Genetic diversity and structure of domestic cavy (Cavia porcellus) populations from smallholder farms in southern Cameroon

Although domestic cavies are widely used in sub-Saharan Africa as a source of meat and income, there are only a few studies of their population structure and genetic relatedness. This seminal study was designed with the main objective to assess the genetic diversity and determine the population structure of cavy populations from Cameroon to guide the development of a cavy improvement program. Sixteen microsatellite markers were used to genotype 109 individuals from five cavy populations (Wouri, Moungo and Nkongsamba in the Littoral region, and Mémé and Fako in the Southwest region of Cameroon). Twelve markers worked in the five populations with a total of 17 alleles identified, with a range of 2.9 to 4.0 alleles per locus. Observed heterozygosity (from 0.022 to 0.277) among populations was lower than expected heterozygosity (from 0.42 to 0.54). Inbreeding rates between individuals of the populations and between individuals in each population were 59.3% and 57.2%, respectively, against a moderate differentiation rate of 4.9%. All the tested loci deviated from Hardy-Weinberg equilibrium, except for locus 3. Genetic distances between populations were small (from 0.008 to 0.277), with a high rate of variability among individuals within each population (54.4%). Three distinct genetic groups were structured. This study has shown that microsatellites are useful for the genetic characterization of cavy populations in Cameroon and that the populations investigated have sufficient genetic diversity that can be used to be deployed as a basis for weight, prolificacy and disease resistance improvement. The genetic of diversity in Southern Cameroon is wide and constitute an opportunity for cavy breeding program

Mycobacterium tuberculosisis the causative agent of tuberculosis in the southern ecological zones of Cameroon, as shown by genetic analysis

BACKGROUND: Tuberculosis (TB) is a major cause of mortality and suffering worldwide, with over 95% of TB deaths occurring in low- and middle-income countries. In recent years, molecular typing methods have been widely used in epidemiological studies to aid the control of TB, but this usage has not been the case with many African countries, including Cameroon. The aims of the present investigation were to identify and evaluate the diversity of the Mycobacterium tuberculosis complex (MTBC) isolates circulating in two ecological zones of Cameroon, seven years after the last studies in the West Region, and after the re-organization of the National TB Control Program (NTBCP). These were expected to shed light also on the transmission of TB in the country. The study was conducted from February to July 2009. During this period, 169 patients with symptomatic disease and with sputum cultures that were positive for MTBC were randomly selected for the study from amongst 964 suspected patients in the savannah mosaic zone (West and North West regions) and the tropical rainforest zone (Central region). After culture and diagnosis, DNA was extracted from each of the MTBC isolates and transported to the BecA-ILRI Hub in Nairobi, Kenya for molecular analysis. METHODS: Genetic characterization was done by mycobacterial interspersed repetitive unit–variable number tandem repeat typing (MIRU-VNTR) and Spoligotyping. RESULTS: Molecular analysis showed that all TB cases reported in this study were caused by infections with Mycobacterium tuberculosis (98.8%) and Mycobacterium africanum (M. africanum) (1.2%) respectively. We did not detect any M. bovis. Comparative analyses using spoligotyping revealed that the majority of isolates belong to major clades of M. tuberculosis: Haarlem (7.6%), Latin American-Mediterranean (34.4%) and T clade (26.7%); the remaining isolates (31.3%) where distributed among the minor clades. The predominant group of isolates (34.4%) corresponded to spoligotype 61, previously described as the “Cameroon family. Further analysis based on MIRU-VNTR profiles had greater resolving power than spoligotyping and defined additional genotypes in the same spoligotype cluster. CONCLUSION: The molecular characterization of MTBC strains from humans in two ecological regions of Cameroon has shown that M. tuberculosis sensu stricto is the predominant agent of TB cases in the zones. Three decades ago, TB was reported to be caused by M. africanum in 56.0% of cases. The present findings are consistent with a major shift in the prevalence of M. tuberculosis in Cameroon

Viral metagenomics demonstrates that domestic pigs are a potential reservoir for Ndumu virus

BACKGROUND: The rising demand for pork has resulted in a massive expansion of pig production in Uganda. This has resulted in increased contact between humans and pigs. Pigs can act as reservoirs for emerging infectious diseases. Therefore identification of potential zoonotic pathogens is important for public health surveillance. In this study, during a routine general surveillance for African swine fever, domestic pigs from Uganda were screened for the presence of RNA and DNA viruses using a high-throughput pyrosequencing method. FINDINGS: Serum samples from 16 domestic pigs were collected from five regions in Uganda and pooled accordingly. Genomic DNA and RNA were extracted and sequenced on the 454 GS-FLX platform. Among the sequences assigned to a taxon, 53% mapped to the domestic pig (Sus scrofa). African swine fever virus, Torque teno viruses (TTVs), and porcine endogenous retroviruses were identified. Interestingly, two pools (B and C) of RNA origin had sequences that showed 98% sequence identity to Ndumu virus (NDUV). None of the reads had identity to the class Insecta indicating that these sequences were unlikely to result from contamination with mosquito nucleic acids. CONCLUSIONS: This is the first report of the domestic pig as a vertebrate host for Ndumu virus. NDUV had been previously isolated only from culicine mosquitoes. NDUV therefore represents a potential zoonotic pathogen, particularly given the increasing risk of human-livestock-mosquito contact

20-Year Risks of Breast-Cancer Recurrence after Stopping Endocrine Therapy at 5 Years

The administration of endocrine therapy for 5 years substantially reduces recurrence rates during and after treatment in women with early-stage, estrogen-receptor (ER)-positive breast cancer. Extending such therapy beyond 5 years offers further protection but has additional side effects. Obtaining data on the absolute risk of subsequent distant recurrence if therapy stops at 5 years could help determine whether to extend treatment

Long-term outcomes for neoadjuvant versus adjuvant chemotherapy in early breast cancer: meta-analysis of individual patient data from ten randomised trials

Background Neoadjuvant chemotherapy (NACT) for early breast cancer can make breast-conserving surgery more feasible and might be more likely to eradicate micrometastatic disease than might the same chemotherapy given after surgery. We investigated the long-term benefits and risks of NACT and the influence of tumour characteristics on outcome with a collaborative meta-analysis of individual patient data from relevant randomised trials. Methods We obtained information about prerandomisation tumour characteristics, clinical tumour response, surgery, recurrence, and mortality for 4756 women in ten randomised trials in early breast cancer that began before 2005 and compared NACT with the same chemotherapy given postoperatively. Primary outcomes were tumour response, extent of local therapy, local and distant recurrence, breast cancer death, and overall mortality. Analyses by intention-to-treat used standard regression (for response and frequency of breast-conserving therapy) and log-rank methods (for recurrence and mortality). Findings Patients entered the trials from 1983 to 2002 and median follow-up was 9 years (IQR 5–14), with the last follow-up in 2013. Most chemotherapy was anthracycline based (3838 [81%] of 4756 women). More than two thirds (1349 [69%] of 1947) of women allocated NACT had a complete or partial clinical response. Patients allocated NACT had an increased frequency of breast-conserving therapy (1504 [65%] of 2320 treated with NACT vs 1135 [49%] of 2318 treated with adjuvant chemotherapy). NACT was associated with more frequent local recurrence than was adjuvant chemotherapy: the 15 year local recurrence was 21·4% for NACT versus 15·9% for adjuvant chemotherapy (5·5% increase [95% CI 2·4–8·6]; rate ratio 1·37 [95% CI 1·17–1·61]; p=0·0001). No significant difference between NACT and adjuvant chemotherapy was noted for distant recurrence (15 year risk 38·2% for NACT vs 38·0% for adjuvant chemotherapy; rate ratio 1·02 [95% CI 0·92–1·14]; p=0·66), breast cancer mortality (34·4% vs 33·7%; 1·06 [0·95–1·18]; p=0·31), or death from any cause (40·9% vs 41·2%; 1·04 [0·94–1·15]; p=0·45). Interpretation Tumours downsized by NACT might have higher local recurrence after breast-conserving therapy than might tumours of the same dimensions in women who have not received NACT. Strategies to mitigate the increased local recurrence after breast-conserving therapy in tumours downsized by NACT should be considered—eg, careful tumour localisation, detailed pathological assessment, and appropriate radiotherapy

Environment and farm factors associated with exposure to Theileria parva infection in cattle under traditional mixed farming system in Mbeere District, Kenya

The objective of this study was to investigate the relationship between seroprevalence to Theileria parva infection in cattle and potential environmental and farm-level effects in 80 farms under traditional crop–livestock system in Mbeere District, Kenya. A standardized questionnaire was used to collect the effects characteristics as related to T. parva infection epidemiology. Serum samples were collected from 440 cattle of all ages for detection of T. parva antibodies by the enzyme-linked immunosorbent assay technique. The association between the variables was assessed using a generalized estimation equation logistic regression model. The overall T. parva seroprevalence, accounting for correlation of responses, was 19.3% (95% confidence interval (CI) 14%, 25%). Two variables, “administrative division” and “presence of the vector tick on the farm”, were significantly associated with the T. parva seroresponse. Respectively, cattle from farms in Gachoka, Evurore, and Mwea divisions were (and their 95% CI) 1.3 (0.36, 4.8), 4.4 (1.2, 15.9), and 15.2 (4.9, 47.1) times more likely to be seropositive relative to those from Siakago Division (P=0.000). Cattle from farms in which the vector tick was present were 2.9 (1.2, 6.7) times more likely to be seropositive (P=0.011). Results of this study suggested that both environmental and farm factors may be associated with T. parva infection epidemiology in Mbeere District. Under such circumstances, characterization of environmental suitability for the vector tick and corresponding environment-specific farm management practices in the district is required both for improved understanding of the disease and in planning disease control programs

Estimating seroprevalence and variation to four tick-borne infections and determination of associated risk factors in cattle under traditional mixed farming system in Mbeere District, Kenya

A cross-sectional study of serum antibody responses of cattle to tick-borne disease (TBD) parasites (Theileria parva, Theileria mutans, Anaplasma marginale and Babesia bigemina) was conducted on traditional smallholder mixed farms in Mbeere District in Kenya. The objective was to estimate the infections’ seroprevalence and variation and identify associated risk factors. A total of 440 cattle in 80 farms, selected by stratified random sampling from the four divisions in the district, were surveyed. Information on animal and on each farm's management practices, particularly on tick control practices, was obtained by personal interview using a standardized questionnaire. Prevalences of serum antibodies were determined using the enzyme-linked immunosorbent assay (ELISA) technique. The relationship between TBDs seroprevalence and the risk factors was assessed by multivariable analysis using standard logistic regression models and mixed models using the farm as a random effect. Overall estimation of seroprevalences and their 95% confidence limits were: T. parva (19% [14%, 25%]), T. mutans (25% [20%, 29%]), A. marginale (58% [52%, 64%]) and B. bigemina (19% [15%, 23%]). Analysis in presence of extra-binomial variation under Analysis Of Variance (ANOVA) yielded relatively larger intra-farm correlation coefficient (ICC) (0.3) and variance-inflation factor (VIF) (2.35) values for T. parva than for the other parasites [range, 0.05–0.07 (for ICC) and 1.02–1.32 (for VIF)]. Both farm- and area-level variables had variably significant and large effects on all infections, but these were more pronounced on T. parva seroprevalence. Inclusion of farm random effect resulted in substantially higher estimate of farm variance component for T. parva infection (1.73) compared to other infections [range, 0.29–0.56], comparable ICC values with those under ANOVA analysis [range, 0.08–0.35] and a substantially better fit than the standard multivariable logistic regressions. The above results serve as possible indicators of existence of endemic instability for the studied TBD infections in the district. A probable differential ecological and climatic variability in vector suitability habitats, particularly for T. parva vector, was likely in Mbeere District and this was suggested to influence farm tick control management across the area. Implications of the design-based sampling and analyses on the above results are also discussed