| 1. |
- Jaén-Luchoro, D., et al.
(författare)
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Complete genome sequence of Mycobacterium chelonae type strain CCUG 47445, a rapidly growing species of nontuberculous mycobacteria
- 2016
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Ingår i: Genome Announcements. - 2169-8287. ; 4:3
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Tidskriftsartikel (refereegranskat)abstract
- Mycobacterium chelonae strains are ubiquitous rapidly growing mycobacteria associated with skin and soft tissue infections, cellulitis, abscesses, osteomyelitis, catheter infections, disseminated diseases, and postsurgical infections after implants with prostheses, transplants, and even hemodialysis procedures. Here, we report the complete genome sequence of M. chelonae type strain CCUG 47445. © 2016 Jaén-Luchoro et al.
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| 2. |
- Salvà-Serra, Francisco, 1989, et al.
(författare)
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Complete genome sequences of Streptococcus pyogenes type strain reveal 100%-match between PacBio-solo and Illumina-Oxford Nanopore hybrid assemblies
- 2020
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 10:1
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Tidskriftsartikel (refereegranskat)abstract
- We present the first complete, closed genome sequences of Streptococcus pyogenes strains NCTC 8198(T) and CCUG 4207(T), the type strain of the type species of the genus Streptococcus and an important human pathogen that causes a wide range of infectious diseases. S. pyogenes NCTC 8198(T) and CCUG 4207(T) are derived from deposit of the same strain at two different culture collections. NCTC 8198(T) was sequenced, using a PacBio platform; the genome sequence was assembled de novo, using HGAP. CCUG 4207(T) was sequenced and a de novo hybrid assembly was generated, using SPAdes, combining Illumina and Oxford Nanopore sequence reads. Both strategies yielded closed genome sequences of 1,914,862 bp, identical in length and sequence identity. Combining short-read Illumina and long-read Oxford Nanopore sequence data circumvented the expected error rate of the nanopore sequencing technology, producing a genome sequence indistinguishable to the one determined with PacBio. Sequence analyses revealed five prophage regions, a CRISPR-Cas system, numerous virulence factors and no relevant antibiotic resistance genes. These two complete genome sequences of the type strain of S. pyogenes will effectively serve as valuable taxonomic and genomic references for infectious disease diagnostics, as well as references for future studies and applications within the genus Streptococcus.
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| 3. |
- Salva-Serra, Francisco, 1989, et al.
(författare)
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Comparative genomics of Stutzerimonas balearica (Pseudomonas balearica): diversity, habitats, and biodegradation of aromatic compounds
- 2023
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Ingår i: Frontiers in Microbiology. - 1664-302X. ; 14
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Tidskriftsartikel (refereegranskat)abstract
- Stutzerimonas balearica (Pseudomonas balearica) has been found principally in oil-polluted environments. The capability of S. balearica to thrive from the degradation of pollutant compounds makes it a species of interest for potential bioremediation applications. However, little has been reported about the diversity of S. balearica. In this study, genome sequences of S. balearica strains from different origins were analyzed, revealing that it is a diverse species with an open pan-genome that will continue revealing new genes and functionalities as the genomes of more strains are sequenced. The nucleotide signatures and intra- and inter-species variation of the 16S rRNA genes of S. balearica were reevaluated. A strategy of screening 16S rRNA gene sequences in public databases enabled the detection of 158 additional strains, of which only 23% were described as S. balearica. The species was detected from a wide range of environments, although mostly from aquatic and polluted environments, predominantly related to petroleum oil. Genomic and phenotypic analyses confirmed that S. balearica possesses varied inherent capabilities for aromatic compounds degradation. This study increases the knowledge of the biology and diversity of S. balearica and will serve as a basis for future work with the species.
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| 4. |
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| 5. |
- Crespi, S., et al.
(författare)
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Legionella maioricensis sp. nov., a new species isolated from the hot water distribution systems of a hospital and a shopping center during routine sampling
- 2023
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Ingår i: International Journal of Systematic and Evolutionary Microbiology. - : Microbiology Society. - 1466-5026 .- 1466-5034. ; 73:1
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Tidskriftsartikel (refereegranskat)abstract
- Two Legionella- like strains isolated from hot water distribution systems in 2012 have been characterized phenotypically, bio-chemically and genomically in terms of DNA relatedness. Both strains, HCPI- 6T and EUR- 108, exhibited biochemical pheno-typic profiles typical of Legionella species. Cells were Gram-negative motile rods which grew on BCYE alpha agar but not on blood agar and displayed phenotypic characteristics typical of the family Legionellaceae, including a requirement for L-cysteine and testing catalase positive. Both strains were negative for oxidase, urease, nitrate reduction and hippurate negative, and non -fermentative. The major ubiquinone was Q12 (59.4 % HCPI- 6T) and the dominant fatty acids were C16:1 omega 7c (28.4 % HCPI- 6T, 216 % EUR- 108), C16: 0 iso (222.5 % and 213 %) and C15: 0 anteiso (19.5 % and 223.5 %, respectively). The percent G+C content of genomic DNA was determined to be 39.3 mol %. The 16S rRNA gene, mip sequence and comparative genome sequence -based analyses (average nucleotide identity, ANI; digital DNA-DNA hybridization, dDDH; and phylogenomic treeing) demonstrated that the strains represent a new species of the genus Legionella. The analysis based on the 16S rRNA gene sequences showed that the sequence similarities for both strains ranged from 98.8-90.1 % to other members of the genus. The core genome- based phylogenomic tree (protein-concatemer tree based on concatenation of 418 proteins present in single copy) revealed that these two strains clearly form a separate cluster within the genus Legionella. ANI and dDDH values confirmed the distinctiveness of the strains. Based on the genomic, genotypic and phenotypic findings from a polyphasic study, the isolates are considered to represent a single novel species, for which the name Legionella maioricensis sp. nov. is proposed. The type strain is HCPI- 6T (=CCUG 75071T=CECT 30569T).
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| 6. |
- Fernández-Juárez, V., et al.
(författare)
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Everything Is Everywhere: Physiological Responses of the Mediterranean Sea and Eastern Pacific Ocean Epiphyte Cobetia Sp. to Varying Nutrient Concentration
- 2022
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Ingår i: Microbial Ecology. - : Springer Science and Business Media LLC. - 0095-3628 .- 1432-184X. ; 83:2, s. 296-313
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Tidskriftsartikel (refereegranskat)abstract
- Bacteria are essential in the maintenance and sustainment of marine environments (e.g., benthic systems), playing a key role in marine food webs and nutrient cycling. These microorganisms can live associated as epiphytic or endophytic populations with superior organisms with valuable ecological functions, e.g., seagrasses. Here, we isolated, identified, sequenced, and exposed two strains of the same species (i.e., identified as Cobetia sp.) from two different marine environments to different nutrient regimes using batch cultures: (1) Cobetia sp. UIB 001 from the endemic Mediterranean seagrass Posidonia oceanica and (2) Cobetia sp. 4B UA from the endemic Humboldt Current System (HCS) seagrass Heterozostera chilensis. From our physiological studies, both strains behaved as bacteria capable to cope with different nutrient and pH regimes, i.e., N, P, and Fe combined with different pH levels, both in long-term (12days (d)) and short-term studies (4 d/96h (h)). We showed that the isolated strains were sensitive to the N source (inorganic and organic) at low and high concentrations and low pH levels. Low availability of phosphorus (P) and Fe had a negative independent effect on growth, especially in the long-term studies. The strain UIB 001 showed a better adaptation to low nutrient concentrations, being a potential N2-fixer, reaching higher growth rates (μ) than the HCS strain. P-acquisition mechanisms were deeply investigated at the enzymatic (i.e., alkaline phosphatase activity, APA) and structural level (e.g., alkaline phosphatase D, PhoD). Finally, these results were complemented with the study of biochemical markers, i.e., reactive oxygen species (ROS). In short, we present how ecological niches (i.e., MS and HCS) might determine, select, and modify the genomic and phenotypic features of the same bacterial species (i.e., Cobetia spp.) found in different marine environments, pointing to a direct correlation between adaptability and oligotrophy of seawater. © 2021, The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.
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| 7. |
- Jaen-Luchoro, Daniel, et al.
(författare)
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First insights into a type II toxin-antitoxin system from the clinical isolate Mycobacterium sp MHSD3, similar to epsilon/zeta systems
- 2017
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Ingår i: Plos One. - : Public Library of Science (PLoS). - 1932-6203. ; 12:12
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Tidskriftsartikel (refereegranskat)abstract
- A putative type II toxin-antitoxin (TA) system was found in the clinical isolate Mycobacterium sp. MHSD3, a strain closely related to Mycobacterium chelonae. Further analyses of the protein sequences of the two genes revealed the presence of domains related to a TA system. BLAST analyses indicated the presence of closely related proteins in the genomes of other recently published M. chelonae strains. The functionality of both elements of the TA system was demonstrated when expressed in Escherichia coli cells, and the predicted structure of the toxin is very similar to those of well-known zeta-toxins, leading to the definition of a type II TA system similar to epsilon/zeta TA systems in strains that are closely related to M. chelonae.
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| 8. |
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| 9. |
- Salvà-Serra, Francisco, 1989, et al.
(författare)
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Proteotyping for Rapid Identifications of Clinically-Relevant Infectious Bacteria
- 2016
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Ingår i: Programme of the XXXV ECCO Meeting 2016.
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Aims The development and application of novel identifications and diagnostics of pathogenic bacteria, virulence and antibiotic resistance factors, to enhance treatment of infectious diseases and to address the pandemic of antimicrobial resistance (1). To apply mass spectrometry (MS)-based ‘proteotyping’, a rapid proteomic-genomic method to identify and use cell biomarkers for pathogen identification and detection of targeted metabolic functions (www.tailored-treatment.eu/). Methods and results The proteins of intact bacterial cells or cell-fractions are bound to a membrane surface, using the patented (WO2006068619) Lipid-based Protein Immobilization (LPI) technology. Peptides are generated from bound proteins, using enzymatic digestion, separated and analyzed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). The MS profiles are compared to those of reference peptide sequences and the peptide sequences are compared against a curated in-house database of genome sequences. Conclusions Analyses of bacterial cell peptides identified protein biomarkers of infectious bacteria, at the species-level, virulence and antibiotic resistance factors. Model samples have been ‘proteotyped’, using well-characterized reference strains, and an enhanced whole-genome sequence database, to demonstrate ‘proof-of-concept’, and the method been applied directly to the analyses of clinical samples, without prior cultivation. Significance of study Proteotyping demonstrates the potential for proteomics-based analyses for detecting expressed genomic markers of bacterial species, virulence and antibiotic resistance, for the identifications and diagnostics of infectious microorganisms. References Cohen A, Bont L, Engelhard D, Moore E, Fernández D, Kreisberg-Greenblatt R, Oved K, Eden E, Hayes J (2015). A multifaceted 'omics' approach for addressing the challenge of antimicrobial resistance. Future Microbiol. 10:365-376
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