Baseline characteristics and clinical symptoms related to respiratory viruses identified among patients presenting with influenza-like illness in primary care.

OBJECTIVES: We aimed to identify patients' clinical characteristics associated with respiratory viruses identified among patients presenting with influenza-like illness (ILI). METHODS: A sample of patients of all ages presenting with ILI was included by physicians of the French Sentinelles network during two seasons (2015/16 and 2016/17). Nasopharyngeal samples were tested for the presence of influenza virus (IV), respiratory syncytial virus (RSV), human rhinovirus (HRV) and human metapneumovirus (HMPV). Patients' characteristics associated with each of the four virus classes were studied using multivariate logistic regressions. RESULTS: A total of 5859 individuals were included in the study: 48.0% tested positive for IV, 7.9% for HRV, 7.5% for RSV and 4.1% for HMPV. Cough was associated with IV (OR 2.14, 95% CI 1.81-2.52) RSV (OR 2.52, 95% CI 1.75-3.74) and HMPV detection (OR 2.15, 95% CI 1.40-3.45). Rhinorrhoea was associated mainly with HRV detection (OR 1.75, 95% CI 1.34-2.32). Headache was associated with IV detection (OR 1.75, 95% CI 1.34-2.32), whereas absence of headache was associated with RSV and HMPV detection. Dyspnoea was associated with RSV detection (OR 2.33, 95% CI 1.73-3.12) and absence of dyspnoea with IV detection. Conjunctivitis was associated with IV detection (OR 1.27, 95% CI 1.08-1.50). Some associations were observed only in children: dyspnoea and cough with RSV detection (age <5 years), conjunctivitis with IV detection (age <15 years). Period of onset of symptoms differed among aetiological diagnoses. Seasonal influenza vaccination decreased the risk of IV detection (OR, 0.67, 95% CI 0.51-0.86). CONCLUSIONS: This study allowed the identification of symptoms associated with several viral aetiologies in patients with ILI. A proper knowledge and understanding of these clinical signs may improve the medical management of patients.

Molecular investigation of tick-borne pathogens in ixodid ticks infesting domestic animals (cattle and sheep) and small rodents (black rats) of Corsica, France.

Although livestock farming (sheep, goats, pigs, and cattle) is an important economic activity in Corsica, a French Mediterranean island, knowledge about the tick fauna and microorganisms carried by them remains scarce. This study aimed to investigate the presence and perform molecular characterization of Anaplasmataceae, Rickettsia spp., and Borrelia burgdorferi sensu lato (sl) in tick species collected in Corsica. Ticks from cattle (Bos taurus), sheep (Ovis aries), and rodents (Rattus rattus) were collected from May to September 2016. DNA was purified from ticks, submitted to quantitative real-time polymerase chain reaction (qPCR) and sequenced for phylogenetic analysis. In total, 660 ticks were collected from 111 animals during the study. The most abundant collected tick species from cattle was Rhipicephalus bursa (n = 495; 84.5%), followed by Hyalomma marginatum (n = 91; 15.5%). Rhipicephalus bursa and Ixodes ricinus were the only tick species collected from sheep and rodents, respectively. Overall, Rickettsia was the most common pathogen group (n = 48; 24%) detected in ticks. Sequence analysis of partial gltA and ompA genes revealed the presence of Ri. aeschlimannii and Candidatus Ri. barbariae. Anaplasmataceae DNA was detected in eight (6%) of the 127 cattle pools and in one (2%) of the 61 R. bursa specimens collected from sheep. Sequence analysis of the rpoB gene revealed the presence of one Anaplasma species, A. marginale. Borrelia burgdorferi sl DNA was detected in one pool of H. marginatum collected from cattle and in two (15%) of the 13 I. ricinus pools collected from nine black rats. To our knowledge, this is the first report of the occurrence and molecular characterization of Candidatus Ri. barbariae, an emerging member of the Rickettsia group causing spotted fever, in Corsica. The detection of B. burgdorferi sl DNA, which was previously believed to be rare in Corsica, confirms the presence of this agent on the island.

Estimation of seasonal influenza vaccine effectiveness using data collected in primary care in France: comparison of the test-negative design and the screening method.

OBJECTIVES: We discussed which method between the test-negative design (TND) and the screening method (SM) could provide more robust real-time and end-of-season vaccine effectiveness (VE) estimates using data collected from routine influenza surveillance in primary care. METHODS: We used data collected during two influenza seasons, 2014-15 and 2015-16. Using the SM, we estimated end-of-season VE in preventing medically attended influenza-like illness and laboratory-confirmed influenza among the population at risk. Using the TND, we estimated end-of-season VE in preventing influenza among both the general and the at-risk population. We estimated real-time VE using both methods. RESULTS: For the SM, the overall adjusted end-of-season VE was 24% (95% confidence interval (CI), 16 to 32) and 12% (95% CI, -16 to 33) during season 2014-15, and 53% (95% CI, 44 to 60) and 47% (95% CI, 23 to 64) during season 2015-16, in preventing influenza-like illness and laboratory-confirmed influenza, respectively. For the TND, the overall adjusted end-of-season VE was -17% (95% CI, -79 to 24) and -38% (95% CI, -199 to 13) in 2014-15, and 10% (95% CI, -31 to 39) and 18% (95% CI, -33 to 50) in 2015-16, among the general and at-risk population, respectively. Real-time VE estimates obtained through the TND showed more variability across each season and lower precision than those estimated with the SM. CONCLUSIONS: Although the worldwide use of the TND allows for comparison of overall VE estimates among countries, the SM performs better in providing robust real-time VE estimates among the population at risk.

Influenza-like illness outbreaks in nursing homes in Corsica, France, 2014-2015: epidemiological and molecular characterization.

BACKGROUND: To study the molecular epidemiology of the influenza outbreaks in nursing homes (NHs) to determine whether multiple influenza strains were involved. METHODS: From September to December 2014, NHs in Corsica were invited to participate in an ongoing daily epidemiological and microbiological surveillance for influenza-like illness (ILI) among residents and health care workers (HCWs). RESULTS: The study involved 12 NHs. Respiratory illness meeting the ILI case definition was observed among 44 residents from whom 22 specimens were collected. Of the 22 residents with a nasopharyngeal sample, 13 (59 %) were positive for at least one of the 11 pathogens analysed. Among these 13 patients, 11 (92 %) presented a confirmed influenza (A/H3N2) and two had another respiratory virus: one human metapneumovirus and one human coronavirus. Of patients with a confirmed influenza A(H3N2), 10 (91 %) were vaccinated against influenza during the 2014-2015 season. Two influenza outbreaks were reported in two NHs, caused by influenza A(H3N2) strains belonging to cluster 3C.3 and 3C.2a. Although antivirals were available, prophylaxis was not used. CONCLUSIONS: Phylogenetic analysis seems to suggest no multiple introduction into the two NHs reporting the two influenza A(H3N2) outbreaks. A number of factors could have contributed to transmitting influenza in NHs including, the absence of administration of antiviral treatment for prophylaxis of all residents/staff regardless of immunization status because of the poor vaccine match during each outbreak, the intensive contacts with incompletely protected residents and HCWs, and the low adherence of NHs to notification of ILI outbreaks to the health authorities.