Genetic diversity of pneumococcal surface protein A (PspA) in paediatric isolates of non-conjugate vaccine serotypes in Japan

Serotype distribution and antimicrobial resistance of Streptococcus pneumoniae isolated from children in Japan, 2023

Background

The prevalence of serotypes and antimicrobial resistance of Streptococcus pneumoniae was characterized among children thirteen years after the licensure of the pneumococcal conjugate vaccine (PCV) in Japan.

Methods

A total of 353 pneumococcal isolates were collected from Japanese children between March and July 2023. All the isolates were serotyped using genetic methods and tested for susceptibility to 14 antimicrobial agents.

Results

Among the 353 isolates, the prevalence rates of non-PCV13 and non-PCV20 serotypes were 96.9 % and 77.9 %, respectively, including the dominant non-PCV13/PCV20 serotypes 23A (16.1 %), 35B (15.3 %), 15A (10.5 %), 15C (9.3 %), and 34 (9.1 %), which accounted for 60.3 % of all isolates. The high non-susceptibility rates were observed for macrolides (erythromycin, azithromycin, and clarithromycin; ≥81.9 %) and tetracycline (80.7 %). Penicillin non-susceptibility and multidrug resistance (MDR) were detected in 49.9 % (6.8 % resistant and 43.1 % intermediate) and 68.3 % of the isolates, respectively. The three most common non-PCV13/PCV20 serotypes 15A, 23A, and 35B exhibited high prevalence rates of penicillin non-susceptibility (≥89.5 %) and MDR (≥81.5 %). Extensive drug resistance was observed in 10.5 % of all isolates belonging to six different serotypes (12F, 23A, 11A, 15A, 35B, and 15B) and in the non-encapsulated strains of S. pneumoniae.

Conclusions

Our study revealed a higher prevalence of non-susceptibility to penicillin with MDR in the three most common non-PCV13/PCV20 serotypes 15A, 23A, and 35B, in Japan, suggesting their persistence in the PCV13 era.

Membrane particles evoke a serotype-independent cross-protection against pneumococcal infection that is dependent on the conserved lipoproteins MalX and PrsA

SignificancePneumococcal infections are major contributors to morbidity and mortality worldwide. Introduction of pneumococcal conjugated vaccines (PCVs) into the childhood vaccination program has led to a decrease in invasive pneumococcal disease (IPD) in vaccinated children but concurrently to an increase of nonvaccine-type IPD, also in nonvaccinated age groups such as the elderly. Thus, novel vaccine approaches are urgently needed, especially for the elderly, targeting all pneumococci causing IPD. Here, we show that pneumococcal membrane particles (MPs) evoke a serotype-independent cross-protection against IPD. This protection is dependent on the presence of the two conserved lipoproteins MalX and PrsA. We suggest that MPs can be used for pneumococcal vaccine development.

A Jack of All Trades: The Role of Pneumococcal Surface Protein A in the Pathogenesis of Streptococcus pneumoniae

Streptococcus pneumoniae (Spn), or the pneumococcus, is a Gram-positive bacterium that colonizes the upper airway. Spn is an opportunistic pathogen capable of life-threatening disease should it become established in the lungs, gain access to the bloodstream, or disseminate to vital organs including the central nervous system. Spn is encapsulated, allowing it to avoid phagocytosis, and current preventative measures against infection include polyvalent vaccines composed of capsular polysaccharide corresponding to its most prevalent serotypes. The pneumococcus also has a plethora of surface components that allow the bacteria to adhere to host cells, facilitate the evasion of the immune system, and obtain vital nutrients; one family of these are the choline-binding proteins (CBPs). Pneumococcal surface protein A (PspA) is one of the most abundant CBPs and confers protection against the host by inhibiting recognition by C-reactive protein and neutralizing the antimicrobial peptide lactoferricin. Recently our group has identified two new roles for PspA: binding to dying host cells via host-cell bound glyceraldehyde 3-phosphate dehydrogenase and co-opting of host lactate dehydrogenase to enhance lactate availability. These properties have been shown to influence Spn localization and enhance virulence in the lower airway, respectively. Herein, we review the impact of CBPs, and in particular PspA, on pneumococcal pathogenesis. We discuss the potential and limitations of using PspA as a conserved vaccine antigen in a conjugate vaccine formulation. PspA is a vital component of the pneumococcal virulence arsenal - therefore, understanding the molecular aspects of this protein is essential in understanding pneumococcal pathogenesis and utilizing PspA as a target for treating or preventing pneumococcal pneumonia.

Distribution and Variation of Serotypes and Pneumococcal Surface Protein A Clades of Streptococcus pneumoniae Strains Isolated From Adult Patients With Invasive Pneumococcal Disease in Japan

Pneumococcal surface protein A (PspA) is a surface protein of Streptococcus pneumoniae that may be a candidate antigen for new pneumococcal vaccines. This study investigates the distribution of PspA clades of the causative strains of adult invasive pneumococcal disease (IPD) in Japan. Of the 1,939 strains isolated from cases of adult IPD during 2014–2019, the PspA clades of 1,932 (99.6%) strains were determined, and no pspA was detected in the remaining 7 strains (0.4%). PspA clades 1–6 were detected in 786 (40.5%), 291 (15.0%), 443 (22.8%), 369 (19.0%), 33 (1.7%), and 6 (0.3%) strains, respectively. New PspA clades (0.2%) were identified in two non-typeable and two serotype 35B pneumococci. The proportions of clade 1 and clade 2 showed significantly decreased and increased trends, respectively. Furthermore, the PspA clade of pneumococcal strains was partially serotype- and sequence type-dependent. The majority of strains belonging to serotypes contained in both the 13-valent pneumococcal conjugate vaccine (PCV13) and the 23-valent pneumococcal polysaccharide vaccine (PPSV23) belonged to PspA clades 1 or 3. In contrast, the distribution of clades in non-vaccine serotypes was wider than that of vaccine serotype pneumococci. Our findings demonstrate that almost all pneumococcal strains from adult IPD express PspA clades 1–4, especially for non-vaccine serotypes. These results may be useful for the development of a new pneumococcal vaccine with PspA.

Clonal lineages and antimicrobial resistance of nonencapsulated Streptococcus pneumoniae in the post-pneumococcal conjugate vaccine era in Japan

OBJECTIVES

The emergence and spread of nonencapsulated Streptococcus pneumoniae (NESp) is a public health concern in the post-pneumococcal conjugate vaccine era. We analyzed the prevalence, molecular characteristics, and antimicrobial resistance of NESp responsible for noninvasive infections in northern Japan.

METHODS

NESp isolates were identified using molecular and phenotypical methods among 4463 S. pneumoniae isolates from noninvasive infection cases during 4 study periods between January 2011 and January 2019. NESp isolates were analyzed for antimicrobial susceptibility, genotype, and virulence-associated genes.

RESULTS

Seventy-one NESp isolates were identified (1.6% of total clinical isolates) and assigned to the null capsule clade (NCC)1 (pspK+) (94.4%) or NCC2 (aliC+/aliD+) (5.6%). The dominant sequence types (STs) were ST7502 (23.9%), ST4845 (19.7%), ST16214 (11.3%), ST11379 (9.9%), and ST7786 (7.0%). These 5 dominant STs and all 7 novel STs were related to the sporadic NESp lineage ST1106 or PMEN clone Denmark¹⁴-ST230. High non-susceptibility rates of NESp were observed for trimethoprim-sulfamethoxazole, erythromycin, and tetracycline (>92.9%), and multidrug resistance was observed in 88.7% of the NESp isolates, including all ST7502, ST4845, and ST11379 isolates.

CONCLUSIONS

The study revealed that the dominant clonal groups of NESp were associated with a high prevalence of non-susceptibility to antimicrobials in northern Japan.

Seroepidemiological analysis of anti-pneumococcal surface protein A (PspA) immunoglobulin G by clades in Japanese population

BACKGROUND

Pneumococcal surface protein A (PspA) is one of the candidates of the novel pneumococcal protein vaccines. The seroepidemiology of naturally acquired anti-PspA immunoglobulin G (IgG) by clades, across a wide range of ages has not been investigated.

METHODS

We examined the concentrations of anti-PspA IgG by clades (1, 2, 3, 4, and 5) in 397 sera from persons aged 0-≥70 years by enzyme-linked immunosorbent assay, and determined the geometric mean concentrations (GMCs) by age group. The relationships between concentrations of anti-PspA IgG antibody for each clade for each person were also assessed.

RESULTS

GMC of anti-PspA IgG was lowest, highest, and plateaued in those aged 6-11 months, 5-9-years, and 20-49 years, respectively. It gradually declined in those aged > 70 years. GMCs patterns in different age groups were similar for all clades. Correlations were found especially within the same PspA family (between clades 1 and 2 or clades 4 and 5).

CONCLUSIONS

Our data suggested that most people acquired anti-PspA IgG across clades 1, 2, 3, 4, and 5 during childhood. These results would be a fundamental data of clade-specific anti-PspA IgG antibodies.

Current situation and need for prevention of invasive pneumococcal disease and pneumococcal pneumonia in 6- to 64-year-olds in Japan

We conducted a systematic review of the literature to evaluate the reported epidemiology and burden of invasive pneumococcal disease (IPD) and pneumococcal pneumonia (PP) among children and adults aged 6-64 years in Japan. Studies published from Japan between September 2009 and September 2019 and indexed in the MEDLINE/PubMed or ICHUSHI databases were evaluated. A majority of the studies reported overlapping age ranges, including children aged <6 years and adults aged >64 years. According to the national surveillance data, 19% of the IPD cases were patients aged 5-59 years, and an increasing trend in IPD cases was reported from 2013 to 2017. Comorbidities were consistent with those reported by the Advisory Committee on Immunization Practices. Deaths from IPD appeared to increase nearly 3-fold between 2013 and 2017. Overall, both 13-valent pneumococcal conjugate vaccine (PCV13) and 23-valent pneumococcal polysaccharide vaccine (PPSV23) coverage was higher for IPD compared with PP. All the serotypes known to be prominent in Japan were also identified as common serotypes (3, 6A, 19A: PCV13 serotypes; 12F: outbreak serotype; 15A, 35B: drug-resistant serotypes). This systematic literature review suggests a substantial burden of IPD and PP in Japanese children and adults aged 6-64 years. The burden of comorbidities, hospitalizations, and mortality was particularly high among adults. Concerted pneumococcal vaccination strategies may help to reduce the incidence and burden of IPD and PP in this large proportion of the Japanese population.

Virulence-Associated Characteristics of Serotype 14 and Serogroup 9 Streptococcus pneumoniae Clones Circulating in Brazil: Association of Penicillin Non-susceptibility With Transparent Colony Phenotype Variants

Streptococcus pneumoniae remains a major agent of invasive diseases, especially in children and the elderly. The presence of pneumococcal capsule, pneumococcal surface protein A (PspA), and pilus type 1 (PI-1) and the ability of colony phase variation are assumed to play important roles in the virulence potential of this microorganism. Differences in the capsular polysaccharide allow the characterization of more than 90 pneumococcal serotypes; among them, serotype 14 and serogroup 9 stand out due to their prevalence in the pre- pneumococcal conjugate vaccine era and frequent association with penicillin non-susceptibility. Here we investigated the distribution of PI-1 and pspA genes and colony phase variants among 315 S. pneumoniae isolates belonging to serotype 14 and serogroup 9, recovered over 20 years in Brazil, and correlated these characteristics with penicillin susceptibility and genotype as determined by multilocus sequence typing. All strains were shown to carry pspA genes, with those of family 2 (pspA2) being the most common, and nearly half of the strains harbored P1-1 genes. The pspA gene family and the presence of PI-1 genes were conserved features among strains belonging to a given clone. A trend for increasing the occurrence of pspA2 and PI-1 genes over the period of investigation was observed, and it coincided with the dissemination of CC156 (Spain^9V-3) clone in Brazil, suggesting a role for these virulence attributes in the establishment and the persistence of this successful clone. Opaque variant was the colony phenotype most frequently observed, regardless of clonal type. On the other hand, the transparent variant was more commonly associated with penicillin-non-susceptible pneumococci and with strains presenting evidence of recombination events involving the genes coding for polysaccharide capsule and PspA, suggesting that pneumococcal transparent variants may present a higher ability to acquire exogenous DNA. The results bring to light new information about the virulence potentials of serotype 14 and serogroup 9 S. pneumoniae isolates representing the major clones that have been associated with the emergence and the dissemination of antimicrobial resistance in our setting since the late 1980s.

High prevalence of antimicrobial resistance in non-vaccine serotypes of non-invasive/colonization isolates of Streptococcus pneumoniae: A cross-sectional study eight years after the licensure of conjugate vaccine in Japan

BACKGROUND

Multidrug resistance (MDR) in non-vaccine serotypes (NVTs)-Streptococcus pneumoniae is a global public health concern after the widespread use of pneumococcal conjugate vaccines (PCVs). The present study aimed to analyze the prevalence of serotypes and antimicrobial susceptibilities of non-invasive/colonization isolates of S. pneumoniae eight years after the introduction of PCV in Japan.

METHODS

A total of 545 non-invasive pneumococcal isolates (460 children, 85 adults) obtained from July 2018 to January 2019 were studied. All isolates were tested for susceptibility to ten antimicrobials and were characterized for serotypes, penicillin binding protein (PBP) genotypes, and macrolide resistance genes.

RESULTS

Among children, 95.0% of isolates belonged to non-13-valent pneumococcal conjugate vaccine (PCV13) serotypes (NVTs), with 15A (15.0%) being dominant, followed by 35B (12.2%), 23A (11.1%), 15B (9.8%), and 15C (9.6%). In contrast, serotype 3 (18.8%) was the most prevalent in adults, while 15A, 10A, and 23A were also common. Serotypes covered by PCV13 and 23-valent pneumococcal polysaccharide vaccine (PPSV23) in all the adult isolates were 25.9% and 48.2%, respectively. High resistance rates were observed against erythromycin, tetracycline, and clindamycin (≥62.4% children, ≥58.8% adults). Penicillin-resistant and penicillin-intermediate isolates represented 2.2% and 33.8% of all isolates, respectively. Most isolates of the three dominant NVTs 15A, 35B, and 23A were non-susceptible to penicillin. Overall, multiple drug resistance (MDR) was detected in 69.0% of all isolates, including dominant NVTs 15A, 35B, 23A, 15B, and 15C. Among all the isolates, 81.8% harbored at least one altered PBP genes, and erm(B), mef(A/E) and both these genes were found in 68.2%, 23.3%, and 6.8%, respectively. High prevalence (>90%) of erm(B) was observed in serogroup 15, and serotypes 23A, 33F, and 12F.

CONCLUSION

The present study revealed the high prevalence of NVTs 15 and 23A, and 35B showing MDR, suggesting their spread after introduction of routine PCV immunization.

Evolution of Streptococcus pneumoniae Serotype 3 in England and Wales: A Major Vaccine Evader

Despite its inclusion in pneumococcal conjugate vaccine 13 (PCV13), Streptococcus pneumoniae serotype 3 remains a major cause of invasive pneumococcal disease in England and Wales. Previous studies have indicated that there are distinct lineages within serotype 3 clonal complex 180 and the clade distributions have shifted in recent years with the emergence of clade II. We undertook whole genome sequencing and genomic analysis of 616 serotype 3 isolates from England and Wales between 2003 and 2018, including invasive and carriage isolates. Our investigations showed that clade II has expanded since 2014 and now represents 50% of serotype 3 invasive pneumococcal disease (IPD) isolates in England and Wales. Genomic analysis of antibiotic resistance and protein antigen genes showed that distinct profiles are present within the clades which could account for the recent emergence of this clade. This investigation highlights the importance and utility of routine whole genome sequencing and its ability to identify new and emerging variation at the single nucleotide level which informs surveillance and will impact future vaccine development.

Prevalence of Various Vaccine Candidate Proteins in Clinical Isolates of Streptococcus pneumoniae: Characterization of the Novel Pht Fusion Proteins PhtA/B and PhtA/D

Pneumococcal proteins unrelated to serotypes are considered to be candidates of antigens in next-generation vaccines. In the present study, the prevalence of vaccine candidate protein genes, along with serotypes and antimicrobial resistance determinants, was investigated in a total of 57 isolates obtained from a tertiary care hospital in Japan. All of the pediatric isolates and 76.6% of the adult isolates did not belong to PCV13 (a 13-valent pneumococcal conjugate vaccine) serotypes, and 70.2% of all isolates showed multidrug resistance. All of the isolates had ply, pavA, nanA, and nanB, and high prevalence was noted for the pspA and pspC genes (96.5% and 78.9%, respectively). Detection rates for the pneumococcal histidine triad protein (Pht) genes phtA, phtB, phtD, and phtE were 49.1%, 26.3%, 61.4%, and 100%, respectively. Two fusion-type genes, phtA/B and phtA/D, were identified, with a prevalence of 36.9% and 14.0%, respectively. These fusion types showed 78.1–90.0% nucleotide sequence identity with phtA, phtB, and phtD. The most prevalent pht profile was phtA + phtD + phtE (26.3%), followed by phtA/B + phtE (19.3%) and phtA/B + phtD + phtE (17.5%), while pht profiles including phtD and/or phtA/phtD were found in 71.9% of isolates. The present study revealed the presence of two fusion types of Pht and their unexpectedly high prevalence. These fusion types, as well as PhtA and PhtB, contained sequences similar to the B cell epitopes that have been previously reported for PhtD.

Association Between Pneumococcal Surface Protein A Family and Genetic/Antimicrobial Resistance Traits of Non-Invasive Pneumococcal Isolates from Adults in Northern Japan

Pneumococcal isolates from adult patients in northern Japan in 2016 were subjected to molecular investigation related to pneumococcal surface protein A (PspA) and drug resistance determinants. Of the 51 isolates, serotype 3/ST180 was the most prevalent (17.6%), followed by 35B (ST2755/ST558) (11.8%) and 15A (ST63/ST7874/ST13068/ST13785) (9.8%). Coverage of serotypes by 13-valent conjugate vaccine and 23-valent polysaccharide vaccine was 27.5% and 49%, respectively. All the isolates expressed PspA family 1 or 2 (51% and 49%, respectively). Each serotype was associated with either of the PspA families (e.g., serotype 3, PspA family 1; serotypes 35B and 15A, PspA family 2). Multidrug resistance (MDR) was found in 84.3% of the isolates. Minimum of one altered penicillin-binding protein gene was detected in 82.4% of isolates, indicating 25.5% non-susceptibility to penicillin. Serotypes 15A and 35B were predominant and demonstrated MDR. An isolate of serotype 15A/ST13785 (single-locus variant of ST242) was resistant to fluoroquinolones associated with double mutation in the quinolone resistance-determining regions of gyrA and parC. The present study indicates the spread of MDR pneumococci represented by isolates of serotypes 3, 15A, and 35B, and prevalence of both PspA family 1 and 2 in isolates obtained from adult patients.