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Africa
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Genotyping and Its Implications for Transmission Dynamics and Tuberculosis Control
Published in Peter D O Davies, Stephen B Gordon, Geraint Davies, Clinical Tuberculosis, 2014
Recent guidance on contact investigation suggests that in low-incidence countries, it should be limited to situations where it is clear that transmission is likely to have occurred [222], and this can be facilitated by genotyping. The United Kingdom, the Netherlands and the United States are countries that carry out prospective genotyping on all culture-confirmed isolates. Molecular clusters are generated using bespoke software or packages such as BioNumerics (www.applied-maths.com/bionumerics) to rapidly detect clusters and potential outbreaks. Epidemiological information on time, person and place is collected on index cases through routine surveillance and/or social networking questionnaires in an attempt to identify epidemiological links, social networks or transmission settings [223]. Further contacts can then be identified and screened for latent infection or active disease. Graphical representations of clusters can be useful to visualise epidemiological links, common features and social networks between cases (Figures 4.5 & 4.6).
Can sequencing improve the diagnosis and management of Clostridioides difficile infection?
Published in Expert Review of Molecular Diagnostics, 2021
Korakrit Imwattana, Daniel R Knight, Thomas V Riley
Beyond individual patients, WGS data can help with infection prevention and control within a healthcare facility. In addition to standard multilocus sequence typing (MLST), WGS can also provide gene-by-gene or allele-based typing of the core genome (cgMLST) and whole-genome (wgMLST) [29]. Combined with commercial analysis software (BioNumerics and Ridom SeqSphere) and an open-source database (EnteroBase), these approaches provide greater discrimination than conventional PCR-based or enzymatic restriction-based typing tools, but also offer portability and standardized nomenclature [30]. WGS-based typing can thus identify patients who are infected with epidemic C. difficile strains or strains that are multi-drug resistant [5,6], which can then lead to appropriate patient isolation and decontamination of the environment. Surveillance of genotypic AMR prevalence can also determine which antimicrobial is likely to trigger a CDI outbreak in the hospital, and proper management can be implemented to mitigate the risk [31]. This should greatly reduce CDI burden, both clinically and economically.
Dynamic analysis of human small intestinal microbiota after an ingestion of fermented milk by small-intestinal fluid perfusion using an endoscopic retrograde bowel insertion technique
Published in Gut Microbes, 2020
Toshihiko Takada, Daisuke Chinda, Tatsuya Mikami, Kensuke Shimizu, Kosuke Oana, Shiro Hayamizu, Kuniaki Miyazawa, Tetsu Arai, Miyuki Katto, Yusuke Nagara, Hiroshi Makino, Akira Kushiro, Kenji Oishi, Shinsaku Fukuda
A series of 10-fold dilutions of oral fluids and ileal fluids wereas prepared with sterilized PBS, and the diluted solutions were spread on DifcoTM Mitis Salivarius agar (Becton Dickinson and Company [cat. no. 229810]) supplemented with 0.001% sodium tellurite. The agar plates were incubated at 37°C for 72 h, aerobically. Each colony with different morphologies were collected, and DNA was extracted as described above.48 RAPD analysis was performed using the random primer 1252 (5ʹ-CCGCAGCCAA-3ʹ). PCR amplifications were performed with initial heating at 94°C for 2 min; 6 cycles of 94°C for 30 s, 36°C for 1 min, and 72°C for 90 s; 30 cycles of 94°C for 20 s, 36°C for 30 min, and 72°C for 90 s; and a final extension at 72°C for 3 min. Fingerprint profiles were separated by gel electrophoresis at 100 V for approximately 30 min in 1.0% agarose gels. The RAPD fingerprint profiles were compared by using BioNumerics software (Applied Math). The similarity index was calculated using the Jaccard coefficient, and the unweighted pair-group method using average linkages was used to construct a dendrogram.
Staphylococcus aureus infected embolic stroke upregulates Orm1 and Cxcl2 in a rat model of septic stroke pathology
Published in Neurological Research, 2019
Lærke Boye Astrup, Kerstin Skovgaard, Rune Skovgaard Rasmussen, Tine Moesgaard Iburg, Jørgen Steen Agerholm, Bent Aalbæk, Henrik Elvang Jensen, Ole Lerberg Nielsen, Flemming Fryd Johansen, Peter Mikael Helweg Heegaard, Páll Skúli Leifsson
In the pilot study, the average bacterial content per 5 mm macroclot was determined based on a total of five fibrin macroclots. Each of the five clots derived from a different rat (Table 1). The macroclots were prepared as described in ‘surgical procedures’. Each macroclot was flushed out of the catheter by 1 mL saline and homogenized. Both undiluted and serial tenfold dilutions of the homogenate were cultured on blood agar plates at 37°C for 24 h. Final detection limit was 1 CFU/embolus. Possible spread of bacteria to the systemic circulation was examined by bacteriological culturing of brain, liver, heart, spleen, and kidney from three rats (Table 2). Each tissue sample/organ was homogenized with 9 mL saline, and both undiluted and serial tenfold dilutions of the homogenate were cultured on blood agar plates at 37°C for 24 h. Detection limit was 1 CFU/g tissue or 1 CFU/organ for organs with a total weight of less than 1 g (spleen and kidney). For each positive sample, a colony was selected for S. aureus protein-A typing (spa-typing). A multiplex PCR [27] and BioNumerics v 6.6 (Applied Maths, Sint-Martens-Latem, Belgium) was used to amplify, sequence and analyse the spa gene and assign the spa type. The infused S. aureus strain was used as positive control.