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Chen YT, Peng HL, Shia WC, Hsu FR, Ken CF, Tsao YM, Chen CH, Liu CE, Hsieh MF, Chen HC, Tang CY, Ku TH. Whole-genome sequencing and identification of Morganella morganii KT pathogenicity-related genes. BMC Genomics 2012; 13 Suppl 7:S4. [PMID: 23282187 PMCID: PMC3521468 DOI: 10.1186/1471-2164-13-s7-s4] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND The opportunistic enterobacterium, Morganella morganii, which can cause bacteraemia, is the ninth most prevalent cause of clinical infections in patients at Changhua Christian Hospital, Taiwan. The KT strain of M. morganii was isolated during postoperative care of a cancer patient with a gallbladder stone who developed sepsis caused by bacteraemia. M. morganii is sometimes encountered in nosocomial settings and has been causally linked to catheter-associated bacteriuria, complex infections of the urinary and/or hepatobiliary tracts, wound infection, and septicaemia. M. morganii infection is associated with a high mortality rate, although most patients respond well to appropriate antibiotic therapy. To obtain insights into the genome biology of M. morganii and the mechanisms underlying its pathogenicity, we used Illumina technology to sequence the genome of the KT strain and compared its sequence with the genome sequences of related bacteria. RESULTS The 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. Moreover, organisation of the 19 genes of the eut operon differs from that found in the other non-Proteeae enterobacterial genomes. CONCLUSIONS This 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.
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Affiliation(s)
- Yu-Tin Chen
- Department of Computer Science, National Tsing Hua University, 101, Section 2, Kuang-Fu Rd., Hsinchu, Taiwan
| | - Hwei-Ling Peng
- Department of Biological Science and Technology, National Chiao Tung University, 1001, University Road, Hsinchu, Taiwan
| | - Wei-Chung Shia
- Cancer Research Center, Changhua Christian Hospital, 135, Nanhsiao St., Changhua, Taiwan
| | - Fang-Rong Hsu
- Master's Program in Biomedical Informatics and Biomedical Engineering, Feng Chia University, 100 Wenhwa Rd., Taichung, Taiwan
- Department of Information Engineering and Computer Sciences, Feng Chia University, 100 Wenhwa Rd., Taichung, Taiwan
| | - Chuian-Fu Ken
- Institute of Biotechnology, National Changhua University of Education, 2 Shi-Da Rd., Changhua, Taiwan
| | - Yu-Ming Tsao
- Department of Anesthesiology, Changhua Christian Hospital, 135, Nanhsiao St., Changhua, Taiwan
| | - Chang-Hua Chen
- The Division of Infectious Diseases, Department of Internal Medicine, Changhua Christian Hospital, 135, Nanhsiao St., Changhua, Taiwan
| | - Chun-Eng Liu
- The Division of Infectious Diseases, Department of Internal Medicine, Changhua Christian Hospital, 135, Nanhsiao St., Changhua, Taiwan
| | - Ming-Feng Hsieh
- Department of Computer Science, National Tsing Hua University, 101, Section 2, Kuang-Fu Rd., Hsinchu, Taiwan
| | - Huang-Chi Chen
- Division of Critical Care Medicine, Department of Internal Medicine, Changhua Christian Hospital, 135, Nanhsiao St., Changhua, Taiwan
| | - Chuan-Yi Tang
- Department of Computer Science, National Tsing Hua University, 101, Section 2, Kuang-Fu Rd., Hsinchu, Taiwan
- Department of Computer Science, Providence University, 200, Chung-Chi Rd., Taichung, Taiwan
| | - Tien-Hsiung Ku
- Department of Anesthesiology, Changhua Christian Hospital, 135, Nanhsiao St., Changhua, Taiwan
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Ruiz JC, D'Afonseca V, Silva A, Ali A, Pinto AC, Santos AR, Rocha AAMC, Lopes DO, Dorella FA, Pacheco LGC, Costa MP, Turk MZ, Seyffert N, Moraes PMRO, Soares SC, Almeida SS, Castro TLP, Abreu VAC, Trost E, Baumbach J, Tauch A, Schneider MPC, McCulloch J, Cerdeira LT, Ramos RTJ, Zerlotini A, Dominitini A, Resende DM, Coser EM, Oliveira LM, Pedrosa AL, Vieira CU, Guimarães CT, Bartholomeu DC, Oliveira DM, Santos FR, Rabelo ÉM, Lobo FP, Franco GR, Costa AF, Castro IM, Dias SRC, Ferro JA, Ortega JM, Paiva LV, Goulart LR, Almeida JF, Ferro MIT, Carneiro NP, Falcão PRK, Grynberg P, Teixeira SMR, Brommonschenkel S, Oliveira SC, Meyer R, Moore RJ, Miyoshi A, Oliveira GC, Azevedo V. Evidence for reductive genome evolution and lateral acquisition of virulence functions in two Corynebacterium pseudotuberculosis strains. PLoS One 2011; 6:e18551. [PMID: 21533164 PMCID: PMC3078919 DOI: 10.1371/journal.pone.0018551] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2010] [Accepted: 03/11/2011] [Indexed: 02/02/2023] Open
Abstract
Background Corynebacterium pseudotuberculosis, a Gram-positive, facultative intracellular pathogen, is the etiologic agent of the disease known as caseous lymphadenitis (CL). CL mainly affects small ruminants, such as goats and sheep; it also causes infections in humans, though rarely. This species is distributed worldwide, but it has the most serious economic impact in Oceania, Africa and South America. Although C. pseudotuberculosis causes major health and productivity problems for livestock, little is known about the molecular basis of its pathogenicity. Methodology and Findings We characterized two C. pseudotuberculosis genomes (Cp1002, isolated from goats; and CpC231, isolated from sheep). Analysis of the predicted genomes showed high similarity in genomic architecture, gene content and genetic order. When C. pseudotuberculosis was compared with other Corynebacterium species, it became evident that this pathogenic species has lost numerous genes, resulting in one of the smallest genomes in the genus. Other differences that could be part of the adaptation to pathogenicity include a lower GC content, of about 52%, and a reduced gene repertoire. The C. pseudotuberculosis genome also includes seven putative pathogenicity islands, which contain several classical virulence factors, including genes for fimbrial subunits, adhesion factors, iron uptake and secreted toxins. Additionally, all of the virulence factors in the islands have characteristics that indicate horizontal transfer. Conclusions These particular genome characteristics of C. pseudotuberculosis, as well as its acquired virulence factors in pathogenicity islands, provide evidence of its lifestyle and of the pathogenicity pathways used by this pathogen in the infection process. All genomes cited in this study are available in the NCBI Genbank database (http://www.ncbi.nlm.nih.gov/genbank/) under accession numbers CP001809 and CP001829.
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Affiliation(s)
- Jerônimo C. Ruiz
- Research Center René Rachou, Oswaldo Cruz Foundation, Belo Horizonte, Minas Gerais, Brazil
| | - Vívian D'Afonseca
- Department of General Biology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Artur Silva
- Department of Genetics, Federal University of Pará, Belém, Pará, Brazil
| | - Amjad Ali
- Department of General Biology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Anne C. Pinto
- Department of General Biology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Anderson R. Santos
- Department of General Biology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Aryanne A. M. C. Rocha
- Department of General Biology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Débora O. Lopes
- Health Sciences Center, Federal University of São João Del Rei, Divinópilis, Minas Gerais, Brazil
| | - Fernanda A. Dorella
- Department of General Biology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Luis G. C. Pacheco
- Department of General Biology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- Department of Biointeraction Sciences, Federal University of Bahia, Salvador, Bahia, Brazil
| | - Marcília P. Costa
- Department of Veterinary Medicine, State University of Ceará, Fortaleza, Ceará, Brazil
| | - Meritxell Z. Turk
- Department of General Biology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Núbia Seyffert
- Department of General Biology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Pablo M. R. O. Moraes
- Department of General Biology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Siomar C. Soares
- Department of General Biology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Sintia S. Almeida
- Department of General Biology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Thiago L. P. Castro
- Department of General Biology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Vinicius A. C. Abreu
- Department of General Biology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Eva Trost
- Department of Genetics, University of Bielefeld, CeBiTech, Bielefeld, Nordrhein-Westfale, Germany
| | - Jan Baumbach
- Department of Computer Science, Max-Planck-Institut für Informatik, Saarbrücken, Saarlan, Germany
| | - Andreas Tauch
- Department of Genetics, University of Bielefeld, CeBiTech, Bielefeld, Nordrhein-Westfale, Germany
| | | | - John McCulloch
- Department of Genetics, Federal University of Pará, Belém, Pará, Brazil
| | | | | | - Adhemar Zerlotini
- Research Center René Rachou, Oswaldo Cruz Foundation, Belo Horizonte, Minas Gerais, Brazil
| | - Anderson Dominitini
- Research Center René Rachou, Oswaldo Cruz Foundation, Belo Horizonte, Minas Gerais, Brazil
| | - Daniela M. Resende
- Research Center René Rachou, Oswaldo Cruz Foundation, Belo Horizonte, Minas Gerais, Brazil
- Department of Pharmaceutical Sciences, Federal University of Ouro Preto, Ouro Preto, Minas Gerais, Brazil
| | - Elisângela M. Coser
- Research Center René Rachou, Oswaldo Cruz Foundation, Belo Horizonte, Minas Gerais, Brazil
| | - Luciana M. Oliveira
- Department of Phisics, Federal University of Ouro Preto, Ouro Preto, Minas Gerais, Brazil
| | - André L. Pedrosa
- Department of Pharmaceutical Sciences, Federal University of Ouro Preto, Ouro Preto, Minas Gerais, Brazil
- Department of Biological Sciences, Federal University of Triangulo Mineiro, Uberaba, Minas Gerais, Brazil
| | - Carlos U. Vieira
- Department of Genetics and Biochemistry, Federal University of Uberlândia, Uberlândia, Minas Gerais, Brazil
| | - Cláudia T. Guimarães
- Brazilian Agricultural Research Corporation (EMBRAPA), Sete Lagoas, Minas Gerais, Brazil
| | - Daniela C. Bartholomeu
- Department of Biochemistry and Immunology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Diana M. Oliveira
- Department of Veterinary Medicine, State University of Ceará, Fortaleza, Ceará, Brazil
| | - Fabrício R. Santos
- Department of General Biology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Élida Mara Rabelo
- Department of Parasitology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Francisco P. Lobo
- Department of Biochemistry and Immunology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Glória R. Franco
- Department of Biochemistry and Immunology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Ana Flávia Costa
- Department of General Biology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Ieso M. Castro
- Department of Pharmacy, Federal University of Ouro Preto, Ouro Preto, Minas Gerais, Brazil
| | - Sílvia Regina Costa Dias
- Department of Parasitology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Jesus A. Ferro
- Department of Technology, State University of São Paulo, Jaboticabal, São Paulo, Brazil
| | - José Miguel Ortega
- Department of Biochemistry and Immunology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Luciano V. Paiva
- Department of Chemistry, Federal University of Lavras, Lavras, Minas Gerais, Brazil
| | - Luiz R. Goulart
- Department of Genetics and Biochemistry, Federal University of Uberlândia, Uberlândia, Minas Gerais, Brazil
| | - Juliana Franco Almeida
- Department of Genetics and Biochemistry, Federal University of Uberlândia, Uberlândia, Minas Gerais, Brazil
| | - Maria Inês T. Ferro
- Department of Technology, State University of São Paulo, Jaboticabal, São Paulo, Brazil
| | - Newton P. Carneiro
- Brazilian Agricultural Research Corporation (EMBRAPA), Sete Lagoas, Minas Gerais, Brazil
| | - Paula R. K. Falcão
- Brazilian Agricultural Research Corporation (EMBRAPA), Campinas, São Paulo, Brazil
| | - Priscila Grynberg
- Department of Biochemistry and Immunology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Santuza M. R. Teixeira
- Department of Biochemistry and Immunology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Sérgio Brommonschenkel
- Department of Plant Pathology, Federal University of Viçosa, Viçosa, Minas Gerais, Brazil
| | - Sérgio C. Oliveira
- Department of Biochemistry and Immunology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Roberto Meyer
- Department of Biointeraction Sciences, Federal University of Bahia, Salvador, Bahia, Brazil
| | | | - Anderson Miyoshi
- Department of General Biology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Guilherme C. Oliveira
- Research Center René Rachou, Oswaldo Cruz Foundation, Belo Horizonte, Minas Gerais, Brazil
- Center of Excellence in Bioinformatics, National Institute of Science and Technology, Research Center René Rachou, Oswaldo Cruz Foundation, Belo Horizonte, Minas Gerais, Brazil
| | - Vasco Azevedo
- Department of General Biology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- * E-mail:
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