Indian Journal of Medical Microbiology IAMM  | About us |  Subscription |  e-Alerts  | Feedback |  Login   
  Print this page Email this page   Small font sizeDefault font sizeIncrease font size
 Home | Ahead of Print | Current Issue | Archives | Search | Instructions  
Users Online: 411 Official Publication of Indian Association of Medical Microbiologists 
 ~  Similar in PUBMED
 ~  Search Pubmed for
 ~  Search in Google Scholar for
 ~Related articles
 ~  Article in PDF (498 KB)
 ~  Citation Manager
 ~  Access Statistics
 ~  Reader Comments
 ~  Email Alert *
 ~  Add to My List *
* Registration required (free)  

 ~  Abstract
 ~ Introduction
 ~  Materials and Me...
 ~ Results
 ~ Discussion
 ~ Acknowledgment
 ~  References
 ~  Article Figures
 ~  Article Tables

 Article Access Statistics
    PDF Downloaded315    
    Comments [Add]    
    Cited by others 1    

Recommend this journal


  Table of Contents  
Year : 2012  |  Volume : 30  |  Issue : 1  |  Page : 39-43

A rapid and reliable species-specific identification of clinical and environmental isolates of Vibrio cholerae using a three-test procedure and recA polymerase chain reaction

1 Department of Bacteriology, Pasteur Institute of Iran
2 Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
3 Faculty of Science, Health and Education, University of the Sunshine Coast, Queensland, Australia

Date of Submission12-Sep-2011
Date of Acceptance19-Dec-2011
Date of Web Publication22-Feb-2012

Correspondence Address:
B Bakhshi
Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran

Login to access the Email id

Source of Support: None, Conflict of Interest: None

DOI: 10.4103/0255-0857.93027

Rights and Permissions

 ~ Abstract 

Purpose: Vibrio cholerae, the cause of cholera, is one of the leading causes of morbidity and mortality in many developing countries. Most laboratories initially rely on biochemical tests for a presumptive identification of these strains, followed by a polymerase chain reaction (PCR)-based method to confirm their identification. The aim of this study is to establish a rapid and reliable identification scheme for V. cholerae using a minimal, but highly specific number of biochemical tests and a PCR assay. Materials and Methods: We developed a species-specific PCR to identify V. cholerae, using a housekeeping gene recA, and used that to evaluate the sensitivity and specificity of 12 biochemical tests commonly used for screening and / or presumptive identification of V. cholerae in the clinical and environmental samples. Results: Here we introduced a combination of three biochemical tests, namely, sucrose fermentation, oxidase test, and growth in trypton broth containing 0% NaCl, as also the PCR of the recA gene, for rapid identification of V. cholerae isolates, with 100% sensitivity and specificity. The established method accurately identified a collection of 47 V. cholerae strains isolated from the clinical cases (n = 26) and surface waters (n = 21), while none of the 32 control strains belonging to different species were positive in this assay. Conclusion: The triple-test procedure introduced here is a simple and useful assay which can be adopted in cholera surveillance programs for efficient monitoring of V. cholerae in surface water and fecal samples.

Keywords: Housekeeping gene, identification, polymerase chain reaction, recA, Vibrio cholera

How to cite this article:
Roozbehani A D, Bakhshi B, Pourshafie M R, Katouli M. A rapid and reliable species-specific identification of clinical and environmental isolates of Vibrio cholerae using a three-test procedure and recA polymerase chain reaction. Indian J Med Microbiol 2012;30:39-43

How to cite this URL:
Roozbehani A D, Bakhshi B, Pourshafie M R, Katouli M. A rapid and reliable species-specific identification of clinical and environmental isolates of Vibrio cholerae using a three-test procedure and recA polymerase chain reaction. Indian J Med Microbiol [serial online] 2012 [cited 2021 Mar 3];30:39-43. Available from:

 ~ Introduction Top

Cholera is a life-threatening diarrhoeal disease with high mortality among human populations. At least eight pandemics of cholera have been recorded, with the first one occurring in 1817. Of these, all but one originated in the Indian subcontinent, with the fifth, sixth, and seventh pandemics being caused by the classical strain of serogroup O1, although the last one introduced a new O1 strain with different phage susceptibility and biochemical properties. [1] The most recent pandemic was caused by a non-O1 serogroup, O139, in the 1990s.

The aetiological agent of the disease, V. cholerae, is a water-borne pathogen for which 209 O serogroups have been recognised. Of these serogroups O1 and O139 have so far, been associated with human diseases. The other serogroups, collectively referred to as non-O1 non-O139 serogroups, have not been associated with epidemics, but can cause sporadic diarrhoea [2] and are ubiquitously distributed in the aquatic environment. Rapid and accurate identification of V. cholerae O1 in potable water, aquatic environment, and fecal samples is important for disease management and the public health system. Identification of V. cholerae is usually achieved by conventional bacteriological methods, such as, culturing stool or surface water samples on a selective medium, Thiosulfate Citrate Bile Salts Sucrose (TCBS) agar, followed by biochemical testing of colonies and confirmation by a slide agglutination test, using specific antisera. [3] The TCBS agar eliminates most non-target bacteria in the clinical samples, but it is not satisfactory for surface water samples, because some bacteria present in the water sources can produce yellow colonies resembling those of V. cholerae. [4] Furthermore, the series of biochemical tests commonly used to identify V. cholerae[5],[6],[7] are originally selected and used for clinical samples in order to specifically detect pathogenic Vibrios. In addition, the close relation between V. cholerae and certain other members of the Vibrionaceae or Aeromonas spp., with respect to their biochemical properties, has often made unambiguous identification of the organism quite difficult.

Although the commercial availability of O1 and / or O139 antisera has helped the identification of the epidemic strains of V. cholerae considerably, it may not be true for the non-O1 / non-O139 strains, which until recently, have been known to range from serogroups O2 to O138 and from the O140 to O193. [8] The problem has become prominent recently, as the non-O1 / non-O139 strains of diverse serogroups have been implicated as the causative agents of a large number of diarrhoeal cases in many developing countries. [9] The use of a 16S rRNA sequence for the identification of V. cholerae strains has not been successful so far due to the lack of appreciable differences between V. cholerae and other members of the Vibrionaceae family. [6] While different molecular-based methods have been developed for the rapid identification of V.cholerae, most laboratories use the biochemical methods for the initial and / or presumptive identification of these bacteria.

In this study, we have evaluated the use of a triple biochemical test procedure and a highly specific recA PCR for the rapid identification of V. cholerae strains, using a collection of 49 clinical and environmental strains of V. cholerae, isolated from different parts of Iran against 29 control strains belonging to different species, and have shown the specificity and sensitivity of the method.

 ~ Materials and Methods Top

Bacterial isolates

Environmental samples were collected from different surface water sources in the north, west, and central parts of Tehran over a three-month period. The processing of water samples has been described previously. [10] Briefly, 500 ml from each water sample was concentrated using a vacuum pressure of 15 to 20 lb / in 2 on filter water samples, through a 0.45-μm pore size membrane, after pre-filtration through filter paper (Wattman No.1; Maidston, UK). After enrichment of the filter papers in phosphate-buffered saline (PBS) and alkaline peptone water (APW), each sample was streaked on TCBS agar plates and incubated overnight at 37΀C. [11] All the yellow colonies on the TCBS agar plates suspected of being V. cholerae were further examined by colony morphology, oxidase test, motility, sucrose, and lactose fermentation, growth in trypton broth containing 0% NaCl, arginine dehydrolase, ornithin decarboxylase, Voges-Proskauer, and indole tests. [4] Alkaline peptone water was used for the enrichment of V. cholerae in clinical samples, which was then streaked on TCBS agar plates and incubated at 37ΊC for 18 to 24 hours. Suspected V. cholerae colonies were confirmed by using the 12 biochemical assays as described earlier. [11] The V. cholerae colonies were further examined for their serogroups by the slide agglutination test using the polyvalent V. cholerae O1 antiserum. All isolates that agglutinated with the polyvalent V. cholerae O1 or O139 antiserum were then serotyped by specific monovalent antisera against Inaba- and Ogawa-specific antigens. [12]

Selection of the biochemical tests

The effectiveness of each biochemical test was evaluated for its sensitivity and specificity, and 100% sensitivity was sought, in order to eliminate false negatives. These were calculated as follows: sensitivity = [(number of positive isolates, as determined by the biochemical tests and PCR) / (total number of positive isolates, as determined by PCR)] Χ 100; and specificity = [(number of negative isolates, as determined by biochemical tests and PCR) / (total number of negative isolates, as determined by PCR)] Χ 100. [13]

Confirmation of presumptive V. cholerae isolates

Presumptive V. cholerae isolates were confirmed by PCR using species-specific primers as described by Chun et al. [7] The PCR primer sets were, prVC-F (5'-TTAAGCSTTTTCRCTGA GAATG-3') and prVCM-R (5'- GTCACTTAACCATACAACCCG-3'), which amplified a portion of the intergenic spacer region between the 16S and 23S RNA genes specific for V. cholerae.

Polymerase chain reaction assay for recA gene

Amplification of the target gene was carried out by a PCR assay, using bacterial cell lysate as the source of template DNA. Bacterial isolates were initially grown overnight at 37΀C on brain-heart infusion (BHI) agar plates. From each plate isolated colonies were picked up and suspended in 100 ml of double-distilled water and boiled for 10 minutes. The cell debris was removed by centrifugation at 1000 rpm for five minutes, and the supernatant containing the template DNA was used for the PCR assay. The PCR amplified a fragment of approximately 1100 bp from the housekeeping gene recA, using primers recA-F (5΄- TGGACGAGAATAAACAGAAGGC-3΄) and recA-R (5΄- AACCTCTTTGCATTCAGCCC-3΄). [14] PCR amplification of the target DNA was carried out in a thermal cycler using 200-μl PCR tubes, with a reaction mixture volume of 25 ml. Each of the reaction mixtures contained 20 ΅L sterile double distilled water, 2.5 ΅L 10x Taq polymerase buffer, 0.3 ΅L dNTPs (10 mM), 0.5 U Taq DNA polymerase, and 25 pmol of each primer. The cycling conditions were as follows: preincubation at 94ΊC for five minutes, 30 cycles of one minute at 94ΊC, for denaturation, one minute at 64ΊC for annealing, two minutes at 72ΊC for elongation, and incubation at 72ΊC for three minutes for final elongation. [3]

 ~ Results Top

Bacterial isolates

In all, 26 clinical and 21 environmental isolates were included in this study. All the clinical isolates belonged to serogroup O1 of different sero- and biotypes, while environmental isolates belonged to the non-O1, non-O139 serogroups [Table 1]. Two culture collection strains of V. cholerae isolated from the clinical cases (i.e., ATCC 14035) and the environment (i.e., CIP 104155) were also included in this study as the control. Other control strains (n = 30) belonged to different Gram-negative species, identified and characterised in different clinical settings [Table 1].
Table 1: Vibrio cholerae included in this study and control strains tested by PCR for the presence of recA gene

Click here to view

Evaluation of the biochemical tests and polymerase chain reaction of recA

The results of the biochemical tests for V. choleae strains isolated in this study and each of the control strains are shown in [Table 2]. As depicted, a combination of oxidase test, sucrose fermentation on TCBS, plus growth in trypton broth containing 0% NaCl, were the selected tests, with 100% sensitivity and specificity for V. cholerae strains. All V. cholerae strains positive for these biochemical tests also showed positive PCR results for the recA gene [Table 2] and [Figure 1]a.
Figure 1: (a) Agarose gel electrophoresis of PCR amplified products with recA specific primers (~1100 bp). Lanes: 1 - 4, environmental isolates; 5 - 8, clinical isolates; 9, Vibrio cholerae ATCC 14035; 10, negative control; 11, DNA Size Marker, and (b) Lanes 1, Aeromonas hydrophila; 2,  Escherichia More Details coli 3, Vibrio fischeri; 4, Acinetobacter spp.; 5, Pseudomonas aeruginosa; 6, Klebsiella pneumonia; 7,Vibrio cholerae reference strain 14035; 8, DNA Size Marker

Click here to view
Table 2: Biochemical tests used to screen for V. cholerae and control strains

Click here to view

To determine the specificity of the primers for detection of V. cholerae strains, DNA obtained from Aeromonas spp., Escherichia coli., V. fischeri, Acinetobacter spp., Pseudomonas spp. and Klebsiella spp. were included in the study and showed no gene amplification by PCR [Figure 1]b, confirming the specificity of the primers for detecting V. cholerae O1.

 ~ Discussion Top

As V. cholerae is autochthonous to the aquatic environment, [6],[10] monitoring of this bacterium in water sources is important for the control of cholera. The simple triple set of tests introduced in this study, provided 100% sensitivity and specificity for the identification and confirmation of the V. cholerae isolates against the control strains that showed distinct biochemical test patterns, different from those of the V. cholerae strains. To verify the application of this set of tests for the successful isolation and detection of V.cholerae in field studies, we used this procedure to isolate and detect V.cholerae from the clinical and water samples. All suspected bacterial colonies, with a biochemical profile of + / + / + from sucrose fermentation on TCBS agar, positive oxidase test, and growth of alkaline peptone water with 0% NaCl, were subjected to tests with PCR, for the presence of recA gene. The results were in complete agreement with those obtained by the procedure, as described earlier. [13] One shortcoming of this study, however, might be that the sensitivity and specificity of the proposed combined tests was not tested for other members of Vibrionaceae that might grow on TCBS medium and partially ferment sucrose. In our study V. fischeri, a species closely related to V.cholerae was found to grow weakly on TCBS. However, this strain showed a characteristic pattern against this triple set of biochemical tests that was different from those obtained from the V. cholerae strains isolated from the clinical and environmental sources.

Several molecular methods for the identification of V. cholerae have been reported previously, which include 16S rRNA [15] and 16S-23S rRNA intergenic sequence analysis. [7] The inability of 16S rRNA sequences to unambiguously distinguish between the different Vibrio species, however, is well-recognised. [6] In this study, we used an assay specific to the V. cholerae species that was developed in our laboratory to confirm the specificity of the triple biochemical tests, for detection of V.cholerae isolates. Amplification of the recA gene by the polymerase chain reaction technique was not reported in the identification of the V. cholerae strains in pure cultures and our results indicated that the presence of the recA gene was consistent with the selected biochemical tests in all these isolates. It should be noted, however, that the primers used were just for the detection of V. cholerae and not for differentiation of the pathogenic and nonpathogenic strains. Thus, according to this study, PCR of the recA gene can be used as a confirmatory alternative test for the accurate identification of the species V.cholerae.

In conclusion, our results indicate that the clinical and aquatic samples can be screened rapidly for the presence of V. cholerae by enriching the samples with alkaline peptone water without NaCl, followed by selecting the yellow colonies on the TCBS agar, and performing an oxidase test. Isolates showing positive reaction in these three tests can then be confirmed by PCR amplification of the recA gene. This protocol can be adopted in cholera surveillance programs for the efficient monitoring of V. cholerae in surface water, and fecal samples as well.

 ~ Acknowledgment Top

The study was funded by the Iranian National Science Foundation grant No. 88002358.

 ~ References Top

1.Yamazaki W, Seto K, Taguchi M, Ishibashi M, Inoue K. Sensitive and rapid detection of cholera toxin-producing Vibrio cholerae using a loop-mediated isothermal amplification. BMC Microbiol 2008;8:94.  Back to cited text no. 1
2.Nusrin S, Khan GY, Bhuiyan NA, Ansaruzzaman M, Hossain MA, Safa A, et al. Diverse CTX phages among toxigenic Vibrio cholerae O1 and O139 strains isolated between 1994 and 2002 in an area where cholera is endemic in Bangladesh. J Clin Microbiol 2004;42:5854-6.  Back to cited text no. 2
3.Ansaruzzaman M, Rahman M, Kibriya AK, Bhuiyan NA, Islam MS, Albert MJ. Isolation of sucrose late-fermenting and nonfermenting variants of Vibrio cholerae O139 Bengal: implications for diagnosis of cholera. J Clin Microbiol 1995;33:1339-40.  Back to cited text no. 3
4.Choopun N, Louis V, Huq A, Colwell RR. Simple procedure for rapid identification of Vibrio cholerae from the aquatic environment. Appl Environ Microbiol 2002;68:995-8.  Back to cited text no. 4
5.Singh DV, Isac SR, Colwell RR. Development of a hexaplex PCR assay for rapid detection of virulence and regulatory genes in Vibrio cholerae and Vibrio mimicus. J Clin Microbiol 2002;40:4321-4.  Back to cited text no. 5
6.Ruimy R, Breittmayer V, Elbaze P, Lafay B, Boussemart O, Gauthier M, et al. Phylogenetic analysis and assessment of the genera Vibrio, Photobacterium, Aeromonas, and Plesiomonas deduced from small-subunit rRNA sequences. Int J Syst Bacteriol 1994;44:416-26.  Back to cited text no. 6
7.Chun J, Huq A, Colwell RR. Analysis of 16S-23S rRNA intergenic spacer regions of Vibrio cholerae and Vibrio mimicus. Appl Environ Microbiol 1999;65:2202-8.  Back to cited text no. 7
8.Yamai S, Okitsu T, Shimada T, Katsube Y. Distribution of serogroups of Vibrio cholerae non-O1 non-O139 with specific reference to their ability to produce cholera toxin, and addition of novel serogroups. Kansenshogaku Zasshi 1997;71:1037-45.  Back to cited text no. 8
9.Dalsgaard A, Serichantalergs O, Pitarangsi C, Echeverria P. Molecular characterization and antibiotic susceptibility of Vibrio cholerae non-O1. Epidemiol Infect 1995;114:51-63.  Back to cited text no. 9
10.Bakhshi B, Pourshafie MR, Navabakbar F, Tavakoli A, Shahcheraghi F, Salehi M, et al. Comparison of distribution of virulence determinants in clinical and environmental isolates of Vibrio cholerae. Iran Biomed J 2008;12:159-65.  Back to cited text no. 10
11.Chakraborty S, Mukhopadhyay AK, Bhadra RK, Ghosh AN, Mitra R, Shimada T, et al. Virulence genes in environmental strains of Vibrio cholerae. Appl Environ Microbiol 2000;66:4022-8.  Back to cited text no. 11
12.Eroshenko GA, Kukleva LM, Shavina N, Kutyrev VV. Molecular-epidemiological characteristic and possible origin of Vibrio cholerae non O1 / non O139 with complete and limited set of virulence genes. Zh Mikrobiol Epidemiol Immunobiol 2007;5:24-8.  Back to cited text no. 12
13.Bakhshi B, Barzelighi HM, Adabi M, Lari AR, Pourshafie MR. A molecular survey on virulence associated genotypes of non-O1 non-O139 Vibrio cholerae in aquatic environment of Tehran, Iran. Water Res 2009;43:1441-7.  Back to cited text no. 13
14.Byun R, Elbourne LD, Lan R, Reeves PR. Evolutionary relationships of pathogenic clones of Vibrio cholerae by sequence analysis of four housekeeping genes. Infect Immun 1999;67:1116-24.  Back to cited text no. 14
15.Hayden RT, Kolbert CP, Hopkins MK, Persing DH. Characterization of culture-derived spiral bacteria by 16S ribosomal RNA gene sequence analysis. Diagn Microbiol Infect Dis 2001;39:55-9.  Back to cited text no. 15


  [Figure 1]

  [Table 1], [Table 2]

This article has been cited by
1 Ribotyping and TCP gene cluster analysis of environmental and clinical Vibrio cholerae strains isolated in Iran
Bita Bakhshi,Hajar Mohammadi-Barzelighi,Neda Hosseini-Aliabad,Mohammad R. Pourshafie
Annals of Microbiology. 2014; 64(1): 49-53
[Pubmed] | [DOI]


Print this article  Email this article


2004 - Indian Journal of Medical Microbiology
Published by Wolters Kluwer - Medknow

Online since April 2001, new site since 1st August '04