Next generation genome sequencing reveals phylogenetic clades with different level of virulence among Salmonella Typhimurium clinical human isolates in Hong Kong.

BACKGROUND: Salmonella Typhimurium is frequently isolated from foodborne infection cases in Hong Kong, but the lack of genome sequences has hindered in-depth epidemiological and phylogenetic studies. In this study, we sought to reconstruct the phylogenetic relationship and investigate the distribution and mutation patterns of virulence determinants among local S. Typhimurium clinical isolates using their genome sequences. RESULTS: We obtained genome sequences of 20 S. Typhimurium clinical isolates from a local hospital cluster using a 454 GS FLX Titanium sequencing platform. Phylogenetic analysis was performed based on single nucleotide polymorphism positions of the core genome against the reference strain LT2. Antimicrobial susceptibility was determined using minimal inhibitory concentration for five antimicrobial agents and analyses of virulence determinants were performed through referencing to various databases. Through phylogenetic analysis, we revealed two distinct clades of S. Typhimurium isolates and three outliers in Hong Kong, which differ remarkably in antimicrobial susceptibility and presentation and mutations of virulence determinants. The local isolates were not closely related to many of the previously sequenced S. Typhimurium isolates, except LT2. As the isolates in the two clades spanned over 10 years of isolation, they probably represent endemic strains. The outliers are possibly introduced from outside of Hong Kong. The close relatedness of members in one of the clades to LT2 and the Japanese stool isolate T000240 suggests the potential reemergence of LT2 progeny in regions nearby. CONCLUSIONS: Our study demonstrated the utility of next-generation sequencing coupled to traditional microbiological testing method in a retrospective epidemiological study involving multiple clinical isolates. The evolution of multidrug- and ciprofloxacin-resistant strains among the more virulent clade is also an increasing concern.

Genome Sequences of Salmonella enterica Serotype Typhimurium Blood Clinical Isolate ST4848/06 and Stool Isolate ST1489/06.

Salmonella enterica serotype Typhimurium human blood strains isolated from outside Africa are rarely sequenced. Here, we report the draft genome sequences of two S. Typhimurium clinical strains isolated in the same year, one from blood and another from stool, in order to gain insights into the genetic basis leading to invasive diseases.

Draft genome sequence of Salmonella enterica serovar Typhimurium ST1660/06, a multidrug-resistant clinical strain isolated from a diarrheic patient.

Salmonella enterica serovar Typhimurium is one of the most prevalent serovars of Salmonella that causes human gastroenteritis. Here, we report the draft genome sequence of the S. Typhimurium multidrug-resistant strain ST1660/06. Comparative genomic analysis unveiled three strain-specific genomic islands that potentially confer the multidrug resistance and virulence of the strain.

Staphylococcus aureus carriage in the anterior nares of close contacts of patients with atopic dermatitis.

OBJECTIVE: To study the prevalence of Staphylococcus aureus colonization in close contacts of patients with atopic dermatitis (AD) and the influence on AD severity. DESIGN: Prospective case-control study. SETTING: Pediatric dermatology clinic in a Hong Kong university hospital. Patients We recruited 211 subjects prospectively, including 50 AD patients, 50 non-AD control subjects, 60 close contacts of AD patients, and 51 close contacts of controls. Intervention Nasal swabs and skin swabs were taken. Severity of AD was assessed using the SCORAD (Scoring Atopic Dermatitis) index. MAIN OUTCOME MEASURES: The prevalence of S aureus colonization in the close contacts of AD patients was compared with that of the close contacts of non-AD controls. Between-group differences were assessed, where appropriate, by unpaired t test or Pearson chi(2) test. Multivariate logistic regression using the forward stepwise method was performed to identify independent predictors of severe AD. A probability value of P < .05 was considered statistically significant. RESULTS: Significantly more nasal carriers of S aureus were found among the close contacts of AD patients (14 of 60 [23%]) than among the close contacts of non-AD controls (4 of 51 [8%] [P = .03]). The difference was still significant after the exclusion of the AD patients' close contacts who also had AD (24% vs 8% [P = .03]). By multivariate analysis, only skin colonization of S aureus was independently associated with severe AD (odds ratio, 17.0; 95% confidence interval, 1.60-181.1 [P = .02]). CONCLUSIONS: Anterior nares of close contacts of AD patients are reservoirs of S aureus. The presence of S aureus carriers among close contacts does not predict AD severity. Skin colonization is associated with severe AD.