Genomic diversity of citrate fermentation in Klebsiella pneumoniae.
BACKGROUND
It has long been recognized that Klebsiella pneumoniae can grow anaerobically on citrate. Genes responsible for citrate fermentation of K. pneumoniae were known to be located in a 13-kb gene cluster on the chromosome. By whole genome comparison of the available K. pneumoniae sequences (MGH 78578, 342, and NTUH-K2044), however, we discovered that the fermentation gene cluster was present in MGH 78578 and 342, but absent in NTUH-K2044. In the present study, the previously unknown genome diversity of citrate fermentation among K. pneumoniae clinical isolates was investigated.


RESULTS
Using a genomic microarray containing probe sequences from multiple K. pneumoniae strains, we investigated genetic diversity among K. pneumoniae clinical isolates and found that a genomic region containing the citrate fermentation genes was not universally present in all strains. We confirmed by PCR analysis that the gene cluster was detectable in about half of the strains tested. To demonstrate the metabolic function of the genomic region, anaerobic growth of K. pneumoniae in artificial urine medium (AUM) was examined for ten strains with different clinical histories and genomic backgrounds, and the citrate fermentation potential was found correlated with the genomic region. PCR detection of the genomic region yielded high positive rates among a variety of clinical isolates collected from urine, blood, wound infection, and pneumonia. Conserved genetic organizations in the vicinity of the citrate fermentation gene clusters among K. pneumoniae, Salmonella enterica, and Escherichia coli suggest that the 13-kb genomic region were not independently acquired.


CONCLUSIONS
Not all, but nearly half of the K. pneumoniae clinical isolates carry the genes responsible for anaerobic growth on citrate. Genomic variation of citrate fermentation genes in K. pneumoniae may contribute to metabolic diversity and adaptation to variable nutrient conditions in different environments.
Chen
Ying-Tsong
YT
Division of Molecular and Genomic Medicine, National Health Research Institutes, Miaoli, Taiwan, Republic of China. onion@nhri.org.tw
Liao
Tsai-Lien
TL
Wu
Keh-Ming
KM
Lauderdale
Tsai-Ling
TL
Yan
Jing-Jou
JJ
Huang
I-Wen
IW
Lu
Min-Chi
MC
Lai
Yi-Chyi
YC
Liu
Yen-Ming
YM
Shu
Hung-Yu
HY
Wang
Jin-Town
JT
Su
Ih-Jen
IJ
Tsai
Shih-Feng
SF
D019343:Citric Acid / Q000378:metabolism*; D055028:Comparative Genomic Hybridization; D003470:Culture Media; D004269:DNA, Bacterial / Q000235:genetics; D005285:Fermentation / Q000235:genetics*; D014644:Genetic Variation; D016680:Genome, Bacterial; D044404:Genomic Islands; D007711:Klebsiella pneumoniae / Q000235:genetics* / Q000378:metabolism; D005810:Multigene Family; D020411:Oligonucleotide Array Sequence Analysis; D017422:Sequence Analysis, DNA
D003470:Culture Media; D004269:DNA, Bacterial; D019343:Citric Acid
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