Poster Abstracts - S518


Can genomics enable genetic evaluations with phenotypes recorded on smallholder dairy farms?

Identification: Powell, Owen

Credits: None available.

Can genomics enable genetic evaluations with phenotypes recorded on smallholder dairy farms?
Owen Powell1, R. Chris Gaynor1, Janez Jenko1, Gregor Gorjanc1, Okeyo Mwai2, Raphael Mrode2,3 & John M. Hickey1
1The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Research Centre, Midlothian EH25 9RG, UK; 2ILRI, International Livestock Research Institute; 3Scotland's Rural College (SRUC), Peter Wilson Building, Kings Buildings, West Mains Road, Edinburgh, EH9 3JG
Background: Genetic evaluation is a central component of genetic improvement programs. In advanced economies, most genetic evaluations depend on large quantities of data that are recorded on commercial farms. Large herd sizes and widespread use of artificial insemination enable the genetic and environmental components of an individual animal's phenotype to be accurately separated. In contrast to this, herds are neither large nor have high genetic connectedness in smallholder farming systems, such as in East Africa. This limits genetic evaluation with pedigree information. Genomic information keeps track of shared haplotypes rather than animals. This information could capture and strengthen connectedness between herds and through this may enable genetic evaluations based on phenotypes recorded on smallholder dairy farms. The objective of this study was to use simulation to quantify the power of genomic information to enable genetic evaluation under such conditions.
Results: The results from this study show; (i) GBLUP produced higher accuracies than PBLUP at all population sizes and herd sizes, (ii) Models with herd fitted as a random effect produced equal or higher accuracies than the model with herd fitted as a fixed effect across all herd size scenarios, (iii) At low levels of genetic connectedness, with four offspring per sire and one to two animals per herd, GBLUP produced EBV accuracies greater than 0.5. Generally, a decrease in the number of sires mated per generation showed consistently higher accuracies compared to when more sires were used.
Conclusions: This study has demonstrated the potential of genomic information to be an enabling technology in smallholder dairy economies by facilitating genetic evaluations with records collected from farms with herd sizes of four cows or less.  The inclusion of smallholder dairy data in genetic evaluations could provide increases in local and national milk production, in regions such as East Africa, with downstream impacts upon wider societal, nutritional and economic outcomes.

First molecular detection of pathogenic Leptospira in livestock from slaughterhouses in Madagascar

Identification: Rahelinirina, Soanandrasana

Credits: None available.

First molecular detection of pathogenic Leptospira in livestock from slaughterhouses in Madagascar
Soanandrasana Rahelinirina1, Mark Moseley2, Minoarisoa Rajerison1, Rakotoharinome Vincent Michel3, Sandra Telfer1,2
1Institut Pasteur de Madagascar, 2The University of Aberdeen, 3Direction des Services Vétérinaires Madagascar
Although leptospirosis has not been considered a significant health problem for humans or livestock in Madagascar, a recent serological study has shown evidence of exposure in humans and identified contact with cattle as a key risk factor.  However, the real role of livestock such as cattle and pig in the epidemiology of human leptospirosis in Madagascar remains to be elucidated. The aims of this study were to determine the prevalence of Leptospira among livestock in Madagascar and characterize the pathogenic Leptospira species found. Kidney and urine samples from 105 cattle and 100 pigs were collected from four slaughterhouses in Madagascar in 2015. The samples were tested by a quantitative real-time PCR TaqMan assay targeting the 16sRNA gene specific to pathogenic Leptospira. Where possible, sequencing of 200-300bp of the lfb1 gene was used to identify infecting Leptospira species. Cattle had a significantly higher overall prevalence than pigs (19% vs 5%). Cattle had 13 infections detected in kidney samples and 11 in urine samples, with only 4 individuals testing positive for both sample types. Of the positive pigs, only one infection was detected in kidney compared to four infections detected in urine.
Sequencing identified L. borgpetersenii and L. kirschneri in cattle. No lfb1 sequences were obtained from positive pig samples. This is the first molecular evidence of leptospirosis in livestock in Madagascar. The high prevalence in cattle provides further evidence that they could be an important source of infection for humans and also suggest that leptospirosis may have significant impacts on animal health and productivity. Moreover, our results highlight the need to consider sampling methodology when comparing studies and planning surveillance. Our results reinforce the need to take a one health approach for zoonoses like leptospirosis.

Genomic Characterization of Zambian Indigenous Cattle Breeds

Identification: Smith, Edward

Credits: None available.

Genomic Characterization of Zambian Indigenous Cattle Breeds
Edward Smith
Virginia Polytechnic Institute and State University, Animal and Poultry Sciences, Blacksburg, VA
Breed characterization is a primary step in designing appropriate management and conservation programs of livestock in developing countries. Since cattle represent a major food animal species in Zambia, its conservation is a major goal for both the government and non-governmental organizations. To support the conservation effort, the objective of this thesis research was to assess the phenotypic and molecular characteristics of indigenous Zambian cattle breeds including Angoni, Barotse, Tonga, and Baila based on body measurements and randomly amplified polymorphic DNA (RAPD) markers, respectively. A total of 100 animals, 25 from each of the four breeds associated with different tribes and region of Zambia, were used in the molecular analysis research. Additionally, 10 Holstein x Jersey crossbred animals were used as a reference and to test the extent of cross-breeding, if any, of the indigenous stock with exotic breeds. To further compare the Zambian indigenous breeds, morphometric measurements including body length, heart girth, and height at withers on 50 animals of each breed were measured. Blood was collected from animals at randomly selected farms and DNA isolated by standard protocols in Zambia. A total of 10 primers, of the 20 evaluated for informativeness, were used in the RAPD-PCR analyses. Differences among the four breeds for all the three morphometric measurements were significant with the Barotse significantly higher than the other three (P<0.05). The average number of bands per primer was 7.1 and the percentage of polymorphic bands per primer ranged from 40 to 71.4 with an average of 64.8%.  Breed divergence was highest between the Tonga and the Barotse and lowest between the Tonga and Baila breeds.  Both the morphometric measurements and RAPD-based distance estimates suggest that the Barotse may be different from the other indigenous breeds while the Tonga and Baila were more closely related. In addition, the genetic distance estimates imply that the Holstein x Jersey crosses are different from the four Zambian indigenous cattle breeds evaluated. This thesis research provides, for the first time, the basic genetic information necessary for conservation of Zambian cattle breeds and the use of these populations for effective crossbreeding. The data suggest that though there is isolated by geographic distance and cultural differences among the tribes, two of the breeds are significantly related.

Genetic diversity of pharmacogenes in a Bantu-speaking cohort and evaluation of variants associated with tenofovir-induced nephrotoxicity

Identification: Tshabalala, Elizabeth

Credits: None available.

Genetic diversity of pharmacogenes in a Bantu-speaking cohort and evaluation of variants associated with tenofovir-induced nephrotoxicity
E. Sibongile Tshabalala1, Ananyo Choudhury2, Natasha Beeton-Kempen1, Faheem Seedat3 and Ebrahim Variava3, Neil Martinson4, Michèle Ramsay2, 5 and Dalu Mancama1
1CSIR, Biosciences Unit, South Africa: 2Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, South Africa; 3Department of Internal Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; 4Perinatal HIV Research Unit, Baragwanath Hospital and Faculty of Health Sciences, University of the Witwatersrand, South Africa; 5Division of Human Genetics, National Health Laboratory Service, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, South Africa
Recent South African studies report an increase in hospital admissions due to adverse drug reactions (ADRs), including to tenofovir disoproxil fumarate (TDF). Growing evidence suggests a genetic contribution to TDF-related ADRs. Given the high genetic diversity observed in African populations, the aim of this study was to elucidate the pharmacological implications of such diversity by identifying and characterizing known and novel pharmacogenetic variants and evaluating their possible association with TDF-induced nephrotoxicity. Using targeted next generation sequencing to screen 40 Bantu-speaking individuals for variants in 65 genes, 1687 variants were identified; including 129 novel and 22 potential loss-of-function variants. Based on allele frequency (MAF>0.1) and prior association with ADRs, nine SNPs within five genes were prioritised for a genetic association study for TDF-induced nephrotoxicity (clinically manifesting as acute kidney injury (AKI)).  A total of 137 HIV positive patients on TDF treatment were subsequently genotyped using TaqMan® assays, 53 of whom presented with AKI. Association analysis was performed with alleles, genotypes and haplotypes using χ2 tests. The ABCC2 1249A allele and ABCC2 haplotypes AAC and AAT displayed associations with TDF-induced AKI (p≤0.05). The ABCC2 GTT haplotype (p=0.02) appeared to be protective against TDF-induced AKI. However, the associations were not significant following corrections for multiple testing. Further evaluation of these ABCC2 variants in larger cohorts is warranted to establish their role, if any, in TDF-induced AKI.

Non-typhoidal Salmonella and Zoonotic E. coli as Potential Drivers of Antimicrobial Resistance in Pastoralist Communities in Kasese District, Uganda

Identification: Walusansa, Abdul

Credits: None available.

Non-typhoidal Salmonella and Zoonotic E. coli as Potential Drivers of Antimicrobial Resistance in Pastoralist Communities in Kasese District, Uganda
Abdul Walusansa
School of Medicine, Islamic University in Uganda

August 2017
Introduction: Non-prescribed use of antimicrobials in Agriculture incurs a transfer risk of resistant pathogens to humans. The aim of this study was to determine the potential of non-typhoidal Salmonella spp and Zoonotic E. coli to serve as drivers of Antimicrobial resistance among animals and humans.
Methodology: A laboratory based cross-sectional study was done using archived Salmonella spp and E. coli isolates previously obtained from individuals among pastoralist communities of Kasese district, Uganda. Recovery of the isolates was done by conventional culture and Identification by biochemical methods, serotyping and PCR. Antimicrobial resistance profiling was done by using Kirby bauer disc diffusion method. Following this; the isolates were screened for resistance mechanisms including Extended Spectrum β-lactamase, Carbapenemase and AmpC production using disc diffusion based methods.
Results: The prevalence of Enterohemorrhagic E.coli (EHEC) and Non Typhoidal salmonella were 16% (28/180) and 50% (1/2) respectively. Of the EHEC, 94% (26/28) were of phylogroup B1, A (3%, 1/28) and B2 (3%, 1/28). The most prevalent virulence gene in the EHEC was Stx1 (100%, 28/28) followed by Stx2e (94%, 26/28), none was Stx2 positive. Highest resistance was seen to Cotrimoxazole (89%, 25/28), Tetracycline (71%,20/28), Ampicillin (65%,18/28) and Nitrofurantoin (28%,8/28), these are commonly used in the agricultural sector, whereas minimal resistance was observed to those commonly used in human medicine especially the β-lactams, β-lactam inhibitors and Carbapenems. 17%, (5/28) of the EHEC were ESBL positive, of these one (3%, 1/28) was a Carbapenemase producer. Though only one Non-typhoidal Salmonella isolate was found, it is worrying to note that it showed resistance to all the three antimicrobial agents (Nalidixic acid, Chloramphenicol and Ciprofloxacin) that are most recommended for treatment of Salmonellosis in this setting.
Conclusion: There is a high prevalence of highly pathogenic and resistant zoonotic E. coli and low prevalence of Non typhoidal salmonella among humans in pastoralist communities in Uganda. We suspect that these pathogens, along with their AMR genes, were acquired from animals because the zoonotic E. coli (EHEC) largely contained the animal specific Vero toxin gene VT2e and majority belonged Pylo-group B1 which has been documented as the most common EHEC phylo-group inhabiting domestic animals. Therefore, it is highly likely that zoonotic bacteria are potential drivers of antimicrobial resistance to humans in these settings and we recommend that studies involving relatedness of drug resistant isolates from humans and animals should be conducted to ascertain the role of enterohemorrhagic E. coli in the zoonotic spread of antimicrobial resistance in pastoralist communities. We recommend that a one health approach should be used to establish drivers of MDR spread in pastoralist communities.

Occurrence and Multiple-Antibiotics Resistance Profile of Enterobacteriaceae Isolated from Bats Faecal Samples in Osun State, Nigeria

Identification: Aladejana, Oluwatoyin

Credits: None available.

Occurrence and Multiple-Antibiotics Resistance Profile of Enterobacteriaceae Isolated from Bats Faecal Samples in Osun State, Nigeria
Aladejana Oluwatoyin Modupe1*, Oluduro Antonia Olufunke2, Famurewa Oladiran1, Thonda Oluwakemi Abike1, Olawoye Abimbola Abosede1.
1 Department of Biological Sciences, Microbiology Unit, Kings University, Odeomu, Osun State Nigeria; 2Department of Microbiology, Faculty of Science, Obafemi Awolowo University, Ile-ife, Osun State, Nigeria  
*Corresponding Author
Members of Enterobacteriaceae are important human pathogens and increasing number of antibiotic-resistant strains among the members are detected worldwide.  Bats are one of the most widely distributed mammals in the world, they are known as either reservoirs or carriers of several zoonosis. A total of 48 faecal samples were collected with 142 isolates recovered from Obafemi Awolowo University Ile Ife, 23 faecal samples were collected with 84 isolates recovered from Nigeria machine Tools, Osogbo and 30 faecal samples were collected with 111 isolates recovered from Oba's Palace Area, Ilesa, all in Osun State South West Nigeria.  Of the 41 different genera detected, 13 were common to the three study locations. Their resistance to fifteen different antibiotics revealed that antibiotic resistance patterns of the Gram-negative bacteria recovered from the different locations correlated well. In all, the susceptibility and resistance patterns of the bacterial isolates varied and 35.9% of the multiple antibiotic-resistant isolates tested for were Extended Spectrum β - Lactamase (ESBL) producers. The level of multiple antibiotic resistance and ESBL producers among isolates in the study areas is of great public health concern considering the health implications.

High Heterozygosity in SNPs of TNF alpha Gene of Women Accessing Breast Cancer Care at a Tertiary Health Facility in Southwest Nigeria

Identification: Alamukii, Nanfizat Abiket

Credits: None available.

High Heterozygosity in SNPs of TNF alpha Gene of Women Accessing Breast Cancer Care at a Tertiary Health Facility in Southwest Nigeria
Nanfizat Abiket Alamukii1,2*, Abayomi Odetunde2, Chinedum Peace Babalola2,,3 Adeyinka Gladys Falusi2, Roseangela Ifeyinwa Nwuba1,4
Department of Zoology, Faculty of Science, University of Ibadan, Nigeria; 2Genetics Research Unit, Institute for Advance Medical Research and Training (IAMRAT), University College Hospital (UCH), University of Ibadan, Nigeria; 3Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ibadan, Nigeria; 4Department of Biological Sciences, Faculty of science, University of Medical Sciences, Ondo, Nigeria
*Presenting author

Introduction: Single Nucleotide Polymorphisms (SNPs) at the promoter region of TNFα gene are involved in the regulation of its expression. Alleles of these SNPs such as TNFα 308-A have been known to increase the production TNF protein. The presence of TNFα at the microevironment of certain tumours including breast cancer have been recorded. We genotyped the SNPs of TNFα and its receptors in breast cancer patients and control individuals to determine their role in the development and progression of breast cancer among women accessing care at a tertiary health facility in southwest Nigeria.
Methodology: This is a case control study of 200 consenting women recruited from the University College Hospital, Ibadan. The study was approved by the UI/UCH Ethical Review Board/Committee. DNA was extracted from blood samples collected from each participant. Allele-specific polymerase chain reaction was used to genotype various SNPS of TNFα and its receptors [TNFα (488 G/A, 238 G/A, 308 G/A, 859 C/T) and its receptor (TNFR1A+IV56+10 -G/A)].
Results: These showed very high heterozygosity of all the TNFα SNPs genotyped in the population which is a deviation from Hardy-Weinberg rule (P<0.0001). There was a significant difference (p-=0.0213) between cases and control for genotypes GA, AA & GG of TNFα 308. On the other hand, there were no significant differences between case and control for genotypes GA, GG & AA of TNFα 488, 238, 380 TNFR1A+IV56+10, and CC, CT, TT of TNFα 859 (P=0.2841, 0.7859, 0.3014 & 0.4922 respectively).
Conclusion: The genotypic results indicate a selection for heterozygote alleles within the population which although not yet linked to breast cancer, may be important in the expression of TNF gene for survival the geographical region. The significant difference in the genotypes of TNFα 308 between breast cancer patients and control individuals is a possible indicator that this SNP may have an important role in the development and progression of breast cancer among Nigerian women.
Keywords: Breast cancer, TNFα, SNPs heterozygosity, Nigerian women.

The influence of CCR2-CCR5 genetic variants on HIV-2 disease progression in West Africa

Identification: Davis, Alberta

Credits: None available.

The influence of CCR2-CCR5 genetic variants on HIV-2 disease progression in West Africa
Alberta Davis1, Weijing He2, Miriam Wautho1, Alfred Amambua Ngwa1, Sunil K Ahuja2, Assan Jaye1      
1MRC Unit Gambia at London School of Hygiene and Tropical Medicine; 2University of Texas Health San Antonio
The host genetic factors that determine susceptibility to HIV/AIDS in contrasting HIV-2 infections remains largely unknown. Here, we assessed the effect of variations in 2 adjacent genes that encode products critical to HIV pathogenesis and disease progression: CCR2 and CCR5 [1]. 157 HIV-2 infected patients sample from Gambia and Guinea Bissau where categorised into low (<100), medium (101 - 10,000) and high (>10,000) viral load (copies/ml). We genotyped 6 SNPs in CCR5 cis-regulatory regions, the CCR5-32 mutation, and the SNP CCR2-V64I, which together form the chemokine receptor 5 (CCR5) human haplotype groups (HHA - HHG). These were tested for their association with plasma viral load and CD4 percentage alongside their frequency distributions. The frequency of HHA was higher in the low (32.8%) and medium (32.3%) groups compared to the high group (25%). In contrast both HHD and HHE were more frequent in the high viral load group (39.6% and 17.7%, respectively) compared to the other two groups. In a multivariable regression model, possession of HHA or HHC haplotypes were associated with 59% (95% CI = 21% - 79%; p = 0.007) or 76% (95% CI = 29% - 92%; p = 0.010) lower odds of having higher viral loads, respectively. We found that the homozygous mutant allele 303A, from which HHE haplotype is derived, was significantly associated with lower CD4 percentage (p = 0.0096). Further analysis showed that CD4 percentage among individuals possessing the HHE haplotype was significantly lower compared to those without HHE (p = 0.0317). These data suggest that HHA and HHC haplotypes have a protective effect on HIV-2 infections in this study population as observed by their association with lower viral load levels, thereby contributing to delayed disease progression. In contrast, HHE showed trends consistent with worse disease outcomes such as lower CD4 percentage. These findings contribute to a better understanding of the human genetics of HIV-2 disease progression.
1.      Gornalusse, G.G., et al., Epigenetic mechanisms, T-cell activation, and CCR5 genetics interact to regulate T-cell expression of CCR5, the major HIV-1 coreceptor. Proc Natl Acad Sci U S A, 2015. 112(34): p. E4762-71.

Mutagenesis in a family with Constitutional Mismatch Repair Deficiency Syndrome

Identification: Lamola, Lindiwe

Credits: None available.

Mutagenesis in a family with Constitutional Mismatch Repair Deficiency Syndrome+
L. Lamola1,2, A. Vorster1, E. Chimusa1, U. Algar3, P. Goldberg3, R. Ramesar1
1Division of Human Genetics, Department of Pathology, Institute of infectious Disease and Molecular Medicine (IDM) University of Cape Town (UCT), 2Division of Human Genetics, National Health Laboratory Service, School of Pathology, University of the Witwatersrand; 3Surgical Gastroenterology Unit, Department of Surgery, Groote Schuur Hospital, (UCT)
Introduction: The mismatch repair (MMR) system plays an important role in maintaining genome integrity. A heterozygous mutation in one of the MMR genes i.e. MLH1, MSH2, MSH6 and PMS2 cause dominant adult cancer syndrome, Lynch syndrome. In a large South African family of mixed ancestry, a c.1528C>T mutation in exon 13 of the MLH1 gene is the most common Lynch syndrome-causing variant in our cohort of patients in the Western Cape Province. A paediatric patient homozygous for this mutation diagnosed with Constitutional Mismatch Repair Deficiency (CMMR-D) syndrome was described within this extended family. CMMR-D syndrome results in an increased predisposition to a range of cancers, most commonly brain and haematological tumours in early childhood. The aims of this study were to focus on the CMMR-D syndrome as a branch of Lynch syndrome and to potentially use the hyper-mutability-status to develop a working hypothesis for carcinogenesis in CMMR-D and Lynch syndromes.  
Methods: Whole exome sequencing (WES) was performed in the blood of the mother and father and the saliva of the CMMR-D proband and her sibling. A cancer panel (designed in house) was used for targeted NGS on seven tissues (including adrenal gland, bowel, cerebellum, cerebrum, kidney, liver, and spleen) and saliva, from the proband who had developed brain cancer and had demised by five (5) years of age. In order to investigate the extent of hyper-mutability in CMMR-D, sequence comparisons were performed to identify new mutations in the proband not present in her parents and to compare mutations across her different tissues. The list of new variants was used to identify genes that were involved and to assess protein-protein interactions and pathway-based analysis to identify the most enriched pathways in hyper-mutability.
Results: No specific regions of the genome were identified as prone to acquiring more variants due to MMR deficiency in CMMR-D. However, a range of pathways that were enriched among genes in which variants were identified, including the extracellular matrix, WNT signalling, TGFβ and p53 and that could be linked to MMR deficiency.  
Discussion and Conclusion: This study points to the potential involvement of a range of pathways associated with cancer development in CMMR-D which may be indirectly involved in tumorigenesis as a result of MMR deficiency.  The study suggests that it is likely that some of these biological processes or pathways are also involved in the emergence of extra-colonic cancers in individuals affected with Lynch syndrome.

Genetic Characterization of H5N1 Influenza A Virus Isolated from Pigs in Ogbomoso, Nigeria

Identification: Oladipo, Kolawole

Credits: None available.

Genetic Characterization of H5N1 Influenza A Virus Isolated from Pigs in Ogbomoso, Nigeria
Oladipo E.K.*1,2, Adeniji J.A.3, Oloke J.K2
1Department of Microbiology, Laboratory of Molecular Biology and Bioinformatics, Adeleke University, Ede, Osun State, Nigeria; 2Department of Pure and Applied Biology (Microbiology / Virology Unit), Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria; 3Department of Virology, College of Medicine, University of Ibadan, Ibadan, Oyo State, Nigeria
Introduction: Pigs are susceptible to infections with both avian and mammalian Influenza A viruses. Pigs play an important role in the ecology of influenza virus. The changing epidemiology of influenza has a significant implications for the circulation of viruses in pigs. Little is known about the circulating strains in this area. To understand the current the current situation regarding influenza viruses circulating among pigs in Ogbomoso, a surveillance study was conducted.
Methods: Viral isolation from nasal swabs collected from one hundred pigs was performed using egg inoculation, MDCK and haemagglutination assay. Reverse transcriptase polymerase chain reaction (RT-PCR) was carried out by amplifying the matrix gene for identification. The sequence was determined by Sanger dideoxy sequencing. The homology analysis was implemented by Influenza Research database (IRD) and phylogenetic analysis was performed by Maximum - Likelihood methods using MEGA 7.10 software package.
Results: Multiple sequence alignment showed that the matrix (M) genes of A/H5N1/Ogbomoso/2014 influenza virus showed highest nucleotide identity with A/Pigeon/Sichuan/NCXN29/2014(H5N1) and A/Duck/Sichuan/NCXN11/2014 (H5N1) {98% and 97% respectively}. The phylogenetic analysis of the matrix gene of A/H5N1/Ogbomoso/2014 indicated that this virus is closely related to H5N1 strains circulating in southwest China.
Conclusion: This is the first report of genetic characterization of influenza A virus H5N1 of swine origin isolate from Ogbomoso. The presented results can further promote Influenza A virus surveillance and epidemiology insight in this community. The potential role of pigs in interspecies transmission remains important.     
Keywords: Pigs, H5N1, Ogbomoso, Influenza A, Genetic Characterization.