| 1. |
- Alygizakis, Nikiforos, et al.
(författare)
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Making waves: The NORMAN antibiotic resistant bacteria and resistance genes database (NORMAN ARB&ARG)–An invitation for collaboration to tackle antibiotic resistance
- 2024
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Ingår i: Water Research. - : Elsevier Ltd. - 0043-1354 .- 1879-2448. ; 257
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Forskningsöversikt (refereegranskat)abstract
- With the global concerns on antibiotic resistance (AR) as a public health issue, it is pivotal to have data exchange platforms for studies on antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) in the environment. For this purpose, the NORMAN Association is hosting the NORMAN ARB&ARG database, which was developed within the European project ANSWER. The present article provides an overview on the database functionalities, the extraction and the contribution of data to the database. In this study, AR data from three studies from China and Nepal were extracted and imported into the NORMAN ARB&ARG in addition to the existing AR data from 11 studies (mainly European studies) on the database. This feasibility study demonstrates how the scientific community can share their data on AR to generate an international evidence base to inform AR mitigation strategies. The open and FAIR data are of high potential relevance for regulatory applications, including the development of emission limit values / environmental quality standards in relation to AR. The growth in sharing of data and analytical methods will foster collaboration on risk management of AR worldwide, and facilitate the harmonization in the effort for identification and surveillance of critical hotspots of AR. The NORMAN ARB&ARG database is publicly available at: https://www.norman-network.com/nds/bacteria/.
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| 2. |
- Bogas, Diana, et al.
(författare)
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Applications of optical DNA mapping in microbiology
- 2017
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Ingår i: BioTechniques. - : Future Science Ltd. - 0736-6205 .- 1940-9818. ; 62:6, s. 255-267
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Forskningsöversikt (refereegranskat)abstract
- Optical mapping (OM) has been used in microbiology for the past 20 years, initially as a technique to facilitate DNA sequence-based studies; however, with decreases in DNA sequencing costs and increases in sequence output from automated sequencing platforms, OM has grown into an important auxiliary tool for genome assembly and comparison. Currently, there are a number of new and exciting applications for OM in the field of microbiology, including investigation of disease outbreaks, identification of specific genes of clinical and/or epidemiological relevance, and the possibility of single-cell analysis when combined with cell-sorting approaches. In addition, designing lab-on-a-chip systems based on OM is now feasible and will allow the integrated and automated microbiological analysis of biological fluids. Here, we review the basic technology of OM, detail the current state of the art of the field, and look ahead to possible future developments in OM technology for microbiological applications.
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| 3. |
- Eckert, EM, et al.
(författare)
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Every fifth published metagenome is not available to science.
- 2020
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Ingår i: PLoS biology. - : Public Library of Science (PLoS). - 1545-7885. ; 18:4
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Tidskriftsartikel (refereegranskat)abstract
- Have you ever sought to use metagenomic DNA sequences reported in scientific publications? Were you successful? Here, we reveal that metagenomes from no fewer than 20% of the papers found in our literature search, published between 2016 and 2019, were not deposited in a repository or were simply inaccessible. The proportion of inaccessible data within the literature has been increasing year-on-year. Noncompliance with Open Data is best predicted by the scientific discipline of the journal. The number of citations, journal type (e.g., Open Access or subscription journals), and publisher are not good predictors of data accessibility. However, many publications in high-impact factor journals do display a higher likelihood of accessible metagenomic data sets. Twenty-first century science demands compliance with the ethical standard of data sharing of metagenomes and DNA sequence data more broadly. Data accessibility must become one of the routine and mandatory components of manuscript submissions-a requirement that should be applicable across the increasing number of disciplines using metagenomics. Compliance must be ensured and reinforced by funders, publishers, editors, reviewers, and, ultimately, the authors.
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| 4. |
- Narciso-da-Rocha, Carlos, et al.
(författare)
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Diversity and antibiotic resistance of Acinetobacter spp. in water from the source to the tap.
- 2013
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Ingår i: Applied Microbiology and Biotechnology. - : Springer Science and Business Media LLC. - 0175-7598 .- 1432-0614. ; 97:1, s. 329-340
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Tidskriftsartikel (refereegranskat)abstract
- Acinetobacter spp. are ubiquitous bacteria in the environment. Acinetobacter spp. isolated from a municipal drinking water treatment plant and from connected tap water were identified to the species level on the basis of rpoB gene partial sequence analysis. Intraspecies variation was assessed based on the analysis of partial sequences of housekeeping genes (rpoB, gyrB, and recA). Antibiotic resistance was characterized using the disk diffusion method and isolates were classified as wild or non-wild type (non-WT), according to the observed phenotype. The strains of Acinetobacter spp. were related to 11 different validly published species, although three groups of isolates, presenting low rpoB sequence similarities with previously described species, may represent new species. Most of the isolates were related to the species A. johnsonii and A. lwoffii. These two groups, as well as others related to the species A. parvus and A. tjernbergiae, were detected in the water treatment plant and in tap water. Other strains, related to the species A. pittii and A. beijerinckii, were isolated only from tap water. Most of the isolates (80%) demonstrated wild type (WT) to all of the 12 antibiotics tested. Non-WT for tetracycline, meropenem, and ceftazidime, among others, were observed in water treatment plant or in tap water samples. Although, in general, this study suggests a low prevalence of acquired antibiotic resistance in water Acinetobacter spp., the potential of some species to acquire and disseminate resistance via drinking water is suggested.
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| 5. |
- Vaz-Moreira, Ivone, et al.
(författare)
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Microbacterium luticocti sp. nov., isolated from sewage sludge compost.
- 2008
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Ingår i: International journal of systematic and evolutionary microbiology. - : Microbiology Society. - 1466-5026 .- 1466-5034. ; 58:7, s. 1700-1704
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Tidskriftsartikel (refereegranskat)abstract
- Strain SC-087B(T), isolated from sewage sludge compost during a study of bacterial diversity in composts, was characterized. The isolate was a Gram-positive, short rod that was motile, catalase- and oxidase-negative and able to grow at 27-45 degrees C, pH 5.5-9.7 and in up to 10 % NaCl. The peptidoglycan was of the B2beta type, containing the characteristic amino acids ornithine, homoserine and hydroxyglutamic acid. The muramic acid residues of the peptidoglycan were partially glycolylated. The major cell-wall sugar was mannose; traces of xylose were also detected. The predominant fatty acids, comprising more than 70 % of the total, were anteiso-C(17 : 0) and anteiso-C(15 : 0), the major respiratory quinone was menaquinone-12 (MK-12) and the G+C content of the genomic DNA was 72 mol%. Based on analysis of the 16S rRNA gene sequence, the closest phylogenetic neighbours of strain SC-087B(T) were members of the family Microbacteriaceae, showing sequence similarity values of around 96 % with members of the species Microbacterium barkeri (96.0 %), Microbacterium gubbeenense (95.6 %) and Microbacterium indicum (95.7 %). The chemotaxonomic and phenotypic traits analysed supported the inclusion of this strain within the genus Microbacterium and the proposal of a novel species. The name Microbacterium luticocti sp. nov. is proposed and the type strain is SC-087B(T) (=DSM 19459(T)=CCUG 54537(T)).
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| 6. |
- Vaz-Moreira, Ivone, et al.
(författare)
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Shinella fusca sp. nov., isolated from domestic waste compost
- 2010
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Ingår i: International journal of systematic and evolutionary microbiology. - : Microbiology Society. - 1466-5026 .- 1466-5034. ; 60:1, s. 144-148
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Tidskriftsartikel (refereegranskat)abstract
- A bacterium, designated strain DC-196(T), isolated from kitchen refuse compost was analysed by using a polyphasic approach. Strain DC-196(T) was characterized as a Gram-negative short rod that was catalase- and oxidase-positive, and able to grow at 10-40 degrees C, pH 6-9 and in NaCl concentrations as high as 3 %. Chemotaxonomically, C(18 : 1) was observed to be the predominant cellular fatty acid and ubiquinone 10 (Q10) was the predominant respiratory quinone. The G+C content of the genomic DNA was determined to be 66 mol%. On the basis of the genotypic, phenotypic and chemotaxonomic characteristics, strain DC-196(T) was assigned to the genus Shinella, although with distinctive features. At the time of writing, 16S rRNA gene sequence similarities of 97.6-96.8 % and the low DNA-DNA hybridization values of 38.2-32.2 % with the type strains of the three recognized Shinella species confirmed that strain DC-196(T) represents a novel species of the genus, for which the name Shinella fusca sp. nov. is proposed (type strain DC-196(T)=CCUG 55808(T)=LMG 24714(T)).
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| 7. |
- Vaz-Moreira, Ivone, et al.
(författare)
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Sphingobium vermicomposti sp. nov., isolated from vermicompost.
- 2009
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Ingår i: International journal of systematic and evolutionary microbiology. - : Microbiology Society. - 1466-5026 .- 1466-5034. ; 59:12, s. 3145-3149
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Tidskriftsartikel (refereegranskat)abstract
- Strain VC-230(T) was isolated from homemade vermicompost produced from kitchen waste. The isolate was a Gram-negative-staining, catalase- and oxidase-positive, motile rod-shaped bacterium able to grow at 15-37 degrees C and pH 6-8. On the basis of 16S rRNA gene sequence analysis, strain VC-230(T) was determined to belong to the family Sphingomonadaceae by its clustering with type strains of the genus Sphingobium, with Sphingobium chlorophenolicum ATCC 33790(T) (97.7 %) and Sphingobium herbicidovorans DSM 11019(T) (97.4 %) as its closest neighbours. The polar lipid pattern, the presence of spermidine and ubiquinone 10, the predominance of the cellular fatty acids C(18 : 1)omega7c/9t/12t, C(16 : 1)omega7c and C(16 : 0) and the G+C content of the genomic DNA supported the affiliation of this organism to the genus Sphingobium. The phylogenetic, chemotaxonomic, phenotypic and DNA-DNA hybridization analyses verify that strain VC-230(T) represents a novel species, for which the name Sphingobium vermicomposti sp. nov. is proposed. The type strain is VC-230(T) (=CCUG 55809(T) =DSM 21299(T)).
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| 8. |
- Vredenburg, Jana, et al.
(författare)
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Quinolone-resistant Escherichia coli isolated from birds of prey in Portugal are genetically distinct from those isolated from water environments and gulls in Portugal, Spain and Sweden
- 2014
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Ingår i: Environmental Microbiology. - : Wiley. - 1462-2912 .- 1462-2920. ; 16:4, s. 995-1004
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Tidskriftsartikel (refereegranskat)abstract
- The influence of geographic distribution and type of habitat on the molecular epidemiology of ciprofloxacin resistant Escherichia coli was investigated. Ciprofloxacin resistant E. coli from wastewater, urban water with faecal contamination and faeces of gulls, pigeons and birds of prey, from Portugal, Spain and Sweden were compared based on multi-locus sequence typing (MLST) and quinolone resistance genetic determinants. Multi-locus sequence typing allowed the differentiation of E. coli lineages associated with birds of prey from those inhabiting gulls and waters. E. coli lineages of clinical relevance, such as the complex ST131, were detected in wastewater, streams and gulls in Portugal, Spain and Sweden. Quinolone resistance was due to gyrA and parC mutations, although distinct mutations were detected in birds of prey and in wastewater, streams and gulls isolates. These differences were correlated with specific MLST lineages, suggesting resistance inheritance. Among the plasmid-mediated quinolone resistance genes, only aac(6 ')-ib-cr and qnrS were detected in wastewater, streams and gulls isolates, but not in birds of prey. The horizontal transfer of the gene aac(6 ')-ib-cr could be inferred from its occurrence in different MLST lineages.
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