Population Genetics of New Zealand Nemadactylus macropterus (tarakihi) and Characterisation of their Mitochondrial Genome

<p>Nemadactylus macropterus, commonly known as tarakihi in New Zealand is highly regarded by commercial and recreational fishers and considered a taonga by iwi and customary fisheries. For many years N. macropterus was New Zealand’s second most important commercial catch and is currently the third most valuable inshore commercial finfish fishery in which 90% is consumed by the domestic market. However, despite the apparent importance, relatively little is known about the population structure of the N. macropterus. In 2017 the first fully quantitative stock assessment was conducted on the east coast N. macropterus fisheries as one stock. Alarmingly, the east coast fishery was estimated to be 15.9% of the unexploited spawning biomass and predicted to have been declining for the past thirty years. In an effort to rebuild the fishery, several rebuild plans have been purposed and commercial catch limits have been reduced. In order to rebuild and successfully manage a viable future N. macropterus fishery, an understanding of demographic connectivity and genetic connectivity among N. macropterus populations is essential. The overall goal of this thesis research was to investigate the population genetic structure, genetic diversity and demographic history of N. macropterus using fish sampled from around New Zealand. This was achieved by analysing hyper variable region one of mitochondrial DNA for 370 N. macropterus collected from 14 locations. No genetic differentiation was observed among the 14 locations, an indication that N. macropterus have a panmictic genetic structure. Furthermore, N. macropterus display a relatively high level of genetic diversity and appear to have a large stable population with a long evolutionary history. The Bayesian skyline analysis indicates the N. macropterus historic population has gone through two expansions. The mostly likely cause of this is an expansion before and after the last glacial maximum. The genetic diversity and demographic history of N. sp was also studied using samples collected from around the Three Kings Islands of New Zealand. The complete mitochondrial genome of N. macropterus was reconstructed from bulk DNA sequencing data and a set of specific mtDNA primers were developed to amplify hyper variable region one. The DNA sequencing data provided by these primers with the addition of published control region sequences was used to reconstruct the Nemadactylus phylogeny.</p>

Population Genetics of New Zealand Nemadactylus macropterus (tarakihi) and Characterisation of their Mitochondrial Genome

<p>Nemadactylus macropterus, commonly known as tarakihi in New Zealand is highly regarded by commercial and recreational fishers and considered a taonga by iwi and customary fisheries. For many years N. macropterus was New Zealand’s second most important commercial catch and is currently the third most valuable inshore commercial finfish fishery in which 90% is consumed by the domestic market. However, despite the apparent importance, relatively little is known about the population structure of the N. macropterus. In 2017 the first fully quantitative stock assessment was conducted on the east coast N. macropterus fisheries as one stock. Alarmingly, the east coast fishery was estimated to be 15.9% of the unexploited spawning biomass and predicted to have been declining for the past thirty years. In an effort to rebuild the fishery, several rebuild plans have been purposed and commercial catch limits have been reduced. In order to rebuild and successfully manage a viable future N. macropterus fishery, an understanding of demographic connectivity and genetic connectivity among N. macropterus populations is essential. The overall goal of this thesis research was to investigate the population genetic structure, genetic diversity and demographic history of N. macropterus using fish sampled from around New Zealand. This was achieved by analysing hyper variable region one of mitochondrial DNA for 370 N. macropterus collected from 14 locations. No genetic differentiation was observed among the 14 locations, an indication that N. macropterus have a panmictic genetic structure. Furthermore, N. macropterus display a relatively high level of genetic diversity and appear to have a large stable population with a long evolutionary history. The Bayesian skyline analysis indicates the N. macropterus historic population has gone through two expansions. The mostly likely cause of this is an expansion before and after the last glacial maximum. The genetic diversity and demographic history of N. sp was also studied using samples collected from around the Three Kings Islands of New Zealand. The complete mitochondrial genome of N. macropterus was reconstructed from bulk DNA sequencing data and a set of specific mtDNA primers were developed to amplify hyper variable region one. The DNA sequencing data provided by these primers with the addition of published control region sequences was used to reconstruct the Nemadactylus phylogeny.</p>

Investigation of the piroplasm diversity circulating in wildlife and cattle of the greater Kafue ecosystem, Zambia

Background Piroplasms are vector-borne intracellular hemoprotozoan parasites that infect wildlife and livestock. Wildlife species are reservoir hosts to a diversity of piroplasms and play an important role in the circulation, maintenance and evolution of these parasites. The potential for likely spillover of both pathogenic and non-pathogenic piroplasm parasites from wildlife to livestock is underlined when a common ecological niche is shared in the presence of a competent vector. Method To investigate piroplasm diversity in wildlife and the cattle population of the greater Kafue ecosystem, we utilized PCR to amplify the 18S rRNA V4 hyper-variable region and meta-barcoding strategy using the Illumina MiSeq sequencing platform and amplicon sequence variant (ASV)-based bioinformatics pipeline to generate high-resolution data that discriminate sequences down to a single nucleotide difference. Results A parasite community of 45 ASVs corresponding to 23 species consisting of 4 genera of Babesia, Theileria, Hepatozoon and Colpodella, were identified in wildlife and the cattle population from the study area. Theileria species were detected in buffalo, impala, hartebeest, sable antelope, sitatunga, wild dog and cattle. In contrast, Babesia species were only observed in cattle and wild dog. Our results demonstrate possible spillover of these hemoprotozoan parasites from wildlife, especially buffalo, to the cattle population in the wildlife-livestock interface. Conclusion We demonstrated that the deep amplicon sequencing of the 18S rRNA V4 hyper-variable region for wildlife was informative. Our results illustrated the diversity of piroplasma and the specificity of their hosts. They led us to speculate a possible ecological cycle including transmission from wildlife to domestic animals in the greater Kafue ecosystem. Thus, this approach may contribute to the establishment of appropriate disease control strategies in wildlife-livestock interface areas.

Investigation of the piroplasm diversity circulating in wildlife and cattle of the greater Kafue ecosystem, Zambia

Background: Piroplasms are vector-borne intracellular hemoprotozoan parasites that infect wildlife and livestock. Wildlife species are reservoir hosts to a diversity of piroplasms and play an important role in the circulation, maintenance and evolution of these parasites. The potential for likely spillover of both pathogenic and non-pathogenic piroplasm parasites from wildlife to livestock is underlined when common ecological niche is shared in the presence of a competent vector. Method: To investigate piroplasm diversity in wildlife and cattle population of the greater Kafue ecosystem, we utilized PCR to amplify the 18S rRNA V4 hyper-variable region and meta-barcoding strategy using illumina MiSeq sequencing platform and amplicon sequence variant (ASV) based bioinformatics pipeline to generate high resolution data which discriminate sequences down to a single nucleotide difference. Results: A parasite community of 45 ASVs corresponding to 23 species consisting of 4 genera of Babesia, Theileria, Hepatozoon and Colpodella, were identified in wildlife and cattle population from the study area. Theileria species were detected in buffalo, impala, hartebeest, sable antelope, sitatunga, wild dog and cattle. In contrast, Babesia species were only observed in cattle and wild dog. Our results demonstrate possible spillover of these hemoprotozoan parasites from wildlife, especially buffalo, to cattle population in the wildlife-livestock interface.Conclusion: We demonstrated that the deep amplicon sequencing of the 18S rRNA V4 hyper-variable region for wildlife was informative. Our results illustrated the diversity of piroplasma and the specificity of their hosts. They led us to speculate possible ecological cycle including transmission from wildlife to domestic animals in the greater Kafue ecosystem. Thus, this approach may contribute to the establishment of appropriate disease control strategies in wildlife-livestock interface areas.

Investigation of the piroplasm diversity circulating in wildlife and cattle of the greater Kafue ecosystem, Zambia

Background Piroplasms are vector-borne intracellular hemoprotozoan parasites that infect wildlife and livestock. Wildlife species are reservoir hosts to a diversity of piroplasms and play an important role in the circulation, maintenance and evolution of these parasites. The potential for likely spillover of both pathogenic and non-pathogenic piroplasm parasites from wildlife to livestock is underlined when common ecological niche is shared in the presence of a competent vector. Method To investigate piroplasm diversity in parasite community in wildlife and cattle population of the greater Kafue ecosystem , we utilized PCR to amplify the 18S rRNA V4 hyper-variable region and meta-barcoding strategy using illumina MiSeq sequencing platform and amplicon sequence variant (ASV) based bioinformatics pipeline to generate high resolution data which discriminate sequences down to a single nucleotide difference. Results A parasite community of 45 ASVs corresponding to 23 species consisting of 4 genera of Babesia , Theileria , Hepatozoon and Colpodella, were identified in wildlife and cattle population from the study area. Theileria species were observed in buffalo, impala, hartebeest, sable antelope, sitatunga, wild dog and cattle. In contrast, Babesia species were only observed in cattle and wild dog. Our results demonstrate possible spillover of these hemoprotozoan parasites from wildlife, especially buffalo, to cattle population in the wildlife-livestock interface. Conclusion We demonstrated that the deep amplicon sequencing of the 18S rRNA V4 hyper-variable region for wildlife was informative. Our results illustrated the diversity of piroplasma and the specificity of their hosts. They led us to speculate possible ecological cycle including transmission from wildlife to domestic animals in the greater Kafue ecosystem. Thus, this approach may contribute to the establishment of appropriate disease control strategies in wildlife-livestock interface areas.

Assessment of inducible clindamycin resistance and Hyper Variable Region (HVR) of mecA gene in clinical staphylococci

Objective: To study the prevalence of inducible clindamycin along with vancomycin and methicillin resistance and assessment of hyper variable region (HVR) of mecA gene among different clinical isolates of Staphylococcus spp. Methods: A total of 176 clinical isolates of Staphylococci were collected from Pakistan Institute of Medical Sciences (PIMS), Islamabad during 2014-2015. The sample sources were pus, blood, urine, sputum, tracheal secretions and tissue fluids. Bacterial identification was done by colony morphology and biochemical tests. Kirby-Bauer disc-diffusion method was carried out to assess the susceptibility against different antibiotics. Minimal inhibitory concentrations (MICs) were done for vancomycin resistance. Double Disk Diffusion test (D-test) was used to detect the clindamycin inducible resistance. PCR was performed to detect erm(C), mecA and HVR genes. Results: Clindamycin inducible resistance among Staphylococcal isolates was found to be 7%, whereas in S. aureus it was 4%, and in coagulase negative Staphylococci (CoNS) it was 11%. The highest resistance was observed against fosfomycin, fusidic acid and cefoxitin. Vancomycin resistance was observed in 23 isolates (13%) of Staphylococci. erm(C), mecA and HVR genes were found in 18%, 50% and 42% respectively. Conclusions: D-test must be performed routinely to avoid clindamycin failure. A high level of resistance against vancomycin in Staphylococcal isolates is a concern for public health. doi: https://doi.org/10.12669/pjms.36.2.665 How to cite this:Khan AA, Farooq J, Abid M, Zahra R. Assessment of inducible clindamycin resistance and Hyper Variable Region (HVR) of mecA gene in clinical staphylococci. Pak J Med Sci. 2020;36(2):---------. doi: https://doi.org/10.12669/pjms.36.2.665 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Isolation and characterization of Infectious bursal disease virus VP2 gene isolated from Tirupati region of Andhra Pradesh, India.

<p>Infectious bursal disease (IBD) is a highly contagious viral disease of birds characterized by lesions in the bursa of Fabricius, immunosuppression, severe morbidity and mortality. Due to amino acids substitutions in this region results in change in the topography of hyper variable region of VP2, where most of the neutralizing epitopes are present. Cloning and characterization of hyper variable region of prevalent strains of IBDV in this part of the country will provide basis for development of better vaccine for future. In the present study, we cloned four full length sequences of IBDV-VP2 with hyper variable region and found that all the cloned sequences have similar epitopes. Phylogenetic analysis showed that they are closely related to each other and are also closely related to strains of Luxembourg, China, and USA. This study will enhance the knowledge on IBDV circulating strains in this part of the country.</p>