Acinetobacter ursingii sp. nov. and Acinetobacter schindleri sp. nov., isolated from human clinical specimens.

Nemec, Alexandr; Baère, Thierry De; Tjernberg, Ingela; Vaneechoutte, Mario; Reijden, T.J. van der; Dijkshoorn, Lenie

doi:10.1099/00207713-51-5-1891

Cited by 157 publications

(188 citation statements)

References 21 publications

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“…Twenty-four (genomic) species are currently recognized within the genus (Bouvet & Grimont, 1986;Tjernberg & Ursing, 1989;Bouvet & Jeanjean, 1989;Gerner-Smidt & Tjernberg, 1993;Vaneechoutte et al, 1999;Nemec et al, 2001) and strains of these species usually form colonies of 1?0-2?0 mm in diameter after 24 h incubation under optimum growth conditions (Bouvet & Grimont, 1986;Nemec et al, 2001). In a taxonomic study of Acinetobacter clinical isolates (Nemec et al, 2000), two strains were found which formed notably small colonies on routine agar media and could not be identified as any known (genomic) species.…”

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confidence: 99%

“…Phenotypic characterization was done essentially according to Bouvet & Grimont (1987) and Gerner-Smidt et al (1991), with some modifications. Details of the methods and their interpretative criteria have been given by Dijkshoorn et al (1998) and Nemec et al (2000Nemec et al ( , 2001. The assimilation tests were performed in tubes containing the fluid medium of Cruze et al (1979) supplemented with 0?1 % (w/v) carbon source.…”

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confidence: 99%

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Acinetobacter parvus sp. nov., a small-colony-forming species isolated from human clinical specimens

Nemec

Dijkshoorn

Cleenwerck

et al. 2003

International Journal of Systematic and Evolutionary Microbiology

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The taxonomic status of seven glucose-non-acidifying, non-proteolytic Acinetobacter strains characterized by forming small colonies on agar media was studied. With one exception, all strains were from human specimens. They could be distinguished from all described Acinetobacter (genomic) species by their ability to grow on ethanol and acetate as sole sources of carbon but not on 22 other substrates tested including DL-lactate or DL-4-aminobutyrate. DNA-DNA hybridization studies, 16S rRNA gene sequence analysis, amplified rDNA restriction analysis and DNA polymorphism analysis by AFLP showed that these strains represent a hitherto unknown species of the genus Acinetobacter, for which the name Acinetobacter parvus (type strain LMG 21765 T =LUH 4616 T =NIPH 384 T =CCM 7030 T ) is proposed.The genus Acinetobacter comprises non-motile, strictly aerobic, oxidase-negative, Gram-negative bacteria that grow well on simple media. Twenty-four (genomic) species are currently recognized within the genus (Bouvet & Grimont, 1986;Tjernberg & Ursing, 1989;Bouvet & Jeanjean, 1989;Gerner-Smidt & Tjernberg, 1993;Vaneechoutte et al., 1999;Nemec et al., 2001) and strains of these species usually form colonies of 1?0-2?0 mm in diameter after 24 h incubation under optimum growth conditions (Bouvet & Grimont, 1986;Nemec et al., 2001). In a taxonomic study of Acinetobacter clinical isolates (Nemec et al., 2000), two strains were found which formed notably small colonies on routine agar media and could not be identified as any known (genomic) species. These strains were glucose-non-acidifying, non-proteolytic, did not utilize any of the 14 carbon sources of the identification scheme of Bouvet & Grimont (1987) and had highly similar amplified rDNA restriction analysis (ARDRA) profiles. Later, five strains similar to the two strains were found among archive strains in our collections. The aim of the present study was to define the taxonomic status of these strains by a polyphasic analysis.The seven strains used in this study are listed in Table 1. All had the properties of the genus Acinetobacter (Juni, 1984), i.e. they were Gram-negative, strictly aerobic, oxidasenegative, non-motile coccobacilli, and were positive in the transformation assay of Juni (1972). The methods for genotypic characterization included ARDRA, AFLP fingerprinting and comparative 16S rDNA sequence analysis. Phenotypic characterization was done essentially according to Bouvet & Grimont (1987) LMG 19082, which produced large amounts of exopolysaccharides, were subjected to a mild alkaline hydrolysis step before cell lysis, as described by Willems et al. (2001). The G+C content of the DNA was determined by HPLC according to the method of Mesbah et al. (1989). Nonmethylated phage l DNA (Sigma) was used as the calibration reference. DNA-DNA hybridizations were performed using a modification of the microplate method described by Ezaki et al. (1989) and Goris et al. (1998). Hybridizations were performed at 37 uC in a hybridization solution [26 SSC, 56Denhardt's solution, ...

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confidence: 99%

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confidence: 99%

Acinetobacter parvus sp. nov., a small-colony-forming species isolated from human clinical specimens

Nemec

Dijkshoorn

Cleenwerck

et al. 2003

International Journal of Systematic and Evolutionary Microbiology

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“…Otra estrategia genómica para la asignación taxonómica es la caracterización de fragmentos de ADN y sus variaciones, que pueden ser sitios de restricción, inserciones, supresiones, secuencias repetidas o microsatélites, polimorfismos de una sola base u otras diferencias de las secuencias (Moore et al 2010). La detección de polimorfismo del tamaño de fragmentos amplificados (AFLP: amplified fragment length polymorphism) ha mostrado ser útil para la delineación de nuevas especies (Nemec et al 2001). Con la intención de utilizar la mayor información posible e incrementar la precisión en la caracterización, también se han propuesto protocolos de asignación de taxones con otras moléculas y con un enfoque polifásico (Moore et al 2010) mediante espectrometría de masas (Ramasamy et al 2014).…”

Section: Specific Databasesunclassified

“…Another genomic approach for taxonomic assignment is the characterization of DNA fragments and their variations, which can be restriction sites, insertions and deletions, DNA sequence repeats or microsatellites, single nucleotide polymorphisms or other sequence variations (Moore et al 2010). Amplified fragment length polymorphism (AFLP) has also proven useful for the delineation of new species (Nemec et al 2001). In order to apply as much information as possible to obtain the most accurate characterization possible, taxonomic assignment protocols using other molecules and a polyphasic approach, including MALD-TOF mass spectrometry (Ramasamy et al 2014), have also been proposed (Moore et al 2010).…”

Section: Asignación De Taxonesmentioning

confidence: 99%

The 16S rRNA gene in the study of marine microbial communities

et al. 2015

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ABSTRACT. New sequencing technologies and analytical capabilities have stimulated the study of microbial communities from specific environments, enabling researchers to understand the complexity of those systems. The 16S rRNA gene has proved very useful in describing the diversity and characterization of marine microbial communities, particularly of uncultivated organisms. The development of new sequencing techniques has contributed to the exponential increase in the number of reported 16S rRNA sequences as barcodes for microorganisms, forcing a review of concepts and methods for the taxonomic classification of these organisms. Manipulation and analysis of large amounts of genetic information have prompted the development of specific databases, specialized algorithms, and computational tools to compare thousands of such sequences and make a taxonomic assignment. Complete 16S rRNA sequences are thus needed for accurate and reproducible taxonomy assignment in the study of marine bacterial communities.Key words: metagenomics, marine microbial communities, 16S rRNA databases. RESUMEN. Las nuevas tecnologías de secuenciación y capacidades analíticas han estimulado el estudio de las comunidades microbianas deambientes específicos, lo cual ha permitido conocer la complejidad de estos sistemas. El gen ARNr 16S ha demostrado ser de gran utilidad para describir y caracterizar las comunidades microbianas marinas, especialmente los organismos no cultivados. Las nuevas técnicas de secuenciación han contribuido al incremento exponencial de registro de secuencias, aunque parciales, del ARNr 16S como elemento de código de barras para microorganismos. Consecuentemente, ha sido necesaria una revisión de conceptos y métodos de clasificación taxonómica para estos organismos. El manejo y análisis de una gran cantidad de información génica han impulsado el desarrollo de bases de datos específicas, algoritmos y herramientas computacionales especializadas para comparar miles de secuencias semejantes y hacer la asignación taxonómica. Por lo tanto, las secuencias completas del ARNr 16S son necesarias para una asignación taxonómica certera y reproducible en los estudios de comunidades microbianas marinas.Palabras clave: metagenómica, comunidades microbianas marinas, bases de datos ARNr 16S.

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“…Selective amplification of genomic restriction fragments using AFLP was performed as described previously [3]. Briefly, purified DNA was digested using EcoRI and MseI, and amplification was carried out with a Cy5-labelled EcoRI + A primer and an MseI + C primer (A and C, selective bases).…”

Section: Amplified Fragment Length Polymorphism Typingmentioning

confidence: 99%

Can Escherichia coli be used as an indicator organism for transmission events in hospitals?

Broek

Bernards

Reijden

et al. 2008

Eur J Clin Microbiol Infect Dis

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Can Escherichia coli be used as an indicator organism for transmission events in hospitals? Perineal and pharyngeal swabs were obtained from patients admitted to a medical or surgical intensive care unit within 24 h of admission and then twice per week. Escherichia coli isolates were typed by random amplification of polymorphic DNA (RAPD) and amplified fragment length polymorphism (AFLP) typing. Based on the typing results, transmission rates for RAPD and AFLP typing were 8.5 and 6.6 per 100 patient-days. Requiring in addition to similarity in genotype parity in time and place for a transmission event, the incidence dropped to 3.8 (RAPD) and 1.7 (AFLP) per 100 patient-days. The two typing methods not only differed with respect to numbers of transmissions identified, but also to individuals involved in transmissions. This study identified a number of problems regarding the use of Escherichia coli as indicator organism for transmission events. The use of Escherichia coli for this purpose cannot be recommended at the moment.

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Acinetobacter ursingii sp. nov. and Acinetobacter schindleri sp. nov., isolated from human clinical specimens.

Cited by 157 publications

References 21 publications

Acinetobacter parvus sp. nov., a small-colony-forming species isolated from human clinical specimens

Acinetobacter parvus sp. nov., a small-colony-forming species isolated from human clinical specimens

The 16S rRNA gene in the study of marine microbial communities

Can Escherichia coli be used as an indicator organism for transmission events in hospitals?

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