Whole genome sequencing of Streptococcus suis revealed potential drug resistance and zoonotic transmission in companion cat

@#Streptococcus suis is a bacterium of clinical importance in diverse animal hosts including companion animals and humans. Companion animals are closely associated in the living environment of humans and are potential reservoirs for zoonotic pathogens. Given the zoonotic potential of S. suis, it is crucial to determine whether this bacterium is present among the companion animal population. This study aimed to detect Streptococcus suis in companion animals namely cats and dogs of the central west coast of Peninsular Malaysia and further characterize the positive isolates via molecular and genomic approach. The detection of S. suis was done via bacterial isolation and polymerase chain reaction assay of gdh and recN gene from oral swabs. Characterization was done by multiplex PCR serotyping, as well as muti-locus sequence typing, AMR gene prediction, MGE identification and phylogenomic analysis on whole genome sequence acquired from Illumina and Oxford Nanopore sequencing. Among the 115 samples, PCR assay detected 2/59 of the cats were positive for S. suis serotype 8 while all screened dog samples were negative. This study further described the first complete whole genome of S. suis strain SS/UPM/MY/F001 isolated from the oral cavity of a companion cat. Genomic analysis revealed a novel strain of S. suis having a unique MLST profile and antimicrobial resistance genes of mefA, msrD, patA, patB and vanY. Mobile genetic elements were described, and pathogenic determinants matched to human and swine strains were identified. Phylogenetic tree analysis on the core genome alignment revealed strain SS/UPM/MY/F001 was distinct from other S. suis strains. This study provided insight into the detection and genomic features of the S. suis isolate of a companion cat and highlighted its potential for antimicrobial resistance and pathogenicity.

Epidemiological risk factors and phylogenetic affinities of Sarcocystis infecting village chickens and pigs in Peninsular Malaysia

@#The intake of food and water containing the Sarcocystis parasite has been linked to a number of outbreaks worldwide, including Malaysia. Nevertheless, the lack of surveys and epidemiological data on Sarcocystis infections in Malaysia makes it difficult to estimate its occurrence in humans and animals. A cross-sectional study was conducted to determine the prevalence of Sarcocystis and the risk factors associated with infection among village chickens and pigs reared under different farm managements in Peninsular Malaysia. Phylogenetic trees were constructed using partial fragments of the 18S rRNA gene and ITS1 sequences. In the present study, 680 sera samples were collected from village chickens (n=250) and commercial pigs (n=433) and anti-Sarcocystis antibodies were screened using the enzymelinked immunosorbent assays (ELISA) kit. At the animal level, the prevalence of Sarcocystis was 9.2% (95% CI: 5.92-13.48) and at the farm level, it was 64.0% (95% CI: 42.52-82.03) in village chickens. The animal-level seroprevalence of Sarcocystis for pigs was 3.7% (95% CI: 2.13-5.93) and 36.8% (95% CI: 16.29-61.64) at the farm-level. Polymerase Chain Reaction (PCR) was conducted on meat samples from various parts of village chickens (n=250) consisting of brain, heart, lung, and pectoralis muscle tissues, and pork (n=121) consisting of intercostal muscle, diaphragm, and tongue. Sarcocystis DNA was detected in 6.4% (95% CI: 4.60-11.60) of village chicken samples but zero in pork samples. A total of 11 unique Sarcocystis haplotypes were isolated from these tissue samples. Multivariable logistic regression analysis of the putative risk factors showed a statistically significant association between Sarcocystis infection in pigs and uncovered storage of feed. Although no zoonotic Sarcocystis was isolated in this study, we reported the first discovery of S. wenzeli in Malaysia.

First molecular detection of porcine circovirus type 4 (PCV4) in Malaysia

@#Porcine circovirus type 4 (PCV4) is the newest member in the porcine circovirus family, first reported in 2020. To date, the presence of PCV4 has only been reported in China, South Korea and most recently in Thailand. Detection of PCV4 have been reported in various production stages of pigs from piglets, finishers to sows; associated with a myriad of clinical manifestations including porcine dermatitis and nephropathy syndrome (PDNS), postweaning multisystemic wasting syndrome (PMWS), respiratory, enteric and neurological diseases. While successful virus isolation and culture has yet to be reported, pathogenicity of PCV4 has been demonstrated through infectious clone studies. The objective of this study is to investigate the presence of PCV4 in Malaysian porcine population to update the epidemiology of porcine circoviruses in Malaysia. A total of 49 samples from commercial intensive pig farms, abattoir and wild boar population were subjected to conventional polymerase chain reaction assay to detect PCV4 capsid (cap) genome. Resulting cap nucleotide sequences were analyzed for maximum likelihood phylogeny relationship. Results revealed that PCV4 is present in Peninsular Malaysia at a molecular prevalence of 4.08% (2 / 49 samples). Both PCV4 positive samples originated from clinically healthy finishers. Malaysian PCV4 strains were classified as genotype PCV4b, and were found to be phylogenetically distinct from the China, South Korea and Thailand strains. With this latest update of the novel PCV4 in Malaysia, it is clear that more attention needs to be given to the investigation of novel porcine circoviruses (PCV) and management of PCV diseases.

Molecular detection of Haemophilus parasuis serotypes 4, 5 or 12 and 13 in Peninsular Malaysia

@#Although the economic importance of Haemophilus parasuis infection causing Glasser’s disease is prevalent throughout pig farms in Peninsular Malaysia, there is a dearth of knowledge on its actual nature. In this study, a multiplex PCR was performed to screen for three major predominant virulent strains of H. parasuis, which are serotypes 4, 5 or 12 and 13. A total of 175 tissues or bodily fluid samples of various parts were collected from diseased animals from October, 2016 to February, 2018; with total of 62.9% positive detection of H. parasuis. The highest detection was found to be in the pericardial sac fibrin (90.9%) followed by pleural fibrin, lung, pleural fluid, tonsil, pericardial sac, peritoneal fluid, abdominal fibrin, joint fluid, brain and pericardium. Serotype 13 was the highest (40/110) followed by serotype 4(37/110), serotype 5(31/110) and 12 samples were nontypable (12/110). The presence of untypable serotype also drives to further identification of other serotypes in Malaysia.

Different porcine reproductive and respiratory syndrome (PRRS) vaccine regimes and its effect on pig immunity status at Southeast Asia pig farms

Porcine reproductive and respiratory syndrome (PRRS) is a disease characterised by late-term reproductive failure in sows and gilts, and respiratory problems in piglets and growing pigs. In this study, 240 sera were collected from four farms that had been practicing different PRRS vaccination regime for more than a year and vaccinations were done at 2 months before sampling. Fifteen sera samples from four age groups: sows, growers, weaners and piglets were collected from each farm and analysed using IDEXX PRRS X3 ELISA for PRRSV antibodies. Pooled serum samples were tested by using nested-PCR that enable the differentiation of Type I and Type II PRRSV. Out of 80 pooled serum samples, none were positive for PRRSV indicating all age groups were not viraemic after vaccination. Results by ELISA test showed all the farms were seropositive for PRRS. ELISA testing showed no significant difference between the farms except for Farm B which practised whole herd US MLV vaccination. Farm B showed significantly lower (p<0.05) S/P ratio in their piglet, grower and sow groups which suggest there was low virus circulation in herd. Farm A which practised US MLV on sow was the only farm found to have seronegative status in their weaners. Data indicates PRRS MLV vaccination will not cause viraemia post four weeks vaccination and whole herd MLV vaccination may help to reduce virus circulation in PRRS endemic farm.