Influenza A Virus in Backyard Pigs and Poultry in Rural Cambodia.

Surveillance of influenza virus in humans and livestock is critical, given the worldwide public health threats and livestock production losses. Livestock farming involving close proximity between humans, pigs and poultry is often practised by smallholders in low-income countries and is considered an important driver of influenza virus evolution. This study determined the prevalence and genetic characteristics of influenza A virus (IAV) in backyard pigs and poultry in Cambodia. A total of 751 animals were tested by matrix gene-based rRT-PCR, and influenza virus was detected in 1.5% of sampled pigs, 1.4% of chickens and 1.0% of ducks, but not in pigeons. Full-length genome sequencing confirmed triple reassortant H3N2 in all IAV-positive pigs and various low pathogenic avian influenza subtypes in poultry. Phylogenetic analysis of the swine influenza viruses revealed that these had haemagglutinin and neuraminidase genes originating from human H3N2 viruses previously isolated in South-East Asia. Phylogenetic analysis also revealed that several of the avian influenza subtypes detected were closely related to internal viral genes from highly pathogenic H5N1 and H9N2 formerly sequenced in the region. High sequence homology was likewise found with influenza A viruses circulating in pigs, poultry and wild birds in China and Vietnam, suggesting transboundary introduction and cocirculation of the various influenza subtypes. In conclusion, highly pathogenic subtypes of influenza virus seem rare in backyard poultry, but virus reassortment, involving potentially zoonotic and pandemic subtypes, appears to occur frequently in smallholder pigs and poultry. Increased targeted surveillance and monitoring of influenza circulation on smallholdings would further improve understanding of the transmission dynamics and evolution of influenza viruses in humans, pigs and poultry in the Mekong subregion and could contribute to limit the influenza burden.

Risk factors associated with Campylobacter detected by PCR in humans and animals in rural Cambodia.

Campylobacter are worldwide-occurring zoonotic bacteria, with the species Campylobacter jejuni and C. coli commonly associated with diarrhoea in children in low-income countries. In this cross-sectional study, the prevalence of C. jejuni and C. coli in human and livestock faecal samples was detected by PCR and zoonotic risk factors associated with human Campylobacter positivity were identified. In total 681 humans and 753 livestock (chickens, ducks, pigs, cattle) from 269 households were sampled. Children aged <16 years were more frequently Campylobacter positive (19%) than adults (8%) and multilevel logistic models revealed that human C. jejuni positivity was associated with the following household practices: home-slaughtering [odds ratio (OR) 2·4, P = 0·01], allowing animals access to sleeping and food preparation areas (OR 2·8, P = 0·02), and eating undercooked meat (OR 6·6, P = 0·05), while frequent consumption of beef was protective (OR 0·9, P = 0·05). Associations were stronger for home-slaughtering (OR 4·9, P = 0·004) with C. jejuni infection in children only. Campylobacter was highly prevalent in pigs (72%) and chickens (56%) and risk factors associated with human Campylobacter positivity were identified throughout the meat production chain. The findings underline the importance of studying source attributions throughout the production chain and the need for upgraded understanding of Campylobacter epidemiology in low-income countries.