Evaluating the cost implications of integrating SARS-CoV-2 genome sequencing for infection prevention and control investigation of nosocomial transmission within hospitals.

BACKGROUND: The COG-UK hospital-onset COVID-19 infection (HOCI) trial evaluated the impact of SARS-CoV-2 whole-genome sequencing (WGS) on acute infection, prevention, and control (IPC) investigation of nosocomial transmission within hospitals. AIM: To estimate the cost implications of using the information from the sequencing reporting tool (SRT), used to determine likelihood of nosocomial infection in IPC practice. METHODS: A micro-costing approach for SARS-CoV-2 WGS was conducted. Data on IPC management resource use and costs were collected from interviews with IPC teams from 14 participating sites and used to assign cost estimates for IPC activities as collected in the trial. Activities included IPC-specific actions following a suspicion of healthcare-associated infection (HAI) or outbreak, as well as changes to practice following the return of data via SRT. FINDINGS: The mean per-sample costs of SARS-CoV-2 sequencing were estimated at £77.10 for rapid and £66.94 for longer turnaround phases. Over the three-month interventional phases, the total management costs of IPC-defined HAIs and outbreak events across the sites were estimated at £225,070 and £416,447, respectively. The main cost drivers were bed-days lost due to ward closures because of outbreaks, followed by outbreak meetings and bed-days lost due to cohorting contacts. Actioning SRTs, the cost of HAIs increased by £5,178 due to unidentified cases and the cost of outbreaks decreased by £11,246 as SRTs excluded hospital outbreaks. CONCLUSION: Although SARS-CoV-2 WGS adds to the total IPC management cost, additional information provided could balance out the additional cost, depending on identified design improvements and effective deployment.

Factors affecting turnaround time of SARS-CoV-2 sequencing for inpatient infection prevention and control decision making: analysis of data from the COG-UK HOCI study.

BACKGROUND: Barriers to rapid return of sequencing results can affect the utility of sequence data for infection prevention and control decisions. AIM: To undertake a mixed-methods analysis to identify challenges that sites faced in achieving a rapid turnaround time (TAT) in the COVID-19 Genomics UK Hospital-Onset COVID-19 Infection (COG-UK HOCI) study. METHODS: For the quantitative analysis, timepoints relating to different stages of the sequencing process were extracted from both the COG-UK HOCI study dataset and surveys of study sites. Qualitative data relating to the barriers and facilitators to achieving rapid TATs were included from thematic analysis. FINDINGS: The overall TAT, from sample collection to receipt of sequence report by infection control teams, varied between sites (median 5.1 days, range 3.0-29.0 days). Most variation was seen between reporting of a positive COVID-19 polymerase chain reaction (PCR) result to sequence report generation (median 4.0 days, range 2.3-27.0 days). On deeper analysis, most of this variability was accounted for by differences in the delay between the COVID-19 PCR result and arrival of the sample at the sequencing laboratory (median 20.8 h, range 16.0-88.7 h). Qualitative analyses suggest that closer proximity of sequencing laboratories to diagnostic laboratories, increased staff flexibility and regular transport times facilitated a shorter TAT. CONCLUSION: Integration of pathogen sequencing into diagnostic laboratories may help to improve sequencing TAT to allow sequence data to be of tangible value to infection control practice. Adding a quality control step upstream to increase capacity further down the workflow may also optimize TAT if lower quality samples are removed at an earlier stage.

Universal use of surgical masks is tolerated and prevents respiratory viral infection in stem cell transplant recipients.

Prevention of respiratory viral infection in stem cell transplant patients is important due to its high risk of adverse outcome. This single-centre, mixed methods study, conducted before the severe acute respiratory syndrome coronavirus-2 pandemic, explored the barriers and facilitators to a policy of universal mask use by visitors and healthcare workers, and examined the impact of the first year of introduction of the policy on respiratory viral infection rates compared with preceding years, adjusted for overall incidence. Education around universal mask use was highlighted as being particularly important in policy implementation. A significant decrease in respiratory viral infection was observed following introduction.

Evaluation of procalcitonin as a contribution to antimicrobial stewardship in SARS-CoV-2 infection: a retrospective cohort study.

It can be a diagnostic challenge to identify patients with coronavirus disease 2019 in whom antibiotics can be safely withheld. This study evaluated the effectiveness of a guideline implemented at Sheffield Teaching Hospitals NHS Foundation Trust that recommends withholding antibiotics in patients with low serum procalcitonin (PCT), defined as ≤0.25 ng/mL. Results showed reduced antibiotic consumption in patients with PCT ≤0.25 ng/mL with no increase in mortality, alongside a reduction in subsequent carbapenem prescriptions during admission. The results support the effectiveness of this guideline, and further research is recommended to identify the optimal cut-off value for PCT in this setting.

Key drivers of cloud response to surface-active organics.

Aerosol-cloud interactions constitute the largest source of uncertainty in global radiative forcing estimates, hampering our understanding of climate evolution. Recent empirical evidence suggests surface tension depression by organic aerosol to significantly influence the formation of cloud droplets, and hence cloud optical properties. In climate models, however, surface tension of water is generally assumed when predicting cloud droplet concentrations. Here we show that the sensitivity of cloud microphysics, optical properties and shortwave radiative effects to the surface phase are dictated by an interplay between the aerosol particle size distribution, composition, water availability and atmospheric dynamics. We demonstrate that accounting for the surface phase becomes essential in clean environments in which ultrafine particle sources are present. Through detailed sensitivity analysis, quantitative constraints on the key drivers - aerosol particle number concentrations, organic fraction and fixed updraft velocity - are derived for instances of significant cloud microphysical susceptibilities to the surface phase.

Joint aspiration, including culture of reaspirated saline after a 'dry tap', is sensitive and specific for the diagnosis of hip and knee prosthetic joint infection.

Aims: The aim of this study was to establish the diagnostic accuracy of culture of joint aspirate with and without saline injection-reaspiration. Patients and Methods: This is a retrospective analysis of 580 hip and knee aspirations in patients who were deemed to have a moderate to high risk of infection, and who subsequently proceeded to revision arthroplasty over a period of 12 years. It was carried out at a large quaternary referral centre where preoperative aspiration is routine. Results: Fluid was aspirated primarily in 313 (54%) cases and after saline injection-reaspiration of a 'dry tap' in 267 (46%) cases. Overall sensitivity and specificity of the diagnostic aspirate were 84% (78% to 89%) and 85% (81% to 88%), respectively. Sensitivity and specificity of saline injection-reaspiration after 'dry tap' were 87% (79% to 92%) and 79% (72% to 84%) compared with 81% (71% to 88%) and 90% (85% to 93%) for direct aspiration. Conclusion: Preoperative joint aspiration and culture is a sensitive and specific test for the confirmation of diagnosis in patients at a moderate to high risk of prosthetic joint infection. Culture of saline injection-reaspiration also provides accurate diagnostic information in the event of a 'dry tap'. Both methods allow susceptibility testing of relevant organisms and are therefore able to guide perioperative antibiotic therapy. Cite this article: Bone Joint J 2018;100-B:749-54.

Microphysical explanation of the RH-dependent water affinity of biogenic organic aerosol and its importance for climate.

A large fraction of atmospheric organic aerosol (OA) originates from natural emissions that are oxidized in the atmosphere to form secondary organic aerosol (SOA). Isoprene (IP) and monoterpenes (MT) are the most important precursors of SOA originating from forests. The climate impacts from OA are currently estimated through parameterizations of water uptake that drastically simplify the complexity of OA. We combine laboratory experiments, thermodynamic modeling, field observations, and climate modeling to (1) explain the molecular mechanisms behind RH-dependent SOA water-uptake with solubility and phase separation; (2) show that laboratory data on IP- and MT-SOA hygroscopicity are representative of ambient data with corresponding OA source profiles; and (3) demonstrate the sensitivity of the modeled aerosol climate effect to assumed OA water affinity. We conclude that the commonly used single-parameter hygroscopicity framework can introduce significant error when quantifying the climate effects of organic aerosol. The results highlight the need for better constraints on the overall global OA mass loadings and its molecular composition, including currently underexplored anthropogenic and marine OA sources.

Revising the hygroscopicity of inorganic sea salt particles.

Sea spray is one of the largest natural aerosol sources and plays an important role in the Earth's radiative budget. These particles are inherently hygroscopic, that is, they take-up moisture from the air, which affects the extent to which they interact with solar radiation. We demonstrate that the hygroscopic growth of inorganic sea salt is 8-15% lower than pure sodium chloride, most likely due to the presence of hydrates. We observe an increase in hygroscopic growth with decreasing particle size (for particle diameters <150 nm) that is independent of the particle generation method. We vary the hygroscopic growth of the inorganic sea salt within a general circulation model and show that a reduced hygroscopicity leads to a reduction in aerosol-radiation interactions, manifested by a latitudinal-dependent reduction of the aerosol optical depth by up to 15%, while cloud-related parameters are unaffected. We propose that a value of κs=1.1 (at RH=90%) is used to represent the hygroscopicity of inorganic sea salt particles in numerical models.

False-positive synovial fluid alpha-defensin test in a patient with acute gout affecting a prosthetic knee.

The alpha-defensin test has demonstrated promising results in studies evaluating it for the diagnosis of prosthetic joint infection. There are limited data in the literature regarding its use in patients with other inflammatory joint conditions, but a high specificity for infection has been reported. We describe a patient with a prosthetic knee joint, who had a positive alpha-defensin lateral flow assay but in whom subsequent results confirmed a diagnosis of acute gout with no evidence of infection.

Case report of a successfully treated gentamicin and ciprofloxacin resistant Serratia marcescens prosthetic joint infection.

We report the case of an eradicated multiresistant Serratia marcescens prosthetic hip joint infection. It is estimated that enteric Gram-negative organisms account for approximately 8% of prosthetic joint infections. However, the evolving multiresistant strains of organisms being encountered in hospital acquired infections is making eradication increasingly difficult. We describe n our surgical and microbiological approach to this in a complex case.

Lessons from a large norovirus outbreak: impact of viral load, patient age and ward design on duration of symptoms and shedding and likelihood of transmission.

BACKGROUND: Hospital norovirus outbreaks cause significant financial and operational disruption which should be minimised by optimal handling of affected areas and use of isolation facilities. AIM: To identify factors associated with increased duration of symptoms and viral excretion and increased probability of transmission. METHODS: Retrospective observational study of a large norovirus outbreak at a UK teaching hospital in the winter of 2009-2010 where patients were diagnosed using a real-time polymerase chain reaction (PCR) assay. FINDINGS: Symptom duration was significantly associated with patient age (Spearman rank correlation coefficient: 0.197; P = 0.002) but not with PCR cycle threshold (C(T)) value. Duration of viral excretion was found to be longer in patients with higher viral loads. Transmission within a ward bay was not significantly associated either with age or with C(T) value but was more likely to occur in some ward blocks than others, which may relate to differences in ward design. Transfer of patients into isolation rooms or cohorted area within two days of symptom onset did not significantly influence probability of onward transmission (52% vs 47%; P = 0.67). CONCLUSIONS: The presented data suggest that C(T) value may guide timing of repeat sample collection if ongoing gastrointestinal symptoms may relate to other pathologies, and that patients developing symptoms of norovirus may remain in their current bay rather than being moved into isolation facilities. The bay or ward should be closed to new admissions but it should be anticipated that duration of symptoms and therefore closure will be longer when the outbreak involves elderly patients.

HIV testing: the boundaries. A survey of HIV testing practices and barriers to more widespread testing in a British teaching hospital.

A survey of HIV testing practices among registrars of all admitting specialties within Sheffield Teaching Hospitals National Health Service Trust was performed in 2007. Respondents from most specialties tested patients for HIV infrequently and several barriers were identified, which prevented testing even when the diagnosis was considered.

Vibrio vulnificus: an unusual mode of acquisition and novel use of rapid susceptibility testing.

Infection with Vibrio vulnificus is uncommon in Europe but is associated with necrotising wound infections and life-threatening septicaemia. This case is one of infection most likely to have been acquired from a thermal pool in Turkey without preceding exposure to seawater or shellfish. The report also describes how early management was optimised using gradient diffusion antibiotic strips to provide rapid susceptibility data.