Impact of metagenomic next-generation sequencing on clinical decision-making at an academic medical center, a retrospective study, Iowa, 2020-2022.

We assessed the impact of metagenomic next-generation sequencing (mNGS) on patient care using previously established criteria. Among 37 patients receiving mNGS testing, 16% showed results that had a positive clinical impact. While mNGS results may offer valuable supplementary information, results should be interpreted within the broader clinical context and evaluation.

Primary spontaneous listerial peritonitis.

A male in his mid-60s with chronic kidney disease, ischemic cardiomyopathy, and nonalcoholic cirrhosis due to congestive hepatopathy presented with fever and abdominal pain for two weeks. He underwent diagnostic paracentesis, which noted an ascitic neutrophil count over 7000/mm3. Gram stain of the ascitic fluid showed Gram-positive cocci. He was diagnosed with spontaneous bacterial peritonitis (SBP) and was started on ceftriaxone. Ascites cultures grew Listeria monocytogenes and antibiotics were changed to ampicillin. He received one week of ampicillin while inpatient and seven weeks of oral amoxicillin, at which point his ascitic neutrophil count was less than 250/mm3. He was continued on suppressive amoxicillin for an additional 14 weeks with no recurrence in over a year after the discontinuation of amoxicillin. Though uncommon, L. monocytogenes should be considered a pathogen causing SBP. Focal listerial infections can be treated with penicillins alone while invasive disease may require the addition of aminoglycosides.

Rates of Antimicrobial Resistance With Extended Oral Antibiotic Prophylaxis After Total Joint Arthroplasty.

Background: There is increased interest and utilization of extended oral antibiotic prophylaxis (EOAP) following primary and revision total hip arthroplasties (THAs) and total knee arthroplasties (TKAs). The purpose of this study was to look for potential associations between EOAP and differential rates of antimicrobial resistance or epidemiology of organisms causing periprosthetic joint infection (PJI) following primary and aseptic revision THAs/TKAs. Methods: Patients who developed PJI following a primary or aseptic revision TKA/THA at a single institution from 2009 to 2020 were retrospectively identified. Patients who received at least 7 days of EOAP following the surgery were noted. Rates of antimicrobial resistance were compared between standard antibiotic prophylaxis and EOAP cohorts using the Fisher's exact test. Results: One hundred twenty-eight cultures were obtained from 119 patients with PJI. Fourty-four cases (37%) developed PJI after EOAP. Staphylococcus aureus was the most frequently isolated organism (30% of all cultures; 78% were methicillin-sensitive). Rates of antimicrobial resistance were similar between standard antibiotic prophylaxis and EOAP cohorts in all but 2 instances: Increased resistance to erythromycin and trimethoprim-sulfamethoxazole was observed in coagulase-negative Staphylococci isolates in the EOAP cohort (89% vs 21%, P < .01; 44% vs 0%, P = .02). An increased frequency of gram-negative organisms was observed in the EOAP group (22% vs 8%, P = .03). Conclusions: Rates of antimicrobial resistance were not significantly different between EOAP and standard antibiotic prophylaxis cohorts except in coagulase-negative Staphylococci. The increased frequency of gram-negative infections was present in the EOAP cohort. Larger, multicenter studies are needed to better understand the impact of EOAP on antimicrobial resistance and PJI epidemiology. Level of Evidence: Level III; retrospective cohort study.

Days of Antibiotic Spectrum Coverage: A Novel Metric for Inpatient Antibiotic Consumption.

BACKGROUND: Days of therapy (DOT), the most widely used benchmarking metric for antibiotic consumption, may not fully measure stewardship efforts to promote use of narrow-spectrum agents and may inadvertently discourage the use of combination regimens when single-agent alternatives have greater adverse effects. To overcome the limitations of DOT, we developed a novel metric, days of antibiotic spectrum coverage (DASC), and compared hospital performances using this novel metric with DOT. METHODS: We evaluated 77 antibiotics in 16 categories of antibacterial activity to develop our spectrum scoring system. DASC was then calculated as cumulative daily antibiotic spectrum coverage (ASC) scores. To compare hospital benchmarking using DOT and DASC, we conducted a retrospective cohort study of adult patients admitted to acute care units within the Veterans Health Administration system in 2018. Antibiotic administration data were aggregated to calculate each hospital's DOT and DASC per 1000 days present (DP) for ranking. RESULTS: The ASC score for each antibiotic ranged from 2 to 15. There was little correlation between DOT per 1000 DP and DASC per DOT, indicating that lower antibiotic consumption at a hospital does not necessarily mean more frequent use of narrow-spectrum antibiotics. The differences in each hospital's ranking between DOT and DASC per 1000 DP ranged from -29.0% to 25.0%, respectively, with 27 hospitals (21.8%) having differences >10%. CONCLUSIONS: We propose a novel composite metric for antibiotic stewardship, DASC, that combines consumption and spectrum as a potential replacement for DOT. Further studies are needed to evaluate whether benchmarking using the DASC will improve evaluations of stewardship.

Laboratory Diagnosis and Monitoring of Viral Hepatitis.

Many microbes, toxins, autoimmune diseases, and neoplastic diseases may cause liver inflammation; however, 5 viruses whose main pathogenesis is liver disease are referred to as hepatitis A, B, C, D, and E viruses. These viruses cause a significant burden of global illness. With the exception of hepatitis A virus, all may cause chronic infection potentially leading to cirrhosis and hepatocellular carcinoma. Excellent serologic and nucleic acid detection methods are available for determining the precise cause and, in some cases, the duration of infection. Diagnostics are critical for identifying individuals needing treatment and for monitoring the treatment success.

Antimicrobial Susceptibility Patterns among a Large, Nationwide Cohort of Abiotrophia and Granulicatella Clinical Isolates.

Antimicrobial susceptibility patterns from 599 A. defectiva, G. adiacens, and G. elegans clinical isolates were determined by broth microdilution. We observed significant differences in susceptibility across species, particularly to penicillin and ceftriaxone, and across geographical regions. A. defectiva was the least susceptible species overall to penicillin. All isolates were susceptible to vancomycin and >90% were susceptible to levofloxacin.

Bacterial and viral co-infections complicating severe influenza: Incidence and impact among 507 U.S. patients, 2013-14.

BACKGROUND: Influenza acts synergistically with bacterial co-pathogens. Few studies have described co-infection in a large cohort with severe influenza infection. OBJECTIVES: To describe the spectrum and clinical impact of co-infections. STUDY DESIGN: Retrospective cohort study of patients with severe influenza infection from September 2013 through April 2014 in intensive care units at 33 U.S. hospitals comparing characteristics of cases with and without co-infection in bivariable and multivariable analysis. RESULTS: Of 507 adult and pediatric patients, 114 (22.5%) developed bacterial co-infection and 23 (4.5%) developed viral co-infection. Staphylococcus aureus was the most common cause of co-infection, isolated in 47 (9.3%) patients. Characteristics independently associated with the development of bacterial co-infection of adult patients in a logistic regression model included the absence of cardiovascular disease (OR 0.41 [0.23-0.73], p=0.003), leukocytosis (>11K/µl, OR 3.7 [2.2-6.2], p<0.001; reference: normal WBC 3.5-11K/µl) at ICU admission and a higher ICU admission SOFA score (for each increase by 1 in SOFA score, OR 1.1 [1.0-1.2], p=0.001). Bacterial co-infections (OR 2.2 [1.4-3.6], p=0.001) and viral co-infections (OR 3.1 [1.3-7.4], p=0.010) were both associated with death in bivariable analysis. Patients with a bacterial co-infection had a longer hospital stay, a longer ICU stay and were likely to have had a greater delay in the initiation of antiviral administration than patients without co-infection (p<0.05) in bivariable analysis. CONCLUSIONS: Bacterial co-infections were common, resulted in delay of antiviral therapy and were associated with increased resource allocation and higher mortality.

Severe Influenza in 33 US Hospitals, 2013-2014: Complications and Risk Factors for Death in 507 Patients.

BACKGROUND: Influenza A (H1N1) pdm09 became the predominant circulating strain in the United States during the 2013-2014 influenza season. Little is known about the epidemiology of severe influenza during this season. METHODS: A retrospective cohort study of severely ill patients with influenza infection in intensive care units in 33 US hospitals from September 1, 2013, through April 1, 2014, was conducted to determine risk factors for mortality present on intensive care unit admission and to describe patient characteristics, spectrum of disease, management, and outcomes. RESULTS: A total of 444 adults and 63 children were admitted to an intensive care unit in a study hospital; 93 adults (20.9%) and 4 children (6.3%) died. By logistic regression analysis, the following factors were significantly associated with mortality among adult patients: older age (>65 years, odds ratio, 3.1 [95% CI, 1.4-6.9], P=.006 and 50-64 years, 2.5 [1.3-4.9], P=.007; reference age 18-49 years), male sex (1.9 [1.1-3.3], P=.031), history of malignant tumor with chemotherapy administered within the prior 6 months (12.1 [3.9-37.0], P<.001), and a higher Sequential Organ Failure Assessment score (for each increase by 1 in score, 1.3 [1.2-1.4], P<.001). CONCLUSION: Risk factors for death among US patients with severe influenza during the 2013-2014 season, when influenza A (H1N1) pdm09 was the predominant circulating strain type, shifted in the first postpandemic season in which it predominated toward those of a more typical epidemic influenza season.

Haemophilus influenzae serotype f as a rare cause of septic arthritis.

Non-type B Haemophilus influenzae emerges as a new pathogen in the post H. influenzae serotype b vaccine era. We describe a case of polyarticular septic arthritis caused by H. influenzae serotype f in an adult. The patient was successfully treated with surgical debridement and antibiotic. To the best of our knowledge, this is the fourth reported case of H. influenzae serotype f septic arthritis in adults.

Pulmonary blastomycosis: a new endemic area in New York state.

We describe three cases of pulmonary blastomycosis in patients from central New York State (NYS). Two of these cases occurred in 2012, and in patients who resided in the same county. Moreover, two of these cases manifested with acute respiratory distress syndrome and survived. Interestingly, one of the two received corticosteroids and was extubated within 1 week. To the best of our knowledge, these are the first cases of human blastomycosis to be reported from NYS and we propose that corticosteroids administration might reduce hospitalisation time and ventilator-associated complications, even though it is not currently recommended in standard treatment.