Phenotypic and molecular characterization of Streptococcus pneumoniae in pre-conjugate vaccine era: A Chinese hospital-based retrospective study

Serotype distribution and antimicrobial resistance of Streptococcus pneumoniae in China among children under 14 years of age post-implementation of the PCV13: a systematic review and meta-analysis (2017-2024)

BACKGROUND

Streptococcus pneumoniae (S. pneumoniae) is a major cause of morbidity and mortality in children worldwide, and its evolving serotype distribution and antibiotic resistance patterns are of global health concern. This meta-analysis aims to investigate the serotype distribution and antimicrobial resistance of S. pneumoniae after the introduction of pneumococcal conjugate vaccine 13-valent (PCV13) as a self-funded vaccine in Chinese pediatric populations.

METHODS

We systematically reviewed studies published between 2017 and 2024 that focused on S. pneumoniae serotypes isolated from children under 14 years old in mainland China. Data sources included PubMed, Embase, Web of Science, CNKI, Wanfang, and SinoMed. The findings were synthesized using either a fixed-effects or random-effects model.

RESULTS

Our meta-analysis included 12 studies, identifying the most common serotypes of S. pneumoniae were 19 F, 19 A, 23 F, 14, 6B and 6 A. Vaccine serotype coverage rates were 52.17% (95%CI: 44.91-59.42%) for PCV10, 74.77% (95%CI: 71.53-78.01%) for PCV13, 76.72% (95%CI: 75.37-78.07%) for PCV15 and 92.90% (95%CI: 92.09-93.71%) for PPSV23. Antimicrobial resistance was most pronounced for erythromycin at 93.73% (95%CI: 90.58-96.88%), followed by azithromycin, tetracycline, clindamycin, and sulfamethoxazole. Serotype prevalence and vaccine coverage varied regionally and by strain type.

CONCLUSION

The distribution of S. pneumoniae serotypes and their antibiotic resistance profiles in children under 14 years in mainland China have remained relatively stable post-PCV13 introduction as a self-funded vaccine. The results support continued use and possible expansion of PCV13 immunization and highlight the importance of ongoing surveillance and vaccine development to cover all prevalent serotypes in China.

Serotype, antibiotic susceptibility and whole-genome characterization of Streptococcus pneumoniae in all age groups living in Southwest China during 2018-2022

Background

Streptococcus pneumoniae is a common pathogen that colonizes the human upper respiratory tract, causing high morbidity and mortality worldwide. This study aimed to investigate the prevalence status of S. pneumoniae isolated from patients of all ages in Southwest China, including serotype, antibiotic susceptibility and other molecular characteristics, to provide a basis for clinical antibiotic usage and vaccine development.

Methods

This study was conducted from January 2018 to March 2022 at West China Hospital, West China Second University Hospital, First People's Hospital of Longquanyi District (West China Longquan Hospital), Meishan Women and Children's Hospital (Alliance Hospital of West China Second University Hospital) and Chengdu Jinjiang Hospital for Women and Children Health. Demographic and clinical characteristics of 263 pneumococcal disease (PD) all-age patients were collected and analyzed. The serotypes, sequence types (STs), and antibiotic resistance of the strains were determined by next-generation sequencing, sequence analysis and the microdilution broth method.

Results

The most common pneumococcal serotypes were 19F (17.87%), 19A (11.41%), 3 (8.75%), 23F (6.46%) and 6A (5.70%). Coverage rates for PCV10, PCV13, PCV15, PCV20 and PCV24 were 36.12, 61.98, 61.98, 63.12 and 64.26%, respectively. Prevalent STs were ST271 (12.55%), ST320 (11.79%), ST90 (4.18%), ST876 (4.18%) and ST11972 (3.42%). Penicillin-resistant S. pneumoniae (PRSP) accounted for 82.35 and 1.22% of meningitis and nonmeningitis PD cases, respectively. Resistance genes msrD (32.7%), mefA (32.7%), ermB (95.8%), tetM (97.3%) and catTC (7.6%) were found among 263 isolates. Most isolates showed high resistance to erythromycin (96.96%) and tetracycline (79.85%), with more than half being resistant to SXT (58.94%). A few isolates were resistant to AMX (9.89%), CTX (11.03%), MEN (9.13%), OFX (1.14%), LVX (1.14%) and MXF (0.38%). All isolates were susceptible to vancomycin and linezolid.

Conclusion

Our study provides reliable information, including the prevalence, molecular characterization and antimicrobial resistance of S. pneumoniae isolates causing pneumococcal diseases in Southwest China. The findings contribute to informed and clinical policy decisions for prevention and treatment.

Molecular epidemiology of Streptococcus pneumoniae isosslated from children with community-acquired pneumonia under 5 years in Chengdu, China

Streptococcus pneumoniae (S. pneumoniae) is one of the most common community-associated pathogens responsible for pneumonia in children. This retrospective study aimed to investigate the molecular characteristics of S. pneumoniae isolated from children with community-acquired pneumonia (CAP) under 5 years in Chengdu, China. Molecular characteristics of S. pneumoniae included serotype and virulence factor performed by using PCR method and sequence types (STs) determined by sequencing seven housekeeping genes. In addition, the potential relationships between molecular characteristics were depicted by minimum spanning tree and correspondence analysis. The prevailing serotypes were 19F (18.52%), 6B (17.59%), 19A (13.89%), 6A (6.48%) and 23F (5.56%) among 108 isolates. The overall coverage rates of 7-valent, 10-valent, 13-valent, 15-valent and 20-valent pneumococcal conjugate vaccines (PCVs) were 47.32, 48.1, 75, 75 and 78.7%, respectively. Meanwhile, the coverage rates of PCV13 among the isolates from CAP patients aged <1 year were high up to 84.2%. MLST analysis results showed that there were 56 different STs identified, of which the dominant STs were ST271 (22.22%) and ST320 (12.04%). Five international clones among STs were observed, including Spain23F-1, Spain6B-2, Taiwan19F-14, Netherlands3-31 and Denmark14-32. Additionally, most of the isolates carried ply, psaA, nanA, pavA, piaA and CC271 isolates expressed more of nanA than non-CC271 isolates. Moreover, there were strong relevant relationships among STs, serotypes and virulence factors. Considering serotypes and virulence factors together can be used as the foundation for the formulation of vaccine strategy.

Identification and molecular characterization of penicillin-nonsusceptible Streptococcus pneumoniae isolates recovered from invasive infections in a pre-pneumococcal vaccine era

BACKGROUND

Given the significant role of penicillin-nonsusceptible Streptococcus pneumoniae in inducing severe infectious diseases, identifying serotypes and genotypes that can mediate antimicrobial resistance has become a pillar of treatment strategies. This study aims to determine the correlation between the minimum inhibitory concentration of antimicrobial agents and amino acid mutations in penicillin-binding proteins. Moreover, molecular serotyping and multiple-locus variable number tandem repeat analysis typing were first-ever performed to characterize the invasive penicillin-nonsusceptible S. pneumoniae isolates in Iran.

METHODS

Of 149 isolates, antimicrobial susceptibility tests were performed against penicillin, ceftriaxone, and cefotaxime by the MIC Test Strip, and sequence analysis of the pbp genes was performed through PCR-sequencing method. All penicillin-nonsusceptible S. pneumoniae isolates were serotyped and genotyped by sequential multiplex PCR and multiple-locus variable-number tandem repeat analysis, respectively.

RESULTS

Among pneumococcal isolates, 53 isolates were classified as penicillin-nonsusceptible S. pneumoniae, of which 38 (71.7%) and 15 (28.3%) were resistant and intermediate to penicillin, respectively. Furthermore, ceftriaxone- and cefotaxime-nonsusceptible pneumococci constituted 33 (62.2%) and 29 cases (54.7%), respectively. Of note, there were 8 and 41 different serotypes and multiple-locus variable-number tandem repeat analysis types, respectively.

CONCLUSIONS

Due to the increasing resistance to antimicrobial agents, the most efficient approach to preventing pneumococcal infection mortality as vaccine-preventable diseases is focusing on wide-spectrum vaccination. Based on our findings, the 13-valent pneumococcal conjugate vaccine could considerably reduce the incidence of invasive pneumococcal diseases due to the high rate of serotype coverage.

Molecular Characterization Based on Whole-Genome Sequencing of Streptococcus pneumoniae in Children Living in Southwest China During 2017-2019

Background

Streptococcus pneumoniae is an important pathogen causing high morbidity and high mortality in children and undergoes frequent recombination for capsule switching to neutralize the 13-valent pneumococcal conjugate vaccine (PCV13). This study aimed to investigate the prevalence, and molecular characteristics including serotypes and antibiotic susceptibility of S. pneumoniae isolated from children living in Southwest China from 2017 to 2019 to facilitate the selection of effective vaccine formulations and appropriate antibiotic treatment regimens.

Methods

This study was conducted at West China Second University Hospital (Chengdu, Sichuan Province, China), Zunyi Medical University Third Affiliated Hospital/First People's Hospital of Zunyi (Zunyi, Guizhou Province, China) and Chengdu Jinjiang District Maternal and Child Healthcare Hospital (Chengdu, Sichuan Province, China). Demographic and clinical characteristics of children infected with S. pneumoniae were collected and analysed. Next-generation sequencing and sequence analysis were used to determine the serotypes, sequence types, antibiotic resistance and potential protein vaccine target genes of the pneumococcal isolates. The coverage rate provided by PCV13 was estimated by calculating the percentage of the specific serotypes that were specifically the PCV13-included serotypes. Antimicrobial susceptibility was determined by the microdilution broth method.

Results

The most prevalent pneumococcal serotypes were 19F (25.8%), 19A (14.1%), 6B (12.5%), 6A (9.4%) and 14 (7.8%). The predominant STs were ST271 (23.3%), ST320 (15.5%) and ST90 (8.6%), dominated by the clonal complex Taiwan^19F-14 (39.1%). The coverage rate of PCV13 was 77.3% in all the isolates, with relatively higher values in invasive isolates (86.4%). Over the decade, the rates of resistance to penicillin, amoxicillin and cefotaxime were 5.6%, 5.3% and 5.1%, respectively, with significantly higher values in invasive isolates (22.4%, 14.9% and 11.9%). Almost all the isolates were resistant to erythromycin (99.1%) and clindamycin (95.9%). All isolates carried virulence-related genes, including ply, psaA, piaA, piuA, phtE, nanA, pepO, danJ, pvaA, clpP, pcsB, stkP, potD, and strH. The carriage of virulence and resistance genes varied among serotypes and clades, with serotype 19F/ST271 showing higher resistance to antibiotics and being more likely to carry pilus genes and other virulence genes.

Conclusion

These data provide valuable information for the understanding of pneumococcal pathogenesis, antimicrobial resistance and the development of protein-based vaccines against pneumococcal infection.

Genotypic and phenotypic characteristics of Streptococcus pneumoniae from community-acquired pneumonia patients and healthy asymptomatic participants in Sichuan province, China

Background

Streptococcus pneumoniae (S. pneumoniae) is the common cause of community-acquired pneumonia (CAP) and is also found in the upper respiratory tract of healthy people. Hence, the study aimed to compare the serotypes, virulence/pili genes, and antibiotic susceptibility of S. pneumoniae from healthy asymptomatic participants and CAP patients.

Methods

Streptococcus pneumoniae were retrospectively collected from health asymptomatic participants and CAP patients in Sichuan, China. The serotypes were tested by multiplex polymerase chain reaction (PCR) or Quellung reaction. Antibiotic susceptibility testing was performed using the broth microdilution method. The molecular epidemiology of S. pneumoniae was analyzed by multilocus sequence typing (MLST). Additionally, the presence of virulence/pili genes were detected using PCR.

Results

A total of 83 pneumococcal isolates were collected in the current study. Of these, 52 and 31 isolates were from healthy asymptomatic participants and CAP patients, respectively. Most of S. pneumoniae were resistant to erythromycin (ERY), clindamycin (CLI), tetracycline (TET) and trimethoprim-sulfamethoxazole (SXT). 90.4% isolates were classified as multidrug resistant (MDR). The predominant serotypes were 3, 19F and 19A in the CAP carriers, whereas 3, 6 and 19F were the main serotypes among the asymptomatic carriers. The overall coverage rates of pneumococcal conjugate vaccine (PCV) 10 and PCV13 serotypes were 34.9% and 66.3%, respectively. The predominant sequence types (STs) were ST271, ST320, and ST3397. There were significant differences in some resistance and virulence characteristics between CAP patients and asymptomatic carriers. Additionally, clonal complex (CC) 271 strains had higher percentage in resistance to cefuroxime (CXM) and cefotaxime (CEF), meropenem (MER) and cefepime (CFP), which mainly carried the rlrA and sipA genes.

Conclusions

High coverage rate of PCV13 and high prevalence of MDR indicated the necessity to expand immunization with PCV13 and rationally use the antibiotics in Sichuan, China. Importantly, long-term surveillance should be conducted to assess effectiveness brought by vaccines. Our findings may supply new guidance for developing new pneumococcal vaccines.

Molecular epidemiology of Streptococcus pneumoniae isolated from pediatric community-acquired pneumonia in pre-conjugate vaccine era in Western China

BACKGROUND

Streptococcus pneumoniae (S. pneumoniae) is one of the most common pathogens which can cause morbidity and mortality in pediatric infections worldwide. This study aimed to describe the phenotypic and molecular characteristics of community-acquired pneumonia (CAP)-causing S. pneumoniae recovered from children in Western China.

METHODS

We retrospectively enrolled pediatric patients younger than 5 years diagnosed with CAP. All 419 S. pneumoniae isolates were tested for antibiotic susceptibility, serotypes, virulence genes, resistance genes, and sequence types. The potential relationships between molecular characteristics were tested by correspondence analysis.

RESULTS

Most of S. pneumoniae isolates were resistant to erythromycin, tetracycline, clindamycin and trimethoprim-sulfamethoxazole, with 93.8% isolates classified as multidrug resistant. The dominant STs were ST271 (30.8%) and ST320 (12.2%), while the prevailing serotypes were 19F (46.8%), 6B (11.5%), 23F (9.5%) and 19A (9.3%). The coverage rates of PCV-7 and PCV-13 were 73.03% and 86.16%, while the coverage rates of PCV13 among children aged < 1 year and 1-2 years were high in 93.18% and 93.62%. We also observed that CC271 expressed more of mef (A/E), lytA, rlrA and sipA than non-CC271 isolates. Moreover, there were strong corresponding relationships between molecular characteristics.

CONCLUSIONS

The high coverage rate of PCV13 suggests the necessity of introducing the PCV13 vaccine in Western China. Our findings underscore the value of monitoring multiple molecular characteristics to provide new guidance for developing future pneumococcal vaccines.

Molecular characterization, antibiotic resistance pattern and capsular types of invasive Streptococcus pneumoniae isolated from clinical samples in Tehran, Iran

Background

Streptococcus pneumoniae causes serious infections worldwide. The aim of this study was to determine the molecular characteristic, antibiotic resistance pattern and capsular types of invasive S. pneumoniae in Tehran, Iran.

Results

Of the 44 pneumococcal invasive isolates, 39 (89%) were isolated from children and 5 (11%) from adults. The results show that all pneumococcal isolates were susceptible to linezolid but had varying resistance to trimethoprim-sulfamethoxazole (86%), erythromycin (73%), tetracycline (66%), clindamycin (43%), penicillin (16%), chloramphenicol (14%) and levofloxacin (2%). The range of erythromycin, tetracycline and penicillin MICs were 2 - ≥ 256 μg/mL, 4 - ≥ 48 μg/mL, and 0.047 - ≥ 256 respectively. All of the penicillin resistant isolates were multidrug resistant (MDR) and in addition to penicillin were resistant to tetracycline, erythromycin and trimethoprim-sulfamethoxazole. The most common capsular types detected in 64% of the pneumococcal isolates was 6A/B, 19A, 15A, 23F. The multilocus sequence typing (MLST) of 10 pneumococcal isolates revealed 9 different sequence types (STs), including ST 15139 (capsular type 19A) and ST 15140 (capsular type 23F), which have not previously been reported.

Conclusions

The study revealed that the S. pneumoniae isolates belonged to diverse capsular types and clones with high rate of resistance to erythromycin, tetracycline, and penicillin.

Phenotypic and molecular characterization of macrolide resistance mechanisms among Streptococcus pneumoniae isolated in Tunisia

Introduction. Streptococcus pneumoniae is responsible for many community infections, with the main ones being pneumonia and meningitis. Pneumococcus has developed increased resistance to multiple classes of antibiotics. The evolution of antibiotic resistance in pneumococcus was influenced by changes in serotype distribution under vaccine selection pressure.Aim. The aim of this study was to determine the genes involved in macrolide resistance, the antimicrobial susceptibility, the serotype distribution and the spread of international antibiotic-resistant clones among clinical isolates of S. pneumoniae.Methodology. We investigated 86 erythromycin-resistant S. pneumoniae strains isolated from respiratory (n=74) or non-respiratory (n=12) samples in Tunisia. Antimicrobial susceptibility was tested using the disk diffusion method. Macrolide-resistant strains were analysed by polymerase chain reaction (PCR) for ermA, ermB, mefA and msrD. We also investigated the macrolide resistance mechanisms in eight isolates (9.3%) by sequencing the L4 and L22 riboprotein-coding genes, plus relevant segments of the three 23S rRNA genes. Capsular serotypes were detected by multiplex PCR. Sequence types (STs) were explored using multilocus sequence typing (MLST).Results. Among the 86 studied strains, 70 (81.4 %) were resistant to penicillin G. The prevalent serotypes were 19F, 14, 19A and 23F. We observed that the cMLSB phenotype (66/86, 76.7%) was the most common in these pneumococci. In addition, ermB was the most frequent resistance gene. No mutation in ribosomal protein L22 or L4 or 23S rRNA was detected. Overall, 44 STs were identified in this study, including 16 that were described for the first time. Resistance to lincomycin, tetracycline and trimethoprim/sulfamethoxazole was observed in 55 (64 %), 34 (39.5 %) and 31 (36 %) isolates, respectively. Furthermore, an increase in fluoroquinolone use in particular may lead to the emergence of levofloxacin-resistant strains. Multidrug resistance was observed in 83 isolates (96.5%). Three global antibiotic-resistant clones were identified: Denmark¹⁴ ST230, Portugal^19F ST177 and Spain^9V ST156.Conclusion. This study shows that macrolide resistance among S. pneumoniae isolated in Tunisia is mainly related to target site modification. Our observations demonstrate a high degree of genetic diversity and capsular types among strains resistant to macrolides.

Changes in serotype distribution and antimicrobial resistance of Streptococcus pneumoniae isolates from adult patients in Asia: Emergence of drug-resistant non-vaccine serotypes

This study was performed to investigate the serotype distribution and antimicrobial susceptibility of Streptococcus pneumoniae in Asian countries. A prospective surveillance study on S. pneumoniae collected from adult patients (≥50 years old) with invasive pneumococcal disease or community-acquired pneumonia was performed at 66 hospitals in Asian countries (Korea, China, Malaysia, Singapore, the Philippines, and Thailand) in 2012-2017. Serotyping and antimicrobial susceptibility tests of 850 pneumococcal isolates were performed. The proportions of isolates with serotypes covered by 13-valent pneumococcal conjugate vaccine (PCV13) were 37.0% in Korea, 53.4% in China, 77.2% in Malaysia, 35.9% in the Philippines, 68.7% in Singapore, and 60.2% in Thailand. Major serotypes were 19F (10.4%), 19A (10.1%), and 3 (8.5%) in 2012-2017, with different serotype distributions in each country. Macrolide resistance in pneumococci was high (66.8%) and prevalence of multidrug resistance (MDR) also remained high (50.8%). MDR non-PCV13 serotypes such as 11A, 15A, 35B, and 23A have emerged in Asian countries. This study showed the persistent prevalence of 19F and 19A with a noteworthy increase of certain non-PCV13 serotypes in Asian countries. High prevalence of macrolide resistance and MDR was also found in pneumococcal isolates. These data emphasize the need for continued surveillance of pneumococcal epidemiology in Asia in the post-pneumococcal vaccine era.

Epidemiology Characteristics of Streptococcus pneumoniae From Children With Pneumonia in Shanghai: A Retrospective Study

Background: Streptococcus pneumoniae is the most common pathogen causing death in children under 5 years old. This retrospective surveillance aimed to analyze serotype distribution, drug resistance, virulence factors, and molecular characteristics of pneumonia isolates from children in Shanghai, China. Methods: A total of 287 clinical pneumococcal isolates were collected from January to December in 2018 and were divided into community-acquired pneumonia (CAP) and healthcare-associated pneumonia (HAP) two groups according to where someone contracts the infection. All isolates were serotyped by multiplex sequential PCR and antimicrobial susceptibility testing was performed using E-test or disk diffusion method. The molecular epidemiology was analyzed using multilocus sequence typing and seven housekeeping genes were sequenced to identified the sequence types (STs). In addition, we investigated the presence of virulence genes via PCR. Results: The most common serotypes were 19F, 6A, 19A, 23F, 14, and 6B, and the coverage rates of the 7-, 10- and 13-valent pneumococcal conjugate vaccines were 58.9, 58.9, and 80.5%, respectively. More PCV13/non-PCV7 serotypes and higher rate of penicillin non-susceptible S. pneumoniae were seen in HAP. Molecular epidemiological typing showed a high level of diversity and five international antibiotic-resistant clones were found, including Taiwan^19F-14, Spain^23F-1, Spain^6B-2, Taiwan^23F-15 and Sweden^15A-25. No significant difference was observed in the presence of virulence genes among the isolates obtained from CAP and HAP. All of the S. pneumoniae isolates carried lytA, ply, psaA, pavA, spxB, htrA, and clpP, and the carriage rate of nanA and piaA were 96.2 and 99.0%. Conversely, cps2A, cbpA, and pspA were present in 33.8-44.3% of the isolates. Conclusions: Serotype changes and emerging multidrug-resistant international clones were found in current study. lytA, ply, psaA, pavA, spxB, htrA, and clpP may be good protein vaccine candidates. Long-term high-quality surveillance should be conducted to assess impact and effectiveness brought by vaccines, and provide a foundation for prevention strategies and vaccine policies.