Open Access Highly Accessed Research article

Genomic diversity of citrate fermentation in Klebsiella pneumoniae

Ying-Tsong Chen1, Tsai-Lien Liao1, Keh-Ming Wu12, Tsai-Ling Lauderdale3, Jing-Jou Yan4, I-Wen Huang3, Min-Chi Lu5, Yi-Chyi Lai5, Yen-Ming Liu1, Hung-Yu Shu6, Jin-Town Wang7, Ih-Jen Su3 and Shih-Feng Tsai128*

Author Affiliations

1 Division of Molecular and Genomic Medicine, National Health Research Institutes, Miaoli, Taiwan, Republic of China

2 Genome Research Center and Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan, Republic of China

3 Division of Infectious Diseases, National Health Research Institutes, Zhunan, Miaoli, Taiwan, Republic of China

4 Department of Pathology, National Cheng Kung University Hospital, Tainan, Taiwan, Republic of China

5 College of Medicine, Chung Shan Medical University, Taichung, Taiwan, Republic of China

6 Department of Bioscience Technology, Chang Jung Christian University, Tainan County, Taiwan, Republic of China

7 Department and Graduate Institute of Microbiology, National Taiwan University, Taipei, Taiwan, Republic of China

8 Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan, Republic of China

For all author emails, please log on.

BMC Microbiology 2009, 9:168  doi:10.1186/1471-2180-9-168

Published: 15 August 2009



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.


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 the13-kb genomic region were not independently acquired.


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.