Class 1 Integrons, Genetic Factor for the Dissemination of Tetracycline and Chloramphenicol Resistance Genes in Escherichia coli isolated from Children with Diarrhea in Rural Burkina Faso

Abstract

Antimicrobial resistance has been declared a global threat to public health, as a massive increase in this problem has been observed worldwide. This study aims to investigate the role of class I integrons (Int1) in the dissemination of tetracycline and chloramphenicol
resistance genes in Escherichia coli in rural Burkina Faso. A study was conducted to screen for E. coli species from 275 stool samples collected from under five age children suffering from diarrhea, in rural area of Burkina Faso. The antimicrobial resistance
determinants were investigated by Polymerase Chain Reaction, checking the presence of class 1, 2, 3 integrons, tet and catA1 resistance genes. Class 1 integrons were reported in all the five (5/5) E. coli isolates. One tetracycline resistant (Tetr) strain (20%) possessed the tet gene and two strains harbored the catA1 gene. There was a coexistence between the tet and catA1 genes and class 1 integrons in one atypical EPEC. Class 1 integrons have been playing an important role in the development of multidrug resistance in E. coli pathovars. A better understanding of the molecular mechanisms by which antimicrobial resistance emerges and spreads should enable us to design intervention strategies to reduce its progression.
Keywords: Antibiotic Resistance Genes; Class 1 Integrons; E. coli; Diarrhea; Children

Full text

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OPEN ACCESS EC MICROBIOLOGY
Research Article
Class 1 Integrons, Genetic Factor for the Dissemination of Tetracycline
and Chloramphenicol Resistance Genes in Escherichia coli isolated
from Children with Diarrhea in Rural Burkina Faso
René Dembélé1,2*, Ali Konaté1, Assèta Kagambèga1,3, Issiaka Soulama4, Wendpoulomdé AD Kaboré5, Oumar Traoré1,2,
Alfred S Traoré1, Awa Aidara-Kane6, Amy Gassama Sow7 and Nicolas Barro1
1Laboratory of Molecular Biology, Epidemiology and Surveillance of Bacteria and Viruses Transmitted by Food (LaBESTA)/Center for
Research in Biological, Food and Nutritional Sciences (CRSBAN)/Graduate School of Science and Technology (EDST)/University of Ouaga I,
Professor Joseph KI-ZERBO, Burkina Faso
2Training and Research Unit in Applied Sciences and Technologies (TRU/AST)/University of Dédougou, Burkina Faso
3Institute of Sciences, Ouagadougou 01, Burkina Faso
4National Centre for Research and Training on Malaria (NCRTM), Ouagadougou 01, Burkina Faso
5Training and Research Unit in Health Sciences (TRU/HS)/University of Ouaga I, Professor Joseph KI-ZERBO, Ouagadougou 03, Burkina Faso
6World Health Organization, WHO-AGISAR, Department of Food Safety and Zoonoses, Switzerland
7Unit of Experimental Bacteriology, Pasteur Institute of Dakar, Dakar, Senegal
Citation: René Dembélé., et al. “Class 1 Integrons, Genetic Factor for the Dissemination of Tetracycline and Chloramphenicol Resistance
Genes in Escherichia coli isolated from Children with Diarrhea in Rural Burkina Faso”. EC Microbiology 15.6 (2019): 463-470.
*Corresponding Author: Rene Dembele, Laboratory of Molecular Biology, Epidemiology and Surveillance of Bacteria and Viruses
Transmitted by Food (LaBESTA), University of Dedougou, Dedougou, Burkina Faso.
Received: April 10, 2019; Published: May 28, 2019
Abstract
Antimicrobial resistance has been declared a global threat to public health, as a massive increase in this problem has been ob-
served worldwide. This study aims to investigate the role of class I integrons (Int1) in the dissemination of tetracycline and chlor-
amphenicol resistance genes in Escherichia coli in rural Burkina Faso. A study was conducted to screen for E. coli species from 275
-
tance determinants were investigated by Polymerase Chain Reaction, checking the presence of class 1, 2, 3 integrons, tet and catA1
 E. coli isolates. One tetracycline resistant (Tetr) strain (20%)
possessed the tet gene and two strains harbored the catA1 gene. There was a coexistence between the tet and catA1 genes and class
1 integrons in one atypical EPEC. Class 1 integrons have been playing an important role in the development of multidrug resistance
in E. coli pathovars. A better understanding of the molecular mechanisms by which antimicrobial resistance emerges and spreads
should enable us to design intervention strategies to reduce its progression.
Keywords: Antibiotic Resistance Genes; Class 1 Integrons; E. coli; Diarrhea; Children
Abbreviations
AR: Antibiotic Resistance; CAT: Chloramphenicol Acetyl Transferase; CMA: Centre Médical avec Antenne Chirugicale; MDR: Multidrug
Resistant
Introduction
Antibiotic resistance (AR) continues to pose a great threat to public health in both developed and developing countries [1]. In many
parts of the world, the emergence of multidrug-resistant Gram-negative bacteria is a major concern in hospital settings. Infections
          

Citation: René Dembélé., et al. “Class 1 Integrons, Genetic Factor for the Dissemination of Tetracycline and Chloramphenicol Resistance
Genes in Escherichia coli isolated from Children with Diarrhea in Rural Burkina Faso”. EC Microbiology 15.6 (2019): 463-470.
Figure 1: Map of Burkina Faso. In dark = Gourcy and Boromo where the study was conducted.
Class 1 Integrons, Genetic Factor for the Dissemination of Tetracycline and Chloramphenicol Resistance Genes in Escherichia coli
isolated from Children with Diarrhea in Rural Burkina Faso
464
and are associated with high morbidity and mortality rates as well as protracted hospital stay [2]. Enterobacteriaceae including Klebsiella
pneumoniae, Escherichia coli as well as Enterobacter spp. and non-lactose fermenting bacteria such as Pseudomonas aeruginosa and
Acinetobacter   Escherichia coli is
a ubiquitous presence in the developing world and is responsible for a range of enteric infections [4]. Antimicrobial resistance occurs
        
tend to be even larger than in industrialized countries. In fact, high resistance rates have often been reported in surveillance studies
dealing with clinical isolates [6,7] and in prevalence studies of commensal bacteria taken as indicators to estimate spread of acquired
resistance [8,9]. Tetracyclines have been used extensively since the late 1940s as broad-spectrum inexpensive antibiotics that are effective
against a wide variety of diseases in humans, animals, and plants. However, resistance to tetracycline has increased dramatically since
Shigella dysenteriae [10]. The transmissibility of resistance in bacterial populations can take
place by either clonal spread of particular strains or horizontal transfer of resistance determinants by plasmid- or transposon-mediated

involved in resistance [12], have been found on resistance plasmids or transposons, making gene transfer the likely method of acquiring
resistance.
One of the best-characterized bacterial antibiotic resistance mechanisms is the synthesis of chloramphenicol acetyl transferase
(CAT) [13]. Production of this enzyme, encoded by the cat gene, is the most common means by which bacteria become resistant to
chloramphenicol [14], a small bacteriostatic antibiotic that interacts with a peptidyl transferase center [15]. Dissemination of antibiotic
resistance genes by horizontal transfer has led to the rapid emergence of antibiotic resistance among clinical isolates of bacteria [16].
In this study, we screened the tet and catA1-producing E. coli to elucidate the dissemination mechanism. In addition, to the best of our
Int1) in the dissemination of tetracycline and chloramphenicol
resistance genes in E. coli in rural Burkina Faso.
Materials and Methods
E. coli isolates

1).

Citation: René Dembélé., et al. “Class 1 Integrons, Genetic Factor for the Dissemination of Tetracycline and Chloramphenicol Resistance
Genes in Escherichia coli isolated from Children with Diarrhea in Rural Burkina Faso”. EC Microbiology 15.6 (2019): 463-470.
Class 1 Integrons, Genetic Factor for the Dissemination of Tetracycline and Chloramphenicol Resistance Genes in Escherichia coli
isolated from Children with Diarrhea in Rural Burkina Faso
465
Trained healthcare personnel using sterile stool containers collected stool samples. All the samples were immediately iced and brought
 
E. coli (EHEC, EPEC, EAEC, EIEC, and ETEC) as
described by Antikainen., et al [18]. The genes investigated and primers used are listed in table 1.
Pathotype Target gene Primer sequence (5’ to 3’) Size (bp) [C] () Ref.
Typical
EPEC bfpB MP3-bfpB-F: GACACCTCATTGCTGAAGTCG 910 0.1 [19]
MP3-bfpB-R: CCAGAACACCTCCGTTATGC 0.1
EHEC and
EPEC
eaeA eae-F: TCAATGCAGTTCCGTTATCAGTT 482 0.1 [19]
eae-R: GTAAAGTCCGTTACCCCAACCTG 0.1
escV MP3-escV-F: ATTCTGGCTCTCTTCTTCTTTATGGCTG 544 0.4 [19]
MP3-escV-R: CGTCCCCTTTTACAAACTTCATCGC 0.4
Ent ent-F: TGGGCTAAAAGAAGACACACTG 629 0.4 [19]
ent-R: CAAGCATCCTGATTATCTCACC 0.4
EHEC
EHEC-hly hlyEHEC-F: TTCTGGGAAACAGTGACGCACATA 688 0.1 [18]
hlyEHEC-R: TCACCGATCTTCTCATCCCAATG 0.1
Stx1 MP4-stx1A-F: CGATGTTACGGTTTGTTACTGTGACAGC 244 0.2 [19]
MP4-stx1A-R: AATGCCACGCTTCCCAGAATTG 0.2
Stx2 MP3-stx2AF: GTTTTGACCATCTTCGTCTGATTATTGAG 324 0.4 [19]
MP3-stx2A-R: AGCGTAAGGCTTCTGCTGTGAC 0.4
EAEC
astA MP-astA-F TGCCATCAACACAGTATATCCG 102 0.4 [19]
MP2-astA-R ACGGCTTTGTAGTCCTTCCAT 0.4
aggR MP2-aggR-F: ACGCAGAGTTGCCTGATAAAG 400 0.2 [19]
MP2-aggR-R:AATACAGAATCGTCAGCATCAGC 0.2
Pic MP2-pic-F: AGCCGTTTCCGCAGAAGCC 1111 0.2 [19]
MP2-pic-R: AAATGTCAGTGAACCGACGATTGG 0.2
EIEC
invE MP2-invE-F: CGATAGATGGCGAGAAATTATATCCCG 766 0.2 [19]
MP2-invE-R: CGATCAAGAATCCCTAACAGAAGAATCAC 0.2
ipaH ipaH-F: GAAAACCCTCCTGGTCCATCAGG 437 0.1 [20]
ipaH-R: GCCGGTCAGCCACCCTCTGAGAGTAC 0.1
ETEC
elt MP2-LT-F: GAACAGGAGGTTTCTGCGTTAGGTG 655 0.1 [19]
MP2-LT-R: CTTTCAATGGCTTTTTTTTGGGAGTC 0.1
estA MP4-STIa-F : CCTCTTTTAGYCAGACARCTGAATCASTTG 157 0.4 [19]
MP4-STIa-R: CAGGCAGGATTACAACAAAGTTCACAG 0.4
estB MP2-STI-F: TGTCTTTTTCACCTTTCGCTC 171 0.2 [19]
MP2-STI-R CGGTACAAGCAGGATTACAACAC 0.2
E. coli uidA MP2-uidA-F: ATGCCAGTCCAGCGTTTTTGC 1487 0.2 [20]
MP2-uidA-R: AAAGTGTGGGTCAATAATCAGGAAGTG 0.2
Table 1: Oligonucleotides primers used for multiplex PCR reaction.
Legend: EAEC: Enteroaggregative E. coli; EPEC: Enteropathogenic E. coli; EIEC: Enteroinvasive E. coli; EHEC: Enterohemorrhagic E. coli;
ETEC: Enteroenterotoxigenic E. coli; : Micromolaire; [C]: Concentration; pb: “Paire de Base”; Ref.: Reference.

Citation: René Dembélé., et al. “Class 1 Integrons, Genetic Factor for the Dissemination of Tetracycline and Chloramphenicol Resistance
Genes in Escherichia coli isolated from Children with Diarrhea in Rural Burkina Faso”. EC Microbiology 15.6 (2019): 463-470.
Class 1 Integrons, Genetic Factor for the Dissemination of Tetracycline and Chloramphenicol Resistance Genes in Escherichia coli
isolated from Children with Diarrhea in Rural Burkina Faso
466
Antimicrobial susceptibility testing
The antimicrobial susceptibility test was performed using the disk diffusion method on Mueller-Hinton agar as described by the
European Committee on Antimicrobial Susceptibility Testing [21]. The following antimicrobials (belonging to 7 different families) were
                
(10 µg), piperacillin (75 µg), piperacillin-tazobactam (100 +10 µg), imipenem (10 µg), tetracycline (30 µg), chloramphenicol (30 µg),

gentamycin (15 µg), netilmicin (10 µg), and tobramycin (10 µg) (Bio-Rad, France). EUCAST guidelines were used to interpret results.
Antimicrobial resistance genes detection
To detect the molecular determinants of resistance, all the multidrug-resistant isolates of E. coli were considered and PCR was carried
catA1) [22], tetracycline (tet) [23] and for integrons (intI1,
intI2, intI3
DNA polymerase (Accu Power, Korea), deoxyribonucleic triphosphate (10 mM), buffer GC (10X), MgCl2 (25 mM), and PCR primers (10

         

visualized under ultraviolet (UV) light (Gel Logic 200).
Genetic resistance
supports Genes Primers sequence (5’to3’) Size (bp) References
Chloramphenicol catA1 F : CGC CTG ATG AAT GCT CAT CCG 456 [22]
R : CCT GCC ACT CAT CGC AGT AC
Tetracycline tet F : GCA GGC AGA GCA AGT AGA GG 956 [23]
R : GTT TCG GGT TCG GGA TGG TC
Integrons
Int1 F: ATT TCT GTC CTG GCT GGC GA 600
[24]
R: ACA TGT GAT GGC GAC GCA CGA
Int2 F : CAC GGA TAT GCG ACA AAA AGG T 806
R : GTA GCA AAC GAC TGA CGA AAT G
Int3 F: GCC CCG GCA GCG ACT TTC AG 600
R: ACG GCT CTG CCA AAC CTG ACT
Table 2: Oligonucleotides primers used for PCR reaction.
Ethical considerations


Results and Discussion
Global prevalence of antibiotic resistance in E. coli isolates
E. coli by 16-plex PCR: three (3) enteroaggregative E. coli (EAEC) and two
(2) atypical enteropathogenic E. coli
classes of antimicrobials) E. coli and harbored resistance patterns to tetracycline, amoxicillin-clavulanic acid and amoxicillin. Eighty

Citation: René Dembélé., et al. “Class 1 Integrons, Genetic Factor for the Dissemination of Tetracycline and Chloramphenicol Resistance
Genes in Escherichia coli isolated from Children with Diarrhea in Rural Burkina Faso”. EC Microbiology 15.6 (2019): 463-470.
Figure 2: 
A = Molecular Weight Marker (100 bp), B = Int1 positive control (600pb),
C-E = Positive Samples (E. coli) to Int1 detection, T = Negative Control.
Class 1 Integrons, Genetic Factor for the Dissemination of Tetracycline and Chloramphenicol Resistance Genes in Escherichia coli
isolated from Children with Diarrhea in Rural Burkina Faso
467
percent (80%) of our isolates were resistant to colistin-sulfate, trimethoprim-sulfamethoxazole and piperacillin. Resistance to nalidixic
E.
coli strains showed resistance to imipenem and chloramphenicol.
Resistance genes and integrons in E. coli isolates
One atypical EPEC (043B) that showed resistance to tetracycline and chloramphenicol was simultaneously positive for the presence
of tet and catA1 genes by PCR. Another atypical EPEC (046B) harbored catE. coli
strains (Table 3). Class 2 and 3 integrons were not detected in this study.
Coexistence of resistance genes and integrons in the same E. coli isolates
Our results showed that catA1 gene and class 1 integrons were simultaneously harbored by one atypical EPEC. Similarly, there was a
coexistence between the tet and catA1 genes and class 1 integrons in one atypical EPEC (Table 3).
Codes Pathovars Antibiotic-resistance phenotype Resistance genes Integrons
025B EAEC AMC, AMX, CTX, ATM, CRO, FEP, CFM,
TET, SXT, NAL, CST, TZP, PIP -Int1
039B EAEC AMC, AMX, TET, SXT, CST, PIP - Int1
043B Atypical EPEC AMC, AMX, CTX, ATM, IPM, CRO, FEP,
CFM, TET, CHL, CST, TZP, PIP, GMI, TMN catA1, tet Int1
044B EAEC AMC, AMX, CTX, ATM, IPM, CRO, FEP,
CFM, TET, CHL, SXT, NAL, CST, TZP -Int1
046B Atypical EPEC AMC, AMX, TET, SXT, NAL, PIP catA1 Int1
Table 3: Antibiotic resistance phenotypes and genes detected in E. coli isolates from clinical samples
Legend : EAEC: Eneteroaggregative E. coli; EPEC: Enteropathogenic E. coli; AMC: Amoxicillin-Clavulanic Acid; AMX: Amoxicillin;

CHL: Chloramphenicol; SXT: Trimethoprim-sulfamethoxazole; NAL: Nalidixic Acid; CST: Colistin sulfate;
TZP: Piperacillin-Tazobactam; GMI: Gentamicin; PIP: Piperacillin; TMN: Tobramycin.

Citation: René Dembélé., et al. “Class 1 Integrons, Genetic Factor for the Dissemination of Tetracycline and Chloramphenicol Resistance
Genes in Escherichia coli isolated from Children with Diarrhea in Rural Burkina Faso”. EC Microbiology 15.6 (2019): 463-470.
Class 1 Integrons, Genetic Factor for the Dissemination of Tetracycline and Chloramphenicol Resistance Genes in Escherichia coli
isolated from Children with Diarrhea in Rural Burkina Faso
468
Discussion
In this study, all isolated strains were resistant to tetracycline while 40% were resistant to chloramphenicol which results are similar
to data reported by Wu., et al. [25] who found 100% resistant to tetracycline and 20% to chloramphenicol. In addition, all the study strains
were multidrug resistant (MDR). Studies showed that MDR Gram-negative bacterial pathogens are a global public health threat [26]. This
tet and catA1 genes in E. coli strains isolated from children in Burkina
Faso. The pattern of antibiotic resistance detected in our isolates is in line with the resistance encountered in different strains of E. coli
isolated from various clinical sources worldwide [27]. In the last few years, it has been shown that E. coli is exhibiting resistance to more
antibiotic classes, hence rendering these drugs ineffective in treating its infections [28].
In the present study, one tetracycline resistant (Tetr) strain (20%) possessed the tet gene. A study by Lanz., et al. [29] showed that the
tet(A) gene alone was the most prevalent tet gene among E. coli isolates from pigs with diarrhea or enterotoxemia. The presence of Int1
was reported in 100% of the study isolates that is higher than 24% of class 1 integrons reported among clinical strains [30]. Integrons
are mobile genetic elements thought to play an important role in the dissemination and accumulation of resistance genes in bacteria
[31]. The presence of an integron is strongly associated with antimicrobial resistance. Thus, class 1 integrons have been associated with
tetracycline resistance genes [32] and have been shown to be selected and maintained by antimicrobial pressure [30]. In addition to
their fungible gene cassettes, which often confer resistance to antimicrobial agents, all class 1 integrons contain an independent sulI gene
encoding sulfonamide resistance. Because the integron system has the ability to create novel combinations of resistance genes, it may be
a dynamic force in the evolution of multidrug-resistant (MDR) bacteria [33].
In this study, one atypical EPEC that showed resistance to chloramphenicol was positive for the presence of catA1 gene by PCR.
However, one strain (atypical EPEC) which were chloramphenicol sensitive also possessed the cat  
antibiotic resistance genes catA1 were present in 40% of the study strains. Our founding is similar to data reported by Deekshit., et al.
2011 who found the catA1 gene in seafood-associated Salmonella Weltevreden (both in a resistant strain and in a susceptible strain)
with a catA1 rate equal to 57.52% [34]. Chloramphenicol resistance can due to degradation of the antibiotic by either chloramphenicol
catA gene has been reported to be located upon plasmid [34,35]. The
gene catA1 reported in the study conducted by Deekshit., et al. [34] was found to identical to that reported from E. coli (FN554766) and
other Salmonella serovars. Concerning the strain susceptible to chloramphenicol in which catA1 gene was detected, it is possible that
the gene was not expressed in this case. Indeed, Deekshit., et al. showed that the reason for the unexpressive characteristic of catA1 gene
of Salmonella  
primers [34]. Silencing of antibiotic-resistant genes in environments, where the gene product does not confer any selective advantage,
may be a phenomenon that has not received much attention and therefore should be adressed in perspectives.
Conclusion
This study highlights that class 1 integrons have been playing an important role in the development of multidrug resistance in
diarrheagenic E. coli pathovars. Further research examining integron persistence over time and determining whether class 1 integrons

move among strains. Indeed, a better understanding of the molecular mechanisms by which antimicrobial resistance emerges and spreads
should enable us to design intervention strategies to reduce its progression.
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Citation: René Dembélé., et al. “Class 1 Integrons, Genetic Factor for the Dissemination of Tetracycline and Chloramphenicol Resistance
Genes in Escherichia coli isolated from Children with Diarrhea in Rural Burkina Faso”. EC Microbiology 15.6 (2019): 463-470.
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isolated from Children with Diarrhea in Rural Burkina Faso
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Citation: René Dembélé., et al. “Class 1 Integrons, Genetic Factor for the Dissemination of Tetracycline and Chloramphenicol Resistance
Genes in Escherichia coli isolated from Children with Diarrhea in Rural Burkina Faso”. EC Microbiology 15.6 (2019): 463-470.
Class 1 Integrons, Genetic Factor for the Dissemination of Tetracycline and Chloramphenicol Resistance Genes in Escherichia coli
isolated from Children with Diarrhea in Rural Burkina Faso
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Volume 15 Issue 6 June 2019
©All rights reserved by René Dembélé., et al.
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