Editor's Choice Articles

Colistin resistance in Enterobacteriaceae is mediated by complex mechanisms that modify their outer membrane and prevent the binding of colistin to its target, the lipopolysaccharide (LPS). The genomic support of this resistance involves several genes involved in the synthesis of sugars that modify this LPS, decreasing the affinity of colistin. Most of genes that have been described in colistin resistance are regulatory genes. Previous studies have identified mutations, deletions, or insertions in these genes in strains that had become resistant to colistin. However, most of these previous studies only focused on colistin-resistant isolates.

In this work, the authors compared the genetic polymorphism of 22 colistin-resistance associated genes in a population of colistin-susceptible and colistin-resistant Klebsiella pneumoniae. Their objective was to identify SNPs, deletions and insertions actually associated with colistin resistance. They showed that most of the previously described mutations, except for mutations, deletion and insertion in mgrB, the main involved mechanism, and some mutations in the pmrA and pmrB genes, are in fact genetic polymorphisms clade associated that are present in both colistin-susceptible and -resistant isolates.

This work underlines the importance of using control strains to study these resistance mechanisms. It also shows the need to associate the antibiotic resistance phenotype of strains whose genomes are deposited on NCBI to use these genomes in this type of analysis.

Antibiotic resistance in Gram-negative bacteria (GNB) is a global threat. One of the strategies used to deal with it is to reposition as antibiotics, molecules already approved in human medicine for another therapeutic indication. Thus, in this work, the authors were interested in the combination of two molecules, pentamidine and auranofin.

Pentamidine is an anti-parasitic agent that has shown a disruptive action on the membrane of GNB by interacting with LPS. Auranofin is a compound used in the treatment of rheumatoid arthritis which has shown an antimicrobial effect essentially on Gram-positive bacteria and to a lesser extent on GNB because of its lower penetration through their membrane. By combining these two molecules, pentamidine permeabilizes the membrane of GNB, allowed a better penetration of auranofin and a better activity. They tested this combination on wild and multidrug resistant strains of Escherichia coli, Klebsiella pneumoniae and Acintobacter baumannii and showed a synergistic action of the combination, also delaying the development of resistance. This association is promising for the development of a new antibiotic active on these multidrug resistant GNB.

Tuberculosis still causes more 1.4 million people worldwide. The treatment of tuberculosis caused by MDR and XDR Mycobacterium tuberculosis is complicated and relies on the use of an effective combination therapy. The used molecules can be injectable aminoglycosides, fluoroquinolones, antibiotics repositioned in the treatment of tuberculosis, such as clofazimine (an anti-leprosy drug) or linezolide (an oxazolidinone), or new molecules such as bedaquiline, delamanid or pretomanid. In 2020, a clinical trial (Nix-TB regimen) based on the combination of bedaquiline, pretomanid and linezolid for 26 weeks showed 90% efficacy on MDR and XDR clinical infections. However, adverse events such as peripheral neuropathy and myelosuppression, mainly related to the use of linezolid, are an issue for the follow-up of the treatment.

In this work, the authors evaluated the potential of clofazimine as an alternative to linezolid in this treatment. They evaluated the efficacy of clofazimine in combination with pretomanid, bedaquiline and linezolid on a M. tuberculosis H37Rv isolate. Despite additive and synergistic effects of clofazimine with each of the three molecules studied, the predicted bacterial cell kill was lowest with clofazimine. However, the authors did not consider the cumulative effect of clofazimine in the target site in their study, which may explain the lower efficacy of clofazimine.

Combination with bedaquiline and pretomanid showed the more promising effects, which should be confirmed in further studies.

Colistin is a last-line antibiotic used in the treatment of multidrug-resistant Gram-negative bacterial infections. Colistin resistance mechanisms in these bacteria involve modification of the target of colistin, lipid A. Sugars, such as aminoarabinose or phosphoethanolamine are added on the lipid A to neutralize its negative charges and thus prevent the binding of the positively charged colistin. Several genes are involved in the synthesis of these sugars, including a transferable gene mcr-1, coding for a phosphoethanolamine transferase.

In this work, the authors sought to understand the genes involved in the regulation of colistin resistance in an Escherichia coli strain carrying a mcr-1 gene. In the presence of colistin, they showed that the expression of both chromosomal and plasmid phosphoethanolamine transferases were mainly modified, in contrast to the operon coding for the synthesis of aminoarabinose. Interestingly, the regulator of the expression of these genes were not altered, suggesting other genes are involved in this regulation. The expression of genes involved in lipid and cell envelope biosynthesis or in the regulation of oxidative stress was also modified, suggesting they play a role in colistin resistance.

This study provides new insights into the complex regulatory mechanisms that bacteria can set up to survive in the presence of colistin.

Carbapenemase-producing Enterobacteriaceae (CPE) often cause Healthcare Associated Infections (HAIs) and confer resistance to other classes of antibiotics, limiting treatment options.

Aminoglycosides are broad-spectrum antibiotics used in combination with other antibiotics to treat enterobacterial infections and often remain active on CPE. However, aminoglycoside-modifying enzymes encoded by transferable genes are widely distributed worldwide, leading to the resistance of one or more aminoglycosides. In recent years, a new family of enzymes, the 16S sRNA methyltransferases (RMTs) which confer a high level of resistance to most aminoglycosides have emerged. The spread of these RMTs genes remains low, especially in Europe, but needs to be monitored.

In this study, the authors performed an epidemiological and molecular analysis of CPE strains isolated in Spain carrying these RMTs genes. Their results provide important information on the bacterial species and clones producing these enzymes as well as on the antibiotic resistance genes and mobile elements that are associated with them.

The increase in antibiotic resistance in human medicine has led researchers to develop therapeutic alternatives for several years. The development of new molecules, the repositioning of old antibiotics or the marketing of new antimicrobial combinations are options that have been proposed in recent years, but which have several limitations.

Other tools are currently being developed. The first one is based on phage therapy, which consists of fighting multi-resistant bacteria by infecting them with a bacteriophage. This method, which has been known for several decades, is currently receiving renewed interest.

The second method consists of using a genome editing tool that has revolutionised genetics in recent years: the CRISPR-Cas system. This system, in the field of antibiotic resistance fighting, targets the antibiotic resistance gene to inactivate it, restoring the antibiotic susceptibility of the bacterium. This promising technique requires, however, to correctly target into the bacteria of interest. The combination of an infecting phage with the CRISPR-Cas system is one of the promising methods summarised in this paper.

Treatment of Gram negative bacterial infections is often based on intravenous (IV) antibiotic therapy. The oral antibiotic therapy step-down, after bacterial identification and antibiotics susceptibility tests, has several advantages as it reduces the length of hospital stay and complications related to catheterisation.

However, there is a lack of randomised controlled studies in the literature in the comparison of oral treatment to IV treatment. As a result, the practices of infectious diseases (ID) specialists vary according to their own experience. Thus, the authors of this study conducted a survey of ID specialists to determine the current state of practice in the management of Gram negative bacterial infections. The results of this survey show that the initiation of PO treatment depends essentially on the source of the infection and the geographic origin of the prescriber. There is also no consensus regarding the duration of IV antibiotic therapy before switching to PO antibiotics.

In summary, this study demonstrates the variability of the management in these infections and highlights the need for a randomised trial to provide recommendations based on a true comparison.

This paper highlights the concept of One Health for transmission of antibiotic resistance genes between animals and humans. Using a set of 480 human isolates and 445 animal isolates of E. coli collected in Italy, the authors found a large prevalence of antibiotic resistance genes among different sequence types (STs) in those strains.

Although different STs were found between human and animal isolates, antibiotic resistance genes were the same, likely suggesting that those genes can spread in different ecosystems and that resistance is linked to the transmission of genes between bacterial communities and not to transmission of specific bacterial clones.

This work is interesting because it shows that during a longitudinal genomic characterisation of carbapenemase-producing bacteria in Hong Kong during a 7-year period that carbapenemase genes that circulate in Hong Kong are diverse and that the epidemiology has changed because increase of carbapenemase-producing Enterobacteriaceae is different since 2015.

This work demonstrates that the evolution of an epidemic situation to an endemic situation in a given country could be due to specific clones and / or spread of specific mobile genetic elements within bacterial communities. Moreover, it shows that some antibiotic resistance may become predominant that raises the question of the fitness and the dynamic of certain genes.

Resistant tuberculosis is of concern worldwide and this work shows that emergence of such strains is ongoing in Brazil and proposes a different scenario to try to stop transmission of such strains.

Using whole genome sequencing and clinical / epidemiology investigation in a retrospective study including more than 300 resistant clinical isolates, authors found that specific lineages associated with resistance may spread in their country.

This work highlights that specific resistant bacterial clones may emerge in a country or worldwide and that active surveillance is now possible thanks to whole-genome sequencing (WGS); this will help in the future to define strategies to control such events and to take decisions.

The use of a combination of antibiotics or of an antibiotic associated with other effective molecules is a solution to treat infections caused by difficult-to-eradicate bacteria.

In this work, the authors were interested in infections caused by Burkholderia cenocepacia, a member of the Burkholderia cepacia complex. This Gram negative bacterium mainly colonises patients with cystic fibrosis, forming biofilms that are difficult to eradicate that can evolve in a necrotising pneumonia and contraindicate lung transplantation.

The authors tested several combinations of molecules including antibiotics and antioxidants on the biofilm induced by B. cenocepacia. They showed the effectiveness of the combination of N-acetyl-cysteine (NAC) and ciprofloxacin in vitro. NAC is an antioxidant with mucolytic properties that is believed to promote the disruption of the biofilm, allowing ciprofloxacin to reach its target and to be effective. This work brings new hopes in the eradication of this bacterium which will have to be confirmed and evaluated on in vivo models.

Drug repurposing and the reuse of old antibiotics are therapeutic solutions being considered to treat multidrug-resistant Gram negative bacterial infections.

Zidovudine, an antiretroviral molecule initially used in the treatment of HIV, has recently been identified as active against carbapenem and / or colistin-resistant enterobacterial isolates. Because of the risk of selection of zidovudine-resistant strains, it has been proposed to use it in combination with other antibiotics, and clinical trials are currently in process in association with colistin.

In this work, the authors studied the use of Zidovudine in combination with Fosfomycin, an old antibiotic that has been abandoned for years or used mostly in the treatment of urinary tract infections. Using in vitro methods (minimum inhibitory concentration, checkerboard assays, time kill study) and an in vivo Galleria mellonella infection model, the authors showed a synergistic effect of the combination of Zidovudine and Fosfomycin on 25 of the 36 strains of multi-resistant enterobacteria tested, mostly Escherichia coli and Klebsiella pneumoniae species. These results are promising for clinical use and now clinical trials are required to confirm its utility in humans.

In this work, authors investigated the prevalence of mcr-mediated colistin resistance in Escherichia coli isolated from healthy food-producing animals from 2012 to 2016 in Belgium.

They studied the resistance profile, the plasmid type and the sequence type of these isolates. Overall, 40 E. coli carried at least one mcr gene, the mcr-1 being the most frequent followed by mcr-4, mcr-2, mcr-3 and mcr-5. Thirty three isolates had a multidrug-resistant (MDR) phenotype, with resistance to ampicillin, tetracycline, sulfamethoxazole, trimethoprim and ciprofloxacin being the most frequent.

No specific clonal lineage of E. coli was identified and mcr genes were carried on different plasmid types. Interestingly, one MDR E. coli carried three mcr genes: mcr-1, mcr-3 and mcr-5. This isolate was co-resistant to all antimicrobial tested excepted meropenem and tigecycline. Twenty seven antibiotic resistance genes were identified and seven different plasmid replicons.

This work reveals the high prevalence and circulation of mcr genes in food-producing animals in Belgium. Some isolates are MDR and carry multiple antibiotic resistance genes and plasmids that can be easily transferrable to other isolates of the same species or other species.

The presence of multiple mcr genes in one isolate is intriguing and suggests that those genes may have functions other than resistance to colistin only. Global surveillance programmes and antibiotic stewardship are warranted to prevent the emergence and spread of MDR isolates in humans, animals and environment.

Methicillin-resistant Staphylococcus aureus (MRSA) bloodstream infections (BSI) currently require the use of intravenous treatment, with a risk of complications such as catheter infections or thrombosis. The oral step-down is an interesting option to limit these adverse effects but requires to be as efficient as the intravenous treatment.

This study was a retrospective, observational, single-centre study that evaluated the efficacy of oral linezolid, an oxazolidinone antibiotic, in the treatment for MRSA BSI as compared to standard parenteral treatment (SPT) (vancomycin or daptomycin). The primary endpoint was infection-related readmission (IRR), the secondary endpoints were mortality, adverse events and a decrease of hospital length stay.

A total of 215 patients were included, 54 in the linezolid group and 161 in the SPT group of which 62% received vancomycin and 38% received daptomycin. Authors showed that linezolid therapy was not inferior to SPT for the treatment of MRSA BSI (IRR 90 days 17% in the linezolid group vs 26% in the SPT group, p=0.159). Linezolid was not associated with a difference in adverse effects, but the use of oral therapy limited the risk of outpatient parenteral antimicrobial therapy.

Although statistical analysis was not significant, the hospital length of stay was reduced by two days on average. These results highlight advantages in terms of cost of care and would notably be interesting for the treatment of people who inject drugs, for whom the use of the intravenous line requires prolonged hospitalizations for monitoring with a risk of leave against medical advice prior to completion of therapy. This study shows also that oral therapy could limit the major risk of catheter related infections.

The mobile colistin resistance genes mcr have been discovered at the end of 2015 and have considerably changed the epidemiology of colistin resistance. Since the discovery of mcr-1 gene, nine other mcrs have been described from mcr-2 to mcr-10.

The mcr-9 gene has been described in Enterobacteriaceae from animals, humans and meat samples. In this study, Wang et al screened for colistin-resistant bacteria and mcr genes in 120 milk samples from healthy cows collected from commercial farms in Jiangsu province, China, in 2019. Overall, the prevalence of mcr-positive isolates was very low (0.83%), with one strain of mcr-9-positive S. enterica isolated.

This mcr-9 gene was located on a transferrable IncHI2A plasmid but did not confer colistin resistance, suggesting that its expression was low. However, surveillance for the dissemination of mcr-9 gene along with other antibiotic resistance genes in plasmids should be monitored to identify a potential spread of mobile antibiotic resistance genes in China’s food industry.

The fight against multidrug-resistant bacteria, including carbapenemase-producing bacteria, requires the search for new therapeutic options. In this field, drug repurposing is an interesting option because it can be rapidly transferred to the clinic. The authors of this work have studied the in vitro efficacy of a combination of colistin, a last-line antibiotic used in the treatment of multidrug-resistant Gram negative bacterial infections, with an antimalarial drug, mefloquine, for the treatment of carbapenemase-producing enterobacterial infections.

This combination showed a synergistic activity against NDM-1-, mcr-1- and ESBL-producing enterobacteria in checkerboard analysis. This activity was confirmed to be bactericidal by time kill study, the addition of mefloquine allowed a lower concentration of colistin to be used, which could reduce its toxicity. An in vivo study on a mouse peritoneal infection model confirmed the efficacy of the treatment with significant reduction of CFU counts at 4-6 hours after the administration of the combination at 20 mg/kg for both drugs.

Mefloquine has been used for malaria prophylaxis for many years and is well known to clinicians. Its use as a booster of colistin activity would reduce the nephrotoxicity and neurotoxicity of this antibiotic. Further studies in humans are still needed to ensure the in vivo activity of this combination.

Digestive carriage of Extended Spectrum Beta-Lactamase-producing Enterobacteriaceae (ESBL-E) in humans represents a reservoir for the transmission of multidrug-resistant bacteria. The transmission of these ESBL-E to immunocompromised people can lead to infections that are difficult to treat and onerous in terms of management. In the Netherlands, the prevalence of ESBL-E carriage in the general population has been evaluated at 8.6% in but specific populations could be at higher risk for ESBL-E carriage.

In this work, authors have evaluated the prevalence of ESBL-E carriage and its association with sexual behaviour among men who have sex with men (MSM) in Amsterdam, the Netherlands. They included 695 MSM between April and December 2018, with a median age of 43 years old. The global prevalence of ESBL-producing enterobacteria carriage was 16.3%, twice as high as in the general population. The ESBL carriage was associated with a higher number of sex partners in the preceding 6 months and practicing certain sexual behaviours with casual partners. The recent use of antibiotics was also a risk factor for ESBL. This finding should be taken into consideration for the management of sepsis in MSM, in order to adapt the empirical antibiotic therapy to the risk of isolation of ESBL-E. 

The spread of antibiotic resistance worldwide is associated with the dissemination of specific multidrug-resistant clones. In Escherichia coli, several multidrug-resistant clones have spread internationally and are particularly monitored. This is the case for E. coli sequence type 131 (ST131), a clone found in human infections and frequently associated with multidrug resistance.

The authors of this work evaluated the antibiotic resistance level of E. coli in fecal samples in healthy people in Osaka, Japan, between 2013 and 2019 and analysed the incidence of this clone in the studied population. Overall, the antimicrobial resistance rate was low, except for resistance to ampicillin and ciprofloxacin. Ampicillin resistance was mostly carried by TEM enzyme. The overall prevalence of 3rd generation cephalosporin resistance was 4.4%, with a slight increase in 2016-2017 and the presence of Extended-Spectrum Beta-lactamase (ESBL) genes was low. The prevalence of the ST131 clone increases from <5% before 2016 to 10% since 2016. Its members carry mostly quinolone resistance, and some ESBL-producers. Overall, they found a lower antimicrobial resistance rate in healthy people as compared to previous studies performed on hospitalised patients. The increasing level of ciprofloxacin resistance and ESBL could be linked to the increase of the ST131 clone since 2016.

Efflux pumps are an important and complex mechanism for antimicrobial resistance in bacteria. Among them, Resistance-nodulation-cell division family (RND) efflux pumps are widely found in enterobacteria and play a role in antibiotic resistance. The most well-known efflux pump in Klebsiella pneumoniae is AcrAB that is upregulated by the ramA transcription regulator gene and downregulated by the repressor acrR.

In this work, authors were interested in another efflux pump, OqxAB, and focused on the role of ramA in the regulation of this pump. They confirmed that ramA gene is overexpressed after inhibition of its repressor ramR and up-regulate both AcrAB and OqxAB efflux pumps. These efflux pumps were able to efflux tigecycline, cefepime, piperacillin-tazobactam, ciprofloxacin, chloramphenicol and nitrofurantoin for AcrAB and tetracycline, ciprofloxacin and nitrofurantoin for OqxAB. These results emphasize the role of ramA in regulation of multidrug resistance efflux pumps in K. pneumoniae.

Ceftolozane-tazobactam is a novel β-lactam / β-lactamase inhibitor active on multidrug resistant enterobacteria, especially Extended-Spectrum-Beta-Lactamase (ESBL) ones.

In this work, Hernandez-Garcia et al evaluated the concordance between the phenotypic susceptibility of ceftolozane-tazobactam in 426 enterobacteria (mostly Escherichia coli and Klebsiella pneumoniae) isolated in intensive care unit from patients hospitalised between 2017 and 2018 in Portugal with the Resistome of these isolates by whole genome sequencing.

They also characterised the clones found in ICU during this period. Interestingly, the most prevalent clones were the international well-known clones ST131 for E. coli and ST307 for K. pneumoniae and the major resistance genes were blaCTX-M-15 for ESBL phenotype and blaKPC-3 for carbapenemase. Surprisingly, the presence of carbapenemase did not correlate with ceftolozane-tazobactam resistance in E. coli, unlike in K. pneumoniae. These results suggest other mechanisms involved in the resistance to ceftolozane-tazobactam in E. coli.

Following the increase in resistance to beta-lactam antibiotics, especially carbapenems, clinicians became interested in an old antibiotic, Fosfomycin. This antibiotic has the advantage of having a unique antibacterial mechanism of action, assuming that it can be active in multidrug-resistant bacteria. However, resistance mechanisms have already been identified, notably by modification of the target, impermeability, but above all, acquisition of a plasmid-mediated fosA gene hydrolysing Fosfomycin.

In China, this antibiotic has been reused for several years now, but the prevalence and mechanisms of Fosfomycin resistance are poorly known. The authors of this work investigated the mechanism of Fosfomycin resistance in 80 carbapenemase KPC-producing Klebsiella pneumoniae isolates, highlighting a rate of 80% of Fosfomycin resistance. They showed that the fosA3 gene of plasmid origin was present in 36.3% of the strains and conferred a high level of resistance to Fosfomycin. All KPC-KP also carried mutations or deletions in the Fosfomycin target genes, notably in the glpt gene, suggesting that this mechanism is also common. Further investigations are needed to understand the role of this Fosfomycin hydrolase, which is present in the genome of various bacterial genera.