Date of Award


Document Type

Open Access Thesis

Degree Name

Master of Public Health (MPH)


School of Public Health

First Advisor

Anne L. Wyllie

Second Advisor

Virginia Pitzer


Pneumococcal carriage is a prerequisite for pneumococcal disease and surveillance of carriage is crucial for evaluating and informing vaccination strategies. In recent years, molecular methods have improved the sensitivity of pneumococcal carriage detection as compared to the gold standard culture-based method. However, nucleic acid extraction from samples collected is resource-intensive, limiting scalability for extensive surveillance, particularly in low-resource settings. We previously developed a saliva-based PCR test for SARS-CoV-2, having identified that nucleic acid extraction can be omitted and replaced with a simple enzymatic lysis or heat treatment step without compromising the accuracy and efficiency of testing. Here, we compared pneumococcus detection in saliva samples collected weekly from an observational longitudinal study in childcare centers in New Haven (CT, USA), using our standard protocol (culture-enrichment followed by DNA extraction) and a DNA extraction-free protocol (addition of proteinase K then incubation at 95°C for 5 min). The presence of pneumococcus was determined by qPCR detection of pneumococcal gene, piaB. Samples were also tested for influenza A (IAV), influenza B (IBV), respiratory syncytial virus (RSV), and human metapneumovirus (hMPV), and parechovirus (PeV). A total of 754 saliva samples were collected from 92 children (median age 3.65 years). Pneumococcus was detected in 358 (47.2%) samples by the extraction-free protocol and in 367 (48.7%) samples by the culture-enrichment protocol. There was a near-perfect agreement (Cohen’s kappa: 0.92) and a high CT correlation (r=0.92) between the two methods, though the extraction-free protocol reported lower bacterial loads (ΔCT = -6.40, p

Open Access

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