scholarly journals Serotype Distribution of Streptococcus pneumoniae Isolates Causing Invasive and Non-Invasive Infections Using Whole-Genome Sequencing in Ethiopia

2021 ◽  
Vol Volume 14 ◽  
pp. 787-794
Author(s):  
Bekele Sharew ◽  
Feleke Moges ◽  
Gizachew Yismaw ◽  
Adane Mihret ◽  
Wondiwossen Abebe ◽  
...  
Keyword(s):  
Streptococcus Pneumoniae ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome ◽  
Serotype Distribution ◽  
Non Invasive ◽  
Invasive Infections

scholarly journals Characterization of Streptococcus pneumoniae strains causing invasive infections using whole-genome sequencing

2020 ◽  
Vol 97 (2) ◽  
pp. 113-118 ◽  
Author(s):  
Konstantin O. Mironov ◽  
Vitaly I. Korchagin ◽  
Yuliya V. Mikhailova ◽  
Yurii G. Yanushevich ◽  
Andrey A. Shelenkov ◽  
...  
Keyword(s):  
Streptococcus Pneumoniae ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Pneumococcal Infection ◽  
Whole Genome ◽  
Multicenter Studies ◽  
Serotype 1 ◽  
Invasive Infections ◽  
Sequence Types

Purpose: antigenic and genetic characterization of Streptococcus pneumoniae strains isolated from patients with invasive forms of pneumococcal infection using whole-genome sequencing.Materials and Methods. The study was performed on 46 S. pneumoniae strains isolated during the PEHASus multicenter studies in 2015-2018. Sequencing was performed using Illumina protocols and equipment. The SPAdes, SeroBA, PneumoCaT software were used for data processing, as well as BIGSdb software (PubMLST.org).Results and Discussion. Whole-genome sequences of strains were obtained; the information was entered into the PubMLST database (id: 51080-51125). Ten (21%) strains were found to have serotype 3. Five (11%) strains belonged to serotype 19F and five to serogroup 6; two of them belonged to serotype 6A; one strain had 6B and 1 had 6BE serotype; 1 strain showed discordant result (6A or 6BE). Serotype 15B was identified in 3 (6.5%) strains. Serotypes 7F, 8, 9V, 14, 22F, 23F and 28A were identified in two strains each; serotypes 1, 4, 9N, 10C, 12F, 18C, 35F, 37 and 38 were found once. The proportion of strains with serotypes included in PCV13 and PPV23 vaccines was 65% and 80%, respectively. 36 sequence types were found in strains; out of them, 6 sequence types were found for the first time. A dominant sequence type or clone complexes could not be identified using multilocus sequence typing except for serotype 3 strains. The inability to identify clonal complexes is in congruence with the previously obtained data on the absence of S. pneumoniae clones associated with pneumococcal meningitis in Russia.Conclusion. The information about serotypes of S. pneumoniae causing invasive infections together with epidemiologic data about strain sources and vaccination allows us to evaluate the effectiveness of pneumococcal vaccines and provide information for improving the PCR-based routine serotyping.

scholarly journals Serotype Distribution of Streptococcus pneumoniae Carriage ‎in Six-Month-Old Infants: A Cross-sectional Study During 2017-18, Tehran, ‎Iran

2021 ◽  
Vol In Press (In Press) ◽  
Author(s):  
Shirin Sayyahfar ◽  
Abdoulreza Esteghamati ◽  
Seyed Alireza Fahimzad ◽  
Safura Hajisadeghi Isfahani ◽  
Ali Nazari Alam ◽  
...  
Keyword(s):  
Streptococcus Pneumoniae ◽  
Multiplex Pcr ◽  
Positive Culture ◽  
Cross Sectional Study ◽  
Sectional Study ◽  
Serotype Distribution ◽  
Cross Sectional ◽  
Non Invasive ◽  
Healthy Infants ◽  
Invasive Infections

Background: Streptococcus pneumoniae is recognized as one of the main pathogens inducing several invasive and non-invasive infections in children. Objective: The present study aimed to evaluate the serotype distribution of S. pneumoniae in six–month–old carriers. Methods: This study encompassed 600 six-month-old healthy infants whose pharyngeal swap samples were collected and then cultured to isolate S. pneumoniae. Twenty- five different serotypes were defined on positive culture samples by multiplex PCR. Results: In this study, 13 cases (2.2%) were positive S. pneumonia. The most common isolated serotypes of S. pneumoniae were serotypes 23F (n = 6, 1%) and 3 (n = 3, 0.5%), respectively. Notably, the most frequent serotype in formula-fed infants (n = 300) was Serotype 23F (n = 5, 1.7%); however, Serotype 3 (n = 3, 1%) was the most frequent one in breastfed participants (n = 300). According to the findings, the overall coverage of PCV10, PCV13, and PPSV23 on the S. pneumoniae serotypes at the age of six months was 50%, 73%, and 85%, respectively. Conclusions: At this age, the type of feeding could not significantly affect the frequency rate of S. pneumoniae colonization, while the serotype distributions in the two breastfed and formula-fed groups were different.

scholarly journals Whole-Genome Sequencing ofAggregatibacterSpecies Isolated from Human Clinical Specimens and Description ofAggregatibacter kilianiisp. nov.

2018 ◽  
Vol 56 (7) ◽  
Author(s):  
May Murra ◽  
Lisbeth Lützen ◽  
Aynur Barut ◽  
Reinhard Zbinden ◽  
Marianne Lund ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Whole Genome ◽  
Content Type ◽  
Clinical Specimens ◽  
Phylogenetic Cluster ◽  
Invasive Infections ◽  
Rrna Gene Sequencing

ABSTRACTAggregatibacterspecies are commensal bacteria of human mucosal surfaces that are sometimes involved in serious invasive infections. During the investigation of strains cultured from various clinical specimens, we encountered a coherent group of 10 isolates that could not be allocated to any validly named species by phenotype, mass spectrometry, or partial 16S rRNA gene sequencing. Whole-genome sequencing revealed a phylogenetic cluster related to but separate fromAggregatibacter aphrophilus. The meanin silicoDNA hybridization value for strains of the new cluster versusA. aphrophiluswas 56% (range, 53.7 to 58.0%), whereas the average nucleotide identity was 94.4% (range, 93.9 to 94.8%). The new cluster exhibited aggregative properties typical of the genusAggregatibacter. Key phenotypic tests for discrimination of the new cluster from validly namedAggregatibacterspecies are alanine-phenylalanine-proline arylamidase,N-acetylglucosamine, and β-galactosidase. The nameAggregatibacter kilianiiis proposed, with PN_528 (CCUG 70536Tor DSM 105094T) as the type strain.

scholarly journals SeroBA: rapid high-throughput serotyping of Streptococcus pneumoniae from whole genome sequence data

2017 ◽  
Author(s):  
Lennard Epping ◽  
Andries J. van Tonder ◽  
Rebecca A. Gladstone ◽  
Stephen D. Bentley ◽  
Andrew J. Page ◽  
...  
Keyword(s):  
Streptococcus Pneumoniae ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome Sequence ◽  
Validation Dataset ◽  
List Type ◽  
Whole Genome ◽  
Link Type ◽  
Computational Performance ◽  
The Impact

ABSTRACTStreptococcus pneumoniae is responsible for 240,000 - 460,000 deaths in children under 5 years of age each year. Accurate identification of pneumococcal serotypes is important for tracking the distribution and evolution of serotypes following the introduction of effective vaccines. Recent efforts have been made to infer serotypes directly from genomic data but current software approaches are limited and do not scale well. Here, we introduce a novel method, SeroBA, which uses a hybrid assembly and mapping approach. We compared SeroBA against real and simulated data and present results on the concordance and computational performance against a validation dataset, the robustness and scalability when analysing a large dataset, and the impact of varying the depth of coverage in the cps locus region on sequence-based serotyping. SeroBA can predict serotypes, by identifying the cps locus, directly from raw whole genome sequencing read data with 98% concordance using a k-mer based method, can process 10,000 samples in just over 1 day using a standard server and can call serotypes at a coverage as low as 10x. SeroBA is implemented in Python3 and is freely available under an open source GPLv3 license from: https://github.com/sanger-pathogens/seroba.DATA SUMMARYThe reference genome Streptococcus pneumoniae ATCC 700669 is available from National Center for Biotechnology Information (NCBI) with the accession number: FM211187Simulated paired end reads for experiment 2 have been deposited in FigShare: https://doi.org/10.6084/m9.figshare.5086054.v1Accession numbers for all other experiments are listed in Supplementary Table S1 and Supplementary Table S2.I/We confirm all supporting data, code and protocols have been provided within the article or through supplementary data files. ⊠IMPACT STATEMENTThis article describes SeroBA, a A-mer based method for predicting the serotypes of Streptococcus pneumoniae from Whole Genome Sequencing (WGS) data. SeroBA can identify 92 serotypes and 2 subtypes with constant memory usage and low computational costs. We showed that SeroBA is able to reliably predict serotypes at a depth of coverage as low as 10x and is scalable to large datasets.

Isolation and whole genome sequencing of fetal cells from maternal blood towards the ultimate non-invasive prenatal testing

2017 ◽  
Vol 37 (13) ◽  
pp. 1311-1321 ◽  
Author(s):  
Fang Chen ◽  
Ping Liu ◽  
Ying Gu ◽  
Zhu Zhu ◽  
Amulya Nanisetti ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Prenatal Testing ◽  
Maternal Blood ◽  
Whole Genome ◽  
Fetal Cells ◽  
Non Invasive

scholarly journals Secondary findings from non-invasive prenatal testing for common fetal aneuploidies by whole genome sequencing as a clinical service

2013 ◽  
Vol 33 (6) ◽  
pp. 602-608 ◽  
Author(s):  
Tze Kin Lau ◽  
Fu Man Jiang ◽  
Robert J. Stevenson ◽  
Tsz Kin Lo ◽  
Lin Wai Chan ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Prenatal Testing ◽  
Clinical Service ◽  
Whole Genome ◽  
Secondary Findings ◽  
Non Invasive ◽  
Fetal Aneuploidies
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