scholarly journals Characterization of Streptococcus pneumoniae serotype 19F-variants occurring in Brazil uncovers a predominant lineage that can lead to misinterpretation in capsular typing

2021 ◽  
Vol 104 ◽  
pp. 580-583
Author(s):  
Laura M.A. Oliveira ◽  
Aline R.V. Souza ◽  
Tatiana C.A. Pinto ◽  
Lucia M. Teixeira
2020 ◽  
Vol 20 (1) ◽  
Author(s):  
S. Garcia-Garcia ◽  
A. Perez-Arguello ◽  
D. Henares ◽  
N. Timoneda ◽  
C. Muñoz-Almagro

Abstract Background Whole genome sequencing has emerged as a useful tool for identification and molecular characterization of pathogens. MinION (Oxford Nanopore) is a real-time third generation sequencer whose portability, affordability and speed in data production make of it an attractive device for whole genome sequencing. The objective of this study is to evaluate MinION sequencer for pathogen identification and molecular characterization of Streptococcus pneumoniae isolated at a children’s Hospital. Whole genome sequencing of 32 Streptococcus pneumoniae invasive isolates, previously characterized by standard methods (Quellung reaction, Multiplex PCR and Sanger-MLST), were performed. DNA was extracted using ZymoBIOMICS DNA Microprep kit. Quantification and purity of DNA was assessed by Qubit and Nanodrop, respectively. Library preparation was performed using the Rapid Barcoding Kit. Real-time workflow EPI2ME platform “What’s it in my pot” was used for species identification. Fast5 sequences were converted into FASTQ by Albacore software. Reads were assembled using CANU software. PathogenWatch, genomic epidemiology and pubmlst online tools were used for capsular typing and/or whole genome-MLST profile. Results Rapid identification of Streptococcus pneumoniae was achieved by “What’s in my pot”. Capsular typing was correctly assigned with PathogenWatch in all 32 isolates at serogroup level and 24 at serotype level. Whole genome-MLST results obtained by genomic epidemiology and pubmlst were consistent with double locus variant clonal complex obtained by Sanger-MLST in 31 isolates. Conclusion MinION sequencer provides a rapid, cost-effective and promising pathway for performing WGS by a pocked-sized device for epidemiological purposes but improving its sequencing accuracy will make it more appealing to be used in clinical microbiology laboratories.


2016 ◽  
Vol 40 ◽  
pp. 200-204 ◽  
Author(s):  
Idrissa Diawara ◽  
Khalid Zerouali ◽  
Khalid Katfy ◽  
Abouddihaj Barguigua ◽  
Houria Belabbes ◽  
...  

PLoS ONE ◽  
2015 ◽  
Vol 10 (3) ◽  
pp. e0120467 ◽  
Author(s):  
Lei Wang ◽  
Yong-Liang Jiang ◽  
Jing-Ren Zhang ◽  
Cong-Zhao Zhou ◽  
Yuxing Chen

2001 ◽  
Vol 355 (2) ◽  
pp. 431 ◽  
Author(s):  
Daniel R. SYLVESTER ◽  
Emilio ALVAREZ ◽  
Arun PATEL ◽  
Kapila RATNAM ◽  
Howard KALLENDER ◽  
...  

2010 ◽  
Vol 192 (9) ◽  
pp. 2346-2358 ◽  
Author(s):  
Alina D. Gutu ◽  
Kyle J. Wayne ◽  
Lok-To Sham ◽  
Malcolm E. Winkler

ABSTRACT The WalRK two-component system plays important roles in maintaining cell wall homeostasis and responding to antibiotic stress in low-GC Gram-positive bacteria. In the major human pathogen, Streptococcus pneumoniae, phosphorylated WalR Spn (VicR) response regulator positively controls the transcription of genes encoding the essential PcsB division protein and surface virulence factors. WalR Spn is phosphorylated by the WalK Spn (VicK) histidine kinase. Little is known about the signals sensed by WalK histidine kinases. To gain information about WalK Spn signal transduction, we performed a kinetic characterization of the WalRK Spn autophosphorylation, phosphoryltransferase, and phosphatase reactions. We were unable to purify soluble full-length WalK Spn . Consequently, these analyses were performed using two truncated versions of WalK Spn lacking its single transmembrane domain. The longer version (Δ35 amino acids) contained most of the HAMP domain and the PAS, DHp, and CA domains, whereas the shorter version (Δ195 amino acids) contained only the DHp and CA domains. The autophosphorylation kinetic parameters of Δ35 and Δ195 WalK Spn were similar [Km (ATP) ≈ 37 μM; k cat ≈ 0.10 min−1] and typical of those of other histidine kinases. The catalytic efficiency of the two versions of WalK Spn ∼P were also similar in the phosphoryltransfer reaction to full-length WalR Spn . In contrast, absence of the HAMP-PAS domains significantly diminished the phosphatase activity of WalK Spn for WalR Spn ∼P. Deletion and point mutations confirmed that optimal WalK Spn phosphatase activity depended on the PAS domain as well as residues in the DHp domain. In addition, these WalK Spn DHp domain and ΔPAS mutations led to attenuation of virulence in a murine pneumonia model.


Author(s):  
In-Hwa Choi ◽  
Jai-Heon Shim ◽  
Seung-Whan Kim ◽  
Su-Nam Kim ◽  
Suhk-Neung Pyo ◽  
...  

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