1) Akiba, M., Sekizuka, T., Yamashita, A., Kuroda, M., Fujii, Y., Murata, M., Lee, K., Joshua, D.I., Balakrishna, K., Bairy, I., Subramanian, K., Krishnan, P., Munuswamy, N., Sinha, R.K., Iwata, T., Kusumoto, M., Guruge, K.S., 2016. Distribution and relationships of antimicrobial resistance determinants among extended-spectrum-cephalosporin-resistant or carbapenem-resistant Escherichia coli isolates from rivers and sewage treatment plants in India. Antimicrob. Agents Chemother. 60,2972-2980.
2) Andino, A., Hanning, I., 2015. Salmonella enterica: survival, colonization, and virulence differences among serovars. Sci. World J. 2015, 520179.
3) Awol, N., Nigusse, D., Ali, M., 2019. Prevalence and antimicrobial susceptibility profile of Salmonella and Shigella among food handlers working in food establishment at Hawassa city, Southern Ethiopia. BMC Res. Notes 12, 712.
4 Branchu, P., Bawn, M., Kingsley, R.A., 2018. Genome variation and molecular epidemiology of Salmonella enterica serovar Typhimurium pathovariants. Infect. Immun. 86, e00079-00018.
5) Cao, G., Allard, M.W., Hoffmann, M., Monday, S.R., Muruvanda, T., Luo, Y., Payne, J., Rump, L., Meng, K., Zhao, S., McDermott, P.F., Brown, E.W., Meng, J., 2015. Complete sequences of six IncA/C plasmids of multidrug-resistant Salmonella enterica subsp. enterica serotype Newport. Genome Announc. 3, e00027-15.
6) Carattoli, A., Zankari, E., García-Fernández, A., Voldby Larsen, M., Lund, O., Villa, L., Moller Aarestrup, F., Hasman, H., 2014. In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing. Antimicrob. Agents Chemother. 58, 3895-3903.
7) Carver, T.J., Rutherford, K.M., Berriman, M., Rajandream, M.A., Barrell, B.G., Parkhill, J., 2005. ACT: the Artemis comparison tool. Bioinformatics 21, 3422-3423.
8) Centers for Disease Control and Prevention, 2014. Foodborne Diseases Active Surveillance Network (FoodNet): FoodNet Surveillance Report for 2012 (Final Report). Centers for Disease Control and Prevention, Atlanta, GA, U.S.A. https://www.cdc.gov/foodnet/PDFs/2012_annual_report_508c.pdf (accessed on September 6th, 2021)
9) Chen, K., Dong, N., Zhao, S., Liu, L., Li, R., Xie, M., Lin, D., Wai-Chi Chan, E., Meng, J., McDermott, P.F., Chen, S., 2018. Identification and characterization of conjugative plasmids that encode ciprofloxacin resistance in Salmonella. Antimicrob. Agents Chemother. 62, 00575-18.
10) Cheng, Q., Jiang, X., Xu, Y., Hu, L., Luo, W., Yin, Z., Gao, H., Yang, W., Yang, H., Zhao, Y., Zhao, X., Zhou, D., Dai, E., 2019. Type 1, 2, and 1/2-hybrid IncC plasmids from China. Front. Microbiol. 10, 2508.
11) Chuma, T., Miyasako, D., Dahshan, H., Takayama, T., Nakamoto, Y., Shahada, F., Akiba, M., Okamoto, K., 2013. Chronological change of resistance to B -lactams in Salmonella enterica serovar Infantis isolated from broilers in Japan. Front. Microbiol. 4, 113.
12) Clinical and Laboratory Standards Institute, 2012. Performance standards for antimicrobial disk susceptibility tests; approved standard-Document M02-A11. Clinical and Laboratory Standards Institute, Wayne, PA, U.S.A.
13) Clinical and Laboratory Standards Institute, 2013. Performance standards for antimicrobial disk and dilution susceptibility tests for bacteria isolated from animal; second informational supplement-Document VET01-S2. Clinical and Laboratory Standards Institute, Wayne, PA, U.S.A.
14) Clinical and Laboratory Standards Institute, 2014. Performance standards for antimicrobial susceptibility testing; twenty-fourth informational supplement-Document M100-S24. Clinical and Laboratory Standards Institute, Wayne, PA, U.S.A.
15) Clinical and Laboratory Standards Institute, 2018. Performance standards for antimicrobial susceptibility testing -Document M100, 28th Edition. Clinical and Laboratory Standards Institute, Wayne, PA, U.S.A.
16) Clinical and Laboratory Standards Institute, 2020. Performance standards for antimicrobial susceptibility testing-_Document M100, 30th Edition. Clinical and Laboratory Standards Institute, Wayne, PA, U.S.A.
17) Cloeckaert, A., Praud, K., Doublet, B., Bertini, A., Carattoli, A., Butaye, P., Imberechts, H., Bertrand, S., Collard, J.M., Arlet, G., Weill, F.X., 2007. Dissemination of an extended -spectrum- B - lactamase blarem-52 gene-carrying IncI1 plasmid in various Salmonella enterica serovars isolated from poultry and humans in Belgium and France between 2001 and 2005. Antimicrob. Agents Chemother. 51, 1872-1875.
18) Coil, D., Jospin, G., Darling, A.E., 2014. A5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeg data. Bioinformatics 31, 587-589.
19) Colom, K., Pérez, J., Alonso, R., Fernández-Aranguiz, A., Lariño, E., Cisterna, R., 2003. Simple and reliable multiplex PCR assay for detection of blarem, blashv and blaoxa-1 genes in Enterobacteriaceae. FEMS Microbiol. Lett. 223, 147-151.
20) Coudron, P.E., 2005. Inhibitor-based methods for detection of plasmid-mediated AmpC B -lactamases in Klebsiella spp., Escherichia coli, and Proteus mirabilis. J. Clin. Microbiol. 43, 4163-4167.
21) Dutil, L., Irwin, R., Finley, R., Ng, L.K., Avery, B., Boerlin, P., Bourgault, A.M., Cole, L., Daignault, D., Desruisseau, A..Demczuk, W., Hoang, L., Horsman, G.B., Ismail, J., Jamieson, F., Maki, A., Pacagnella, A., Pillai, D.R., 2010. Ceftiofur resistance in Salmonella enterica serovar Heidelberg from chicken meat and humans, Canada. Emerg. Infect. Dis. 16, 48-54.
22) Eng, S., Pusparajah, P., Ab Mutalib, N., Ser, H., Chan, K., Lee, L., 2015. Salmonella: A review on pathogenesis, epidemiology and antibiotic resistance. Front. Life Sci. 8, 284-293.
23) European Parliament, 2019. The EU poultry meat and egg sector: Main features, challenges and prospects. https://www.europarl.europa.eu/RegData/etudes/IDAN/2019/6 44195/EPRS_IDA(2019)644195_EN.pdf (accessed on October5th, 2020)
24) Fabre, L., Delauné, A., Espié, E., Nygard, K., Pardos, M., Polomack, L., Guesnier, F., Galimand, M., Lassen, J., Weill, F.X., 2009. Chromosomal integration of the extended-spectrum B -lactamase gene blac-m-1s in Salmonella enterica serotype Concord isolates from internationally adopted children. Antimicrob. Agents Chemother. 53, 1808-1816.
25) Fernández-Alarcón, C., Singer, R.S., Johnson, T.J., 2011. Comparative genomics of multidrug resistance-encoding IncA/C plasmids from commensal and pathogenic Escherichia coli from multiple animal sources. PLoS One 6, e23415.
26) Grimont, P.A.D., Weill, F.X., 2007. Antigenic formulae of the Salmonella serovars, 9th revision. World Health Organization Collaborating Center for Reference and Research on Salmonella, Pasteur Institute, Paris, France. https://www.pasteur.fr/sites/default/files/veng_0.pdf (accessed on September 8th, 2021)
27) Gut, A.M., Vasiljevic, T., Yeager, T., Donkor, O.N., 2018. Salmonella infection - prevention and treatment by antibioticsand probiotic yeasts: a review. Microbiology 164, 1327-1344.
28) Hammerum, A.M., Heuer, O.E., Emborg, H.-D., Bagger-Skjot, L., Jensen, V.F., Rogues, A.M., Skov, R.L., Agerso, Y., Brandt, C.T., Seyfarth, A.M., Muller, A., Hovgaard, K., Ajufo, J., Bager, F., Aarestrup, F.M., Frimodt-Moller, N., Wegener, H.C., Monnet, D.L., 2007. Danish integrated antimicrobial resistance monitoring and research program. Emerg. Infect. Dis. 13, 1632- 1639.
29) Harada, K., Asai, T., 2010. Role of antimicrobial selective pressure and secondary factors on antimicrobial resistance prevalence in Escherichia coli from food-producing animals in Japan. J. Biomed. Biotechnol. 2010, 180682.
30) 橋本信一郎，2017.養鶏現場での薬剤耐性間題への取り組み、鶏病研究会報 53,29-34.
31) Hasman, H., Mevius, D., Veldman, K., Olesen, I., Aarestrup, F.M., 2005. B -lactamases among extended-spectrum B - lactamase (ESBL) -resistant Salmonella from poultry, poultry products and human patients in The Netherlands. J. Antimicrob. Chemother. 56, 115-121.
32) Hedican, E., Hooker, C., Jenkins, T., Medus, C., Jawahir, S., Leano, F., Smith, K., 2009. Restaurant Salmonella Enteritidis outbreak associated with an asymptomatic infected food worker. J. Food Prot. 72, 2332-2336.
33) Hiki, M., Kawanishi, M., Abo, H., Kojima, A., Koike, R., Hamamoto, S., Asai, T., 2015. Decreased resistance to broad - spectrum cephalosporin in Escherichia coli from healthy broilers at farms in Japan after voluntary withdrawal of ceftiofur. Foodborne Pathog. Dis. 12, 639-643.
34) Hiki M., Usui M., Kojima A., Ozawa M., Ishii Y., Asai T., 2013. Diversity of plasmid replicons encoding the blacmy-2 gene in broad-spectrum cephalosporin-resistant Escherichia coli from livestock animals in Japan. Foodborne Pathog. Dis. 10, 243-249.
35） 樋脇 弘， 椿本 亮， 久保倉宏一，栗原淑子，本田己喜子，小田隆弘，1995.鶏卵，液卵および加工品におけるサルモネラ対策について.福岡市衛生試験所報 20,59-68.
36) Hohmann, E.L., 2001. Nontyphoidal salmonellosis. Clin. Infect. Dis. 32, 263-269.
37) Holt, K.E., Dolecek, C., Chau, T.T., Duy, P.T., La, T.T., Hoang, N.V., Nga, T.V., Campbell, J.I., Manh, B. H., Vinh Chau, N.V., Hien, T.T., Farrar, J., Dougan, G., Baker, S., 2011. Temporal fluctuation of multidrug resistant salmonella typhi haplotypes in the mekong river delta region of Vietnam. PLoS Negl. Trop. Dis. 5, e929.
38) Holt, K.E., Thomson, N.R., Wain, J., Phan, M.D., Nair, S., Hasan, R., Bhutta, Z.A., Quail, M.A., Norbertczak, H., Walker, D., Dougan, G., Parkhill, J., 2007. Multidrug-resistant Salmonella enterica serovar paratyphi a harbors IncHI1 plasmids similar to those found in serovar typhi. J. Bacteriol. 189, 4257- 4264.
39) Hunt, M., Silva, N.D., Otto, T.D., Parkhill, J., Keane, J.A., Harris, S.R., 2015. Circlator: automated circularization of genome assemblies using long sequencing reads. Genome Biol. 16, 294.
40) 兵庫県食肉衛生検査センター, 2020. 令和2年度事業概要（令和元年度実績)、兵庫，兵庫県食肉衛生検査センター，30.
41) Iwabuchi, E., Maruyama, N., Hara, A., Nishimura, M., Muramatsu, M., Ochiai, T., Hirai, K., 2010. Nationwide survey of Salmonella prevalence in environmental dust from layer farms in Japan. J. Food Prot. 73, 1993-2000.
42) Jacoby, G. B -lactamase classification and amino acid sequences for TEM, SHV and OXA extended-spectrum and inhibitor resistant enzymes. http://www.lahey.org/Studies/ (accessed on June 19th, 2017)
43) Jeon, H.Y., Seo, K.W., Kim, Y.B., Kim, D.K., Kim, S.W., Lee, Y.J., 2019. Characteristics of third-generation cephalosporin-resistant Salmonella from retail chicken meat produced by integrated broiler operations. Poult. Sci. 98, 1766-1774.
44) Johnson, T.J., Bielak, E.M., Fortini, D., Hansen, L.H., Hasman, H., Debroy, C., Nolan, L.K., Carattoli, A., 2012. Expansion of the IncX plasmid family for improved identification and typing of novel plasmids in drug-resistant Enterobacteriaceae. Plasmid 68, 43-50.
45) Kataoka, Y., Murakami, K., Tori, Y., Kimura, H., Maeda-Mitani, E., Shigemura, H., Fujimoto, S., Murakami, S., 2017. Reduction in the prevalence of AmpC B -lactamase CMY-2 in Salmonella from chicken meat following cessation of the use of ceftiofur in Japan. J. Glob. Antimicrob. Resist. 10, 10-11.
46) 川西路子，2016.JVARM （動物由来薬剤耐性菌モニタリング）の取り組み、日本豚病研究会報 68,12-18.
47) Kim, J.S., Yun, Y.S., Kim, S.J., Jeon, S.E., Lee, D.Y., Chung, G.T., Yoo, C.K., Kim, J., 2016. Rapid emergence and clonal dissemination of CTX-M-15-producing Salmonella enterica serotype Virchow, South Korea. Emerg. Infect. Dis. 22, 68-70.
48) Klare, I., Badstübner, D., Konstabel, C., Böhme, G., Claus, H., Witte, W., 1999. Decreased incidence of VanA-type vancomycin- resistant enterococci isolated from poultry meat and from fecal samples of humans in the community after discontinuation of avoparcin usage in animal husbandry. Microb. Drug Resist. 5, 45-52.
49) Kleinheinz, K.A., Jensen, K.G., Larsen, M.V., 2014. Applying the ResFinder and VirulenceFinder web-services for easy identification of acquired antibiotic resistance and E. coli virulence genes in bacteriophage and prophage nucleotide sequences. Bacteriophage 4, e27943.
50) 国立医薬品食品衛生研究所，2016.サルモネラ属菌標準試験法 NIHSJ-01-ST4 (090218). http://www.nihs.go.jp/fhm/kensa/sal/Salmonells%20ST4- 091014F.pdf (アクセス日 2021年9月8日）
51) Kolmogorov, M., Yuan, J., Lin, Y., Pevzner, P.A., 2019. Assembly of long, error-prone reads using repeat graphs. Nat. Biotechnol. 37, 540-546.
52) 駒井享，2007. 鶏肉の生産、処理加工および流通の現状・独立行政法人農畜産業振興機構 月報「畜産の情報」（国内編）2007年 9 A. https://lin.alic.go.jp/alic/month/dome/2007/sep/chousal.htm (アクセス日 2021年9月8日）
53) Koren, S., Walenz, B.P., Berlin, K., Miller, J.R., Bergman, N.H., Phillippy, A.M., 2017. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res. 27, 722-736.
54) 厚生労働省，薬事・食品衛生審議会食品衛生分科会乳肉水産食品部会食肉等の生食に関する調査会資料 平成 26年 3月 17 日開催資料6 https://www.mhlw.go.jp/file/05-Shingikai-11121000- Iyakushokuhinkyoku-Soumuka/0000040840.pdf (アクセス日 2021年9月6日）
55) Kubasova, T., Cejkova, D., Matiasovicova, J., Sekelova, Z., Polansky, O., Medvecky, M., Rychlik, I., Juricova, H., 2016. Antibiotic resistance, core-genome and protein expression in IncHI1 plasmids in Salmonella Typhimurium. Genome Biol. Evol. 8, 1661-1771.
56) Langridge, G.C., Wain, J., Nair, S., 2012. Invasive Salmonellosis in Humans. EcoSal Plus, 5. https://journals.asm.org/doi/10.1128/ecosalplus.8.6.2.2?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_ pub%20%200pubmed (accessed on September 26th, 2021)
57) Lee, C.S., Li, J.J., Doi, Y., 2015. Complete sequence of conjugative IncA/C plasmid encoding CMY-2 B -lactamase and RmtE 16S rRNA methyltransferase. Antimicrob. Agents Chemother. 59, 4360-4361.
58) Leinberger, D.M., Grimm, V., Rubtsova, M., Weile, J., Schröppel, K., Wichelhaus, T.A., Knabbe, C., Schmid, R.D., & Bachmann, T.T., 2010. Integrated detection of extended - spectrum-beta-lactam resistance by DNA microarray-based genotyping of TEM, SHV, and CTX-M genes. J. Clin.Microbiol., 48, 460-471.
59) Leverstein-van Hall, M.A., Dierikx, C.M., Cohen Stuart, J., Voets, G.M., van den Munckhof, M.P., van Essen -Zandbergen, A., Platteel, T., Fluit, A.C., van de Sande-Bruinsma, N., Scharinga, J., Bonten, M.J., Mevius, D.J., 2011. Dutch patients, retail chicken meat and poultry share the same ESBL genes, plasmids and strains. Clin. Microbiol. Infect. 17, 873-880.
60) Li, H., 2016. Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences. Bioinformatics 32, 2103- 2110.
61) Li, H., Durbin, R., 2010. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 26, 589-595.
62) Liakopoulos, A., Geurts, Y., Dierikx, C.M., Brouwer, M.S., Kant, A., Wit, B., Heymans, R., van Pelt, W., Mevius, D.J., 2016. Extended-spectrum cephalosporin-resistant Salmonella enterica serovar Heidelberg Strains, the Netherlands. Emerg. Infect. Dis. 22, 1257-1261.
63) Liu, J.H., Wei, S.Y., Ma, J.Y., Zeng, Z.L., Lü, D.H., Yang, G.X., Chen, Z.L., 2007. Detection and characterisation of CTX-M and CMY-2 B -lactamases among Escherichia coli isolates from farm animals in Guangdong Province of China. Int. J. Antimicrob. Agents. 29, 576-581.
64) Mahrouki, S., Belhadj, O., Chihi, H., Mohamed, B.M., Celenza, G., Amicosante, G., Perilli, M., 2012. Chromosomal b/acT×-M-15 associated with IS EcpI in Proteus mirabilis and Morganella morgani isolated at the military hospital of Tunis, Tunisia. J. Med. Microbiol. 61, 1286-1289.
65) Majowicz, S.E., Musto, J., Scallan, E., Angulo, F.J., Kirk, M., O'Brien, S.J., Jones, T.F., Fazil, A., Hoekstra, R.M., 2010. The global burden of nontyphoidal Salmonella gastroenteritis. Clin. Infect. Dis. 50, 882-889.
66) Matsumoto, Y., Izumiya, H., Sekizuka, T., Kuroda, M., Ohnishi, M., 2014. Characterization of blatem-52-carrying plasmids of extended-spectrum-ß-lactamase-producing Salmonella enterica isolates from chicken meat with a common supplier in Japan. Antimicrob. Agents Chemother. 58, 7545-7547.
67) Medeiros, M.A., Oliveira, D.C., Rodrigues Ddos, P., Freitas, D.R., 2011. Prevalence and antimicrobial resistance of Salmonella in chicken carcasses at retail in 15 Brazilian cities. Rev. Panam. Salud Publica. 30, 555-560.
68) Medus, C., Smith K.E., Bender, J.B., Leano, F., Hedberg C.W., 2010. Salmonella infections in food workers identified through routine Public Health Surveillance in Minnesota: impact on outbreak recognition. J. Food Prot. 73, 2053-2058.
69) 見上彪，2003.獃医微生物学 第2版. 東京，文永堂，29-32.
70) Moffatt, C.R., Musto, J., Pingault, N., Miller, M., Stafford, R., Gregory, J., Polkinghorne, B.G., Kirk, M.D., 2016. Salmonella Typhimurium and outbreaks of egg-associated disease in Australia, 2001 to 2011. Foodborne Pathog. Dis 13, 379-385.
71) Murakami, K., Ishihara, T., Horikawa, K., Oda, T., 2007. Features of Salmonella serovars among food handlers in Kyushu, Japan. New Microbiol. 30, 155-159.
72) Murakami, K., Noda, T., Maeda, E., Sera, N., Fujimoto, S., 2014. Easy washing of lysed cell plugs for bacterial typing by pulsed - field gel electrophoresis using simple equipment. J. Microbiol. Methods 101, 67-69.
73) National Center for Biotechnology Information. https://www.ncbi.nlm.nih.gov/genbank/wgs/ (accessed on September 24th, 2021)
74) National Center for Biotechnology Information. https://www.ncbi.nlm.nih.gov/nuccore/?term= (accessed on September 24th, 2021)
75) National Institute of Genetics DNA Data Bank of Japan. https://dfast.ddbj.nig.ac.jp/ (accessed on January 22nd, 2021)
76) National Veterinary Assay Laboratory Ministry of Agriculture Forestry and Fisheries 2018. Sales amounts and sales volumes (active substance) of antibiotics, synthetic antibacterials, anthelmintics and antiprotozoals. https://www.maff.go.jp/nval/iyakutou/hanbaidaka/pdf/h30_han baidaka.pdf (accessed on December 6th, 2020).
77) Noda, T., Murakami, K., Etoh, Y., Okamoto, F., Yatsuyanagi, J., Sera, N., Furuta, M., Onozuka, D., Oda, T., Asai, T., Fujimoto, S., 2015. Increase in resistance to extended-spectrum cephalosporins in Salmonella isolated from retail chicken products in Japan. PLoS One 10, e0116927.
78) Noda, T., Murakami, K., Ishiguro, Y., Asai, T., 2010. Chicken meat is an infection source of Salmonella serovar Infantis for humans in Japan. Foodborne Pathog. Dis. 7, 727-735.
79) 能登 優，高瀬識之，高橋裕里香，松本貴嗣，吉川博文，土金恵 子， 細山哲，藤田信之， 岡田憲典，山根久和，野尻秀昭,2012. プラスミド保持に伴う負荷を軽減化する宿主染色体因子. 環境バイ オテクノロジー学会誌,12,135-139.
80) 農林水産省，2005.鶏卵のサルモネラ総合対策指針 https://www.maff.go.jp/j/syouan/douei/eisei/e_kanri_kizyun/sa 1/pdf/kei ran_sogo.pdf (アクセス日 2021年 12月2日）
81) 農林水産省，2009.薬剤耐性菌についてのQ&A. https://www.maff.go.jp/nval/tyosa_kenkyu/taiseiki/pdf/taiseiki n_q_a_20100107.pdf (アクセス日 2021年 11月26日）
82) Ochoa, J.T., and Santisteban-Ponce, J., 2019. Salmonella (non- typhoidal), vol 1. Elsevier, Philadelphia, PA, U.S.A.
83) 小栗克之，三品和世，杉山道雄，荒幡克己，1997.GP センターにおける加工卵製造と今後の展望．岐阜大学農学部研究報告， 65-73. http://repository.lib.gifu-u.ac.jp/bitstream/20.500.12099 /5468/1/KJ00000737337.pdf (アクセス日 2021年9月22日）
84) Oliva, M., Monno, R., Addabbo, P., Pesole, G., Scrascia, M., Calia, C., Dionisi, A.M., Chiara, M., Horner, D.S., Manzari, C., Pazzani, C., 2018. IS26 mediated antimicrobial resistance gene shuffling from the chromosome to a mosaic conjugative FII plasmid. Plasmid 100, 22-30.
85) Pagani, L., Dell'Amico, E., Migliavacca, R., D'Andrea, M.M., Giacobone, E., Amicosante, G., Romero, E., Rossolini, G.M., 2003. Multiple CTX-M-type extended-spectrum B -lactamases in nosocomial isolates of Enterobacteriacee from a hospital in northern Italy. J. Clin. Microbiol. 41, 4264-4269.
86) Papagiannitsis, C.C., Dolejska, M., Izdebski, R., Giakkoupi, P. Skalova, A., Chudejova, K., Dobiasova, H., Vatopoulos, A.C., Derde, L.P., Bonten, M.J., Gniadkowski, M., Hrabak, J., 2016. Characterisation of IncA/C plasmids carrying an In 416-like integron with the blavim-19 gene from Klebsiella pneumoniae ST383 of Greek origin. Int. J. Antimicrob. Agents 47, 158-162.
87) Parkhill, J., Dougan, G., James, K.D., Thomson, N.R., Pickard, D., Wain, J., Churcher, C., Mungall, K.L., Bentley, S.D., Holden, M.T., Sebaihia, M., Baker, S., Basham, D., Brooks, K., Chillingworth, T., Connerton, P., Cronin, A., Davis, P., Davies, R.M., Dowd, L., White, N., Farrar, J., Feltwell, T., Hamlin, N., Haque, A., Hien, T.T., Holroyd, S., Jagels, K., Krogh, A., Larsen, T.S., Leather, S., Moule, S., O'Gaora, P., Parry, C., Quail, M., Rutherford, K., Simmonds, M., Skelton, J., Stevens, K., Whitehead, S., Barrell, B.G., 2001. Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18. Nature 413, 848-852.
88) Partridge, S.R., Kwong, S.M., Firth, N., Jensen, S.O., 2018. Mobile genetic elements associated with antimicrobial resistance. Clin. Microbiol. Rev. 31, e00088-17.
89) Parveen, S., Taabodi, M., Schwarz, J.G., Oscar, T.P., Harter- Dennis, J., White, D.G., 2007. Prevalence and antimicrobial resistance of Salmonella recovered from processed poultry. J. Food Prot. 70, 2466-2472.
90) Perilli, M., Dell'Amico, E., Segatore, B., de Massis, M.R., Bianchi, C., Luzzaro, F., Rossolini, G.M., Toniolo, A., Nicoletti, G., Amicosante, G., 2002. Molecular characterization of extended-spectrum B -lactamases produced by nosocomial isolates of Enterobacteriaceae from an Italian nationwide survey. J. Clin. Microbiol. 40, 611-614.
91) Pether, J.V.S., Scott, R.J.D., 1982. Salmonella carriers; are they dangerous? A study to identify finger contamination with Salmonellae by convalescent carriers. J. Infection 5, 81-88.
92) Poirel, L., Decousser, J.W., Nordmann, P., 2003. Insertion sequence IS Ecp1B is involved in expression and mobilization of a blacr×-m B -lactamase gene. Antimicrob. Agents Chemother. 47, 2938-2945.
93) Riaño, I., Moreno, M.A., Teshager, T., Sáenz, Y., Domínguez, L., Torres, C., 2006. Detection and characterization of extended-spectrum B -lactamases in Salmonella enterica strains of healthy food animals in Spain. J. Antimicrob. Chemother. 58, 844-847.
94) Rodríguez, I., Thomas, K., Van Essen, A., Schink, A.K., Day, M., Chattaway, M., Wu, G., Mevius, D., Helmuth, R., Guerra, B., 2014. Chromosomal location of blacrx-m genes in clinical isolates of Escherichia coli from Germany, The Netherlands and the UK. Int. J. Antimicrob. Agents 43, 553-557.
95) Rozwandowicz, M., Brouwer, M.S.M., Fischer, J., Wagenaar, J.A., Gonzalez-Zorn, B., Guerra, B., Mevius, D.J., Hordijk, J., 2018. Plasmids carrying antimicrobial resistance genes in Enterobacteriaceae. J. Antimicrob. Chemother. 73, 1121-1137.
96) Saito, S., Koori, Y., Ohsaki, Y., Osaka, S., Oana, K., Nagano, Y., Arakawa, Y., Nagano, N., 2017. Third-generation cephalosporin-resistant non-typhoidal Salmonella isolated from human feces in Japan. Jpn. J. Infect. Dis. 70, 301-304.
97) Sánchez-Salazar, E., Gudiño, M.E., Sevillano, G., Zurita, J., Guerrero-López, R., Jaramillo, K., Calero-Cáceres, W., 2020. Antibiotic resistance of Salmonella strains from layer poultry farms in central Ecuador. J. Appl. Microbiol. 128, 1347-1354.
98) Sannat, C., Patyal, A., Rawat, N., Ghosh, R.C., Jolhe, D. K., Shende, R.K., Hirpurkar, S.D., Shakya, S., 2017. Characterization of Salmonella Gallinarum from an outbreak in Raigarh, Chhattisgarh. Vet. World. 10, 144-148.
99) 笹川千尋，林哲地，2008. 医科細菌学（改訂第4版）・東京，南江堂，27-44.
100) Sccmann, T., 2014. Prokka: rapid prokaryotic genomc annotation. Bioinformatics 30, 2068-2069.
101) Sekizuka, T., Yatsu, K., Inamine, Y., Segawa, T., Nishio, M., Kishi, N., Kuroda, M., 2018. Complete genome sequence of a blapc-2-positive Klebsiella pneumonia strain isolated from the effluent of an urban sewage treatment plant in Japan. mSphere 3, e00314-18.
102) Shahada, F., Sekizuka, T., Kuroda, M., Kusumoto, M., Ohishi, D., Matsumoto, A., Okazaki, H., Tanaka, K., Uchida, I., Izumiya, H., Watanabe, H., Tamamura, Y., Iwata, T., Akiba, M., 2011. Characterization of Salmonella enterica serovar Typhimurium isolates harboring a chromosomally encoded CMY-2 ₽ - lactamase gene located on a multidrug resistance genomic island. Antimicrob. Agents Chemother. 55, 4114-4121.
103) Sherburne, C.K., Lawley, T.D., Gilmour, M.W., Blattner, F.R., Burland, V., Grotbeck, E., Rose, D.J., Taylor, D.E., 2000. The complete DNA sequence and analysis of R27, a large IncHI plasmid from Salmonella typhi that is temperature sensitive for transfer. Nucleic Acids Res. 28, 2177-2786.
104) 品川邦汎，1999.卵及び卵加工品におけるサルモネラエンテリティディスの汚染とその対策。食品衛生学雑誌 40,7-18.
105) Siddiqui, T.R., Bibi, S., Mustufa, M.A., Ayaz, S.M., Khan, A., 2015. High prevalence of typhoidal Salmonella enterica serovarsexcreting food handlers in Karachi-Pakistan: a probable factor for regional typhoid endemicity. J. Health Popul. Nutr. 33, 27.
106) Siguier, P., Filée, J., Chandler, M., 2006. Insertion sequences in prokaryotic genomes. Curr. Opin. Microbiol. 9, 526-531.
107) Siguier, P., Gourbeyre, E., Chandler, M., 2014. Bacterial insertion sequences: their genomic impact and diversity. FEMS Microbiol. Rev. 38, 865-891.
108) Siguier, P., Perochon, J., Lestrade, L., Mahillon, J., Chandler, M., 2006. ISfinder: the reference centre for bacterial insertion sequences. Nucleic Acids Res. 34, D32-36.
109) Sirichote, P., Hasman, H., Pulsrikarn, C., Schonheyder, H.C., Samulioniené, J., Pornruangmong, S., Bangtrakulnonth, A., Aarestrup, F.M., Hendriksen, R.S., 2010. Molecular characterization of extended-spectrum cephalosporinase- producing Salmonella enterica serovar Choleraesuis isolates from patients in Thailand and Denmark. J. Clin. Microbiol. 48, 883- 888.
110) Smet, A., Van Nieuwerburgh, F., Vandekerckhove, T.T., Martel, A., Deforce, D., Butaye, P., Haesebrouck, F., 2010. Complete nucleotide sequence of CTX-M-15-plasmids from clinical Escherichia coli isolates: insertional events of transposons and insertion sequences. PLoS One 5, e11202.
111) Sokal, R.R., Michener, C.D., 1958. A statistical method for evaluating systematic relationships. Univ. Kans. Sci. Bull. 38, 1409-1438.
112) Someya, A., Otsuki, K., Murase, T., 2005. Antimicrobial susceptibilities of Salmonella isolates obtained from layer chicken houses on a commercial egg-producing farm in Japan, 1997 to 2002. J. Food Prot. 68, 2030-2034.
113) 総務省統計局，平成27年国勢調査 https://www.stat.go.jp/data/kokusei/2015/kekka.html (T4 tス日 2021年9月23日）
114) Sullivan, M.J., Petty, N.K., Beatson, S.A., 2011. Easyfig: a genome comparison visualizer. Bioinformatics 27, 1009-1010.
115） 食品安全委員会，2010. 食品健康影響評価のためのリスクプロファイル 〜 鶏卵中のサルモネラ・エンテリティディス 〜（改訂版）https://www.fsc.go.jp/sonota/risk_profile/risk_salmonella.pdf(アクセス日 2021年9月 21日）
116) Tagg, K.A., Francois Watkins, L., Moore, M.D., Bennett, C., Joung, Y.J., Chen, J.C., Folster, J.P., 2019. Novel trimethoprim resistance gene dfrA34 identified in Salmonella Heidelberg in the USA. J. Antimicrob. Chemother. 74, 38-41.
117) 高槻森水，柳村俊介，2015.採卵養鶏業における大規模企業経営と家族経営の展開、北海道大学農經論叢 70,53-61.
118) Tate, H., Folster, J.P., Hsu, C.H., Chen, J., Hoffmann, M., Li, C., Morales, C., Tyson, G.H., Mukherjee, S., Brown, A.C., Green, A., Wilson, W., Dessai, U., Abbott, J., Joseph, L., Haro, J., Ayers, S., McDermott, P.F., Zhao, S., 2017. Comparative analysis of extended-spectrum-ß-lactamase CTX-M-65- producing Salmonella enterica serovar Infantis isolates from humans, food animals, and retail chickens in the United States. Antimicrob. Agents Chemother. 61, e00488-17.
119) United States Department of Agriculture - Animal and Plant Health Inspection Service. 2013. Foreign Animal Disease Preparedness and Response Plan (FAD PReP) /National Animal Health Emergency Management System (NAHEMS) Guidelines, Poultry Industry Manual. https://www.aphis.usda.gov/animal_health/emergency_manage ment/downloads/documents_manuals/poultry_ind_manual.pdf (accessed on October 5th, 2020).
120) U.S. Food and Drug Administration 2019. 2018 Summary report on antimicrobials sold or distributed for use in food-producing animals. https://www.fda.gov/media/133411/download (accessed on December 6th, 2020)
121) van Schothorst, M., Beckers, H.J., 1978. Persistent excretion of salmonellas. Br. Med. J. 2, 1301.
122) Vandecraen, J., Chandler, M., Aertsen, A., Van Houdt, R., 2017. The impact of insertion sequences on bacterial genome plasticity and adaptability. Crit. Rev. Microbiol. 43, 709-730.
123) Vaser, R., Sovic, I., Nagarajan, N., Sikic, M., 2017. Fast and accurate de novo genome assembly from long uncorrected reads. Genome Res. 27, 737-746.
124) Vincent, A.T., Trudel, M.V., Paquet, V.E., Boyle, B., Tanaka, K.H., Dallaire-Dufresne, S., Daher, R.K., Frenette, M., Derome, N., Charette, S.J., 2014. Detection of variants of the pRAS3, pAB5S9, and pSN254 plasmids in Aeromonas salmonicida subsp. salmonicida: multidrug resistance, interspecies exchanges, and plasmid reshaping. Antimicrob. Agents Chemother. 58, 7367- 7374.
125） 和知野純一，2020.薬剤耐性獲得機構～グラム陰性菌を中心に〜。 日本臨床徴生物学会雑誌 30,1-12.
126) Wain, J., Diem Nga, L.T., Kidgell, C., James, K., Fortune, S., Song Diep, T., Ali, T., O Gaora, P., Parry, C., Parkhill, J., Farrar, J., White, N.J., Dougan, G., 2003. Molecular analysis of incHI1 antimicrobial resistance plasmids from Salmonella serovar Typhi strains associated with typhoid fever. Antimicrob. Agents Chemother. 47, 2732-2739.
127) Walker, B.J., Abeel, T., Shea, T., Priest, M., Abouelliel, A., Sakthikumar, S., Cuomo, C.A., Zeng, Q., Wortman, J., Young, S.K., Earl, A.M., 2014. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One 9, e112963.
128) Weill, F.X., Demartin, M., Fabre, L., Grimont, P.A., 2004. Extended-spectrum-ß-lactamase (TEM-52) -producing strains of Salmonella enterica of various serotypes isolated in France. J. Clin. Microbiol. 42, 3359-3362.
129) Wick, R.R., Judd, L.M., Gorrie, C.L., Holt, K.E., 2017. Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput. Biol. 13, e1005595.
130) Winokur, P.L., Vonstein, D.L., Hoffman, L.J., Uhlenhopp, E. K., Doern, G.V., 2001. Evidence for transfer of CMY-2 AmpC B - lactamase plasmids between Escherichia coli and Salmonella isolates from food animals and humans. Antimicrob. Agents Chemother. 45, 2716-2722.
131） 山本 勲，2015.実証分析のための計量経済学 正しい手法と結果の読み方.東京，中央経済社，93-103.
132) Yu, F., Chen, Q., Yu, X., Li, Q., Ding, B., Yang, L., Chen, C., Qin, Z., Parsons, C., Zhang, X., Huang, J., Luo, Y., Wang, L., Pan, J., 2011. High prevalence of extended-spectrum beta lactamases among Salmonella enterica Typhimurium isolates from pediatric patients with diarrhea in China. PLoS One 6, e16801.
133) Zhang, D., Zhao, Y., Feng, J., Hu, L., Jiang, X., Zhan, Z., Yang, H., Yang, W., Gao, B., Wang, J., Li, J., Yin, Z., Zhou, D., 2019. Replicon-based typing of IncI-complex plasmids, and comparative genomics analysis of Incl y / K1 plasmids. Front. Microbiol. 10, 48.
134) Zhang, L., Fu, Y., Xiong, Z., Ma, Y., Wei, Y., Qu, X., Zhang, H.. Zhang, J., Liao, M., 2018. Highly prevalent multidrug-resistant Salmonella from chicken and pork meat at retail markets in Guangdong, China. Front. Microbiol. 9, 2104.
135) Zhang, W.H., Lin, X.Y., Xu, L., Gu, X.X., Yang, L., Li, W., Ren, S.Q., Liu, Y.H., Zeng, Z.L., Jiang, H.X., 2016. CTX-M-27 Producing Salmonella enterica serotypes Typhimurium and Indiana are prevalent among food-producing animals in China. Front. Microbiol. 7, 436.
136) Zhao, Q.Y., Chen, P.X., Yang, L., Cai, R.M., Zhu, J.H., Fang, L.X., Webber, M.A., Jiang, H.X., 2020. Transmission of plasmid-borne and chromosomal blacr×-m-64 among Escherichia coli and Salmonella isolates from food-producing animals via IS Ecp1- mediated transposition. J. Antimicrob. Chemother. 75, 1424- 1427.
137) Zhao, S., Qaiyumi, S., Friedman, S., Singh, R., Foley, S.L., White, D.G., McDermott, P.F., Donkar, T., Bolin, C., Munro, S., Baron, E.J., Walker, R.D., 2003. Characterization of Salmonella enterica serotype Newport isolated from humans and food animals. J. Clin. Microbiol. 41, 5366-5371.
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