Population
A total of 48 critically ill patients were included in the study and swabbed at the time of ICU admission and 72 hours later (Table 1). This 72-hour window was selected because antibiotic discontinuation in the ICU is often first considered after 72 hours of antibiotic treatment. Median sequential organ failure (SOFA) score was 16 (IQR, 10-18) at ICU admission and 17 (IQR, 15-19) after 72 hours (Supplemental Table 2). Raw data for the study is given in Data Supplement 1 (phenotype) and Data Supplement 2 (genotype).
Receipt of antibiotics
Patients were eligible for inclusion in the study if they did or did not receive antibiotics. In sum, 41/48 (85%) of patients in the study received antibiotics and 37/48 (77%) received broad-spectrum antibiotics, most often a 3rd generation cephalosporin or an extended spectrum penicillin with a β-lactamase inhibitor. Figure 1A shows the antibiotics received by class, and Figure 1B shows pairwise combinations of antibiotics. Almost all antibiotics were intravenous. Of 91 antibiotics dosed to the 48 patients, 93% were given intravenously (1 patient received oral azithromycin, 1 received oral vancomycin, and 4 received oral rifaximin).
Overall changes in antimicrobial resistance phenotype and genotype
First, antimicrobial resistance phenotype was examined by culturing rectal swabs and performing susceptibility testing. No differences were evident comparing summary data for resistance phenotype at ICU admission versus 72 hours later for MRSA (RR 1.4, 95% CI 0.6 - 3.4; p = 0.59), VRE (RR 1.4, 95% CI 0.6 - 3.1; p = 0.61), or Gram-negative bacteria showing β-lactam resistance (RR 1.4, CI 0.8 - 2.4; p = 0.27 (Figure 2). Summing all antimicrobial resistance phenotype categories, there were no differences in rates of antimicrobial resistance for Gram-negative bacteria comparing ICU admission (non-susceptibility for 88/960 antibiotics tested, 9.1%) versus 72 hours later (non-susceptibility for 107/960 antibiotics tested, 11.1%) (chi-squared p = 0.17).
Next, antimicrobial resistance genotype was examined by performing qPCR across 87 common antibiotic resistance genes from the rectal swabs. No differences were evident comparing summary genotype data from ICU admission versus 72 hours later for genes conferring resistance to β-lactams (chi-squared p = 0.27), vancomycin (p =1.0), macrolides (p = 0.93), or fluoroquinolones (p = 0.74) (Supplemental Figure 1). Summing all resistance genes, there were no differences in rates of antimicrobial resistance comparing ICU admission (positive qPCR for 392 of 4,176 genes, 9%) versus 72 hours later (positive qPCR for 421 of 4,176 genes, 10%) (chi-squared p = 0.30).
Effect of antibiotics on antimicrobial resistance phenotype
For patients that did not carry individual resistant bacteria at admission, the carriage rate after 72 hours for those that received relevant antibiotics was compared to the carriage rate for those that did not receive relevant antibiotics (e.g., comparing β-lactam non-susceptibility in culture based on receipt of β-lactam antibiotics). Antibiotics had no significant association with resistance phenotype (Figure 3). Emergence of Gram-negative bacteria showing resistance to at least one β-lactam antibiotic after 72 hours was seen in 8/24 (33%) of patients who received β-lactam antibiotics and in 2/10 (20 %) of patients who did not (RR 1.7, 95% CI 0.43 - 6.51; Fisher’s p = 0.68). VRE was present in 1/13 (8%) patients who received vancomycin and in 2/27 (7%) of patients who did not (RR 1.0, 95% CI 0.10 - 10.4; p = 1.0). MRSA was present in 5/31 (16%) patients who received β-lactams and in 0/10 (0%) of patients who did not (RR unable; p = 0.31). No other clinical interventions (enteral feeding, opioids, mechanical ventilation, and proton pump inhibitors) associated with detectable differences in resistance phenotype.
Effect of antibiotics on antimicrobial resistance genotype
Change in antimicrobial resistance gene abundance was tested after stratifying by receipt of antibiotic class (Figure 4). This was first done with change in genotype classified as a continuous variable based on within-individual change in CT values (ICU admission CT minus 72-hour CT). There was no association between the changes within relevant resistance genes after 72 hours and receipt of any of the 3 most common antibiotic categories (β-lactams, vancomycin, or macrolides). There was also no overall difference in the within-individual change in CT values comparing combined antibiotic gene categories (t-test p = 0.49 for β-lactams, p = 0.28 for vancomycin, and p = 0.19 for macrolides) (Figure 4). This analysis was then repeated classifying within-individual change in genotype categorically (i.e., present versus absent). Again, there was no association between receipt of antibiotics and changes within relevant antibiotic resistance genotypes. Last, other ICU interventions were examined. Opioids were associated with modestly reduced within-individual risk of an increase in combined genotype (RR 0.79, 95% CI 0.69 - 0.91; p<0.01). No other clinical interventions associated with detectable differences in resistance genotype.
ICU admission antimicrobial resistance pattern as a predictor of resistance phenotype and genotype after 72 hours
Last, the ICU admission antimicrobial resistance pattern was examined as a predictor of resistance after 72 hours for both phenotype and genotype. For 7 of the 9 antimicrobial resistance categories tested, presence of the resistant phenotype (i.e., non-susceptibility in culture) at the time of ICU admission was significantly associated with non-susceptibility 72 hours later (Figure 5A). For 14 of the 26 genes tested, presence of the resistance genotype (i.e., positive qPCR) at the time of ICU admission was significantly associated with positive qPCR 72 hours later (Figure 5B).