Serotype distribution and susceptibility to penicillin and erythromycin among noninvasive or colonization isolates of Streptococcus pneumoniae in northern Japan: a cross-sectional study in the pre-PCV7 routine immunization period

Spread of multidrug resistance in non-PCV13/PCV20 serotypes of Streptococcus pneumoniae: A cross-sectional study ten years after the introduction of pneumococcal conjugate vaccine in Japan

Ten years after the introduction of the pneumococcal conjugate vaccine (PCV) in Japan, the prevalence rates of non-PCV13 and non-PCV20 serotypes among pediatric pneumococcal isolates were 94.0% and 73.7%, respectively. The predominant non-PCV13/PCV20 serotypes (15A, 35B, and 23A) were mostly multidrug-resistant (≥80.5%), exhibiting non-susceptibility to penicillin.

High prevalence of multiple serotypes of pneumococci in patients with pneumonia and their associated risk factors

BACKGROUND

Multiple serotypes of pneumococci have epidemiological and clinical implications, such as the emergence of non-vaccine serotypes and the acquisition of antimicrobial resistance. Prevalence of multiple serotypes of pneumococci in adults and their risk factors are not known.

METHODS

We enrolled adult patients from age ≥15 years with radiologically confirmed pneumonia in four hospitals across Japan. Pneumococcal pneumonia was defined with a pneumococcal bacterial density of ≥104/mL in sputum by lytA quantitative PCR, and serotypes were determined. Pneumonias with a single serotype were categorised as single-serotype pneumococcal pneumonia and with two or more serotypes as multiple-serotype pneumococcal pneumonia. Multivariable logistic regression was used to assess the risk factors.

RESULTS

3470 patients (median age 77 years, IQR 65-85) were enrolled. Pneumococcal pneumonia was identified in 476 (18.3%, n=2605) patients. Multiple serotypes were detected in 42% of them. Risk of having multiple serotypes was low among patients who had received 23-valent pneumococcal polysaccharide vaccine (PPSV23) vaccines (adjusted OR 0.51 (95% CI 0.27 to 0.94)). Proportion of non-PCV7 PPSV23 serotypes in overall distribution of multiple serotypes was 67.4% (n=324/481) compared with 46.4% (n=128/276) in that of single serotypes (p=0.001). Serotypes 5, 9N/9L, 10A, 12/22/46, 17F and 35F were associated with multiple-serotype pneumonia, and serotypes 6A/6B, 23F, 11 and 6C/6D were associated with single-serotype pneumonia. Proportion of more invasive serotypes (serotypes 1, 5, 7F, 8) was significantly higher in multiple-serotype pneumonia (p=0.001).

CONCLUSIONS

Multiple serotypes of pneumococci are common in sputum of adult patients with pneumonia. The risk of multiple-serotype pneumococcal pneumonia is lower than that of single-serotype pneumococcal pneumonia among PPSV23-vaccinated patients.

TRIAL REGISTRATION NUMBER

UMIN000006909.

Burden of illness associated with pneumococcal infections in Japan - a targeted literature review

INTRODUCTION

Pneumococcal diseases (PDs) are among the leading causes of mortality and morbidity worldwide. However, the evidence on epidemiology, health economic, and patient-reported outcomes has not been systematically reviewed and published in Japan. This study aimed to assess the burden, treatment adherence and compliance, and serotype distribution associated with PDs in Japan.

METHOD

One hundred and eight studies were identified between January 2005 and June 2020. The identified studies were mostly regional and with a limited scale, clinical settings, and populations.

RESULTS

In 2013-2017, invasive PD incidence rates were 4.98-9.47/100,000 in <4-year-olds, 0.36/100,000 in 5-14-year-olds, 0.46/100,000 in 15-64-year-olds, and 1.50-5.38/100,000 in the elderly. The incidence of invasive PDs in children decreased from 24.6/100,000 in 2008 to 10.7/100,000 in 2013 after the introduction of PCV7 and further declined to 10.3/100,000 in 2014 after PCV13 was introduced. From 2014, the prevalence of PCV13 serotypes decreased across all age groups along with a decrease of PPV23 serotypes, but an increase of PPV23 serotypes not included in PCV13 among adults and the elderly. No study reported health-related quality-of-life data for PDs. In children, direct costs were 340,905-405,978 JPY (3,099-3,691 USD) per pneumococcal bacteraemia, 767,447-848,255 JPY (6,977-7,711 USD) per pneumococcal meningitis, and 79,000 JPY (718 USD) per pneumococcal acute otitis media episodes. In adults and the elderly, the direct cost of pneumococcal pneumonia was 348,280-389,630 JPY (3,166-3,542 USD). The average hospital stay length was 7.2-31.9 days in children, 9.0 days in adults and 9.0-28.7 days in adults and the elderly.

CONCLUSIONS

The epidemiological burden of PDs remains high in Japan, especially among children and the elderly with invasive PDs accounting for a very small proportion of all PDs. A significant impact of the PCV13 vaccine program was reported, while the PPV23's impact remains unclear. A substantial decrease in quality-adjusted life years in adults and the elderly and a high economic burden may exist.

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.

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.

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.

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.

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

PURPOSE

Among the pneumococcal proteins, pneumococcal surface protein A (PspA) is considered the most promising candidate for a serotype-independent vaccine. This study aimed to investigate the serotype, genetic diversity of PspA, lineage (genotype) and drug resistance traits of pneumococcal isolates from paediatric patients.

METHODOLOGY

A total of 678 non-invasive pneumococcal isolates obtained from June to November 2016 were analysed. All isolates were characterized for PspA families, serotypes and macrolide resistance genes. Seventy-one representative isolates of non-vaccine serotypes (NVTs) were genetically analysed for the clade-defining region (CDR) of PspA, as well as multi-locus sequence typing (MLST).

RESULTS

The detection rate of NVTs was 87.9 % (n=596), including dominant NVTs 15A (14.5 %, n=98), 35B (11.8 %, n=80), 15C (9.3 %, n=63) and 23A (9.0 %, n=61). Most isolates (96.6 %) possessed macrolide resistance genes erm(B) and/or mef(A/E). PspA families 1, 2 and 3 were detected in 42.3, 56.6 and 0.6 % of isolates, respectively. Nucleotide sequences of CDR showed high identity (90-100 %) within the same PspA clade, although the CDR identity among different PspA families ranged from 53 to 69 %. All isolates of NVTs 23A, 10A, 34, 24, 22F/22A, 33F, 23B and 38 were from PspA family 1, while NVTs 35B, 15C, 15B and 11A/11D isolates were from family 2. In contrast, genetically distinct PspAs were found in NVTs 6C and 15A. PspA family 3/clade 6 was detected in only NVT serotype 37 isolates assigned to ST447 and ST7970, showing the mucoid phenotype.

CONCLUSION

The present study revealed the predominance of PspA families 1 and 2 in NVTs, and the presence of family 3 in serotype 37.

Ten-Year Trends and Clinical Relevance of the Antimicrobial Resistance Genotype in Respiratory Isolates of Streptococcus pneumoniae

Background: Antimicrobial resistance of Streptococcus pneumoniae, especially against β-lactam antibiotics, is a global concern. We aimed to analyze a 10-year trend in the antimicrobial resistance genotype of respiratory isolates of S. pneumoniae and to clarify whether resistance genotypes were correlated with phenotypic drug susceptibility, pathogenicity, and host clinical background. Methods: Respiratory isolates of S. pneumoniae from 2003 to 2012 were analyzed with polymerase chain reaction for the presence of β-lactam resistance gene mutations on pbp1a, pbp2x, and pbp2b. Sixty-eight strains isolated from different patients in 2012 were particularly analyzed for the association between genotypes and clinical data. Results: The 10-year trend analysis showed a recent increase in gPRSP (genotypic penicillin-resistant S. pneumoniae) with all 3 β-lactam resistance genes (from 21.7 to 35.3% in 3 years) and a steady level of gPSSP (genotypic penicillin-susceptible S. pneumoniae) without any β-lactam resistance genes (13.2% in 2012). This resistance trend in genotypes was more prominent than resistance phenotypes determined with a drug susceptibility test. The probability of being a causative pathogen did not differ in gPSSP (55.6%), gPISP (genotypic penicillin-intermediate resistant S. pneumoniae; 54.3%), and gPRSP (54.2%). There was no significant difference in the ratio of patients who presented with respiratory failure in respiratory infection caused by gPSSP, gPISP, or gPRSP. Host clinical characteristics including age and gender were not different among resistance genotypes. Conclusions: There was no difference in pathogenicity or clinical background between gPSSP, gPISP, and gPRSP. Antimicrobial resistance in respiratory isolates of S. pneumoniae was more prevalent in genotypes than in phenotypes.

Serotype Replacement in Adult Pneumococcal Pneumonia after the Introduction of Seven-Valent Pneumococcal Conjugate Vaccines for Children in Japan: a Systematic Literature Review and Pooled Data Analysis

Streptococcus pneumoniae is the major causative agent for adult pneumonia. Following the introduction of pneumococcal conjugate vaccines (PCV) for children, serotype replacement has been reported in adult invasive pneumococcal diseases but has not been well studied for cases of pneumococcal pneumonia in adults in Asia. To investigate serotype replacement in adult pneumococcal pneumonia in Japan, we conducted a systematic review of the literature across 5 databases using terms, including pneumococcus, serotype, their synonyms, and derivatives. After the assessment of the identified articles, data on the pneumococcal serotype distribution among adult pneumonia cases were extracted from relevant studies. Twenty-two studies were reviewed, and 4 relevant articles were included in the pooled data analysis. The proportion of the 7-valent PCV (PCV7)-covered serotypes from before and after the introduction of PCV7 for children (－18.1%, p ＜ 0.001) significantly decreased; moreover, the proportions of serotypes covered by PCV13 but not PCV7 (＋9.9%, p = 0.003) and those covered by the 23-valent polysaccharide vaccine but not PCV7 (＋9.4%, p = 0.007) significantly increased. Serotype replacement occurred in adult cases of pneumococcal pneumonia following vaccination of children with PCV7 in Japan. Further nationwide surveillance is warranted to investigate serotype replacement in the post-PCV13 phase.

Macrolide Resistance in Streptococcus pneumoniae

Streptococcus pneumoniae is a common commensal and an opportunistic pathogen. Suspected pneumococcal upper respiratory infections and pneumonia are often treated with macrolide antibiotics. Macrolides are bacteriostatic antibiotics and inhibit protein synthesis by binding to the 50S ribosomal subunit. The widespread use of macrolides is associated with increased macrolide resistance in S. pneumoniae, and the treatment of pneumococcal infections with macrolides may be associated with clinical failures. In S. pneumoniae, macrolide resistance is due to ribosomal dimethylation by an enzyme encoded by erm(B), efflux by a two-component efflux pump encoded by mef (E)/mel(msr(D)) and, less commonly, mutations of the ribosomal target site of macrolides. A wide array of genetic elements have emerged that facilitate macrolide resistance in S. pneumoniae; for example erm(B) is found on Tn917, while the mef (E)/mel operon is carried on the 5.4- or 5.5-kb Mega element. The macrolide resistance determinants, erm(B) and mef (E)/mel, are also found on large composite Tn916-like elements most notably Tn6002, Tn2009, and Tn2010. Introductions of 7-valent and 13-valent pneumococcal conjugate vaccines (PCV-7 and PCV-13) have decreased the incidence of macrolide-resistant invasive pneumococcal disease, but serotype replacement and emergence of macrolide resistance remain an important concern.

Multidrug Resistance in Non-PCV13 Serotypes of Streptococcus pneumoniae in Northern Japan, 2014

Since the implementation of routine PCV13 immunization in Japan, nonvaccine serotypes (NVTs) have been increasing among clinical isolates of Streptococcus pneumoniae. In this study, susceptibility to 18 antibiotics was tested for all the 231 isolates with NVTs, which were collected from children <16 years of age in northern Japan in 2014 (July-November). High resistance rates were observed for macrolides (>90.9%), tetracycline (91.3%), and clindamycin (75.3%), while penicillin (PEN) nonsusceptibility (PNSP; MIC ≥0.12 μg/ml) was detected in 42.9% of the pneumococci [39.4%; PEN-intermediate S. pneumoniae (PISP), 3.5%; PEN-resistant S. pneumoniae (PRSP)]. All serotype 15A isolates were PRSP (MIC, ≥2 μg/ml) or PISP, and PNSP was prevalent in also serotypes 23A (96.9%), 6C (41%), and 35B (33.3%). Overall, 42.0% of the isolates showed multidrug resistance (MDR). Sequence types (STs) determined for 20 PNSP isolates with NVTs were ST63 (15A), STs 242 or 5832 (6C), STs 338 or 5242 (23A), and ST558 (35B). All the PNSP isolates possessed tet(M), and erm(B) or mefA(A/E), and 70% of them were gPRSP having three altered genes pbp1a, pbp2x, and pbp2b. Among alterations in transpeptidase-coding region of penicillin-binding proteins (PBPs), two substitutions of T₃₇₁S in the STMK motif and TSQF_574-577NTGY in PBP1a were common to all PRSP isolates. The present study showed the spread of PNSP in NVTs 15A, 23A, 6C, and 35B, and the emergence of the MDR international clone Sweden^15A-ST63 in northern Japan.

Emerging non-PCV13 serotypes of noninvasive Streptococcus pneumoniae with macrolide resistance genes in northern Japan

In Japan, the 7-valent pneumococcal conjugate vaccine (PCV7) was introduced to the nation's routine immunization program in April 2013 and was replaced by the 13-valent pneumococcal conjugate vaccine (PCV13) in November 2013. Distribution of serotypes and macrolide resistance genotypes was investigated for a total of 1097 (975 children, 122 adults) and 960 (873 children, 87 adults) clinical isolates of Streptococcus pneumoniae from noninvasive infections in Hokkaido (northern main island of Japan) in the routine immunization periods for PCV7 and PCV13 (April–October 2013 and November 2013–November 2014, respectively). Serotype was determined by sequential multiplex PCR and additional genetic analyses. Macrolide resistance genes erm(B) and mef(A/E) were detected by multiplex PCR. Although the most prevalent serotypes in children were 23A and 6C in the PCV7 period, after replacement with PCV13, 19A became the most common, followed by 6C, 15A and 23A. Among adults, serotype 3 was consistently the most frequent throughout the study periods. Compared with values from the pre-PCV7 routine immunization period, PCV7 serotypes decreased from 48.3 to 3.3% in the PCV13 period among children, while the rates of non-PCV13 serotypes (particularly 15A, 23A, 11A, 10A and 35B) increased from 39.7 to 75.1% (p < 0.001). In the PCV13 period, erm(B), mef(A/E) and both of these genes were detected in 75.8, 31.6 and 11.3% of all isolates, respectively. Serotype 19A accounted for 76.9% of the isolates with both the macrolide resistance genes, and emerging non-PCV13 serotypes 15A, 15C and 23A mostly harboured erm(B).

Serotype distribution and antimicrobial resistance of Streptococcus pneumoniae causing noninvasive diseases in a Children's Hospital, Shanghai

Background

Streptococcus pneumoniae, which cause noninvasive pneumococcal diseases, severely impair children's health. This study analyzed serotype distribution and antimicrobial resistance of S. pneumoniae from January 2012 to December 2012 in a Children's Hospital, Shanghai.

Methods

A total of 328 pneumococcal isolates were serotyped by multiplex sequential PCR and/or capsule-quellung reaction. The minimum inhibitory concentrations for 11 antimicrobial agents were determined by broth microdilution method.

Results

Among 328 strains, 19F (36.3%), 19A (13.4%), 6A (11.9%), 23F (11.0%), 14 (5.8%), 6B (5.2%), and 15B/C (4.3%) were the most common serotypes. The coverage rates of 7-, 10-, and 13-valent conjugate vaccines (PCV7, PCV10, and PCV13) were 58.2%, 58.2%, and 84.1%, respectively. Out of the isolates, 26 (7.9%) strains were penicillin resistant. Most of the strains displayed high resistance rate to macrolides (98.5% to erythromycin, 97.9% to azithromycin, and 97.0% to clindamycin).

Conclusions

The potential coverage of PCV13 is higher than PCV7 and PCV10 because of the emergence of 19A and there should be long-term and systematic surveillance for non-vaccine serotypes.

High prevalence of genotype 6E (putative serotype 6E) among noninvasive/colonization isolates of Streptococcus pneumoniae in northern Japan

Serogroup 6 of Streptococcus pneumoniae contains four established serotypes (6A-6D). Recently, putative serotype 6E (genotype 6E) was proposed as a novel type, which is cross-reactive with 6B-specific antiserum, but its capsular polysaccharide synthesis (cps) locus is genetically distinct from those of serotypes 6A and 6B. In the present study, prevalence of genotype 6E was analyzed by a newly designed multiplex polymerase chain reaction (PCR) for noninvasive or colonizing S. pneumoniae isolates in northern Japan assigned to serogroup 6 in our previous study by the sequential multiplex PCR developed by Pai et al. Among the isolates previously assigned to 6A and 6B, 2.2% (1/45) and 77.3% (140/181) of isolates, respectively, were revealed to have cps genes of genotype 6E. Eight 6E isolates selected for further analysis were found to have identical or highly similar sequences of cps genes (wzg, wzh, wze, wciN, wciP, and wzy) to those of strains previously reported as putative serotype 6E, and all the isolates were classified into sequence type 90 (ST90). Reanalysis of genetic traits on penicillin and macrolide resistance clarified significantly higher rates of three pbp mutations (gPRSP) and ermB in genotype 6E than in serotypes 6A and 6B. These findings suggested a need for detection of genotype 6E in the surveillance of S. pneumoniae serotypes.