Background Appropriate storage and transport conditions are crucial for ensuring bacterial viability within biological specimens. Nasopharyngeal carriage studies are common for Streptococcus pneumoniae . However, storing or transporting specimens at ultra-low temperatures as recommended by the World Health Organization is not possible in all settings. Here, we assess the impact of alternative storage conditions on pneumococcal viability and density using laboratory-prepared samples. Methods Flocked swabs were inoculated with low (n = 395) or medium (n = 395) loads of single pneumococcal isolates. Twenty different serotypes were tested. Swabs were stored in skim milk, tryptone, glucose and glycerol (STGG) medium at -80°C (gold standard), -20°C and 4°C, and in silica desiccant packets (SDPs) at 4°C and 30°C. Viable counts were performed at inoculation (baseline), and 2, 7, 14, 21 and 28 days post storage. A subset of samples from baseline and 28 days post storage were assessed for pneumococcal detection and density using culture-independent, molecular methods. Results Using culture-based methods, pneumococcal recovery was high (≥ 80%) up to 28 days when samples were stored at -20°C and − 80°C in STGG. Samples stored at 4°C in both STGG and SDPs had inconsistent recovery (< 80%) by 28 days, and samples stored at 30°C in SDPs had very low recovery (< 15%) at all timepoints. Overall, when compared by culture to the inoculum load, density was substantially reduced when alternative storage conditions were used. When density was assessed by lytA qPCR, pneumococci could be detected for most (99%) samples in select storage conditions. Conclusions Improper storage of specimens may lead to underestimations of pneumococcal prevalence and density, especially when culture-based methods are used. Given this, study outcomes and methods of testing should be considered when determining feasible transport and storage conditions. We identified alternative storage conditions to the gold standard that could enable studies in remote or complex settings.

Background:Streptococcus pneumoniae (the pneumococcus) is one of the main causes of childhood mortality. Understanding pneumococcal serotype and lineage distribution in children is important for vaccine decision-making. We undertook a secondary analysis of nasopharyngeal swabs collected from unvaccinated children as part of pneumococcal vaccine studies to provide a comprehensive picture of pneumococcal carriage epidemiology in Vietnamese children during the first 60 months of life. Methods:We analysed 4375 nasopharyngeal swabs from unvaccinated children to assess overall and vaccine-type pneumococcal carriage at 6, 12, 18, 24, and 60 months of age. For the latter three age groups, serotype distribution and genetic lineages (Global Pneumococcal Sequence Cluster, GPSCs) were described overall and by age. We also evaluated the prevalence of antimicrobial resistance (AMR) genes and multi-drug resistance (MDR), comparing vaccine-type and non-vaccine-type pneumococci. Findings:Overall pneumococcal carriage was 21·7% (952/4375) with a total of 27 serotypes detected. Serotype coverage was similar across products Pneumosil (68·6% [95% CI 65·5-71·7%], 595/867), Prevenar13 (70·0% [95% CI 67·0-73·1%], 607/867), and Vaxneuvance (70·0% [95% CI 67·0-73·1%], 607/867), and lower for Synflorix (41·5% [95% CI 38·2-44·8%], 360/867) p < 0·05 vs Pneumosil, Prevenar13 or Vaxneuvance. In total, 2444 swabs were tested at 18, 24, and 60 months. Thirty distinct GPSCs were identified, with their distribution remaining stable across these ages. AMR genes were highly prevalent, detected in 98·9% (360/364) of samples. Interpretation:Synflorix provided lower serotype coverage than other PCVs, largely driven by the prevalence of serotype 6A, which is not included in Synflorix formulation. Serotype, lineage distribution, and prevalence of AMR genes across the sampled age groups remained consistent, indicating that these distributions are broadly representative of young unvaccinated children, helping to guide optimal approaches for pneumococcal surveillance in low- and middle-income countries. Funding:National Health and Medical Research Council, Bill & Melinda Gates Foundation, Murdoch Children's Research Institute.

Background: Pneumococcal conjugate vaccine (PCV) prevents pneumococcal disease and pneumonia, but indirect effects are poorly understood in low-coverage, high-burden settings like Papua New Guinea (PNG). PNG introduced 13-valent PCV (PCV13) in 2014. We aimed to assess direct and indirect effectiveness of PCV13 against vaccine-type pneumococcal carriage among children with pneumonia or suspected meningitis in PNG. Methods: Children aged <= 59 months with pneumonia or suspected meningitis (cases) were enrolled at Eastern Highlands Provincial Hospital and nearby clinics (April 2016-December 2019). Clinical data, PCV13 status, and nasopharyngeal swabs were collected. Pneumococci were detected by lytA real-time PCR and serotyped by microarray. PCV13 coverage among village children <= 59 months was estimated via household surveys. Vaccine-type carriage by case-level PCV13 status was estimated. Associations between carriage and case PCV13 status (direct effects), and village-level coverage (indirect effects) were estimated using GEE logistic regression with village clustering. Results: Among 1214 cases, vaccine-type carriage was lower in vaccinated (24.8%) than under-vaccinated (41.3%) cases. Adjusted PCV13 effectiveness against vaccine-type carriage was 46.6% (95% CI 27.0-60.9). Coverage surveys occurred in 148 villages (5978 children). Median village-level coverage increased from 2016 (12.5% [IQR 0-37.5]) to 2019 (28.6% [IQR 0-53.8]). Each percent increase in village coverage corresponded to a 0.5% (95% CI 0.0-1.0) decrease in vaccine-type carriage. Conclusions: PCV13 vaccination reduced vaccine-type carriage in PNG. Despite low coverage, indirect effects were evident, consistent with emerging herd protection. These findings highlight the importance of strengthening PCV13 programs to optimise individual and community protection.

Streptococcus pneumoniae (the pneumococcus) is a leading cause of community-acquired pneumonia. Pneumococci are categorised into serotypes, based on the type of capsular polysaccharide produced, which has important implications for virulence, vaccine impact and global surveillance. Recently, we identified a novel serotype, which we named 33G, that is comprised of an O-acetylated hexasaccharide repeat unit. In this study, we report and describe variants of 33G, designated 33G-like, which we isolated from the nasopharynx of two adults hospitalised with pneumonia in Mongolia. Serological comparison of 33G and 33G-like pneumococci were conducted by Quellung serotyping. Genetic analysis of the capsular polysaccharide loci was performed using whole genome sequencing. Polysaccharide composition was determined using 1H nuclear magnetic resonance. By Quellung serotyping, 33G pneumococci type as both 10B and 33B whereas 33G-like pneumococci type as both 10B and 33F. Genomic analysis of the capsular polysaccharide locus revealed 33G-like loci are identical to 33G, except for frameshift mutations in the wciG gene which encodes an acetyltransferase responsible for the O-acetylation of beta-galactofuranose (β-Galf) in the capsular polysaccharide repeat unit. We constructed an artificial 33G-like by deleting wciG in a 33G strain and confirmed this gene was responsible for the serological differences between 33G and 33G-like pneumococci. Lastly, 1H nuclear magnetic resonance confirmed the O-acetylation present in the 33G polysaccharide is absent in the 33G-like polysaccharide. Here, we have provided serological, genetic and biochemical evidence that the 33G-like capsule differs to 33G and all other pneumococcal serotypes, meeting the requirements to be designated as a new serotype, which we have named 33H.

BACKGROUND:Chronic pulmonary infection with pathogens such as Pseudomonas aeruginosa is associated with lung function decline and increased mortality in people with cystic fibrosis (CF). The relationship between sputum bacterial load and the severity of pulmonary exacerbations remains unclear. This study aimed to explore the relationship between sputum bacterial load and clinical response to antibiotic treatment of pulmonary exacerbations in children with CF. METHODS:Multicentre prospective longitudinal study of children with CF receiving IV tobramycin for a pulmonary exacerbation who had prior isolation of Gram-negative bacteria and able to expectorate sputum. Lung function (FEV1) and sputum bacterial load were assessed. Bacterial load was performed using quantitative PCR on either intact (live) bacterial cells or all bacterial DNA (live + dead) and targeted either P. aeruginosa only or all bacteria. RESULTS:Twelve children (14 admissions) were enrolled and each provided ≥2 sputum samples; 11 children (13 admissions) also had ≥2 FEV1 measurements. In 10 admissions where FEV1 improved, five showed a reduction in all live bacteria, with a median reduction by 8.65 × 106 copies/g (73 % reduction). Live P. aeruginosa was detected in 8/10 children and in seven, a median reduction of 2.99 × 107 copies/g (90 % reduction) was observed. Improved FEV1 correlated with greater reductions in live + dead P. aeruginosa (ρ = -0.63, p = 0.04). CONCLUSION:A greater reduction in total sputum P. aeruginosa bacterial load (live + dead) was associated with improved lung function (FEV1) in children with CF receiving tobramycin.

ABSTRACTBackgroundData available for RSV and influenza infections among children < 2 years in Mongolia are limited. We present data from four districts of Ulaanbaatar from April 2015 to June 2021.MethodsThis study was nested in an enhanced surveillance project evaluating pneumococcal conjugate vaccine (PCV13) impact on the incidence of hospitalized lower respiratory tract infections (LRTIs). Our study was restricted to children aged < 2 years with arterial O2 saturation < 93% and children with radiological pneumonia. Nasopharyngeal (NP) swabs collected at admission were tested for RSV and influenza using qRT‐PCR. NP swabs of all patients with radiological pneumonia and of a subset of randomly selected NP swabs were tested for S. pneumoniae (S.p.) by qPCR and for serotypes by culture and DNA microarray.ResultsAmong 5705 patients, 2113 (37.0%) and 386 (6.8%) had RSV and influenza infections, respectively. Children aged 2–6 months had a higher percentage of very severe RSV infection compared to those older than 6 months (42.2% versus 31.4%, p‐value Fisher's exact = 0.001). S.p. carriage was detected in 1073/2281 (47.0%) patients. Among S.p. carriage cases, 363/1073 (33.8%) had S.p. and RSV codetection, and 82/1073 (7.6%) had S.p. and influenza codetection. S.p. codetection with RSV/influenza was not associated with more severe LRTIs, compared to only RSV/influenza cases.ConclusionIn Mongolia, RSV is an important pathogen causing more severe LRTI in children under 6 months of age. Codetection of RSV or influenza virus and S.p. was not associated with increased severity.

Abstract 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.

BACKGROUND:Data on changes in pneumococcal serotypes in hospitalised children following the introduction of the pneumococcal conjugate vaccine (PCV) in low-income and middle-income countries are scarce. In 2016, Mongolia introduced the 13-valent PCV (PCV13) into the national immunisation programme. We aimed to describe the trend and impact of PCV13 introduction on pneumococcal carriage in hospitalised children aged 2-59 months with pneumonia in Mongolia over a 6-year period. METHODS:In this active surveillance programme, children aged 2-59 months with pneumonia who met the study case definition (cough or difficulty breathing with either respiratory rate ≥50 beats per min, oxygen saturation <90%, or clinical diagnosis of severe pneumonia) were enrolled between April 1, 2015, and June 30, 2021, from four districts in Ulaanbaatar. We tested nasopharyngeal samples collected at enrolment for pneumococci using lytA real-time quantitative PCR and conducted molecular serotyping and detection of antimicrobial resistance (AMR) genes with DNA microarray. We used log-binomial regression to estimate prevalence ratios (PRs) of pneumococcal carriage, comparing prevalence in the periods before and after the introduction of PCV13 and between vaccinated and unvaccinated children for three outcomes: overall, PCV13 vaccine-type, and non-PCV13 vaccine-type carriage. PRs were adjusted with covariates that were identified by use of a directed acyclic graph, informed by relevant literature. FINDINGS:A total of 17 688 children were enrolled, of whom 17 607 (99·5%) met the study case criteria. 6545 (42·5%) of 15 411 collected nasopharyngeal swabs were tested for pneumococci. In all age groups, a similar prevalence of pneumococcal carriage was shown between the pre-PCV13 period and post-PCV13 period (882 [48·0%] of 1837 vs 2174 [46·2%] of 4708; adjusted PR 0·98 [95% CI 0·92-1·04]; p=0·60). Overall, vaccine-type carriage reduced by 43·6% after the introduction of PCV13 (adjusted PR 0·56 [95% CI 0·51-0·62]; p<0·0001). Younger children (aged 2-23 months) showed a 47·7% reduction in vaccine-type carriage (95% CI 41·2-53·5; adjusted PR 0·52 [95% CI 0·46-0·59]; p<0·0001), whereas children aged 24-59 months had a 29·3% reduction (12·6-42·8; 0·71 [0·57-0·87]; p=0·0014). Prevalence of 6A, 6B, 14, 19F, and 23F decreased following the introduction of PCV13; however, 19F and 6A remained common (5·8% and 2·9%). Non-vaccine-type carriage increased (adjusted PR 1·49 [95% CI 1·32-1·67]), with 15A, NT2, and 15B/C being the most prevalent serotypes. Overall, 1761 (89·3%) of 1978 analysed samples contained at least one AMR gene. The percentage of samples with any AMR gene decreased with vaccine introduction (92·3% in the pre-PCV13 period vs 85·3% in the post-PCV13 period; adjusted odds ratio 0·49 [95% CI 0·34-0·70]), with similar decreases for samples with at least three AMR genes (46·8% vs 27·6%; 0·44 [0·36-0·55]). INTERPRETATION:6 years after the introduction of PCV13 in Mongolia, the prevalence of vaccine-type carriage and AMR genes showed a reduction among young hospitalised children with pneumonia. Reductions in vaccine-type carriage are likely to result in reductions in pneumococcal pneumonia. FUNDING:GAVI, the Vaccine Alliance.

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. Pneumococcal carriage is a useful outcome to evaluate pneumococcal conjugate vaccine (PCV) introduction. Here the authors conducted cross-sectional carriage surveys before (2015) and after 13-valent PCV introduction (2017 and 2022) in Mongolia to determine vaccine impact.

Pneumococcal Conjugate Vaccines (PCVs) have substantially reduced the burden of disease caused by Streptococcus pneumoniae (the pneumococcus). However, protection is limited to vaccine serotypes, and when administered to children who are colonized with pneumococci at the time of vaccination, immune responses to the vaccine are blunted. Here, we investigate the potential of a killed whole cell pneumococcal vaccine (WCV) to reduce existing pneumococcal carriage and mucosal disease when given therapeutically to infant mice colonized with pneumococci. We show that a single dose of WCV reduced pneumococcal carriage density in an antibody-dependent manner. Therapeutic vaccination induced robust immune responses to pneumococcal surface antigens CbpA, PspA (family 1) and PiaA. In a co-infection model of otitis media, a single dose of WCV reduced pneumococcal middle ear infection. Lastly, in a two-dose model, therapeutic administration of WCV reduced nasal shedding of pneumococci. Taken together, our data demonstrate that WCV administered in colonized mice reduced pneumococcal density in the nasopharynx and the middle ear, and decreased shedding. WCVs would be beneficial in low and middle-income settings where pneumococcal carriage in children is high.

Background: Data on pneumococcal serotype changes in hospitalised children following pneumococcal conjugate vaccine (PCV) introduction in low-middle income countries are limited. Mongolia introduced the 13-valent PCV (PCV13) into the national immunisation programme from 2016. We measured the effect of PCV13 introduction on pneumococcal nasopharyngeal carriage in hospitalised children with pneumonia in Mongolia over a six-year period.Methods: Children aged 2-59 months with pneumonia (n=17,607) were enrolled during April 2015 to June 2021 from four districts in Ulaanbaatar. Nasopharyngeal swabs (n=6,545) were tested to detect pneumococci using lytA real-time quantitative PCR and molecular serotyping and antimicrobial resistance (AMR) gene detection conducted by DNA microarray. Participant characteristics and risk factors were described. Log-binomial regression was used to estimate pneumococcal carriage prevalence ratios for all, PCV13 vaccine type (VT) and non-PCV13 vaccine type (NVT) carriage prevalence.Results: Pneumococcal carriage prevalence was similar between pre-PCV13 and post-PCV13 periods (48% vs 46%, p=0·18). Overall, VT carriage reduced by 44% (adjusted prevalence ratio [aPR] =0·56, 95% CI 0·51-0·62). Children aged 2-23 months had a substantial reduction (48%) in VT carriage, which was greater than for older children (29%). Prevalence of 6A, 6B, 14, 19F and 23F declined following PCV13 introduction, however 19F and 6A remained common (6% and 3%, respectively). NVT carriage increased (aPR=1·41, 95% CI 1·24-1·59), with 15A, NT2 and 15B/C most prevalent. Overall, 89% of samples contained at least one AMR gene. The percentage of samples with any AMR gene decreased with vaccine introduction (92% pre-PCV vs 85% post-PCV, p<0·0001) with similar decreases for samples with ≥3 AMR genes (47% vs 28% p<0·0001).Conclusions: Six years after PCV13 vaccine introduction in Mongolia, VT carriage and AMR gene prevalence declined among hospitalised children with pneumonia. Reductions in VT carriage are likely to result in reductions in disease.Funding: Gavi, The Vaccine Alliance.Declaration of Interest: CVM, MU, CDN, PB, BS, DL, CS, TM and EKM are investigators on a Pfizer collaborative research project outside this work. EMD is currently employed by Pfizer. CS, EKM and CDN are investigators on a Merck Investigator Studies Program grant funded by MSD outside this work. JH is co-founder and shareholder of BUGS Bioscience Ltd., a not-for-profit spin-out company of St George's, University of London. The other authors have no relevant conflicts of interest to declare.Ethical Approval: The study was approved by the Medical Ethics Review Committee at the Mongolian Ministry of Health and the Royal Children's Hospital Human Research Ethics Committee (HREC 33203). Written informed consent was obtained by study staff from all parents/caregivers for enrolled children prior to any study procedures being conducted.

ABSTRACT Streptococcus pneumoniae (the pneumococcus) is a human pathogen responsible for a spectrum of diseases such as pneumonia, sepsis, and meningitis. The capsule is the major pneumococcal virulence factor and is encoded by the capsular polysaccharide (cps) locus, a recombination hotspot that has resulted in over 100 distinct capsular polysaccharide types (serotypes) identified to date. Recently, 33X (also known as 10X) was proposed as a putative novel serotype, but the capsule structure had not been elucidated. Here, we provide an in-depth investigation of 33X, demonstrating it is a new pneumococcal capsular serotype. In this study, we screened 12,850 nasopharyngeal swabs from both healthy children and pneumonia patients (adults and children) in Mongolia collected between 2015 and 2022. We identified 20 pneumococcal 33X isolates. Using whole genome sequencing, we found that the 33X cps locus is a chimera of genes from pneumococcal serogroups 35, 10, and 33, as well as other Streptococcal species. Serotyping of 33X pneumococci by the Quellung reaction revealed a unique serological profile, typing as both 10B and 33B. Competitive ELISAs confirmed that antibodies that were generated in mice directed against 33X were inhibited by 33X pneumococci but not 10B or 33B. Lastly, the elucidation of the 33X capsule structure revealed that the polysaccharide is distinct from other serotypes, consisting of an O-acetylated hexasaccharide repeat unit of →5)-β-Galf-(1→3)-β-Glcp-(1→5)-β-Galf 2Ac-(1→3)-β-GalpNAc-(1→3)-α-Galp-(1→4)-Rib-ol-(5→P→. Therefore, 33X meets the requisite genetic, serological, and biochemical criteria to be designated as a new serotype, which we have named 33G. IMPORTANCE Streptococcus pneumoniae (the pneumococcus) is a bacterial pathogen with the greatest burden of disease in Asia and Africa. The pneumococcal capsular polysaccharide has biological relevance as a major virulence factor as well as public health importance as it is the target for currently licensed vaccines. These vaccines have limited valency, covering up to 23 of the >100 known capsular types (serotypes) with higher valency vaccines in development. Here, we have characterized a new pneumococcal serotype, which we have named 33G. We detected serotype 33G in nasopharyngeal swabs (n = 20) from children and adults hospitalized with pneumonia, as well as healthy children in Mongolia. We show that the genetic, serological, and biochemical properties of 33G differ from existing serotypes, satisfying the criteria to be designated as a new serotype. Future studies should focus on the geographical distribution of 33G and any changes in prevalence following vaccine introduction.

INTRODUCTION:Infections are a leading cause of neonatal mortality globally and can be transmitted from mother-to-child vertically or horizontally. Fiji has higher rates of serious neonatal infections and infant skin and soft tissue infections (SSTIs) than high-income countries. Research from the Gambia found that a single dose of oral azithromycin in labour decreased bacterial carriage and infections in mothers and infants, particularly infant skin infections. The Bulabula MaPei clinical trial evaluates the safety and efficacy of a single dose of azithromycin in labour in reducing the incidence of maternal and infant SSTIs and other infections and the impact on bacterial carriage. It will also describe the effect of azithromycin on antimicrobial (AMR) resistance, the maternal and infant microbiome, and infant dysbiosis. METHODS AND ANALYSIS:We are conducting a blinded, placebo-controlled randomised clinical trial administering 2 g of oral azithromycin, or placebo, given to healthy, pregnant women (≥18 years) in labour in Suva, Fiji. The primary outcome is the cumulative incidence of SSTIs in infants by 3 months of age. Secondary outcomes include the incidence of other infant and maternal infections, and safety and tolerability of azithromycin in mother and infant. Following informed consent, 2110 pregnant women will be randomised in a 1:1 ratio, with all study staff and participants masked to group allocation. Mother/infant pairs will be followed up for 12 months over six visits collecting clinical data on infections, antimicrobial use, safety and anthropometrics, in addition to nasopharyngeal, oropharyngeal, rectovaginal and vaginal swabs, maternal breastmilk and infant stool samples, in order to compare bacterial carriage, AMR rates and microbiome. Recruitment for Bulabula MaPei started in June 2019. ETHICS AND DISSEMINATION:This trial was approved and is being conducted according to the protocol approved by The Royal Children's Hospital Human Research Ethics Committee, Australia, and the Fiji National Health Research and Ethics Review Committee. The findings of this study will be disseminated in peer-reviewed journals and presented at conferences. TRIAL REGISTRATION NUMBER:NCT03925480.

Background: Papua New Guinea (PNG) introduced the 13-valent pneumococcal conjugate vaccine (PCV13) in 2014, with administration at 1, 2, and 3 months of age. PCV13 has reduced or eliminated carriage of vaccine types in populations with low pneumococcal carriage prevalence, carriage density and serotype diversity. This study investigated PCV13 impact on serotype-specific pneumococcal carriage prevalence, density, and serotype diversity in PNG infants, who have some of the highest reported rates of pneumococcal carriage and disease in the world. Methods: Nasopharyngeal swabs were collected at 1, 4 and 9 months of age from PCV13-vaccinated infants (n = 57) and age-/season-matched, unvaccinated infants (at approximately 1 month, n = 53; 4 months, n = 57; 9 months, n = 52). Serotype-specific pneumococcal carriage density and antimicrobial resistance genes were identified by qPCR and microarray. Results: Pneumococci were present in 89% of swabs, with 60 different serotypes and four non-encapsulated variants detected. Multiple serotype carriage was common (47% of swabs). Vaccine type carriage prevalence was similar between PCV13-vaccinated and unvaccinated infants at 4 and 9 months of age. The prevalence of non-vaccine type carriage was also similar between cohorts, with non-vaccine types present in three-quarters of samples (from both vaccinated and unvaccinated infants) by 4 months of age. The median pneumococcal carriage density was high and similar at each age group (similar to 7.0 log(10)-in genome equivalents/mL). PCV13 had no effect on overall pneumococcal carriage density, vaccine type density, non-vaccine type density, or the prevalence of antimicrobial resistance genes. Conclusion: PNG infants experience dense and diverse pneumococcal colonisation with concurrent serotypes from 1 month of age. PCV13 had no impact on pneumococcal carriage density, even for vaccine serotypes. The low prevalence of vaccine serotypes, high pneumococcal carriage density and abundance of non-vaccine serotypes likely contribute to the lack of PCV13 impact on carriage in PNG infants. Indirect effects of the infant PCV programs are likely to be limited in PNG. Alternative vaccines with broader coverage should be considered. (C) 2021 The Authors. Published by Elsevier Ltd.

BackgroundWithin Ulaanbaatar, Mongolia, risk factors for pneumonia are concentrated among children living in informal settlements comprised of temporary shelters (gers). We used pneumococcal carriage surveillance among children from formal and informal settlements hospitalised with pneumonia to evaluate the direct and indirect effects of 13-valent pneumococcal conjugate vaccine (PCV13) against vaccine-type (VT) pneumococcal carriage following a phased introduction of PCV13.MethodsWe enrolled and collected nasopharyngeal swabs from children 2-59 months of age presenting to hospital. Pneumococci were detected using lytA qPCR and serotyped using microarray on a random monthly selection of swabs between November 2015 and March 2019 from two districts in Ulaanbaatar. PCV13 status was determined using written records. We quantified the associations between individual PCV13 status (direct effects) and district-level PCV13 coverage (indirect effects) and VT carriage using generalised estimating equations and explored interactions by settlement type.FindingsA total of 1 292 swabs from 6 046 participants were tested for pneumococci. Receipt of PCV13 and increasing PCV13 coverage independently reduced the risk of VT carriage. For each percent increase in PCV13 coverage, the adjusted odds of VT carriage decreased by 1•0% (OR 95% CI 0•983-0•996; p=0•001), with a predicted decrease in VT carriage rate from 29•1% to 13•1% as coverage reached 100%. There was a trend towards a slower decline within informal settlements (p=0•100). Adjusted PCV13 vaccine effectiveness against VT carriage was 39•1% (95% CI 11•4-58•1%, p=0•009).InterpretationSubstantial indirect effects were observed following PCV13 introduction, including among children living within informal settlements.FundingBill & Melinda Gates Foundation; Gavi, the Vaccine Alliance.

Introduction Empiric data on indirect (herd) effects of pneumococcal conjugate vaccines (PCVs) in settings with low or heterogeneous PCV coverage are limited. The indirect effects of PCV, which benefits both vaccinated and non-vaccinated individuals, are mediated by reductions in vaccine-type (VT) carriage (a prerequisite for disease). The aim of this study among hospitalised children in Lao People’s Democratic Republic (Lao PDR) is to determine the effectiveness of a 13-valent PCV (PCV13) against VT pneumococcal nasopharyngeal carriage (direct effects) and the association between village-level PCV13 coverage and VT carriage (indirect effects). Methods Pneumococcal nasopharyngeal carriage surveillance commenced in December 2013, shortly after PCV13 introduction (October 2013). We recruited and swabbed children aged 2–59 months admitted to hospital with acute respiratory infection. Pneumococci were detected using lytA quantitative real-time PCR and serotyped using microarray. PCV13 status and village-level PCV13 coverage were determined using written immunisation records. Associations between both PCV13 status and village-level PCV13 coverage and VT carriage were calculated using generalised estimating equations, controlling for potential confounders. Results We enrolled 1423 participants and determined PCV13 coverage for 368 villages (269 863 children aged under 5 years). By 2017, median village-level vaccine coverage reached 37.5%, however, the IQR indicated wide variation among villages (24.1–56.4). Both receipt of PCV13 and the level of PCV13 coverage were independently associated with a reduced odds of VT carriage: adjusted PCV13 effectiveness was 38.1% (95% CI 4.1% to 60.0%; p=0.032); and for each per cent increase in PCV13 coverage, the estimated odds of VT carriage decreased by 1.1% (95% CI 0.0% to 2.2%; p=0.056). After adjustment, VT carriage decreased from 20.0% to 12.8% as PCV13 coverage increased from zero to 60% among under 5. Conclusions Despite marked heterogeneity in PCV13 coverage, we found evidence of indirect effects in Lao PDR. Individual vaccination with PCV13 was effective against VT carriage.

Objectives: Nasopharyngeal carriage of Streptococcus pneumoniae underpins disease development and transmission. This study was performed to examine pneumococcal carriage dynamics, including density and multiple serotype carriage, in Indonesian infants during the first year of life. Methods: Two hundred healthy infants were enrolled at 2 months of age. Eight nasopharyngeal swabs were collected from enrolment until 12 months of age. Pneumococci were detected using quantitative PCR and serotyped by microarray. Regression models assessed factors influencing pneumococcal carriage and density. Results: Eighty-five percent of infants carried pneumococci at least once during the study. The median age at first acquisition was 129 days (interquartile range 41-216 days). The median duration of carriage was longer for the first pneumococcal acquisition compared with subsequent acquisitions (151 days vs. 95 days, p < 0.0001). Of the 166 infants who carried pneumococci during the study, the majority (63.9%) carried a single pneumococcal serotype at a time. Pneumococcal carriage density was higher when upper respiratory tract infection symptoms were present, lower during antibiotic usage, decreased with age, and tended to decrease over time during a carriage episode. Conclusions: The majority of Indonesian infants carry pneumococcus at least once during the first year of life. Pneumococcal carriage is a dynamic process, with pneumococcal density varying during a carriage episode. (C) 2019 The Authors. Published by Elsevier Ltd on behalf of International Society for Infectious Diseases.

Background: Nasopharyngeal carriage of Streptococcus pneumoniae precedes disease, is the source of pneumococcal community spread, and the mechanism for herd protection provided by pneumococcal conjugate vaccines (PCVs). There are few PCV impact studies in low- and middle-income countries, particularly in Asia. In 2016, Mongolia introduced the 13-valent PCV (PCV13) in a phased manner using a 2 + 1 schedule, with catch-up. We aimed to assess the impact of PCV13 introduction on nasopharyngeal pneumococcal carriage and density in children in Mongolia. Methods: We conducted two cross-sectional carriage surveys (pre- and one year post-PCV) at community health clinics in two districts of the capital city, Ulaanbaatar in both May July 2015 and 2017. The study analysis included 961 children too young to be vaccinated (5-8 weeks old) and 989 children eligible for vaccination (12-23 months old). Pneumococci were detected by quantitative real-time PCR and molecular serotyping performed using DNA microarray. Findings: One year post-PCV introduction, PCV13 serotype carriage reduced by 52% in 12-23 month olds (adjusted prevalence ratio [aPR] 0.48 [95% confidence interval [CI] 0.39-0.59]), with evidence of non-PCV13 serotype replacement (aPR 1.55 [95% CI 130-1.85]), compared with the pre-PCV period. In 5-8 week olds, PCV13 serotype carriage reduced by 51% (aPR 0.49 [95% Cl 0.33-0.73]) with no significant change in non-PCV13 serotype carriage (aPR 1.10 [95% CI 0.83-1.46]). An increase was observed in both PCV13 and non-PCV13 pneumococcal density post-PCV introduction. Antimicrobial resistance (AMR) genes were common, with 82.3% of samples containing at least one of the 10 AMR genes assessed. Conclusion: This study demonstrates substantive PCV13 impact on pneumococcal carriage one year post-vaccine introduction in Mongolia. The reductions in PCV13 serotype carriage are likely to result in reductions in pneumococcal disease including indirect effects. Increases in non-PCV13 serotypes require further monitoring. (C) 2019 The Authors. Published by Elsevier Ltd.

BACKGROUND:The indirect effects of pneumococcal conjugate vaccines (PCVs) are mediated through reductions in carriage of vaccine serotypes. Data on PCVs in Asia and the Pacific are scarce. Fiji introduced the ten-valent PCV (PCV10) in 2012, with a schedule consisting of three priming doses at 6, 10, and 14 weeks of age and no booster dose (3 + 0 schedule) without catch-up. We investigated the effects of PCV10 introduction using cross-sectional nasopharyngeal carriage surveys. METHODS:We did four annual carriage surveys (one pre-PCV10 and three post-PCV10) in the greater Suva area in Fiji, during 2012-15, of 5-8-week-old infants, 12-23-month-old children, 2-6-year-old children, and their caregivers (total of 8109 participants). Eligible participants were of appropriate age, had axillary temperature lower than 37°C, and had lived in the community for at least 3 consecutive months. We used purposive quota sampling to ensure a proper representation of the Fiji population. Pneumococci were detected by real-time quantitative PCR, and molecular serotyping was done with microarray. FINDINGS:3 years after PCV10 introduction, vaccine-serotype carriage prevalence declined, with adjusted prevalences (2015 vs 2012) of 0·56 (95% CI 0·34-0·93) in 5-8-week-old infants, 0·34 (0·23-0·49) in 12-23-month-olds, 0·47 (0·34-0·66) in 2-6-year-olds, and 0·43 (0·13-1·42) in caregivers. Reductions in PCV10 serotype carriage were evident in both main ethnic groups in Fiji; however, carriage of non-PCV10 serotypes increased in Indigenous Fijian infants and children. Density of PCV10 serotypes and non-PCV10 serotypes was lower in PCV10-vaccinated children aged 12-23 months than in PCV10-unvaccinated children of the same age group (PCV10 serotypes -0·56 [95% CI -0·98 to -0·15], p=0·0077; non-PCV10 serotypes -0·29 [-0·57 to -0·02], p=0·0334). INTERPRETATION:Direct and indirect effects on pneumococcal carriage post-PCV10 are likely to result in reductions in pneumococcal disease, including in infants too young to be vaccinated. Serotype replacement in carriage in Fijian children, particularly Indigenous children, warrants further monitoring. Observed changes in pneumococcal density might be temporal rather than vaccine related. FUNDING:Department of Foreign Affairs and Trade of the Australian Government through the Fiji Health Sector Support Program; Victorian Government's Operational Infrastructure Support Program; Bill & Melinda Gates Foundation.