The application of omics in ruminant production: a review in the tropical and sub-tropical animal production context

The demand for animal products (e.g. dairy and beef) in tropical regions is expected to increase in parallel with the public demand for sustainable practices, due to factors such as population growth and climate change. The necessity to increase animal production output must be achieved with better management and production technologies. For this to happen, novel research methodologies, animal selection and postgenomic tools play a pivotal role. Indeed, improving breeder selection programs, the quality of meat and dairy products as well as animal health will contribute to higher sustainability and productivity. This would surely benefit regions where resource quality and quantity are increasingly unstable, and research is still very incipient, which is the case of many regions in the tropics. The purpose of this review is to demonstrate how omics-based approaches play a major role in animal science, particularly concerning ruminant production systems and research associated to the tropics and developing countriesinfo:eu-repo/semantics/acceptedVersio

A metagenomic study of the rumen virome in domestic caprids

AbstractThis project sought to investigate the domestic caprid rumen virome by developing a robust viral DNA isolation and enrichmentprotocol (utilizing membrane filtration, ultra-centrifugation, overnight PEG treatment and nuclease treatment) and usingRSD-PCR and high throughput sequencing (HTS) techniques. 3.53% of the reads obtained were analogous to those of virusesdenoting Siphoviridae, Myoviridae, Podoviridae, Mimiviridae, Microviridae, Poxviridae, Tectiviridae and Marseillevirus.Most of the sequenced reads from the rumen were similar to those of phages, which are critical in maintaining the rumenmicrobial populations under its carrying capacity. Though identified in the rumen, most of these viruses have been reportedin other environments as well. Improvements in the viral DNA enrichment and isolation protocol are required to obtain datathat are more representative of the rumen virome. The 102,130 unknown reads (92.31%) for the goat and 36,241 unknownreads (93.86%) for the sheep obtained may represent novel genomes that need further study

Anti-tuberculosis drug resistance among new and previously treated sputum smear-positive tuberculosis patients in Uganda: results of the first national survey.

BACKGROUND: Multidrug resistant and extensively drug resistant tuberculosis (TB) have become major threats to control of tuberculosis globally. The rates of anti-TB drug resistance in Uganda are not known. We conducted a national drug resistance survey to investigate the levels and patterns of resistance to first and second line anti-TB drugs among new and previously treated sputum smear-positive TB cases. METHODS: Sputum samples were collected from a nationally representative sample of new and previously treated sputum smear-positive TB patients registered at TB diagnostic centers during December 2009 to February 2011 using a weighted cluster sampling method. Culture and drug susceptibility testing was performed at the national TB reference laboratory. RESULTS: A total of 1537 patients (1397 new and 140 previously treated) were enrolled in the survey from 44 health facilities. HIV test result and complete drug susceptibility testing (DST) results were available for 1524 (96.8%) and 1325 (85.9%) patients, respectively. Of the 1209 isolates from new cases, resistance to any anti-TB drug was 10.3%, 5% were resistant to isoniazid, 1.9% to rifampicin, and 1.4% were multi drug resistant. Among the 116 isolates from previously treated cases, the prevalence of resistance was 25.9%, 23.3%, 12.1% and 12.1% respectively. Of the 1524 patients who had HIV testing 469 (30.7%) tested positive. There was no association between anti-TB drug resistance (including MDR) and HIV infection. CONCLUSION: The prevalence of anti-TB drug resistance among new patients in Uganda is low relative to WHO estimates. The higher levels of MDR-TB (12.1%) and resistance to any drug (25.3%) among previously treated patients raises concerns about the quality of directly observed therapy (DOT) and adherence to treatment. This calls for strengthening existing TB control measures, especially DOT, routine DST among the previously treated TB patients or periodic drug resistance surveys, to prevent and monitor development and transmission of drug resistant TB

Analysis of factors associated with Multi drug resistance in Uganda; December 2009–February 2011.

<p>Variable included in the multivariate model were, age, sex, residence and previous history of TB treatment.</p>**<p>Analysis limited to univariate level as inclusion at multivariate level masked the apparent association between MDR and potential risk factors.</p

Flow Chart of patient enrollment in the National Anti-TB drug resistance survey in Uganda; December 2009–February 2011.

<p>Figure legend: **NTM = Non Tuberculous Mycobacteria.</p