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Project ID: ICA4-CT-2001-10028
Finanziato nell'ambito di: FP5-INCO 2
Paese: Belgium

Taxonomic description of chloramphenicol-resistant heterotrophs from aquaculture environments

A reliable identification programme was carried out for the taxonomic characterization of C isolates collected during the project. Replicate or clonally related isolates were first identified by DNA fingerprinting using repetitive chromosomal element-PCR analysis (rep-PCR).

On the basis of the relatedness of the profiles obtained, 92 - possible duplicate - isolates were identified and not considered further. Following dereplication, a first step in the identification strategy included gas-liquid chromatographic analysis of cellular fatty acid methyl esters (FAMEs). The extraction and analysis of FAMEs was performed according to the standardized protocol of the Sherlock Identification System (Microbial ID Inc., Newark, DE, USA).

For identification, FAME profiles of unknown isolates were compared with the general TSBA database (MIDI) for heterotrophs. Depending on the taxonomic diversity of the strain collection, second choice techniques such as API, AFLP fingerprinting and 16S rDNA sequencing were included for species identifications of specific bacterial groups. FAME analysis allowed to classify all 558 investigated isolates at least at the bacterial family level.

Distribution analysis of the identification results revealed that the majority of the C isolates belong to six bacterial families i.e. the Enterobacteriaceae (n=350; 63%) followed by members of the Pseudomonadaceae (n=67; 12%), Moraxellaceae (n=62; 11%), Bacillaceae (n=33; 6%), Micrococcaceae (n=19; 3%) and Aeromonadaceae (n=11; 2%). A total of 15 C isolates belonged to other families i.e. Alcaligenaceae, Comamonadaceae, Enterococcaceae, Flavobacteriaceae and Sphingobacteriaceae. One isolate belonging to the g-Proteobacteria could not be unequivocally placed in a specific bacterial family.

For the first time, a comprehensive view was generated on the taxonomic diversity of CHL-resistant heterotrophs in Southeast Asian aquaculture environments.

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