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Collecting a nasopharyngeal swab.

Collecting a nasopharyngeal swab.

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In 2003 the World Health Organization (WHO) convened a working group and published a set of standard methods for studies measuring nasopharyngeal carriage of Streptococcus pneumoniae (the pneumococcus). The working group recently reconvened under the auspices of the WHO and updated the consensus standard methods. These methods describe the collecti...

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... standard method, summarized here. Hold the infant or young child's head securely. Tip their head backwards slightly and pass the swab directly backwards, paral- lel to the base of the NP passage. The swab should move without resistance until reaching the nasopharynx, located about one-half to two-thirds the distance from the nostril to ear lobe (Fig. ...

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... For all patients enrolled in the study after signing informed consent, trained nursing staff collected NPA samples with an 8 mm nelaton probe (Medex, INVIMA 2008DM-0001689 R2, Colombia) and 8-10 cc rinsing infusion of physiological saline solution (PSS) of sodium chloride 0. 9% (Baxter, Viaflex) at 10-15 cm in the posterior nostril of each participant according to the guidelines of the WHO (World Health Organization) Pneumococcal Carriage Working Group in 2013 [19]. ...
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Purpose Streptococcus pneumoniae (Spn) is the primary bacterial cause of lower respiratory tract infections (LRTI) globally, particularly impacting older adults and children. While Spn colonization in children is linked to LRTI, its prevalence, and consequences in adults with comorbidities remain uncertain. This study aims to provide novel data in that regard. Methods This prospective study of outpatient adults with chronic diseases was conducted in Colombia. Data on demographics, vaccination, and clinical history was collected in a RedCap database. Nasopharyngeal aspirate samples were examined for Spn colonization using traditional cultures and quantitative—real time polymerase chain reaction (q-rtPCR). Patients were followed for 18 months, with colonization prevalence calculated and factors influencing colonization and its impact on clinical outcomes analyzed through logistic regressions. Results 810 patients were enrolled, with 10.1% (82/810) identified as colonized. The mean (SD) age was 62 years (±15), and 48.6% (394/810) were female. Major comorbidities included hypertension (52.2% [423/810]), cardiac conditions (31.1% [252/810]), and chronic kidney disease (17.4% [141/810]). Among all, 31.6% (256/810) received the influenza vaccine in the previous year, and 10.7% (87/810) received anti-Spn vaccines. Chronic kidney disease (OR 95% CI; 2.48 [1.01–6.15], p = 0.04) and chronic cardiac diseases (OR 95% CI; 1.62 [0.99–2.66], p = 0.05) were independently associated with Spn colonization. However, colonization was not associated with the development of LRTI (OR 95%CI; 0.64 [0.14–2.79], p = 0.55) or unfavorable outcomes (OR 95% CI;1.17 [0.14–2.79], p = 0.54) during follow-up. Conclusions Chronic kidney and cardiac diseases are independently associated with Spn colonization. However, Spn colonization was not associated with LRTI/unfavorable outcomes in adult patients with chronic comorbidities in our cohort.
... Trained nurses collected nasopharyngeal swabs from each participant using flexible paediatric-(Ultra Minitip) or adult-size (Flexible Minitip) flocked swabs (FLO-QSwabs; Copan Diagnostics, USA), following WHO recommendations [13,14]. Paediatric-sized swabs were used for children under 15y. ...
... We collected nasopharyngeal swabs and assessed these using lytA qPCR and microarray consistent with the WHO guideline [14]. We did not examine oropharyngeal carriage which may have underestimated prevalence in adults [45]. ...
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Background Populations affected by humanitarian crises likely experience high burdens of pneumococcal disease. Streptococcus pneumoniae carriage estimates are essential to understand pneumococcal transmission dynamics and the potential impact of pneumococcal conjugate vaccines (PCV). Over 100 million people are forcibly displaced worldwide, yet here we present only the second pneumococcal carriage estimates for a displaced population. Methods In October 2019, we conducted a cross-sectional survey among internally displaced people (IDP) living in Digaale, a permanent IDP camp in Somaliland where PCV has not been implemented. We collected nasopharyngeal swab samples from 453 residents which were assessed for presence of pneumococci and serotyped using DNA microarray. Results We found that pneumococcal carriage prevalence was 36% (95%CI 31–40) in all ages, and 70% (95%CI 64–76) in children under 5. The three most common serotypes were vaccine serotypes 6B, 19F, and 23F. We estimated that the serotypes included in the 10-valent PNEUMOSIL vaccine were carried by 41% (95%CI 33–49) of all pneumococcal carriers and extrapolated that they caused 52% (95%CI 35–70) of invasive pneumococcal disease. We found some evidence that pneumococcal carriage was associated with recent respiratory symptoms, the total number of physical contacts made, and with malnutrition in children under 5. Through linking with a nested contact survey we projected that pneumococcal exposure of children under 2 was predominantly due to contact with children aged 2–5 (39%; 95%CI 31–48) and 6–14 (25%; 95%CI 17–34). Conclusions These findings suggest considerable potential for direct and indirect protection against pneumococcal disease in Digaale through PCV use in children and potentially adolescents.
... Surveys of pneumococcal colonization in older adults have reported v astl y differ ent estimates, depending on the sampling and testing methodology used. Using culture-based detection of pneu-mococcus from nasopharyngeal swabs (Satzke et al. 2013 ), carria ge is r ar el y detected ( < 5%). When saliv a samples ar e tested using qPCR, higher rates of colonization are detected (Krone et al. 2015 ). ...
... The current gold standard recommendations for the detection of pneumococcus (Satzke et al. 2013 ) ar e insensitiv e when applied for carriage detection in adults (Wyllie et al. 2016a, Miellet et al. 2023b, Krone et al. 2015. As suc h, mor e sensitiv e methods of pneumococcal carria ge surv eillance m ust be established and a ppr opriatel y a pplied (Miellet et al. 2023a ). ...
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... BMC Medicine (2024) 22:419 NP swabs were taken during 17 total visits: at baseline (visit 1) and then weekly during the next 16 visits of the study period per protocol, resulting in 3152 total NP samples from 195 individuals adjusted for missed visits. The swabs were tested for the presence of pneumococci using the World Health Organisation (WHO) NP sampling procedure and standard microbiological culture [22]. Serotyping of every positive pneumococcal sample was done using latex agglutination, based on picking a single colony, to identify serotypes or serogroups [23]. ...
... Ethics approval and consent to participate Nasomune study nasopharyngeal (NP) samples were obtained from each Malawian adult through written consent. Study ethics approval was granted by the Malawi National Health Sciences Research Ethics Committee (NHSRC) (21/24/2680) and the Liverpool School of Tropical Medicine Research Ethics (21)(22)(23)(24)(25)(26)(27)(28)(29)(30)(31)(32)(33)(34)(35) in accordance with the Declaration of Helsinki. Written informed consent to participate was obtained from all of the participants in the study. ...
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... NP swabs were taken using the World Health Organization (WHO)-recommended methodology. The specimens were processed based on the WHO recommendations for characterizing S. pneumoniae (14). Broth enrichment for 4 h was an approach used to increase the sensitivity of cultures (15). ...
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Objectives To describe the carriage rate, serotype distribution, and antimicrobial susceptibility patterns of Streptococcus pneumoniae (S. pneumoniae) nasopharyngeal (NP) isolates among healthy children aged 30 days to <60 months in the cities of Beijing and Shenzhen during 2018–2021. Methods A NP swab sample was collected among four annual cohorts of healthy children at routine well-child visits. S. pneumoniae was identified by culture, optochin sensitivity and bile solubility, serotypes determined by latex agglutination and Quellung, and antimicrobial susceptibility testing performed using E-test strips. Results S. pneumoniae NP carriage was 13.1% (645/4,911), with the highest S. pneumoniae carriage prevalence (15.3%) observed in 25 to <60 months. The carriage prevalence was 15.1% in children 13–24 months, 13.2% in children 7–12 months, and 8.2% in children 30 days to 6 months (P < 0.01). Living with siblings [20.0% vs. 9.4%: OR: 2.42 (95% CI: 2.05–2.87)] or attending day-care [31.8% vs. 11.3%: OR: 3.67 (95% CI: 2.94–4.57)] increased the risk (P < 0.01). During the period (January 2020–April 2021) of strict non-pharmaceutical interventions to prevent and control the COVID-19 pandemic, the proportion of children with S. pneumoniae colonization declined from 16.0% (94/587) to 5.8% (108/1,848) in Beijing while increasing from 14.5% (64/443) to 18.6% (379/2,033) in Shenzhen. Among S. pneumoniae isolates, 36.7% (237/645) belonged to 13-valent pneumococcal conjugate vaccine (PCV13) serotypes, 64.3% (408/645) were non-PCV13 serotypes, including 20.8% (134/645) non-serotypeable S. pneumoniae (NST). A total of 158/644 isolates (24.5%) were MDR. For the PCV13 isolates, MDR was detected in 36.3% (86/237) of isolates; in comparison, 17.6% (72/407) of non-PCV13 serotypes, including NST, were MDR (P < 0.01). S. pneumoniae NP carriage was detected in 10.7% of children with previous pneumococcal vaccination (PCV7 or PCV13 only) compared with 14.9% in children without previous pneumococcal vaccination. Conclusions The highest S. pneumoniae carriage prevalence were found in the oldest age group (25 to <60 months) and in children living with siblings or attending day-care. Vaccination with PCV7 or PCV13 was associated with lower PCV13-serotype colonization. In Beijing, S. pneumoniae carriage significantly declined during the COVID-19 pandemic.
... Nasopharyngeal swab specimens were collected and transported at 2-8 • C from the field site to the Infectious Disease Research Laboratory (IDRL) in Karachi within 8 h of collection as per established World Health Organization's (WHO) consensus methods [12]. In the lab, samples were vortexed in skim milk tryptone-glucose-glycerol (STGG) medium for 10-20 s to disperse the organisms, and afterward, they were frozen at − 80 • C in an upright position until further processing. ...
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Background: In early 2021, the 10-valent Pneumococcal conjugate vaccine (PCV10) was replaced with 13-valent (PCV13) by the federal directorate of immunization (FDI), Pakistan. We assessed the impact of a higher valent vaccine, PCV13, on the serotype distribution of nasopharyngeal carriage in rural Pakistan. Methods: Children <2 years were randomly selected from two rural union councils of Matiari, Sindh in Pakistan between September-October,2022. Clinical, sociodemographic and vaccination histories were recorded. Na-sopharyngeal swabs were collected and processed at Infectious Disease Research Laboratory, Aga Khan University , Karachi. Whole genome sequencing was performed on the culture positive isolates. Results: Of the 200 children enrolled, pneumococcus was detected in 140(70 %) isolates. Majority of age-eligible children (60.1 %,110/183) received 3 PCV13 doses. PCV10 carriage declined from 13.2 %(78/590) in 2017/18 to 7.2 % (10/140) in 2022, additional PCV13 serotypes (3, 6A/6C and 19A) decreased from 18.5 %(109/590) to 11.4 %(16/140) while non-PCV13 serotypes increased from 68.3 %(403/590) to 81.4 %(114/140). There were 88.5 %(n = 124), 80.7 %(n = 113), 55.0 %(n = 77), and 46.0 %(n = 65) isolates predicted to be resistant to cotrimoxazole, penicillin(meningitis cutoff), tetracycline, and erythromycin respectively. Conclusion: Replacing PCV10 with PCV13 rapidly decreased prevalence of PCV13 carriage among vaccinated children in Matiari, Pakistan. Vaccine-driven selection pressure may have been responsible for the increase of non-PCV13 serotypes.
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... World Health Organization recommended methods were followed for nasopharyngeal sample collection, handling and transport 42 . Swab processing and DNA extraction (MagNA Pure LC machine) for the earlier surveys (2015 and 2017) was previously described 17 . ...
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Limited data from Asia are available on long-term effects of pneumococcal conjugate vaccine introduction on pneumococcal carriage. Here we assess the impact of 13-valent pneumococcal conjugate vaccine (PCV13) introduction on nasopharyngeal pneumococcal carriage prevalence, density and antimicrobial resistance. Cross-sectional carriage surveys were conducted pre-PCV13 (2015) and post-PCV13 introduction (2017 and 2022). Pneumococci were detected and quantified by real-time PCR from nasopharyngeal swabs. DNA microarray was used for molecular serotyping and to infer genetic lineage (Global Pneumococcal Sequence Cluster). The study included 1461 infants (5–8 weeks old) and 1489 toddlers (12–23 months old) enrolled from family health clinics. We show a reduction in PCV13 serotype carriage (with non-PCV13 serotype replacement) and a reduction in the proportion of samples containing resistance genes in toddlers six years post-PCV13 introduction. We observed an increase in pneumococcal nasopharyngeal density. Serotype 15 A, the most prevalent non-vaccine-serotype in 2022, was comprised predominantly of GPSC904;9. Reductions in PCV13 serotype carriage will likely result in pneumococcal disease reduction. It is important for ongoing surveillance to monitor serotype changes to potentially inform new vaccine development.
... The surveillance of pneumococcal carriage dynamics relies on establishing methods of detection that are sufficiently sensitive across all ages and scalable in different settings, particularly in settings with a high disease burden (8). While the current recommended gold standard method for detecting pneumococcal carriage in the URT is the conventional culture of a nasopharyngeal swab (9), molecular detection methods improve the sensitivity of pneumococcal carriage detection when applied to nasophar yngeal swabs and other URT sample types including oropharyngeal swabs and saliva (10)(11)(12)(13). Despite being more sensitive for pneumococcal carriage detection, molecular methods are resource-intensive, requiring extraction of DNA from the sample prior to testing. ...
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Molecular methods have improved the sensitivity of the detection of pneumococcal carriage in saliva. However, they typically require sample culture enrichment and nucleic acid extraction prior to performing the detection assay and may limit scalability for extensive surveillance of pneumococcus, particularly in low-resource settings. We evaluated the performance of a DNA-extraction-free method for the detection of pneumococcus in saliva. We 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 the detection of pneumococcus using saliva lysates as compared to purified DNA extracted from culture-enriched aliquots of the paired samples using qPCR targeting the pneumococcal piaB gene. Of the 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 culture-enriched samples. We observed near-perfect agreement between the two protocols (Cohen’s kappa: 0.92; 95% CI: 0.90–0.95). Despite a high correlation between CT values generated by the two methods (r = 0.93, P < 0.0001), the CT values generated from saliva lysates were higher (lower concentration) than those from culture-enriched samples (ΔCT = 6.69, P < 0.00001). The cost of detecting pneumococcus using saliva lysates was at least fivefold lower (US2.53)comparedtothecostofthecultureenrichedmethod(range:US2.53) compared to the cost of the culture-enriched method (range: US13.60–US$19.46). For 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. IMPORTANCE Surveillance for carriage of pneumococcus is a key component of evaluating the performance of pneumococcal vaccines and informing new vaccination strategies. To improve the scalability of pneumococcal carriage surveillance, we show that molecular detection of pneumococcus in saliva from children can be performed without culture enrichment and DNA extraction. Our findings show that using the extraction-free method can improve surveillance efforts for pneumococcal carriage in children, overcoming the resource-intensive hurdle that comes with the use of molecular methods, particularly in low-resource settings.
... Nasopharyngeal swabs collected in skim milktryptone-glucose-glycerin (STGG) transport media were transferred to the National Center of Public Health Laboratories, Aden City. S. pneumoniae was identified from swabs following the Centers for Disease Control and Prevention (CDC) and the World Health Organization (WHO) guidelines, and with the use of S. pneumoniae ATCC 49619 for quality control [22,23]. The confirmed colonies were cultured in Serum Todd Hewitt broth (HIMEDIA, Mumbai, India) for serotyping using the Pneumotest-Latex Kit (Staten Serum Institute, Copenhagen, Denmark) [24]. ...
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Introduction: Streptococcus pneumoniae cause a significant global health challenge. We aimed to determine nasopharyngeal carriage, serotypes distribution, and antimicrobial profile of pneumococci among the children of Aden. Methodology: A total of 385 children, aged 2-17 years, were included. Asymptomatic samples were randomly collected from children in selected schools and vaccination centers. Symptomatic samples were obtained from selected pediatric clinics. The nasopharyngeal swabs were tested for pneumococci using culture and real time polymerase chain reaction (RT-PCR). Serotyping was done with a pneumotest-latex kit and antimicrobial susceptibility was tested by disc diffusion and Epsilometer test. Results: The total pneumococcal carriage was 44.4% and 57.1% by culture and RT-PCR, respectively. There was a statistically significant association between carriage rate and living in single room (OR = 7.9; p = 0.00001), sharing a sleeping space (OR = 15.1; p = 0.00001), and low monthly income (OR = 2.02; p = 0.007). The common serotypes were 19, 1, 4, 5, 2, and 23. The proportion of non-pneumococcal conjugate vaccine (non-PCV13) serotypes was 24%. Pneumococci were resistant to penicillin (96.5%), cefepime (15.8%), ceftriaxone (16.4%), and amoxicillin-clavulanate (0%). Erythromycin, azithromycin, and doxycycline had resistance rates of 48%, 31%, and 53.3%, respectively. Conclusions: A high pneumococcal carriage rate was observed in Yemeni children, particularly in low-income households and shared living conditions. There was significant penicillin resistance at meningitis breakpoint. Furthermore, non-PCV13 serotypes were gradually replacing PCV13 serotypes. The findings underscore the urgent need for enhanced surveillance and stewardship to improve vaccination and antibiotic policies in Yemen.
... PCR was more sensitive at detecting colonization than culture, particularly in the oropharynx, where bacterial densities were highest. Our sampling methods were consistent with those recommended by the World Health Organization utilizing both culture and molecular methods (detection of the autolysin gene lytA) of NP and OP samples separately [36]. The 2 methods have shown close correlation when used in populations of children and adults with high colonization prevalence but were less consistent among those with a lower Spn Colonization and Microbiota in HIV-1 • JID • 5 prevalence and with older age [37]. ...
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Background The substantial risk for respiratory and invasive infections with Streptococcus pneumoniae (Spn) among people with HIV-1 (PWH) begins with asymptomatic colonization. The frequency of Spn colonization among U.S. adults with and without HIV-1 infection is not well-characterized in the conjugate vaccine era. Methods We determined Spn colonization frequency by culture and specific lytA gene QPCR and microbiota profile by 16S rRNA gene sequencing in nasopharyngeal (NP) and oropharyngeal (OP) DNA from 138 PWH and 93 control adults and associated clinical characteristics. Results The frequencies of Spn colonization among PWH and controls did not differ (11.6% vs 8.6%, respectively; p=0.46) using combined results of culture and PCR, independent of vaccination or behavioral risks. PWH showed altered microbiota composition (i.e., beta-diversity. NP: p=0.0028, OP: p=0.0098), decreased alpha-diversity (NP: p=0.024, OP: p=0.0045), and differences in the relative abundance of multiple bacterial taxa. Spn colonization was associated with altered beta-diversity in the NP (p=0.011), but not OP (p=0.21). Conclusions Despite widespread conjugate vaccine and antiretroviral use, frequencies of Spn colonization among PWH and controls are currently consistent with those reported in the pre-conjugate era. The persistently increased risk of pneumococcal disease despite ART may relate to behavioral and immunologic variables other than colonization.