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.

Pulmonary artery injury in left atrial appendage closure device implantation: a systematic review of a potentially fatal complication

Background

Pulmonary artery (PA) injury is a rarely reported complication following percutaneous left atrial appendage closure (LAAC). This study aims to systematically review all reported cases of PA injury associated with LAAC.

Methods

PubMed/Medline, SCOPUS, EMBASE, Google Scholar and the MAUDE databases were searched to find studies reporting PA injury during or after LAAC with the Amplatzer Amulet (AA), Amplatzer Cardiac Plug (ACP) or Watchman device through October 2019. Categorical data were reported in terms of numbers and/or percentages (%).

Results

We found 13 cases (mean age 71.4 yrs) with reported PA injury associated with LAAC. Of these, 9 were case reports, 3 were reported in observational studies, and 1 was in the MAUDE database. Most cases (n=8) were reported in Europe followed by Australia (n=2) and Asia (n=2). The indication for device implantation in all patients was a high bleeding risk with anticoagulation for atrial fibrillation. Five cases were reported with the ACP (1/5 patients died), 5 with AA (2/5 patients died), and 3 with the Watchman (1/2 patients died). Acute and late presentations following implantation were reported for all three devices. 69.2% of cases (9/13) occurred acutely (during or within 24 hours of intervention). Of these, 3/9 occurred during device implantation. 2/4 of the delayed cases occurred >2 weeks following implantation. The mortality rate for acute and delayed cases was 22% (2/9 patients) and 50% (2/4 patients), respectively. A majority of the cases were attributable to barb/strut/hook injury of the PA. PA injury was associated with a mortality rate of approximately 31%. All surviving patients were managed with surgical intervention.

Conclusion

PA injury is an infrequently reported complication following LAAC and is associated with high mortality. Cases can present acutely (intra-procedurally or within 24 hours) or delayed (>24 hours post-implantation). A majority of cases are due to direct injury of the PA by the struts/hooks/barbs of the device. Practitioners should be cognizant of this life-threatening complication, which requires a high index of suspicion for diagnosis and can occur weeks after device implantation.

Funding Acknowledgement

Type of funding source: None

Geochemical behavior and environmental risks related to the use of abandoned base-metal tailings as construction material in the upper-Moulouya district, Morocco

In some developing countries, base-metal residues that were abandoned in tailing ponds or impoundments are increasingly used as construction material without any control, engineering basis, or environmental concern. This uncontrolled reuse of mine tailings may constitute a new form of pollution risks for humans and ecosystems through metal leaching. Therefore, the aim of the current study is to assess mine drainage, metal mobility, and geochemical behavior of two abandoned mine tailings commonly used in the upper-Moulouya region (eastern Morocco) as fine aggregates for mortar preparation. Their detailed physical, chemical, and mineralogical properties were subsequently evaluated in the context of developing appropriate alternative reuses to replace their conventional disposal and limit their weathering exposure. The obtained results showed that both tailings contain relatively high quantities of residual metals and metalloids with lead (ranging between 3610 and 5940 mg/kg) being the major pollutant. However, the mineralogical investigations revealed the presence of abundant neutralizing minerals and low sulfide content which influence mine drainage geochemistry and subsequently lower metals mobility. In fact, leachate analyses from weathering cell kinetic tests showed neutral conditions and low sulfide oxidation rates. According to these results, the tailings used as construction material in the upper-Moulouya region have very low generating potential of contaminated effluents and their reuse as aggregates may constitute a sustainable alternative method for efficient tailing management.

Diagnosis of human metapneumovirus by immunofluorescence staining with monoclonal antibodies in the North-East of England

BACKGROUND

Since its discovery in 2001 human metapneumovirus (hMPV) has been shown to be a significant cause of human respiratory disease, responsible for 5-8% of respiratory infections in hospitalised children. Diagnosis hitherto has been largely carried out by reverse tanscriptase polymerase chain reaction (RT-PCR) but immunofluorescence staining of cells from nasopharyngeal secretions (IF) offers advantages for some laboratories and may produce a more rapid result in urgent cases. We have recently demonstrated that IF with a rabbit antiserum gave sensitivity equal to that of RT-PCR. However, monoclonal antibodies offer a more plentiful, uniform IF reagent.

OBJECTIVES

Here we have evaluated a pool of anti-hMPV monoclonal antibodies in the routine diagnosis of respiratory infections in hospitalised infants and children.

STUDY DESIGN

Eight hundred and fifty-seven routine respiratory specimens were tested by IF with rabbit polyclonal antiserum and monoclonal antibody pool in parallel. A further 1003 specimens were tested with the monoclonal antibody pool alone. All specimens were also tested for a panel of other respiratory viruses by IF.

RESULTS

Both rabbit polyclonal antiserum and monoclonal antibody pool gave positive results in 56 and negative results in 797 specimens. The rabbit polyclonal antibody detected virus in a further two specimens which were negative when tested with the monoclonal pool giving a concordance of 96.6% and a specificity of 100% for the monoclonal antibody pool. Overall hMPV was detected in 5% of specimens whilst 18.4% were positive for hRSV.

CONCLUSIONS

The monoclonal antibody pool-based IF is a robust assay suitable for routine use with a sensitivity only slightly less than that of the other major diagnostic methodologies available.

Varicella-zoster-virus genotypes in East London: a prospective study in patients with herpes zoster

A total of 298 patients with herpes zoster were recruited as part of 2 community-based studies in East London between 1998 and 2003. Single nucleotide-polymorphism analysis of 4 regions (genes 1, 21, 37, and 60) found that most genotypes were European strains C and B, representing 58% and 21% of all samples collected. No change in the proportion of these European clades has occurred during the past 80 years, strongly supporting the hypothesis that these strains are indigenous to the United Kingdom. White patients almost exclusively had reactivation of genotypes C (66%) and B (21%), whereas patients from Africa, Asia, or the Caribbean mainly had reactivation of genotypes A and J. An increase in BglI-positive A and J genotypes in UK cases of zoster is only partly explained by immigration from endemic regions. The data presented provide a baseline against which to evaluate changes in the molecular epidemiology of varicella-zoster virus and the effect of immunization with the Japanese Oka vaccine strain.

Genotyping of varicella-zoster virus and the discrimination of Oka vaccine strains by TaqMan real-time PCR

Single nucleotide polymorphisms (SNPs) in five genes have been used to identify four major subtypes of wild-type varicella-zoster virus (VZV) A, B, C, and J. Additional SNPs, located in the IE62 major transactivating gene can be used to differentiate the Oka vaccine strain (vOka) from wild-type VZV. Primer-probe sets for the detection of the five polymorphic loci were designed by Applied Biosystems for the ABI 7900HT platform. Probes for each allele were labeled with VIC or 6-carboxyfluorescein fluorogenic markers. Each primer-probe set was validated to establish assay sensitivity and specificity using VZV DNA of predetermined copy number and genotype. Further evaluation was carried out using DNA samples from the vesicle fluid or skin swab of the rash of adult patients with herpes zoster or rashes due to vOka. Assay sensitivity ranged from 10 and 10(8) copies/ml of VZV DNA (equivalent to 2 to 20 copies per reaction). Statistical analyses showed that for each genotype, a set of two probes clearly differentiated the nucleotide present (allele) at that locus (P < 0.0001). It was possible to determine the genotype of wild-type VZV using one of four SNP assays and also to differentiate wild type from vOka using a single SNP assay. The assay can be used for diagnostic and epidemiological studies of VZV, including the differentiation of vOka from wild-type strains, investigation of breakthrough infections, and varicella outbreaks following immunization.

Reactivation of 2 genetically distinct varicella-zoster viruses in the same individual

Varicella-zoster viruses recovered from 2 episodes of herpes zoster in an immunocompetent man were found to be different genotypes. The fact that the 2 isolates came from the same individual was confirmed by DNA fingerprinting. Immunity following chickenpox may not always protect against systemic reinfection. This finding raises questions about varicella-zoster virus pathogenesis and may have an impact on public health policy.

IL-5 and TNF-alpha participate in recruitment of eosinophils to intestinal mucosa in ulcerative colitis

There is an increased influx of activated eosinophils to the intestinal mucosa in active ulcerative colitis, and an increased release of eosinophil-derived proteins, such as ECP, has also been observed. These findings indicate that eosinophils may contribute to tissue damage and intestinal inflammation in this disease. The relative importance of different chemotactic factors and the impact of steroid treatment on their effect in active ulcerative colitis are not known. We measured the eosinophil chemotactic activity in perfusion fluids from 11 patients with ulcerative colitis before and after steroid treatment and from 7 control patients. The effect of neutralizing antibodies to IL-5 and -8, RANTES, eotaxin, MCP-3, TNF-alpha, GM-CSF was investigated. The chemotactic activity was higher in perfusion fluids from patients than from controls (P = 0.0043). Anti-IL-5 (P = 0.005) and -TNF-alpha (P = 0.017) inhibited the activity in perfusion fluids obtained before treatment. Steroid treatment prevented the effect of all antibodies but had no significant effect on the chemotactic activity. The chemotactic activity correlated with the levels of eosinophil granule proteins in the perfusion fluids. In conclusion, in ulcerative colitis, eosinophils are attracted to the intestinal tissue by chemotactic factors, of which IL-5 and TNF-alpha may be the most prominent steroid-sensitive ones. The steroid-insensitive chemotactic activities remain unidentified.

Evidence of local eosinophil activation and altered mucosal permeability in collagenous colitis

The local release of the inflammatory mediators eosinophil cationic protein and myeloperoxidase and the permeability marker albumin was studied in collagenous colitis using a new technique for segmental perfusion of the rectum and descending colon. Perfusion of both segments was successful in 19/25 (76%) of patients with collagenous colitis and controls with noninflammatory conditions. The concentration of myeloperoxidase was increased in the perfusion fluids from both segments in only one patient with collagenous colitis and in none of the controls. On the other hand, concentrations of eosinophil cationic protein and albumin in the perfusate from the rectum were significantly increased in collagenous colitis compared with controls, and similar trends were seen in the perfusates from the descending colon. Furthermore, there was a significant correlation between the increased concentrations of eosinophil cationic protein and albumin, indicating a possible relation between eosinophil activation and disturbed mucosal permeability in collagenous colitis.