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1.
Microorganisms ; 9(7)2021 Jul 18.
Artigo em Inglês | MEDLINE | ID: mdl-34361965

RESUMO

Clavibacter michiganensis subsp. michiganensis (Cmm) is the causal agent of bacterial canker of tomato. Differences in virulence between Cmm strains have been reported. The aim of this study was the characterization of nine Cmm strains isolated in Chile to reveal the causes of their differences in virulence. The virulence assays in tomato seedlings revealed different levels of severity associated with the strains, with two highly virulent strains and one causing only mild symptoms. The two most virulent showed increased cellulase activity, and no cellulase activity was observed in the strain causing mild symptoms. In three strains, including the two most virulent strains, PCR amplification of the 10 virulence genes analyzed was observed. In the strain causing mild symptoms, no amplification was observed for five genes, including celA. Sequence and cluster analyses of six virulence genes grouped the strains, as has been previously reported, except for gene pelA1. Gene sequence analysis from the genomes of five Chilean strains revealed the presence of deletions in the virulence genes, celB, xysA, pat-1, and phpA. The results of this study allow us to establish correlations between the differences observed in disease severity and the presence/absence of genes and deletions not previously reported.

2.
Artigo em Inglês | MEDLINE | ID: mdl-34342563

RESUMO

Following the International Committee on Systematics of Prokaryotes electronic discussion and vote on proposals to resolve the status of the Cyanobacteria in the prokaryotic nomenclature, we announce here the results of the ballot. We also present the emended versions of General Consideration 5 and Rules 18a, 24a and 30, based on the outcome of the ballot, to be included in the new revision of the International Code of Nomenclature of Prokaryotes.


Assuntos
Cianobactérias , Filogenia , Cianobactérias/classificação , Terminologia como Assunto
3.
Front Cell Infect Microbiol ; 11: 634215, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34381737

RESUMO

Bloodstream infections (BSIs), the presence of microorganisms in blood, are potentially serious conditions that can quickly develop into sepsis and life-threatening situations. When assessing proper treatment, rapid diagnosis is the key; besides clinical judgement performed by attending physicians, supporting microbiological tests typically are performed, often requiring microbial isolation and culturing steps, which increases the time required for confirming positive cases of BSI. The additional waiting time forces physicians to prescribe broad-spectrum antibiotics and empirically based treatments, before determining the precise cause of the disease. Thus, alternative and more rapid cultivation-independent methods are needed to improve clinical diagnostics, supporting prompt and accurate treatment and reducing the development of antibiotic resistance. In this study, a culture-independent workflow for pathogen detection and identification in blood samples was developed, using peptide biomarkers and applying bottom-up proteomics analyses, i.e., so-called "proteotyping". To demonstrate the feasibility of detection of blood infectious pathogens, using proteotyping, Escherichia coli and Staphylococcus aureus were included in the study, as the most prominent bacterial causes of bacteremia and sepsis, as well as Candida albicans, one of the most prominent causes of fungemia. Model systems including spiked negative blood samples, as well as positive blood cultures, without further culturing steps, were investigated. Furthermore, an experiment designed to determine the incubation time needed for correct identification of the infectious pathogens in blood cultures was performed. The results for the spiked negative blood samples showed that proteotyping was 100- to 1,000-fold more sensitive, in comparison with the MALDI-TOF MS-based approach. Furthermore, in the analyses of ten positive blood cultures each of E. coli and S. aureus, both the MALDI-TOF MS-based and proteotyping approaches were successful in the identification of E. coli, although only proteotyping could identify S. aureus correctly in all samples. Compared with the MALDI-TOF MS-based approaches, shotgun proteotyping demonstrated higher sensitivity and accuracy, and required significantly shorter incubation time before detection and identification of the correct pathogen could be accomplished.


Assuntos
Bacteriemia , Infecções Estafilocócicas , Bacteriemia/diagnóstico , Candida albicans , Escherichia coli , Humanos , Espectrometria de Massas por Ionização e Dessorção a Laser Assistida por Matriz , Infecções Estafilocócicas/diagnóstico , Staphylococcus aureus
4.
Artigo em Inglês | MEDLINE | ID: mdl-34191704

RESUMO

The Editorial Board for the International Code of Nomenclature of Prokaryotes (ICNP) has compiled proposed revisions of the ICNP. As outlined previously (Oren et al., Int J Syst Evol Microbiol 2021;71:004598; https://doi.org/10.1099/ijsem.0.004598) and to comply with Articles 13(b)(4) and 4(d) of the statutes of the International Committee on Systematics of Prokaryotes, a public discussion of the document will start on 1 July 2021, to last for 6 months. Here, we present the procedure for this discussion.


Assuntos
Classificação , Células Procarióticas/classificação , Terminologia como Assunto
5.
Artigo em Inglês | MEDLINE | ID: mdl-34161220

RESUMO

Following the International Committee on Systematics of Prokaryotes electronic discussion and vote on proposals to include the rank of phylum in the rules of the International Code of Nomenclature of Prokaryotes, we here announce the results of the ballot. We also present draft versions of the emended Rules 5b, 8, 15 and 22, based on the outcome of the ballot, to be included in the proposal for the preparation of a new revision of the International Code of Nomenclature of Prokaryotes.


Assuntos
Filogenia , Células Procarióticas/classificação , Terminologia como Assunto
6.
Artigo em Inglês | MEDLINE | ID: mdl-33605868

RESUMO

The International Journal of Systematic and Evolutionary Microbiology (IJSEM) will move to 'true continuous publication' during the first months of 2021 to modernize the workflow and align it with the current online-only nature of the journal. In the new format, articles will be cited using an article number rather than page numbering. The article number will be the Digital Object Identifier (DOI) suffix, i.e., the last six digits of the DOI. Benefits of the new system include streamlining in-house processes, hence, reducing time and costs, and speeding up the publication time of the final 'Version of Record'. Because of the new format of the IJSEM, it is necessary to emend Rule 24b (2) and Note 1 paragraph 3 of Rule 27 of the International Code of Nomenclature of Prokaryotes (ICNP) to regulate matters of priority for papers published after January 2021. We also propose adding another example to Note 2 of Rule 33b to clarify how nomenclatural authorities of names published in the IJSEM from 2021 onward must be cited.

7.
Artigo em Inglês | MEDLINE | ID: mdl-33300858

RESUMO

The Editorial Board of the International Code of Nomenclature of Prokaryotes here explains the proposed procedure towards the production of the next revision of the Prokaryotic Code, to include public discussion of a draft version, to be prepared by the editors, followed by balloting of the members of the International Committee on Systematics of Prokaryotes.

8.
Microorganisms ; 8(11)2020 Oct 29.
Artigo em Inglês | MEDLINE | ID: mdl-33137950

RESUMO

The genus Clavibacter has been associated largely with plant diseases. The aims of this study were to characterize the genomes and the virulence factors of Chilean C. michiganensis subsp. michiganensis strains VL527, MSF322 and OP3, and to define their phylogenomic positions within the species, Clavibacter michiganensis. VL527 and MSF322 genomes possess 3,396,632 and 3,399,199 bp, respectively, with a pCM2-like plasmid in strain VL527, with pCM1- and pCM2-like plasmids in strain MSF322. OP3 genome is composed of a chromosome and three plasmids (including pCM1- and pCM2-like plasmids) of 3,466,104 bp. Genomic analyses confirmed the phylogenetic relationships of the Chilean strains among C.michiganensis subsp. michiganensis and showed their low genomic diversity. Different virulence levels in tomato plants were observable. Phylogenetic analyses of the virulence factors revealed that the pelA1 gene (chp/tomA region)-that grouped Chilean strains in three distinct clusters-and proteases and hydrolases encoding genes, exclusive for each of the Chilean strains, may be involved in these observed virulence levels. Based on genomic similarity (ANIm) analyses, a proposal to combine and reclassify C. michiganensis subsp. phaseoli and subsp. chilensis at the species level, as C. phaseoli sp. nov., as well as to reclassify C. michiganensis subsp. californiensis as the species C. californiensis sp. nov. may be justified.

9.
Int J Syst Evol Microbiol ; 70(8): 4544-4554, 2020 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-32618559

RESUMO

The taxonomic status of six strains of Acinetobacter obtained from meat samples, collected from supermarkets in Porto, Portugal, was investigated using polyphasic analysis. Partial rpoB sequence similarities lower than 95 % to other Acinetobacter species with validly published names led to the hypothesis that these strains represented novel species. This was confirmed based on comparative multilocus sequence analysis, which included the gyrB, recA and 16S rRNA genes, revealing that these strains represented two coherent lineages that were distinct from each other and from all known species. The names Acinetobacter portensis sp. nov. (comprising four strains) and Acinetobacter guerrae sp. nov. (comprising two strains) are proposed for these novel species. The species status of these two groups was confirmed by low (below 95 %) whole-genome sequence average nucleotide identity values and low (below 70 %) digital DNA-DNA hybridization similarities between the whole-genome sequences of the proposed type strains of each novel species and the representatives of the known Acinetobacter species. Phylogenomic treeing from core genome analysis supported these results. The coherence of each new species lineage was supported by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry differentiation of the species at the protein level, by cellular fatty acid profiles, and by unique and differential combinations of metabolic and physiological properties shared by each novel species. The type strain of A. portensis sp. nov. is AC 877T (=CCUG 68672T=CCM 8789T) and the type strain of A. guerrae sp. nov. is AC 1271T (=CCUG 68674T=CCM 8791T).


Assuntos
Acinetobacter/classificação , Microbiologia de Alimentos , Carne/microbiologia , Filogenia , Acinetobacter/isolamento & purificação , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Genes Bacterianos , Tipagem de Sequências Multilocus , Hibridização de Ácido Nucleico , Portugal , RNA Ribossômico 16S/genética , Análise de Sequência de DNA
10.
Sci Rep ; 10(1): 11656, 2020 07 15.
Artigo em Inglês | MEDLINE | ID: mdl-32669560

RESUMO

We present the first complete, closed genome sequences of Streptococcus pyogenes strains NCTC 8198T and CCUG 4207T, 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 8198T and CCUG 4207T are derived from deposit of the same strain at two different culture collections. NCTC 8198T was sequenced, using a PacBio platform; the genome sequence was assembled de novo, using HGAP. CCUG 4207T 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.


Assuntos
Mapeamento Cromossômico , DNA Bacteriano/genética , Sequenciamento de Nucleotídeos em Larga Escala , Streptococcus pyogenes/genética , Fatores de Virulência/genética , Sequenciamento Completo do Genoma/métodos , Técnicas de Tipagem Bacteriana , Sequência de Bases , Sistemas CRISPR-Cas , DNA Bacteriano/metabolismo , Genoma Bacteriano , Nanoporos , Prófagos/genética , Análise de Sequência de DNA , Streptococcus pyogenes/classificação , Streptococcus pyogenes/virologia , Fatores de Virulência/metabolismo
11.
Int J Syst Evol Microbiol ; 70(6): 3639-3646, 2020 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-32501783

RESUMO

A Gram-stain-negative, microaerophilic, non-motile, rod-shaped bacterium strain designated PMP191FT, was isolated from a human peritoneal tumour. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the organism formed a lineage within the family Chitinophagaceae that was distinct from members of the genus Pseudoflavitalea (95.1-95.2 % sequence similarity) and Pseudobacter ginsenosidimutans (94.4 % sequence similarity). The average nucleotide identity values between strain PMP191FT and Pseudoflavitalea rhizosphaerae T16R-265T and Pseudobacter ginsenosidimutans Gsoil 221T was 68.9 and 62.3% respectively. The only respiratory quinone of strain PMP191FT was MK-7 and the major fatty acids were iso-C15 : 0, iso-C15 : 1 G and summed feature 3 (C16:1 ω7c and/or C16:1 ω6c). The polar lipids consisted of phosphatidylethanolamine and some unidentified amino and glycolipids. The G+C content of strain PMP191FT calculated from the genome sequence was 43.4 mol%. Based on phylogenetic, phenotypic and chemotaxonomic evidence, strain PMP191FT represents a novel species and genus for which the name Parapseudoflavitalea muciniphila gen. nov., sp. nov. is proposed. The type strain is PMP191FT (=DSM 104999T=ATCC BAA-2857T = CCUG 72691T). The phylogenetic analyses also revealed that Pseudobacter ginsenosidimutans shared over 98 % sequence similarly to members of the genus Pseudoflavitalea. However, the average nucleotide identity value between Pseudoflavitalea rhizosphaerae T16R-265T, the type species of the genus and Pseudobacter ginsenosidimutans Gsoil 221T was 86.8 %. Therefore, we also propose that Pseudobacter ginsenosidimutans be reclassified as Pseudoflavitalea ginsenosidimutans comb. nov.


Assuntos
Bacteroidetes/classificação , Neoplasias Peritoneais/microbiologia , Filogenia , Técnicas de Tipagem Bacteriana , Bacteroidetes/isolamento & purificação , Baltimore , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Glicolipídeos/química , Humanos , Fosfatidiletanolaminas/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Vitamina K 2/análogos & derivados , Vitamina K 2/química
12.
Artigo em Inglês | MEDLINE | ID: mdl-32509595

RESUMO

Correct identifications of isolates and strains of the Mitis-Group of the genus Streptococcus are particularly difficult, due to high genetic similarity, resulting from horizontal gene transfer and homologous recombination, and unreliable phenotypic and genotypic biomarkers for differentiating the species. Streptococcus pneumoniae and Streptococcus pseudopneumoniae are the most closely related species of the clade. In this study, publicly-available genome sequences for Streptococcus pneumoniae and S. pseudopneumoniae were analyzed, using a pangenomic approach, to find candidates for species-unique gene markers; ten species-unique genes for S. pneumoniae and nine for S. pseudopneumoniae were identified. These species-unique gene marker candidates were verified by PCR assays for identifying S. pneumoniae and S. pseudopneumoniae strains isolated from clinical samples. All determined species-level unique gene markers for S. pneumoniae were detected in all S. pneumoniae clinical isolates, whereas fewer of the unique S. pseudopneumoniae gene markers were present in more than 95% of the clinical isolates. In parallel, taxonomic identifications of the clinical isolates were confirmed, using conventional optochin sensitivity testing, targeted PCR-detection for the "Xisco" gene, as well as genomic ANIb similarity analyses for the genome sequences of selected strains. Using mass spectrometry-proteomics, species-specific peptide matches were observed for four of the S. pneumoniae gene markers and for three of the S. pseudopneumoniae gene markers. Application of multiple species-level unique biomarkers of S. pneumoniae and S. pseudopneumoniae, is proposed as a protocol for the routine clinical laboratory for improved, reliable differentiation, and identification of these pathogenic and commensal species.


Assuntos
Genômica , Streptococcus pneumoniae , Streptococcus , Genótipo , Streptococcus/genética , Streptococcus pneumoniae/genética
13.
Microorganisms ; 8(6)2020 Jun 13.
Artigo em Inglês | MEDLINE | ID: mdl-32545759

RESUMO

Escherichia coli strain CCUG 78773 is a virulent extended-spectrum ß-lactamase (ESBL)-producing ST131-O25b type strain isolated during an outbreak at a regional university hospital. The complete and closed genome sequence, comprising one chromosome (5,076,638 bp) and six plasmids (1718-161,372 bp), is presented. Characterization of the genomic features detected the presence of 59 potential antibiotic resistance factors, including three prevalent ß-lactamases. Several virulence associated elements were determined, mainly related with adherence, invasion, biofilm formation and antiphagocytosis. Twenty-eight putative type II toxin-antitoxin systems were found. The plasmids were characterized, through in silico analyses, confirming the two ß-lactamase-encoding plasmids to be conjugative, while the remaining plasmids were mobilizable. BLAST analysis of the plasmid sequences showed high similarity with plasmids in E. coli from around the world. Expression of many of the described virulence and AMR factors was confirmed by proteomic analyses, using bottom-up, liquid chromatography-tandem mass spectrometry (LC-MS/MS). The detailed characterization of E. coli strain CCUG 78773 provides a reference for the relevance of genetic elements, as well as the characterization of antibiotic resistance and the spread of bacteria harboring ESBL genes in the hospital environment.

14.
BMC Microbiol ; 20(1): 134, 2020 05 25.
Artigo em Inglês | MEDLINE | ID: mdl-32450819

RESUMO

BACKGROUND: Environmental surveillance of antibiotic resistance can contribute towards better understanding and management of human and environmental health. This study applied a combination of long-read Oxford Nanopore MinION and short-read Illumina MiSeq-based sequencing to obtain closed complete genome sequences of two CTX-M-producing multidrug-resistant Escherichia coli strains isolated from blue mussels (Mytilus edulis) in Norway, in order to understand the potential for mobility of the detected antibiotic resistance genes (ARGs). RESULTS: The complete genome sequence of strain 631 (E. coli sequence type 38) was assembled into a circular chromosome of 5.19 Mb and five plasmids (between 98 kb and 5 kb). The majority of ARGs cluster in close proximity to each other on the chromosome within two separate multidrug-resistance determining regions (MDRs), each flanked by IS26 transposases. MDR-1 carries blaTEM-1, tmrB, aac(3)-IId, aadA5, mph(A), mrx, sul1, qacEΔ1 and dfrA17; while MDR-2 harbors aph(3″)-Ib, aph(6)-Id, blaTEM-1, catA1, tet(D) and sul2. Four identical chromosomal copies of blaCTX-M-14 are located outside these regions, flanked by ISEc9 transposases. Strain 1500 (E. coli sequence type 191) exhibited a circular chromosome of 4.73 Mb and two plasmids (91 kb and 4 kb). The 91 kb conjugative plasmid belonging to IncI1 group carries blaCTX-M-15 and blaTEM-1 genes. CONCLUSION: This study confirms the efficacy of combining Nanopore long-read and Illumina short-read sequencing for determining complete bacterial genome sequences, enabling detection and characterization of clinically important ARGs in the marine environment in Norway, with potential for further dissemination. It also highlights the need for environmental surveillance of antibiotic resistance in low prevalence settings like Norway.


Assuntos
Mapeamento Cromossômico/métodos , Infecções por Escherichia coli/veterinária , Proteínas de Escherichia coli/genética , Escherichia coli/genética , Mytilus edulis/microbiologia , Análise de Sequência de DNA/métodos , beta-Lactamases/genética , Animais , Conjugação Genética , Farmacorresistência Bacteriana Múltipla , Monitoramento Ambiental , Escherichia coli/classificação , Escherichia coli/isolamento & purificação , Tamanho do Genoma , Genoma Bacteriano , Sequenciamento de Nucleotídeos em Larga Escala , Família Multigênica , Noruega , Filogenia , Plasmídeos/genética
15.
Environ Microbiol ; 22(6): 1997-2000, 2020 06.
Artigo em Inglês | MEDLINE | ID: mdl-32342578

RESUMO

The current SARS-CoV-2 pandemic is wreaking havoc throughout the world and has rapidly become a global health emergency. A central question concerning COVID-19 is why some individuals become sick and others not. Many have pointed already at variation in risk factors between individuals. However, the variable outcome of SARS-CoV-2 infections may, at least in part, be due also to differences between the viral subspecies with which individuals are infected. A more pertinent question is how we are to overcome the current pandemic. A vaccine against SARS-CoV-2 would offer significant relief, although vaccine developers have warned that design, testing and production of vaccines may take a year if not longer. Vaccines are based on a handful of different designs (i), but the earliest vaccines were based on the live, attenuated virus. As has been the case for other viruses during earlier pandemics, SARS-CoV-2 will mutate and may naturally attenuate over time (ii). What makes the current pandemic unique is that, thanks to state-of-the-art nucleic acid sequencing technologies, we can follow in detail how SARS-CoV-2 evolves while it spreads. We argue that knowledge of naturally emerging attenuated SARS-CoV-2 variants across the globe should be of key interest in our fight against the pandemic.


Assuntos
Betacoronavirus , Vírus da SARS , COVID-19 , Infecções por Coronavirus , Surtos de Doenças , Humanos , Pandemias , Pneumonia Viral , SARS-CoV-2
16.
Mol Cell Proteomics ; 19(3): 518-528, 2020 03.
Artigo em Inglês | MEDLINE | ID: mdl-31941798

RESUMO

Mass spectrometry (MS) and proteomics offer comprehensive characterization and identification of microorganisms and discovery of protein biomarkers that are applicable for diagnostics of infectious diseases. The use of biomarkers for diagnostics is widely applied in the clinic and the use of peptide biomarkers is increasingly being investigated for applications in the clinical laboratory. Respiratory-tract infections are a predominant cause for medical treatment, although, clinical assessments and standard clinical laboratory protocols are time-consuming and often inadequate for reliable diagnoses. Novel methods, preferably applied directly to clinical samples, excluding cultivation steps, are needed to improve diagnostics of infectious diseases, provide adequate treatment and reduce the use of antibiotics and associated development of antibiotic resistance. This study applied nano-liquid chromatography (LC) coupled with tandem MS, with a bioinformatics pipeline and an in-house database of curated high-quality reference genome sequences to identify species-unique peptides as potential biomarkers for four bacterial pathogens commonly found in respiratory tract infections (RTIs): Staphylococcus aureus; Moraxella catarrhalis; Haemophilus influenzae and Streptococcus pneumoniae The species-unique peptides were initially identified in pure cultures of bacterial reference strains, reflecting the genomic variation in the four species and, furthermore, in clinical respiratory tract samples, without prior cultivation, elucidating proteins expressed in clinical conditions of infection. For each of the four bacterial pathogens, the peptide biomarker candidates most predominantly found in clinical samples, are presented. Data are available via ProteomeXchange with identifier PXD014522. As proof-of-principle, the most promising species-unique peptides were applied in targeted tandem MS-analyses of clinical samples and their relevance for identifications of the pathogens, i.e. proteotyping, was validated, thus demonstrating their potential as peptide biomarker candidates for diagnostics of infectious diseases.


Assuntos
Proteínas de Bactérias/metabolismo , Haemophilus influenzae/metabolismo , Moraxella catarrhalis/metabolismo , Peptídeos/metabolismo , Staphylococcus aureus/metabolismo , Streptococcus pneumoniae/metabolismo , Biomarcadores/metabolismo , Haemophilus influenzae/isolamento & purificação , Humanos , Moraxella catarrhalis/isolamento & purificação , Sistema Respiratório/microbiologia , Infecções Respiratórias/microbiologia , Especificidade da Espécie , Staphylococcus aureus/isolamento & purificação , Streptococcus pneumoniae/isolamento & purificação , Espectrometria de Massas em Tandem
17.
Syst Appl Microbiol ; 43(1): 126039, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31776051

RESUMO

Clinical and environmental-associated strains (n=17), genotypically related to Corynebacterium spp., yet distinct from any species of the genus Corynebacterium with validly published names, have been isolated during the last 20 years and tentatively identified as Corynebacterium sanguinis, although the combination, "Corynebacterium sanguinis" was never validly published. The comprehensive genotypic and phenotypic characterisations and genomic analyses in this study support the proposal for recognizing the species within the genus Corynebacterium, for which the name, Corynebacterium sanguinis sp. nov., is reaffirmed and proposed. Strains of Corynebacterium sanguinis are Gram-positive, non-motile, non-spore-forming, short, pleomorphic and coryneform bacilli, growing aerobically, with CO2. They contain mycolic acids, major respiratory menaquinones, MK-8 (II-H2) and MK-9 (II-H2), and polar lipids, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol, phosphoglycolipid, glycolipids and a novel lipid that remains to be characterized and identified. Strains of Corynebacterium sanguinis are genotypically most similar to Corynebacterium lipophiliflavum, with 16S rRNA gene sequence similarities of 98.3% and rpoB sequence similarities of 94.9-95.2%. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) analysis were able to clearly differentiate Corynebacterium sanguinis from the most closely related species. The genome size of Corynebacterium sanguinis is 2.28-2.37Mbp with 65.1-65.5mol% G+C content. A total of 2202-2318 ORFs were predicted, comprising 2141-2251 protein-encoding genes. The type strain is CCUG 58655T (=CCM 8873T=NCTC 14287T).


Assuntos
Infecções por Corynebacterium/microbiologia , Corynebacterium/classificação , Microbiologia Ambiental , Proteínas de Bactérias/genética , Composição de Bases , Corynebacterium/química , Corynebacterium/citologia , Corynebacterium/fisiologia , DNA Bacteriano/genética , Ácidos Graxos/química , Tamanho do Genoma , Genoma Bacteriano/genética , Glicolipídeos/química , Humanos , Hibridização de Ácido Nucleico , Fosfolipídeos/química , Filogenia , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Especificidade da Espécie , Vitamina K 2/química
18.
Sci Rep ; 9(1): 16868, 2019 11 14.
Artigo em Inglês | MEDLINE | ID: mdl-31727989

RESUMO

Septic arthritis is one of the most aggressive joint diseases. Although caused predominantly by S. aureus, Gram-negative bacteria, Pseudomonas aeruginosa among them, account for a significant percentage of the causal agents of septic arthritis. However, septic arthritis caused by P. aeruginosa has not been studied thus far, due to lack of an animal model. NMRI mice were inoculated with different doses of P. aeruginosa. The clinical course of septic arthritis and radiological changes of joints were examined. Furthermore, the host molecular and cellular mechanisms involved in P. aeruginosa-induced septic arthritis were investigated. Inoculation of mice with P. aeruginosa caused septic arthritis in a dose-dependent manner. Neutrophil depletion led to higher mortality and more severe joint destruction (p < 0.01). In contrast, monocyte depletion resulted in higher mortality (p < 0.05) but similar arthritis severity compared to controls. Mice depleted of CD4+ T-cells inoculated with P. aeruginosa displayed less severe bone damage (p < 0.05). For the first time, a mouse model for P. aeruginosa septic arthritis is presented. Our data demonstrate that neutrophils play a protective role in P. aeruginosa septic arthritis. Monocytes/macrophages, on the other hand, are only essential in preventing P. aeruginosa-induced mortality. Finally, CD4+ T-cells are pathogenic in P. aeruginosa septic arthritis.


Assuntos
Artrite Infecciosa/patologia , Modelos Animais de Doenças , Articulações/patologia , Neutropenia/patologia , Infecções por Pseudomonas/patologia , Pseudomonas aeruginosa/patogenicidade , Animais , Artrite Infecciosa/imunologia , Artrite Infecciosa/microbiologia , Artrite Infecciosa/mortalidade , Linfócitos T CD4-Positivos/imunologia , Linfócitos T CD4-Positivos/microbiologia , Linfócitos T CD4-Positivos/patologia , Feminino , Humanos , Articulações/imunologia , Articulações/microbiologia , Contagem de Leucócitos , Depleção Linfocítica , Camundongos , Camundongos Endogâmicos , Monócitos/imunologia , Monócitos/microbiologia , Monócitos/patologia , Neutropenia/imunologia , Neutropenia/microbiologia , Neutropenia/mortalidade , Neutrófilos/imunologia , Neutrófilos/microbiologia , Neutrófilos/patologia , Especificidade de Órgãos , Infecções por Pseudomonas/imunologia , Infecções por Pseudomonas/microbiologia , Infecções por Pseudomonas/mortalidade , Pseudomonas aeruginosa/crescimento & desenvolvimento , Pseudomonas aeruginosa/imunologia , Índice de Gravidade de Doença , Análise de Sobrevida
19.
Front Microbiol ; 10: 2511, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31781055

RESUMO

The family Enterobacteriaceae is a taxonomically diverse and widely distributed family containing many human commensal and pathogenic species that are known to carry transferable antibiotic resistance determinants. Characterization of novel taxa within this family is of great importance in order to understand the associated health risk and provide better treatment options. The aim of the present study was to characterize a Gram-negative bacterial strain (CCUG 66741) belonging to the family Enterobacteriaceae, isolated from a wound infection of an adult patient, in Sweden. Initial phenotypic and genotypic analyses identified the strain as a member of the family Enterobacteriaceae but could not assign it to any previously described species. The complete 16S rRNA gene sequence showed highest similarity (98.8%) to four species. Whole genome sequencing followed by in silico DNA-DNA similarity analysis and average nucleotide identity (ANI) analysis confirmed that strain CCUG 66741 represents a novel taxon. Sequence comparisons of six house-keeping genes (16S rRNA, atpD, dnaJ, gyrB, infB, rpoB) with those of the type strains of the type species of related genera within the family Enterobacteriaceae indicated that the strain embodies a novel species within the family. Phylogenomic analyses (ANI-based and core genome-based phylogeny) showed that strain CCUG 66741 forms a distinct clade, representing a novel species of a distinct, new genus within the family Enterobacteriaceae, for which the name Scandinavium goeteborgense gen. nov., sp. nov. is proposed, with CCUG 66741T as the type strain (= CECT 9823T = NCTC 14286T). S. goeteborgense CCUG 66741T carries a novel variant of a chromosomally-encoded quinolone resistance gene (proposed qnrB96). When expressed in Escherichia coli, the qnrB96 gene conferred five-fold increase in minimum inhibitory concentration against ciprofloxacin. This study highlights the importance and the utility of whole genome sequencing for pathogen identification in clinical settings.

20.
Microbiol Resour Announc ; 8(33)2019 Aug 15.
Artigo em Inglês | MEDLINE | ID: mdl-31416868

RESUMO

Acinetobacter radioresistens strain DD78 (= CCUG 69565) is a soil hydrocarbon-degrading and biosurfactant-producing bacterium isolated from chronically crude oil-polluted soil of the Aconcagua River mouth in Chile. The 3.25-Mb A. radioresistens DD78 genome (41.8% GC content) was completely sequenced, with 4 replicons, 2,970 coding sequences, and 77 tRNAs.

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