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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

The TR region in A. fumigatus gene Afu3g08990 containing a leader sequence and GPI anchor shows size variability. The TR region of Afu3g08990 was amplified by PCR in 11 clinical A. fumigatus isolates, including the genome-sequenced reference strain Af293. This figure shows size variation of the TR region between the strains.
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fig3: The TR region in A. fumigatus gene Afu3g08990 containing a leader sequence and GPI anchor shows size variability. The TR region of Afu3g08990 was amplified by PCR in 11 clinical A. fumigatus isolates, including the genome-sequenced reference strain Af293. This figure shows size variation of the TR region between the strains.

Mentions: Importantly, the repeat containing region of Afu3g08990 or CSP (cell-surface protein) was shown to vary significantly between A. fumigatus isolates from various origin (Levdansky et al. 2007; Balajee et al. 2007) (Fig. 3) By simply sequencing the Afu3g08990 repeat region in the various isolates and performing a phylogenetic analysis using the maximum parsimony method, it was possible to successfully “sub-type” fifty five epidemiologically linked A. fumigatus isolates from six nosocomial outbreaks of invasive aspergillosis. The results were concordant with another discriminatory genotyping technique, the Afut1 RFLP typing method. However, while Afut1 typing is labor and time intensive, needs specialised equipment and is not high throughput, Afu3g08990/CSP-typing requires only the ability to perform PCR and have access to an automated sequencer. Also, interpretation of the sequence information does not require sophisticated algorithms nor dedicated software and thus can be seamlessly integrated into any clinical microbiology laboratory.


Aspergillus strain typing in the genomics era.

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

The TR region in A. fumigatus gene Afu3g08990 containing a leader sequence and GPI anchor shows size variability. The TR region of Afu3g08990 was amplified by PCR in 11 clinical A. fumigatus isolates, including the genome-sequenced reference strain Af293. This figure shows size variation of the TR region between the strains.
© Copyright Policy
Related In: Results  -  Collection

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

fig3: The TR region in A. fumigatus gene Afu3g08990 containing a leader sequence and GPI anchor shows size variability. The TR region of Afu3g08990 was amplified by PCR in 11 clinical A. fumigatus isolates, including the genome-sequenced reference strain Af293. This figure shows size variation of the TR region between the strains.
Mentions: Importantly, the repeat containing region of Afu3g08990 or CSP (cell-surface protein) was shown to vary significantly between A. fumigatus isolates from various origin (Levdansky et al. 2007; Balajee et al. 2007) (Fig. 3) By simply sequencing the Afu3g08990 repeat region in the various isolates and performing a phylogenetic analysis using the maximum parsimony method, it was possible to successfully “sub-type” fifty five epidemiologically linked A. fumigatus isolates from six nosocomial outbreaks of invasive aspergillosis. The results were concordant with another discriminatory genotyping technique, the Afut1 RFLP typing method. However, while Afut1 typing is labor and time intensive, needs specialised equipment and is not high throughput, Afu3g08990/CSP-typing requires only the ability to perform PCR and have access to an automated sequencer. Also, interpretation of the sequence information does not require sophisticated algorithms nor dedicated software and thus can be seamlessly integrated into any clinical microbiology laboratory.

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