Re-evaluation of Streptococcus pneumoniae carriage in Portuguese elderly by qPCR increases carriage estimates and unveils an expanded pool of serotypes

Abstract

Statistical analysis. The geometric mean was used to summarize the distribution of Ct values from lytA and piaB of nasopharyngeal and oropharyngeal samples. To look for associations between Ct values from nursing home vs family home and nasopharynx vs oropharynx an adjusted generalized linear model (GLM) using a Gaussian distribution and a log link function was used. The McNemar's test was used to compare culture and real-time PCR methods based on paired individuals. The Chi-square test was used to compare prevalence of S. pneumoniae between nasopharyngeal and oropharyngeal samples and between nursing home and family home by real-time PCR or culture-based methods. A p-value of <0.05 was considered statistically significant for all the tests used. The Gini-Simpson index of diversity (GSID) was used to calculate serotype diversity. All analyses were performed using R version 3.2.3 41. ethics statement. This study was conducted in accordance with the European Statements for Good Clinical Practice and the declaration of Helsinki of the World Health Medical Association. In addition, it was registered and approved at health care centers of Oeiras and Montemor-o-Novo that report to Administração Regional de Saúde (ARS, "Regional Health Administration") of Lisboa e Vale do Tejo, and Alentejo, respectively, from the Ministry of Health. Informed written consent was obtained from all participants. All samples and questionnaires were attributed a numeric code and were processed anonymously.

Molecular surveillance of pneumococcal carriage following completion of immunization with the 13-valent pneumococcal conjugate vaccine administered in a 3 + 1 schedule

“…However, the organism also resides in the oropharynx 5 – 7 , and colonization of any part of the upper airway may lead to pneumococcal disease and transmission 4 . Therefore, it is not surprising that sampling of saliva in older children 5 and the posterior oropharyngeal wall in adults 6 – 8 has also been used as a site for pneumococcal detection.…”

“…Pneumococcal pharyngeal colonization and serotype characterization is routinely investigated by culture of the dominant isolate, followed by serotyping with specific antisera 9 . However, the use of traditional culture-based methods may miss serotypes present at a lower density 6 , 10 . This problem has been addressed by the recent development of molecular diagnostic methods, which offer high-sensitivity detection of multiple serotypes from a single naso-/oropharyngeal sample and are able to unveil co-colonization of S. pneumoniae , especially in cultures of polymicrobial samples 6 , 10 .…”

Insights Into the Effects of Mucosal Epithelial and Innate Immune Dysfunction in Older People on Host Interactions With Streptococcus pneumoniae

“…Why older people are so vulnerable to disease caused by S. pneumoniae is likely to be multifactorial including co-morbidities, relative immunodeficiency, malnutrition and defective swallowing ( Janssens and Krause, 2004 ; Zalacain, 2004 ; Arndt, 2015 ). Disease follows pneumococcal carriage and reported nasopharyngeal and oropharyngeal carriage rates in older people vary between 0–39% ( Krone et al., 2015 ; Adler et al., 2020 ; Almeida et al., 2020 ; Smith et al., 2020 ; Yasuda et al., 2020 ). Unlike adults aged 18–64yrs, older adults do not appear to benefit from the natural immune effects of pneumococcal colonization events that are thought to protect against re-colonization and disease ( Ferreira et al., 2013 ; Adler et al., 2020 ).…”

Prevalence of antimicrobial-resistant Streptococcus species among respiratory patients and meat products, and antibacterial effects of oregano oil nanoemulsion

“…Although S. mitis is considered to have low pathogenicity, it is associated with serious clinical conditions, such as sepsis, pancreatic diseases, and endocarditis, especially in patients with impaired immunity [3]. Streptococcus pneumoniae colonies the human nasopharynx and oropharynx, and is responsible for several human infections, including otitis media, bronchitis, bacteremia, pneumonia, septicemia, septic arthritis, endocarditis, cellulitis, osteomyelitis, peritonitis, and meningitis [4,5].…”