Skin abscess caused by Trueperella bernardiae: Case report and literature review.

We investigated a skin abscess caused by Trueperella bernardiae in a patient with comorbidities. Initial empirical therapy with Clindamycin did not yield a response, and follow-up culture revealed the presence of T. bernardiae through MALDI-TOF and NGS. Since no CLSI or FDA breakpoints have been published for this strain, resistant gene screening of the genetic sequence showed the presence of the erm(X) gene (with 95 % identity). This gene confers resistance to erythromycin, clindamycin, lincomycin, pristinamycin, quinupristin, and virginiamycin. Subsequent therapy with oral amoxicillin/clavulanate led to complete healing.

Lowering the Acquisition of Multi-drug Resistant Organism (MDROs) with Pulsed-xenon (LAMP) Study: a cluster randomized controlled, double-blinded, interventional crossover trial.

BACKGROUND: Environmental disinfection is essential for reducing spread of healthcare associated infections (HAIs). Previous studies report conflicting results regarding the effects of ultraviolet light (UV) in reducing infections. This trial evaluated the impact of adding pulsed xenon UV (PX-UV) to standard terminal cleaning in reducing environmentally-implicated HAIs (eiHAIs). METHODS: The LAMP trial was conducted in 2 hospitals (15 inpatient wards) utilizing a cluster randomized controlled, double-blinded, interventional crossover trial comparing standard terminal cleaning followed by either pulsed xenon ultraviolet (PX-UV) disinfection (intervention arm) or sham disinfection (control arm). The primary outcome was incidence of eiHAIs from clinical microbiology tests on the 4th day of stay or later or within 3 days after discharge from the study unit. EiHAIs included clinical cultures positive for vancomycin-resistant enterococci (VRE), extended spectrum beta-lactamase-producing Escherichia coli or Klebsiella pneumonia, methicillin-resistant Staphylococcus aureus (MRSA), and Acinetobacter baumannii, and stool PCR positive for Clostridiodes difficile. FINDINGS: Between May 18, 2017 to Jan 7, 2020, 25,732 patients were included, with an incidence of 601 eiHAI and 180,954 patient days. There was no difference in the rate of eiHAIs in the intervention and sham arms (3.49 vs 3.17 infections/1000 patient days respectively, RR 1.10 CI (0.94, 1.29, p= 0.23)). Study results were similar when stratified by eiHAI type, hospital, and unit type. CONCLUSION: The LAMP study failed to demonstrate an effect of the addition of UV light disinfection following terminal cleaning on reductions in rates of eiHAIs. Further investigations targeting hospital environmental surfaces and the role of no touch technology to reduce HAIs are needed.

Transmission of Severe Acute Respiratory Syndrome Coronavirus 2 Among Residents and Employees in a Veterans Affairs Community Living Center: A 42-Month Prospective Cohort Study.

Background: Understanding routes of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission in long-term care facilities is essential for the development of effective control measures. Methods: Between March 1, 2020, and August 31, 2023, we identified coronavirus disease 2019 (COVID-19) cases among residents and employees in a Veterans Affairs community living center that conducted routine screening for asymptomatic COVID-19. Contact tracing was conducted to identify suspected transmission events, and whole genome sequencing was performed to determine the relatedness of SARS-CoV-2 samples. Results: During the 42-month study period, 269 cases of COVID-19 were diagnosed, including 199 employees and 70 residents. A total of 48 (24.1%) employees and 30 (42.9%) residents were asymptomatic. Sequencing analysis provided support for multiple events in which employees transmitted SARS-CoV-2 to co-workers and residents. There was 1 episode of likely transmission of SARS-CoV-2 from one resident to another resident, but no documented transmissions from residents to employees. Conclusions: Transmission of SARS-CoV-2 in the community living center predominantly involved transmission from employees to co-workers and residents. There is a need for improved measures to prevent transmission of SARS-CoV-2 by healthcare personnel.

Evolution of a Distinct SARS-CoV-2 Lineage Identified during an Investigation of a Hospital Outbreak.

The SARS-CoV-2 virus steadily evolves, and numerous antigenically distinct variants have emerged over the past three years. Tracking the evolution of the virus would help us understand the process that generates the diverse variants and predict the future evolutionary trajectory of SARS-CoV-2. Here, we report the evolutionary trajectory of a unique Omicron lineage identified during an outbreak investigation that occurred in a residence unit in the healthcare system. The new lineage had four distinct non-synonymous and two distinct synonymous mutations apart from its parental lineage. Since this lineage of virus was exclusively found during the outbreak, we were able to track the detailed evolutionary history of the entire lineage along the transmission path. Furthermore, we estimated the evolutionary rate of the SARS-CoV-2 Omicron variant from the analysis of the evolution of the lineage. This new Omicron sub-lineage acquired 3 mutations in a 12-day period, and the evolutionary rate was estimated as 3.05 × 10-3 subs/site/year. This study provides more insight into an ever-evolving virus.

Risk of Hepatitis B Reactivation in Patients Receiving Ibrutinib: The National Veterans Affairs Cohort.

Background: Ibrutinib has been a first-line treatment for chronic lymphocytic leukemia since 2014. Case reports of hepatitis B virus (HBV) reactivation after ibrutinib initiation have been presented. The association between the risk of HBV reactivation and ibrutinib initiation remains unclear. This nationwide study aimed to estimate the incidence of HBV reactivation after ibrutinib initiation. Method: This study included patients who received ibrutinib between 1 February 2014 and 31 October 2019. Possible reactivations were searched by (1) changes in HBV surface antigen or HBV DNA from no data or negative status to positive after ibrutinib initiation, (2) alanine aminotransferase levels that were at least 3 times the baseline value after ibrutinib initiation, and (3) new antiviral prescriptions against HBV after ibrutinib initiation. Individual chart reviews were conducted to identify HBV reactivation attributed to ibrutinib. The cumulative incidence of HBV reactivation was calculated. Results: A total 4130 patients were eligible during the study period. Of these, patients with negative HBV core antibody (anti-HBcAb; n = 1670) and patients who were taking antivirals against HBV (n = 60) were excluded. There were 2219 patients without anti-HBcAb testing results. Among the remaining 181 patients with positive anti-HBcAb, 7 HBV reactivations were directly attributable to ibrutinib treatment after chart review, for a 3.9% cumulative incidence. Conclusions: Our study revealed a low cumulative incidence of HBV reactivation after ibrutinib initiation among patients with previous anti-HBcAb positivity, indicating a moderate risk of HBV reactivation.

Understanding the significance of microbiota recovered from health care surfaces.

BACKGROUND: Microbial contamination of hospital surfaces remains despite adherence to routine disinfection. Our study demonstrates bioburden from various types of hospital high-touch surfaces and the pathogenicity of all bacteria recovered. METHODS: Several high-touch hospital surfaces from a single medical-surgical unit were sampled and cultured using replicate organism detection and counting (RODAC) Tryptic Soy agar plates. Colonies were then subcultured to blood agar plates and speciated using MALDI-TOF. The local microbiology laboratory database was queried for any clinical isolate match with the environmental samples recovered. RESULTS: Manikins, bed rails, and workstations-on-wheels were the most contaminated surfaces with the largest variety of bacteria isolated from manikins and bed rails. A total of 60 different types of pathogens were isolated, 18 of which were well-known pathogens, and 7 were classified as important in the health care setting by CDC. Our clinical microbiology laboratory identified 29 of 60 hospital surface bacteria in clinical isolates. Urine, soft tissue, and blood were the most common sources of clinical isolates. CONCLUSIONS: Surfaces in the health care environment harbor both well-known and not-so-well-known human pathogens. Several not-so-well-known pathogens are skin flora or environmental bacteria, which in the right setting, can become pathogenic and cause diseases including meningitis, brain abscess, endocarditis, and bacteremia.

Nursing home wastewater surveillance for early warning of SARS-CoV-2-positive occupants-Insights from a pilot project at 8 facilities.

BACKGROUND: Wastewater surveillance for SARS-CoV-2 has been used widely in the United States for indication of community incidence during the COVID-19 pandemic, but less is known about the feasibility of its use on a building level in nursing homes to provide early warning and prevent transmission. METHODS: A pilot study was conducted at 8 Department of Veterans Affairs nursing homes across the United States to examine operational feasibility. Wastewater from the participating facilities was sampled daily during the week for 6 months (January 11, 2021-July 2, 2021) and analyzed for SARS-CoV-2 genetic material. Wastewater results were compared to new SARS-CoV-2 infections in nursing home residents and employees to determine if wastewater surveillance could provide early warning of a COVID-19-positive occupant. RESULTS: All 8 nursing homes had wastewater samples positive for SARS-CoV-2 and COVID-19-positive occupants. The sensitivity of wastewater surveillance for early warning of COVID-19-positive residents was 60% (3/5) and for COVID-19-positive employees was 46% (13/28). CONCLUSIONS: Wastewater surveillance may provide additional information for reinforcing infection control practices and lead to preventing transmission in a setting with high-risk residents. The low sensitivity for early warning in this real-world pilot highlights limitations and insights for applicability in buildings.

Diagnostic performance of DNA probe-based and PCR-based molecular vaginitis testing.

Vaginitis is usually diagnosed empirically, microscopically, via cultures, or by molecular testing for the detection of bacterial vaginosis (BV), vulvovaginal candidiasis (VVC), or Trichomonas vaginalis (TV). The DNA probe-based technique detects BV by identifying Gardnerella vaginalis, VVC by identifying Candida spp., while real-time PCR-based detection methods identify BV by algorithmic analysis of the absence or presence of known vaginal flora. We examined 8,878 total orders placed for DNA probe-based identification (ID) and 10,464 total orders placed for molecular panel ID. We found that PCR-based BV test positivity reduced from 30% to 23% compared with the population tested with DNA probe-based testing. We also found that PCR-based testing VVC positivity increased from 6.3% and 11.6% when compared with DNA probe-based testing. Bayesian generalized linear analysis estimated a lower mean proportion of positive tests for BV in PCR-based molecular panels than DNA probe testing suggesting an under-call of BV. The same models estimated a higher mean proportion of positive tests for molecular vaginal panels than DNA probe testing suggesting an increased detection of candidal vaginitis. In addition, the mean (SD) age for patients with Candida albicans was 40.5 (40.0-41.1) years. Patients with Candida glabrata (now N. glabrata) were 5.2-8.1 (mean 6.7) years older than patients with Candida albicans. Our retrospective data analysis found that BD Max MVP's ability to discriminate between vaginal candidiasis versus other yeast will help to implement CDC (Centers for Disease Control and Prevention)-recommended treatment options. We also believe that providers' inattention to non-albicans treatment could be an issue nationwide. IMPORTANCE Using retrospective data from U.S. Food and Drug Administration-approved/cleared molecular vaginal panels, molecular methods were found to have higher detection for Candida vaginitis and lower detection for bacterial vaginitis when compared to probe-based methods. In addition, the differentiation of Candida and non-Candida yeast has not reached the physician community as we observed noncompliance in recommended therapy. Furthermore, the pros and cons of migrating to molecular testing from conventional microscopy for identifying bacterial vaginitis and fungal vaginitis have been examined and reported in this paper. Interestingly, the mean (SD) age for patients with Candida albicans was 40.5 (40.0-41.1) years. Patients with N. glabrata were 5.2-8.1 (mean 6.7) years older than patients with Candida albicans.

Using a handheld UV device for disinfection in the patient care environment: A descriptive qualitative study.

Frontline nurses play a critical role in the prevention of healthcare-acquired infections (HAIs) through daily practices of hand hygiene and decontamination of surfaces. Despite these practices, environmental contamination and HAIs persist. Emerging use of UV light at wavelengths safe for human exposure provides additional strategies for disinfecting the patient care environment. The purpose of this qualitative study is to explore frontline nursing feedback regarding a novel handheld UV device prototype. A convenience sample of nurses were invited to participate in facilitated individual or small group discussions led by one member of the research team. Thematic analysis of discussion transcripts was completed by two members of the research team. Sixteen registered nurses participated. Four themes found in the study were time considerations, complexity, safety (patient and nurse), and characteristics of technology to improve patient care. Findings suggest that while nursing staff are willing to use technology, it must be considered valuable to patient care and should not hinder the provision of care. Inclusion of inputs from nursing staff for development of technology identifies potential barriers to acceptance and use in the practice environment.

Case of Extensively Drug-Resistant Shigella sonnei Infection, United States.

We report extensively drug-resistant (XDR) Shigella sonnei infection in an immunocompromised patient in Texas, USA. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry failed to identify XDR Shigella, but whole-genome sequencing accurately characterized the strain. First-line antimicrobials are not effective against emerging XDR Shigella. Fosfomycin, carbapenems, and tigecycline are potential alternatives.

Efficacy of a filtered far-UVC handheld disinfection device in reducing the microbial bioburden of hospital surfaces.

BACKGROUND: The filtered far-UV-C (FFUV) handheld disinfection device is a small portable device that emits far UV-C at 222 nm. The objective of this study was to evaluate the device's ability to kill microbial pathogens on hospital surfaces and compare it to manual disinfection using germicidal sodium hypochlorite wipes. METHODS: A total of 344 observations (4 observations from 86 objects' surfaces) were sampled with 2 paired samples per surface: a pre- and a post-sodium hypochlorite and FFUV sample. The results were analyzed via a Bayesian multilevel negative binomial regression model. RESULTS: The estimated mean colony counts for the sodium hypochlorite control and treatment groups were 20.5 (95% uncertainty interval: 11.7-36.0) and 0.1 (0.0-0.2) colony forming units (CFUs), respectively. The FFUV control and treatment groups had mean colony counts of 22.2 (12.5-40.1) and 4.1 (2.3-7.2) CFUs. The sodium hypochlorite group and the FFUV group had an estimated 99.4% (99.0%-99.7%) and 81.4% (76.2%-85.7%) reduction in colony counts, respectively. CONCLUSIONS: The FFUV handheld device effectively reduced the microbial bioburden on surfaces in the health care setting. The major benefit of FFUV is likely seen when manual disinfection is not possible or when supplementing cleaners or disinfectants with the low-level disinfection properties.

Assessment of microbial bioburden on portable medical equipment in a hospital setting.

Objectives: Although routine disinfection of portable medical equipment is required in most hospitals, frontline staff may not be able to disinfect portable medical equipment at a rate that adequately maintains low bioburden on high-use equipment. This study quantified bioburden over an extended time period for two types of portable medical equipment, workstations on wheels and vitals machines, across three hospital wards. Methods: Bioburden was quantified via press plate samples taken from high touch surfaces on 10 workstations on wheels and 5 vitals machines on each of 3 medical surgical units. The samples were taken at three timepoints each day over a 4-week period, with random rotation of timepoints and portable medical equipment, such that frontline staff were not aware at which timepoint their portable medical equipment would be sampled. The mean bioburden from the different locations and portable medical equipment was estimated and compared with Bayesian multilevel negative binomial regression models. Results: Model estimated mean colony counts (95% credible interval) were 14.4 (7.7-26.7) for vitals machines and 29.2 (16.1-51.1) for workstations on wheels. For the workstations on wheel, colony counts were lower on the mouse, 0.22 (0.16-0.29), tray, 0.29 (0.22, 0.38), and keyboard, 0.43 (0.32-0.55), when compared to the arm, as assessed by incident rate ratios. Conclusions: Although routine disinfection is required, bioburden is still present across portable medical equipment on a variety of surfaces. The difference in bioburden levels among surfaces likely reflects differences in touch patterns for the different portable medical equipment and surfaces on the portable medical equipment. Although the association of portable medical equipment bioburden to healthcare-associated infection transmission was not assessed, this study provides evidence for the potential of portable medical equipment as a vector for healthcare-associated infection transmission despite hospital disinfection requirements.

Campylobacter coli bacteremia associated with diarrhea.

Campylobacter coli (C. coli) is a gram negative, non-spore forming, mobile, curved, or spiral-shaped rod organisms and one of the most common gastrointestinal human pathogens. Campylobacter very rarely causes bacteremia. However, there are reports of bloodstream infection of C. coli and most of the Campylobacterbacteremia have been found among immunocompromised patients. In this study, a case of C. coli blood stream infection that was associated with diarrhea in an immunocompetent patient.

Nationwide Genomic Surveillance and Response to COVID-19: The VA SeqFORCE and SeqCURE Consortiums.

Background: The US Department of Veterans Affairs (VA) has dedicated significant resources toward countering the COVID-19 pandemic. Sequencing for Research Clinical and Epidemiology (SeqFORCE) and Sequencing Collaborations United for Research and Epidemiology (SeqCURE) were developed as clinical and research consortiums, respectively, focused on the genetic COVID-19 surveillance. Observations: Through genetic sequencing, VA SeqFORCE and SeqCURE collaborations contributed to the COVID-19 pandemic response and scientific understanding. Future directions for each program include the assessment of the unique impact of COVID-19 on the veteran population, as well as the adaptation of these programs to future infectious disease threats. We foresee the use of these established platforms beyond infectious diseases. Conclusions: VA SeqFORCE and SeqCURE were established as clinical and research programs dedicated to sequencing COVID-19 as part of ongoing clinical and surveillance efforts. In the future, we anticipate that having these programs embedded within the largest integrated health care system in the US will enable the study of pathogens and pandemics beyond COVID-19 and at an unprecedented scale. The investment in these programs will form an integral part of our nation's response to emerging infectious diseases, with future applications to precision medicine and beyond.

Extended Remdesivir Infusion for Persistent Coronavirus Disease 2019 Infection.

Persistent severe acute respiratory syndrome coronavirus 2 infection is difficult to treat. Here, we report a case of 5-month persistent coronavirus disease 2019 in an immunocompromised patient who was successfully treated with 30 consecutive days of remdesivir. Prolonged remdesivir infusion with concurrent cycle threshold monitoring might provide a potential solution to cure these patients with difficult-to-treat infections.

Factors That Affect Legionella Positivity in Healthcare Building Water Systems from a Large, National Environmental Surveillance Initiative.

Legionella growth in healthcare building water systems can result in legionellosis, making water management programs (WMPs) important for patient safety. However, knowledge is limited on Legionella prevalence in healthcare buildings. A dataset of quarterly water testing in Veterans Health Administration (VHA) healthcare buildings was used to examine national environmental Legionella prevalence from 2015 to 2018. Bayesian hierarchical logistic regression modeling assessed factors influencing Legionella positivity. The master dataset included 201,146 water samples from 814 buildings at 168 VHA campuses. Overall Legionella positivity over the 4 years decreased from 7.2 to 5.1%, with the odds of a Legionella-positive sample being 0.94 (0.90-0.97) times the odds of a positive sample in the previous quarter for the 16 quarters of the 4 year period. Positivity varied considerably more at the medical center campus level compared to regional levels or to the building level where controls are typically applied. We found higher odds of Legionella detection in older buildings (OR 0.92 [0.86-0.98] for each more recent decade of construction), in taller buildings (OR 1.20 [1.13-1.27] for each additional floor), in hot water samples (O.R. 1.21 [1.16-1.27]), and in samples with lower residual biocide concentrations. This comprehensive healthcare building review showed reduced Legionella detection in the VHA healthcare system over time. Insights into factors associated with Legionella positivity provide information for healthcare systems implementing WMPs and for organizations setting standards and regulations.

Presumptive positive with the Cepheid Xpert Xpress SARS-CoV-2 assay due to N mutations in the Delta variant.

The Cepheid Xpert® Xpress SARS-CoV-2 assay is 1 of the several real-time reverse transcription polymerase chain reaction (RT-PCR) assays that received Emergency Use Authorization from the United States Food and Drug Administration (FDA) for detection of SARS-CoV-2. Here we report 4 SARS-CoV-2 samples that were reported as presumptive positives on the Cepheid platform while reported as positives on alternative RT-PCR platforms. Whole genome sequencing indicated that the samples were Delta variants and had point mutations in the N gene which potentially interfered with SARS-CoV-2 detection. Two types of point mutations were found in these samples in the US CDC 2019-nCoV Real time PCR N2 Probe region: C29203T and C29200T. C29203T is a novel point mutation, and C29200T has not been previously reported in the Delta variants. This underlines the fact that mutations in the real-time RT-PCR assay target region could hinder accurate detection of SARS-CoV-2.

Effect of a "feedback prompt" from a disinfection tracking system on portable medical equipment disinfection.

BACKGROUND: Portable medical equipment (PME) may contribute to transmission of multidrug-resistant organisms without proper disinfection. We studied whether a Disinfection Tracking System (DTS) with feedback prompt, attached to PME, can increase the frequency of PME disinfection. METHODS: DTS devices were placed on 10 workstations-on-wheels (WOWs) and 5 vitals machine (VM). After a 25 day "screen-off" period, the DTS device screens were turned on to display the number of hours since the last recorded disinfection event for a 42 day period. We used a Bayesian multilevel zero-inflated negative binomial model to compare the number of events in the display "screen-off" to the "screen-on" period. RESULTS: During the "screen-off" period, there were 1.26 and 0.49 mean disinfection events and during the "screen-on" period, there were 1.76 and 0.50 mean disinfection events for WOWs and VM, respectively, per day. The model estimated mean events per device per day in the the "screen-on" period for WOW's were 1.32 (1.10 - 1.57) times greater than those in the "screen-off" period and the "screen-on" period for VM devices was 1.37 (0.89 - 2.01) times greater than those in the "screen-off" period. CONCLUSIONS: The rate of disinfection events for WOWs increased following the implementation of the DTS feedback prompt.

The viral phoenix: enhanced infectivity and immunity evasion of SARS-CoV-2 variants.

SARS-CoV-2 pandemic continues with emergence of new variants of concerns. These variants are fueling the third and fourth waves of pandemic across many nations. Here we describe the new emerging variants of SARS-CoV-2 and why they have enhanced infectivity and possess the ability to evade immunity.