Date Published: February 7, 2017
Publisher: Public Library of Science
Author(s): John Joseph Farrell, Huaping Wang, Rangarajan Sampath, Kristin S. Lowery, Robert A. Bonomo, Massimiliano Galdiero.
Initial antimicrobial treatment of patients with deep seated or invasive infections is typically empiric. Usually, cultures of specimens obtained from the suspected source of infection are performed to identify pathogens and guide continued antimicrobial treatment. When patients present with signs and symptoms of infection, but sterile body fluid or tissue specimens cannot be obtained in a timely fashion, growth of bacterial pathogens in culture may be inhibited following initiation of empiric antibiotic treatment. To address this clinical dilemma, we performed a prospective evaluation of conventional culture vs. PCR coupled to electrospray ionization mass spectrometry (PCR/ESI-MS) on sterile body fluids and tissues submitted to the diagnostic microbiology lab following initiation of empiric antibiotic treatment for patients with suspected infection. In this series of surgical samples, PCR/ESI-MS identified bacterial pathogen(s) in 56% (49/87) of patients with non-diagnostic cultures. Examination of patients stratified by antibiotic treatment duration demonstrated that PCR/ESI-MS sustains high rates of bacterial DNA detection over time by generalized estimating equation models (p<0.0001).
Sepsis management guidelines recommend that blood cultures be obtained before the initiation of antibiotics. But even when blood culture collection precedes antibiotic treatment, blood cultures are negative in up to 50% of patients with severe sepsis or septic shock. [1, 2] Guidelines also encourage sampling of the suspected source of infection in a timely fashion, when the clinical circumstances allow. When the suspected source of infection cannot be readily sampled, several doses of empiric antibiotics may be administered prior to sampling or drainage, reducing the sensitivity for detection of bacteria in culture. 
Following completion of a PCR/ESI-MS pilot study, approval was obtained from the University of Illinois College of Medicine and St. Francis Medical Center Institutional Review Boards for prospective PCR/ESI-MS testing of specimens submitted to the microbiology laboratory from inpatients receiving antimicrobial treatment at St. Francis Medical Center, Peoria, IL. All specimens were collected as part of the routine care of the patient and submitted to the microbiology laboratory by the treating physicians for conventional cultures. None of the patients included in this study were participates in the original pilot study.
Our study population included 65 men and 63 women (51% and 49%, respectively). The average patient age was 55 years. Sterile specimens were obtained by PA for 56% (72/128) of patients. The mean and median DOT were 9 (S.D = 17.5) and 4 days, respectively with a range from 1–165 days. As expected, the treatment groups were slightly weighted towards DOT ≤ 2 days: 47 patients (37%) were treated for ≤ 2 days; 43 patients (33%) were treated for 3 to 7 days; and 38 patients (30%) were treated for ≥ 8 days. Sex and age were equally distributed for all three treatment groups, and no significant difference was observed among the three DOT groups in terms of sample source (PA vs. OR), number of SIRS present at admission, or WBC count. In contrast, patients with a DOT ≤ 2 days were much less likely to have received multiple empiric antibiotics than patients in the two longer DOT treatment groups (p<0.001). (Table 1) In our prospective investigation, PCR/ESI-MS was significantly more likely to detect bacteria than culture in sterile surgical specimens and body fluids obtained from patients who had received more than 2 days of antibiotic treatment (p<0.0001). PCR/ESI-MS also appeared useful for detection of bacterial pathogens at much longer antibiotic treatment durations. Predictive probability plots demonstrate a significant disparity between culture and PCR/ESI-MS for all patients with DOT > 2, with sustained high probability of pathogen detection for patients treated with antibiotics in both of the longer DOT groups (Fig 2).