Qing-Hua Zou

Salmonella paratyphi C: Genetic Divergence from Salmonella choleraesuis and Pathogenic Convergence with Salmonella typhi

Background Although over 1400 Salmonella serovars cause usually self-limited gastroenteritis in humans, a few, e.g., Salmonella typhi and S. paratyphi C, cause typhoid, a potentially fatal systemic infection. It is not known whether the typhoid agents have evolved from a common ancestor (by divergent processes) or acquired similar pathogenic traits independently (by convergent processes). Comparison of different typhoid agents with non-typhoidal Salmonella lineages will provide excellent models for studies on how similar pathogens might have evolved. Methodologies/Principal Findings We sequenced a strain of S. paratyphi C, RKS4594, and compared it with previously sequenced Salmonella strains. RKS4594 contains a chromosome of 4,833,080 bp and a plasmid of 55,414 bp. We predicted 4,640 intact coding sequences (4,578 in the chromosome and 62 in the plasmid) and 152 pseudogenes (149 in the chromosome and 3 in the plasmid). RKS4594 shares as many as 4346 of the 4,640 genes with a strain of S. choleraesuis, which is primarily a swine pathogen, but only 4008 genes with another human-adapted typhoid agent, S. typhi. Comparison of 3691 genes shared by all six sequenced Salmonella strains placed S. paratyphi C and S. choleraesuis together at one end, and S. typhi at the opposite end, of the phylogenetic tree, demonstrating separate ancestries of the human-adapted typhoid agents. S. paratyphi C seemed to have suffered enormous selection pressures during its adaptation to man as suggested by the differential nucleotide substitutions and different sets of pseudogenes, between S. paratyphi C and S. choleraesuis. Conclusions S. paratyphi C does not share a common ancestor with other human-adapted typhoid agents, supporting the convergent evolution model of the typhoid agents. S. paratyphi C has diverged from a common ancestor with S. choleraesuis by accumulating genomic novelty during adaptation to man.

Helicobacter pylori in the oral cavity and gastric mucosa: a meta-analysis.

BACKGROUND Helicobacter pylori have been found in the oral cavity and stomach. This study is to establish whether there might be any associations between isolates of H. pylori in the oral cavity and those in the stomach by meta-analysis. METHODS Studies reporting raw data on the prevalence of H. pylori infection in the oral cavity in gastric H. pylori-positive and H. pylori-negative patients, in patients with gastroesophageal diseases, and in healthy individuals and studies reporting data on the eradication rate in the oral cavity or stomach, published in the English language, were identified through MEDLINE and EMBASE up to May 2010. RESULTS The prevalence of H. pylori infection in the oral cavity in gastric H. pylori-positive patients was significantly higher (45.0%) than that in gastric H. pylori-negative patients (23.9%). The pooled odds ration (OR) was 3.61 and the 95% CI was 1.91-6.82 (P < 0.0001). Different diagnostic methods produced different pooled ORs with PCR the highest (OR = 5.11, 95% CI: 2.08-12.54, P = 0.0004) and rapid urease test (RUT) the lowest (OR = 2.00, 95% CI: 0.80-5.00, P = 0.14). The 44.8% (91/203) prevalence of H. pylori infection in the oral cavity in patients with clinical and/or histological gastroesophageal diseases was significantly higher than the 13.2% (21/159) in patients with non-ulcerous dyspepsia or healthy controls (OR = 5.15, 95% CI: 2.97-8.92, P < 0.00001). The eradication efficiency in stomach is 85.8% (187/218), while in oral cavity it is only 5.7% (9/158). The OR is 55.59, P < 0.00001. CONCLUSIONS There is a close relation between the infection of H. pylori in the oral cavity and stomach. H. pylori in the oral cavity are more difficult to be eradicated than in the stomach. It may be a source of reinfection.

SPC-P1: a pathogenicity-associated prophage of Salmonella paratyphi C

BackgroundSalmonella paratyphi C is one of the few human-adapted pathogens along with S. typhi, S. paratyphi A and S. paratyphi B that cause typhoid, but it is not clear whether these bacteria cause the disease by the same or different pathogenic mechanisms. Notably, these typhoid agents have distinct sets of large genomic insertions, which may encode different pathogenicity factors. Previously we identified a novel prophage, SPC-P1, in S. paratyphi C RKS4594 and wondered whether it might be involved in pathogenicity of the bacteria.ResultsWe analyzed the sequence of SPC-P1 and found that it is an inducible phage with an overall G+C content of 47.24%, similar to that of most Salmonella phages such as P22 and ST64T but significantly lower than the 52.16% average of the RKS4594 chromosome. Electron microscopy showed short-tailed phage particles very similar to the lambdoid phage CUS-3. To evaluate its roles in pathogenicity, we lysogenized S. paratyphi C strain CN13/87, which did not have this prophage, and infected mice with the lysogenized CN13/87. Compared to the phage-free wild type CN13/87, the lysogenized CN13/87 exhibited significantly increased virulence and caused multi-organ damages in mice at considerably lower infection doses.ConclusionsSPC-P1 contributes pathogenicity to S. paratyphi C in animal infection models, so it is possible that this prophage is involved in typhoid pathogenesis in humans. Genetic and functional analyses of SPC-P1 may facilitate the study of pathogenic evolution of the extant typhoid agents, providing particular help in elucidating the pathogenic determinants of the typhoid agents.

mutL as a genetic switch of bacterial mutability: turned on or off through repeat copy number changes.

Bacterial adaptation to changing environments can be achieved through the acquisition of genetic novelty by accumulation of mutations and recombination of laterally transferred genes into the genome, but the mismatch repair (MMR) system strongly inhibits both these types of genetic changes. As mutation and recombination do occur in bacteria, it is of interest to understand how genetic novelty may be achieved in the presence of MMR. Previously, we observed associations of a defective MMR genotype, 6bpΔmutL, with greatly elevated bacterial mutability in Salmonella typhimurium. To validate these observations, we experimentally converted the mutL gene between the wild-type and 6bpΔmutL in S. typhimurium and inspected the bacterial mutability status. When 6bpΔmutL was converted to mutL, the originally highly mutable Salmonella strains regained genetic stability; when mutL was converted to 6bpΔmutL, the mutability was elevated 100-fold. Interestingly, mutL cells were found to grow out of 6bpΔmutL cells; the new mutL cells eventually replaced the original 6bpΔmutL population. As conversion between mutL and 6bpΔmutL may occur readily during DNA replication, it may represent a previously unrecognized mechanism to modulate bacterial mutability at the population level, allowing bacteria to respond rapidly to changing environments while minimizing the risks associated with persistent hypermutability.

Identification of Genes to Differentiate Closely Related Salmonella Lineages

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.

Genotyping of Salmonella with lineage-specific genes: correlation with serotyping

BACKGROUND The bacterial genus Salmonella encompasses a large number of serotypes that are genetically very similar but biologically quite different, especially in pathogenic properties and host specificity. Serotyping has been used for the classification, identification, and epidemiological investigation due to its excellent discriminating power, but it cannot distinguish the different pathogenic lineages within a polyphyletic serotype. Additionally, very few institutions have the comprehensive set of antisera for typing. Therefore various studies have been performed to explore alternative assays to differentiate Salmonella isolates, such as the search for genes that can be used as potential molecular substitutes for serotyping. However, the genes tested so far have often given inconsistent results. METHODS In this study, the discriminating power of seven genes to differentiate 309 Salmonella strains representing 26 serotypes was evaluated and the results were compared with those of other methods. RESULTS The seven newly selected genes have a good power to differentiate different serovars. The tree based on the concatenated sequences of these genes revealed phylogenetic relationships of the bacteria consistent with that of the whole genome tree. CONCLUSION Individual Salmonella lineages each have specific genes that can be used to differentiate Salmonella isolates on a phylogenetic basis.

Comparative genomic analysis between typhoidal and non-typhoidal Salmonella serovars reveals typhoid-specific protein families.

BACKGROUND The genus Salmonella contains more than 2600 serovars. While most cause a self-limiting gastroenteritis, four serovars, S. Typhi, S. Paratyphi A, B and C, elicit typhoid, a potentially fatal systemic infection. Because of the prevalence in certain regions, such as South Asia, and the disease severity of typhoidal Salmonella infections, comprehensive studies are needed to elucidate the pathogenesis of diseases caused by these typhoidal serovars. RESULTS We performed comparative genomic analyses on eight human typhoidal strains and 27 non-human typhoidal Salmonella strains to elucidate their evolutionary relationships and identify the genes specific to the four typhoidal serovars. Our results indicate that Salmonella may have an open pan-genome. A core-genome based phylogeny demonstrated that divergence between S. Paratyphi A and S. Typhi took place not long ago and S. Paratyphi B shared a recent common ancestor with S. Paratyphi C. Of great interest, the divergence between S. Paratyphi B and S. Paratyphi C was shown to be more recent than that between S. Paratyphi A and S. Typhi. Alignment and comparisons of the genomes identified unique complements of protein families to each of the typhoidal serovars. Most of these protein families are phage related and some are candidate virulence factors. Importantly, we found 88 protein families specific to two to three of the four typhoidal serovars. All but two of the 88 genes are present in S. Typhi, with a few in the three paratyphoidal serovars but none in the non-human typhoidal serovars. Most of these genes are predicted to encode hypothetical proteins and some are known to code for virulence factors such as Vi polysaccharide related proteins. CONCLUSIONS By comprehensive genomic comparisons, we identified protein families specific to the human typhoidal serovars, which will greatly facilitate investigations on typhoid pathogenesis.