Genomic diversity of citrate fermentation in Klebsiella pneumoniae. 2009

Ying-Tsong Chen, and Tsai-Lien Liao, and Keh-Ming Wu, and Tsai-Ling Lauderdale, and Jing-Jou Yan, and I-Wen Huang, and Min-Chi Lu, and Yi-Chyi Lai, and Yen-Ming Liu, and Hung-Yu Shu, and Jin-Town Wang, and Ih-Jen Su, and Shih-Feng Tsai
Division of Molecular and Genomic Medicine, National Health Research Institutes, Miaoli, Taiwan, Republic of China. onion@nhri.org.tw

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.

UI MeSH Term Description Entries
D007711 Klebsiella pneumoniae Gram-negative, non-motile, capsulated, gas-producing rods found widely in nature and associated with urinary and respiratory infections in humans. Bacillus pneumoniae,Bacterium pneumoniae crouposae,Hyalococcus pneumoniae,Klebsiella pneumoniae aerogenes,Klebsiella rhinoscleromatis
D003470 Culture Media Any liquid or solid preparation made specifically for the growth, storage, or transport of microorganisms or other types of cells. The variety of media that exist allow for the culturing of specific microorganisms and cell types, such as differential media, selective media, test media, and defined media. Solid media consist of liquid media that have been solidified with an agent such as AGAR or GELATIN. Media, Culture
D004269 DNA, Bacterial Deoxyribonucleic acid that makes up the genetic material of bacteria. Bacterial DNA
D005285 Fermentation Anaerobic degradation of GLUCOSE or other organic nutrients to gain energy in the form of ATP. End products vary depending on organisms, substrates, and enzymatic pathways. Common fermentation products include ETHANOL and LACTIC ACID. Fermentations
D005810 Multigene Family A set of genes descended by duplication and variation from some ancestral gene. Such genes may be clustered together on the same chromosome or dispersed on different chromosomes. Examples of multigene families include those that encode the hemoglobins, immunoglobulins, histocompatibility antigens, actins, tubulins, keratins, collagens, heat shock proteins, salivary glue proteins, chorion proteins, cuticle proteins, yolk proteins, and phaseolins, as well as histones, ribosomal RNA, and transfer RNA genes. The latter three are examples of reiterated genes, where hundreds of identical genes are present in a tandem array. (King & Stanfield, A Dictionary of Genetics, 4th ed) Gene Clusters,Genes, Reiterated,Cluster, Gene,Clusters, Gene,Families, Multigene,Family, Multigene,Gene Cluster,Gene, Reiterated,Multigene Families,Reiterated Gene,Reiterated Genes
D014644 Genetic Variation Genotypic differences observed among individuals in a population. Genetic Diversity,Variation, Genetic,Diversity, Genetic,Diversities, Genetic,Genetic Diversities,Genetic Variations,Variations, Genetic
D016680 Genome, Bacterial The genetic complement of a BACTERIA as represented in its DNA. Bacterial Genome,Bacterial Genomes,Genomes, Bacterial
D017422 Sequence Analysis, DNA A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis. DNA Sequence Analysis,Sequence Determination, DNA,Analysis, DNA Sequence,DNA Sequence Determination,DNA Sequence Determinations,DNA Sequencing,Determination, DNA Sequence,Determinations, DNA Sequence,Sequence Determinations, DNA,Analyses, DNA Sequence,DNA Sequence Analyses,Sequence Analyses, DNA,Sequencing, DNA
D044404 Genomic Islands Distinct units in some bacterial, bacteriophage or plasmid GENOMES that are types of MOBILE GENETIC ELEMENTS. Encoded in them are a variety of fitness conferring genes, such as VIRULENCE FACTORS (in "pathogenicity islands or islets"), ANTIBIOTIC RESISTANCE genes, or genes required for SYMBIOSIS (in "symbiosis islands or islets"). They range in size from 10 - 500 kilobases, and their GC CONTENT and CODON usage differ from the rest of the genome. They typically contain an INTEGRASE gene, although in some cases this gene has been deleted resulting in "anchored genomic islands". Pathogenicity Islands,Anchored Genomic Islands,Genomic Islets,Pathogenicity Islets,Symbiosis Islands,Symbiosis Islets,Anchored Genomic Island,Genomic Island,Genomic Island, Anchored,Genomic Islands, Anchored,Genomic Islet,Island, Anchored Genomic,Island, Genomic,Island, Pathogenicity,Island, Symbiosis,Islands, Anchored Genomic,Islands, Genomic,Islands, Pathogenicity,Islands, Symbiosis,Islet, Genomic,Islet, Pathogenicity,Islet, Symbiosis,Islets, Genomic,Islets, Pathogenicity,Islets, Symbiosis,Pathogenicity Island,Pathogenicity Islet,Symbiosis Island,Symbiosis Islet
D055028 Comparative Genomic Hybridization A method for comparing two sets of chromosomal DNA by analyzing differences in the copy number and location of specific sequences. It is used to look for large sequence changes such as deletions, duplications, amplifications, or translocations. Array Comparative Genomic Hybridization,Array-Based Comparative Genomic Hybridization,Comparative Genome Hybridization,Array Based Comparative Genomic Hybridization,Comparative Genome Hybridizations,Comparative Genomic Hybridizations,Genome Hybridization, Comparative,Genome Hybridizations, Comparative,Genomic Hybridization, Comparative,Genomic Hybridizations, Comparative,Hybridization, Comparative Genome,Hybridization, Comparative Genomic,Hybridizations, Comparative Genome,Hybridizations, Comparative Genomic

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