View More View Less
  • 1 Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Science and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
  • | 2 Aix Marseille University, IRD, APHM, MEPHI, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, 19-21 Boulevard Jean Moulin, 13385, Marseille CEDEX 05, France
  • | 3 Laboratory of Clinical Biology, NINI Hospital, Tripoli, Lebanon
Restricted access

Purchase article

USD  $25.00

1 year subscription (Individual Only)

USD  $784.00

Abstract

This study aimed to evaluate the routine identification tools available in Lebanon for differentiation of Escherichia coli and Shigella spp. The identification of 43 isolates defined as Shigella spp. by Api 20E was accessed using MALDI-TOF, serological testing, duplex PCR targeting ipaH (present in Shigella spp. and enteroinvasive E. coli “EIEC”) and lacY (found in E. coli including EIEC but not Shigella spp.) as well as gyrB gene sequencing. Antibiotic susceptibility was investigated as well as Shiga-toxin production. All isolates were identified as E. coli by MALDI-TOF while the PCR showed a disparate group of 26 EIEC, 11 Shigella spp., 5 E. coli and 1 inactive E. coli. However, the sequencing of gyrB gene, which was recently described as a suitable marker for distinguishing E. coli and Shigella spp., identified all isolates as E. coli. Antibiotic resistance was noticeable against ß-lactams, rifampicin, trimethoprim-sulfamethoxazole, gentamicin, and ciprofloxacin. The most common variants of beta-lactamase genes were blaTEM-1, blaCTX-M-15, and blaCTX-M-3. A great discordance between the used methods in identification was revealed herein. An accurate identification technique able to distinguish E. coli from Shigella spp. in routine laboratories is a pressing need in order to select the appropriate treatment and assess the epidemiology of these bacteria.

  • [1]

    WHO. By category | Number of deaths by region – diarrhoeal diseases, http://apps.who.int/gho/data/view.main.CM1002015REG6-CH3?lang=en.

    • Search Google Scholar
    • Export Citation
  • [2]

    Schroeder GN, Hilbi H. Molecular pathogenesis of Shigella spp.: controlling host cell signaling, invasion, and death by type III secretion. Clin Microbiol Rev 2008; 21: 134156.

    • Crossref
    • Search Google Scholar
    • Export Citation
  • [3]

    Lima IFN, Havt A, Lima AAM. Update on molecular epidemiology of Shigella infection. Curr Opin Gastroenterol 2015; 31: 3037.

  • [4]

    Keusch GT, Walker CF, Das JK, Horton S, Habte D. Diarrheal diseases. In: Black RE, Laxminarayan R, Temmerman M, Walker N, editors. Reproductive, maternal, newborn, and child health: disease control priorities. 3rd ed., vol. 2. Washington (DC): The International Bank for Reconstruction and Development | The World Bank; 2016.

    • Search Google Scholar
    • Export Citation
  • [5]

    Kotloff KL, Platts-Mills JA, Nasrin D, Roose A, Blackwelder WC, Levine MM. Global burden of diarrheal diseases among children in developing countries: incidence, etiology, and insights from new molecular diagnostic techniques. Vaccine 2017; 35: 67836789.

    • Crossref
    • Search Google Scholar
    • Export Citation
  • [6]

    Zuo G, Xu Z, Hao B. Shigella strains are not clones of Escherichia coli but sister species in the genus Escherichia. Dev Reprod Biol 2013; 11: 6165.

    • Search Google Scholar
    • Export Citation
  • [7]

    The HC, Thanh DP, Holt KE, Thomson NR, Baker S. The genomic signatures of Shigella evolution, adaptation and geographical spread. Nat Rev Microbiol 2016; 14: 235250.

    • Crossref
    • Search Google Scholar
    • Export Citation
  • [8]

    van den Beld MJC, Reubsaet FAG. Differentiation between Shigella, enteroinvasive Escherichia coli (EIEC) and noninvasive Escherichia coli. Eur J Clin Microbiol Infect Dis 2012; 31: 899904.

    • Crossref
    • Search Google Scholar
    • Export Citation
  • [9]

    Yang C, Li P, Zhang X, Ma Q, Cui X, Li H, et al. Molecular characterization and analysis of high-level multidrug-resistance of Shigella flexneri serotype 4s strains from China. Sci Rep 2016; 6: 29124.

    • Crossref
    • Search Google Scholar
    • Export Citation
  • [10]

    Pavlovic M, Luze A, Konrad R, Berger A, Sing A, Busch U, et al. Development of a duplex real-time PCR for differentiation between E. coli and Shigella spp. J Appl Microbiol 2011; 110: 12451251.

    • Crossref
    • Search Google Scholar
    • Export Citation
  • [11]

    Rahi P, Prakash O, Shouche YS. Matrix-assisted laser desorption/ionization time-of-flight mass-spectrometry (MALDI-TOF MS) based microbial identifications: challenges and scopes for microbial ecologists. Front Microbiol 2016; 7: 1359.

    • Crossref
    • Search Google Scholar
    • Export Citation
  • [12]

    Løbersli I, Wester AL, Kristiansen Å, Brandal LT. Molecular differentiation of Shigella spp. from enteroinvasive E. coli. Eur J Microbiol Immunol 2016; 6: 197205.

    • Crossref
    • Search Google Scholar
    • Export Citation
  • [13]

    Chattaway MA, Schaefer U, Tewolde R, Dallman TJ, Jenkins C. Identification of Escherichia coli and Shigella species from whole-genome sequences. J Clin Microbiol 2017; 55: 616623.

    • Crossref
    • Search Google Scholar
    • Export Citation
  • [14]

    Pettengill EA, Pettengill JB, Binet R. Phylogenetic Analyses of Shigella and Enteroinvasive Escherichia coli for the identification of molecular epidemiological markers: whole-genome comparative analysis does not support distinct genera designation. Front Microbiol 2015; 6: 1573.

    • Crossref
    • Search Google Scholar
    • Export Citation
  • [15]

    Al Bayssari C, Olaitan AO, Dabboussi F, Hamze M, Rolain JM. Emergence of OXA-48-producing Escherichia coli clone ST38 in fowl. Antimicrob Agents Chemother 2015; 59: 745746.

    • Crossref
    • Search Google Scholar
    • Export Citation
  • [16]

    Dhiviya Prabaa MS, Naveen Kumar DR, Yesurajan IF, Anandan S, Kamini W, Balaji V. Identification of nonserotypeable Shigella spp. using genome sequencing: a step forward. Future Sci OA 2017; 3: FSO229.

    • Crossref
    • Search Google Scholar
    • Export Citation
  • [17]

    Bélanger SD, Boissinot M, Ménard C, Picard FJ, Bergeron MG. Rapid detection of Shiga toxin-producing bacteria in feces by multiplex PCR with molecular beacons on the smart cycler. J Clin Microbiol 2002; 40: 14361440.

    • Crossref
    • Search Google Scholar
    • Export Citation
  • [18]

    EUCAST. The European committee on antimicrobial susceptibility testing, http://www.eucast.org/.

  • [19]

    Roschanski N, Fischer J, Guerra B, Roesler U. Development of a multiplex real-time PCR for the rapid detection of the predominant beta-lactamase genes CTX-M, SHV, TEM and CIT-type AmpCs in Enterobacteriaceae. PloS One 2014; 9:e100956.

    • Crossref
    • Search Google Scholar
    • Export Citation
  • [20]

    Edelstein M, Pimkin M, Palagin I, Edelstein I, Stratchounski L. Prevalence and molecular epidemiology of CTX-M extended-spectrum beta-lactamase-producing Escherichia coli and Klebsiella pneumoniae in Russian hospitals. Antimicrob Agents Chemother 2003; 47: 37243732.

    • Crossref
    • Search Google Scholar
    • Export Citation
  • [21]

    Tajbakhsh M, Garcia Migura L, Rahbar M, Svendsen CA, Mohammadzadeh M, Zali MR, et al. Antimicrobial-resistant Shigella infections from Iran: an overlooked problem?. J Antimicrob Chemother 2012; 67: 11281133.

    • Crossref
    • Search Google Scholar
    • Export Citation
  • [22]

    Yagi T, Kurokawa H, Shibata N, Shibayama K, Arakawa Y. A preliminary survey of extended-spectrum beta-lactamases (ESBLs) in clinical isolates of Klebsiella pneumoniae and Escherichia coli in Japan. FEMS Microbiol Lett 2000; 184: 5356.

    • Search Google Scholar
    • Export Citation
  • [23]

    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: 37113716.

    • Crossref
    • Search Google Scholar
    • Export Citation
  • [24]

    Hsu BM, Wu SF, Huang SW, Tseng YJ, Ji DD, Chen JS, et al. Differentiation and identification of Shigella spp. and enteroinvasive Escherichia coli in environmental waters by a molecular method and biochemical test. Water Res 2010; 44: 949955.

    • Crossref
    • Search Google Scholar
    • Export Citation
  • [25]

    Ekwall E, Dimander M. Comparison of micro-ID with API 20E for identification of Salmonella, Shigella and Yersinia species. Eur J Clin Microbiol 1982; 1: 134137.

    • Crossref
    • Search Google Scholar
    • Export Citation
  • [26]

    Li B, Liu H, Wang W. Multiplex real-time PCR assay for detection of Escherichia coli O157:H7 and screening for non-O157 Shiga toxin-producing E. coli .BMC Microbiol 2017; 17: 215.

    • Crossref
    • Search Google Scholar
    • Export Citation
  • [27]

    Khot PD, Couturier MR, Wilson A, Croft A, Fisher MA. Optimization of matrix-assisted laser desorption ionization-time of flight mass spectrometry analysis for bacterial identification. J Clin Microbiol 2012; 50: 38453852.

    • Crossref
    • Search Google Scholar
    • Export Citation
  • [28]

    Kim HJ, Ryu JO, Song JY, Kim HY. Multiplex polymerase chain reaction for identification of Shigellae and Four Shigella species using novel genetic markers screened by comparative genomics. Foodborne Pathog Dis 2017; 14: 400406.

    • Crossref
    • Search Google Scholar
    • Export Citation
  • [29]

    Liu B, Knirel YA, Feng L, Perepelov AV, Senchenkova SN, Wang Q, et al. Structure and genetics of Shigella O antigens. FEMS Microbiol Rev 2008; 32: 627653.

    • Crossref
    • Search Google Scholar
    • Export Citation
  • [30]

    Anandan S, Muthuirulandi Sethuvel DP, Gajendiren R, Verghese VP, Walia K, Veeraraghavan B. Molecular characterization of antimicrobial resistance in clinical Shigella isolates during 2014 and 2015: trends in South India. Germs 2017; 7: 115122.

    • Crossref
    • Search Google Scholar
    • Export Citation
  • [31]

    Shakya G, Acharya J, Adhikari S, Rijal N. Shigellosis in Nepal: 13 years review of nationwide surveillance. J Health Popul Nutr 2016; 35: 36.

  • [32]

    Devanga Ragupathi NK, Muthuirulandi Sethuvel DP, Inbanathan FY, Veeraraghavan B. Accurate differentiation of Escherichia coli and Shigella serogroups: challenges and strategies. New Microbes New Infect 2018; 21: 5862.

    • Crossref
    • Search Google Scholar
    • Export Citation
  • [33]

    Ashida H, Sasakawa C. Shigella IpaH family effectors as a versatile model for studying Pathogenic Bacteria. Front Cell Infect Microbiol 2015; 5: 100.

    • Search Google Scholar
    • Export Citation
  • [34]

    Ashida H, Toyotome T, Nagai T, Sasakawa C. Shigella chromosomal IpaH proteins are secreted via the type III secretion system and act as effectors. Mol Microbiol 2007; 63: 680693.

    • Crossref
    • Search Google Scholar
    • Export Citation
  • [35]

    Hazen TH, Leonard SR, Lampel KA, Lacher DW, Maurelli AT, Rasko DA. Investigating the relatedness of Enteroinvasive Escherichia coli to other E. coli and Shigella isolates by using comparative genomics. Infect Immun 2016; 84: 23622371.

    • Crossref
    • Search Google Scholar
    • Export Citation
  • [36]

    Kasai H, Tamura T, Harayama S. Intrageneric relationships among Micromonospora species deduced from gyrB-based phylogeny and DNA relatedness. Int J Syst Evol Microbiol 2000; 50: 127134.

    • Crossref
    • Search Google Scholar
    • Export Citation
  • [37]

    Wang LT, Lee FL, Tai CJ, Kasai H. Comparison of gyrB gene sequences, 16S rRNA gene sequences and DNA-DNA hybridization in the Bacillus subtilis group. Int J Syst Evol Microbiol 2007; 57: 18461850.

    • Crossref
    • Search Google Scholar
    • Export Citation
  • [38]

    Vos M, Quince C, Pijl AS, de Hollander M, Kowalchuk GA. A Comparison of rpoB and 16S rRNA as markers in pyrosequencing studies of bacterial diversity. PLoS One 2012; 7:e30600.

    • Crossref
    • Search Google Scholar
    • Export Citation
  • [39]

    Chamoun K, Farah M, Araj G, Daoud Z, Moghnieh R, Salameh P, et al. Lebanese Society of Infectious Diseases study group (LSID study group): surveillance of antimicrobial resistance in Lebanese hospitals: retrospective nationwide compiled data. Int J Infect Dis 2016; 46: 6470.

    • Crossref
    • Search Google Scholar
    • Export Citation
  • [40]

    Daoud Z, Hakime N. Prevalence and susceptibility patterns of extended-spectrum beta-lactamase-producing Escherichia coli and Klebsiella pneumoniae in a general university hospital in Beirut, Lebanon. Rev Esp Quimioter 2003; 16: 233238.

    • Search Google Scholar
    • Export Citation
  • [41]

    Keddy KH, Sooka A, Crowther-Gibson P, Quan V, Meiring S, Cohen C, et al. Group for Enteric, Respiratory, and Meningeal Disease Surveillance in South Africa (GERMS-SA): systemic shigellosis in South Africa. Clin Infect Dis 2012; 54: 14481454.

    • Crossref
    • Search Google Scholar
    • Export Citation
  • [42]

    Madhavan A, Balakrishnan S, Vasudevapanicker J. Antibiotic susceptibility pattern of Shigella isolates in a tertiary healthcare center. J Lab Phys 2018; 10: 140144.

    • Search Google Scholar
    • Export Citation
  • [43]

    Liu Y, Cheng Y, Yang H, Hu L, Cheng J, Ye Y, et al. Characterization of extended-spectrum β-lactamase genes of Shigella flexneri isolates with fosfomycin resistance from patients in China. Ann Lab Med 2017; 37: 415419.

    • Crossref
    • Search Google Scholar
    • Export Citation
  • [44]

    Dekker JP, Frank KM. Salmonella, Shigella, and Yersinia. Clin Lab Med 2015; 35: 225246.

  • [45]

    Valenzuela C, Legarraga P, Peña A, Arenas A, Berkowitz L, Ramírez G, et al. Etiologic and clinical characterization of community acquired gastroenteritis in adult patients in a Chilean emergency room by the film array GI panel. PLoS One 2018; 13: e0207850.

    • Crossref
    • Search Google Scholar
    • Export Citation

Monthly Content Usage

Abstract Views Full Text Views PDF Downloads
Jan 2021 25 0 0
Feb 2021 38 1 1
Mar 2021 37 2 4
Apr 2021 89 0 1
May 2021 27 0 0
Jun 2021 24 0 0
Jul 2021 0 0 0