Identification of  Streptococcus pneumoniae  and other Mitis streptococci: importance of molecular methods

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Abstract

The Mitis group of streptococci includes an important human pathogen, Streptococcus pneumoniae (pneumococcus) and about 20 other related species with much lower pathogenicity. In clinical practice, some representatives of these species, especially Streptococcus pseudopneumoniae and Streptococcus mitis, are sometimes mistaken for S. pneumoniae based on the results of classical microbiological methods, such as optochin susceptibility and bile solubility. Several various molecular approaches that address the issue of correct identification of pneumococci and other Mitis streptococci have been proposed and are discussed in this review, including PCR- and gene sequencing-based tests as well as new developments in the genomic field that represents an important advance in our understanding of relationships within the Mitis group.

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Kraken: ultrafast metagenomic sequence classification using exact alignments

Derrick E Wood, Steven L Salzberg (2014)

Kraken is an ultrafast and highly accurate program for assigning taxonomic labels to metagenomic DNA sequences. Previous programs designed for this task have been relatively slow and computationally expensive, forcing researchers to use faster abundance estimation programs, which only classify small subsets of metagenomic data. Using exact alignment of k-mers, Kraken achieves classification accuracy comparable to the fastest BLAST program. In its fastest mode, Kraken classifies 100 base pair reads at a rate of over 4.1 million reads per minute, 909 times faster than Megablast and 11 times faster than the abundance estimation program MetaPhlAn. Kraken is available at http://ccb.jhu.edu/software/kraken/.

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Burden of Streptococcus pneumoniae and Haemophilus influenzae type b disease in children in the era of conjugate vaccines: global, regional, and national estimates for 2000–15

Brian Wahl, Katherine L O'Brien, Adena Greenbaum … (2018)

Summary Background Pneumococcal conjugate vaccine (PCV) and Haemophilus influenzae type b (Hib) vaccine are now used in most countries. To monitor global and regional progress towards improving child health and to inform national policies for disease prevention and treatment, we prepared global, regional, and national disease burden estimates for these pathogens in children from 2000 to 2015. Methods Using WHO and Maternal and Child Epidemiology Estimation collaboration country-specific estimates of pneumonia and meningitis mortality and pneumonia morbidity from 2000 to 2015, we applied pneumococcal and Hib cause-specific proportions to estimate pathogen-specific deaths and cases. Summary estimates of the proportion of pneumonia deaths and cases attributable to these pathogens were derived from four Hib vaccine and six PCV efficacy and effectiveness study values. The proportion of meningitis deaths due to each pathogen was derived from bacterial meningitis aetiology and adjusted pathogen-specific meningitis case–fatality data. Pneumococcal and Hib meningitis cases were inferred from modelled pathogen-specific meningitis deaths and literature-derived case–fatality estimates. Cases of pneumococcal and Hib syndromes other than pneumonia and meningitis were estimated using the ratio of pathogen-specific non-pneumonia, non-meningitis cases to pathogen-specific meningitis cases from the literature. We accounted for annual HIV infection prevalence, access to care, and vaccine use. Findings We estimated that there were 294 000 pneumococcal deaths (uncertainty range [UR] 192 000–366 000) and 29 500 Hib deaths (18 400–40 700) in HIV-uninfected children aged 1–59 months in 2015. An additional 23 300 deaths (15 300–28 700) associated with pneumococcus and fewer than 1000 deaths associated Hib were estimated to have occurred in children infected with HIV. We estimate that pneumococcal deaths declined by 51% (7–74) and Hib deaths by 90% (78–96) from 2000 to 2015. Most children who died of pneumococcus (81%) and Hib (76%) presented with pneumonia. Less conservative assumptions result in pneumococcccal death estimates that could be as high as 515 000 deaths (302 000–609 000) in 2015. Approximately 50% of all pneumococcal deaths in 2015 occurred in four countries in Africa and Asia: India (68 700 deaths, UR 44 600–86 100), Nigeria (49 000 deaths, 32 400–59 000), the Democratic Republic of the Congo (14 500 deaths, 9300–18 700), and Pakistan (14 400 deaths, 9700–17 000]). India (15 600 deaths, 9800–21 500), Nigeria (3600 deaths, 2200–5100), China (3400 deaths, 2300–4600), and South Sudan (1000 deaths, 600–1400) had the greatest number of Hib deaths in 2015. We estimated 3·7 million episodes (UR 2·7 million–4·3 million) of severe pneumococcus and 340 000 episodes (196 000–669 000) of severe Hib globally in children in 2015. Interpretation The widespread use of Hib vaccine and the recent introduction of PCV in countries with high child mortality is associated with reductions in Hib and pneumococcal cases and deaths. Uncertainties in the burden of pneumococcal disease are largely driven by the fraction of pneumonia deaths attributable to pneumococcus. Progress towards further reducing the global burden of Hib and pneumococcal disease burden will depend on the efforts of a few large countries in Africa and Asia. Funding Bill & Melinda Gates Foundation.

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Clinical presentation, etiology, and outcome of infective endocarditis in the 21st century: the International Collaboration on Endocarditis-Prospective Cohort Study.

David R. Murdoch, G Ralph Corey, Bruno Hoen … (2009)

We sought to provide a contemporary picture of the presentation, etiology, and outcome of infective endocarditis (IE) in a large patient cohort from multiple locations worldwide. Prospective cohort study of 2781 adults with definite IE who were admitted to 58 hospitals in 25 countries from June 1, 2000, through September 1, 2005. The median age of the cohort was 57.9 (interquartile range, 43.2-71.8) years, and 72.1% had native valve IE. Most patients (77.0%) presented early in the disease (<30 days) with few of the classic clinical hallmarks of IE. Recent health care exposure was found in one-quarter of patients. Staphylococcus aureus was the most common pathogen (31.2%). The mitral (41.1%) and aortic (37.6%) valves were infected most commonly. The following complications were common: stroke (16.9%), embolization other than stroke (22.6%), heart failure (32.3%), and intracardiac abscess (14.4%). Surgical therapy was common (48.2%), and in-hospital mortality remained high (17.7%). Prosthetic valve involvement (odds ratio, 1.47; 95% confidence interval, 1.13-1.90), increasing age (1.30; 1.17-1.46 per 10-year interval), pulmonary edema (1.79; 1.39-2.30), S aureus infection (1.54; 1.14-2.08), coagulase-negative staphylococcal infection (1.50; 1.07-2.10), mitral valve vegetation (1.34; 1.06-1.68), and paravalvular complications (2.25; 1.64-3.09) were associated with an increased risk of in-hospital death, whereas viridans streptococcal infection (0.52; 0.33-0.81) and surgery (0.61; 0.44-0.83) were associated with a decreased risk. In the early 21st century, IE is more often an acute disease, characterized by a high rate of S aureus infection. Mortality remains relatively high.

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Author and article information

Contributors

Ewa Sadowy:

ORCID: http://orcid.org/0000-0003-0284-6440

e.sadowy@nil.gov.pl , https://orcid.org/0000-0003-0284-6440

Journal

Journal ID (nlm-ta): Eur J Clin Microbiol Infect Dis

Journal ID (iso-abbrev): Eur J Clin Microbiol Infect Dis

Title: European Journal of Clinical Microbiology & Infectious Diseases

Publisher: Springer Berlin Heidelberg (Berlin/Heidelberg )

ISSN (Print): 0934-9723

ISSN (Electronic): 1435-4373

Publication date (Electronic): 24 July 2020

Publication date PMC-release: 24 July 2020

Publication date (Print): 2020

Volume: 39

Issue: 12

Pages: 2247-2256

Affiliations

[1 ]GRID grid.419694.7, ISNI 0000 0004 0622 0266, Department of Molecular Microbiology, , National Medicines Institute, ; Chełmska 30/34, 00-725 Warsaw, Poland

[2 ]GRID grid.419694.7, ISNI 0000 0004 0622 0266, Department of Epidemiology and Clinical Microbiology, , National Medicines Institute, ; Chełmska 30/34, 00-725 Warsaw, Poland

Author information

Ewa Sadowy http://orcid.org/0000-0003-0284-6440

Waleria Hryniewicz https://orcid.org/0000-0002-3651-9790

Article

Publisher ID: 3991

DOI: 10.1007/s10096-020-03991-9

PMC ID: 7669753

PubMed ID: 32710352

SO-VID: b014476d-f45d-486d-ac8c-fb5b510e2208

License:

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

History

Date received : 20 May 2020

Date accepted : 15 July 2020

Funding

Funded by: FundRef http://dx.doi.org/10.13039/501100004281, Narodowe Centrum Nauki;

Award ID: 2013/10/M/NZ2/00259

Funded by: Ministerstwo Zdrowia

Award ID: Narodowy Program Ochrony Antybiotyków (NPOA)

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ScienceOpen disciplines: Infectious disease & Microbiology

Keywords: streptococcus,pcr,sequencing,mlsa,wgs

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ScienceOpen disciplines: Infectious disease & Microbiology

Keywords: streptococcus, pcr, sequencing, mlsa, wgs

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Identification of Streptococcus pneumoniae and other Mitis streptococci: importance of molecular methods

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Most cited references 109

Kraken: ultrafast metagenomic sequence classification using exact alignments

Burden of Streptococcus pneumoniae and Haemophilus influenzae type b disease in children in the era of conjugate vaccines: global, regional, and national estimates for 2000–15

Clinical presentation, etiology, and outcome of infective endocarditis in the 21st century: the International Collaboration on Endocarditis-Prospective Cohort Study.

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