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1.
Genome Announc ; 6(15)2018 Apr 12.
Artigo em Inglês | MEDLINE | ID: mdl-29650570

RESUMO

Aeromonas lusitana sp. nov. is an isolate derived from a study aimed at characterizing Aeromonas spp. from water sources used for recreation and agricultural purposes and assessing the implications these organisms have for human and animal health. We present here the 4.52-Mbp draft genome sequence of this novel species.

2.
Genome Announc ; 6(15)2018 Apr 12.
Artigo em Inglês | MEDLINE | ID: mdl-29650571

RESUMO

Species of the Aeromonas genus can be found in numerous environmental milieus, including various water sources, and some species cause disease in animals. We present here the draft genome sequence for Aeromonas cavernicola DSM 24474T, a novel species isolated from a freshwater brook within a cavern in the Czech Republic.

3.
Foodborne Pathog Dis ; 9(8): 713-8, 2012 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-22816989

RESUMO

"Alheira" is a traditional smoked meat sausage produced in the north of Portugal, representing an important economic resource for the region. This meat product has been subjected to research studies with the aim of detecting the presence of common foodborne pathogens, but, to our knowledge, isolation of emerging foodborne Aeromonas from alheira has never been previously described. Present work attempts to evaluate the Aeromonas species diversity of 84 isolates of Aeromonas spp. collected from 32 alheira samples. All presumptive Aeromonas isolates were subjected to genotyping by enterobacterial repetitive intergenic consensus-polymerase chain reaction analysis. The isolates presenting a different pattern were subjected to gyrB gene sequencing for species classification, and the species A. hydrophila, A. salmonicida, A. caviae, A. media, and A. allosaccharophila were identified. The Aeromonas species diversity found has not been previously described in any other meat product evaluated in previous studies. It is also important to highlight the presence of A. hydrophila and A. caviae because they were previously associated with illness in humans, including gastroenteritis.


Assuntos
Aeromonas/genética , Aeromonas/isolamento & purificação , Produtos da Carne/microbiologia , Filogenia , Aeromonas/classificação , Aeromonas/patogenicidade , Animais , Técnicas de Tipagem Bacteriana , DNA Girase/genética , DNA Girase/metabolismo , DNA Bacteriano/genética , Contaminação de Alimentos/análise , Microbiologia de Alimentos , Genótipo , Reação em Cadeia da Polimerase , Portugal , Suínos
4.
Int J Food Microbiol ; 146(2): 118-22, 2011 Mar 30.
Artigo em Inglês | MEDLINE | ID: mdl-21402427

RESUMO

In the present study, 710 isolates of Aeromonas spp. have been collected from pig carcasses, diaphragm muscle, faeces, dehairing equipment and water in slaughterhouses at the North of Portugal. The isolates were obtained from a total of 154 samples. All presumptive Aeromonas isolates were subjected to ERIC-PCR analysis and those which presented a different pattern were taken and the species classified by gyrB gene sequencing. We have found the species A. hydrophila, A. salmonicida, A. bestiarum, A. caviae, A. media, A. veronii, A. allosaccharophila, A. simiae and A. aquariorum. To our knowledge, this extent of Aeromonas species diversity has not been previously described from meat or from the slaughter environment, perhaps due to the unreliability of available identification methods. A noticeable level of isolate redundancy (strains with identical gyrB sequence) from different samples collected in different dates was also obtained, indicating that only a few predominant strains of these species persist at the slaughter system. It is also important to emphasise the presence of Aeromonas species previously associated with illness in man.


Assuntos
Aeromonas/genética , Carne/microbiologia , Suínos/microbiologia , Matadouros , Aeromonas/classificação , Aeromonas/isolamento & purificação , Animais , DNA Girase/genética , DNA Bacteriano/genética , Genes Bacterianos , Filogenia , Portugal
5.
Int J Syst Evol Microbiol ; 61(Pt 2): 242-248, 2011 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-20207806

RESUMO

Two freshwater isolates (WB4.1-19(T) and WB4.4-101), sharing 99.9 % 16S rRNA gene sequence similarity, were highly related to Aeromonas sobria (99.7 % similarity; 6 bp differences). A phylogenetic tree derived from a multi-locus phylogenetic analysis (MLPA) of the concatenated sequences of five housekeeping genes (gyrB, rpoD, recA, dnaJ and gyrA; 3684 bp) revealed that both strains clustered as an independent phylogenetic line next to members of Aeromonas molluscorum and Aeromonas bivalvium. The DNA-DNA reassociation value between the two new isolates was 89.3 %. Strain WB4.1-19(T) had a DNA-DNA relatedness value of <70 % with the type strains of the other species tested. Phenotypic characterization differentiated the two novel strains from all other type strains of species of the genus Aeromonas. It is concluded that the two new strains represent a novel species of the genus Aeromonas, for which the name Aeromonas rivuli sp. nov. is proposed, with the type strain WB4.1-19(T) (=CECT 7518(T)=DSM 22539(T)=MDC 2511(T)).


Assuntos
Aeromonas/classificação , Técnicas de Tipagem Bacteriana , Água Doce/microbiologia , Aeromonas/isolamento & purificação , DNA Bacteriano/genética , Genes Bacterianos , Dados de Sequência Molecular , Tipagem de Sequências Multilocus , Fenótipo , Filogenia , RNA Ribossômico 16S/genética , Análise de Sequência de DNA
6.
Int J Syst Evol Microbiol ; 58(Pt 5): 1169-75, 2008 May.
Artigo em Inglês | MEDLINE | ID: mdl-18450708

RESUMO

During a survey to determine the prevalence of Aeromonas strains in water and skin of imported ornamental fish, 48 strains presumptively identified as Aeromonas were isolated but they could not be identified as members of any previously described Aeromonas species. These strains were subjected to a polyphasic approach including phylogenetic analysis derived from gyrB, rpoD and 16S rRNA gene sequencing, DNA-DNA hybridization, MALDI-TOF MS analysis, genotyping by RAPD and extensive biochemical and antibiotic susceptibility tests in order to determine their taxonomic position. Based on the results of the phylogenetic analyses and DNA-DNA hybridization data, we describe a novel species of the genus Aeromonas, for which the name Aeromonas aquariorum sp. nov. is proposed, with strain MDC47T (=DSM 18362T =CECT 7289T) as the type strain. This is the first Aeromonas species description based on isolations from ornamental fish.


Assuntos
Aeromonas/classificação , Aquicultura , Doenças dos Peixes/microbiologia , Infecções por Bactérias Gram-Negativas/veterinária , Microbiologia da Água , Aeromonas/genética , Aeromonas/isolamento & purificação , Animais , Técnicas de Tipagem Bacteriana , DNA Girase/genética , DNA Bacteriano/análise , RNA Polimerases Dirigidas por DNA/genética , Peixes/microbiologia , Genes de RNAr , Infecções por Bactérias Gram-Negativas/microbiologia , Dados de Sequência Molecular , Hibridização de Ácido Nucleico , Fenótipo , Filogenia , RNA Ribossômico 16S/genética , Técnica de Amplificação ao Acaso de DNA Polimórfico , Análise de Sequência de DNA , Fator sigma/genética , Pele/microbiologia , Espectrometria de Massas por Ionização e Dessorção a Laser Assistida por Matriz
7.
Int J Syst Evol Microbiol ; 56(Pt 10): 2481-2487, 2006 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-17012583

RESUMO

Recent phylogenetic studies of the genus Aeromonas based on gyrB and rpoD gene sequences have improved the phylogeny based on 16S rRNA gene sequences first published in 1992, particularly in the ability to split closely related species. These studies did not include the recently described species Aeromonas simiae and Aeromonas molluscorum and only a single strain of Aeromonas culicicola was available for analysis at that time. In the present work, these Aeromonas species and newly isolated strains of A. culicicola were examined. Sequence analysis indicates that A. simiae and A. molluscorum belong to non-described phylogenetic lines of descent within this genus, which supports the original description of both species. The most closely related species are Aeromonas schubertii and Aeromonas encheleia, respectively, which is consistent with 16S rRNA gene sequencing results. However, while the five strains of A. molluscorum showed nucleotide differences in their gyrB and rpoD gene sequences, the only two known A. simiae strains exhibited identical gene sequences, suggesting that they are isolates of the same strain. On the basis of the rpoD gene sequence phylogeny, A. culicicola strains from the original description and new isolates from drinking water and ornamental fish clustered within the species Aeromonas veronii, suggesting inconsistencies with previous results. Other strains with previously controversial taxonomy and new isolates from other studies were included in this study in order to clarify their phylogenetic affiliation at the species level.


Assuntos
Aeromonas/classificação , Aeromonas/genética , DNA Girase/genética , RNA Polimerases Dirigidas por DNA/genética , Filogenia , Fator sigma/genética , Animais , Técnicas de Tipagem Bacteriana , DNA Bacteriano/análise , Humanos , Dados de Sequência Molecular , RNA Ribossômico 16S/genética , Análise de Sequência de DNA
8.
Appl Environ Microbiol ; 71(1): 538-41, 2005 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-15640231

RESUMO

We describe the recovery of the rare species Aeromonas culicicola, so far known only in mosquitoes in India, from a drinking water supply in Spain. Typing, using enterobacterial repetitive intergenic consensus-PCR, revealed that the 27 new isolates belonged to 3 very closely related strains. These strains were genetically identified by 16S rRNA gene sequencing. Spanish strains differed from the mosquito strains in three nucleotide positions. The AHCYTOEN gene was present in these water strains, which may have a public health significance.


Assuntos
Aeromonas/classificação , Aeromonas/isolamento & purificação , Culicidae/microbiologia , Ingestão de Líquidos , Abastecimento de Água , Aeromonas/genética , Animais , Proteínas de Bactérias/genética , Técnicas de Tipagem Bacteriana , DNA Bacteriano/análise , Enterotoxinas/genética , Água Doce/microbiologia , Genes de RNAr , Dados de Sequência Molecular , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Espanha
9.
Int J Syst Evol Microbiol ; 54(Pt 5): 1511-1519, 2004 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-15388703

RESUMO

The phylogenetic relationships of all known species of the genus Aeromonas, and especially Aeromonas bestiarum and Aeromonas salmonicida, were investigated on 70 strains using the rpoD sequence, which encodes the sigma70 factor. This analysis was complemented with the sequence of gyrB, which has already proven useful for determining the phylogenetic relationships in the genus. Nucleotide sequences of rpoD and gyrB showed that both genes had similar substitution rates (< 2 %) and a similar number of variable positions (34 % for rpoD versus 32 % for gyrB). Strain groupings by analysis of rpoD, gyrB and a combination of both genes were consistent with the taxonomic organization of all Aeromonas species described to date. However, the simultaneous analysis of both clocks improved the reliability and the power to differentiate, in particular, closely related taxa. At the inter-species level, gyrB showed a better resolution for differentiating Aeromonas sp. HG11/Aeromonas encheleia and Aeromonas veronii/Aeromonas culicicola/Aeromonas allosaccharophila, while rpoD more clearly differentiated A. salmonicida from A. bestiarum. The analysis of rpoD provided initial evidence for clear phylogenetic divergence between the latter two species.


Assuntos
Aeromonas/classificação , Aeromonas/genética , DNA Girase/genética , RNA Polimerases Dirigidas por DNA/genética , Filogenia , Fator sigma/genética , Aeromonas salmonicida/classificação , Aeromonas salmonicida/genética , Proteínas de Bactérias/genética , DNA Bacteriano/química , DNA Bacteriano/isolamento & purificação , Genes Bacterianos , Dados de Sequência Molecular , Análise de Sequência de DNA , Homologia de Sequência
10.
Int J Syst Evol Microbiol ; 53(Pt 3): 875-883, 2003 May.
Artigo em Inglês | MEDLINE | ID: mdl-12807216

RESUMO

The phylogenetic relationships of all known species of the genus Aeromonas were investigated by using the sequence of gyrB, a gene that encodes the B-subunit of DNA gyrase. Nucleotide sequences of gyrB were determined from 53 Aeromonas strains, including some new isolates, which were also characterized by analysis of the 16S rDNA variable regions. The results support the recognition of the family Aeromonadaceae, as distinct from Plesiomonas shigelloides and other enteric bacteria. This phylogenetic marker revealed strain groupings that are consistent with the taxonomic organization of all Aeromonas species described to date. In particular, gyrB results agreed with 16S rDNA analysis; moreover, the former showed a higher capacity to differentiate between species. The present analysis was useful for the elucidation of reported discrepancies between different DNA-DNA hybridization sets. Additionally, due to the sequence diversity found at the intraspecies level, gyrB is proposed as a useful target for simultaneous identification of species and strains. In conclusion, the gyrB gene has proved to be an excellent molecular chronometer for phylogenetic studies of the genus Aeromonas.


Assuntos
Aeromonas/classificação , DNA Girase/genética , Filogenia , Análise de Sequência de DNA , Aeromonas/genética , Animais , DNA Ribossômico/análise , Humanos , Dados de Sequência Molecular , Hibridização de Ácido Nucleico , RNA Ribossômico 16S/genética , Especificidade da Espécie
11.
Clin Microbiol Infect ; 7(7): 345-51, 2001 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-11531978

RESUMO

OBJECTIVE: To determine whether Escherichia coli strains isolated from patients with uncomplicated acute pyelonephritis can be distinguished from those isolated from patients with complicated acute pyelonephritis on the basis of the genetic background. METHODS: In total, 103 E. coli strains isolated from patients with acute pyelonephritis (59 uncomplicated pyelonephritis (UAP) and 44 complicated pyelonephritis (CAP)) were characterized by RFLP of the intergenic spacer region 16S-23S rRNA, the presence of three alternative sequences found in the polymorphic V6 loop of the 16S rRNA gene, the presence of the pap gene, and antibiotic susceptibility. RESULTS: At similarity levels of 70%, four RFLP groups (alpha1, alpha2, beta1 and beta2) were discerned. Strains from UAP were statistically significant for alpha RFLP, with a strong association with the presence of the pap gene, V6-I sequence and antibiotic multisensitivity. Strains from CAP randomly belonged to the alpha or beta RFLP groups, with a very low presence of the pap gene, and random presence of V6 sequences, and were multiresistant to antibiotics. When the CAP strains were distributed according to underlying pathology, non-obstructive cases had RFLP and V6 polymorphisms similar to those of UAP cases, while obstructive cases were clearly distinct. CONCLUSIONS: UAP and non-obstructive CAP E. coli strains are sensitive to antimicrobials, show a high level of the pap gene and belong to the selective, homogeneous and highly protected molecular alpha2 group, where no recombinations, deletions or insertions are present. On the contrary, obstructive and vesicorenal reflux E. coli strains show significant antimicrobial resistance, high intercistronic heterogenicity (wide presence of block nucleotidic substitutions, deletions or insertions) and significantly lower virulence.


Assuntos
Infecções por Escherichia coli/microbiologia , Escherichia coli/genética , Pielonefrite/microbiologia , Óperon de RNAr/genética , Doença Aguda , Sequência de Bases , Primers do DNA , DNA Bacteriano/química , Farmacorresistência Bacteriana/genética , Eletroforese em Gel de Ágar , Escherichia coli/efeitos dos fármacos , Escherichia coli/patogenicidade , Humanos , Testes de Sensibilidade Microbiana , Dados de Sequência Molecular , Reação em Cadeia da Polimerase , Polimorfismo de Fragmento de Restrição , RNA Ribossômico 16S/genética , RNA Ribossômico 23S/genética , Homologia de Sequência do Ácido Nucleico , Virulência
12.
Actas Fund. Puigvert ; 20(3): 149-160, jul. 2001. ilus, tab
Artigo em Es | IBECS | ID: ibc-5937

RESUMO

A un total de 103 cepas de E. Boli aisladas de enfermos con pielonefritis aguda (59 cepas de pielonefritis no complicadas (PNAnoC) y 44 de pielonefritis complicadas (PNAC)) y 72 cepas de la colección ECOR se les ha determinado el tipo de secuencia V6 (posiciones 1000-1040) del gen 16S-rRNA, la posesión del gen pap y la secuencia espacio intergénico 16S-23S-rRNA mediante amplificación por PCR usando 7 cebadores específicos, digestión con endonucleasas, electroforesis y análisis de los polimorfismos de longitud de fragmentos de restricción (RFLP). Con niveles de similaridad del 70 por ciento se han formado 4 grupos denominados a-1, a-2, beta-1 y beta-2. El subgrupo a-2 se ha correlacionado con el B-2 de MLEE considerado de maxima virulencia.Las cepas aisladas de PNAnoC mostraron una asociación causal significativa (p <0,01) con el subgrupo molecular a-2 (74 por ciento) , secuencia V6-1(91,2 por ciento) y presencia del gen pap (85,3 por ciento). Por contra, en las cepas aisladas de PNAC no se observó relación de causalidad (p = n. s.) entre los grupos moleculares, la secuencia V6-I y la presencia del gen pap. La agrupación de las cepas de PNAC según el diagnóstico de la patología de base (no obstructiva: 13 casos, obstructiva: 20 casos y reflujo vesico-renal: 11 casos) demostró que para los casos no obstructivos se conservaba una estructura molecular estrechamente relacionada a los casos de PNAnoC, mientras que para el resto la pertenencia al grupo alfa/beta y tipo de secuencia era aleatorio con una presencia del gen pap muy baja (12,9 por ciento). La incidencia de polirresistencia a los antibióticos en el grupo a fue bastante menor que en el grupo beta (5,6 por ciento versus 25 por ciento respectivamente).En el grupo beta la frecuencia del gen pap en cepas polirresistentes disminuyó más de 4 veces respecto a las cepas sensibles o con monorresistencia de su propio grupo o más de 6 veces respecto a las del grupo a Se concluye que las cepas de PNAnoC poseen una elevada virulencia y homogeneidad y están altamente protegidas de recombinaciones o reordenaciones con patrón molecular de: subgrupo a-2 + presencia gen pap + secuencia V6-I + multisensibilidad a los antibióticos. Las cepas de PNAC (excepto los casos no obstructivos) tienen gran variabilidad intercistrónica (grupo alfa/beta, tipo de secuencia V6), poseen una baja virulencia y son mas polirresistentes a los antibióticos. (AU)


Assuntos
Humanos , Pielonefrite/etiologia , Escherichia coli/genética , Pielonefrite/genética , Pielonefrite/microbiologia , Escherichia coli/patogenicidade , Escherichia coli/isolamento & purificação , Resistência Microbiana a Medicamentos , Variação Genética
13.
FEMS Immunol Med Microbiol ; 28(3): 225-32, 2000 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-10865175

RESUMO

Genetic relationships of Aeromonas veronii strains isolated from human and environmental sources were investigated by restriction fragment length polymorphism (RFLP) of the polymerase chain reaction-amplified intergenic spacer region (ISR) flanked by the 16S and 23S rRNA genes. When using endonucleases AluI, HinfI and CfoI the 16S-23S rDNA-RFLP patterns showed considerable overall similarity, although most strains yielded specific profiles. Several intra-specific lines of descent comprised clinical strains linked to isolates from environmental sources. Strains having identical patterns may be individuals derived from highly similar, if not the same, microorganism. Results suggest that the ISR sequence-based method can be used to demonstrate colonization of a public water supply with a particular microorganism. In addition it could be very useful for tracing recurrent episodes of diarrhea and Aeromonas infection outbreaks.


Assuntos
Aeromonas/classificação , Microbiologia Ambiental , RNA Ribossômico 16S/genética , RNA Ribossômico 23S/genética , Aeromonas/genética , Primers do DNA , DNA Bacteriano/análise , DNA Ribossômico/análise , Infecções por Bactérias Gram-Negativas/epidemiologia , Humanos , Polimorfismo de Fragmento de Restrição , Especificidade da Espécie
14.
Int J Syst Evol Microbiol ; 50 Pt 6: 2069-2073, 2000 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-11155981

RESUMO

A previously described molecular method, based on 16S rDNA RFLP analysis, for the identification of Aeromonas spp. was unable to separate the species Aeromonas salmonicida, Aeromonas bestiarum and the recently described Aeromonas popoffii. In this study, the method has been extended with endonucleases AIwNI and PstI for the identification of these species. A molecular frame for the identification of all known Aeromonas spp. is presented.


Assuntos
Aeromonas/classificação , Aeromonas/genética , DNA Ribossômico/análise , Polimorfismo de Fragmento de Restrição , RNA Ribossômico 16S/genética , Animais , Desoxirribonucleases de Sítio Específico do Tipo II/metabolismo , Humanos , Análise de Sequência de DNA
15.
Int J Syst Bacteriol ; 49 Pt 4: 1403-8, 1999 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-10555319

RESUMO

The 16S rDNA sequences of the recently described Aeromonas encheleia and Aeromonas popoffii, were determined and compared with data from all known Aeromonas sp. Diagnostic 16S rDNA regions were also sequenced for some strains previously considered as an extension of A. encheleia and a strain of Aeromonas Group 501 (formerly Enteric Group 501). Results indicated that A. encheleia and A. popoffii are phylogenetically separated species as originally described. A conclusion about HG11 taxonomic status is not recommended until previous discrepancies are clarified by further DNA-DNA hybridization and sequencing studies.


Assuntos
Aeromonas/classificação , Aeromonas/genética , Filogenia , RNA Ribossômico 16S/genética , DNA Bacteriano/genética , DNA Ribossômico/genética , Hibridização de Ácido Nucleico , Análise de Sequência de DNA
16.
Int J Syst Bacteriol ; 49 Pt 2: 601-10, 1999 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-10319482

RESUMO

Sequence heterogeneities of variable positions located at regions V1 and V6 of 56 cloned 16S rRNA genes were determined from six Escherichia coli strains. These nucleotides were involved in secondary structure base-pairing of stem-loops. Compensatory and single mutations have occurred but secondary structure was conserved. Eight different sequences were found in the stem at region V1 indicating that in these sites mutation rates are higher than those of homogenizatin processes. Region V6 showed two different structures (V6-I and V6-II) although heterogeneities were determined in nine sites. Strains ECOR52 and ECOR56 only showed the V6-I sequence, ECOR35 showed V6-II, whereas clones from ECOR42 and ECOR49 showed both types of V6 structures. Results were confirmed by PCR using V6 sequence-specific probes. Stem V6-II was also found in 16S rRNA sequences deposited in the RDP (Ribosomal Database Project) belonging to distantly related taxa; ancestral sequence V6-II seems to be homogenized in all rrn operons of the multigene family of strain ECOR35 producing effects of distortion in the molecular clock, similar to those that homoplasies could produce. V6 sequence-specific probes were applied to the 72 ECOR strains: half showed both V6-I and V6-II, and the rest had one or another. Only strain ECOR24 did not yield products in the PCR test and sequencing of 12 cloned 16S rRNA genes revealed a third form, V6-III, also found in the RDP. Concerted evolution by homogenization of the rRNA family may induce chronometric distortions responsible for a loss of ultrametricity in phylogenetic trees, particularly, of very closely related micro-organisms.


Assuntos
Escherichia coli/genética , Genes de RNAr , Variação Genética , Família Multigênica/genética , RNA Ribossômico 16S/genética , Sequência de Bases , DNA Bacteriano/química , DNA Bacteriano/genética , DNA Ribossômico/química , DNA Ribossômico/genética , Genes Bacterianos , Dados de Sequência Molecular , Mutação , Conformação de Ácido Nucleico , Reação em Cadeia da Polimerase/métodos , Análise de Sequência de DNA
17.
J Bacteriol ; 181(9): 2703-9, 1999 May.
Artigo em Inglês | MEDLINE | ID: mdl-10217757

RESUMO

The molecular microevolution of the 23S rRNA gene (rrl) plus the spacer downstream has been studied by sequencing of different operons from some representative strains of the Escherichia coli ECOR collection. The rrl gene was fully sequenced in six strains showing a total of 67 polymorphic sites, a level of variation per nucleotide similar to that found for the 16S rRNA gene (rrs) in a previous study. The size of the gene was highly conserved (2902 to 2905 nucleotides). Most polymorphic sites were clustered in five secondary-structure helices. Those regions in a large number of operons were sequenced, and several variations were found. Sequences of the same helix from two different strains were often widely divergent, and no intermediate forms existed. Intercistronic variability was detected, although it seemed to be lower than for the rrs gene. The presence of two characteristic sequences was determined by PCR analysis throughout all of the strains of the ECOR collection, and some correlations with the multilocus enzyme electrophoresis clusters were detected. The mode of variation of the rrl gene seems to be quite similar to that of the rrs gene. Homogenization of the gene families and transfer of sequences from different clonal lines could explain this pattern of variation detected; perhaps these factors are more relevant to evolution than single mutation. The spacer region between the 23S and 5S rRNA genes exhibited a highly polymorphic region, particularly at the 3' end.


Assuntos
DNA Ribossômico/genética , Escherichia coli/genética , Genes Bacterianos , Variação Genética , RNA Ribossômico 23S/genética , Técnicas de Tipagem Bacteriana , Sequência de Bases , Bancos de Espécimes Biológicos , DNA Ribossômico/classificação , Escherichia coli/classificação , Evolução Molecular , Técnicas de Transferência de Genes , Dados de Sequência Molecular , Conformação de Ácido Nucleico , Sondas de Ácido Nucleico , Óperon , RNA Ribossômico 23S/classificação , RNA Ribossômico 5S/genética , Análise de Sequência de DNA , Homologia de Sequência do Ácido Nucleico , Especificidade da Espécie
18.
J Mol Evol ; 47(1): 62-72, 1998 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-9664697

RESUMO

The ribosomal RNA multigene family in Escherichia coli comprises seven rrn operons of similar, but not identical, sequence. Four operons (rrnC, B, G, and E) contain genes in the 16S-23S intergenic spacer region (ISR) for tRNA(Glu-2) and three (rrnA, D, and H) contain genes for tRNA(Ile-1) and tRNA(Ala-1B). To increase our understanding of their molecular evolution, we have determined the ISR sequence of the seven operons in a set of 12 strains from the ECOR collection. Each operon was specifically amplified using polymerase chain reaction primers designed from genes or open reading frames located upstream of the 16S rRNA genes in E. coli K12. With a single exception (ECOR 40), ISRs containing one or two tRNA genes were found at the same respective loci as those of strain K12. Intercistronic heterogeneity already found in K12 was representative of most variation among the strains studied and the location of polymorphic sites was the same. Dispersed nucleotide substitutions were very few but 21 variable sites were found grouped in a stem-loop, although the secondary structure was conserved. Some regions were found in which a stretch of nucleotides was substituted in block by one alternative, apparently unrelated, sequence (as illustrated by the known putative insertion of rsl in K12). Except for substitutions of different sizes and insertions/deletions found in the ISR, the pattern of nucleotide variation is very similar to that found for the 16S rRNA gene in E. coli. Strains K12 and ECOR 40 showed the highest intercistronic heterogeneity. Most strains showed a strong tendency to homogenization. Concerted evolution could explain the notorious conservation of this region that is supposed to have low functional restrictions.


Assuntos
DNA Ribossômico/genética , Escherichia coli/genética , Evolução Molecular , RNA Ribossômico 16S/genética , RNA Ribossômico 23S/genética , Sequência de Bases , Bancos de Espécimes Biológicos , DNA Bacteriano/genética , Escherichia coli/classificação , Dados de Sequência Molecular , Família Multigênica , Mutação , Conformação de Ácido Nucleico , Óperon , RNA de Transferência de Ácido Glutâmico/genética , Homologia de Sequência do Ácido Nucleico
19.
J Clin Microbiol ; 35(7): 1671-4, 1997 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-9196171

RESUMO

Identification of Aeromonas species, emergent pathogens for humans, has long been controversial due to their phenotypic and genomic heterogeneities. Computer analysis of the published 16S rRNA gene sequences revealed that restriction fragment length polymorphism of the PCR-amplified 16S rRNA gene is a good and rapid way of assessing the identities of all known species of Aeromonas. The method was evaluated with the reference strains of all species (or DNA homology groups) and 76 clinical isolates of diverse origin. Most results from the two approaches were in agreement, but some discrepancies were discerned. Advantages over previous phenotypic and genetic methods are discussed.


Assuntos
Aeromonas/classificação , Técnicas de Tipagem Bacteriana , Infecções por Bactérias Gram-Negativas/microbiologia , RNA Bacteriano/análise , Técnica de Amplificação ao Acaso de DNA Polimórfico , Aeromonas/genética , Aeromonas/isolamento & purificação , Humanos , RNA Bacteriano/genética , RNA Ribossômico 16S/análise , RNA Ribossômico 16S/genética
20.
Appl Environ Microbiol ; 63(4): 1261-7, 1997 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-9097422

RESUMO

The intraspecific genetic diversity of Oenococcus oeni, the key organism in the malolactic fermentation of wine, has been evaluated by random amplified polymorphic DNA (RAPD), ribotyping, small-plasmid content, and sequencing of RAPD markers with widespread distribution among the strains. Collection strains representing the diversity of this species have been studied together with some new isolates, many of which were obtained from wines produced by spontaneous malolactic fermentation. The RAPD profiles were strain specific and discerned two main groups of strains coincident with clusters obtained by macrorestriction typing in a previous work. Ribotyping and the conservation of RAPD markers indicates that O. oeni is a relatively homogeneous species. Furthermore, identical DNA sequences of some RAPD markers among strains representative of the most divergent RAPD clusters indicates that O. oeni is indeed a phylogenetically tight group, probably corresponding to a single clone, or clonal line of descent, specialized to grow in the wine environment and universally spread.


Assuntos
DNA Bacteriano/genética , Genoma Bacteriano , Cocos Gram-Positivos/genética , Impressões Digitais de DNA , Variação Genética , Cocos Gram-Positivos/classificação , Leuconostoc/classificação , Leuconostoc/genética , Dados de Sequência Molecular , Análise de Sequência de DNA
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