Background: Methicillin-resistant S. aureus (MRSA) is known to cause frequent and severe infections in community living centers, potentially resulting in significant mortality for elderly patients. More research is needed to understand how to utilize genomic and epidemiological data to understand characteristics that may lead to increased transmission. We hypothesized that combining genomic and epidemiological information to sample patients and their environments during long-term stays, we will be able to capture a diverse set of MRSA strains. Method: This work included genome sequencing of patient and environmental samples from 11 patients within the VA Ann Arbor Healthcare System from May 4, 2021- November 16, 2022. All 11 patients tested positive for MRSA during their stay (mean days = 31). Patient and environmental samples were taken throughout their stays, screened for MRSA, and whole-genome sequenced. Single nucleotide variants (SNVs) were identified by mapping reads and calling variants against strain-specific reference genomes. We used ape v5.6-2 in R v4.2.2 to analyze and infer evolution, acquisition, and transmission events based on pairwise SNV distances. Genomic clusters were determined using stats v3.6.2, with a SNV distance threshold of 20. Result: Samples that were collected from patient bodily sites were able to reveal 20 distinct genomic clusters of MRSA (patient hands: n = 10, nares: n = 7, groin: n = 3). Environmental samples from patient environments also revealed distinct genomic MRSA clusters (tv remote: n = 9, toilet seat and bed rail: n = 6, table top, bed control, and call button: n = 5, bed curtain: n = 4, pulse ox = 2, cell phone, tray, pulse ox, mat, body hoist wrap, and bed: n = 1). Conclusion: The identification of various genomic clusters from patients and their environmental reservoirs suggests intrahost variation that can only be captured by using a more holistic approach of integrating epidemiology and genomic sequencing. Developing studies that incorporate genomic data, various environmental sources, and multiple isolates over time within community living centers can increase our understanding of strains that are more likely to transmit, survive on living and non-living surfaces and therefore lead to improved recommendation for infection prevention interventions and drivers of endemicity.

Disclosure: Lona Mody: NIH, VA, CDC, Kahn Foundation; Honoraria: UpToDate; Contracted Research: Nano-Vibronix

Background: Nursing homes (NHs) have high prevalence of multi-drug resistant organisms (MDROs) with rates exceeding those in hospitals. This study proposes quantifying patients’ risk of MDRO colonization and creating a risk profile for the NH patient populations to assist in reducing MDRO burden in health care facilities. Methods: We assessed a risk classification model using data from a prospective cohort study (2018 Pathways study). Patient sample included 783 newly admitted patients followed for up to 180 days and 9,587 samples collected from patients during 2,089 visits. Individual risk factors of MDRO colonization were assessed using unadjusted logistic regression, and patients were risk classified based on number of risk factors. Multivariate regression was performed to obtain odds of MDRO colonization for patient risk groups adjusting for patient age, sex, race, and length of NH stay (LOS). The risk classification tool developed using Pathways data was also tested among a sample of NH residents from Veterans Administration (N=190). Results: The patient sample (Pathways data) was 43.2% male, 37.2% Black with a mean age 74 years. 69.3% were colonized with a MDRO during the study. In unadjusted regression, recent antibiotic use (p<.001), open wounds (p<.05), use of urinary catheter or feeding tube (p<.001), functional disability (p<.001), diabetes (p<.01), and preadmission hospital stay over 14 days (p<.001) were associated with colonization, while Charlson comorbidity score, age, sex, and race were not. In adjusted analysis (c-statistic=0.75), a patient’s colonization risk increased with the number of risk factors (Figure 1), with 47.2% expected colonization among patients with none of the risk factors and 86.7% expected colonization among patients with four or more risk factors. The risk classification model had similar performance among male and female patients, and among Black and White patients (Figure 2). Secondary analysis using data obtained from separate, Veterans Administration facilities provided preliminary validation of the risk scoring tool. The model had acceptable fit (c-statistic=0.71). Veterans with four or more risk factors had 87.8% expected probability of MDRO colonization compared with 39.6% colonization among those without any risk factors. Veterans with less than four risk factors also had higher colonization, but these differences were not statistically significant. Conclusions. Despite system-wide efforts to reduce MDRO burden, prevalence of MDRO colonization remains high in NHs. The risk classification tool can assist in early identification of most vulnerable NH patients to direct targeted interventions such as education, enhanced environmental cleaning, and active surveillance.

Disclosure: Lona Mody: NIH, VA, CDC, Kahn Foundation; Honoraria: UpToDate; Contracted Research: Nano-Vibronix

Background: Nursing home (NH) residents are at high risk of COVID-19 from exposure to infected staff and other residents. Understanding SARS-CoV-2 viral RNA kinetics in residents and staff can guide testing, isolation, and return to work recommendations. We sought to determine the duration of antigen test and polymerase chain reaction (PCR) positivity in a cohort of NH residents and staff. Methods: We prospectively collected data on SARS-CoV-2 viral kinetics from April 2023 through November 2023. Staff and residents could enroll prospectively or upon a positive test (identified through routine clinical testing, screening, or outbreak response testing). Participating facilities performed routine clinical testing; asymptomatic testing of contacts was performed within 48 hours if an outbreak or known exposure occurred and upon (re-) admission. Enrolled participants who tested positive for SARS-CoV-2 were re-tested daily for 14 days with both nasal antigen and nasal PCR tests. All PCR tests were run by a central lab with the same assay. We conducted a Kaplan-Meier survival analysis on time to first negative test restricted to participants who initially tested positive (day zero) and had at least one test ≥10 days after initially testing positive with the same test type; a participant could contribute to both antigen and PCR survival curves. We compared survival curves for staff and residents using the log-rank test. Results: Twenty-four nursing homes in eight states participated; 587 participants (275 residents, 312 staff) enrolled in the evaluation, participants were only tested through routine clinical or outbreak response testing. Seventy-two participants tested positive for antigen; of these, 63 tested PCR-positive. Residents were antigen- and PCR-positive longer than staff (Figure 1), but this finding is only statistically significant (p=0.006) for duration of PCR positivity. Five days after the first positive test, 56% of 50 residents and 59% of 22 staff remained antigen-positive; 91% of 44 residents and 79% of 19 staff were PCR-positive. Ten days after the first positive test, 22% of 50 residents and 5% of 22 staff remained antigen-positive; 61% of 44 residents and 21% of 19 staff remained PCR-positive. Conclusions: Most NH residents and staff with SARS-CoV-2 remained antigen- or PCR-positive 5 days after the initial positive test; however, differences between staff and resident test positivity were noted at 10 days. These data can inform recommendations for testing, duration of NH resident isolation, and return to work guidance for staff. Additional viral culture data may strengthen these conclusions.

Disclosure: Stefan Gravenstein: Received consulting and speaker fees from most vaccine manufacturers (Sanofi, Seqirus, Moderna, Merck, Janssen, Pfizer, Novavax, GSK, and have or expect to receive grant funding from several (Sanofi, Seqirus, Moderna, Pfizer, GSK). Lona Mody: NIH, VA, CDC, Kahn Foundation; Honoraria: UpToDate; Contracted Research: Nano-Vibronix

Background: Veterans Health Administration (VHA) community living centers (CLCs) provide postacute and long-term care. CLC veterans visit myriad locations outside their rooms (eg, rehabilitation, dialysis). Pathogen transmission during out-of-room visits is unknown. Methods: We recruited newly admitted veterans at 3 CLCs. After obtaining informed consent, we cultured nares, groin, hands, and 7 surfaces in the patient rooms. We accompanied veterans to up to 5 out-of-room visits and cultured patients’ hands and surfaces they touched. We tested for multidrug-resistant organisms (MDROs) including methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant Enterococcus (VRE), and quinolone, carbapenem, and/or ceftazidime-resistant gram-negative bacteria (R-GNB). We defined transmission as a positive culture following an initial negative culture during the same visit. Results: We enrolled 137 veterans (median follow-up, 29 days; mean, 5.9 visits); 97% were postacute patients. We conducted 539 patient-room sampling visits (mean, 3.9 per veteran; 5,490 swabs) and accompanied 97 veterans to 266 out-of-room sampling visits (mean, 2.7 per veteran; 2,360 swabs). Of 137 patients, 47 (35%) were colonized with an MDRO at enrollment and 74 (58%) of 128 patients were colonized on any follow-up patient-room visits. Of 133 patients, 55 (41%) acquired a new MDRO, most often VRE (31 of 97, 32%). In patient rooms, toilet seats [114 (21%) of 538], curtains [101 (19%) of 530] and bedrails [98 (18%) of 539] were most frequently contaminated. Among 266 out-of-room visits, 17% had surfaces contaminated with MDROs, most commonly involving dialysis [4 (31%) of 13], radiology [2 (25%) of 8], and rehabilitation therapy [29 (18%) of 159] (Fig. 1).Transmission of MDROs during out-of-room visits was common and occurred in 18% of visits with 8% (9 MRSA and 12 VRE) acquiring a new MDRO on their hands and 12% (9 MRSA and 23 VRE) of MDRO transmission occurring from hands to a surface that the patient touched (Fig. 1). In 18 (58%) of 31 cases, the organism transmitted to a surface was on patient hands at the start of the visit. Transmission was most common during visits to dialysis (3 to patients and 2 to surfaces), radiology (1 to a patient and 2 to surfaces), and rehabilitation therapy (13 to patients and 21 to surfaces) (Fig. 2). Conclusions: New MDRO acquisition during VHA CLC stay was common, and nearly one-fifth of out-of-room visits resulted in MDRO transmission. Our analyses suggest that veterans’ hands may shed MDROs (MRSA and VRE) to surfaces. Interventions to reduce MDRO transmission during visits for rehabilitation, dialysis, and other therapies are needed.

Disclosures: None

Background and objectives: Patients with functional disabilities are at higher risk of adverse outcomes, including infections. Although healthcare worker hand contamination has long been recognized as an important source of pathogen acquisition, the role of patient hands has been less clearly defined. We sought to determine whether the presence of functional disabilities is correlated with patient hand contamination by multidrug-resistant organisms (MDROs) and thus a potential target for patient hand hygiene (PHH) interventions. Methods: Case–control study of hand contamination with methicillin-resistant S. aureus, vancomycin-resistant enterococci, and gram-negative bacilli resistant to cephalosporins, fluoroquinolones, and/or carbapenems in 2 acute-care hospitals in southeastern Michigan. Cases (n = 40) and controls (n = 359) were defined as patients with or without hand contamination by MDROs, respectively. We assigned 3 exposure categories based on Katz activities of daily living scores: no functional disabilities (independent, reference group), 1–3 functional disabilities (partially dependent), and 4+ functional disabilities (dependent). We used stepwise logistic regression to identify confounding variables. Logistic regression was then used to establish the relationship between a patient’s functional dependence level and their hand contamination by MDROs. Results: The distribution of hand contamination of each target MDRO by level of patient dependence is shown in the Table. Overall, methicillin-resistant Staphylococcus aureus (MRSA) was the most represented, followed by resistant gram-negatives and vancomycin-resistant enterococci (VRE). Hospital site, sex, and history of MDROs were included in the model based on stepwise regression. The odds ratio (OR) of MRSA hand contamination in the dependent category was 3.19 (95% CI, 1.18–5.54) compared to the independent category, and for any MDRO the OR was 2.77 (95% CI, 1.22–6.32) (Fig. 1). The OR of MRSA hand contamination in the partially dependent category was 1.38 (95% CI, 0.27–7.07) compared to the independent group, and for any MDRO the OR was 0.86 (95% CI, 0.24–3.10) (Fig. 1). Feeding dependence had the highest single association with hand contamination (OR, 3.79, 95% CI, 1.26–11.43), with dressing dependence having the second highest association with hand contamination (OR, 2.82; 95% CI, 1.31–6.05) (Fig. 2). Conclusions: Patients with more functional dependencies were more likely to have MDRO hand contamination. This finding suggests a need for targeted PHH interventions in patients with functional disabilities to help prevent the spread of MDROs in the acute-care setting.

Disclosures: None

Background: Postacute sequelae of SARS-CoV-2 (PASC) include fatigue, dyspnea, anxiety, and cognitive impairment. Few studies have explored the prevalence or presentation of PASC among nursing home (NH) residents. Method: A case–control study was conducted at 1 NH in Michigan in December 2021. Cases were defined as residents with SARS-CoV-2 infection between November 2, 2020, and October 8, 2021. Controls lived at the same NH during this interval and never tested positive for SARS CoV-2. Patient characteristics were compared between cases and controls using the Fisher exact test and Wilcoxon rank-sum test. Primary outcomes were functional decline, cognition, and adverse health outcomes. Outcomes were assessed by comparing measures on last observation to observations before COVID-19 diagnosis (cases) or to earliest observation (controls). Multivariable logistic regression assessed correlation between COVID-19 diagnosis and outcomes. Results: In total, 152 residents were identified for inclusion (147 included in final analyses, 76 cases, 71 controls); 5 were excluded due to insufficient data. We collected the following resident characteristics: 66% were aged ≥80 years; 73% were female; 95% were non-Hispanic white; 82% were long-stay residents; median of 3 comorbidities (IQR, 2–4). The mean number of follow-up observations was 2.60 (SD, 1.25). No significant differences in population characteristics were detected between cases and controls. Moreover, 106 patients (46 cases and 60 controls) had at least 1 follow-up visit and were thus included in the analyses to evaluate long-term outcomes. Among them, cases experienced significant declines in completing transfers (OR 5.65, p Conclusions: Nursing home residents with COVID-19 are more likely to enter hospice and have a higher mortality rate in the year following infection. Survivors experience significant functional decline in basic activities of daily living, specifically in the ability to transfer and dress. Larger studies are needed to further characterize our findings and to design interventions that can help overcome these long-term sequelae from COVID-19.

Funding: None

Disclosures: None

Background: Persistent colonization with resistant gram-negative bacteria (R-GNB) increases risk of clinical infection and intra-facility transmission among nursing home (NH) patients. Limited data exist on the roles of age and function on duration of R-GNB colonization. Methods: Secondary data analysis was performed from a cohort study of patients admitted to 6 Michigan NHs between November 2013 and May 2018. Swabs obtained upon enrollment, day 14, day 30, then monthly until NH discharge from 6 anatomical sites were cultured for GNB. R-GNB were defined as resistant to ciprofloxacin, ceftazidime, or imipenem. Positive R-GNB culture from a single visit followed by negative cultures for the same organism from ≥2 subsequent visits were defined as transient R-GNB colonization. All other patients with positive R-GNB cultures from multiple visits were considered persistently colonized. Demographic data, antibiotic use, device use, and physical self-maintenance scales (PSMSs) were obtained upon enrollment. Characteristics were compared between patients with transient versus persistent R-GNB and uncolonized patients using multinomial logistic regression. Results: We recruited 896 patients (median age, 75 years; 41% male; 46% nonwhite) and followed them for 2,437 total visits. Of 896 patients, 407 (45.4%) were colonized with ≥1 R-GNB during their stay. Of 171 patients with ≥ 2 follow-up visits after R-GNB detection, 94 (55%) remained persistently colonized with the same R-GNB (Table 1). Escherichia coli (30%) and Proteus mirabilis (22%) were the most frequently identified R-GNB. The most common anatomical colonization sites were perirectal (368 [24.3%] of 1,147) groin (340 [14.3%] of 2,046), and hands (115 [4.8%] of 2283). Compared to uncolonized patients, patients with persistent (1.09; 95% CI, 1.00–1.19, P = .048) and transient R-GNB colonization (1.13; 95% CI, 1.04–1.23; P = .003) had lower PSMS (Tables 2 and 3). Compared to uncolonized and transiently colonized patients, patients with persistent R-GNB colonization had prolonged lengths of NH stay (1.01; 95% CI, 1.00–1.01; P = .003). Conclusions: R-GNB colonization in vulnerable NH patients is common (407 [45.5%] of 896 and often persistent (94 [55%] of 171 patients with sufficient follow-up to assess persistence). Patients with persistent R-GNB had lower functional status, longer LOS, and higher readmission rates than those without. R-GNB decolonization should be investigated as a strategy to potentially improve outcomes among NH patients.

Funding: None

Disclosures: None

Background: SARS-CoV-2, the virus causing COVID-19 infection, can significantly contaminate environmental surfaces and can remain viable on surfaces for up to 9 days. Although respiratory route remains the most significant mode of transmission, fomites and environmental sources of infection remain a concern for healthcare personnel who are working in dedicated COVID-19 units. We investigated the extent of detectable SARS-CoV-2 contamination in the environment of COVID-19 patients at a single VA hospital, with the intent of identifying potential high-touch surfaces at risk for viral contamination, which could be used to inform the development of simple COVID-19 prevention strategies. Methods: We conducted a cohort study at 1 VA hospital in a unit housing adult veterans admitted with COVID-19 between October and December 2020. In total, 11 swab specimens were collected for PCR analysis (SARS-CoV-2 env gene) from environmental surfaces inside and just outside the rooms of COVID-19 patients one time. Retrospective chart reviews were conducted to provide the SARS-CoV-2 epidemiologic context for environmental detection. Results: In total, 297 swabs were collected from the unit and environmental areas surrounding 27 hospitalized patients: average age, 72.5 years (range, 34–94); 100% male; 92% non-Hispanic white; average comorbidities, 1.8 (SD, 1.1). Of 297 swabs, 80 (27%) were positive for SARS-CoV-2 and 19 (70%) of 27 patients had at least 1 positive site. The most contaminated site was the floor just outside the patient room (78% positive samples), followed by the patient’s bedrail (37%) and chair handle (37%) (Fig. 1). Traditionally high-touch surfaces, such as the door handle (outside patient room) and the light switch, did not have high positivity rates (<15%). Interestingly, both the personal protective equipment (PPE) cart outside patient’s room (33%) and the double doors leading out of the unit (19%) were positive, which are surfaces often touched with bare hands after handwashing. Analyses of clinical data are underway to examine whether specific care needs, based on activities of daily living disability, comorbidities, and clinical presentation of COVID-19, predict SARS-CoV-2 environmental contamination. Conclusions: The presence of environmental contamination by SARS-CoV-2 highlights the importance of transmission via direct or indirect contact. Studies targeting high-risk populations are needed to better understand the transmission of SARS-CoV-2 between infected patients and their environment. Our findings also suggest that handwashing and attention to using disinfecting wipes may mitigate the risk of transmission of virus from surfaces that one might consider safe to touch.

Funding: None

Disclosures: None

Background: Transmission of methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococcus (VRE) is of special concern among frail patients in nursing homes. To understand environmental contamination patterns in this setting, we screened a suitable section of a nursing home over time and assessed MRSA and VRE prevalence in patients and their rooms. We were especially interested in assessing whether MRSA and VRE strains persist in rooms during changes of occupancy after patient discharge. Methods: We conducted a prospective cohort study of MRSA and VRE colonization and contamination among successive patients in a cluster of 9 single-occupancy rooms. Using flocked swabs, 5 high-touch surfaces were screened 3 times a week for 34 weeks. Patients were also screened (ie, nares, groin, and hands), if they agreed to participate. Whole-genome sequencing was performed on 67 nonredundant MRSA and VRE strains. Single-nucleotide polymorphism heatmaps and similarity trees were generated to evaluate strain diversity and persistence the facility. Results: Overall, 146 distinct occupancy events were captured during the study (16.5 average per room; range, 11–22), with 387 study visits and 4,670 total swabs collected. All rooms were contaminated with VRE, and 8 of 9 were contaminated with MRSA at least once during the study period. New contamination of a room with MRSA or VRE was observed in 43 (23%) of 185 opportunities, with potential persistence during occupancy changes in 25 (32.9%) of 76 opportunities. Sequencing of 67 nonredundant isolates identified at least 6 enterococcal clades and 10 MRSA clades (6 USA100 and 4 USA300), indicating a high degree of diversity and probably multiple introductions in the facility during the study time. In 3 separate cases, whole-genome sequencing confirmed persistence of a specific MRSA strain during a change of room occupancy, including 1 case of a MRSA strain persisting in a clean room before admission of the next patient. For VRE, 2 cases of persistence during room occupancy changes were confirmed, along with 6 cases of possible persistence (contamination across noncontiguous room occupancy events). Conclusions: Active surveillance screening and a recurring evaluation of terminal cleaning procedures should be considered due to high levels of circulation and persistence of MRSA and VRE in the nursing home setting.

Funding: None

Disclosures: None

Background: Patient colonization and shedding of vancomycin-resistant enterococci (VRE) is a major source of environmental contamination leading to VRE transmission in nursing homes. We hypothesize that we can inform mitigation strategies by identifying patient clinical and microbiota features associated with environmental contamination with VRE. Methods: During a 6-month period of active surveillance in 6 Michigan nursing homes, 245 patients (with 806 follow-up visits) were enrolled. Patient clinical data and swabs for VRE were collected from multiple body sites and high-touch environmental surfaces. In total, 316 perirectal swabs were collected from 137 patients for gut microbiota analysis and community status type (CST) assignment based on taxonomic composition. The associations between VRE colonization pattern, gut microbial CST, and patient factors were examined using multivariable generalized estimating equations, adjusting for patient-and facility-level clustering. We used VRE colonization patterns to group study visits: “uncolonized” (patient−/environment−); “environment-only” (patient−/environment+); “patient-only” (patient+/environment−); “both” (patient+/environment+). Results: Across all study visits, VRE colonization on patient hand and groin/perirectal area was positively correlated with VRE contamination of high-touch environmental surfaces, suggesting direct transfer of VRE between patient and environment via patient hands (Figure 1A). We next set out to identify patient factors associated with patient colonization and environmental contamination. At baseline, while patients in the “both” group had anticipated risk factors such as longer prior hospitalization and more frequent broad-spectrum antibiotic use, they were unexpectedly younger than “uncolonized” patients and had similar functional status. This last feature contrasted with the “patient-only” group, characterized by higher urinary catheter use and higher functional dependence, suggestive of lower functional dependence facilitating patient contamination of their environment. No clinical features distinguished “uncolonized” and “environment-only” patients (Table 1). Lastly, in multivariable analyses, we determined the contribution of patient functional status and gut microbiota features to environmental contamination. Low-diversity CST, characterized by reduced anaerobic taxa, was weakly associated with “patient-only” and significantly associated with “both.” Notably, high functional dependence was significantly associated with “environment-only” and “patient-only” but not “both,” indicating high-functioning patients with disrupted gut microbiota as drivers of environmental contamination (Figure 1B). Conclusions: Our findings suggest that antimicrobial exposure disrupts patient gut microbiota, a significant mediator of colonization dynamics between patients and their environment, and that high-functioning patients may be more likely to spread VRE between their body sites and high-touch environmental surfaces (Figure 2). These findings highlight both antibiotic stewardship and patient hand hygiene as important targets for interrupting transmission mediated by environmental contamination.

Funding: No

Disclosures: None

Figure 1.

Table 1.

Figure 2.

Perianal screening can be intrusive. The sensitivities of multianatomical, nonperianal surveillance were 92.3% for methicillin-resistant Staphylococcus aureus (MRSA), 58.7% for vancomycin-resistant enterococci (VRE), and 54.9% for resistant Gram-negative bacilli (R-GNB). Sensitivities improved upon adding environmental surveillance (95.5%, 82.9%, and 67.9%, respectively). Multianatomical, nonperianal screening and room environment surveillance may replace perianal screening and reduce healthy participant bias in nursing homes.

This SHEA white paper identifies knowledge gaps and challenges in healthcare epidemiology research related to coronavirus disease 2019 (COVID-19) with a focus on core principles of healthcare epidemiology. These gaps, revealed during the worst phases of the COVID-19 pandemic, are described in 10 sections: epidemiology, outbreak investigation, surveillance, isolation precaution practices, personal protective equipment (PPE), environmental contamination and disinfection, drug and supply shortages, antimicrobial stewardship, healthcare personnel (HCP) occupational safety, and return to work policies. Each section highlights three critical healthcare epidemiology research questions with detailed description provided in supplementary materials. This research agenda calls for translational studies from laboratory-based basic science research to well-designed, large-scale studies and health outcomes research. Research gaps and challenges related to nursing homes and social disparities are included. Collaborations across various disciplines, expertise and across diverse geographic locations will be critical.