Getting Repeated Species in cell free DNA profiles

[arpit20328]

Hi authors,

I have paired end fastq files of cell free DNA patients infected with sepsis. I have 6 patients files

For these 6 patients the distribution is as follows

Patient 1:
Leuconostoc sp. DORA_2
Escherichia coli
Chlamydia trachomatis
Streptococcus pneumoniae
Vibrio vulnificus
Staphylococcus aureus
Enterococcus faecalis
Mycobacterium leprae
cyanobacterium G8-9
Bacillus paranthracis
Acinetobacter baumannii
Klebsiella pneumoniae
Streptococcus oralis
Lactobacillus crispatus
Mycobacterium tuberculosis
Levilactobacillus brevis
Staphylococcus hominis
Staphylococcus epidermidis
Cutibacterium acnes
Plasmodium ovale
Listeria monocytogenes

Patient 2:

Leuconostoc sp. DORA_2
Chlamydia trachomatis
Escherichia coli
Streptococcus pneumoniae
Vibrio vulnificus
Cutibacterium acnes
Staphylococcus aureus
Enterococcus faecalis
Mycobacterium leprae
Saccharomycodes ludwigii
Acinetobacter baumannii
Lactobacillus crispatus
Klebsiella pneumoniae
Streptococcus oralis
cyanobacterium G8-9
Pseudomonas aeruginosa
Bacillus paranthracis
Staphylococcus hominis
Plasmodium ovale

Patient 3:

Leuconostoc sp. DORA_2
Mycoplasmopsis arginini
Paracoccus acridae
Escherichia coli
Chlamydia abortus
Wenyingzhuangia marina
Klebsiella pneumoniae
Streptomyces malachitofuscus
Streptococcus pneumoniae
Nocardioides sp. OK12
Enterococcus faecium
Chlamydia trachomatis
Staphylococcus aureus
Staphylococcus epidermidis
Enterococcus faecalis
Cutibacterium acnes
Lactobacillus crispatus
Streptomyces gancidicus
Levilactobacillus brevis
Rhodococcus fascians
Mycobacterium leprae
Acinetobacter baumannii
Enterobacter hormaechei
Streptococcus oralis
Bacillus yapensis
Staphylococcus hominis
Streptosporangium violaceochromogenes

Similarly for patients 4,5,6 we are getting at top Leuconostoc sp. DORA_2 and in second spot Escherichia coli

My Question is why the spectrum is not getting changed patient wise. ? It is getting changed when bowtie2 or karken2 based classification is used.

[pmenzel]

These might all be false positive hits, either contamination from the DNA extraction or library prep kits or from kaiju's database search itself.
Cell-free DNA sequencing from blood requires strict measurements of negative controls to filter out background noise!

[arpit20328]

@pmenzel yes. so these results are after wet lab negative template control data removal.

Now question comes of false hits computationally. which is tough to decipher.

False fastq files with fabricated reads might be the best way. but I have figure it out on how to do it.