Estimating the number of probable new SARS-CoV-2 infections among tested subjects from the number of confirmed cases.

OBJECTIVES: In most African countries, confirmed COVID-19 case counts underestimate the number of new SARS-CoV-2 infection cases. We propose a multiplying factor to approximate the number of biologically probable new infections from the number of confirmed cases. METHODS: Each of the first thousand suspect (or alert) cases recorded in South Kivu (DRC) between 29 March and 29 November 2020 underwent a RT-PCR test and an IgM and IgG serology. A latent class model and a Bayesian inference method were used to estimate (i) the incidence proportion of SARS-CoV-2 infection using RT-PCR and IgM test results, (ii) the prevalence using RT-PCR, IgM and IgG test results; and, (iii) the multiplying factor (ratio of the incidence proportion on the proportion of confirmed -RT-PCR+- cases). RESULTS: Among 933 alert cases with complete data, 218 (23%) were RT-PCR+; 434 (47%) IgM+; 464 (~ 50%) RT-PCR+, IgM+, or both; and 647 (69%) either IgG + or IgM+. The incidence proportion of SARS-CoV-2 infection was estimated at 58% (95% credibility interval: 51.8-64), its prevalence at 72.83% (65.68-77.89), and the multiplying factor at 2.42 (1.95-3.01). CONCLUSIONS: In monitoring the pandemic dynamics, the number of biologically probable cases is also useful. The multiplying factor helps approximating it.

Influence of observable and unobservable exposure on the patient's risk of acquiring influenza-like illness at hospital.

During outbreaks of hospital-acquired influenza-like illness (HA-ILI) healthcare workers (HCWs), patients, and visitors are each a source of infection for the other. Quantifying the effects of these various exposures will help improve prevention and control of HA-ILI outbreaks. We estimated the attributability of HA-ILI to: (1) exposure to recorded or unrecorded sources; (2) exposure to contagious patient or contagious HCW; (3) exposure during observable or unobservable contagious period of the recorded sources; and, (4) the moment of exposure. Among recorded sources, 59% [95% credible interval (CrI) 34-83] of HA-ILI of patients was associated with exposure to contagious patients and 41% (95% CrI 17-66) with exposure to contagious HCWs. Exposure during the unobservable contagiousness period of source patients accounted for 49% (95% CrI 19-75) of HA-ILI, while exposure during the unobservable contagiousness period of source HCWs accounted for 82% (95% CrI 51-99) of HA-ILI. About 80% of HA-ILIs were associated with exposure 1 day earlier. Secondary cases of HA-ILI might appear as soon as the day after the detection of a primary case highlighting the explosive nature of HA-ILI spread. Unobservable transmission was the main cause of HA-ILI transmission suggesting that symptom-based control measures alone might not prevent hospital outbreaks. The results support the rapid implementation of interventions to control influenza transmission.

Community-acquired Legionnaires' disease in a renal transplant recipient with unclear incubation period: the importance of molecular typing.

Transplant recipients are at risk of developing Legionnaires' disease (LD) because of impaired cellular immunity. Here, we describe a renal transplant recipient who developed LD at least 10 days after hospital admission and transplantation. The hospital water network was initially suspected, but further testing determined that the probable source was the patient's domestic water supply. Our report also suggests that the patient's immunosuppressed state may have switched potential colonization to pneumonia.

Is diabetes a risk factor for central venous access port-related bloodstream infection in oncological patients?

It was a dogma that patients with diabetes mellitus (DM) are at increased risk of infection or death associated with an infection. However, in cancer patients, this has not been well investigated. The aim was to investigate whether diabetic patients with cancer are at high risk of central venous access port (CVAP)-related bloodstream infection (BSI), and to analyse mortality after CVAP-BSI. A total of 17 patients with type 1 DM (T1DM), 66 with type 2 DM (T2DM) and 307 non-diabetic patients were included. Each patient was followed up until the first late CVAP-BSI or for a maximum for 1 year in the absence of a CVAP-BSI. Fifty-three CVAP-BSIs occurred in 66,528 catheter-days. The cumulative incidence of CVAP-BSI was not higher in T1DM (5.9 %; p = 0.17) and T2DM (19.7 %; p = 0.70) compared with the non-diabetic patients (12.7 %). However, in patients with CVAP-BSI, the 1-month crude mortality rate was higher in DM patients (42.9 % vs. 15.4 %; p = 0.04), whereas the mortality in patients without CVAP-BSI was similar in both groups of patients (19.8 % vs. 17.1 %; p = 0.58). Of the 12 deaths that occurred within 1 month of CVAP-BSI, 16.66 % was attributable to CVAP-BSI. The predictive factor of 1-month mortality was DM (p = 0.04). Parenteral nutrition (PN) was independently associated with CVAP-BSI in diabetic patients (p = 0.001). In this study, diabetes did not increase the risk of CVAP-BSI, but mortality was higher in diabetic patients who had a CVAP-BSI. This suggests, in addition to medical treatment, CVAP should be withdrawn after infection onset.

Benefits of smart pumps for automated changeovers of vasoactive drug infusion pumps: a quasi-experimental study.

BACKGROUND: Manual changeover of vasoactive drug infusion pumps (CVIP) frequently lead to haemodynamic instability. Some of the newest smart pumps allow automated CVIP. The aim of this study was to compare automated CVIP with manual 'Quick Change' relays. METHODS: We performed a prospective, quasi-experimental study, in a university-affiliated intensive care unit (ICU). All adult patients receiving continuous i.v. infusion of vasoactive drugs were included. CVIP were successively performed manually (Phase 1) and automatically (Phase 2) during two 6-month periods. The primary endpoint was the frequency of haemodynamic incidents related to the relays, which were defined as variations of mean arterial pressure >15 mm Hg or heart rate >15 bpm. The secondary endpoints were the nursing time dedicated to relays and the number of interruptions in care because of CVIP. A multivariate mixed effects logistic regression was fitted for analytic analysis. RESULTS: We studied 1329 relays (Phase 1: 681, Phase 2: 648) from 133 patients (Phase 1: 63, Phase 2: 70). Incidents related to CVIP decreased from 137 (20%) in Phase 1 to 73 (11%) in Phase 2 (P<0.001). Automated relays were independently associated with a 49% risk reduction of CVIP-induced incidents (adjusted OR=0.51, 95% confidence interval 0.34-0.77, P=0.001). Time dedicated to the relays and the number of interruptions in care to manage CVIP were also significantly reduced with automated relays vs manual relays (P=0.001). CONCLUSIONS: These results demonstrate the benefits of automated CVIP using smart pumps in limiting the frequency of haemodynamic incidents related to relays and in reducing the nursing workload.

Factors associated with hospital mortality in community-acquired legionellosis in France.

The aims of this study were to describe the clinical, biological and radiological features of community-acquired (CA) Legionnaires' disease (LD) and identify the predictors of mortality in hospitalised patients. Demographic data, risk factors, clinical and biological features, medical management, complications, and outcome from 540 hospitalised patients with confirmed CA LD were prospectively recorded. 8.1% of patients (44 out of 540) died. The predictors of survival after Kaplan-Meier analysis were male sex (p = 0.01), age <60 yrs (p = 0.02), general symptoms (p = 0.006), intensive care unit (ICU) stay (p<0.001), and class II-III Pneumonia Severity Index score (p = 0.004). Six predictors of death were identified by multivariate analysis: age (per 10-yr increment) (relative hazard (RH) 1.50, 95% CI 1.21-1.87), female sex (RH 2.00, 95% CI 1.08-3.69), ICU admission (RH 3.31, 95% CI 1.67-6.56), renal failure (RH 2.73, 95% CI 1.42-5.27), corticosteroid therapy (RH 2.54, 95% CI 1.04-6.20) and C-reactive protein (CRP) >500 mg · L(-1) (RH 2.14, 95% CI 1.02-4.48). Appropriate antibiotic therapy was prescribed for 70.8% (292 out of 412) of patients after admission and for 99.8% (537 out of 538) of patients after diagnosis confirmation. In conclusion, female sex, age, ICU stay, renal failure, corticosteroid treatment and increased level of CRP are significant risk factors for mortality in CA LD.

Invasive aspergillosis: an important risk factor on the short- and long-term survival of acute myeloid leukemia (AML) patients.

Invasive aspergillosis (IA) during induction chemotherapy of acute myeloid leukemia (AML) could worsen the prognosis. Our objective was to study how the development of IA during AML interferes with the therapeutic strategy and to evaluate its impact on the short- and long-term survival. Newly diagnosed AML patients between the years 2004 and 2007 were retrospectively analyzed. The outcome was death of the patient. A Cox proportional hazards model with the diagnosis of IA and post-induction response evaluation as the main exposure was fitted. Overall, 262 patients were analyzed and 58 IA were observed. The 2-year survival of patients having had remission of AML was 54% and, for patients with failure of chemotherapy, it was 5% (p < 0.001). The 2-year survival of patients having had IA was 14%, and without IA, it was 32% (p = 0.01). Multivariate analysis showed that IA was associated with a higher risk of death in case of remission compared to no IA (hazard ratio [HR] = 1.66 [1.05-2.65], p = 0.031) and also in case of failure (HR = 6.43, p < 0.001). IA was associated with an increased risk of death for patients if they were either in remission or in failure after induction chemotherapy.

A report on the large measles outbreak in Lyon, France, 2010 to 2011.

In 2010 and 2011, the city of Lyon, located in the Rhône-Alpes region (France), has experienced one of the highest incidences of measles in Europe. We describe a measles outbreak in the Lyon area, where cases were diagnosed at Lyon University hospitals (LUH) between 2010 and mid-2011. Data were collected from the mandatory notification system of the regional public health agency, and from the virology department of the LUH. All patients and healthcare workers who had contracted measles were included. Overall, 407 cases were diagnosed, with children of less than one year of age accounting for the highest proportion (n=129, 32%), followed by individuals between 17 and 29 years-old (n=126, 31%). Of the total cases, 72 (18%) had complications. The proportions of patients and healthcare workers who were not immune to measles were higher among those aged up to 30 years. Consequently, women of childbearing age constituted a specific population at high risk to contract measles and during this outbreak, 13 cases of measles, seven under 30 years-old, were identified among pregnant women. This study highlights the importance of being vaccinated with two doses of measles vaccine, the only measure which could prevent and allow elimination of the disease.

Consumption of psychoactive substances among 535 women entering a Lyon prison (France) between June 2004 and December 2008.

BACKGROUND: In France, recent data on the consumption of psychoactive substances (PASs) among women entering prison are virtually nonexistent. The objective of this study was to describe the characteristics of female entrants at Montluc prison in Lyon (France) and to estimate their PAS consumption. METHODS: Between June 1, 2004 and December 31, 2008, of 841 women entering the Lyon correctional facility, 535 had an entrance interview, conducted by a nurse, during which a questionnaire was systematically proposed; 306 detainees did not have this interview and could not be included in the study because of an immediate transfer to another prison or emergency hospitalization. Socioeconomic and incarceration characteristics, PAS consumption, as well as consumption level (occasional, regular, abusive or dependence) and psychological distress of the 535 interviewed detainees were systematically noted. This psychological distress was defined by the presence in the entrant talks or behavior suggesting clinical symptoms such as anxiety, depression, delusion, delirium, and mood or behavior disorders. Descriptive analysis was undertaken with the Chi(2) test and Fisher's exact test for differences between the proportions observed. RESULTS: The average age of the 534 responding detainees was 31.5 years; 59.2% had had no ongoing professional activity in the 12 months prior to incarceration, and 21.6% had already been imprisoned before; 37.5% of the entrants reported dependence on tobacco and 13.7% on alcohol; 6.6% reported regular, abusive use or dependence on cannabis, 20.4% on psychotropic medications, and 7.7% on other drugs (heroin, cocaine, synthetic drugs) in the 6 months preceding their incarceration; 39.2% of the consumers at risk reported using at least two substances; 7.1% of detainees were on opioid substitution treatment. A multiple correspondence factor analysis was used to note specific characteristics of three groups of PAS consumers. CONCLUSIONS: More frequent among young women detainees, overall PAS consumption was quite close to that of male entrants, was greater than in the general female population, and was very often accompanied by psychological distress. Effective screening upon entry into detention should be carried out so that female consumers can be offered psychological and/or psychiatric care adapted to a prison environment.

A randomized trial of viral hepatitis prevention among underprivileged people in the Lyon area of France.

BACKGROUND: We compared the efficacy of two viral hepatitis B and C (VHBC) screening strategies, relative to no intervention, among underprivileged people (UP) living in shelters in the Lyon area. METHODS: Eighteen of 37 shelters were randomly sampled after stratification based on the accommodation capacity and the screening centres/shelters distance. Through randomization, the S0 strategy (no intervention), the S1 strategy [group information (GI) and referral for screening] and the S2 strategy (GI and in situ screening) were each applied in six shelters. A standardized questionnaire was offered to each participant. Follow-up of positive cases was organized via the reference centre of VHBC of Lyon. RESULTS: The screening completion rate (SCR) among 1276 included subjects in S0, S1 and S2 was 1.5, 42.8 and 59.7%, respectively (P < 10(-6)). This rate was higher in S2 regardless of the sociodemographic variable considered. Odds ratios (OR) of screening completion (SC) was significantly higher in S1 versus S0, OR = 49.8 [95% confidence interval (CI): 26.1-102.1], in S2 versus S0, OR = 98.5 (95% CI: 51.9-200.8) and in S2 versus S1, OR = 2.0 (95% CI: 1.3-2.9). Age, country of birth and professional inactivity were independently associated with SC. CONCLUSIONS: Health authorities must ensure widespread screening of UP, which is more effective when conducted in shelters than in screening centres.

Automated surveillance in French ICUs: is it feasible? Results from a survey in French ICUs participating in a surveillance network.

A survey was undertaken to evaluate the level of computerization in intensive care units (ICUs) within a French network dedicated to the surveillance of healthcare-associated infections, antimicrobial use (AMU) and antimicrobial resistance (AMR) in ICUs (REA-REZO). Ninety-eight ICUs responded, and patient records were computerized in 57%, antimicrobial prescriptions were computerized in 59% and AMR epidemiology was computerized in 72%. AMU and AMR feedback was provided to the ICU itself for 77% and 65% of ICUs, respectively, and feedback was provided to the national surveillance for 79% and 65% of ICUs, respectively. This study suggests that the level of computerization in ICUs requires further improvement.

Characteristics of human metapneumovirus infection in adults hospitalized for community-acquired influenza-like illness in France, 2012-2018: a retrospective observational study.

OBJECTIVES: To describe the prevalence, clinical features and complications of human metapneumovirus (hMPV) infections in a population of adults hospitalized with influenza-like illness (ILI). METHODS: This was a retrospective, observational, multicenter cohort study using prospectively collected data from adult patients hospitalized during influenza virus circulation, for at least 24 h, for community-acquired ILI (with symptom onset <7 days). Data were collected from five French teaching hospitals over six consecutive winters (2012-2018). Respiratory viruses were identified by multiplex reverse transcription polymerase chain reaction (RT-PCR) on nasopharyngeal specimens. hMPV + patients were compared with hMPV- patients, influenza+ and respiratory syncytial virus (RSV)+ patients using multivariate logistic regressions. Primary outcome was the prevalence of hMPV in patients hospitalized for ILI. RESULTS: Among the 3148 patients included (1449 (46%) women, 1988 (63%) aged 65 and over; 2508 (80%) with chronic disease), at least one respiratory virus was detected in 1604 (51%, 95% confidence interval (CI) 49-53), including 100 cases of hMPV (100/3148, 3% 95% CI 3-4), of which 10 (10%) were viral co-infection. In the hMPV + patients, mean length of stay was 7 days, 62% (56/90) developed a complication, 21% (14/68) were admitted to intensive care unit and 4% (4/90) died during hospitalization. In comparison with influenza + patients, hMPV + patients were more frequently >65 years old (adjusted odds ratio (aOR) = 3.3, 95% CI 1.9-6.3) and presented more acute heart failure during hospitalization (aOR = 1.8, 95% CI 1.0-2.9). Compared with RSV + patients, hMPV + patients had less cancer (aOR = 0.4, 95% CI 0.2-0.9) and were less likely to smoke (aOR = 0.5, 95% CI 0.2-0.9) but had similar outcomes, especially high rates of respiratory and cardiovascular complications. CONCLUSIONS: Adult hMPV infections mainly affect the elderly and patients with chronic conditions and are responsible for frequent cardiac and pulmonary complications similar to those of RSV infections. At-risk populations would benefit from the development of antivirals and vaccines targeting hMPV.

Influenza increases invasive meningococcal disease risk in temperate countries.

OBJECTIVES: Invasive meningococcal disease (IMD) is a severe bacterial infection that displays wintertime seasonality in temperate countries. Mechanisms driving seasonality are poorly understood and may include environmental conditions and/or respiratory virus infections. We evaluated the contribution of influenza and environmental conditions to IMD risk, using standardized methodology, across multiple geographical regions. METHODS: We evaluated 3276 IMD cases occurring between January 1999 and December 2011 in 11 jurisdictions in Australia, Canada, France and the United States. Effects of environmental exposures and normalized weekly influenza activity on IMD risk were evaluated using a case-crossover design. Meta-analytic methods were used to evaluate homogeneity of effects and to identify sources of between-region heterogeneity. RESULTS: After adjustment for environmental factors, elevated influenza activity at a 2-week lag was associated with increased IMD risk (adjusted odds ratio (OR) per standard deviation increase 1.29; 95% confidence interval, 1.04-1.59). This increase was homogeneous across the jurisdictions studied. By contrast, although associations between environmental exposures and IMD were identified in individual jurisdictions, none was generalizable. CONCLUSIONS: Using a self-matched design that adjusts for both coseasonality and case characteristics, we found that surges in influenza activity result in an acute increase in population-level IMD risk. This effect is seen across diverse geographic regions in North America, France and Australia. The impact of influenza infection on downstream meningococcal risk should be considered a potential benefit of influenza immunization programmes.

Hospital-acquired influenza: a synthesis using the Outbreak Reports and Intervention Studies of Nosocomial Infection (ORION) statement.

Nosocomial influenza outbreaks occur in almost all types of hospital wards, and their consequences for patients and hospitals in terms of morbidity, mortality and costs are considerable. The source of infection is often unknown, since any patient, healthcare worker (HCW) or visitor is capable of transmitting it to susceptible persons within hospitals. Nosocomial influenza outbreak investigations should help to identify the source of infection, prevent additional cases, and increase our knowledge of disease control to face future outbreaks. However, such outbreaks are probably underdetected and underreported, making routes of transmission difficult to track and describe with precision. In addition, the absence of standardised information in the literature limits comparison between studies and better understanding of disease dynamics. In this study, reports of nosocomial influenza outbreaks are synthesised according to the ORION guidelines to highlight existing knowledge in relation to the detection of influenza cases, evidence of transmission between patients and HCWs and measures of disease incidence. Although a body of evidence has confirmed that influenza spreads within hospitals, we should improve clinical and virological confirmation and initiate active surveillance and quantitative studies to determine incidence rates in order to assess the risk to patients.

[Orion (Outbreak Reports and Intervention studies of Nosocomial Infection) used for evaluating interventions and investigations of nosocomial infection outbreaks]. / Orion (Outbreak Reports and Intervention Studies of Nosocomial Infection) pour l'évaluation des interventions et des investigations d'épidémie dans le domaine des infections nosocomiales.

INTRODUCTION: British colleagues have developed the Outbreak Reports and Intervention studies of Nosocomial Infection (Orion) guidelines with the aim to promote transparency of publications in the field of health-care associated infections and particularly for reports of outbreak investigation or intervention studies. The aim of this study was to translate the Orion criteria and to promote their use in France. RESULTS: The Orion guidelines include a checklist of 22 commented items related to the title, abstract, introduction, methods, results, and discussion sections of a scientific article. Specific points for each item are developed to enhance its relevance. CONCLUSION: The use of Orion guidelines by authors and editors should be encouraged and should improve the quality of standards in research, intervention studies, and publications on nosocomial infections and health-care associated infections.

Effect of early initiation of highly active antiretroviral therapy on CD4 cell count and HIV-RNA viral load trends within 24 months of the onset of acute retroviral syndrome.

OBJECTIVES: The effect of starting highly active antiretroviral therapy (HAART) early after the onset of acute retroviral syndrome (ARS) on CD4 and HIV-RNA trends was studied over a 2-year follow-up period. METHODS: Four groups of HIV-infected patients stratified according to the time interval from ARS onset to HAART initiation and a control group of untreated patients were compared. RESULTS: The results indicated that the earlier the start of HAART, the faster was the rate of CD4 increase and HIV-RNA decrease. However, this difference did not seem to persist at 24 months. CONCLUSIONS: The optimal treatment strategy for HIV-infected patients needs to be explored further.

Incidence of methicillin-resistant Staphylococcus aureus nosocomial infections in intensive care units in Lyon University hospitals, France, 2003-2006.

We describe the trends in the incidence of methicillin-resistant Staphylococcus aureus nosocomial infection in intensive care units in Lyon hospitals from January 1, 2003, through December 31, 2006. The incidence rate decreased from 1.77 cases per 100 ICU patients in 2003 to 1.16 cases per 100 ICU patients in 2006, a reduction of 38.0% (P = .05).

Susceptibilities of clinical Clostridium difficile isolates to antimicrobials: a systematic review and meta-analysis of studies since 1970.

OBJECTIVES: Although exposure to antibiotics can cause Clostridium difficile infection, certain antibiotics are used to treat C. difficile. Measurements of antimicrobial C. difficile activity could help to identify antibiotic risk and emergent resistance. Here, we describe publication patterns relating to C. difficile susceptibilities and estimate minimum inhibitory concentrations (MIC) for antibiotic classes in the published literature between January 1970 and June 2014. METHODS: We queried PUBMED and EMBASE for studies reporting antibiotic C. difficile MIC in English or French. We used mixed-effects models to obtain pooled estimates of antibiotic class median MIC (MIC50), 90th percentile of MIC (MIC90), and MIC90:MIC50 ratio. RESULTS: Our search identified 182 articles that met our inclusion criteria, of which 27 were retained for meta-analysis. Aminoglycosides (MIC50 120 mg/L, 95% CI 62-250), 3rd (MIC50 75 mg/L, 95% CI 39-130) and 2nd generation cephalosporins (MIC50 64 mg/L, 95% CI 27-140) had the least C. difficile activity. Rifamycins (MIC50 0.034 mg/L, 95% CI 0.012-0.099) and tetracyclines (MIC50 0.29 mg/L, 95% CI 0.054-1.7) had the highest level of activity. The activity of 3rd generation cephalosporins was more than three times lower than that of 1st generation agents (MIC50 19 mg/L, 95% CI 7.0-54). Time-trends in MIC50 were increasing for carbapenems (70% increase per 10 years) while decreasing for tetracyclines (51% decrease per 10 years). CONCLUSIONS: We found a 3500-fold variation in antibiotic C. difficile MIC50, with aminoglycosides as the least active agents and rifamycins as the most active. Further research is needed to determine how in vitro measures can help assess patient C. difficile risk and guide antimicrobial stewardship.

Prospective survey of azole drug resistance among environmental and clinical isolates of Aspergillus fumigatus in a French University hospital during major demolition works.

OBJECTIVES: Recent studies have reported the emerging worldwide problem of azole drug resistance of A. fumigatus isolates. The aim of this study was to evaluate the antifungal susceptibilities of A. fumigatus isolates recovered from air and clinical samples collected in a French University hospital (Lyon), which underwent major deconstruction works over a one year-period. METHODS: A daily surveillance of fungal contamination was implemented during 11-months. Environmental survey was realized by air samplings, outdoor and indoor, with an automatic agar sampler. In parallel, surveillance of IA infection cases was conducted by epidemiological investigation. Environmental and clinical isolates of A. fumigatus were identified by conventional methods and ß-tubulin sequencing. Susceptibility testing of A. fumigatus isolates against Itraconazole (ITZ), Voriconazole (VCZ) was performed using Etest method. RESULTS: A total of 3885 air samples (1744 outdoor samples and 2141 indoor samples) were collected. From the 3073 identified colonies of A. fumigatus, 400 A. fumigatus isolates were tested for their susceptibility to ITZ and VCZ, including 388 isolates coming from the environment (indoor n:157, outdoor n:231) and 12 isolates coming from clinical samples. All the 400 isolates were susceptible to azoles (≤1µg/mL). CONCLUSIONS: No environmental reservoir of A. fumigatus azole resistant strains was found in our hospital which was undergoing major demolition works. Further studies with larger number of A. fumigatus clinical isolates and environmental isolates from agricultural areas and healthcare establishments are needed to better appreciate the occurrence and prevalence of azole resistance.