A novel marker for the species-specific detection and quantitation of Shigella sonnei by targeting a methylase gene

Shigella sonnei is a causal agent of fever, nausea, stomach cramps, vomiting, and diarrheal disease. The present study describes a quantitative polymerase chain reaction (qPCR) assay for the specific detection of S. sonnei using a primer pair based on the methylase gene for the amplification of a 325 bp DNA fragment. The qPCR primer set for the accurate diagnosis of Shigella sonnei was developed from publically available genome sequences. This quantitative PCR-based method will potentially simplify and facilitate the diagnosis of this pathogen and guide disease management.     

Nationwide groundwater surveillance of noroviruses in South Korea, 2008

To inspect the norovirus contamination of groundwater in South Korea, a nationwide study was performed in the summer (June to August) and winter (October to December) of 2008. Three-hundred sites designated by the government ministry were inspected. Water samples were collected for analysis of water quality, microorganism content, and viral content. Water quality was assessed by temperature, pH, turbidity, residual chlorine, and nitrite nitrogen content. Microorganism contents were analyzed bacteria, total coliforms, Escherichia coli, and bacteriophage. Virus analyses included panenterovirus and norovirus. Two primer sets were used for the detection of norovirus genotypes GI and GII, respectively. Of 300 samples, 65 (21.7%) were norovirus positive in the summer and in 52 (17.3%) were norovirus positive in the winter. The genogroup GI noroviruses that were identified were GI-1, GI-2, GI-3, GI-4, GI-5, GI-6, and GI-8 genotypes; those in the GII genogroup were GII-4 and GII-Yuri genotypes. The analytic data showed correlative relationships between the norovirus detection rate and the following parameters: water temperature and turbidity in physical-chemical parameters and somatic phage in microbial parameters. It is necessary to periodically monitor waterborne viruses that frequently cause epidemic food poisoning in South Korea for better public health and sanitary conditions.     

Full sequence analysis and characterization of a human astrovirus type 1 isolate from South Korea

Human astroviruses are recognized as an important cause of infantile gastroenteritis around the world. In South Korea, sporadic cases of HAstV infection have been reported since 2002. However, hitherto, there have been no studies reporting the whole genome sequence of an HAstV isolate from South Korea. Hence, we sequenced and analyzed the entire genome of an HAstV-1 strain (lhar) that was isolated in Seoul, South Korea. The whole-genome sequence analysis revealed 3 open reading frames comprising the whole genome: ORF1a (2,763 bp), ORF1b (1,548 bp), and ORF2 (2,364 bp). The lhar strain showed amino acid identities with 8 other reference strains of 87.6–98.7%, 94.2–98.8%, and 62.6–99.0% in the ORF1a, ORF1b, and ORF2 regions, respectively. The amino acid sequence of the capsid region encoded by ORF2 was compared with a total of 19 HAstV-1 strains and 8 HAstVs reference strains isolated in various countries. This revealed 1 amino acid substitution, at aa412 (Pro → Arg) in ORF2. This study, the first to report the full-length sequence of an HAstV isolated in South Korea, is meaningful in that it can be used as a full-length HAstV sequence standard for future comparison studies. It may also prove useful to the field of public health field by facilitating the diagnosis and the prediction of new emerging variants.     

A 5‐year survey (2007–2011) of enteric viruses in Korean aquatic environments and the use of coliforms as viral indicators

Three hundred and thirty‐nine water samples obtained from 90 locations in Korea from 2007 to 2011 were tested for the presence of enteric viruses (EV), total coliforms (TC), and fecal coliforms (FC). A total culturable virus assay revealed that 89 samples (26.3%) were positive for EVs, the average concentration being 5.8 most probable number (MPN)/100 L. The Han river basin exhibited the highest contamination by EVs (occurrence, 41.3%; average concentration, 24.0 MPN/100 L). EV contamination was found more frequently in river water (occurrence, 33.6%; concentration, 8.4 MPN/100 L) than in lake water or groundwater. The concentration of EVs was highest in spring (7.7 MPN/100 L), whereas it was found most frequently in winter (36.1%). The number of TCs ranged from 0 – 1.2 × 10⁵ colony forming units (CFU)/100 mL and that of FCs from 0–6.2 × 10³ CFU/100 mL per sample. Statistical analyses showed that the presence of EVs, TCs and FCs did not correlate significantly with temperature or turbidity. In addition, presence of TCs and FCs was not significantly correlated with presence of EVs. In conclusion, TCs and FCs may not be accurate microbial indicators of waterborne EVs in Korean aquatic environments.