Persistence of pneumococcal carriage among older adults in the community despite COVID-19 mitigation measures

Abstract

Background. Reported rates of invasive pneumococcal disease were markedly lower than normal during the 2020/2021 winter in the Northern Hemisphere, the first year after the start of the COVID-19 pandemic. However, little is known about rates of carriage of pneumococcus among adults during this period. Methods. Between October 2020-August 2021, couples living in the Greater New Haven Area were enrolled if both individuals were aged 60 years and above and did not have any individuals under the age of 60 years living in the household. Saliva samples and questionnaires regarding social activities and contacts and medical history were obtained every 2 weeks for a period of 10 weeks. Following culture-enrichment, extracted DNA was tested using qPCR for pneumococcus-specific sequences piaB and lytA. Individuals were considered positive for pneumococcal carriage when Ct-values for piaB were less than 40. Results. We collected 567 saliva samples from 95 individuals aged 60 years and above (47 household pairs and one singleton). Of those, 7.1% of samples tested positive for pneumococcus by either piaB only (n=6) or both piaB and lytA (n=34), representing 22/95 (23.2%) individuals and 16/48 (33.3%) households over the course of the 10-week study period. Study participants attended few social events during this period. However, many participants continued to have regular contact with children. Individuals who had regular contact with preschool and school aged children (i.e., 2-9 year olds) had a higher prevalence of carriage (15.9% vs 5.4%). Conclusions. Despite COVID-19-related disruptions, a large proportion of older adults carried pneumococcus at least once during the 10-week study period. Prevalence was particularly high among those who had contact with school-aged children, but carriage was not limited to this group.

High levels of detection of non-pneumococcal species ofStreptococcusin saliva from adults in the USA

“…Updated World Health Organization recommendations made in 2013 by the Pneumococcal Carriage Working Group advised the inclusion of oropharyngeal swabs from adults when possible [30]. A number of studies have demonstrated that the sensitivity of carriage detection can be further improved when molecular methods are applied [15,[31][32][33][34] to alternative sample types such as saliva [21,23]. With increased use of molecular methods however, there have been increased reports of confounding by non-pneumococcal species of Streptococcus, leading to uncertainty regarding the accuracy of culture-independent approaches [13,24,35].…”

“…The lytA -positive/ piaB -negative strains were thawed on ice, cultured on blood agar plates using a 10 μl inoculating loop and incubated overnight at 37ºC with 5% CO 2 . Colonies were harvested using a 10 μl inoculating loop and DNA was extracted via the boilate method [21]. For each strain, the 408 bp variable region of the rpsB gene encoding the ribosomal protein S2 was amplified with conventional PCR using the primers previously described [24] with a modified protocol.…”

“…Culture-enriched saliva samples were thawed on wet ice. DNA was extracted from 200 μl of each sample as previously described [21]. Each DNA template was tested in qPCR for pneumococcal genes piaB [3,16] and lytA [13].…”

Impact of Temporary Storage Conditions on the Viability of Streptococcus pneumoniae in Saliva

“…Culture-enriched saliva samples were thawed on ice. DNA was extracted from 200 μL of each sample using the MagMAX Ultra viral/pathogen nucleic acid isolation kit (Thermo Fisher Scientific) on the KingFisher Apex instrument (Thermo Fisher Scientific), with modifications ( 22 ). Each DNA template was tested by qPCR for the pneumococcal genes piaB ( 23 , 24 ) and lytA ( 25 ).…”

A low-cost culture- and DNA extraction-free method for the molecular detection of pneumococcal carriage in saliva

“…A real-time qPCR assay targeting the pneumococcal iron uptake ABC transporter lipoprotein piaB gene was used to detect the presence of pneumococcal DNA in both the DNA extracted from culture-enriched samples and saliva lysates, as previously described. 12,19,20 Both DNA extracts and saliva lysates (2.5 µL) were tested in 20 µL reaction volumes using Advanced Universal Probe Supermix (BioRad, USA) and a primer/probe mix at concentrations of 250 nM (1 μL per reaction) (Iowa Black quenchers, USA).…”