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Aspergillus strain typing in the genomics era.

Klaassen CH, Osherov N - Stud. Mycol. (2007)

Bottom Line: Multiple reasons may justify a need for strain typing purposes, but the most common reason is to delineate the epidemiological relationships between isolates.The availability of whole genome sequences has greatly influenced our ability to develop highly targeted and efficient strain typing methods fur these purposes.Some strain typing methods may serve dual goals: not only can they be used to discriminate between multiple isolates of a certain species, they can also aid in the recognition, identification, description and validation process of a fungal species.

View Article: PubMed Central - PubMed

Affiliation: Department of Medical Microbiology and Infectious Diseases, Canisius Wilhelmina Hospital, Nijmegen, The Netherlands.

ABSTRACT
Multiple reasons may justify a need for strain typing purposes, but the most common reason is to delineate the epidemiological relationships between isolates. The availability of whole genome sequences has greatly influenced our ability to develop highly targeted and efficient strain typing methods fur these purposes. Some strain typing methods may serve dual goals: not only can they be used to discriminate between multiple isolates of a certain species, they can also aid in the recognition, identification, description and validation process of a fungal species.

No MeSH data available.


Related in: MedlinePlus

Example of AFLP analysis showing the discriminatory power as well as the ability to discriminate between isolates belonging to different species. The figure shows 16 fingerprints from A. fumigatus cultured from 16 IA patients (1 isolate per patient). Based on the differential presence or absence of one or more bands, all isolates can be discriminated from each other. One isolate with a clearly different fingerprint turned out to be N. fisheri. The dendrogram was calculated by UPGMA clustering using the Pearson correlation coefficient. The scale bar indicates the percentage similarity.
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fig2: Example of AFLP analysis showing the discriminatory power as well as the ability to discriminate between isolates belonging to different species. The figure shows 16 fingerprints from A. fumigatus cultured from 16 IA patients (1 isolate per patient). Based on the differential presence or absence of one or more bands, all isolates can be discriminated from each other. One isolate with a clearly different fingerprint turned out to be N. fisheri. The dendrogram was calculated by UPGMA clustering using the Pearson correlation coefficient. The scale bar indicates the percentage similarity.

Mentions: Whereas AFLP has originally been presented as a tool for strain typing purposes, it is also very well suited to simultaneously resolve isolates belonging to different species from each other. This is relevant in the case where the identification of a microorganism may be uncertain such as the species from the morphologically very similar section Fumigati. If not properly identified, use of such typing data could easily lead to false conclusions. In a way, AFLP can be considered the perfect PCR alternative to DNA-DNA reassociation studies. Classical DNA-DNA reassociation studies rely on sequence similarities. If two species share a certain amount of sequence information, it is to be expected that they will also share a certain amount of similarity in banding patterns from an AFLP fingerprint. In fact, this has already been demonstrated for a variety of bacterial and fungal species. According to our own observations, AFLP fingerprints of isolates of the same species are usually > 60 % similar whereas fingerprints for isolates representing different species are usually < 40 % similar (Fig. 2). We also used AFLP analysis for confirmation of the identity of 67 isolates representing 26 species in Aspergillus section Fumigati. These isolates have previously been identified using a variety of other methods. Although the majority of isolates were correctly identified, this exercise clearly showed that: i some isolates were misidentified, ii that some recognised species are comprised of multiple clearly discernible subgroups and iii that several isolates that are currently recognised as different species should actually be grouped into a single species. Thus, AFLP can very well complement the use of MLST and other methods in the recognition and validation process of fungal species.


Aspergillus strain typing in the genomics era.

Klaassen CH, Osherov N - Stud. Mycol. (2007)

Example of AFLP analysis showing the discriminatory power as well as the ability to discriminate between isolates belonging to different species. The figure shows 16 fingerprints from A. fumigatus cultured from 16 IA patients (1 isolate per patient). Based on the differential presence or absence of one or more bands, all isolates can be discriminated from each other. One isolate with a clearly different fingerprint turned out to be N. fisheri. The dendrogram was calculated by UPGMA clustering using the Pearson correlation coefficient. The scale bar indicates the percentage similarity.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2275195&req=5

fig2: Example of AFLP analysis showing the discriminatory power as well as the ability to discriminate between isolates belonging to different species. The figure shows 16 fingerprints from A. fumigatus cultured from 16 IA patients (1 isolate per patient). Based on the differential presence or absence of one or more bands, all isolates can be discriminated from each other. One isolate with a clearly different fingerprint turned out to be N. fisheri. The dendrogram was calculated by UPGMA clustering using the Pearson correlation coefficient. The scale bar indicates the percentage similarity.
Mentions: Whereas AFLP has originally been presented as a tool for strain typing purposes, it is also very well suited to simultaneously resolve isolates belonging to different species from each other. This is relevant in the case where the identification of a microorganism may be uncertain such as the species from the morphologically very similar section Fumigati. If not properly identified, use of such typing data could easily lead to false conclusions. In a way, AFLP can be considered the perfect PCR alternative to DNA-DNA reassociation studies. Classical DNA-DNA reassociation studies rely on sequence similarities. If two species share a certain amount of sequence information, it is to be expected that they will also share a certain amount of similarity in banding patterns from an AFLP fingerprint. In fact, this has already been demonstrated for a variety of bacterial and fungal species. According to our own observations, AFLP fingerprints of isolates of the same species are usually > 60 % similar whereas fingerprints for isolates representing different species are usually < 40 % similar (Fig. 2). We also used AFLP analysis for confirmation of the identity of 67 isolates representing 26 species in Aspergillus section Fumigati. These isolates have previously been identified using a variety of other methods. Although the majority of isolates were correctly identified, this exercise clearly showed that: i some isolates were misidentified, ii that some recognised species are comprised of multiple clearly discernible subgroups and iii that several isolates that are currently recognised as different species should actually be grouped into a single species. Thus, AFLP can very well complement the use of MLST and other methods in the recognition and validation process of fungal species.

Bottom Line: Multiple reasons may justify a need for strain typing purposes, but the most common reason is to delineate the epidemiological relationships between isolates.The availability of whole genome sequences has greatly influenced our ability to develop highly targeted and efficient strain typing methods fur these purposes.Some strain typing methods may serve dual goals: not only can they be used to discriminate between multiple isolates of a certain species, they can also aid in the recognition, identification, description and validation process of a fungal species.

View Article: PubMed Central - PubMed

Affiliation: Department of Medical Microbiology and Infectious Diseases, Canisius Wilhelmina Hospital, Nijmegen, The Netherlands.

ABSTRACT
Multiple reasons may justify a need for strain typing purposes, but the most common reason is to delineate the epidemiological relationships between isolates. The availability of whole genome sequences has greatly influenced our ability to develop highly targeted and efficient strain typing methods fur these purposes. Some strain typing methods may serve dual goals: not only can they be used to discriminate between multiple isolates of a certain species, they can also aid in the recognition, identification, description and validation process of a fungal species.

No MeSH data available.


Related in: MedlinePlus