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

Genomic characterization of Streptococcus pneumoniae isolates obtained from carriage and disease among paediatric patients in Addis Ababa, Ethiopia

Background and aims. Despite the introduction of pneumococcal conjugate vaccines (PCVs), Streptococcus pneumoniae still remains an important cause of morbidity and mortality, especially among children under 5 years in sub-Saharan Africa. We sought to determine the distribution of serotypes, lineages and antimicrobial resistance of S. pneumoniae from carriage and disease among children presenting to health facilities, 5-6 years after the introduction of PCV10 in Ethiopia.Methods. Whole-genome sequencing (WGS) was performed on 103 S. pneumoniae (86 from nasopharyngeal swabs, 4 from blood and 13 from middle ear discharge) isolated from children aged <15 years at 3 healthcare facilities in Addis Ababa, Ethiopia, from September 2016 to August 2017. Using the WGS data, serotypes were predicted, isolates were assigned to clonal complexes, global pneumococcal sequence clusters (GPSCs) were inferred and screening for alleles and mutations that confer resistance to antibiotics was performed using multiple bioinformatic pipelines.Results. The 103 S. pneumoniae isolates were assigned to 38 serotypes (including nontypeable) and 46 different GPSCs. The most common serotype was serotype 19A. Common GPSCs were GPSC1 [14.6% (15/103), sequence type (ST) 320, serotype 19A], GPSC268 [8.7% (9/103), ST 6882 and novel STs; serotypes 16F, 11A and 35A] and GPSC10 [8.7% (9/103), STs 2013, 230 and 8804; serotype 19A]. The four invasive isolates were serotype 19A (n=2) and serotype 33C (n=2). Resistance to penicillin (>0.06 µg ml-1, CLSI meningitis cutoff) was predicted in 57% (59/103) of the isolates, and 43% (25/58) penicillin-binding protein allele combinations were predicted to be associated with penicillin resistance. Resistance mutations in folA (I100L) and/or folP (indel between fifty-sixth and sixty-seventh aa) were identified among 66% (68/103) of the isolates, whilst tetracycline (tetM) and macrolide (ermB and mefA) resistance genes were found in 46.6% (48/103), 20.4% (21/103) and 20.4% (21/103) of the isolates, respectively. Multidrug resistance (MDR) (≥3 antibiotic classes) was observed in 31.1% (32/103) of the isolates. GPSC1 and GPSC10 accounted for 46.8% (15/32) and 18.7% (6/32) of the overall MDR.Conclusion. Five to 6 years after the introduction of PCV10 in Ethiopia, the S. pneumoniae obtained from carriage and disease among paediatric patients showed diverse serotype and pneumococcal lineages. The most common serotype identified was 19A, expressed by the MDR lineages GPSC1 and GPSC10, which is not covered by PCV10 but is included in PCV13. Continued assessment of the impact of PCV on the population structure of S. pneumoniae in Ethiopia is warranted during and after PCV13 introduction.

Changes in population genetic structure of serotype 19A Streptococcus pneumoniae after universal childhood use of the 10-valent pneumococcal conjugate vaccine in Brazil

BACKGROUND

The introduction of the 10-valent pneumococcal conjugate vaccine (PCV10) for nationwide childhood immunization in 2010 led to a significant reduction in colonization and invasive pneumococcal disease (IPD) by vaccine serotypes in young. However, non-vaccine serotypes have emerged, and serotype 19A is now the leading cause of IPD in Brazil.

METHODS

We analyzed 32 serotype 19A isolates of Streptococcus pneumoniae recovered from children and adults who attended different health facilities in the state of Rio de Janeiro, Brazil, between 2010 and 2023. The capsular types of the isolates were determined by sequential multiplex PCR or by cpsB gene sequencing. All isolates were subjected to antimicrobial susceptibility testing and MLST.

RESULTS

Of the 32 serotype 19A isolates, 29 (90.6 %) isolates were recovered from children aged ≤5 years and three (9.4 %) isolates were recovered from adults. Nineteen (59.4 %) isolates were associated with colonization, and 13 (40.6 %) isolates were from diseases. All isolates were susceptible to chloramphenicol, levofloxacin, linezolid, rifampin, and vancomycin. The highest frequencies of non-susceptibility (intermediate + resistant) were observed for sulfamethoxazole-trimethoprim (n = 30; 93.8 %), penicillin (n = 24; 75 %), and erythromycin (n = 23; 71.9 %). Twenty-two (68.8 %) isolates were multidrug resistant (MDR). MICs for penicillin among penicillin-non-susceptible pneumococci (PNSP) ranged from 0.12 to 8.0 μg/mL. MICs for erythromycin ranged from 0.064 to >256 μg/mL. MICs for ceftriaxone ranged from 0.023 to 4 μg/mL. The most common genetic lineages were ST733 (n = 7; 21.9 %), mostly found before and in the early years of PCV10 introduction, and CC320 (n = 25; 78.1 %), mostly found in the late-PCV10 period. All 25 isolates within CC320 were PNSP and mostly (n = 22; 88 %) MDR.

CONCLUSIONS

We observed a shift in antimicrobial susceptibility profiles and genetic lineages after long-term use of PCV, mostly PCV10, for routine childhood immunization, characterized by clonal expansion of the MDR lineage CC320.

Fourier transform infrared spectroscopy for Streptococcus pneumoniae capsular serotype classification in pediatric patients with invasive infections

Invasive pneumococcal disease (IPD) is a major cause of morbidity and mortality worldwide, particularly in the pediatric population (children and infants), with high rates of hospitalization and death. This study aimed to create and validate a classifier for Streptococcus pneumoniae serotyping using Fourier-transform infrared (FT-IR) spectroscopy as a rapid alternative to the classical serotyping technique. In this study, a database comprising 76 clinical isolates, including 18 serotypes (predominantly serotypes 19A, 6C, and 3) of S. pneumoniae from pediatric patients with IPD, was tested at a tertiary pediatric hospital in southern Brazil during 2016-2023. All isolates were previously serotyped using the Quellung reaction, and 843 FT-IR spectra were obtained to create a classification model using artificial neural network (ANN) machine learning. After the creation of this classifier, internal validation was performed using 384 spectra as the training dataset and 459 as the testing dataset, resulting in a predictive accuracy of 98% for serotypes 19A, 6, 3, 14, 18C, 22F, 23A, 23B, 33F, 35B, and 9N. In this dataset, serotypes 10A/16F, 15ABC, and 7CF could not be differentiated and were, therefore, grouped as labels. FT-IR is a promising, rapid, and low-cost method for the phenotypic classification of S. pneumoniae capsular serotypes. This methodology has significant implications for clinical and epidemiological practice, improving patient management, monitoring infection trends, and developing new vaccines.

High prevalence of 19A pneumococcal serotype carriage during the COVID-19 pandemic in Brazil

INTRODUCTION

Streptococcus pneumoniae colonization patterns are influenced by host and environmental factors, which may be related to Invasive Pneumococcal Disease (IPD). Interestingly, COVID-19 pandemic witnessed a decline in the incidence of IPDs. Investigations with diligent data collection on the prevalence of nasopharyngeal colonization and associated serotypes during this unique period can yield novel insights. The aim of the current study was to assess the prevalence of S. pneumoniae carriage among children and adults who have sought care at emergency departments with suspected COVID-19.

METHODS

In this cross-sectional study, adults and children presenting with signs and symptoms likely associated with COVID-19 in two outpatient clinics in Southern Brazil were invited to participate. RT-PCR with a comprehensive molecular panel for pneumococcal identification of the 21 most prevalent serotypes in Latin America was performed on all enrolled subjects. Prevalence of pneumococcal carriage was assessed in the age groups (< 2, ≥ 2-5, ≥ 5-11, ≥ 11-18, ≥ 18-60, ≥ 60).

RESULTS

A total of 1644 subjects were included in the study. Pneumococcal carriage was detected by PCR testing in 14.9% (245/1,644), and serotype identification occurred in 42.0% (103/245) of the participants, with a total frequency of 111. The most frequent serotype identified was 19A (25.2%, n = 28/111), followed by 6C/6D (17.1%, n = 19/111), and 23A (11.7%, n = 13/111), also highlighting the high frequency of non-vaccine serotypes found across all age groups.

DISCUSSION

19A serotype, as well other most frequent serotypes identified are not covered by the PCV-10 in a community setting where PCV-10 is widely available. This finding reinforces the need for continuous surveillance to determine the impact of pneumococcal vaccination and guide public health decision-making. High 19A serotype prevalence is critical in the decision-making process for electing the best options for pneumococcal conjugate vaccines.

Immunization in women's lives: present and future

•The negative impact of infectious diseases and their immunoprevention during the different stages of a woman's life requires a broad approach including adolescence, adulthood, pregnancy and the postmenopausal phase. •Immunization of pregnant women should be a priority for the protection of the maternal-fetal dyad, especially in regions with high rates of infections preventable by immunization. •Brazil has one of the most comprehensive vaccination programs in the world - the National Immunization Program (Programa Nacional de Imunizações, PNI) - that serves all age groups: newborns, children, adolescents, adults, pregnant women and older adults, as well as groups with special needs, such as adolescents, pregnant and older adult women. •However, vaccination coverage remains below ideal for all available vaccines, especially among adolescents and pregnant women, and Febrasgo is committed to collaborating with the PNI to combat vaccine hesitancy. •The gynecologist/obstetrician is the reference physician for women, therefore the access to information and updates regarding all vaccines recommended for their patients is extremely important for this professional, aiming at the greatest possible protection. •The objective of this Febrasgo Position Statement is to bring an update to women's vaccination schedule, covering some vaccines that are available, including new approved vaccines and those in the commercialization phase. •This work is a compilation of the First Febrasgo Scientific Immunization Forum held in the city of São Paulo in October 2023 with the objective to update recommendations for vaccines in use and new innovative vaccines soon to be available.

Rebound of pediatric invasive pneumococcal disease in Portugal after the COVID-19 pandemic was not associated with significant serotype changes

OBJECTIVES

The COVID-19 pandemic led to the institution of public health measures in many countries which reduced respiratory infections. We aimed to identify and characterize changes in pediatric (<18 years) invasive pneumococcal disease (pIPD) in Portugal in 2018-2023.

METHODS

pIPD cases were identified by culture and molecular methods and stratified by age and serotype. When available the susceptibility of the isolates to antimicrobials was evaluated.

RESULTS

pIPD cases were markedly reduced in the last trimester of 2019-2020 and the entire 2020-2021 season. While 2021-2022 was in line with pre-pandemic seasons, in 2022-2023, the number of pIPD cases exceeded those found pre-pandemic. Molecular tests were responsible for identifying and serotyping 30% of cases, highlighting their importance in evaluating pIPD. Among the 316 pIPD cases, 37 different serotypes were detected, of which serotypes 3 (n = 85, 26.9%), 8 (n = 25, 7.9%), 10A (n = 21, 6.6%) and 24F (n = 20, 6.3%) were the most frequent. The post-pandemic serotype distribution reflected mostly pre-pandemic trends and the rebound was not driven by particular serotypes. We identified many vaccine failures, most (n = 37) representing serotype 3 infections. Penicillin non-susceptibility increased from 14% pre-pandemic to 29%, with serotype 24F becoming particularly significant.

CONCLUSIONS

The higher number of cases of pIPD post-COVID-19 in Portugal raises the possibility of a higher burden of pneumococcal disease in Europe post-pandemic. The relatively stable serotype distribution and the current availability of the higher valency conjugate vaccines PCV15 and PCV20, potentially preventing a large proportion of pIPD (43% and 67%, respectively), offer an opportunity to control this increase.

Serotype Distribution and Antimicrobial Susceptibility Pattern of Streptococcus pneumoniae in COVID-19 Pandemic Era in Brazil

Despite the introduction of the pneumococcal vaccine, Streptococcus pneumoniae remains a cause of invasive diseases in Brazil. This study provides the distribution of serotypes and antimicrobial susceptibility patterns for pneumococcal isolates before and during the years of the COVID-19 pandemic in two age groups, <5 and ≥50 years. This is a national laboratory-based surveillance study that uses data from the Brazilian national laboratory for invasive S. pneumoniae from the pre-COVID-19 (January 2016 to January 2020) and COVID-19 (February 2020 to May 2022) periods. Antimicrobial resistance was evaluated by disk diffusion and minimum inhibitory concentration. The year 2020 was marked by a 44.6% reduction in isolates received and was followed by an upward trend from 2021 onwards, which became evident in 2022. No differences were observed in serotypes distribution between the studied periods. The COVID-19 period was marked by the high prevalence of serotypes 19A, 3, and 6C in both age groups. Serotypes 19A and 6C were related to non-antimicrobial susceptibility. We observed a reduction in S. pneumoniae, without changes in serotypes distribution and epidemiological capsular switch during the COVID-19 period. We observed elevated resistance rates, mainly to penicillin and ceftriaxone for non-meningitis cases in children under 5 years of age.

Antimicrobial Resistance in Streptococcus pneumoniae before and after the Introduction of Pneumococcal Conjugate Vaccines in Brazil: A Systematic Review

Streptococcus pneumoniae causes serious illnesses, such as pneumonia, bacteremia, and meningitis, mainly in immunocompromised individuals and those of extreme ages. Currently, pneumococcal conjugate vaccines (PCVs) are the best allies against pneumococcal diseases. In Brazil, the 10-valent and 13-valent PCVs have been available since 2010, but the threat of antimicrobial resistance persists and has been changing over time. We conducted a systematic review of the literature with works published since 2000, generating a parallel between susceptibility data on isolates recovered from colonization and invasive diseases before and after the implementation of PCVs for routine childhood use in Brazil. This systematic review was based on the Cochrane Handbook for Systematic Reviews of Interventions and Preferred Reporting Items for Systematic Literature Reviews and Meta-Analyses (PRISMA) guidelines. Despite the inclusion of PCVs at a large scale in the national territory, high frequencies of non-susceptibility to important drugs used in pneumococcal diseases are still observed, especially penicillin, as well as increasing resistance to macrolides. However, there are still drugs for which pneumococci have a comprehensive sensitivity profile.

Streptococcus pneumoniae serotype 19A in hospitalized children with invasive pneumococcal disease after the introduction of conjugated vaccines in Lima, Peru

BACKGROUND

The Pneumococcal conjugate vaccine (PCV) has decreased cases of invasive pneumococcal disease (IPD) worldwide. However, the impact of PCVs introduction may be affected by the serotype distribution in a specific context.

METHODS

Cross-sectional multicenter passive surveillance study of IPD cases in pediatric patients hospitalized in Lima, Peru between 2016 and 2019 (after PCV13 introduction) to determine the serotype distribution and antimicrobial resistance of Streptococcus pneumoniae. Serotyping was performed by a sequential multiplex PCR and confirmed by whole genome sequencing.

RESULTS

Eighty-five S. pneumoniae isolates were recovered (4.07/100,000 among children <60 months of age). Serotype 19A was the most common (49.4%). Children infected with serotype 19A in comparison with children infected with other serotypes were younger, had a lower rate of meningitis and higher rates of pneumonia, complicated pneumonia and antimicrobial resistance; 28.6% of patients with serotype 19A have received at least one dose of PCV13 vs. 62.8% of patients with other serotypes. Using MIC-breakpoints, 81.2% (56/69) of non-meningitis strains and 31.2% (5/16) of meningitis strains were susceptible to penicillin; 18.8% (3/16) of meningitis strains had intermediate resistance to ceftriaxone. Resistance to azithromycin was 78.8% (67/85). Serotype 19A frequency increased over time in the same study population, from 4.2% (4/96) in 2006-2008, to 8.6% (5/58) in 2009-2011, to 49.4% (42/85) in the current study (2016-2019) (p < 0.001).

CONCLUSIONS

After PCV13 introduction in Peru, serotype 19A remains the most prevalent; however, the vaccination coverage is still not optimal. Therefore, additonal surveillance studies are needed to determine the remaining IPD burden.

Trends in Pneumococcal and Bacterial Meningitis in Brazil from 2007 to 2019

The pneumococcal conjugate vaccination (PCV) was introduced into the Brazilian Childhood National Immunization Program in 2010; however, universal pneumococcal vaccination for older adults has not been implemented yet. Our aim is to evaluate the trends in pneumococcal meningitis incidence and case fatality rate (CFR) across all age groups from 2007 to 2019 using data from the National Surveillance System. The pre-PCV (2007-2009) and post-PCV (2011-2019) periods were compared; changes in incidence and CFR were assessed by joinpoint regression. Additional analyses of bacterial meningitis were performed to compare the patterns and trends. Over the 13-year period, 81,203 and 13,837 cases were classified as bacterial and pneumococcal meningitis, respectively. S. pneumoniae was the main etiological agent of bacterial meningitis in adults aged ≥50 years and the most lethal in all age groups. In the post-PCV period, a 56.5% reduction in the average incidence was seen in pneumococcal meningitis in the pediatric population. In contrast, there was an increasing trend among adults. The CFR for pneumococcal and bacterial meningitis remained stable in most age groups during the study period. These findings highlight the value of expanding pneumococcal vaccination policies, including vaccines that provide better indirect protection from children to adults and broadening vaccination to older adults.