Muhammad Abbas
About
My research project
New tools for sustainable control of liver fluke in ruminantsAchieving food security is a significant challenge due to the continuing expansion of the global population. Food-producing animals play a significant role in our diet. Food animals such as cattle and sheep can be infected by multiple parasites, which compromise animal health and welfare and cause significant production losses, thus negatively impacting food security. The liver fluke Fasciola is a particularly important parasite of ruminants worldwide. This parasite can also transmit to humans, so it has zoonotic importance. In the UK, the liver fluke species F. hepatica is endemic in ruminants, costing the cattle industry about £13 to £40 million annually; it reduces net profit by an average of 12% for dairy farms and 6% for beef farms. Climate change and porous boundaries directly influence parasite occurrence, making it difficult to control the disease. Understanding parasite genetic diversity, population genetics and multiplicity of infection (MOI), and the number of parasite genotypes in an infected host, can provide insights into infection rates, parasite self/cross mating behaviour, and potential for genetic exchange. Moreover, there is a need for user-friendly genetic markers with good genome coverage for in-depth analysis of F. hepatica population structure, and their impact on the emergence and spread of anthelmintic resistance, especially as markers for triclabendazole resistance, has not been identified. The current project has developed a sensitive and rapid diagnostic tool, based on qPCR technology, to screen F. hepatica DNA from the faecal samples concentrated by sedimentation method from different farms in the UK. Secondly, new whole-genome data has been generated from well-characterized F. hepatica isolates from sheep and cattle hosts from two geographical areas of the UK. Thirdly, based on the genomic data, high-quality genetic markers are under development and validation. These markers and the mitochondrial markers will then be used to determine the population genetics structure, MOI, and the potential for genetic exchange among F. hepatica populations in sheep and cattle in different locations in the UK. Control of Fasciola involves strategic treatment of ruminants with flukicides, guided by “fluke forecasts” based on models using climate data. Therefore, finally, we will integrate genetic data into climate-based models of F. hepatica transmission to improve "fluke forecasting."
Supervisors
Achieving food security is a significant challenge due to the continuing expansion of the global population. Food-producing animals play a significant role in our diet. Food animals such as cattle and sheep can be infected by multiple parasites, which compromise animal health and welfare and cause significant production losses, thus negatively impacting food security. The liver fluke Fasciola is a particularly important parasite of ruminants worldwide. This parasite can also transmit to humans, so it has zoonotic importance. In the UK, the liver fluke species F. hepatica is endemic in ruminants, costing the cattle industry about £13 to £40 million annually; it reduces net profit by an average of 12% for dairy farms and 6% for beef farms. Climate change and porous boundaries directly influence parasite occurrence, making it difficult to control the disease. Understanding parasite genetic diversity, population genetics and multiplicity of infection (MOI), and the number of parasite genotypes in an infected host, can provide insights into infection rates, parasite self/cross mating behaviour, and potential for genetic exchange. Moreover, there is a need for user-friendly genetic markers with good genome coverage for in-depth analysis of F. hepatica population structure, and their impact on the emergence and spread of anthelmintic resistance, especially as markers for triclabendazole resistance, has not been identified. The current project has developed a sensitive and rapid diagnostic tool, based on qPCR technology, to screen F. hepatica DNA from the faecal samples concentrated by sedimentation method from different farms in the UK. Secondly, new whole-genome data has been generated from well-characterized F. hepatica isolates from sheep and cattle hosts from two geographical areas of the UK. Thirdly, based on the genomic data, high-quality genetic markers are under development and validation. These markers and the mitochondrial markers will then be used to determine the population genetics structure, MOI, and the potential for genetic exchange among F. hepatica populations in sheep and cattle in different locations in the UK. Control of Fasciola involves strategic treatment of ruminants with flukicides, guided by “fluke forecasts” based on models using climate data. Therefore, finally, we will integrate genetic data into climate-based models of F. hepatica transmission to improve "fluke forecasting."
Research
Publications
-lactam antibiotics are essential medications for treating human diseases. The spread of extended-spectrum β-lactamase-producing (ESBL-PE) exists globally in multiple reservoirs and the natural environment and poses an immense threat to public health. Plasmid incompatibility groups, such as IncFIA, IncI1, IncY, IncFIB, IncN, IncFIC, IncX4, IncB/O/K/Z, IncHI1/2, and IncA/C, which exist in humans, animals, and the environment, carrying , , and genes. The IS upstream and orf477 downstream of genes, as well as other mobile genetic elements (MGEs) such as IS and IS , are involved in capturing and mobilizing antibiotic-resistant genes (ARGs). The gene is the most common among all discussed reservoirs. The environmental reservoir and propagation mode of ESBL-PE are increasing and difficult to control. The reasons include but are not limited to bacterial adaptability and horizontal gene transfer (HGT) mediated by MGEs and plasmids. Conjugation is a pathway of HGT that is almost uncontrollable. MGEs and plasmids such as Tn , IS families, IncI1, IncK, and IncN are facilitating HGT of genes. This review highlights the need to monitor trends in antimicrobial resistance (AMR) in the natural environment. Therefore, policies such as antibiotic management plans, training for healthcare providers and/or patients, cautious use of antibiotics, the need for epidemiological networks, pre-travel consultations, World Health Organization (WHO) infection control and biosafety guidelines, and other intervention measures are considered desirable.
Dicrocoelium lancet flukes cause significant production loss in ruminant livestock. Although co-infection with multiple Dicrocoelium species within a host is common, techniques for studying the composition of these complex parasite communities are lacking. The pathogenicity, epidemiology, and therapeutic susceptibility of different helminth species vary, and little is known about the interactions that take place between co-infecting species and their hosts. Here, we describe the first applicationof metabarcoding deep amplicon sequencing method to studythe Dicrocoelium species in sheep and goats. First, rDNA ITS-2 sequences of four Dicrocoelium species (Dicrocoelium dendriticum, Dicrocoelium hospes, Dicrocoelium orientalis, and Dicrocoelium chinensis) were extracted from the NCBI public database. Phylogenetic analysis revealed separate clades of Dicrocoelium species; hence, molecular differentiation between each species is possible in co-infections. Second, 202 flukes belonging to seventeen host populations (m