Objective:Leukemic and hematopoietic cell transplant patients have one of the highest incidences of C. difficile infection (CDI). While CDI patients are considered the primary source of transmission, asymptomatic colonized patients (AC) can progress to CDI or contribute to in-unit transmission. We aim to quantify the roles of CDI and AC patients in C. difficile importation and transmission within oncological units. Design:Prospective cohort study. Setting:Two leukemia and HCT transplant units in a large tertiary care hospital in the US. Methods:We developed a stochastic, individual-based network model to simulate C. difficile acquisition and transmission. Data from cultures and nucleic acid amplification testing (NAAT) obtained at admission and weekly, and toxin enzyme immunoassay (EIA) tests used for CDI diagnosis were used to calibrate the model. Healthcare worker room assignments informed the network structure. Key parameters were estimated via particle filtering. Results:The model reproduced observed weekly test counts and transmission pairs. AC patients were the primary source of new colonizations: 51% were due to importation (of those, 88% were admitted as AC), and 49% were due to transmission (AC was the source in 92% of transmissions). Sensitivity analysis showed that these findings were most influenced by the colonization rate and rates of environmental contamination and cleaning. Conclusions:These findings reinforce the role of AC, particularly via admission importation, in sustaining C. difficile transmission in high-risk hospital settings. Infection control focused on CDI effectively reduced onward transmission, as indicated by CDI's low contribution to new colonizations.

In this prospective cohort study, 30 health care personnel with a known SARS-CoV-2 exposure provided oropharyngeal swabs for polymerase chain reaction (PCR) testing and blood specimens for serologic testing at 2 time points postexposure. At a median 7days postexposure (range, 1-13days), none had a positive PCR and 1 (3%) had a reactive antibody test. No additional participants were PCR or antibody-positive at a median 25days postexposure (range, 14-36days).

BACKGROUND:Opportunistic premise plumbing pathogens (OPPPs) can establish reservoirs in hospital plumbing and cause healthcare associated infections (HAIs). There is currently no widely accepted protocol for sink drain cleaning to reduce OPPP burden. METHODS:We implemented a sink cleaning intervention in 12 intensive care unit (ICU) rooms. At low frequency (1×/week) and high frequency (5×/week) intervals, we wiped sink surfaces with 10% bleach wipes and pumped a foamed preacid disinfectant into sink drains. We also maintained untreated rooms (0×/week). We used E-swabs to sample sink drains and surrounding surfaces during one baseline, two intervention, and two post-intervention periods over 23 months. Samples were selectively cultured for bacterial growth and antimicrobial resistant organism (ARO) isolation. We conducted whole-genome sequencing (WGS) on Pseudomonas spp. and Stenotrophomonas spp. isolates to track impacts on reservoirs over time. We also collected and analysed clinical isolates from patients occupying the study rooms and information about HAIs that occurred. FINDINGS:The intervention reduced the proportion of sink drains yielding Gram-negative bacteria by up to 85% (95% CI: 56-114%) in high frequency rooms versus the baseline period, but this was not significant in low frequency rooms. It also reduced the proportion of sink drains yielding Pseudomonas spp. and Stenotrophomonas spp. by up to 100% (95% CI: 79-121%) and 95% (95% CI: 65-125%) versus the baseline period in high frequency rooms and up to 71% (95% CI: 50-92%, p < 0.001) and 66% (95% CI: 27-105%, p < 0.05) in low frequency rooms, respectively. WGS showed strains of Pseudomonas aeruginosa and Stenotrophomonas maltophilia that colonised sink drains for over 3 years across two studies. Following the intervention periods, P. aeruginosa reservoirs were replaced with new strains, while S. maltophilia reservoirs returned with the same strains. INTERPRETATION:This environmental hygiene intervention may be effective in reducing the burden of OPPPs in hospital sinks. FUNDING:Agency for Healthcare Research and Quality (R01HS027621), National Institute of Allergy and Infectious Diseases (U01AI123394, 1K23AI137321), Barnes-Jewish Hospital Foundation (5102), Washington University Institute of Clinical and Translational Sciences (4462) from the National Center for Advancing Translational Sciences (UL1TR002345).

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 Escherichia coli (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. Multivariate statistical models were used to assess the relationship between uropathogen colonization and recurrent UTI (rUTI), controlling for clinical characteristics. 644 stool samples and 895 UPEC isolates were interrogated for taxonomic composition, antimicrobial resistance genes, and phenotypic resistance. Cohort UTI gut microbiome pro fi les were compared against published healthy and UTI reference microbiomes, as well as assessed within-cohort for timepoint- and recurrence-speci fi c differences. Findings Risk of rUTI was not independently associated with clinical characteristics. The UTI gut microbiome was distinct from healthy reference microbiomes in both taxonomic composition and antimicrobial resistance gene (ARG) burden, with 11 differentially abundant taxa at the genus level. rUTI and non-rUTI gut microbiomes in the cohort did not generally differ, but gut microbiomes from urinary tract colonized patients were elevated in E. coli abundance 7 - 14 days post-antimicrobial treatment. Corresponding UPEC gut isolates from urinary tract colonizing lineages showed elevated phenotypic resistance against 11 of 23 tested drugs compared to noncolonizing lineages. Interpretation The gut microbiome is implicated in UPEC urinary tract colonization during rUTI, serving as an ARGenriched reservoir for UPEC. UPEC can asymptomatically colonize the gut and urinary tract, and post-antimicrobial blooms of gut E. coli among urinary tract colonized patients suggest that cross -habitat migration of UPEC is an important mechanism of rUTI. Thus, treatment duration and UPEC populations in both the urinary and gastrointestinal tract should be considered in treating rUTI and developing novel therapeutics. Copyright (c) 2024 The Authors. Published by Elsevier Ltd. This is an open access article under the CC BY -NC -ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). Copyright (c) 2024 The Authors. Published by Elsevier Ltd. This is an open access article under the CC BY -NC -ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).

ABSTRACT Nucleic acid amplification tests (NAATs) are frequently used in Clostridioides difficile research and diagnostic testing, but the effect of freezing specimens on C. difficile NAAT performance is not well characterized. We compared C. difficile NAAT results between fresh and frozen fecal ( n = 354) and rectal swab specimens (eSwab) ( n = 132) using the Xpert system. Specimens were collected prospectively from 384 hospitalized patients admitted to the hematopoietic cell transplant and acute leukemia wards at a tertiary care hospital. Categorical concordance of NAAT results (agreement of positive/positive or negative/negative) was excellent between fresh and frozen conditions for fecal specimens (Kappa = 0.92) and very good for rectal swabs (Kappa = 0.78). Cycle threshold value correlation was similarly consistent between fresh and frozen conditions for swabs and stool specimens (Spearman’s correlation = 0.88). These results support the use of frozen fecal and rectal swab specimens to provide accurate results for research purposes when C. difficile NAAT testing on fresh specimens is not available or feasible. IMPORTANCE Nucleic acid amplification tests (NAATs) are frequently used in Clostridioides difficile research and diagnostic testing, but the effect of freezing specimens on C. difficile 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 C. difficile NAAT testing in research when fresh specimens are not available.

Clostridioides difficile 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 C. difficile from patients (n = 384) and their environments. Whole-genome sequencing (WGS) of 146 isolates revealed that most C. difficile isolates were from clade 1 (131/146, 89.7%), while only one isolate of the hypervirulent ST1 was recovered. Of culture-positive admissions (n = 79), 19 (24%) patients were colonized with toxigenic C. difficile on admission to the hospital. We defined 25 strain networks at ≤2 core gene single nucleotide polymorphisms; two of these networks contain strains from different patients. Strain networks were temporally linked (P < 0.0001). To understand the genomic correlates of the disease, we conducted WGS on an additional cohort of C. difficile (n = 102 isolates) from the same hospital and confirmed that clade 1 isolates are responsible for most CDI cases. We found that while toxigenic C. difficile isolates are associated with the presence of cdtR, nontoxigenic isolates have an increased abundance of prophages. Our pangenomic analysis of clade 1 isolates suggests that while toxin genes (tcdABER and cdtR) were associated with CDI symptoms, they are dispensable for patient colonization. These data indicate that toxigenic and nontoxigenic C. difficile contamination persist in a hospital setting and highlight further investigation into how accessory genomic repertoires contribute to C. difficile colonization and disease. IMPORTANCE:Clostridioides difficile infection remains a leading cause of hospital-associated diarrhea, despite increased antibiotic stewardship and transmission prevention strategies. This suggests a changing genomic landscape of C. difficile. Our study provides insight into the nature of prevalent C. difficile strains in a hospital setting and transmission patterns among carriers. Longitudinal sampling of surfaces and patient stool revealed that both toxigenic and nontoxigenic strains of C. difficile clade 1 dominate these two wards. Moreover, quantification of transmission in carriers of these clade 1 isolates underscores the need to revisit infection prevention measures in this patient group. We identified unique genetic signatures associated with virulence in this clade. Our data highlight the complexities of preventing transmission of this pathogen in a hospital setting and the need to investigate the mechanisms of in vivo persistence and virulence of prevalent lineages in the host gut microbiome.

Abstract Background Clostridioides difficile (CD) colonization is common among hospitalized patients. Screening for toxigenic CD (TCD) colonization with rectal swab nucleic acid amplification tests (NAAT) may identify people at risk for CDI and help prevent onward TCD transmission, especially in immunocompromised patients with long hospitalizations. The study objective was to test whether rectal swab NAAT could detect TCD colonized patients and whether NAAT results identify patients that contribute to environmental contamination. Methods This was a prospective cohort study on two BMT/Leukemia units. Stool specimens, rectal swabs, and environmental swabs (bedrail, room sink, keyboard) were collected from patients at admission and weekly and cultured semi-quantitatively for TCD. NAAT (Cepheid) was performed on rectal swabs (eSwabs; Copan Diagnostics). The relationship between stool TCD concentration, NAAT Ct, and a positive environmental culture was evaluated using univariate logistic regression. Bleach was used for daily and terminal discharge cleaning of all rooms. Toxigenicity was determined by detection of tcdA or tcdB by whole genome sequencing (WGS). Results From January 2019 - July 2019, 659 stool specimens and 495 rectal swabs were collected from 384 patients. Specimens from 554 patient-days were cultured and 126 (23%) were positive. Of those, 88 (70%) were TCD. 21 of 987 (2%) environmental swabs were TCD positive; 18 (86%) were from bedrails. Among 61 unique patient calendar days with paired rectal swab NAAT and stool culture results (paired samples), overall sensitivity of rectal swab NAAT to detect toxigenic CD colonization compared to culture was 44%, with 4/16 (25%) of people colonized with > 0 - < 10,000 CFU/g of TCD and 7/9 (78%) with ≥ 10,000 CFU/g TCD (Figure 1). There was no relationship between stool culture or rectal swab NAAT result and risk of a positive environmental swab (Figure 2). Figure 1. Toxigenic C. difficile semi-quantitative culture and rectal swab NAAT on paired patient-day of specimen collection (N=61 patient-days) Figure 2. Toxigenic C. difficile semi-quantitative stool and rectal swab NAAT results and environmental contamination by paired patient-day of specimen collection Conclusion Rectal swab NAAT may not be sufficiently sensitive to screen for TCD colonization that contributes to environmental contamination. Disclosures Erik R. Dubberke, MD, MSPH, Abbott: Advisor/Consultant|AstraZeneca: Advisor/Consultant|Ferring Pharmaceuticals: Advisor/Consultant|Ferring Pharmaceuticals: Grant/Research Support|Merck and Co.: Advisor/Consultant|Pfizer: Advisor/Consultant|Pfizer: Grant/Research Support|Seres Therapeutics: Advisor/Consultant|Summit: Advisor/Consultant|Theriva Biologics: Grant/Research Support

AbstractClostridioides difficileinfection (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 culturedC. difficilefrom patients (n=384) and their environments. Whole-genome sequencing (WGS) of 146 isolates revealed that mostC. difficileisolates were from clade 1 (131/146, 89.7%), while only one isolate of the hypervirulent ST1 was recovered. Of culture-positive admissions (n=79), 19 (24%) of patients were colonized with toxigenicC. difficileon admission to the hospital. We defined 25 strain networks at ≤ 2 core gene SNPs; 2 of these networks contain strains from different patients. Strain networks were temporally linked (p<0.0001). To understand genomic correlates of disease, we conducted WGS on an additional cohort ofC. difficile(n=102 isolates) from the same hospital and confirmed that clade 1 isolates are responsible for most CDI cases. We found that while toxigenicC. difficileisolates are associated with the presence ofcdtR, nontoxigenic isolates have an increased abundance of prophages. Our pangenomic analysis of clade 1 isolates suggests that while toxin genes (tcdABER and cdtR) were associated with CDI symptoms, they are dispensable for patient colonization. These data indicate toxigenic and nontoxigenicC. difficilecontamination persists in a hospital setting and highlight further investigation into how accessory genomic repertoires contribute toC. difficilecolonization and disease.

Abstract Objective: To determine the prevalence of severe acute respiratory coronavirus virus 2 (SARS-CoV-2) IgG nucleocapsid (N) antibodies among healthcare personnel (HCP) with no prior history of COVID-19 and to identify factors associated with seropositivity. Design: Prospective cohort study. Setting: An academic, tertiary-care hospital in St. Louis, Missouri. Participants: The study included 400 HCP aged ≥18 years who potentially worked with coronavirus disease 2019 (COVID-19) patients and had no known history of COVID-19; 309 of these HCP also completed a follow-up visit 70–160 days after enrollment. Enrollment visits took place between September and December 2020. Follow-up visits took place between December 2020 and April 2021. Methods: At each study visit, participants underwent SARS-CoV-2 IgG N-antibody testing using the Abbott SARS-CoV-2 IgG assay and completed a survey providing information about demographics, job characteristics, comorbidities, symptoms, and potential SARS-CoV-2 exposures. Results: Participants were predominately women (64%) and white (79%), with median age of 34.5 years (interquartile range [IQR], 30–45). Among the 400 HCP, 18 (4.5%) were seropositive for IgG N-antibodies at enrollment. Also, 34 (11.0%) of 309 were seropositive at follow-up. HCP who reported having a household contact with COVID-19 had greater likelihood of seropositivity at both enrollment and at follow-up. Conclusions: In this cohort of HCP during the first wave of the COVID-19 pandemic, ∼1 in 20 had serological evidence of prior, undocumented SARS-CoV-2 infection at enrollment. Having a household contact with COVID-19 was associated with seropositivity.

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. We show that lineages persisting in both niches within a patient exhibit increased allelic diversity. Habitat-specific selection results in niche-specific adaptive mutations and genes, putatively mediating fitness in either environment. Within-lineage inter-habitat genomic plasticity mediated by mobile genetic elements (MGEs) provides the opportunistic pathogen with a mechanism to adapt to the physiological conditions of either habitat, and reduced MGE richness is associated with recurrence in gut-adapted UPEC lineages. Collectively, our results establish niche-specific adaptation as a driver of UPEC within-host evolution.

Abstract In a prospective cohort of healthcare personnel (HCP), we measured severe acute respiratory syndrome coronavirus virus 2 (SARS-CoV-2) nucleocapsid IgG antibodies after SARS-CoV-2 infection. Among 79 HCP, 68 (86%) were seropositive 14–28 days after their positive PCR test, and 54 (77%) of 70 were seropositive at the 70–180-day follow-up. Many seropositive HCP (95%) experienced an antibody decline by the second visit.

A gold standard diagnostic for Clostridioides difficile infection (CDI) does not exist. An area of controversy is how to manage patients whose stool tests positive by nucleic acid amplification tests but negative by toxin enzyme immunoassay.