Identification of Genes to Differentiate Closely Related Salmonella Lineages

Zou, Qing-Hua; Li, Ren-Qing; Wang, Ye-Jun; Liu, Shu-Lin
February 2013
PLoS ONE;Feb2013, Vol. 8 Issue 2, p1
Academic Journal
Background: Salmonella are important human and animal pathogens. Though highly related, the Salmonella lineages may be strictly adapted to different hosts or cause different diseases, from mild local illness like gastroenteritis to fatal systemic infections like typhoid. Therefore, rapid and accurate identification of Salmonella is essential for timely and correct diagnosis of Salmonella infections. The current identification methods such as 16S rRNA sequencing and multilocus sequence typing are expensive and time consuming. Additionally, these methods often do not have sufficient distinguishing resolution among the Salmonella lineages. Methodologies/Principal Findings: We compared 27 completely sequenced Salmonella genomes to identify possible genomic features that could be used for differentiation of individual lineages. We concatenated 2372 core genes in each of the 27 genomes and constructed a neighbor-joining tree. On the tree, strains of each serotype were clustered tightly together and different serotypes were unambiguously separated with clear genetic distances, demonstrating systematic genomic divergence among the Salmonella lineages. We made detailed comparisons among the 27 genomes and identified distinct sets of genomic differences, including nucleotide variations and genomic islands (GIs), among the Salmonella lineages. Two core genes STM4261 and entF together could unambiguously distinguish all Salmonella lineages compared in this study. Additionally, strains of a lineage have a common set of GIs and closely related lineages have similar sets of GIs. Conclusions: Salmonella lineages have accumulated distinct sets of mutations and laterally acquired DNA (e.g., GIs) in evolution. Two genes entF and STM4261 have diverged sufficiently among the Salmonella lineages to be used for their differentiation. Further investigation of the distinct sets of mutations and GIs will lead to novel insights into genomic evolution of Salmonella and greatly facilitate the elucidation of pathogeneses of Salmonella infections.


Related Articles

  • Codon and Base Biases after the Initiation Codon of the Open Reading Frames in the Escherichia coli Genome and Their Influence on the Translation Efficiency1. Sato, Toru; Terabe, Mahito; Watanabe, Hidemi; Gojobori, Takashi; Hori-Takemoto, Chie; Miura, Kin-ichiro // Journal of Biochemistry;2001, Vol. 129 Issue 6, p851 

    Nucleotide sequences around the boundaries of all open reading frames in the Escherichia coli whole genome were analyzed. Characteristic base biases were observed after the initiation codon and before the termination codon. We examined the effect of the base sequence after the initiation codon...

  • Comparative Genomics of the Bacterial Genus Streptococcus Illuminates Evolutionary Implications of Species Groups. Gao, Xiao-Yang; Zhi, Xiao-Yang; Li, Hong-Wei; Klenk, Hans-Peter; Li, Wen-Jun // PLoS ONE;Jun2014, Vol. 9 Issue 6, p1 

    Members of the genus Streptococcus within the phylum Firmicutes are among the most diverse and significant zoonotic pathogens. This genus has gone through considerable taxonomic revision due to increasing improvements of chemotaxonomic approaches, DNA hybridization and 16S rRNA gene sequencing....

  • Charge versus sequence for nuclear/nucleolar localization of plant ribosomal proteins. Savada, Raghavendra; Bonham-Smith, Peta // Plant Molecular Biology;Mar2013, Vol. 81 Issue 4/5, p477 

    Ribosomal subunit assembly in the nucleolus is dependent on efficient targeting of ribosomal proteins (RPs) from the cytoplasm into the nucleus and nucleolus. Nuclear/nucleolar localization of a protein is generally mediated by one or more specific stretches of basic amino...

  • Identification of the Microbiota in Carious Dentin Lesions Using 16S rRNA Gene Sequencing. Obata, Junko; Takeshita, Toru; Shibata, Yukie; Yamanaka, Wataru; Unemori, Masako; Akamine, Akifumi; Yamashita, Yoshihisa // PLoS ONE;Aug2014, Vol. 9 Issue 8, p1 

    While mutans streptococci have long been assumed to be the specific pathogen responsible for human dental caries, the concept of a complex dental caries-associated microbiota has received significant attention in recent years. Molecular analyses revealed the complexity of the microbiota with the...

  • Characterization of the Two Intra-Individual Sequence Variants in the 18S rRNA Gene in the Plant Parasitic Nematode, Rotylenchulus reniformis. Nyaku, Seloame T.; Sripathi, Venkateswara R.; Kantety, Ramesh V.; Gu, Yong Q.; Lawrence, Kathy; Sharma, Govind C. // PLoS ONE;Apr2013, Vol. 8 Issue 4, p1 

    The 18S rRNA gene is fundamental to cellular and organismal protein synthesis and because of its stable persistence through generations it is also used in phylogenetic analysis among taxa. Sequence variation in this gene within a single species is rare, but it has been observed in few metazoan...

  • Changes in microbiota during experimental human Rhinovirus infection. Hofstra, J. J.; Matamoros, S.; van de Pol, M. A.; de Wever, B.; Tanck, M. W.; Wendt-Knol, H.; Deijs, M.; van der Hoek, L.; Wolthers, K. C.; Molenkamp, R.; Visser, C. E.; Sterk, P. J.; Lutter, R.; de Jong, M. D. // BMC Infectious Diseases;Aug2015, Vol. 15 Issue 1, p1 

    Background: Human Rhinovirus (HRV) is responsible for the majority of common colds and is frequently accompanied by secondary bacterial infections through poorly understood mechanisms. We investigated the effects of experimental human HRV serotype 16 infection on the upper respiratory tract...

  • Escherichia coli O157:H7 Super-Shedder and Non-Shedder Feedlot Steers Harbour Distinct Fecal Bacterial Communities. Xu, Yong; Dugat-Bony, Eric; Zaheer, Rahat; Selinger, Lorna; Barbieri, Ruth; Munns, Krysty; McAllister, Tim A.; Selinger, L. Brent // PLoS ONE;May2014, Vol. 9 Issue 5, p1 

    Escherichia coli O157:H7 is a major foodborne human pathogen causing disease worldwide. Cattle are a major reservoir for this pathogen and those that shed E. coli O157:H7 at >104 CFU/g feces have been termed “super-shedders”. A rich microbial community inhabits the mammalian...

  • Rapid 16S rRNA Next-Generation Sequencing of Polymicrobial Clinical Samples for Diagnosis of Complex Bacterial Infections Salipante, Stephen J.; Sengupta, Dhruba J.; Rosenthal, Christopher; Costa, Gina; Spangler, Jessica; Sims, Elizabeth H.; Jacobs, Michael A.; Miller, Samuel I.; Hoogestraat, Daniel R.; Cookson, Brad T.; McCoy, Connor; Matsen, Frederick A.; Shendure, Jay; Lee, Clarence C.; Harkins, Timothy T.; Hoffman, Noah G. // PLoS ONE;May2013, Vol. 8 Issue 5, p1 

    Classifying individual bacterial species comprising complex, polymicrobial patient specimens remains a challenge for culture-based and molecular microbiology techniques in common clinical use. We therefore adapted practices from metagenomics research to rapidly catalog the bacterial composition...

  • The Microbiome of the Middle Meatus in Healthy Adults. Ramakrishnan, Vijay R.; Feazel, Leah M.; Gitomer, Sarah A.; Ir, Diana; Robertson, Charles E.; Frank, Daniel N. // PLoS ONE;Dec2013, Vol. 8 Issue 12, p1 

    Rhinitis and rhinosinusitis are multifactorial disease processes in which bacteria may play a role either in infection or stimulation of the inflammatory process. Rhinosinusitis has been historically studied with culture-based techniques, which have implicated several common pathogens in disease...


Read the Article


Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics