Highly Penicillin-Resistant Multidrug-Resistant Pneumococcus-Like Strains Colonizing Children in Oeiras, Portugal: Genomic Characteristics and Implications for Surveillance

Abstract

While performing surveillance studies in Oeiras, Portugal, designed to describe the impact of pneumococcal conjugate vaccine on colonization, we observed an increase from 0.7% in 2003 to 5% in 2006 in the prevalence of penicillin resistance (MIC of 2 to 6 mg/liter) among presumptively identified pneumococcal isolates. Although 15 of the 22 penicillin-resistant isolates obtained in 2006 were optochin resistant, they were bile soluble and thus considered to be bona fide pneumococci. This study aimed to clarify the nature of these isolates by using a combination of phenotypic and genotypic approaches that included routine strategies for pneumococcal identification, multilocus sequence analysis (MLSA), and comparative genomic hybridization (CGH). By MLSA, all isolates were classified as "streptococci of the mitis group" that, however, were distinct from typical Streptococcus pneumoniae or Streptococcus mitis. A single isolate was identified as Streptococcus pseudopneumoniae. CGH confirmed these findings and further indicated that a considerable part of the proposed pneumococcal core genome is conserved in these isolates, including several pneumococcal virulence genes (e.g., pavA, spxB, cbpE, and cbpD). These results suggest that among pneumococci and closely related streptococci, universal unique phenotypic and genetic properties that could aid species identification are virtually impossible to define. In pneumococcal colonization studies, when atypical strains are found, MLSA and CGH are informative tools that can be used to complement routine tests. In our study, after correct identification of the penicillin-resistant true pneumococci, we found that penicillin resistance levels among pneumococci remained stable from 2003 to 2006.Streptococcus pneumoniae is a bacterial pathogen that frequently colonizes the nasopharynx of humans, particularly young children of preschool age. Colonization is mostly asymptomatic and only rarely results in disease (3). However, when disease does occur, it may range from a mild infection such as otitis media to severe septicemia or meningitis. Globally, the morbidity and mortality associated with pneumococcal infections are extremely high. A recent report from the WHO estimated that 0.7 to 1.0 million deaths occur annually among children Ͻ5 years of age as a result of pneumococcal infections (50).Four phenotypic characteristics are classically used in the diagnostic laboratory for the presumptive identification of S. pneumoniae: colony morphology (colonies with a depression in the center showing alpha-hemolysis on sheep blood agar), optochin susceptibility, deoxycholate (DOC) solubility (commonly referred to as bile solubility), and a positive reaction with antipneumococcal polysaccharide capsule antibodies (20). In particular, optochin susceptibility and deoxycholate solubility have been associated with high sensitivity and specificity (between 98% and 100%). However, a number of studies have reported on sporadic optochin-resistant S. pneumoniae isolates (28, 34) and rare deoxycholat...

Characterization of Nontypeable and Atypical Streptococcus pneumoniae Pediatric Isolates from 1994 to 2010

“…All group III isolates were negative by Quellung testing using the omni-sera. Six of eight (1,17,20). We initiated this study to gain a better understanding of the phenotypic and genotypic characteristics of our nontypeable S. pneumoniae isolates.…”

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

“…1). CSP sequences of four strains (IS7493, PT5479, PT5779, and SK674) were available from reports in earlier publications (25,41,48). All but that of SK674 were identical to CSPps1.…”

DNA bacterial load in children and adolescents with pneumococcal pneumonia and empyema

“…However, we may consider that in our study the consecutively serotyping by Real-Time PCR (which included tested with capsular genes of pneumococci) and the detection of a virulent gene (ply gene) of pneumococci in sterile sample of patients with clinical symptoms and radiologically confirmed pneumonia and empyema may have significant clinical value. Up to date, the clinical role of S.pseudopneumoniae and others quasi-pneumococcus in invasive disease is unknown, but some authors have alerted about the increase of these strains in the nasopharynx [28]. So, the clinical role of these closely related pneumococcal strains isolated in sterile samples need to be clarified.…”