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Phylogenetic analysis of Salmonella and shiga toxin E. coli isolated from wild animal fecal pellets
Rahman Md. Mafizur,Sang Jin Lim,Yung Chul Park 강원대학교 산림과학연구소 2018 강원대학교 산림과학연구소 학술대회 Vol.2018 No.09
Feces of wild animals are the harbor and potential vectors of Salmonella and Shiga toxinproducing Escherichia coli (STEC) that cause many infectious diseases of human and animals. This study includes the molecular phylogeny and median joining network (MJN) of Salmonella and STEC. Based on median joining network and haplotype analyses, 10 Salmonella haplotypes were clearly discovered in Korean wild animal fecal samples. Of them, the haplotype H8 and H1 belong to S. enterica diarizonae and the other 8 haplotypes belonged to S. e. enterica. The haplotype H7, H6 and H9 (green color) of birds, H4 and H5 (red color) of leopard cats and H13 of Korean National Culture Collection (NCCP) might be disseminated from same origin. The phylogentic tree shows that a total 54 Salmonella strains from worldwide and Korea were grouped into main two species of S. enterica and S. bongori. Salmonella enterica formed separated clades of four subspecies of S. e. enterica, S. e. salamae, S. e. arizonae and S. e. diarizonae. In case of STEC, 6 types of serovas were discovered from the 93 samples. Strains of the serovar E. coli 083:H1 were well clustered genetically together and widely distributed over various localities and various host species. This kind of analysis might be better understanding of genetic relatedness of Korean Salmonella to others. In addition to gene network analysis more important part of this section because of genealogical analysis might be understanding transmission mode of pathogen
Rahman Md Mafizur,Sang Jin Lim,Yung Chul Park 강원대학교 산림과학연구소 2017 강원대학교 산림과학연구소 학술대회 Vol.2017 No.11
We examined presence of Escherichia coli, Shiga toxin-producing E. coli, and Salmonella species in feces of six rodent species (Apodemus agrarius, A. peninsulae, A. sylvaticus, Micromys minutus, Myodes regulus, and Rattus norvegicus) captured from different agricultural regions of South Korea. By culture methods and PCR assay, we detected E. coli in 50% of 56 individuals of the six species and various Shiga toxin-producing E. coli strains in 32.7% of them, but no Salmonella species. All of three types of the Shiga toxin-producing E. coli (O83:H1, O104:H4 and O157:H16) were detected in A. agrarius and A. sylvaticus. E. coli O104:H4, as well as E. coli O157:H7 3.6% (2/56), was associated with a widespread and foodborne disease. Although E. coli O104:H4 has rarely been found in feces of wild rodents until now, in the present study E. coli O104:H4 was detected in feces of the wild rodents in South Korea. Wild mice of A. agrarius, which account for 60.7% of total 56 individuals, are most widely distributed and abundant in various agroecosystems of South Korea. Of 36 individuals of A. agrarius, feces of 12 individuals contained Shiga toxin-producing E. coli, which account for 23.1% of total 56 individuals of the six rodent species and 70.6% of total 17 individuals with Shiga toxin-producing E. coli. The three types of the Shiga toxin-producing E. coli (O83:H1, O104:H4, and O157:H7) were detected in A. agrarius. Thus, A. agrarius would be important reservoirs of the pathogenic bacteria which cause zoonotic diseases in different agroecosystem s.
Rahman Md Mafizur,Sang Jin Lim,Yung Chul Park 강원대학교 산림과학연구소 2017 강원대학교 산림과학연구소 학술대회 Vol.2017 No.11
Wildlife damage to agriculture has increased over the last 20 years in Korea. They will cause damage for various aspects of agriculture, including great damage to the crops by water deer (Hydropotes inermis), wild boar (Sus scrofa) and rodent. Nowadays, the Rural Development Adminstration of Korea (RDA) starts to pay attention to zoonotic microorganisms of wildlife which visit agricultural area, as well as wildlife damage to the crops. Wild mice of Apodemus agrarius, wild boar (Sus scrofa) and water deer (Hydropotes inermis) are very common in South Korea and widely distributed over various agricultural farm area and mountainous forests in South Korea. They will have high possibility to disseminates zoonotic microorganisms which are great threat to farmers’ health. In this study, so, in this study, we collect 756 fecal pellet of mammal (Wild boar, Water dear, Wild cat, raccoon, rodent), birds (magpies, crows, sparrow etc) and environmental sample (soil, water). We detected total 27 different Salmonella strain from 21 (2.78%) individual fecal and 98 shiga toxin E.coli from 91 (10.97%) individual fecal, 4 (0.52%) E.coli. we will introduce distribution map of Salmonella spp. and Shiga toxin Escherichia coli, E.coli O157:H7 which were disseminated from fecal of various wildlife to visit farm area, focusing on fecal-disseminated microorganisms of wild animal.
M Mafizur Rahman,Sangjin Lim,Yungchul Park 강원대학교 산림과학연구소 2021 강원대학교 산림과학연구소 학술대회 Vol.2021 No.10
The zoonotic diseases, virus and bacteria-borne, are major concern to the global security. African swine fever (ASF) is high contagious and high mortality haemorrhagic viral disease in domestic and wild boar (Sus scrofa). Bacteria-borne zoonotic diseases such as Salmonella and Shiga toxin-producing Escherichia coli were detected in wild boar (S. scrofa) in Korea. However, ASF is found in almost all countries around the world, particularly in sub-Saharan Africa. The outbreaks have spread through China, Mongolia and Vietnam, South Korea, North Korea, India as well as northeast region Myanmar, Bhutan, and Bangladesh during the last two years. But on 17 September 2019, the first outbreak of African swine fever in a pig farm was confirmed in South Korea. Based on genetic sequence with the phylogenetic analysis ASFV isolates were in South Korea belong to genotype II and serogroup 8. However, genomic characterization whole genomic sequence of ASFV isolates are required for typing, control measures, management, and development of vaccine against ASFV. Till date, there is no effective approved vaccine or antiviral drugs in the market against ASF infection. Therefore, control/prevention and management is the best strategy to handle of the ASF infection. ASF is a transboundary animal disease (TAD) that can be spread by live or dead pigs, domestic or wild, and pork products. The prevention strategies of ASF are early detection, design more cost-effective surveillance e.g. modelling for transmission dynamics, find out the risk factors including role of wild boar and soft ticks, and biosafety and biosecurity measures. In our presentation, we discuss about the viral and bacterial zoonotic diseases in future concerns, cost-effective surveillance, and mitigation measures of zoonotic (ASF) diseases.
Md-Mafizur Rahman,Jiyeong Shin,Jungwon Jeon,Changhee Han,Juil Kim,David G. Heckel,Celso Omoto 한국응용곤충학회 2023 한국응용곤충학회 학술대회논문집 Vol.2023 No.10
To elucidate the mechanism of pyrethroid resistance in Helicoverpa armigera, the study explored three possibilities based on deltamethrin as a model pyrethroid; 1) the existence of mutations in the target site of deltamethrin, 2) the existence of variation at the genomic level between insecticide-susceptible and resistant strains, 3) differences in gene expression patterns between the strains. Based on these hypotheses, three levels of resistant strains and a susceptible strain as well as nine Korean field populations were used. As results, 1) any point mutations were not detected in sodium channel gene. 2) based on newly set Korean reference genome (GCA_026262555.1), approximately 3,369,837 and 1,032,689 variants (SNPs and Indels) were revealed from genome and ORFs, respectively. However, any specific variants were not found to be highly correlated with the level of insecticide resistance. 3) based on DEG analysis, some of detoxification enzyme genes were differently expressed particularly cytochrome P450 genes. Therefore, H. armigera possibly acquires deltamethrin resistance through a combination of actions, including over-expression of various detoxification enzymes such as CYP3 subfamilies and cuticular proteins.
M. Mafizur Rahman,윤광배,김지영,Mohamed Zakaria Hussin,박영철 한국통합생물학회 2016 Animal cells and systems Vol.20 No.2
We characterized the complete mitogenome of Pipistrellus coromandra (Indian pipistrelle) for comparative analysis of mitogenomes and for resolving the phylogenetic relationship of four tribes in the subfamily Vespertilioninae. The mitogenome size of P. coromandra was 17,153 bp, with a control region and a typical set of 37 mitochondrial genes. The nucleotide composition of the P. coromandra mitogenome showed an AT bias with a nucleotide composition of 33.5% A, 30.7% T, 13.3% G, and 22.5% C. The mitochondrial protein-coding genes in P. coromandra use the standard start codon (ATN), two stop codons (TAA and AGA), and two incomplete stop codons (TA- and T–). The intertribal relationship of four tribes was highly resolved from the phylogenetic analysis of mitogenome sequences.
Md. Maharub Hossain Fahim,Walid Hassan,Afia Afsin,Md. Mahfuzur Rahman,Md. Tanvir Rahman,임상진,Oh Yeonsu,박영철,Hossain Md. Faruquee,Md. Mafizur Rahman 한국생태학회 2024 Journal of Ecology and Environment Vol.48 No.2
Background: Fruit bats are natural carriers of Nipah virus (NiV ). The primary objective of this study is to identify potential reservoir species in a selected geographic regions. It is necessary to determine an accurate species identification of the associated reservoir bat species distributed in a specific region. Results: In this study, we collected 20 different bat specimens from the NiV-prone area of the Kushtia district. Among these, 14 were tissue samples (BT-1–14) and six were fecal sam- ples (BF-1–6). We used the mitochondrial gene cytochrome b, one of the most abundant and frequently used genetic markers, for polymerase chain reaction amplification and se- quencing. Out of the 20 samples, 12 tissue samples and 2 fecal samples were successfully amplified and sequenced. However, two tissue samples and four fecal samples yielded chimeric sequences, rendering them unsuitable for annotation. The sequences of the suc- cessfully amplified samples were compared to those deposited in the National Center for Biotechnology Information database using basic local alignment search tool to identify the bat specimen collected. The study identified six different bat species using both morpho- logical and genetic data, which may carriers of the NiV. Conclusions: Our results suggest that additional research should be conducted to gath- er more information on fruit bats from different localities across the country. The study contributes to the establishment of appropriate measures for NiV carrying disease control and management.
Md. Maharub Hossain Fahim,Walid Hassan,Afia Afsin,Md. Mahfuzur Rahman,Md. Tanvir Rahman,Sang Jin Lim,Yeonsu Oh,Yung Chul Park,Hossain Md. Faruquee,Md. Mafizur Rahman The Ecological Society of Korea 2024 Journal of Ecology and Environment Vol.48 No.1
Background: Fruit bats are natural carriers of Nipah virus (NiV). The primary objective of this study is to identify potential reservoir species in a selected geographic regions. It is necessary to determine an accurate species identification of the associated reservoir bat species distributed in a specific region. Results: In this study, we collected 20 different bat specimens from the NiV-prone area of the Kushtia district. Among these, 14 were tissue samples (BT-1-14) and six were fecal samples (BF-1-6). We used the mitochondrial gene cytochrome b, one of the most abundant and frequently used genetic markers, for polymerase chain reaction amplification and sequencing. Out of the 20 samples, 12 tissue samples and 2 fecal samples were successfully amplified and sequenced. However, two tissue samples and four fecal samples yielded chimeric sequences, rendering them unsuitable for annotation. The sequences of the successfully amplified samples were compared to those deposited in the National Center for Biotechnology Information database using basic local alignment search tool to identify the bat specimen collected. The study identified six different bat species using both morphological and genetic data, which may carriers of the NiV. Conclusions: Our results suggest that additional research should be conducted to gather more information on fruit bats from different localities across the country. The study contributes to the establishment of appropriate measures for NiV carrying disease control and management.