1
|
Williams AN, Ma A, Croxen MA, Demczuk WHB, Martin I, Tyrrell GJ. Genomic analysis of Streptococcus pneumoniae serogroup 20 isolates in Alberta, Canada from 1993-2019. Microb Genom 2023; 9:001141. [PMID: 38015202 PMCID: PMC10711305 DOI: 10.1099/mgen.0.001141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 11/09/2023] [Indexed: 11/29/2023] Open
Abstract
In the province of Alberta, Canada, invasive disease caused by Streptococcus pneumoniae serogroup 20 (serotypes 20A/20B) has been increasing in incidence. Here, we characterize provincial invasive serogroup 20 isolates collected from 1993 to 2019 alongside invasive and non-invasive serogroup 20 isolates from the Global Pneumococcal Sequencing (GPS) Project collected from 1998 to 2015. Trends in clinical metadata and geographic location were evaluated, and serogroup 20 isolate genomes were subjected to molecular sequence typing, virulence and antimicrobial resistance factor mining, phylogenetic analysis and pangenome calculation. Two hundred and seventy-four serogroup 20 isolates from Alberta were sequenced, and analysed along with 95 GPS Project genomes. The majority of invasive Alberta serogroup 20 isolates were identified after 2007 in primarily middle-aged adults and typed predominantly as ST235, a sequence type that was rare among GPS Project isolates. Most Alberta isolates carried a full-length whaF capsular gene, suggestive of serotype 20B. All Alberta and GPS Project genomes carried molecular resistance determinants implicated in fluoroquinolone and macrolide resistance, with a few Alberta isolates exhibiting phenotypic resistance to azithromycin, clindamycin, erythromycin, tetracycline and trimethoprim-sulfamethoxazole, as well as non-susceptibility to tigecycline. All isolates carried multiple virulence factors including those involved in adherence, immune modulation and nutrient uptake, as well as exotoxins and exoenzymes. Phylogenetically, Alberta serogroup 20 isolates clustered with predominantly invasive GPS Project isolates from the USA, Israel, Brazil and Nepal. Overall, this study highlights the increasing incidence of invasive S. pneumoniae serogroup 20 disease in Alberta, Canada, and provides insights into the genetic and clinical characteristics of these isolates within a global context.
Collapse
Affiliation(s)
- Ashley N. Williams
- Department of Laboratory Medicine and Pathology, University of Alberta, 5-411 Edmonton Clinic Health Academy, Edmonton, Alberta, T6G 1C9 Canada
- Alberta Precision Laboratory – Public Health Laboratory, 8440 112 Street NW, Edmonton, Alberta, T6G 2B7 Canada
| | - Angela Ma
- Department of Laboratory Medicine and Pathology, University of Alberta, 5-411 Edmonton Clinic Health Academy, Edmonton, Alberta, T6G 1C9 Canada
- Department of Pathology, University of Utah School of Medicine, 15 North Medical Drive East, Ste. #1100, Salt Lake City, UT, 84112 USA
| | - Matthew A. Croxen
- Department of Laboratory Medicine and Pathology, University of Alberta, 5-411 Edmonton Clinic Health Academy, Edmonton, Alberta, T6G 1C9 Canada
- Alberta Precision Laboratory – Public Health Laboratory, 8440 112 Street NW, Edmonton, Alberta, T6G 2B7 Canada
- Li Ka Shing Institute of Virology, University of Alberta, 6-010 Katz Centre for Health Research, 11315 - 87 Ave NW, Edmonton, Alberta, T6G 2E1 Canada
- Women & Children’s Health Research Institute (WCHRI), University of Alberta, 5-083 Edmonton Clinic Health Academy (ECHA), 11405 87 Avenue NW Edmonton, AB, T6G 1C9 Canada
| | - Walter H. B. Demczuk
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba, R3E 3R2 Canada
| | - Irene Martin
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba, R3E 3R2 Canada
| | - Gregory J. Tyrrell
- Department of Laboratory Medicine and Pathology, University of Alberta, 5-411 Edmonton Clinic Health Academy, Edmonton, Alberta, T6G 1C9 Canada
- Alberta Precision Laboratory – Public Health Laboratory, 8440 112 Street NW, Edmonton, Alberta, T6G 2B7 Canada
- Li Ka Shing Institute of Virology, University of Alberta, 6-010 Katz Centre for Health Research, 11315 - 87 Ave NW, Edmonton, Alberta, T6G 2E1 Canada
| |
Collapse
|
2
|
Till P. RNA Characterization in Trichoderma reesei. Methods Mol Biol 2021; 2234:191-235. [PMID: 33165790 DOI: 10.1007/978-1-0716-1048-0_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
This chapter provides an overview on different methods for the characterization of RNAs in Trichoderma reesei. In the first section, protocols for the extraction of total RNA from fungal mycelia and the identification of 5' and 3' ends of certain RNAs of interest via rapid amplification of cDNA ends (RACE) are presented. In the next section, this knowledge on the transcriptional start and end points is used for in vitro synthesis and fluorescence labeling of the RNA of interest. The in vitro synthesized RNA can then be applied for in vitro analyses such as RNA electrophoretic mobility shift assays (RNA-EMSA) and RNA in vitro footprinting. RNA-EMSA is a method suitable for the identification and characterization of RNA-protein interactions or interactions of an RNA with other nucleic acids. RNA in vitro footprinting allows exact mapping of protein-binding sites on RNA molecules and also the determination of RNA secondary and tertiary structures at singe-nucleotide resolution. All protocols presented in this chapter are optimized for the analysis of noncoding RNAs (ncRNAs), especially long ncRNAs (lncRNAs) or other specific RNA species of more than 200 nt in length.
Collapse
Affiliation(s)
- Petra Till
- Christian Doppler laboratory for optimized expression of carbohydrate-active enzymes, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria.
| |
Collapse
|
3
|
Fourmy D, Yoshizawa S. Protein-RNA footprinting: an evolving tool. WILEY INTERDISCIPLINARY REVIEWS-RNA 2012; 3:557-66. [PMID: 22566372 DOI: 10.1002/wrna.1119] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
As more RNA molecules with important cellular functions are discovered, there is a strong need to characterize their structures, functions, and interactions. Chemical and enzymatic footprinting methods are used to map RNA secondary and tertiary structure, to monitor ligand interactions and conformational changes, and in the study of protein-RNA interactions. These methods provide data at single-nucleotide resolution that nicely complements the structural information available from X-ray diffraction, nuclear magnetic resonance spectroscopy (NMR), or cryo-electron microscopy. Footprinting methods also complement the dynamic information derived from single-molecule Förster resonance energy transfer. RNA footprinting tools have been used for decades, but we have recently seen spectacular advances, for instance, the use in combination with massive parallel sequencing techniques. Large libraries of RNA molecules (small or large in size) can now be probed in high-throughput manner when RNA footprinting methods are combined with fluorescent probe technologies and automation. In this article, after a brief historical overview, we summarize recent advances in RNA-protein footprinting methodologies that now integrate tools for massive parallel analysis.
Collapse
Affiliation(s)
- Dominique Fourmy
- Centre de Génétique Moléculaire UPR 3404, CNRS, Université Paris-Sud, Gif-sur-Yvette, France.
| | | |
Collapse
|
4
|
Fleishman SJ, Corn JE, Strauch EM, Whitehead TA, Andre I, Thompson J, Havranek JJ, Das R, Bradley P, Baker D. Rosetta in CAPRI rounds 13-19. Proteins 2011; 78:3212-8. [PMID: 20597089 PMCID: PMC2952713 DOI: 10.1002/prot.22784] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Modeling the conformational changes that occur on binding of macromolecules is an unsolved challenge. In previous rounds of the Critical Assessment of PRediction of Interactions (CAPRI), it was demonstrated that the Rosetta approach to macromolecular modeling could capture side chain conformational changes on binding with high accuracy. In rounds 13-19 we tested the ability of various backbone remodeling strategies to capture the main-chain conformational changes observed during binding events. These approaches span a wide range of backbone motions, from limited refinement of loops to relieve clashes in homologous docking, through extensive remodeling of loop segments, to large-scale remodeling of RNA. Although the results are encouraging, major improvements in sampling and energy evaluation are clearly required for consistent high accuracy modeling. Analysis of our failures in the CAPRI challenges suggest that conformational sampling at the termini of exposed beta strands is a particularly pressing area for improvement.
Collapse
Affiliation(s)
- Sarel J Fleishman
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|