Highly Pathogenic Avian Influenza A(H5N1) Clade 2.3.4.4b Virus in Poultry, Benin, 2021.

In August 2021, we detected highly pathogenic avian influenza A(H5N1) clade 2.3.4.4b viruses in poultry in southern Benin. The isolates were genetically similar to H5N1 viruses of clade 2.3.4.4b isolated during the same period in Africa and Europe. We also found evidence for 2 separate introductions of these viruses into Benin.

Redesign and Validation of a Real-Time RT-PCR to Improve Surveillance for Avian Influenza Viruses of the H9 Subtype.

Avian influenza viruses of the H9 subtype cause significant losses to poultry production in endemic regions of Asia, Africa and the Middle East and pose a risk to human health. The availability of reliable and updated diagnostic tools for H9 surveillance is thus paramount to ensure the prompt identification of this subtype. The genetic variability of H9 represents a challenge for molecular-based diagnostic methods and was the cause for suboptimal detection and false negatives during routine diagnostic monitoring. Starting from a dataset of sequences related to viruses of different origins and clades (Y439, Y280, G1), a bioinformatics workflow was optimized to extract relevant sequence data preparatory for oligonucleotides design. Analytical and diagnostic performances were assessed according to the OIE standards. To facilitate assay deployment, amplification conditions were optimized with different nucleic extraction systems and amplification kits. Performance of the new real-time RT-PCR was also evaluated in comparison to existing H9-detection methods, highlighting a significant improvement of sensitivity and inclusivity, in particular for G1 viruses. Data obtained suggest that the new assay has the potential to be employed under different settings and geographic areas for a sensitive detection of H9 viruses.

Serological Surveillance of Influenza D Virus in Ruminants and Swine in West and East Africa, 2017-2020.

Influenza D virus (IDV) was first isolated in 2011 in Oklahoma, USA from pigs presenting with influenza-like symptoms. IDV is known to mainly circulate in ruminants, especially cattle. In Africa, there is limited information on the epidemiology of IDV, although the virus has likely circulated in the region since 2012. In the present study, we investigated the seropositivity of IDV among domestic ruminants and swine in West and East Africa from 2017 to 2020. Serum samples were analyzed using the hemagglutination inhibition (HI) assay. Our study demonstrated that IDV is still circulating in Africa, with variations in seropositivity among countries and species. The highest seropositivity was detected in cattle (3.9 to 20.9%). Our data highlights a need for extensive surveillance of IDV in Africa in order to better understand the epidemiology of the virus in the region.

Antigenic and molecular characterization of low pathogenic avian influenza A(H9N2) viruses in sub-Saharan Africa from 2017 through 2019.

Sub-Saharan Africa was historically considered an animal influenza cold spot, with only sporadic highly pathogenic H5 outbreaks detected over the last 20 years. However, in 2017, low pathogenic avian influenza A(H9N2) viruses were detected in poultry in Sub-Saharan Africa. Molecular, phylogenetic, and antigenic characterization of isolates from Benin, Togo, and Uganda showed that they belonged to the G1 lineage. Isolates from Benin and Togo clustered with viruses previously described in Western Africa, whereas viruses from Uganda were genetically distant and clustered with viruses from the Middle East. Viruses from Benin exhibited decreased cross-reactivity with those from Togo and Uganda, suggesting antigenic drift associated with reduced replication in Calu-3 cells. The viruses exhibited mammalian adaptation markers similar to those of the human strain A/Senegal/0243/2019 (H9N2). Therefore, viral genetic and antigenic surveillance in Africa is of paramount importance to detect further evolution or emergence of new zoonotic strains.

Assessment of the Presence of Resistance Genes Detected from the Environment and Selected Food Products in Benin.

Gram-negative bacilli can spread from the environment and through food products. This study aimed to characterize ESBL production and virulence genes from multidrug-resistant Gram-negative bacilli isolated from specimen collected from the environment, kitchen, and food products. A total of 130 samples were collected at local markets in seven different communities in Benin (Abomey-Calavi, Ouidah, Bohicon, Abomey, Parakou, Djougou, and Grand-Popo). Samples were cultured on McConkey and ChromID™ ESBL agar plates. The isolates were identified by the API 20E gallery. An antibiotic susceptibility test was carried out, and the detection of ESBL production and virulence-associated genes was carried out by Polymerase Chain Reaction (PCR). The data collected was coded and analyzed using GraphPad prism 7 software and Excel. The software R was used to calculate the correlation coefficient between the results of the detection of ESBL+ on agar and by the effect of the double synergy. The results showed that sixty-three (63) bacterial strains were isolated from the 130 samples, of which the dominant species was Chryseomonas luteola (10/63). The kitchen samples were the most contaminated with 36.50%. More than 40% of the isolates were resistant to at least three different classes of antibiotics. Also, blaSHV gene was detected in 33.33% (21/63) of the isolates and in all isolates of Pseudomonas aeruginosa (5/5%). 11.11% (7/63) of isolates were virulent with dominance of the fimH gene, especially with Escherichia coli (83.33%). The kitchen samples showed a high prevalence of ESBL-producing strains with fimH gene. This raises the problem of non-compliance with hygiene rules in community cooking and food handling.

Capacity Building Efforts for Rabies Diagnosis in Resource-Limited Countries in Sub-Saharan Africa: A Case Report of the Central Veterinary Laboratory in Benin (Parakou).

Rabies has been listed as a priority zoonotic disease in many African countries and the countdown to reach the goal of eliminating dog-mediated human rabies deaths by 2030 means that disease control measures need to be applied fast. In this context, an essential pillar of any national plan to control rabies is the implementation of reliable diagnostic techniques to ensure the success of field surveillance systems. Although many African countries have received international support for the control of rabies-some countries, like Benin, have not received a similar level of support. Indeed, until 2018, Benin was not able to diagnose rabies and rabies diagnosis in animals as well as humans relied solely on observed clinical symptoms. Although the Central Veterinary Laboratory (CVL) of Parakou had the equipment to implement two recommended tests, the lack of specific reagents and skills prevented the implementation of a rabies diagnostic service. Here we present the joint efforts of the national authorities in Benin, intergovernmental agencies, and non-governmental organizations to assess the strengths and weaknesses of the government's rabies control efforts. We have applied the Stepwise Approach toward Rabies Elimination (SARE) analysis, implemented rabies diagnostic capacities at the CVL of Parakou, characterized strains of rabies virus circulating in Benin, and finally integrated an inter-laboratory comparison program.

Resistance and virulence determinants of faecal Salmonella spp. isolated from slaughter animals in Benin.

OBJECTIVE: Salmonella spp. are one of the leading foodborne pathogens worldwide naturally found in the intestines of many animals. People that are in direct contact with the infected animals or their cages may become ill. The aim of this study was to determine the prevalence, antibiogram and virulence genes associated with Salmonella serovars from fecal samples of animals intended for consumption in Southern Benin. RESULTS: Out of a total of 406 samples, 2.46% were positive. The isolates identified were multidrug-resistant Salmonella spp. to penicillins, first generation cephalosporins and some aminoglycosides. All Salmonella isolates produced invA gene of 284 bp, fimA of 85 bp and stn of 260 bp. The spvC gene (571 bp) was present in 10% of the isolates whereas the spvR gene (310 bp) was found in 20% of the isolates. The control strain possessed all the tested genes. The invA gene implies that strains are able to invade epithelial cells. The fimA and stn genes present in all isolates show that they are capable of causing gastrointestinal illness in humans. The presence of spvC and spvR genes suggests the possibility of these strains to produce toxins.