Acquired Resistance to Colistin via Chromosomal And Plasmid-Mediated Mechanisms in Klebsiella pneumoniae : Infectious Microbes & Diseases

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Review Article

Acquired Resistance to Colistin via Chromosomal And Plasmid-Mediated Mechanisms in Klebsiella pneumoniae

Berglund, Björn1,2,✉

Editor(s): van der Veen, Stijn

Author Information
Infectious Microbes & Diseases 1(1):p 10-19, September 2019. | DOI: 10.1097/IM9.0000000000000002
  • Open


The increasing prevalence of resistance to the last-resort antibiotics carbapenems is leading to increasing difficulties in treating infections caused by multidrug-resistant carbapenem-resistant Gram-negative bacteria such as Klebsiella pneumoniae. The situation has led to the reintroduction of a drug previously discontinued for use in humans - colistin. Colistin is a cationic polypeptide which binds to the negatively charged lipid A of the lipopolysaccharide on the outer membrane of Gram-negative bacteria, causing membrane destabilization, cell leakage and death. Although colistin can be used to successfully treat infections caused by carbapenem-resistant K. pneumoniae, colistin resistance is known to be inducible during colistin treatment and can be engendered via mutations and genetic alterations in chromosomal genes involved in the regulatory network controlling chemical modifications of the lipid A moiety on the lipopolysaccharide, reducing the negative charge of lipid A and its affinity for colistin. Furthermore, the recent discovery of plasmid-mediated colistin resistance via the mcr-genes, and the potential for plasmid-mediated resistance determinants to rapidly disseminate between strains, has given rise to concerns regarding the future usefulness of colistin as a last-resort antibiotic. This review describes the known colistin resistance mechanisms in K. pneumoniae and the epidemiology of plasmid-mediated colistin resistance determinants in association to the species.


Klebsiella pneumoniae are Gram-negative bacteria of the Enterobacteriaceae family and common colonizers of the human gastrointestinal tract.1,2K. pneumoniae are opportunistic pathogens which can cause different types of healthcare-associated infections including pneumonia, bloodstream infections, urinary tract infections, wound infections, and surgical site infections. Infections caused by these bacteria are becoming increasingly difficult to treat due to the increasing prevalence of antibiotic resistance. Third-generation cephalosporins are the drugs preferentially used to treat infections caused by multidrug-resistant K. pneumoniae. The utility of these drugs has; however, been considerably limited by the widespread dissemination of extended-spectrum β-lactamases (ESBLs), enzymes which can hydrolyze third-generation cephalosporins.3 Since the 2000s, these enzymes have become globally occurring at high rates.4 The last-resort antibiotics used against multidrug-resistant and ESBL-producing K. pneumoniae are carbapenems.5 Unfortunately, the recent decade has seen a worldwide increase of carbapenem-resistant K. pneumoniae (CRKP), an increase which has mainly been due to the rapid dissemination of K. pneumoniae carbapenemase (KPC), New Delhi metallo-β-lactamase (NDM), and oxacillinase-48 (OXA-48) type carbapenemases. The treatment options for infections caused by multidrug-resistant CRKP are narrow indeed, and the increasing prevalence of the multidrug and carbapenem resistance phenotypes in clinical settings among K. pneumoniae and other bacteria such as Escherichia coli, Pseudomonas aeruginosa, and Acinetobacter baumannii, has prompted the reintroduction of an antibiotic previously discontinued for human use – colistin.6

Colistin (also known as polymyxin E) is, together with polymyxin B, the only drug from the polymyxin class of antibiotics used to treat infections in humans.7 Colistin was originally isolated from Paenibacillus polymyxa in the 1940s. It was clinically used to treat infections in humans from 1959, but the nephrotoxicity of the compound led to a decline in its use from the early 1970s in favor of newly introduced drugs (eg, aminoglycosides). In recent decades, colistin has seen increased usage as a last-resort option against infections caused by multidrug- and carbapenem-resistant P. aeruginosa, A. baumannii, and Enterobacteriaceae, and K. pneumoniae among the latter in particular.8 However, the utility of colistin against K. pneumoniae is limited both by the relatively high rates of colistin resistance among the species and by that colistin resistance can be induced by treatment with the antibiotic.9,10 The resistance rate among clinical isolates in many studies lie between approximately 5%–10%, but has been reported as high as approximately 20%–40% among CRKP in Italy and Greece.11 The colistin resistance rate of K. pneumoniae among clinical isolates collected worldwide in the SENTRY Antimicrobial Surveillance Program between 2014 and 2015 has been reported as 4.4%.12 In a case-control study conducted at six Italian hospitals during 2010 to 2014, the 30-day mortality of patients with bloodstream infections caused by colistin-resistant CRKP was found to be as high as 51%.13 In the same study, an increase in prevalence of colistin resistance among CRKP causing bloodstream infections was observed over the study period from less than 10% to more than 30%.

Whereas colistin was phased out of human medicine in the 1970s, the antibiotic saw increased usage as a therapeutic, prophylactic, and growth promoter in animal food-production, including poultry and pig farming.14,15 The extensive usage of colistin in animal production, and the associated selection pressure exerted on bacteria in the animal guts, have been linked to the emergence and dissemination of the plasmid-mediated colistin resistance gene mcr-1, which was discovered in 2015 in China.14,16 The fear of a rapid dissemination of colistin resistance made possible by plasmid-mediated resistance determinants have led to a growing number of voices calling for the banning of colistin for use as a growth promoter and prophylactic in animal production in order to preserve the drug's usefulness in human medicine.14 As a result, colistin has already been banned for use as a feed additive in some countries such as China,17 and the European Medicines Agency, in their updated advice on colistin usage published in 2016, recommended minimizing usage of colistin and reserving the drug for treating clinical conditions for which there are no alternative treatments.18

There is an increasing need for colistin to treat infections caused by multidrug-resistant CRKP, nevertheless, the emergence of colistin resistance and the recent discovery of plasmid-mediated colistin resistance in K. pneumoniae calls into question the future usefulness of colistin as a last-resort antibiotic. This review describes the known colistin resistance mechanisms and the epidemiology of plasmid-mediated colistin resistance determinants in K. pneumoniae.

Colistin mode of action and resistance mechanisms

Colistin is a cationic polypeptide and narrow-spectrum antibiotic with activity mainly against Gram-negative bacteria.8 Susceptible species among Enterobacteriaceae include Klebsiella spp., E. coli, Enterobacter spp., Salmonella spp., Shigella spp., Citrobacter spp., and Kluyvera spp. Although the exact mechanism of antibacterial activity of colistin has not been fully elucidated, the main target has clearly been established to be lipid A of the lipopolysaccharide (LPS) of the outer membrane of Gram-negative bacteria.19 The positively charged colistin molecule binds to the negatively charged lipid A causing destabilization and permeability changes in the cell membrane leading to leakage of cell content and cell death. Whereas colistin's major mode of action is on the bacterial cell membrane, a secondary mode of action by inhibition of respiratory enzymes – type II NADH-quinone oxidoreductases, has also been proposed.20

Among Enterobacteriaceae, decreased susceptibility to polymyxins has been attributed mainly to chemical modifications of the lipid A moiety by addition of either or both of amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine (pEtN).21,22 These modifications lead to a net reduction in negative charge and as a consequence, to lower affinity for the positively charged colistin molecule. Lipid A modifications are regulated by signal transduction systems which mediate adaptive responses to environmental stimuli including low concentrations of Mg2+ and pH, and high concentrations of Fe3+ and Al3+.22 The chemical decoration of lipid A with L-Ara4N is mediated by the pmrHFIJKLM operon (also known as arnBCADTEF or pbgPE) whereas the addition of pEtN to lipid A is catalyzed by PmrC which gene is located on the pmrCAB operon (Figure 1). The expression of these operons is in turn regulated by the PmrA/PmrB two-component system (2CS). PmrB is a sensor kinase located in the inner membrane and is autophosphorylated by environmental stimuli (including low pH and high concentrations of Fe3+ and Al3+). Upon phosphorylation, the phosphoryl group is transferred to PmrA, the cognate response regulator of PmrB. The phosphorylated form of PmrA can bind to the promoter regions of the pmrHFIJKLM and pmrCAB operons and promote their expression, which leads to increases in levels of lipid A modifications with L-Ara4N and pEtN. Since pmrA and pmrB are both located on the pmrCAB operon, induction of the PmrA/PmrB 2CS is positively autoregulated by increased expression of pmrA and pmrB, leading to an increased signal response. However, increased PmrB kinase activity leads to a switch in PmrB to increasing phosphatase activity, which in turn leads to an increase in removal of the phosphoryl groups from phosphorylated PmrA, thus hampering its ability to bind to PmrA-dependent promoters and repressing the signal response.

Figure 1:
Proteins and genes involved in the regulatory network modulating chemical modifications of the lipid A moiety on the lipopolysaccharide with L-Ara4N and pEtN in K. pneumoniae. Two-component systems PmrA/PmrB and PhoP/PhoQ are activated by environmental stimuli and regulate the transcription of genes pmrHFIJKLM and pmrC via phosphorylation of the cognate response regulators PmrA and PhoP. The PhoP/PhoQ system is further under autoregulation by MgrB, and the PhoP/PhoQ signal is additionally transduced via the connector protein PmrD. In the figure, proteins are denoted by white ellipses and genes are denoted by gold arrows. The figure is not to scale. L-Ara4N: amino-4-deoxy- L-arabinose; pEtN: phosphoethanolamine.

In several species of Enterobacteriaceae, including K. pneumoniae, chemical modification of lipid A with L-Ara4N and pEtN are further regulated by another 2CS, PhoP/PhoQ.22 Like PmrA/PmrB, PhoP/PhoQ is constituted by an inner membrane sensor kinase, PhoQ, which induces phosphorylation of its cognate response regulator PhoP upon exposure to certain environmental stimuli. In the case of PhoQ, its autophosphorylation is induced by low concentrations of Mg2+ and some cationic antimicrobial peptides. The PhoP/PhoQ response signal induces lipid A modifications via genes in the PmrA/PmrB regulon, but the specific way in which the interaction occurs is different between different species. In K. pneumoniae, the phosphorylated form of PhoP promotes transcription of the connector protein PmrD. PmrD protects PmrA from dephosphorylation, thus indirectly increasing the PmrA/PmrB signal.23 The phosphorylated form of PhoP can also bind directly to the pmrHFIJKLM operon and promote modification of lipid A with L-Ara4N.22

The PhoP/PhoQ 2CS is under further regulation of another transmembrane protein, MgrB, which functions as a negative feedback regulator on the PhoP/PhoQ 2CS.24 Induction of PhoQ by environmental stimuli leads to phosphorylation of PhoP, the phosphorylated form of which acts as a transcriptional activator on several genes in the PhoP/PhoQ regulon, including mgrB. MgrB in turn directly acts to repress PhoQ, thereby repressing phosphorylation of PhoP and dampening the signal response.

Chromosomally mediated colistin resistance

Alterations in the genes regulating the chemical additions of L-Ara4N and pEtN to the lipid A moiety are the most common and well-characterized mechanisms of acquired colistin resistance in K. pneumoniae (Table 1).9 One such mechanism is via deleterious alterations in mgrB, leading to disruption of the negative feedback loop of the PhoP/PhoQ 2CS, overexpression of PhoP-regulated genes and abnormally high levels of lipid A modifications. A wide range of different disruptive alterations in mgrB leading to decreased colistin susceptibility have been observed (Table 1 and Figure 2). Mutations in mgrB engendering a dysfunctional MgrB and elevated MICs to colistin which have been observed include nonsense mutations,25–28 frameshift deletions leading to the introduction of premature stop codons,25–27 large deleted sections of the gene,29 non-stop mutations leading to elongated gene products,27,30 and amino acid substitutions25,31,32 (Table 1). However, the most prevalently reported mechanism of mgrB inactivation is transposition of insertion sequences (ISs) into the gene, which leads to complete loss-of-function of MgrB and subsequent upregulation of the PhoP/PhoQ 2CS and colistin resistance (Figure 2).33 A large number of different ISs have been associated with transposition into mgrB including IS10R,26,27,30 IS5,28 IS5-like,9,25,26,30,34 IS903,27,34 ISKpn14,25,26 and ISKpn26,27,28 with ISs of the IS5-family being the most commonly reported.33 Apart from IS transposition directly into the gene, MgrB disruption has also been reported to be brought on by transposition of IS90326,27,30 and IS5-like30 ISs into the promoter region of mgrB, presumably leading to hampered expression of MgrB. Judging from the number of reports of colistin resistance by inactivation of mgrB, this mechanism seems to be the most common colistin resistance mechanism in K. pneumoniae,25,33 and has been reported to occur in patients treated with colistin.9,10 Furthermore, mgrB inactivation has been shown to occur fairly easily in vitro, at a low fitness cost,35 and the inactivation of mgrB in mutants of clinical isolates has been shown to lead to colistin resistance without loss of virulence in Galleria mellonella (waxmoth) larvae36,37 and murine in vivo infection models.37 These attributes make mgrB inactivation a clinically problematic mechanism of colistin resistance.

Table 1:
Amino acid substitutions experimentally verified to confer colistin resistance in K. pneumoniae by using complementation assays or similar methods.
Figure 2:
Mutations and genetic alterations in mgrB engendering a dysfunctional gene product and colistin resistance in K. pneumoniae. A: Major deletions or IS transpositions can truncate mgrB leading to a dysfunctional gene product. IS transpositions into the promoter region of mgrB can lead to disrupted expression of the gene. B: Point mutations in mgrB can lead to an elongated protein via non-stop mutations, a truncated protein via nonsense mutations or altered protein functionality via amino acid substitutions arising from missense mutations. In the figure, genes are denoted with large arrows and proteins are denoted as green ellipses. ISs are depicted as red arrows. The figure is not to scale. IS: insertion sequence.

Mutations in the genes directly involved in the PmrA/PmrB and PhoP/PhoQ 2CSs can also cause colistin resistance via upregulation of L-Ara4N and pEtN modifications to lipid A (Table 1). In pmrB, mutations including those leading to A20P,38 L82R,39 and T157P40 have been shown to engender colistin resistance through complementation assays, although several additional mutations have been observed which putatively reduce colistin susceptibility in K. pneumoniae.8,34,41,42 Mutations in pmrA are more rarely reported. The missense mutation leading to the amino acid substitution G53C in PmrA has been reported in colistin-resistant K. pneumoniae, and since the analogous mutation has been observed to cause resistance in Klebsiella aerogenes and Salmonella enterica, it is conceivable that it has the same effect in K. pneumoniae.34 Amino acid substitutions R81C32 and D191Y43 in PhoP and A21S,44 L26P,30 T281M and G358C31 in PhoQ have also been confirmed by complementation assays and site-directed mutagenesis to confer colistin resistance in K. pneumoniae. As with pmrA and pmrB, several additional mutations in phoP and phoQ in colistin-resistant K. pneumoniae have been observed and predicted to engender elevated MICs to colistin.8,42 Clearly, there are still numerous mutations in genes related to the PmrA/PmrB regulatory network leading to colistin resistance that remain to be discovered.

CrrA/CrrB is another 2CS whose function seems to be associated with the PmrA/PmrB regulatory network.29 The function of the CrrA/CrrB 2CS has not yet been fully elucidated; however, the CrrA/CrrB 2CS likely affects the PmrA/PmrB 2CS via a connector protein CrrC. CrrA/CrrB can be found in some strains of K. pneumoniae and mutations in crrB have been shown to lead to elevated MICs of colistin.29,45 These include mutations leading to amino substitutions L94M, Q10L, Y31H, W140R, N141I, P151S, and S195N (Table 1).29,45 A dysfunctional CrrB likely affects the regulation of the PmrA/PmrB 2CS leading to reduced colistin susceptibility via overexpression of the pmrHFIJKLM and pmrCAB operons; however, it has also been proposed that mutations in genes related to CrrA/CrrB additionally mediate resistance to colistin via a putative efflux pump.46

Another 2CS, QseB/QseC has been shown to be involved in colistin resistance in K. pneumoniae. Pitt et al.32 showed that either mutations causing S8R and I283L in qseC could cause colistin and polymyxin B resistance (Table 1). The role of QseB/QseC is not well-characterized in K. pneumoniae but the 2CS has been shown to be involved in cross-talk with PmrA/PmrB in E. coli. One study also showed that mutations in the genes yciM and lpxM, leading to V43G and V30G, respectively, could each confer colistin resistance in clinical isolates of K. pneumoniae.44 The mechanism of resistance via these mutations has not been elucidated, but yciM is involved in the biosynthesis of LPS whereas lpxM encodes a lipid A acyltransferase, and so it is conceivable that mutations in these genes lead to colistin resistance via alterations in LPS production and lipid A morphology, respectively.

A few studies have shown that the capsule may also be involved in polymyxin resistance in K. pneumoniae. In Campos et al.,47 increased capsular polysaccharide (CPS) production was shown to be linked to decreased susceptibility to polymyxin B, and Llobet et al.,48 showed that exposure of K. pneumoniae to purified CPS increased the MICs of polymyxin B, likely via binding of the positively charged polymyxin to the negatively charged CPS. Formosa et al.,19 used atomic force microscopy to characterize morphological differences in the capsule and its interaction with colistin in colistin-susceptible and colistin-resistant isolates and showed that the capsule was removed by colistin in the susceptible, but not in the resistant isolate, indicating a role of the capsule in colistin resistance. In contrast, in another study, a wild-type K. pneumoniae isolate and its capsule-deficient mutant was found to exhibit no difference in susceptibility to colistin.49 Further studies are clearly needed to elucidate the role of the capsule in colistin resistance in K. pneumoniae.

Heteroresistance, or the existence of resistant subpopulations in otherwise phenotypically susceptible populations as determined by routine susceptibility testing methods, is known to occur in K. pneumoniae with regards to colistin.50,51 The size of the subpopulations vary; Poudyal et al.50 reported the ratio of resistant subpopulations among K. pneumoniae isolates heteroresistant to colistin as ranging from one out of 10−9 to 10−5 of the main populations. Meletis et al.51 similarly reported the range of the resistant subpopulations as ranging from one out of 10−7 to 10−5 of the main populations. Due to the very nature of heteroresistance (ie, indeterminable by routine susceptibility testing), the prevalence is largely unknown.1 Although based on relatively few isolates, two studies investigating the issue showed remarkably high prevalences of 75% (12 out of 16) and 94% (15 out of 16), respectively.50,51 Several studies have shown that heteroresistance to colistin in K. pneumoniae is related to mutations and genetic alterations among the resistant subpopulations in genes associated with LPS biosynthesis and modifications.43,44,52 Specifically, elevated MICs in resistant subpopulations of clinical isolates of K. pnemoniae have been shown to be engendered by inactivation of mgrB,44,52 and mutations in phoP,43phoQ, lpxM, and yciM.44 Cain et al.53 further linked colistin heteroresistance in K. pneumoniae to mutations in crrB. Regardless of the mechanism, it is likely that resistant subpopulations with chromosomal alterations can become dominant during a colistin selection pressure, thus facilitating emergence of resistance during colistin therapy leading to treatment failure. Although the clinical significance of colistin heteroresistance in K. pneumoniae is still largely unknown, Band et al.54 showed that clinically obtained, multidrug-resistant CRKP isolates with subpopulations showing colistin resistance could cause treatment failure in an in vivo murine infection model indicating that the phenomenon merits further study and consideration as a potentially serious clinical issue.

Plasmid-mediated colistin resistance

Mutations in chromosomal genes were the only known mechanisms of acquired colistin resistance until 2015, when the plasmid-mediated gene mcr-1 was reported for the first time.16mcr-1 encodes a pEtN transferase which confers reduced susceptibility to colistin by catalyzing the addition of pEtN to the lipid A moiety. The gene was initially discovered among isolates of E. coli and K. pneumoniae originating from China. Isolates of E. coli carrying mcr-1 were found among pigs at slaughter, retail meat from pigs and chicken, and from inpatients at hospitals, whereas, K. pneumoniae carrying mcr-1 were only isolated from inpatients. The news of the discovery of mcr-1 prompted screenings worldwide throughout sample collections and databases, and it was soon discovered that the gene was already globally disseminated, and present in several different species of Enterobacteriaceae, including Salmonella typhimurium, Salmonella Paratyphi B, and Shigella sonnei.55 Since the discovery of mcr-1, several other mcr-genes have been reported.56 To date, these include mcr-2 up to mcr-8, although mcr-1 is still by far the most commonly reported colistin resistance gene worldwide. Aside from mcr-1, only mcr-3 and mcr-8 among the mcr-genes have been reported in K. pneumoniae (Table 2).56–58

Table 2:
Publications reporting on isolates of K. pneumoniae carrying mcr-genes including specimen type, location, numbers of isolates, multilocus sequence type (MLST) of isolates, carbapenemases, and Inc-type of the mcr-carrying plasmid.

A list of publications reporting on the isolation of mcr-carrying K. pneumoniae is summarized in Table 2. Although K. pneumoniae was one of the initial species in which mcr-1 was discovered,16 the gene is by far more commonly reported in isolates of E. coli. A survey on mcr-1 carriage in isolates from the SENTRY Program based on 13 526 E. coli isolates and seven 480 K. pneumoniae isolates collected from hospitals worldwide during 2014 and 2015 detected mcr-1 among 19 of 59 isolates of colistin-resistant E. coli (32%), but none among 331 isolates of colistin-resistant K. pneumoniae.12 In an updated repeat of the survey based on isolates from 2016, two K. pneumoniae isolates (from Spain and Italy) and 10 E. coli isolates were detected carrying mcr-1 out of a total of 11 493 isolates.59 Screening for mcr-genes among clinical isolates from the INFORM global surveillance program detected no mcr-1 among 481 K. pneumoniae isolates, but one isolate carried mcr-3 (0.21%).58 Similarly, low prevalence rates of mcr-1 in K. pneumoniae have been reported in several studies. In the original report on mcr-1, K. pneumoniae with mcr-1 was detected in three out of 420 clinical isolates (0.7%).16 In a multicenter study including 28 tertiary hospitals in China, only one isolate of K. pneumoniae with mcr-1 was detected among 571 K. pneumoniae isolates (0.2%) from bloodstream infections collected from 2013 to 2014.60 A similar prevalence rate was observed in another Chinese multicenter study in which 979 isolates of K. pneumoniae, collected between 2014 and 2016 from patients with bloodstream infections at 48 tertiary hospitals, were screened and only two isolates were found to carry mcr-1 (0.2%).61 A retrospective study conducted at two hospitals in Hangzhou and Guangzhou, China, reported a higher prevalence: 13 mcr-1-carrying isolates of K. pneumoniae were detected among 348 K. pneumoniae isolates in total (3.7%).62 Regardless of a fairly low prevalence rate reported in most studies, mcr-genes have been reported in clinical isolates of K. pneumoniae from countries worldwide including Brazil,63 France,64 Italy,65 India,66 Japan,67 South Africa,68 Thailand,69 Vietnam,70 and USA.71

Overall, the prevalence of mcr-1-carrying strains appears to be higher in animals than humans, which is likely a consequence of the high usage of colistin in animal food production, particularly among pigs and chicken which have been suggested to serve as reservoirs for the gene.14,16 As with clinical studies, E. coli has been more widely reported in the context, nevertheless, several studies report on K. pneumoniae carrying mcr-genes isolated from animals. Among 100 rectal swabs from pigs at two pig farms in Portugal, two isolates of K. pneumoniae with mcr-1 were found (2%).72 A Chinese study on broiler, swine and cattle farms from four provinces in China found two isolates carrying mcr-1 among 44 K. pneumoniae isolates from animal sources (4.5%).73 Another study from China reported mcr-carrying K. pneumoniae (mcr-1 and mcr-8) in isolates from six pigs and three chicken.56mcr-1-carrying K. pneumoniae have also been reported in pigs at Malaysian farms.74

K. pneumoniae carrying mcr-genes have also been isolated from environmental sources. One study investigating mcr-1-carrying bacteria on surfaces in the environment of public transportation in Guangzhou, China, found K. pneumoniae carrying mcr-1 on surfaces on an elevator handrail at the bus route and on a ticket machine and escalator handrail in the metro.75 Interestingly, K. pneumoniae carrying mcr-genes have also been detected in flies collected from the environment.57,76 One study isolated 17 K. pneumoniae with mcr-1 from flies collected from a rural area and suburbs of a city in Thailand.76 Interestingly, all isolates were ST43 and carried mcr-1 on an IncX4-plasmid. Another study, also conducted in Thailand, isolated 2 mcr-3-carrying K. pneumoniae from flies collected at pig farms.57 These results indicate that the environment may be an important route for transmission and dissemination of mcr-genes and K. pneumoniae.

The vast majority of reports on mcr-1 pertain to carriage in E. coli, and the published data indicate that the gene has disseminated to a diverse array of different strains among that species. In a meta-study compiling data from publications on mcr-1 in E. coli, it was shown that the gene had been reported in 112 unique multilocus sequence types (STs), although there was a predominance of reports among ST10 (12.8%), implying a dissemination driven by plasmid transfer rather than clonal expansion.77 Although the data on mcr-1 in K. pneumoniae is scarcer, studies reporting STs show a similar diversity as E. coli. Out of 35 studies reporting (or partially reporting) on STs among findings of mcr-1-carrying K. pneumoniae (Table 2), 34 different STs are reported, and only eight STs appear in more than one study: ST15 (n = 5), ST11 (n = 3), ST45 (n = 3), ST307 (n = 3), ST16 (n = 2), ST37 (n = 2), ST512 (n = 2), and ST526 (n = 2). Carriage in clinically prevalent strains such as ST11 and ST15 may; however, be overrepresented as these strains are much more common among clinical isolates. As with E. coli, mcr-1 has likely expanded through the K. pneumoniae population via highly transferable plasmids rather than relied on the expansion of single clones.

No single plasmid seems to be responsible for the worldwide dissemination of mcr-1, indeed the gene has thus far been observed to be carried on a wide array of different Inc-types of plasmids (>10).77,78 Overall, the gene seems to be most commonly carried on IncI2, IncX4, and IncHI2 plasmids, with geographical differences in prevalence.77 For K. pneumoniae specifically, 12 out of 19 studies reporting on Inc-type of the mcr-1-carrying plasmid found the gene to be carried on an IncX4 plasmid, making it the most common Inc-type reported in the species (Table 2). Other Inc-types are more sporadically reported and include carriage on IncI2,79,80 IncHI2,72,81 IncP,72,82 and IncFIIB.83 Notably, mcr-1 has also been found in K. pneumoniae to be carried on the chromosome66 and on a P7 phage-like plasmid.84 Acquisition of mcr-1-carrying plasmids has been shown to incur significant fitness costs to K. pneumoniae both in in vitro assays and in vivo animal models.85,86 Interestingly, acquisition of mcr-1-carrying plasmids in E. coli has been associated with lower fitness costs compared to K. pneumoniae,86 which may explain the higher prevalence of the gene among E. coli. These results also indicate that the dissemination of mcr-1 in K. pneumoniae is contingent on colistin selection pressures, and by extension, that by limiting colistin usage, further dissemination of the gene in K. pneumoniae could be stopped. On the other hand, the fitness cost conferred by mcr-1-carrying IncX4 plasmids has not been tested in K. pneumoniae, and as this is the most common type of plasmids carrying mcr-1 detected in the species, it is not inconceivable that these plasmids confer a significantly lower fitness cost.

Colistin is a last-resort antibiotic which can be used to treat infections caused by multidrug-resistant CRKP. The dissemination of plasmid-mediated colistin resistance determinants among K. pneumoniae threatens the utility of colistin as a last-resort antibiotic and the risk of emergence of colistin-resistant CRKP for which few therapeutic options remain is a public health concern. Unfortunately, several reports of clinical isolates of K. pneumoniae carrying both mcr-1 and carbapenem resistance genes have already been published and indicate an already worldwide presence of this type of strains. The reports are mainly from Southeast Asia and include isolates carrying KPC-, NDM-, and OXA-48 type carbapenemases,66,70,87–90 whereas mcr-1-producing K. pneumoniae carrying KPC type carbapenemases have also been reported from Europe, in Italy and Portugal,65,91 and from South America, in Brazil.63,92,93 Although most of the abovementioned studies report only the findings of a few isolates, one outbreak of KPC-3- and mcr-1-producing K. pneumoniae isolated from 16 patients at a Portuguese hospital has been reported,91 indicating the potential healthcare burden posed by these strains. Currently, outbreaks of CRKP carrying mcr-genes are not commonly reported; however, this situation may change if plasmid-mediated colistin resistance determinants continue to disseminate unabated.


The rapid dissemination of carbapenemases among multidrug-resistant K. pneumoniae worldwide has necessitated the use of colistin as a last-resort antibiotic. Colistin resistance emerges in K. pneumoniae most commonly via mutations or IS transpositions into mgrB, a negative regulator gene involved in regulation of lipid A modifications, but resistance can also emerge via single mutations in genes involved in the same regulatory network. A further complication to the situation is the recent emergence of plasmid-mediated colistin resistance via the mcr-genes, and mcr-1 in particular. The clinical impact of mcr-1 in K. pneumoniae has thus far been limited as the gene is much more commonly observed in E. coli. Nevertheless, plasmid-mediated resistance determinants have the propensity to spread rapidly and caution is warranted as is a continued screening for the gene, particularly among clinical isolates. The relative ease with which colistin resistance can emerge in K. pneumoniae via spontaneous genetic events in the chromosome, together with the low fitness cost associated, is worrying from a therapeutic perspective and induction of resistance in patients treated with colistin has been observed. Antibiotic stewardship and a prudent and restrained use of colistin are likely necessary to preserve the future usefulness of colistin as a last-resort antibiotic.


Thanks to Lennart E. Nilsson for critical evaluation of the manuscript.


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Klebsiella pneumoniae; colistin; mutation; antibiotic resistance; plasmid, mcr-1

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