Background
Extensive and irrational use of antibiotics has led to the emergence and spread of antimicrobial resistance (AMR)—a condition in which pathogenic strains of bacteria develop resistance to the therapeutic antibiotics prescribed against it [
1]. Realising the AMR as a global crisis, World Health Organization (WHO) and US Centres of Disease Control and Prevention (CDC) have already warned of an imminent global disaster and possibility of returning to the post-antibiotic era [
2]. Gram-negative bacteria, mainly
Enterobacterales,
Acinetobacter baumannii and
Pseudomonas aeruginosa are able to produce enzymes such as extended-spectrum beta-lactamases (ESBLs), AmpC beta-lactamases, carbapenemase and metallo-beta-lactamases (MBL), which enable the host bacteria to develop resistance to most classes of antibiotics in use [
3]. All of these enzymes possess a similar mechanism to hydrolyse β-lactam ring of the antibiotics. ESBLs are class A β-lactamases that are responsible for resistant against oxy-imino cephalosporins (cefotaxime, ceftazidime, ceftriaxone, cefuroxime, and cefepime) and monobactams (aztreonam) [
4]. Carbapenemase are the members of class A, B and D β-lactamases. Class A and D carbapenemase bring out the serine based hydrolytic mechanism while the class B carbapenemase are metallo- β-lactamases (MBL) that contain zinc based hydrolytic mechanism [
5]. A novel kind of MBL, known as New Delhi metallo-β-Lactamase (NDM) possesses the ability to resist virtually all β-lactam antibiotics (except aztreonam) and carbapenems [
6]. Similarly,
K. pneumoniae carbapenemase (KPC), a derivative of carbapenemase (class A β-lactamases) also has become prominent because of their ability to inactivate carbapenems [
7]. Although KPC is prevalent among
K. pneumoniae, the enzyme has been frequently isolated from other Gram-negative bacilli [
8].
Multidrug-resistant (MDR) bacteria—better known as superbugs—seriously limit the treatment options and thus are associated with increased mortalities, morbidities and economic burden [
9]. On the other hand, narrowed treatment option is forcing clinicians to rely upon the “last line” drugs, primarily colistin (a polymyxin E antibiotics), which is reintroduced to counter the rapidly surging carbapenemase-producing Gram-negative bacteria [
10]. Polymyxins (polymyxin B and polymyxin E) are cyclic lipopeptide discovered in the late 1940s [
11] that were introduced in the treatment of infections caused by Gram-negative bacteria. However, they were no longer used due to their neuro- and nephro-toxicity and also due to the availability of comparatively ‘safer’ drugs such as beta-lactams [
12]. Although their toxic effects were standstill, polymyxins were re-introduced in 1990s to counter the uncontrolled emanation of carbapenem resistant bacteria [
13]. Polymyxins are now extensively used in modern clinics due to paucity of novel, effective and safer antibiotics [
14]. Like with all other antibiotics, bacteria have managed to develop resistant to colistin, as a large number of studies suggest the emergence and globalization of colistin-resistance [
10].
Until the first report of a variant of noble plasmid-mediated mobilized colistin resistance gene (
mcr-1) in late 2015 in China, polymyxin (particularly, colistin) resistance was solely attributed to the regulatory changes mediated by the chromosomal genes (phoPQ, pmrAB, and mgrB) [
2]. Since the first identification of
mcr-1, several variants (from
mcr-1 to
mcr-9) have been reported from more than 40 countries across five different continents [
15]. The
mcr-1 encodes for phosphoethanolamine (pEtN) transferase enzyme (discovered in late 2015), which modifies the outer membrane lipopolysaccharides by adding pEtN to the phosphate groups in Lipid A thereby decreasing the net negative charges [
2]. The resulting modification reduces the binding affinity of polymyxins to the bacterial cell wall [
16,
17]. Unlike chromosomal mutation, acquisition of
mcr is a matter of serious concern because of its potential transferability, as the gene is spread rapidly through the horizontal transfer at a higher rate than occurring through spontaneous mutation [
18]. In addition, plasmids resistant to multiple classes of antibiotics can be transferred to other bacteria [
19,
20]. Elevated endemicity of
mcr genes all over the world in a short span of time is attributable to their ability to proliferate at a higher pace [
21].
Since
mcr gene was first isolated in an
E. coli from animal sources in China, the plasmid-mediated colistin resistance may have transmitted from animals (colistin was extensively used as growth promoters for long times) to humans [
22].
E. coli is the most prevalent species harbouring the
mcr gene, accounting for approximately 91% of the entire load of
mcr-positive bacteria, which is followed by
Salmonella enterica (~ 7%) and
K. pneumoniae (~ 2%) [
23]. Higher burden of
mcr among
S. enterica than
K. pneumoniae also supports the fact that the former is the food-borne pathogen and is very likely to be transmitted via food chain [
24]. Moreover, these drug-resistant bacteria are isolated from humans, animals, and environments so that the perspective of ‘One Health’ has been jeopardized [
25].
Implementation of effective surveillance programs and infection controls are considered as the two pillars to check the growth and spread of AMR [
26]. However, in the developing countries like Nepal, circulation and co-circulation of resistant genes may go undetected, underreported and poorly characterized due to poor diagnostic facilities [
27,
28]. In addition, irrational use of antibiotics among humans and animals (often as growth promoters) is putting pressure of potential outbreaks in the future [
10]. Moreover, there are a limited number of studies on colistin resistance and the prevalence of resistance can vary and change over the time within and between the countries. Therefore, this study was conducted in a tertiary care center with an attempt to determine the prevalence of beta-lactamases including ESBL, MBL, KPC and colistin resistance among Gram-negative MDR pathogens. At the same time, we also aimed to explore the possible role of
mcr genes in conferring resistance to colistin. Furthermore, antibiogram of the resistant strains to a variety of antibiotics was carried out to recognize the possible therapeutic options for combating superbugs.
Discussion
Drug-resistance, especially pan-drug resistance and MDR is emerging as a major challenge in the treatment of infections caused by Gram-negative bacteria. As surveillance of AMR and early response to the infection control are crucial steps to address the issues, this study also aimed to determine the status of MDR among E. coli and K. pneumoniae isolates and to investigate possible acquisition of mcr-1 in colistin resistant isolates. In this study, most of the isolates were resistant to commonly prescribed broad-spectrum antibiotics. In addition, prevalence of colistin resistance and acquisition of mcr-1 among the drug-resistant isolates was also observed in this study.
In this study, 16.4% (529/3216) specimens showed bacterial growth in which prevalence of Gram-negative bacteria from different clinical specimens was much higher than the Gram-positives. This finding concords with previous studies reported from Nepal [
9,
10,
40‐
44]. Higher prevalence of
E. coli in comparison to other species could be due to being normal flora of human gut which is highly opportunistic in immunocompromised patients. When
E. coli reaches out to the tissues other than its common site, it serves as an opportunistic pathogen. A number of virulence factors encoded by pathogenic strains of
E. coli enable them to colonize the human body in spite of effective host defence [
45].
In this study, all of the isolates of
E. coli and
K. pnemoniae were susceptible to colistin, polymyxin B and tigecycline, which is comparable to some previous findings [
46,
47]. These classes of antibiotics can be effective drugs in the management of Gram-negatives. Conversely, all of the isolates were resistant towards azithromycin. Previous exposure of the isolates to these antibiotics as well as the state of resistance genes of corresponding antibiotics may be the reasons for their susceptibility patterns [
48].
In this study, increased resistance to third-generation cephalosporins was observed, as more than half of the isolates were non-susceptible to those drugs. Similar findings have been reported by some previous studies [
47,
49,
50]. Higher rate of resistance to cephalosporins can be attributable to their irrational prescription and uses [
51].
Resistance rate of
E. coli to fluoroquinolones in this study ranged from 47 to 55% which are in agreement with earlier studies from Nepal [
52,
53] and India [
54]. Resistance to fluroquinolones among MDR Gram-negative bacteria is common and is expected to sustain and perhaps accelerate even if other antibiotics are used [
55]. The prevalence of fluroquinolone resistance is related to the intensity of antibiotics used, which may reduce the efficacy of drug in a progressive manner [
56].
In this study, almost one fourth of
E. coli isolates were resistant to carbapenem antibiotics. The resistance rate towards these antibiotics ranged from < 3.0% to 21.0% in some of the previous studies from Nepal [
50,
52,
53] whereas 100% sensitivity towards imipenem was reported in some other studies [
47,
57]. Production of beta-lactamase enzymes and the upregulation of efflux pump are suggested as the reasons for reduced susceptibility [
58]. However, comparatively low resistance to carbapenem antibiotics reported in this study could be due to the lower use of these antibiotics in the treatment of infections [
59].
In AST assay of
K. pneumoniae, two-third of the isolates were susceptible to fluoroquinolones and gentamicin. This finding is similar to another study reported from Nepal [
60]. However, some other studies have reported lower sensitivity rates (less than 50.0%) [
57,
61]. This variation may be due to the difference in the specimens included in the study as well as the exposure of isolates towards the antibiotics. All of the
K. pneumoniae isolates were resistant to amoxicillin. Similar findings were reported in other studies [
52,
60]. In addition, reduced sensitivity towards cephalosporin and carbapenem antibiotics was observed in this study. High resistant rate towards cephalosporins was also reported in previous studies [
50,
52,
62,
63]. Multiple factors such as extensive use of drugs, production of beta-lactamases, or efflux pumps (which actively pump out these antibiotics) are attributable to the rise in the resistance against carbapenems [
26,
64].
Among the total (343) isolates of
E. coli and
K. pneumoniae, more than half (58.0%) were MDR. MDR strains were predominant among the isolates of
E. coli in comparison to
K. pneumoniae. This result was in consistent with previous findings which also reported the rate of MDR in a range of 41.0%–67.7% [
9,
20,
28,
52,
60] while lower than some other findings [
8,
10]. In this study, the prevalence of MDR
E. coli and
K. pneumoniae was 59.3% and 48.8% respectively. Common risk factors associated with development of MDR are poor hygiene, misuse of antibiotics and absence of antimicrobial surveillance program [
65,
66]. Higher rate of antibiotic resistance among
E. coli and
Klebsiella spp
. is associated with their ability to produce different kinds of β-lactamases primarily ESBL, AmpC and MBL, and carriage of resistance trait for quinolones and aminoglycosides in the plasmid [
67]. In several hospitals in Nepal, the antibiotics used for the treatment of infected patients are effective in curing only a half of the cases whereas other half of the treatment course shows no response [
68]. In addition, development of partial resistance by bacteria, most antibiotics intended to cure people are becoming less effective which might also be the reason of increasing prevalence of MDR reported in this study [
26].
In this study, the prevalence of ESBL producing strains was found to be 41.1% among Gram-negative isolates. This result is comparable to some previous reports from Nepal [
52,
69]. The prevalence of ESBL production was reported low in other studies [
70‐
72]. The difference in the prevalence of ESBL production can be partially due to geographical variations, type of specimens processed, and local practices of antibiotics prescription and use [
73].
In our study, among 343 isolates of
E. coli and
K. pneumoniae, 12.5% were resistant to carbapenem. In earlier study reported from Kathmandu Model Hospital, the prevalence of carbapenem resistant ranged from 4.5% to 20.0% among the members of Enterobacteriaceae [
74]. However, higher rate of carbapenem resistant among Enterobacteriaceae was reported in other studies [
75,
76]. The difference in utilization of carbapenem antibiotics to treat infections in different study settings may be responsible for these variations [
75].
Carbapenem resistant isolates were subjected to KPC and MBL production test phenotypically. In this assay, 30.2% and 60.5% isolates were KPC and MBL-producers respectively. Our findings are comparable to a previous finding [
77]. The prevalence of KPC production in
E. coli and
K. pneumoniae was 33.3% and 20.0% respectively in our study. Similarly, MBL production was reported 63.6% in
E. coli and 50.0% in
K. pneumoniae. In a previous study, KPC production in
E. coli was reported as 14.4% and 7.1% in
K. pneumoniae [
8]. Accordingly, another study reported comparatively lower incidence of MBL producing-
E. coli and
K. pneumoniae in different clinical samples in Central Nepal [
78]. Similarly, lower rate of MBL (9.0%) and KPC (6.5%) production was reported in
E. coli [
79]. Another study from Iran reported 80.5% of
K. pneumoniae isolates as KPC-producers [
80]. This study revealed higher prevalence of MBL and KPC production in
E. coli and
K. pneumoniae which may be due to dissemination of plasmid encoded carbapenem resistance genes [
59].
This study reported comparatively low prevalence (3.0%) of colistin resistant
E. coli and
K. pneumoniae isolates (3.0%). Similar result was reported in previous findings of 0.3% in Switzerland [
81], 0.7% in Spain [
82] and in a previous report of global antimicrobial surveillance programs [
83,
84]. Low prevalence of the resistant isolates in our study may be attributable to the presence of low number of
mcr-1 positive bacteria and lesser use of colistin use for the treatment of community acquired infections [
81]. However, other studies from India [
85] and Thailand [
86] reported the prevalence rate of colistin resistant as high as 32.0% and 71.3% respectively. In this study, rates of colistin resistance were different among the bacterial species. Higher prevalence of colistin resistance was reported in
K. pneumoniae (10.0%) when compared to
E. coli (2.2%). Different studies also showed that higher prevalence of colistin resistant
K. pneumoniae than
E. coli [
87,
88]. The main risk factor for the development of colistin resistance is related to the extensive and irrational use of colistin in antimicrobial therapy [
89].
MIC range of colistin for
E. coli ranged from ≤ 2 µg/ml to 8 µg/ml which was lesser than that of
K. pneumoniae (≤ 2 µg/ml to 16 µg/ml). This finding is in agreement with a previous study from China [
90]. MIC range of
mcr-1 positive
Enterobacteriaceae typically have a moderate level 4–16 mg/l of colistin resistant strains [
91]. MIC of colistin resistant isolates carrying
mcr-1 was lower in this study. Exceptionally, MIC range of colistin in colistin resistant
K. pneumoniae without
mcr-1 was high in this study. This result suggests that colistin resistance in
K. pneumoniae might be associated with chromosomal mutations in
mgrB, phoP/phoQ, pmrA, pmrB, pmrC and
crrABC [
92]. High MIC may also be due to strong selective pressure in the isolates. These strains may carry another variant of
mcr gene [
93].
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