NDM-Producing E coli Harboring PBP Insert Variants Emerges as New Threat

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New Delhi metallo-β-lactamase (NDM) was first detected in 2009 in Klebsiella pneumoniae.¹ Since then, the bla_NDM genes, responsible for encoding NDM-type enzymes, have been identified in Acinetobacter, Pseudomonas, and, most commonly, Escherichia coli and other Enterobacterales bacteria. As with other metallo-β-lactamases (MBLs), NDM is capable of hydrolyzing nearly all β-lactams, including carbapenems but notably not aztreonam. Data from the Centers for Disease Control and Prevention from 2017 to 2019 revealed that nearly 9% of all carbapenem-resistant Enterobacterales and approximately 1% of Pseudomonas isolates in the US harbored bla_NDM, a figure expected to increase over time.²

The emergence and dissemination of NDM are facilitated by various factors, including increased global travel, widespread antibiotic usage, and inadequate infection control measures in health care settings.³ The Infectious Diseases Society of America recommends β-lactam antibiotics as a treatment option for NDM-producing organisms, specifically ceftazidime/avibactam in combination with aztreonam or cefiderocol as monotherapy.⁴ Cefiderocol is a novel siderophore-conjugated cephalosporin that harnesses the bacterial iron transport system to access the periplasmic compartment. Cefiderocol is stable to hydrolysis by a broad array of β-lactamases, including MBLs.⁵ In the CREDIBLE - CR study (NCT02714595), cefiderocol was seen to be effective in the treatment of organisms producing MBLs.^6,7 Although aztreonam itself is active against MBL-producing organisms due to stability to hydrolysis by MBLs,^8,9 it remains susceptible to hydrolysis by extended-spectrum β-lactamases, AmpC β-lactamases, KPCs, or OXA-48–like carbapenemases, which are commonly coproduced alongside NDMs.⁹ Partnering aztreonam with an inhibitor of these enzymes, such as avibactam, prevents hydrolysis of aztreonam and allows for activity against MBL-producing organisms. Indeed, aztreonam paired with ceftazidime/avibactam is highly effective in the treatment of infections caused by MBL-producing organisms.¹⁰ However, emerging resistance to these frontline treatment options poses a growing challenge in managing infections caused by NDM-producing organisms, complicating treatment strategies.³

β-lactam antibiotics exert bactericidal effects by disrupting the formation of bacterial cell walls through covalent binding to crucial penicillin-binding proteins (PBPs). These enzymes play a vital role in the final stages of peptidoglycan cross-linking. In gram-negative bacteria, crucial PBPs are PBP1a and PBP1b, which participate in cell lysis; PBP2, whose inhibition halts cell division; and PBP3, whose inhibition arrests cell division, causing filamentation. Inhibition of 1 or more of these PBPs can lead to cell death.¹¹ Cephalosporins preferentially target PBP3 and PBP1a, whereas aztreonam binds exclusively to PBP2, PBP3, and PBP4. Resistance to β-lactams in Enterobacterales, including to cefiderocol, is often mediated through β-lactamases, which hydrolyze the functional β-lactam ring and prevent binding to PBPs.¹² However, NDM-5–producing E coli bacteria harboring PBP3 variants, specifically YRIN or YRIK insertions after residue 333 (333YRIN/K334), are increasingly prevalent worldwide and account for nearly a quarter of NDM-producing E coli bacteria in India.^13-15 Additionally, E coli bacteria that carry PBP3 variants frequently harbor variants of CMY-42, a transferable AmpC enzyme.¹⁶ Together, these mechanisms lead to dramatically increased minimum inhibitory concentrations (MICs) to both aztreonam/ avibactam and cefiderocol.^13-15,17-19 Concerningly, these enzymes and PBP mutations are now frequently identified in a successful E coli clone, ST167, which has begun to spread globally.²⁰ Sadek et al completed whole-gene sequencing of 19 NDM-producing E coli isolates exhibiting high MICs for aztreonam/avibactam (> 4 μg/mL). All the isolates had either a 333YRIK or YRIN334 insertion, with YRIN being more commonly observed.²¹

Additionally, each isolate carried a plasmid-borne CMY β-lactamase gene, most commonly CMY-42. The MIC of aztreonam/avibactam was 4-fold higher for the CMY-42–producing isolates compared with CMY-2. Livermore et al specifically assessed the independent contribution of different insert variants and CMY enzymes to the aztreonam/ avibactam MIC.¹⁹ Isolates harboring YRIN were typically less resistant than those harboring YRIK, with MICs generally in the range of 0.5 to 2 μg/mL for those harboring YRIN vs at least 8 μg/mL for those harboring YRIK. CMY-42 and other CMY variants led to an additional increase in MIC of 1- or 2-fold relative to isolates with the insertion alone.

Mutations in PBPs pose a relatively unique challenge in antimicrobial drug development. In contrast to β-lactamase– mediated resistance, where addition of a β-lactamase inhibitor allows for restoration of activity for the parent compound, this approach does not work for PBP mutations. The addition of a β-lactamase inhibitor alone does not restore activity of the partner β-lactam compound due to the presence of non–β-lactamase–mediated resistance. For example, cefepime/ taniborbactam is a broad-spectrum cephalosporin/ boronic acid–based β-lactamase inhibitor in late-stage development specifically for the treatment of MBL-producing organisms.²² Although taniborbactam usually readily inhibits most NDM variants, inhibition of NDM-5 is insufficient to restore activity of cefepime/taniborbactam against PBP3 mutations due to inability of cefepime to bind to PBP3.^23,24 This is in contrast to organisms harboring NDM-9 or NDM-30, which are NDM variants resistant to inhibition by taniborbactam. In these isolates, cefepime is hydrolyzed before it has the opportunity to interact with PBP3. Therefore, the activity of any MBL-active β-lactamase inhibitor combination will depend not only on the spectrum of the inhibitor but also on the PBP-binding spectrum of the parent β-lactam compound and specifically inhibition of PBPs other than PBP3.

Several such compounds are in development or commercially available. Among these, the compound with the longest track record of use is mecillinam or the oral prodrug pivmecillinam. Mecillinam is a β-lactam that inhibits PBP2 and is widely used in Scandinavia for treatment of urinary tract infection. Pivmecillinam was recently approved by the US Food and Drug Administration in the US for treatment of uncomplicated urinary tract infection.²⁵ Mecillinam is generally active against a broad array of β-lactamase– producing Enterobacterales bacteria, including those producing NDM enzymes.²⁶ Zidebactam, a novel diazabicycloooctane (DBO) β-lactamase inhibitor, serves a dual role as both a broad-spectrum inhibitor of serine β-lactamases and β-lactam enhancer due to its complementary inhibition of PBP2.²⁷ Cefepime/ zidebactam is highly active in vitro against NDM-producing E coli bacteria harboring PBP insert variants.^28,29 Durlobactam, another broad-spectrum DBO inhibitor, is similarly active against NDM-producing E coli bacteria with PBP inserts, although whether it has an enhancer effect similar to zidebactam is presently unknown.^30,31 Historically, rapid development of resistance to PBP2 inhibitors has been a significant concern, and thus, any successful use of these compounds is likely dependent on partnering with a drug with some residual inhibition of PBP3 or other PBPs, such as carbapenems or aztreonam.³²

In conclusion, the emergence and spread of NDM-producing organisms harboring PBP insert mutations pose significant threats to existing therapeutics. Efforts to address PBP-mediated resistance require a multifaceted approach, encompassing enhanced surveillance, stringent infection control measures, and the development of novel therapeutics targeting resistance mechanisms. Furthermore, continued research into the molecular basis of resistance and the identification of new drug targets are essential to stay ahead of antimicrobial resistance.

References

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