Historical development of typing methods for Streptococcus pneumoniae

John, James; Gopalkrishnan, Sangeetha; Marie, Mohammed Ali M.; Gowda, K. Lakshmana

doi:10.1097/mrm.0000000000000001

Cited by 2 publications

(2 citation statements)

References 42 publications

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“…It is also important to differentiate NESp from other closely related nonencapsulated streptococcal species, such as S. pseudopneumoniae ( 41 ) and S. tigurinus ( 42 ), which are often confused with S. pneumoniae . Molecular approaches can be used to confirm both species and capsule status with greater precision and accuracy to demonstrate true prevalence ( 43 , 44 ). These approaches include multilocus sequence typing (MLST), which has allowed reliable species identification of streptococcal isolates ( 45 ).…”

Section: Classificationmentioning

confidence: 99%

Nonencapsulated Streptococcus pneumoniae: Emergence and Pathogenesis

Keller

Robinson

McDaniel

2016

mBio

130

153

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While significant protection from pneumococcal disease has been achieved by the use of polysaccharide and polysaccharide-protein conjugate vaccines, capsule-independent protection has been limited by serotype replacement along with disease caused by nonencapsulated Streptococcus pneumoniae (NESp). NESp strains compose approximately 3% to 19% of asymptomatic carriage isolates and harbor multiple antibiotic resistance genes. Surface proteins unique to NESp enhance colonization and virulence despite the lack of a capsule even though the capsule has been thought to be required for pneumococcal pathogenesis. Genes for pneumococcal surface proteins replace the capsular polysaccharide (cps) locus in some NESp isolates, and these proteins aid in pneumococcal colonization and otitis media (OM). NESp strains have been isolated from patients with invasive and noninvasive pneumococcal disease, but noninvasive diseases, specifically, conjunctivitis (85%) and OM (8%), are of higher prevalence. Conjunctival strains are commonly of the so-called classical NESp lineages defined by multilocus sequence types (STs) ST344 and ST448, while sporadic NESp lineages such as ST1106 are more commonly isolated from patients with other diseases. Interestingly, sporadic lineages have significantly higher rates of recombination than classical lineages. Higher rates of recombination can lead to increased acquisition of antibiotic resistance and virulence factors, increasing the risk of disease and hindering treatment. NESp strains are a significant proportion of the pneumococcal population, can cause disease, and may be increasing in prevalence in the population due to effects on the pneumococcal niche caused by pneumococcal vaccines. Current vaccines are ineffective against NESp, and further research is necessary to develop vaccines effective against both encapsulated and nonencapsulated pneumococci.

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Section: Classificationmentioning

confidence: 99%

Nonencapsulated Streptococcus pneumoniae: Emergence and Pathogenesis

Keller

Robinson

McDaniel

2016

mBio

130

153

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“…This method is expensive and time-consuming and requires expertise (3). With the sequencing of the capsular biosynthesis loci of all 90 pneumococcal serotypes, new molecular methods for pneumococcal serotyping have been developed (4).…”

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confidence: 99%

Direct Detection and Prediction of All Pneumococcal Serogroups by Target Enrichment-Based Next-Generation Sequencing

Liyanapathirana

Ang

et al. 2014

J Clin Microbiol

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Despite the availability of standard methods for pneumococcal serotyping, there is room for improvement in the available methods, in terms of throughput, multiplexing capacity, and the number of serotypes identified. We describe a target enrichmentbased next-generation sequencing method applied to nasopharyngeal samples for direct detection and serogroup prediction of all known serotypes of Streptococcus pneumoniae, 32 to the serotype level and the rest to the closely related serogroup level. The method was applied to detect and to predict the serogroups of pneumococci directly in clinical samples and from sweeps of primary culture DNA, with increased detection rates versus culture-based identification and agreement with the serotypes/serogroups determined by conventional serotyping methods. We propose this method, in conjunction with traditional serotyping methods, as an alternative to rapid detection and serotyping of pneumococci. The introduction of conjugate vaccination has dramatically altered the prevalence and community structure of pneumococcal serotypes, in both disease and carriage (1). As the serotype valency of conjugate vaccines increased from 7 to 13, the serotypes and their prevalence were subjected to dynamic changes to less common serotypes. Thus, there is a need for laboratory methods that are capable of identifying the maximum possible number of serotypes with a limited number of assays, in order to monitor serotype replacement and any emerging serotypes (2).The Quellung reaction remains the standard method for identification of pneumococcal serotypes. This method is expensive and time-consuming and requires expertise (3). With the sequencing of the capsular biosynthesis loci of all 90 pneumococcal serotypes, new molecular methods for pneumococcal serotyping have been developed (4). The most widely used of these methods remain sequential multiplex PCRs. The Centers for Disease Control and Prevention (CDC) (Atlanta, GA) recommends a set of 8 multiplex PCRs that are capable of differentiating 40 seroidentities, 22 to the serotype level (5) (http://www.cdc.gov/streplab/pcr .html). More recently, a set of seven real-time PCR assays capable of differentiating 21 serotypes was also recommended by the CDC (6). However, the number of tests to be performed still remains relatively high, due to the limited multiplexing capabilities associated with gel-based differentiation and quencher dye combinations. Thus, there is a need for alternative serotyping methods capable of differentiating the greatest number of serotypes at least to closely related serogroups, with a minimal number of assays, in a rapid and cost-effective manner.Next-generation sequencing (NGS) is an attractive alternative platform for the development of diagnostic methods. The high throughput, the increasingly simple and fast methods for sample preparation, and the ability to pool samples together make these platforms versatile for adaptation. Target enrichment-based sequencing through selective enrichment of the regions of interest enabl...

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Historical development of typing methods for Streptococcus pneumoniae

Cited by 2 publications

References 42 publications

Nonencapsulated Streptococcus pneumoniae: Emergence and Pathogenesis

Nonencapsulated Streptococcus pneumoniae: Emergence and Pathogenesis

Direct Detection and Prediction of All Pneumococcal Serogroups by Target Enrichment-Based Next-Generation Sequencing

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