Abstract
Bacterial strains belonging to family Enterobacteriaceae are well-established enteric pathogens of humans and animals which are the major cause of mortality worldwide. So to deal with these infections, it is necessary to identify the disease-causing pathogens along with their virulence mechanism. The characterization and detection of these pathogens rely on conventional culturing and biochemical techniques. But these conventional techniques are low sensitive and time intense. This led to search for more rapid, sensitive, and advanced technique for their detection. In the present scenario, the molecular methods are most commonly applied to identify the pathogenic bacterial strains. The molecular methods include DNA-based methods, such as restriction endonuclease analysis of genomic and plasmid DNA, plasmid profiling, chromosomal DNA profiling using pulsed field gel electrophoresis, polymerase chain reaction (PCR)-based methods, 16S rRNA sequencing methods, polyphasic taxonomic approaches, etc. These are the more rapid and more sensitive techniques which overcome the issues of identification by conventional techniques. Hence, these techniques are considered the most promising for bacterial identification.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Reference
Kramer MN, Coto D, Weidner JD (2005) The science of recalls. Meat Sci 71:158–163
Invitski D, Abdel-Hamid I, Atanasov P, Wilkins E (1999) Biosensors for the detection of pathogenic bacteria. Biosens Bioelectron 14:599–624
Hook EW (1990) Salmonella species (including typhoid fever). In: Mandell GL, Douglas RG, Bennett JE (eds) Principles and practices of infectious diseases. Churchill Livingstone, New York, pp 1700–1715
Vidic J, Manzano M, Chang CM, Jaffrezic-Renault N (2018) Advanced biosensors for detection of pathogens related to livestock and poultry. Vet Res 48:11
Dougan G, Huett A, Clare S (2002) Vaccines against human enteric bacterial pathogens. Br Med Bull 62:113–123
Koneman EW, Allen SD, Janda WM, Schreckenberger PC, Winn WC (1997) Diagnostic microbiology, 5th edn. Lipponcott Raven Publishers Philadelphia, New York, pp 50–56
Wong HC, Ho CY, Kuo LP, Wang TK, Lee CL, Shih YC (1999) Ribotyping of the Vibrio paraheamolyticus isolates obtained from food poisoning outbreaks in Taiwan. Microbiol Immunol 43:631–636
de Boer RF, Ott A, Kesztyus B, Kooistra-Smid A (2010) Improved detection of five major gastrointestinal pathogens by use of a molecular screening approach. J Clin Microbiol 48:4140–4146
Hobson NS, Tothill I, Turner AP (1996) Microbial detection. Biosens Bioelectron 11:455–477
Fournier-Wirth C, Deschaseaux M, Defer C, Godreuil S, Carrière C, Bertrand X, Tunez V, Schneider T, Coste J, Morel P (2006) Evaluation of the enhanced bacterial detection system for screening of contaminated platelets. Transfusion 46:220–224
Seno M, Sakaki M, Ogawa H (2004) Genotypic diversity of Salmonella enteritidis isolates from sporadic patients in limited area during one year. J Infect 49:291–296
Tekeli A, Erdem B, Sahin F, Koyuncu E, Karasartova D et al (2006) Plasmid profiles and randomly amplified polymorphic DNA analysis of Salmonella enterica serotype Enteritidis strains from outbreaks and sporadic cases in Turkey. New Microbiol 29:251–260
Kilic A, Bedir O, Kocak N, Levent B, Eyigun CP et al (2010) Analysis of an outbreak of Salmonella enteritidis by repetitive-sequence-based PCR and pulsed-field gel electrophoresis. Intern Med 49:36–46
Us E, Erdem B, Tekeli A, Gerceker D, Saran B et al (2011) Investigation of Salmonella serotype enteritidis isolates by plasmid profile analysis and pulsed-field gel electrophoresis. Microbiyol Bul 45:210–222
Merino LA, Ronconi MC, Navia MM, Ruiz J, Sierra JM et al (2003) Analysis of the clonal relationship among clinical isolates of Salmonella enterica serovar Infantis by different typing methods. Rev Inst Med Trop Sao Paulo 45:119–123
Almeida PF, Almeida RCC (2000) A PCR protocol using inl gene as a target for specific detection of Listeria monocytogenes. Food Control 11:97–101
Singh A, Goering RV, Simjee S, Foley SL, Zervos MJ (2006) Application of molecular techniques to the study of hospital infection. Clin Microbiol Rev 19:512–530
Towner KJ, Cockkayne E (1995) Molecular methods for microbial identification typing, 1st edn. Chapman & Hall, Ltd, London, pp 3–10
Ranjbar R, Hosseini MJ, Kaffashian AR, Farshad S (2010) An outbreak of shigellosis due to serotype 3a in a prison in Iran. Arch Iran Med 11:413–416
Vaneechoutte M, Verschraegen G, Struelens MJ (1997) Typing of Staphylococcus aureus and Staphylococcus epidermidis strains by PCR analysis of inter-IS256 spacer length polymorphisms. J Clin Microbiol 35:2580–2587
Khan AA, Nawaz MS, Khan SA, Cerniglia CE (2000) Detection of multidrug-resistant Salmonella typhimurium DT104 by multiplex polymerase chain reaction. FEMS Microbiol Lett 82:355–360
Islam M, Hossain M, Hasan M, Rahman M, Fuchs G, Mahalanabis D et al (1998) Detection of Shigella from stools of dysentery patients by culture and polymerase chain reaction techniques. J Diarrhoeal Dis Res 16:248–251
Kulkarni SP, Lever S, Logan JM, Lawson AJ, Stanley J, Shafi MS (2002) Detection of Campylobacter species: a comparison of culture and polymerase chain reaction based methods. J Clin Pathol 55:749–753
Lampel K, Orlandi P, Kornegay L (2000) Improved template preparation for PCR-based assays for detection of food-borne bacterial pathogens. Appl Environ Microbiol 66:4539–4542
Radstrom P, WA AL-S (1998) Capacity of nine thermostable DNA polymerases to mediate DNA amplification in the presence of PCR inhibiting samples. Appl Environ Microbiol 64:3748–3753
Schweitzer B, Kingsmore S (2001) Combining nucleic acid amplification and detection. Curr Opin Biotechnol 12:21–27
Christine CG (2004) Life beyond PCR: alternative target amplification technologies for the diagnosis of infectious diseases, part II. Clin Microbiol Newsl 26:129–136
Schwartz DC, Cantor CR (1984) Separation of yeast chromosome-sized DNAs by pulsed field gradient gel electrophoresis. Cell 37:67–75
Finney M (2000) Pulsed field gel electrophoresis. Curr Protoc Mol Biol 51:2.5B.1–2.5B.9
Liebisch B, Schwarz S (1996) Molecular typing of Salmonella enterica sub sp. enterica serovar Enteritidis isolates. J Med Microbiol 44:52–59
Mitsuda T, Muto T, Yamada M, Kobayashi N, Toba M, Aihara Y, Ito A, Yokota S (1998) Epidemiological study of a food-borne outbreak of enterotoxigenic Escherichia coli O25: NM by pulsed-field gel electrophoresis and randomly amplified polymorphic DNA analysis. J Clin Microbiol 36:652–656
Philippe B, Lalande V, Salauze B, Burghoffer B, Avesani V, Delmée M, Rossier A, Barbut F, Petit JC (2000) Comparison of PCR-Ribotyping, arbitrarily primed PCR, and pulsed-field gel electrophoresis for typing Clostridium difficile. J Clin Microbiol 38:2484–2487
Ahmed R, Soule G, Demczuk WH, Clark C, Khakhria R, Ratnam S, Marshall S, Ng LK, Woodward DL, Johnson WM, Rodgers FG (2000) Epidemiologic typing of Salmonella enterica serotype enteritidis in a Canada-wide outbreak of gastroenteritis due to contaminated cheese. J Clin Microbiol 38:2403–2406
Mendoza MC, Landeras E (1999) In: Saeed AM, Gast RE, Potter ME, Wall PG (eds) Molecular epidemiological methods for differentiation of Salmonella enterica serovar Enteritidis strains in humans and animals: epidemiology, pathogenesis, and control. Iowa University Press, Ames, pp 125–140
Bidet P, Barut F, Lalande V, Burghoffer B, Piet JC (1999) Development of a new PCR-ribotyping method for Clostridium difficile based on ribosomal RNA gene sequencing. FEMS Microbiol Lett 175:261–266
Sechi LA, Leori G, Lollai SA, Dupre I, Muloicotti P, Fadda G (1999) Different strategies for the molecular characterization of the Mycobacterium bovis strain isolated in Sardinia Italy. Appl Environ Microbiol 65:1781–1785
Lagatolla C, Dolzani L, Tomin E, Lavenia A, Michele M, Tommasini T (1996) PCR-Ribotyping for characterization Salmonella isolates of different serotypes. J Clin Microbiol 34:2440–2443
Landeras E, onzalez-Hevia MA, Alzugaray R, Mendoza MC (1996) Epidemiological differentiation of pathogenic strains of Salmonella enteritidis by ribotyping. J Clin Microbiol 34:2294–2296
Lin AW, Usera MA, Barrett TJ, Goldsby RA (1996) Application of random amplified polymorphic DNA analysis to differentiate strains of Salmonella enteritidis. J Clin Microbiol 34:870–876
Fernandes SA, Ghilardi ACR, Tavechio AT, Machado AMO, Pignatari ACC (2003) Phenotypic and molecular characterization of Salmonella enteritidis strains isolated in São Paulo, Brazil. Rev Inst Med Trop 45:59–63
Dambaugh TR, Mangiaterra E, Fritschel S (1997) Ribotype characterization of Salmonella and E. coli O157:H7 with PvuII on the RiboPrinter microbial characterization system. Am Soc Microbiol (Washington, DC) 439:14
Busse HJ, Kainz A, Tsitko IV, Salkinoja-Salonen M (2000) Riboprints as a tool for rapid preliminary identification of sphingomonads. Syst Appl Microbiol 23:115–123
Satokari R, Mattila-Sandholm T, Suihko ML (2000) Identification of pediococci by ribotyping. J Appl Microbiol 88:260–265
Clermont D, Harmant C, Bizet C (2001) Identification of strains of Alcaligenes and Agrobacterium by a polyphasic approach. J Clin Microbiol 39:3104–3109
Fontana J, Stout A, Bolstorff B, Timperi R (2003) Automated Ribotyping and pulsed-field gel electrophoresis for rapid identification of multidrug-resistant Salmonella serotype Newport. Emerg Infect Dis 9:496–499
Navarro F, Llovet T, Echeita MA, Coll P, Aladuena A, Usera MA, Prats G (1996) Molecular typing of Salmonella enterica serovar typhi. J Clin Microbiol 34:2831–2834
Liebana E, Garcia-Migura L, Breslin MF, Davies RH, Woodward MJ (2001) Diversity of strains of Salmonella enterica serotype enteritidis from English poultry farms assessed by multiple genetic fingerprinting. J Clin Microbiol 39:154–161
Swaminathan B, Barrett TJ, Hunter SB, Tauxe RV (2001) PulseNet: the molecular subtyping network for foodborne bacterial disease surveillance, United States. Emerg Infect Dis 7:382–389
Riley LW (2004) Molecular epidemiology of infectious diseases: principles and practices. ASM Press, Washington, p 337
Maiden M, Bygraves JA, Feil E, Morelli G, Russell JE, Urwin R, Zhang Q, Zhou J, Zurth K, Caugant DA, Feavers IM, Achtman M, Spratt BG (1998a) Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms. Proc Natl Acad Sci U S A 95:3140–3145
Maiden MCJ (2006) Multilocus sequence typing of bacteria. Annu Rev Microbiol 60:561–588
Call DR, Orfe L, Davis MA, Lafrentz S, Kang MS (2008) Impact of compounding error on strategies for subtyping pathogenic bacteria. Foodborne Pathog Dis 5:505–516
Sabat AJ, Chlebowicz MA, Grundmann H, Arends JP, Kampinga G, MEESSEN NE, Friedrich AW, Van Dijl JM (2012) Microfluidic-chip based multiple-locus variable-number tandem repeat fingerprinting with new primer sets for methicillin-resistant Staphylococcus aureus. J Clin Microbiol 50:2255–2262
Maiden MCJ, Ygraves JA, Feil E, Morelli G, Russell JE, Urwin R, Zhang Q, Zhou J, Zurth K, Caugant DA, Feavers IM, Achtman M, Spratt BG (1998b) Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms. Proc Natl Acad Sci U S A 95:3140–3145
Yan SS, Pendrak ML, Abela-Ridder B, Punderson JW, Fedorko DP, Foley SL (2003) An overview of Salmonella typing public health concern. Clin Appl Immunol Rev 4:189–204
Francisco AP, Vaz C, Monteiro PT, Melo-Cristino J, Ramirez M, Carriço JA (2012) PHYLOViZ: phylogenetic inference and data visualization for sequence based typing methods. BMC Bioinformatics 13:87
Kotetishvili M, Stine OC, Kreger A, Morris JG, Sulakvelidze A (2002) Multilocus sequence typing for characterization of clinical and environmental Salmonella strains. J Clin Microbiol 40:1626–1635
Chen Y, Zhang W, Knabel SJ (2007) Multi-virulence locus sequence typing identifies single nucleotide polymorphisms which differentiate epidemic clones and outbreak strains of Listeria monocytogenes. J Clin Microbiol 45:835–846
Wang RF, Cao WW, Cerniglia CE (1994) A 16S rDNA-based PCR method for rapid and specific detection of Clostridium perfringens in food. Mol Cell Probes 8:131–137
Fox GE, Magrum LJ, Balch WE, Wolfe RS, Woese CR (1977) Classification of methanogenic bacteria by 16S ribosomal RNA characterization. Proc Natl Acad Sci U S A 74:4537–4541
Woese CR (1987) Bacterial evolution. Microbiol Rev 51:221–271
Olsen GJ, Overbeek NL, Larsen N et al (1992) The ribosomal database project. Nucleic Acids Res 20(Suppl):2199–2200
Olsen GJ, Woese CR (1993) Ribosomal RNA: a key to phylogeny. FASEB J 7:113–123
Tang YW, Ellis NM, Hopkins MK et al (1998) Comparison of phenotypic and genotypic techniques for identification of unusual aerobic pathogenic gram-negative bacilli. J Clin Microbiol 36:3674–3679
Clarridge JE III (2004) Impact of 16S rRNA gene sequence analysis for identification of bacteria on clinical microbiology and infectious diseases. Clin Microbiol Rev 17:840–862
Relman DA, Falkow S (1992) Identification of uncultured microorganisms: expanding the spectrum of characterized microbial pathogens. Infect Agents Dis 1:245–253
Brouqui P, Raoult D (2001) Endocarditis due to rare and fastidious bacteria. Clin Microbiol Rev 14:177–207
Harris KA, Fidler KJ, Hartley JC, Vogt J, Klein NJ, Monsell F, Novelli VM (2002) Unique case of Helicobacter sp. osteomyelitis in an immunocompetent child diagnosed by broad-range 16S PCR. J Clin Microbiol 40:3100–3103
Ekblom R, Jochen BW (2014) A field guide to whole-genome sequencing, assembly and annotation. Evol Appl 7:1026–1042
Colwell RR (1970) Polyphasic taxonomy of the genus Vibrio: numerical taxonomy of Vibrio cholerae, Vibrio parahaemolyticus and related Vibrio species. J Bacteriol 104:410–433
Platts-Mills JA, Liu J, Houpt ER (2003) New concepts in diagnostics for infectious diarrhea. Mucosal Immunol 5:876–885
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2018 Springer Nature Singapore Pte Ltd.
About this chapter
Cite this chapter
Shrivastava, A., Singhal, P.K., Shrivastava, P. (2018). Molecular Diagnosis of Enteric Bacterial Pathogens. In: Dash, H., Shrivastava, P., Mohapatra, B., Das, S. (eds) DNA Fingerprinting: Advancements and Future Endeavors. Springer, Singapore. https://doi.org/10.1007/978-981-13-1583-1_9
Download citation
DOI: https://doi.org/10.1007/978-981-13-1583-1_9
Published:
Publisher Name: Springer, Singapore
Print ISBN: 978-981-13-1582-4
Online ISBN: 978-981-13-1583-1
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)