Commensal-pathogen dynamics structure disease outcomes during Clostridioides difficile colonization.

Gastrointestinal colonization by Clostridioides difficile is common in healthcare settings and ranges in presentation from asymptomatic carriage to lethal C. difficile infection (CDI). We used a systems biology approach to investigate why patients colonized with C.

Commensal-pathogen dynamics structure disease outcomes during colonization.

Gastrointestinal colonization by is common in healthcare settings and ranges in clinical presentation from asymptomatic carriage to lethal infection (CDI). We used a systems biology approach to investigate why patients colonized with have a range of outcomes. Microbiota-humanization of germ-free mice with fecal samples from toxigenic C.

Gut microbiome correlates of recurrent urinary tract infection: a longitudinal, multi-center study.

Background: Urinary tract infections (UTI) affect approximately 250 million people annually worldwide. Patients often experience a cycle of antimicrobial treatment and recurrent UTI (rUTI) that is thought to be facilitated by a gut reservoir of uropathogenic (UPEC).

Methods: 125 patients with UTI caused by an antibiotic-resistant organism (ARO) were enrolled from July 2016 to May 2019 in a longitudinal, multi-center cohort study.

Genomic surveillance of transmission and virulence in a healthcare setting.

Unlabelled: infection (CDI) is a major cause of healthcare-associated diarrhea, despite the widespread implementation of contact precautions for patients with CDI. Here, we investigate strain contamination in a hospital setting and the genomic determinants of disease outcomes. Across two wards over 6 months, we selectively cultured from patients ( = 384) and their environments.

Genomic surveillance of transmission and virulence in a healthcare setting.

infection (CDI) is a major cause of healthcare-associated diarrhea, despite the widespread implementation of contact precautions for patients with CDI. Here, we investigate strain contamination in a hospital setting and genomic determinants of disease outcomes. Across two wards over six months, we selectively cultured from patients (n=384) and their environments.

Comparison of nucleic acid amplification test (NAAT) results using fresh and frozen stool specimens and rectal swabs.

Nucleic acid amplification tests (NAATs) are frequently used in research and diagnostic testing, but the effect of freezing specimens on NAAT performance is not well characterized. This study evaluated the concordance of NAAT results between fresh and frozen specimens (fecal and rectal swabs) and found it to be very good to excellent. The results indicate that frozen fecal and rectal swab specimens may be used for NAAT testing in research when fresh specimens are not available.

Early coronavirus disease 2019 (COVID-19) pandemic effects on individual-level risk for healthcare-associated infections in hospitalized patients.

Objective: We compared the individual-level risk of hospital-onset infections with multidrug-resistant organisms (MDROs) in hospitalized patients prior to and during the coronavirus disease 2019 (COVID-19) pandemic. We also quantified the effects of COVID-19 diagnoses and intrahospital COVID-19 burden on subsequent MDRO infection risk.

Design: Multicenter, retrospective, cohort study.

Risk factors for hospital-onset Clostridioides difficile infections before and during the severe acute respiratory syndrome coronavirus 2 pandemic.

In this retrospective cohort from 3 Missouri hospitals from January 2017 to August 2020, hospital-onset Clostridioides difficile infections were more common during the severe acute respiratory syndrome coronavirus 2 pandemic at the tertiary care hospital. Risk factors associated with hospital-onset C difficile infection included the year of hospitalization, age, high-risk antibiotic use, acid-reducing medications, chronic comorbidities, and severe acute respiratory syndrome coronavirus 2 infection.

Microbiology Clinical Culture Diagnostic Yields and Antimicrobial Resistance Proportions before and during the COVID-19 Pandemic in an Indian Community Hospital and Two US Community Hospitals.

Studies comparing the impact of the COVID-19 pandemic on diagnostic microbiology culture yields and antimicrobial resistance proportions in low-to-middle-income and high-income countries are lacking. A retrospective study using blood, respiratory, and urine microbiology data from a community hospital in India and two community hospitals (Hospitals A and B) in St. Louis, MO, USA was performed.

Personal protective equipment use among dental healthcare personnel during the coronavirus disease 2019 (COVID-19) pandemic and the impact of an educational video in clinical practice.

Objective: Dental healthcare personnel (DHCP) are at high risk of exposure to coronavirus disease 2019 (COVID-19). We sought to identify how DHCP changed their use of personal protective equipment (PPE) as a result of the COVID-19 pandemic, and to pilot an educational video designed to improve knowledge of proper PPE use.

Design: The study comprised 2 sets of semistructured qualitative interviews.

Longitudinal analysis of risk factors associated with severe acute respiratory coronavirus virus 2 (SARS-CoV-2) infection among hemodialysis patients and healthcare personnel in outpatient hemodialysis centers.

In this prospective, longitudinal study, we examined the risk factors for severe acute respiratory coronavirus virus 2 (SARS-CoV-2) infection among a cohort of chronic hemodialysis (HD) patients and healthcare personnel (HCPs) over a 6-month period. The risk of SARS-CoV-2 infection among HD patients and HCPs was consistently associated with a household member having SARS-CoV-2 infection.

Predictors of humoral response to SARS-CoV-2 mRNA vaccine BNT162b2 in patients receiving maintenance dialysis.

Objective: Patients on dialysis are at high risk for severe COVID-19 and associated morbidity and mortality. We examined the humoral response to SARS-CoV-2 mRNA vaccine BNT162b2 in a maintenance dialysis population.

Design: Single-center cohort study.

Assessment of dental health care personnel protocol deviations and self-contamination during personal protective equipment donning and doffing.

Background: Dental health care personnel (DHCP) may be at increased risk of exposure to severe acute respiratory syndrome coronavirus 2, the virus that causes COVID-19, as well as other clinically important pathogens. Proper use of personal protective equipment (PPE) reduces occupational exposure to pathogens. The authors performed an assessment of PPE donning and doffing practices among DHCP, using a fluorescent marker as a surrogate for pathogen transmission.

Epidemiology of Plasmid Lineages Mediating the Spread of Extended-Spectrum Beta-Lactamases among Clinical Escherichia coli.

The prevalence of extended-spectrum beta-lactamases (ESBLs) among clinical isolates of Escherichia coli has been increasing, with this spread driven by ESBL-encoding plasmids. However, the epidemiology of ESBL-disseminating plasmids remains understudied, obscuring the roles of individual plasmid lineages in ESBL spread. To address this, we performed an in-depth genomic investigation of 149 clinical ESBL-like E.

Persisting uropathogenic Escherichia coli lineages show signatures of niche-specific within-host adaptation mediated by mobile genetic elements.

Large-scale genomic studies have identified within-host adaptation as a hallmark of bacterial infections. However, the impact of physiological, metabolic, and immunological differences between distinct niches on the pathoadaptation of opportunistic pathogens remains elusive. Here, we profile the within-host adaptation and evolutionary trajectories of 976 isolates representing 119 lineages of uropathogenic Escherichia coli (UPEC) sampled longitudinally from both the gastrointestinal and urinary tracts of 123 patients with urinary tract infections.

Acute and persistent effects of commonly used antibiotics on the gut microbiome and resistome in healthy adults.

Antibiotics are deployed against bacterial pathogens, but their targeting of conserved microbial processes means they also collaterally perturb the commensal microbiome. To understand acute and persistent effects of antibiotics on the gut microbiota of healthy adult volunteers, we quantify microbiome dynamics before, during, and 6 months after exposure to 4 commonly used antibiotic regimens. We observe an acute decrease in species richness and culturable bacteria after antibiotics, with most healthy adult microbiomes returning to pre-treatment species richness after 2 months, but with an altered taxonomy, resistome, and metabolic output, as well as an increased antibiotic resistance burden.

SARS-CoV-2 Infection Risk Factors among Maintenance Hemodialysis Patients and Health Care Personnel In Outpatient Hemodialysis Centers.

Increased risk of SARS-CoV-2 infection was associated with community prevalence.Increased risk of SARS-CoV-2 infection was associated with exposure to infected family members and personal infection prevention measures.

Isolation of SARS-CoV-2 in Viral Cell Culture in Immunocompromised Patients With Persistently Positive RT-PCR Results.

Immunocompromised adults can have prolonged acute respiratory syndrome coronavirus 2 (SARS-CoV-2) positive RT-PCR results, long after the initial diagnosis of coronavirus disease 2019 (COVID-19). This study aimed to determine if SARS-CoV-2 virus can be recovered in viral cell culture from immunocompromised adults with persistently positive SARS-CoV-2 RT-PCR tests. We obtained 20 remnant SARS-CoV-2 PCR positive nasopharyngeal swabs from 20 immunocompromised adults with a positive RT-PCR test ≥14 days after the initial positive test.

Multi-omics investigation of -colonized patients reveals pathogen and commensal correlates of pathogenesis.

infection (CDI) imposes a substantial burden on the health care system in the United States. Understanding the biological basis for the spectrum of -related disease manifestations is imperative to improving treatment and prevention of CDI. Here, we investigate the correlates of asymptomatic colonization using a multi-omics approach.

Alternative Causes of Infectious Diarrhea in Patients with Negative Tests for Clostridoides Difficile.

Background: Hospitalized patients with diarrhea who have a negative Clostridoides difficile (C. difficile) test are not routinely evaluated for alternative causes of infectious diarrhea. This study assessed for potential infectious causes of diarrhea in hospitalized patients with an order for repeat C.

A randomized controlled trial of GG on antimicrobial-resistant organism colonization.

Objective: Alteration of the colonic microbiota following antimicrobial exposure allows colonization by antimicrobial-resistant organisms (AROs). Ingestion of a probiotic, such as Lactobacillus rhamnosus GG (LGG), could prevent colonization or infection with AROs by promoting healthy colonic microbiota. The purpose of this trial was to determine the effect of LGG administration on ARO colonization in hospitalized patients receiving antibiotics.

The Role of Diagnostic Stewardship in Testing: Challenges and Opportunities.

Purpose Of Review: Accurate and timely diagnosis of infection (CDI) is imperative to prevent transmission and reduce morbidity and mortality due to CDI, but CDI laboratory diagnostics are complex. The purpose of this article is to review the role of laboratory tests in the diagnosis of CDI, and the role of diagnostic stewardship in optimization of testing.

Recent Findings: Results from diagnostic tests should be interpreted with an understanding of the strengths and limitations inherent in each testing approach.

Microbiota restoration reduces antibiotic-resistant bacteria gut colonization in patients with recurrent Clostridioides difficile infection from the open-label PUNCH CD study.

Background: Once antibiotic-resistant bacteria become established within the gut microbiota, they can cause infections in the host and be transmitted to other people and the environment. Currently, there are no effective modalities for decreasing or preventing colonization by antibiotic-resistant bacteria. Intestinal microbiota restoration can prevent Clostridioides difficile infection (CDI) recurrences.

Randomized Controlled Trial of Oral Vancomycin Treatment in Clostridioides difficile-Colonized Patients.

infection (CDI) is most commonly diagnosed using nucleic acid amplification tests (NAAT); the low positive predictive value of these assays results in patients colonized with unnecessarily receiving CDI treatment antibiotics. The risks and benefits of antibiotic treatment in individuals with such cases are unknown. Fecal samples of NAAT-positive, toxin enzyme immunoassay (EIA)-negative patients were collected before, during, and after randomization to vancomycin ( = 8) or placebo ( = 7).

Impact of investigational microbiota therapeutic RBX2660 on the gut microbiome and resistome revealed by a placebo-controlled clinical trial.

Background: Intestinal microbiota restoration can be achieved by complementing a subject's perturbed microbiota with that of a healthy donor. Recurrent Clostridioides difficile infection (rCDI) is one key application of such treatment. Another emerging application of interest is reducing antibiotic-resistant genes (ARGs) and organisms (AROs).