What is PhenePlate system ?
The PhenePlate system is an automated system for simple and rapid subtyping of bacteria for epidemiological, nosocomial and ecological studies. The system is based on the evaluation of the kinetics of biochemical reactions (by reading test results at several occasions), performed in 96 well microplates. The system contains 2 to 8 sets of dehydrated reagents, which have been specifically selected for various groups of microorganisms.
Typing of bacteria is defined as identification of strains below the species level. Typing is critical in tracking the spread of specific bacterial strains, such as in epidemiological or nosocomial investigations, and is very useful in studies of the diversity or stability of bacterial populations in ecological investigations.
Based on different characteristics of the bacteria, there are different typing methods, such as Genotyping (DNA/RNA), Chemotyping (Chemical characterization of bacterial cell), and Phenotyping (Morphology or Metabolic reaction). Since the chemotype and the phenotype of a bacterial cell depend on the expression of its DNA, they are both indirect measures of the bacterial genotype.
Why do we need Phenotyping instead of Genotyping?
First, we need to ask ourselves, why do we normally use photographic portraits in order to recognize humans instead of their DNA-fingerprints? – It is of course because the photographic portrait of the human (the phenotype) is so simple, rapid and cheap, and, if it is properly done, gives all the information that is required to recognize a particular individual. However, in some instances, the genotype may give additional information that cannot be obtained in other ways, or may be needed to verify important findings. The same is applicable for bacteria: phenotyping is normally much simpler to use than genotyping, and often gives the required information, but in some cases phenotyping cannot be performed, and in some cases genotyping is required in order to obtain information that the phenotype cannot yield. So the answer is: use phenotyping when possible, and genotyping as its complement.
PhenePlate system is a high resolution macro-array phenotyping system
PhenePlate system uses biochemical fingerprinting technic in which bacterial strains can be characterized by quantifying bacterial metabolic reaction on different substrates. Main concept is that bacterial isolates with identical genotypes, i.e. belonging to the same clone, share identical metabolic properties, whereas isolates with different genotypes also have differences in one or more of the measured metabolic processes, and thus will show different activities in the reactions involved.
What is PhenePlate system used for?
PhenePlate is used to select important isolates from bacterial populations for further investigation as the first screening system. It can be used to characterize whole bacterial population (Maximum 600 isolates), and the diversity of each population, as well as the similarity between different populations, automatically calculated by using the PhPWin software.
Important application includes:
Vaccine development – Screening/Selection/Characterization of target bacteria suitable for use as vaccines
Probiotics development – Quality assurance of probiotics organisms in Nutritional Supplement, Food and Therapeutic Products.
Environmental monitoring – Tracking the source of microbial pollution by Carbon Source Utilization profiling with PhenePlate system.
Hospital infection monitoring – Tracking the source of microbial contamination in hospital by Carbon Source Utilization profiling with PhenePlate system / Examine bacterial population changes with high reproducibility.
Publications on PhenePlate system Applications
Interspecies transfer of vancomycin, erythromycin and tetracycline resistance among Enterococcus species recovered from agrarian sources. Conwell M, Daniels V, Naughton PJ, Dooley JS. BMC Microbiol. 2017 Jan; 17 (1): 19.
Pseudomonas-related populations associated with reverse osmosis in drinking water treatment. Sala-Comorera L, Blanch AR, Vilaró C, Galofré B, García-Aljaro C. J Environ Manage. 2016; 182: 335-341.
Characterization of methicillin resistant Staphylococcus aureus strains among inpatients and outpatients in a referral hospital in Tehran, Iran. Rahimia F and Shokoohizadehb L. Microbial Pathogenesis 2016; 97: 89-93
Characterization of Resistance to Aminoglycosides in Methicillin-Resistant Staphylococcus aureus Strains Isolated From a Tertiary Care Hospital in Tehran, Iran. Rahimi F. Jundishapur J Microbiol. 2016 Jan 2; 9 (1): e29237.
Highly Heterogeneous Probiotic Lactobacillus Species in Healthy Iranians with Low Functional Activities.Rohani M, Noohi N, Talebi M, Katouli M, Pourshafie MR. PLoS One. 2015 Dec; 10 (12): e0144467.
Viability and stability of Escherichia coli and enterococci populations in fecal samples upon freezing. Masters N, Christie M, Stratton H, Katouli M. Can J Microbiol. 2015 Jul; 61 (7): 495-501.
Isolation and Biochemical Fingerprinting of Vancomycin-Resistant Enterococcus faecium From Meat, Chicken and Cheese.Talebi M, Sadeghi J, Rahimi F, Pourshafie MR. Jundishapur J Microbiol. 2015 Apr; 8 (4): e15815
Neem (Azadirachta indica A. Juss) Oil to Tackle Enteropathogenic Escherichia coli. Del Serrone P, Toniolo C and Nicoletti M. Biomed Res Int. 2015; 2015: 343610.
Surveillance of antimicrobial resistance among Escherichia coli in wastewater in Stockholm during 1 year: does it reflect the resistance trends in the society? Kwak YK, Colque P, Byfors S, Giske CG, Möllby R, Kühn I. Int J Antimicrob Agents. 2015 January; 45 (1): 25-32
Probiotic and technological properties of Lactobacillus spp. strains from the human stomach in the search for potential candidates against gastric microbial dysbiosis. Delgado S, Leite AM, Ruas-Madiedo P and Mayo B. Front Microbiol. 2015 Jan; 5: 766.
Characterization of CTX-M-producing Escherichia coli by repetitive sequence-based PCR and real-time PCR-based replicon typing of CTX-M-15 plasmids. Onnberg A, Soderquist B, Persson K and Olling PM. APMIS 2014; 122: 1136-1143
Antibiotic resistance in environmental Escherichia coli – a simple screening method for simultaneous typing and resistance determination. Colque Navarro P, Fernandez H, Möllby R, Otth L, Tiodolf M, Wilson M, Kühn I. J Water Health. 2014 Dec; 12 (4): 692-701.
Phenotypic Characteristics and Probiotic Potentials of Lactobacillus spp. Isolated From Poultry. Noohi N, Ebrahimipour G, Rohani M, Talebi M, Pourshafie MR. Jundishapur J Microbiol. 2014 Sep; 7 (9): e17824.
Determination of Vancomycin Resistant Enterococcus faecium Diversity in Tehran Sewage Using Plasmid Profile, Biochemical Fingerprinting and Antibiotic Resistance. Borhani K, Ahmadi A, Rahimi F, Pourshafie MR and Talebi M. Jundishapur J Microbiol. 2014 Feb; 7 (2): e8951
Alteration of the colonization pattern of coagulase-negative staphylococci in patients undergoing treatment for hematological malignancy. Ahlstrand E, Persson L, Tidefelt U, Söderquist B. Eur J Clin Microbiol Infect Dis. 2012 Jul; 31 (7): 1679-87.
Diarrheagenic Escherichia coli markers and phenotypes among fecal E. coli isolates collected from Nicaraguan infants. Reyes D, Vilchez S, Paniagua M, Colque-Navarro P, Weintraub A, Möllby R, Kühn I. J Clin Microbiol. 2010 Sep; 48 (9): 3395-6.
Diversity of intestinal Escherichia coli populations in Nicaraguan children with and without diarrhoea. Reyes D, Vilchez S, Paniagua M, Colque P, Weintraub A, Möllby R, Kühn I. J Med Microbiol. 2009 Dec; 58 (Pt 12): 1593-600.
Molecular and phenotypic characterization of Escherichia coli and Klebsiella pneumoniae producing extended-spectrum β-lactamases with focus on CTX-M in a low-endemic area in Sweden. Onnberg A, Mölling P, Zimmermann J, Söderquist B. APMIS. 2011 Apr; 119 (4-5): 287-95.
Characterization, and comparison, of human clinical and black-headed gull (Larus ridibundus) extended-spectrum beta-lactamase-producing bacterial isolates from Kalmar, on the southeast coast of Sweden. Bonnedahl J, Drobni P, Johansson A, Hernandez J, Melhus A, Stedt J, Olsen B, Drobni M: J Antimicrob Chemother. 2010 Sep; 65 (9): 1939-44.
Vancomycin resistant enterococci (VRE) in Swedish sewage sludge. Sahlström L, Rehbinder V, Albihn A, Aspan A, Bengtsson B: Acta Vet Scand. 2009 May; 29; 51:24.
Characterization of bacterial coliform occurrences in different zones of a drinking water distribution system. Blanch AR, Galofré B, Lucena F, Terradillos A, Vilanova X, Ribas F. J Appl Microbiol. 2007 Mar; 102 (3): 711-721.
Occurrence and relatedness of vancomycin resistant enterococci in animals, humans and the environment in different European regions. Kühn I, Iversen A, Finn M, Greko C, Burman LG, Blanch AR, Vilanova X, Manero A, Taylor H, Caplin J, Domínguez L, Inmaculada A. Herrero, Moreno MA, Möllby R. Applied and Environmental Microbiology 2005; 71 (9): 5383-5390.
Diversity among 2481 Escherichia coli from women with community acquired lower urinary tract infections in 17 countries. Landgren M, Odén H, Kühn I, Österlund A, Kahlmeter G. J Antimicrob Chemother. 2005 Jun; 55 (6): 928-937.
Prevalence of antibiotic resistant Enterococcus spp in waste waters in the north of Chile.
Silva A J, Loyola S P, Galleguillos O J, Rodriguez G Y, Colque-Navarro P, Mollby R, Kühn I. Rev Med Chil. 2005 Oct; 133 (10): 1201-10.
Host species-specific metabolic fingerprint database for enterococci and Escherichia coli and its application to identify sources of fecal contamination in surface waters. Ahmed W, Neller R, Katouli M. Appl Environ Microbiol. 2005 Aug; 71 (8): 4461-4468.
Clonal origin of ciprofloxacin- and ampicillin resistant Enterococcus faecium strains emerging in Sweden. Torell E, Kühn I, Olsson-Liljequist B, Hoffman BM, Haeggman S, Lindahl C and Burman LG. Clinical Microbiology and Infection 2003; 9: 1011-1019.
The PhenePlate system for studies of the diversity of enterococcal populations from the food chain and the environment. Kühn I, Iversen A, Mollby R. Int J Food Microbiol. 2003; 88 (2-3): 189-96.
Comparison of enterococcal populations in animals, humans, and the environment – a European study. Kühn I, Iversen A, Burman LG, Olsson-Liljequist B, Franklin A, Finn M, Aarestrup F, Seyfarth AM, Blanch AR, Vilanova X, Taylor H, Caplin J, Moreno MA, Dominguez L, Herrero IA, Mollby R. Int J Food Microbiol. 2003; 88 (2-3): 133-45.
Evidence for a Transmission Between Humans and the Environment of a Nosocomial Strain of Enterococcus faecium. Iversen A, Kühn I, Rahman M, Franklin A, Burman LG, Olsson-Liljequist B, Torell E, Möllby R . Environmental Microbiology 2004; 6 (1): 55-59.
Phenotypic population characteristics of the enterococci in wastewater and animal faeces: implications for the new European directive on the quality of bathing waters. Wallis JL, Taylor HD. Water Sci Technol. 2003; 47 (3): 27-32.
High prevalence of vancomycin resistant enterococci in Swedish sewage. Iversen A, Kühn I, Franklin A, Möllby R. Appl Environ Microbiol. 2002; 68: 2838-2842.
An anthroposophic lifestyle and intestinal microflora in infancy. Alm JS, Swartz J, Bjorksten B, Engstrand L, Engstrom J, Kuhn I, Lilja G, Mollby R, Norin E, Pershagen G, Reinders C, Wreiber K, Scheynius A. Pediatr Allergy Immunol. 2002; 13 (6): 402-411.
Gastrointestinal transit survival of an Enterococcus faecium probiotic strain administered with or without vancomycin. Lund B, Adamsson I, Edlund C. Int J Food Microbiol. 2002; 77: 109-115.
The effect of a sewage treatment plant effluent on the faecal coliforms and enterococci populations of the reception river waters. Vilanova X. Manero A. Cerda-Cuellar M. Blanch AR.
Journal of Applied Microbiology 2002; 92 (2): 210-214.
Diversity of Vibrio spp. populations in several exhibition aquaria with a shared water supply. Blanch AR. Cerda-Cuellar M. Hispano C. Letters in Applied Microbiology 2001; 33 (2): 137-143.
Weaning of piglets. Effects of an exposure to a pathogenic strain of Escherichia coli. Melin L, Katouli M, Lindberg A, Fossum C, Wallgren P. J Vet Med. 2000; 47: 663-675.
Clonality of Vibrio anguillarum strains isolated from fish from the Scandinavian countries, Sweden, Finland and Denmark. Pedersen K, Kühn I, Seppänen J, Hellström A, Tiainen T, Rimaila-Pärnänen E, Larsen JL. J Appl Microbiol. 1999; 86: 337-347.
Epidemiological typing of international collections of Klebsiella spp: computerized biochemical fingerprinting compared with serotyping, phage typing, and pulsed-field gel electrophoresis. Tullus K, Burman LG, Haeggman S, Hutchingson G, Kühn I. Clin Microbiol Infect. 1999; 5: 184-189.
Characterization of Aeromonas spp isolated from humans with diarrhoea, from healthy controls, and from surface water in Bangladesh. Kühn I, Albert J, Ansaruzzaman M, Alabi SA, Bhuiyanand NA, Huys G, Islam MS, Jansen P, Kersters K, Neogi PKB, Möllby R. J Clin Microbiol. 1997; 35 (2): 369-373.
Diversity, stability, and virulence properties of Aeromonas strains from Swedish water distribution systems. Kühn I, Allestam G, Huys G, Janssen P, Kersters K, Krovacek K, and Stenström T.A. Appl Environ Microbiol. 1997; 63: 2708-2715.
Biochemical fingerprinting of coliform bacterial populations – comparisons between polluted river water and factory effluents. Kühn I, Allestam G, Engdahl M, and Stenström T.-A.
Wat Sci Tech. 1997; 35: 343-350.
Phenotypic characterization of the intestinal Escherichia coli of pigs during suckling, post-weaning and fattening periods. Katouli M, Lund A, Wallgren P, Kühn I, Söderlind O, Möllby R.
Appl Environ Microbiol. 1995; 61: 778-783.