses towards high traffic sections. • Reducing barrier effects should take into account species behavioural traits.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2016

Strategic Environmental Assessment practices in European small islands: Insights from Azores and Orkney islands

The literature concerning Strategic Environmental Assessment (SEA) often refers to the importance of context-specific approaches. However, there is a lack of systematised and consistent studies that enhance tailor-made SEA practices and procedures. Small islands are bounded units of study which may help explore SEA theory and practice in special territories. Small islands present particular features and unique values, such as, small size and population, geographic isolation, limited resources and vulnerable ecosystems. Hence, the main goal of this research was to profile SEA practices and procedures in European small islands and provide a background for future research aiming to improve context-specific SEA applications. To achieve this goal, an exploratory case study was developed using Azores (Portugal) and Orkney (Scotland) archipelagos. An analysis of the corresponding mainland was also carried out to contextualise both case studies. The data collection was achieved through a qualitative content analysis of 43 Environmental Reports. The research found that there is not an SEA context-specific approach used within these European small islands, including guidelines, assessment topics, assessment techniques, follow-up and stakeholders engagement. The debate concerning specific approaches to small islands must be re-focused on the enhancement of SEA capacity-building amongst different stakeholders (including decision-makers), on the development and implementation of collaborative approaches, and on the exchange of knowledge and experiences between small islands networks. - Highlights: • Reviewed the differences between the Portuguese and Scottish SEA system • Showed a low integration of SEA specific features in reports of European small islands • Provides background for future SEA research for small islands approaches.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2015

A critical view on microplastic quantification in aquatic organisms

Microplastics, plastic particles and fragments smaller than 5 mm, are ubiquitous in the marine environment. Ingestion and accumulation of microplastics have previously been demonstrated for diverse marine species ranging from zooplankton to bivalves and fish, implying the potential for microplastics to accumulate in the marine food web. In this way, microplastics can potentially impact food safety and human health. Although a few methods to quantify microplastics in biota have been described, no comparison and/or intercalibration of these techniques have been performed. Here we conducted a literature review on all available extraction and quantification methods. Two of these methods, involving wet acid destruction, were used to evaluate the presence of microplastics in field-collected mussels (Mytilus galloprovincialis) from three different “hotspot” locations in Europe (Po estuary, Italy; Tagus estuary, Portugal; Ebro estuary, Spain). An average of 0.18±0.14 total microplastics g{sup −1} w.w. for the Acid mix Method and 0.12±0.04 total microplastics g{sup −1} w.w. for the Nitric acid Method was established. Additionally, in a pilot study an average load of 0.13±0.14 total microplastics g{sup −1} w.w. was recorded in commercial mussels (Mytilus edulis and M. galloprovincialis) from five European countries (France, Italy, Denmark, Spain and The Netherlands). A detailed analysis and comparison of methods indicated the need for further research to develop a standardised operating protocol for microplastic quantification and monitoring.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2018

Ecosystem services: Urban parks under a magnifying glass

Highlights: • We mapped ecosystem services in an urban park with high spatial detail. • Ecosystem services varied widely with vegetation type. • Native forest provided the most ecosystem services. • Urban parks should not be seen homogenous units regarding ecosystem services. • Nature-based solutions can help managers to optimize ecosystem services provision. Urban areas’ population has grown during the last century and it is expected that over 60% of the world population will live in cities by 2050. Urban parks provide several ecosystem services that are valuable to the well-being of city-dwellers and they are also considered a nature-based solution to tackle multiple environmental problems in cities. However, the type and amount of ecosystem services provided will vary with each park vegetation type, even within same the park. Our main goal was to quantify the trade-offs in ecosystem services associated to different vegetation types, using a spatially detailed approach. Rather than relying solely on general vegetation typologies, we took a more ecologically oriented approach, by explicitly considering different units of vegetation structure and composition. This was demonstrated in a large park (44 ha) located in the city of Almada (Lisbon metropolitan area, Portugal), where six vegetation units were mapped in detail and six ecosystem services were evaluated: carbon sequestration, seed dispersal, erosion prevention, water purification, air purification and habitat quality. The results showed that, when looking at the park in detail, some ecosystem services varied greatly with vegetation type. Carbon sequestration was positively influenced by tree density, independently of species composition. Seed dispersal potential was higher in lawns, and mixed forest provided the highest amount of habitat quality. Air purification service was slightly higher in mixed forest, but was high in all vegetation types, probably due to low background pollution, and both water purification and erosion prevention were high in all vegetation types. Knowing the type, location, and amount of ecosystem services provided by each vegetation type can help to improve management options based on ecosystem services trade-offs and looking for win-win situations. The trade-offs are, for example, very clear for carbon: tree planting will boost carbon sequestration regardless of species, but may not be enough to increase habitat quality. Moreover, it may also negatively influence seed dispersal service. Informed practitioners can use this ecological knowledge to promote the role of urban parks as a nature-based solution to provide multiple ecosystem services, and ultimately improve the design and management of the green infrastructure. This will also improve the science of Ecosystem Services, acknowledging that the type of vegetation matters for the provision of ecosystem services and trade-offs analysis.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2018

UV-filters and musk fragrances in seafood commercialized in Europe Union: Occurrence, risk and exposure assessment

Highlights: • Largest survey on UV-Fs and musks in seafood commercialized in Europe. • Farmed seabream showed the highest average concentration of UV-Fs. • Wild mackerel showed the highest average concentration of polycyclic musks. • UV-Fs and musks in raw samples were far below the estimated toxicological reference value. In the framework of the FP7 ECsafeSeafood project, 62 seafood samples commercialized in Europe Union from several representative species – mackerel, tuna, salmon, seabream, cod, monkfish, crab, shrimp, octopus, perch and plaice – were analysed for residues of 21 personal care products (PCPs), including 11 UV-filters (UV-Fs) and 10 musk fragrances (musks). PCPs analysis were performed by Quick, Easy, Cheap, Effective Rugged, Safe (QuEChERS), combined with liquid-liquid extraction (LLE) or dispersive solid-phase extraction (dSPE), followed by gas chromatography-tandem mass spectrometry (GC-MS/MS). The results showed the presence in a wide range of samples of nine out of eleven UV-Fs compounds analysed, namely 2-ethylhexyl salicylate (EHS), 2-ethylhexyl,4-methoxycinnamate (EHMC), 4-methylbenzylidenecamphor (4-MBC), benzophenone-1 (BP1), benzophenone-3 (BP3), isoamyl-4-methoxycinnamate (IMC), 2,2′-dihydroxy-4,4′-dimethoxybenzophenone (DHMB), homosalate (HS), and octocrylene (OC), whereas galaxolide (HHCB), galaxolide lactone (HHCB-lactone), and tonalide (AHTN) were the most found musks. The potential risks to human health associated with the exposure to eight of the more prevalent PCPs – EHS, EHMC, 4-MBC, BP1, BP3, IMC, HHCB, and AHTN - through seafood consumption were assessed for consumers from five European countries (Belgium, Ireland, Italy, Portugal and Spain). Results showed that the human exposure to UV-Fs and musks estimated from the concentration values found in seafood and the daily consumption of concerned seafood species, were far below toxicological reference values.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2018

Occurrence of cyclic imines in European commercial seafood and consumers risk assessment

Highlights: • First study of cyclic imines in commercial shellfish samples from Europe. • First study including samples from eight European countries during two years. • First report dealing risk assessment on pinnatoxins. • Completes information regarding spirolides from the EFSA report on 2010. • Increases database on levels of CIs in shellfish to perform a risk assessment. Cyclic imines constitute a quite recently discovered group of marine biotoxins that act on neural receptors and that bioaccumulate in seafood. They are grouped together due to the imino group functioning as their common pharmacore, responsible for acute neurotoxicity in mice. Cyclic imines (CIs) have not been linked yet to human poisoning and are not regulated in the European Union (EU), although the European Food Safety Authority (EFSA) requires more data to perform conclusive risk assessment for consumers. Several commercial samples of bivalves including raw and processed samples from eight countries (Italy, Portugal, Slovenia, Spain, Ireland, Norway, The Netherlands and Denmark) were obtained over 2 years. Emerging cyclic imine concentrations in all the samples were analysed on a LC-3200QTRAP and LC-HRMS QExactive mass spectrometer. In shellfish, two CIs, pinnatoxin G (PnTX-G) and 13-desmethylspirolide C (SPX-1) were found at low concentrations (0.1–12 µg/kg PnTX-G and 26–66 µg/kg SPX-1), while gymnodimines and pteriatoxins were not detected in commercial (raw and processed) samples. In summary, SPX-1 (n: 47) and PnTX-G (n: 96) were detected in 9.4% and 4.2% of the samples, respectively, at concentrations higher than the limit of quantification (LOQ), and in 7.3% and 31.2% of the samples at concentrations lower than the LOQ (25 µg/kg for SPX-1 and 3 µg/kg for PnTX-G), respectively. For the detected cyclic imines, the average exposure and the 95th percentile were calculated. The results obtained indicate that it is unlikely that a potential health risk exists through the seafood diet for CIs in the EU. However, further information about CIs is necessary in order to perform a conclusive risk assessment.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2018

Polycyclic aromatic hydrocarbons bioaccessibility in seafood: Culinary practices effects on dietary exposure

Highlights: • PAHs bioaccessibility in seafood was assessed. • Raw shrimp present the lowest and dried seaweed the highest content of PAH. • There was a significant interaction effect between species and culinary treatment. This work aimed to determine the effect of culinary practices on the contamination level and bioaccessibility of polycyclic aromatic hydrocarbons (PAHs) in seafood. The selected farmed seafood species (marine shrimp, clams and seaweed) were commercially available in Portugal. The mean concentrations of PAHs varied between 0.23 and 51.8 µg kg{sup −1}, with the lowest value being observed in raw shrimp and the highest in dried seaweed. The number of compounds detected in seaweed and clams (naphthalene, acenaphthene, fluorene, phenanthrene, benzo(b)fluoranthene and benzo(j)fluoranthene) were higher than in shrimp (fluorene and pyrene). Among the PAHs measured, fluorene was the predominant one. There was a significant interaction effect between species and culinary treatment (p < 0.05), thus boiled and dried seaweed samples presented the lowest and the highest levels of fluorene (0.13 and 1.8 µg kg{sup −1}), respectively. The daily intake of PAHs decreased with bioaccessibility, varying from 22% for benzo(k)fluoranthene (in raw clam) to 84% for phenanthrene (in steamed clam). According to the potency equivalent concentrations, screening values and bioaccessibility of PAHs, the consumption of marine shrimp, clam and seaweed is considered as safe for consumers.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

The economic value of photovoltaic performance loss mitigation in electricity spot markets

Photovoltaic (PV) performance is affected by reversible and irreversible losses. These can typically be mitigated through responsive and proactive operations and maintenance (O&M) activities. However, to generate profit, the cost of O&M must be lower than the value of the recovered electricity. This value depends both on the amount of recovered energy and on the electricity prices, which can vary significantly over time in spot markets. The present work investigates the impact of the electricity price variability on the PV profitability and on the related O&M activities in Italy, Portugal, and Spain. Here, it is found that the PV revenues varied by 1.6 × to 1.8 × within the investigated countries in the last 5 years. Moreover, forecasts predict higher average prices in the current decade compared to the previous one. These will increase the future PV revenues by up to 60% by 2030 compared to their 2015–2020 mean values. These higher revenues will make more funds available for better maintenance and for higher quality components, potentially leading to even higher energy yield and profits. Linearly growing or constant price assumptions cannot fully reproduce these expected price trends. Furthermore, significant price fluctuations can lead to unexpected scenarios and alter the predictions.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

DOE OSTI2019

Review of wind generation within adequacy calculations and capacity markets for different power systems

The integration of renewable energy sources, including wind power, in the adequacy assessment of electricity generation capacity becomes increasingly important as renewable energy generation increases in volume and replaces conventional power plants. The contribution of wind power to cover the electricity demand is less certain than conventional power sources; therefore, the capacity value of wind power is smaller than that of conventional plants. This article presents an overview of the adequacy challenge, how wind power is handled in the regulation of capacity adequacy, and how wind power is treated in a selection of jurisdictions. The jurisdictions included in the overview are Sweden, Great Britain, France, Ireland, United States (PJM and ERCOT), Finland, Portugal, Spain, Norway, Denmark, Belgium, Germany, Italy and the Netherlands.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2017

Soap production: A green prospective

Highlights: • Reducing the amount of different types of municipal waste. •Recycling waste to obtain a useful green soap, which is good quality and cheap. • Inspiring community projects meant to convey recycling and ecological approach. • Contributing to families’ economy and stimulating the use of healthier products. - Abstract: A green prospective based on the reuse of waste materials such as almond shells, orange peel and used cooking oil to manufacture soap is presented. In Portugal, thousands of tons of waste are generated from used cooking oil and production of nut shells’ residues is growing every year. In addition, the high consumption of citrus fruits, oranges in particular, generates large amounts of citrus peel. Therefore, it is necessary to diversify reuse mechanisms of these wastes, in order to make them back into raw materials. Complying with this trend, this work was carried out by processing and grinding almond shells, treating used oil, processing orange peels and extracting limonene, formulating and producing soap, and performing an acceptance study of the final product. Results validated a high potential of the idea in the field of environmental education, so it can be replicated in practical classes. It can also be useful for waste management, and it can support the development of community projects on an ecological approach.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2021

Controlling the pandemic during the SARS-CoV-2 vaccination rollout

There is a consensus that mass vaccination against SARS-CoV-2 will ultimately end the COVID-19 pandemic. However, it is not clear when and which control measures can be relaxed during the rollout of vaccination programmes. We investigate relaxation scenarios using an age-structured transmission model that has been fitted to age-specific seroprevalence data, hospital admissions, and projected vaccination coverage for Portugal. Our analyses suggest that the pressing need to restart socioeconomic activities could lead to new pandemic waves, and that substantial control efforts prove necessary throughout 2021. Using knowledge on control measures introduced in 2020, we anticipate that relaxing measures completely or to the extent as in autumn 2020 could launch a wave starting in April 2021. Additional waves could be prevented altogether if measures are relaxed as in summer 2020 or in a step-wise manner throughout 2021. We discuss at which point the control of COVID-19 would be achieved for each scenario.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2015

Electronic journals: Their use by teachers/researchers of engineering and social sciences

Libraries must attend the needs of their different users. Academics are usually a particular kind of users with specific needs. Universities are environments where scientific communication is essential and where electronic format of journals is becoming more and more frequently used. This way it becomes increasingly important to understand how academics from different scientific areas use the available electronic resources. The aim of this study is to better understand the existing differences among the users of electronic journals in Engineering and Social Sciences. The research undertaken was mainly focused on the study of the use of electronic journals by teachers/researchers from the Faculties of Engineering and of Arts from the University of Porto, Portugal. In this study an international survey was used in order to characterize the levels of use and access of electronic journals by these communities. The ways of seeking and using scientific information, namely in terms frequency of access, the number of articles consulted, the use of databases and the preference of publishing in electronic journals were analyzed. A set of comparisons were established and results indicate an extensive use of the electronic format, regardless the faculty. However, some differences emerge when it comes to details. Such is the case of the usage rate of reference management software which is considerably more used by Engineering academics than Social Science ones. Generally, electronic journals meeting the information needs of its users and are increasingly used as a preferred means of research. Though, some particular differences in the use of them have emerged, when comparing academics from these two faculties.

99 GENERAL AND MISCELLANEOUS↗

DOE OSTI2015

Preface to Special Topic: Marine Renewable Energy

Marine renewable energy (MRE) is generates from waves, currents, tides, and thermal resources in the ocean. MRE has been identified as a potential commercial-scale source of renewable energy. This special topic presents a compilation of works selected from the 3rd IAHR Europe Congress, held in Porto, Portugal, in 2014. Here, it covers different subjects relevant to MRE, including resource assessment, marine energy sector policies, energy source comparisons based on levelized cost, proof-of-concept and new-technology development for wave and tidal energy exploitation, and assessment of possible inference between wave energy converters (WEC).

16 TIDAL AND WAVE POWER↗

DOE OSTI2018

A GIS-based framework for addressing conflicting objectives in the context of an ecosystem approach to fisheries management—a case study of the Portuguese sardine fishery

Abstract An ecosystem approach to fisheries management (EAFM) is as a new paradigm in fisheries management. In this study, a combination of geographic information systems (GISs) and multi-criteria decision-making method (MCDM) is proposed as a framework supporting an ecosystem approach to European sardine (Sardina pilchardus, Clupeidae) fishery management in Portugal. This case study was chosen due to the recent severe decline shown by the species. To develop an EAFM for the sardine fishery, a set of criteria were defined based on literature review and expert knowledge. To address multiple conflicting objectives, namely conservation and fisheries, five scenarios were considered: (i) baseline; (ii) nurseries protection; (iii) spawning areas protection; (iv) fishery profit driven, and (v) safeguarding dependent fishing communities. Combination of GIS and MCDM methods highlighted important areas to implement spatial conservation measures for sardine. The analyses indicate that some areas are suitable for conservation in several scenarios, such as the area near Aveiro and the area near the Tejo estuary. However, conservation measures implemented in the area near Aveiro would imply higher economic trade-offs when compared with the actions applied in the region near the Tejo estuary. Results also suggested some of the conservation objectives, such as the protection of sardine eggs and juveniles, to not be compatible. The proposed framework is an important tool supporting EAFM by addressing conflicting objectives, trade-offs and identifying areas that could be considered as potential fishery closure sites or subjected to further analyses.

Szalaj, D.↗

DOE OSTI2018

How fishing intensity affects the spatial and trophic ecology of two gull species breeding in sympatry

Abstract Fisheries produce large quantities of discards, an important resource for scavenging seabirds. However, a policy reform banning discards, which is soon to be implemented within the EU, will impose a food shortage upon scavengers, and it is still largely unknown how scavengers will behave. We studied the diet (hard remains), trophic (stable isotope analysis), and foraging (individual tracking) ecology of two gull species breeding in sympatry: Audouin’s gull Larus audouinii (AG) and yellow-legged gull Larus michahellis (YLG), in South Portugal, under normal fishery activity (NFA; work days) and low fishery activity (LFA; weekends), over two consecutive years. We established a pattern of dietary, spatial, and temporal segregation between the two gull species. Under LFA, yellow-legged gulls reduced their time spent at-sea, thus foraging more in alternative habitats (e.g. refuse dumps) and widening their isotopic niche (i.e. generalist behaviour). Contrastingly, Audouin’s gull had a narrower trophic niche (i.e. specialist behaviour), foraging exclusively at-sea, reducing the amount of demersal fish and increasing the amount of pelagic fish in their diet. Under NFA, both species foraged mostly at-sea, feeding almost exclusively on fish, with increased consumption of demersal species (i.e. fishery discards). In general, yellow-legged gull had a broader trophic niche (i.e. generalist behaviour) when compared with the narrower isotopic niche of Audouin’s gull (i.e. specialist behaviour). Overall, both gull species relied heavily on fishery discards. However, there was visible dietary, spatial, and temporal segregation between the two species, associated with their dietary and habitat preferences that could be attributed to the availability of anthropogenic resources, such as fishery discards.

Matos, Diana M.↗

DOE OSTI2020

The success of particular Acinetobacter baumannii clones: accumulating resistance and virulence inside a sugary shield

Abstract Background In Portugal, carbapenem-resistant Acinetobacter baumannii (CRAB) has been associated with ST98, ST103 and ST208 (Oxford Scheme, Oxf) and a clone has usually been associated with a particular period of time. These clonal shifts were primarily explained by an increased antimicrobial resistance profile. Here we explore genomic and biochemical differences among these and more recent clones, which could further explain the diversity and evolution of this species. Methods A total of 116 CRAB isolates (2010–15), together with representatives of a previously described CRAB collection (4 isolates, 2001–06) were characterized by attenuated total reflection Fourier transform infrared spectroscopy (FTIR-ATR) and MLST. Representatives of different FTIR-ATR/MLST clusters were selected for WGS (n = 13), which allowed the in silico extraction of resistance and virulence genes, capsule locus and SNP analysis. Results A. baumannii clonal shifts of OXA-58-producing ST103Oxf (2001–04), OXA-40-producing ST98Oxf (2002–06), OXA-23-producing ST208Oxf (2006–10) and OXA-23-producing ST218Oxf (2010–15) were accompanied by an increase in AMR genes and virulence factors. FTIR-ATR clustering was congruent with sugar composition predicted from the capsular locus: a fucosamine cluster comprising ST98Oxf, ST103Oxf and a single ST218Oxf isolate; a pseudaminic acid cluster of ST208Oxf and ST1557Oxf isolates; and legionaminic acid, resembling the sialic acid from mammalian cells, in a cluster comprising ST218Oxf isolates. The whole-genome phylogenetic tree was congruent with MLST, with isolates presenting 5–28 938 SNPs. ST208Oxf and ST218Oxf presented ∼1900 SNPs while ST103Oxf and ST1557Oxf showed a greater number of SNPs (∼28 000). Conclusions Clonal shifts of CRAB were promoted, in our country, by consecutive virulence and AMR gene pool enlargement, together with features increasing pathogen–host adaptation. Worldwide dominance of ST218Oxf is supported by the combination of high AMR and virulence levels.

Silva, Liliana↗