Current challenges in the accurate identification of Streptococcus pneumoniae and its serogroups/serotypes in the vaccine era

Varghese, Rosemol; Jayaraman, Ranjith; Veeraraghavan, Balaji

doi:10.1016/j.mimet.2017.07.015

Cited by 45 publications

(30 citation statements)

References 76 publications

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“…The primary virulence factor of Sp is its polysaccharide capsule, which also determines the serotype. More than 95 serotypes exist and they vary in their capacity to activate the host immune system and to invade [12][13][14][15]. PCVs provide direct protection to the vaccinated individuals against a number of clinically relevant serotypes [12].…”

Section: Introductionmentioning

confidence: 99%

How nasopharyngeal pneumococcal carriage evolved during and after a PCV13-to-PCV10 vaccination programme switch in Belgium, 2016 to 2018

et al. 2020

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Background: The current carriage study was set up to reinforce surveillance during/after the PCV13-to-PCVC10 switch in Belgium. Aim: This observational study monitored carriage of Streptococcus pneumoniae (Sp) serotypes, particularly those no longer covered (3, 6A, 19A), as well as Haemophilus influenzae (Hi), because PCV10 contains the non-typeable Hi protein D. Methods: A total of 2,615 nasopharyngeal swabs from children (6-30 months old) attending day care were collected in three periods over 2016-2018. Children's demographic and clinical characteristics and vaccination status were obtained through a questionnaire. Sp and Hi were identified by culture and PCR. Pneumococcal strains were tested for antimicrobial (non-)susceptibility by disc diffusion and serotyped by Quellung-reaction (Quellung-reaction and PCR for serotypes 3, 6A, 19A). Results: The carriage prevalence of Sp (> 75%) remained stable over the successive periods but that of Hi increased (87.4%, 664 Hi-carriers/760 in 2016 vs 93.9%, 895/953 in 2017-2018). The proportion of non-PCV13 vaccine serotypes decreased (94.6%, 438 isolates/463 in 2016 vs 89.7%, 599/668 in 2017-2018) while that of PCV13-non-PCV10 vaccine serotypes (3 + 6A + 19A) increased (0.9%, 4 isolates/463 in 2016 vs 7.8%, 52/668 in 2017-2018), with serotype 19A most frequently identified (87.9%, 58/66 isolates). Non-susceptibility of pneumococci against any of the tested antibiotics was stable over the study period (> 44%). Conclusions: During and after the PCV13-to-PCV10 vaccine switch, the proportion of non-PCV13 serotypes decreased, mainly due to a serotype 19A carriage prevalence increase. These results complement invasive pneumococcal disease surveillance data, providing further basis for pneumococcal vaccination programme policy making.

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Section: Introductionmentioning

confidence: 99%

How nasopharyngeal pneumococcal carriage evolved during and after a PCV13-to-PCV10 vaccination programme switch in Belgium, 2016 to 2018

et al. 2020

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“…As stated by WHO, S. pneumoniae is the fourth most common microbial cause of death and the cause of mucosal and invasive diseases with a high mortality rate. This pathogen belongs to the Streptococcal mitis group and is part of the normal flora of the upper respiratory tract (61)(62)(63)(64) . S. pneumonia growth increases at 5-10% CO 2 (29) .…”

Section: Streptococcus Pneumoniaementioning

confidence: 99%

A Review on Bacterial Respiratory Infections and Optimization of Their Identification

Mirhoseini

Heydari

Abednezhad

et al. 2020

IEM

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Background: The current narrative review aims to describe microbial agents causing pneumonia briefly. In addition, the ongoing review tries to introduce the diagnostic methods from biochemical to molecular tests used routinely and the promising molecular methods which will be used in near future. Materials & Methods: PubMed was searched for all review and original articles related to the lung infection. Studies providing insights into clinical symptoms, microbiology, risk factors, and diagnosis were included. Conclusion: Untreated respiratory infections are one of the most common health care problems worldwide. We tried to provide a collective view of new aspects of bacteriology and diagnosis methodology of lung infection detection.

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“…In contrast, individual house-keeping gene PCRand sequence-based assays have proven to be less reliable for differentiating the other closely related species of the Mitis-Group streptococci from each other (Gonzales-Siles et al, 2019). Several PCR-based methods, mostly targeting genes for specific pneumococcal virulence factors (lytA, ply, cpsA, pspA), specific intergenic DNA sequences, and specific regions of the 16S rRNA gene, have been proposed to be pneumococcal species-specific (El Aila et al, 2010;Varghese et al, 2017). Recently, a unique molecular marker, SPS0002, was described (Croxen et al, 2018).…”

Section: Introductionmentioning

confidence: 99%

A Pangenome Approach for Discerning Species-Unique Gene Markers for Identifications of Streptococcus pneumoniae and Streptococcus pseudopneumoniae

Gonzales-Silès

Karlsson

Schmidt

et al. 2020

Front. Cell. Infect. Microbiol.

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Correct identifications of isolates and strains of the Mitis-Group of the genus Streptococcus are particularly difficult, due to high genetic similarity, resulting from horizontal gene transfer and homologous recombination, and unreliable phenotypic and genotypic biomarkers for differentiating the species. Streptococcus pneumoniae and Streptococcus pseudopneumoniae are the most closely related species of the clade. In this study, publicly-available genome sequences for Streptococcus pneumoniae and S. pseudopneumoniae were analyzed, using a pangenomic approach, to find candidates for species-unique gene markers; ten species-unique genes for S. pneumoniae and nine for S. pseudopneumoniae were identified. These species-unique gene marker candidates were verified by PCR assays for identifying S. pneumoniae and S. pseudopneumoniae strains isolated from clinical samples. All determined species-level unique gene markers for S. pneumoniae were detected in all S. pneumoniae clinical isolates, whereas fewer of the unique S. pseudopneumoniae gene markers were present in more than 95% of the clinical isolates. In parallel, taxonomic identifications of the clinical isolates were confirmed, using conventional optochin sensitivity testing, targeted PCR-detection for the "Xisco" gene, as well as genomic ANIb similarity analyses for the genome sequences of selected strains. Using mass spectrometry-proteomics, species-specific peptide matches were observed for four of the S. pneumoniae gene markers and for three of the S. pseudopneumoniae gene markers. Application of multiple species-level unique biomarkers of S. pneumoniae and S. pseudopneumoniae, is proposed as a protocol for the routine clinical laboratory for improved, reliable differentiation, and identification of these pathogenic and commensal species.

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Current challenges in the accurate identification of Streptococcus pneumoniae and its serogroups/serotypes in the vaccine era

Cited by 45 publications

References 76 publications

How nasopharyngeal pneumococcal carriage evolved during and after a PCV13-to-PCV10 vaccination programme switch in Belgium, 2016 to 2018

How nasopharyngeal pneumococcal carriage evolved during and after a PCV13-to-PCV10 vaccination programme switch in Belgium, 2016 to 2018

A Review on Bacterial Respiratory Infections and Optimization of Their Identification

A Pangenome Approach for Discerning Species-Unique Gene Markers for Identifications of Streptococcus pneumoniae and Streptococcus pseudopneumoniae

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