Novel pneumococcal capsule type 33E results from the inactivation of glycosyltransferase WciE in vaccine type 33F

Optimizing nanopore adaptive sampling for pneumococcal serotype surveillance in complex samples using the graph-based GNASTy algorithm

Serotype surveillance of Streptococcus pneumoniae (the pneumococcus) is critical for understanding the effectiveness of current vaccination strategies. However, existing methods for serotyping are limited in their ability to identify co-carriage of multiple pneumococci and detect novel serotypes. To develop a scalable and portable serotyping method that overcomes these challenges, we employed nanopore adaptive sampling (NAS), an on-sequencer enrichment method that selects for target DNA in real-time, for direct detection of S. pneumoniae in complex samples. Whereas NAS targeting the whole S. pneumoniae genome was ineffective in the presence of nonpathogenic streptococci, the method was both specific and sensitive when targeting the capsular biosynthetic locus (CBL), the operon that determines S. pneumoniae serotype. NAS significantly improved coverage and yield of the CBL relative to sequencing without NAS and accurately quantified the relative prevalence of serotypes in samples representing co-carriage. To maximize the sensitivity of NAS to detect novel serotypes, we developed and benchmarked a new pangenome-graph algorithm, named GNASTy. We show that GNASTy outperforms the current NAS implementation, which is based on linear genome alignment, when a sample contains a serotype absent from the database of targeted sequences. The methods developed in this work provide an improved approach for novel serotype discovery and routine S. pneumoniae surveillance that is fast, accurate, and feasible in low-resource settings. Although NAS facilitates whole-genome enrichment under ideal circumstances, GNASTy enables targeted enrichment to optimize serotype surveillance in complex samples.

Intra-serotype variation of Streptococcus pneumoniae capsule and its quantification

Streptococcus pneumoniae (Spn) is a leading respiratory pathogen that depends on a thick layer of capsular polysaccharide (CPS) to evade immune clearance. Disease prevention by CPS-based vaccines is limited because of the species' high genome plasticity and ability to express over 100 different capsule types (serotypes). Generally, intra-serotype variations in capsulation are overlooked, despite the genetic variability of the bacterium. This oversight may result from a lack of standardized, reliable, and easily available methodology to quantify capsulation. Here, we have modified two methods to analyze the Spn capsule: immunoblot quantification of CPS in bacterial lysates and light microscopy to assess capsule thickness. Two assays were used because each measures distinct aspects of capsulation that could be differentially affected by the density of CPS. Quantification of either CPS amount or capsule thickness predicted the effectiveness of immune serum in opsonophagocytic killing assays for isogenic strains. Our standardized approaches both revealed significant differences in both CPS amount and capsule thickness among clinical isolates of the same serotype, challenging the assumption that intra-serotype capsulation is a conserved feature. As expected, these two methods show limited intra-strain correlation between amounts of CPS production and capsule thickness.

IMPORTANCE

Despite the availability of vaccines, Streptococcus pneumoniae remains a leading cause of respiratory and invasive diseases. These vaccines target a polysaccharide capsule the bacterium uses to evade the immune system. Variation of the capsule composition subdivides the organism into serotypes and influences its protective potency. Another critical factor affecting this protection is capsule size. It is commonly assumed that S. pneumoniae strains of the same serotype produce capsules of consistent size, despite the organism's heterogeneity. In this study, we challenge this assumption by analyzing clinical isolates of the same serotype. Existing methods were modified to achieve high reproducibility and increase accessibility. Our data reveal significant fluctuations in capsule production within a given serotype. Our findings suggest that S. pneumoniae research should consider capsule size, not just its presence and type. The results imply that standardized vaccine efficacy tests may yield variable results depending on the capsule production of target strains.

Integrated and high-throughput method to collect, store, recover, and manage microbial isolates in mini-arrays

Clinical studies of vaccines generally require collections of microbial isolates obtained from various body sites over multiple years. Further, large microbe collections are needed for research due to increasing appreciation for the phenotypic and genotypic diversity among a single microbial species. However, large collections are not generally available due to method limitations. We show a new way to create, recover, and manage microbe collections in 96- or 384-well plates using 50% glycerol at -20°C. Fifty percent glycerol remains liquid at -20°C and permits only the chosen isolates to be reliably sampled without first thawing all other isolates in the plate. Consequently, the glycerol sampling allows integration of microbe collection, labeling, recovery, and storage steps. Creating a microbe collection as an array in microplates reduces physical storage space by 6- or 23-fold with 96-well or 384-well plates, respectively. The array permits direct analysis of the collection with high-throughput assay systems. Further, we show that Streptococcus pneumoniae could be stored for 11 years as a microplate array. Standardized microbe arrays created in microplates with the new method could be easily distributed for studies of microbial structures, genetic diversity, antibiotics, and microbe-host interactions. This integrated method suggests how automated microbe management systems can be created.IMPORTANCEEpidemiologic and microbiology studies require large microbial collections, and the use of microplates could facilitate the creation and management of these collections. However, recovering individual isolates from microplates is manual and tedious. In this study, we demonstrate a simple method for recovering a selected individual isolate from a microplate at -20°C using 50% glycerol. Additionally, we found that Streptococcus pneumoniae could be revived for more than 10 years in microplates. This new method of recovering microbes from frozen microplates could greatly streamline many large-scale epidemiologic studies, particularly those related to pneumococcal vaccine studies. This new method may ultimately automate the collection, management, and storage of microbial isolates.

Streptococcus pneumoniae serotype 33H: a novel serotype with frameshift mutations in the acetyltransferase gene wciG

BACKGROUND

Streptococcus pneumoniae (the pneumococcus) is a leading cause of community-acquired pneumonia. Pneumococci are categorised into serotypes, based on the type of capsular polysaccharide produced, which has important implications for virulence, vaccine impact and global surveillance. Recently, we identified a novel serotype, which we named 33G, that is comprised of an O-acetylated hexasaccharide repeat unit. In this study, we report and describe variants of 33G, designated 33G-like, which we isolated from the nasopharynx of two adults hospitalised with pneumonia in Mongolia.

METHODS

Serological comparison of 33G and 33G-like pneumococci were conducted by Quellung serotyping. Genetic analysis of the capsular polysaccharide loci was performed using whole genome sequencing. Polysaccharide composition was determined using 1H nuclear magnetic resonance.

RESULTS

By Quellung serotyping, 33G pneumococci type as both 10B and 33B whereas 33G-like pneumococci type as both 10B and 33F. Genomic analysis of the capsular polysaccharide locus revealed 33G-like loci are identical to 33G, except for frameshift mutations in the wciG gene which encodes an acetyltransferase responsible for the O-acetylation of beta-galactofuranose (β-Galf) in the capsular polysaccharide repeat unit. We constructed an artificial 33G-like by deleting wciG in a 33G strain and confirmed this gene was responsible for the serological differences between 33G and 33G-like pneumococci. Lastly, 1H nuclear magnetic resonance confirmed the O-acetylation present in the 33G polysaccharide is absent in the 33G-like polysaccharide.

CONCLUSIONS

Here, we have provided serological, genetic and biochemical evidence that the 33G-like capsule differs to 33G and all other pneumococcal serotypes, meeting the requirements to be designated as a new serotype, which we have named 33H.

Update on the evolving landscape of pneumococcal capsule types: new discoveries and way forward

SUMMARYStreptococcus pneumoniae (the "pneumococcus") is a significant human pathogen. The key determinant of pneumococcal fitness and virulence is its ability to produce a protective polysaccharide (PS) capsule, and anti-capsule antibodies mediate serotype-specific opsonophagocytic killing of bacteria. Notably, immunization with pneumococcal conjugate vaccines (PCVs) has effectively reduced the burden of disease caused by serotypes included in vaccines but has also spurred a relative upsurge in the prevalence of non-vaccine serotypes. Recent advancements in serotyping and bioinformatics surveillance tools coupled with high-resolution analytical techniques have enabled the discovery of numerous new capsule types, thereby providing a fresh perspective on the dynamic pneumococcal landscape. This review offers insights into the current pneumococcal seroepidemiology highlighting important serotype shifts in different global regions in the PCV era. It also comprehensively summarizes newly discovered serotypes from 2007 to 2024, alongside updates on revised chemical structures and the de-novo determinations of structures for previously known serotypes. Furthermore, we spotlight emerging evidence on non-pneumococcal Mitis-group strains that express capsular PS that are serologically and biochemically related to the pneumococcal capsule types. We further discuss the implications of these recent findings on capsule nomenclature, pneumococcal carriage detection, and future PCV design. The review maps out the current status and also outlines the course for future research and vaccine strategies, ensuring a continued effective response to the evolving pneumococcal challenge.

Natural antibodies to polysaccharide capsules enable Kupffer cells to capture invading bacteria in the liver sinusoids

The interception of blood-borne bacteria in the liver defines the outcomes of invasive bacterial infections, but the mechanisms of this antibacterial immunity are not fully understood. This study shows that natural antibodies (nAbs) to capsules enable liver macrophage Kupffer cells (KCs) to rapidly capture and kill blood-borne encapsulated bacteria in mice. Affinity pulldown with serotype-10A capsular polysaccharides (CPS10A) of Streptococcus pneumoniae (Spn10A) led to the identification of CPS10A-binding nAbs in serum. The CPS10A-antibody interaction enabled KCs to capture Spn10A bacteria from the bloodstream, in part through complement receptors on KCs. The nAbs were found to recognize the β1-6-linked galactose branch of CPS10A and similar moieties of serotype-39 S. pneumoniae and serotype-K50 Klebsiella pneumoniae capsules. More importantly, the nAbs empowered KCs to capture serotype-39 S. pneumoniae and serotype-K50 K. pneumoniae in the liver. Collectively, our data have revealed a highly effective immune function of nAb against encapsulated bacteria and emphasize the concept of treating septic encapsulated bacterial diseases with monoclonal antibodies.

Massively parallel barcode sequencing revealed the interchangeability of capsule transporters in Streptococcus pneumoniae

Multidrug/oligosaccharidyl-lipid/polysaccharide (MOP) family transporters are essential in glycan synthesis, flipping lipid-linked precursors across cell membranes. Yet, how they select their substrates remains enigmatic. Here, we investigate the substrate specificity of the MOP transporters in the capsular polysaccharide (CPS) synthesis pathway in Streptococcus pneumoniae. These capsule flippases collectively transport more than 100 types of capsule precursors. To determine whether they can substitute for one another, we developed a high-throughput approach to systematically examine nearly 6000 combinations of flippases and substrates. CPS flippases fall into three groups: relaxed, type-specific, and strictly specific. Cargo size and CPS acetylation affect transport, and we isolated additional gain-of-function flippase variants that can substitute for the peptidoglycan flippase YtgP (MurJ). We also showed that combining flippase variants in a single cassette allows various CPS precursors to be flipped, which may aid glycoengineering. This study reveals that MOP flippases exhibit broad specificity, shaping the evolution of glycan synthesis.

New pneumococcal serotype 20C is a WciG O-acetyltransferase deficient variant of canonical serotype 20B

The polysaccharide (PS) capsule of Streptococcus pneumoniae (pneumococcus) is the immunodominant surface structure that shields the bacteria from the host immune system. Since the capsule is the primary target of currently available pneumococcal vaccines, anti-capsular antibodies are highly protective but serotype-specific. Pneumococci may evade host or vaccine-induced immunity as a result of variation in capsule structure mediated via multiple mechanisms, such as the loss or gain of O-acetylation. Previous biochemical studies of serogroup 20 isolates have identified two subtypes-20A and 20B, whose capsule PS differs in the WhaF-mediated glucose side chain. Herein, we characterize a newly discovered capsule type, 20C, that differs from serotype 20B via the inactivation of capsule O-acetyltransferase gene, wciG. Structural analysis demonstrated that 20C and 20B share an identical repeat unit [→3)-α-D-GlcpNAc-[β-D-Galf-(1→4)][α-D-Glcp-(1→6)]-(1→P→6)-α-D-Glcp-(1→6)- β-D-Glcp-(1→3)-β-D-Galf 5,6Ac2-(1→3)-β-D-Glcp-(1→], except for the absence of WciG-mediated O-acetyl group at terminal galactofuranose (β-D-Galf). We confirmed that deletion of the wciG gene in a 20B strain resulted in the expression of the 20C capsule. Serotype 20C is serologically indistinguishable from the canonical 20A and 20B using conventional serotyping antibodies, but serogroup 20 subtypes can be distinguished by sequencing of cps genes-whaF, wciG, and wcjE. While genetic screening suggests 20C to be globally less prevalent, a new variant was identified which appears to have both wciG and whaF genes inactive, potentially indicating it to be a new serotype. Consequently, genome-based serotyping/bioinformatic tools must scrutinize all cps genes for mutations that might inactivate/modify cps-encoded enzymes, ensuring effective tracking of emerging capsule variants in response to ongoing vaccination efforts.

IMPORTANCE

Streptococcus pneumoniae (pneumococcus) is a significant human pathogen known for producing a wide array of antigenically and structurally diverse capsule types, a fact that poses a serious challenge to the effectiveness of vaccines targeting pneumococcal capsule polysaccharide (PS). Herein, we provide a comprehensive analysis-genetic, antigenic, and biochemical of a newly identified capsule type, 20C, which differs from the canonical serotype 20B due to the inactivation of the capsule O-acetyltransferase gene, wciG. Our findings highlight how pneumococci can alter their capsule PS structure and immunological characteristics through minor genetic modifications. Since the appearance of new capsule types can directly affect pneumococcal conjugate vaccine (PCV) implementation, a deeper understanding of capsule PS at the genetic, immunological, and biochemical levels is critical for the development of future diagnostic tools and vaccines.

Pneumococcal disease burden in high-risk older adults: Exploring impact of comorbidities, long-term care facilities, antibiotic resistance, and immunization policies through a narrative literature review

This study aims to provide a comprehensive review of literature on pneumococcal disease burden in high-risk older adults aged ≥65 with focus on impact of comorbidities, long-term care facilities (LTCFs), antibiotic resistance, and vaccination policies across various countries. Research showed that the disease burden and the prevalence of antibiotic-resistant pneumococci was higher in the elderly, particularly those residing in LTCFs, and with comorbidities. These individuals are at high risk of infection with antibiotic-resistant serotypes 10A, 11A, and 15B. The vaccination strategies and national guidelines for pneumococcal vaccines in the elderly vary across countries. Some countries focus on single-dose strategies, while others recommend sequential vaccinations with varying intervals. Although vaccination policies are well-established for the elderly, they are not as well-established for high-risk elderly groups, and this review underscores the need for more tailored vaccination strategies for these groups.

Pre- & post-vaccine trends in pneumococcal serotypes & antimicrobial resistance patterns

Background & objectives The Pneumococcal vaccines were introduced under the Universal Immunization Programme (UIP) in 2021 in India. Drawing from the collective experience of various nations, it is anticipated that there will be a substantial shift in serotype patterns following the introduction of this vaccine. The available data is limited to years until 2018 when the vaccine was introduced in only five States. The present study was carried out to estimate the changes in serotypes and antimicrobial resistance patterns pre- and post-vaccine introduction from a tertiary care centre. Methods All isolates from various clinical specimens in the pre-vaccine era (January 2015-July 2021, except for 2019) and post-vaccine era (August 2021- March 2023) were included. Antimicrobial susceptibility was tested using disc diffusion or VITEK2, and serotyping was performed using the Quellung test (post-vaccine introduction) or sequential multiplex PCR (pre-vaccine introduction). The Chi-square or Fisher exact test was used to identify associations between antimicrobial resistance and serotypes. The z-test for proportions was used to identify significant changes in serotype frequencies between the pre- and post-vaccine era; P<0.05 was considered as the level of significance. Results Overall, the resistance rates increased for most of the antibiotics in the post-vaccine era, and there was no significant increase in the non-vaccine serotypes. The proportion of serotypes 19F and 15B/C increased, and serotypes 23F and 14 reduced in the post-vaccine era. The majority of the 19F and 19A isolates (89.7% and 80%, respectively) were multidrug resistant in the post-vaccine era. Interpretation & conclusions Introducing pneumococcal vaccination reduced the burden of many vaccine serotypes, while the burden of non-vaccine serotypes slightly increased. Most of the vaccine serotypes (like 19F and 19A) that persisted in the post-vaccine era were drug resistant.

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.

Evaluation of GC-MS for identification and characterization of pneumococcal serotype 24A, 24B, and 24F capsular polysaccharide

Analysis of pneumococcal polysaccharides (PnPs) has been an arduous task, especially in similar serotypes. Pneumococci invades the host immune response by modulating capsule structure with small genetic changes making them indistinguishable from similar serotypes by conventional modes of analysis. The new serotype 24F causing invasive pneumococcal-resistant infection is an analytical challenge for its analysis as related serotypes 24A and 24B Ps share a common backbone. The difference in the branched chain which contains arabinitol and ribitol in 24F and 24B respectively are stereoisomers making their identification even more challenging. The composition analysis by GC-MS revealed distinct peaks for arabinitol in 24F and 24A Ps and ribitol in Pn 24B serotype polysaccharide. The mass spectral analysis confirmed their identification along with a heterologous cross-reactivity which confirmed anti-Pn-24F mAb reactive to Pn 24B than Pn 24A. The quantitative analysis of pneumococcal 24A, 24B and 24F using GC-MS showed sensitive analysis over the concentration range 3.125-200 μg/mL with regression coefficient >0.99 making ideal modality for the characterization, identification, and quantitation of pneumococcal 24A, 24B and 24F similar serotypes.

Genome sequences of 36 Streptococcus pneumoniae strains optimized for the multiplexed opsonophagocytosis killing assay

A multiplexed opsonophagocytosis assay (MOPA) was developed as a cost-effective, high-throughput biological assay to evaluate the efficacy of pneumococcal vaccines by in vitro measurement of opsonophagocytic activity of anti-capsular antibodies. Here, we report draft genomes of the 36 strains of Streptococcus pneumoniae developed for use in the reference pneumococcal MOPA.

A low-cost culture- and DNA extraction-free method for the molecular detection of pneumococcal carriage in saliva

Molecular methods have improved the sensitivity of the detection of pneumococcal carriage in saliva. However, they typically require sample culture enrichment and nucleic acid extraction prior to performing the detection assay and may limit scalability for extensive surveillance of pneumococcus, particularly in low-resource settings. We evaluated the performance of a DNA-extraction-free method for the detection of pneumococcus in saliva. We developed a streamlined qPCR-based protocol for the detection of pneumococcus, omitting culture enrichment and DNA extraction. Using saliva samples collected from children attending childcare centers (New Haven, CT, USA), we evaluated the detection of pneumococcus using saliva lysates as compared to purified DNA extracted from culture-enriched aliquots of the paired samples using qPCR targeting the pneumococcal piaB gene. Of the 759 saliva samples tested from 92 children [median age 3.65 years; IQR (2.46-4.78)], pneumococcus was detected in 358 (47.2%) saliva lysates prepared using the extraction-free protocol and in 369 (48.6%) DNA extracted from culture-enriched samples. We observed near-perfect agreement between the two protocols (Cohen's kappa: 0.92; 95% CI: 0.90-0.95). Despite a high correlation between CT values generated by the two methods (r = 0.93, P < 0.0001), the CT values generated from saliva lysates were higher (lower concentration) than those from culture-enriched samples (ΔCT = 6.69, P < 0.00001). The cost of detecting pneumococcus using saliva lysates was at least fivefold lower (US$2.53) compared to the cost of the culture-enriched method (range: US$13.60-US$19.46). For pneumococcal carriage surveillance in children, our findings suggest that a DNA extraction-free approach may offer a cost-effective alternative to the resource-intensive culture-enrichment method.IMPORTANCESurveillance for carriage of pneumococcus is a key component of evaluating the performance of pneumococcal vaccines and informing new vaccination strategies. To improve the scalability of pneumococcal carriage surveillance, we show that molecular detection of pneumococcus in saliva from children can be performed without culture enrichment and DNA extraction. Our findings show that using the extraction-free method can improve surveillance efforts for pneumococcal carriage in children, overcoming the resource-intensive hurdle that comes with the use of molecular methods, particularly in low-resource settings.

Implications of Cross-Reactivity and Cross-Protection for Pneumococcal Vaccine Development

Pneumococcal vaccines are a cornerstone for the prevention of pneumococcal diseases, reducing morbidity and mortality in children and adults worldwide. Pneumococcal vaccine composition is based on the polysaccharide capsule of Streptococcus pneumoniae, which is one of the most important identified contributors to the pathogen's virulence. Similarities in the structural composition of polysaccharides included in licensed pneumococcal vaccines may result in cross-reactivity of immune response against closely related serotypes, including serotypes not included in the vaccine. Therefore, it is important to understand whether cross-reactive antibodies offer clinical protection against pneumococcal disease. This review explores available evidence of cross-reactivity and cross-protection associated with pneumococcal vaccines, the challenges associated with the assessment of cross-reactivity and cross-protection, and implications for vaccine design and development.

Biological puzzles solved by using Streptococcus pneumoniae: a historical review of the pneumococcal studies that have impacted medicine and shaped molecular bacteriology

The major human pathogen Streptococcus pneumoniae has been the subject of intensive clinical and basic scientific study for over 140 years. In multiple instances, these efforts have resulted in major breakthroughs in our understanding of basic biological principles as well as fundamental tenets of bacterial pathogenesis, immunology, vaccinology, and genetics. Discoveries made with S. pneumoniae have led to multiple major public health victories that have saved the lives of millions. Studies on S. pneumoniae continue today, where this bacterium is being used to dissect the impact of the host on disease processes, as a powerful cell biology model, and to better understand the consequence of human actions on commensal bacteria at the population level. Herein we review the major findings, i.e., puzzle pieces, made with S. pneumoniae and how, over the years, they have come together to shape our understanding of this bacterium's biology and the practice of medicine and modern molecular biology.

Streptococcus pneumoniae serotype 33G: genetic, serological, and structural analysis of a new capsule type

IMPORTANCE

Streptococcus pneumoniae (the pneumococcus) is a bacterial pathogen with the greatest burden of disease in Asia and Africa. The pneumococcal capsular polysaccharide has biological relevance as a major virulence factor as well as public health importance as it is the target for currently licensed vaccines. These vaccines have limited valency, covering up to 23 of the >100 known capsular types (serotypes) with higher valency vaccines in development. Here, we have characterized a new pneumococcal serotype, which we have named 33G. We detected serotype 33G in nasopharyngeal swabs (n = 20) from children and adults hospitalized with pneumonia, as well as healthy children in Mongolia. We show that the genetic, serological, and biochemical properties of 33G differ from existing serotypes, satisfying the criteria to be designated as a new serotype. Future studies should focus on the geographical distribution of 33G and any changes in prevalence following vaccine introduction.

Antimicrobial resistance in Streptococcus pneumoniae: a retrospective analysis of emerging trends in the United Arab Emirates from 2010 to 2021

INTRODUCTION

Although pneumococcal conjugate vaccines (PCV) have been effective in reducing the burden of Streptococcus pneumoniae infections, there is a paucity of data on the relationship with antimicrobial resistance (AMR) trends in the Arabian Gulf region. This study was carried out to assess S. pneumoniae resistance trends in the United Arab Emirates (UAE) where PCV-13 vaccination was introduced in 2011.

METHODS

Retrospective analysis of S. pneumoniae demographic and microbiological data collected as part of the national AMR surveillance program from 2010 to 2021 was carried out. A survey of reporting sites and hand searching of annual reports of local health authorities was carried out to identify data on S. pneumoniae serotypes as this is not included in the AMR surveillance database.

RESULTS

From 2010 to 2021, 11,242 non-duplicate S. pneumoniae isolates were reported, increasing from 324 in 2010 to 1,115 in 2021. Factoring in annual increment in the number of surveillance sites, the number of isolates per site showed an upward trajectory from 2015 to 2018 and declined in 2020 with the onset of the pandemic. The majority of isolates (n/N = 5,751/11,242; 51.2%) were from respiratory tract specimens with 44.5% (n/N = 2,557/5,751) being nasal colonizers. Up to 11.9% (n/N = 1,337/11,242) were invasive pneumococcal disease (IPD) isolates obtained from sterile site specimens including blood (n = 1,262), cerebrospinal (n = 52), pleural (n = 19) and joint (n = 4) fluid; and were predominantly from pediatric patients. The downward trend for amoxicillin and for penicillin G at the non-meningitis and meningitis as well as oral penicillin breakpoints was statistically significant. In contrast, increasing trends of resistance were seen for levofloxacin, moxifloxacin, trimethoprim/sulfamethoxazole and erythromycin. IPD and non-IPD isolates showed similar demographic and AMR trends. None of the surveillance sites carried out S. pneumoniae serotyping and handsearching of annual reports did not yield this information.

CONCLUSION

The increasing trend of pneumococcal disease and AMR with emergence of isolates with MDR phenotype despite is of concern. In the absence of S. pneumoniae serotyping the role of non-vaccine serotypes in driving this pattern remains unknown. There is an urgent need for serotype, genomic and AMR surveillance of S. pneumoniae isolates in the UAE.