Microbiome compositions and resistome levels after antibiotic treatment of critically ill patients – An observational cohort study

Background: Hospitalization and treatment with antibiotics increase the risk of acquiring multidrug-resistant bacteria due to antibiotic-mediated changes in patient microbiota. This study aimed to investigate how broad and narrow antibiotics affect the gut microbiome and the resistome in antibiotic naïve patients during neurointensive care.Materials/methods: Patients admitted to neurointensive care unit were treated with broad-spectrum (meropenem or piperacillin/tazobactam) or narrow-spectrum antibiotic treatment (including ciprofloxacin, cefuroxime, vancomycin and dicloxacillin) according to clinical indications. A rectal swab was collected from each patient before and after 5-7 days of antibiotic therapy (N=34). Shotgun metagenomic sequencing was performed and composition of metagenomic species (MGS) was determined. The resistome (as collection of antibiotic resistance genes) was characterized with CARD RGI software and CARD database. As a measure for selection pressure in the patient, we used sum of number of days with each antibiotic (antibiotic days).Results: We observed a significant increase in richness and a tendency for an increase in Shannon index after narrow-spectrum treatment. For broad-spectrum treatment the effect was more diverse with some patients increasing and some decreasing in richness and Shannon index. This was studied further by comparison of patients who had gained or lost >10 MGS, respectively. Selection pressure was significantly higher in patients with decreased richness (p = 0.0054) and decreased Shannon index (p = 0.012); these patients tended to have received a higher number of antibiotics (for richness: P= 0.063; for Shannon index: P = 0.086). A decrease in MGS richness was significantly correlated to number of drugs administered and selection pressure of the patient. Bray-Curtis dissimilarities were significant between the pre- and post-treatment of samples in the narrow group, indicating that the longer the narrow-spectrum treatment, the higher the differences between the pre- and the post-treatment microbial composition. Changes in resistome followed MGS composition and was independent of administered antibiotics. We did not find significant differences between pre- and at post-treatment for both antibiotic spectrum treatments, however we observed that most of the antibiotic class resistance genes were higher in abundance in post-treatment after broad-spectrum treatment Conclusions:The MGS composition of the microbiome changed independently of the applied antibiotic treatment. Patients who received narrow-spectrum treatment exhibited an increase in alpha diversity, whereas patients who received broad-spectrum treatment exhibited opposite effects depending on the duration of the treatment with selection pressure and duration of treatment being higher in patients with a decreased MGS diversity. The selection pressure in the patient may be a better predictor of the effect on the microbiome than the spectrum of the antibiotics.