Whole-Genome-Sequencing characterization of bloodstream infection-causing hypervirulent Klebsiella pneumoniae of capsular serotype K2 and ST374

Figures & data

Table 1. The capsular serotype, MLST type and distribution of ten virulence factor genes in the 20 hypermucoviscous K. pneumoniae isolates with ultra-long viscous string (>20 mm).

Isolate	Patient Gender	Patient Age	Collection Date	Source	Department	MLST	CPS	magA	allS	rmpA	mrkD	kfuBC	cf29a	fimH	uge	wabG	ureA
RJA360	m	77	Sept., 2014	sputum	neurology	23	K1	+	+	+	+	+	+	+	+	+	+
RJF67-2	m	63	Oct., 2014	blood	EICU	23	K1	+	+	+	+	+		+	+	+	+
RJA2570	f	75	Dec., 2014	abscess	trauma surgery	23	K1	+	+	+	+	+	+	+	+	+	+
RJF999	m	46	Jan., 2015	blood	ICU	23	K1	+	+	+	+	+		+	+	+	+
RJA166	m	47	Apr., 2015	sputum	cardiac surgery	23	K1	+	+	+	+	+		+	+	+	+
RJF271	m	54	Apr., 2014	abscess	emergency	680	K1	+	+	+	+	+	+	+	+	+	+
RJA277	m	55	Nov., 2014	abscess	intervention	2846	K1	+		+	+		+	+	+	+	+
RJA304	f	64	Sept., 2014	sputum	dermatology	86	K2			+	+			+	+	+	+
RJB442	f	71	Oct., 2014	urine	nephrology	86	K2			+	+			+	+	+	+
RJF293	m	54	Sept., 2014	blood	ICU	374	K2		+	+	+	+		+	+	+	+
RJF294	m	54	Sept., 2014	blood	ICU	374	K2		+	+	+	+		+	+	+	+
RJA898	m	54	Sept., 2014	sputum	ICU	374	K2		+	+	+	+		+	+	+	+
RJA2225	m	61	Nov., 2014	abscess	general surgery	375	K2			+	+			+	+	+	+
RJA1385	m	38	Feb., 2015	drainage	EICU	11	Not tested				+			+	+	+	+
RJA1253	m	59	Mar., 2014	hydrothorax	thoracic surgery	412	Not tested			+	+			+	+	+	+
RJA1657	f	71	Sept., 2014	sputum	thoracic surgery	412	Not tested			+	+			+	+	+	+
RJA565	f	43	Sept., 2014	sputum	hematology	412	Not tested			+	+			+	+	+	+
RJA1547	f	74	Nov., 2014	bile	transplantation	412	Not tested			+	+			+	+	+	+
RJA1504	f	44	Dec., 2014	sputum	respiratory	412	Not tested			+	+			+	+	+	+
RJA1887	m	74	Sept., 2014	sputum	respiratory	2845	No tested			+	+	+		+	+	+	+

^a Virulence factor genes of K. pneumoniae: magA, coding for polysaccharides polymerase specific for K. pneumoniae serotype K1; allS, activator of the allantoin regulon;rmpA, transcriptional activator of cps gene transcription; mrkD, adhesin subunit of type 3 fimbriae; kfuBC, iron transport and phosphotransferase protein; cf29a, CF504 protein precursor; fimH, minor adhesin subunit of type 1; uge, uridinediphosphate galacturonate 4-epimerase; wabG, glucosyltransferase; ureA, urease subunit gamma; fimbriae.

^b Multilocus Sequence Typing (MLST) was determined by BIGSdb (http://bigsdb.pasteur.fr/klebsiella/).

Figure 1. Kaplan-Meier survival curves for K. pneumoniae RJF293 infected mice. Mice were infected with 10³ CFU of different K. pneumoniae strains intraperitoneally. The previously reported hvKP strain NTUH-K2044 (ST23, K1 serotype), cKP strain HS11286 (ST11, KL103 serotype) and saline were applied as the controls. RJF293 showed virulence not statistically significant from that of NTUH-K2044 (p > 0.6, by log-rank test). No death of mice in the HS11286 or saline groups was observed during seven days.

Figure 2. Putative virulence genes (gene clusters) detected among the 106 completely sequenced K. pneumoniae genomes (Supplementary Table S3). (A) A parsimony tree generated from 429,267 SNPs using kSNP3 for the 106 completely sequenced K. pneumoniae chromosomes and displayed by iTOL with midpoint rooting. The hvKP and cKP isolates listed in Supplementary Table S4 are highlighted by color (red or orange, hvKP; blue, cKP). (B) The virulence genes predicted in the RJF293 genome are listed as an example in Supplementary Table S5. The presence of genes in the chromosome and/or plasmid is indicated in different gray scales.

Table 2. Large genomic island-like regions (>10 kb) identified on the K. pneumoniae RJF293 chromosome.

Region	Coordinates [CDS]	Length (kb)	G+C%	Features
GI1	406,963-417,086 [RJF2_RS01995-02030]	10.1	44.6	Fimbrial assembly protein
GI2	564,594-609,498 [RJF2_RS02780-03005]	44.9	47.0	Insertion site: tRNA^Leu; integrase (RJF2_RS02780)
GI3	1,066,669-1,077,261 [RJF2_RS05225-05250]	10.6	44.7	Radical SAM protein (RJF2_RS05240); integrase (RJF2_RS05250)
GI4	2,033,163-2,043,180 [RJF2_RS09775-09830]	10.0	50.2
GI5 (prophage)	2,364,000-2,417,629 [RJF2_RS11405-11765]	53.6	51.7	Intact prophage; integrase (RJF2_RS11765)
GI6 (ICE)	3,380,804-3,439,781 [RJF2_RS16675-16850]	59.0	53.1	Yersiniabactin synthesis, Type IV secretion system. Insertion site:tRNA^Asn;integrase (RJF2_RS16670)
GI7 (T6SS)	3,762,797-3,804,165 [RJF2_RS18280-18450]	41.4	50.7	Type VI secretion system (T6SS-3)
GI8	4,379,704-4,400,294 [RJF2_RS21295-21365]	20.6	46.8	Two-component regulatory system KvgAS; Fimbrial assembly protein

^a The G+C content of the RJF293 chromosome is 57.5%.