[Distribution in different Salmonella serovars and integration sites of Salmonella paratyphi C phage SPC-P1].

OBJECTIVE: To determine the prevalence of Salmonella paratyphi C phage (SPC-P1) in different Salmonella serovars and to identify the integration sites in host genome. METHODS: Based on the complete genome of SPC-P1 in S. paratyphi C RKS4594, 6 pairs of primers were designed and used to amplify the fragments of SPC-P1 in 11 S. typhi, 11 S. paratyphi A, 12 S. paratyphi B and 23 S. paratyphi C strains. At the same time, 100 complete genomes of Salmonella including 20 serovars available in National Center for Biotechnology Information (NCBI) database were downloaded and aligned by Mauve 2.3.1 to determine the prevalence of SPC-P1 in these serovars. Primers were designed according to the integration sites of SPC-P1 in the genome of RKS4594, and used to amplify ten strains having SPC-P1 in the genome. The PCR products were sequenced to investigate the integration sites of SPC-P1. RESULTS: SPC-P1 was widely distributed in S.paratyphi C genome. In the study, 14 strains had all 6 fragments and 2 strains had 3-5 fragments. All the amplified fragments showed expected sizes. In contrast, in the genomes of S. typhi, S. paratyphi A and S. paratyphi B, no or only 1-2 fragments could be amplified, and the sizes were smaller than expected. The results from Mauve showed that only in the genome of S.choleraesuis, which was a close relative of S. paratyphi C, there existed an almost complete genome of SPC-P1. The insertion site of SPC-P1 in all the ten S. paratyphi C strains tested was between pgtE and yfdC genes. CONCLUSION: SPC-P1 is a unique virulence factor of S. paratyphi C. It may play roles in the host range and pathogenicity of S.paratyphi C.

Gene sequencing and variable site analyzing of coding region of two enterovirus A71 isolates with different clinical phenotypes.

Currently, it is still controversial that if the pathogenicity of EV-A71 causing severe or mild hand, foot, and mouth disease (HFMD) is associated with viral nucleotide or amino acid sequence(s). In this study, 19 clinical strains were detected in samples from diagnosed patients of EV-A71-caused HFMD with mild or severe symptoms. Then, VP1-2A fragment sequences of 19 EV-A71 isolates were determined, the phylogenetic analysis, based on VP1 sequences of 19 EV-A71 stains in this study and which of 62 EV-A71 strains with different clinical phenotypes reported before, were carried out. Our results showed that no difference in the genotype and evolution distribution was observed among the EV-A71 strains mentioned above. Furthermore, two EV-A71 isolates, which with much close evolutionary relationship but different clinical manifestations, were purified by plaque assay, the complete genome sequencing was done, and deduced amino acid sequence analysis of 11 proteins coded by EV-A71 was carried out. Eight variable amino acid sites were found and further verified with those of 62 strains reported before. Our study provides further evidence that the potential pathogenicity of EV-A71 causing severe or mild HFMD seems not to be associated with viral genotype and even the amino acid substitution.

A genome map of Salmonella enterica serovar Agona: numerous insertions and deletions reflecting the evolutionary history of a human pathogen.

Salmonella enterica serovar Agona is an important zoonotic pathogen, causing serious human illness worldwide, but knowledge about its genetics and evolution, especially regarding the genomic events that might have contributed to the formation of S. Agona as an important pathogen, is lacking. As a first step toward understanding this pathogen and characterizing its genomic differences with other salmonellae, we constructed a physical map of S. Agona in strain SARB1 using I-CeuI, XbaI, AvrII and Tn10 insertions with pulsed-field gel electrophoresis techniques. On the 4815-kb genomic map, we located 82 genes, revealed one inversion of about 1000 kb and resolved seven deletions and seven insertions ranging from 10 to 67 kb relative to the genome of Salmonella typhimurium LT2. These genomic features clearly distinguish S. Agona from other previously analyzed salmonellae and provide clues to the molecular basis for its genomic divergence. Additionally, these kinds of physical maps, combined with emerging high-speed sequencing technologies, such as the Solexa or SOLiD techniques, which require a pre-existing high-resolution physical map such as the S. Agona map reported here, will play important roles in genomic comparative studies of bacteria involving large numbers of strains.

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.

[Frequency of transfusion transmitted virus in healthy infants in Jiujiang city Jiangxi province].

OBJECTIVE: Transfusion transmitted virus (TTV) DNA was detected in serum samples obtained from healthy infants and volunteer blood donors living in Jiujiang city in an attempt to shed light on the prevalence of TTV infection and the transmission route of TTV infection in infants. METHODS: Modified untranslated region, polymerase chain reaction (UTR PCR) and N22 PCR were performed to test TTV DNA in serum samples from 86 infants and 58 blood donors. RESULTS: TTV DNA was detected by UTR PCR in 51 (53.5%) infants and 58 (100%) in blood donors, while that tested by N22 PCR was 14 (16.3%) and 22 (37.3%) in infants and blood donors, respectively. Among infants younger than 30 days, 1 - 6 months and 7 - 12 months of age, TTV DNA was detected by UTR PCR and N22 PCR at rates of 0, 33.3%, 95.0% and 0, 7.4%, 30.0%, respectively. CONCLUSION: The prevalence rates of TTV DNA detected by UTR PCR were 95% in infants of 7 - 12 months after birth and 100% in healthy blood donors in Jiujiang city. However the results obtained by N22 PCR were much less frequently in the same population. Results showed that significant difference did exist in the prevalence of TTV DNA detected by the two different PCR systems. Age-dependent increase of TTV infection was observed in early childhood, while environmental sources were considered to be the most common route of TTV acquisition as the primary infection in infants. However, the prevalence of TTV in infants of 7 - 12 months was similar to that in healthy adults in the same region.