IDDT Journal

Introduction

The 2024 Infectious Diseases Society of America (IDSA) guidelines classify carbapenem-resistant Enterobacterales (CRE) as organisms within the Enterobacterales order demonstrating resistance to at least one carbapenem antibiotic—such as ertapenem, Meropenem, Imipenem, or doripenem [1]. CRE encompass a diverse group of pathogens, exhibiting various resistance mechanisms. They can be categorized as either carbapenemase-producing or noncarbapenemase-producing. Common carbapenemases include Klebsiella pneumoniae carbapenemases (KPCs), New Delhi metallo-β-lactamases (NDMs), Verona integron-encoded metallo-β-lactamases (VIMs), Imipenem-hydrolyzing metallo-βlactamases (IMPs), and OXA-48-like oxacillinases. NDM, VIM, and IMP carbapenemases are collectively known as metallo-βlactamases (MBLs) [1]. The genes responsible for these enzymes include blaKPC, blaNDM, blaVIM, blaIMP, and blaOXA-48-like. Identifying the specific carbapenemase produced by a CRE isolate is crucial for determining appropriate treatment, as the efficacy of newer β-lactam antibiotics varies depending on the carbapenemase present [1].

CRE Infection Epidemiology:

Antimicrobial resistance (AMR) contributed to over one million deaths globally in 2021, with projections suggesting a potential rise to 1.91 million annual deaths by 2050 [2]. Since their initial detection in 1980, the prevalence of CRE has significantly increased, leading the World Health Organization to designate them as a critical-priority pathogen, emphasizing the urgent need for effective treatment strategies [3]. CRE infections pose a substantial global public health threat, with India experiencing a notably high incidence. This is often linked to the widespread dissemination of the NDM-1 carbapenemase gene, making it endemic within the Indian subcontinent. In India, the predominant factor contributing to Carbapenem-Resistant Enterobacteriaceae (CRE) is frequently linked to the synthesis of New Delhi Metallo-beta-lactamase (NDM) enzymes, especially the NDM-1 variant. Conversely, in Western countries, the Klebsiella pneumoniae carbapenemase (KPC) is more typically connected with CRE. Additionally, various geographical areas may display distinct patterns of carbapenemase production, such as OXA-48 observed in certain regions of Europe and North Africa. In India, the situation is quite similar, as indicated by the recent ICMR-AMRSN 2022 report, which reveals that CRKP (56%) and CREco (30%) rank among the three most prevalent isolates from all samples, excluding feces and urine, obtained from ICUs in Indian hospitals. [4] CRE infections are associated with high mortality rates, ranging from 26% to 50% [5]. Notably, carbapenem resistance has doubled between 2017 and 2022, according to the ICMR-AMR report [4].

CRE Infection Risk Factors:

Analysis of recent research indicates several factors that elevate the risk of developing carbapenem-resistant Enterobacterales (CRE) infections. These include pre-existing medical conditions, the use of urinary catheters, the presence of indwelling vascular devices, extended periods of hospitalization, prolonged courses of antibiotic therapy, the need for mechanical respiratory support, and a history of exposure to fluoroquinolone, carbapenem, or cephalosporin antibiotics [6].

CRE Detection Techniques:

Diverse methodologies employed for detecting carbapenemresistant Enterobacterales (CRE), highlighting their respective sensitivities, specificities, and limitations summarised in Table 1 [7]. Culture-based techniques, such as the modified Hodge test (MHT) enhanced with boronic acid, E-test strips that utilize EDTA (ethylenediaminetetraacetic acid), and targeted combination disk diffusion assays, have enhanced antimicrobial susceptibility testing (AST). These methods demonstrate commendable sensitivity and specificity in identifying KPC and MBL, although their effectiveness is diminished when it comes to detecting OXA48 [8]. Phenotypic methods include the Modified Hodge Test (MHT), which is effective for KPC but not MBL, and carbapeneminactivation methods (CIM), which can detect all carbapenemases [9]. Selective media offer varying sensitivity and specificity. Rapid phenotypic methods like colorimetric assays and MALDI-TOF MS are useful but may miss OXA-48 [10]. Genotypic methods, such as PCR-based techniques (including qPCR, RT-PCR, and mPCR), are considered the gold standard for rapid and accurate detection and typing of all carbapenemases [7]. Loop-mediated isothermal amplification (LAMP) offers a simpler and more cost-effective alternative [11]. Whole genome sequencing (WGS) provides comprehensive information but has a longer turnaround time [12]. Immunological methods, such as ELISA, have demonstrated poor performance [13]. Biosensors, including electrochemical and optical assays, are emerging technologies but require further development for reliable carbapenemase detection [14]. Emerging Techniques such as microfluidic and Raman spectroscopic techniques, show promise, but more research is required [15].

In India, the identification of Non-Carbapenemase Producing Carbapenem-Resistant Enterobacteriaceae (Non-CP CRE) is primarily conducted through conventional microbiological laboratory methods. This process involves the culture-based identification of Enterobacteriaceae, followed by phenotypic susceptibility testing utilizing disk diffusion or E-test to ascertain carbapenem resistance. Further confirmation is achieved through phenotypic tests such as the modified Hodge test (MHT) or the Carba NP test, which help distinguish between Carbapenemase Producing CRE (CP-CRE) and non-CP CRE. If necessary, molecular techniques may be employed to detect the specific resistance genes associated with non-CP CRE mechanisms [16].

Rapid commercial tests offer significant benefits within the Indian healthcare landscape. A variety of these tests, which are either cleared by the Food and Drug Administration (FDA) or bear the Conformité Européenne (CE) mark, are accessible for the identification of carbapenemase-producing carbapenem-resistant Enterobacteriaceae (CP CRE). These tests can be divided into two primary categories: phenotypic and molecular tests. The phenotypic detection of carbapenemase-producing organisms can be performed using biochemical assays such as Carba NP®, Blue Carba®, and Carba® tests. Although these assays confirm the presence of carbapenemases in bacterial cultures or isolates, they have limitations in recognizing other antimicrobial resistance (AMR) mechanisms, such as efflux pumps and porin losses, and they do not identify the specific type of carbapenemase enzyme present. Additionally, these methods require the availability of bacterial isolates. In contrast, nucleic acid-based molecular tests, including Xpert Carba-R®, BioFire film Array®, and Nanosphere Verigene BC-GN®, offer several advantages over traditional culture-based phenotypic tests. These benefits include a rapid turnaround time of less than six hours, precise identification of specific carbapenemase genes, and, in certain instances, the ability to directly analyze clinical specimens without prior culture. Nevertheless, molecular tests also encounter challenges, such as the inability to differentiate between mutant and wild-type enzymes, the distinction between silenced and expressed genes, and the detection of increased carbapenemase gene dosage as well as offpanel carbapenemase genes.The potential for misinterpretation regarding susceptibility and resistance to carbapenems and novel beta-lactam/beta-lactamase inhibitors is significant. It is advisable to interpret FDA/CE-validated molecular tests for resistance mechanisms alongside phenotypic tests to effectively manage suspected carbapenem-resistant Enterobacteriaceae (CRE) infections in critically ill patients in India. However, the financial burden associated with molecular testing methods limits their broader implementation in clinical laboratories. Conversely, innovative phenotypic lateral flow immunoassays have emerged as cost-effective alternatives within clinical environments. Previous research has shown that the NG-Test® CARBA 5 lateral flow assay possesses outstanding specificity (100%), sensitivity (98%), and positive predictive value (100%), demonstrating excellent concordance with molecular tests in identifying Enterobacterales that produce carbapenemases, with a rapid turnaround time of approximately 15 minutes. FDA/CE-approved lateral flow tests for detecting phenotypic carbapenemase production offer a swift turnaround time, strong agreement with molecular tests, and userfriendly application for suspected CRE infections in critically ill patients in India [17].

Table 1: CRE Detection techniques for most common carbapenemases.

Carbapenemases with representing gene [18]:

The concise overview of the major carbapenemase families, their associated genes, and the bacterial species in which they originate, highlighting the diverse mechanisms of carbapenem resistance are mentioned in Table 2. This table categorizes the most common carbapenemase enzymes based on the Ambler classification system (A, B, and D) and identifies the corresponding genes and bacterial origins.

Table 2: The Most common Carbapenemases with representing gene in bacteria.

Newer Agents for Management of CRE Infections

Research into novel antimicrobial therapies against carbapenemresistant Enterobacterales (CRE) is a priority, with several new agents either recently approved or currently undergoing development, providing potential advancements in combating these resistant infections.

BETA-LACTAM/BETA-LACTAMASE INHIBITOR COMBINATIONS (Serine Carbapenemase Focus):

Ceftazidime-Avibactam:

Ceftazidime-Avibactam is frequently employed as an initial treatment choice for numerous carbapenem-resistant Enterobacterales (CRE) infections, owing to its extensive activity against a range of carbapenemases. Avibactam, a unique non-beta-lactam beta-lactamase inhibitor, effectively recovers the antimicrobial efficacy of ceftazidime against many CRE isolates, including those producing KPC and certain OXA-type carbapenemases. However, it lacks activity against metalloβ-lactamases (MBLs). A systematic review and meta-analysis published in 2025 highlighted the global trends of CAZ-AVI resistance in Gram-negative bacteria, revealing an increase in resistance proportions from 5.6% in 2015-2020 to 13.2% in 20212024 [19]. CAZ-AVI frequently exhibits synergistic bactericidal activity when combined with other antimicrobials against carbapenem-resistant Gram-negative bacteria. These findings underscore the importance of considering CAZ-AVI in treatment guidelines and emphasize the need for ongoing monitoring to maintain its effectiveness against resistant infections.

Meropenem-Vaborbactam

Vaborbactam, a novel beta-lactamase inhibitor, specifically targets Klebsiella pneumoniae carbapenemase (KPC) enzymes. It effectively restores the activity of Meropenem against KPCproducing carbapenem-resistant Enterobacterales (CRE). Similar to Avibactam, Vaborbactam does not exhibit activity against metalloβ-lactamases (MBLs). Real-world studies have demonstrated both the efficacy and safety of Meropenem-Vaborbactam in treating CRE infections, with clinical efficacy and survival rates, including 30-day and 90-day survival, as primary endpoints [20]. Pooled data revealed a clinical success rate of 75% (95% CI, 66%-82%), with 30-day and 90-day survival rates of 75% (95% CI, 71%-78%) and 69% (95% CI, 61%-76%), respectively [21]. A retrospective, multicenter cohort study comparing Meropenem-Vaborbactam (MEV) to ceftazidime-Avibactam (CZA) in hospitalized adults with serious infections, including sepsis, urinary tract infections (UTIs), complicated intra-abdominal infections (cIAIs), and pneumonia, was conducted [22]. The analysis showed that less than a third of patients received either drug within two days of infection onset (30.6% MEV vs. 33.0% CZA, p = 0.313). MEVtreated patients required mechanical ventilation less frequently than those receiving CZA (35.0% vs. 41.4%, p = 0.010) [22]. Furthermore, MEV treatment was associated with a lower adjusted mortality rate (17.0% [95% CI 13.6%, 20.3%] vs. 20.6% [95% CI 19.0%, 22.2%], p = 0.048) compared to CZA [22].

Aztreonam-Avibactam [23]:

Recently a study examining bacterial isolates from 69 medical centers between 2020 and 2022 evaluated the activity of aztreonamAvibactam, using a fixed Avibactam concentration of 4 mg/L and a susceptibility breakpoint of ≤ 8 mg/L. The findings revealed that aztreonam-Avibactam inhibited 100% of Enterobacterales isolates at ≤ 8 mg/L and 99.9% at ≤ 4 mg/L, demonstrating potent activity against carbapenem-resistant Enterobacterales (CRE) with MIC50/90 values of 0.25/1 mg/L. In comparison, ceftazidimeAvibactam and Meropenem-Vaborbactam exhibited activity against 89.4% and 88.5% of CRE isolates, respectively. The most prevalent carbapenemases identified were KPC (69.2%), NDM (9.6%), and SME (4.8%), with 16.3% of CRE isolates lacking identifiable carbapenemase genes. Ceftazidime-Avibactam and Meropenem-Vaborbactam showed strong activity against KPC and SME producers but limited efficacy against metallo-βlactamase (MBL) producers. Tigecycline (95.2% susceptible), amikacin (73.1% susceptible), and gentamicin (60.6% susceptible) were the most active comparators against CRE. AztreonamAvibactam inhibited 79.1% of Pseudomonas aeruginosa isolates at ≤ 8 mg/L, while 77.2% were susceptible to both Meropenem and Piperacillin-Tazobactum. Furthermore, aztreonam-Avibactam demonstrated significant activity against Stenotrophomonas maltophilia, inhibiting 99.5% of isolates at ≤ 8 mg/L.”

Imipenem-Cilastatin/Relebactam:

Relebactam, a new beta-lactamase inhibitor, expands the antimicrobial spectrum of Imipenem-Cilastatin, providing activity against certain serine carbapenemases. While this combination presents a valuable treatment alternative for carbapenem-resistant Enterobacterales (CRE) infections, its efficacy against metalloβ-lactamases (MBLs) is restricted. A meta-analysis of four randomized controlled trials involving 948 patients found that IMI/REL therapy had similar clinical responses to comparator therapies across various treatment visits, with relative risks (RR) of 1.00 (0.88, 1.12) at discontinuation of intravenously administered therapy (DCIV), 1.00 (0.89, 1.14) at early follow-up (EFU), and 1.00 (0.88, 1.13) at late follow-up (LFU) [24]. Another study on patients with complicated urinary tract infections (cUTI) or acute pyelonephritis showed microbiological response rates of 95.5%, 98.6%, and 98.7% for IMI/REL 250 mg, IMI/REL 125 mg, and IMI/Cilastatin alone, respectively [25]. Additionally, a study on hospital-acquired or ventilator-associated bacterial pneumonia (HABP/VABP) found that clinical response rates were comparable between IMI/REL and piperacillin/Tazobactum across different renal function categories, with a higher response rate (91.7% vs. 44.4%) in patients with augmented renal clearance [26].

BETA-LACTAMASE INHIBITORS (DEVELOPMENTAL):

Zidebactam (with Cefepime) [27]:

Study reported over 97% clinical efficacy in infections caused by carbapenem-resistant Gram-negative pathogens Clinical and Laboratory Standards Institute (CLSI) awarded high susceptibility breakpoints to Zidebactam/Cefepime, indicating its effectiveness against Enterobacterales, Pseudomonas, and Acinetobacter combination is currently undergoing a multinational Phase 3 study, expected to be completed by FY 2025, which will further facilitate its global registration and marketing authorization.

Taniborbactam (with Cefepime) [28]:

The CERTAIN-1 Phase 3 study, which included 661 adult patients with complicated urinary tract infections (cUTI) and acute pyelonephritis, found that CEF/TAN achieved a composite microbiologic and clinical success rate of 70% compared to 58% for meropenem, with a treatment difference of 11.9 percentage points (95% CI, 2.4, 21.6). Another study reported that CEF/TAN was superior to meropenem in terms of composite success at the Test-of-Cure visit, with a difference of 12.6 percentage points (95% CI, 3.1, 22.2). The safety profile of CEF/TAN was comparable to meropenem, with treatment-emergent adverse events occurring in 35.5% of CEF/TAN-treated patients and 29.0% of meropenemtreated patients.

Nacubactam (with meropenem) [29,30]:

The ROSCO Global Surveillance study, which included 4,695 clinical isolates from 50 sites in the United States and Europe, found that MEM/NAC inhibited 99.5%, 99.7%, and 99.9% of Enterobacteriaceae isolates at concentrations of ≤2, ≤4, and ≤8 mg/L, respectively. Another study reported that MEM/NAC displayed MIC ≤8 mg/L for 33 out of 37 CAZ/AVI-resistant multidrug-resistant Enterobacteriaceae isolates.

LYS228 [31]:

It is a Monobactam antibiotic, sharing structural similarities with aztreonam. It maintains activity against metallo-β-lactamases (MBLs) and, through specific structural modifications, also gains activity against serine β-lactamases by targeting penicillin-binding protein 3. Laboratory studies have indicated strong activity against both Class A (KPC) and Class B (NDM) carbapenemases. Pharmacokinetic evaluations have demonstrated a favourable safety and tolerability profile. Although two phase 2 clinical trials were initiated for LYS228, they were subsequently discontinued. Currently, there are no registered clinical trials for LYS228 or its related compound, BOS228.

CEPHALOSPORIN (SIDEROPHORE):

Cefiderocol [32-35]:

Cefiderocol leverages the bacterial iron uptake mechanism to enhance its cellular entry and bypass bacterial resistance. The United States Food and Drug Administration (FDA) granted approval to Cefiderocol in 2019 for the treatment of complicated urinary tract infections (cUTI) and hospital-acquired/ventilatorassociated pneumonia (HAP/VAP). This approval followed successful phase 2 and 3 non-inferiority trials, which compared Cefiderocol to Imipenem-Cilastatin for cUTI and to meropenem for nosocomial pneumonia, respectively, both caused by gramnegative pathogens. Cefiderocol exhibits a strong binding affinity for multiple penicillin-binding proteins, disrupting peptidoglycan synthesis and leading to bacterial cell death. Its safety profile is generally comparable to that of other cephalosporin antibiotics. The CREDIBLE-CR study assessed Cefiderocol’s efficacy in severe carbapenem-resistant infections. However, the FDA label now includes a boxed warning concerning an observed increase in all-cause mortality associated with Acinetobacter infections, specifically in cases of bloodstream infections (BSI), nosocomial pneumonia, and sepsis. The largest European real-world evidence study (PERSEUS) included 261 critically ill adult patients and found an overall clinical success rate of 84.3% and a 28-day all-cause mortality of 21.5%. Another study, the PROVE study, included 244 patients and reported a clinical cure rate of 64.8%, a clinical response rate of 74.2%, and a 30-day in-hospital allcause mortality (IH-ACM) of 18.4%. Resistance to Cefiderocol in Enterobacterales has been observed when both serine and metallobeta-lactamases are co-produced; this resistance mechanism can be potentially circumvented by the addition of Avibactam.

AMINOGLYCOSIDE:

Plazomicin [36-38]:

Plazomicin, a newly developed aminoglycoside, demonstrates antimicrobial activity against certain carbapenem-resistant Enterobacterales (CRE) isolates, including those exhibiting resistance to other aminoglycosides. This agent is less susceptible to specific enzymes that modify aminoglycosides. It displays a broad spectrum of activity against Enterobacterales, encompassing strains with extended-spectrum beta-lactamase (ESBL) enzymes and various CRE classes, such as Class A (KPC), Class B (VIM, IMP), and Class D (OXA-48). However, its clinical effectiveness may be reduced in regions with a high prevalence of NDM-1-

producing CRE, due to its variable activity against these strains. The CARE trial, a multicenter, randomized, open-label trial, evaluated Plazomicin compared to colistin for serious CRE infections. The study included 39 patients, with 18 receiving Plazomicin and 21 receiving colistin. The primary endpoint event occurred in 24% of patients receiving Plazomicin compared to 50% of those receiving

colistin, with a difference of -26 percentage points (95% CI, -55 to 6). Among patients with bloodstream infections, the primary endpoint event occurred in 14% of patients receiving Plazomicin compared to 53% of those receiving colistin, with a difference of -39 percentage points (95% CI, -69 to -4). Another meta-analysis of three randomized controlled trials involving 761 patients found that Plazomicin had a clinical remission rate similar to comparators (OR, 1.02; 95% CI, 0.60–1.73) and a lower microbiologic recurrence rate (OR, 0.38; 95% CI, 0.17–0.86) Resistance to Plazomicin can occur through modifications mediated by 16S ribosomal methyltransferases, and bacteria harboring these resistance genes can facilitate their horizontal transfer.

Table 3: Summary of Newer Antimicrobial to Manage CRE Infections.

Table 4: Summary of Antibiotic (Combination) Positioning For Different Types Of Carbapenemase Enzymes