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Whole-genome sequencing (WGS) shotgun metagenomics (metagenomics) attempts to sequence the entire genetic content straight from the sample. Diagnostic advantages lie in the ability to detect unsuspected, uncultivatable, or very slow-growing organisms.
To evaluate the clinical and economic effects of using WGS and metagenomics for outbreak management in a large metropolitan hospital.
Intensive care unit and burn unit of large metropolitan hospital.
Simulated intensive care unit and burn unit patients.
We built a complex simulation model to estimate pathogen transmission, associated hospital costs, and quality-adjusted life years (QALYs) during a 32-month outbreak of carbapenem-resistant Acinetobacter baumannii (CRAB). Model parameters were determined using microbiology surveillance data, genome sequencing results, hospital admission databases, and local clinical knowledge. The model was calibrated to the actual pathogen spread within the intensive care unit and burn unit (scenario 1) and compared with early use of WGS (scenario 2) and early use of WGS and metagenomics (scenario 3) to determine their respective cost-effectiveness. Sensitivity analyses were performed to address model uncertainty.
On average compared with scenario 1, scenario 2 resulted in 14 fewer patients with CRAB, 59 additional QALYs, and $75,099 cost savings. Scenario 3, compared with scenario 1, resulted in 18 fewer patients with CRAB, 74 additional QALYs, and $93,822 in hospital cost savings. The likelihoods that scenario 2 and scenario 3 were cost-effective were 57% and 60%, respectively.
The use of WGS and metagenomics in infection control processes were predicted to produce favorable economic and clinical outcomes.
To examine the effectiveness of antimicrobial and antithrombogenic materials incorporated into peripherally inserted central catheters (PICCs) to prevent bloodstream infection, thrombosis, and catheter occlusion.
Prospective cohort study involving 52 hospitals participating in the Michigan Hospital Medicine Safety Consortium. Sample included adult hospitalized medical patients who received a PICC between January 2013 and October 2019. Coated and impregnated catheters were identified by name, brand, and device marketing or regulatory materials. Multivariable Cox proportional hazards models with robust sandwich standard error estimates accounting for the clustered nature of data were used to identify factors associated with PICC complications in coated versus noncoated devices across general care, intensive care unit (ICU), and oncology patients. Results were expressed as hazard ratios (HRs) with corresponding 95% confidence intervals (CIs).
Of 42,562 patients with a PICC, 39,806 (93.5%) were plain polyurethane, 2,263 (5.3%) incorporated antimicrobial materials, and 921 (2.2%) incorporated antithrombogenic materials. Most were inserted in general ward settings (n = 28,111, 66.0%), with 12, 078 (28.4%) and 1,407 (3.3%) placed in ICU and oncological settings, respectively. Within the entire cohort, 540 (1.3%) developed thrombosis, 745 (1.8%) developed bloodstream infection, and 4,090 (9.6%) developed catheter occlusion. Adjusting for known risk factors, antimicrobial PICCs were not associated with infection reduction (HR, 1.16; 95% CI, 0.82–1.64), and antithrombogenic PICCs were not associated with reduction in thrombosis and occlusion (HR, 1.15; 95% CI, 0.92–1.44). Results were consistent across populations and care settings.
Antimicrobial and antithrombogenic PICCs were not associated with a reduction in major catheter complications. Guidance aimed at informing use of these devices, balancing benefits against cost, appear necessary.
Finely laminated (cm–μm scale) metalliferous precipitates are widespread in the surficial environment, especially around mineral deposits and reflect biogeochemical processes that can pervade near-surface environments on a larger scale. Examples in this paper involve precipitates of the transition metals Fe, Cu and Mn with minor Co, Ni, V and Zn; the metalloids As and Sb; and authigenic Au. Mobility and re-precipitation are driven primarily by geochemical disequilibrium, especially with respect to pH and redox states, that arises from complex interactions between biological processes, geological processes, and variations in the surrounding environment. Different degrees of chemical disequilibrium arise on small spatial scales on time scales of days to millennia. Interactions between biota, waters and rocks in these small near-surface settings affect the biogeochemical environments. Sulfur- and iron-oxidising bacteria are common biogeochemical agents associated with sulfide-bearing lithologies, but localised reductive environments can also develop, leading to gradients in pH and redox state and differential metal mobility. In general, there is commonly a spatial separation of Fe-rich precipitates from those with Cu and Mn, and other transition metals also follow Cu and Mn rather than Fe. Metalloids As and Sb have a strong affinity for Fe under oxidising conditions, but not under more reducing conditions. However, complex biogeochemical parageneses of laminated metalliferous deposits preclude prediction of finer formation details. The textures, mineral species, and metal associations within these deposits are likely to be encountered in all facets of mineral deposit development: initial exploration activity of near-surface locations, mining of shallow portions of orebodies, especially supergene zones, and downstream environmental management with respect to discharging metalliferous waters.
To compare the epidemiology, clinical characteristics, and mortality of patients with bloodstream infections (BSI) caused by extended-spectrum β-lactamase (ESBL)-producing Escherichia coli (ESBL-EC) versus ESBL-producing Klebsiella pneumoniae (ESBL-KP) and to examine the differences in clinical characteristics and outcome between BSIs caused by isolates with CTX-M versus other ESBL genotypes
As part of the INCREMENT project, 33 tertiary hospitals in 12 countries retrospectively collected data on adult patients diagnosed with ESBL-EC BSI or ESBL-KP BSI between 2004 and 2013. Risk factors for ESBL-EC versus ESBL-KP BSI and for 30-day mortality were examined by bivariate analysis followed by multivariable logistic regression.
The study included 909 patients: 687 with ESBL-EC BSI and 222 with ESBL-KP BSI. ESBL genotype by polymerase chain reaction amplification of 286 isolates was available. ESBL-KP BSI was associated with intensive care unit admission, cardiovascular and neurological comorbidities, length of stay to bacteremia >14 days from admission, and a nonurinary source. Overall, 30-day mortality was significantly higher in patients with ESBL-KP BSI than ESBL-EC BSI (33.7% vs 17.4%; odds ratio, 1.64; P=.016). CTX-M was the most prevalent ESBL subtype identified (218 of 286 polymerase chain reaction-tested isolates, 76%). No differences in clinical characteristics or in mortality between CTX-M and non–CTX-M ESBLs were detected.
Clinical characteristics and risk of mortality differ significantly between ESBL-EC and ESBL-KP BSI. Therefore, all ESBL-producing Enterobacteriaceae should not be considered a homogeneous group. No differences in outcomes between genotypes were detected.
Asbestos bodies are the histological hallmarks of asbestos exposure. Both conventional and advanced techniques are used to evaluate abundance and composition in histological samples. We previously reported the possibility of using synchrotron X-ray fluorescence microscopy (XFM) for analyzing the chemical composition of asbestos bodies directly in lung tissue samples. Here we applied a high-performance synchrotron X-ray fluorescence (XRF) set-up that could allow new protocols for fast monitoring of the occurrence of asbestos bodies in large histological sections, improving investigation of the related chemical changes. A combination of synchrotron X-ray transmission and fluorescence microscopy techniques at different energies at three distinct synchrotrons was used to characterize asbestos in paraffinated lung tissues. The fast chemical imaging of the XFM beamline (Australian Synchrotron) demonstrates that asbestos bodies can be rapidly and efficiently identified as co-localization of high calcium and iron, the most abundant elements of these formations inside tissues (Fe up to 10% w/w; Ca up to 1%). By following iron presence, we were also able to hint at small asbestos fibers in pleural spaces. XRF at lower energy and at higher spatial resolution was afterwards performed to better define small fibers. These analyses may predispose for future protocols to be set with laboratory instruments.
Accurate discrimination of two morphologically similar species of Patella limpets has been facilitated by using qPCR amplification of species-specific mitochondrial genomic regions. Cost-effective and non-destructive sampling is achieved using a mucus swab and simple sample lysis and dilution to create a PCR template. Results show 100% concurrence with dissection and microscopic analysis, and the technique has been employed successfully in field studies. The use of highly sensitive DNA barcoding techniques such as this hold great potential for improving previously challenging field assessments of species abundance.
Clostridium difficile infection (CDI) has been extensively described in healthcare settings; however, risk factors associated with community-acquired (CA) CDI remain uncertain. This study aimed to synthesize the current evidence for an association between commonly prescribed medications and comorbidities with CA-CDI.
A systematic search was conducted in 5 electronic databases for epidemiologic studies that examined the association between the presence of comorbidities and exposure to medications with the risk of CA-CDI. Pooled odds ratios were estimated using 3 meta-analytic methods. Subgroup analyses by location of studies and by life stages were conducted.
Twelve publications (n=56,776 patients) met inclusion criteria. Antimicrobial (odds ratio, 6.18; 95% CI, 3.80–10.04) and corticosteroid (1.81; 1.15–2.84) exposure were associated with increased risk of CA-CDI. Among the comorbidities, inflammatory bowel disease (odds ratio, 3.72; 95% CI, 1.52–9.12), renal failure (2.64; 1.23–5.68), hematologic cancer (1.75; 1.02–5.68), and diabetes mellitus (1.15; 1.05–1.27) were associated with CA-CDI. By location, antimicrobial exposure was associated with a higher risk of CA-CDI in the United States, whereas proton-pump inhibitor exposure was associated with a higher risk in Europe. By life stages, the risk of CA-CDI associated with antimicrobial exposure greatly increased in adults older than 65 years.
Antimicrobial exposure was the strongest risk factor associated with CA-CDI. Further studies are required to investigate the risk of CA-CDI associated with medications commonly prescribed in the community. Patients with diarrhea who have inflammatory bowel disease, renal failure, hematologic cancer, or diabetes are appropriate populations for interventional studies of screening.
Interventions that prevent healthcare-associated infection should lead to fewer deaths and shorter hospital stays. Cleaning hands (with soap or alcohol) is an effective way to prevent the transmission of organisms, but rates of compliance with hand hygiene are sometimes disappointingly low. The National Hand Hygiene Initiative in Australia aimed to improve hand hygiene compliance among healthcare workers, with the goal of reducing rates of healthcare-associated infection.
We examined whether the introduction of the National Hand Hygiene Initiative was associated with a change in infection rates. Monthly infection rates for healthcare-associated Staphylococcus aureus bloodstream infections were examined in 38 Australian hospitals across 6 states. We used Poisson regression and examined 12 possible patterns of change, with the best fitting pattern chosen using the Akaike information criterion. Monthly bed-days were included to control for increased hospital use over time.
The National Hand Hygiene Initiative was associated with a reduction in infection rates in 4 of the 6 states studied. Two states showed an immediate reduction in rates of 17% and 28%, 2 states showed a linear decrease in rates of 8% and 11% per year, and 2 showed no change in infection rates.
The intervention was associated with reduced infection rates in most states. The failure in 2 states may have been because those states already had effective initiatives before the national initiative’s introduction or because infection rates were already low and could not be further reduced.