Table 2 Comparison of BAL sample analysis results obtained by DAMIAN, Taxonomer BETA, PathoScope and metaMix.

DAMIAN

23,828,285 reads 99,23% human sequences

3,265,314 reads 51,74% human sequences

2,370,210 reads 98,13% human sequences

✓ Influenza A (39,810 reads; 42%)

• H1N1 all 8 segments (8 contigs) 97–100% id.

○ Influenza A

○ A/Singapore/TT198/2011 (H1N1)

○ A/Swine/France/71-130116/2013 (H1N1)

○ A/Swine/France/71-130116/2013 (H1N1)

○ A/Singapore/TT198/2011 (H1N1)

○ A/Santa Clara/YGA_03065/2013(H1N1),

○ A/Arizona/M2/2012(H1N1)

○ A/Swine/France/71-130116/2013 (H1N1)

✓ Candida albicans (14,249 reads, 15.15%)

✓ Influenza A (1,886 reads, 1.57%)

• H3N2 all 8 segments (8 contigs) 99% id.

○ PB2, A/Connecticut/Flu140/2013(H3N2)

○ PB1, A/Connecticut/Flu140/2013(H3N2)

○ PA, A/Connecticut/Flu140/2013(H3N2)

○ HA, A/Connecticut/Flu140/2013(H3N2)

○ NP, A/Connecticut/Flu140/2013(H3N2)

○ NA, A/Connecticut/Flu140/2013(H3N2)

○ M2, M1, A/Connecticut/Flu140/2013(H3N2)

○ NEP,NS1, A/Connecticut/Flu140/2013(H3N2)

✓ human parainfluenza 3 virus (1 read) 99% id.

✓ human herpes simplex virus 1 (4 reads) 99% id.

✓ Candida albicans (10,207 reads, 7.65%)

✓ Chlamydophila psittaci (237 reads; 4.13%) 100%id.

• Chlamydophila psittacci 6BC, 4 contigs, 16S and 23S rRNA

• Chamydophila VS225, 1 contig, 16S rRNA

• Chlamydophila Mat116, 1 contig, 16S rRNA

Taxonomer

BETA

9,900,000 reads sampled^*; 5% classified

Bacteria: 62,128 reads; Viruses: 10,723 reads; Fungi: 86 reads

3,200,000 reads samples; 13% classified

Bacteria: 300,309 reads; Viruses: 7,686 reads; Fungi: 17,878 reads

2,300,000 reads samples; 4% classified

Bacteria: 24,960 reads; Viruses: 950 reads;

✓ Influenza A (1,227 reads)

• H1N1 (1,227 reads)

✓ α-retrovirus (9,677 reads)

✓ dsDNA virus (505 reads)

✓ Influenza A (1,433 reads)

• H3N2 (354 reads)

✓ Human parainfluenza 3 virus (13 reads)

✓ α-retrovirus (907 reads)

✓ Caudovirales (1,299 reads)

✓ Herpesviridae (184 reads)

✓ Candida albicans (15,537 reads)

✓ Chlamydia (75 reads)

• Chlamydia psittaci (33 reads)

• Chlamydia trachomatis (30 reads)

✓ Proteobacteria (510 reads)

✓ Firmicutes (33 reads)

✓ α-retrovirus (169 reads)

✓ Herpesviridae (52 reads)

PathoScope

   45,576 aligned reads; 2,234 hits

✓ Influenza A (12,234 reads)

• Subtypes H3N2; H5N1; H1N1; H9N2; H2N2

✓ Hepatitis C (224 reads)

• Genotype 2; 1; 6

✓ Encephalomyocarditis Virus (115 reads)

   184,719 aligned reads; 2,434 hits

✓ Influenza A (1,337 reads)

✓ Subtypes H3N2

✓ Avian leukosis virus (1,256 reads)

✓ human herpes simplex virus 1 (102 reads)

✓ Veillonella parvula (130,363 reads)

✓ Enterococcus faecium (21,178 reads)

   4,408 aligned reads; 1,752 hits

✓ Chlamydophila psittaci (23.83 reads)#

metaMix

26 hits; 7,328,046 human reads

✓ Influenza A (1 contig; 46,698 reads)

• H1N1, 1 contig; A/Canela/LACENRS-418/2013

✓ Candida albicans SC5314 2 contigs (601,527 reads)

Bacteria 3 contigs (372 reads)

44 hits; 201,764 human reads

✓ Influenza A (3 contigs; 2,244 reads)

• H3N2, 2 contigs; A/Bage/LACENRS-205/2013;

A/Porto Alegre/LACENRS-275/2013

✓ Candida albicans, 1 contig (97,816reads)

Bacteria; 15 contigs (109,048 reads)

16 hits; 142,965 human reads

✓ Chlamydia psittaci (1 contig; 252 reads)