Emergence of KPC-31, a KPC-3 Variant Associated with Ceftazidime-Avibactam Resistance, in an Extensively Drug-Resistant ST235 Pseudomonas aeruginosa Clinical Isolate

Emerging resistance mechanisms to newer β-lactams in Pseudomonas aeruginosa

BACKGROUND

Although the introduction of novel β-lactams and/or combinations with β-lactamase inhibitors over the last decade is helping to mitigate the threat of extensively drug-resistant/difficult-to-treat-resistant (XDR/DTR) Pseudomonas aeruginosa infections, the problem is far from being solved, due to the capacity of this pathogen for developing resistance.

OBJECTIVES

This study aims to provide a comprehensive analysis of the emerging/evolving resistance mechanisms to the antipseudomonal β-lactams introduced over the last decade.

SOURCES

Sources include literature review of published studies before December 31 2024 analysing P. aeruginosa resistance mechanisms for ceftolozane/tazobactam, ceftazidime/avibactam, cefiderocol, imipenem/relebactam, meropenem/vaborbactam, and/ aztreonam/avibactam.

CONTENT

Among the emerging resistance mechanisms are noteworthy the mutations in the catalytic centres (mostly the Ω-loop) of AmpC, the horizontally acquired OXA-2/OXA-10 enzymes or of the class A carbapenemases (GES/KPC). These mutations typically confer ceftolozane/tazobactam and ceftazidime/avibacm resistance. They also frequently increase cefiderocol Minimal Inhibitory Concentrations (MICs), and some of them, such as the L320P AmpC mutation, affect cefiderocol specifically. However, most of these mutations confer collateral susceptibility to carbapenems. Efflux pumps are also relevant, given their capacity to extrude both, the β-lactam and their partner β-lactamase inhibitor. Moreover, beyond the classical mutational overexpression of efflux pumps, emerging resistance is driven by the selection of structural mutations leading to modified (enhanced) substrate recognition. Other emerging mechanisms include β-lactam target mutations (particularly Penicillin-binding protein 3 (PBP3)), large genomic deletions, the activation of two-component regulators (such as ParRS or CpxRS) or the mutations in iron transport systems (such as Piu or Pir) involved in cefiderocol resistance.

IMPLICATIONS

A deep understanding of emerging resistance mechanisms, including their conferred cross-resistances and collateral susceptibilities, should be useful for the optimization of treatments of severe XDR/DTR P. aeruginosa infections.

Characterization of Klebsiella pneumoniae carbapenemase (KPC)-14, a KPC variant conferring resistance to ceftazidime-avibactam in the extensively drug-resistant ST463 Pseudomonas aeruginosa clinical isolate

OBJECTIVE

We studied two Klebsiella pneumoniae carbapenemase (KPC)-14 variants from clinical Pseudomonas aeruginosa isolates (C137 and C159) to better understand the genomic diversity, mechanisms, and genes that confer antibiotic resistance and pathogenicity.

METHODS

Genomic DNA from C137/159 was subjected to Illumina and Oxford Nanopore sequencing. Horizontal transmission of the plasmid was evaluated using cloning experiments. The expression of efflux pumps, the outer membrane protein OprD, and the enzyme AmpC was quantified using qRT-PCR. The detectability of KPC-14 was evaluated using different methods, and biofilm formation assays and growth curves were assessed.

RESULTS

C137 and C159, sequence type 463 ExoU-positive multidrug-resistant strains, were concurrently resistant to carbapenems and ceftazidime-avibactam. Both strains possessed five intrinsic antimicrobial resistance genes (fosA, catB7, crpP, blaPAO, and a blaOXA-486 variant) as well as blaKPC-14. In strain C137, blaKPC-14 was located on a plasmid (pC137). Both strains expressed the blaKPC-14 gene, concurrent inactivation of OprD, overexpression of the MexX efflux pump, and a pronounced capacity for biofilm formation. The genomic environment of KPC-14 consisted of IS26/IS26/TnpR_Tn3/ISKpn27/ISKpn6/IS26, which classified it as pseudo-compound transposon (PCT). IS26-mediated PCTs may store a variety of resistance genes, including blaKPC-2 and KPC variants, which are currently disseminating in this region.

CONCLUSIONS

The KPC-14 variant presents significant challenges for clinical treatment. The blaKPC-14 gene carried by PCTs was integrated into the chromosome and exhibited stability throughout bacterial inheritance. Our research highlights the need for improved clinical surveillance of KPC-producing P. aeruginosa.

KPC variants conferring resistance to ceftazidime-avibactam in Pseudomonas aeruginosa strains

BACKGROUND

This study aimed to characterize three KPC variants (KPC-33, KPC-100, and KPC-201) obtained from a clinical isolate of Pseudomonas aeruginosa (#700), along with two induced strains C109 and C108.

METHODS

Genomic DNAs of #700 (ST235), C109 (ST463), and C108 (ST1076) were sequenced using Illumina and Oxford Nanopore technologies. The transferability and stability of the plasmid was assessed through conjugation experiments and plasmid stability experiments, respectively. Minimum inhibitory concentrations of bacterial strains were determined using broth microdilution methods. In vitro induction was performed using ceftazidime-avibactam (CZA) at concentrations of 6/4 µg/ml. Linear genomic alignments were visualized using Easyfig, and protein structure modeling of the novel KPC variant (KPC-201) was conducted using PyMol.

RESULTS

The plasmids carrying the KPC variants in the three CZA-resistant strains (C109, C108, and #700) had sizes of 39,251 bp (KPC-100), 394,978 bp (KPC-201), and 48,994 bp (KPC-33). All three plasmids belonged to the IncP-like incompatibility (Inc) groups, and the plasmid exhibited relatively high plasmid stability, KPC-33 and KPC-201-harboring plasmids were successfully transferred to the recipient strain P. aeruginosa PAO1rifR. The genetic environments of the three blaKPC genes differed from each other. The mobile elements of the three blaKPC genes were as follows, TnAS1-IS26-ΔISKpn27-blaKPC-33-ISKpn6-IS26, IS6-ΔISKpn27-blaKPC-100-ISKpn6-IS26-Tn3-IS26, and IS6100-ISKpn27-blaKPC-201-ISKpn6-TnAS1. Notably, the length of ΔISKpn27 upstream of the blaKPC-33 and blaKPC-100 genes were remarkably short, measuring 114 bp and 56 bp, respectively, deviating significantly from typical lengths associated with ISKpn27 elements. Moreover, the novel KPC variant, KPC-201, featured a deletion of amino acids LDR at positions 161-163 in KPC-3, resulting in a looser pocket structure contributing to its avibactam resistance.

CONCLUSIONS

KPC-201, identified as a novel KPC variant, exhibits resistance to CZA. The presence of multiple mobile elements surrounding the blaKPC-variant genes on stable plasmids is concerning. Urgent preventive measures are crucial to curb its dissemination in clinical settings.

Mechanisms leading to in vivo ceftazidime/avibactam resistance development during treatment of GES-5-producing Pseudomonas aeruginosa infections

The mechanisms underlying ceftazidime/avibactam resistance development in four ceftazidime/avibactam susceptible/resistant pairs of GES-5-producing ST235 Pseudomonas aeruginosa clinical isolates were investigated. In three of the cases, ceftazidime/avibactam resistance was driven by a single mutation leading to GES-27 (P162Q), GES-29 (P162A), or the novel GES-60 (N136S), as confirmed through cloning experiments. Moreover, these mutations were associated with increased cefiderocol MICs but reduced carbapenem, particularly imipenem/relebactam, resistance. Understanding the complexity of resistance mechanisms to the growing repertoire of antipseudomonal β-lactams is crucial to guide optimized treatments and antimicrobial stewardship measures.

Impact of chromosomally encoded resistance mechanisms and transferable β-lactamases on the activity of cefiderocol and innovative β-lactam/β-lactamase inhibitor combinations against Pseudomonas aeruginosa

OBJECTIVES

We aimed to compare the stability of the newly developed β-lactams (cefiderocol) and β-lactam/β-lactamase inhibitor combinations (ceftazidime/avibactam, ceftolozane/tazobactam, aztreonam/avibactam, cefepime/taniborbactam, cefepime/zidebactam, imipenem/relebactam, meropenem/vaborbactam, meropenem/nacubactam and meropenem/xeruborbactam) against the most clinically relevant mechanisms of mutational and transferable β-lactam resistance in Pseudomonas aeruginosa.

METHODS

We screened a collection of 61 P. aeruginosa PAO1 derivatives. Eighteen isolates displayed the most relevant mechanisms of mutational resistance to β-lactams. The other 43 constructs expressed transferable β-lactamases from genes cloned in pUCP-24. MICs were determined by reference broth microdilution.

RESULTS

Cefiderocol and imipenem/relebactam exhibited excellent in vitro activity against all of the mutational resistance mechanisms studied. Aztreonam/avibactam, cefepime/taniborbactam, cefepime/zidebactam, meropenem/vaborbactam, meropenem/nacubactam and meropenem/xeruborbactam proved to be more vulnerable to mutational events, especially to overexpression of efflux operons. The agents exhibiting the widest spectrum of activity against transferable β-lactamases were aztreonam/avibactam and cefepime/zidebactam, followed by cefepime/taniborbactam, cefiderocol, meropenem/xeruborbactam and meropenem/nacubactam. However, some MBLs, particularly NDM enzymes, may affect their activity. Combined production of certain enzymes (e.g. NDM-1) with increased MexAB-OprM-mediated efflux and OprD deficiency results in resistance to almost all agents tested, including last options such as aztreonam/avibactam and cefiderocol.

CONCLUSIONS

Cefiderocol and new β-lactam/β-lactamase inhibitor combinations show promising and complementary in vitro activity against mutational and transferable P. aeruginosa β-lactam resistance. However, the combined effects of efflux pumps, OprD deficiency and efficient β-lactamases could still result in the loss of all therapeutic options. Resistance surveillance, judicious use of new agents and continued drug development efforts are encouraged.

Complex evolutionary trajectories in vivo of two novel KPC variants conferring ceftazidime-avibactam resistance

More and more ceftazidime-avibactam-resistant KPC-producing Klebsiella pneumoniae have been reported with its widespread use, and the detection rate of KPC variants has increased dramatically. However, the evolutionary mechanism and fitness effects during KPC mutation remained unknown. Here, we report the complex in vivo evolutionary trajectories of two novel KPC variants, KPC-155 (L169P/GT242A) and KPC-185 (D179Y/GT242A), from K. pneumoniae in the same patient. The novel variants were shown to confer ceftazidime-avibactam resistance but restore carbapenem susceptibility based on the results of plasmid transformation assays, cloning experiments, and enzyme kinetic measurements. In vitro, competition experiments highlighted the adaptive advantage conferred by strains carrying these KPC variants, which could lead to the rapid spread of these ceftazidime-avibactam-resistant strains. The growth curve indicated that blaKPC-185 had better growth conditions at lower avibactam concentration compared to blaKPC-155, which was consistent with ceftazidime-avibactam use in vivo. In addition, replicative transposition of the IS26-flanked translocatable unit (IS26-ISKpn6-blaKPC-ISKpn27-IS26) also contributes to the blaKPC amplification and formation of two copies (blaKPC-2 and blaKPC-185), conferring both carbapenem and ceftazidime-avibactam resistance. However, strains with double copies showed reduced competitive advantage and configuration stability. The comparative plasmid analysis of IS26 group (IS26-blaKPC-IS26) and Tn1721 group (Tn1721-blaKPC-IS26) revealed that IS26-insertion could influence the distribution of resistance genes and ability of self-conjugation. The dynamic changes in blaKPC configuration highlight the need for consistent monitoring including antimicrobial susceptibility testing and determination of blaKPC subtypes - during clinical treatment, especially when ceftazidime-avibactam is administered.

First report of KPC variants conferring ceftazidime-avibactam resistance in Colombia: introducing KPC-197

Resistance to ceftazidime-avibactam (CZA) due to Klebsiella pneumoniae carbapenemase (KPC) variants is increasing worldwide. We characterized two CZA-resistant clinical Klebsiella pneumoniae strains by antimicrobial susceptibility test, conjugation assays, and WGS. Isolates belonged to ST258 and ST45, and produced a KPC-31 and a novel variant KPC-197, respectively. The novel KPC variant presents a deletion of two amino acids on the Ω-loop (del_168-169_EL) and an insertion of two amino acids in position 274 (Ins_274_DS). Continued surveillance of KPC variants conferring CZA resistance in Colombia is warranted.

IMPORTANCE

Latin America and the Caribbean is an endemic region for carbapenemases. Increasingly high rates of Klebsiella pneumoniae carbapenemase (KPC) have established ceftazidime-avibactam (CZA) as an essential antimicrobial for the treatment of infections due to MDR Gram-negative pathogens. Although other countries in the region have reported the emergence of CZA-resistant KPC variants, this is the first description of such enzymes in Colombia. This finding warrants active surveillance, as dissemination of these variants could have devastating public health consequences.

Pseudomonasaeruginosa antimicrobial susceptibility profiles, resistance mechanisms and international clonal lineages: update from ESGARS-ESCMID/ISARPAE Group

SCOPE

Pseudomonas aeruginosa, a ubiquitous opportunistic pathogen considered one of the paradigms of antimicrobial resistance, is among the main causes of hospital-acquired and chronic infections associated with significant morbidity and mortality. This growing threat results from the extraordinary capacity of P. aeruginosa to develop antimicrobial resistance through chromosomal mutations, the increasing prevalence of transferable resistance determinants (such as the carbapenemases and the extended-spectrum β-lactamases), and the global expansion of epidemic lineages. The general objective of this initiative is to provide a comprehensive update of P. aeruginosa resistance mechanisms, especially for the extensively drug-resistant (XDR)/difficult-to-treat resistance (DTR) international high-risk epidemic lineages, and how the recently approved β-lactams and β-lactam/β-lactamase inhibitor combinations may affect resistance mechanisms and the definition of susceptibility profiles.

METHODS

To address this challenge, the European Study Group for Antimicrobial Resistance Surveillance (ESGARS) from the European Society of Clinical Microbiology and Infectious Diseases launched the 'Improving Surveillance of Antibiotic-Resistant Pseudomonas aeruginosa in Europe (ISARPAE)' initiative in 2022, supported by the Joint programming initiative on antimicrobial resistance network call and included a panel of over 40 researchers from 18 European Countries. Thus, a ESGARS-ISARPAE position paper was designed and the final version agreed after four rounds of revision and discussion by all panel members.

QUESTIONS ADDRESSED IN THE POSITION PAPER

To provide an update on (a) the emerging resistance mechanisms to classical and novel anti-pseudomonal agents, with a particular focus on β-lactams, (b) the susceptibility profiles associated with the most relevant β-lactam resistance mechanisms, (c) the impact of the novel agents and resistance mechanisms on the definitions of resistance profiles, and (d) the globally expanding XDR/DTR high-risk lineages and their association with transferable resistance mechanisms.

IMPLICATION

The evidence presented herein can be used for coordinated epidemiological surveillance and decision making at the European and global level.

The balance between antibiotic resistance and fitness/virulence in Pseudomonas aeruginosa: an update on basic knowledge and fundamental research

The interplay between antibiotic resistance and bacterial fitness/virulence has attracted the interest of researchers for decades because of its therapeutic implications, since it is classically assumed that resistance usually entails certain biological costs. Reviews on this topic revise the published data from a general point of view, including studies based on clinical strains or in vitro-evolved mutants in which the resistance phenotype is seen as a final outcome, i.e., a combination of mechanisms. However, a review analyzing the resistance/fitness balance from the basic research perspective, compiling studies in which the different resistance pathways and respective biological costs are individually approached, was missing. Here we cover this gap, specifically focusing on Pseudomonas aeruginosa, a pathogen that stands out because of its extraordinary capacity for resistance development and for which a considerable number of recent and particular data on the interplay with fitness/virulence have been released. The revised information, split into horizontally-acquired vs. mutation-driven resistance, suggests a great complexity and even controversy in the resistance-fitness/virulence balance in the acute infection context, with results ranging from high costs linked to certain pathways to others that are seemingly cost-free or even cases of resistance mechanisms contributing to increased pathogenic capacities. The elusive mechanistic basis for some enigmatic data, knowledge gaps, and possibilities for therapeutic exploitation are discussed. The information gathered suggests that resistance-fitness/virulence interplay may be a source of potential antipseudomonal targets and thus, this review poses the elementary first step for the future development of these strategies harnessing certain resistance-associated biological burdens.

Worldwide Dissemination of blaKPC Gene by Novel Mobilization Platforms in Pseudomonas aeruginosa: A Systematic Review

The dissemination of blaKPC-harboring Pseudomonas aeruginosa (KPC-Pa) is considered a serious public health problem. This study provides an overview of the epidemiology of these isolates to try to elucidate novel mobilization platforms that could contribute to their worldwide spread. A systematic review in PubMed and EMBASE was performed to find articles published up to June 2022. In addition, a search algorithm using NCBI databases was developed to identify sequences that contain possible mobilization platforms. After that, the sequences were filtered and pair-aligned to describe the blaKPC genetic environment. We found 691 KPC-Pa isolates belonging to 41 different sequence types and recovered from 14 countries. Although the blaKPC gene is still mobilized by the transposon Tn4401, the non-Tn4401 elements (NTEKPC) were the most frequent. Our analysis allowed us to identify 25 different NTEKPC, mainly belonging to the NTEKPC-I, and a new type (proposed as IVa) was also observed. This is the first systematic review that consolidates information about the behavior of the blaKPC acquisition in P. aeruginosa and the genetic platforms implied in its successful worldwide spread. Our results show high NTEKPC prevalence in P. aeruginosa and an accelerated dynamic of unrelated clones. All information collected in this review was used to build an interactive online map.