dnaJ gene sequence-based assay for species identification and phylogenetic grouping in the genus Staphylococcus

Abstract

In the last few years, many attempts have been made to use conserved gene sequences for identification and for phylogenetic studies of Staphylococcus species. In an effort to identify a more reliable approach, a dnaJ gene sequence-based database was created. In this study, an approximately 883 bp portion of the dnaJ gene sequence from 45 staphylococcal type strains was compared with 16S rRNA and other conserved gene (hsp60, sodA and rpoB) sequences available in public databases. Nucleotide sequence comparisons revealed that the staphylococcal dnaJ gene showed higher discrimination (mean similarity 77.6 %) than the 16S rRNA (mean similarity 97.4 %), rpoB (mean similarity 86 %), hsp60 (mean similarity 82 %) and sodA (mean similarity 81.5 %) genes. Analysis of the dnaJ gene sequence from 20 Staphylococcus isolates representing two clinically important species showed <1 % sequence divergence. Phylogenetic data obtained from the dnaJ gene sequence were in general agreement with those of 16S rRNA gene sequence analysis and DNA-DNA reassociation studies. In conclusion, the dnaJ gene sequence-based assay is an effective alternative to currently used methods, including 16S rRNA gene sequencing, for identification and taxonomical analysis of Staphylococcus species.

Identification of Coagulase-Negative Staphylococci by SodA Gene Sequence Analysis

“…In addition, the partial sodA gene sequence failed to differentiate between the two subspecies of S. capitis, S. carnosus, S. saprophyticus and S. succinus and also the three subspecies of S. sciuri as the similarity among the subspecies was 100%. This finding is consistent with other conserved genes used for staphylococcal identification including dnaJ (Shah et al, 2007), hsp60 (Kwok and Chow, 2003) and 16S rRNA (Ghebremedhin et al, 2008;Kwok and Chow, 2003) where majority of complete discrimination at subspecies level was unsuccessful due to of high similarities among the subspecies.…”

“…In general, the results suggest that apart from the subspecies level, the sodA internal sequence is able to show more species discrimination as compared to the sequence of other conserved genes such as the 16S rRNA with mean similarity of 90% (Shah et al, 2007), rpoB with mean similarity of 86% (Drancourt and Raoult, 2002;Mellmann et al, 2006) and hsp60 with mean similarity of 82% (Kwok et al, 1999). Following general convention, a 95% identity threshold was adopted as the limit for a positive identification and unambiguous assignment to a particular species.…”

“…However, the use of this gene is limited due to high degree of sequence similarity between closely related species (Becker et al, 2004;Goh et al, 1996;Gribaldo et al, 1997;Kwok et al, 1999). Hence, other highly conserved sequence has been exploited which includes sodA (Poyart et al, 2001), gap (Bergeron et al, 2011;Ghebremedhin et al, 2008), hsp60 (Ghebremedhin et al, 2008;Kwok et al, 1999), rpoB (Drancourt and Raoult, 2002;Mellmann et al, 2006), tuf (Heikens et al, 2005) and dnaJ (Shah et al, 2007) gene sequencing methods. However, the sequences of some genes are not sufficient to discriminate between closely related Staphylococcus at both species and subspecies level and the databases only includes a limited number of species.…”

Quarter- and cow-level risk factors for intramammary infection with coagulase-negative staphylococci species in Swiss dairy cows

“…Isolates with scores ≥2.0 were identified to the species level according to manufacturer's guidelines. Each time an isolate displayed a score below 2.0, it was further identified by sequencing of the 16S rRNA gene using universal primers (Kuhnert et al, 1996) as well as by sequencing of the rpoB or dnaJ genes (Drancourt and Raoult, 2002;Shah et al, 2007). Its spectral profile was introduced into the MALDI-TOF MS database thereafter.…”

hsp60 and 16S rRNA gene sequence relationships among species of the genus Bacteroides with the finding that Bacteroides suis and Bacteroides tectus are heterotypic synonyms of Bacteroides pyogenes

“…The taxonomy of the genus Bacteroides has undergone significant changes in the last two decades (Dewhirst et al, 1990;Moore & Moore, 1994;Rautio et al, 2003;Sakamoto et al, 2002Sakamoto et al, , 2007Sakamoto & Benno, 2006;Shah & Collins, 1988. It has also been reported that 16S rRNA gene sequencing is useful for the identification of isolates of clinically significant species of the genus Bacteroides (Song et al, 2005).To date, a multilocus sequence typing (MLST) approach has been widely used to infer the phylogeny of organisms (Alexandre et al, 2008; Itoh et al, 2006;Shah et al, 2007;Yamamoto & Harayama, 1995). However, only limited information has been accumulated for species of the genus Bacteroides.…”