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 Table of Contents  
Year : 2016  |  Volume : 3  |  Issue : 4  |  Page : 288-290

Importance of identification of lactose nonfermenting Escherichia coli and their prevalence in urinary isolates

1 Department of Microbiology, Sri Aurobindo Institute of Medical Sciences, Medical College and Post Graduate Institute, Indore, Madhya Pradesh; Department of Biochemistry, SOS, IGNOU, New Delhi, India
2 Department of Biochemistry, SOS, IGNOU, New Delhi, India
3 Department of Biochemistry, Sri Aurobindo Institute of Medical Sciences, Medical College and Post Graduate Institute, Indore, Madhya Pradesh, India
4 Department of Microbiology, Sri Aurobindo Institute of Medical Sciences, Medical College and Post Graduate Institute, Indore, Madhya Pradesh, India

Date of Web Publication14-Sep-2016

Correspondence Address:
Dr. Trupti Bajpai
Assistant Professor, Department of Microbiology, Sri Aurobindo Institute of Medical Sciences Medical College and PG Institute, Indore-Ujjain Road, MR-10 Crossing, Indore, Madhya Pradesh
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Source of Support: None, Conflict of Interest: None

DOI: 10.4103/2348-3334.190581

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Introduction: Escherichia coli is one of the most common bacteria causing urinary tract infection. Accurate identification of urinary isolates is highly desirable and frequently challenging. Our study aims at identifying the “atypical” phenotype of E. coli by conventional, automated, and molecular methods and studying its prevalence among all the urinary isolates of E. coli. Materials and Methods: The present prospective study was conducted in the Department of Microbiology of a teaching tertiary care hospital of Central India for 6 months during the year 2014–2015. A total of 592 urine samples were processed. Identification of different urinary isolates was done by conventional and automated methods and by molecular method in special cases. Results: Two hundred and sixty-one uropathogens were isolated during the study. Among these, 110 (42.1%) isolates were E. coli, of which 4 (3.6%) isolates were confirmed as “atypical” E. coli by automated and molecular method. Conclusions: Our study highlights the challenges in the identification of atypical urinary isolates of E. coli. Accurate identification is essential for implicating proper antibiotic treatment.

Keywords: 16S ribosomal RNA sequencing, atypical Escherichia coli, VITEK-2 Compact

How to cite this article:
Bajpai T, Pandey M, Varma M, Bhatambare G. Importance of identification of lactose nonfermenting Escherichia coli and their prevalence in urinary isolates. CHRISMED J Health Res 2016;3:288-90

How to cite this URL:
Bajpai T, Pandey M, Varma M, Bhatambare G. Importance of identification of lactose nonfermenting Escherichia coli and their prevalence in urinary isolates. CHRISMED J Health Res [serial online] 2016 [cited 2023 Mar 28];3:288-90. Available from: https://www.cjhr.org/text.asp?2016/3/4/288/190581

  Introduction Top

Urinary tract infection (UTI) is one of the most important causes of morbidity and mortality and  Escherichia More Details coli is the most frequently isolated urinary pathogen. It exists as a commensal in the gastrointestinal tract and provides the pool for the initiation of UTI. These isolates express chromosomally encoded virulence markers, which are responsible for their varying levels of pathogenicity.[1],[2]

Some of the strains of these isolates are often multi-drug resistant. Proper susceptibility data from the specified area are required, if empirical antibiotics are to be administered in this group of patients. Moreover, this demands accurate identification which is frequently challenging in the need of proper sample collection and transport due to variation in phenotypic characteristics such as motility, gas production, and lactose-fermenting capabilities, and also due to the lack of full battery of biochemical tests in several laboratories.[3]

Our study aims at identifying the “atypical” phenotype of E. coli by conventional, automated, and molecular methods and studying its prevalence among all the urinary isolates of E. coli.

  Materials and Methods Top

The present prospective study was conducted from October 2014 to March 2015 in the Department of Microbiology of a teaching tertiary care hospital located in the Central India. Clean catch, midstream urine samples from 592 patients clinically suspected of UTI were subjected to microscopy and culture on blood agar, MacConkey agar, and UTI chromogenic media (HiMedia, Mumbai, India). The uropathogens isolated from the culture-positive samples were identified up to species level by conventional method (biochemical tests).[4],[5] The isolates were further confirmed by automated method (VITEK 2-Compact System, BioMérieux Inc., France). If required, then, further confirmation was done by molecular method (16S ribosomal RNA [16S rRNA] sequencing) (Yaazh Xenomics, Mumbai, India). In 16S rRNA sequencing, genomic DNA was extracted, followed by its amplification (polymerase chain reaction). The amplified fragments were purified prior to sequencing. Bidirectional sequencing was performed for each amplified product by an automated sequencer.[6],[7] Analysis of sequencing data was performed by MicroSeq 500 software (Thermo Fisher Scientific, 168 Third Avenue, Waltham, MA USA). The consensus sequences were compared (online) with the published sequences available in GenBank at the website (http://www.ncbi.nlm.nih.gov/) using the nucleotide Basic Local Alignment Search Tool of the National Center for Biotechnology Information. The phylogenetic tree of the identified E. coli was analyzed. Data for the phylogenetic analysis were obtained from sequences contained in the GenBank nucleotide sequences database.[8],[9]

  Results Top

Out of 592 patient samples processed, a total of 243 (41%) urine samples were found to be culture-positive. Two hundred and sixty-one uropathogens were isolated from the 243 culture-positive samples (18 samples had mixed flora, i.e. two pathogens). Among these, 161 (61.6%) isolates were Gram-negative Bacilli, 56 (21.4%) were Gram-positive cocci, and 44 (16.8%) were Candida species. Among the 161 Gram-negative isolates, 149 (92.8%) were members of Enterobacteriaceae, 8 (4.9%) were Pseudomonas aeruginosa, and 4 (2.4%) were Acinetobacter species. Of the 149 members of Enterobacteriaceae, 110 (73.8%) were detected as E. coli. Among these 110 E. coli isolates, 4 (3.6%) isolates were confirmed as E. coli only by automated and molecular methods.

  Discussion Top

It has traditionally been described that certain serotypes of E. coli were consistently associated with uropathogenicity. They were recognized for the first time in 1970s and are currently known as uropathogenic E. coli (UPEC).[1] These are typical E. coli strains that differ from “atypical” or inactive strains of E. coli, which were identified as the causative agents of diarrheal diseases in 1971 known to present shigellosis-like symptoms. At present, they are known as enteroinvasive E. coli.[10] The prevalence of “atypical” E. coli has been frequently reported from diarrheal cases.[11] Here, we have reported their prevalence as uropathogens.

E. coli are Gram-negative bacilli, commonly found in the lower intestine of warm-blooded animals including humans. The harmless strains are a part of normal gut flora and benefit the host by producing Vitamin K2 and preventing the establishment of pathogenic bacteria in the intestine. UPECs are responsible for approximately 90% of UTIs in individuals with ordinary anatomy.[12] These strains are motile, aerogenic lactose fermenters that can be very easily identified by conventional methods of identification in all clinical microbiology laboratories.[2]

However, there are variants of E. coli that are termed as “inactive.” They are nonmotile, anaerogenic, nonlactose fermenters. Biochemically, they are very similar to Shigella species and such isolates pose a significant diagnostic challenge.[1],[13] Although biochemical and serological methods are typically used to distinguish these species, these approaches have suboptimal performance. Phenotypically, they share many common characteristics, but genotypically they could be considered as same species.[13]

Even during our study, these isolates could not be confirmed as E. coli by conventional methods. Automated method could identify it as E. coli, but again 16S rRNA sequencing identified it as either Shigella sonnei or E. coli. It was finally confirmed as E. coli on the basis of the clinical sample from which it was isolated. Being a urinary isolate, it was finally confirmed as enteroinvasive strain of E. coli resembling Shigella species [Figure 1].
Figure 1: Phylogenetic tree of Escherichia coli based on the nucleotide sequences of 16S ribosomal RNA genes

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A total of 3.6% of nonlactose fermenting E. coli urinary isolates were detected during our study. Our results were consistent with those of Thompson et al.[14] (approximately 4%) and Versalovic et al.[15] (approximately 5%), while it varied from 6.3%[1] to 9% and 12.4%, respectively, in the studies conducted by Radha and Jeya [11] and Bhat and Bhat.[16] It was found to be as high as 19.7% in the study authored by Chang et al.[17]

  Conclusion Top

Our study highlights some important points. First, unless colony characteristics are observed minutely and full battery of biochemical tests are put up and analyzed properly, E. coli isolates can often be misidentified as other members of Enterobacteriaceae and such misidentification can frequently lead to improper antibiotic treatment. Second, if the isolates are misidentified by conventional methods, then they should be identified by automated methods and further confirmed by molecular methods. Molecular methods cannot be introduced on the regular basis, but can be helpful during epidemiological studies. Based on our observation, the results of 16S rRNA should be interpreted carefully to avoid any kind of discrepancies.


The authors wish to thank the management, technical, and clinical staff of SAIMS Medical College and PG Institute, for their kind support.

Financial support and sponsorship


Conflicts of interest

There are no conflicts of interest.

  References Top

Raksha R, Srinivasa H, Macaden RS. Occurrence and characterisation of uropathogenic Escherichia coli in urinary tract infections. Indian J Med Microbiol 2003;21:102-7.  Back to cited text no. 1
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March SB, Ratnam S. Sorbitol-MacConkey medium for detection of Escherichia coli O157:H7 associated with hemorrhagic colitis. J Clin Microbiol 1986;23:869-72.  Back to cited text no. 2
Bhattacharyya S, Sarfraz A, Ansari MA, Jaiswal N. Characterization and antibiogram of uropathogenic Escherichia coli from a tertiary care hospital in Eastern India. Int J Curr Microbiol Appl Sci 2015;4:701-5.  Back to cited text no. 3
Cheesbrough M. Microbiology. Medical Laboratory Manual for Tropical Countries. Vol. 2. England: Cambridgeshire; 1984. p. 985.  Back to cited text no. 4
Collee JG, Duguid JP, Fraser AG, Marmion BP, Simmons A, editors. Laboratory strategy in the diagnosis of infective syndromes. In: Mackie and McCartney Practical Medical Microbiology. 14th ed. Ch. 4. New York: Churchill Livingstone; 1996. p. 53-94.  Back to cited text no. 5
Bakkali ME, Chaoui I, Zouhdi M, Melloul M, Arakrak A, Mzibri ME, et al . Comparison of the conventional technique and 16s rDNA gene sequencing method in identification of clinical and hospital environmental isolates in Morocco. Afr J Mircobiol Res 2013;7:5637-44.  Back to cited text no. 6
Fontana C, Favaro M, Pelliccioni M, Pistoia ES, Favalli C. Use of the MicroSeq 500 16S rRNA gene-based sequencing for identification of bacterial isolates that commercial automated systems failed to identify correctly. J Clin Microbiol 2005;43:615-9.  Back to cited text no. 7
Fukushima M, Kakinuma K, Kawaguchi R. Phylogenetic analysis of Salmonella, Shigella , and Escherichia coli strains on the basis of the gyrB gene sequence. J Clin Microbiol 2002;40:2779-85.  Back to cited text no. 8
Dereeper A, Guignon V, Blanc G, Audic S, Buffet S, Chevenet F, et al. Phylogeny.fr: Robust phylogenetic analysis for the non-specialist. Nucleic Acids Res 2008;36:465-9.  Back to cited text no. 9
Gadage D, Wankhade A, Muley VV, Paralikar AV, Bhore A. Are inactive E. coli always commensals? Sch J Appl Sci 2014;1:426-7.  Back to cited text no. 10
Radha TR, Jeya M. Prevalence of atypical E. coli causing urinary tract infection in a tertiary care hospital. Aust Med J 2010;3:545.  Back to cited text no. 11
Singleton P. Bacteria in Biology, Biotechnology and Medicine. 5th ed. Newyork: Wiley; 1999. p. 444-54.  Back to cited text no. 12
Khot PD, Fisher MA. Novel approach for differentiating Shigella species and Escherichia coli by matrix-assisted laser desorption ionization-time of flight mass spectrometry. J Clin Microbiol 2013;51:3711-6.  Back to cited text no. 13
Thompson JS, Hodge DS, Borczyk AA. Rapid biochemical test to identify verocytotoxin-positive strains of Escherichia coli serotype O157. J Clin Microbiol 1990;28:2165-8.  Back to cited text no. 14
Versalovic J, Carroll KC, Funke G, Jorgensen JH, Landry ML, Warnock DW. Manual of Clinical Microbiology. 10th ed. Washington, D.C.: American Society for Microbiology; 2011.  Back to cited text no. 15
Bhat KG, Bhat MG. Atypical Escherichia coli in urinary tract infection. Trop Doct 1995;25:127.  Back to cited text no. 16
Chang J, Yu J, Lee H, Ryu H, Park K, Park YJ. Prevalence and characteristics of lactose non-fermenting Escherichia coli in urinary isolates. J Infect Chemother 2014;20:738-40.  Back to cited text no. 17


  [Figure 1]

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