Emergence of a multidrug-resistant and virulent Streptococcus pneumoniae lineage mediates serotype replacement after PCV13: an international whole-genome sequencing study.

BACKGROUND: Serotype 24F is one of the emerging pneumococcal serotypes after the introduction of pneumococcal conjugate vaccine (PCV). We aimed to identify lineages driving the increase of serotype 24F in France and place these findings into a global context. METHODS: Whole-genome sequencing was performed on a collection of serotype 24F pneumococci from asymptomatic colonisation (n=229) and invasive disease (n=190) isolates among individuals younger than 18 years in France, from 2003 to 2018. To provide a global context, we included an additional collection of 24F isolates in the Global Pneumococcal Sequencing (GPS) project database for analysis. A Global Pneumococcal Sequence Cluster (GPSC) and a clonal complex (CC) were assigned to each genome. Phylogenetic, evolutionary, and spatiotemporal analysis were conducted using the same 24F collection and supplemented with a global collection of genomes belonging to the lineage of interest from the GPS project database (n=25 590). FINDINGS: Serotype 24F was identified in numerous countries mainly due to the clonal spread of three lineages: GPSC10 (CC230), GPSC16 (CC156), and GPSC206 (CC7701). GPSC10 was the only multidrug-resistant lineage. GPSC10 drove the increase in 24F in France and had high invasive disease potential. The international dataset of GPSC10 (n=888) revealed that this lineage expressed 16 other serotypes, with only six included in 13-valent PCV (PCV13). All serotype 24F isolates were clustered in a single clade within the GPSC10 phylogeny and long-range transmissions were detected from Europe to other continents. Spatiotemporal analysis showed GPSC10-24F took 3-5 years to spread across France and a rapid change of serotype composition from PCV13 serotype 19A to 24F during the introduction of PCV13 was observed in neighbouring country Spain. INTERPRETATION: Our work reveals that GPSC10 alone is a challenge for serotype-based vaccine strategy. More systematic investigation to identify lineages like GPSC10 will better inform and improve next-generation preventive strategies against pneumococcal diseases. FUNDING: Bill & Melinda Gates Foundation, Wellcome Sanger Institute, and the US Centers for Disease Control and Prevention.

Triumph of Pneumococcal Conjugate Vaccines: Overcoming a Common Foe.

Pneumococcal conjugate vaccine (PCV) has reduced the burden of pneumococcal disease by the near elimination of vaccine serotypes from countries giving a booster dose at >9 months of life. Herd protection, induced by interruption of pneumococcal vaccine type transmission has protected children too young to be immunized, children and adults with underlying risk conditions for invasive pneumococcal disease, and the elderly. PCV has rolled out in most poor countries, but millions of children remain un-immunized especially in middle income countries because of cost constraints. These are being met by considering fewer doses to maintain herd protection, and support for more affordable vaccine from developing country manufacturers. While 3rd generation PCV's with potential inclusion of 20+ serotypes are close to market in adults, it will be their introduction into childhood immunization and herd protection that is most likely to maximize the public health benefits of these vaccines.

Differences in clinical severity of respiratory viral infections in hospitalized children.

It is uncertain whether clinical severity of an infection varies by pathogen or by multiple infections. Using hospital-based surveillance in children, we investigate the range of clinical severity for patients singly, multiply, and not infected with a group of commonly circulating viruses in Nha Trang, Vietnam. RT-PCR was performed to detect 13 respiratory viruses in nasopharyngeal samples from enrolled patients. We apply a novel clinical severity score and examine associations with the odds of being severe and differences in raw severity scores. We find no difference in severity between 0-, 1-, and 2-concurrent infections and little differences in severity between specific viruses. We find RSV and HMPV infections to be associated with 2- and 1.5-fold increase in odds of being severe, respectively, and that infection with ADV is consistently associated with lower risk of severity. Clinically, based on the results here, if RSV or HMPV virus is suspected, PCR testing for confirmatory diagnosis and for detection of multiple coinfecting viruses would be fruitful to assess whether a patient's disease course is going to be severe.

Seasonality of respiratory viruses causing hospitalizations for acute respiratory infections in children in Nha Trang, Vietnam.

BACKGROUND: Acute respiratory infections (ARIs) are the most common causes of death in children under 5 years of age. While the etiology of most pneumonia and ARI episodes is undiagnosed, a broad range of ARI-causing viruses circulate widely in South East Asia. However, the patterns and drivers of the seasonal transmission dynamics are largely unknown. Here we identify the seasonal patterns of multiple circulating viruses associated with hospitalizations for ARIs in Nha Trang, Vietnam. METHODS: Hospital based enhanced surveillance of childhood ARI is ongoing at Khanh Hoa General Hospital in Nha Trang. RT-PCR was performed to detect 13 respiratory viruses in nasopharyngeal samples from enrolled patients. Seasonal patterns of childhood ARI hospital admissions of various viruses were assessed, as well as their association with rainfall, temperature, and dew point. RESULTS: Respiratory syncytial virus peaks in the late summer months, and influenza A in April to June. We find significant associations between detection of human parainfluenza 3 and human rhinovirus with the month's mean dew point. Using a cross-wavelet transform we find a significant out-of-phase relationship between human parainfluenza 3 and temperature and dew point. CONCLUSIONS: Our results are important for understanding the temporal risk associated with circulating pathogens in Southern Central Vietnam. Specifically, our results can inform timing of routing seasonal influenza vaccination and for when observed respiratory illness is likely viral, leading to judicious use of antibiotics in the region.

PERCH in Perspective: What Can It Teach Us About Pneumonia Etiology in Children?

The pneumonia team at the Bill & Melinda Gates Foundation congratulates the Pneumonia Etiology Research for Child Health (PERCH) study on delivering on their grant to collect high-quality data from thousands of children with World Health Organization-defined severe and very severe pneumonia and from controls in 9 diverse sites in 7 low- and middle-income countries. This supplement sets the foundation to understanding this complex study by providing an in-depth description of the study methodology, including discussion of key aspects such as antibiotic pretreatment, chest radiograph interpretation, utility of induced sputum in children, measurement of pathogen density, and use of C-reactive protein, and how these affect pneumonia etiology.

Surveillance of the impact of pneumococcal conjugate vaccines in developing countries.

Infection due to Streptococcus pneumoniae is a leading cause of morbidity and mortality in young children, especially in developing countries. With the support of Gavi, the Vaccine Alliance, the majority of these countries have introduced pneumococcal conjugate vaccines (PCV) into their national immunization programs and early data demonstrate a high degree of effectiveness, translating to enormous public health benefit through both direct and indirect (herd) effects. Future vaccination strategy may be focused on maintaining herd effects rather than individual protection. Evaluation of vaccine-type carriage, particularly in pneumonia cases, may be an easy, feasible way of measuring continued vaccine impact.

Immune response to 13-valent pneumococcal conjugate vaccine with a reduced dosing schedule.

BACKGROUND: The 7-valent pneumococcal conjugate vaccine (PCV7) has demonstrated effectiveness against pneumococcal illnesses when administered as 3 infant doses plus a toddler dose (3+1 schedule) or as an abbreviated schedule of 2 infant doses plus a toddler dose (2+1 schedule). The 13-valent pneumococcal conjugate vaccine (PCV13) is approved and World Health Organization-prequalified for administration in a 2+1 schedule when used as part of routine immunization programs. OBJECTIVE: To summarize immunologic responses elicited by PCV13 administered in a 2+1 schedule and following 2 doses in a 3+1 schedule. METHODS: Studies were double-blind, randomized, active-controlled, multicenter studies except the Mexico study (open-label, single-arm). In 2+1 studies, PCV13 was administered at 2, 4, and 12 (UK) or 3, 5, and 11 (Italy) months. In 3+1 studies (Spain and Mexico), assessment was made postdose 2 of the primary series (2, 4, and 6 months). The primary immunogenicity endpoint was the proportion of participants achieving serotype-specific antipolysaccharide immunoglobulin (Ig)G concentrations ≥ 0.35µg/mL (i.e., responders) 1 month postdose 2. Pneumococcal IgG geometric mean concentrations (GMCs), opsonophagocytic activity (OPA), and concomitant vaccine responses were assessed. RESULTS: PCV13 and PCV7 elicited comparable immune responses for the 7 common serotypes after 2 infant doses. The proportion of PCV13 responders postdose 2 was >85% for most of the 7 common and 6 additional serotypes, except common serotypes 6B (27.9-81.4%) and 23F (55.8-77.5%) and additional serotypes 3 (73.8-96.9%) and 6A (79.2-94.4%). Serotypes 6B and 23F elicited lower IgG GMCs postdose 2 compared with other serotypes; all serotypes demonstrated boosting posttoddler dose. All serotypes demonstrated functional activity; >95% of participants achieved OPA levels ≥ 1:8 postdose 2. Concomitant vaccine responses were similar between PCV13 and PCV7 groups. CONCLUSION: Immune responses elicited by PCV13 following 2 infant doses support transition from PCV7 to PCV13 in countries using a 2+1 schedule.

Vigilancia epidemiológica prospectiva de la enfermedad neumocócica invasora y de la neumonía en niños de San José, Costa Rica / Prospective epidemiologic surveillance of invasive pneumoccal disease and pneumonia in children in San Jos‚, Costa Rica

Justificación y objetivo: Streptococcus pneumoniae es globalmente la primera causa de muertes inmunoprevenibles en niños menores de 5 años. Métodos: entre 2007 y 2009 se realizó una vigilancia prospectiva con base poblacional en niños de 28 días a 36 meses en San José, Costa Rica. Se determinaron la incidencia de la enfermedad neumocócica invasora y de neumonía confirmada clínicamente y por radiografía, la distribución de serotipos y la sensibilidad a los antibióticos. Resultados: participaron 8801 sujetos (mediana de edad: 13,0 meses). En 25 niños se detectó enfermedad neumocócica invasora mediante aislamiento en cultivos (22) o mediante reacción de polimerasa en cadena y un cuadro clínico compatible con enfermedad neumocócica invasora. En los casos diagnosticados únicamente por cultivo, la tasa de incidencia de enfermedad neumocócica invasora en niños de 28 días a 36 meses de edad fue de 33,7/100000 por año para los años 1 y 2 combinados. Al considerar los casos adicionales diagnosticados por reacción de polimerasa en cadena, la incidencia aumnetó a 46,/100 000. El serotipo más frecuente fue el 14 (28,6 por ciento), seguido por los serotipos 3, 4, 6A, 19A, 22F. 42,9 por ciento de los aislamientos eran insensibles a la penicilina y al cotrimoxazol. La incidencia de neumonía confirmada clínicamente y de neumonía confirmada por radiografía fue de 1968/100 000 y 551/100 000, respectivamente. Conclusión: la incidencia de enfermedad neumocócica invasora y neumonía en niños de San José es considerable. Estos datos epidemiológicos sirven como línea de base para evaluar la efectividad de nuevas vacunas antineumocócicas conjugadas.

Bacteriology of community-acquired invasive disease found in a multicountry prospective, population-based, epidemiological surveillance for Pneumococcus in children in Latin America.

Several bacteria cause community-acquired invasive bacterial disease in children; many are vaccine preventable. Knowledge of pathogens causing community-acquired invasive bacterial disease is important when selecting antimicrobial therapy and implementing vaccine prevention strategies. We describe bacteriology of community-acquired invasive disease observed among 31,641 blood and sterile fluid cultures from children aged 28 days to 36 months in 3 Latin American countries over 2 years.

Population-based surveillance for invasive pneumococcal disease and pneumonia in infants and young children in Bogotá, Colombia.

BACKGROUND: In children <5 years of age, Streptococcus pneumoniae (SP) is, globally, the leading cause of vaccine-preventable death. Surveillance conducted in Bogotá, Colombia estimated incidence rates of invasive pneumococcal disease (IPD), clinical and chest radiograph-confirmed pneumonia (CXR+Pn); SP serotype distribution and antimicrobial susceptibility. METHODS: This prospective population-based surveillance was conducted from 2006 to 2008 in children 28 days to <36 months of age seeking care at SaludCoop centers. We determined incidence rates of IPD and pneumonia (clinical and CXR+Pn). Eligibility criteria included: temperature ≥39.0°C within 24h and/or clinical suspicion of IPD or pneumonia. Blood was obtained for culture in all children. Other sterile site specimens were obtained per routine practice. RESULTS: Of 8261 subjects enrolled, a total of 64 had invasive pneumococcal disease detected by isolation of SP from nonduplicative cultures (62) or detected solely by PCR and a clinical picture consistent with IPD (2). The overall IPD incidence rates for culture-positive only cases for children aged 28 days to <36 months was 76.4/100,000 per year for years 1 and 2 combined. Age stratification found the highest rates in children 6-12 and 12 to <24 months of age. IPD incidence rates were assessed for bacteremic pneumonia (54.2/100,000), bacteremia (17.2/100,000), meningitis (3.7/100,000), and sepsis (1.2/100,000). Most common serotypes causing IPD were: 14 (51.6%), 6B (9.7%), and 19F (9.7%). Coverage of IPD cases by pneumococcal conjugate vaccine (PCV) 7, PCV10, and PCV13 was 77.4%, 85.5%, and 91.9%, respectively. Twenty-eight isolates (45.2%) were penicillin-nonsusceptible; PCV7 covered 96.3% of these; PCV10 covered 96.3% and PCV13 covered 100%. The overall incidence of clinical pneumonia and CXR+Pn was 6276/100,000 and 2120/100,000, respectively. CONCLUSION: Pneumococcal disease and pneumonia burden is considerable in children in Bogotá, Colombia. Vaccination with pneumococcal conjugate vaccines has the potential to decrease this burden. Epidemiologic data are critical in assessing the potential impact of introduction of PCVs into national immunization schedules.

Prospective epidemiologic surveillance of invasive pneumococcal disease and pneumonia in children in San José, Costa Rica.

BACKGROUND: Streptococcus pneumoniae (SP) is the leading cause of vaccine-preventable death in children <5 years of age, globally. This surveillance determined incidence rates of invasive pneumococcal disease (IPD), clinical and chest radiograph-confirmed pneumonia (CXR+Pn); and SP serotype distribution and antimicrobial susceptibility in children in San José, Costa Rica. METHODS: This was a 2-year prospective, population-based surveillance conducted in 2007-2009 in children aged 28 days to 36 months presenting to participating healthcare centers. Eligibility criteria for study inclusion were as follows: temperature ≥ 39.0°C within 24h and/or clinical suspicion of IPD or pneumonia. RESULTS: 8801 subjects were enrolled. Median age: 14.5 months. A total of 25 children had invasive pneumococcal disease with S. pneumoniae isolated from nonduplicative cultures (22) or detected solely by PCR and a clinical picture consistent with IPD (3). Sources of positive cultures (some children had >1 positive culture) were: blood (20), pleural fluid (4), and cerebrospinal fluid (3). Of the 3 cases detected solely by PCR, 2 were from cerebrospinal fluid and 1 from pleural fluid. The overall IPD incidence rates for culture-positive only cases for children aged 28 days to <3 years was 33.7/100,000 per year for years 1 and 2 combined. Age stratification of culture-positive only subjects showed a peak during year 1 (106.8/100,000) in children 28 days to <6 months of age group, and in year 2 (45.5/100,000) in children 12 months to <24 months of age group. Most common serotypes were 14 (28.6%), followed by 3, 4, 6A, 19A, and 22F (9.5% each). Of 22 nonduplicative IPD isolates, 42.9% were penicillin- and trimethoprim/sulfamethoxazole nonsusceptible isolates. Consideration of PCR-positive cases increases the incidence of IPD for children aged 28 days to <3 years to 46.0/100,000. Overall incidence of clinical pneumonia and CXR+Pn was 1968/100,000 and 551/100,000, respectively. CONCLUSIONS: There is a considerable burden of IPD and pneumonia in children in San José. These epidemiologic data serve as a baseline to evaluate the effectiveness of the incorporation of new conjugate pneumococcal vaccines into the National Immunization Program in Costa Rican children.

Population-based surveillance for invasive pneumococcal disease and pneumonia in infants and young children in Goiânia, Brazil.

BACKGROUND: Streptococcus pneumoniae is the leading cause of vaccine-preventable death in children <5 years of age globally. We determined incidence rates of invasive pneumococcal disease (IPD), clinical and chest X-ray-confirmed pneumonia (CXR+Pn), S. pneumoniae serotype distribution, and antimicrobial susceptibility in children in Goiânia, Brazil. METHODS: Prospective, population-based surveillance was conducted from May 2007 to May 2009 in children 28 days to <36 months of age presenting to all 33 pediatric healthcare services (outpatient departments, emergency rooms, hospitals) in Goiânia. Eligibility criteria were temperature ≥39.0 °C in the previous 24h and/or clinical suspicion of pneumonia or IPD. RESULTS: 14,509 subjects were enrolled. Median age was 14.0 months. S. pneumoniae was detected in 64 samples from 62 subjects: 58 (90.6%) blood; 4 (6.3%) cerebrospinal fluid; and 2 (3.1%) pleural fluid. Incidence rate of IPD (culture- and polymerase chain reaction-positive) for all children aged 28 days to <36 months was 57.5/100,000; overall incidence for culture-positive only was 54.9/100,000. Age stratification of culture-positive-only subjects found the highest rates were, 114.6/100,000 and 69.8/100,000, respectively, for the 6 months to <12 months and 12 months to <24 months age groups. The overall incidence of invasive pneumonia and pneumococcal meningitis was 37.2/100,000 and 5.3/100,000, respectively. The most common IPD serotypes were 14 (45.0%), 6B (13.3%), 18C (6.7%), and 23F (5.0%). Eight isolates (13.3%) were penicillin nonsusceptible. The cumulative percentages of serotypes included in 7-valent, 10-valent, and 13-valent pneumococcal conjugate vaccines were 78.3%, 80.0%, and 88.3%, respectively. The overall incidence of clinical pneumonia and CXR+Pn was, 9598/100,000 and 3428/100,000, respectively. CXR+Pn rates for hospitalized and non-hospitalized subjects were 1751/100,000 and 1677/100,000, respectively. CONCLUSIONS: The burden of IPD and pneumonia is considerable in children in a large Brazilian city, and is seen in hospitalized as well as ambulatory subjects. Vaccination with pneumococcal conjugate vaccines has the potential to decrease this burden.