Molecular epidemiology, virulence traits and antimicrobial resistance signatures of Aeromonas spp. in the critically endangered Iberochondrostoma lusitanicum follow geographical and seasonal patterns

This research was supported by CIISA—Centro de Investigação Interdisciplinar em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, Project UIDB/00276/2020 (funded by FCT—Fundação para a Ciência e Tecnologia IP) and by MARE (MARE-ISPA), MARE/UIDB/MAR/04292/2020 and strategic project MARE/UIDP/MAR/04292/2020 (also funded by FCT). M.L.G. thanks funding by the University of Lisbon (PhD fellowship C10571K). T.A.M. and C.S.M. thank partial support by CEAUL (funded by FCT, Portugal, through the project UIDB/00006/2020).Despite the fact that freshwater fish populations are experiencing severe declines worldwide, our knowledge on the interaction between endangered populations and pathogenic agents remains scarce. In this study, we investigated the prevalence and structure of Aeromonas communities isolated from the critically endangered Iberochondrostoma lusitanicum, a model species for threatened Iberian leuciscids, as well as health parameters in this species. Additionally, we evaluated the virulence profiles, antimicrobial resistance signatures and genomic relationships of the Aeromonas isolates. Lesion prevalence, extension and body condition were deeply affected by location and seasonality, with poorer performances in the dry season. Aeromonas composition shifted among seasons and was also different across river streams. The pathogenic potential of the isolates significantly increased during the dry season. Additionally, isolates displaying clinically relevant antimicrobial resistance phenotypes (carbapenem and fluroquinolone resistance) were detected. As it inhabits intermittent rivers, often reduced to disconnected pools during the summer, the dry season is a critical period for I. lusitanicum, with lower general health status and a higher potential of infection by Aeromonas spp. Habitat quality seems a determining factor on the sustainable development of this fish species. Also, these individuals act as reservoirs of important antimicrobial resistant bacteria with potential implications for public health.Publisher PDFPeer reviewe

Mesophilic Aeromonas in threatened Iberian leuciscids : conservation and public health implications

Tese de Doutoramento em Ciências Veterinárias na Especialidade de Sanidade AnimalDespite the high risk of extinction of the Iberian leuciscids, the impact of bacterial diseases on their conservation is unknown. A comprehensive knowledge of the interaction between these species and pathogens, such as mesophilic Aeromonas, as well as the development of biosafety measures for ex situ programs, are considered essential for the success of their conservation. The main objectives of this thesis are the evaluation of the epidemiology of mesophilic Aeromonas in Iberochondrostoma lusitanicum, as well as the characterization of their antimicrobial resistance and virulence profiles, the detection of differences in the diversity of Aeromonas spp. of I. lusitanicum and Squalius pyrenaicus, the evaluation of the potential of biosecurity measures in the control of Aeromonas spp. in ex situ programs and testing the effect of climate change on Aeromonas spp. The results showed that I. lusitanicum presented lower general health status in the dry season, varying with location. Aeromonas communities varied between seasons and locations, while their pathogenic potential increased in the dry season. Relevant resistance phenotypes (carbapenems and fluoroquinolones) were detected. Furthermore, I. lusitanicum and S. pyrenaicus showed different levels of skin lesions, with S. pyrenaicus being the most affected species. Aeromonas communities differed between the two fish species. Additionally, the use of biosecurity measures suggests a decrease in the prevalence of Aeromonas spp. in ex situ programs, as well as its pathogenicity to fish, while an increase in antimicrobial resistance was observed throughout the program. Finally, climate change predicted by the International Panel on Climate Change for water temperature and pH influenced the growth, biofilm production and antimicrobial resistance profiles of Aeromonas spp. The current results clarify the epidemiology of mesophilic Aeromonas in threatened Iberian leuciscids and contribute to the establishment of adequate conservation measures.RESUMO - Apesar do elevado risco de extinção dos leuciscídeos ibéricos, desconhece-se o impacto das doenças bacterianas na sua conservação. Um conhecimento abrangente sobre a interação entre estas espécies e agentes patogénicos, como Aeromonas mesofílicas, bem como o desenvolvimento de medidas de biossegurança para programas ex situ, são considerados essenciais para o sucesso da sua conservação. Os principais objetivos desta tese são a avaliação da epidemiologia de Aeromonas mesofílicas em Iberocondrostoma lusitanicum, bem como a caracterização dos seus perfis de resistência antimicrobiana e virulência, a deteção de diferenças na diversidade de Aeromonas spp. de I. lusitanicum e Squalius pyrenaicus, a avaliação do potencial de medidas de biossegurança no controlo de Aeromonas spp. em programas ex situ e a testagem do efeito de alterações climáticas em Aeromonas spp. Os resultados mostraram que I. lusitanicum apresentaram estado geral de saúde inferior na época seca, variando com a localização. As comunidades de Aeromonas variaram entre épocas e localizações, enquanto o seu potencial patogénico aumentou na época seca. Foram detetados fenótipos de resistência relevantes (carbapenemos e fluroquinolonas). Além disso, I. lusitanicum e S. pyrenaicus apresentaram diferentes níveis de lesões cutâneas, sendo S. pyrenaicus a espécie mais afetada. As comunidades de Aeromonas diferiram entre as duas espécies de peixes. Adicionalmente, o uso de medidas de biossegurança sugere uma diminuição na prevalência de Aeromonas spp. em programas ex situ, bem como da sua patogenicidade para peixes, enquanto foi observado um aumento da resistência antimicrobiana ao longo do programa. Finalmente, as alterações climatéricas previstas pelo Painel Internacional sobre Mudanças Climáticas para a temperatura e pH da água influenciaram o crescimento, a produção de biofilme e os perfis de resistência antimicrobiana de Aeromonas spp. Os resultados atuais esclarecem sobre a epidemiologia de Aeromonas mesofílicas em leuciscídeos ibéricos ameaçados e contribuem para o estabelecimento de medidas de conservação adequadasN/

Integrated human exposure to air pollution

The book “Integrated human exposure to air pollution” aimed to increase knowledge about human exposure in different micro-environments, or when citizens are performing specific tasks, to demonstrate methodologies for the understanding of pollution sources and their impact on indoor and ambient air quality, and, ultimately, to identify the most effective mitigation measures to decrease human exposure and protect public health. Taking advantage of the latest available tools, such as internet of things (IoT), low-cost sensors and a wide access to online platforms and apps by the citizens, new methodologies and approaches can be implemented to understand which factors can influence human exposure to air pollution. This knowledge, when made available to the citizens, along with the awareness of the impact of air pollution on human life and earth systems, can empower them to act, individually or collectively, to promote behavioral changes aiming to reduce pollutants’ emissions. Overall, this book gathers fourteen innovative studies that provide new insights regarding these important topics within the scope of human exposure to air pollution. A total of five main areas were discussed and explored within this book and, hopefully, can contribute to the advance of knowledge in this field

Genomic analysis of diverse bacterial pathogens

Bacterial pathogens have been a historical scourge for the entirety of human existence but have been significantly thwarted since the 20th century due to the development of antibiotics. However, owing to the large selection pressure of antibiotics on bacterial populations, phenotypic antibiotic resistance from the development of vertically transmitted mutations and horizontally acquired antibiotic resistance genes (ARGs) is increasing. The sum has produced multidrug resistant organisms (MDROs) which have extremely limited treatment options. Epidemiological studies have determined that carbapenem resistant Enterobacteriaceae (CRE), Acinetobacter baumannii, and vancomycin resistant Enterococcus (VRE) are some of the most problematic MDRO infections. The advent of cost-effective and accurate next-generation sequencing has resulted in a proliferation of bacterial genomes available. ARGs, antibiotic resistance conferring single nucleotide polymorphism (SNPs), and virulence genes can be identified within an assembled genome by comparison to known databases. The combination of the genetic information encoded within the genome of an isolate along with metadata related to important phenotypes or clinical context can be used to identify trends in ARG carriage, evolution over time, and viii differences in gene burden. This information can also be used in understanding the effects of antibiotic treatment on multi organism infections such as bacterial vaginosis. My thesis intends to investigate features related to natural populations of bacterial isolates in the Enterobacteriaceae family and Acinetobacter baumannii in Chapters 2, 3, 4 and the Gram-positive organisms Enterococcus faecium, Gardnerella, and Corynebacterium in Chapters 5, 6, and 7. In Chapter 2 we identify the carbapenem resistance gene blaIMP-27 in a clinical isolate of carbapenem resistance Providencia rettgeri. We then acquired two blaIMP-27 bearing Proteus mirabilis and determine that one isolate (PM187) also has it on a plasmid. We were able to completely close the blaIMP-27 bearing plasmids pPR1 and pPM187 and determine that the local genetic context was similar but the background of the plasmids were different. In Chapter 3 we collect a cohort of longitudinally antibiotic resistant organisms recovered from hospital surfaces in the United States and Pakistan. We compare the phenotypic identification with the genomic identification to determine that several isolates represent novel taxonomic groups, we identify a severe degree of phenotypic antibiotic resistance in the collected important human pathogens and elucidate a network of ARGs common amongst the bacteria. Importantly, we demonstrate that E. faecium and A. baumannii co-occur greater than predicted by chance a lone and that laboratory strains of these organisms are capable of forming synergistic growth in biofilms. In Chapter 4 we collect a cohort of Klebsiella variicola from Washington University and use whole genome sequencing to determine the population structure of all publicly available K. variicola genomes and identify genes relevant for infection related phenotypes. We show that these differences may have a functional consequence as some K. variicola strains can be more competent uropathogens than Klebsiella pneumoniae. In Chapter 5 we compare linezolid resistance mechanisms within a cohort to VRE from the United States and Pakistan to determine that all of the US isolates were resistant due to SNPs in the 23S rRNA sequence, but the Pakistan isolates all had acquired ARGs. Two of six these ARGs were the limited scope efflux pumps optrA and poxtA but the other ARGs are novel variants of the cfr family. In Chapter 6 we analyze a set of publicly available Gardnerella vaginalis genomes and metatranscriptomes of women with bacterial vaginosis to determine that what is commonly considered a single species can be interpreted as 9 different species with differences in accessory genome function and varying presence in bacterial vaginosis cases. Different genomospecies are present at varying abundance and putative virulence genes have high expression values during infection. Finally, in chapter 7 we determine the effects of acquired daptomycin resistance on the biology of Corynebacterium striatum. In summation this work provides novel insights on the relatedness of important human pathogens to one another and the content of their genes relevant toward infection across a wide range of species

A comparative analysis employing a gene- and genome-centric metagenomic approach reveals changes in composition, function, and activity in waterworks with different treatment processes and source water in Finland

The emergence and development of next-generation sequencing technologies (NGS) has made the analysis of the water microbiome in drinking water distribution systems (DWDSs) more accessible and opened new perspectives in microbial ecology studies. The current study focused on the characterization of the water microbiome employing a gene- and genome-centric metagenomic approach to five waterworks in Finland with different raw water sources, treatment methods, and disinfectant. The microbial communities exhibit a distribution pattern of a few dominant taxa and a large representation of low-abundance bacterial species. Changes in the community structure may correspond to the presence or absence and type of disinfectant residual which indicates that these conditions exert selective pressure on the microbial community. The Archaea domain represented a small fraction (up to 2.5%) and seemed to be effectively controlled by the disinfection of water. Their role particularly in non-disinfected DWDS may be more important than previously considered. In general, non-disinfected DWDSs harbor higher microbial richness and maintaining disinfectant residual is significantly important for ensuring low microbial numbers and diversity. Metagenomic binning recovered 139 (138 bacterial and 1 archaeal) metagenome-assembled genomes (MAGs) that had a >50% completeness andPeer reviewe