Molecular epidemiology of Shigella flexneri isolated from pediatrics in a diarrhea-endemic area of Khyber Pakhtunkhwa, Pakistan

  • Iqbal Nisa
  • Muhammad QasimEmail author
  • Arnold Driessen
  • Jeroen Nijland
  • Fazli Bari
  • Mohammad Haroon
  • Hazir Rahman
  • Nusrat Yasin
  • Taj Ali Khan
  • Mubbashir Hussain
  • Waheed Ullah
Original Article


Shigella flexneri is considered as an important causative agent of Shigellosis causing diarrhea in the countries with a low socioeconomic status. No study has been carried out on the molecular prevalence of S. flexneri in Khyber Pakhtunkhwa, Pakistan. So this study was designed to evaluate the molecular prevalence of S. flexneri and their associated risk factors. A total of 2014 diarrheal stool samples were collected from January 2016 to May 2017 from pediatrics patients of Khyber Pakhtunkhwa followed by identification of S. flexneri through biochemical, serological, and molecular methods. The overall prevalence of Shigella species was found to be 7.9% (n = 160). The predominant Shigella specie was S. flexneri (n = 155, 96.8%) followed by S. boydii (n = 5, 3.1%). Interestingly, no sample was found positive for S. sonnei and S. dysenteriae. The majority of Shigellosis cases occurred from June to September. Potential risk factors related with Shigellosis were unhygienic latrine usage, bad hand washing, and consumption of unhygienic food and water, and pipe leakage in the sewage system. In this study, we have observed a high number of Shigellosis cases especially those caused by S. flexneri. It is suggested that effective health awareness programs should be organized by the regional health authorities to minimize the magnitude of pediatrics Shigellosis.


S. flexneri Pediatrics Molecular epidemiology Diarrhea Endemic area Pakistan 


Authors’ contributions

Muhammad Qasim, Iqbal Nisa, Arnold Driessen, Jeroen Nijland, and Fazli Bari designed the study, carried out the experiments, analyzed the data, and drafted the manuscript. Muhammad Qasim, Iqbal Nisa, and Jeroen Nijland helped in data analysis and results interpretation. Muhammad Qasim, Arnold Driessen, Jeroen Nijland, Fazli Bari, Mohammad Haroon, Hazir Rehman, Nusrat Yasin, Taj Ali Khan, Mubbashir Hussain, and Waheed Ullah critically reviewed and commented on the manuscript.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical approval

All procedures followed were in accordance with the ethical standards of the responsible committee on human experimentation (institutional and national) and with the Helsinki Declaration of 1975, as revised in 2000. In addition, the institutional research ethical committee approved the present study.

Informed consent

Informed consent was obtained from all patients/guardian for being included in the study.


  1. 1.
    Mardaneh J, Abbas S, Afrugh P (2013) Prevalence of Shigella species and antimicrobial resistance patterns of isolated strains from infected pediatrics in Tehran. Int J Enteric Pathog 1:28–31CrossRefGoogle Scholar
  2. 2.
    Saima SA, Abbas F et al (2018) Isolation & identification of Shigella species from food and water samples of Quetta, Pakistan. Pure Appl Biol 7:227–235Google Scholar
  3. 3.
    Ashkenazi S (2004) Shigella infections in children: new insights. Semin Pediatr Infect Dis 15:246–252CrossRefGoogle Scholar
  4. 4.
    Fan W, Qian H, Shang W et al (2017) Low distribution of genes encoding virulence factors in Shigella flexneri serotypes 1b clinical isolates from eastern Chinese populations. Gut Pathog 9:76CrossRefGoogle Scholar
  5. 5.
    Sharma A, Singh SK, Bajpai D (2010) Phenotypic and genotypic characterization of Shigella spp. with reference to its virulence genes and antibiogram analysis from river Narmada. Microbiol Res 165:33–42CrossRefGoogle Scholar
  6. 6.
    Wang S, Chen JHAW (2012) A rapid and specific PCR method for the detection of Shigella spp. in spiked samples. J Food Drug Anal 20:59–65Google Scholar
  7. 7.
    Khalil IA, Troeger C, Blacker BF et al (2018) Morbidity and mortality due to Shigella and enterotoxigenic Escherichia coli diarrhea: the global burden of disease study 1990–2016. Lancet Infect Dis 18:1229–1240CrossRefGoogle Scholar
  8. 8.
    Warren BR, Parish ME, Schneider KR (2006) Shigella as a foodborne pathogen and current methods for detection in food. Crit Rev Food Sci Nutr 46:551–567CrossRefGoogle Scholar
  9. 9.
    Muthuirulandi Sethuvel DP, Devanga Ragupathi NK, Anandan S, Veeraraghavan B (2017) Update on: Shigella new serogroups/serotypes and their antimicrobial resistance. Lett Appl Microbiol 64:8–18CrossRefGoogle Scholar
  10. 10.
    Rahimi E, Shirazi F, Khamesipour F (2017) Isolation and study of the antibiotic resistance properties of Shigella Species in meat and meat products. J Food Process Preserv 41:e12947CrossRefGoogle Scholar
  11. 11.
    Platts-Mills JA, McCormick BJJ, Kosek M et al (2014) Methods of analysis of enteropathogen infection in the MAL-ED cohort study. Clin Infect Dis 59:S233–S238CrossRefGoogle Scholar
  12. 12.
    Koneman EW, Allen SD, Janda WM, Schreckenberger PC, Winn WC (1997) Colour atlas and textbook of diagnostic microbiology (5th edition) Lippincott, NY, USAGoogle Scholar
  13. 13.
    Carlos J, Junior R, Tamanini R et al (2016) Efficiency of boiling and four other methods for genomic DNA extraction of deteriorating spore-forming bacteria from milk. Semina: Ciencias Agrarias 37:3069–3078Google Scholar
  14. 14.
    James G (2010) Universal bacterial identification by PCR and DNA sequencing of 16S rRNA gene. In: Schuller M, Sloots PT, James SG, Halliday LC, Carter WJI (eds) PCR for clinical microbiology. Springer, Dordrecht, pp 209–214CrossRefGoogle Scholar
  15. 15.
    Wang XY, Du L, Von Seidlein L et al (2005) Occurrence of Shigellosis in the young and elderly in rural China: results of a 12-month population-based surveillance study. Am J Trop Med Hyg 73:416–422CrossRefGoogle Scholar
  16. 16.
    Opintan JA, Newman MJ (2007) Distribution of serogroups and serotypes of multiple drug resistant Shigella isolates. Ghana Med J 41:7–11Google Scholar
  17. 17.
    Nisar M, Ahmed MD, Hassan Mushtaq M et al (2014) Clinico-epidemiology of Shigellosis in children suffering from diarrhea in district Lahore, Pakistan. Int J Curr Microbiol App Sci 3:950–957Google Scholar
  18. 18.
    Orrett FA (2008) Prevalence of Shigella serogroups and their antimicrobial resistance patterns in southern Trinidad. J Health Popul Nutr 26:456–462PubMedPubMedCentralGoogle Scholar
  19. 19.
    Ghaemi EO, Aslani MM, Moradi AV et al (2007) Epidemiology of Shigella-associated diarrhea in Gorgan, north of Iran. Saudi J Gastroenterol 13:129–132CrossRefGoogle Scholar
  20. 20.
    Khan AAI, Huq S, Malek MA et al (2004) Shigella serotypes among hospitalized patients in urban Bangladesh and their antimicrobial resistance. Epidemiol Infect 132:773–777CrossRefGoogle Scholar
  21. 21.
    Mache A (2001) Antibiotic resistance and sero-groups of Shigella among paediatric out-patients in Southwest Ethiopia. East Afr Med J 78:296–299CrossRefGoogle Scholar
  22. 22.
    Thompson CN, Duy PT, Baker S (2015) The rising dominance of Shigella sonnei: an intercontinental shift in the etiology of bacillary dysentery. PLoS Negl Trop Dis 9:e0003708CrossRefGoogle Scholar
  23. 23.
    Abdu A, Aboderin AO, Elusiyan JB et al (2013) Serogroup distribution of Shigella in Ile-Ife, southwest Nigeria. Trop Gastroenterol 34:164–169CrossRefGoogle Scholar
  24. 24.
    Yismaw G, Negeri C, Kassu A (2008) A five-year antimicrobial resistance pattern of Shigella isolated from stools in the Gondar university hospital, Northwest Ethiopia. Trop Dr 38:43–45CrossRefGoogle Scholar
  25. 25.
    Shapiro RL, Kumar L, Phillips-Howard P et al (2001) Antimicrobial resistant bacterial diarrhea in rural Western Kenya. J Infect Dis 183:1701–1704CrossRefGoogle Scholar
  26. 26.
    Brooks JT, Ochieng JB, Kumar L et al (2006) Surveillance for bacterial diarrhea and antimicrobi resistance in rural Western Kenya, 1997-2003. Clin Infect Dis 43:393–401CrossRefGoogle Scholar
  27. 27.
    Chang Z, Zhang J, Ran L et al (2016) The changing epidemiology of bacillary dysentery and characteristics of antimicrobial resistance of Shigella isolated in China from 2004–2014. BMC Infect Dis 16:685CrossRefGoogle Scholar
  28. 28.
    Cui X, Wang J, Yang C et al (2015) Prevalence and antimicrobial resistance of Shigella flexneri serotype 2 variant in China. Front Microbiol 6:435CrossRefGoogle Scholar
  29. 29.
    Abu-elyazeed RR, Wierzba TF, Frenck RW, Putnam SD, Rao MR, Savarino SJ, Kamal KA, Peruski JR, Abd-El messih IA, El-Alkamy S, Naficy AB (2004) Epidemiology of Shigella-associated diarrhea in rural Egyptian children. Am J Trop Med Hyg 71:367–372CrossRefGoogle Scholar
  30. 30.
    Molbak K (2000) The epidemiology of diarrhoeal diseases in early childhood. A review of community studies in Guinea-Bissau. Dan Med Bull 47:340–358PubMedGoogle Scholar
  31. 31.
    Hossain MA, Albert MJ, Hasan KZ (1990) Epidemiology of Shigellosis in teknaf, a coastal area of Bangladesh: a 10-year survey. Epidemiol Infect 105:41–49CrossRefGoogle Scholar
  32. 32.
    Sousa ABM, Mendes EN, Collares GB et al (2013) Shigella in Brazilian children with acute diarrhea: prevalence, antimicrobial resistance and virulence genes. Mem Inst Oswaldo Cruz 108:30–35CrossRefGoogle Scholar
  33. 33.
    Anteneh ZA, Andargie K, Tarekegn M (2017) Prevalence and determinants of acute diarrhea among children younger than five years old in Jabithennan district, Northwest Ethiopia, 2014. BMC Public Health 17:99CrossRefGoogle Scholar
  34. 34.
    Mamo A, Hailu A (2014) Assessment of prevalence and related factors of diarrheal diseases among under-five year’s children in debrebirehan referral hospital, Debrebirehan town, North shoa zone, Amhara region, Ethiopia. OALib 01:1–14CrossRefGoogle Scholar
  35. 35.
    Thiam S, Diene AN, Fuhrimann S et al (2017) Prevalence of diarrhea and risk factors among children under five years old in Mbour, Senegal: a cross-sectional study. Infect Dis Poverty 6:109CrossRefGoogle Scholar
  36. 36.
    Godana W (2013) Environmental factors associated with acute diarrhea among children under five years of age in derashe district, Southern Ethiopia. Sci J Public Health 1:119CrossRefGoogle Scholar
  37. 37.
    Chompook P, Todd J, Wheeler JG et al (2006) Risk factors for Shigellosis in Thailand. Int J Infect Dis 10:425–433CrossRefGoogle Scholar
  38. 38.
    Swaddiwudhipong W, Karintraratana SKS (1995) A common-source outbreak of Shigellosis involving a piped public water supply in northern Thai communities. J Trop Med Hyg 98:145–150PubMedGoogle Scholar
  39. 39.
    Egoz N, Shmilovitz M, Kretzer B et al (1991) An outbreak of Shigella sonnei infection due to contamination of a municipal water supply in northern Israel. J Inf Secur 22:87–93Google Scholar
  40. 40.
    Mengistie B, Berhane Y, Worku A (2013) Prevalence of diarrhea and associated risk factors among children under-five years of age in Eastern Ethiopia: a cross-sectional study. Open J Prev Med 03:446–453CrossRefGoogle Scholar

Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2020

Authors and Affiliations

  • Iqbal Nisa
    • 1
  • Muhammad Qasim
    • 1
    Email author
  • Arnold Driessen
    • 2
  • Jeroen Nijland
    • 2
  • Fazli Bari
    • 3
    • 4
  • Mohammad Haroon
    • 5
  • Hazir Rahman
    • 6
  • Nusrat Yasin
    • 1
  • Taj Ali Khan
    • 1
  • Mubbashir Hussain
    • 1
  • Waheed Ullah
    • 1
  1. 1.Department of MicrobiologyKohat University of Science and TechnologyKohatPakistan
  2. 2.Department of Molecular Microbiology, Groningen Biomolecular Sciences, and Biotechnology Institute, Faculty of Science and EngineeringRijksuniversiteit GroningenGroningenThe Netherlands
  3. 3.Department of PathologyLady Reading HospitalPeshawarPakistan
  4. 4.Department of MicrobiologyNowshera Medical CollegeNowsheraPakistan
  5. 5.Department of MedicineKhyber Teaching HospitalPeshawarPakistan
  6. 6.Department of MicrobiologyAbdul Wali Khan UniversityMardanPakistan

Personalised recommendations