Antibiotic Resistance Profile and Random Amplification
Antibiotic Resistance Profile and Random Amplification
Antibiotic Resistance Profile and Random Amplification
483
Original article
Keywords: Antibiotic resistance, E.coli, Klebsiella pneumoniae, RAPD typing, Saudi Arabia
Gram-negative bacteria are potential causes of ESBLs are primarily produced by gram-negative
both nosocomial and community-acquired infections. organisms of the Enterobacteriaceae family, especially
Multiple antibiotic resistance to broad-spectrum Escherichia coli and Klebsiella pneumoniae [4, 5].
β-lactams are considered one of the most important The Ambler classification, clusters the enzymes
traits. Antibiotic resistance of Enterobacteriaceae is into 4 molecular classes (A–D) according to their
mainly accompanied by the production of extended amino acid sequences [6]. ESBLs are class A
spectrum β-lactamases (ESBLs) that hydrolyze third- β-lactamases that cleave oxyimino-cephalosporins and
generation cephalosporins and aztreonam, but can be monobactams, but not cephamycins or carbapenems.
inhibited by clavulanic acid [1−3]. Although there are many genotypes of ESBLs, SHV,
TEM, and CTX-M types are considered the most
Correspondence to: Ahmed S. Abdel-Moneim, College of common [7]. CTX-M-type ESBLs, which are non-
Medicine, Taif University, Al-Taif 5700, Saudi Arabia. TEM and non-SHV derivatives, represent a new and
E-mail: [email protected]; [email protected] rapidly growing family of molecular class-A ESBLs
220 Ali K. Alzahrani, et al.
[8]. According to their amino acid sequence similarities, the current study, we intended to conduct antibiotic
they have been classified into five groups: 1, 2, 8, 9, susceptibility screening of E. coli and K. pneumoniae
and 25/26, and, to date, more than 40 CTX-M from inpatients and detect the common ESBL genes.
β-lactamases have been reported. Meanwhile, we intended to genotype the ESBL positive
ESBL-producing bacteria are among the common bacteria with random amplified polymorphic DNA
microorganisms that produce severe diarrhoea, (RAPD) polymerase chain reaction (PCR).
postoperative abdominal wound sepsis, urinary
tract infections, and respiratory tract infections [2]. Materials and methods
Cephalosporins commonly used in patients with
septic infections are ineffective in the case of Bacterial culture and identification
ESBL-producing bacteria. ESBL-producing bacteria Our study protocol was approved by Taif
can acquire resistance to antimicrobials such as the University Medical Ethics Review Board (project
aminoglycosides, cotrimoxazole, tetracyclines, No. 3364-435-1) in accordance with the guidelines for
trimethoprim, and quinolones with the potential of the the protection of human subjects. Samples were
development of multidrug resistant microbes [9−12]. collected for clinical purposes from inpatients from
There is a shortage of the new antibiotics the local area of Al-Taif and nearby cities at King
especially for gram-negative bacteria that produce Abdul-Aziz Hospital, Al-Taif, Saudi Arabia between
ESBLs [13]. Delays in laboratory diagnosis and the February 1st and August 30th 2015 after patient
use of inappropriate antibiotic therapy are among consent documented on standard hospital forms. The
factors that increase the severity of the disease clinical samples were from various origins: 38 were
with a subsequent increase in mortality [14, 15]. from urinary tract infections, and 5 were from
Accordingly, rapid detection of ESBL-producing suppurative wounds in the perineum, sepsis of various
bacteria may aid in selecting the appropriate antibiotic postoperative wounds, and the liver. We received 43
with a subsequent improvement in the antibacterial bacterial isolates anonymized by coding linked to
outcomes [16]. Rapid detection is also necessary to patient identities from the clinical laboratory, which
screen patients and subsequently improve hospital were derived from the samples originally collected
infection control policies, avoid misuse of antibiotics, for clinical purposes. The isolates were subcultured
thus prolonging the efficacy of the currently available on selective media including blood agar and
antibiotic armamentarium [17, 18]. MacConkey agar [22] and gram-negative rods were
Current techniques for detecting ESBL producers selected for further identification [23].
are based on the determination of susceptibility to
expanded-spectrum cephalosporins followed by the Bacterial isolates confirmation and antimicrobial
inhibition of the ESBL activity, mostly by the use of susceptibility tests
clavulanic acid or tazobactam [19]. The double-disk Cultured bacteria were resuspended in 0.45%
synergy test and the ESBL “E-test” were proposed saline and matched to the required McFarland
for that purpose. Sensitivities and specificities of units. Two milliliters of bacterial suspension were
the double-disk test and of the E-test are good, ranging automatically loaded into a VITEK 2 microbial
from 80% to 95% [20]. Automated bacterial identification system (bioMérieux, Durham, NC, USA)
identification and antibiotic susceptibility testing for identification with gram-negative bacilli and
are also used in the detection of ESBL-producing antimicrobial susceptibility testing-GN04 cards.
organisms. The performances of those systems differ Reference strains including E. coli American Type
depending on the species investigated, with much higher Culture Collection 25922 were used as controls.
sensitivity (80%−99%) than specificity (50%−80%) Criteria used to characterize ESBL are those of the
[19, 20]. Clinical and Laboratory Standards Institute (CLSI,
Those tests require overnight growth, meaning that formerly National Committee for Clinical Laboratory
up to 24 to 48 h can elapse, before ESBL production Standards) [24]. The gram-negative bacilli were
is detected once the isolate has grown [19, 20]. This tested for their susceptibility to ampicillin, amoxicillin/
may result in a delay in the initiation of appropriate clavulanic acid, piperacillin/tazobactam, cefalothin,
antibiotic therapy [17]. Molecular detection of ESBL cefoxitin, ceftazidime, ceftriaxone, cefepime,
genes by PCR is an attractive alternative [19−21]. In imipenem, meropenem, amikacin, gentamicin,
Vol. 10 No. 3 Resistance and typing of Enterobacteriaceae 221
June 2016
Table1. Oligonucleotide sequences used to identify genes encoding important β-lactamase (bla) genes and random
primers used for genotyping of the bacteria
Bacterial genotyping using RAPD analysis missing data as “9”. The genetic associations between
For RAPD analysis, 11 different 10-mer random isolates were evaluated by calculating the Jaccard
primers, which were preselected for their performance similarity coefficient for pairwise comparisons based
with DNA from isolates of Enterobacteriaceae on the proportion of shared bands produced by the
(Table 1) were used (Amersham Pharmacia Biotech, primers. The similarity matrix was subjected to cluster
Piscataway, NJ, USA). Following experiments to analysis by an unweighted pair group method for
optimize component concentrations, PCR amplification arithmetic mean and a dendrogram was generated.
of random primers was conducted according to The computations were performed using the program
published methods [26, 27]. Briefly, 1 μL (20 ng) of NTSYS-PC version 2.01 [28]. Jaccard’s similarity
genomic DNA, 12.5 μL of Go Taq Green Master Mix, matrix was subjected to principal component analysis.
Promega, USA, 1 μL of primer (20 pmol), and
deionized ultrapure distilled water up to a total volume Results and Discussion
of 25 L were used. For DNA amplification, an initial There is a current increase in ESBL-producing
denaturation at 94°C for 5 min was conducted, and bacteria worldwide mainly E. coli. Among the 43
followed by 94°C for 30 s, 35°C for 1.5 min, and 72°C tested samples, 27 isolates were E. coli and 16 were
for 2.5 min for 40 cycles and a final elongation step K. pneumoniae (Table 2).
at 72°C for 7 min. DNA amplicons were separated ESBL-producing bacteria were detected in 17/
by electrophoresis in 1.5% agarose gel in TBE. The 43 isolates (39.5%): 14 strains were E. coli and 3
gels were stained with ethidium bromide (5 μg ml–1). strains were K. pneumoniae. All E. coli isolates
A 100 bp DNA ladder (with 1500 bp and 500 bp and 2/3 of K. pneumoniae were positive for blaTEM
reference bands) was used to provide molecular (Table 3).
weight markers suitable to determine DNA fragment Only 2/14 E coli and 2/3 K. pneumoniae showed
sizes (AccuRuler 100 bp DNA RTU Ladder, Ready- resistance to nitrofurantoin. Ten of 14 E. coli and
To-Use Cat. No. 02001-500; Maestrogen, Las Vegas, 3/3 K. pneumoniae ESBL strains were resistant
NV, USA). DNA was visualized by illumination with to ciprofloxacin. ESBLs confer resistance to the
ultraviolet light and then photographed using a Gel oxyimino-cephalosporins (i.e., cefotaxime, ceftriaxone,
Doc 2000 device (Bio-Rad Laboratories, Hercules, ceftazidime) and monobactams (i.e., aztreonam)
CA, USA). [29]. ESBLs do not hydrolyze the cephamycins
(e.g., cefoxitin and cefotetan), or the carbapenems
Data analysis (imipenem and meropenem), and their hydrolytic
The amplification products of RAPD-PCR were activity can be inhibited by several β-lactamase
scored for the presence “1” or absence “0” and inhibitors such as clavulanic acid and tazobactam [29].
Table 2. Antibiotic sensitivity of the examined samples (Escherichia coli and Klebsiella pneumoniae).
Two of 14, E. coli and 1/3 K. pneumoniae showed (31.4%) were considered as monomorphic (Table 4).
resistance to cefoxitin and clavulanic acid inhibition, The number of amplified fragments scored for each
while all the tested strains were sensitive to imipenem isolate was recorded. The amplified products
and meropenem (Table 3). In a Russian study, 39.7% among the E. coli and K. pneumoniae isolates were
of E. coli isolates and 21.8% of K. pneumoniae polymorphic.
isolates, which were ESBL-producing strains were A phylogenetic tree was constructed for the 14
resistant to ciprofloxacin [30]. Unfortunately, ESBL- different bla E. coli strains compared with an ESBL-
producing organisms often also possess resistance negative E. coli control that showed a different pattern
determinants to other important antibiotic groups, such of DNA fragments with the different primers (data
as aminoglycosides and fluoroquinolones, leaving not shown). The total number of bands varied from
an extremely limited range of effective agents [31]. 22 with primer OPA-10, to 15 with primer OPA-09
Only four E. coli strains were found to be resistant (Table 4). The RAPD-PCR results using OPA-06-
to gentamicin, while all E.coli strains were sensitive primer showed the highest polymorphism, the 16
to amikacin. A single K. pneumoniae strain was found fragments showed 100% polymorphism (Table 4).
to be resistant to both gentamicin and amikacin. The molecular size of the amplicon products ranged
In the present study, the majority of the blaTEM- from 75 bp to 1450 bp. These findings denote that
type ESBLs were predominant (16/17) followed RAPD markers are effective in detecting similarity
by blaCTX-M group 1, 3/3 K. pneumoniae, and 2/14 between E. coli strains and provide a potential tool
E. coli isolates were positive for blaCTX-M genes for studying the interstrain genetic similarity and the
from CTX-M group 1. Only a single E. coli isolate establishment of genetic relationships.
was positive for the CTX-M-group 2, and none According to genetic similarity and intraspecies
were positive results for the CTX-M group 9 gene differentiation, the 14 E. coli strains and an ESBL-
(Table 3). K. pneumoniae isolate 5 (negative for negative E. coli control strain were grouped into
TEM positive for CTX-M-1) was more resistant different clusters with about 54% genetic similarity.
than the other two K. pneumoniae (positive to TEM E17 was clustered in a separate tree branch far distant
and CTX-M-1) because they showed resistance from other isolates. E6 and E9 formed another cluster
to amikacin and gentamicin. The negative PCR while the rest were clustered in two main subclusters:
results in this report do not negate the possibility the first one included (E1, E3, E4, and E7), while the
that modified blaCTX-M were present in these isolates. second included (E8 and E10−15). E17, and to lesser
Because of the increased complexity of β-lactam extent E6 and E9, were found distant from the other
resistance in gram-negative organisms, the key to tested ESBL-positive E. coli strains (Figure 2).
effective surveillance is the use of both phenotypic RAPDs proved to be useful as genetic markers
and genotypic analyses in concert [32]. in bacteria fingerprinting as previously described [33].
Molecular markers are efficient tools for Although major bands from RAPD reactions are highly
molecular identification and estimation of relatedness reproducible, minor bands can be difficult to reproduce
through DNA fingerprinting. RAPD markers were because of the random priming nature of this PCR
developed by Williams et al. [26]. RAPD technique reaction and potential confounding effects associated
using single-arbitrary-10-mer oligonucleotides was with comigration with other markers. The use of
used to amplify discrete fragments of DNA using multiple primers sets in RAPD analysis can be used
PCR. This technique has been used extensively in as a rapid method for preliminary biotyping of the
many different applications and in different bacterial E. coli.
species because of its simplicity [27]. Genomic Pairwise genetic distance and homogeneity tests
diversity of K. pneumoniae and E. coli isolates were performed to determine the relatedness between
(n = 17) was investigated by RAPD analysis. The the different bacterial strains. Smaller genetic distance
RAPD results showed polymorphic numbers of between E. coli reflected the geographical proximity
the amplicons in different E. coli (n = 14) and between them and the results supported the hypothesis
K. pneumoniae (n = 3) isolates described in Table 4 that the geographical distance is an important factor
(Figure 1). influencing the genetic relatedness of E. coli strains
The random primers yielded 207 distinct bands, [34, 35]. A previous study used fingerprinting for
142 (68.6%) were considered as polymorphic and 65 resistant different bacteria in Al-Taif in determining
224
Table 3. Results of polymerase chain reaction of genes encoding important β-lactamases (bla) genes in selected bacteria and relevant antibiotic sensitivity
a c
Sample Isolated TEM CTX-M group Antibiotic sensitivity
Number bacteria CTX-1 CTX-2 CTX-9 bAmp Am/Cla Pip/Taz Cefo Cefta Cefe Imi Mer Amk Gen Cip Tig Nit Tri/Sulf
1 E. coli + – – – R R I R R R S S S S R S S R
2 K. pneumoniae + + – – R R I R R R S S S S R S I R
3 E. coli + – – – R S R S R R S S S S R S S R
4 E. coli + – – – R I R S R R S S S S R S S S
5 K. pneumoniae – + – – R I R I R R S S R R R I R R
6 E. coli + – – – R S S S R R S S S S R S S R
7 E. coli + – – – R I S I R R S S S R R S I R
8 E. coli + – + – R S R S R R I S S R R S S S
9 E. coli + + – – R S S S R R S S S S S S S S
10 E. coli + – – – R I S S R R S S S S R S R R
11 E. coli + – – – R R R S R R S S S S R S S R
12 E. coli + – – – R S S S R R S S S S S S S R
13 E. coli + – – – R S S I R R S S S R S S S R
14 E. coli + + – – R S S R R R S S S S R S S S
15 E. coli + – – – R S S I R R S S S R S S S R
16 K. pneumoniae + + – – R S R S R R S S S S R S R R
17 E. coli + – – – R I R S R R S S S S R S R S
Ali K. Alzahrani, et al.
a
TEM variants including TEM-1 and TEM-2. bAmp (ampicillin), Am/Cla (amoxicillin/clavulanic acid), Pip/Taz (piperacillin/tazobactam), Cefo (cefoxitin), Cefta (ceftazidime), Cefe
(cefepime), Imi (imipenem), Mer (meropenem), Amk (amikacin), Gen (gentamicin), Cip (ciprofloxacin), Tig (tigecycline), Nit (nitrofurantoin), Tri/Sul (trimethoprim/sulfamethoxazole),
E. coli = Escherichia coli and K. pneumoniae = Klebsiella pneumoniae. cR (resistant), S (sensitive), I (intermediate).
Vol. 10 No. 3 Resistance and typing of Enterobacteriaceae 225
June 2016
pairwise genetic distance and homogeneity [27]. from Al-Taif and surrounds in Saudi Arabia. blaTEM
However, including strains from different genera of and blaCTX-M-1 were the most commonly detected
bacteria in the same tree did not provide clear picture. genes. There was evidence for the existence of
We concluded that a considerably high incidence polymorphic genetic patterns among ESBL-producing
of ESBL-producing bacteria was present in patients bacteria.
Figure 1. Agarose gel (1.5%) electrophoresis of random amplified polymorphic DNA profiles of extended-spectrum
β-lactamase (ESBL)-producing Escherichia coli and Klebsiella pneumoniae. All isolates are E. coli except
Nos. 2, 5, and 16 as shown in Table 3 (in lanes 2, 5, 16 respectively) are K. pneumoniae. In the first left hand
lane of each gel a 100 bp DNA ladder was used to provide discrete DNA molecular weight markers (1500 bp
reference band, then 1000 to 100 bp in 100 bp steps with a 500 bp reference band) to determine DNA fragment
sizes (AccuRuler 100 bp DNA RTU Ladder; Maestrogen, Las Vegas, NV, USA). Primers (a) OPA-01, (b) OPA-03,
(c) OPA-04, (d) OPA-05, (e) OPA-06, (f) OPA-07, (g) OPA-08, (h) OPA-09, (i) OPA-10, (j) OPB-07, and (k) OPD-05.
An ESBL-negative E. coli control showed a different pattern of DNA fragments with the different primers (data
not shown).
226 Ali K. Alzahrani, et al.
Table 4. Polymorphic bands of each genetic primers and percentage of polymorphism in the extended spectrum
β-lactamase-producing bacterial isolates
Figure 2. Dendrogram of the 14 Escherichia coli isolates collected from inpatients at King Abdul-Aziz Hospital, Al-Taif,
Saudi Arabia based on the 11 random amplified polymorphic DNA primers compared with an extended spectrum
β-lactamase-negative strain (from our laboratory)
Acknowledgment References
This study was supported by Taif University, 1. Coque TM, Baquero F, Canton R. Increasing
through a grant for project No. 3364-435-1. prevalence of ESBL-producing Enterobacteriaceae in
Europe. Euro Surveill. 2008; 13:pii: 19044. [online]
Conflict of interest statement Available from http://www.eurosurveillance.org/View
The authors declare that there is no conflict of Article.aspx?ArticleId=19044
interest in this research. 2. Pitout JD, Laupland KB. Extended-spectrum β-
Vol. 10 No. 3 Resistance and typing of Enterobacteriaceae 227
June 2016