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Multidrug-Resistant
I n f e c t i o n s i n C y s t i c F i b ro s i s
Thomas S. Murray, MD, PhDa,*, Gail Stanley, MD
b,c,d,
*,
Jonathan L. Koff, MDc,d,e,*
KEYWORDS
Cystic fibrosis Multidrug-resistant organisms Bacteriophage Gallium
KEY POINTS
Despite the introduction of cystic fibrosis transmembrane conductance regulator (CFTR)
modulator therapy, multidrug-resistant organism (MDRO) pulmonary infections remain a
significant problem for patients with cystic fibrosis (CF), and new therapeutic strategies
are needed.
Standard antibiotic dosing regimens may produce subtherapeutic levels for patients with
CF, as the pharmacokinetics/pharmacodynamics often differ from patients without CF.
Novel therapies, such as gallium and bacteriophage(s), are emerging as exciting options
to treat MDRO infections but additional studies are required to determine the optimal
dosing, and patient populations, which will benefit the most.
INTRODUCTION
Chronic Multidrug-Resistant Organism Infections in Cystic Fibrosis
Patients with cystic fibrosis (CF) are colonized early in life with bacteria and treated
with repeated cycles of antibiotics. This leads to the emergence of pathogenic
chronic multidrug-resistant organism (MDROs), defined as microorganisms resistant
to one or more different classes of antibiotics.1 Organisms that are problematic
This article was previously published in Clinics in Chest Medicine 43:4 December 2022.
a
Department of Pediatrics, Section Infectious Diseases and Global Health, Yale University
School of Medicine, PO Box 208064, 333 Cedar Street, New Haven, CT 06520-8064, USA;
b
Department of Internal Medicine, Section Pulmonary, Critical Care and Sleep Medicine, Yale
University School of Medicine, PO Box 208057, 300 Cedar Street TAC-441 South, New Haven, CT
06520-8057, USA; c Adult Cystic Fibrosis Program; d Yale University Center for Phage Biology &
Therapy; e Department of Internal Medicine, Section Pulmonary, Critical Care and Sleep
Medicine, Yale University School of Medicine, PO Box 208057, 300 Cedar Street TAC-455A
South, New Haven, CT 06520-8057, USA
* Corresponding authors.
E-mail addresses: Thomas.s.murray@yale.edu (T.S.M.); gail.stanley@yale.edu (G.S.); jon.koff@
yale.edu (J.L.K.)
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150 Murray et al
include, but are not limited to, the gram-positive methicillin-resistant Staphylo-
coccus aureus (MRSA), and a variety of gram-negative organisms that include
Pseudomonas aeruginosa, Burkholderia sp., Stenotrophomonas maltophilia, Achro-
mobacter xylosoxidans, and nontuberculous mycobacteria (NTM). In 2019, 16.9% of
P. aeruginosa infections in patients with CF were multidrug-resistant (MDR), while
more than 50% of patients had a respiratory culture that grew MRSA.2 As highly
effective cystic fibrosis transmembrane conductance regulator (CFTR) modulator
therapy is introduced at younger ages, there is optimism that this will reduce the inci-
dence and/or severity of chronic infections and decrease the acquisition of new
pathogens.3,4 However, this is tempered by the observation that while the initiation
of ivacaftor initially leads to decreases in P. aeruginosa, this effect is not maintained
long term.5 In addition, for some individuals with CF currently on CFTR modulator
therapy, evidence suggests there is little change to the microbes in the airway.6
Therefore, antibiotics remain integral to treatment regimens during pulmonary exac-
erbations,4 and novel antimicrobial approaches or interventions are needed to treat
these infections.
Several different therapeutic approaches have been tried in recent years to improve
outcomes for patients with CF with chronic MDRO pulmonary infection (Table 1). One
such approach is to improve the efficacy of existing antibiotics by optimizing the phar-
macokinetics/pharmacodynamics (PK/PD), which may be achieved by altering the
dosing regimen.7 Another strategy to extend the benefits of a currently available
drug (eg, vancomycin, ciprofloxacin, levofloxacin, and amikacin), is to develop an
inhaled formulation that allows for higher concentrations in the lung while reducing
systemic adverse effects.8–10 Finally, existing beta-lactam drugs, such as ceftazidime
and meropenem, have been combined with novel beta-lactamase inhibitors to create
new drugs that target gram-negative MDROs that produce extended-spectrum beta-
lactamases (ESBLs) and carbapenemases.11
While optimizing the delivery of existing drugs has been helpful, it is not surprising
that resistant organisms continue to emerge. The above approaches also highlight
the limitation of the existing antibiotic pipeline where few new drugs with
novel mechanisms of action have been introduced in recent years. The result is inno-
vative therapies currently being studied that either: (1) target the host to improve the
immune response to infection [for example, granulocyte macrophage-colony stimu-
lating factor (GM-CSF)] or (2) target the organism with a completely different class
of molecule(s) that have antimicrobial activity (eg, gallium or bacteriophages).
DISCUSSION
Optimizing the Pharmacokinetics/Pharmacodynamics of Available Antibiotics
Based on pancreatic insufficiency and impaired gastrointestinal tract absorption,
increased renal and hepatic drug clearance, and increased volume of distribution of
hydrophilic drugs12–14 standard antimicrobial dosing may not be appropriate for pa-
tients with CF as they require higher and/or more frequent drug administration to
achieve therapeutic levels.15–17 One review of anti-MRSA agents found that for both
intravenous (IV) and oral administration, none of the currently recommended doses
for any of the studied drugs achieved therapeutic levels for a sufficient time.15 In
each case either a higher dose or more frequent dosing was recommended to achieve
the required minimum inhibitory concentrations (MICs) for the appropriate time. For
certain beta-lactam antibiotics, such as meropenem, continuous infusions increase
the time the drug concentration is above the MIC, which increases drug activity
against isolates with higher MICs.17,18 These data highlight the importance of studying
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Table 1
Novel approaches to treat MDRO infections in patients with CF
151
152 Murray et al
the PK/PD of novel antimicrobials in CF children and adults as they come to market
because suboptimal dosing will potentially select for resistant strains.19
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Multidrug Resistant Infections in CF 153
negatives but very little data are available to support its use in CF.35 One study of 8
patients with CF who received 12 courses of cefiderocol for MDR A. xylosoxidans
noted a clinical response after 11/12 (91.7%) courses, but only one patient cleared
the infection.36 Additional studies are needed to determine if there is a role for cefider-
ocol when other agents have failed to generate a clinical response.
Although the correlation between in vitro antibiotic resistance and clinical outcomes
is often absent in CF,37,38 it is important to note that variable rates of in vitro resistance
have been described for all of the above antibiotics.11,25,27,39 Mechanisms of resis-
tance to these agents include, but are not limited to, increased activity of efflux pumps,
porin mutations, and overexpression of the AmpC beta-lactamase.11,40 Additionally,
none of the currently available new beta-lactam/beta-lactamase inhibitors bind class
B metalloprotease b-lactamases, such that isolates with these enzymes will remain
resistant.11
Methicillin-Resistant S. aureus
Fewer new agents have been developed in recent years for MRSA treatment. Ceftaro-
line is a fifth-generation IV cephalosporin that targets the penicillin-binding protein 2A,
which confers methicillin resistance to S. aureus. As with other antimicrobials, the PK/
PD of ceftaroline in CF may require nonstandard dosing to achieve therapeutic
levels.15,41 There are little data for the use of ceftaroline to treat MRSA-associated pul-
monary exacerbations.42,43 One retrospective study of 90 patients with CF who
received ceftaroline compared with 90 patients treated with vancomycin showed no
difference in forced expiratory volume in 1 second (FEV1), which suggested equiva-
lence between the 2 drugs.42 Thus, ceftaroline may be an option for patients with renal
dysfunction or those who are unable to tolerate vancomycin for other reasons. Impor-
tantly, carbapenem use in patients with CF has been linked to ceftaroline resistance,
which makes susceptibility testing a consideration for patients who have previously
received carbapenems for MDR gram-negative organisms.44
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154 Murray et al
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Multidrug Resistant Infections in CF 155
after 48 weeks) showed that no significant sputum culture conversions occurred in the
inhaled GM-CSF group. Based on these results, the use of inhaled GM-CSF in CF for
NTM has been discontinued.
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156 Murray et al
find naturally occurring phages that infect bacterial pathogens of interest. In addition,
phages can be genetically engineered to be used therapeutically.72
It is important to note that there are limited data on the safety and efficacy of phage
therapy in traditionally defined clinical studies. However, the Eliava Institute in Georgia
and the Ludwik Hirszfeld Institute in Poland have provided phage therapy to many pa-
tients.73 There is an increasing experience in the United States with FDA-approved
compassionate cases and clinical trials,70 although early attempts to show phage
therapy efficacy in randomized clinical trials have been largely unsuccessful. The
lack of efficacy in clinical trials may be attributed to poor study design, challenges
in phage stabilization, or administration of phage at concentrations too low to be ther-
apeutically active. One hypothetical concern with phage therapy is a toxic response
caused by target pathogen lysis that releases bacterial toxins (eg, lipopolysaccharides
and other virulence factors) that could trigger an inflammatory response. It is important
to highlight that this effect has not been observed in animal studies of phage therapy.
Notably, studies have shown that exposure to clinically relevant beta-lactam antibi-
otics leads to a higher release of bacterial endotoxin compared with phages.74
Specific to CF, there are case reports of the addition of phage therapy to standard
clinical care in compassionate cases.75 These include pediatric and adult patients
whereby phage therapy was delivered either via nebulization or IV to target bacteria
such as P. aeruginosa, S. aureus, or A. xylosoxidans.75 Since the publication of these
reports, interest in phage therapy in the United States has increased with several
phage therapy programs starting or expanding [Tailored Antibacterials & Innovative
Laboratories for Phage Research (TAIL4R) at Baylor University, Army & Navy Labora-
tories, Mayo Clinic, Center for Phage Technology (CPT) at Texas A&M University, Cen-
ter for Innovative Phage Applications & Therapeutics (IPATH) at University of
California, San Diego, University of Pittsburgh (expertise in NTM phage), Center for
Phage Biology & Therapy at Yale University]. Current or planned clinical trials to inves-
tigate phage therapy to treat P. aeruginosa are independently investigating single
phage (clinicaltrials.gov NCT04684641) or phage cocktails (multiple phages given at
the same time; clinicaltrials.gov NCT04596319 & NCT05010577), and different routes
of administration (eg, nebulized vs IV).
It will be important to study each of these approaches. For example, while phage
cocktails may provide a broader range of coverage for a specific bacterium, there is
evidence that cocktails may increase genetic mutations in P. aeruginosa that could
result in increased virulence.76 Such an effect will need to be investigated in clinical
strains of P. aeruginosa and other bacteria. In addition, there is evidence that multiple
phages may interfere with phage replication within the same bacteria, potentially
reducing the effectiveness of phage therapy.77 However, single phage therapy may
be limited by evolving bacterial resistance.78 Recognizing that bacteria continue to
evolve resistance to phage(s), investigators have developed a strategy to identify
phages that target specific virulence factors on bacteria so that the result of phage
therapy are surviving bacteria mutants with decreased expression or production of
such virulence factors.66 For example, phage therapy targeting P. aeruginosa anti-
biotic efflux pumps, responsible for resistance to multiple antibiotics, restored anti-
biotic susceptibility79 and was reported in a compassionate use case to treat an
infected aortic graft.80 Compassionate use of phage therapy in patients with CF is per-
formed by a few centers in the United States targeting MDR P. aeruginosa,
A. xylosoxidans and NTM.72 Currently a phase 2 randomized, double-blinded, sin-
gle-site clinical trial studying the safety and effectiveness of single nebulized phage
therapy is enrolling patients with CF with P. aeruginosa (clinicaltrials.gov
NCT04684641).
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Multidrug Resistant Infections in CF 157
Gallium and phage therapy are examples of additional strategies to treat MDR bacteria.
Continued well-designed and executed clinical trials are required to confirm initial
observations.
Compassionate treatment may be available for these types of therapies for carefully selected
candidates.
SUMMARY
While MDRO infections have recently been recognized as an emerging global threat, in-
dividuals with CF, and their care teams, have been challenged with the complexities
involved in the clinical care of MRSA, P. aeruginosa, Burkholderia sp., S. maltophilia,
A. xylosoxidans, and NTM for far too long. While we await the discovery and development
of additional antimicrobials with novel mechanisms of action, this article summarizes ap-
proaches that have been used to: (1) optimize the PK/PD of existing antibiotics, (2) admin-
isternew antibiotic combinations, and (3) repurpose existing antibiotics into inhaled
formulations. However, because MDROs continue to evolve, additional approaches
are required beyond the existing antibiotic pipeline. Novel approaches include: (1) target-
ing the host to improve the immune response(s) to infection [for example, GM-CSF] or (2)
targeting the pathogen with a completely different class of molecule(s) that have antimi-
crobial activity (eg, gallium or bacteriophages). These approaches require additional clin-
ical studies before they can be considered for routine clinical use.
FINANCIAL SUPPORT
DISCLOSURE
T.S. Murray-none. J.L. Koff is the PI for bacteriophage clinical trial NCT04684641 and
a national Co-PI for bacteriophage clinical trial NCT05010577. J.L. Koff & G.L. Stanley:
Colleagues at Yale University have licensed intellectual property related to bacterio-
phage therapy to a company although neither J.L. Koff nor G.L. Stanley has a financial
interest in this process.
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158 Murray et al
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