1,720,984 research outputs found
Achromobacter spp. in Cystic Fibrosis Patients: A Genomic-Based Approach to Unravel Microbe-Host Adaptation
Full text linkBacteria belonging to the genus Achromobacter are widely distributed in natural environments and have been recognized as emerging nosocomial pathogens for their contribution to a wide range of human infections. Achromobacter spp. can establish chronic infections associated with inflammation, produce biofilm, resist common disinfectants, readily acquire antibiotic resistance and outcompete resident microbiota. In particular, cystic fibrosis (CF) patients with lung disease are the most frequently colonized and infected by Achromobacter species usually developing persistent respiratory tract infections. In the last five years the number of publications regarding these pathogens has doubled in comparison to the preceding five-year period and their whole genome sequencing data availability has seen a steep increase, underlining both the growing research interest for these microorganisms as well as their emergence in the clinical setting. Nonetheless, many clinical aspects and pathogenic mechanisms still remain to be elucidated. The main focus of this thesis has been to unravel underlying key processes and to investigate the adaptive mechanisms exploited by these microorganisms during lung infection in CF patients. This has been pursued by analysing both genomic and phenotypic data of 103 Achromobacter spp. clinical isolates from 40 CF patients followed at the CF centres in Verona (Italy), Rome (Italy), and Copenhagen (Denmark). The work presented in this thesis provides new knowledge on the onset of Achromobacter spp. infections and their adaptation to the CF lung environment. With further genomic and phenotypic studies it will be possible to translate these results into the clinical setting, leading to better predictions of the infection course and improvement of treatment strategies to the benefit of CF patients
Start 2024 by asking: 'Why do science?'
No full textStep back from the usual lab-meeting format, and ask yourself and your colleagues why you all do what you do, say Mirko Treccani and Laura Veschetti
Microbial genomes metadata on public repositories: friends or foes?
No full textMotivation: Genome sequences uploaded and stored on public repositories are of crucial importance for a plethora of microbial analyses, among them: genomes comparison, phylogenetic analysis and species identification. In particular, microbial genomic sequences are uploaded by laboratories all around the world and metadata input is left to the discretion of the submitter. Based on our experience, we want to raise attention to the fact that metadata is not always fully correct – even for relevant information like taxonomical classification, which could still prove to be difficult for some microorganisms in the wet-lab. Therefore, we encourage researchers to perform some pre-analytical quality control steps before running downstream analyses. Methods: Klebsiella michiganensis and Achromobacter xylosoxidans complete assembly sequences were downloaded from NCBI RefSeq (respectively n=350 downloaded on 05-11-2021, and n=142 downloaded on 13-11-2019). Average Nucleotide Identity (ANI), which is a measure of nucleotide-level genomic similarity between the coding regions of two genomes, was calculated using fastANI v1.33 tool. Genomes showing ANI>=95% were considered as belonging to the same species. R version 4.1.1, pheatmap and colorspace R packages were used for ANI analyses results visualization purposes. Results: We performed an in silico taxonomical analysis of publicly available microbial genomes belonging to two bacterial species: Klebsiella michiganensis and Achromobacter xylosoxidans. We chose to perform such analysis focusing on these species since they both are opportunistic pathogens – i.e. microorganisms that do not usually infect healthy hosts, but establish infections in immunodepressed individuals or patients with underlying diseases – that contribute to the spread of antibiotic resistance in nosocomial settings. The analysis results (Figure 1) indicate that 9% of K. michiganensis genomes (n=31/350) were misclassified as belonging to this species, in fact they showed ANI<95% when compared to all the other genomic sequences. Moreover, as regards A. xylosoxidans, we found that 62% of genomes (n=88/142) resulted as misclassified. In conclusion, we found discrepancies among the reported taxonomic classification at species level and ANI results, suggesting a probable misclassification of some microorganisms that might compromise downstream analyses. In light of these results, we strongly suggest to perform pre-analytical quality control steps to ensure the correctness of taxonomical information. Examples of such quality controls are ANI calculation and 16S rRNA sequence analysis (same species if identity>98%) for species evaluation, or in silico multi-locus sequence typing (also known as MLST, MLST schemes for each species are available at https://pubmlst.org) for sequence type classification
The BioVRPi project: a valuable and sustainable alternative for genomic analysis
Full text linkSince 2012, the Raspberry Pi Foundation has started developing pocket-sized and low-cost devices, originally meant to teach computer science in developing Countries. Its growing interest and constant improvement led Raspberry Pi devices to find different applications and to suit the needs of various research areas. In the previous years, different researchers already reported applications of Raspberry Pi devices in bioinformatics, such as basic train- ing and proteomics. In the beginning of 2021, we gave birth to BioVRPi, a project which aims to develop and offer a low-cost and stable bioinformatic environment for students and re- searchers involved in the genomics and transcriptomics fields. We evaluated performances and software compatibilities of different scenarios, focusing on Genome-Wide Association Studies for complex traits in Homo sapiens, transcriptomic analyses on RNA-seq data from Strongyloides stercoralis samples and alignment of small organisms, such as SARS-CoV-2 (virus), Escherichia Coli (bacterium) and Caenorhabditis elegans (nematode). Results from both the bioinformatic and benchmarking analyses showed that Raspberry Pi devices are capable of accomplishing different bioinformatic tasks in terms of results and performances. Moreover, they proved to be a valuable low-cost and sustainable alternative, in accordance with the United Nation 2030 Agenda, to answer the needs and the challenges of the current socio-economic situation
The Interplay between Microbiota and Human Complex Traits
Full text linkMicroorganisms have been one of the most influential drivers propelling some of the greatest environmental and evolutionary changes in the landscape and biology of the entire planet [...]
Genomic Instability Evolutionary Footprints on Human Health: Driving Forces or Side Effects?
Full text linkIn this work, we propose a comprehensive perspective on genomic instability comprising not only the accumulation of mutations but also telomeric shortening, epigenetic alterations and other mechanisms that could contribute to genomic information conservation or corruption. First, we present mechanisms playing a role in genomic instability across the kingdoms of life. Then, we explore the impact of genomic instability on the human being across its evolutionary history and on present-day human health, with a particular focus on aging and complex disorders. Finally, we discuss the role of non-coding RNAs, highlighting future approaches for a better living and an expanded healthy lifespan
Genomic characterization of Achromobacter species isolates from chronic and occasional lung infection in cystic fibrosis patients
Full text linkAchromobacter species are increasingly being detected in cystic fibrosis (CF) patients, where they can establish chronic infections by adapting to the lower airway environment. To better understand the mechanisms contributing to a successful colonization by Achromobacter species, we sequenced the whole genome of 54 isolates from 26 patients with occasional and early/late chronic lung infection. We performed a phylogenetic analysis and compared virulence and resistance genes, genetic variants and mutations, and hypermutability mechanisms between chronic and occasional isolates. We identified five Achromobacter species as well as two non-affiliated genogroups (NGs). Among them were the frequently isolated Achromobacter xylosoxidans and four other species whose clinical importance is not yet clear: Achromobacter insuavis, Achromobacter dolens, Achromobacter insolitus and Achromobacter aegrifaciens. While A. insuavis and A. dolens were isolated only from chronically infected patients and A. aegrifaciens only from occasionally infected patients, the other species were found in both groups. Most of the occasional isolates lacked functional genes involved in invasiveness, chemotaxis, type 3 secretion system and anaerobic growth, whereas the great majority (>60%) of chronic isolates had these genomic features. Interestingly, almost all (n=22/23) late chronic isolates lacked functional genes involved in lipopolysaccharide production. Regarding antibiotic resistance, we observed a species-specific distribution of blaOXA genes, confirming what has been reported in the literature and additionally identifying blaOXA-2 in some A. insolitus isolates and observing no blaOXA genes in A. aegrifaciens or NGs. No significant difference in resistance genes was found between chronic and occasional isolates. The results of the mutator genes analysis showed that no occasional isolate had hypermutator characteristics, while 60% of early chronic (<1 year from first colonization) and 78% of late chronic (>1 year from first colonization) isolates were classified as hypermutators. Although all A. dolens, A. insuavis and NG isolates presented two different mutS genes, these seem to have a complementary rather than compensatory function. In conclusion, our results show that Achromobacter species can exhibit different adaptive mechanisms and some of these mechanisms might be more useful than others in establishing a chronic infection in CF patients, highlighting their importance for the clinical setting and the need for further studies on the less clinically characterized Achromobacter species
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
- …
