Antibiotic resistance pattern, capsular types, and molecular characterization of invasive isolates of Streptococcus pneumoniae in the south of Tunisia from 2012 to 2018

Population structure, antibiotic resistance and molecular characteristics of Streptococcus pneumoniae causing invasive disease in Hubei, China

Introduction. This research sought to examine the epidemiological features, antibiotic resistance profiles and molecular characteristics of Streptococcus pneumoniae infections among hospitalized patients in Hubei, China, thus providing epidemiological evidence to inform the effective prevention and management of pneumococcal infections.Hypothesis/Gap Statement. Current research predominantly focuses on large urban centres, leaving a substantial knowledge gap regarding pneumococcal infections and resistance patterns in smaller city-level hospitals, such as those in Hubei Province.Aim. This study aimed to investigate the epidemiological features, antibiotic resistance profiles and molecular characteristics of invasive S. pneumoniae isolates from hospitalized patients in Tianmen City, Hubei, China.Methodology. S. pneumoniae strains were isolated from hospitalized patients at the First People's Hospital of Tianmen, Hubei, China, between September 2021 and September 2022. Epidemiological characteristics, serological typing and antimicrobial susceptibility of the isolates were analysed. Whole-genome sequencing was performed on the strains to identify resistance genes and virulence genes.Results. A total of 194 S. pneumoniae isolates were analysed, with 90% (174/194) from community-acquired pneumonia cases. Respiratory samples accounted for 96% of isolates, and children under 5 years old comprised 78% of cases. Seasonal variation was observed, with infections peaking in winter and spring. Antibiotic resistance analysis revealed notable age-related differences: penicillin resistance was 12.37% overall but absent in elderly patients. Ceftriaxone showed no resistance, whereas cefotaxime and meropenem exhibited higher resistance in children than in the elderly. Multilocus sequence typing identified 56 sequence types (STs), with ST271 (24.2%) being the most prevalent. Serotyping revealed 24 serotypes, with 19F (27.8%, 54/194) as the dominant type. Phylogenetic analysis showed two major clades, with strong correlations between serotype and ST distribution. Resistance genes ermB and tetM were highly prevalent (99.0% and 97.9%, respectively). Comparative genomic analysis demonstrated significantly higher resistance rates in ST271 strains than in non-ST271 strains, particularly for cefotaxime (76.60% vs. 4.76%) and meropenem (53.19% vs. 14.29%). ST271 strains predominantly expressed serotype 19F, accounting for 87% (47/54) of all serotype 19F isolates, carrying distinct resistance and virulence genes, highlighting its clinical significance.Conclusion. This study highlights a significant burden of invasive S. pneumoniae infections, predominantly affecting children under five, with notable peaks during winter and spring. ST271, predominantly associated with serotype 19F, exhibited significantly higher antibiotic resistance rates compared with other strains, indicating the necessity of tailored antibiotic strategies and robust local antibiotic stewardship programmes. The widespread presence of resistance and virulence genes underscores the evolutionary adaptability of S. pneumoniae, emphasizing the importance of continuous genetic surveillance. The current pneumococcal vaccination (13-valent pneumococcal conjugate vaccine) coverage of the predominant serotype provides a favourable outlook for disease control.

Single nucleotide polymorphisms and penicillin non-susceptibility among invasive Streptococcus pneumoniae from Vietnam and India: Insights from a comparative genomics study

OBJECTIVES

Streptococcus pneumoniae (S. pneumoniae) is a significant cause of global morbidity and mortality across all age groups. Antimicrobial resistance (AMR), particularly penicillin resistance, is a significant treatment challenge. The study investigates AMR patterns among S. pneumoniae isolates from Vietnam, a country with high penicillin non-susceptibility, and India which in comparison has lower penicillin non-susceptibility. The present study focuses on penicillin resistance-associated genes and single nucleotide polymorphisms (SNPs), that contribute to pathogenicity.

METHODS

Invasive S. pneumoniae belonging to serotypes 23F (n = 13) and 19F (n = 20) genome sequences from Vietnam (n = 13) and India (n = 20) were retrieved and annotated to identify core genes. These genes were screened for antimicrobial resistance using the database. The genome sequences were mapped to a reference genome to detect the gene variants and were analysed for identifying specific mutations that contribute to pathogenicity.

RESULTS

Annotations identified pbp1a, pbp2b, and pbp2x (pbpX) as relevant AMR genes. In Vietnam, pbpX was a core gene, with 41 SNPs detected, of which 7 were deleterious mutations contributing to penicillin resistance. In contrast, pbpX was completely absent in the Indian genomes analysed.

CONCLUSIONS

The current study highlights the genetic basis of penicillin non-susceptibility among invasive S. pneumoniae serotypes 23F and 19F and focuses on regional variations in resistance between India and Vietnam. The pbpX was identified as a core gene among penicillin-resistant pneumococci in Vietnam. In India, the absence of pbpX highlights genomic diversity, distinct from the uniformity observed in Vietnamese genomes. The study further predicts that deleterious SNPs are associated with pathogenicity.

The Evolution of the Antimicrobial Resistance of Streptococcus pneumoniae in Tunisia: A Multicentric Analysis over Two Decades (2000-2019)

Background/Objectives: Streptococcus pneumoniae is a leading respiratory pathogen responsible for significant morbidity and mortality, particularly among vulnerable populations. Understanding its antimicrobial resistance patterns and serotype distribution is crucial for guiding treatment and prevention strategies. This study aims to examine these trends in S. pneumoniae isolates from Tunisia over a two-decade period (2000-2019). Methods: A retrospective time series analysis was conducted on data (n = 4284) gathered from eight university hospital centers across Tunisia. Antimicrobial susceptibility testing was performed according to the European Committee on Antimicrobial Susceptibility Testing (EUCAST) guidelines. Pneumococcal serotypes were determined for a subset of samples from 2012 to 2019 (n = 903) using multiplex PCR and latex agglutination. Results: Penicillin G resistance decreased from 9-13.7% during 2000-2002 to 4.3% by 2019, while amoxicillin resistance increased until reaching 10% in 2019. Erythromycin resistance initially increased before stabilizing between 61.9% and 66.3% during 2014-2019, whereas tetracycline resistance declined from 2000 to 2008 and fluctuated around 40% during 2009-2019. Levofloxacin resistance did not exceed 1.2% throughout the study period. The most prevalent serotypes were 14, 19F, 19A, 23F, 3, 6B, 6A, and 9V. Among them, serotype 3 was the most susceptible overall. Serotypes 23F, 14, 9V, and 6B displayed the highest levels of multi-drug resistance. Conclusions: Penicillin G (high-dosage), cefotaxime, and levofloxacin are still effective against most S. pneumoniae strains in Tunisia, while erythromycin and tetracycline are not reliable options for treating pneumococcal infections. Alarming resistance rates among prevalent serotypes, except serotype 3, underscore the need for preventive measures, rational antibiotic use, and ongoing surveillance.

Detection of Macrolide-Resistant Streptococcus pneumoniae Genes and Its Clinical Outcomes in a Tertiary Teaching Hospital in Malaysia

Background

Streptococcus pneumoniae is one of the leading causes of mortality and morbidity worldwide. The dramatic increase in in-vitro resistance of antimicrobial agents, particularly beta-lactams and macrolides, makes pneumococcal infections difficult to treat. The aim of this study was to describe the drug resistance rate, assess the prevalence of macrolide-resistant genes and review the clinical complications of pneumococcal infections among patients presented to Hospital Universiti Sains Malaysia (HUSM), Kelantan, Malaysia.

Methods

This is a descriptive cross-sectional study. All S. pneumoniae isolates collected from clinical specimens within a 1-year period were subjected to selected antimicrobial susceptibility testing using E-test strips. Polymerase chain reaction (PCR) analysis was conducted to detect macrolide-resistant determinants. The patient's clinical data were obtained from clinical notes.

Results

A total of 113 patients with a positive growth of S. pneumoniae were included in the study. The most common predisposing factors among them were bronchopulmonary diseases (15.9%). The penicillin-resistant rate was 7.1%, with minimal inhibitory concentration (MIC) ranging between 0.012 μg/mL and >32 μg/mL, and the erythromycin-resistant rate was 26.5%, with a MIC range of 0.03 μg/mL-> 256 μg/mL. Most of the erythromycin-resistant isolates were found to have the mef(A) gene (50.4%) and the erm(B) gene (20%); 16.7% had a combination of genes mef(A) and erm(B), and 13.3% had none of the two genes. Community-acquired pneumonia is the predominant type of pneumococcal infection. There was no significant association between the presence of macrolide resistance determinants and mortality (P = 0.837) or complications (P > 0.999 for empyema and cardiac complication; P = 0.135 for subdural abscess).

Conclusion

The majority of erythromycin-resistant isolates were found to have the mef(A) gene, followed by the erm(B) gene and a combination of genes mef(A) and erm(B).

High Prevalence of Novel Sequence Types in Streptococcus pneumoniae That Caused Invasive Diseases in Kuwait in 2018

BACKGROUND

Multilocus sequence typing (MLST) is used to gain insight into the population genetics of bacteria in the form of sequence type (ST). MLST has been used to study the evolution and spread of virulent clones of Streptococcus pneumoniae in many parts of the world. Such data for S. pneumoniae are lacking for the countries of the Arabian Peninsula, including Kuwait.

METHODS

We determined the STs of all 31 strains of S. pneumoniae from invasive diseases received at a reference laboratory from various health centers in Kuwait during 2018 by MLST. The relationship among the isolates was determined by phylogenetic analysis. We also determined the serotypes by Quellung reaction, and antimicrobial susceptibility by Etest, against 15 antibiotics belonging to 10 classes.

RESULTS

There were 28 STs among the 31 isolates, of which 14 were new STs (45.2%) and 5 were rare STs (16.1%). Phylogenetic analysis revealed that 26 isolates (83.9%) were unrelated singletons, and the Kuwaiti isolates were related to those from neighboring countries whose information was gleaned from unpublished data available at the PubMLST website. Many of our isolates were resistant to penicillin, erythromycin, and azithromycin, and some were multidrug-resistant. Virulent serotype 8-ST53, and serotype 19A with new STs, were detected.

CONCLUSIONS

Our study detected an unusually large number of novel STs, which may indicate that Kuwait provides a milieu for the evolution of novel STs. Novel STs may arise due to recombination and can result in capsular switching. This can impact the effect of vaccination programs on the burden of invasive pneumococcal disease. This first report from the Arabian Peninsula justifies the continuous monitoring of S. pneumoniae STs for the possible evolution of new virulent clones and capsular switching.

Monitoring Over a Decade in the Serotype Prevalence of Streptococcus pneumoniae in Iran: A Systematic Review and Meta-analysis

BACKGROUND

There is no comprehensive information about the circulating serotypes of Streptococcus pneumoniae in Iran in recent years. This study aimed to summarize information about the changes over a decade in the serotype prevalence of S. pneumoniae in Iran.

METHODS

We performed a comprehensive search in PubMed/Medline, Web of Science, Science Direct, and the Iranian Database, such as Magiran and SID, from January 2011 to February 2023. The systematic process, in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA), was carried out by two researchers who were both independent and calibrated. Statistical analyses were carried out using Comprehensive Meta-Analysis software. Identifying and measuring heterogeneity were done using I2 and the chi-square test. Finally, Begg's rank correlation test was used in combination with a funnel plot to evaluate any possible publication bias.

RESULTS

The search returned 16 relevant results, with a total of 1575 isolates. Of those studies, eight studies reported the distribution of S. pneumoniae serotypes among patients, three studies among healthy individuals, and five studies among both groups. As the meta-analysis revealed, the most common serotypes were 23F (n = 299, 14.1% [95% CI: 9.7-19.9]; I2 = 84.3%; P<0.001 for heterogeneity), 19F (n = 221, 13.4% [95% CI: 9.9-17.9; I2 = 76.7%; P<0.001 for heterogeneity]), and 19A (n = 102, 8.7% [95% CI: 6.5-11.7; I2 = 54.3%; P<0.001 for heterogeneity]). Moreover, Begg's test (P = 0.160, 0.173, and 0.176 for 23F, 19F, and 19A, respectively) showed no evidence of publication bias.

CONCLUSION

Based on our pooled results, the majority of the serotypes of pneumococci in the Iranian population were 23F, 19F, and 19A, respectively, over the last decade. The findings can be valuable in selecting effective pneumococcal vaccine candidates and targeted antibiotics in Iranian patients.