Virological and epidemiological patterns of swine influenza A virus infections in France: Cumulative data from the RESAVIP surveillance network, 2011-2018.

Swine influenza A viruses (swIAVs) cause acute respiratory syndromes in pigs and may also infect humans. Following the 2009 pandemic, a network was established in France to reinforce swIAV monitoring. This study reports virological and epidemiological data accumulated through passive surveillance conducted during 1,825 herd visits from 2011 to 2018. Among them, 887 (48.6 %) tested swIAV-positive. The proportion of positive cases remained stable year-on-year and year-round. The European avian-like swine H1N1 (H1avN1) virus was the most frequently identified (69.6 %), and was widespread across the country. The European human-like reassortant swine H1N2 (H1huN2) virus accounted for 22.1 % and was only identified in the north-western quarter and recently in the far north. The 2009 pandemic H1N1 (H1N1pdm) virus (3.6 %) was detected throughout the country, without settling in areas of higher pig densities. Its proportion increased in winter, during the seasonal epidemics in humans. The European human-like reassortant swine H3N2 as well as H1avN2 viruses were identified sporadically. In up to 30 % of swIAV-positive cases, pigs exhibited clinical signs of high intensity, regardless of the viral subtype and vaccination program. The recurrent pattern of the disease, i.e., an endemic infection at the herd level, was reported in 41% of cases and mainly affected post-weaning piglets (OR = 5.11 [3.36-7.76]). Interestingly, the study also revealed a significant association between the recurrent pattern and sow vaccination (OR = 1.96 [1.37-2.80]). Although restricted to the studied pig population, these results bring new knowledge about swIAV dynamics and infection patterns in pig herds in France.

Infection of Wildlife by Mycobacterium bovis in France Assessment Through a National Surveillance System, Sylvatub.

Mycobacterium bovis infection was first described in free-ranging wildlife in France in 2001, with subsequent detection in hunter-harvested ungulates and badgers in areas where outbreaks of bovine tuberculosis (TB) were also detected in cattle. Increasing concerns regarding TB in wildlife led the French General Directorate for Food (DGAL) and the main institutions involved in animal health and wildlife management, to establish a national surveillance system for TB in free-ranging wildlife. This surveillance system is known as "Sylvatub." The system coordinates the activities of various national and local partners. The main goal of Sylvatub is to detect and monitor M. bovis infection in wildlife through a combination of passive and active surveillance protocols adapted to the estimated risk level in each area of the country. Event-base surveillance relies on M. bovis identification (molecular detection) (i) in gross lesions detected in hunter-harvested ungulates, (ii) in ungulates that are found dead or dying, and (iii) in road-killed badgers. Additional targeted surveillance in badgers, wild boars and red deer is implemented on samples from trapped or hunted animals in at-risk areas. With the exception of one unexplained case in a wild boar, M. bovis infection in free-living wildlife has always been detected in the vicinity of cattle TB outbreaks with the same genotype of the infectious M. bovis strains. Since 2012, M. bovis was actively monitored in these infected areas and detected mainly in badgers and wild boars with apparent infection rates of 4.57-5.14% and 2.37-3.04%, respectively depending of the diagnostic test used (culture or PCR), the period and according to areas. Sporadic infection has also been detected in red deer and roe deer. This surveillance has demonstrated that M. bovis infection, in different areas of France, involves a multi-host system including cattle and wildlife. However, infection rates are lower than those observed in badgers in the United Kingdom or in wild boars in Spain.

Real-time PCR for identification of Brucella spp.: a comparative study of IS711, bcsp31 and per target genes.

Culture is considered as the reference standard assay for diagnosis of Brucella spp. in humans and animals but it is time-consuming and hazardous. In this study, we evaluated the performances of newly designed real-time PCR assays using TaqMan probes and targeting the 3 following specific genes: (i) the insertion sequence IS711, (ii) bcsp31 and (iii) per genes for the detection of Brucella at genus level. The real-time PCR assays were compared to previously described conventional PCR assays targeting the same genes. The genus-specificity was evaluated on 26 Brucella strains, including all species and biovars. The analytical specificity was evaluated on a collection of 68 clinically relevant, phylogenetically related or serologically cross-reacting micro-organisms. The analytical sensitivity was assessed using decreasing DNA quantities of Brucella ovis, B. melitensis bv. 1, B. abortus bv. 1 and B. canis reference strains. Finally, intra-assay repeatability and inter-assay reproducibility were assessed. All Brucella species DNA were amplified in the three tests. However, the earliest signal was observed with the IS711 real-time PCR, where it varied according to the IS711 copy number. No cross-reactivity was observed in all three tests. Real-time PCR was always more sensitive than conventional PCR assays. The real-time PCR assay targeting IS711 presented an identical or a greater sensitivity than the two other tests. In all cases, the variability was very low. In conclusion, real-time PCR assays are easy-to-use, produce results faster than conventional PCR systems while reducing DNA contamination risks. The IS711-based real-time PCR assay is specific and highly sensitive and appears as an efficient and reproducible method for the rapid and safe detection of the genus Brucella.