We conclude that the most effective way to prevent human HPAI cases is to intervene directly in the poultry sector. Our study further suggests that implementing preventive measures in backyard chicken farming and limiting transport of live poultry and their products are promising options to this end.

Vaccines are used in integrated control strategies to protect poultry against H5N1 high-pathogenicity avian influenza (HPAI). H5N1 HPAI was first reported in Indonesia in IMPORTANCEH5N1 high-pathogenicity avian influenza (HPAI) virus has become endemic in Indonesian poultry, and such poultry are the source of virus for birds and mammals, including humans. Vaccination has become a part of the poultry control strategy, but vaccine failures have occurred in the field. This study identified possible causes of vaccine failure, which included the use of an unlicensed virus seed strain and induction of low levels of protective antibody because of an insufficient quantity of vaccine antigen. However, the most important cause of vaccine failure was the appearance of drift variant field viruses that partially or completely overcame commercial vaccine-induced immunity. Furthermore, experimental vaccines using inactivated wild-type virus or reverse genetics-generated vaccines containing the hemagglutinin and neuraminidase genes of wild-type drift variant field viruses were protective. These studies indicate the need for surveillance to identify drift variant viruses in the field and update licensed vaccines when such variants appear.

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An epidemiological investigation was conducted in an unvaccinated dairy farming enterprise in which three workers on one of the milking herds (Herd 1) were diagnosed with leptospirosis due to serovars Hardjo (H) (n = 2) and Pomona (P) (n = 1) between January and March 2015. Blood and urine samples were collected from milking cows in Herd 1 (N = 230) and Herd 2 (N = 400), rising one‐ (R1, N = 125) and rising two‐year‐old (R2, N = 130) replacement heifers, and four pigs associated with Herd 1, in March 2015. Sera were tested using the MAT for serovars H, P, Copenhageni (C), Ballum (B) and Tarassovi (T), and urine samples were tested by qPCR. Seventy‐five per cent of 109 cows in Herd 1 and 36% of 121 in Herd 2 were seropositive (≥48), predominantly to H and P, and 23% of 74 cows in Herd 1 and 1% of 90 cows in Herd 2 were qPCR positive. Fifty‐five per cent of 42 R2 heifers were seropositive to T. No R1 and 17% of 42 R2 heifers were qPCR positive. Subsequently, all cattle were vaccinated for H and P, and Herds 1 and 2 were given amoxicillin. After the booster vaccination, 7% of 91 in Herd 1, 2% of 82 in Herd 2 and 11% of 38 R1 heifers (sampled as R2) were PCR positive. After the amoxicillin treatment, no cows in Herd 1 and 5% of 62 cows in Herd 2 were urine PCR positive. Calves and pigs were seropositive to H, P, C and B. Vaccination and antibiotic treatment appeared effective in reducing the risk of exposure of workers to vaccine serovars. However, evidence of non‐vaccine serovars indicated that workers likely remain at risk of exposure to Leptospira.

This study aimed to evaluate risk factors associated with shedding of pathogenic Leptospira species in urine at animal and herd levels. In total, 200 dairy farms were randomly selected from the DairyNZ database. Urine samples were taken from 20 lactating, clinically normal cows in each herd between January and April 2016 and tested by real-time polymerase chain reaction (PCR) using gyrB as the target gene. Overall, 26.5% of 200 farms had at least one PCR positive cow and 2.4% of 4000 cows were shedding Leptospira in the urine. Using a questionnaire, information about risk factors at cow and farm level was collected via face-to-face interviews with farm owners and managers. Animals on all but one farm had been vaccinated against Hardjo and Pomona and cows on 54 of 200 (27%) farms had also been vaccinated against Copenhageni in at least one age group (calves, heifers and cows). Associations found to be statistically significant in univariate analysis (at P < 0.2) were assessed by multivariable logistic regression. Factors associated with shedding included cattle age (Odds ratio (OR) 0.82, 95% CI 0.71-0.95), keeping sheep (OR 5.57, 95% confidence interval (CI) 1.46-21.25) or dogs (OR 1.45, 95% CI 1.07-1.97) and managing milking cows in a single as opposed to multiple groups (OR 0.45, 95% CI 0.20-0.99). We conclude that younger cattle were more likely to be shedding Leptospira than older cattle and that the presence of sheep and dogs was associated with an increased risk of shedding in cows. Larger herds were at higher risk of having Leptospira shedders. However, none of the environmental risk factors that were assessed (e.g. access to standing water, drinking-water source), or wildlife abundance on-farm, or pasture were associated with shedding, possibly due to low statistical power, given the low overall shedding rate.

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Foot and mouth disease (FMD) is a highly contagious disease affecting cloven-hoofed animals which has been well documented as one of the major animal diseases that causing serious economic loss of livestock sectors. The disease is endemic in many countries, particularly in Asia and Africa. Indonesia has declared disease-free country since 1986 and the World Organization of Animal Health (WOAH/OIE) has recognised Indonesia as FMD-free country without vaccination in 1990. However, FMD virus was detected from a number of disease outbreaks in cattle and goat in Indonesia in May 2022. This study report for the first time the detection and identification of serotype O/ME-SA/Ind-2001 lineage in Indonesia. Although the Indonesian serotype O/ME-SA/Ind-2001 viruses appeared belonging to the Ind-2001e sublineage, they formed a unique cluster with 95.3% average nucleotide sequence similarity to Ind-2001e viruses from other Asia countries. The source of virus incursion into Indonesia is still unresolved; however, illegal trade of live animals from endemic areas in Southeast Asia is the suspected route which should be further investigated.