Strain-resolved metagenomic analysis of the gut as a reservoir for bloodstream infection pathogens among premature infants in Singapore

Heston, Sarah M.; Lim, Charis Shu En; Ong, Chengsi; Chua, Mei Chien; Kelly, Matthew S.; Yeo, Kee Thai

doi:10.1186/s13099-023-00583-8

Gut Pathogens

Table 3 Genomic concordance of bacterial strains in fecal samples to blood culture isolates

From: Strain-resolved metagenomic analysis of the gut as a reservoir for bloodstream infection pathogens among premature infants in Singapore

Patient	BSI isolate	DOL of BSI	DOL of fecal sample	Coverage overlap (%)	popANI (%)	Population SNPs	conANI (%)
AD8134	Streptococcus agalactiae	0	No strains with popANI > 99.999% in sequenced fecal samples
AT4275	Streptococcus anginosus	0	1	99.9964	100.0000	0	99.9999
HJ2545	Proteus mirabilis	9	5	99.9894	100.0000	0	99.9995
		9	13	99.9883	100.0000	0	99.9995
		9	33	99.8263	99.9999	4	99.9966
		9	38	99.9911	100.0000	0	99.9995
		9	47	89.0305	100.0000	0	99.9956
		9	53	94.5055	99.9998	7	99.9662
		9	59	99.8561	99.9999	4	99.9050
JU9212	Staphylococcus aureus	46	No strains with popANI > 99.999% in sequenced fecal samples
NR7313	Staphylococcus epidermidis	4	2	99.9965	100.0000	0	99.9995
		4	17	90.3569	99.9998	4	99.9933
NZ7258	Klebsiella pneumoniae	15	15	99.9984	100.0000	1	99.9972
		15	49	99.9985	100.0000	0	99.9999
		15	60	99.9986	100.0000	0	99.9999
PL2596	S. agalactiae	65	56	99.9872	100.0000	0	99.9086
		65	61	99.9688	100.0000	0	99.9044
		65	66	99.9788	100.0000	0	99.8543
QA9843	S. agalactiae	32	28	99.9641	100.0000	0	99.9904
RN6899	K. pneumoniae	10	8	99.9991	100.0000	2	99.9998
		10	10	99.9997	100.0000	2	99.9998
RX6831	K. pneumoniae BC120-140220.sorted.bam BC120-140220.sorted.bam BC120-140220.sorted.bam	18	7	99.9946	100.0000	0	99.9998
		18	15	99.9944	100.0000	0	99.9998
		18	35	99.9948	100.0000	1	99.9997
		18	61	99.9943	100.0000	0	99.9995
RX8994	Escherichia coli	14	12	99.9909	100.0000	0	100.000
		14	14	99.9892	100.0000	0	100.000
		14	21	99.9923	100.0000	0	100.000
		14	39	99.9907	100.0000	0	100.000
		14	47	99.9895	100.0000	0	100.000
		14	53	99.9896	100.0000	0	100.000
		14	60	99.9906	100.0000	0	100.000
SG3906	S. epidermidis	50	10	95.0561	99.9999	2	99.9993
		50	19	99.9931	100.0000	1	99.9996
		50	31	99.9935	100.0000	0	99.9980
TN3774	E. coli	6	2	99.9826	100.0000	1	99.9980
		6	5	99.9565	100.0000	0	99.9973
		6	29	99.9325	100.0000	0	99.9978
YC2596	S. aureus	25	No strains with popANI > 99.999% in sequenced fecal samples
YH3562	S. agalactiae	0	3	99.9933	100.0000	0	100.0000
		0	21	99.9983	100.0000	0	99.9975
		0	28	99.9991	100.0000	0	99.9943
		0	35	99.9959	100.0000	0	99.9905
		0	56	99.9662	100.0000	0	99.9836
ZR1676	S. agalactiae	35	No strains with popANI > 99.999% in sequenced fecal samples

BSI bloodstream infection, DOL day of life, popANI population average nucleotide identify, SNP single nucleotide polymorphism, conANI consensus average nucleotide identity

Back to article page

ISSN: 1757-4749

Contact us

Submission enquiries: journalsubmissions@springernature.com