scholarly journals Whole genome sequencing of penicillin-resistant Streptococcus pneumoniae reveals mutations in penicillin-binding proteins and in a putative iron permease

2011 ◽  
Vol 12 (11) ◽  
pp. R115 ◽  
Author(s):  
Fereshteh Fani ◽  
Philippe Leprohon ◽  
Danielle Légaré ◽  
Marc Ouellette
Keyword(s):  
Streptococcus Pneumoniae ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Binding Proteins ◽  
Whole Genome ◽  
Penicillin Binding Proteins

scholarly journals Penicillin-Binding Protein Transpeptidase Signatures for Tracking and Predicting β-Lactam Resistance Levels inStreptococcus pneumoniae

mBio ◽  
2016 ◽  
Vol 7 (3) ◽  
Author(s):  
Yuan Li ◽  
Benjamin J. Metcalf ◽  
Sopio Chochua ◽  
Zhongya Li ◽  
Robert E. Gertz ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Binding Proteins ◽  
Whole Genome Sequencing Data ◽  
Whole Genome ◽  
Sequencing Data ◽  
Pneumococcal Infections ◽  
Penicillin Binding Proteins ◽  
Major Discrepancy ◽  
Sequence Signatures

ABSTRACTβ-Lactam antibiotics are the drugs of choice to treat pneumococcal infections. The spread of β-lactam-resistant pneumococci is a major concern in choosing an effective therapy for patients. Systematically tracking β-lactam resistance could benefit disease surveillance. Here we developed a classification system in which a pneumococcal isolate is assigned to a “PBP type” based on sequence signatures in the transpeptidase domains (TPDs) of the three critical penicillin-binding proteins (PBPs), PBP1a, PBP2b, and PBP2x. We identified 307 unique PBP types from 2,528 invasive pneumococcal isolates, which had known MICs to six β-lactams based on broth microdilution. We found that increased β-lactam MICs strongly correlated with PBP types containing divergent TPD sequences. The PBP type explained 94 to 99% of variation in MICs both before and after accounting for genomic backgrounds defined by multilocus sequence typing, indicating that genomic backgrounds made little independent contribution to β-lactam MICs at the population level. We further developed and evaluated predictive models of MICs based on PBP type. Compared to microdilution MICs, MICs predicted by PBP type showed essential agreement (MICs agree within 1 dilution) of >98%, category agreement (interpretive results agree) of >94%, a major discrepancy (sensitive isolate predicted as resistant) rate of <3%, and a very major discrepancy (resistant isolate predicted as sensitive) rate of <2% for all six β-lactams. Thus, the PBP transpeptidase signatures are robust indicators of MICs to different β-lactam antibiotics in clinical pneumococcal isolates and serve as an accurate alternative to phenotypic susceptibility testing.IMPORTANCEThe human pathogenStreptococcus pneumoniaeis a leading cause of morbidity and mortality worldwide. β-Lactam antibiotics such as penicillin and ceftriaxone are the drugs of choice to treat pneumococcal infections. Some pneumococcal strains have developed β-lactam resistance through altering their penicillin-binding proteins (PBPs) and have become a major concern in choosing effective patient therapy. To systematically track and predict β-lactam resistance, we obtained the sequence signatures of PBPs from a large collection of clinical pneumococcal isolates using whole-genome sequencing data and found that these “PBP types” were predictive of resistance levels. Our findings can benefit the current era of strain surveillance when whole-genome sequencing data often lacks detailed resistance information. Using PBP positions that we found are always substituted within highly resistant strains may lead to further refinements. Sequence-based predictions are accurate and may lead to the ability to extract critical resistance information from nonculturable clinical specimens.

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.

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 Whole genome sequencing of macrolide resistant Streptococcus pneumoniae serotype 19A sequence type 416

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Petra Spanelova ◽  
Vladislav Jakubu ◽  
Lucia Malisova ◽  
Martin Musilek ◽  
Jana Kozakova ◽  
...  
Keyword(s):  
Streptococcus Pneumoniae ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Sequence Type ◽  
Whole Genome

scholarly journals Phylogenetic analysis of emergent Streptococcus pneumoniae serotype 22F causing invasive pneumococcal disease using whole genome sequencing

PLoS ONE ◽  
2017 ◽  
Vol 12 (5) ◽  
pp. e0178040 ◽  
Author(s):  
Walter H. B. Demczuk ◽  
Irene Martin ◽  
Linda Hoang ◽  
Paul Van Caeseele ◽  
Brigitte Lefebvre ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Streptococcus Pneumoniae ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Invasive Pneumococcal Disease ◽  
Pneumococcal Disease ◽  
Whole Genome

scholarly journals In Vivo Capsular Switch in Streptococcus pneumoniae – Analysis by Whole Genome Sequencing

PLoS ONE ◽  
2012 ◽  
Vol 7 (11) ◽  
pp. e47983 ◽  
Author(s):  
Fen Z. Hu ◽  
Rory Eutsey ◽  
Azad Ahmed ◽  
Nelson Frazao ◽  
Evan Powell ◽  
...  
Keyword(s):  
Streptococcus Pneumoniae ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome

scholarly journals Whole genome sequencing of macrolide resistant Streptococcus pneumoniae serotype 19A sequence type 416

2020 ◽  
Author(s):  
Petra Spanelova ◽  
Vladislav Jakubu ◽  
Lucia Malisova ◽  
Martin Musilek ◽  
Jana Kozakova ◽  
...  
Keyword(s):  
Czech Republic ◽  
Streptococcus Pneumoniae ◽  
The Netherlands ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Illumina Miseq ◽  
Sequence Type ◽  
Macrolide Resistance ◽  
Whole Genome ◽  
Recent Origin

Abstract Background: The resistance of Streptococcus pneumoniae to macrolides is becoming an increasingly important issue and thus it is important to understand the genetics related to adaptation of this species to the widespread use of antibiotics in Europe. The 58 isolates of S. pneumoniae belonging to sequence type 416 and serotype 19A and to several different phenotypes originated from Italy, Portugal and Czech Republic were thus sequenced on Illumina MiSeq. The aim of the study was to describe the relation between isolates in this collection and the Netherlands15B-37 clone, which belongs to serotype 15B and sequence type 199. The association of sequence type 416 with macrolide resistance was also investigated. Results: Investigation of genes associated with serotype confirmed common recent origin of inquired isolates in the serotype switch between 15B and 19A serotypes. The genes associated with the macrolide resistance are to be quite variable even within closely genetically relative isolates. Conclusions: This tendency to interchange and modification of genes associated with macrolide resistance and surrounding sequences could lead to adaptation to different circumstances and thus to accelerate spreading of this sequence type in regions with high macrolide consumption.

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