Detection of Enteric Bacteria in Raw Food Samples from Vietnam ...

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TBS Tris buffer saline TE Tris, EDTA buffer TET Tetracycline TRI Trimethoprim Tris Tris (hydroxymethyl) amino methane SDS Sodium dodecyl sulfate SGI1 Salmonella genomic island 1 Tm 0 C Melting temperature TCBS Thiosulfate citrate bile salts sucrose agar TSI Triple sugar iron agar TSA Tryticase soy agar VP Voges-Proskauer v/v Volume per volume w/v Weight per volume XLD Xylose lysine deoxycholate agar WHO World Health Organisation µg Microgram µL Microlitre xv
List of Figures Figure 1.1: The possible routes of transmission of antibiotic resistant bacteria from farm ........................................................................................................................ 32 Figure 1.2: General structures of integrons. ............................................................................ 37 Figure 1.3: Genetic organization of the antibiotic resistance gene region of SGI1 in DT104. ................................................................................................................... 42 Figure 3.1: PFGE gels which were used for Gel Compar analysis ....................................... 104 Figure 3.2: Dendrogram generated by the Gel Compar II software showing the relationship of DNA fingerprinting profiles of Salmonella spp. isolates.. .......... 106 Figure 3.3: Resistance of Salmonella spp. isolates of difference origins to antibiotics ........ 110 Figure 3.4: Resistance of E. coli isolates of different origins to antibiotics .......................... 124 Figure 4.1: Genetic organisation of the antibiotic resistance gene cluster of SGI1 of DT104. ................................................................................................................. 153 Figure 4.2: Agarose gel electrophoresis of PCRs amplification of antibiotic resistance genes multiplex PCR set 2. .................................................................................. 161 Figure 4.3: Agarose gel electrophoresis of PCRs amplification of antibiotic resistance gene tetA. ............................................................................................................. 162 Figure 4.4: Plasmids content of Salmonella spp. and E.coli isolates using different plasmid extraction method. .................................................................................. 181 Figure 4.5: High molecular weight (95 kb) plasmid of S. Typhimurium 82/6915 ................ 182 Figure 4.6: Agarose gel electrophoresis of PCR amplification of class 1 integron .............. 189 Figure 4.7: Agarose gel electrophoresis of PCR amplification of class 1 integron. ............. 190 xvi
Page 1 and 2: Detection of Enteric Bacteria in Ra
Page 3 and 4: Acknowledgement I would first like
Page 5 and 6: Table of Content List of Abbreviati
Page 7 and 8: 2.1.6. Media and solutions for tiss
Page 9 and 10: Chapter 3: The Detection of Enteric
Page 11 and 12: 4.2.6. The transfer ability of anti
Page 13 and 14: Term Meaning AMP Ampicillin AMO Amo
Page 15: LDC Lysine Decarboxylase MDR Multid
Page 19 and 20: Figure 5.5: Agarose gel electrophor
Page 21 and 22: Table 4.2: E. coli isolates used to
Page 23 and 24: Abstract 1 ABSTRACT Food is essenti
Page 25 and 26: 3 ABSTRACT was also observed. In co
Page 27 and 28: 5 ABSTRACT The ownership of resista
Page 29 and 30: Chapter 1: Introduction 1.1. Enteri
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Page 51 and 52: 29 CHAPTER 1: INTRODUCTION antibiot
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45 CHAPTER 1: INTRODUCTION Morabito
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47 CHAPTER 2: GENERAL MATERIALS AND
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Petri dish Nunc, Denmark 49 CHAPTER
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2.1.3. General media and solutions
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Trypan blue solution: 1% (w/v) tryp
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2.2.2.1.3. Isolation and identifica
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Table 2.2: Bacterial strains and ba
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2.2.3.2. Inoculation of test plates
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2.2.4.3. Polymerase Chain Reaction
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CHAPTER 3: THE DETECTION OF ENTERIC
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CHAPTER 4: MOLECULAR GENETIC MECHAN
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4.2. Method CHAPTER 4: MOLECULAR GE
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Isolate name Sources CHAPTER 4: MOL
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Isolates Sources CHAPTER 4: MOLECUL
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Integron size (kb CHAPTER 4: MOLECU
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CHAPTER 5: PATHOGENICITY OF SALMONE
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Primer set CHAPTER 5: PATHOGENICITY
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Primer set CHAPTER 5: PATHOGENICITY
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Isolate name CHAPTER 5: PATHOGENICI
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Chapter 6: General Discussion 251 C
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253 CHAPTER 6: GENERAL DISCUSSION s
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255 CHAPTER 6: GENERAL DISCUSSION I
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257 CHAPTER 6: GENERAL DISCUSSION m
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259 CHAPTER 6: GENERAL DISCUSSION r
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261 CHAPTER 6: GENERAL DISCUSSION p
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263 REFERENCE Angkititrakul, S., C.
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265 REFERENCE Bauernfeind, A., S. W
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267 REFERENCE Boyd, D. A., G. A. Pe
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269 REFERENCE Catry, B., H. Laevens
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271 REFERENCE enterica serovars Typ
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273 REFERENCE multiple-antibiotic r
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275 REFERENCE Shiga toxin-producing
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277 REFERENCE Fitzgerald, C., K. St
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279 REFERENCE Graninger, W., K. Zed
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281 REFERENCE Heffernan, E. J., J.
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283 REFERENCE Jarrett, P., and M. S
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285 REFERENCE Kauffmann, F. 1972. S
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287 REFERENCE Leverstein-van Hall,
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289 REFERENCE Maguire, H. C., A. A.
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291 REFERENCE Meng, J., M. P. Doyle
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293 REFERENCE Nakamura, M., S. Sato
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295 REFERENCE Christenson, M. L. Bi
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297 REFERENCE Phan, Q., P. Mshar, T
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299 REFERENCE Refsum, T., E. Heir,
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301 REFERENCE Salyers, A. A. 1993.
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303 REFERENCE Identification of ant
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305 REFERENCE patterns produced by
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307 REFERENCE Vaudaus, P., and F. A
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309 REFERENCE White, D. G., S. Zhao
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311 REFERENCE Yavzori, M., N. Porat
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APPENDIX Table A1: Salmonella spp.
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Isolates Source Group Serotype 315
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Table A2: E. coli isolates which we
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Isolates Source AMP AMO AUG TET 319
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Table A3: V. parahaemolyticus isola
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323 CONFERENCES/ PROCEEDINGS and PU
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