Investigation of healthcare-associated COVID-19 in a large French hospital group by whole-genome sequencing

OBJECTIVES

Despite the quick implementation of infection prevention and control procedures and the use of personal protective equipment within healthcare facilities, many cases of nosocomial COVID-19 transmission have been reported. We aimed to estimate the frequency and impact of healthcare-associated COVID-19 (HA-COVID-19) and evaluate the contribution of whole-genome sequencing (WGS) in cluster investigation.

METHODS

We estimated the frequency and mortality of HA-COVID-19 infections from September 1 to November 30, 2020, with a focus on the evolution of hospitalized community-associated COVID-19 (CA-COVID-19) cases and cases detected among healthcare workers (HCWs) within the Sorbonne University Hospital Group (Paris, France). We thoroughly examined 12 clusters through epidemiological investigations and WGS.

RESULTS

Overall, 209 cases of HA-COVID-19 were reported. Evolution of HA-COVID-19 incidence closely correlated with the incidence of CA-COVID-19 and COVID-19 among HCWs. During the study period, 13.9 % of hospitalized patients with COVID-19 were infected in the hospital and the 30-day mortality rate of HA-COVID-19 was 31.5 %. Nosocomial transmission of SARS-CoV-2 led to clusters involving both patients and HCWs. WGS allowed the exclusion of one-third of cases initially assigned to a cluster.

CONCLUSIONS

WGS analysis combined with comprehensive epidemiological investigations is essential to understand transmission routes and adapt the IPC response to protect both patients and HCWs.

Economic impact of an outbreak of carbapenemase producing-Enterobacteriaceae in a surgical intensive care unit

BACKGROUND

A 15-month outbreak of carbapenemase-producing Enterobacterales (CPE) occurred in the surgical intensive care unit (SICU) of our institution. We aimed to estimate the financial impact of this outbreak from the perspective of the French public health insurance system.

METHODS

The characteristics of the colonised/infected CPE patients and outbreak management according to French national guidelines were prospectively collected. Loss of productivity was assessed in terms of the reduction in total number of admissions (TNA) and discharges and in ICU length of stay (LoS). The additional financial burden associated with this outbreak was estimated by the accounting department of the hospital, including the impact of the extended LoS and restricted admissions.

RESULTS

Sixteen CPE patients (19 stays) were hospitalised in the SICU (10/2016-01/2018). The median ICU LoS for the CPE cases was 17 [8-36] days versus 6.5 and 6.1 days in 2016 and 2017, respectively, for the whole SICU population. The total number of lost bed days during the outbreak was 452. The TNA dropped dramatically in 2017 (decrease of 20.6%). The estimated costs were 768,386 EUR for bed days lost; 297,176 EUR and 63,675 EUR for the extended LoS for the CPE cases and the patients on contact precautions, respectively; 34,045 EUR for staff reinforcements; 85,764 EUR for bacteriological screening tests; and 42,857 EUR for antimicrobial treatment. The total financial burden of the outbreak was 1,291,903 EUR.

CONCLUSION

Management of a CPE outbreak in the SICU is associated with a huge financial burden for the unit and for the institution.

Bathroom contamination by antibiotic-resistant Enterobacterales (ESBLPE and CPE): an experimental study

BACKGROUND

Extended-spectrum β-lactamase-producing Enterobacterales (ESBLPE) and carbapenemase-producing Enterobacterales (CPE) cause serious infections. Their presence in urine may lead to environmental contamination potentially responsible for cross-transmission.

AIM

To evaluate the level of spraying and contamination after emptying urine in the toilet and rinsing in the sink, a common practice in the healthcare setting.

METHODS

For each test, the procedure was similar: seat raised, emptying urinal bottle into the toilet at the height of the bowl, rinsing in the sink and flushing. To study splash-drops, water and fluorescein were mixed in the urinal bottle. In each area, the splash-drops frequency and level were assessed with UV. To study contamination, three ESBLPE and one CPE were diluted in saline, 10⁶/mL. Contamination was assessed by sampling before, immediately after and 3 h after the test. The swabs were cultured and the colonies counted and identified.

FINDINGS

The areas at the highest risk of spraying were the toilet bowl contour (N = 36/36), the underside of the toilet seat (N = 34) and the inside of the sink (N = 34). Except for gloves (N = 14), there was low clothing contamination. The most frequently contaminated areas were inside the sink (40/48), where the highest levels of contamination were found (14/48).

CONCLUSION

Emptying the urinal bottles in the toilet followed by sink rinsing is associated with a significant risk of projection and contamination, depending on the area (highest risk at the sink), but the bacteria did not survive beyond 3 h. This practice, which carries a risk of cross-transmission, should be reviewed.

Factors responsible for Ixodes ricinus nymph abundance: Are soil features indicators of tick abundance in a French region where Lyme borreliosis is endemic?

In Europe, the hard tick Ixodes ricinus (Acari: Ixodidae) is the main vector of Lyme borreliosis spirochetes (Borrelia burgdorferi sensu lato group). A field study was conducted to evaluate the abundance of Ixodes nymphs in the French region of Alsace, where Lyme borreliosis is endemic, and to determine whether environmental factors such as soil moisture and composition may be associated with nymph abundance. In the ten sites studied, ticks were collected by drag sampling from March to October in 2013 and 2014. Temperature, relative humidity, saturation deficit, soil pH, humus composition and type of vegetation were recorded at each site. The abundance of I. ricinus was highly variable from one site to another. Inter-annual variations were also observed, since the nymph abundance were higher in 2013 than in 2014. This study shows that humus type can be indicative of nymph abundance. Three types of humus were observed: (1) moder, (2) mull, and (3) mull-moder humus. One of them, moder humus, which is characterized by a thick layer of fragmented leaves, was found in multivariate analyses to be strongly associated with the nymph abundance. This study demonstrates that factors such as saturation deficit do not suffice to explain the differences in nymph abundance among sites. The composition of the soil and especially the type of humus should also be taken into consideration when assessing acarological risk.

ICE SLURRY APPLICATIONS

The role of secondary refrigerants is expected to grow as the focus on the reduction of greenhouse gas emissions increases. The effectiveness of secondary refrigerants can be improved when phase changing media are introduced in place of single phase media. Operating at temperatures below the freezing point of water, ice slurry facilitates several efficiency improvements such as reductions in pumping energy consumption as well as lowering the required temperature difference in heat exchangers due to the beneficial thermo-physical properties of ice slurry. Research has shown that ice slurry can be engineered to have ideal ice particle characteristics so that it can be easily stored in tanks without agglomeration and then be extractable for pumping at very high ice fraction without plugging. In addition ice slurry can be used in many direct contact food and medical protective cooling applications. This paper provides an overview of the latest developments in ice slurry technology.

Virus-specific secretory IgA antibodies as a means of rapid diagnosis of measles and mumps infection

A highly sensitive solid-phase radioimmunoassay has been developed for the detection of virus-specific IgA antibodies in saliva obtained from infants and children. Serial saliva samples from infants and children under 3 years of age with acute measles or mumps infection, or after measles immunization, were examined for their content of virus-specific IgA antibodies. Virus-specific antibodies appeared transiently in the saliva in both illnesses and after immunization with live attenuated measles vaccine. The significance of this finding for rapid diagnosis of these infections without the necessity of drawing a blood sample is discussed.

Detection of IgG antibodies specific for measles virus by enzyme-linked immunosorbent assay (ELISA)

A solid-phase, enzyme-linked immunosorbent assay (ELISA) for determination of IgG antibodies against measles virus is described. The assay utilized antigen-coated polystyrene microplates. The antigen consisted of a sonicated extract of measles-infected Vero cells. Goat and anti-human IgG-peroxidase conjugate was used to detect human IgG bound to viral antigen. Sera taken from 63 healthy adults, 11 young children and 36 patients were evaluated for their IgG titer against measles virus. Comparison of results obtained by ELISA with those obtained by hemagglutination-inhibition (HI) assay or by complement fixation showed good agreement between the tests. The geometric mean titer (GMT) for healthy adults was 753 for ELISA and 32.8 for HI. If these averages are taken as a measure of comparison, then ELISA is approximately 23 times more sensitive than HI. ELISA technique is rapid to perform and could be recommended for routine diagnosis.

Detection of antibodies to varicella zoster virus by radioimmunoassay and enzyme immunoassay techniques

An enzyme assay for the detection of antibodies to varicella-zoster membrane antigen (IPAMA) and a solid phase radioimmunoassay (RIA) which utilizes infected cell lysates as antigen are described. The results have been compared with those obtained by the indirect fluorescent antibody to membrane antigen (IFAMA) technique. It was found that IPAMA was equal in sensitivity to IFAMA. No cross-reactivity was found with other herpes group viruses. The IPAMA appears to give objective results, is easily and rapidly performed, and is recommended as a routine test for serological diagnosis of varicella-zoster infection. The RIA method is about 100 times more sensitive than IPAMA and IFAMA. The RIA is specific and has the potential of determining lower levels of antibody than other serological methods currently in use.