Deployment of whole genome next-generation sequencing of SARS-CoV-2 in a military maritime setting.

BACKGROUND: SARS-CoV-2 can spread rapidly on maritime platforms. Several outbreaks of SARS-CoV-2 have been reported on warships at sea, where transmission is facilitated by living and working in close quarters. Core components of infection control measures such as social distancing, patient isolation and quarantine of exposed persons are extremely difficult to implement. Whole genome sequencing (WGS) of SARS-CoV-2 has facilitated epidemiological investigations of outbreaks, impacting on outbreak management in real time by identifying transmission patterns, clusters of infection and guiding control measures. We suggest such a capability could mitigate against the impact of SARS-CoV-2 in maritime settings. METHODS: We set out to establish SARS-CoV-2 WGS using miniaturised nanopore sequencing technology aboard the Royal Fleet Auxiliary ARGUS while at sea. Objectives included designing a simplified protocol requiring minimal reagents and processing steps, the use of miniaturised equipment compatible for use in limited space, and a streamlined and standalone data analysis capability to allow rapid in situ data acquisition and interpretation. RESULTS: Eleven clinical samples with blinded SARS-CoV-2 status were tested at sea. Following viral RNA extraction and ARTIC sequencing library preparation, reverse transcription and ARTIC PCR-tiling were performed. Samples were subsequently barcoded and sequenced using the Oxford Nanopore MinION Mk1B. An offline version of the MinKNOW software was used followed by CLC Genomics Workbench for downstream analysis for variant identification and phylogenetic tree construction. All samples were correctly classified, and relatedness identified. CONCLUSIONS: It is feasible to establish a small footprint sequencing capability to conduct SARS-CoV-2 WGS in a military maritime environment at sea with limited access to reach-back support. This proof-of-concept study has highlighted the potential of deploying such technology in the future to military environments, both maritime and land-based, to provide meaningful clinical data to aid outbreak investigations.

Enhanced chlorhexidine skin penetration with 1,8-cineole.

BACKGROUND: Chlorhexidine (CHG) penetrates poorly into skin. The purpose of this study was to compare the depth of CHG skin permeation from solutions containing either 2% (w/v) CHG and 70% (v/v) isopropyl alcohol (IPA) or 2% (w/v) CHG, 70% (v/v) IPA and 2% (v/v) 1,8-cineole. METHODS: An ex-vivo study using Franz diffusion cells was carried out. Full thickness human skin was mounted onto the cells and a CHG solution, with or without 2% (v/v) 1,8-cineole was applied to the skin surface. After twenty-four hours the skin was sectioned horizontally in 100 µm slices to a depth of 2000 µm and the concentration of CHG in each section quantified using high performance liquid chromatography (HPLC). The data were analysed with repeated measures analysis of variance. RESULTS: The concentration of CHG in the skin on average was significantly higher (33.3% [95%, CI 1.5% - 74.9%]) when a CHG solution which contained 1,8-cineole was applied to the skin compared to a CHG solution which did not contain this terpene (P = 0.042). CONCLUSIONS: Enhanced delivery of CHG can be achieved in the presence of 1,8-cineole, which is the major component of eucalyptus oil. This may reduce the numbers of microorganisms located in the deeper layers of the skin which potentially could decrease the risk of surgical site infection.

Impact of surgical site infection on healthcare costs and patient outcomes: a systematic review in six European countries.

BACKGROUND: Surgical site infections (SSIs) are associated with increased morbidity and mortality. Furthermore, SSIs constitute a financial burden and negatively impact on patient quality of life (QoL). AIM: To assess, and evaluate the evidence for, the cost and health-related QoL (HRQoL) burden of SSIs across various surgical specialties in six European countries. METHODS: Electronic databases and conference proceedings were systematically searched to identify studies reporting the cost and HRQoL burden of SSIs. Studies published post 2005 in France, Germany, the Netherlands, Italy, Spain, and the UK were eligible for data extraction. Studies were categorized by surgical specialty, and the primary outcomes were the cost of infection, economic evaluations, and HRQoL. FINDINGS: Twenty-six studies met the eligibility criteria and were included for analysis. There was a paucity of evidence in the countries of interest; however, SSIs were consistently associated with elevated costs, relative to uninfected patients. Several studies reported that SSI patients required prolonged hospitalization, reoperation, readmission, and that SSIs increased mortality rates. Only one study reported QoL evidence, the results of which demonstrated that SSIs reduced HRQoL scores (EQ-5D). Hospitalization reportedly constituted a substantial cost burden, with additional costs arising from medical staff, investigation, and treatment costs. CONCLUSION: Disparate reporting of SSIs makes direct cost comparisons difficult, but this review indicated that SSIs are extremely costly. Thus, rigorous procedures must be implemented to minimize SSIs. More economic and QoL studies are required to make accurate cost estimates and to understand the true burden of SSIs.

Microbiologic contamination of a positive- and a neutral- displacement needleless intravenous access device in clinical use.

The use of a positive-displacement needleless intravenous access device was associated with lower microbial contamination rates compared with a neutral-displacement device when used on central venous catheters in hemato-oncology patients. In addition, rates of central line-associated bloodstream infection did not differ when either device was used.

Antimicrobial activity and skin permeation of iodine present in an iodine-impregnated surgical incise drape.

OBJECTIVES: The antimicrobial efficacy of an iodine-impregnated incise drape against MRSA was evaluated in a skin model. The permeation of iodine from this drape into the skin was also assessed. METHODS: The antimicrobial efficacy was evaluated in ex vivo studies following application of the surgical incise drape for various times on the surface of donor skin, which was inoculated with either 1 × 10(3) or 1 × 10(6) cfu MRSA/cm(2) skin and mounted on Franz diffusion cells. In some experiments the MRSA-inoculated skin was pre-incubated for 18 h at room temperature prior to applying the drape. Permeation of iodine into the skin using this model was also determined following application of the incise drape for 6 h. RESULTS: The iodine-impregnated drape demonstrated antimicrobial activity compared with the non-use of drape. This reached significance when a high inoculum of MRSA was applied with no pre-incubation period and when a low inoculum of MRSA was applied with a pre-incubation period (P = 0.002 and P = 0.014, respectively). Furthermore, in experiments wherein a high inoculum of MRSA was applied with no pre-incubation period, the iodine-impregnated drape demonstrated superior antimicrobial activity compared with the use of a non-antimicrobial drape (P < 0.001). MIC and MBC values of iodine were attained to 1500 µm below the skin surface. CONCLUSIONS: The iodine-impregnated surgical incise drape had detectable antimicrobial activity. Furthermore, iodine penetrated into the deeper layers of the skin. This property should suppress microbial regrowth at and around a surgical incision site, making its use preferable to the use of a standard drape or non-use of a drape.

Microbiological comparison of a silver-coated and a non-coated needleless intravascular connector in clinical use.

BACKGROUND: The potential for microbial contamination of needleless intravascular (IV) connectors and the risk of subsequent infection are currently a subject of debate. AIM: To compare the number of micro-organisms associated with silver-coated and non-coated connectors in a clinical setting. METHODS: Twenty-five patients with haematological malignancies who required a central venous catheter (CVC) as part of their clinical management were studied. Each patient's CVC was randomly designated to have attached either silver-coated or non-coated connectors. Before and after each manipulation of the connectors, the compression seals were decontaminated with a wipe incorporating 2% (w/v) chlorhexidine gluconate in 70% (v/v) isopropyl alcohol. Following four days in situ, the number of micro-organisms recovered from 119 silver-coated and 117 non-coated connectors was determined. FINDINGS: Thirty-six (30.3%) silver-coated connectors had micro-organisms present on the external silicone compression seal compared to 41 (35%) non-coated connectors [odds ratio (OR): 0.8; 95% confidence interval (CI): 0.47-1.39; P = 0.49]. Conversely, the internal fluid pathway of 31 (26.1%) silver-coated connectors had micro-organisms present compared to 55 (47.0%) of the non-coated connectors (OR: 0.40; 95% CI: 0.23-0.69; P = 0.001). In addition, the total number of micro-organisms present was less in the silver-coated connectors as compared to non-coated devices (P = 0.001). CONCLUSION: The use of a silver-coated connector with a dedicated decontamination regime may reduce the risk of catheter-related bloodstream infection acquired via the intraluminal route.

The antimicrobial efficacy of copper alloy furnishing in the clinical environment: a crossover study.

OBJECTIVE: To determine whether copper incorporated into hospital ward furnishings and equipment can reduce their surface microbial load. DESIGN: A crossover study. SETTING: Acute care medical ward with 19 beds at a large university hospital. METHODS: Fourteen types of frequent-touch items made of copper alloy were installed in various locations on an acute care medical ward. These included door handles and push plates, toilet seats and flush handles, grab rails, light switches and pull cord toggles, sockets, overbed tables, dressing trolleys, commodes, taps, and sink fittings. Their surfaces and those of equivalent standard items on the same ward were sampled once weekly for 24 weeks. The copper and standard items were switched over after 12 weeks of sampling to reduce bias in usage patterns. The total aerobic microbial counts and the presence of indicator microorganisms were determined. RESULTS: Eight of the 14 copper item types had microbial counts on their surfaces that were significantly lower than counts on standard materials. The other 6 copper item types had reduced microbial numbers on their surfaces, compared with microbial counts on standard items, but the reduction did not reach statistical significance. Indicator microorganisms were recovered from both types of surfaces; however, significantly fewer copper surfaces were contaminated with vancomycin-resistant enterococci, methicillin-susceptible Staphylococcus aureus, and coliforms, compared with standard surfaces. CONCLUSIONS: Copper alloys (greater than or equal to 58% copper), when incorporated into various hospital furnishings and fittings, reduce the surface microorganisms. The use of copper in combination with optimal infection-prevention strategies may therefore further reduce the risk that patients will acquire infection in healthcare environments.

Role of copper in reducing hospital environment contamination.

The environment may act as a reservoir for pathogens that cause healthcare-associated infections (HCAIs). Approaches to reducing environmental microbial contamination in addition to cleaning are thus worthy of consideration. Copper is well recognised as having antimicrobial activity but this property has not been applied to the clinical setting. We explored its use in a novel cross-over study on an acute medical ward. A toilet seat, set of tap handles and a ward entrance door push plate each containing copper were sampled for the presence of micro-organisms and compared to equivalent standard, non-copper-containing items on the same ward. Items were sampled once weekly for 10 weeks at 07:00 and 17:00. After five weeks, the copper-containing and non-copper-containing items were interchanged. The total aerobic microbial counts per cm(2) including the presence of 'indicator micro-organisms' were determined. Median numbers of microorganisms harboured by the copper-containing items were between 90% and 100% lower than their control equivalents at both 07:00 and 17:00. This reached statistical significance for each item with one exception. Based on the median total aerobic cfu counts from the study period, five out of ten control sample points and zero out of ten copper points failed proposed benchmark values of a total aerobic count of <5cfu/cm(2). All indicator micro-organisms were only isolated from control items with the exception of one item during one week. The use of copper-containing materials for surfaces in the hospital environment may therefore be a valuable adjunct for the prevention of HCAIs and requires further evaluation.

Staphylococci.

Staphylococci are among the leading causes of nosocomial infections. Increasing insusceptibility to beta-lactams and the glycopeptides complicates treatment of these infections. This review examines the current status and future perspectives for the therapy of infections caused by Staphylococcus aureus and coagulase-negative staphylococci.

A prospective clinical trial to evaluate the microbial barrier of a needleless connector.

Needleless connectors are being increasingly used for direct access to intravascular catheters. However, the potential for microbial contamination of these devices and subsequent infection risk is still widely debated. In this study the microbial contamination rate associated with three-way stopcock luers with standard caps attached was compared to those with Y-type extension set luers with Clearlink needleless connectors attached. Fifty patients undergoing cardiothoracic surgery who required a central venous catheter (CVC) as part of their peri- and postoperative management were studied for microbial contamination of CVC luers following 72 hrs in situ. Each patient's CVC was randomly designated to have either the three-way stopcocks with caps (control patients) or Clearlink Y-type extension sets (test patients). Prior to, and following each manipulation of the three-way stopcock luers or Clearlink devices, a 70% (v/v) isopropyl alcohol swab was used for disinfection of the connections. The microbial contamination of 393 luers, 200 with standard caps and 193 with Clearlink attached, was determined. The internal surfaces of 20 of 200 (10%) three-way stopcock luers with standard caps were contaminated with micro-organisms whereas only one of 193 (0.5%) luers with Clearlink attached was contaminated (P<0.0001). These results demonstrate that the use of the Clearlink device with a dedicated disinfection regimen reduces the internal microbial contamination rate of CVC luers compared with standard caps. The use of such needle-free devices may therefore reduce the intraluminal risk of catheter-related bloodstream infection and thereby supplement current preventive guidelines.

RAPD for the typing of coagulase-negative staphylococci implicated in catheter-related bloodstream infection.

OBJECTIVES: A rapid random amplification of polymorphic DNA (RAPD) technique was developed to distinguish between strains of coagulase-negative staphylococci (CoNS) involved in central venous catheter (CVC)-related bloodstream infection. Its performance was compared with that of pulsed-field gel electrophoresis (PFGE). METHODS: Patients at the University Hospital Birmingham NHS Foundation Trust, U.K. who underwent stem cell transplantation and were diagnosed with CVC-related bloodstream infection due to CoNS whilst on the bone marrow transplant unit were studied. Isolates of CoNS were genotyped by PFGE and RAPD, the latter employing a single primer and a simple DNA extraction method. RESULTS: Both RAPD and PFGE were highly discriminatory (Simpson's diversity index, 0.96 and 0.99, respectively). Within the 49 isolates obtained from blood cultures of 33 patients, 20 distinct strains were identified by PFGE and 25 by RAPD. Of the 25 strains identified by RAPD, nine clusters of CoNS contained isolates from multiple patients, suggesting limited nosocomial spread. However, there was no significant association between time of inpatient stay and infection due to any particular strain. CONCLUSION: The RAPD technique presented allows CoNS strains to be genotyped with high discrimination within 4h, facilitating real-time epidemiological investigations. In this study, no single strain of CoNS was associated with a significant number of CVC-related bloodstream infections.

Rapid serodiagnosis of Staphylococcus aureus surgical site infection following median sternotomy.

OBJECTIVES: To determine the sensitivity and specificity of a novel ELISA for the serodiagnosis of surgical site infection (SSI) due to staphylococci following median sternotomy. METHODS: Twelve patients with a superficial sternal SSI and 19 with a deep sternal SSI due to Staphylococcus aureus were compared with 37 control patients who also underwent median sternotomy for cardiac surgery but exhibited no microbiological or clinical symptoms of infection. A further five patients with sternal SSI due to coagulase-negative (CoNS) staphylococci were studied. An ELISA incorporating a recently recognised exocellular short chain form of lipoteichoic acid (lipid S) recovered from CoNS, was used to determine serum levels of anti-lipid S IgG in all patient groups. RESULTS: Serum anti-lipid S IgG titres of patients with sternal SSI due to S. aureus were significantly higher than the control patients (P<0.0001). In addition, patients with deep sternal SSI had significantly higher serum anti-lipid S IgG titres than patients with superficial sternal SSI (P = 0.03). Serum anti-lipid S IgG titres of patients with sternal SSI due to CoNS were significantly higher than the control patients (P = 0.001). CONCLUSION: The lipid S ELISA may facilitate the diagnosis of sternal SSI due to S. aureus and could also be of value with infection due to CoNS.

A randomized, prospective clinical trial to assess the potential infection risk associated with the PosiFlow needleless connector.

The microbial contamination rate of luers of central venous catheters (CVCs) with either PosiFlow needleless connectors or standard caps attached was investigated. The efficacy of 70% (v/v) isopropyl alcohol, 0.5% (w/v) chlorhexidine in gluconate 70% (v/v) isopropyl alcohol and 10% (w/v) aqueous povidone-iodine to disinfect the intravenous connections was also assessed. Seventy-seven patients undergoing cardiac surgery who required a CVC as part of their clinical management were randomly allocated either needleless connectors or standard caps. Patients were also designated to receive chlorhexidine/alcohol, isopropyl alcohol or povidone-iodine for pre-CVC insertion skin preparation and disinfection of the connections. After 72 h in situ the microbial contamination rate of 580 luers, 306 with standard caps and 274 with needleless connectors attached, was determined. The microbial contamination rate of the external compression seals of 274 needleless connectors was also assessed to compare the efficacy of the three disinfectants. The internal surfaces of 55 out of 306 (18%) luers with standard caps were contaminated with micro-organisms, whilst only 18 out of 274 (6.6%) luers with needleless connectors were contaminated (P<0.0001). Of those needleless connectors disinfected with isopropyl alcohol, 69.2% were externally contaminated with micro-organisms compared with 30.8% disinfected with chlorhexidine/alcohol (P<0.0001) and 41.6% with povidone-iodine (P<0.0001). These results suggest that the use of needleless connectors may reduce the microbial contamination rate of CVC luers compared with the standard cap. Furthermore, disinfection of needleless connectors with either chlorhexidine/alcohol or povidone-iodine significantly reduced external microbial contamination. Both these strategies may reduce the risk of catheter-related infections acquired via the intraluminal route.