TrueBac™ ID

Sample name

Decision

Genome size 3,619,905
No. of contigs 68
GC content 46.35 %
N50 157,623
DB ver. 20191105
Pipeline ver. 1.92
Sequencing depth N/A
No. of UBCG (paralogs) 92/92 (2)

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ID results

Sequence file(s)

Clostridium scindens ATCC 35704 is identified as Clostridium scindens by genomic evidence.

No.	Hit taxon	ANI (%)	ANI coverage (%)	16S (%)	recA (%)	rplC (%)	Taxonomy
1	Clostridium scindens	99.9651	100.0	100.0	100.0	100.0	Bacteria;;;Firmicutes;;Clostridia;;Clostridiales;;Lachnospiraceae;;Clostridium_g21;Clostridium scindens;
2	KE159781_s	86.6025	5.7229	93.94			Bacteria;;;Firmicutes;;Clostridia;;Clostridiales;;Lachnospiraceae;;Clostridium_g21;KE159781_s;
3	Dorea longicatena	86.0168	4.4707	93.6	81.23		Bacteria;;;Firmicutes;;Clostridia;;Clostridiales;;Lachnospiraceae;;Dorea;Dorea longicatena;
4	QUII_s	88.03	2.0696	93.6			Bacteria;;;Firmicutes;;Clostridia;;Clostridiales;;Lachnospiraceae;;Mediterraneibacter;QUII_s;
5	KQ236749_s	85.8898	6.9158	93.54		84.42	Bacteria;;;Firmicutes;;Clostridia;;Clostridiales;;Lachnospiraceae;;Extibacter;KQ236749_s;
6	QSVN_s	85.0932	3.8749	93.53	81.4		Bacteria;;;Firmicutes;;Clostridia;;Clostridiales;;Lachnospiraceae;;Dorea;QSVN_s;
7	Clostridium hylemonae	83.4999	5.5674	93.2		85.01	Bacteria;;;Firmicutes;;Clostridia;;Clostridiales;;Lachnospiraceae;;Extibacter;Clostridium hylemonae;
8	OEPZ_s	85.2237	5.7166	92.98	81.2	84.58	Bacteria;;;Firmicutes;;Clostridia;;Clostridiales;;Lachnospiraceae;;Dorea;OEPZ_s;
9	Dorea formicigenerans	88.2499	3.5995	92.63		85.02	Bacteria;;;Firmicutes;;Clostridia;;Clostridiales;;Lachnospiraceae;;Dorea;Dorea formicigenerans;
10	QUDV_s	85.1491	2.726	92.42		84.15	Bacteria;;;Firmicutes;;Clostridia;;Clostridiales;;Lachnospiraceae;;QUDV_g;QUDV_s;
11	Extibacter muris	85.3425	7.6063	92.22			Bacteria;;;Firmicutes;;Clostridia;;Clostridiales;;Lachnospiraceae;;Extibacter;Extibacter muris;
12	LT990039_s	84.4296	5.1309	91.75	80.85		Bacteria;;;Firmicutes;;Clostridia;;Clostridiales;;Lachnospiraceae;;LT990039_g;LT990039_s;
13	Lachnoclostridium phocaeense	85.777	3.3426	91.68		84.8	Bacteria;;;Firmicutes;;Clostridia;;Clostridiales;;Lachnospiraceae;;Lachnoclostridium;Lachnoclostridium phocaeense;
14	Merdimonas faecis	83.8897	5.3288	91.48	81.53	83.99	Bacteria;;;Firmicutes;;Clostridia;;Clostridiales;;Lachnospiraceae;;Merdimonas;Merdimonas faecis;

Index	Decision	Drug class	Mechanism	AMR Gene Family	ARO (Best hit)	ARO ID	Bitscore/Cutoff	Identity (%)
1	Strict	tetracycline antibiotic	antibiotic efflux	major facilitator superfamily (MFS) antibiotic efflux pump	tetA(P)	3000180	18.8606/800.0	100.0
2	Strict	tetracycline antibiotic	antibiotic target protection	tetracycline-resistant ribosomal protection protein	tet(W/N/W)	3004442	946.421/500.0	69.59
3	Perfect	phenicol antibiotic	antibiotic inactivation	chloramphenicol acetyltransferase (CAT)	catI	3002683	465.692/400.0	100.0
4	Strict	tetracycline antibiotic	antibiotic target protection	tetracycline-resistant ribosomal protection protein	tetO	3000190	1312.36/1200.0	99.37

Index	Ref ID	Contig	Location	Description	E-value	% Identity	% Coverage
1	VFG001967	52	114586..115722	(gb\|NP_282580) (glf) UDP-galactopyranose mutase [Capsule (VF0323)] [Campylobacter jejuni subsp. jejuni NCTC 11168]	6.0E-42	65.52	63.59
2	VFG002182	52	114586..115722	(gb\|NP_816133) (cpsI) UDP-galactopyranose mutase [Capsule (VF0361)] [Enterococcus faecalis V583]	5.0E-30	65.37	51.36
3	VFG000077	52	158877..159458	(gb\|NP_465991) (clpP) ATP-dependent Clp protease proteolytic subunit [ClpP (VF0074)] [Listeria monocytogenes EGD-e]	3.0E-29	65.54	95.02

How to cite

Ha, S.M., Kim, C.K., Roh, J., Byun, J.H., Yang, S.J., Choi, S.B., Chun, J., and Yong, D. (2019). Application of the whole genome-based bacterial identification system, TrueBac ID, in clinical isolates which were not identified with three MALDI-TOF M/S systems. Ann Lab Med. 39(6):530-536.

Feldgarden, M., Brover, V., Haft, D.H., Prasad, A.B., Slotta, D.J., Tolstoy, I., Tyson, G.H., Zhao, S., Hsu, C.-H., McDermott, P.F., Tadesse, D.A., Morales, C., Simmons, M., Tillman, G., Wasilenko, J., Folster, J.P., and Klimke, W. (2019). Validating the NCBI AMRFinder Tool and Resistance Gene Database Using Antimicrobial Resistance Genotype-Phenotype Correlations in a Collection of NARMS Isolates.Antimicrob. Agents Chemother. 63 no. 11 (November 1, 2019): e00483-19.

Liu, B., Zheng, DD., Jin, Q., Chen, LH., and Yang, J. (2019). VFDB 2019: a comparative pathogenomic platform with an interactive web interface.Nucleic Acids Res. 47(D1):D687-D692.