Evolutionary genomics of Salmonella : Gene acquisitions revealed by microarray analysis

Abstract

The presence of homologues of Salmonella enterica sv. Typhimurium LT2 genes was assessed in 22 other Salmonella including members of all seven subspecies and Salmonella bongori. Genomes were hybridized to a microarray of over 97% of the 4,596 annotated ORFs in the LT2 genome. A phylogenetic tree based on homologue content, relative to LT2, was largely concordant with previous studies using sequence information from several loci. Based on the topology of this tree, homologues of genes in LT2 acquired by various clades were predicted including 513 homologues acquired by the ancestor of all Salmonella, 111 acquired by S. enterica, 105 by diphasic Salmonella, and 216 by subspecies 1, most of which are of unknown function. Because this subspecies is responsible for almost all Salmonella infections of mammals and birds, these genes will be of particular interest for further mechanistic studies. Overall, a high level of gene gain, loss, or rapid divergence was predicted along all lineages. For example, at least 425 close homologues of LT2 genes may have been laterally transferred into Salmonella and then between Salmonella lineages. S almonellae are divided taxonomically into two species, Salmonella enterica, and Salmonella bongori. S. enterica is comprised of more than 2,000 serovars assigned to seven subspecies (ssp): I, II, IIIa, IIIb, IV, VI, and VII. S. bongori, formerly referred to as ssp. V, was assigned a separate species based initially on its different biotype and phylogenetic data acquired by multilocus enzyme electrophoresis (MLEE) (1, 2).The Salmonella Reference Collection C (SARC) contains 16 strains used in DNA sequence studies encompassing two strains each from all seven subgroups of S. enterica and S. bongori (3). Data from MLEE analysis of 24 loci and from the combined sequences of five housekeeping genes both are consistent in their prediction of S. bongori as an outgroup. The common ancestor of ssp. I, II, IIIb, and VI acquired the mechanism of flagellar antigen shifting, which is thought to play an important role in adaptation of the salmonellae to warm-blooded hosts (4). Subsequently, ssp. I became highly specialized for mammals and birds, with some serovars adapting to a single host species (e.g., S. enterica sv. Typhi in humans). Overall, ssp. I accounts for more than 99% of enteric and systemic infections in humans (5).DNA microarray technology is an emerging technique to investigate genetic relationships between closely related bacterial strains. Species analyzed with this method include Helicobacter pylori (6-8), Campylobacter (9), mycobacteria (10), Staphylococcus aureus (11), obligate endosymbionts of the tsetse fly (12, 13), Shewanella oneidensis (14), Pseudomonas species (15), and Vibrio cholerae (16).The completed genome sequence of S. enterica sv. Typhimurium (STM) LT2 (17) allowed us to construct an LT2 microarray of PCR-amplified whole ORFs representing over 97% of the 4,596 coding sequences assigned to the bacterium. With this LT2 chip we compared the genetic content of the Salmonell...

Comparative Genetics of the rdar Morphotype inSalmonella

“…arizonae (group IIIa) and S. bongori (group V) isolates. This is consistent with previous DNA microarray studies (14,45). However, only S. enterica subsp.…”

“…For pathogenic Salmonella spp., genome sequencing efforts have identified over 15 distinct fimbrial types (Salmonella enterica serovars Typhimurium [42], Typhi [44], and Paratyphi [41]). Pioneering work by Baumler et al (5) and subsequent genomic comparisons (14,45,61) revealed that most fimbrial operons have a scattered distribution throughout the salmonellae. Early hypotheses that fimbriae were involved in adherence to host cells suggested that numerous fimbrial types would contribute to the host specificities and tissue tropisms of different Salmonella spp.…”

Isolation of Salmonella enterica serotype choleraesuis resistant to ceftriaxone and ciprofloxacin

“…In an analysis of Salmonella genomes by microarray techniques using the genome of serotype Typhimurium LT2 as a standard, approximately 90% of the annotated LT2 open reading frames (ORFs) were homologous among members of all seven subgroups (112). Comparative genomic analysis of serotypes Typhimurium and Typhi (full genome sequences), and serotypes Dublin, Enteritidis, and Paratyphi (draft sequences) revealed that in each genome approximately 10 to 12% of unique DNA was acquired by horizontal gene transfer (96,109).…”

Identification of resistance and virulence factors in an epidemic Enterobacter hormaechei outbreak strain

“…Comparative genomic hybridization (CGH) is a powerful genetic tool for the study of bacteria (Dobrindt et al, 2003;Fitzgerald et al, 2001Fitzgerald et al, , 2003Fukiya et al, 2004;Israel et al, 2001;Leavis et al, 2007;Lindsay et al, 2006;Paauw et al, 2008;Porwollik et al, 2002;Salama et al, 2000). Most CGH arrays have been designed from annotated wholegenome sequences.…”