Streptococcus pseudopneumoniae Identification by Pherotype: a Method To Assist Understanding of a Potentially Emerging or Overlooked Pathogen

Abstract

bThe recent identification of Streptococcus pseudopneumoniae (pseudopneumococcus) has complicated classification schemes within members of the "mitis" streptococcal group. Accurate differentiation of this species is necessary for understanding its disease potential and identification in clinical settings. This work described the use of the competence-stimulatory peptide ComC sequence for identification of S. pseudopneumoniae. ComC sequences from clinical sources were determined for 17 strains of S. pseudopneumoniae, Streptococcus pneumoniae, and Streptococcus oralis. An additional 58 ComC sequences from a range of sources were included to understand the diversity and suitability of this protein as a diagnostic marker for species identification. We identified three pherotypes for this species, delineated CSP6.1 (10/14, 79%), CSP6.3 (3/14, 21%), and SK674 (1/14, 7%). Pseudopneumococcal ComC sequences formed a discrete cluster within those of other oral streptococci. This suggests that the comC sequence could be used to identify S. pseudopneumoniae, thus simplifying the study of the pathogenic potential of this organism. To avoid confusion between pneumococcal and pseudopneumococcal pherotypes, we have renamed the competence pherotype CSP6.1, formerly reported as an "atypical" pneumococcus, CSPps1 to reflect its occurrence in S. pseudopneumoniae.T he mitis group of streptococci includes nasopharyngeal colonizers such as Streptococcus mitis, Streptococcus oralis, Streptococcus pneumoniae, and the recently classified Streptococcus pseudopneumoniae (2). Of these, S. pneumoniae (pneumococcus) is responsible for more than a million deaths annually and is responsible for diseases such as otitis media, pneumonia, septicemia, and meningitis. However, invasive diseases caused by other related viridans group streptococci had been documented (16,26,31).Some strains of S. pseudopneumoniae, along with S. mitis and S. oralis, have often been classified previously as "atypical pneumococci," because of their similarity to S. pneumoniae. These organisms share Ն99% identity in 16S rRNA gene sequences (2,21,43). Optochin sensitivity and bile solubility, the two standard pneumococcal phenotypic identification tests, have proven to be inconclusive for differentiating pneumococci from these atypical strains (3,4,9,10,17,19,20,22,27,29,32,34,38,39,49). Virulence factors that were once thought to be exclusive to the pneumococcus, such as pneumolysin (encoded by ply) and autolysin A (encoded by lytA), have been detected in commensal streptococcal species (18,35,49), compromising their specificity as species identification markers. The pathogenic potential of S. pseudopneumoniae (the pseudopneumococcus) has been demonstrated in a murine model (12) as well as in humans (2,18,23,24,28,40). Rapid, correct identification of this organism in the clinical setting is essential for diagnosis and for understanding its disease potential. A simple, unequivocal method to identify S. pseudopneumoniae would be valuable.Streptococci are competent for gene...

Clinical and Antimicrobial Susceptibility Data of 140 Streptococcus pseudopneumoniae Isolates in France

“…treptococcus pseudopneumoniae is a recently designated species included in the S. oralis-S. mitis group and closely related to Streptococcus pneumoniae that may be identified using appropriate phenotypic and/or molecular assays (1,8,11,12). Pathogenic significance of S. pseudopneumoniae in respiratory tract diseases is still unclear in spite of its association with both a history of chronic obstructive pulmonary disease (COPD) and exacerbation of COPD (4,6).…”

“…Species identification was based on optochin (Oxoid Ltd., Basingstoke, England) susceptibility in an ambient atmosphere and resistance or intermediate susceptibility in a 5% CO 2 atmosphere, insolubility in 1% sodium deoxycholate (BD Diagnostics, Heidelberg, Germany), and a positive reaction with the AccuProbe Pneumococcus test (bioMérieux, Marcy l'Etoile, France) (1,6). Despite recent reports recommending molecular methods, such as recA gene sequencing or real-time PCR assays targeting the Spn9802 fragment and the autolysin gene lytA, for accurate identification of S. pseudopneumoniae (8,12), the association of one molecular and two phenotypic assays we used here allowed confident identification, because optochin-resistant or deoxycholate-insoluble S. pneumoniae isolates are rarely observed (as reviewed in reference 10).…”

Identifying Divergent Streptococcal Strains Using Pherotype: Implications for Pathogen Emergence and Epidemiology

“…Despite a previous report that S. pseudo pneumoniae does not have a comC gene [43], we subsequently located this gene from their published genome sequence [50]. In addition, our study found that the comC gene was present in a further 17 clinical strains of the pseudopneumococcus [50].…”

“…In addition, our study found that the comC gene was present in a further 17 clinical strains of the pseudopneumococcus [50]. The majority of these pseudopneumococci carried the same pherotype, CSP6.1 [50] that had previously been identified as a rare pneumococcal pherotype [51].…”

A novel quantitative PCR assay for the detection of Streptococcus pneumoniae using the competence regulator gene target comX

“…Of these targets, the lytA primer/probe set designed by Carvalho et al (2007) has been tested most extensively in clinical studies (Cvitkovic Spik et al, 2013;Wu et al, 2013). This target has been shown not to cross-react with the recently described species Streptococcus pseudopneumoniae (Arbique et al, 2004), which is genetically very similar to Streptococcus pneumoniae and can be misidentified as atypical pneumococci with traditional identification methods (Leung et al, 2012;Rolo et al, 2013). Many of the other qPCR assays also give a positive result for Streptococcus pseudopneumoniae (Carvalho et al, 2007) and are therefore not specific for Streptococcus pneumoniae.…”