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2.
Arq. bras. med. vet. zootec. (Online) ; 72(3): 1039-1046, May-June, 2020. ilus, tab, graf
Article in English | LILACS, VETINDEX | ID: biblio-1129747

ABSTRACT

O objetivo deste comunicado é desenvolver um método quantitativo PCR em tempo real, baseado em guia molecular (MB) (MB-qPCR) para detecção de infecção por espécies de Brucella, e avaliar seu potencial de utilização clínica. Os primers e as sondas MB foram desenhados para amplificação específica e determinação de sequência conservada do código do gene para os primeiros 58-aa da proteína de membrana externa OMP-2a, que é compartilhada em cinco espécies de Brucella epidêmicas. A avaliação metodológica foi realizada por análise de sensibilidade, especificidade, coeficiente de variação intra e inter, e a linearidade do qPCR. O potencial diagnóstico foi avaliado comparando-se o método qPCR desenvolvido com ensaios de exames bacteriológicos convencionais, incluindo os testes de soroaglutinação convencionais (SATs) e os testes do Rosa Bengala (RBPTs). O método exibiu alta sensibilidade (tão baixo quanto 50 cópias) e grande faixa de linearidade (102-108 cópias). Nenhuma reação cruzada foi encontrada com bactéria clínica comum. A sensibilidade diagnóstica foi superior ao exame bacteriológico, e a especificidade diagnóstica foi superior ao SAT ou ao RBPT. Um método MB-qPCR altamente sensível e específico para DNA de Brucella foi estabelecido com sucesso, provando ser uma ferramenta útil no diagnóstico molecular de brucelose.(AU)


Subject(s)
Brucella/isolation & purification , Genome, Bacterial , Real-Time Polymerase Chain Reaction/methods
3.
Rev. Soc. Bras. Med. Trop ; 53: e20190470, 2020. tab, graf
Article in English | ColecionaSUS, LILACS, ColecionaSUS, SES-SP | ID: biblio-1136864

ABSTRACT

Abstract INTRODUCTION: Tuberculosis is listed among the top 10 causes of deaths worldwide. The resistant strains causing this disease have been considered to be responsible for public health emergencies and health security threats. As stated by the World Health Organization (WHO), around 558,000 different cases coupled with resistance to rifampicin (the most operative first-line drug) have been estimated to date. Therefore, in order to detect the resistant strains using the genomes of Mycobacterium tuberculosis (MTB), we propose a new methodology for the analysis of genomic similarities that associate the different levels of decomposition of the genome (discrete non-decimated wavelet transform) and the Hurst exponent. METHODS: The signals corresponding to the ten analyzed sequences were obtained by assessing GC content, and then these signals were decomposed using the discrete non-decimated wavelet transform along with the Daubechies wavelet with four null moments at five levels of decomposition. The Hurst exponent was calculated at each decomposition level using five different methods. The cluster analysis was performed using the results obtained for the Hurst exponent. RESULTS: The aggregated variance, differenced aggregated variance, and aggregated absolute value methods presented the formation of three groups, whereas the Peng and R/S methods presented the formation of two groups. The aggregated variance method exhibited the best results with respect to the group formation between similar strains. CONCLUSION: The evaluation of Hurst exponent associated with discrete non-decimated wavelet transform can be used as a measure of similarity between genome sequences, thus leading to a refinement in the analysis.


Subject(s)
Humans , Genome, Bacterial/genetics , Wavelet Analysis , Models, Genetic , Mycobacterium tuberculosis/genetics
4.
Article in English | WPRIM | ID: wpr-772954

ABSTRACT

Identifying antimicrobial resistant (AMR) bacteria in metagenomics samples is essential for public health and food safety. Next-generation sequencing (NGS) technology has provided a powerful tool in identifying the genetic variation and constructing the correlations between genotype and phenotype in humans and other species. However, for complex bacterial samples, there lacks a powerful bioinformatic tool to identify genetic polymorphisms or copy number variations (CNVs) for given genes. Here we provide a Bayesian framework for genotype estimation for mixtures of multiple bacteria, named as Genetic Polymorphisms Assignments (GPA). Simulation results showed that GPA has reduced the false discovery rate (FDR) and mean absolute error (MAE) in CNV and single nucleotide variant (SNV) identification. This framework was validated by whole-genome sequencing and Pool-seq data from Klebsiella pneumoniae with multiple bacteria mixture models, and showed the high accuracy in the allele fraction detections of CNVs and SNVs in AMR genes between two populations. The quantitative study on the changes of AMR genes fraction between two samples showed a good consistency with the AMR pattern observed in the individual strains. Also, the framework together with the genome annotation and population comparison tools has been integrated into an application, which could provide a complete solution for AMR gene identification and quantification in unculturable clinical samples. The GPA package is available at https://github.com/IID-DTH/GPA-package.


Subject(s)
Bacteria , Genetics , Bayes Theorem , DNA Copy Number Variations , Genome, Bacterial , Genotyping Techniques , High-Throughput Nucleotide Sequencing , Humans , Klebsiella pneumoniae , Genetics , Metagenomics , Methods , Polymorphism, Genetic , Software
5.
Article in English | WPRIM | ID: wpr-772945

ABSTRACT

Emerging antibiotic resistance is a major global health threat. The analysis of nucleic acid sequences linked to susceptibility phenotypes facilitates the study of genetic antibiotic resistance determinants to inform molecular diagnostics and drug development. We collected genetic data (11,087 newly-sequenced whole genomes) and culture-based resistance profiles (10,991 out of the 11,087 isolates comprehensively tested against 22 antibiotics in total) of clinical isolates including 18 main species spanning a time period of 30 years. Species and drug specific resistance patterns were observed including increased resistance rates for Acinetobacter baumannii to carbapenems and for Escherichia coli to fluoroquinolones. Species-level pan-genomes were constructed to reflect the genetic repertoire of the respective species, including conserved essential genes and known resistance factors. Integrating phenotypes and genotypes through species-level pan-genomes allowed to infer gene-drug resistance associations using statistical testing. The isolate collection and the analysis results have been integrated into GEAR-base, a resource available for academic research use free of charge at https://gear-base.com.


Subject(s)
Acinetobacter baumannii , Genetics , Bacteria , Genetics , Cell Culture Techniques , Methods , Drug Resistance, Microbial , Genetics , Escherichia coli , Genetics , Genome, Bacterial , Genotype , Humans , Internet , Microbial Sensitivity Tests , Phenotype , Whole Genome Sequencing
6.
Article in Chinese | WPRIM | ID: wpr-776033

ABSTRACT

Objective To describe the microbiological characteristics of ()CGMCC 12426 and determine and analyze its complete genome sequences.Methods strain CGMCC 12426 genomic DNA sequencing was performed on a single molecule real-time sequencing(SMRT)platform and the annotation was completed in the NCBI Prokaryotic Genomic Annotation Pipeline(pGAP).Results The complete genomic sequences of the released CGMCC 12426 consisted of a 4 138 265-bp circular chromosome and a 74 165-bp plasmid,which resulted in the prediction of 4581 genes including 4222 coding sequences,87 tRNAs,and 30 rRNAs(which included 5S rRNA,16S rRNA,and 23S rRNA).Conclusion The genome sequencing provided a basis for further investigations on the genetic background of and on the metabolic and regulatory mechanisms.


Subject(s)
Bacillus subtilis , Genetics , Genome, Bacterial , Plasmids , RNA, Ribosomal, 16S , Genetics , RNA, Ribosomal, 23S , Genetics , RNA, Ribosomal, 5S , Genetics , Sequence Analysis, DNA
7.
Chinese Journal of Biotechnology ; (12): 541-557, 2019.
Article in Chinese | WPRIM | ID: wpr-771354

ABSTRACT

The emergence and spread of antimicrobial resistance has become a serious global issue. Bacterial characteristics, such as antimicrobial resistance genes, virulence-associated genes, plasmid types, and phylogenetic relationship among different strains, are the keys to unravel the occurrence and dissemination of antimicrobial resistance. However, the accuracy and efficiency of the traditional techniques, such as polymerase chain reaction and pulsed field gel electrophoresis is insufficient to underlying the mystery of antimicrobial resistance. Recently, the whole genome sequencing and high-throughput bioinformatics analysis have been successfully used in antimicrobial resistance studies, helping scientists to obtain the nature of antimicrobial resistance bacteria quickly, and more precisely to paint the evolutionary relationship among different strains. Therefore, in this study, we aim to systematically introduce the recent development of whole genome sequencing analysis, including different methods and corresponding characteristics of library preparation, platform sequencing, data analysis, and the latest application of the technology in the antimicrobial resistance research. We hope that this review can provide more comprehensive knowledge about whole genome sequencing and bioinformatic analysis for antimicrobial resistance research.


Subject(s)
Anti-Bacterial Agents , Computational Biology , Drug Resistance, Bacterial , Genome, Bacterial , Phylogeny , Whole Genome Sequencing
8.
Rio de Janeiro; s.n; 2019. 2019 p. ilus.
Thesis in Portuguese | LILACS | ID: biblio-1050352

ABSTRACT

Klebsiella pneumoniae é um patógeno oportunista que causa principalmente infecções respiratórias e do trato urinário. A ocorrência frequente de isolados virulentos resistentes a múltiplas drogas levou a inclusão dessa espécie na lista da OMS das principais prioridades para pesquisa e desenvolvimento de alternativas terapêuticas. O conhecimento abrangente dos mecanismos moleculares subjacentes à virulência da K. pneumoniae pode levar à proposta de medicamentos mais eficientes e específicos. O Sistema de Secreção Tipo VI (T6SS) contribui para a competição bacteriana, invasão celular e colonização in vivo. Apesar dos estudos que mostram o envolvimento do T6SS na patogênese da K. pneumoniae, pouco se conhece sobre a regulação de sua expressão. O entendimento dos mecanismos regulatórios pode fornecer pistas sobre a função desse sistema e contribuir para o desenvolvimento de novas abordagens terapêuticas para o tratamento de infecções por K. pneumoniae. Esse trabalho teve como objetivo identificar mecanismos de regulação transcricional dos genes do T6SS de K. pneumoniae


Para isso, analisamos os genomas de três cepas (Kp52.145, HS11286 e NTUH-K2044) de forma a predizer e padronizar a anotação dos genes de T6SS através de buscas de similaridade. Foram encontrados 38 genes do T6SS em Kp52.145, 29 em HS11286 e 30 em NTUH-K2044. Nas adjacências dos genes do T6SS foram encontrados genes envolvidos em sistemas de captação de ferro, sugerindo que o T6SS de K. pneumoniae também pode desempenhar um papel na importação de íons. Foram identificadas 17 regiões promotoras dependentes de σ70 em Kp52.145, 12 em HS11286 e 12 em NTUH-K2044. Identificamos ainda 17, 12 e 15 sequências promotoras a partir dos sítios putativos de σ54. Também identificamos 165 sítios de ligação para reguladores transcricionais em Kp52.145, 125 em HS11286 e 134 em NTUH-K2044. Nossos resultados in silico sugerem que o T6SS de K. pneumoniae seja regulado em resposta a sinais ambientais e devem direcionar experimentos in vitro que testem a resposta de K. pneumoniae a variações de temperatura (H-NS), de nutrientes (GcvA e Fis), estresse oxidativo (OxyR) e osmolaridade (RscAB e OmpR). (AU)


Subject(s)
Animals , Genome, Bacterial , Type VI Secretion Systems , Klebsiella pneumoniae
9.
Braz. j. microbiol ; 49(4): 703-713, Oct.-Dec. 2018. tab, graf
Article in English | LILACS | ID: biblio-974305

ABSTRACT

ABSTRACT The leguminous inoculation with nodule-inducing bacteria that perform biological nitrogen fixation is a good example of an "eco-friendly agricultural practice". Bradyrhizobium strains BR 3267 and BR 3262 are recommended for cowpea (Vigna unguiculata) inoculation in Brazil and showed remarkable responses; nevertheless neither strain was characterized at species level, which is our goal in the present work using a polyphasic approach. The strains presented the typical phenotype of Bradyrhizobium with a slow growth and a white colony on yeast extract-mannitol medium. Strain BR 3267 was more versatile in its use of carbon sources compared to BR 3262. The fatty acid composition of BR 3267 was similar to the type strain of Bradyrhizobium yuanmingense; while BR 3262 was similar to Bradyrhizobium elkanii and Bradyrhizobium pachyrhizi. Phylogenetic analyses based on 16S rRNA and three housekeeping genes placed both strains within the genus Bradyrhizobium: strain BR 3267 was closest to B. yuanmingense and BR 3262 to B. pachyrhizi. Genome average nucleotide identity and DNA-DNA reassociation confirmed the genomic identification of B. yuanmingense BR 3267 and B. pachyrhizi BR 3262. The nodC and nifH gene analyses showed that strains BR 3267 and BR 3262 hold divergent symbiotic genes. In summary, the results indicate that cowpea can establish effective symbiosis with divergent bradyrhizobia isolated from Brazilian soils.


Subject(s)
Bradyrhizobium/isolation & purification , Bradyrhizobium/genetics , Agricultural Inoculants/isolation & purification , Agricultural Inoculants/genetics , Vigna/microbiology , Phylogeny , Symbiosis , Brazil , DNA, Bacterial/genetics , RNA, Ribosomal, 16S/genetics , Genome, Bacterial , Evolution, Molecular , Bradyrhizobium/classification , Bradyrhizobium/physiology , Genomics , Root Nodules, Plant/microbiology , Agricultural Inoculants/classification , Agricultural Inoculants/physiology , Vigna/physiology
10.
Braz. j. microbiol ; 49(2): 210-211, Apr.-June 2018.
Article in English | LILACS | ID: biblio-889231

ABSTRACT

Abstract Paraburkholderia tropica (syn Burkholderia tropica) are nitrogen-fixing bacteria commonly found in sugarcane. The Paraburkholderia tropica strain Ppe8 is part of the sugarcane inoculant consortium that has a beneficial effect on yield. Here, we report a draft genome sequence of this strain elucidating the mechanisms involved in its interaction mainly with Poaceae. A genome size of approximately 8.75 Mb containing 7844 protein coding genes distributed in 526 subsystems was de novo assembled with ABySS and annotated by RAST. Genes related to the nitrogen fixation process, the secretion systems (I, II, III, IV, and VI), and related to a variety of metabolic traits, such as metabolism of carbohydrates, amino acids, vitamins, and proteins, were detected, suggesting a broad metabolic capacity and possible adaptation to plant association.


Subject(s)
Genome, Bacterial , Burkholderiaceae/genetics , Endophytes/genetics , Bacterial Proteins/genetics , Sequence Analysis, DNA , Computational Biology , Saccharum/microbiology , Burkholderiaceae/isolation & purification , Metabolic Networks and Pathways/genetics , Molecular Sequence Annotation , Endophytes/isolation & purification
11.
Braz. j. microbiol ; 49(2): 207-209, Apr.-June 2018. tab
Article in English | LILACS | ID: biblio-889240

ABSTRACT

Abstract Streptomycetes remain as one of the important sources for bioactive products. Isolated from the mangrove forest, Streptomyces gilvigriseus MUSC 26T was previously characterised as a novel streptomycete. The high quality draft genome of MUSC 26T contained 5,213,277 bp with G + C content of 73.0%. Through genome mining, several gene clusters associated with secondary metabolites production were revealed in the genome of MUSC 26T. These findings call for further investigations into the potential exploitation of the strain for production of pharmaceutically important compounds.


Subject(s)
Streptomyces/genetics , Genome, Bacterial , Environmental Microbiology , Streptomyces/isolation & purification , Base Composition , Biological Products/metabolism , Sequence Analysis, DNA , Computational Biology , Wetlands , Metabolic Networks and Pathways/genetics , Secondary Metabolism
12.
Electron. j. biotechnol ; 33: 36-38, May. 2018. tab
Article in English | LILACS | ID: biblio-1024852

ABSTRACT

Background: Draft and complete genome sequences from bacteria are key tools to understand genetic determinants involved in pathogenesis in several disease models. Piscirickettsia salmonis is a Gram-negative bacterium responsible for the Salmon Rickettsial Syndrome (SRS), a bacterial disease that threatens the sustainability of the Chilean salmon industry. In previous reports, complete and draft genome sequences have been generated and annotated. However, the lack of transcriptome data underestimates the genetic potential, does not provide information about transcriptional units and contributes to disseminate annotation errors. Results: Here we present the draft genome and transcriptome sequences of four P. salmonis strains. We have identified the transcriptional architecture of previously characterized virulence factors and trait-specific genes associated to cation uptake, metal efflux, antibiotic resistance, secretion systems and other virulence factors. Conclusions: This data has provided a refined genome annotation and also new insights on the transcriptional structures and coding potential of this fish pathogen.


Subject(s)
Animals , Salmonidae , Piscirickettsiaceae Infections/veterinary , Piscirickettsia/genetics , Fish Diseases/microbiology , Genome, Bacterial , Piscirickettsia/pathogenicity , Transcriptome
13.
Braz. j. microbiol ; 49(1): 7-9, Jan.-Mar. 2018.
Article in English | LILACS | ID: biblio-889192

ABSTRACT

ABSTRACT In this report, we present a draft genome of 2,886,173 bp of an Exiguobacterium aurantiacum strain PN47 isolate from the sediment of a saline pond named "Salar del Huasco" in the Altiplano in the North of Chile. Strain PN47 encodes adaptive characteristics enabling survival in extreme environmental conditions of high heavy metal and salt concentrations and high alkalinity.


Subject(s)
Bacillaceae/isolation & purification , Bacillaceae/genetics , Ponds/microbiology , Genome, Bacterial , Phylogeny , Bacillaceae/classification , Bacillaceae/metabolism , DNA, Bacterial/genetics , Base Sequence , Sodium Chloride/analysis , Sodium Chloride/metabolism , Ponds/chemistry , Chile , Metals, Heavy/analysis , Metals, Heavy/metabolism
14.
Braz. j. microbiol ; 49(1): 13-15, Jan.-Mar. 2018. tab, graf
Article in English | LILACS | ID: biblio-889194

ABSTRACT

ABSTRACT As the largest genus in Actinobacteria family, Streptomyces species have the ability to synthesize numerous compounds of diverse structures with bioactivities. Streptomyces mangrovisoli MUSC 149T was previously isolated as a novel streptomycete from mangrove forest in east coast of Peninsular Malaysia. The high quality draft genome of MUSC 149T comprises 9,165,825 bp with G + C content of 72.5%. Through bioinformatics analysis, 21 gene clusters identified in the genome were associated with the production of bioactive secondary metabolites. The presence of these biosynthetic gene clusters in MUSC 149T suggests the potential exploitation of the strain for production of medically important compounds.


Subject(s)
Streptomyces/isolation & purification , Genome, Bacterial , Geologic Sediments/microbiology , Phylogeny , Streptomyces/classification , Streptomyces/genetics , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Base Composition , DNA, Bacterial/genetics , Molecular Sequence Data , Base Sequence , Malaysia
15.
Braz. j. microbiol ; 49(1): 5-6, Jan.-Mar. 2018.
Article in English | LILACS | ID: biblio-889197

ABSTRACT

ABSTRACT The type strain SUR2 of the novel species Chryseobacterium limigenitum was isolated from a dehydrated sludge of the municipal sewage treatment plant in Dogoše near Maribor in Slovenia. The draft genome, with 60 contigs, 4,697,725 bp, 34.4% of G+C content, was obtained using the Illumina HiSeq 2500-1 platform. Joint Genome Institute Microbial Genome Annotation Pipeline (MGAP v.4) has identified 4322 protein-coding sequences including resistance genes against arsenic and other heavy metals. In addition, a subclass B3 metallo-β-lactamase, which confers resistance to penicillins, cephalosporins and carbapenems, was also present in the genome. The genome sequence provides important information regarding bioremediation potential and pathogenic properties of this newly identified species.


Subject(s)
Sewage/microbiology , Genome, Bacterial , Chryseobacterium/genetics , Penicillins/pharmacology , Phylogeny , Sewage/chemistry , Base Composition , DNA, Bacterial/genetics , Molecular Sequence Data , Base Sequence , Microbial Sensitivity Tests , Carbapenems/pharmacology , Chryseobacterium/isolation & purification , Chryseobacterium/classification , Chryseobacterium/drug effects , Anti-Bacterial Agents/pharmacology
16.
Braz. j. microbiol ; 49(1): 10-12, Jan.-Mar. 2018. tab
Article in English | LILACS | ID: biblio-889198

ABSTRACT

ABSTRACT Vitellibacter aquimaris D-24T (=KCTC 42708T = DSM 101732T), a halophilic marine bacterium, was isolated from seawater collected from Desaru beach, Malaysia. Here, we present the draft genome sequence of D-24T with a genome size of approximately 3.1 Mbp and G + C content of 39.93%. The genome of D-24T contains genes involved in reducing a potent greenhouse gas (N2O) in the environment and the degradation of proteinaceous compounds. Genome availability will provide insights into potential biotechnological and environmental applications of this bacterium.


Subject(s)
Seawater/microbiology , Genome, Bacterial , Flavobacteriaceae/genetics , Phylogeny , Base Composition , DNA, Bacterial/genetics , Molecular Sequence Data , Base Sequence , Flavobacteriaceae/isolation & purification , Flavobacteriaceae/classification , Malaysia
17.
Braz. j. microbiol ; 49(1): 18-19, Jan.-Mar. 2018.
Article in English | LILACS | ID: biblio-889201

ABSTRACT

ABSTRACT Bacillus anthracis strain SPV842_15 was isolated from bovine fetus, while B. anthracis strain Brazilian vaccinal was recovered from a commercial vaccine. We report here the genome sequences of both strains. The SPV842_15 genome is composed of a single circular chromosome with a length of 5,228,664 base pairs, and comprises 5911 coding sequences. In turn, the Brazilian vaccinal genome remains in 201 contigs with 5733 coding sequences. Both genomes have an overall C + G content of 35.4%, and 11 genes encoding the ribosomal RNAs (rRNAs) 5S, 16S and 23S. Only the plasmid pX01 sequence, which carries genes for toxins synthesis, was detected and completely assembled for both strains. These plasmids have a length of 181,684 base pairs and a C + G content of 32.5%. These genomic data generate insights about vaccinal B. anthracis virulence.


Subject(s)
Animals , Cattle , Bacillus anthracis/isolation & purification , Bacillus anthracis/genetics , Bacterial Vaccines/genetics , Cattle Diseases/microbiology , Genome, Bacterial , Phylogeny , Plasmids/genetics , Bacillus anthracis/classification , Base Composition , DNA, Bacterial/genetics , Molecular Sequence Data , Bacterial Vaccines/isolation & purification , Base Sequence
18.
Braz. j. microbiol ; 49(1): 16-17, Jan.-Mar. 2018.
Article in English | LILACS | ID: biblio-889216

ABSTRACT

ABSTRACT Kosakonia cowanii type strain 888-76T is a human pathogen which was originally isolated from blood as NIH group 42. In this study, we report the complete genome sequence of K. cowanii 888-76T. 888-76T has 1 chromosome and 2 plasmids with a total genome size of 4,857,567 bp and C+G 56.15%. This genome sequence will not only help us to understand the virulence features of K. cowanii 888-76T but also provide us the useful information for the study of evolution of Kosakonia genus.


Subject(s)
Humans , Genome, Bacterial , Enterobacteriaceae/isolation & purification , Enterobacteriaceae/genetics , Enterobacteriaceae Infections/microbiology , Phylogeny , Plasmids/genetics , Base Composition , DNA, Bacterial/genetics , Molecular Sequence Data , Base Sequence , Enterobacteriaceae/classification
19.
Salud pública Méx ; 60(1): 29-40, Jan.-Feb. 2018. tab, graf
Article in English | LILACS | ID: biblio-903844

ABSTRACT

Abstract: Objective: To compare the genetic determinants involved in plant colonization or virulence in the reported genomes of K. variicola, K. quasipneumoniae and K. pneumoniae. Materials and methods: In silico comparisons and Jaccard analysis of genomic data were used. Fimbrial genes were detected by PCR. Biological assays were performed with plant and clinical isolates. Results: Plant colonization genes such as cellulases, catalases and hemagglutinins were mainly present in K. variicola genomes. Chromosomal β-lactamases were characteristic of this species and had been previously misclassified. K. variicola and K. pneumoniae isolates produced plant hormones. Conclusions: A mosaic distribution of different virulence- and plant-associated genes was found in K. variicola and in K. quasipneumoniae genomes. Some plant colonizing genes were found mainly in K. variicola genomes. The term plantanosis is proposed for plant-borne human infections.


Resumen: Objetivo: Comparar genes de colonización de plantas o de virulencia en los genomas reportados de K. variicola, K. quasipneumoniae y K. pneumoniae. Material y métodos: Se utilizaron análisis in silico y de Jaccard. Por PCR se detectaron genes de fimbrias. Se realizaron ensayos biológicos con aislados de plantas y clínicos. Resultados: Los genes de colonización de plantas como celulasas, catalasas y hemaglutininas se encontraron principalmente en genomas de K. variicola. Las β-lactamasas cromosómicas son características de la especie y en algunos casos estaban mal clasificadas. K. variicola y K. pneumoniae producen hormonas vegetales. Conclusiones: Se encontró una distribución en mosaico de los genes de asociación con plantas y de virulencia en K. variicola y K. quasipneumoniae. Principalmente en K. variicola se encontraron algunos genes involucrados en la colonización de plantas. Se propone el término plantanosis para las infecciones humanas de origen vegetal.


Subject(s)
Humans , Plants/microbiology , Klebsiella Infections/microbiology , Klebsiella/physiology , Bacterial Proteins/physiology , Bacterial Proteins/genetics , Virulence/genetics , Computer Simulation , Disease Reservoirs , Adaptation, Biological/genetics , Genome, Bacterial , Drug Resistance, Multiple, Bacterial , Gene Ontology , Genes, Bacterial , Klebsiella/enzymology , Klebsiella/genetics , Klebsiella/pathogenicity
20.
Salud pública Méx ; 60(1): 56-62, Jan.-Feb. 2018. tab, graf
Article in English | LILACS | ID: biblio-903842

ABSTRACT

Abstract: Objective: Due to the fact that K. variicola, K. quasipneumoniae and K. pneumoniae are closely related bacterial species, misclassification can occur due to mistakes either in normal biochemical tests or during submission to public databases. The objective of this work was to identify K. variicola and K. quasipneumoniae genomes misclassified in GenBank database. Materials and methods: Both rpoB phylogenies and average nucleotide identity (ANI) were used to identify a significant number of misclassified Klebsiella spp. genomes. Results: Here we report an update of K. variicola and K. Quasipneumoniae genomes correctly classified and a list of isolated genomes obtained from humans, plants, animals and insects, described originally as K. pneumoniae or K. variicola, but known now to be misclassified. Conclusions: This work contributes to recognize the extensive presence of K. variicola and K. quasipneumoniae isolates in diverse sites and samples.


Resumen: Objetivo: Identificar genomas mal clasificados de K. variicola, y K. quasipneumoniae en la base de datos del GenBank. Material y métodos: En el presente estudio se usaron tanto análisis filogenéticos usando rpoB como la identidad media de nucleótidos (ANI, por sus siglas en ingles) para identificar un número significativo de genomas del género Klebsiella. Resultados: Se reportó una actualización de genomas de K. variicola y K. quasipneumoniae correctamente clasificados y una lista de aquellos aislamientos obtenidos de seres humanos, plantas, animales e insectos, descritos originalmente como K. pneumoniae o K. variicola pero ahora se conoce que están mal clasificados. Conclusiones: Este trabajo contribuye a la presencia extensiva de aislamientos de K. variicola y K. quasipneumoniae en diversos sitios y muestras.


Subject(s)
Animals , Plants/microbiology , Ursidae/microbiology , Klebsiella Infections/microbiology , Bacterial Typing Techniques , Genome, Bacterial , Insecta/microbiology , Klebsiella/classification , Phylogeny , DNA, Bacterial , Sequence Analysis, DNA
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