Dense genomic sampling identifies highways of pneumococcal recombination

Chewapreecha, Claire; Harris, Simon R.; Croucher, Nicholas J.; Turner, Claudia; Marttinen, Pekka; Cheng, Lu; Pessia, Alberto; Aanensen, David M.; Mather, Alison E.; Page, Andrew J.; Salter, Susannah J.; Harris, David; Nosten, François; Green, David; Corander, Jukka; Parkhill, Julian; Turner, Paul; Bentley, Stephen D.

doi:10.1038/ng.2895

Cited by 368 publications

(538 citation statements)

References 44 publications

Supporting

Mentioning

511

Contrasting

Order By: Relevance

“…While non-typeable pneumococcal isolates are more commonly associated with carriage rather than invasive disease, non-typeable pneumococci has been isolated from children with IPD. 17,30,31 Furthermore, recent evidence suggests that non-typeable pneumococci have high genetic recombination potential leading to the possibility of spreading antibiotic resistance making their identification important for surveillance studies 32,33,34 Approximately 50% of the pneumococcal isolates found during our study were non-PCV13 serotypes (with an additional 44% of the types being non-typeable). One-third of the a CLSI breakpoints used for determination of susceptibility ( 2 mg/mL penicillin, 2 mg/mL cefotaxime, 2 mg/mL trimethoprim-sulfamethoxazole).…”

Section: Discussionmentioning

confidence: 90%

Nasopharyngeal pneumococcal carriage rates among HIV-infected adults following widespread pediatric use of conjugate pneumococcal vaccine-13

Feola

Bonville

Cibula

et al. 2016

Human Vaccines & Immunotherapeutics

View full text Add to dashboard Cite

Background: Nasopharyngeal pneumococcal carriage rates among HIV-infected adults has not been described since conjugate pneumococcal vaccine-13 (PCV13) was added to the universal infant and childhood vaccination schedule in 2010. Methods: HIV-infected adults presenting for routine health care visits to the Designated AIDS Center in Syracuse, NY between December 2013 and June 2015 were eligible for enrollment. Demographic, medical, and social history were recorded after obtaining informed consent. Nasopharyngeal samples were collected and cultured for the presence of Streptococcus pneumoniae using standard microbiologic techniques. Antibiotic susceptibility testing was performed using E-test!. Results: 707 nasopharyngeal samples were collected from 414 HIV-infected adults. 18 samples were culture positive for S. pneumoniae; 1 (6%) isolate was of vaccine-type, 9 (50%) were non-vaccine types, and 8 (44%) were non-typeable. The 18 isolates were recovered from 15 different patients (4% of those enrolled). Three patients were culture positive for pneumococcus isolated from 2 consecutive samples, with non-typeable pneumococci identified consecutively from 2 patients and serotype 35B identified consecutively from 1 patient. The most commonly identified non-vaccine serotypes were 35B and 15B/C. Identified pneumococci were penicillin and cefotaxime susceptible. Conclusion: Four percent of HIVinfected adults in our study population were colonized with S. pneumoniae. The non-vaccine serotypes 35B and 15B/C predominated.

show abstract

Section: Discussionmentioning

confidence: 90%

Nasopharyngeal pneumococcal carriage rates among HIV-infected adults following widespread pediatric use of conjugate pneumococcal vaccine-13

Feola

Bonville

Cibula

et al. 2016

Human Vaccines & Immunotherapeutics

View full text Add to dashboard Cite

show abstract

“…This whole genome alignment allowed calculation of SNP and INDEL rates across recent S. pneumoniae evolutionary history. We used previously determined parameters for the rate of codon evolution 14 , relative rate of SNPs to indels in coding regions 15 , rates of gene loss and horizontal gene transfer 16 when running the simulation. We then used ALF with these parameters to simulate the evolution of coding sequences from the root genome along the given phylogeny.…”

Section: Methodsmentioning

confidence: 99%

Evaluation of phylogenetic reconstruction methods using bacterial whole genomes: a simulation based study

Lees¹,

Kendall²,

Parkhill³

et al. 2018

Wellcome Open Res

Self Cite

View full text Add to dashboard Cite

Background: Phylogenetic reconstruction is a necessary first step in many analyses which use whole genome sequence data from bacterial populations. There are many available methods to infer phylogenies, and these have various advantages and disadvantages, but few unbiased comparisons of the range of approaches have been made. Methods: We simulated data from a defined “true tree” using a realistic evolutionary model. We built phylogenies from this data using a range of methods, and compared reconstructed trees to the true tree using two measures, noting the computational time needed for different phylogenetic reconstructions. We also used real data from Streptococcus pneumoniae alignments to compare individual core gene trees to a core genome tree. Results: We found that, as expected, maximum likelihood trees from good quality alignments were the most accurate, but also the most computationally intensive. Using less accurate phylogenetic reconstruction methods, we were able to obtain results of comparable accuracy; we found that approximate results can rapidly be obtained using genetic distance based methods. In real data we found that highly conserved core genes, such as those involved in translation, gave an inaccurate tree topology, whereas genes involved in recombination events gave inaccurate branch lengths. We also show a tree-of-trees, relating the results of different phylogenetic reconstructions to each other. Conclusions: We recommend three approaches, depending on requirements for accuracy and computational time. Quicker approaches that do not perform full maximum likelihood optimisation may be useful for many analyses requiring a phylogeny, as generating a high quality input alignment is likely to be the major limiting factor of accurate tree topology. We have publicly released our simulated data and code to enable further comparisons.

show abstract

“…In large-scale genome sequencing of bacterial strains, we see thousands of recombination events [15], and indeed, on occasion, explaining phenotypes requires methods that explicitly need to account for and remove vertical transmission signals [16]. One thousand eubacterial genes have flowed into the stem lineage of halophilic Archaebacteria and identification of this important evolutionary event required the modelling of horizontal, rather than vertical gene flows [17].…”

Section: Introductionmentioning

confidence: 99%

The ring of life hypothesis for eukaryote origins is supported by multiple kinds of data

McInerney

Pisani

O’Connell

2015

Phil. Trans. R. Soc. B

View full text Add to dashboard Cite

One contribution of 17 to a theme issue 'Eukaryotic origins: progress and challenges'. The literature is replete with manuscripts describing the origin of eukaryotic cells. Most of the models for eukaryogenesis are either autogenous (sometimes called slow-drip), or symbiogenic (sometimes called big-bang). In this article, we use large and diverse suites of 'Omics' and other data to make the inference that autogeneous hypotheses are a very poor fit to the data and the origin of eukaryotic cells occurred in a single symbiosis.

show abstract

Dense genomic sampling identifies highways of pneumococcal recombination

Cited by 368 publications

References 44 publications

Nasopharyngeal pneumococcal carriage rates among HIV-infected adults following widespread pediatric use of conjugate pneumococcal vaccine-13

Nasopharyngeal pneumococcal carriage rates among HIV-infected adults following widespread pediatric use of conjugate pneumococcal vaccine-13

Evaluation of phylogenetic reconstruction methods using bacterial whole genomes: a simulation based study

The ring of life hypothesis for eukaryote origins is supported by multiple kinds of data

Contact Info

Product

Resources

About