Evaluation of the authenticity of haloarchaeal strains by random-amplified polymorphic DNA

Aeromonas aquariorum sp. nov., isolated from aquaria of ornamental fish

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.

Phylogenetic identification of Aeromonas strains isolated from carcasses of pig as new members of the species Aeromonas allosaccharophila

The first description of the species Aeromonas allosaccharophila was only based on two strains (the type strain CECT4199, and a duplicate CECT4200) isolated from diseased elvers (Anguilla anguilla) of an eel-farm located in Valencia, Spain, and one stool isolate (ATCC35942) from a female with diarrhoea and food poisoning in South Carolina, U.S.A. In the present study, 17 Aeromonas isolates obtained from carcasses of pigs and from the equipment for the cleaning process, and one strain recently isolated from a clinical case of gastroenteritis, were genetically identified as Aerornonas allosaccharophila on the basis of gyrB and 16S rRNA gene sequencing. In addition, this phylogenetic approach also supports the classification of Aeromonas veronii biogroup sobria reference strains LMG13071, LMG13073 and LMG13074 within the species A. allosaccharophila. The A. allosaccharophila strains isolated from pig carcasses processed in a single slaughterhouse presented a clonal origin, on the basis of random amplified polymorphic DNA genetic typing. To our knowledge, this is the first time since the species description that A. allosaccharophila has been newly identified, being on this occasion isolated from the environment of a slaughterhouse. Our findings indicate that this species may be readily identified by a sequencing approach and, consequently, the present work supports the existence of this phylogenetic cluster.

Application of four molecular techniques for typing outbreak-associated Mycobacterium tuberculosis strains

We applied four molecular techniques for the typing of strains of Mycobacterium tuberculosis associated with outbreaks: RFLP of the IS6110 insertion sequence, spoligotyping, RAPD, and PCR-IS6110. All 4 techniques were applied to 18 strains which were shown by epidemiological data to be involved in 6 outbreaks. All the methods classified the strains into the same groups as the classical epidemiological data did, but RFLP of the IS6110 insertion sequence and spoligotyping are laborious techniques requiring more than a full day's work, whilst RAPD and PCR IS6110 are simple methods easily incorporated into the daily routine. Nevertheless, a large-scale process of standardization and evaluation is necessary in order to be able to establish the true value of the latter two methods as intraspecific characterization markers for M. tuberculosis isolates.

Intraspecific genetic diversity of Oenococcus oeni as derived from DNA fingerprinting and sequence analyses

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.