Impact of IS1111 insertion on the MLVA genotyping of Coxiella burnetii.
Q fever epidemiological investigations of the likely sources of contamination may involve Coxiella burnetii MLVA for direct and rapid typing from clinical samples. However, little information is available with regards to PCR amplification failures in C. burnetii MLVA typing. This paper focuses on difficulties encountered with MLVA loci that may impact the interpretation of MLVA data and shows that some loci may constitute hotspots for mutational events. MLVA genotyping, using 17 different loci, was used on vaginal swabs (VS) from clinically infected animals as described elsewhere (Chmielewski et al., 2009). Amplicons of interest were sequenced and identified using the BLAST software by comparison with sequences available in GenBank. All VS samples produced MLVA patterns. However, amplification failures or unexpected sizes amplicons (>to 1.5 kbp), making the interpretation of MLVA complicated, were also observed. Sequencing of these amplicons revealed the presence of IS1111 element insertion. In this C. burnetii MLVA study some difficulties encountered with genotyping are highlighted and the role of IS1111 element in genome plasticity is confirmed. Finally, the need for the selection of a set of VNTRs for an efficient MLVA scheme and the question of standardization and harmonization for comparable MLVA typing data are raised again.
Anses, Sophia-Antipolis Laboratory, Animal Q Fever Unit, Sophia-Antipolis, France. Electronic address: Karim.SIDI-BOUMEDINE@anses.fr.
Karim
K
Sidi-Boumedine
Anses, Sophia-Antipolis Laboratory, Animal Q Fever Unit, Sophia-Antipolis, France.
Véronique
V
Duquesne
Anses, Sophia-Antipolis Laboratory, Animal Q Fever Unit, Sophia-Antipolis, France.
Myriam
M
Prigent
Anses, Sophia-Antipolis Laboratory, Animal Q Fever Unit, Sophia-Antipolis, France.
Elise
E
Yang
Unité d'Epidémiologie Animale UR0346, Institut National de la Recherche Agronomique (INRA), Saint Genès Champanelle, France.
Aurélien
A
Joulié
Anses, Sophia-Antipolis Laboratory, Animal Q Fever Unit, Sophia-Antipolis, France.
Richard
R
Thiéry
Anses, Sophia-Antipolis Laboratory, Animal Q Fever Unit, Sophia-Antipolis, France.
Elodie
E
Rousset
D000818:Animals; D001483:Base Sequence; D016997:Coxiella burnetii / Q000145:classification* / Q000235:genetics*; D004251:DNA Transposable Elements / Q000235:genetics*; D004269:DNA, Bacterial / Q000235:genetics; D005838:Genotype; D060005:Genotyping Techniques / Q000379:methods*; D015511:Goat Diseases / Q000382:microbiology; D006041:Goats / Q000382:microbiology; D006801:Humans; D018598:Minisatellite Repeats / Q000235:genetics*; D008969:Molecular Sequence Data; D058889:Molecular Typing / Q000379:methods*; D011778:Q Fever / Q000382:microbiology; D017422:Sequence Analysis, DNA
D004251:DNA Transposable Elements; D004269:DNA, Bacterial
Coxiella burnetii; IS1111 element insertion; MLVA genotyping; Q fever; Standardization and harmonization of MLVA typing