Table of Contents  
Year : 2014  |  Volume : 5  |  Issue : 1  |  Page : 39-43  

Broad spectrum β-lactam resistance in faecal Escherichia coli isolated from severely malnourished and nourished children attending Mbagathi district hospital, Nairobi: A case-control study

1 Department of Medical Microbiology, College of Health Sciences, Jomo Kenyatta Univesity of Agriculture and Technology, Nairobi, Kenya
2 Department of Molecular Biology, Centre for Microbiology Research, Kenya Medical Research Institute, KNH Grounds, Nairobi, Kenya

Date of Web Publication25-Mar-2014

Correspondence Address:
Samuel Mwangi Njoroge
Jomo Kenyatta University of Agriculture and Technology, College of Health Sciences, Department of Medical Microbiology, P. O. Box 620000, Nairobi
Login to access the Email id

Source of Support: None, Conflict of Interest: None

DOI: 10.4103/2229-5186.129336

Rights and Permissions

Context: Severely malnourished children have increased risk of being put on antibiotics due to co-morbidities. Aim: The study's objective was to characterize the Escherichia coli β-lactamase mediated resistance to the broad spectrum β-lactam antimicrobials among this population and compare them with nourished children as controls. Settings and Design: In this case-control, hospital-based setup, 109 E. coli isolates were obtained from each group, one isolate per subject. Materials and Methods: Stool or anal swabs were collected, enriched in buffered peptone water and cultured on MacConkey and eosin methylene blue agars. Biochemical test were used to identify E. coli. antibiograms to determine phenotypic resistance were determined using a panel of 14 drugs. Only the isolates showing synergy between ampicillin-calvulanic acid and one or more third generation cephalosporins were picked as extended spectrum β-lactamase (ESBL) producers. Statistical Analysis: Differences in ESBL rates and susceptibility percentages between cases and controls were evaluated for significance using 2-tailed Fisher's exact test. Results: Prevalence of ESBL phenotype was higher in severely malnourished children (39%) as compared to the controls (7%). The plasmid-encoded AmpC's (pAmpC)-like phenotype was observed in 11% isolates. Conclusions: Isolation of ESBL-E. coli among severely malnourished children is high. Surveillance of ESBL producers, both in the community and hospital settings needs to be stepped up in Kenya.

Keywords: Antimicrobial resistance, diarrhea, Escherichia coli, extended spectrum β-lactamase-Escherichia coli, severely malnourished children, Kenya

How to cite this article:
Njoroge SM, Kiiru JN, Kikuvi GM. Broad spectrum β-lactam resistance in faecal Escherichia coli isolated from severely malnourished and nourished children attending Mbagathi district hospital, Nairobi: A case-control study. Chron Young Sci 2014;5:39-43

How to cite this URL:
Njoroge SM, Kiiru JN, Kikuvi GM. Broad spectrum β-lactam resistance in faecal Escherichia coli isolated from severely malnourished and nourished children attending Mbagathi district hospital, Nairobi: A case-control study. Chron Young Sci [serial online] 2014 [cited 2017 Mar 25];5:39-43. Available from:

   Introduction Top

Severely malnourished children are at a higher risk of enteric infection, making them more prone to diarrhea than healthy children. [1],[2] They often have other complications such as diarrhea, pneumonia and bacteremia. [3],[4] This may warrant the empiric use of antimicrobials to boost their survival, but in the case of severe acute malnutrition complicated by diarrhea only, this predisposes a child to inappropriate antimicrobial use. [5],[6]

Antimicrobial resistance among Escherichia coli is of increasing global concern. [7] This has been associated with the emergence and spread of extended spectrum β-lactamase (ESBL)-producing E. coli, which are also frequently associated with resistance to quinolone and aminoglycosides. [8] Serious infections with ESBL producing E. coli are associated with high mortality rates as therapeutic options are limited to carbapenems. [9],[10] ESBL producers are resistant to penicillins, oxyimino-cephalosporins, monobactams and are inhibited by β-lactamase inhibitor combinations. [11] ESBL are generally derived from temoneira (TEM) and sulfhydryl variable (SHV)-type enzymes. [12] Lately, cefotaximases (CTX-M) enzymes are substituting parent SHV and TEM enzymes as the more common type of ESBLs, mainly in community-acquired infections caused by E. coli.[13] ESBL's have been isolated before in in hospital settings Kenya. [10],[14] Furthermore, plasmid-encoded AmpC (pAmpC) β-lactamases such as cephamycinases (CMYs) mediate resistance to most classes of β-lactams except to cefepime. [15]

Currently, no data exits showing the extent and consequence of drug resistant E. coli among severely malnourished children under 5 years of age in Kenya. This cross-sectional study therefore aimed to characterize E. coli antimicrobial resistance patterns to the broad spectrum β-lactam antimicrobials among severely malnourished children with diarrhea attending Mbagathi District Hospital and not to link E. coli with diarrhea.

   Materials and Methods Top

In this hospital-based, case-control study, 109 non-duplicate E. coli isolates from severely malnourished children and 109 from matched healthy children were obtained in accordance with the National ethical standards on human experimentation (ERC Protocol No. 2382) using homogenous sampling. All the children were 2-60 months of age across both genders and patient categories (cases and controls). Severely malnourished children had a mid-upper arm circumference of less 110 mm (−3 Z scores from the mean) and were also recruited in the Cotrimoxazole Prophylaxis in Severely Malnourished Children (CTX)-clinical trial. All the children recruited in the study were from Kibera, an informal settlement in Kenya's capital city, Nairobi. Majority of the cases were hospitalized at Mbagathi District Hospital pediatric ward. Controls were children visiting out-patient department but requiring microbiology investigations. Specimens from cases were predominantly rectal swabs while stool samples were preferred for controls.

Rectal swab or stool sample was collected from each study participant, enriched overnight in 5% buffered peptone water and plated on MacConkey and Eosin Methylene Blue agar (Oxoid, Basingstoke, United Kingdom). Incubation was carried out for 18 h at 37°C. A single E. coli colony was picked from each specimen to yield one isolate per patient average. Antimicrobial susceptibility tests were performed using Kirby-Bauer disc diffusion technique. [16] This was carried out with antibiotic discs (Cypress diagnostics, Langdorp, Belgium) on Mueller Hinton agar (Oxoid). E. coli ATCC 25922 was included as a control strain on each test batch which in this case, was always susceptible to all the drugs. Antibiogram panel included; ampicillin (10 μg), cefpodoxime (30 μg), CTX (30 μg), ceftazidime (30 μg), cefepime (30 μg), cefoxitin (30 μg) represented, amoxicillin/clavulanic acid (20/10 μg), tazobactam/piperacillin (100/10 μg), gentamicin (5 μg), streptomycin (25 μg), ciprofloxacin (30 μg), nalidixic acid (30 μg), chloramphenicol (30 μg) and sulfamethoxazole/trimethoprim (23.75/1.25 μg). An isolate was defined as resistant to third generation cephalosporins, when the inhibition zone diameter of cefpodoxime (30 μg) and CTX (30 μg) was <17 mm and 22 mm, respectively. [17] Phenotypic ESBL detection was first performed by disk diffusion and double disk synergy test using CLSI 2012 guidelines. Only isolates showing synergy zones between amoxicillin/clavulanic and one- or more- third generation cephalosporins were picked as ESBL producers [Figure 1]. Antimicrobial susceptibility test results of all the isolates were analyzed using the WHONET 5.6 software. Fisher's exact test, 2-tailed was used to evaluate for significance on ESBL susceptibility profiles differences between cases and controls.
Figure 1: Phenotypic identification of extended spectrum β-lactam producing Escherichia coli (AMC – Amoxicillin-clavulanic acid, CPD – Cefpodoxime, FOX – Cefoxitin, CTX – Cefotaxime, FEP – Cefepime, CAZ – Ceftazidime, AMP – Ampicillin, SXT – Trimethoprim-sulfamethoxazole, CIP – Ciprofloxacin, TZP – Tazobactam-piperacillin, NA – Nalidixic acid, C – Chloramphenicol, S – Streptomycin, CN – Gentamicin. Occurrence of "ghost inhibition zones" between β-lactam/β-lactamase and β-lactam only antibiotic discs is suggestive of an ESBL phenotype)

Click here to view

   Results and Discussions Top

Antimicrobial resistance patterns

Although the purpose of the study was not to ascertain virulence or the pathotypes of the E. coli isolated, surveillance of drug resistance among these isolates is of equal importance. Out of the 109 E. coli non-duplicate isolates from each group, 43 (39%) and 8 (7%) were of ESBL phenotypes from cases and controls respectively [Figure 2]. In a similar study, fecal isolation rate of ESBL's among severely malnourished children in a pediatric re-nutrition center was slightly lower at 31% in 2011 compared with 39% in this study. [18] The increase could be a result of different antibiotic exposures between the two countries and/or an increase in the propensity of ESBL occurrence with time.
Figure 2: Distribution of ESBLæs among patient categories extended spectrum β-lactamase producing (ESBL) Escherichia coli, non-ESBL- E. coli isolates not exhibiting ESBL phenotype. Actual number of E. coli isolates from both cases and controls was 109 each

Click here to view

ESBLs also confer co-resistance to quinolones and aminoglycosides. [19] This was also observed in this study with high rates of resistance to nalidixic acid, ciprofloxacin, gentamicin and chloramphenicol. There were significant differences in resistance antibiograms in ESBLs and non-ESBLs among cases and controls [Figure 3] and [Figure 4]. Differences in ESBL-E. coli antibiograms among cases and controls was only observed in cefotaxime, streptomycin and gentamicin [Table 1]. The incidence of co-resistance in ESBL producing enterobacteriaceae is an emerging public health concern due to their occurrence in both hospital and community setting, co-resistance with other classes of antimicrobials, higher cost and toxic treatment options in developing countries. [10],[12],[18],[20],[21],[22],[23]
Figure 3: Distribution of resistance in extended spectrum β-lactamase producing (ESBL) Escherichia coli (ESBL- E. coli) among cases and controls. (AMC – Amoxicillin-clavulanic acid, CPD – Cefpodoxime, FOX – Cefoxitin, CTX – Cefotaxime, FEP – Cefepime, CAZ – Ceftazidime, AMP – Ampicillin, SXT – Trimethoprim-sulfamethoxazole, CIP – Ciprofloxacin, TZP – Tazobactam-piperacillin, NA – Nalidixic acid, C- Chloramphenicol, S – Streptomycin, CN – Gentamicin. ESBL – Extended spectrum β-lactamase. Resistant isolates were grouped together with intermediate

Click here to view
Figure 4: Resistance profiles of the non-extended spectrum β-lactamase producing (none-ESBL's) Escherichia coli among cases and controls AMC - amoxicillin-clavulanic acid, CPD - Cefpodoxime, FOX - Cefoxitin, CTX - Cefotaxime, FEP - Cefepime, CAZ - Ceftazidime, AMP - Ampicillin, SXT - Trimethoprimsulfamethoxazole, CIP - Ciprofloxacin, TZP - Tazobactampiperacillin, NA - Nalidixic acid, C - Chloramphenicol, S - Streptomycin, CN - Gentamicin. Resistant isolates were grouped together with Intermediate

Click here to view
Table 1: Comparison of ESBL-E. coli antibiograms from cases and controls

Click here to view

A recent study carried out in Kibera showed a high percentage of environmental E. coli being resistant to commonly used drugs; tetracycline, ampicillin and sulphamethoxazole/trimethoprim. [24] Malnutrition increases the risk of entero-toxigenic E. coli colonization which is associated with diarrheal illness. [1] In addition, malnutrition aggravates enteric infections affecting morbidity, mortality and therapy. [25],[26] Diarrhea was found to a common morbidity among severely malnourished children in Dhaka, Bangladesh. [27]

ESBL E. coli isolates were from 20 male (47%) and 23 female (53%) subjects in cases. Controls constituted five females (63%) and three males (37%). AmpC CMYs are β-lactamase enzymes that hydrolyze cephamycins (cefoxitin) and third generation cephalosporins. [28] They are either plasmid or chromosomally encoded, but our interest was on pAmpC's enzymes. [28] Majority of plasmid mediated cephamycin resistance is characterized by resistance to cefoxitin and susceptibility to cefepime: A fourth generation cephalosporin. [15] Cefoxitin resistance using disc diffusion has 97% sensitivity and 64% specificity. [29] Out of the 23 cefoxitin resistant E. coli isolates from the study, 23 (100%) showed resistance to cefoxitin but susceptibility to cefepime [Figure 5]. Cefoxitin resistance observed in the 23 isolates is more likely to be plasmid mediated than chromosomally induced. Amp-C β-lactamase are found throughout the world but are not prevalent as ESBL's. [15]
Figure 5: Antibiograms of 23 Escherichia coli isolates resistant to FOX showing no extended spectrum β-lactamase (ESBL) production. AMC – Amoxicillin-clavulanic acid, CPD – Cefpodoxime, FOX – Cefoxitin, CTX – Cefotaxime, FEP – Cefepime, CAZ – Ceftazidime, AMP – Ampicillin, SXT – Trimethoprimsulfamethoxazole, CIP – Ciprofloxacin, TZP – Tazobactampiperacillin, NA – Nalidixic acid, C – Chloramphenicol, S – Streptomycin, CN – Gentamicin

Click here to view

   Conclusion Top

The prevalence of ESBL-E. coli among severely malnourished children is unusually high. ESBL's also manifest co-resistance to other classes of antimicrobials rendering treatment a toxic and costly affair. Therefore, ESBL screening among severely malnourished children is of great importance since it affects treatment outcome. ESBL surveillance should be stepped up by creation of sentinel sites throughout the Country.

   Acknowledgments Top

Indebted to Dr. Sam Kariuki, Dr. James Berkley, CMR-KEMRI KNH ground staff, Mbagathi District Hospital Administration and Laboratory staff, CTX-Study Nairobi station staff. Thank you.

   References Top

1.Mondal D, Haque R, Sack RB, Kirkpatrick BD, Petri WA Jr. Attribution of malnutrition to cause-specific diarrheal illness: Evidence from a prospective study of preschool children in Mirpur, Dhaka, Bangladesh. Am J Trop Med Hyg 2009;80:824-6.  Back to cited text no. 1
2.Das SK, Chisti MJ, Huq S, Malek MA, Salam MA, Ahmed T, et al. Etiology of diarrhea among severely malnourished infants and young children: Observation of urban-rural differences over one decade in Bangladesh. Food Nutr Sci 2013; Mar;4:233-9.  Back to cited text no. 2
3.Talbert A, Thuo N, Karisa J, Chesaro C, Ohuma E, Ignas J, et al. Diarrhoea complicating severe acute malnutrition in Kenyan children: A prospective descriptive study of risk factors and outcome. PLoS One 2012;7:e38321.  Back to cited text no. 3
4.Schlaudecker EP, Steinhoff MC, Moore SR. Interactions of diarrhea, pneumonia, and malnutrition in childhood: Recent evidence from developing countries. Curr Opin Infect Dis 2011;24:496-502.  Back to cited text no. 4
5.Ashworth A, Khanum S, Jackson A, Schofield C. Guidelines for the Inpatient Treatment of Severely Malnourished Children. Geneva; World Health Organisation. 2003:1-50.  Back to cited text no. 5
6.Alcoba G, Kerac M, Breysse S, Salpeteur C, Galetto-Lacour A, Briend A, et al. Do children with uncomplicated severe acute malnutrition need antibiotics? A systematic review and meta-analysis. PLoS One 2013;8:e53184.  Back to cited text no. 6
7.Peirano G, van Greune CH, Pitout JD. Characteristics of infections caused by extended-spectrum β-lactamase-producing Escherichia coli from community hospitals in South Africa. Diagn Microbiol Infect Dis 2011;69:449-53.  Back to cited text no. 7
8.Fatima EL, Meriem EL, Said B. Plasmid mediated quinolones resistance ESBL-Enterobactériaceae in Moroccan. Pham Anal Acta 2012; S15:006.  Back to cited text no. 8
9.Al-Muharrmi Z, Rafay A, Balkhair A, Jabri AA. Antibiotic combination as empirical therapy for extended spectrum beta-lactamase. Oman Med J 2008;23:78-81.  Back to cited text no. 9
10.Maina D, Makau P, Nyerere A, Revathi G. Antimicrobial resistance patterns in extended-spectrum β-lactamase producing Escherichia coli and Klebsiella pneumoniae isolates in a private tertiary hospital, Kenya. Microbiol Discov 2013;1:5.   Back to cited text no. 10
11.Bush K, Fisher JF. Epidemiological expansion, structural studies, and clinical challenges of new β-lactamases from gram-negative bacteria. Annu Rev Microbiol 2011;65:455-78.  Back to cited text no. 11
12.Rupp ME, Fey PD. Extended spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae: Considerations for diagnosis, prevention and drug treatment. Drugs 2003;63:353-65.  Back to cited text no. 12
13.Falagas ME, Karageorgopoulos DE. Extended-spectrum beta-lactamase-producing organisms. J Hosp Infect 2009;73:345-54.  Back to cited text no. 13
14.Kiiru J, Kariuki S, Goddeeris BM, Butaye P. Analysis of β-lactamase phenotypes and carriage of selected β-lactamase genes among Escherichia coli strains obtained from Kenyan patients during an 18-year period. BMC Microbiol 2012;12:155.   Back to cited text no. 14
15.Jacoby GA. AmpC beta-lactamases. Clin Microbiol Rev 2009;22:161-82.  Back to cited text no. 15
16.Bauer AW, Kirby WM, Sherris JC, Turck M. Antibiotic susceptibility testing by a standardized single disk method. Am J Clin Pathol 1966;45:493-6.  Back to cited text no. 16
17.CLSI. Performance Standards for Antimicrobial Susceptibility Testing; Twenty-Second Informational Supplement. Vol. 32. No. 3. Wayne, PA: Clinical Laboratory Standards Institute; 2012.  Back to cited text no. 17
18.Woerther PL, Angebault C, Jacquier H, Hugede HC, Janssens AC, Sayadi S, et al. Massive increase, spread, and exchange of extended spectrum β-lactamase-encoding genes among intestinal Enterobacteriaceae in hospitalized children with severe acute malnutrition in Niger. Clin Infect Dis 2011;53:677-85.  Back to cited text no. 18
19.Schwaber MJ, Navon-Venezia S, Schwartz D, Carmeli Y. High levels of antimicrobial coresistance among extended-spectrum-beta-lactamase-producing Enterobacteriaceae. Antimicrob Agents Chemother 2005;49:2137-9.  Back to cited text no. 19
20.Herindrainy P, Randrianirina F, Ratovoson R, Ratsima Hariniana E, Buisson Y, Genel N, et al. Rectal carriage of extended-spectrum beta-lactamase-producing gram-negative bacilli in community settings in Madagascar. PLoS One 2011;6:e22738.  Back to cited text no. 20
21.Bazzaz BS, Naderinasab M, Mohamadpoor AH, Farshadzadeh Z, Ahmadi S, Yousefi F. The prevalence of extended-spectrum beta-lactamase-producing Escherichia coli and Klebsiella pneumoniae among clinical isolates from a general hospital in Iran. Acta Microbiol Immunol Hung 2009;56:89-99.  Back to cited text no. 21
22.Wassef MA, El Shenoufy AE, Ghaith DM. Phenotypic and genotype patterns of aminoglycoside resistance in gram negative bacilli. J Am Sci 2010;6:781-6. Available from:   Back to cited text no. 22
23.Nibedita D, Borthakur A. Antibiotic coresistance among extended-spectrum beta lactamase-producing urinary isolates in a tertiary medical center: A prospective study. Chron Young Sci 2012;3:53-6.  Back to cited text no. 23
24.Christabel M, Budambula N, Kiiru J, Kariuki S. Characterization of antibiotic resistance in environmental enteric pathogens from Kibera slum in Nairobi-Kenya. J Bacteriol Res 2012;4:46-54.  Back to cited text no. 24
25.Guerrant RL, Oriá RB, Moore SR, Oriá MO, Lima AA. Malnutrition as an enteric infectious disease with long-term effects on child development. Nutr Rev 2008;66:487-505.  Back to cited text no. 25
26.Irena AH, Mwambazi M, Mulenga V. Diarrhea is a major killer of children with severe acute malnutrition admitted to inpatient set-up in Lusaka, Zambia. Nutr J 2011;10:110.  Back to cited text no. 26
27.Ashraf H, Alam NH, Chisti MJ, Mahmud SR, Hossain I. A follow-up experience of 6 months after treatment of children with severe acute malnutrition in Dhaka, Bangladesh. J Trop Pediatr 2012;58:253-57.  Back to cited text no. 27
28.Pfeifer Y, Cullik A, Witte W. Resistance to cephalosporins and carbapenems in Gram-negative bacterial pathogens. Int J Med Microbiol 2010;300:371-9.  Back to cited text no. 28
29.Ingram PR, Inglis TJ, Vanzetti TR, Henderson BA, Harnett GB, Murray RJ. Comparison of methods for AmpC β-lactamase detection in Enterobacteriaceae. J Med Microbiol 2011;60:715-21.  Back to cited text no. 29


  [Figure 1], [Figure 2], [Figure 3], [Figure 4], [Figure 5]

  [Table 1]


    Similar in PUBMED
   Search Pubmed for
   Search in Google Scholar for
 Related articles
    Access Statistics
    Email Alert *
    Add to My List *
* Registration required (free)  

  In this article
    Materials and Me...
    Results and Disc...
    Article Figures
    Article Tables

 Article Access Statistics
    PDF Downloaded263    
    Comments [Add]    

Recommend this journal