Persistence of Pneumococcal Carriage Among Older Adults in the Community Despite COVID-19 Mitigation Measures

Wyllie, Anne L.; Mbodj, Sidiya; Thammavongsa, Darani A; Hislop, Maikel S; Yolda-Carr, Devyn; Waghela, Pari; Nakahata, Maura; Watkins, Anne E.; Vega, Noel; Allicock, Orchid M; Wilkins, Geisa; Ouyang, Andrea; Siqueiros, Laura; Strong, Yvette; Anastasio, Kelly; Alexander-Parrish, Ronika; Arguedas, Adriano; Gessner, Bradford; Weinberger, Daniel M

doi:10.2139/ssrn.4166776

Cited by 7 publications

(18 citation statements)

References 16 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…30,32 Therefore, to evaluate our sample processing methods for their impact on pneumococcal carriage detection and to exclude confounding from other streptococci, we limited our analyses to piaB . 19,30 Nonetheless, results obtained here, when testing the culture-enriched saliva samples using piaB , highly correlated with results obtained when targeting the lytA gene in the same culture-enriched saliva samples (see Supplementary Figure 2). However, a multiplex PCR assay of the key targets used for pneumococcal carriage detection could be further evaluated.…”

Section: Discussionsupporting

confidence: 82%

“…Samples were thawed on ice, and 100 μL of raw saliva was inoculated on trypticase soy agar (TSA II) supplemented with 5% defibrinated sheep blood and 10 mg/L gentamicin (Gent plates, ThermoFisher Scientific) and incubated overnight at 37°C with 5% CO 2. 19 Bacterial growth was harvested into 2,100 μL of BHI supplemented with 10% glycerol and stored at -80°C until further processing. These samples were considered as culture-enriched for pneumococcus.…”

Section: Methodsmentioning

confidence: 99%

“…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). A standard curve prepared from five 1:10 serial dilutions of pneumococcal DNA, ranging from 1 ng/μL to 0·00001 ng/μL was included as a positive control.…”

Section: Methodsmentioning

confidence: 99%

“…Samples were classified as positive for pneumococcus when a piaB cycle threshold (C T ) value was <40. 19,20…”

Section: Methodsmentioning

confidence: 99%

See 3 more Smart Citations

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

Peno,

Lin,

Hislop

et al. 2023

Preprint

Self Cite

View full text Add to dashboard Cite

BackgroundMolecular methods have improved the sensitivity of detection of pneumococcal carriage in saliva. However, they typically require sample culture-enrichment and nucleic acid extraction, prior to performing the detection assay. These factors may limit scalability for extensive surveillance of pneumococcus, particularly in low-resource settings. In this study, we evaluated the performance of a DNA-extraction-free method for the detection of pneumococcus in saliva.MethodsWe developed a streamlined qPCR-based protocol for the detection of pneumococcus, omitting culture-enrichment and DNA extraction. Using saliva samples collected from children attending childcare centers (New Haven, CT, USA), we evaluated detection of pneumococcus using saliva lysates as compared to purified DNA extracted from culture-enriched aliquots of the paired samples using qPCR targeting the pneumococcalpiaBgene.ResultsOf 759 saliva samples tested from 92 children (median age 3.65 years; IQR (2.46-4.78), pneumococcus was detected in 358 (47.2%) saliva lysates prepared using the extraction-free protocol and in 369 (48.6%) DNA extracted from the culture-enriched samples. We observed a near-perfect agreement between the two protocols (Cohen’s kappa: 0.92; 95%CI: 0.90-0.95). While we also observed a high correlation between the qPCR CTvalues generated by the two methods (r=0.93,p<0.0001), the CTvalues generated from the extraction-free, saliva lysates were higher (lower concentration) than those obtained from DNA extracted from culture-enriched samples (ΔCT= 6.68,p<0.00001).ConclusionsFor pneumococcal carriage surveillance in children, our findings suggest that a DNA extraction-free approach may offer a cost-effective alternative to the resource-intensive culture-enrichment method. While, as expected, we observed higher qPCR CTvalues (lower bacterial load) in the absence of culture-enrichment, the overall rate of detection remained unaffected.

show abstract

Section: Discussionsupporting

confidence: 82%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

“…Samples were classified as positive for pneumococcus when a piaB cycle threshold (C T ) value was <40. 19,20…”

Section: Methodsmentioning

confidence: 99%

See 2 more Smart Citations

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

Peno,

Lin,

Hislop

et al. 2023

Preprint

Self Cite

View full text Add to dashboard Cite

show abstract

“…Saliva samples and demographic data were collected every 2 weeks for 6 total visits (10 week study inclusion), as previously described. 6 At the final visit, study participants also provided a urine sample. Participants from the first season were invited to participate again in the second season.…”

Section: Methodsmentioning

confidence: 99%

Contact with young children is a major risk factor for pneumococcal colonization in older adults

Wyllie,

Yolda-Carr,

Hislop

et al. 2024

Preprint

Self Cite

View full text Add to dashboard Cite

BackgroundImportant questions remain about the sources of transmission of pneumococcus to older adults in the community. This is a critical question for understanding the potential indirect effects of using pneumococcal conjugate vaccines (PCVs) in children and older adults. For non-institutionalized individuals, the most likely source of adult-to-adult transmission is in the household. The goal of this study was to characterize the dynamics and risk factors for acquisition of pneumococcus in older adults.MethodsWe designed a longitudinal study to sample adults >60 years of age living in the same household (New Haven, CT, USA), and without younger contacts residing in the household. Saliva samples and questionnaires regarding social behaviors and health status were obtained every 2 weeks for a period of 10 weeks. DNA extracted from culture-enriched saliva was tested using qPCR for pneumococcus genespiaBandlytA.ResultsAcross two study seasons (November 2020-August 2021, November 2021-September 2022), 121 individuals from 61 households were followed for 6 study visits; 62 individuals were enrolled in both seasons. Overall, 52/1088 (4.8%) samples tested positive for pneumococcus based onpiaB, with 27/121 (22.3%) individuals colonized on at least one time point. Several individuals were colonized at multiple timepoints including two individuals who were colonized throughout the 10-week sampling period; two others were colonized at 5 of 6 time points. In 5 instances, both members of the household were carriers in the same season, though not necessarily at the same time point. Pneumococcal carriage was substantially higher among individuals who had contact with children (10.0% vs 1.6%). Participants who reported recent contact with <5-year-olds and 5-9-year-olds had particularly elevated prevalence (13.8%; 14.1%, respectively).ConclusionsContact with young children was the most important factor that influenced pneumococcal acquisition rates. While there were several instances where both adult household members were colonized at the same time or at sequential visits, these individuals also both typically had contact with children.

show abstract

Collateral impacts of pandemic COVID-19 drive the nosocomial spread of antibiotic resistance

Shirreff

Temime

et al. 2022

Preprint

View full text Add to dashboard Cite

Circulation of multidrug-resistant bacteria (MRB) in healthcare facilities is a major public health problem. These settings have been greatly impacted by the COVID-19 pandemic, notably due to surges in COVID-19 caseloads and the implementation of infection control measures. Yet collateral impacts of pandemic COVID-19 on MRB epidemiology remain poorly understood. Here, we present a dynamic transmission model in which SARS-CoV-2 and MRB co-circulate among patients and staff in a hospital population in an early pandemic context. Responses to SARS-CoV-2 outbreaks are captured mechanistically, reflecting impacts on factors relevant for MRB transmission, including contact behaviour, hand hygiene compliance, antibiotic prescribing and population structure. In a first set of simulations, broad parameter ranges are accounted for, representative of diverse bacterial species and hospital settings. On average, COVID-19 control measures coincide with MRB prevention, including fewer incident cases and fewer cumulative person-days of patient MRB colonization. However, surges in COVID-19 caseloads favour MRB transmission and lead to increased rates of antibiotic resistance, especially in the absence of concomitant control measures. In a second set of simulations, methicillin-resistant Staphylococcus aureus and extended-spectrum beta-lactamase-producing Escherichia coli are simulated in specific hospital wards and pandemic response scenarios. Antibiotic resistance dynamics are highly context-specific in these cases, and SARS-CoV-2 outbreaks significantly impact bacterial epidemiology only in facilities with high underlying risk of bacterial transmission. Crucially, antibiotic resistance burden is reduced in facilities with timelier, more effective implementation of COVID-19 control measures. This highlights the control of antibiotic resistance as an important collateral benefit of robust pandemic preparedness.

show abstract

Persistence of Pneumococcal Carriage Among Older Adults in the Community Despite COVID-19 Mitigation Measures

Cited by 7 publications

References 16 publications

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

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

Contact with young children is a major risk factor for pneumococcal colonization in older adults

Collateral impacts of pandemic COVID-19 drive the nosocomial spread of antibiotic resistance

Contact Info

Product

Resources

About