The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

Whole genome sequencing (WGS) of Mycobacterium tuberculosis has rapidly progressed from a research tool to a clinical application for the diagnosis and management of tuberculosis and in public health surveillance. This development has been facilitated by drastic drops in cost, advances in technology and concerted efforts to translate sequencing data into actionable information. There is, however, a risk that, in the absence of a consensus and international standards, the widespread use of WGS technology may result in data and processes that lack harmonization, comparability and validation. In this Review, we outline the current landscape of WGS pipelines and applications, and set out best practices for M. tuberculosis WGS, including standards for bioinformatics pipelines, curated repositories of resistance-causing variants, phylogenetic analyses, quality control and standardized reporting.

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Whole genome sequencing of Mycobacterium tuberculosis: current standards and open issues.

The molecular clock and its phylogenetic applications to genomic data have changed how we study and understand one of the major human pathogens, Mycobacterium tuberculosis (MTB), the etiologic agent of tuberculosis. Genome sequences of MTB strains sampled at different times are increasingly used to infer when a particular outbreak begun, when a drug-resistant clone appeared and expanded, or when a strain was introduced into a specific region. Despite the growing importance of the molecular clock in tuberculosis research, there is a lack of consensus as to whether MTB displays a clocklike behavior and about its rate of evolution. Here we performed a systematic study of the molecular clock of MTB on a large genomic data set (6,285 strains), covering different epidemiological settings and most of the known global diversity. We found that sampling times below 15-20 years were often insufficient to calibrate the clock of MTB. For data sets where such calibration was possible, we obtained a clock rate between 1x10-8 and 5x10-7 nucleotide changes per-site-per-year (0.04-2.2 SNPs per-genome-per-year), with substantial differences between clades. These estimates were not strongly dependent on the time of the calibration points as they changed only marginally when we used epidemiological isolates (sampled in the last 40 years) or three ancient DNA samples (about 1,000 years old) to calibrate the tree. Additionally, the uncertainty and the discrepancies in the results of different methods were sometimes large, highlighting the importance of using different methods, and of considering carefully their assumptions and limitations.

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The molecular clock of Mycobacterium tuberculosis.

We analyzed human papillomavirus (HPV) prevalences during prevaccination and postvaccination periods to consider possible changes in nonvaccine HPV genotypes after introduction of vaccines that confer protection against 2 high-risk types, HPV16 and HPV18 Our meta-analysis included 9 studies with data for 13,886 girls and women ≤19 years of age and 23,340 women 20–24 years of age We found evidence of cross-protection for HPV31 among the younger age group after vaccine introduction but little evidence for reductions of HPV33 and HPV45 For the group this same age group, we also found slight increases in 2 nonvaccine high-risk HPV types (HPV39 and HPV52) and in 2 possible high-risk types (HPV53 and HPV73) However, results between age groups and vaccines used were inconsistent, and the increases had possible alternative explanations; consequently, these data provided no clear evidence for type replacement Continued monitoring of these HPV genotypes is important

Population-Level Effects of Human Papillomavirus Vaccination Programs on Infections with Nonvaccine Genotypes.

Mycobacterium tuberculosis (M.tb) is a globally distributed, obligate pathogen of humans that can be divided into seven clearly defined lineages. An emerging consensus places the origin and global dispersal of M.tb within the past 6,000 years: identifying how the ancestral clone of M.tb spread and differentiated within this timeframe is important for identifying the ecological drivers of the current pandemic. We used Bayesian phylogeographic inference to reconstruct the migratory history of M.tb in Africa and Eurasia and to investigate lineage specific patterns of spread from a geographically diverse sample of 552 M.tb genomes. Applying evolutionary rates inferred with ancient M.tb genome calibration, we estimated the timing of major events in the migratory history of the pathogen. Inferred timings contextualize M.tb dispersal within historical phenomena that altered patterns of connectivity throughout Africa and Eurasia: trans-Indian Ocean trade in spices and other goods, the Silk Road and its predecessors, the expansion of the Roman Empire, and the European Age of Exploration. We found that Eastern Africa and Southeast Asia have been critical in the dispersal of M.tb. Our results further reveal that M.tb populations have grown through range expansion, as well as in situ, and delineate the independent evolutionary trajectories of bacterial subpopulations underlying the current pandemic.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/mec.15120

Lineage specific histories of Mycobacterium tuberculosis dispersal in Africa and Eurasia.

On the basis of population genomic and phylogeographic analyses of 1669 Mycobacterium tuberculosis lineage 4 (L4) genomes, we find that dispersal of L4 has been completely dominated by historical migrations out of Europe. We demonstrate an intimate temporal relationship between European colonial expansion into Africa and the Americas and the spread of L4 tuberculosis (TB). Markedly, in the age of antibiotics, mutations conferring antimicrobial resistance overwhelmingly emerged locally (at the level of nations), with minimal cross-border transmission of resistance. The latter finding was found to reflect the relatively recent emergence of these mutations, as a similar degree of local restriction was observed for susceptible variants emerging on comparable time scales. The restricted international transmission of drug-resistant TB suggests that containment efforts at the level of individual countries could be successful.

/pdf/global-expansion-of-mycobacterium-tuberculosis-lineage-4-1ec85t1r9v.pdf

Global expansion of Mycobacterium tuberculosis lineage 4 shaped by colonial migration and local adaptation

We report here the draft genome sequence of a Streptococcus species belonging to the S. mitis group. While a clear species identification cannot be made for the isolate, it appears that its most recent common ancestor is the species S. pseudopneumoniae.

https://journals.asm.org/doi/pdf/10.1128/genomeA.00620-18

Draft Genome Sequence of a Potentially Novel Streptococcus Species Belonging to the Streptococcus mitis Group.

BACKGROUND Whether type-specific human papillomavirus (HPV) infection influences the risk of acquiring infections with other HPV types is unclear. We studied concurrent HPV infections in 17-year-old girls from two birth cohorts; the first vaccine-eligible cohort in Norway and a pre-vaccination cohort. METHODS Urine samples were collected and tested for 37 HPV genotypes. This study was restricted to unvaccinated girls from the pre-vaccination cohort (n=5245) and vaccinated girls from the vaccine-eligible cohort (n=4904). Risk of HPV infection was modelled using mixed-effect logistic regression. Expected frequencies of concurrent infection with each pairwise combination of the vaccine types and high-risk types (6/11/16/18/31/33/35/39/45/51/52/56/58/59) were compared to observed frequencies. RESULTS Infection with multiple HPV types was more common among unvaccinated girls than vaccinated girls (9.2% vs. 3.7%). HPV33 and HPV51 was the only HPV-pair that was detected together more often than expected among both unvaccinated (p=0.002) and vaccinated girls (p<0.001). No HPV-pairs were observed significantly less often than expected. CONCLUSIONS HPV33 and HPV51 tended to be involved in co-infection among both unvaccinated and vaccinated girls. The introduction of HPV vaccination does not seem to have had an effect on the tendency of specific HPV types to cluster together.

/pdf/concurrent-infection-with-multiple-human-papillomavirus-5d1f0d96tu.pdf

Ingerid Ørjansen Kirkeleite

Papers

Global expansion of Mycobacterium tuberculosis lineage 4 shaped by colonial migration and local adaptation

Draft Genome Sequence of a Potentially Novel Streptococcus Species Belonging to the Streptococcus mitis Group.

Concurrent infection with multiple human papillomavirus types among unvaccinated and vaccinated 17-year-old Norwegian girls.