Carbapenem Resistance Profiles of Pathogenic Escherichia coli in Uganda


  •   Kenneth Ssekatawa

  •   Denis K. Byarugaba

  •   Jesca L. Nakavuma

  •   Charles D. Kato

  •   Francis Ejobi

  •   Robert Tweyongyere

  •   Eddie M. Wampande


Escherichia coli has been implicated as one of the main etiological agents of diarrhea, urinary tract infections, meningitis and septicemia worldwide. The ability to cause diseases is potentiated by presence of virulence factors. The virulence factors influence the capacity of E. coli to infect and colonize different body systems. Thus, pathogenic E. coli are grouped into DEC strains that are mainly clustered in phylogenetic group B1 and A; ExPEC belonging to A, B2 and D. Coexistence of virulence and beta-lactamase encoding genes complicates treatment outcomes. Therefore, this study aimed at presenting the carbapenem resistance (CR) profiles among pathogenic E. coli. This was a retrospective cross-sectional study involving use of 421 archived E. coli clinical isolates collected in 2019 from four Uganda tertiary hospitals. The isolates were subjected to antibiotics sensitivity assays to determine phenotypic resistance. Four sets of multiplex PCR were performed to detect CR genes, DEC pathotypes virulence genes, ExPEC PAI and the E. coli phylogenetic groups. Antibiotic susceptibility revealed that all the 421 E. coli isolates used were MDR as they exhibited 100% resistance to more than one of the first-line antibiotics. The study registered phenotypic and genotypic CR prevalence of 22.8% and 33.0% respectively. The most predominant gene was blaOXA-48 with genotypic frequency of 33.0%, then blaVIM (21.0%), blaIMP (16.5%), blaKPC (14.8%) and blaNDM (14.8%). Spearman’s correlation revealed that presence of CR genes was highly associated with phenotypic resistance. Furthermore, of 421 MDR E. coli isolates, 19.7% harboured DEC virulence genes, where EPEC recorded significantly higher prevalence (10.8%) followed by S-ETEC (3.1%), STEC (2.9%), EIEC (2.0%) and L-ETEC (2.0%). Genetic analysis characterized 46.1% of the isolates as ExPEC and only PAI IV536 (33.0%) and PAI IICFT073 (13.1%) were detected. Phylogenetic group B2 was predominantly detected (41.1%), followed by A (30.2%), B1(21.6%), and D (7.1%). Furthermore, 38.6% and 23.1% of the DEC and ExPEC respectively expressed phenotypic resistance. Our results exhibited significant level of CR carriage among the MDR DEC and ExPEC clinical isolates belonging to phylogenetic groups B1 and B2 respectively. Virulence and CR genetic factors are mainly located on mobile elements. Thus, constitutes a great threat to the healthcare system as this promotes horizontal gene transfer.

Keywords: Carbapenem resistance, Virulence genes, Pathogenicity islands, Pathogenic E. coli, E. coli phylogenetic groups


Ali, M.M.M., et al., Molecular characterization of diarrheagenic Escherichia coli from Libya. J The American journal of tropical medicine hygiene, 2012. 86(5): p. 866-871.

Sader, H.S., et al., Four-year evaluation of frequency of occurrence and antimicrobial susceptibility patterns of bacteria from bloodstream infections in Latin American medical centers. J Diagnostic microbiology infectious disease, 2002. 44(3): p. 273-280.

Kaper, J.B., J.P. Nataro, and H.L. Mobley, Pathogenic escherichia coli. J Nature reviews microbiology, 2004. 2(2): p. 123-140.

Russo, T.A. and J.R. Johnson, Proposal for a new inclusive designation for extraintestinal pathogenic isolates of Escherichia coli: ExPEC. J The Journal of infectious diseases, 2000. 181(5): p. 1753-1754.

Smith, J.L., et al., Extraintestinal pathogenic Escherichia coli. 2007. 4(2): p. 134-163.

Aranda, K.R., et al., Single multiplex assay to identify simultaneously enteropathogenic, enteroaggregative, enterotoxigenic, enteroinvasive and Shiga toxin-producing Escherichia coli strains in Brazilian children. 2007. 267(2): p. 145-150.

Brandal, L.T., et al., Octaplex PCR and fluorescence-based capillary electrophoresis for identification of human diarrheagenic Escherichia coli and Shigella spp. 2007. 68(2): p. 331-341.

Diamant, E., et al., Phylogeny and strain typing of Escherichia coli, inferred from variation at mononucleotide repeat loci. 2004. 70(4): p. 2464-2473.

Clements, A., et al., Infection strategies of enteric pathogenic Escherichia coli. 2012. 3(2): p. 71-87.

Johnson, J.R. and A.L. Stell, Extended virulence genotypes of Escherichia coli strains from patients with urosepsis in relation to phylogeny and host compromise. J The Journal of infectious diseases, 2000. 181(1): p. 261-272.

Johnson, T.J., et al., Identification of minimal predictors of avian pathogenic Escherichia coli virulence for use as a rapid diagnostic tool. Journal of clinical microbiology, 2008. 46(12): p. 3987-3996.

Le Bouguenec, C., M. Archambaud, and A. Labigne, Rapid and specific detection of the pap, afa, and sfa adhesin-encoding operons in uropathogenic Escherichia coli strains by polymerase chain reaction. J Journal of clinical microbiology, 1992. 30(5): p. 1189-1193.

Clermont, O., S. Bonacorsi, and E. Bingen, Rapid and simple determination of theEscherichia coli phylogenetic group. Applied environmental microbiology, 2000. 66(10): p. 4555-4558.

Barzan, M., D. Gharibi, and M. Ghorbanpoor, Phylogenetic grouping and phenotypic detection of extended-spectrum β-lactamases among Escherichia coli from calves and dairy cows in Khuzestan, Iran. Haji, Hajikolaei Mohammad Rahim Pourmehdi, Boroujeni Mehdi 2017.

Ssekatawa, K., et al., Prevalence of pathogenic Klebsiella pneumoniae based on PCR capsular typing harbouring carbapenemases encoding genes in Uganda tertiary hospitals. Antimicrobial Resistance & Infection Control, 2021. 10(1): p. 57.

Ssekatawa, K., et al., A systematic review: the current status of carbapenem resistance in East Africa. BMC Res Notes, 2018. 11(1): p. 629.

CLSI., Performance Standards for Antimicrobial Disk Susceptibility Tests for Bacteria Isolated from Animals: CLSI Supplement VET01SEd5E; Replaces VET01-S2. 2020: Clinical and Laboratory Standards Institute.

Dallenne, C., et al., Development of a set of multiplex PCR assays for the detection of genes encoding important β-lactamases in Enterobacteriaceae. 2010. 65(3): p. 490-495.

Fischer, J., et al., Escherichia coli producing VIM-1 carbapenemase isolated on a pig farm. 2012. 67(7): p. 1793-1795.

Ochman, H. and R.K. Selander, Standard reference strains of Escherichia coli from natural populations. J Journal of bacteriology, 1984. 157(2): p. 690-693.

Toma, C., et al., Multiplex PCR assay for identification of human diarrheagenic Escherichia coli. 2003. 41(6): p. 2669-2671.

Sabaté, M., et al., Pathogenicity island markers in commensal and uropathogenic Escherichia coli isolates. 2006. 12(9): p. 880-886.

Dias, M.T., et al., Molecular characterization and evaluation of antimicrobial susceptibility of enteropathogenic E. coli (EPEC) isolated from minas soft cheese. J Food Science Technology, 2012. 32(4): p. 747-753.

Oswald, E., et al., Typing of intimin genes in human and animal enterohemorrhagic and enteropathogenic Escherichia coli: characterization of a new intimin variant. 2000. 68(1): p. 64-71.

Yamasaki, S., et al., Typing of verotoxins by DNA colony hybridization with poly‐and oligonucleotide probes, a bead‐enzyme‐linked immunosorbent assay, and polymerase chain reaction. 1996. 40(5): p. 345-352.

López-Saucedo, C., et al., Single multiplex polymerase chain reaction to detect diverse loci associated with diarrheagenic Escherichia coli. 2003. 9(1): p. 127.

Sethabutr, O., et al., Detection of Shigellae and enteroinvasive Escherichia coli by amplification of the invasion plasmid antigen H DNA sequence in patients with dysentery. 1993. 167(2): p. 458-461.

Ratchtrachenchai, O.-A., S. Subpasu, and K. Ito, Investigation on enteroaggregative Escherichia coli infection by multiplex PCR. J Bull. Dept. Med. Sci, 1997. 39(4): p. 211-220.

Mushi, M.F., et al., Carbapenemase genes among multidrug resistant gram negative clinical isolates from a tertiary hospital in Mwanza, Tanzania. 2014. 2014.

Ogbolu, D. and M. Webber, High-level and novel mechanisms of carbapenem resistance in Gram-negative bacteria from tertiary hospitals in Nigeria. J International journal of antimicrobial agents, 2014. 43(5): p. 412-417.

Olalekan, A., et al., High proportion of carbapenemase-producing Escherichia coli and Klebsiella pneumoniae among extended-spectrum β-lactamase-producers in Nigerian hospitals. J Glob Antimicrob Resist, 2020. 21: p. 8-12.

Oduyebo, O.O., et al., Phenotypic determination of carbapenemase producing enterobacteriaceae isolates from clinical specimens at a tertiary hospital in Lagos, Nigeria. Niger Postgrad Med J, 2015. 22(4): p. 223-7.

Pawar, S.K., et al., Carbapenem–resistant Enterobacteriaceae: Prevalence and bacteriological profile in a tertiary teaching hospital from rural western India. 2018. 5(3): p. 342-347.

Hackman, H.K., et al., Emergence of Carbapenem-resistant Enterobacteriaceae among Extended-spectrum Beta-lactamase Producers in Accra, Ghana. 2017. 7(24).

Mahrach, Y., et al., Phenotypic and molecular study of carbapenemase-producing Enterobacteriaceae in a regional hospital in northern Morocco. 2019. 3: p. 113.

Eshetie, S., et al., Multidrug resistant and carbapenemase producing Enterobacteriaceae among patients with urinary tract infection at referral Hospital, Northwest Ethiopia. Antimicrobial Resistance and Infection Control, 2015. 4(1): p. 12.

Perovic, O., et al., Carbapenem-resistant Enterobacteriaceae in patients with bacteraemia at tertiary hospitals in South Africa, 2015 to 2018. European Journal of Clinical Microbiology & Infectious Diseases, 2020. 39(7): p. 1287-1294.

Singh-Moodley, A. and O. Perovic, Antimicrobial susceptibility testing in predicting the presence of carbapenemase genes in Enterobacteriaceae in South Africa. %J BMC infectious diseases, 2016. 16(1): p. 536.

Kotb, S., et al., Epidemiology of carbapenem-resistant Enterobacteriaceae in Egyptian intensive care units using National Healthcare–associated Infections Surveillance Data, 2011–2017. 2020. 9(1): p. 1-9.

ElMahallawy, H.A., et al., Spread of carbapenem resistant Enterobacteriaceae at tertiary care cancer hospital in Egypt. 2018. 50(7): p. 560-564.

Tawfick, M.M., et al., The emergence of carbapenemase blaNDM genotype among carbapenem-resistant Enterobacteriaceae isolates from Egyptian cancer patients. European Journal of Clinical Microbiology & Infectious Diseases, 2020. 39(7): p. 1251-1259.

Okoche, D., et al., Prevalence and characterization of carbapenem-resistant Enterobacteriaceae isolated from Mulago National Referral Hospital, Uganda. 2015. 10(8): p. e0135745.

Ampaire, L.M., et al., Epidemiology of carbapenem resistance among multi-drug resistant enterobacteriaceae in Uganda. 2015. 8(2): p. 418.

Mahmoud, N.E., H.N. Altayb, and R.M. Gurashi, Detection of Carbapenem-Resistant Genes in Escherichia coli Isolated from Drinking Water in Khartoum, Sudan. Journal of Environmental and Public Health, 2020. 2020: p. 2571293.

Kollenda, H., et al., Screening for carbapenemases in ertapenem-resistant Enterobacteriaceae collected at a Tunisian hospital between 2014 and 2018. 2019. 9(1): p. 9-13.

Baran, I. and N. Aksu, Phenotypic and genotypic characteristics of carbapenem-resistant Enterobacteriaceae in a tertiary-level reference hospital in Turkey. J Annals of clinical microbiology antimicrobials, 2016. 15(1): p. 20.

Demir, Y., Y. Zer, and I. Karaoglan, Investigation of VIM, IMP, NDM-1, KPC AND OXA-48 enzymes in Enterobacteriaceae strains. J Pakistan journal of pharmaceutical sciences, 2015. 28.

Nordmann, P., L. Dortet, and L. Poirel, Carbapenem resistance in Enterobacteriaceae: here is the storm! J Trends in molecular medicine, 2012. 18(5): p. 263-272.

Nordmann, P., T. Naas, and L. Poirel, Global spread of Carbapenemase-producing Enterobacteriaceae. Emerg Infect Dis, 2011. 17(10): p. 1791-8.

Codjoe, F.S. and E.S. Donkor, Carbapenem Resistance: A Review. Med Sci (Basel), 2017. 6(1).

Bou, G., et al., Characterization of a nosocomial outbreak caused by a multiresistant Acinetobacter baumannii strain with a carbapenem-hydrolyzing enzyme: high-level carbapenem resistance in A. baumannii is not due solely to the presence of beta-lactamases. J Clin Microbiol, 2000. 38(9): p. 3299-305.

Crowley, B., V. Benedí, and A. Doménech-Sánchez, Expression of SHV-2 beta-lactamase and of reduced amounts of OmpK36 porin in Klebsiella pneumoniae results in increased resistance to cephalosporins and carbapenems. Antimicrob Agents Chemother, 2002. 46(11): p. 3679-82.

Yang, D., Y. Guo, and Z. Zhang, Combined porin loss and extended spectrum β-lactamase production is associated with an increasing imipenem minimal inhibitory concentration in clinical Klebsiella pneumoniae strains. J Current microbiology, 2009. 58(4): p. 366.

Queenan, A. and K. Bush, Carbapenemases: the versatile beta-lactamases. Clin Microbiol Rev, 2007. 20(3): p. 440-58, table of contents.

Okeke, I.N., Diarrheagenic Escherichia coli in sub-Saharan Africa: status, uncertainties and necessities. J The journal of infection in developing countries, 2009. 3(11): p. 817-842.

Keskimäki, M., et al., Prevalence of diarrheagenic Escherichia coli in finns with or without diarrhea during a round-the-world trip. J Clin Microbiol, 2000. 38(12): p. 4425-9.

Zhou, Y., et al., Characteristics of diarrheagenic Escherichia coli among children under 5 years of age with acute diarrhea: a hospital based study. 2018. 18(1): p. 63.

Mandomando, I.M., et al., Etiology of diarrhea in children younger than 5 years of age admitted in a rural hospital of southern Mozambique. Am J Trop Med Hyg, 2007. 76(3): p. 522-7.

Aijuka, M., et al., Enteroaggregative Escherichia coli is the predominant diarrheagenic E. coli pathotype among irrigation water and food sources in South Africa. Int J Food Microbiol, 2018. 278: p. 44-51.

Tanih, N., et al., Prevalence of diarrheagenic Escherichia coli in young children from rural South Africa: The Mal-ED cohort. 2014. 21: p. 149.

Moyo, S.J., et al., Identification of diarrheagenic Escherichia coli isolated from infants and children in Dar es Salaam, Tanzania. BMC Infectious Diseases, 2007. 7(1): p. 92.

Bisi-Johnson, M.A., et al., Molecular basis of virulence in clinical isolates of Escherichia coli and Salmonella species from a tertiary hospital in the Eastern Cape, South Africa. 2011. 3(1): p. 9.

Nataro, J.P. and J.B. Kaper, Diarrheagenic Escherichia coli. Clin Microbiol Rev, 1998. 11(1): p. 142-201.

Herzog, K., et al., Diarrheagenic enteroaggregative Escherichia coli causing urinary tract infection and bacteremia leading to sepsis. Infection, 2014. 42(2): p. 441-444.

Tangi, S.C., et al., Prevalence of pathogenicity island markers genes in uropathogenic Escherichia coli isolated from patients with urinary tract infectious. Asian Pacific Journal of Tropical Disease, 2015. 5(8): p. 662-666.

Middendorf, B., et al., The Pathogenicity Islands (PAIs) of the Uropathogenic Escherichia coli Strain 536: Island Probing of PAI II536. The Journal of Infectious Diseases, 2001. 183(Supplement_1): p. S17-S20.

Parham, N.J., et al., Prevalence of pathogenicity island IICFT073 genes among extraintestinal clinical isolates of Escherichia coli. J Clin Microbiol, 2005. 43(5): p. 2425-34.

Sarowska, J., et al., Virulence factors, prevalence and potential transmission of extraintestinal pathogenic Escherichia coli isolated from different sources: recent reports. Gut Pathogens, 2019. 11(1): p. 10.

Desvaux, M., et al., Pathogenicity Factors of Genomic Islands in Intestinal and Extraintestinal Escherichia coli. 2020. 11(2065).

Katongole, P., et al., Biofilm formation, antimicrobial susceptibility and virulence genes of Uropathogenic Escherichia coli isolated from clinical isolates in Uganda. BMC Infectious Diseases, 2020. 20(1): p. 453.

Schmidt, H. and M. Hensel, Pathogenicity islands in bacterial pathogenesis. Clin Microbiol Rev, 2004. 17(1): p. 14-56.

Iranpour, D., et al., Phylogenetic Groups of Escherichia coli Strains from Patients with Urinary Tract Infection in Iran Based on the New Clermont Phylotyping Method. BioMed Research International, 2015. 2015: p. 846219.

Ahumada-Santos, Y.P., et al., Association of phylogenetic distribution and presence of integrons with multidrug resistance in Escherichia coli clinical isolates from children with diarrhoea. Journal of Infection and Public Health, 2020. 13(5): p. 767-772.

Stoppe, N.C., et al., Worldwide Phylogenetic Group Patterns of Escherichia coli from Commensal Human and Wastewater Treatment Plant Isolates. Front Microbiol, 2017. 8: p. 2512.

Duriez, P., et al., Commensal Escherichia coli isolates are phylogenetically distributed among geographically distinct human populations. Microbiology (Reading), 2001. 147(Pt 6): p. 1671-1676.

Li, B., et al., Phylogenetic Groups and Pathogenicity Island Markers in Fecal Escherichia coli Isolates from Asymptomatic Humans in China. 2010. 76(19): p. 6698-6700.

Al-Mayahie, S.M., et al., Phylogenetic grouping of dominant fecal escherichia coli isolates from healthy males and females in Al-Kut/Wasit Province. 2015. 6.

Escobar-Pa´ramo, P., et al., Large-scale population structure of human commensal Escherichia coli isolates. Appl. Environ. Microbiol. 70:5698–5700., 2004.

Lee, J.H., et al., Phylogenetic group distributions, virulence factors and antimicrobial resistance properties of uropathogenic Escherichia coli strains isolated from patients with urinary tract infections in South Korea. 2016. 62(1): p. 84-90.

Kazemnia, A., M. Ahmadi, and M. Dilmaghani, Antibiotic resistance pattern of different Escherichia coli phylogenetic groups isolated from human urinary tract infection and avian colibacillosis. Iran Biomed J, 2014. 18(4): p. 219-24.

Staji, H., M. Rassouli, and S. Jourablou, Comparative virulotyping and phylogenomics of Escherichia coli isolates from urine samples of men and women suffering urinary tract infections. Iran J Basic Med Sci, 2019. 22(2): p. 211-214.

Bailey, J.K., et al., Distribution of Human Commensal Escherichia coli Phylogenetic Groups. Journal of clinical microbiology, 2010. 48(9): p. 3455-3456.

Poirel, L., et al., Plasmid-mediated carbapenem and colistin resistance in a clinical isolate of Escherichia coli. 2016. 16(3): p. 281.

Tischendorf, J., R.A. de Avila, and N. Safdar, Risk of infection following colonization with carbapenem-resistant Enterobactericeae: A systematic review. Am J Infect Control, 2016. 44(5): p. 539-43.

Middendorf, B., et al., Instability of pathogenicity islands in uropathogenic Escherichia coli 536. 2004. 186(10): p. 3086-3096.

Schneider, G., et al., Mobilisation and remobilisation of a large archetypal pathogenicity island of uropathogenic Escherichia coli in vitrosupport the role of conjugation for horizontal transfer of genomic islands. 2011. 11(1): p. 210.


How to Cite
Ssekatawa, K., Byarugaba, D. K., Nakavuma, J. L., Kato, C. D., Ejobi, F., Tweyongyere, R., & Wampande, E. M. (2021). Carbapenem Resistance Profiles of Pathogenic Escherichia coli in Uganda. European Journal of Biology and Biotechnology, 2(2), 63-73.