Identification of isolated or mixed strains from long reads: a challenge met on Streptococcus thermophilus using a MinION sequencer

This study aimed to provide efficient recognition of bacterial strains on personal computers from MinION (Nanopore) long read data. Thanks to the fall in sequencing costs, the identification of bacteria can now proceed by whole genome sequencing. MinION is a fast, but highly error-prone sequencing device and it is a challenge to successfully identify the strain content of unknown simple or complex microbial samples. It is heavily constrained by memory management and fast access to the read and genome fragments. Our strategy involves three steps: indexing of known genomic sequences for a given or several bacterial species; a request process to assign a read to a strain by matching it to the closest reference genomes; and a final step looking for a minimum set of strains that best explains the observed reads. We have applied our method, called ORI, on 77 strains of Streptococcus thermophilus. We worked on several genomic distances and obtained a detailed classification of the strains, together with a criterion that allows merging of what we termed 'sibling' strains, only separated by a few mutations. Overall, isolated strains can be safely recognized from MinION data. For mixtures of several non-sibling strains, results depend on strain abundance.

Stamp-Perforation-Inspired Micronotch for Selectively Tearing Fiber-Bridged Carbon Nanotube Thin Films and Its Applications for Strain Classification

Cracks typically deteriorate the structural and electrical properties of materials when not properly controlled. A few papers recently reported the controlling methods of crack formation in the brittle materials utilizing the lateral V-notch structure. For ductile materials, however, there have been few papers reporting cracking phenomenon, but full cracking control including predesigned initiation, propagation, and termination has not been reported yet. Therefore, we report a predesigned full cracking control in ductile conductive carbon nanotube (CNT) films by introducing inkjet-printed L-shape micronotch (LMN) structures inspired by directional stamp perforation marks. In spite of the high fracture toughness of CNT films, the LMNs determine locations of initial crack formation and guide crack propagation in a predesigned way. Selective connection of isolated cracks in the CNT film increases its resistance monotonically under tensile strain and thus tremendously well maintains high linearity (adj. R² value > 0.99) in resistance change over record large strain ranges of 0.01-100%, which enables us to quantitatively classify strain values accurately for previously reported practical body signals for the first time. We believe that our facile printing-based crack control strategy not only provides a comprehensive solution to various stretchable sensor applications but also builds a new milestone for cracking mechanism studies in fracture mechanics.

Phylogenetic Analysis of SARS-CoV-2 Data Is Difficult

Numerous studies covering some aspects of SARS-CoV-2 data analyses are being published on a daily basis, including a regularly updated phylogeny on nextstrain.org. Here, we review the difficulties of inferring reliable phylogenies by example of a data snapshot comprising a quality-filtered subset of 8,736 out of all 16,453 virus sequences available on May 5, 2020 from gisaid.org. We find that it is difficult to infer a reliable phylogeny on these data due to the large number of sequences in conjunction with the low number of mutations. We further find that rooting the inferred phylogeny with some degree of confidence either via the bat and pangolin outgroups or by applying novel computational methods on the ingroup phylogeny does not appear to be credible. Finally, an automatic classification of the current sequences into subclasses using the mPTP tool for molecular species delimitation is also, as might be expected, not possible, as the sequences are too closely related. We conclude that, although the application of phylogenetic methods to disentangle the evolution and spread of COVID-19 provides some insight, results of phylogenetic analyses, in particular those conducted under the default settings of current phylogenetic inference tools, as well as downstream analyses on the inferred phylogenies, should be considered and interpreted with extreme caution.

Strain classification of Mycobacterium tuberculosis: congruence between large sequence polymorphisms and spoligotypes

Spoligotyping is used in molecular epidemiological studies, and signature patterns have identified strain families. However, homoplasy occurs in the markers used for spoligotyping, which could lead to identical spoligotypes in phylogenetically unrelated strains. We determined the accuracy of strain classification based on spoligotyping using the six large sequence and single nucleotide polymorphisms-defined lineages as a gold standard. Of 919 Mycobacterium tuberculosis isolates, 870 (95%) were classified into a spoligotype family. Strains from a particular spoligotype family belonged to the same lineage. We did not find convergence to the same spoligotype. Spoligotype families appear to be sub-lineages within the main lineages.