Researchers have successfully used bacteriophages to treat an antibiotic-resistant mycobacterial lung infection


For the first time, researchers have successfully used bacteriophages – viruses that kill bacteria – to treat an antibiotic-resistant mycobacterial lung infection, clearing the way for a young National Jewish Health patient with cystic fibrosis to receive a life-saving lung transplant.

The successful use of phages to treat a Mycobacterium abscessus lung infection was reported in a case study published today in the journal Cell.

“We had tried unsuccessfully for years to clear the mycobacterial infection with a variety of antibiotics,” said Jerry Nick, MD, lead author on the study and director of the Adult Cystic Fibrosis Program at National Jewish Health. “When we used the bacteria’s own natural enemies, we were able to clear the infection which resulted in a successful lung transplant.”

“I am so grateful for the effort, persistence and creativity of all the people who were involved in my treatment,” said Jarrod Johnson, recipient of the lung transplant. “I thought I was going to die. They have literally saved my life.”

Cystic fibrosis is an inherited disease that causes a buildup of thick mucus in the lungs, leading to repeated bacterial infections that damage the lungs and can cause respiratory failure. Although new treatments have greatly improved the prognosis for people with cystic fibrosis, life expectancy still remains significantly reduced.

Mycobacteria are a common and widespread genus of bacteria that can cause tuberculosis, leprosy and nontuberculous mycobacterial (NTM) infections. Mycobacterium abscessus is a particularly aggressive and challenging NTM infection. Combinations of multiple antibiotics and treatment extending a year or longer are often unsuccessful. National Jewish Health has the largest adult Cystic Fibrosis Program in the country and is a leading center for treatment of NTM infections.

Johnson is a 26-year-old cystic fibrosis patient who has suffered repeated lung infections throughout his life. As a child, he was admitted to various hospitals several times a year. As an adult, he experienced a rapid decline in his lung function following a persistent Mycobacterium abscessus infection over a six-year period and received a number of unsuccessful treatments.

By 2020, his lung function had fallen below 30%. Without a lung transplant, doctors felt he was likely to die in only a few years.

Johnson had been refused transplants by three transplant centers, primarily because of his mycobacterial infection. Mycobacteria can spread from the lungs to the skin and other tissues, which can plague transplant recipients on immunosuppressive medications. Dr. Nick and his team at National Jewish Health considered phages as a potential treatment option. Johnson was hospitalized at Saint Joseph Hospital in Denver, where he spent more than 200 days the year before receiving phage treatment.

Bacteriophages – or phages, for short – are viruses that attack bacteria. Interest in using them to treat bacterial infections has grown in recent years as more and more bacteria have become resistant to antibiotics. Graham Hatfull, Ph.D., professor of Biological Sciences at the University of Pittsburgh and an author in the study, is a leader in discovery and use of phages to treat mycobacterial infections, and provided the phages used to treat Johnson.

Phages are often specific for only a few types of bacteria. In 2016, Dr. Nick and his colleagues sent samples of the Mycobacterium abscessus from Johnson’s lungs in search of a phage that could kill the mycobacterium. Dr. Hatfull and his team in Pittsburgh screened dozens of phage candidates and identified two that efficiently killed the mycobacterium infecting Johnson’s lungs. These were genetically engineered to optimize their potential.

“This research can serve as a roadmap for future use of phages to treat patients with severe Mycobacterium abscessus lung infection and to save lives,” said Dr. Nick.

Doctors at National Jewish Health received authorization from the U.S. Food and Drug Administration for compassionate use of the experimental treatment. Johnson received his first infusion of phages in September 2020, followed by 500 days of twice-daily infusions. Within two months, a variety of genomic, cell culture and clinical markers indicated that the treatment was succeeding. Just over a year after the phage treatment began, Johnson’s infection appeared to have cleared.

Alice L. Gray, MD, Medical Director of the University of Colorado Lung Transplant Program believed the transplant was now safe and placed him on the active list. He received his new lungs in October 2021 at the UCHealth Transplant Center, and in collaboration with Dr. Gray, remained on phage therapy throughout the procedure and during his recovery. A range of markers has indicated no evidence of the infection following the transplant. Johnson has now discontinued all treatment for Mycobacterium abscessus and is living a normal life.

Two other successful responses of severe Mycobacteria infection to phage have been reported by Dr. Hatfull’s team at the University of Pittsburgh. These cases were related to patients primarily with skin infections. The use of phages to treat a broader spectrum of patients will help to determine the roles of antibodies and phage resistance, guided by these successful case studies.

Bacteriophages as a Treatment Option for Mycobacterial Infections

Antibiotic resistance is becoming a major public health issue throughout the world. The spread of multidrug-resistant (MDR) bacteria is a threat to human health and extensive antibiotic resistance has developed in various bacteria, including mycobacteria, due both to innate resistance in some species and the fact that some bacteria are highly adept at acquiring antibiotic-resistant determinants from each other or during treatment [37].

Bacteriophages have been proposed for decades for the treatment of common bacterial infections, but mycobacterial infections have generally been excluded [38]. We can only speculate that the availability of effective oral antimycobacterial drugs and the prolonged length of treatment for most of mycobacterial infections did not make intravenous mycobacteriophages an appealing field to be pursued.

With the rise of drug resistance, their clinical utility has been re-discovered and their use has been successfully demonstrated, both as treatment options, but also as possible alternatives for the disinfection of water systems, in animal health and in the food industry [39,40,41,42]. Phage preparations have successfully been approved for use against Escherichia coli and Listeria monocytogenes in meat contamination [43].

Although phages have been extensively used therapeutically in former Soviet Union countries, their clinical use in the Western world is generally case-by-case, under the compassionate use route, when all other treatment options have failed. There have been no commercial preparations and there are no standard regulations on their use in the United States, leaving the choice of phage treatments as the last resort for very few desperate cases and relying on the ability and connections of clinical teams to source them.

The first patient treated with intravenous phage therapy in the United States suffered from a systemic infection caused by a multidrug-resistant Acinetobacter baumannii, although a complete recovery was achieved [44]. Some case series on the compassionate use of phage therapy (PT) in Europe have also highlighted significant clinical improvement in the infections after phage treatment [45,46], and clinical trials on the use of PT to treat chronic otitis and other infections caused by Pseudomonas aeruginosa, Staphylococcus aureus and Enterobacterales have been published, with promising results [47,48,49]. However, the use of mycobacteriophages (phages active against different mycobacterial species) is still very limited, and no clinical trials have been reported to date.

Mycobacterium spp. belong to the family Mycobacteriaceae of the class Actinobacteria. The taxonomy of mycobacteria is regularly updated, and the most recent classification was released in 2017 with over 170 recognized species [50]. Based on phenotypic and genetic differences, the genus can be classified into two main groups: slowly growing mycobacteria, including Mycobacterium tuberculosis complex; and rapid growers, NTMs, that are generally environmental organisms that cause opportunistic infections [51].

The worldwide impact of TB has already been mentioned. Other NTM infections are also increasing worldwide, due to the expanding numbers of immunocompromised individuals (including those with HIV infection and hematological disorders), as well as patients with cystic fibrosis (CF) and chronic lung disorders [52,53]. Among the various NTMs, the MAB complex comprises a group of rapidly growing, multidrug-resistant mycobacteria that are responsible for a wide spectrum of skin and soft tissue diseases, lung and central nervous system infections, bacteremia, ocular and other infections. These infections are often problematic and difficult to treat, due to the innate resistance of MAB to many antibiotics [54,55]. Typically, patients are treated with last-line antibiotics that have extreme toxicities for an extended amount of time (~12 months) and, in many cases, they cannot tolerate the side-effects of these drug regimens.

Phage activity has been successfully demonstrated against different mycobacterial species, including M. abscessus [56], M. ulcerans [57], M. avium and M. tuberculosis [58,59,60]. However, most of the data is based on laboratory and animal models and reports of clinical cases are very scant thus far. The first clinical case of phage treatment (PT) against drug-resistant MAB was a 15-year-old patient suffering from cystic fibrosis, who had a double lung transplant and persistent disseminated infection [61].

The treatment consisted of a cocktail of three different phages administered intravenously (IV), two of which were temperate and genetically engineered to convert into lytic phages, twice daily, at 109 PFU/dose [61]. Most importantly, the administration of the phage IV was safe, with no toxicities or side-effects. After 6 weeks of treatment, complete resolution of an infected liver node was seen, along with an increase in the patient’s weight and lung function.

Skin nodules were slower to improve. After 121 days of treatment, the patient’s MAB isolates were still susceptible to each of the three phages in the cocktail, and a neutralizing immune response was not seen. In a more recent case study, using the same three-phage cocktail, a phage-neutralizing antibody response was demonstrated to be the cause of phage treatment failure [62].

The patient, an immunocompetent 81-year-old male with MAB lung disease, was given the cocktail IV twice daily at 109 PFU/dose. Colony-forming unit (CFU) counts from sputum revealed a 1-log decrease in MAB after one month of PT. However, MAB CFU then increased steadily from two to six months of PT. The patient’s MAB samples were still fully susceptible to two of the phages used in the cocktail, but had an intermittent 1–2 log decrease in susceptibility to one phage. Patient serum revealed a strong neutralizing antibody response to all three phages in the cocktail, which was further analyzed using ELISAs and found to be primarily IgG-mediated [62].

PT for patients with MAB infections is complicated, because strain variability is extensive [62] and phage susceptibility is unpredictable due to MAB variations. Dedrick et al. [62] found that colony morphotypes (smooth or rough) influence phage susceptibility, because smooth isolates are more resistant to phage infection. Additionally, clinical MAB isolates have various prophages (1–6 per strain) integrated into their genomes, which can influence phage susceptibility due to phage defense systems [63,64].

A recent review of all the clinical requests for PT at the Center for Innovative Phage Applications and Therapeutics (IPATH) in San Diego showed that over a two-year period, there were 90 requests for PT against different mycobacterial infections (47 M. abscessus, 23 M. avium, 7 M. chimaera, and 13 other Mycobacterium species, including M. chelonae, M. smegmatis, M. xenopi, and M. genavense). However, PT was approved and administered to only four patients with M. abscessus infection (with a further three patients pending administration at the time of publication) and only one patient with M. chimaera [65]. In all cases, PT was given intravenously with topical administration in patients with skin lesions.

Antibiotic resistance in M. tuberculosis is certainly a growing concern, particularly with the emergence of extensively drug-resistant (XDR) and totally drug-resistant (TDR) strains. Successful XDR-TB treatment, particularly in resource-limited settings, may be very challenging. In a 2006 XDR-TB outbreak in KwaZulu-Natal, South Africa, 52 of 53 people who contracted the disease died within months [66], even with survival rates significantly improving in more recent years [67]. Delivery of phages to the lungs could benefit from aerosolization; however, it is uncertain whether phages could target intracellular or intra-granuloma M. tuberculosis as well as extracellular M. tuberculosis [68]. Although phages may not be taken up directly by macrophages, they may be dynamically cycled among the broader population by piggybacking on the natural bacterium–macrophage dynamics [69].

The use of a nonvirulent mycobacterium, specifically, M. smegmatis, has been proposed as both a potential delivery system (carrier) and as a bacterial host that can lead to the high proliferation of bacteriophages [60]. Recently, some authors have demonstrated that a cocktail of three to five different mycobacteriophages was effective against M. smegmatis under low-pH, hypoxic and stationary conditions (mimicking the granuloma) and showed synergy with rifampicin.

Similarly, they have found that three mycobacteriophages (DS6A, D29 and TM4) were also able to prevent the growth of M. tuberculosis [59]. The same D29 mycobacteriophage (already mentioned for diagnostic testing and treatment option) has also been proposed as potential prophylaxis to prevent tuberculosis in the mice model with an optimized inhalation device. The bacteriophage aerosol pre-treatment significantly decreased the M. tuberculosis burden in mouse lungs at 24 h and 3 weeks post-challenge [70,71].

In addition to the phages already mentioned, other bacteriophages have also been investigated against M. tuberculosis as therapeutic options (including phages TM4, T7, P4, PDRPv, BTCU-1, Bo4, SWU1, GR-21/T, My-327, Ms6 and Bxz2) [72]. More recently, colleagues from Pittsburgh have assembled a five-phage cocktail that minimized the emergence of phage resistance and cross-resistance to multiple phages (AdephagiaΔ41Δ43, D29, FionnbharthΔ45Δ47, Fred313_cpmΔ33, and Muddy_HRMN0157-2), and which efficiently killed a series of M. tuberculosis reference strains representing its common lineages [58].

Other authors have also been successful in encapsulating mycobacteriophages into giant liposomes and showing their uptake into eukaryotic cells more efficiently than free bacteriophages [73]. This could represent an ideal formulation for inhaled administration, as recently demonstrated for liposomal amikacin in the treatment of NTM lung infection [74].

The administration of treatment, the need for multiple active phages and the potential development of resistance are only some of the multiple challenges that phage therapy against mycobacterial infections still needs to overcome [42] (Table 2). More than 18,000 actinobacteriophages have been described; the selection of an active phage is a laborious process [75].

Due to phage specificity, tailored treatments are necessary and very few centers in the world are able to perform this personalized manufacturing, causing significant delays from request to administration. Resident prophages may strongly influence the phage infection profiles and influence which phages are therapeutically useful [63], and some bacterial strains, such as the smooth morphotypes of M. abscessus, may be intrinsically resistant [56].

The production of neutralizing antibodies to the phages can also significantly limit their therapeutic efficacy. All bacteriophages are capable of inducing a specific antibody response (IgM and IgG), as demonstrated in animal models and as observed in humans. These antibodies might impact phage bioavailability, although further in vivo studies are needed to assess the impact on treatment outcomes [76]. Hence, the selection process of active phages is far from an easy task.

Table 2 – Challenges of phage therapy against mycobacterial infections, from the selection of phages, the necessary regulatory approvals and treatment considerations.

Challenges of Phage Therapy Against Mycobacterial Infections
Selection of phagesLaborious screening process of thousands of different phages
A cocktail of 3 to 6 active phages may be needed
Few centers in the world are able to perform this personalized manufacturing
AdministrationIntravenous route for disseminated infection is required
Topical administration for skin lesion is easily performed
Still under development:
Use of a nonvirulent mycobacterium as carrier to reach the lung
Liposomal formulations for inhalation in case of lung infection
Development of resistanceIntrinsically resistance strain (i.e., smooth morphotype of M. abscessus)
Acquired resistance after treatment/bacterial defense mechanisms
Production of neutralizing antibody against the phages
Regulatory processEach clinical case required multiple local approvals, including ethical committee and national approval body
Genetic characterization of the phage(s), sterility of the final product and minimal endotoxin concentration required prior to approval

It is important to note that the concept of phage resistance is different from the mechanisms of resistance against antibiotics. For example, the phage resistance in vitro is very pathogen and phage-specific, and it is not widely transferable, such as the extended-spectrum-β-lactamase resistance observed in Gram-negative bacteria [77]. For MAB, it has been observed at a very low level [56] and it may lead to different degrees of resistance in vivo relative to in vitro. It can be hypothesized that phage-resistant mutants of M. tuberculosis might be less fit due to a loss of virulence.

This will inevitably influence therapeutic strategies, where phage monotherapy may be plausible without resistance being a major concern in MAB, but the impact of PT on M. tuberculosis still needs to be assessed in clinical practice. If the development of resistance in TB is not going to be a relevant problem, it raises the possibility of using phages for long-term treatments, where the goal is to suppress active disease and dissemination rather than to effect a ‘cure’ as the outcome in MDR compassionate cases or where nebulized bacteriophages can be used as an adjuvant strategy in addition to antibiotics with the aim of shortening the overall length of treatment to only few months.

It is also important not to forget the necessary regulatory process. Phage therapy remains experimental; therefore, each clinical case will require multiple local approvals (i.e., ethical committee, FDA in the United States, NHSE in the United Kingdom and other national bodies in different European countries).

The majority of compassionate cases generally include evidence of clinical need and failure of previous treatments, proof of in vitro bacterial susceptibility to the phage(s), sequencing and genetic characterization of the phage(s), with particular focus on delineating any potential risk of transmitting plasmids and genetic material encoding for resistance mechanisms (both in phages and bacteria), lack of lysogenic activity, sterility of the final product and minimal endotoxin concentration [65,78,79].

Recently, colleagues from San Diego have proposed a standardized bacteriophage purification protocol for personalized phage therapy (requiring 16–21 days in total), with a systematic procedure for phage isolation, liter-scale cultivation, concentration and purification [80]. Despite the various challenges, mycobacteriophages are a promising alternative option for the treatment of mycobacterial infections, and further research and future clinical trials are needed to assess their role as adjuvants in order to reduce the total duration of treatment.

reference link :

More information: Jerry A. Nick et al, Host and pathogen response to bacteriophage engineered against Mycobacterium abscessus lung infection, Cell (2022). DOI: 10.1016/j.cell.2022.04.024



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