Improved identification of Gordonia, Rhodococcus and Tsukamurella species by 5'-end 16S rRNA gene sequencing.
OBJECTIVE
The identification of fastidious aerobic Actinomycetes such as Gordonia, Rhodococcus, and Tsukamurella has remained a challenge leading to clinically significant misclassifications. This study is intended to examine the feasibility of partial 5'-end 16S rRNA gene sequencing for the identification of Gordonia, Rhodococcus, and Tsukamurella, and defined potential reference sequences for species from each of these genera.


METHODS
The 16S rRNA gene sequence based identification algorithm for species identification was used and enhanced by aligning test sequences with reference sequences from the List of Prokaryotic Names with Standing in Nomenclature.


RESULTS
Conventional PCR based 16S rRNA gene sequencing and the alignment of the isolate 16S rRNA gene sequence with reference sequences accurately identified 100% of clinical strains of aerobic Actinomycetes. While partial 16S rRNA gene sequences of reference type strains matched with the 16S rRNA gene sequences of 19 isolates in our data set, another 13 strains demonstrated a degree of polymorphism with a 1-4 bp difference in the regions of difference.


CONCLUSIONS
5'-end 606 bp 16S rRNA gene sequencing, coupled with the assignment of well defined reference sequences to clinically relevant species of bacteria, can be a useful strategy for improving the identification of clinically relevant aerobic Actinomycetes.
Department of Neurosurgery, Beijing Tian Tan Hospital, Capital Medical University, Beijing, PR China.
Tao
T
Wang
Fanrong
F
Kong
Sharon
S
Chen
Meng
M
Xiao
Tania
T
Sorrell
Xiaoyan
X
Wang
Shuo
S
Wang
Vitali
V
Sintchenko
D024506:5' Flanking Region / Q000235:genetics*; D000193:Actinomycetales Infections / Q000175:diagnosis / Q000382:microbiology; D004269:DNA, Bacterial / Q000032:analysis / Q000235:genetics; D033601:Gordonia Bacterium / Q000235:genetics / Q000302:isolation & purification*; D006801:Humans; D008828:Microbiological Techniques; D008969:Molecular Sequence Data; D012329:RNA, Bacterial / Q000032:analysis / Q000235:genetics; D012336:RNA, Ribosomal, 16S / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D012240:Rhodococcus / Q000235:genetics / Q000302:isolation & purification*; D012680:Sensitivity and Specificity; D017423:Sequence Analysis, RNA; D013045:Species Specificity
D004269:DNA, Bacterial; D012329:RNA, Bacterial; D012336:RNA, Ribosomal, 16S