Nasopharyngeal Bacterial Carriage in the Conjugate Vaccine Era with a Focus on Pneumococci

Nasopharyngeal carriage and antibiotic susceptibility patterns of streptococcus pneumoniae, haemophilus influenzae, moraxella catarrhalis and staphylococcus aureus among urban Ugandan children post-PCV10 introduction: a cross-sectional study

In 2013, Uganda introduced the PCV10 pneumococcal vaccine and it is given to children at 6, 10 and 14 weeks after birth. Carriage prevalence studies post PCV10-introduction are necessary for monitoring the impact of vaccination and trends in antibiotic resistance. Here, we studied carriage/antibiotic resistance of Streptococcus pneumoniae (pneumococcus), Haemophilus influenzae, Moraxella catarrhalis, and Staphylococcus aureus isolated from 194 children at the Mulago Assessment Centre clinic in Kampala-Uganda, 5 years post-PCV10 introduction. Almost all the children were vaccinated with PCV10 (98.5%, 191/194). The overall carriage prevalence (any species) was 62% (120/194), and it was associated with a history of antibiotics use (p=0.0159) and having respiratory symptoms (p=0.0003). The pneumococcus, H. influenzae, M. catarrhalis, and S. aureus carriage prevalence was 46% (90/194), 21% (40/194), 7% (14/194), and 6% (12/194), respectively. Species co-carriage occurred in 32 children (17%, 32/194), predominantly multidrug resistant pneumococcus + H. influenzae (23 children). Furthermore, pneumococci were highly resistant to cotrimoxazole (100%), erythromycin (76%), and tetracycline (52%), 42% being multidrug-resistant. Overall, we note an increase in antibiotic resistance post-PCV10 introduction, and microbial shifts i.e., a decrease in pneumococcus, M. catarrhalis and S. aureus carriage and an increase in H. influenzae carriage suggesting vaccine-associated perturbation of the respiratory ecology.

Impact of PCV10 on pediatric pneumococcal disease burden in Brazil: time for new recommendations?

OBJECTIVE

To describe the impact of the 10-valent pneumococcal conjugate vaccine on the pediatric burden of pneumococcal infections, carriage, serotype replacement, and antimicrobial resistance in Brazil since its introduction in 2010.

DATA SOURCE

A narrative review of English, Spanish, and Portuguese articles published in online databases and in Brazilian epidemiological surveillance databases was performed. The following keywords were used: Streptococcus pneumoniae, pneumococcal disease, conjugate vaccine, PCV10, antimicrobial resistance, and meningitis.

SUMMARY OF THE FINDINGS

Declines in hospitalization rates of all-cause pneumonia occurred in the target age groups and some age groups not targeted by vaccination early after the use of PCV10. Large descriptive studies of laboratory-confirmed pneumococcal meningitis and hospital-based historical series of hospitalized children with IPD have evidenced a significant impact on disease burden, in-hospital fatality rates, and admission to the intensive care unit before and after the inclusion of the vaccine. Impact data on otitis media is limited and inconsistent; the main benefit remains the prevention of complicated diseases. During the late post-vaccine years, a significant and progressive increase in high-level penicillin non-susceptibility pneumococci has been described. Since 2014 serotype 19A has been the leading serotype in all ages and was responsible for 28.2%-44.6% of all IPD in children under 5 yrs.

CONCLUSIONS

PCV10 has performed a significant impact on IPD in Brazil since 2010, however, progress has been continuously hampered by replacement. Broader spectrum PCVs could provide expanded direct and indirect protection against ST19A and other additional serotypes of increasing importance if administered to children in the Brazilian National Immunization Program.

Uncovering the core principles of the gut-lung axis to enhance innate immunity in the chicken

Research in mammals has evidenced that proper colonization of the gut by a complex commensal microbial community, the gut microbiota (GM), is critical for animal health and wellbeing. It greatly contributes to the control of infectious processes through competition in the microbial environment while supporting proper immune system development and modulating defence mechanisms at distant organ sites such as the lung: a concept named ‘gut-lung axis’. While recent studies point to a role of the GM in boosting immunity and pathogen resilience also in poultry, the mechanisms underlying this role are largely unknown. In spite of this knowledge gap, GM modulation approaches are today considered as one of the most promising strategies to improve animal health and welfare in commercial poultry production, while coping with the societal demand for responsible, sustainable and profitable farming systems. The majority of pathogens causing economically important infectious diseases in poultry are targeting the respiratory and/or gastrointestinal tract. Therefore, a better understanding of the role of the GM in the development and function of the mucosal immune system is crucial for implementing measures to promote animal robustness in commercial poultry production. The importance of early gut colonization in the chicken has been overlooked or neglected in industrial poultry production systems, where chicks are hampered from acquiring a complex GM from the hen. Here we discuss the concept of strengthening mucosal immunity in the chicken through GM modulation approaches favouring immune system development and functioning along the gut-lung axis, which could be put into practice through improved farming systems, early-life GM transfer, feeding strategies and pre-/probiotics. We also provide original data from experiments with germ-free and conventional chickens demonstrating that the gut-lung axis appears to be functional in chickens. These key principles of mucosal immunity are likely to be relevant for a variety of avian diseases and are thus of far-reaching importance for the poultry sector worldwide.

Colonization by Streptococcus pneumoniae among children in Porto Velho, Rondônia, Western Brazilian Amazon

Streptococcus pneumoniae is one of the primary pathogens that are associated with acute respiratory infections (ARI) that cause high rates of morbidity and mortality among children under five years of age in developed and developing countries. This study aimed to determine the prevalence of nasopharyngeal colonization, the antimicrobial resistance profile, and the capacity for biofilm formation by S. pneumoniae isolated from children aged 0-6 years with ARI throughout the Porto Velho-RO. A total of 660 swabs were collected from children with ARI. Molecular and biochemical tests were performed to characterize the isolates. The disk-difusion method and the E-test were used for antimicrobial sensitivity testing (TSA). Biofilm formation capacity was assessed using microtiter plate assays, and serotype detection was acheived using polymerase chain reaction (PCR) analyses. The colonization rate for S. pneumoniae was 8.9% (59/660) and exhibited a high prevalence in children under 23 months of age 64.4% (38/59). The observed serotypes were 9V and 19F with frequencies of 1.7% (1/59) and 13.6% (8/59), respectively. The antimicrobial susceptibility test revealed 100% (59/59) sensitivity to vancomycin. In contrast, trimethoprim and oxacillin exhibited high resistance rates of 76.3% (45/59) and 52.5% (31/59), respectively. Of the biofilm-forming isolates, 54.8% (23/42) possessed resistance to some antimicrobials. In this study, S. pneumoniae showed high rates of antimicrobial resistance and the ability to form biofilms, as these are factors that favor bacterial persistence and can cause serious damage to the host.

Impact of Therapeutics on Unified Immunity During Allergic Asthma and Respiratory Infections

Asthma is a common chronic respiratory disease that affects millions of people worldwide. Patients with allergic asthma, the most prevalent asthma endotype, are widely considered to possess a defective immune response against some respiratory infectious agents, including viruses, bacteria and fungi. Furthermore, respiratory pathogens are associated with asthma development and exacerbations. However, growing data suggest that the immune milieu in allergic asthma may be beneficial during certain respiratory infections. Immunomodulatory asthma treatments, although beneficial, should then be carefully prescribed to avoid misuse and overuse as they can also alter the host microbiome. In this review, we summarize and discuss recent evidence of the correlations between allergic asthma and the most significant respiratory infectious agents that have a role in asthma pathogenesis. We also discuss the implications of current asthma therapeutics beyond symptom prevention.

Nasal colonization by potential bacterial pathogens in healthy kindergarten children of Nepal: a prevalence study

INTRODUCTION

In low- and middle-income countries including Nepal, respiratory tract infection (RTI) is considered as one of the most prominent public health problems in children. Multiple carriage of respiratory pathogens is common in children, especially in preschoolers as they are easily transmitted through close contact and poor hygienic condition. Thus, this research is based on the study of prevalence, co-existence, associated factors and antibiogram of nasal isolates among healthy preschoolers.

METHODS

The study was conducted in four randomly selected kindergarten schools (two government run and two private run) of Bhaktapur Municipality. Out of a total 140 students, 136 eligible participants of age group 2-5 years old were involved in the study. Nasal swab was collected for the isolation of five target isolates (Staphylococcus aureus, Streptococcus pneumoniae, Moraxella catarrhalis, Haemophilus influenzae and Haemophilus parainfluenzae) and their antibiotic resistance determination.

RESULTS

Of 136 participants involved, 128 (94.5%) were positive for carriage of at least one of the target bacteria. The most common isolate was M. catarrhalis 62.5% (80/128) followed by S. aureus 43.0% (55/128). There was a significant difference in bacterial carriage with respect to type of school (p value<0.05, OR=0.50, CI=0.20-0.90). Regarding bacterial co-existence, the most common co-existence was of S. aureus and M. catarrhalis & S. pneumoniae and M. catarrhalis 48.8%. Multiple logistic regression analysis showed that S. aureus was negatively associated with S. pneumoniae, M. catarrhalis and H. influenzae and S. pneumoniae was positively associated with M. catarrhalis and H. influenzae. Multidrug resistance was seen in 63 isolates (29.4%).

CONCLUSIONS

Nepalese kindergarten children are at a high risk of respiratory tract infection by multidrug resistant bacteria.

Urban and Rural Disparities in Pneumococcal Carriage and Resistance in Jordanian Children, 2015-2019

BACKGROUND

A pneumococcal carriage surveillance study took place examining Jordanian children in urban and rural areas in the period 2015-2019.

OBJECTIVES

To determine urban and rural differences in pneumococcal carriage rate, resistance, and serotypes among healthy Jordanian children from Amman (urban) and eastern Madaba (rural).

METHODS

Nasopharyngeal swabs (NP) were taken from 682 children aged 1 to 163 months. Pneumococcal identification, serotyping, and resistance were performed according to standard method.

RESULTS

The number of cases tested for Amman was 267 and there were 415 cases tested for eastern Madaba. Carriage rate for eastern Madaba was 39.5% and 31.1% for Amman. Predominant serotypes for eastern Madaba and Amman were 19F (21.3%; 15.7%), 23F (12.2%; 9.6%), 14 (6.7%; 2.4%), 19A (4.9%; 2.4%), and 6A (5.5%; 3.6%). Resistance rates for eastern Madaba and Amman were as follows: penicillin (95.8%; 81.9%), clarithromycin (68.9%; 59.0%), clindamycin (40.8%; 31.3%), and trimethoprim-sulfamethoxazole (73.2%; 61.4%). Coverage of PCV7, PCV13, and the future PCV20 for Amman was 42.2%, 48.2%, and 60.2%; for eastern Madaba, coverage was 50.0%, 62.2%, and 73.2%, respectively. In Amman 25.8% of children received 1-3 PCV7 injections compared to 1.9% of children in eastern Madaba.

CONCLUSIONS

There were significant differences in carriage, resistance, and coverage between both regions. The potential inclusion of a PCV vaccination program for rural areas is essential.

Efficacy and tolerability of immunotherapy in advanced nasopharyngeal carcinoma with or without chemotherapy: a meta-analysis

INTRODUCTION

Evidence of programmed death-1 inhibitors in nasopharyngeal carcinoma has been accumulated. However, previous clinical studies were basically small sample size.

OBJECTIVE

This study aimed to summarize existing studies to comprehensively compare programmed death-1 inhibitors in nasopharyngeal carcinoma with or without chemotherapy.

METHODS

Different databases were searched for full-text publications with a programmed death-1 inhibitor with or without chemotherapy. No study-to-study heterogeneity was detected, and fixed-effect models were applied to synthesize data.

RESULTS

Seven studies were included. The mean progression-free survival duration of programmed death-1 inhibitors treatment was 4.66 months. The 6 month progression-free survival rate was 50%, however, the12 month progression-free survival rate fell to 27%. Comparing with programmed death-1 inhibitor monotherapy, the objective response rate was higher in combination therapy (pooled RR=2.90, 95% CI: 2.07-4.08). The partial response rate was higher in patients receiving programmed death-1 in association with chemotherapy (pooled RR=3.09, 95% CI: 2.15-4.46), In contrast, the progressive disease rate was lower in combination therapy group (pooled RR=0.06, 95% CI: 0.01-0.31). Stable disease condition was comparable (pooled RR=0.90, 95% CI: 0.50-1.64) with or without chemotherapy. Programmed death-1 single use or combined with chemotherapy did not influence the total adverse events occurrence (pooled RR=0.99, 95% CI: 0.93-1.05). However, combination therapy could increase the risk of serious adverse events such as anemia, thrombocytopenia, and neutropenia.

CONCLUSION

The present study summarized the efficacy and safety of programmed death-1 inhibitors in nasopharyngeal carcinoma. Combination therapy showed higher anti-tumor activity except for higher risk of myelosuppression.

Nasopharyngeal Carriage of Methicillin-Resistant Staphylococcus aureus (MRSA) among Sickle Cell Disease (SCD) Children in the Pneumococcal Conjugate Vaccine Era

The aim of this cross-sectional study was to investigate Staphylococcus aureus nasopharyngeal carriage epidemiology in relation to other nasopharyngeal bacterial colonizers among sickle cell disease (SCD) children about five years into pneumococcal conjugate vaccine 13 (PCV-13) introduction in Ghana. The study involved bacteriological culture of nasopharyngeal swabs obtained from 202 SCD children recruited from the Princess Marie Louise Children's Hospital. S. aureus isolates were identified using standard methods and subjected to antimicrobial susceptibility testing using the Kirby-Bauer disc diffusion method. Cefoxitin-resistant S. aureus isolates were screened for carriage of the mecA, pvl, and tsst-1 genes using multiplex polymerase chain reaction. The carriage prevalence of S. aureus was 57.9% (n = 117), and that of methicillin-resistant S. aureus (MRSA) was 3.5% (n = 7). Carriage of the mecA, pvl, and tsst-1 genes were respectively demonstrated in 20.0% (n = 7), 85.7% (n = 30), and 11.4% (n = 4) of the cefoxitin-resistant S. aureus isolates. PCV-13 vaccination (OR = 0.356, p = 0.004) and colonization with coagulase-negative staphylococci (CoNS) (OR = 0.044, p < 0.0001) each protected against S. aureus carriage. However, none of these and other features of the participants emerged as a determinant of MRSA carriage. The following antimicrobial resistance rates were observed in MRSA compared to methicillin-sensitive S. aureus: clindamycin (28.6% vs. 4.3%), erythromycin (42.9% vs. 19.1%), tetracycline (100% vs. 42.6%), teicoplanin (14.3% vs. 2.6%), penicillin (100% vs. 99.1%), amoxiclav (28.6% vs. 3.5%), linezolid (14.3% vs. 0.0%), ciprofloxacin (42.9% vs. 13.9%), and gentamicin (42.9% vs. 13.0%). The proportion of S. aureus isolates that were multidrug resistant was 37.7% (n = 46). We conclude that S. aureus was the predominant colonizer of the nasopharynx of the SCD children, warranting the continuous monitoring of this risk group for invasive S. aureus infections.

Nasopharyngeal Carriage and Antimicrobial Susceptibility Profile of Staphylococcus aureus among Children under Five Years in Accra

This cross-sectional study investigated the Staphylococcus aureus (S. aureus) and methicillin-resistant S. aureus (MRSA) nasopharyngeal carriage epidemiology in Accra approximately five years post-pneumococcal conjugate vaccines introduction in the country. Archived nasopharyngeal swabs collected from 410 children aged under five years old were bacteriologically cultured. The resultant S. aureus isolates were subjected to antimicrobial susceptibility testing and screening for carriage of the mecA and LukF-PV (pvl) genes, following standard procedures. The data obtained were analyzed with Statistical Products and Services Solutions (SPSS) using descriptive statistics and Chi square tests of associations. The isolated bacteria decreased across coagulase-negative Staphylococci (47.3%, n = 194), S. aureus (23.2%, n = 95), Diphtheroids (5.4%, n = 22), Micrococcus species (3.7%, n = 15), Klebsiella pneumoniae (3.2%, n = 13), Moraxella species and Citrobacter species (1.5% each, n = 6), Escherichia coli, Enterobacter species, and Pseudomonas species (0.9% each, n = 2). The MRSA carriage prevalence was 0.49% (n = 2). Individuals aged 37-48 months recorded the highest proportion of S. aureus carriage (32.6%, 31/95). Resistance of S. aureus to the antibiotics tested were penicillin G (97.9%, n = 93), amoxiclav (20%, n = 19), tetracycline (18.9%, n = 18), erythromycin (5.3%, n = 5), ciprofloxacin (2.1%, n = 2), gentamicin (1.1%, n = 1), cotrimoxazole, clindamycin, linezolid, and teicoplanin (0% each). No inducible clindamycin resistance was observed for the erythromycin-resistant isolates. Three (3.2%) of the isolates were multidrug resistant, of which 66.7% (2/3) were MRSA. The pvl gene was associated with 59.14% (55/93) of the methicillin-sensitive S. aureus (MSSA) isolates, but was not detected among any of the MRSA isolates.

Biannual Treatment of Preschool Children with Single Dose Azithromycin to Reduce Mortality: Impact on Azithromycin Resistance in the MORDOR Trial in Tanzania

The Macrolides Oraux pour Réduire les Décès avec un Oeil sur la Résistance study showed that administration of biannual, single-dose azithromycin to preschool children reduces mortality. We sought to evaluate its impact on azithromycin resistance. Thirty randomly selected communities in Kilosa district, Tanzania, were randomized to receive 6-monthly single-dose azithromycin (∼20 mg/kg) versus placebo treatment of children aged 1–59 months. From each community, 40 children (aged 1–59 months) were randomly selected at baseline, 12 and 24 months. Isolation and resistance testing of Streptococcus pneumoniae and Escherichia coli were evaluated using nasopharyngeal and rectal swabs, respectively. The carriage prevalence and the proportion of azithromycin-resistant isolates were determined using disk diffusion. At baseline, the characteristics of the randomly selected children were similar by treatment arms. Both at baseline and in annual cross-sectional surveys, rates of S. pneumoniae and E. coli isolation between treatment arms were similar. The proportions of azithromycin-resistant S. pneumoniae isolates in the children in communities treated with azithromycin versus placebo at baseline, 12 months, and 24 months were 26.5% (18.1%; P = 0.26), 26.8% (16.5%; P = 0.29), and 13.4% (17.0%; P = 0.57), respectively. The proportions of azithromycin-resistant E. coli isolates at baseline, 12 months, and 24 months in the azithromycin (versus placebo) arms were 14.9% (18.9%; P = 0.16), 21.5% (16.6%; P = 0.10), and 14.9% (14.7%; P = 0.95), respectively. Over the 24 months, the mean treatment coverage for the azithromycin and placebo was 76.9% and 74.8%, respectively (P = 0.49). Biannual administration of single-dose azithromycin to children did not appear to result in excess azithromycin resistance in S. pneumoniae and E. coli isolates over 24 months of follow-up.

Clival defect in the pathogenesis of recurrent meningitis: a case report and literature review

Background

Meningitis is a life-threatening infection often associated with high morbidity. Recurrent bacterial meningitis poses a clinical challenge, both clinically and diagnostically. To prevent further recurrences, the underlying causes of recurrent bacterial meningitis should be investigated intensively.

Case presentation

Here, we aim to present a patient referred to our clinic with rhinorrhea and found to the Staphylococcus aureus meningitis related to a clival defect. The patient reported no history of trauma, surgery, or brain neoplasm, and the cerebrospinal fluid leakage was classified as spontaneous. The patient had two episodes of meningitis in the last 4 years, but etiologic data of the previous episodes were absent. A pneumococcal vaccine was administered following her second attack, suggesting a possible Staphylococcus aureus infection due to altered colonization in the sinuses. She was successfully treated with linezolid but refused surgery to correct the defect and was discharged without neurologic sequelae.

Conclusion

Spontaneous cerebrospinal fluid leakage from the clivus which could provoke recurrent meningitis is a rare situation. In conjunction with appropriate rapid antibiotherapy for the prevention of recurrent meningitis, the removal of anatomical risk factors should be a principal aim. Effective surgical procedures prevent recurrences.

Host-Pathogen Interactions in Gram-Positive Bacterial Pneumonia

Community-acquired pneumonia (CAP) is a leading cause of morbidity and mortality worldwide. Despite broad literature including basic and translational scientific studies, many gaps in our understanding of host-pathogen interactions remain. In this review, pathogen virulence factors that drive lung infection and injury are discussed in relation to their associated host immune pathways. CAP epidemiology is considered, with a focus on Staphylococcus aureus and Streptococcus pneumoniae as primary pathogens. Bacterial factors involved in nasal colonization and subsequent virulence are illuminated. A particular emphasis is placed on bacterial pore-forming toxins, host cell death, and inflammasome activation. Identified host-pathogen interactions are then examined by linking pathogen factors to aberrant host response pathways in the context of acute lung injury in both primary and secondary infection. While much is known regarding bacterial virulence and host immune responses, CAP management is still limited to mostly supportive care. It is likely that improvements in therapy will be derived from combinatorial targeting of both pathogen virulence factors and host immunomodulation.

Trends in Antimicrobial Drug Resistance of Streptococcus pneumoniae Isolates at Jordan University Hospital (2000⁻2018)

Antimicrobial drug resistance (AMR) in pneumococci complicates the treatment of serious pneumococcal infections. Country-specific AMR patterns can help to establish guidelines for empiric therapy. The aim of the current study was to analyze the distribution of AMR among Streptococcus pneumoniae isolates at Jordan University Hospital (JUH) during 2000⁻2018. Paper-based and electronic clinical data registry records from 2000 to 2018 were retrospectively analyzed to study the AMR among pneumococcal isolates at JUH. Temporal trend analysis was done using two-tailed linear-by-linear test for association. The total number of unique pneumococcal isolates that were identified was 556, of which 544 isolates had antimicrobial susceptibility testing results. The most frequent specimens were eye (n = 117, 21.0%), bloodstream (n = 93, 16.7%) and sputum (n = 81, 14.6%). Invasive infections represented 23.6% of all unique isolates. The overall susceptibility of S. pneumoniae isolates during the study period to different antimicrobials was: 100% to vancomycin, 97.7% to ceftriaxone, 97.1% to cefotaxime, 94.9% to chloramphenicol, 89.7% to penicillin, 83.8% to levofloxacin, 67.7% to clindamycin and 52.1% to erythromycin. The prevalence of multi-drug resistance (MDR) was 8.6% (95% confidence interval: 6.4⁻11.5%). Trend analysis showed an increase in the prevalence of non-susceptibility to erythromycin, clindamycin and levofloxacin (p < 0.001). MDR prevalence increased from 1.6% in the first quarter to 14.6% in the fourth quarter (p < 0.001). The incidence of invasive infections declined over the study period (p < 0.001). The increase in the prevalence of AMR and MDR among pneumococcal isolates in Jordan demands judicious use of antimicrobials and regular surveillance of resistance.

Rocking Pneumonia and the Boogie Woogie Flu

The relation between pneumonia and influenza is regularly addressed in modern music. Epidemiological data obtained during influenza pandemics, as well as during seasonal influenza, illustrate and underscore this association. Even though the number of pneumonia cases are generally under-reported and blood tests show a lack of sensitivity, a clear link between influenza and pneumonia can still be observed. In fact, the majority of mortality during influenza pandemics is due to pneumonia caused by a bacterial superinfection, in most cases Streptococcus pneumoniae. Vaccination is a powerful tool to prevent the development of both influenza and pneumonia in children, as well as in the elderly. Cellular and molecular data show that influenza can lead to changes in the integrity of lung epithelial cells, including desialysation of carbohydrate moieties, which favour attachment and invasion of S. pneumoniae. Further elucidation of these mechanisms could lead to targeted intervention strategies, in which universal influenza vaccines could play a role.

Nasopharyngeal carriage of Streptococcus pneumoniae in children under 5 years of age before introduction of pneumococcal vaccine (PCV10) in urban and rural districts in Pakistan

Background

Benefits of pneumococcal conjugate vaccine programs have been linked to the vaccine’s ability to disrupt nasopharyngeal carriage and transmission. The 10-valent pneumococcal vaccine (PCV10) was included in the Expanded Program on Immunization (EPI) in Sindh, Pakistan in February 2013. This study was carried out immediately before PCV10 introduction to establish baseline pneumococcal carriage and prevalent serotypes in young children and to determine if carriage differed in urban and rural communities.

Methods

Nasopharyngeal specimens were collected from a random sample of children 3-11 and 12-59 months of age in an urban community (Karachi) and children 3-11 months of age in a rural community (Matiari). Samples were processed in a research laboratory in Karachi. Samples were transported in STGG media, enriched in Todd Hewitt broth, rabbit serum and yeast extract, cultured on 5% sheep blood agar, and serotyped using the CDC standardized sequential multiplex PCR assay. Serotypes were categorized into PCV10-type and non-vaccine types.

Results

We enrolled 670 children. Pneumococci were detected in 73.6% and 79.5 % of children in the infant group in Karachi and Matiari, respectively, and 78.2% of children 12 to 59 months of age in Karachi. In infants, 38.9% and 33.5% of those carrying pneumococci in Karachi and Matiari, respectively, had PCV10 types. In the older age group in Karachi, the proportion was 30.7%, not significantly different from infants. The most common serotypes were 6A, 23F, 19A, 6B and 19F.

Conclusion

We found that about 3 of 4 children carried pneumococci, and this figure did not vary with age group or urban or rural residence. Planned annual surveys in the same communities will inform change in carriage of PCV10 serotype pneumococci after the introduction and uptake of PCV10 in these communities

Electronic supplementary material

The online version of this article (10.1186/s12879-018-3608-5) contains supplementary material, which is available to authorized users.

Molecular characterization of Streptococcus pneumoniae, particularly serotype19A/ST320, which emerged in Krasnoyarsk, Russia

Streptococcus pneumoniae, a common human pathogen, colonizes the nasopharynx and causes diseases including acute otitis media (AOM). Herein, pneumococcal serotype distributions in children before and after PCV7 vaccination and in patients with pneumococcal disease in Siberian Russia (Krasnoyarsk) are reported. Analyses included antimicrobial susceptibility testing, sequence typing (ST), pulsed field gel electrophoresis, virulence‐related surface protein gene (VSG) typing with novel primers and structural analysis by scanning electron microscopy. In healthy children (HC) prior to administration of PCV7, drug‐susceptible serotype23F/ST1500 was a major pneumococcal genotype. In the PCV7 trial, multidrug‐resistant serotype19A/ST320 emerged in vaccinees after PCV7, exhibiting a PCV7‐induced serotype replacement. Multidrug‐resistant serotype19A/ST320 was evident in patients with AOM. Community‐acquired pneumonia (CAP) isolates showed genetic similarities to the AOM (ST320) genotype, constituting a common non‐invasive AOM–CAP group. In contrast, meningitis isolates were more divergent. Overall, 25 ST types were identified; five (20%) of which were Krasnoyarsk‐native. Regarding VSGs, PI‐1 (rlrA/rrgB), PI‐2 (pitA/B), psrP and cbpA were present at 54.3%, 38.6%, 48.6%, and 95.7%, respectively, with two major VSG content types, PI‐1⁻/PI‐2⁻/psrP⁺/cbpA⁺ and PI‐1⁺/PI‐2⁺/psrP^‐/cbpA⁺, being found for HC and non‐invasive diseases, respectively. A major clone of serotype19A/ST320 (PI‐1⁺/PI‐2⁺) produced the longest pneumococcal wire (pilus) structures in colonies. ST1016 (PI‐1⁻/PI‐2⁻) in HC had HEp‐2 cell‐adherent pili. These results suggest that serotype19A/ST320 and related genotypes, with the VSG content type PI‐1⁺/PI‐2⁺/psrP⁻/cbpA⁺, emerged in vaccinees after PCV7 in Siberia, accompanying diseases in non‐vaccinated children, and that some genotypes (serotypes19A/ST320 and 18/ST1016) produced novel pneumococcal structures, predicting their roles in colony formation and adherence.

Age-related differences in the respiratory microbiota of chickens

In this era of next generation sequencing technologies it is now possible to characterise the chicken respiratory microbiota without the biases inherent to traditional culturing techniques. However, little research has been performed in this area. In this study we characterise and compare buccal, nasal and lung microbiota samples from chickens in three different age groups using 16S rRNA gene analysis. Buccal and nasal swabs were taken from birds aged 2 days (n = 5), 3 weeks (n = 5) and 30 months (n = 6). Bronchoalveolar lavage (BAL) samples were also collected alongside reagent only controls. DNA was extracted from these samples and the V2-V3 region of the 16S rRNA gene was amplified and sequenced. Quality control and OTU clustering were performed in mothur. Bacterial DNA was quantified using qPCR, amplifying the V3 region of the 16S rRNA gene. We found significant differences between the quantity and types of bacteria sampled at the three different respiratory sites. We also found significant differences in the composition, richness and diversity of the bacterial communities in buccal, nasal and BAL fluid samples between age groups. We identified several bacteria which had previously been isolated from the chicken respiratory tract in culture based studies, including lactobacilli and staphylococci. However, we also identified bacteria which have not previously been cultured from the respiratory tract of the healthy chicken. We conclude that our study can be used as a baseline that future chicken respiratory microbiota studies can build upon.

Influence of the pneumococcal conjugate vaccines on the temporal variation of pneumococcal carriage and the nasal microbiota in healthy infants: a longitudinal analysis of a case-control study

BACKGROUND

Bacterial colonization of the upper airways is a prerequisite for subsequent invasive disease. With the introduction of the 7- and 13-valent pneumococcal conjugate vaccines (PCV7 and PCV13), changes in pneumococcal upper airway colonization have been described. It is, however, less evident whether the vaccines lead to compositional changes of the upper airway microbiota. Here, we performed a case-control study using samples from a longitudinal infant cohort from Switzerland. We compared pneumococcal carriage and the nasal microbiota within the first year of life of healthy infants vaccinated with either PCV7 (n = 20, born in 2010) or PCV13 (n = 21, born between 2011 and 2013). Nasal swabs were collected every second week (n = 763 in total). Pneumococcal carriage was analyzed by quantitative PCR of the pneumococcal-specific lytA gene. Analysis of the bacterial core microbiota was performed based on 16S rRNA sequencing and subsequent oligotyping. We exclusively performed oligotyping of the core microbiota members, which were defined as the five most abundant bacterial families (Moraxellaceae, Streptococcaceae, Staphylococcaceae, Corynebacteriaceae, and Pasteurellaceae). Linear mixed effect (LME) and negative binomial regression models were used for statistical analyses.

RESULTS

We found a higher number of samples positive for pneumococcal carriage in PCV7- compared to PCV13-vaccinated infants (LME model; P = 0.01). In contrast, infants vaccinated in the PCV13 era had an increased alpha diversity as measured by the richness and the Shannon Diversity Index (LME model; P = 0.003 and P = 0.01, respectively). Accordingly, the PCV13 era was associated with clusters of a higher diversity than PCV7-associated clusters. Furthermore, infants vaccinated with PCV13 had a higher binary-based within-subject microbiota similarity, as well as a decreased Jensen-Shannon distance over time as compared to PCV7-vaccinated infants, indicating a higher microbiota stability in the PCV13 era (LME model and t test; P = 0.06 and P = 0.03, respectively).

CONCLUSIONS

We hypothesize that the higher diversity and stability of the upper airway microbiota in the PCV13 era is the result of the lower pneumococcal carriage rate. This seems to indicate that the nasal bacterial microbiota of infants has changed in recent years as compared to the beginning of this study.

Efficacy of a novel, protein-based pneumococcal vaccine against nasopharyngeal carriage of Streptococcus pneumoniae in infants: A phase 2, randomized, controlled, observer-blind study

BACKGROUND

Conserved pneumococcal proteins are potential candidates for inclusion in vaccines against pneumococcal diseases. In the first part of a two-part study, an investigational vaccine (PHiD-CV/dPly/PhtD-30) containing 10 pneumococcal serotype-specific polysaccharide conjugates (10VT) combined with pneumolysin toxoid and pneumococcal histidine triad protein D (30μg each) was well tolerated by Gambian children. Part two, presented here, assessed the efficacy of two PHiD-CV/dPly/PhtD formulations against pneumococcal nasopharyngeal carriage (NPC) prevalence in infants.

METHODS

In this phase 2, randomized, controlled, observer-blind trial, healthy infants aged 8-10weeks, recruited from a peri-urban health center, were randomized (1:1:1:1:1:1) into six groups. Four groups received PHiD-CV/dPly/PhtD (10 or 30μg of each protein), PHiD-CV, or 13-valent pneumococcal conjugate vaccine at ages 2-3-4months (3+0 infant schedule) and two groups PHiD-CV/dPly/PhtD-30 or PHiD-CV at 2-4-9months (2+1 infant schedule). The primary objective was impact on non-10VT NPC at ages 5-9-12months. Secondary objectives included confirmatory analysis of protein dose superiority and safety/reactogenicity. Impact on pneumococcal NPC acquisition, bacterial load, and ply and phtD gene sequencing were explored.

RESULTS

1200 infants were enrolled between June 2011 and May 2012. Prevalences of pneumococcal (60-67%) and non-10VT (55-61%) NPC were high at baseline. Across all post-vaccination time points, efficacy of PHiD-CV/dPly/PhtD-10 and PHiD-CV/dPly/PhtD-30 against non-10VT NPC (3+0 schedule) was 1.1% (95% CI -21.5, 19.5) and 2.1% (-20.3, 20.3), respectively; efficacy of PHiD-CV/dPly/PhtD-30 (2+1 schedule) was 0.5% (-22.1, 18.9) versus PHiD-CV. No differences were observed in pneumococcal NPC acquisition, clearance, or bacterial load. Both protein-based vaccines elicited immune responses to pneumococcal proteins.

CONCLUSIONS

In this high carriage prevalence setting, inclusion of pneumococcal proteins in the PHiD-CV/dPly/PhtD investigational vaccine had no impact on pneumococcal NPC in infants, regardless of protein dose or schedule. Future evaluations will assess its impact against pneumococcal disease endpoints.

FUNDING

PATH, GlaxoSmithKline Biologicals SA. ClinicalTrials.gov identifier NCT01262872.

Of the Phrensy: an update on the epidemiology and pathogenesis of bacterial meningitis in the pediatric population

In the past century, advances in antibiotics and vaccination have dramatically altered the incidence and clinical outcomes of bacterial meningitis. We review the shifting epidemiology of meningitis in children, including after the implementation of vaccines that target common meningitic pathogens and the introduction of intrapartum antibiotic prophylaxis offered to mothers colonized with Streptococcus agalactiae. We also discuss what is currently known about the pathogenesis of meningitis. Recent studies of the human microbiome have illustrated dynamic relationships of bacterial and viral populations with the host, which may potentiate the risk of bacterial meningitis.

Pneumococcal conjugate vaccine introduction in Latin America and the Caribbean: progress and lessons learned

In Latin America and the Caribbean, pneumococcus has been estimated to cause 12,000-28,000 deaths, 182,000 hospitalizations, and 1.4 million clinic visits annually. Countries in the Americas have been among the first developing nations to introduce pneumococcal conjugate vaccines into their Expanded Programs on Immunization, with 34 countries and territories having introduced these vaccines as of September 2015. Lessons learned for successful vaccine introduction include the importance of coordination between political and technical decision makers, adjustments to the cold chain prior to vaccine introduction, and the need for detailed plans addressing the financial and technical sustainability of introduction. Though many questions on the Pneumococcal Conjugate Vaccine remain unanswered, the experience of the Americas suggests that the vaccines can be introduced quickly and effectively.