Burden of Antimicrobial Resistance in Adult Hospitalized Patients With Cancer: A Multicenter Analysis.

Background: Infections are a leading cause of death in patients with cancer, but the proportion and rate of antimicrobial resistance (AMR) in hospitalized patients with cancer are not well understood.

Methods: This retrospective, cross-sectional evaluation of AMR assessed hospitalized adult patients in 168 United States (US) healthcare facilities between April 2018 and December 2022. Nonduplicate, noncontaminant Gram-negative and Gram-positive bacteria recovered from various samples (blood, respiratory, urine, etc.

Emergence of transmissible SARS-CoV-2 variants with decreased sensitivity to antivirals in immunocompromised patients with persistent infections.

We investigated the impact of antiviral treatment on the emergence of SARS-CoV-2 resistance during persistent infections in immunocompromised patients (n = 15). All patients received remdesivir and some also received nirmatrelvir-ritonavir (n = 3) or therapeutic monoclonal antibodies (n = 4). Sequence analysis showed that nine patients carried viruses with mutations in the nsp12 (RNA dependent RNA polymerase), while four had viruses with nsp5 (3C protease) mutations.

Clinical Course, Antifungal Susceptibility, and Genomic Sequencing of Trichophyton indotineae.

Importance: Trichophyton indotineae is an emerging dermatophyte causing outbreaks of extensive tinea infections often unresponsive to terbinafine. This species has been detected worldwide and in multiple US states, yet detailed US data on infections with T indotineae are sparse and could improve treatment practices and medical understanding of transmission.

Objective: To correlate clinical features of T indotineae infections with in vitro antifungal susceptibility testing results, squalene epoxidase gene sequence variations, and isolate relatedness using whole-genome sequencing.

High touch surface bioburden associated with the use of disinfectants with and without continuously active disinfection in ambulatory care settings.

A quaternary ammonium and alcohol-based disinfectant with reported continuous activity demonstrated reduced microbial buildup on surfaces over time compared to routine disinfectants without continuous activity in and hospital studies. We compared these disinfectants in ambulatory settings and found no difference in bioburden on high-touch surfaces over time.

Comparative genomics reveals the correlations of stress response genes and bacteriophages in developing antibiotic resistance of .

is the second most common bacteria associated with urinary tract infections (UTIs) in women. The antimicrobial treatment regimen for uncomplicated UTI is normally nitrofurantoin, trimethoprim-sulfamethoxazole (TMP-SMX), or a fluoroquinolone without routine susceptibility testing of recovered from urine specimens. However, TMP-SMX-resistant has been detected recently in UTI patients, as well as in our cohort.

A Distinct Nasal Microbiota Signature in Peritoneal Dialysis Patients.

Key Points: , , , and are the most common genera in the anterior nares. The nasal abundance of is inversely correlated with the nasal abundance of . Peritoneal dialysis patients have a distinctly diverse representation of and in their anterior nares.

Uncharacterized and lineage-specific accessory genes within the pan-genome landscape.

is a Gram-negative bacterium recognized for its unique swarming motility and urease activity. A previous proteomic report on four strains hypothesized that, unlike other Gram-negative bacteria, may not exhibit significant intraspecies variation in gene content. However, there has not been a comprehensive analysis of large numbers of genomes from various sources to support or refute this hypothesis.

A Distinct Nasal Microbiota Signature in Peritoneal Dialysis Patients.

Rationale & Objective: The nasal passages harbor both commensal and pathogenic bacteria. In this study, we sought to characterize the anterior nasal microbiota in PD patients using 16S rRNA gene sequencing.

Study Design: Cross-sectional.

Distinct Laboratory Test Result Profiles Between SARS-CoV-2 and Seasonable Influenza Infected Patients.

Objective: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and influenza viruses are contagious respiratory pathogens with similar symptoms but require different treatment and management strategies. This study investigated the differences in laboratory test result profiles between SARS-CoV-2 and influenza infected patients upon presentation to emergency department (ED).

Methods: Laboratory test results and demographic information from 723 influenza positive (2018/1/1 to 2020/3/15) and 1,281 SARS-CoV-2 positive (2020/3/11 to 2020/6/30) ED patients were retrospectively analyzed.

Successful diagnostic stewardship for testing in pediatrics.

Objective: To reduce both inappropriate testing for and diagnosis of healthcare-onset (HO) infections (CDIs).

Design: We performed a retrospective analysis of testing from hospitalized children before (October 2017-October 2018) and after (November 2018-October 2020) implementing restrictive computerized provider order entry (CPOE).

Setting: Study sites included hospital A (a ∼250-bed freestanding children's hospital) and hospital B (a ∼100-bed children's hospital within a larger hospital) that are part of the same multicampus institution.

Comparison between Perianal Swab and Stool Specimens for Detecting Colonization with Extended-Spectrum Beta-Lactamase-Producing and Fluoroquinolone-Resistant .

Stool specimens are frequently used to detect gastrointestinal tract colonization with antimicrobial-resistant enteric bacteria, but they cannot be rapidly collected. Perianal swab specimens can be collected more quickly and efficiently, but data evaluating their suitability as a specimen type for this purpose are sparse. We performed selective culture for extended-spectrum β-lactamase-producing (ESBL-E) and fluoroquinolone-resistant (FQRE) using paired perianal swab and stool specimens that were collected within 1 day of each other from hematopoietic cell transplant recipients and patients with acute leukemia.

Laboratory Interventions to Eliminate Unnecessary Rapid COVID-19 Testing During a Reagent Shortage.

Objectives: In the fall of 2020, US medical centers were running out of rapid coronavirus disease 2019 (COVID-19) tests. The aim of this study is to evaluate the impact of an intervention to eliminate rapid test misutilization and to quantify the effect of the countermeasures to control rapid test ordering using a test utilization dashboard.

Methods: Interventions were made to preserve a severely limited supply of rapid diagnostic tests based on real-time analysis of a COVID-19 test utilization dashboard.

Partial ORF1ab Gene Target Failure with Omicron BA.2.12.1.

Mutations in the genome of SARS-CoV-2 can affect the performance of molecular diagnostic assays. In some cases, such as S-gene target failure, the impact can serve as a unique indicator of a particular SARS-CoV-2 variant and provide a method for rapid detection. Here, we describe partial ORF1ab gene target failure (pOGTF) on the cobas SARS-CoV-2 assays, defined by a ≥2-thermocycle delay in detection of the ORF1ab gene compared to that of the E-gene.

Prevalence and Characterization of the Cefazolin Inoculum Effect in North American Methicillin-Susceptible Staphylococcus aureus Isolates.

Antistaphylococcal penicillins and cefazolin remain the primary treatments for infections with methicillin-susceptible Staphylococcus aureus (MSSA). The cefazolin inoculum effect (CzIE) causes the cefazolin MIC to be elevated in proportion to the number of bacteria in the inoculum. The objective of this multicenter study was to evaluate the prevalence of the CzIE in North American MSSA isolates.

Impact of a Rapid Molecular Test for Klebsiella pneumoniae Carbapenemase and Ceftazidime-Avibactam Use on Outcomes After Bacteremia Caused by Carbapenem-Resistant Enterobacterales.

Background: Patients with bacteremia due to carbapenem-resistant Enterobacterales (CRE) experience delays until appropriate therapy and high mortality rates. Rapid molecular diagnostics for carbapenemases and new β-lactam/β-lactamase inhibitors may improve outcomes.

Methods: We conducted an observational study of patients with CRE bacteremia from 2016 to 2018 at 8 New York and New Jersey medical centers and assessed center-specific clinical microbiology practices.

System-wide transcriptome damage and tissue identity loss in COVID-19 patients.

The molecular mechanisms underlying the clinical manifestations of coronavirus disease 2019 (COVID-19), and what distinguishes them from common seasonal influenza virus and other lung injury states such as acute respiratory distress syndrome, remain poorly understood. To address these challenges, we combine transcriptional profiling of 646 clinical nasopharyngeal swabs and 39 patient autopsy tissues to define body-wide transcriptome changes in response to COVID-19. We then match these data with spatial protein and expression profiling across 357 tissue sections from 16 representative patient lung samples and identify tissue-compartment-specific damage wrought by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, evident as a function of varying viral loads during the clinical course of infection and tissue-type-specific expression states.

Mechanism of Action and Resistance Evasion of an Antimicrobial Oligomer against Multidrug-Resistant Gram-Negative Bacteria.

The last resort for treating multidrug-resistant (MDR) and other MDR Gram-negative bacteria is a class of antibiotics called the polymyxins; however, polymyxin-resistant isolates have emerged. In response, antimicrobial peptides (AMPs) and their synthetic mimetics have been investigated as alternative therapeutic options. Oligothioetheramides (oligoTEAs) are a class of synthetic, sequence-defined oligomers composed of -allylacrylamide monomers and an abiotic dithiol backbone that is resistant to serum degradation.

Peritoneal Effluent Cell-Free DNA Sequencing in Peritoneal Dialysis Patients With and Without Peritonitis.

Rationale & Objective: Conventional culture can be insensitive for the detection of rare infections and for the detection of common infections in the setting of recent antibiotic usage. Patients receiving peritoneal dialysis (PD) with suspected peritonitis have a significant proportion of negative conventional cultures. This study examines the utility of metagenomic sequencing of peritoneal effluent cell-free DNA (cfDNA) for evaluating the peritoneal effluent in PD patients with and without peritonitis.

The Diagnostic Accuracy Of Procalcitonin for Urinary Tract Infection in Hospitalized Older Adults: a Prospective Study.

Background: The diagnosis of urinary tract infection (UTI) is challenging among hospitalized older adults, particularly among those with altered mental status.

Objective: To determine the diagnostic accuracy of procalcitonin (PCT) for UTI in hospitalized older adults.

Design: We performed a prospective cohort study of older adults (≥65 years old) admitted to a single hospital with evidence of pyuria on urinalysis.