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.

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.

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.

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.

[French recommendations on control measures to reduce the infectious risk in immunocompromised patients]. / Quelles mesures pour maîtriser le risque infectieux chez les patients immunodéprimés ? Recommandations formalisées d'experts.

The increase use of immunosuppressive treatments in patients with solid cancer and/or inflammatory diseases requires revisiting our practices for the prevention of infectious risk in the care setting. A review of the literature by a multidisciplinary working group at the beginning of 2014 wished to answer the following 4 questions to improve healthcare immunocompromised patients: (I) How can we define immunocompromised patients with high, intermediate and low infectious risk, (II) which air treatment should be recommended for this specific population? (III) What additional precautions should be recommended for immunocompromised patients at risk for infection? (IV) Which global environmental control should be recommended? Based on data from the literature and using the GRADE method, we propose 15 recommendations that could help to reduce the risk of infection in these exposed populations.

Association between Pseudomonas aeruginosa positive water samples and healthcare-associated cases: nine-year study at one university hospital.

OBJECTIVE: To study the association between the results of water samples and Pseudomonas aeruginosa healthcare-associated cases in a French university hospital. METHODS: Generalized Estimating Equations were used on complete case and imputed datasets. The spatial unit was the building and the time unit was the quarter. RESULTS: For the period 2004-2013, 2932 water samples were studied; 17% were positive for P. aeruginosa. A higher incidence of P. aeruginosa cases was associated with a higher proportion of positive water samples (P=0.056 in complete case analysis and P=0.031 with the imputed dataset). The association was no longer observed when haematology and intensive care units were excluded, but was significant in analyses of data concerning intensive care units alone (P<0.001). CONCLUSION: This study suggests that water outlet contamination in hospitals can lead to an increase in healthcare-associated P. aeruginosa cases in wards dealing with susceptible patients, but does not play a significant role in other wards.

Clinical characteristics and outcome of respiratory syncytial virus infection among adults hospitalized with influenza-like illness in France.

OBJECTIVES: The aim of this study was to analyse characteristics and outcome of respiratory syncytial virus (RSV) infection in adults hospitalized with influenza-like illness (ILI). METHODS: Patients hospitalized with ILI were included in this prospective, multicentre study carried out in six French hospitals during three consecutive influenza seasons (2012-2015). RSV and other respiratory viruses were detected by multiplex PCR in nasopharyngeal swabs. Risk factors for RSV infection were identified by backward stepwise logistic regression analysis. RESULTS: A total of 1452 patients hospitalized with ILI were included, of whom 59% (861/1452) were >65 years and 83% (1211/1452) had underlying chronic illnesses. RSV was detected in 4% (59/1452), and influenza virus in 39% (566/1452). Risk factors for RSV infection were cancer (adjusted OR 2.1, 95% CI 1.1-4.1, p 0.04), and immunosuppressive treatment (adjusted OR 2.0, 95% CI 1.1-3.8, p 0.03). Patients with RSV had a median length of stay of 9 days (6-25), and 57% of them (30/53) had complications, including pneumonia (23/53, 44%) and respiratory failure (15/53, 28%). Fifteen per cent (8/53) were admitted to an intensive care unit, and the in-hospital mortality rate was 8% (4/53). Pneumonia was more likely to occur in patients with RSV than in patients with RSV-negative ILI (44% (23/53) versus 26% (362/1393), p 0.006) or with influenza virus infection (44% versus 28% (157/560), p 0.02). CONCLUSION: RSV is an infrequent cause of ILI during periods of influenza virus circulation but can cause severe complications in hospitalized adults. Risk factors for RSV detection in adults hospitalized with ILI include cancer and immunosuppressive treatment. Specific immunization and antiviral therapy might benefit patients at risk.

Detection of temporal clusters of health care-associated infections or colonizations with Pseudomonas aeruginosa.

We investigated temporal clusters of Pseudomonas aeruginosa cases between 2005 and 2014 in 1 French university hospital, overall and by ward, using the Kulldorff method. Clusters of positive water samples were also investigated at the whole hospital level. Our results suggest that water outlets are not closely involved in the occurrence of clusters of P aeruginosa cases.

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.

Hospitalization in double-occupancy rooms and the risk of hospital-acquired influenza: a prospective cohort study.

Hospitalization in double-occupancy rooms and the risk of hospital-acquired influenza were assessed prospectively. The incidence was 2.0 for 100 patient-days in double- vs. 0.7 in single-occupancy rooms (p 0.028). The adjusted hazard ratio of hospital-acquired influenza was 2.67 (95% confidence interval 1.05-6.76) in patients hospitalized in double- compared to single-occupancy rooms.

Influenza vaccine effectiveness among healthcare workers in comparison to hospitalized patients: A 2004-2009 case-test, negative-control, prospective study.

The objective of this study was to calculate Vaccine Effectiveness (VE) in healthcare workers (HCW) and to compare VE between patients and HCW. A case-control investigation based on the prospective study was conducted between 2004 and 2009 in a teaching hospital. All HCW with influenza-like illness (ILI) from participating units (n = 24) were included, and vaccination status was characterized by interview. A total of 150 HCW presented ILI; 130 (87%) were female, 27 (18%) were positive for influenza, and 42 (28%) were vaccinated. Adjusted VE was 89% (95% CI 39 to 98). Among patients, adjusted VE was 42% (95% CI -39 to 76). The difference of VE (VEhcw - VEpat) was 46.15% (95% CI 2.41 to 144). The VE ratio (VEhcw / VEpat) was 2.09 (95% CI -1.60 to 134.17). Influenza VE differed between HCW and patients when the flu season was taken into account. This finding confirms the major impact of host determinants on influenza VE.

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.

Hospital management of Clostridium difficile infection: a review of the literature.

BACKGROUND: The emergence of the epidemic Clostridium difficile 027 strain has renewed interest in infection control practices. AIM: To review the effectiveness of different practices to reduce hospital C. difficile infection (CDI) in non-outbreak settings. METHODS: Data sources were identified by a MEDLINE search in English and French. The ORION statement was used to extract key data from articles describing interventions to manage CDI. FINDINGS: Twenty-one studies, published between 1982 and December 2013, were reviewed. Most studies were before-after interventions, and a few studies were planned, formal, prospective investigations. The effects of the following single or combined interventions were described: antibiotic management; environmental disinfection and/or cleaning; hand hygiene; bathing; surveillance; cohorting; and isolation of infected patients in private rooms. CONCLUSION: With many methodological weaknesses and some inadequate research reporting, the observed reduction in CDI may not be entirely attributable to interventions. Although infection control programmes involving education and handwashing/gloving protocols were found to have contributed to a reduction in the incidence of CDI, these measures were usually a component of multi-faceted interventions that did not provide for evaluation of the relative impact of each factor. Appropriate environmental disinfection and antibiotic stewardship would appear to offer the most effective benefits.

Pertussis vaccination coverage among adults in the Lyon area.

BACKGROUND: The compliance with recommendations for Pertussis vaccination was assessed in the Lyon population through vaccination coverage (VC). METHODS: A cross-sectional study was conducted in collaboration with 10 private biological analysis laboratories between October 2010 and March 2012, on 1930 adults (>19 years of age) from the Lyon area. Proof of vaccination (PV) was requested to prove the current vaccination status. RESULTS: A percentage of 30.3% (585/1930) of surveyed individuals provided a PV. A positive vaccination status was confirmed in 10.76% [CI 95% 8.45-13.48] (63/585) and didn't vary in relation to gender (P=0.57), age (P=0.06), or level of schooling (P=0.41). Coverage vaccination was not updated in parents with childbearing project (84.2% (64/76) [CI 95% 74.7-91.2]) or people in contact with children less than 6 years of age (83.6% (87/104) [CI 95% 75.6-89.8]). Pertussis vaccination wasn't confirmed in 80.0% (124/155) of those who thought being vaccine up to date. CONCLUSIONS: The Lyon population poorly complied with the cocooning strategy implemented in 2004. The pertussis vaccine coverage confirmed by a PV proved the inadequate rate of vaccination compared to objectives. It is mandatory to strengthen the vaccinal policy for this vaccine booster.