Clinical detection of human probiotics and human pathogenic bacteria by using a novel high-throughput platform based on next generation sequencing

Table 3 The quantities (matched sequenced reads) of pathogens identified in the samples in the case study

Pathogens	B011	B012	B013	B014	B016	B017	B018	B019	B020	B031	B033	B034
Bordetella pertussis	0	1	0	0	0	1	0	0	0	0	0	0	2
Brucella abortus	0	0	0	0	0	0	0	0	0	0	0	0	0
Brucella melitensis	0	0	0	0	0	0	0	0	0	0	0	0	0
Campylobacter jejuni	0	0	0	11	0	0	0	0	0	11	1	40	63
Clostridium botulinum	0	38	5048	4	5	2	1	361	153	1211	115	59	6997
Clostridium difficile	0	0	1	0	0	0	0	0	0	0	0	0	1
Clostridium perfringens	0	1	2	0	0	0	0	3	10	24	12	93	145
Corynebacterium diphtheriae	0	1	0	1	0	0	0	0	0	1	0	0	3
Enterococcus faecalis	57	13	1	4	8	4	0	20	5	19	6	38	175
Enterococcus faecium	41	8	2	6	5	2	1	22	3	13	1	32	136
*Escherichia coli	1744	8560	7900	3637	10651	4404	5691	1424	1733	210	165	4483	50602
*Haemophilus influenzae	2	1771	2	1055	8	49	1	171	15	1802	2322	4502	11700
Neisseria meningitidis	0	2	0	3	1	0	1	1	1	1	1	1	12
Pseudomonas aeruginosa	1	6	6	4	2	2	3	1	3	0	0	3	31
*Salmonella enterica	1570	9291	7978	1849	9864	4209	5726	622	1658	303	44	4495	47609
Shigella sonnei	41	243	239	32	308	122	192	8	41	1	1	98	1326
Staphylococcus aureus	0	0	0	0	0	0	0	0	1	0	0	0	1
Staphylococcus epidermidis	0	0	0	0	0	0	0	1	1	0	0	0	2
Streptococcus agalactiae	0	69	3	0	5	0	1	0	0	3	6	5	92
Streptococcus pneumoniae	46	26	9	16	1	36	3	46	25	272	5	154	639
Streptococcus pyogenes	7	76	149	14	10	112	9	94	23	417	45	1428	2384
Vibrio cholerae	0	3	0	0	0	1	1	0	1	0	1	0	7
Yersinia pestis	0	0	1	29	2	0	0	1	0	906	0	5	944
	3509	20109	21341	6665	20870	8944	11630	2775	3673	5194	2725	15436

For each species, if the number of reads is 0 for all samples, that species was not shown.
*The leading three pathogens are Escherichia coli, Salmonella enterica and Haemophilus influenzae.