Detection of Mpox Virus Using Microbial Cell-Free DNA: The Potential of Pathogen-Agnostic Sequencing for Rapid Identification of Emerging Pathogens

BACKGROUND

The 2022 global outbreak of Monkeypox virus (MPXV) highlighted challenges with polymerase chain reaction detection as divergent strains emerged and atypical presentations limited the applicability of swab sampling. Recommended testing in the United States requires a swab of lesions, which arise late in infection and may be unrecognized. We present MPXV detections using plasma microbial cell-free DNA (mcfDNA) sequencing.

METHODS

Fifteen plasma samples from 12 case-patients were characterized through mcfDNA sequencing. Assay performance was confirmed through in silico inclusivity and exclusivity assessments. MPXV isolates were genotyped using mcfDNA, and phylodynamic information was imputed using publicly available sequences.

RESULTS

MPXV mcfDNA was detected in 12 case-patients. Mpox was not suspected in 5, with 1 having documented resolution of mpox >6 months previously. Six had moderate to severe mpox, supported by high MPXV mcfDNA concentrations; 4 died. In 7 case-patients, mcfDNA sequencing detected coinfections. Genotyping by mcfDNA sequencing identified 22 MPXV mutations at 10 genomic loci in 9 case-patients. Consistent with variation observed in the 2022 outbreak, 21 of 22 variants were G > A/C > T. Phylogenetic analyses imputed isolates to sublineages arising at different time points and from different geographic locations.

CONCLUSIONS

We demonstrate the potential of plasma mcfDNA sequencing to detect, quantify, and, for acute infections with high sequencing coverage, subtype MPXV using a single noninvasive test. Sequencing plasma mcfDNA may augment existing mpox testing in vulnerable patient populations or in patients with atypical symptoms or unrecognized mpox. Strain type information may supplement disease surveillance and facilitate tracking emerging pathogens.

193. Rapid Diagnostic Testing and Vancomycin Utilization for Contaminated Blood Cultures

Background

Bacteremia is a prevalent hospital acquired infection that affects nearly one in ten hospitalized patients. Rates of contaminated blood cultures have ranged from 0.6% to 6% in the literature. Vancomycin is often chosen as empiric coverage for gram positive organisms while awaiting bacterial identification. The purpose of this study was to evaluate the impact of GenMark ePlex Blood Culture Identification Panel (BCID) implementation on the duration of vancomycin therapy for blood cultures contaminated with coagulase negative staphylococci (CoNS).

Methods

A retrospective chart review was conducted on patients meeting inclusion criteria during a six month period prior to BCID implementation and post BCID implementation, from 03/01/2019 to 08/31/2019 and 03/01/2021 to 08/31/2021. The primary outcome analyzed was the duration of vancomycin therapy, in hours, in patients with a contaminated blood culture. Contaminated blood cultures was defined as a single blood culture growing CoNS. Secondary outcomes included hospital length of stay, readmission for treatment of contaminated blood cultures, and nephrotoxicity.

Results

This IRB-approved study included 190 patients, 75 in the pre-BCID group and 115 in the post-BCID group. The average duration of vancomycin therapy was 53.7 hours in the pre-BCID group and 20.5 hours in the post-BCID group (p = 0.04). Time to organism identification was reduced from 22.8 hours in the pre-BCID group to 12 hours in the post-BCID group (p = 0.5). Additionally, our study did not find a difference in nephrotoxicity, hospital length of stay, or readmissions between the two groups.

Conclusion

Following implementation of the GenMark ePlex Blood Culture Identification Panel (BCID), there was a reduction in both duration of vancomycin therapy and time to culture identification for blood cultures contaminated with CoNS. Rapid diagnostic testing is helpful in clinical decision-making and can lead to earlier discontinuation of empiric antibiotics, such as vancomycin.

Disclosures

All Authors: No reported disclosures.

Reductions in inpatient fluoroquinolone use and postdischarge Clostridioides difficile infection (CDI) from a systemwide antimicrobial stewardship intervention

Objective

To determine the impact of an inpatient stewardship intervention targeting fluoroquinolone use on inpatient and postdischarge Clostridioides difficile infection (CDI).

Design

We used an interrupted time series study design to evaluate the rate of hospital-onset CDI (HO-CDI), postdischarge CDI (PD-CDI) within 12 weeks, and inpatient fluoroquinolone use from 2 years prior to 1 year after a stewardship intervention.

Setting

An academic healthcare system with 4 hospitals.

Patients

All inpatients hospitalized between January 2017 and September 2020, excluding those discharged from locations caring for oncology, bone marrow transplant, or solid-organ transplant patients.

Intervention

Introduction of electronic order sets designed to reduce inpatient fluoroquinolone prescribing.

Results

Among 163,117 admissions, there were 683 cases of HO-CDI and 1,104 cases of PD-CDI. In the context of a 2% month-to-month decline starting in the preintervention period (P < .01), we observed a reduction in fluoroquinolone days of therapy per 1,000 patient days of 21% after the intervention (level change, P < .05). HO-CDI rates were stable throughout the study period. In contrast, we also detected a change in the trend of PD-CDI rates from a stable monthly rate in the preintervention period to a monthly decrease of 2.5% in the postintervention period (P < .01).

Conclusions

Our systemwide intervention reduced inpatient fluoroquinolone use immediately, but not HO-CDI. However, a downward trend in PD-CDI occurred. Relying on outcome measures limited to the inpatient setting may not reflect the full impact of inpatient stewardship efforts.

Induction of human plasmablasts during infection with antibiotic-resistant nosocomial bacteria

OBJECTIVES

Nosocomial pathogens such as Acinetobacter baumannii are a growing public health threat, due in part to their increasing resistance to antibiotics. Since some strains are resistant to all available antibiotics, novel therapies are urgently needed. Plasmablasts are short-lived B cells found in the blood that can be collected and harnessed to produce therapeutic antibodies. We set out to determine whether plasmablasts are induced during infection with A. baumannii and other nosocomial pathogens.

METHODS

We obtained blood samples from patients infected with antibiotic-resistant nosocomial pathogens, and analysed their plasmablast response by flow cytometry.

RESULTS

We observed a strong induction of plasmablasts in patients with antibiotic-resistant A. baumannii infection. Furthermore, plasmablasts were also induced in response to other drug-resistant nosocomial pathogens.

CONCLUSIONS

These data suggest that plasmablasts may be broadly harnessed to develop therapeutic antibodies to combat otherwise untreatable antibiotic-resistant infections.