Grys, Thomas E.

Abstract Background There is growing interest in the use of rapid blood culture identification (BCID) in antimicrobial stewardship programs (ASPs). Although many studies have looked at its clinical and economic utility, its comparative utility in gram-positive and gram-negative blood stream infections (BSIs) has not been as well characterized. Methods The study was a quasi-experimental retrospective study at the Mayo Clinic in Phoenix, Arizona. All adult patients with positive blood cultures before BCID implementation (June 2015 to December 2015) and after BCID implementation (June 2016 to December 2016) were included. The outcomes of interest included time to first appropriate antibiotic escalation, time to first appropriate antibiotic de-escalation, time to organism identification, length of stay, infectious diseases consultation, discharge disposition, and in-hospital mortality. Results In total, 203 patients were included in this study. There was a significant difference in the time to organism identification between the pre- and post-BCID cohorts (27.1 hours vs 3.3 hours, P < .0001). BCID did not significantly reduce the time to first appropriate antimicrobial escalation or de-escalation for either gram-positive BSIs (GP-BSIs) or gram-negative BSIs (GN-BSIs). Providers were more likely to escalate antimicrobial therapy in GP-BSIs after gram stain and more likely to de-escalate therapy in GN-BSIs after susceptibilities. Although there were no significant differences in changes in antimicrobial therapy for organism identification by BCID vs traditional methods, more than one-quarter of providers (28.1%) made changes after organism identification. There were no differences in hospital length of stay or in-hospital mortality comparing pre- vs post-BCID. Conclusions Although BCID significantly reduced the time to identification for both GP-BSIs and GN-BSIs, BCID did not reduce the time to first appropriate antimicrobial escalation and de-escalation.

Objective. To determine whether results of the nasopharyngeal FilmArray respiratory panel (NP-FARP) influenced antibiotic decisions. Methods. We reviewed the medical records of nonintensive care unit (ICU) inpatients that had an NP-FARP performed at our institution between June 2013 and June 2014. The inpatient records were reviewed 48 hours after the NP-FARP for the following data: demographic information; NP-FARP, serum procalcitonin, and methicillin-resistant Staphylococcus aureus nasal swab (MRSA NS) results; antibiotics prior and post-48 hours of the NP-FARP result; and the current immunosuppression status. Clinical outcome data were not obtained. Patients were categorized into those who had a positive (+) or a negative (−) NP-FARP. We further subdivided these two categories into groups A, B, and C based on the antibiotic modifications 48 hours after their NP-FARP result. Group A included patients who were never initiated on antimicrobial therapy. Patients whose antibiotics were discontinued or deescalated were placed in group B. Patients with antibiotic escalation or continuation without change constituted group C. We compared and analyzed groups A, B, and C in the (+) and (−) NP-FARP cohorts. Results. A total of 545 patients were included. There were 143 (26%) patients with positive and 402 (74%) patients with negative NP-FARPs. Comparison of groups A, B, and C between those with a (+) and (−) NP-FARP were as follows: (+) A and (−) A, 28/143 (20%) and 84/402 (21%); (+) B and (−) B, 59/143 (41%) and 147/402 (37%); and (+) C and (−) C, 56/143 (39%) and 171/402 (43%), respectively. We found no statistically significant differences between groups (+) A versus (−) A, (+) B versus (−) B, and (+) C versus (−) C with respect to age, gender, MRSA NS result, procalcitonin result, or concurrent immunosuppression. Conclusion. In non-ICU inpatients, NP-FARP alone or in combination with procalcitonin or MRSA NS did not influence antibiotic decisions during the study period.

Background. The FilmArray Respiratory Panel (FARP) (BioFire Diagnostics, Inc.) is a multiplex, polymerase chain reaction (PCR) technique that can detect 17 respiratory viruses and 3 bacterial targets in a single reaction. Immunocompromised hosts (ICH) with respiratory illnesses often undergo bronchoscopy with bronchoalveolar lavage (BAL). This prospective study aimed to evaluate the yield and concordance of NP and BAL FARP testing when performed on the same patient concurrently. Methods. From February to December 2016, 125 patients (100 ICH and 25 non-ICH) were enrolled. NP swabs and BAL samples were sent for FARP testing. Results. The yield of the BAL FARP among ICH and non-ICH was 24% (24/100) and 8% (2/25), respectively. The yield of positive NP swabs in ICH was 27% (27/100) versus 4% (1/25) in non-ICH. The majority of patients (89%; 111/125) had concordant results between NP and BAL specimens. Of the 24 ICH patients who had a positive BAL FARP, the majority (79%) had the same pathogen detected from the NP swab. Conclusion. The FARP may be useful in the ICH. Given the high concordance, in patients whom a pathogen is identified on the NP FARP, a FARP performed on BAL will likely yield the same result. However, if the NP FARP is negative, performing the test on a BAL sample may have an incremental yield.

Abstract Background/aims In an investigator-initiated, prospective study, we evaluated the feasibility of a five-gene sequence point-of-care (POC) testing strategy (Xpert CARBA-R Assay, Cepheid Inc., Sunnyvale, CA, USA), compared to reference laboratory PCR (48 – 72 hours turnaround time, two gene sequences), in patients undergoing endoscopic retrograde cholangiopancreatography (ERCP) and in a hospital outbreak investigation. Methods After informed consent, patients undergoing ERCP (September 2015 – April 2016, n = 191) at Mayo Clinic and potential hospital contacts (n = 9) of an index carbapenem-resistant organism (CRO)-positive inpatient were included. Two rectal swabs, one each for reference and POC assays were obtained. The Xpert CARBA-R Assay enables qualitative rapid detection of five beta-lactamase gene sequences associated with carbapenem-non-susceptibility in Gram-negative bacteria. Feasibility parameters (specimen processing and assay run time, ease of use) and percent agreement between the tests were calculated using JMP Pro11 (SAS Corp, Cary, NC, USA). Results Mean age was 62 ± 15 years; 108 (54 %) were male. Both tests were successfully performed in all patients. The POC test was rated by endoscopy nurses as easy/very easy to conduct in 193 patients (97 %); median assay run time and median time for specimen collection and processing were 55 minutes (interquartile range IQR: 53 – 55 minutes) and 3 minutes (IQR: 3 – 6 minutes), respectively. In 200/201 (99.5 %) tests, there was agreement between the POC and reference PCR. Conclusions The more comprehensive POC CRO testing of patients in the endoscopy suite is feasible and results are available in < 1 hour. This strategy may enable rapid risk stratification of duodenoscope exposure to CRO and potentially improve operational efficiency and decrease costs.

AbstractThe aims of this study are to provide protein‐based evidence upon which to reannotate the genome of Coccidiodes posadasii, one of two closely related species of Coccidioides, a dimorphic fungal pathogen that causes coccidioidomycosis, also called Valley fever. Proteins present in lysates and filtrates of in vitro grown mycelia and parasitic phase spherules from C. posadasii strain Silveira are analyzed using a GeLC‐MS/MS method. Acquired spectra are processed with a proteogenomics workflow comprising a Silveira proteome database, a six‐frame translation of the Silveira genome and an ab initio gene prediction tool prior to validation against published ESTs. This study provides evidence for 837 genes expressed at the protein level, of which 169 proteins (20.2%) are putative proteins and 103 (12.3%) are not annotated in the Silveira genome. Additionally, 275 novel peptides are derived from intragenic regions of the genome and 13 from intergenic regions, resulting in 172 gene refinements. Additionally, we are the first group to report translationally active retrotransposon elements in a Coccidioides spp. Our study reveals that the currently annotated genome of C. posadasii str. Silveira needs refinement, which is likely to be the case for many nonmodel organisms.