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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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Context 1
... 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. ...Similar publications
Objectives:
The 23-valent pneumococcal polysaccharide vaccine (PPV) is recommended for prevention of pneumococcal diseases in adults at risk. Few data exist on time- age- and sex-dependent vaccine effectiveness on outcomes in pneumonia.
Methods:
We performed a population based cohort study including adults ≥ 60 years of age (n=738.927) based on...
Background In the UK, primary care records are electronic and require doctors to ascribe disease codes to direct care plans and facilitate safe prescribing. We investigate factors associated with coding of chronic kidney disease (CKD) in patients with reduced kidney function and the impact this has on patient management. Methods We identified patie...
Older adults, particularly those with chronic obstructive pulmonary disease, are advised to receive 23-valent pneumococcal polysaccharide vaccine (PPV23). However, the PPV23 vaccination rate in Taiwan and the determinants of receipt remain unclear.
We analyzed the data of 1475 community-dwelling older adults aged ≥75 years who participated in the H...
Background:
The capsular polysaccharide is the principal virulence factor of Streptococcus pneumoniae and a target for current pneumococcal vaccines. However, some pathogenic pneumococci are serologically nontypeable [nontypeable pneumococci (NTPn)]. Due to their relative rarity, NTPn are poorly characterized, and, as such, limited data exist whic...
Pneumococcal vaccination is frequently used to assess a patient's humoral immune function. Comparison of pre- and post-vaccination levels of anti-pneumococcal antibodies is widely held to be the gold standard for documenting response. However, many of the published criteria for defining an adequate response are based on assays that are no longer wi...
Citations
... The prevalence of nasal pathogens will be determined via nasal swabs, collected from infants at ages 4 and 12 months. Swabs will be screened for key respiratory bacteria (Streptococcus pneumoniae, non-typeable Haemophilus influenzae (NTHi)) and viruses (RSV) using WHO culture 39 and standardised RT-PCR methods, respectively. 40 41 Tertiary outcomes Immune function will be assessed through analysis of whole blood, isolated cord blood mononuclear cells (CBMCs), 42 plasma, breast milk and saliva samples. ...
Introduction:
Globally, acute respiratory infections (ARIs) are a leading cause of childhood morbidity and mortality. While ARI-related mortality is low in Australia, First Nations infants are hospitalised with ARIs up to nine times more often than their non-First Nations counterparts. The gap is widest in the Northern Territory (NT) where rates of both acute and chronic respiratory infection are among the highest reported in the world. Vitamin D deficiency is common among NT First Nations neonates and associated with an increased risk of ARI hospitalisation. We hypothesise that perinatal vitamin D supplementation will reduce the risk of ARI in the first year of life.
Methods and analysis:
'D-Kids' is a parallel (1:1), double-blind (allocation concealed), randomised placebo-controlled trial conducted among NT First Nations mother-infant pairs. Pregnant women and their babies (n=314) receive either vitamin D or placebo. Women receive 14 000 IU/week or placebo from 28 to 34 weeks gestation until birth and babies receive 4200 IU/week or placebo from birth until age 4 months. The primary outcome is the incidence of ARI episodes receiving medical attention in the first year of life. Secondary outcomes include circulating vitamin D level and nasal pathogen prevalence. Tertiary outcomes include infant immune cell phenotypes and challenge responses. Blood, nasal swabs, breast milk and saliva are collected longitudinally across four study visits: enrolment, birth, infant age 4 and 12 months. The sample size provides 90% power to detect a 27.5% relative reduction in new ARI episodes between groups.
Ethics and dissemination:
This trial is approved by the NT Human Research Ethics Committee (2018-3160). Study outcomes will be disseminated to participant families, communities, local policy-makers, the broader research and clinical community via written and oral reports, education workshops, peer-reviewed journals, national and international conferences.
Trial registration number:
ACTRN12618001174279.
... Pneumococcal vaccination is intended to reduce the incidence, complications, sequelae, and mortality from pneumonia and invasive pneumococcal disease. Two types of vaccines are available: a polysaccharide vaccine against 23 serotypes (PPSV23) and a conjugate vaccine against 13 serotypes (PCV13) [33]. ...
Laboratory surveillance of Streptococcus pneumoniae serotypes is crucial for the successful implementation of vaccines to prevent invasive pneumococcal diseases. The reference method of serotyping is the Quellung reaction, which is labor-intensive and expensive. In the last few years, the introduction of MALDI-TOF MS into the microbiology laboratory has been revolutionary. In brief, this new technology compares protein profiles by generating spectra based on the m/z ratio. We evaluated the performance of MALDI-TOF MS for typing serotypes of S. pneumoniae isolates included in the PCV13 vaccine using a machine learning approach. We challenged our classification algorithms in "real time" with a total of new 100 isolates of S. pneumoniae from Argentinian nationwide surveillance. Our best approach could correctly identify the isolates with a sensitivity of 58.33% ([95%CI 40.7-71.7]); specificity of 81.48% ([95%CI 53.6-79.7]); accuracy of 63.0% ([95%CI 61.9-93.7]); PPV of 80.77% ([95%CI 64.5-90.6]) and NPV of 59.46% ([95%CI 48.9-69.2]). Furthermore, this approach allowed us to optimize the use of the antiserum used for capsular typing by 10.2% compared to the traditional "blind" typing scheme. In this work, it was possible to demonstrate that the combination of MALDI-TOF mass spectrometry and multivariate analysis allows the development of new strategies for the identification and characterization of Spn isolates of clinical importance.
... Additionally, participants contributed dual samples to improve detection. Culture of NP samples has been considered the gold standard for detection of pneumococci [22], but this method may be insufficient in adults [23], as evidence suggests that the density of pneumococci in the nasopharynx decreases with age [24]. Analysis of OP or saliva samples by molecular methods has been shown to increase the sensitivity of pneumococcal detection in adults [13,15,17,[25][26][27][28][29][30] as compared with conventional culture [16,31,32]. ...
Background
COVID-19 containment measures reduced the burden of invasive pneumococcal disease. Data on pneumococcal carriage rates among adults during the pandemic are scarce.
Methods
Naso- and oropharyngeal swabs and questionnaires were collected during January 2019 to December 2021 from adults ≥64 years of age. Carriage was determined by lytA/piaB PCR.
Results
A total of 1556 participants provided paired naso- and oropharyngeal swabs. Their median age was 74 years (IQR, 70–79). Streptococcus pneumoniae DNA was detected in 146 (9.4%) oropharyngeal swabs and 34 (2.2%) nasopharyngeal. The carriage rate decreased from 12.9% (95% CI, 10.1%–16.1%, n = 66/511) prelockdown (January 2019–February 2020) to 4.2% (95% CI, 2.0%–7.5%, n = 10/240) during lockdown (March 2020–February 2021) and increased to 12.1% (95% CI, 9.8%–14.7%, n = 87/719) with the reopening of society (March 2021–December 2021; P = .0009).
Conclusions
Pneumococcal carriage prevalence declined significantly during pandemic mitigation measures and rebounded to prepandemic levels as measures were lifted.
... Confirmed pneumococcal isolates were stored in duplicate in 1.5 mL cryotubes containing STGG (skim-milk-tryptone-glucose-glycerin) broth at −80 °C until being transported to the central laboratory for serotyping plus further characterization [31]. ...
: Introduction. Streptococcus pneumonia infections are a major cause of mortality and morbidity worldwide. In Jordan, pneumococcal conjugate vaccines (PCVs) are not included in the national vaccination program. Due to the current availability of several PCVs including PCV-10, PCV-13 and PCV-15, along with PCV-20, currently undergoing pediatric approvals globally, the decision to introduce PCVs and their selection should be based on valid local data on the common serotypes of Streptococcus pneumonia. Methods: This cross-sectional study aimed to identify the frequency of serotypes of Streptococcus pneumonia in children aged below 5 years hospitalized with invasive pneumococcal diseases (IPD) including pneumonia, septicemia and meningitis during the study’s duration in representative areas of Jordan. Serotyping for culture-positive cases was based on the capsular reaction test, known as the Quellung reaction. qPCR was conducted on blood samples of patients with lobar pneumonia identified via X-ray or on cerebrospinal fluid for those with a positive latex agglutination test for Streptococcus pneumonia. Results. This study was based on the analysis of the serotypes of 1015 Streptococcus pneumonia cases among children younger than the age of 5; 1006 cases with pneumonia, 6 cases with meningitis, and 3 cases with septicemia. Only 23 culture-positive cases were identified, in comparison to 992 lobar pneumonia cases which were PCR-positive but culture-negative, with a PCR positivity rate of 92%. Serotypes 6B, 6A, 14 and 19F were the most common serotypes identified in the study, with prevalence rates of 16.45%, 13.60%, 12.12% and 8.18%, respectively. PCV-10, PCV-13, PCV-15 and PCV-20 coverage rates were 45.32%, 61.87%, 64.14% and 68.47%, respectively. Discussion: To the best of our knowledge, this is largest prospective study from the Middle East and one of the largest studies worldwide showing the serotypes of Streptococcus pneumonia. It reveals the urgency for the introduction of PCV vaccination in Jordan, utilizing recently developed vaccines with broader serotype coverage.
... In addition, carriage and IPD serotype distributions, IPD disease burden, and pneumococcal vaccine uptake differ between the US and South Africa and thus these populations may not be directly comparable (21). The age effect observed in this study may be related to lower detection of S. pneumoniae among adults compared to children as S. pneumoniae carriage density is generally lower among adults and we used nasal rather than more sensitive nasopharyngeal swabs and did not collect oropharyngeal swabs among adults, as recommended by the WHO (41,42). Alternatively, this may reflect differences in the processes leading to increased pneumococcal carriage between children and adults, a potential impact of a different serotype distribution between children and adults, differences in prior S. pneumoniae infection and vaccination histories, or differences in the distribution of respiratory viruses co-detected. ...
... For example, ear pain and headache were infrequently reported among symptomatic children aged <5 years relative to older children. Third, we tested self-collected mid-turbinate and anterior nasal swabs rather than nasopharyngeal swabs, which are the current gold standard for detecting pneumococcal carriage in children, and we did not collect nasopharyngeal in addition to oropharyngeal swabs among adults, the current gold standard (41). Therefore, we likely underestimated detection of S. pneumoniae, such as in low S. pneumoniae density specimens (51). ...
Background
Respiratory viruses might influence Streptococcus pneumoniae nasal carriage and subsequent disease risk. We estimated the association between common respiratory viruses and semiquantitative S. pneumoniae nasal carriage density in a household setting before and during the COVID-19 pandemic.
Methods
From November 2019–June 2021, we enrolled participants in a remote household surveillance study of respiratory pathogens. Participants submitted weekly reports of acute respiratory illness (ARI) symptoms. Mid-turbinate or anterior nasal swabs were self-collected at enrollment, when ARI occurred, and, in the second year of the study only, from household contacts after SARS-CoV-2 was detected in a household member. Specimens were tested using multiplex reverse-transcription PCR for respiratory pathogens, including S. pneumoniae , rhinovirus, adenovirus, common human coronavirus, influenza A/B virus, respiratory syncytial virus (RSV) A/B, human metapneumovirus, enterovirus, and human parainfluenza virus. We estimated differences in semiquantitative S. pneumoniae nasal carriage density, estimated by the inverse of S. pneumoniae relative cycle threshold (Crt) values, with and without viral detection for any virus and for specific respiratory viruses using linear generalized estimating equations of S. pneumoniae Crt values on virus detection adjusted for age and swab type and accounting for clustering of swabs within households.
Results
We collected 346 swabs from 239 individuals in 151 households that tested positive for S. pneumoniae ( n = 157 with and 189 without ≥1 viruses co-detected). Difficulty breathing, cough, and runny nose were more commonly reported among individuals with specimens with viral co-detection compared to without (15%, 80% and 93% vs. 8%, 57%, and 51%, respectively) and ear pain and headache were less commonly reported (3% and 26% vs. 16% and 41%, respectively). For specific viruses among all ages, semiquantitative S. pneumoniae nasal carriage density was greater with viral co-detection for enterovirus, RSV A/B, adenovirus, rhinovirus, and common human coronavirus ( P < 0.01 for each). When stratified by age, semiquantitative S. pneumoniae nasal carriage density was significantly greater with viral co-detection among children aged <5 ( P = 0.002) and 5–17 years ( P = 0.005), but not among adults aged 18–64 years ( P = 0.29).
Conclusion
Detection of common respiratory viruses was associated with greater concurrent S. pneumoniae semiquantitative nasal carriage density in a household setting among children, but not adults.
... Sociodemographic and clinical information was obtained from carriage survey participants using an interviewer-administered questionnaire. Nasopharyngeal swabbing, transport, storage and culture were done according to WHO-recommended standards 36 . We collected one swab specimen per participant from the posterior wall of the nasopharynx using nylon-tipped flexible flocked swabs (FloQS-wabs®). ...
... We identified serotypes using latex agglutination confirmed by Quellung Reaction. For isolates with inconclusive serotyping, we confirmed species and serotype by polymerase chain reaction (PCR) for autolysin (lytA) and capsular locus genes, respectively 36 . ...
Pneumococcal conjugate vaccines (PCVs) protect against invasive pneumococcal disease (IPD) among vaccinees. However, at population level, this protection is driven by indirect effects. PCVs prevent nasopharyngeal acquisition of vaccine-serotype (VT) pneumococci, reducing onward transmission. Each disease episode is preceded by infection from a carrier, so vaccine impacts on carriage provide a minimum estimate of disease reduction in settings lacking expensive IPD surveillance. We documented carriage prevalence and vaccine coverage in two settings in Nigeria annually (2016–2020) following PCV10 introduction in 2016. Among 4,684 rural participants, VT carriage prevalence fell from 21 to 12% as childhood (<5 years) vaccine coverage rose from 7 to 84%. Among 2,135 urban participants, VT carriage prevalence fell from 16 to 9% as uptake rose from 15 to 94%. Within these ranges, carriage prevalence declined with uptake. Increasing PCV10 coverage reduced pneumococcal infection at all ages, implying at least a comparable reduction in IPD.
... U/SERC/49/2018). The sample collection was carried out during the period of 1 May to 31 August 2018. ...
... A questionnaire to collect socio-demographic and healthrelated data was completed for each subject, including the subject's gender, age, ethnicity, vaccination status, self-reported respiratory symptoms and antibiotic consumption in the previous month. A nasal (anterior nares) swab and an oropharyngeal swab were taken from each subject by using sterile cotton swabs of the DRYSWAB™ range (MWE, Wiltshire, UK) in accordance with the WHO Pneumococcal Carriage Working Group guidelines [31]. The swab was placed in the skim milk, tryptone, glucose and glycerol (STGG) medium for laboratory analysis and long-term storage. ...
The carriage of bacterial pathogens in the human upper respiratory tract (URT) is associated with a risk of invasive respiratory tract infections, but the related epidemiological information on this at the population level is scarce in Malaysia. This study aimed to investigate the URT carriage of Streptococcus pneumoniae, Haemophilus influenzae, Neisseria meningitidis, Staphylococcus aureus, Klebsiella pneumoniae and Pseudomonas aeruginosa among 100 university students by nasal and oropharyngeal swabbing. The presence of S. aureus, K. pneumoniae and P. aeruginosa was assessed via swab culture on selective media and PCR on the resulting isolates. For S. pneumoniae, H. influenzae and N. meningitidis, their presence was assessed via multiplex PCR on the total DNA extracts from chocolate agar cultures. The carriage prevalence of H. influenzae, S. aureus, S. pneumoniae, K. pneumoniae, N. meningitidis and P. aeruginosa among the subjects was 36%, 27%, 15%, 11%, 5% and 1%, respectively, by these approaches. Their carriage was significantly higher in males compared to females overall. The S. aureus, K. pneumoniae and P. aeruginosa isolates were also screened by the Kirby-Bauer assay, in which 51.6% of S. aureus were penicillin-resistant. The outcomes from carriage studies are expected to contribute to informing infectious disease control policies and guidelines.
... S. pneumoniae strains are "dissolved" in rabbit bile (66), and this is the basis of a phenotypic assay (i.e., bile solubility test) utilized to differentiate S. pneumoniae strains from other alpha-hemolytic streptococci (67,68). At a more physiological concentration, such as that utilized in the current study (1.27 mM), DoC specifically killed S. pneumoniae strains but had little to no activity against other streptococci. ...
Streptococcus pneumoniae (pneumococcus) colonizes the upper respiratory tract, including the nasopharynx, of children and the elderly. Despite antibiotics and vaccines readily available, pneumococcus kills millions worldwide yearly. We have found that the secondary bile acid metabolite and endogenous salt deoxycholic acid (DoC) affects the viability of this human pathogen while also playing multiple roles in host physiology. Via in vitro studies, we assessed the anti-microbial activity of DoC and investigated its potential to eradicate S. pneumoniae colonization using a model of human nasopharyngeal colonization and an in vivo mouse model. At a physiological concentration, DoC (0.5 mg/ml; 1.27 mM) killed all tested strains of S. pneumoniae (n=48) 2 hours post-inoculation. Our model of nasopharyngeal colonization showed that DoC eradicated colonization by S. pneumoniae strains as quickly as 10 minutes post-exposure. The mechanism of action did not involve activating autolysis since autolysis-defective double mutant strains (Δ lytAΔ lytC and Δ spxBΔ lctO) were found to be as susceptible to DoC as the wild-type strain (WT). Oral streptococcal species (n=20) were, however, not as susceptible to DoC at 0.5 mg/ml. Unlike trimethoprim, whose spontaneous resistance frequency (srF) for TIGR4 or EF3030 was ≥ 1 x 10 ⁻⁹ , no spontaneous resistance was observed with DoC. Finally, the efficacy of DoC to eradicate S. pneumoniae colonization was assessed in vivo using an intranasal topical route (i.n.) and separately as prophylactic treatment. Mice that were challenged with S. pneumoniae EF3030 carried a median of 4.05 x 10 ⁵ CFU/ml four days post-inoculation compared to 6.67 x 10 ⁴ CFU/ml for mice treated with DoC. Furthermore, mice in the prophylactic DoC group had approximately a 99% reduction of pneumococcal density illustrating the possibility of deoxycholic acid as a safe, endogenous human bile salt with therapeutic potential against increasingly-resistant S. pneumoniae strains.
This study was in part supported by grants from the National Institutes of Health (NIH; 1R21AI144571-01 and 1R21AI151571-01A1 to J.E.V.). B.A. was supported by a Fulbright scholarship awarded by the U.S. Department of State. The content is solely the responsibility of the authors and does not necessarily represent the official view of the NIH or the U.S. Department of State.
This is the full abstract presented at the American Physiology Summit 2023 meeting and is only available in HTML format. There are no additional versions or additional content available for this abstract. Physiology was not involved in the peer review process.
... This is because large community-based surveillance studies involving repeated sampling of individuals across a wide age range are difficult to conduct due to the nature of the currently recommended URT sampling methods. To detect pneumococcal carriage in the URT, a pre-requisite for disease occurrence, the World Health Organisation (WHO) recommends the use of nasopharyngeal swabs (NPS) in children and both NPS and oropharyngeal swabs in adults [16]. However, sampling, especially in children, . ...
Background: Monitoring the presence of commensal and pathogenic microorganisms in the human oral, nasal and hand niches as determinants for respiratory tract infections is of critical global relevance as was evident during the COVID-19 pandemic. However, community-based surveillance is difficult because current sampling methods are not optimal for a wide age range of participants, particularly young children. We designed a platform of minimally invasive self-sampling at home and assessed its use for longitudinal monitoring of the oral, nasal and hand microbiota of adults and children within families.
Methods: Healthy families with two adults and up to three children, living in and near Liverpool, United Kingdom, self-collected saliva, nasal lining fluid using synthetic absorptive matrices and hand swabs at home every two weeks for six months. Questionnaires were used to collect demographic and epidemiological data and assess feasibility and acceptability. At the end of the study, participants were invited to take part in an interview.
Results: Thirty-three families completed the study. Sample collection using our approach was acceptable to 25/33 (76%) families, as sampling was fast (76%), easy (76%) and painless (60%). Saliva and hand sampling was acceptable to all participants of any age, whereas nasal sampling was accepted mostly by adults and children older than 5 years.
Conclusion: Multi-niche self-sampling at home can be used by adults and children for longitudinal microbial surveillance, providing key data for monitoring respiratory infections.
... The current gold standard method for the detection of pneumococcal carriage is testing nasopharyngeal swabs by conventional culture. Updated World Health Organization (WHO) recommendations made in 2013 by the Pneumococcal Carriage Working Group advised the inclusion of oropharyngeal swabs from adults when possible (20). A number of studies have demonstrated that the sensitivity of carriage detection can be further improved when molecular methods are applied (21)(22)(23)(24)(25)(26) and when alternative sample types such as saliva are used (4, 12, 27). ...
While the sensitivity of detection of pneumococcal carriage can be improved by testing respiratory tract samples with quantitative PCR (qPCR), concerns have been raised regarding the specificity of this approach. We therefore investigated the reliability of the widely used lytA qPCR assay when applied to saliva samples from older adults in relation to a more specific qPCR assay (piaB). During the autumn/winter seasons of 2018/2019 and 2019/2020, saliva was collected at multiple time points from 103 healthy adults aged 21 to 39 (n = 34) and >64 (n = 69) years (n = 344 total samples). Following culture enrichment, extracted DNA was tested using qPCR for piaB and lytA. By sequencing the variable region of rpsB (S2 typing), we identified the species of bacteria isolated from samples testing lytA-positive only. While 30 of 344 (8.7%) saliva samples (16.5% individuals) tested qPCR-positive for both piaB and lytA, 52 (15.1%) samples tested lytA-positive only. No samples tested piaB-positive only. Through extensive reculture attempts of the lytA-positive samples collected in 2018/2019, we isolated 23 strains (in 8 samples from 5 individuals) that were also qPCR-positive for only lytA. Sequencing determined that Streptococcus mitis and Streptococcus infantis were predominantly responsible for this lytA-positive qPCR signal. We identified a comparatively large proportion of samples generating positive signals with the widely used lytA qPCR and identified nonpneumococcal Streptococcus species responsible for this signal. This highlights the importance of testing for the presence of multiple gene targets in tandem for reliable and specific detection of pneumococcus in polymicrobial respiratory tract samples. IMPORTANCE Testing saliva samples with quantitative PCR (qPCR) improves the sensitivity of detection of pneumococcal carriage. The qPCR assay targeting lytA, the gene encoding the major pneumococcal autolysin, has become widely accepted for the identification of pneumococcus and is even considered the "gold standard" by many. However, when applying this approach to investigate the prevalence of pneumococcal carriage in adults in New Haven, CT, USA, we identified nonpneumococcal Streptococcus spp. that generate positive signals in this widely used assay. By testing also for piaB (encoding the iron acquisition ABC transporter lipoprotein, PiaB), our findings demonstrate the importance of testing for the presence of multiple gene targets in tandem for reliable molecular detection of pneumococcus in respiratory tract samples; targeting only lytA may lead to an overestimation of true carriage rates.
