Antibiotic resistance, bacterial transmission and improved prediction of bacterial infection in patients with antibody deficiency
Background Antibody-deficient patients are at risk of respiratory tract infections despite use of immunoglobulin-replacement therapy, therefore many receive antibiotic prophylaxis and have access to antibiotics for self-administration in the event of breakthrough infections which may increase antimicrobial-resistance (AMR). Methods Sputum samples were collected from patients with antibody deficiency in a cross-sectional and prospective study; comprehensive bacteriology culture, 16S rRNA profiling and PCR detecting macrolide resistance determinants were performed. Bacterial isolates were identified using MALDI-TOF, their antimicrobial-susceptibility was determined by the disc-diffusion technique, WGS of selected isolates was done using Illumina NextSeq. Neutrophil-elastase was measured by a Protease Tag immunoassay (ProAxsis). Results 343 bacterial isolates from sputum of 43 patients were tested. Haemophilus influenzae (4%), Streptococcus pneumoniae (3%) and Pseudomonas aeruginosa (2%), were the most common bacterial pathogens isolated. Macrolide and tetracycline resistance were highly prevalent in the whole cohort (82% and 35% of isolates). ermB and mefA were the most common determinants of macrolide resistance in the resistome, detected in 25% and 43% of the sputum samples respectively. tet(M), tet(O) and tet A/B were the most common determinants of tetracycline resistance. WGS revealed the source of AMR genes was the viridans streptococci, 23% of which also carried conjugative plasmids linked with AMR genes and other mobile genetic elements. 96% of the tet(M) detected were linked with the repUS43 plasmid and/or integrative conjugative elements (ICE); mefA and msrD were frequently detected in close proximity (84% of tested isolates); 92% of the ermB detected were linked with repUS43 plasmids, 85% of which were additionally linked with ICE and 85% were in conjugation with tetM.  In the prospective study, a negative correlation between sputum neutrophil elastase concentration and Shannon-entropy a-diversity index (Spearman's ?=-0.306, p=0.005) and a positive relationship with Berger-Parker dominance index (?=0.502, p <0.001) were found. Similar relationships were noted for the change in elastase concentration between consecutive samples, with increases associated with lower a-diversity and higher dominance. Samples testing positive for pathogenic viruses had low elastase concentration. Phylogenetic analysis of H. influenzae isolates suggests possible transmission between patients attending clinic.  Conclusions  Neutrophil elastase may be useful as a marker of infection to guide the use of antibiotics for respiratory infection. Measures to limit transmission of infection and spread of AMR should be implemented in immunodeficiency clinics.