Multilocus Sequence Typing of Klebsiella pneumoniae Nosocomial Isolates

DOI: 10.1128/JCM.43.8.4178-4182.2005

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FIG. 1.
Allelic profiles, ribotype patterns, sequence type (ST), ribotype (RT), source information, and MIC of ceftazidime (CAZ) and ciprofloxacin (CIP) of the 67 K. pneumoniae strains. The two first letters of the original strain name correspond to the code of the source medical center. Clinical sources were blood, respiratory tract (RTI), urinary tract (UTI), and soft tissue infections. Epidemiological clusters initially suspected on the basis of the medical center and susceptibility to CAZ (resistance breakpoint, 64 mg/liter) and to CIP (resistance breakpoint, 2 mg/liter) are indicated in the last column. All clinical strains were collected between 1997 and 2001. The UPGMA dendrogram was built from the pairwise distances between allelic profiles using BioNumerics.

TABLE 1.

Gene loci included in the Klebsiella pneumoniae MLST scheme, PCR and sequencing primers, and variation indices for 67 strains^a

Locus	Putative function of gene	Primer sequence^b^,^c	Size (bp)	Location^d	Temp (°C)	No. of alleles	Nucleotide diversity	Polymorphic sites (nonsynonymous substitutions)
rpoB	Beta-subunit of RNA polymerase B	VIC3: GGC GAA ATG GCW GAG AAC CA	501	4,771,502-4,772,002	50	8	0.00166	7 (1)
		VIC2: GAG TCT TCG AAG TTG TAA CC
gapA	Glyceraldehyde 3-phosphate dehydrogenase	gapA173: TGA AAT ATG ACT CCA CTC ACG G	450	1,347,540-1,347,091	60	6	0.00136	5 (0)
		gapA181: CTT CAG AAG CGG CTT TGA TGG CTT
mdh	Malate dehydrogenase	mdh130: CCC AAC TCG CTT CAG GTT CAG	477	4,004,045-4,003,569	50	10	0.00161	10 (3)
		mdh867: CCG TTT TTC CCC AGC AGC AG
pgi	Phosphoglucose isomerase	pgi1F: GAG AAA AAC CTG CCT GTA CTG CTG GC	432	4,831,091-4,831,522	50	6	0.00092	5 (0)
		pgi1R: CGC GCC ACG CTT TAT AGC GGT TAA T
		pgi2F(seq): CTG CTG GCG CTG ATC GGC AT
		pgi2R(seq): TTA TAG CGG TTA ATC AGG CCG T
phoE	Phosphoporine E	phoE604.1: ACC TAC CGC AAC ACC GAC TTC TTC GG	420	320,309-320,728	50	14	0.00727	18 (2)
		phoE604.2: TGA TCA GAA CTG GTA GGT GAT
infB	Translation initiation factor 2	infB1F: CTC GCT GCT GGA CTA TAT TCG	318	3,937,568-3,937,885	50	10	0.0038	11 (0)
		infB1R: CGC TTT CAG CTC AAG AAC TTC
		infB2F(seq): ACT AAG GTT GCC TCC GGC GAA GC
tonB	Periplasmic energy transducer	tonB1F: CTT TAT ACC TCG GTA CAT CAG GTT	414	2,394,251-2,394,664	45	21	0.01019	14 (5)
		tonB2R: ATT CGC CGG CTG RGC RGA GAG

↵a Genes aroA, tyrB, and ureD were also amplified and sequenced successfully but were not included due to lower sequence quality in general. Genes gyrA and parC used previously (7) were excluded as amino acid changes may be selected by the clinical use of quinolones.
↵b Sequencing primers were the same as the PCR primers, except when indicated.
↵c Primer sources were as follows: for mdh, reference 25; for phoE, reference 9; for pgi1F and pgi1R, reference 29; gapA173, reference 8; for rpoB, E. Ageron and P. Grimont, unpublished. All other primers were designed in this study.
↵d Based on the complete sequence of strain MGH78578 available at http://genome.wustl.edu/projects/bacterial/kpneumoniae/.