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Supplemental Information

Detection and characterisation of Mycobacterium tuberculosis in sputum samples using shotgun metagenomics Figure S1 Detailed phylogenetic placement of metagenome-derived genomes

For each sample, the majority bases at each reference SNP position (or gaps if there was no coverage at that position) were concatenated and the sequence was placed in the reference tree using pplacer (see Methods). The output from pplacer (jplace file) was parsed and a new file produced, such that each alternative placement for a sample could be displayed in the tree along with the posterior probability of that placement. Trees were generated from the modified place file, using guppy from the pplacer suite of programs. Only the top 3 placements for each sample are shown. The combined pp values for each alternative placement of sample in a clade were used to ascertain the likelihood of that sample belonging to that clade.

DOI: 10.7287/peerj.preprints.482v1/supp-1

SNP matrix used to generate tree shown in Figure 1

DOI: 10.7287/peerj.preprints.482v1/supp-2

Repetitive genes excluded from SNP calling

DOI: 10.7287/peerj.preprints.482v1/supp-3

Additional Information

Competing Interests

There are no competing interests.

Author Contributions

Emma L Doughty conceived and designed the experiments, performed the experiments, analyzed the data, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

Martin J Sergeant conceived and designed the experiments, performed the experiments, analyzed the data, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

Ifedayo M.O Adetifa conceived and designed the experiments, contributed reagents/materials/analysis tools.

Martin Antonio conceived and designed the experiments, reviewed drafts of the paper.

Mark J Pallen conceived and designed the experiments, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

Human Ethics

The following information was supplied relating to ethical approvals (i.e., approving body and any reference numbers):

The joint Gambia Government/MRC Ethics Committee approved this investigation under reference SCC 1232 and informed written consent was obtained for all participants.

DNA Deposition

The following information was supplied regarding the deposition of DNA sequences:

Metagenomic sequence reads from this study (excluding those that mapped to the human genome) will be deposited in the European Nucleotide Archive (project accession number pending).

Funding

Support for Emma Doughty's PhD studentship and research costs was provided by Warwick Medical School and MRC Unit, The Gambia. Support for Martin Sergeant's salary was provided by Warwick Medical School. The Enhanced Case Finding project was funded and sponsored by the MRC Unit, The Gambia. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.


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