• Journal of the Korean Data and Information Science Society
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• 제25권2호
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• pp.271-280
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• 2014

구제역은 전염성이 높고 치명적 결과를 유발하는 우제류 전염병이며, 2010/2011년도에 국내에서 발생한 구제역 (2010/2011 구제역)은 사회 및 경제적으로 국가에 재난 수준의 손실을 끼쳤다. 따라서 국가적 차원에서 구제역의 예방과, 발병 시 피해를 줄이려는 많은 노력을 하고 있다. 이러한 노력의 하나로 구제역의 전염 현상을 확률적으로 모형화하고 이해하려는 노력이 필요하다. 영국에서 발생한 2001년 구제역은 그 규모와 피해가 막대하여, 영국에서는 다양한 확률적 모형으로 구제역 전파 현상에 대한 이해를 통하여 미래의 발생에 대비하려는 연구가 이루어져 왔다. 그러나 2010/2011 구제역에 대하여는 확률적 모형을 활용한 연구가 미미한 편이다. 따라서 본 연구에서는 2010/2011 구제역에 대하여 시간-공간 확률 SIR 확률모형을 가정하고 시간과 공간에 따르는 전파 현상에 대하여 고찰한다. 농림수산검역검사본부에서 발표한 구제역 감염데이터와 통계청의 전국농가센서스 자료의 일부인 전체 우제류 농가의 데이터가 본 연구의 분석에 필요한 정도로 상세하지 않으므로 추정 및 보정작업을 통하여 데이터를 보완하였다. 감염데이터를 이용하여 커널함수를 추정하고, 전국 우제류 농장데이터를 이용하여 시뮬레이션을 통하여 모형의 모수를 추정하였다.

• Journal of Microbiology and Biotechnology
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• 제22권4호
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• pp.555-562
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• 2012

PCR was performed to analyze the ${\beta}$-lactamase genes carried by ampicillin-resistant Vibrio spp. strains isolated from marine environments in Korea between 2006 and 2009. All 36 strains tested showed negative results in PCR with the primers designed from the nucleotide sequences of various known ${\beta}$-lactamase genes. This prompted us to screen new ${\beta}$-lactamase genes. A novel ${\beta}$-lactamase gene was cloned from Vibrio alginolyticus KV3 isolated from the aquaculture water of Geoje Island of Korea. The determined nucleotide sequence (VAK-3 ${\beta}$-lactamase) revealed an open reading frame (ORF) of 852 bp, encoding a protein of 283 amino acids (aa), which displayed low homology to any other ${\beta}$-lactamase genes reported in public databases. The deduced 283 aa sequence of VAK-3, consisting of a 19 aa signal peptide and a 264 aa mature protein, contained highly conserved peptide segments specific to class A ${\beta}$-lactamases including the specific amino acid residues STFK (62-65), SDN (122-124), E (158), and RTG (226-228). Results from PCR performed with primers specific to the VAK-3 ${\beta}$-lactamase gene identified 3 of the 36 isolated strains as V. alginolyticus, Vibrio cholerae, and Photobacterium damselae subsp. damselae, indicating the utilization of various ${\beta}$-lactamase genes including unidentified ones in ampicillin-resistant Vibrio spp. strains from the marine environment. In a mating experiment, none of the isolates transfered the VAK-3 ${\beta}$-lactamase gene to the Escherichia coli recipient. This lack of mobility, and the presence of a chromosomal acyl-CoA flanking sequence upstream of the VAK-3 ${\beta}$-lactamase gene, led to the assumption that the location of this new ${\beta}$-lactamase gene was in the chromosome, rather than the mobile plasmid. Antibiotic susceptibility of VAK-3 ${\beta}$-lactamase was indicated by elevated levels of resistance to penicillins, but not to cephalosporins in the wild type and E. coli harboring recombinant plasmid pKV-3, compared with those of the host strain alone. Phylogenetic analysis showed that VAK-3 ${\beta}$-lactamase is a new and separate member of class A ${\beta}$-lactamases.

• Reproductive and Developmental Biology
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• 제35권4호
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• pp.479-483
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• 2011

The objective of this study was to determine the effects of E. coli isolated from porcine semen on sperm viability, motility, and semen pH. Semen samples were prepared using commercial extender, $Seminark^{Pro}$ (Noahbio Tech, Korea) that did not contain antibiotics. And 4 different levels of E. coli were artificially innoculated to semen with following concentrations; 4,000 of sperms with 1 of E. coli (T1), 400 with 1 (T2), 40 with 1 (T3), and 4 with 1 (T4). Semen samples were preserved at $17^{\circ}C$ for 5 days in semen storage box until analyzed by flowcytometer. Aliquots were subjected to measure the sperm viability (Live/$Dead^{(R)}$ stain), motility (mitochondrial function), and semen acidity (pH) from day 0 (day of semen collection) to day 5. Sperm motility and viability were significantly decreased (p<0.05) on day 0 (4 hrs after preservation at $17^{\circ}C$) in T3 and T4 compared to control groups and were significantly decreased (p<0.05) in all groups from day 3. Sample pH was acidic in T3 (6.90~6.86) and T4 (6.86~6.65) from day 3 to day 5 (p<0.05). On the other hand, sample pH was maintained 7.0~7.1 in control, T1, and T2 during the experimental period. Sperm motility and viability were significantly decreased from day 0 to day 5 compared to control in samples contaminated with E. coli above a value of 40:1 ($20{\times}10^6$ sperm cells/ml : $5{\times}10^5$ cfu/ml). Even on day 1 in T4 and on day 3 in T3, semen pH was acidic probably due to the acidification of dead spermatozoa. These results suggest that E. coli contamination has a concentration-dependent detrimental effect on extended porcine semen quality.

• 한국임상수의학회지
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• 제30권4호
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• pp.258-263
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• 2013

The primary goal of this study was to compute sample sizes required to achieve the each aim of a variety of foot-and-mouth disease (FMD) surveillance programs, using a statistically valid technique that takes the following factors into account: sensitivity (Se) and specificity (Sp) of diagnostic test system, desired minimum detectable prevalence, precision, population size, and desired power of the survey. In addition, sample sizes to detect FMD if the disease is present and also as proof of freedom were computed. The current FMD active surveillance programs consist of clinical, virological, and serological surveillance. For the 2012 serological surveillance, annual sample sizes (n = 265,065) are planned at four separate levels: statistical (n = 60,884) and targeted (n = 115,232) at breeding pig farms and slaughter house, in together with the detection of structural proteins (SP) antibodies against FMD (n = 88,949). Overall, the sample size was not designed taking the specific aims of each surveillance stream into account. The sample sizes for statistical surveillance, assuming stratified two-stage sampling technique, was based to detect at least one FMD-infected case in the general population. The resulting sample size can be used to obtain evidence of freedom from FMD infection, not for detecting animals that have antibodies against FMD virus non-structural proteins (NSP). Additionally, sample sizes for targeted surveillance were not aimed for the population at risk, and also without consideration of statistical point of view. To at least the author's knowledge, sampling plan for targeted, breeding pig farms and slaughter house is not necessary and need to be included in the part of statistical surveillance. Assuming design prevalence of 10% in an infinite population, a total of 29 animals are required to detect at least one positive with probability of 95%, using perfect diagnostic test system (Se = Sp = 100%). A total of 57,211 animals needed to be sampled to give 95% confidence of estimating SP prevalence of 80% at the individual animal-level with a precision of ${\pm}5%$, assuming 800 herds with an average 200 heads per farm, within-farm variance of 0.2, between-farm variance of 0.05, cost ratio of 100:1 of farm against animals. Furthermore, 779,736 animals were required to demonstrate FMD freedom, and the sample size can further be reduced depending on the parameters assumed.

• 한국식품조리과학회지
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• 제30권5호
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• pp.603-612
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• 2014

According to the microbiological standard, Staphylococcus aureus, Clostridium perfringens and Listeria monocytogenes should not be detected in milk and egg products in Korea. Refrigerated food such as milk must be kept under $10^{\circ}C$ at retail markets. However, temperature abuse of refrigerated foods at such markets is often observed. We compared the growth and survival kinetics of S. aureus and C. perfringens at 10 and $15^{\circ}C$, and the growth kinetics of L. monocytogenes at 4 and $10^{\circ}C$ in whole and skim milk and ready-to-eat (RTE) quail eggs to evaluate their growth possibilities at retail markets. Regardless of storage temperature, the level of S. aureus reached the maximum level ($10^8-10^9CFU/ml$) in whole milk, non-fat milk and RTE quail eggs within the expiration date. Even low contamination levels of S. aureus (10 CFU/mL) grew rapidly in milk and quail eggs to reach the maximum level within the shelf life. Survival of C. perfringens in whole milk was greater than that in non-fat milk, indicating that the fat content in milk influences the survival of C. perfringens. For L. monocytogenes, the population in milk increased by 0.5-1 log CFU/mL at $4^{\circ}C$, while the populations reached the maximum level at $10^{\circ}C$ within the expiration date, regardless of initial contamination levels. In quail eggs, L. monocytogenes grew to the maximum level within the expiration date (60 days) at both temperatures. S. aureus and L. monocytogenes must be controlled to be negative, and proper temperature management should be emphasized at retail markets to protect the consumer. Since C. perfringens did not grow in milk and RTE quail eggs, there is no risk due to the growth of C. perfringens in these products at retail markets.

• 한국균학회소식:학술대회논문집
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• 한국균학회 2015년도 추계학술대회 및 정기총회
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• pp.41-41
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• 2015

Oomycetes belong to the kingdom Straminipila, a remarkably diverse group which includes brown algae and planktonic diatoms, although they have previously been classified under the kingdom Fungi. These organisms have evolved both saprophytic and pathogenic lifestyles, and more than 60% of the known species are pathogens on plants, the majority of which are classified into the order Peronosporales (includes downy mildews, Phytophthora, and Pythium). Recent phylogenetic investigations based on DNA sequences have revealed that the diversity of oomycetes has been largely underestimated. Although morphology is the most valuable criterion for their identification and diversity, morphological species identification is time-consuming and in some groups very difficult, especially for non-taxonomists. DNA barcoding is a fast and reliable tool for identification of species, enabling us to unravel the diversity and distribution of oomycetes. Accurate species determination of plant pathogens is a prerequisite for their control and quarantine, and further for assessing their potential threat to crops. The mitochondrial cox2 gene has been widely used for identification, taxonomy and phylogeny of various oomycete groups. However, recently the cox1 gene was proposed as a DNA barcode marker instead, together with ITS rDNA. To determine which out of cox1 or cox2 is best suited as universal oomycete barcode, we compared these two genes in terms of (1) PCR efficiency for 31 representative genera, as well as for historic herbarium specimens, and (2) in terms of sequence polymorphism, intra- and interspecific divergence. The primer sets for cox2 successfully amplified all oomycete genera tested, while cox1 failed to amplify three genera. In addition, cox2 exhibited higher PCR efficiency for historic herbarium specimens, providing easier access to barcoding type material. In addition, cox2 yielded higher species identification success, with higher interspecific and lower intraspecific divergences than cox1. Therefore, cox2 is suggested as a partner DNA barcode along with ITS rDNA instead of cox1. Including the two barcoding markers, ITS rDNA and cox2 mtDNA, the multi-locus phylogenetic analyses were performed to resolve two complex clades, Bremia lactucae (lettuce downy mildew) and Peronospora effuse (spinach downy mildew) at the species level and to infer evolutionary relationships within them. The approaches discriminated all currently accepted species and revealed several previously unrecognized lineages, which are specific to a host genus or species. The sequence polymorphisms were useful to develop a real-time quantitative PCR (qPCR) assay for detection of airborne inoculum of B. lactucae and P. effusa. Specificity tests revealed that the qPCR assay is specific for detection of each species. This assay is sensitive, enabling detection of very low levels of inoculum that may be present in the field. Early detection of the pathogen, coupled with knowledge of other factors that favor downy mildew outbreaks, may enable disease forecasting for judicious timing of fungicide applications.

• 한국지리정보학회지
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• 제18권3호
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• pp.89-101
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• 2015

본 연구는 질병역학의 관점에서 2014년 발생한 HPAI(H5N8)의 시간적 분포와 공간적 분포 그리고 시 공간을 동시에 고려한 분포를 지리정보시스템과 연계하여 분석함으로써 2014년 발생한 HPAI의 전파 및 확산 특징을 알아보고자 한다. 분석 결과 2014년 HPAI는 시간적으로는 모두 3 번의 파동을 형성하였으며, 공간적으로는 경기도 충청북도 충청남도가 인접하는 지역, 전라북도의 곰소만 일대, 전라남도의 영암과 나주 등 영산강과 인접한 지역에서 높은 밀도를 보였다. 시 공간적으로도 공간 밀도가 높은 충청북도 음성지역, 전라북도 부안 고창지역, 나주지역에서 군집이 형성되었다. 다만, 충청북도 음성 진천, 충청남도 천안, 경기도 안성 이천 지역과 전라남도 영암 지역에서는 공간적인 밀도는 높음에도 불구하고 시간적인 범위가 넓음으로써 시 공간 군집이 형성되지 못하였다. 이는 이들 지역의 방역에 문제가 있음을 의미한다. 반면에 곰소만과 인접하고 있는 전라북도 부안 고창 장수 지역은 시 공간 군집이 형성됨으로써, 상대적으로 효과적인 방역이 수행되었다고 볼 수 있다.

• Reproductive and Developmental Biology
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• 제37권4호
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• pp.263-267
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• 2013

Pig producers have been shown keen interest of the number of spermatozoa in a semen dose since pig artificial insemination introduce. However, determining the minimal number of spermatozoa need per AI without detrimental effect on overall reproductive performances is not an easy question to answer. To increase the efficiency of semen utilization in pig AI, optimum number of spermatozoa per dose needed to determine. The objective of this study was to determine the reproductive performance and factors that affect on-farm application of low-dose semen insemination in sows. Data were collected from Darby Genetics AI studs from 4th of June to 7th of July, 2012 (n=401). The numbers of parturition were 84, 234 and 83 in sows inseminated with doses of $1.5{\times}10^9$, $2.0{\times}10^9$ and $2.5{\times}10^9$ spermatozoa in 100ml extender, respectively. There were no significant differences on reproductive performances such as gestation period, total born, total born alive, stillbirth and mummy in sows inseminated with different semen doses. The average number of born alive was 10.5, 11.0 and 10.4 from sows inseminated with $1.5{\times}10^9$, $2.0{\times}10^9$ and $2.5{\times}10^9$ sperms, respectively. Also, number of spermatozoa per dose did not affect litter size (p>0.10). There were no significant differences of maternal genetic line difference on gestation period, total number born, number born alive, born dead and mummy. The estimated correlation coefficients of the different semen doses with total number born, number born alive, born dead and mummy were r=-0.00, -0.01, 0.02 and 0.02, respectively. Taken together, the result of this study suggested that when semen was appropriately inseminated after induced ovulation, insemination with low-dose ($1.5{\sim}2.0{\times}10^9$) semen dose not adversely affect sow's fertility.

• 한국동물위생학회지
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• 제39권4호
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• pp.211-219
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• 2016

For determining the prevalence of major enteric pathogens, clinical examination and etiological diagnosis were carried out on 75 Korean pig farms. Enteric disease-suspected signs were observed in 90.7% of the farms and the incidence and severity were higher in younger age groups of the pigs. Five of seven pathogens were detected in 375 fecal samples collected from the 75 farms, and the farm-level prevalence of porcine rotavirus group A (PoRVA), pathogenic Escherichia (E.) coli, Lawsonia (L.) intracelluraris, Salmonella spp., and Brachyspira (B.) hyodysenteriae was 54.7%, 54.7%, 16.0%, 10.7% and 2.7%, respectively. PoRVA was extensively infected in suckling and weaning pig groups. The prevalence of pathogenic E. coli was highest in suckling period, and after the period, it exhibited a tendency to decrease. Salmonella spp. and L. intracelluraris were detected in all feeding groups of pigs in a ratio of 1.3~6.7%. B. hyodysenteriae was detected in 1.3~2.7% of growing and fattening pig groups but not detected in suckling and weaning pig groups. At least one or more pathogens were detected in 30.1% of 375 fecal samples. Among these, 25.0% or 5.1% of cases were single or mixed infection. Enteric disease signs of the pigs were significantly co-related with the detection of PoRVA, pathogenic E. coli or Salmonella spp. (P<0.01) but not with L. intracelluraris or B. hyodysenteriae (P>0.05). Conclusively, it will be expected that these data obtained in this study are very useful for subsequent studies and prevention strategies for swine enteric disease in Korean pig farms.

• 한국동물위생학회지
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• 제43권2호
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• pp.79-88
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• 2020

The aim of this study was to investigate the prevalence of CTX-M β-lactamase and plasmid-mediated quinolone resistance (PMQR) genes, and the pattern of antibiotic resistance in cefotaxime-resistant gramnegative bacteria. A total 126 gram-negative bacteria were isolated from hospitalized dogs and cats between 2018 and 2019. The most predominant isolates were E. coli (n=41), followed by Pseudomonas aeruginosa (n=25), Proteus mirabilis (n=14), Klebsiella pneumoniae (n=9), Sphingomonas paucimobilis (n=7), and Enterobacter cloacae and Serratia marcescens (respectively, n=5). Cefotaxime-resistant isolates were identified in 26.2% (33 isolates) of 126 gram-negative bacteria. CTX-M type β-lactamase were found in 15 isolates (10 E. coli, 1 Ent, cloacae and 4 K. pneumoniae, respectively). Among the CTX-M producing gram-negative bacteria, CTX-M-1 and CTX-M-9 were detected in 10 (66.7%) and 5 (33.3%) isolates, respectively. While, CTX-M-2 and CTX-M-8 were not found. PMQR genes were detected in 12 (36.4%) isolates (4 E. coli, 2 Ent, cloacae and 6 K. pneumoniae, respectively), and the predominant PMQR gene was aac(6')-lb-cr (n=9), followed by qnrB (n=8) and qnrS (n=1) alone or in combination. qnrA and qepA were not found. Additionally, 9 (60%) of 12 PMQR positive isolates were co-existence with CTX-M-1 or CTX-M-9. CTX-M or PMQR producing isolates showed highly resistance to penicillins (100%), cephalosporins (100~66.7%), monobactams (72.2%), and non-β-lactam antibiotics (94.4~61.1%) such as quinolones, trimethoprim/sulfamethoxazole, tetracycline and gentamicin. These findings showed CTX-M-1, CTX-M-9, aac(6')-lb-cr and qnrB were highly prevalent in cefotaxime-resistant Enterobacteriaceae isolates from companion animals in our region. Moreover, PMQR genes were closely associated with CTX-M type β-lactamase.