Browsing by Author "Ramos, Beatriz"
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- À superfície (2022): Aldeia Mineira do LousalPublication . Vicente, Sérgio; Alves, Luzia; Ramos, Beatriz; Farinha, Catarina; Ferreira, Diogo; Saldanha, Diogo; Lopes, Francisco Figueiredo; Pontes, Guilherme; Cabaceira, Joana; André, Mafalda; Pato, Maria; Serafim, Pedro; Imperial, Ricardo
- Animal tuberculosis: impact of disease heterogeneity in transmission, diagnosis, and controlPublication . Pereira, André C.; Reis, Ana C.; Ramos, Beatriz; Cunha, Mónica V.Animal tuberculosis (TB) in terrestrial mammals is mainly caused by Mycobacterium bovis. This pathogen is adapted to a wide range of host species, representing a threat to livestock, wildlife and human health. Disease heterogeneity is a hallmark of multi-host TB and a challenge for control. Drivers of animal TB heterogeneity are very diverse and may act at the level of the causative agent, the host species, the interface between mycobacteria and the host, community of hosts, the environment and even policy behind control programmes. In this paper, we examine the drivers that seem to contribute to this phenomenon. We begin by reviewing evidence accumulated to date supporting the consensus that a complex range of genetic, biological and socio-environmental factors contribute to the establishment and maintenance of animal TB, setting the grounds for heterogeneity. We then highlight the complex interplay between individual, species-specific and community protective factors with risk/maintenance variables that include animal movements and densities, co-infection and super-shedders. We finally consider how current interventions should seek to consider and explore heterogeneity in order to tackle potential limitations for diagnosis and control programmes, simultaneously increasing their efficacy.
- Antimicrobial resistance in commensal Staphylococcus aureus from wild ungulates is driven by agricultural land cover and livestock farmingPublication . Ramos, Beatriz; Rosalino, L. M.; Palmeira, Josman D.; Torres, Rita T.; Cunha, Mónica V.Staphylococcus aureus is a human pathobiont (i.e., a commensal microorganism that is potentially pathogenic under certain conditions), a nosocomial pathogen and a leading cause of morbidity and mortality in humans. S. aureus is also a commensal and pathogen of companion animals and livestock. The dissemination of antimicrobial resistant (AMR) S. aureus, particularly methicillin-resistant (MRSA), has been associated to its ability for establishing new reservoirs, but limited attention has been devoted to the role of the environment. To fill this gap, we aimed to characterize animal carrier status, AMR phenotypes, predominant clonal lineages and their relationship with clinical and food-chain settings, as well as to find predictors of AMR occurrence. Nasal swabs (n = 254) from wild boar (n = 177), red deer (n = 54) and fallow deer (n = 23) hunted in Portugal, during the season 2019/2020, yielded an overall carrier proportion of 35.8%, ranging from 53.7% for red deer and 32.2% for wild boar to 21.7% for fallow deer. MRSA from wild boar and phenotypically linezolid-resistant S. aureus from wild boar and red deer were isolated, indicating that resistance to antimicrobials restricted to clinical practice also occurs in wildlife. The most prevalent genotypes were t11502/ST2678 (29.6%) and t12939/ST2678 (9.4%), previously reported in wild boar from Spain. Clonal lineages reported in humans and livestock, like CC1, CC5 or CC8 (19.1%) and ST425, CC133 or CC398 (23.5%), respectively, were also found. The sequence type ST544, previously restricted to humans, is described in wildlife for the first time. We also identified that land use (agricultural land cover), human driven disturbance (swine abundance) and host-related factors (sex) determine resistance occurrence. These findings suggest that antibiotics used in clinical settings, agriculture and livestock farming, spill over to wildlife, leading to AMR emergence, with potential biological, ecological, and human health effects. This work is one of the most comprehensive surveys in Europe of S. aureus occurrence and determinants among widely distributed wild ungulates.
- Antimicrobial resistance phylodynamics and source attribution under a One Health frameworkPublication . Ramos, Beatriz; Cunha, Mónica Vieira; Rosalino, Luís Miguel do CarmoAntimicrobial resistance (AMR) is a significant public health threat and has recently been recognized as a One Health issue, reflecting the interconnected nature of human, animal, and environmental health. This thesis aimed to increase knowledge on the burden, drivers and transmission dynamics of AMR at the human-animal-environment interfaces, for which Staphylococcus aureus, wild ungulates and genomics were central. Wastewater-based surveillance (WBS) of urban and hospital sewersheds by shotgun metagenomics depicted microbiota signatures of public health importance, while showing that the urban resistome is not restricted to clinically relevant pathogens, being strongly related with the most consumed antimicrobials in Europe. Through molecular, phenotypic and ecological modelling analyses, we show that AMR in commensal Staphylococcus aureus strains from wild ungulates in Portugal is driven by agricultural land cover and livestock farming. We then generate and explore a large dataset of S. aureus draft genomes from wild ungulates to address with high resolution the hypotheses that wildlife colonization and AMR occurrence are related with human activities and that host adaptation is accompanied by genome diversification with phenotypic impacts. For source attribution purposes, we dissect host-informative mobile genetic elements (MGE) and, in parallel, perform ancestral host state reconstruction via phylodynamics. Based on cgMLST, we demonstrate high genomic similarity of S. aureus at the animal-human interface, with MGE biomarkers for host adaptation further supporting epidemiological connections. Phylodynamic inferences on relevant molecular types across Iberia indicate that several clonal lineages were widespread among humans before jumping to new hosts, highlighting recent spillover events from livestock to wildlife. Pangenome analyses retrieved S. aureus antimicrobial and heavy metals resistance determinants in the accessory genome. This thesis provides new insights on AMR transmission across interfaces, encouraging environmental and animal surveillance to help curb AMR, and confirms that genomic data-driven approaches are powerful to track AMR trends and drivers.
- Enterotoxin- and Antibiotic-Resistance-Encoding Genes Are Present in Both Coagulase-Positive and Coagulase-Negative Foodborne Staphylococcus StrainsPublication . Salamandane, Acácio; Oliveira, Jessica; Coelho, Miguel; Ramos, Beatriz; Cunha, Mónica V.; Malfeito-Ferreira, Manuel; Brito, LuisaFood poisoning by staphylococcal enterotoxins (SE) is a major cause of foodborne illness, often associated with coagulase-positive staphylococci (CPS). The increase in the number of methicillin-resistant Staphylococcus aureus (MRSA) strains is another major problem associated with CPS. However, reports of the association of SE and methicillin-resistant Staphylococcus with coagulase-negative staphylococci (CNS) are beginning to re-emerge. In this context, the aim of this study is to investigate the presence of staphylococcal enterotoxin genes and to characterize the phenotypic and genotypic antimicrobial resistance in 66 isolates of Staphylococcus spp. (47 CNS and 19 CPS) recovered from ready-to-eat (RTE) street food sold in Maputo, Mozambique. Seven virulence genes encoding SE (sea, seb, sec, sed and see) and two toxins (hlb and sak) were screened by multiplex PCR (MPCR). Antimicrobial resistance against 12 antibiotics was evaluated by the disk diffusion method. The presence of genes encoding resistance to penicillin, methicillin, vancomycin and erythromycin (blaZ, mecA, vancA, vancB, ermA, ermB and ermC) were also screened by PCR. At least one of the seven virulence genes assessed in this study was detected in 57.9% and 51% of CPS and CNS isolates, respectively. In CPS isolates, the most frequent gene was hlb (47.4%), followed by sec (15.8%) and sea, seb and sed genes with 5.3% each. In CNS isolates, the most frequent gene was sec (36.2%) followed by sak (17%), hlb (14.9%), sed (12.8%) and seb (6.4%). Five of the twelve CPS in which virulence genes were detected were also antibiotic-resistant. All the CNS isolates harboring virulence genes (n = 27, 57.4%) were antimicrobial-resistant. The prevalence of multidrug resistance was higher (59.6%) in CNS than in CPS (26.3%) isolates. Regarding the presence of antibiotic-resistance genes, blaZ (penicillin-resistant) was the most frequent in both CPS (42.1%) and CNS (87.2%), followed by the mecA (encoding methicillin resistance) and vancA genes (vancomycin-resistant), which represented 36.8% and 31.6% in CPS isolates and 46.8% in CNS isolates, respectively. The prevalence of vancomycin-resistant staphylococci has been increasing worldwide and, to our knowledge, this is the first study to report the occurrence of vancomycin-resistant staphylococci in Mozambique. These results emphasize the need to investigate CNS isolates in parallel with CPS, as both constitute public health hazards, given their potential to produce SE and spread antimicrobial resistance genes.
- Estimates of the global and continental burden of animal tuberculosis in key livestock species worldwide: A meta-analysis studyPublication . Ramos, Beatriz; Pereira, André C.; Reis, Ana C.; Cunha, Mónica V.Zoonotic animal tuberculosis (TB) is a One Health paradigm infectious disease, caused by Mycobacterium tuberculosis complex bacteria, that affects different host species with varying levels of management. In most developed countries, official surveillance and control strategies support the longitudinal reporting of herd and/or animal prevalence. However, for under resourced countries without surveillance plans, this information may be obtained from cross-sectional studies only. The objective of this meta-analysis was to perform a worldwide estimate of the overall prevalence of animal TB in different livestock species whose importance in production systems varies according to the region of the world. The ISI's Web of Science and Google Scholar were searched combining keywords and related database-specific subject terms to identify relevant cohort or cross-sectional work published in this topic. A total of 443 articles were retrieved, screened, and a final set of 182 references included. Potential sources of variation were investigated using subgroup analyses and meta-regression. Prevalence estimates in five mammalian host groups were stratified according to host species, host characteristics, anatomical localization of lesions, sample size, geographical location, and diagnostic tests. The multivariable meta-regression analysis accounted for a range between 0% (farmed wild boar) and 68.71% (camelids) of the overall observed heterogeneity, indicating that the pondered predictors partially explain the observed variability. Differences in the overall prevalence of TB across hosts were small, with most groups showing values around 10%, except farmed wild boar (41%). The sample size emerged as an important moderator, with small size studies leading to the overestimation of prevalence. TB prevalence rates were very heterogeneous across continents and depended on the host, with lower values (below 10%) in Africa and Asia, while North America (33.6%, cattle), Europe (51%, goats), and South America (85.7%, pigs) exhibited higher rates, possibly related to greater densities of specific host groups managed on more intensive production systems. Stratification by diagnostic tests evidenced heterogeneous prevalence rates depending on the host group, possibly reflecting differences in test performance across different hosts. Results from this study highlight different TB burden scenarios, pinpointing host groups and diagnostics that should be prioritized in surveillance systems in different regions, thus providing policy-relevant information to catalyse TB control in settings with lower installed capacity and better resource allocation at the human-animal-environment interface.
- Genomic epidemiology of Staphylococcus aureus from the Iberian Peninsula highlights the expansion of livestock associated-CC398 towards wildlifePublication . Ramos, Beatriz; Cunha, Mónica V.Staphylococcus aureus is a versatile pathobiont, exhibiting a broad host range, including humans, other mammals, and avian species. Host specificity determinants, virulence, and antimicrobial resistance genes are often shared by strains circulating at the animal-human interface. While transmission dynamics studies have shown strain exchange between humans and livestock, knowledge of the source, genetic diversification, and transmission drivers of S. aureus in wildlife lag behind. In this work, we explore a wide array of S. aureus genomes from different sources in the Iberian Peninsula to understand population structure, gene content and niche adaptation at the human-livestock-wildlife nexus. Through Bayesian inference, we address the hypothesis that S. aureus strains in wildlife originate from humanized landscapes, either from contact with humans or through interactions with livestock. Phylogenetic reconstruction applied to whole genome sequence data was completed with a dataset of 450 isolates featuring multiple clones from the 1990–2022 period and a subset of CC398 strains representing the 2008–2022 period. Phylodynamic signatures of S. aureus from the Iberian Peninsula suggest widespread circulation of most clones among humans before jumping to other hosts. The number of transitions of CC398 strains within each host category (human, livestock, wildlife) was high (88.26 %), while the posterior probability of transitions from livestock to wildlife was remarkably high (0.99). Microbial genome-wide association analysis did not evidence genome rearrangements nor biomarkers suggesting S. aureus niche adaptation to wildlife, thus supporting recent spill overs. Altogether, our findings indicate that S. aureus isolates collected in the past years from wildlife most likely represent multiple introduction events from livestock. The clonal origin of CC398 and its potential to disseminate and evolve through different animal host species are highlighted, calling for management practices at the livestock-wildlife axis to improve biosecurity and thus restrict S. aureus transmission and niche expansion along gradients of human influence.
- Global trends of epidemiological research in livestock tuberculosis for the last four decadesPublication . Reis, Ana C.; Ramos, Beatriz; Pereira, André C.; Cunha, Mónica V.Animal tuberculosis (TB) caused by Mycobacterium tuberculosis complex (MTC) bacteria remains as one of the most significant infectious diseases of livestock, despite decades of eradication programmes and research efforts, in an era where the livestock sector is among the most important and rapidly expanding commercial agricultural segments worldwide. This work provides a global overview of the spatial and temporal trends of reported scientific knowledge of TB in livestock, aiming to gain insights into research subtopics within the animal TB epidemiology domain and to highlight territorial inequalities regarding data reporting and research outputs over the years. To deliver such information, peer-reviewed reports of TB studies in livestock were retrieved from the Web of Science and Google Scholar, systematized and dissected. The validated data set contained 443 occurrence observations, covering the 1981-2020 period (39 years). We highlight a clear move towards transdisciplinary areas and the One Health approach, with a global temporal increase in publications combining livestock with wildlife and/or human components, which reflect the importance of non-prototypical hosts as key to understanding animal TB. It becomes evident that cattle is the main host across works from all continents; however, many regions remain poorly surveyed. TB research in livestock in low-/middle-income countries is markedly growing, reflecting changes in animal husbandry, but also mirroring the globalization era, with a marked increase in international collaboration and capacitation programmes for scientific and technological development. This review gives an overview of the most prolific continents, countries and research fields in animal TB epidemiology, clearly outlining knowledge gaps and key priority topics. The estimated growth trend of livestock production until 2050, particularly in Asia and Africa, in response to human population growth and animal-protein demand, will require further investment in early surveillance and adaptive research to accommodate the higher diversity of livestock species and MTC members and raising the possibility to fine-tune funding schemes.
- Metagenomic profiling of raw wastewater in Portugal highlights microbiota and resistome signatures of public health interest beyond the usual suspectsPublication . Ramos, Beatriz; Lourenço, Artur B.; Monteiro, Silvia; Santos, Ricardo; Cunha, Mónica V.In response to the rapid emergence and dissemination of antimicrobial resistant bacteria (ARB) and genes (ARGs), integrated surveillance systems are needed to address antimicrobial resistance (AMR) within the One Health Era. Wastewater analyses enable biomarker monitoring at the sewershed level, offering timely insights into pathogen circulation and ARB/ARGs trends originating from different compartments. During two consecutive epidemic waves of the COVID-19 pandemic in Portugal, taxonomic and functional composition of raw urban wastewater from two wastewater treatment plants (WWTPs) representing one million in equivalent population, located in the main urban areas of the country, were profiled by shotgun metagenomics. Hospital wastewater from two central hospitals located in the WWTPs catchment areas were also sequenced. The resistome and virulome were profiled using metagenomic assemblies without taxonomic constraint, and then specifically characterized for ESKAPE pathogens. Urban and hospital wastewater exhibited specific microbiota signatures, Pseudomonadota dominated in the first and Bacteroidota in the latter. Correlation network analyses highlighted 85 (out of top 100) genera co-occurring across samples. The most frequent ARGs were classified in the multidrug, tetracyclines, and Macrolides, Lincosamides, Streptogramins (MLS) classes. Links established between AMR determinants and bacterial hosts evidenced that the diversity and abundance of ARGs is not restricted to ESKAPE, being also highly predominant among emergent enteropathogens, like Aeromonas and Aliarcobacter, or in the iron (II) oxidizer Acidovorax. The Aliarcobacter genus accumulated high abundance of sulphonamides and polymyxins ARGs, while Acinetobacter and Aeromonas hosted the highest abundance of ARGs against beta-lactams. Other bacteria (e.g. Clostridioides, Francisella, Vibrio cholerae) and genes (e.g. vanA-type vancomycin resistance) of public health interest were detected, with targeted monitoring efforts being needed to establish informative baseline data. Altogether, results highlight that wastewater monitoring is a valuable component of pathogen and AMR surveillance in healthy populations, providing a community-representative snapshot of public health trends beyond priority pathogens.
- Non-Tuberculous Mycobacteria: Molecular and Physiological Bases of Virulence and Adaptation to Ecological NichesPublication . Pereira, André C.; Ramos, Beatriz; Reis, Ana C.; Cunha, Mónica V.Non-tuberculous mycobacteria (NTM) are paradigmatic colonizers of the total environment, circulating at the interfaces of the atmosphere, lithosphere, hydrosphere, biosphere, and anthroposphere. Their striking adaptive ecology on the interconnection of multiple spheres results from the combination of several biological features related to their exclusive hydrophobic and lipid-rich impermeable cell wall, transcriptional regulation signatures, biofilm phenotype, and symbiosis with protozoa. This unique blend of traits is reviewed in this work, with highlights to the prodigious plasticity and persistence hallmarks of NTM in a wide diversity of environments, from extreme natural milieus to microniches in the human body. Knowledge on the taxonomy, evolution, and functional diversity of NTM is updated, as well as the molecular and physiological bases for environmental adaptation, tolerance to xenobiotics, and infection biology in the human and non-human host. The complex interplay between individual, species-specific and ecological niche traits contributing to NTM resilience across ecosystems are also explored. This work hinges current understandings of NTM, approaching their biology and heterogeneity from several angles and reinforcing the complexity of these microorganisms often associated with a multiplicity of diseases, including pulmonary, soft-tissue, or milliary. In addition to emphasizing the cornerstones of knowledge involving these bacteria, we identify research gaps that need to be addressed, stressing out the need for decision-makers to recognize NTM infection as a public health issue that has to be tackled, especially when considering an increasingly susceptible elderly and immunocompromised population in developed countries, as well as in low- or middle-income countries, where NTM infections are still highly misdiagnosed and neglected.