Enhancing clinical genomic accuracy with panelGC: a novel metric and tool for quantifying and monitoring GC biases in hybridization capture panel sequencing.

Accurate assessment of fragment abundance within a genome is crucial in clinical genomics applications such as the analysis of copy number variation (CNV). However, this task is often hindered by biased coverage in regions with varying guanine-cytosine (GC) content. These biases are particularly exacerbated in hybridization capture sequencing due to GC effects on probe hybridization and polymerase chain reaction (PCR) amplification efficiency. Such GC content-associated variations can exert a negative impact on the fidelity of CNV calling within hybridization capture panels. In this report, we present panelGC, a novel metric, to quantify and monitor GC biases in hybridization capture sequencing data. We establish the efficacy of panelGC, demonstrating its proficiency in identifying and flagging potential procedural anomalies, even in situations where instrument and experimental monitoring data may not be readily accessible. Validation using real-world datasets demonstrates that panelGC enhances the quality control and reliability of hybridization capture panel sequencing.

Analytical and clinical validation of direct detection of antimicrobial resistance markers by plasma microbial cell-free DNA sequencing.

Sequencing of plasma microbial cell-free DNA (mcfDNA) has gained increased acceptance as a valuable adjunct to standard-of-care testing for diagnosis of infections throughout the body. Here, we report the analytical and clinical validation of a novel application of mcfDNA sequencing, the non-invasive detection of seven common antimicrobial resistance (AMR) genetic markers in 18 important pathogens. The AMR markers include SCCmec, mecA, mecC, vanA, vanB, blaCTX-M, and blaKPC. The AMR markers were computationally linked to the pathogens detected. Analytical validation showed high reproducibility (100%), inclusivity (54 to 100%), and exclusivity (100%). Clinical accuracy was assessed with 114 unique plasma samples from patients at seven study sites with concordant culture results for target bacteria from a variety of specimen types and correlated with available phenotypic antimicrobial susceptibility test results and genotypic results. The positive percent agreement (PPA), negative percent agreement (NPA), and diagnostic yield (DY) were estimated for each AMR marker. DY was defined as the percentage of tests that yielded an actionable result of either detected or not detected. The results for the combination of SCCmec and mecA for staphylococci were PPA 19/20 (95.0%), NPA 21/22 (95.4%), DY 42/60 (70.0%); vanA for enterococci were PPA 3/3 (100%), NPA 2/2 (100%), DY 5/6 (83.3%); blaCTX-M for gram-negative bacilli were PPA 5/6 (83.3%), NPA 29/29 (100%), DY 35/49 (71.4%); and blaKPC for gram-negative bacilli were PPA 0/2 (0%), NPA: 23/23 (100%), DY 25/44 (56.8%). The addition of AMR capability to plasma mcfDNA sequencing should provide clinicians with an effective new culture-independent tool for optimization of therapy. IMPORTANCE: This manuscript is ideally suited for the Innovative Diagnostic Methods sections as it reports the analytical and clinical validation of a novel application of plasma microbial cell-free DNA sequencing for direct detection of seven selected antimicrobial resistance markers in 18 target pathogens. Clearly, it has potential clinical utility in optimizing therapy and was incorporated into the Karius test workflow in September 2023. In addition, the workflow could readily be adapted to expand the number of target bacteria and antimicrobial resistance markers as needed.

Epidemiology and treatment of invasive Bartonella spp. infections in the United States.

OBJECTIVES: Bartonella spp., renowned for cat-scratch disease, has limited reports of dissemination. Tissue and blood cultures have limitations in detecting this fastidious pathogen. Molecular testing (polymerase chain reaction, PCR) and cell-free DNA have provided an avenue for diagnoses. This retrospective observational multicenter study describes the incidence of disseminated Bartonella spp. and treatment-related outcomes. METHODS: Inclusion criteria were diagnosis of bartonellosis via diagnosis code, serology testing of blood, polymerase chain reaction (PCR) of blood, 16/18S tests of blood or tissue, cultures of blood or tissue, or cell-free DNA of blood or tissue from January 1, 2014, through September 1, 2021. Exclusions were patients who did not receive treatment, insufficient data on treatment course, absence of dissemination, or retinitis as dissemination. RESULTS: Patients were primarily male (n = 25, 61.0%), white (n = 28, 68.3%), with mean age of 50 years (SD 14.4), and mean Charlson comorbidity index of 3.5 (SD 2.1). Diagnosis was primarily by serology (n = 34, 82.9%), with Bartonella henselae (n = 40, 97.6%) as the causative pathogen. Treatment was principally doxycycline with rifampin (n = 17, 41.5%). Treatment failure occurred in 16 (39.0%) patients, due to escalation of therapy during treatment (n = 5, 31.3%) or discontinuation of therapy due to an adverse event or tolerability (n = 5, 31.3%). CONCLUSIONS: In conclusion, this is the largest United States-based cohort of disseminated Bartonella spp. infections to date with a reported 39% treatment failure. This adds to literature supporting obtaining multiple diagnostic tests when Bartonella is suspected and describes treatment options.

Trimethoprim/Sulfamethoxazole vs Minocycline for the Treatment of Nonurinary Monomicrobial Stenotrophomonas maltophilia Infections in Hospitalized Patients.

BACKGROUND: Stenotrophomonas maltophilia is an opportunistic, gram-negative bacillus with few therapeutic options due to a high level of intrinsic resistance. Trimethoprim/sulfamethoxazole (SXT) is recommended as the first-line treatment; however, minocycline (MIN) has been shown to have similar clinical outcomes in treating S. maltophilia and addresses concern for increasing resistance to SXT. OBJECTIVE: The objective of this study is to evaluate the efficacy and safety outcomes of nonurinary, monomicrobial infections due to S. maltophilia in hospitalized patients treated with MIN or SXT. METHODS: This was a retrospective study of hospitalized adult patients receiving MIN or SXT for nonurinary monomicrobial S. maltophilia infection from April 1, 2018 to March 31, 2020. The primary outcome was clinical disposition classified as rates of clinical failure, clinical improvement, or clinical success. RESULTS: Eighty-two patients (88.2%) received MIN and 11 patients (11.8%) received SXT initially. Clinical failure occurred in 16 (19.5%) patients in the MIN group and in 4 (36.4%) patients in the SXT group (P = 0.242). Clinical improvement occurred in 11 (13.4%) patients in the MIN group and in 1 (9.1%) patient in the SXT group (P = 1.0). Clinical success occurred in 55 (67.1%) patients in the MIN group and in 6 (54.5%) patients in the SXT group (P = 0.503). Total duration of antimicrobial therapy (P = 0.3198), in-hospital mortality (P = 1.0), hospital length of stay (P = 0.9668), intensive care unit (ICU) length of stay (P = 0.1384), and 30-day readmission (P = 0.686) were similar between groups. CONCLUSIONS AND RELEVANCE: Rates of clinical failure, clinical improvement, or clinical success were similar between MIN and SXT for nonurinary monomicrobial S. maltophilia infections.

Pharmacist-Driven Methicillin-Resistant S. aureus Polymerase Chain Reaction Testing for Pneumonia.

BACKGROUND: Nasal colonization with methicillin-resistant Staphylococcus aureus (MRSA) can be detected using nasal swab polymerase chain reaction (PCR) assay and is associated with clinical MRSA infection. The MRSA nasal PCR has a rapid turnaround time and a negative predictive value for MRSA pneumonia of >98%; however, data are limited in critically ill patients. OBJECTIVE: The purpose of this study is to determine the impact of a pharmacist-driven algorithm, utilizing MRSA PCR nasal screening on duration of anti-MRSA therapy in patients admitted to the intensive care unit (ICU) with suspected pneumonia. METHODS: A single-center pre/post study was conducted in 4 ICUs at a large tertiary care community hospital. Adult patients admitted to the ICU initiated on vancomycin or linezolid for pneumonia managed using a pharmacist-driven MRSA PCR algorithm were included in the algorithm cohort. A historical cohort with standard management was matched 1:1 by age, type of pneumonia, and Acute Physiology and Chronic Health Evaluation II (APACHE II) score. The primary outcome was duration of anti-MRSA therapy. Secondary outcomes included MRSA rates, number of vancomycin levels, new onset of acute kidney injury (AKI), ICU length of stay (LOS), hospital LOS, and mortality. RESULTS: Of the 245 patients screened, 50 patients met inclusion criteria for the algorithm cohort and were matched to 50 patients in the historical cohort. The duration of anti-MRSA therapy was significantly lower compared with the historical cohort (47 vs 95 hours; P < 0.001). Secondary outcomes were similar between groups for MRSA rates, new onset of AKI, LOS, and mortality. There were less vancomycin levels ordered in the algorithm cohort (2 vs 3, P = 0.026). CONCLUSIONS: A pharmacist-driven MRSA PCR algorithm significantly reduced anti-MRSA duration of therapy in critically ill patients with pneumonia. Future studies should validate these results in critically ill populations and in settings where MRSA pneumonia is more prevalent.

Cefiderocol for the Treatment of Adult and Pediatric Patients With Cystic Fibrosis and Achromobacter xylosoxidans Infections.

Treatment options for Achromobacter xylosoxidans are limited. Eight cystic fibrosis patients with A. xylosoxidans were treated with 12 cefiderocol courses. Pretreatment in vitro resistance was seen in 3 of 8 cases. Clinical response occurred after 11 of 12 treatment courses. However, microbiologic relapse was observed after 11 of 12 treatment courses, notably without emergence of resistance.

A Baker's Dozen of Top Antimicrobial Stewardship Intervention Publications in 2022.

Keeping abreast of the antimicrobial stewardship-related articles published each year is challenging. The Southeastern Research Group Endeavor identified antimicrobial stewardship-related, peer-reviewed literature that detailed an actionable intervention during 2022. The top 13 publications were selected using a modified Delphi technique. These manuscripts were reviewed to highlight actionable interventions used by antimicrobial stewardship programs to capture potentially effective strategies for local implementation.

ICU outcomes and survival in patients with severe COVID-19 in the largest health care system in central Florida.

BACKGROUND: Observational studies have consistently described poor clinical outcomes and increased ICU mortality in patients with severe coronavirus disease 2019 (COVID-19) who require mechanical ventilation (MV). Our study describes the clinical characteristics and outcomes of patients with severe COVID-19 admitted to ICU in the largest health care system in the state of Florida, United States. METHODS: Retrospective cohort study of patients admitted to ICU due to severe COVID-19 in AdventHealth health system in Orlando, Florida from March 11th until May 18th, 2020. Patients were characterized based on demographics, baseline comorbidities, severity of illness, medical management including experimental therapies, laboratory markers and ventilator parameters. Major clinical outcomes analyzed at the end of the study period were: hospital and ICU length of stay, MV-related mortality and overall hospital mortality of ICU patients. RESULTS: Out of total of 1283 patients with COVID-19, 131 (10.2%) met criteria for ICU admission (median age: 61 years [interquartile range (IQR), 49.5-71.5]; 35.1% female). Common comorbidities were hypertension (84; 64.1%), and diabetes (54; 41.2%). Of the 131 ICU patients, 109 (83.2%) required MV and 9 (6.9%) received ECMO. Lower positive end expiratory pressure (PEEP) were observed in survivors [9.2 (7.7-10.4)] vs non-survivors [10 (9.1-12.9] p = 0.004]. Compared to non-survivors, survivors had a longer MV length of stay (LOS) [14 (IQR 8-22) vs 8.5 (IQR 5-10.8) p< 0.001], Hospital LOS [21 (IQR 13-31) vs 10 (7-1) p< 0.001] and ICU LOS [14 (IQR 7-24) vs 9.5 (IQR 6-11), p < 0.001]. The overall hospital mortality and MV-related mortality were 19.8% and 23.8% respectively. After exclusion of hospitalized patients, the hospital and MV-related mortality rates were 21.6% and 26.5% respectively. CONCLUSIONS: Our study demonstrates an important improvement in mortality of patients with severe COVID-19 who required ICU admission and MV in comparison to previous observational reports and emphasizes the importance of standard of care measures in the management of COVID-19.

Renin Angiotensin Aldosterone System Antagonism in 2019 Novel Coronavirus Acute Lung Injury.

It has been established that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) uses angiotensin-converting enzyme 2 (ACE2), a membrane-bound regulatory peptide, for host cell entry. Renin-angiotensin-aldosterone system (RAAS) inhibitors have been reported to increase ACE2 in type 2 pneumocyte pulmonary tissue. Controversy exists for the continuation of ACE inhibitors, angiotensin II receptor blockers, and mineralocorticoid receptor antagonists in the current pandemic. ACE2 serves as a regulatory enzyme in maintaining homeostasis between proinflammatory angiotensin II and anti-inflammatory angiotensin 1,7 peptides. Derangements in these peptides are associated with cardiovascular disease and are implicated in the progression of acute respiratory distress syndrome. Augmentation of the ACE2/Ang 1,7 axis represents a critical target in the supportive management of coronavirus disease 2019-associated lung disease. Observational data describing the use of RAAS inhibitors in the setting of SARS-CoV-2 have not borne signals of harm to date. However, equipoise persists, requiring an analysis of novel agents including recombinant human-ACE2 and existing RAAS inhibitors while balancing ongoing controversies associated with increased coronavirus infectivity and virulence.

Evaluating predictors of invasive candidiasis in patients with and without candidemia on micafungin.

Numerous risk factors have been linked to invasive candidiasis; however, they are nonspecific and often trigger empiric antifungal therapy in a large number of patients. Identification of more precise predictors could promote judicious use of empiric echinocandins. In this retrospective review, 127 patients with blood cultures positive for Candida spp. were compared to a randomly selected cohort of 134 patients on empiric micafungin for ≥3 days and with blood cultures negative for Candida spp. Factors associated with candidemia included total parenteral nutrition (TPN; 26.0% vs 15.7%, P = 0.040), multifocal Candida colonization (23.6% vs 3.0%, P < 0.001), and positive 1,3-ß-d-glucan assay (95.0% vs 35.0%, P < 0.001). Patients without candidemia on empiric micafungin were more likely to receive antibiotic therapy in the previous 10 days (55.9% vs 79.9%, P < 0.001) and to be taking immunosuppressive medications (11.0% vs 30.6%, P < 0.001). Receipt of TPN (odds ratio [OR] = 2.07, 95% confidence interval [CI], 1.02-4.21), severe sepsis (OR = 2.20, 95% CI, 1.00-4.83), and multifocal Candida colonization (OR = 13.87, 95% CI, 4.43-43.37) were independently associated with candidemia in the multivariable logistic regression model. Therefore, the absence of these risk factors, especially in conjunction with a negative 1,3-ß-d-glucan assay, may be used to recommend de-escalation of empiric micafungin therapy.

Clinical Utility of Methicillin-Resistant Staphylococcus aureus Nasal Screening for Antimicrobial Stewardship: A Review of Current Literature.

Significant clinical and financial consequences are associated with both inadequate and unnecessary exposure to broad-spectrum antibiotics. As such, antimicrobial stewardship programs seek objective, reliable, and cost-effective tests to identify patients at highest or lowest risk for drug-resistant organisms to guide empirical antimicrobial selection. Use of methicillin-resistant Staphylococcus aureus (MRSA) nasal screening to rule out MRSA in lower respiratory tract infections has led to significant reductions in duration of vancomycin therapy. The clinical utility of MRSA nasal screening in other types of infection remains less clear. This review describes the performance of MRSA nasal screening in predicting MRSA infection, highlights practical considerations for use of MRSA nasal screening, and provides guidance for incorporating MRSA nasal screening into clinical practice. With a high negative predictive value when the prevalence of MRSA is low, MRSA nasal screening is a valuable antimicrobial stewardship tool with potential applications beyond lower respiratory tract infections. In appropriately selected patients, negative MRSA nasal screening can prevent initiation or guide discontinuation of anti-MRSA therapy. Antimicrobial stewardship programs should develop institutional guidelines to promote proper use of MRSA nasal screening. Pharmacists are well positioned to assist with education, interpretation, and application of MRSA nasal screening results.

Prospective evaluation of the incidence of wound infection in rattlesnake envenomation in dogs.

OBJECTIVE: To evaluate the incidence of wound infection following crotalidae envenomation in dogs and determine if the use of prophylactic antibiotics is warranted. DESIGN: Prospective observational study. SETTING: A 24-hour private practice specialty and emergency center in Murrieta, California. ANIMALS: One hundred and two dogs with acute rattlesnake envenomation. INTERVENTIONS: One hundred and forty-three consecutive cases of suspected acute rattlesnake envenomation were evaluated between March of 2012 and May of 2013. One hundred and two cases received no antimicrobials as part of management. Eight cases were placed on prophylactic antimicrobials by the primary care veterinarian prior to referral and were excluded. Two cases were excluded because they were initiated on antimicrobials during hospitalization for reasons unrelated to snakebite. Three cases involved cats and were excluded. Three patients died acutely near the time of presentation and were excluded. Twenty-one cases of suspected envenomation were excluded for lack of strong evidence of snakebite. Four cases were lost to follow-up and were excluded. Follow-up was conducted within 2 weeks either by phone or by direct inspection of the wound. RESULTS: Of the 102 patients included in the study only 1 infection developed. This patient developed an abscess subsequent to suspected compartment syndrome. CONCLUSION: The incidence of wound infection in rattlesnake envenomation is low, and the use of prophylactic antimicrobials is not recommended. The use of antimicrobials should be reserved for wounds with necrosis or abscess and the choice of antimicrobial should be based on a culture and sensitivity of the wound.

Localization of ISG15 and conjugated proteins in bovine endometrium using immunohistochemistry and electron microscopy.

The interferon-stimulated gene ISG15, a ubiquitin homolog, becomes conjugated to and regulates uterine proteins in response to conceptus-derived interferon-tau on d 18 of pregnancy. It was hypothesized here that cellular localization of ISG15 within endometrial cells might provide insight regarding function. Uteri were collected from cows (approximately 21-d estrous cycle) on d 17-21/0 of the estrous cycle and pregnancy and d 23, 45, and 50 of pregnancy. Intracellular ISG15 and its conjugates were present on d 17 of pregnancy, peaked to highest levels from d 18 to 23 and then declined to low but detectable levels by d 45 (P < 0.05) based on Western blotting. ISG15 and its conjugates were not detected on d 50 of pregnancy or during the estrous cycle. Immunohistochemistry revealed that ISG15 was localized throughout the endometrium on d 18-23, with heaviest staining in the sublumenal stratum compactum and the glandular epithelium throughout the stratum spongiosum. By d 45 and 50, ISG15 was lightly stained only in the stratum compactum immediately beneath the lumenal epithelium. Using transmission electron microscopy and immunogold labeling, ISG15 was specifically localized to organelles and compartments of endometrial epithelial cells and stromal cells: nucleus, perinuclear space, cytosol, mitochondria, rough endoplasmic reticulum, and cell membrane. This specific localization in epithelial and stromal cells led to the conclusion that ISG15 has diverse intracellular functions. The sustained presence of conjugated ISG15 through d 50 of pregnancy might reflect stabilization of conjugated proteins in response to implantation and the development of the placenta.

Retrospective analysis of clinical findings and outcome of cats with suspected rattlesnake envenomation in Southern California: 18 cases (2007-2010).

OBJECTIVE: To evaluate treatment and survival rates of cats with suspected rattlesnake envenomation. DESIGN: Retrospective study. SETTING: Veterinary emergency referral hospital in Southern California. ANIMALS: Client-owned animals. INTERVENTIONS: None. MEASUREMENTS AND MAIN RESULTS: Eighteen cats were treated for suspected rattlesnake envenomation between January 2007 and August 2010. There were 3 fatalities and 15 cats survived (16% mortality rate). Two cases developed pelvic limb paresis 3-4 days post envenomation. There were no apparent adverse reactions to treatment with antivenom. CONCLUSIONS: Cats are presented infrequently for treatment of envenomation compared to dogs. Envenomation in cats should be treated according to guidelines established for people and dogs and administration of antivenom does not appear to be associated with adverse events. The mortality rate in this study was found to be 16%, which is higher than the mortality rate reported for dogs suspected of rattlesnake envenomation in a similar region (4.1%). Pelvic limb paresis may develop 3-4 days post envenomation but can resolve within 24 hours.

Mojave toxin-type ascending flaccid paralysis after an envenomation by a Southern Pacific Rattlesnake in a dog.

OBJECTIVE: To describe the clinical presentation and case management of a dog that developed ascending flaccid paralysis after being envenomated by a Southern Pacific rattlesnake. CASE SUMMARY: A dog was presented after it was bitten by a Southern Pacific rattlesnake. Only mild local edema and a minor coagulapathy developed, which is atypical for the Southern Pacific envenomation where hemotoxic effects are more commonly observed. Instead, a severe, rapidly progressing, ascending flaccid paralysis leading to acute respiratory failure, consistent with Mojave toxin, was seen. The patient was treated with repeated doses of antivenin and supported with mechanical ventilation. Despite clinical improvement of the paralysis over subsequent 3 days and successful weaning off the ventilator, the dog decompensated and succumbed to acute respiratory distress syndrome. NEW OR UNIQUE INFORMATION PROVIDED: The geographic region where this envenomation occurred has a documented population of Southern Pacific rattlesnakes with Mojave toxin in their venom. To the knowledge of the authors, this is the first reported case in the veterinary literature of an ascending flaccid paralysis, consistent with Mojave toxin, developing after an envenomation by a Southern Pacific rattlesnake.