Increased performance of DNA metabarcoding of macroinvertebrates by taxonomic sorting.

DNA-based identification through the use of metabarcoding has been proposed as the next step in the monitoring of biological communities, such as those assessed under the Water Framework Directive (WFD). Advances have been made in the field of metabarcoding, but challenges remain when using complex samples. Uneven biomass distributions, preferential amplification and reference database deficiencies can all lead to discrepancies between morphological and DNA-based taxa lists.

Risk Factors of Typhoid Infection in the Indonesian Archipelago.

Background: Knowledge of risk factors and their relative importance in different settings is essential to develop effective health education material for the prevention of typhoid. In this study, we examine the effect of household level and individual behavioural risk factors on the risk of typhoid in three Indonesian islands (Sulawesi, Kalimantan and Papua) in the Eastern Indonesian archipelago encompassing rural, peri-urban and urban areas.

Methods: We enrolled 933 patients above 10 years of age in a health facility-based case-control study between June 2010 and June 2011.

Multi-locus variable-number tandem repeat profiling of Salmonella enterica serovar Typhi isolates from blood cultures and gallbladder specimens from Makassar, South-Sulawesi, Indonesia.

Multi-locus variable-number tandem repeat analysis differentiated 297 Salmonella enterica serovar Typhi blood culture isolates from Makassar in 76 genotypes and a single unique S. Typhi genotype was isolated from the cholecystectomy specimens of four patients with cholelithiasis. The high diversity in S.

Application of a point-of-care test for the serodiagnosis of typhoid fever in Nigeria and the need for improved diagnostics.

Introduction: There is an urgent need for affordable point-of-care diagnostics for the differentiation of febrile illnesses and the confirmation of typhoid in endemic countries.

Methodology: Blood samples were collected from febrile patients with clinical suspicion of typhoid and screened for typhoid fever using the Widal and Typhi Dri Dot tests, while stool and blood samples were screened for Salmonella Typhi using the culture method as well as PCR as a confirmatory test.

Results: A high proportion of febrile patients from Lagos with clinical suspicion of typhoid fever reacted positively in a simple and rapid latex agglutination assay for typhoid fever, indicating that this illness is a common and presumably under-diagnosed health problem in this metropolis.

Infection of cattle in Kenya with Brucella abortus biovar 3 and Brucella melitensis biovar 1 genotypes.

Brucella melitensis biovar 1 was isolated from bovine milk samples from a herd in central Kenya, and Brucella abortus biovar 3 was isolated from aborted fetus materials and vaginal discharge fluids from cattle in central and eastern provinces of Kenya. All infections including those with B. melitensis were in cattle with reproductive problems kept in mixed herds indicating that cross infection occurs from small ruminants.

Validation of the Dri-Dot Latex agglutination and IgM lateral flow assays for the diagnosis of typhoid fever in an Egyptian population.

Laboratory confirmation of typhoid fever is essential for appropriate medical treatment. Blood culture is a standard test for diagnosis of typhoid fever, but well-equipped diagnostic facilities to perform culture are seldom available in endemic areas. We retrospectively compared 2 diagnostic field tests, a latex agglutination Dri-Dot assay and an IgM Lateral Flow assay, to blood culture, in patients with clinically diagnosed typhoid fever.

Typhoid fever among hospitalized febrile children in Siem Reap, Cambodia.

Typhoid fever was confirmed by positive blood culture in 5 (3.7%) of 134 febrile children hospitalized in Cambodia. Typhoid was suspected in an additional 25 (18.

New flagellin gene for Salmonella enterica serovar Typhi from the East Indonesian archipelago.

Phase variation is a property unique of some Salmonella enterica serovar Typhi strains from Indonesia. Salmonella Typhi isolates from Indonesia have been described that in addition to the phase 1 Hd flagellin gene contain a second flagellin gene named z66. S.

Characterization of the Microbial Community Involved in the Suppression of Pythium aphanidermatum in Cucumber Grown on Rockwool.

ABSTRACT The root pathogen Pythium aphanidermatum induced lower levels of disease in cucumber (Cucumis sativus) plants on unsterilized, re-used rockwool slabs than on heat-sterilized, re-used rockwool. Several recolonization treatments of the sterilized rockwool enhanced the suppressiveness of the rockwool. Microbial community structures in the different rockwool treatments were investigated by plate counts on selective media.

Simple, rapid, and affordable point-of-care test for the serodiagnosis of typhoid fever.

We developed a point-of-care test for the serodiagnosis of typhoid fever in the format of an immunochromatographic lateral flow assay. The flow assay for typhoid fever is based on the detection of Salmonella enterica serotype Typhi lipopolysaccharide-specific immunoglobulin M (IgM) antibodies. The assay was evaluated on serum samples collected in a hospital in South Sulawesi, Indonesia, where typhoid fever is endemic, and the results were compared with culture and Widal test.

Laboratory evaluation of a simple and rapid latex agglutination assay for the serodiagnosis of typhoid fever.

A latex agglutination assay for the serodiagnosis of typhoid fever was evaluated on samples collected from patients with clinical suspicion of typhoid fever in South Sulawesi, Indonesia, where the disease is endemic. The latex assay is very easy to use, gives a rapid result and may be used as a point-of-care diagnostic test. For acute phase samples collected on average 6 days after the onset of illness, the sensitivity is 42.