This study aims to identify biomarkers associated with response to phage therapy for refractory bacterial infections. This includes mycobacteriophage treatment for patients with nontuberculous mycobacterial infections. Blood and airway samples will be obtained from follow up visits of patients with refractory bacterial infections that are considered for phage therapy. Samples will be compared between those that receive phage therapy and those that did not. Biomarkers will include changes in the airway microbiome, transcriptome, inflammatory cytokines, and development of neutralizing antibody against phages. The primary endpoint is to identify biomarkers associated with clinical and/or radiographic improvement and/or culture improvement which includes clearing of cultures or decrease in qualitative or resolution of signs and symptoms of infection after at least 6-8 weeks of bacteriophage therapy.

Inclusion Criteria:

1. Adults 18 years of age or older
2. Provision of appropriate written consent
3. Willingness and ability to participate in study procedures
4. Diagnosis of bacterial/mycobacterial infection that meets criteria for treatment (clinical, radiographic, and microbiologic data)
5. Patients are being considered by clinician for phage therapy as a part of their standard of care

Exclusion Criteria:

1. Patients under 18 years of age
2. Pregnant individuals as this population is not considered for phage treatment due to unknown risks of the treatment
3. Breastfeeding Individuals who are breastfeeding as this population is not considered for phage treatment due to unknown risk to the infant

Patients with Nontuberculous Mycobacterial (NTM) disease who are considered for treatment with phage therapy will be recruited. Those that have a positive match for their NTM isolate and starts on mycobacteriophage treatment will be considered cases while those that do not have a positive match and/or does not start on mycobacteriophage treatment will be considered controls.

The de-identified participant data from the final research dataset will be shared upon reasonable request beginning 3 months and ending 5 years following article publication, provided the requesting investigator executes a data use agreement with NYU Langone Health. This instance of data sharing will also require separate IRB review as well as review from NYU Langone's Data Sharing Strategy Board (DSSB). Requests should be directed to: Doreen.Addrizzo@nyulangone.org. The protocol and statistical analysis plan will be posted on Clinicaltrials.gov only as required by federal regulation or supporting awards and agreements.

Beginning 3 months and ending 5 years following article publication

The investigator who proposed to use the data will be granted access upon reasonable request. Requests should be directed to Doreen.Addrizzo@nyulangone.org. To gain access, data requestors will need to sign a data access agreement. This instance of data sharing will also require separate IRB review as well as review from NYU Langone's DSSB.