在次世代定序技術的發展，生命體遺傳解碼速度加快，解碼與基因相關分析工具也在累積，進行比較基因體分析，用於辨認物種內基因功能與可能致病原因。針對全序列定序之微生物基因體發展一套軟體分析平台，適合處理高通量且短序列的次世代定序。從原始序列產出，應用字串演算程式於品質、組裝、分析與找尋致病相關基因。在本地醫院患者分離排名第九於G(-)的伺機型微生物 Morganella morganii，有時會造成社區感染，菌血症，複雜型態泌尿道或膽管結石，且相關於患者插管。為了解它的基因體和致病機轉，從病患分離株KT，進行全序列測序且與相近物種進行比較基因體分析。基因體骨幹建置流程：嶄新組序(de novo)或貼序程式(re-sequence)配合組序混合策略，有許多字串演算法應用和發展於此。在案例， ABySS組序較優。組序KT菌後，搭配分析距離關係，得十二個連續序列。光學限制圖譜和分析顯示，最大的十個連續序列可以被並排。設計引子對、定序和補縫隙，來完成全基因體序列。案例A. baumannii CH 1-43，貼序配合組序混合策略，而剩下一個縫隙則可完成染色體全序列。基因體分析利用序列比對和累積的各物種序列為來源。包括基因預測，定義同源，功能分析和比較基因體分析差異流程：在Morganella morganii KT和Leptospira santarosai serovar Shermani，成功的揭露多種類致病基因，新基因結構和新基因的發現。Morganella morganii KT菌株共有3.8-Mb，其GC比例為51.15%，3565蛋白編碼基因，72個tRNA基因，和10個rRNA基因被預測和推定。致病相關基因含有抗藥因子，纖毛，鞭毛，鐵捕捉系統，第三型分泌系統等基因群，溶血基因和昆蟲毒素都是藉由比較14種相關的腸道科物種基因體得到。而乙醇胺利用基因組(eut operon)發現有19個基因組成，比原本腸道科17個基因更多，更有利於其潛藏於人體腸道內。M. morganii PC也進行全序列測序，約大KT 390-kb。分析指出有一個90-kb的ICE和ICEPm1相像，其它差異為數個prophage基因群。KT菌株是第一個被解開基因體密碼的M. morganii 物種並且有臨床致病力的菌株。比較基因體分析得到許多致病相關的基因和只在Proteeae亞科中發現的新基因。這基因體序列在細菌致病毒素與適存利基上提供了重要資訊。

As the sequencing technology advanced, genome of life decode also accelerate, related genome analysis tools also accumulated, comparative genomic analysis is current trend, which could applied to identify gene function and possible pathogenicity mechanism in organism. We develop a software pipeline for microbial genome project, which is suitable to high throughput and short read next generation sequencing analysis. The opportunistic enterobacterium, Morganella morganii, which can cause bacteraemia, is the ninth most prevalent cause of clinical infections in patients at local hospital. It is sometimes encountered in nosocomial settings and has been causally linked to catheter-associated bacteriuria, complex infections of the urinary and/or hepatobiliary tracts infection. To obtain insights into the genome biology of M. morganii and the mechanisms underlying its pathogenicity, the patient isolate strain KT was whole genome sequencing the genome and compared with the genome sequences of related bacteria. Genome backbone build rely on de novo assembly or re-sequence method, many string algorithm applications and developments. Genome backbone build: de novo assembler or re-sequencing compensate with assembler, a mix approach, many string algorithm applications and developments here. In cases, ABySS assembler performs better. Assembly results of two different distance libraries and scaffolder of M. morganii KT, twelve scaffolds remain. Align and fit ten scaffolds in the KT with optical map. PCR and sequencing for gap fill were conduct and toward the completion of the KT genome. In case, the A. baumannii CH 1-43 successful used mix approach and left one gap to complete genome. Genome analysis, use sequence alignment and accumulated organisms’ sequences as comparative genomics resources. The gene prediction, orthologous identification, functional analysis and comparative genomics analysis workflow: Morganella morganii KT and Leptospira santarosai serovar Shermani were successfully find pathogenicity or virulence related functional genes bring from those organisms and novel gene structures. The M. morganii KT possess genomic sequence of 3,826,919-bp sequence contained in 58 contigs has a GC content of 51.15% and includes 3,565 protein-coding sequences, 72 tRNA genes, and 10 rRNA genes. The pathogenicity-related genes encode determinants of drug resistance, fimbrial adhesins, an IgA protease, haemolysins, ureases, and insecticidal and apoptotic toxins as well as proteins found in flagellae, the iron acquisition system, a type-3 secretion system (T3SS), and several two-component systems. Comparison with 14 genome sequences from other members of Enterobacteriaceae revealed different degrees of similarity to several systems found in M. morganii. The most striking similarities were found in the IS4 family of transposases, insecticidal toxins, T3SS components, and proteins required for ethanolamine use (eut operon) and cobalamin (vitamin B12) biosynthesis. The eut operon and the gene cluster for cobalamin biosynthesis are not present in the other Proteeae genomes analysed. The second selected M. morganii PC strain were whole genome sequencing, and compare with KT, genome size are larger 390-kb in length. One ICE of 90-kb were similar ICE Pm1 were appeared, and several prophage gene clusters are mainly contribute to other differences. The strain KT is the first genome sequence of M. morganii, which is a clinically relevant pathogen. Comparative genome analysis revealed several pathogenicity-related genes and novel genes not found in the genomes of other members of Proteeae. Thus, the genome sequence of M. morganii provides important information concerning virulence and determinants of fitness in this pathogen. The M. morganii KT genome deposited in the DDBJ/EMBL/GenBank under the accession number ALJX00000000.

Bibliography
1. Fleischmann, R.D., et al., Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. science, 1995. 269(5223): p. 496-512.
2. Fraser, C.M., J.A. Eisen, and S.L. Salzberg, Microbial genome sequencing. Nature, 2000. 406(6797): p. 799-803.
3. Venter, J.C., et al., The sequence of the human genome. Science's STKE, 2001. 291(5507): p. 1304.
4. Peltonen, L. and V.A. McKusick, Dissecting human disease in the postgenomic era. science, 2001. 291(5507): p. 1224-1229.
5. Eisenberg, D., et al., Protein function in the post-genomic era. NATURE-LONDON-, 2000: p. 823-826.
6. Bentley, S., et al., Complete genome sequence of the model actinomycete Streptomyces coelicolor A3 (2). Nature, 2002. 417(6885): p. 141-147.
7. Bentley, D.R., Whole-genome re-sequencing. Current opinion in genetics & development, 2006. 16(6): p. 545-552.
8. Margulies, M., et al., Genome sequencing in microfabricated high-density picolitre reactors. Nature, 2005. 437(7057): p. 376-380.
9. Lee, H. and H. Tang, Next-generation sequencing technologies and fragment assembly algorithms. Evolutionary genomics, 2012. 855: p. 155-174.
10. Scholz, M.B., C.C. Lo, and P.S.G. Chain, Next generation sequencing and bioinformatic bottlenecks: the current state of metagenomic data analysis. Current opinion in biotechnology, 2011.
11. Arnold, D.L., et al., Evolution of microbial virulence: the benefits of stress. Trends in genetics, 2007. 23(6): p. 293-300.
12. Mena, A., et al., Characterization of a large outbreak by CTX-M-1-producing Klebsiella pneumoniae and mechanisms leading to in vivo carbapenem resistance development. Journal of clinical microbiology, 2006. 44(8): p. 2831-2837.
13. Hawkey, P.M. and A.M. Jones, The changing epidemiology of resistance. Journal of antimicrobial chemotherapy, 2009. 64(suppl 1): p. i3-i10.
14. Gilbert, J.A. and C.L. Dupont, Microbial metagenomics: beyond the genome. Annual review of marine science, 2011. 3: p. 347-371.
15. Thomas, T., J. Gilbert, and F. Meyer, Metagenomics-a guide from sampling to data analysis. Microbial Informatics and Experimentation, 2012. 2(1): p. 3.
16. Batzoglou, S., et al., ARACHNE: a whole-genome shotgun assembler. Genome research, 2002. 12(1): p. 177-189.
17. Myers, E.W., et al., A whole-genome assembly of Drosophila. science, 2000. 287(5461): p. 2196-2204.
18. Havlak, P., et al., The Atlas genome assembly system. Genome research, 2004. 14(4): p. 721-732.
19. Li, Z., et al., Comparison of the two major classes of assembly algorithms: overlap–layout–consensus and de-bruijn-graph. Briefings in functional genomics, 2012. 11(1): p. 25-37.
20. Pevzner, P.A., H. Tang, and M.S. Waterman, An Eulerian path approach to DNA fragment assembly. Proceedings of the National Academy of Sciences, 2001. 98(17): p. 9748.
21. Myers, E.W., The fragment assembly string graph. Bioinformatics, 2005. 21(suppl 2): p. ii79-ii85.
22. Chaisson, M.J. and P.A. Pevzner, Short read fragment assembly of bacterial genomes. Genome research, 2008. 18(2): p. 324-330.
23. Zerbino, D.R. and E. Birney, Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome research, 2008. 18(5): p. 821-829.
24. Butler, J., et al., ALLPATHS: de novo assembly of whole-genome shotgun microreads. Genome research, 2008. 18(5): p. 810-820.
25. Li, Y., et al., State of the art de novo assembly of human genomes from massively parallel sequencing data. Human genomics, 2010. 4(4): p. 271-277.
26. Simpson, J.T., et al., ABySS: a parallel assembler for short read sequence data. Genome research, 2009. 19(6): p. 1117.
27. Boetzer, M., et al., Scaffolding pre-assembled contigs using SSPACE. Bioinformatics, 2011. 27(4): p. 578-579.
28. Li, R., et al., SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics, 2009. 25(15): p. 1966-1967.
29. Schneeberger, K., et al., Reference-guided assembly of four diverse Arabidopsis thaliana genomes. Proceedings of the National Academy of Sciences, 2011. 108(25): p. 10249.
30. Bendich, A.J. and K. Drlica, Prokaryotic and eukaryotic chromosomes: what's the difference? Bioessays, 2000. 22(5): p. 481-486.
31. Phil, L., et al., Optical mapping as a routine tool for bacterial genome sequence finishing. BMC genomics, 2007. 8.
32. BRISKA, A., A Software System for Validating and Orienting Sequence Contigs Using Optical Maps.
33. Delcher, A.L., et al., Improved microbial gene identification with GLIMMER. Nucleic acids research, 1999. 27(23): p. 4636-4641.
34. Besemer, J., A. Lomsadze, and M. Borodovsky, GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions. Nucleic acids research, 2001. 29(12): p. 2607-2618.
35. Lowe, T.M. and S.R. Eddy, tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic acids research, 1997. 25(5): p. 0955-964.
36. Lagesen, K., et al., RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic acids research, 2007. 35(9): p. 3100-3108.
37. Needleman, S.B. and C.D. Wunsch, A general method applicable to the search for similarities in the amino acid sequence of two proteins. Journal of molecular biology, 1970. 48(3): p. 443-453.
38. Smith, T.F. and M.S. Waterman, Identification of common molecular subsequences. J Mol Biol, 1981. 147(1): p. 195-7.
39. Altschul, S.F., et al., Basic local alignment search tool. Journal of molecular biology, 1990. 215(3): p. 403-410.
40. Tatusova, T.A. and T.L. Madden, BLAST 2 Sequences, a new tool for comparing protein and nucleotide sequences. FEMS microbiology letters, 1999. 174(2): p. 247-250.
41. Morgulis, A., et al., Database indexing for production MegaBLAST searches. Bioinformatics, 2008. 24(16): p. 1757-1764.
42. Kent, W.J., BLAT--the BLAST-like alignment tool. Genome Res, 2002. 12(4): p. 656-64.
43. Tatusov, R.L., E.V. Koonin, and D.J. Lipman, A genomic perspective on protein families. science, 1997. 278(5338): p. 631-637.
44. Tatusov, R.L., et al., The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res, 2001. 29(1): p. 22-8.
45. O'Hara, C.M., F.W. Brenner, and J.M. Miller, Classification, identification, and clinical significance of Proteus, Providencia, and Morganella. Clinical microbiology reviews, 2000. 13(4): p. 534.
46. Nicolle, L.E., Resistant pathogens in urinary tract infections. Journal of the American Geriatrics Society, 2002. 50: p. 230-235.
47. Lee, I. and J. Liu, Clinical characteristics and risk factors for mortality in Morganella morganii bacteremia. Journal of microbiology, immunology, and infection= Wei mian yu gan ran za zhi, 2006. 39(4): p. 328.
48. Hu, L., et al., Morganella morganii urease: purification, characterization, and isolation of gene sequences. Journal of bacteriology, 1990. 172(6): p. 3073-3080.
49. Gebhart-Mueller, E.Y., P. Mueller, and B. Nixon, Unusual case of postoperative infection caused by< i> Morganella morganii</i>. The Journal of foot and ankle surgery, 1998. 37(2): p. 145-147.
50. Kim, B., et al., Bacteraemia due to tribe Proteeae: a review of 132 cases during a decade (1991-2000). Scandinavian journal of infectious diseases, 2003. 35(2): p. 98-103.
51. Berger, S.A., Proteus bacteraemia in a general hospital 1972-1982. Journal of Hospital Infection, 1985. 6(3): p. 293-298.
52. Watanakunakorn, C. and S.C. Perni, Proteus mirabilis bacteremia: a review of 176 cases during 1980-1992. Scandinavian journal of infectious diseases, 1994. 26(4): p. 361-367.
53. Chen, C.M., et al., Bacterial infection in association with snakebite: A 10-year experience in a northern Taiwan medical center. Journal of Microbiology, Immunology and Infection, 2011.
54. Chang, H.Y., et al., Neonatal Morganella morganii sepsis: a case report and review of the literature. Pediatrics International, 2011. 53(1): p. 121-123.
55. Kim, J.H., et al., Morganella morganii sepsis with massive hemolysis. Journal of Korean medical science, 2007. 22(6): p. 1082.
56. Ghosh, S., et al., Fatal Morganella morganii bacteraemia in a diabetic patient with gas gangrene. Journal of medical microbiology, 2009. 58(7): p. 965-967.
57. McDermott, C. and J.M. Mylotte, Morganella morganii: epidemiology of bacteremic disease. Infection Control, 1984: p. 131-137.
58. Fulton, M.D., The identity of Bacterium columbensis Castellani. Journal of bacteriology, 1943. 46(1): p. 79-82.
59. BRENNER, D.O.N.J., et al., Deoxyribonucleic acid relatedness of Proteus and Providencia species. International Journal of Systematic Bacteriology, 1978. 28(2): p. 269-282.
60. Hickman, F., et al., Unusual groups of Morganella (" Proteus") morganii isolated from clinical specimens: lysine-positive and ornithine-negative biogroups. Journal of clinical microbiology, 1980. 12(1): p. 88-94.
61. Poirel, L., et al., Cloning, sequence analyses, expression, and distribution of ampC-ampR from Morganella morganii clinical isolates. Antimicrobial agents and chemotherapy, 1999. 43(4): p. 769-776.
62. Matsen, J.M., et al., Characterization of indole-positive Proteus mirabilis. Applied and Environmental Microbiology, 1972. 23(3): p. 592.
63. Kelly, M.T. and C. Leicester, Evaluation of the Autoscan Walkaway system for rapid identification and susceptibility testing of gram-negative bacilli. Journal of clinical microbiology, 1992. 30(6): p. 1568.
64. Philippon, A., G. Arlet, and G.A. Jacoby, Plasmid-determined AmpC-type β-lactamases. Antimicrobial agents and chemotherapy, 2002. 46(1): p. 1-11.
65. Flannery, E.L., L. Mody, and H.L.T. Mobley, Identification of a modular pathogenicity island that is widespread among urease-producing uropathogens and shares features with a diverse group of mobile elements. Infection and immunity, 2009. 77(11): p. 4887.
66. Song, W., et al., Chromosome-encoded AmpC and CTX-M extended-spectrum β-lactamases in clinical isolates of Proteus mirabilis from Korea. Antimicrobial agents and chemotherapy, 2011. 55(4): p. 1414-1419.
67. Harada, S., et al., Chromosomal Integration and Location on IncT Plasmids of the blaCTX-M-2 Gene in Proteus mirabilis Clinical Isolates. Antimicrobial agents and chemotherapy, 2012. 56(2): p. 1093-1096.
68. Toleman, M.A. and T.R. Walsh, Combinatorial events of insertion sequences and ICE in Gram‐negative bacteria. FEMS microbiology reviews, 2011.
69. Flannery, E.L., S.M. Antczak, and H.L.T. Mobley, Self-transmissibility of the integrative and conjugative element ICEPm1 between clinical isolates requires a functional integrase, relaxase, and Type IV secretion system. Journal of bacteriology, 2011. 193(16): p. 4104.
70. Shi, D.S., et al., Identification of bla KPC-2 on different plasmids of three Morganella morganii isolates. European Journal of Clinical Microbiology & Infectious Diseases, 2011: p. 1-7.
71. Rojas, L., et al., Integron presence in a multiresistant< i> Morganella morganii</i> isolate. International journal of antimicrobial agents, 2006. 27(6): p. 505-512.
72. Livermore, D.M. and N. Woodford, The β-lactamase threat in Enterobacteriaceae,< i> Pseudomonas</i> and< i> Acinetobacter</i>. TRENDS in Microbiology, 2006. 14(9): p. 413-420.
73. Cantón, R. and T.M. Coque, The CTX-M [beta]-lactamase pandemic. Current opinion in microbiology, 2006. 9(5): p. 466-475.
74. Flannery, E.L., L. Mody, and H.L.T. Mobley, Identification of a modular pathogenicity island that is widespread among urease-producing uropathogens and shares features with a diverse group of mobile elements. Infection and immunity, 2009. 77(11): p. 4887-4894.
75. Macleod, S.M. and D.J. Stickler, Species interactions in mixed-community crystalline biofilms on urinary catheters. Journal of medical microbiology, 2007. 56(11): p. 1549-1557.
76. Pearson, M.M., et al., Complete genome sequence of uropathogenic Proteus mirabilis, a master of both adherence and motility. Journal of bacteriology, 2008. 190(11): p. 4027.
77. Nuccio, S.P. and A.J. Baumler, Evolution of the chaperone/usher assembly pathway: fimbrial classification goes Greek. Microbiology and Molecular Biology Reviews, 2007. 71(4): p. 551.
78. Rocha, S.P.D., J.S. Pelayo, and W.P. Elias, Fimbriae of uropathogenic Proteus mirabilis. FEMS Immunology & Medical Microbiology, 2007. 51(1): p. 1-7.
79. Nielubowicz, G.R. and H.L.T. Mobley, Host–pathogen interactions in urinary tract infection. Nature Reviews Urology, 2010. 7(8): p. 430-441.
80. Jacobsen, S.M. and M.E. Shirtliff, Proteus mirabilis biofilms and catheter-associated urinary tract infections. Virulence, 2011. 2(5).
81. Jacobsen, S., et al., Complicated catheter-associated urinary tract infections due to Escherichia coli and Proteus mirabilis. Clinical microbiology reviews, 2008. 21(1): p. 26-59.
82. Heermann, R. and T. Fuchs, Comparative analysis of the Photorhabdus luminescens and the Yersinia enterocolitica genomes: uncovering candidate genes involved in insect pathogenicity. BMC genomics, 2008. 9(1): p. 40.
83. Garsin, D.A., Ethanolamine utilization in bacterial pathogens: roles and regulation. Nature Reviews Microbiology, 2010. 8(4): p. 290-295.
84. Toleman, M.A. and T.R. Walsh, Combinatorial events of insertion sequences and ICE in Gram‐negative bacteria. FEMS microbiology reviews, 2011. 35(5): p. 912-935.
85. Harada, S., et al., Chromosomally encoded blaCMY-2 located on a novel SXT/R391-related integrating conjugative element in a Proteus mirabilis clinical isolate. Antimicrobial agents and chemotherapy, 2010. 54(9): p. 3545-3550.
86. Mohd-Zain, Z., et al., Transferable antibiotic resistance elements in Haemophilus influenzae share a common evolutionary origin with a diverse family of syntenic genomic islands. Journal of bacteriology, 2004. 186(23): p. 8114-8122.
87. Coetzee, J., N. DATTA, and R. Hedges, R factors from Proteus rettgeri. Journal of general microbiology, 1972. 72(3): p. 543-552.
88. Beaber, J.W., B. Hochhut, and M.K. Waldor, Genomic and functional analyses of SXT, an integrating antibiotic resistance gene transfer element derived from Vibrio cholerae. Journal of bacteriology, 2002. 184(15): p. 4259-4269.
89. Böltner, D., et al., R391: a conjugative integrating mosaic comprised of phage, plasmid, and transposon elements. Journal of bacteriology, 2002. 184(18): p. 5158-5169.
90. Wozniak, R.A.F., et al., Comparative ICE genomics: insights into the evolution of the SXT/R391 family of ICEs. PLoS genetics, 2009. 5(12): p. e1000786.
91. Li, R., et al., SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics, 2009. 25(15): p. 1966.
92. Schwartz, D.C., et al., Ordered restriction maps of Saccharomyces cerevisiae chromosomes constructed by optical mapping. Science (New York, NY), 1993. 262(5130): p. 110.
93. Lowe, T.M. and S.R. Eddy, tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic acids research, 1997. 25(5): p. 0955.
94. Lagesen, K., et al., RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic acids research, 2007. 35(9): p. 3100.
95. Gao, F. and C.T. Zhang, Ori-Finder: a web-based system for finding oriCs in unannotated bacterial genomes. BMC bioinformatics, 2008. 9(1): p. 79.
96. Tatusov, R.L., et al., The COG database: an updated version includes eukaryotes. BMC bioinformatics, 2003. 4(1): p. 41.
97. Rice, P., I. Longden, and A. Bleasby, EMBOSS: the European molecular biology open software suite. Trends in genetics, 2000. 16(6): p. 276-277.
98. Maniatis, T., Molecular cloning: a laboratory manual/J. Sambrook, EF Fritsch, T. Maniatis1989: New York: Cold Spring Harbor Laboratory Press.
99. Cock, P.J.A., et al., The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic acids research, 2010. 38(6): p. 1767-1771.
100. Zhou, H., et al., Genomic analysis of the multidrug-resistant Acinetobacter baumannii strain MDR-ZJ06 widely spread in China. Antimicrobial agents and chemotherapy, 2011. 55(10): p. 4506-4512.
101. Lee, C.M., et al., Estimation of 16S rRNA gene copy number in several probiotic Lactobacillus strains isolated from the gastrointestinal tract of chicken. FEMS microbiology letters, 2008. 287(1): p. 136-141.
102. Barnaud, G., et al., Cloning and sequencing of the gene encoding the AmpC β‐lactamase of Morganella morganii. FEMS microbiology letters, 1997. 148(1): p. 15-20.
103. Power, P., et al., Cefotaxime-hydrolysing beta lactamases in Morganella morganii. European Journal of Clinical Microbiology & Infectious Diseases, 1999. 18(10): p. 743-747.
104. Miriagou, V., et al., Providencia stuartii with VIM-1 metallo-β-lactamase. Journal of antimicrobial chemotherapy, 2007. 60(1): p. 183.
105. Lincopan, N., et al., Enterobacteria producing extended-spectrum β-lactamases and IMP-1 metallo-β-lactamases isolated from Brazilian hospitals. Journal of medical microbiology, 2006. 55(11): p. 1611-1613.
106. Pearson, M.M. and H.L.T. Mobley, Repression of motility during fimbrial expression: identification of 14 mrpJ gene paralogues in Proteus mirabilis. Molecular microbiology, 2008. 69(2): p. 548-558.
107. Sabri, M., S. Houle, and C.M. Dozois, Roles of the extraintestinal pathogenic Escherichia coli ZnuACB and ZupT zinc transporters during urinary tract infection. Infection and immunity, 2009. 77(3): p. 1155.
108. Nielubowicz, G.R., S.N. Smith, and H.L.T. Mobley, Zinc uptake contributes to motility and provides a competitive advantage to Proteus mirabilis during experimental urinary tract infection. Infection and immunity, 2010. 78(6): p. 2823-2833.
109. Pearson, M.M. and H.L.T. Mobley, The type III secretion system of Proteus mirabilis HI4320 does not contribute to virulence in the mouse model of ascending urinary tract infection. Journal of medical microbiology, 2007. 56(10): p. 1277-1283.
110. Massé, E. and S. Gottesman, A small RNA regulates the expression of genes involved in iron metabolism in Escherichia coli. Proceedings of the National Academy of Sciences, 2002. 99(7): p. 4620.
111. Kilcoyne, M., et al., Structural investigation of the O-specific polysaccharides of Morganella morganii consisting of two higher sugars. Carbohydrate Research, 2002. 337(18): p. 1697-1702.
112. Young, N.M., et al., Structural characterization and MHCII-dependent immunological properties of the zwitterionic O-chain antigen of Morganella morganii. Glycobiology, 2011. 21(10): p. 1266-1276.
113. Vörös, S. and B. Senior, New O antigens of Morganella morganii and the relationships between haemolysin production. O antigens and morganocin types of strains. Acta microbiologica Hungarica, 1990. 37(4): p. 341.
114. Makela, P. and H. Mayer, Enterobacterial common antigen. Microbiology and Molecular Biology Reviews, 1976. 40(3): p. 591.
115. Cady, K.C., et al., Prevalence, conservation and functional analysis of Yersinia and Escherichia CRISPR regions in clinical Pseudomonas aeruginosa isolates. Microbiology, 2011. 157(2): p. 430-437.
116. Deveau, H., J.E. Garneau, and S. Moineau, CRISPR/Cas system and its role in phage-bacteria interactions. Annual review of microbiology, 2010. 64: p. 475-493.
117. Rodriguez-Siek, K.E., et al., Comparison of Escherichia coli isolates implicated in human urinary tract infection and avian colibacillosis. Microbiology, 2005. 151(6): p. 2097-2110.
118. Welch, R.A., Identification of two different hemolysin determinants in uropathogenic Proteus isolates. Infection and immunity, 1987. 55(9): p. 2183-2190.
119. Koronakis, V., et al., The secreted hemolysins of Proteus mirabilis, Proteus vulgaris, and Morganella morganii are genetically related to each other and to the alpha-hemolysin of Escherichia coli. Journal of bacteriology, 1987. 169(4): p. 1509-1515.
120. Fraser, G.M., et al., Swarming-coupled expression of the Proteus mirabilis hpmBA haemolysin operon. Microbiology, 2002. 148(7): p. 2191-2201.
121. Eberspacher, B., et al., Functional similarity between the haemolysins of Escherichia coli and Morganella morganii. Journal of medical microbiology, 1990. 33(3): p. 165-170.
122. O'Hara, C.M., F.W. Brenner, and J.M. Miller, Classification, identification, and clinical significance of Proteus, Providencia, and Morganella. Clinical microbiology reviews, 2000. 13(4): p. 534-546.
123. Griffith, D.P., D. Musher, and C. Itin, Urease. The primary cause of infection-induced urinary stones. Investigative urology, 1976. 13(5): p. 346.
124. Jones, B., et al., Construction of a urease-negative mutant of Proteus mirabilis: analysis of virulence in a mouse model of ascending urinary tract infection. Infection and immunity, 1990. 58(4): p. 1120.
125. Tsoy, O., D. Ravcheev, and A. Mushegian, Comparative genomics of ethanolamine utilization. Journal of bacteriology, 2009. 191(23): p. 7157-7164.
126. Rodionov, D.A., et al., Comparative genomics of the vitamin B12 metabolism and regulation in prokaryotes. Journal of Biological Chemistry, 2003. 278(42): p. 41148-41159.
127. Zhang, Y., et al., Comparative genomic analyses of nickel, cobalt and vitamin B12 utilization. BMC genomics, 2009. 10(1): p. 78.
128. Srikumar, S. and T.M. Fuchs, Ethanolamine utilization contributes to proliferation of Salmonella enterica serovar Typhimurium in food and in nematodes. Applied and Environmental Microbiology, 2011. 77(1): p. 281-290.
129. Vanaporn, M., et al., Superoxide dismutase C is required for intracellular survival and virulence of Burkholderia pseudomallei. Microbiology, 2011. 157(8): p. 2392.
130. Model, P., G. Jovanovic, and J. Dworkin, The Escherichia coli phage‐shock‐protein (psp) operon. Molecular microbiology, 1997. 24(2): p. 255-261.
131. Jovanovic, G., et al., Properties of the phage-shock-protein (Psp) regulatory complex that govern signal transduction and induction of the Psp response in Escherichia coli. Microbiology, 2010. 156(10): p. 2920-2932.
132. Darwin, A.J., The phage‐shock‐protein response. Molecular microbiology, 2005. 57(3): p. 621-628.
133. Samuel, A., D.H. Julie, and T. Hervé, Improving pan-genome annotation using whole genome multiple alignment. BMC bioinformatics. 12.
134. Dutta, S. and A. Narang, Early onset neonatal sepsis due to Morganella morganii. Indian pediatrics, 2004. 41(11): p. 1155-1157.
135. Sinha, A.K., et al., EARLY ONSET MORGANELLA MORGANII SEPSIS IN A NEWBORN INFANT WITH EMERGENCE OF CEPHALOSPORIN RESISTANCE CAUSED BY DEREPRESSION OF AMPC [beta]-LACTAMASE PRODUCTION. The Pediatric infectious disease journal, 2006. 25(4): p. 376.
136. Falagas, M., et al., Morganella morganii infections in a general tertiary hospital. Infection, 2006. 34(6): p. 315-321.
137. Medeiros, A.A., Evolution and dissemination of β-lactamases accelerated by generations of β-lactam antibiotics. Clinical Infectious Diseases, 1997. 24(Supplement 1): p. S19.
138. Marmur, J. and P. Doty, Determination of the base composition of deoxyribonucleic acid from its thermal denaturation temperature. Journal of molecular biology, 1962. 5(1): p. 109-118.
139. Vanyushin, B., A view of an elemental naturalist at the DNA world (base composition, sequences, methylation). Biochemistry (Moscow), 2007. 72(12): p. 1289-1298.
140. Cornelis, G., M. Van Bouchaute, and G. Wauters, Plasmid-encoded lysine decarboxylation in Proteus morganii. Journal of clinical microbiology, 1981. 14(4): p. 365-369.
141. Janda, J.M., et al., Biochemical investigations of biogroups and subspecies of Morganella morganii. Journal of clinical microbiology, 1996. 34(1): p. 108-113.
142. Jensen, K.T., et al., Recognition of Morganella Subspecies, with Proposal of Morganella morganii subsp. morganii subsp. nov. and Morganella morganii subsp. sibonii subsp. nov. International Journal of Systematic Bacteriology, 1992. 42(4): p. 613-620.
143. Senior, B., Media and tests to simplify the recognition and identification of members of the Proteeae. Journal of medical microbiology, 1997. 46(1): p. 39-44.
144. Sheets, J.J., et al., Insecticidal Toxin Complex Proteins from Xenorhabdus nematophilus. Journal of Biological Chemistry, 2011. 286(26): p. 22742.
145. Sergeant, M., et al., Interactions of insecticidal toxin gene products from Xenorhabdus nematophilus PMFI296. Applied and Environmental Microbiology, 2003. 69(6): p. 3344-3349.
146. Liu, J.R., et al., Molecular Cloning and Characterization of an Insecticidal Toxin from Pseudomonas taiwanensis. Journal of agricultural and food chemistry, 2010.
147. Dowling, A. and N.R. Waterfield, Insecticidal toxins from Photorhabdus bacteria and their potential use in agriculture. Toxicon, 2007. 49(4): p. 436-451.
148. Blackburn, M., et al., A novel insecticidal toxin from Photorhabdus luminescens, toxin complex a (Tca), and its histopathological effects on the midgut of Manduca sexta. Applied and Environmental Microbiology, 1998. 64(8): p. 3036-3041.
149. Yeates, T.O., C.S. Crowley, and S. Tanaka, Bacterial microcompartment organelles: protein shell structure and evolution. Annual review of biophysics, 2010. 39: p. 185-205.
150. Izoré, T., V. Job, and A. Dessen, Biogenesis, regulation, and targeting of the type III secretion system. Structure, 2011. 19(5): p. 603-612.
151. Khor, C.C. and M.L. Hibberd, Host–pathogen interactions revealed by human genome-wide surveys. Trends in genetics, 2012.
152. Kline, T., et al., The Type III Secretion System as a Source of Novel Antibacterial Drug Targets. Current Drug Targets, 2012. 13(3): p. 338-351.
153. Chanumolu, S.K., C. Rout, and R.S. Chauhan, UniDrug-Target: A Computational Tool to Identify Unique Drug Targets in Pathogenic Bacteria. PloS one, 2012. 7(3): p. e32833.
154. Kvist, M., V. Hancock, and P. Klemm, Inactivation of efflux pumps abolishes bacterial biofilm formation. Applied and Environmental Microbiology, 2008. 74(23): p. 7376-7382.
155. May, T., A. Ito, and S. Okabe, Induction of multidrug resistance mechanism in Escherichia coli biofilms by interplay between tetracycline and ampicillin resistance genes. Antimicrobial agents and chemotherapy, 2009. 53(11): p. 4628-4639.
156. Klemm, P., R.M. Vejborg, and V. Hancock, Prevention of bacterial adhesion. Applied microbiology and biotechnology, 2010. 88(2): p. 451-459.