Detection of Colistin-Resistant MCR-1-Positive Escherichia coli by Use of Assays Based on Inhibition by EDTA and Zeta Potential

A Review on Colistin Resistance: An Antibiotic of Last Resort

Antibiotic resistance has emerged as a significant global public health issue, driven by the rapid adaptation of microorganisms to commonly prescribed antibiotics. Colistin, previously regarded as a last-resort antibiotic for treating infections caused by Gram-negative bacteria, is increasingly becoming resistant due to chromosomal mutations and the acquisition of resistance genes carried by plasmids, particularly the mcr genes. The mobile colistin resistance gene (mcr-1) was first discovered in E. coli from China in 2016. Since that time, studies have reported different variants of mcr genes ranging from mcr-1 to mcr-10, mainly in Enterobacteriaceae from various parts of the world, which is a major concern for public health. The co-presence of colistin-resistant genes with other antibiotic resistance determinants further complicates treatment strategies and underscores the urgent need for enhanced surveillance and antimicrobial stewardship efforts. Therefore, understanding the mechanisms driving colistin resistance and monitoring its global prevalence are essential steps in addressing the growing threat of antimicrobial resistance and preserving the efficacy of existing antibiotics. This review underscores the critical role of colistin as a last-choice antibiotic, elucidates the mechanisms of colistin resistance and the dissemination of resistant genes, explores the global prevalence of mcr genes, and evaluates the current detection methods for colistin-resistant bacteria. The objective is to shed light on these key aspects with strategies for combating the growing threat of resistance to antibiotics.

Challenges in the Detection of Polymyxin Resistance: From Today to the Future

Antimicrobial resistance is known to be one of the greatest global threats to human health, and is one of the main causes of death worldwide. In this scenario, polymyxins are last-resort antibiotics to treat infections caused by multidrug-resistant bacteria. Currently, the reference test to evaluate the susceptibility of isolates to polymyxins is the broth microdilution method; however, this technique has numerous complications and challenges for use in laboratory routines. Several phenotypic methods have been reported as being promising for implementation in routine diagnostics, including the BMD commercial test, rapid polymyxin NP test, polymyxin elution test, culture medium with polymyxins, and the Polymyxin Drop Test, which require materials for use in routines and must be easy to perform. Furthermore, Sensititre®, molecular tests, MALDI-TOF MS, and Raman spectroscopy present reliable results, but the equipment is not found in most microbiology laboratories. In this context, this review discusses the main laboratory methodologies that allow the detection of resistance to polymyxins, elucidating the challenges and perspectives.

Genomic characterization of colistin-resistant Klebsiella pneumoniae isolated from intensive care unit patients in Egypt

BACKGROUND

Egypt has witnessed elevated incidence rates of multidrug-resistant Klebsiella pneumoniae infections in intensive care units (ICUs). The treatment of these infections is becoming more challenging whilst colistin-carbapenem-resistant K. pneumoniae is upsurging. Due to the insufficiently available data on the genomic features of colistin-resistant K. pneumoniae in Egypt, it was important to fill in the gap and explore the genomic characteristics, as well as the antimicrobial resistance, the virulence determinants, and the molecular mechanisms of colistin resistance in such a lethal pathogen.

METHODS

Seventeen colistin-resistant clinical K. pneumoniae isolates were collected from ICUs in Alexandria, Egypt in a 6-month period in 2020. Colistin resistance was phenotypically detected by modified rapid polymyxin Nordmann/Poirel and broth microdilution techniques. The isolates susceptibility to 20 antimicrobials was determined using Kirby-Bauer disk diffusion method. Whole genome sequencing and bioinformatic analysis were employed for exploring the virulome, resistome, and the genetic basis of colistin resistance mechanisms.

RESULTS

Out of the tested K. pneumoniae isolates, 82.35% were extensively drug-resistant and 17.65% were multidrug-resistant. Promising susceptibility levels towards tigecycline (88.24%) and doxycycline (52.94%) were detected. Population structure analysis revealed seven sequence types (ST) and K-types: ST383-K30, ST147-K64, ST17-K25, ST111-K63, ST11-K15, ST14-K2, and ST525-K45. Virulome analysis revealed yersiniabactin, aerobactin, and salmochelin siderophore systems in ˃ 50% of the population. Hypervirulence biomarkers, iucA (52.94%) and rmpA/A2 (5.88%) were detected. Extended-spectrum β-lactamase- and carbapenemase-producers accounted for 94.12% of the population, with blaCTX-M-15, blaNDM-5, and blaOXA-48 reaching 64.71%, 82.35%, and 82.35%, respectively. Chromosomal alterations in mgrB (82.35%) were the most prevailing colistin resistance-associated genetic change followed by deleterious mutations in ArnT (23.53%, L54H and G164S), PmrA (11.76%, G53V and D86E), PmrB (11.76%, T89P and T134P), PmrC (11.76%, S257L), PhoQ (5.88%, L322Q and Q435H), and ArnB (5.88%, G47D) along with the acquisition of mcr-1.1 by a single isolate of ST525.

CONCLUSIONS

In this study, we present the genotypic colistin resistance mechanisms in K. pneumoniae isolated in Egypt. More effective antibiotic stewardship protocols must be implemented by Egyptian health authorities to restrain this hazard and safeguard the future utility of colistin. This is the first characterization of a complete sequence of mcr-1.1-bearing IncHI2/IncHI2A plasmid recovered from K. pneumoniae clinical isolate belonging to the emerging high-risk clone ST525.

Mobile colistin resistance (mcr) genes and recent developments in colistin resistance detection

The peptide antibiotic colistin has been reserved as a last resort antibiotic treatment option for cases where other antibiotics including carbapenems have failed. Recent emergence of colistin resistance and discovery of mobile colistin resistance (mcr) genes, which encode the cell wall modifying phosphoethanolamine transferase enzyme, complicates the issue. The mcr genes have been associated with conjugative plasmids and can be horizontally transferred between different bacterial species. The global spread of mcr genes has been extensively documented and this warrants surveillance of the resistance genes in the community. However, susceptibility testing of colistin is fraught with practical challenges owing to the chemical nature of the drug and multiple mechanisms of resistance. Although broth microdilution is the current gold standard for colistin susceptibility testing, the method poses technical challenges. Hence, alternative detection methods for screening colistin resistance are the need of the hour. Several methods have been studied in the recent times to address this issue. In this review, we discuss some of the recent developments in the detection of colistin resistance.

Klebsiella pneumoniae co-harbouring bla NDM-1 , armA and mcr-10 isolated from blood samples in Myanmar

Background. The spread of Enterobacteriaceae coproducing carbapenemases, 16S rRNA methylase and mobile colistin resistance proteins (MCRs) has become a serious public health problem worldwide. This study describes two clinical isolates of Klebsiella pneumoniae coharbouring bla IMP-1, armA and mcr-10.Methods. Two clinical isolates of K. pneumoniae resistant to carbapenems and aminoglycosides were obtained from two patients at a hospital in Myanmar. Their minimum inhibitory concentrations (MICs) were determined by broth microdilution methods. The whole-genome sequences were determined by MiSeq and MinION methods. Drug-resistant factors and their genomic environments were determined.Results. The two K. pneumoniae isolates showed MICs of ≥4 and ≥1024 µg ml-1 for carbapenems and aminoglycosides, respectively. Two K. pneumonaie harbouring mcr-10 were susceptible to colistin, with MICs of ≤0.015 µg ml-1 using cation-adjusted Mueller-Hinton broth, but those for colistin were significantly higher (0.5 and 4 µg ml-1) using brain heart infusion medium. Whole-genome analysis revealed that these isolates coharboured bla NDM-1, armA and mcr-10. These two isolates showed low MICs of 0.25 µg ml-1 for colistin. Genome analysis revealed that both bla NDM-1 and armA were located on IncFIIs plasmids of similar size (81 kb). The mcr-10 was located on IncM2 plasmids of sizes 220 or 313 kb in each isolate. These two isolates did not possess a qseBC gene encoding a two-component system, which is thought to regulate the expression of mcr genes.Conclusion. This is the first report of isolates of K. pneumoniae coharbouring bla NDM-1, armA and mcr-10 obtained in Myanmar.

High mortality from carbapenem-resistant Klebsiella pneumoniae bloodstream infection

In this study, it was evaluated clinical data of 107 patients with bloodstream infection (BSI) by Klebsiella pneumoniae and performed phenotypic and molecular analyzes in 50.5% (54/107) of the samples, those that showed a resistance profile to carbapenemics. The bla_KPC gene was present in 90.4% (49/54) of the samples, bla_NDM gene in one sample and, in 7.4% (4/54) of the samples, no carbapenemase gene was found. In the similarity analysis, it was found 4 main clones and 11 samples were not genetically related. The median age of the patients was 58 (40-70) years old and 60.7% (65/107) were male. When comparing two groups of patients with BSI due to K. pneumoniae with and without resistance to carbapenems, the variables ICU permanence, renal failure (IR), previous use of antimicrobials, Charlson's comorbidity index (ICCi), some invasive procedures and death showed a statistically significant difference (p < 0.05). And when relating death as a dependent variable, IR, liver failure and patients with BSI XDR or PDR, were predictors of increased mortality. Our study showed a higher mortality rate in patients with BSI due to carbapenem-resistant pneumonia with additional resistance or not to polymyxins.

Re-sensitization of mcr carrying multidrug resistant bacteria to colistin by silver

Superbugs carrying a mobile colistin resistance gene (mcr) are jeopardizing the clinical efficacy of the last-line antibiotic colistin. The development of MCR inhibitors is urgently required to cope with antibiotic-resistance emergencies. Here, we show that silver (Ag⁺) fully restores the susceptibility of mcr-1–carrying superbugs against colistin both in vitro and in vivo. We found an unprecedented tetra-silver center in the active-site pocket of MCR-1 through the substitution of the essential Zn²⁺ ions in the intact enzyme, leading to the prevention of substrate binding (i.e. the dysfunction of MCR-1 in transferring phosphorylethanolamine to lipid A). Importantly, the ability of Ag⁺ to suppress resistance evolution extends the lifespan of currently used antibiotics, providing a strategy to treat infections by mcr-positive bacteria.

Colistin is considered the last-line antimicrobial for the treatment of multidrug-resistant gram-negative bacterial infections. The emergence and spread of superbugs carrying the mobile colistin resistance gene (mcr) have become the most serious and urgent threat to healthcare. Here, we discover that silver (Ag⁺), including silver nanoparticles, could restore colistin efficacy against mcr-positive bacteria. We show that Ag⁺ inhibits the activity of the MCR-1 enzyme via substitution of Zn²⁺ in the active site. Unexpectedly, a tetra-silver center was found in the active-site pocket of MCR-1 as revealed by the X-ray structure of the Ag-bound MCR-1, resulting in the prevention of substrate binding. Moreover, Ag⁺ effectively slows down the development of higher-level resistance and reduces mutation frequency. Importantly, the combined use of Ag⁺ at a low concentration with colistin could relieve dermonecrotic lesions and reduce the bacterial load of mice infected with mcr-1–carrying pathogens. This study depicts a mechanism of Ag⁺ inhibition of MCR enzymes and demonstrates the potentials of Ag⁺ as broad-spectrum inhibitors for the treatment of mcr-positive bacterial infection in combination with colistin.

Polyclonal emergence of MDR Enterobacter cloacae complex isolates producing multiple extended spectrum beta-lactamases at Maputo Central Hospital, Mozambique

Enterobacter spp. are important nosocomial pathogens responsible of a wide variety of infections, mainly due to Extended Spectrum β-Lactamase (ESBL) producing isolates, constituting a global public health issue in terms of clinical treatment and infection control, especially in low-income countries, where last-line treatment is often unavailable and there is weak nosocomial surveillance. In this study, we conducted a phenotypic and molecular characterization of 8 clinical Enterobacter spp. strains, isolated from patient’s blood in three hospitals in Mozambique. Isolates were identified by MALDI-TOF and antimicrobial Susceptibility Testing was performed by VITEK 2 system. Half of isolates were analyzed by PCR for β-lactamases genes, other isolates by Whole Genome Sequencing. We identified all isolates as Enterobacter cloacae complex (ECC), those from Maputo Central Hospital were polyclonal, multidrug resistant (5/8), and ESBL producers (50%), carrying blaCTX-M-15 and different assortment of blaSHV-12, blaTEM-1B and blaOXA-1, and AmpCs blaCMH-3, blaACT-7 and blaACT-9 genes. Resistance determinants linked to fluoroquinolone (aac(6')Ib-cr and qnrB1) and others antimicrobials were also found. Notably, one isolate showed phenotypically resistance to colistin, while another colistin susceptible isolate carried a silent mcr-9 gene. ECC nosocomial surveillance is urgently needed to contain and prevent the dissemination of ESBLs producing clones, and mcr-9 spread to other Enterobacteriaceae.

Analysis of colistin resistance in carbapenem-resistant Enterobacterales and XDR Klebsiella pneumoniae

Introduction:

Increasing occurrence of infections caused by multidrug-resistant Gram-negative bacteria resulted in colistin being the last agent for treatment. Apart from plasmid-mediated mcr genes, mutations involving several genes like mgrB, phoP/phoQ, pmrA, pmrB, pmrC, and crrABC genes, are leading causes of colistin resistance. Four colistin susceptibility testing methods were compared against broth microdilution (BMD) and determined the presence of the mcr1-5 gene.

Methodology:

A total of 100 carbapenem-resistant Enterobacterales isolates were tested for colistin susceptibility by commercial broth microdilution (cBMD), E-test, VITEK-2, and rapid polymyxin NP assay (RPNP) and compared with BMD. The presence of the mcr1-5 gene was determined by modified RPNP and PCR. Two non-mcr colistin-resistant XDR isolates were subjected to whole-genome sequencing using Illumina MiSeq sequencing platform.

Results:

Among 100 carbapenem-resistant Enterobacterales isolates, 15% were resistant to colistin. Essential agreement, categorical agreement, major error, and very major error for cBMD/E-test/VITEK-2/RPNP were 96%/73%/82%/NA; 99%/86%/88%/91%, 1.2%/9.4%/11.8%/8.2% and 0%/40%/13.3%/13.3%, respectively. Only one Klebsiella pneumoniae isolate harbored the mcr-1 gene, observed by both methods. Whole-genome sequencing of two non-mcr XDR Klebsiella pneumoniae showed multiple mutations in 10 genes responsible for lipopolysaccharide biosynthesis.

Conclusions:

The performance of cBMD was excellent, whereas the E-test was unacceptable. VITEK-2 and RPNP performed better but remained unreliable due to high error rates. Multiple mutations in the target proteins involving lipopolysaccharide formation, modification, and regulation were seen, resulting in colistin resistance.

Current and emerging polymyxin resistance diagnostics: A systematic review of established and novel detection methods

The emergence of polymyxin resistance, due to transferable mcr genes, threatens public and animal health as there are limited therapeutic options. As polymyxin is one of the last-line antibiotics, there is a need to contain the spread of its resistance to conserve its efficacy. Herein, we describe current and emerging polymyxin resistance diagnostics to inform faster clinical diagnostic choices. A literature search in diverse databases for studies published between 2016 and 2020 was performed. English articles evaluating colistin resistance methods/diagnostics were included. Screening resulted in the inclusion of 93 journal articles. Current colistin resistance diagnostics are either phenotypic or molecular. Broth microdilution is currently the only gold standard for determining colistin MICs (minimum inhibitory concentration). Phenotypic methods comprise of agar-based methods such as CHROMagar™ Col-APSE, SuperPolymyxin, ChromID^® Colistin R, LBJMR and LB medium; manual MIC-determiners viz., UMIC, MICRONAUT MIC-Strip and ComASP Colistin; automated antimicrobial susceptibility testing systems such as BD Phoenix, MICRONAUT-S, MicroScan, Sensititre and Vitek 2; MCR-detectors such as lateral flow immunoassay (LFI) and chelator-based assays including EDTA- and DPA-based tests, that is, combined disk test, modified colistin broth-disk elution (CBDE), Colispot, and Colistin MAC test as well as biochemical colorimetric tests, that is, Rapid Polymyxin NP test and Rapid ResaPolymyxin NP test. Molecular methods only characterize mobile colistin resistance; they include PCR, LAMP and whole-genome sequencing. Due to the faster turnaround time (≤3 h), improved sensitivity (84%-100%) and specificity (93.3%-100%) of the Rapid ResaPolymyxin NP test and Fastinov^® , we recommend this test for initial screening of colistin-resistant isolates. This can be followed by CBDE with EDTA or the LFI as they both have 100% sensitivity and a specificity of ≥94.3% for the rapid screening of mcr genes. However, molecular assays such as LAMP and PCR may be considered in well-equipped clinical laboratories.

Zeta potential beyond materials science: Applications to bacterial systems and to the development of novel antimicrobials

This review summarizes the theory of zeta potential (ZP) and the most relevant data about how it has been used for studying bacteria. We have especially focused on the discovery and characterization of novel antimicrobial compounds. The ZP technique may be considered an indirect tool to estimate the surface potential of bacteria, a physical characteristic that is key to maintaining optimal cell function. For this reason, targeting the bacterial surface is of paramount interest in the development of new antimicrobials. Surface-acting agents have been found to display a remarkable bactericidal effect and have simultaneously revealed a low tendency to trigger resistance. Changes in the bacterial surface as a result of various processes can also be followed by ZP measurements. However, due to the complexity of the bacterial surface, some considerations regarding the assessment of ZP must first be taken into account. Evidence on the application of ZP measurements to the characterization of bacteria and biofilm formation is presented next. We finally discuss the feasibility of using the ZP technique to assess antimicrobial-induced changes in the bacterial surface. Among these changes are those related to the interaction of the agent with different components of the cell envelope, membrane permeabilization, and loss of viability.

Resensitizing carbapenem- and colistin-resistant bacteria to antibiotics using auranofin

Global emergence of Gram-negative bacteria carrying the plasmid-borne resistance genes, bla_MBL and mcr, raises a significant challenge to the treatment of life-threatening infections by the antibiotics, carbapenem and colistin (COL). Here, we identify an antirheumatic drug, auranofin (AUR) as a dual inhibitor of metallo-β-lactamases (MBLs) and mobilized colistin resistance (MCRs), two resistance enzymes that have distinct structures and substrates. We demonstrate that AUR irreversibly abrogates both enzyme activity via the displacement of Zn(II) cofactors from their active sites. We further show that AUR synergizes with antibiotics on killing a broad spectrum of carbapenem and/or COL resistant bacterial strains, and slows down the development of β-lactam and COL resistance. Combination of AUR and COL rescues all mice infected by Escherichia coli co-expressing MCR-1 and New Delhi metallo-β-lactamase 5 (NDM-5). Our findings provide potential therapeutic strategy to combine AUR with antibiotics for combating superbugs co-producing MBLs and MCRs.

Multi-drug resistant pathogens remain a serious public health threat. Here, Sun and colleagues identify a role for auranofin, which is normally used as a drug for rheumatoid arthritis, for reversing antibiotic resistance to carbapenem and colistin.

Rapid Detection and Antibiotic Susceptibility of Uropathogenic Escherichia coli by Flow Cytometry

Background: Early preliminary data on antibiotic resistance patterns available before starting the empiric therapy of urinary tract infections (UTIs) in patients with risk factors for acquiring antibiotic resistance could improve both clinical and epidemiological outcomes. The aim of the present study was two-fold: (i) to assess the antibiotic susceptibility of uropathogenic Escherichia coli isolates, exhibiting different antibiotic resistance phenotypes, directly in artificially contaminated urine samples using a flow cytometry (FC) based protocol; (ii) to optimize the protocol on urine samples deliberately contaminated with bacterial suspensions prepared from uropathogenic E. coli strains. Results: The results of the FC based antimicrobial susceptibility testing (AST) protocol were compared with the reference AST methods results (disk diffusion and broth microdilution) for establishing the sensitivity and specificity. The proposed FC protocol allowed the detection and quantification of uropathogenic E. coli strains susceptibility to nitrofurantoin, trimethoprim–sulfamethoxazole, ciprofloxacin, and ceftriaxone within 4 h after the inoculation of urine specimens. The early availability of preliminary antibiotic susceptibility results provided by direct analysis of clinical specimens could essentially contribute to a more targeted emergency therapy of UTIs in the anticipation of AST results obtained by reference methodology. Conclusions: This method will increase the therapeutic success rate and help to prevent the emergence and dissemination of drug resistant pathogens.

New insights into novel Escherichia coli colistin-resistant strains isolated from Argentina

Colistin is a polymyxin antibiotic (polymyxin E) that has in recent years re-emerged as an option for treatment of multidrug-resistant bacteria. Recently, the re-introduction of colistin resulted in the appearance of colistin-resistant bacteria, which is usually caused by LPS modifications. The fact that this modification is mediated by a plasmid carrying the mcr-1 gene, implies a horizontal transfer of colistin resistance. In Argentina, the National Reference Laboratory in Antimicrobial Resistance (NRLAR), has recently screened several bacteria for the MCR-1 plasmid, detecting nine Escherichia coli isolates carrying the plasmid with the mcr-1 gene, among others. In this context, we proposed to assess the effect of surface charge modifications induced by the plasmid MCR-1 and its impact on the resulting colistin resistance in two clinical isolates of colistin-resistant E. coli. Using zeta potential assays, we confirmed the reduction of negative charge exposure on clinical isolates compared to the reference strain of E. coli. In addition, through permeabilization assays, we were able to correlate this reduction in charge exposure with the extent of damage to the bacterial membrane. The fact that this surface charge modification through substitution of lipid A is plasmid encoded, represents an important concern for future antimicrobial peptide drug development.

Emergence of carbapenem-resistant and colistin-susceptible Enterobacter cloacae complex co-harboring blaIMP-1 and mcr-9 in Japan

Background

The spread of Enterobacteriaceae producing both carbapenemases and Mcr, encoded by plasmid-mediated colistin resistance genes, has become a serious public health problem worldwide. This study describes three clinical isolates of Enterobacter cloacae complex co-harboring bla_IMP-1 and mcr-9 that were resistant to carbapenem but susceptible to colistin.

Methods

Thirty-two clinical isolates of E. cloacae complex non-susceptible to carbapenems were obtained from patients at 14 hospitals in Japan. Their minimum inhibitory concentrations (MICs) were determined by broth microdilution methods and E-tests. Their entire genomes were sequenced by MiSeq and MinION methods. Multilocus sequence types were determined and a phylogenetic tree constructed by single nucleotide polymorphism (SNP) alignment of whole genome sequencing data.

Results

All 32 isolates showed MICs of ≥2 μg/ml for imipenem and/or meropenem. Whole-genome analysis revealed that all these isolates harbored bla_IMP-1, with three also harboring mcr-9. These three isolates showed low MICs of 0.125 μg/ml for colistin. In two of these isolates, bla_IMP-1 and mcr-9 were present on two separate plasmids, of sizes 62 kb and 280/290 kb, respectively. These two isolates did not possess a qseBC gene encoding a two-component system, which is thought to regulate the expression of mcr-9. In the third isolate, however, both bla_IMP-1 and mcr-9 were present on the chromosome.

Conclusion

The mcr-9 is silently distributed among carbapenem-resistant E. cloacae complex isolates, of which are emerging in hospitals in Japan. To our knowledge, this is the first report of isolates of E. cloacae complex harboring both bla_IMP-1 and mcr-9 in Japan.

Evaluation of the NG-Test MCR-1 Lateral Flow Assay and EDTA-Colistin Broth Disk Elution Methods To Detect Plasmid-Mediated Colistin Resistance among Gram-Negative Bacterial Isolates

Plasmid-mediated colistin resistance (PMCR) is a global public health concern, given its ease of transmissibility. The purpose of this study was to evaluate two methods for the detection of PMCR from bacterial colonies: (i) the NG-Test MCR-1 lateral flow immunoassay (LFA; NG Biotech, Guipry, France) and (ii) the EDTA-colistin broth disk elution (EDTA-CBDE) screening test method. These methods were evaluated using a cohort of contemporary, clinical Gram-negative bacillus isolates from 3 U.S. academic medical centers (126 isolates of the Enterobacterales, 50 Pseudomonas aeruginosa isolates, and 50 Acinetobacter species isolates; 1 isolate was mcr positive) and 12 mcr-positive CDC-FDA Antibiotic Resistance (AR) Isolate Bank isolates for which reference broth microdilution colistin susceptibility results were available. Eleven (4.6%) isolates were strongly positive by the MCR-1 LFA, with an additional 8 (3.4%) isolates yielding faintly positive results. The positive percent agreement (PPA) and negative percent agreement (NPA) for MCR-1 detection were 100% and 96.1%, respectively. Upon repeat testing, only a single false-positive MCR-2 producer remained, as the isolates with initially faintly positive results were negative. The EDTA-CBDE screening method had an overall PPA and NPA of 100% and 94.3%, respectively. The NPA for the EDTA-CBDE method was slightly lower at 94.2% with Enterobacterales, whereas it was 96.0% with P. aeruginosa The MCR-1 LFA and EDTA-CBDE methods are both accurate and user-friendly methods for the detection of PMCR. Despite the rarity of PMCR among clinical isolates in the United States, these methods are valuable tools that may be implemented in public health and clinical microbiology laboratories to further discern the mechanism of resistance among colistin-resistant Gram-negative isolates and to detect PMCR for infection prevention and control purposes.

Phenotypic Detection of Plasmid-Mediated Colistin Resistance in Enterobacteriaceae

The aim of this work was to evaluate an easy-to-perform assay based upon inhibition of mobile colistin resistance (MCR) activity by EDTA. We included 92 nonrelated isolates of Enterobacteriaceae (74 Escherichia coli, 17 Klebsiella pneumoniae, and 1 Serratia marcescens). Our proposed method is based on a modification of the colistin agar-spot screening test (CAST), a plate containing 3 μg/ml colistin, by adding an extra plate of colistin agar-spot supplemented with EDTA (eCAST). Bacterial growth was evaluated after 24 h of incubation at 35°C. All the colistin-resistant isolates showed development on the CAST plates. Colistin-resistant K. pneumoniae without mcr-1 and S. marcescens also grew on the eCAST plates. In contrast, colistin-resistant MCR-producing E. coli was not able to grow in eCAST plates. The combined CAST/eCAST test could provide a simple and easy-to-perform method to differentiate MCR-producing Enterobacteriaceae from those in which colistin resistance is mediated by chromosomal mechanisms.

Prevalence and Some Possible Mechanisms of Colistin Resistance Among Multidrug-Resistant and Extensively Drug-Resistant Pseudomonas aeruginosa

Background and Aim

The emergence of colistin-resistant strains is considered a great threat for patients with severe infections. Here, we investigate the prevalence and some possible mechanisms of colistin resistance among multidrug-resistant (MDR) and extensively drug-resistant (XDR) Pseudomonas aeruginosa (P. aeruginosa).

Methods

Antimicrobial susceptibility was performed using disc diffusion methods while colistin resistance was detected by agar dilution method. Possible mechanisms for colistin resistance were studied by detection of mcr-1 and mcr-2 genes by conventional PCR, detection of efflux mechanisms using Carbonyl Cyanide 3-Chlorophenylhydrazone (CCCP), studying outer membrane protein profile and Lipopolysaccharide (LPS) profile of resistant isolates.

Results

It was found that MDR and XDR represented 96% and 87% of the isolated P. aeruginosa, respectively, and colistin resistance represented 21.3%. No isolates were positive for mcr-2 gene while 50% of colistin-resistant isolates were positive for mcr-1. Efflux mechanisms were detected in 3 isolates. Protein profile showed the presence of a band of 21.4 KDa in the resistant strains which may represent OprH while LPS profile showed differences among colistin-resistant mcr-1 negative strains, colistin-resistant mcr-1 positive strains and susceptible strains.

Conclusion

The current study reports a high prevalence of colistin resistance and mcr-1 gene in P. aeruginosa strains isolated from Egypt that may result in untreatable infections. Our finding makes it urgent to avoid unnecessary clinical use of colistin.

Evaluation of EDTA and Dipicolinic Acid in Broth Microdilution with Polymyxin B as a Phenotypic Test to Detect the mcr-1 Gene

Polymyxins (colistin and polymyxin B) have recently regained significant importance as last-line drugs to treat infectious diseases due to multidrug-resistant gram-negative bacteria. However, resistance to polymyxins has increased, and the recognition of plasmid-mediated resistance (by the mcr gene) has led to an epidemiological concern. We aimed to evaluate the reduction of the polymyxin B minimum inhibitory concentration (MIC) in the presence of EDTA or dipicolinic acid (DPA) by using the broth microdilution (BMD) method for phenotypic screening of acquired polymyxin resistance mediated by the mcr-1 gene. Overall, 94 Enterobacterales (48 polymyxin-resistant and 46 polymyxin-susceptible) were evaluated: 47 mcr-1 positive (36 Escherichia coli, 2 Klebsiella pneumoniae, and 9 Salmonella spp.) and 47 mcr-1 negative (3 E. coli and 44 K. pneumoniae-27 isolates with MIC from ≤0.125 to 8 μg/mL and 20 isolates with MIC from 16 to 64 μg/mL). Results were categorized as positive when the chelator decreased the original BMD MIC by ≥2 logs. The majority (95.7%) of mcr-1 positive isolates displayed at least a 3 log dilution decrease in the MIC of polymyxin B with EDTA or DPA. The EDTA-based BMD assay detected 45 mcr-1-positive isolates, with only one false-positive among the mcr-1-negative isolates (sensitivity [SN], 95.7%; specificity [SP], 97.9%), whereas the DPA-based BMD assay detected 44 mcr-1-positive isolates (SN, 93.6%; SP, 95.7%), with two false-positive results. The accuracy of EDTA- and DPA-based BMD assays were 97% and 95%, respectively. The EDTA- and DPA-based assays were demonstrated to be reliable methods to detect mcr-1 positive isolates with excellent accuracy.

Colistin-resistance-mediated bacterial surface modification sensitizes phage infection

Colistin is a drug of last resort for the treatment of many multidrug resistant Gram-negative bacteria, including Klebsiella pneumoniae However, bacteria readily acquire resistance to this antibiotic via lipopolysaccharide modifications caused by spontaneous mutations or from enzymes acquired by lateral gene transfer. The fitness cost associated with these modifications remains poorly understood. In this study, we show that colistin-resistant K. pneumoniae are more susceptible to killing by a newly isolated lytic phage than the colistin sensitive parent strain. We observe this behavior for colistin-resistance conferred by a horizontally transferred mcr-1 containing plasmid and also from the inactivation of the chromosomal gene mgrB By measuring zeta potentials, we found that the phage particles were negatively charged at neutral pH and that colistin-resistant bacteria had less negative zeta potentials than did wildtype. These results suggest that the decreased negative surface charge of colistin-resistant cells lowers the electrostatic repulsion between the phage and bacteria, thereby promoting phage adherence and subsequent infection. To further explore this, we tested the effect of phage treatment on K. pneumoniae growing in several different environments. We found that colistin-resistant cells were more susceptible to phage than were the wildtype cells when growing in biofilms or infected moth larvae and when colonizing the mammalian gut. A better understanding of these fitness costs may lead to new treatment approaches that minimize the emergence and spread of colistin-resistant pathogens in human and environmental reservoirs.

Emergent Polymyxin Resistance: End of an Era?

Until recently, the polymyxin antibiotics were used sparingly due to dose limiting toxicities. However, the lack of therapeutic alternatives for infections caused by highly resistant Gram-negative bacteria has led to the increased use of the polymyxins. Unfortunately, the world has witnessed increased rates of polymyxin resistance in the last decade, which is likely in part due to its irrational use in human and veterinary medicine. The spread of polymyxin resistance has been aided by the dissemination of the transferable polymyxin-resistance gene, mcr, in humans and the environment. The mortality of colistin-resistant bacteria (CoRB) infections varies in different reports. However, poor clinical outcome was associated with prior colistin treatment, illness severity, complications, and multidrug resistance. Detection of polymyxin resistance in the clinic is possible through multiple robust and practical tests, including broth microdilution susceptibility testing, chromogenic agar testing, and molecular biology assays. There are multiple risk factors that increase a person’s risk for infection with a polymyxin-resistant bacteria, including age, prior colistin treatment, hospitalization, and ventilator support. For patients that are determined to be infected by polymyxin-resistant bacteria, various antibiotic treatment options currently exist. The rising trend of polymyxin resistance threatens patient care and warrants effective control.

A Novel Phenotypic Method To Screen for Plasmid-Mediated Colistin Resistance among Enterobacteriales

Plasmid-mediated colistin resistance (PMCR), a consequence of the mcr genes, is a significant public health concern given its potential to easily spread among clinical pathogens. Recently, it was discovered that MCR enzymes require zinc for activity. Thus, we modified the colistin broth-disk elution (CBDE) test to screen for plasmid-mediated colistin resistance (PMCR) genes based on any reduction of colistin MIC in the presence of EDTA. Eighty-five isolates of the order Enterobacteriales (12 mcr positive) were tested by CBDE ± EDTA. The sensitivity and specificity of the EDTA-CBDE method to detect PMCR compared to the molecular genotype results were 100% and 95.8%, respectively. Isolates positive by the EDTA-CBDE test should be further evaluated to confirm the presence of mcr genes.

Discovery of a potential MCR-1 inhibitor that reverses polymyxin activity against clinical mcr-1-positive Enterobacteriaceae

The recent emergence of the plasmid-mediated colistin resistance gene mcr-1 poses a substantial clinical threat to the severe infections caused by CRE (Carbapenem Resistant Enterobacteriaceae), as the treatment failure of the mcr-1-positive CRE "Superbug" most likely occurs by using the combination of carbapenem and polymixins. Therefore, our study aims to seek a potent MCR-1 inhibitor to fight this infection. A checkerboard MIC (Minimum Inhibitory Concentration) assay, time-killing assay, MPNP (Modified rapid polymyxin Nordmann/Poirel) test, combined disk test and molecular modelling analysis were performed on different mcr-1-positive strains to confirm the synergistic effects of the combination of colistin and osthole (OST). And a thigh mouse infection model was also used to evaluate such synergies. We identified that OST regained the bactericidal activity of polymyxins (FIC (Fractional Inhibitory Concentration) index = 0.11±0.04 - 0.29±0.10) against mcr-1-positive Enterobacteriaceae including Escherichia coli and Klebsiella pneumoniae. The in-vitro time-killing assays showed that either OST or polymyxins failed to eradicate mcr-1-positive Enterobacteriaceae, but the combination eliminated mcr-1-positive Enterobacteriaceae by 3-7-h post-inoculation. The mouse infection model demonstrated that the combination therapy significantly reduced the bacterial load in the thighs following subcutaneous administration. Our results established that OST is a promising natural compound that could be used to extend the life of polymyxins and to tackle the inevitability of serious infections caused by polymyxin-resistant bacteria.

Rapid detection of colistin resistance protein MCR-1 by LC-MS/MS

Background

Colistin (polymyxin E) and polymixin B are important bactericidal antibiotics used in the treatment of serious infections caused by multi-drug resistant Gram-negative organisms. Transferrable plasmid-mediated colistin resistance, conferred by the product of the mcr-1 gene, has emerged as a global healthcare threat. Consequently, the rapid detection of the MCR-1 protein in clinical bacterial isolates has become increasingly important. We used a genoproteomic approach to identify unique peptides of the MCR-1 protein that could be detected rapidly by liquid chromatography tandem mass spectrometry (LC–MS/MS).

Methods

MCR-1 tryptic peptides that were efficiently ionized and readily detectable were characterized in a set of mcr-1-containing isolates with triple quadrupole LC–MS. Three optimal peptides were selected for the development of a rapid multiple reaction monitoring LC–MS/MS assay for the MCR-1 protein. To investigate the feasibility of rapid detection of the MCR-1 protein in bacterial isolates using this assay, a blinded 99-sample test set was built that included three additional mcr-1-containing clinical isolates tested in triplicate (9 samples) and 90 negative control isolates.

Results

All of the mcr-1-containing isolates in the test set were accurately identified with no false positive detections by three independent, blinded operators, yielding an overall performance of 100% sensitivity and specificity for multiple operators. Among the three peptides tested in this study, the best performing was DTFPQLAK. The isolate-to-result time for the assay as implemented is less than 90 min.

Conclusions

This work demonstrates the feasibility of rapid detection of the MCR-1 protein in bacterial isolates by LC–MS/MS.

Electronic supplementary material

The online version of this article (10.1186/s12014-019-9228-2) contains supplementary material, which is available to authorized users.

Development of New Tools to Detect Colistin-Resistance among Enterobacteriaceae Strains

The recent discovery of the plasmid-mediated mcr-1 gene conferring resistance to colistin is of clinical concern. The worldwide screening of this resistance mechanism among samples of different origins has highlighted the urgent need to improve the detection of colistin-resistant isolates in clinical microbiology laboratories. Currently, phenotypic methods used to detect colistin resistance are not necessarily suitable as the main characteristic of the mcr genes is the low level of resistance that they confer, close to the clinical breakpoint recommended jointly by the CLSI and EUCAST expert systems (S ≤ 2 mg/L and R > 2 mg/L). In this context, susceptibility testing recommendations for polymyxins have evolved and are becoming difficult to implement in routine laboratory work. The large number of mechanisms and genes involved in colistin resistance limits the access to rapid detection by molecular biology. It is therefore necessary to implement well-defined protocols using specific tools to detect all colistin-resistant bacteria. This review aims to summarize the current clinical microbiology diagnosis techniques and their ability to detect all colistin resistance mechanisms and describe new tools specifically developed to assess plasmid-mediated colistin resistance. Phenotyping, susceptibility testing, and genotyping methods are presented, including an update on recent studies related to the development of specific techniques.

Evaluation of EDTA- and DPA-Based Microdilution Phenotypic Tests for the Detection of MCR-Mediated Colistin Resistance in Enterobacteriaceae

The emergence of the colistin-resistant (COL-R) Enterobacteriaceae represents a worrying health issue. However, only a portion of these strains may carry the plasmid-mediated mcr colistin resistance genes. We evaluated the ability of both ethylenediaminetetraacetic acid (EDTA)-based and dipicolinic acid (DPA)-based broth microdilution (BMD) tests to detect mcr-1 to mcr-5 producers. Of 92 Enterobacteriaceae (85 COL-R), 44 mcr-positive strains (39 Escherichia coli, 3 Klebsiella pneumoniae, and 2 Salmonella spp.) were tested. EDTA (100 μg/mL) was tested in Mueller-Hinton broth (MHB), whereas the DPA (900 μg/mL) was used in cation-adjusted MHB. Results were categorized as positive if in presence of chelator strains exhibited ≥3 two fold MIC decrease compared to the COL MIC alone. The EDTA-based BMD assay detected 41 mcr-positive strains, but 22 false-positive strains (including 12 E. coli and 4 K. pneumoniae) were recorded (sensitivity [SN], 93.2%; specificity [SP], 54.2%). The DPA-based BMD assay detected 37 mcr-positive strains, with 7 false-negative (2 E. coli, 3 K. pneumoniae, 2 Salmonella spp.) strains (SN, 84.1%; SP, 100%). Overall, the EDTA-based BMD assay is not accurate to detect mcr producers, whereas the DPA-based BMD test ("colistin-MAC test") demonstrated good accuracy, but only when implemented for E. coli strains (SN, 94.9%; SP, 100%). With the aim to prevent the dissemination of mcr-possessing E. coli strains, the COL-MAC test could be implemented by clinical laboratories that are unable to perform molecular tests. Moreover, this assay could be applied to screen large collections of isolates to reveal the expression of new mcr-like genes not yet targeted by the current molecular assays.

The EDTA-based disk-combination tests are unreliable for the detection of MCR-mediated colistin-resistance in Enterobacteriaceae

We evaluated several EDTA-based combined-disk tests to detect 25 mcr producers among 48 Enterobacteriaceae. Colistin disks plus EDTA (292/584 μg) on MH and CAMH agar were used. Results were positive if with chelator there was an inhibition zone increase ≥3 mm compared to colistin alone. All tests resulted unreliable (sensitivity ≤68%).

In Vitro/Vivo Activity of Potential MCR-1 Inhibitor in Combination With Colistin Againsts mcr-1-Positive Klebsiella pneumonia

Carbapenem resistance among strains of the nosocomial pathogen Klebsiella pneumoniae is increasing worldwide, causing serious clinical infections and higher mortality rates. Polymyxins are some of the few “last resort” options for treatment of carbapenem-resistant Enterobacteriaceae, including K. pneumoniae, however, the emergence of plasmid-mediated colistin resistance gene mcr-1 has largely rendered polymyxin-class antibiotics ineffective in a clinical setting. We previously identified a natural compound, pterostilbene, which has a synergistic effect in combination with polymyxins. Here, we aimed to determine whether pterostilbene application can restore the bactericidal activity of polymyxins against mcr-1-positive K. pneumoniae. Checkerboard MIC studies confirmed that pterostilbene reduces the MIC of colistin against mcr-1-positive clinical K. pneumoniae isolates, with the bacteria going from resistant to sensitive, and also demonstrated a synergistic effect with colistin (FIC index = 0.11 ± 0.04 or 0.28 ± 0.00). Time-killing assays showed that individually, both pterostilbene and colistin failed to eradicate K. pneumoniae strains, while in combination, the two drugs effectively eliminated K. pneumoniae ZJ02 and K. pneumoniae ZJ05 by 1–3 h post-inoculation. The combined disk test also showed increases in the zones of inhibition only for mcr-1-positive Escherichia coli and K. pneumoniae isolates. A mouse infection model demonstrated that the survival rate of mice at 7 days post-intraperitoneal injection with a lethal dose of K. pneumoniae ZJ05 was significantly promoted from 0 to 67% following combination therapy. This is the first time a MCR-1 inhibitor has successfully been used in combination with colistin against human clinical MCR-1 producing K. pneumoniae ZJ05 isolate.

Mcr colistin resistance gene: a systematic review of current diagnostics and detection methods

Resistance to colistin, mediated by chromosomal mutations and more recently, by plasmid‐borne mcr genes, is increasingly being reported in bacterial isolates taken from humans, animals, farms, foods, and the environment. To easily identify and contain this quickly spreading menace, efficient diagnostics that are cheaper, faster, simpler, sensitive, and specific have become indispensable and urgently necessary. A thorough and systematic review of the literature available at Pubmed, ScienceDirect and Web of Science was thus undertaken to identify articles describing novel and efficient colistin resistance‐ and mcr gene‐detecting methods. From the final 23 studies included in this review, both phenotypic and molecular tests were found. The phenotypic tests consisted of novel culture media viz., SuperPolymyxin™, CHROMagar COL‐APSE and LBJMR media, commercial automated MIC‐determining instruments such as MICRONAUT‐S, Vitek 2, BD Phoenix, Sensititre and MicroScan, and novel assays such as Colistin MAC test, Colispot, rapid polymxin NP test (RPNP), alteration of Zeta potential, modified RPNP test, MICRONAUT‐MIC Strip, MIC Test Strip, UMIC System, and Sensitest™ Colistin. Molecular diagnostics consisted of the CT103XL microarray, eazyplex^® SuperBug kit, and Taqman^®/SYBR Green^® real‐time PCR assays, with 100% sensitivity and specificity plus a shorter turnaround time (<3 hr). Based on the sensitivity, specificity, cost, required skill and turnaround time, the RPNP test and/or novel culture media is recommended for under‐resourced laboratories while the Multiplex PCR or Taqman^®/SYBR Green^® real‐time PCR assay alongside the RPNP or novel culture media is suggested for well‐resourced ones.

Genetic and Functional Characterization of an MCR-3-Like Enzyme-Producing Escherichia coli Isolate Recovered from Swine in Brazil

A collection of 126 pigs was screened for carriage of colistin-resistant Enterobacteriaceae in a farm in Minas Gerais, Brazil. Out of this collection, eight colistin-resistant Escherichia coli isolates were recovered, including one from Minas Gerais State producing a new MCR-3 variant (MCR-3.12). Analysis of the lipopolysaccharide revealed that MCR-3.12 had a function similar to that of MCR-1 and MCR-2 as a result of the addition of a phosphoethanolamine group to the lipid A moiety. Genetic analysis showed that the mcr-3.12 gene was carried by an IncA/C₂ plasmid and was embedded in an original genetic environment. This study reports the occurrence of the MCR-3-like determinant in South America and is the first to demonstrate the functionality of this group of enzymes as a phosphoethanolamine transferase.

An Improved Medium for Colistin Susceptibility Testing

The plasmid-located colistin resistance gene mcr-1 confers low-level resistance to colistin, a last-line antibiotic against multidrug-resistant Gram-negative bacteria. Current CLSI-EUCAST recommendations require the use of a broth microdilution (BMD) method with cation-adjusted Mueller-Hinton (CA-MH) medium for colistin susceptibility testing, but approximately 15% of all MCR-1 producers are classified as sensitive in that broth. Here we report on an improved calcium-enhanced Mueller-Hinton (CE-MH) medium that permits simple and reliable determination of mcr-1-containing Enterobacteriaceae Colistin susceptibility testing was performed for 50 mcr-1-containing Escherichia coli and Klebsiella pneumoniae isolates, 7 intrinsically polymyxin-resistant species, K. pneumoniae and E. coli isolates with acquired resistance to polymyxins due to mgrB and pmrB mutations, respectively, and 32 mcr-1-negative, colistin-susceptible isolates of Acinetobacter baumannii, Citrobacter freundii, Enterobacter cloacae, E. coli, K. pneumoniae, and Salmonella enterica serovar Typhimurium. A comparison of the colistin MICs determined in CA-MH medium and those obtained in CE-MH medium was performed using both the BMD and strip-based susceptibility test formats. We validated the data using an isogenic IncX4 plasmid lacking mcr-1 Use of the CE-MH broth provides clear separation between resistant and susceptible isolates in both BMD and gradient diffusion assays; this is true for both mcr-1-containing Enterobacteriaceae isolates and those exhibiting either intrinsic or acquired colistin resistance. CE-MH medium is simple to prepare and overcomes current problems associated with BMD and strip-based colistin susceptibility testing, and use of the medium is easy to implement in routine diagnostic laboratories, even in resource-poor settings.

Towards Understanding MCR-like Colistin Resistance

Antibiotic resistance has become a global public health priority. Polymyxins, a family of cationic polypeptide antibiotics, act as a final line of refuge against severe infections by Gram-negative pathogens with pan-drug resistance. Unfortunately, this last-resort antibiotic has been challenged by the emergence and global spread of mobilized colistin resistance determinants (mcr). Given the fact that it has triggered extensive concerns worldwide, we present here an updated view of MCR-like colistin resistance. These studies provide a basic framework for understanding the molecular epidemiology and resistance mechanism of MCR-like genes. However, further large-scale epidemiology and functional studies are urgently needed to better understand the biology of this clinically important antibiotic resistance.