Pig Origin Research Articles

Potential new methods to analyze basal and total endogenous protein losses of host and bacterial origin in pigs. Methods to analyze endogenous protein in pigs.

BackgroundCurrent systems for assessing protein quality such as the Digestible Indispensable Amino Acid Score (DIAAS) correct apparent amino acid digestibility for basal endogenous protein losses (bEPL), ignoring the potential influence of the diet on these losses. However, the quantification of total endogenous protein losses (tEPL) poses a challenge. ObjectiveTo evaluate different methods for quantifying tEPL and bEPL, and to assess their potential in discriminating between tEPL originating from bacteria and host. MethodsUsing an incomplete Youden square design, twelve ileal cannulated pigs received ten different protein sources, and a nitrogen-free (NF) diet. Ileal digesta were collected on days 6 and 7 of each 1-week feeding period, to quantify endogenous protein losses (EPL) and analyze apparent ileal digestibility. Ileal EPL were estimated based on 1) 16S-+18S gene copy qPCR, 2) diaminopimelic acid (DAPA)+18S, 3) differential AA profiles in digesta, EPL and bacteria, equaling tEPL, and 4) an NF diet and 5) whey protein isolate (WPI), equaling bEPL. ResultsIleal bEPL based on the NF and WPI method correlated moderately-highly (r=0.69, P<0.05), but the NF method probably underestimated bEPL. In pigs fed the WPI diet, EPL based on the WPI and AA profile method were highly correlated (r=0.88, P<0.01). Overall, tEPL based on the AA profile method were moderately correlated with the 16S+18S method (r=0.58, P<0.001), and DAPA+18S (r=0.57, P<0.001). Low correlations were observed between bacterial tEPL based on the AA profile method and 16S or DAPA. Host tEPL based on the AA profile method and 18S were weakly correlated (r=0.39, P<0.001). ConclusionsThe AA profile method seems the most appropriate method for tEPL quantification, while the WPI method is preferred for bEPL quantification. Despite challenges in distinguishing between bacterial and host EPL, it is evident that bacterial proteins substantially (on average 37-83%, depending on method) contribute to the EPL.

Campylobacter coli of porcine origin exhibits an open pan-genome within a single clonal complex: insights from comparative genomic analysis.

Although Campylobacter spp., including Campylobacter coli, have emerged as important zoonotic foodborne pathogens globally, the understanding of the genomic epidemiology of C. coli of porcine origin is limited. As pigs are an important reservoir of C. coli, we analyzed C. coli genomes that were isolated (n= 3) from pigs and sequenced (this study) them along with all other C. coli genomes for which pig intestines, pig feces, and pigs were mentioned as sources in the NCBI database up to January 6, 2023. In this paper, we report the pan-genomic features, the multi-locus sequence types, the resistome, virulome, and mobilome, and the phylogenomic analysis of these organisms that were obtained from pigs. Our analysis revealed that, in addition to having an open pan-genome, majority (63%) of the typeable isolates of C. coli of pig origin belonged to a single clonal complex, ST-828. The resistome of these C. coli isolates was predominated by the genes tetO (53%), blaOXA-193 (49%), and APH (3')-IIIa (21%); however, the virulome analysis revealed a core set of 37 virulence genes. Analysis of the mobile genetic elements in the genomes revealed wide diversity of the plasmids and bacteriophages, while 30 transposons were common to all genomes of C. coli of porcine origin. Phylogenomic analysis showed two discernible clusters comprising isolates originating from Japan and another set of isolates comprising mostly copies of a type strain stored in three different culture collections.

Unraveling the origin of the wild pig (Sus scrofa Linnaeus, 1758) from the northwest Patagonian region: evidence of hybridization processes and a possible pure wild boar population in a protected area

Unraveling the origin of the wild pig (Sus scrofa Linnaeus, 1758) from the northwest Patagonian region: evidence of hybridization processes and a possible pure wild boar population in a protected area

P24 Antimicrobial susceptibility profiles of hypervirulent strains of Clostridioides difficile of pig and human origin

P24 Antimicrobial susceptibility profiles of hypervirulent strains of <i>Clostridioides difficile</i> of pig and human origin

The shelf life of pork depends on its quality and microbial and non-microbial meat destructors

This work aimed to establish the maximum shelf life of pork of different quality classes depending on the action of non-microbial and microbial destructors. To achieve this goal, samples were taken from the longest back muscles of domestic and industrial pig carcasses. Depending on the results of organoleptic research, pork was divided into three quality classes: 1) NOR (close to optimal quality indicators), 2) PSE (pale, soft, exudative), and 3) DFD (dark, firm, dry). After that, each of the samples was divided into 1 equal parts and placed for storage in a refrigerator (t = 3 ± 1 °C). Each day, one part of the samples was used for laboratory research. The purpose of laboratory research was to establish the freshness of meat by determining the reaction to peroxidase, amino-ammonia nitrogen, reaction to ammonia with Nessler's reagent, and the content of short-chain fatty acids. In addition, the level of MAFAnM was determined. The results of laboratory studies showed that the fastest signs of spoilage were registered in pork, with signs of PSE obtained after the slaughter of pigs on small farms. The first signs of deterioration appeared already on the sixth day of storage. The second fastest spoilage rate (on the eighth day) was meat samples of the PSE quality class taken from pigs of industrial origin. At the same time, the highest increase in microbial contamination during storage was registered in meat samples of industrial origin with signs of DFD. We found that the microbial contamination of pork depends not only on the initial contamination at the production site but also on the quality class of the meat. On the 12th day of pork storage, only NOR-class meat samples of industrial origin remained fresh. Comparing meat samples of the same quality classes, asserting a shorter shelf life and a higher risk of meat products obtained due to domestic origin and backyard slaughter of pigs is possible. The main reason is a combination of factors, the main of which are the impossibility of observing proper hygienic conditions for animal slaughter, poor bleeding, unbalanced diet, and others.

Was the Lanyu pig independently domesticated in the Philippines? A meta-analysis review on the prehistoric expansion of the unique Lanyu pigs

Due to the paucity of molecular studies, the origin of the unique Lanyu pigs has been described as “cryptic.” Recent evidence of the presence of Lanyu pigs with Type I signatures spanning from Northern Luzon (NL) through the western and central Philippine regions suggests the possibility of independent domestication of Lanyu pigs in the Philippines. To clarify the spatio-temporal dispersal of Lanyu pigs, this study meta-analyzed all D-loop sequences of Lanyu pigs with Type I signatures (n=323) from Taiwan and the Philippines and elucidated the role of humans in their expansion. The result supported the existence of two subclades of Type I Lanyu pigs, the Taiwanese Lanyu and the Philippine Lanyu subclades. While the two subclades shared certain morphological traits, the latter had signs of morphological patterns that had undergone feralization. Long-distance movement of these pigs during the post-Neolithic era may have been facilitated by the known back-and-forth migration between the islanders of Lanyu (Orchid Island) and the Batanes Archipelago, the northernmost region of the Philippines. Due to the absence of Lanyu pig signatures in Borneo and the fascinating presence of Lanyu signatures in Palawan, two possible scenarios are being proposed. First, the Lanyu pig originated in Taiwan and was introduced by humans (e.g., through trade after domestication into the Philippines) moving to the west of the Philippines where a new population later became established. Secondly, the ancestral origin of the Lanyu pig radiated from mainland Southeast Asia into the Philippines but was extirpated, leaving the subsequent population. The latter suggests the allopatric expansion of the unique Lanyu pigs, which could likely support that Sus scrofa is native to the Philippines. This finding provides new perspectives on the complex evolutionary and anthropogenic history of pig dispersal into Island Southeast Asia.

Label-Free Quantitative Analysis of Pig Liver Proteome after Hepatitis E Virus Infection.

Hepatitis E represents an emerging zoonotic disease caused by the Hepatitis E virus (HEV), for which the main route of transmission is foodborne. In particular, infection in humans has been associated with the consumption of contaminated undercooked meat of pig origin. The aim of this study was to apply comparative proteomics to determine if porcine liver protein profiles could be used to distinguish between pigs seropositive and seronegative for HEV. Preliminarily, an ELISA was used to evaluate the presence of anti-HEV antibodies in the blood serum of 136 animals sent to slaughter. Among the analyzed samples, a seroprevalence of 72.8% was estimated, and it was also possible to identify 10 animals, 5 positive and 5 negative, coming from the same farm. This condition created the basis for the quantitative proteomics comparison between homogeneous animals, in which only the contact with HEV should represent the discriminating factor. The analysis of the proteome in all samples of liver exudate led to the identification of 554 proteins differentially expressed between the two experimental groups, with 293 proteins having greater abundance in positive samples and 261 more represented in negative exudates. The pathway enrichment analysis allowed us to highlight the effect of the interaction between HEV and the host biological system in inducing the potential enrichment of 69 pathways. Among these, carbon metabolism stands out with the involvement of 41 proteins, which were subjected to interactomic analysis. This approach allowed us to focus our attention on three enzymes involved in glycolysis: glucose-6-phosphate isomerase (GPI), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), and fructose-bisphosphate aldolase A (ALDOA). It therefore appears that infection with HEV induced a strengthening of the process, which involves the breakdown of glucose to obtain energy and carbon residues useful for the virus's survival. In conclusion, the label-free LC-MS/MS approach showed effectiveness in highlighting the main differences induced on the porcine liver proteome by the interaction with HEV, providing crucial information in identifying a viral signature on the host metabolism.

The Origin of Indonesian Guinea Pig (Cavia porcellus) Inferred from Mitochondrial Cytochrome-b Gene

The Origin of Indonesian Guinea Pig (Cavia porcellus) Inferred from Mitochondrial Cytochrome-b Gene

Copro-prevalence of &lt;i&gt;Cryptosporidium &lt;/i&gt;in pigs of selected districtsin West coast of India: A preliminary study

In India, Cryptosporidium spp. have been detected and characterised from humans and domestic animals, mostly ruminants. Although pigs can act as an important reservoir of Cryptosporidium infection to humans, comprehensive studies have not been conducted in pig population in India. Hence, present study attempt to elucidate the prevalence and diversity of Cryptosporidium infection in pigs in the selected districts of three states situated in the West coast of India. The pig faecal samples (n=221) were subjected to coprological examination using modified Ziehl Neelsen (mZN) staining method, followed by polymerase chain reaction to detect Cryptosporidium spp. Using mZN staining method, 1.35% (95% CI, 0.46%–3.91%) of the samples were found positive for Cryptosporidium oocyst. However, the DNA from Cryptosporidium positive faecal samples could not be amplified using polymerase chain reaction probably because of the low sensitivity of the PCR and or low oocyst number in the faecal sample. Cryptosporidium spp. of pig origin have zoonotic potential and a certain proportion of pigs infected with Cryptosporidium may be apparently healthy. Therefore, the pig farmers need to be made aware of hygienic practices while handling pigs and pig manure and and general public must be made sensitised about the good agricultural practices and standard food hygiene practices to prevent foodborne Cryptosporidium infection.

83 Developing Mortality Risk Profiles to Better Feed and Manage High-Producing Sows

Abstract The sow is the origin of pigs born, maternal care, and nutrition in the most critical, neonatal period of life of the pig. Increasing pigs born, birth weight, age, and body weight of pigs at weaning remain effective predictors of the measures of productivity in swine production systems: pigs weaned, growth rate, and full value market pigs. Factors that impact the health and longevity of the sow affect the measures of production. However, as prolificacy continues to increase in sows, a parallel trend for increasing sow mortality reduces the potential gains in productivity. Lameness and musculoskeletal issues account for nearly one-half of the current mortality while sudden non-euthanasia deaths account for the remainder. The increasing mortality of first or second parity sows that is sudden, non-euthanasia, such as prolapses, torsions, gastrointestinal ulcers, and others has exposed our limited knowledge of the metabolism and physiology of the high-producing sow. General risk factors for increased mortality in a herd are age, season, flooring, feeding, body condition, and disease/health status of the sow. A greater understanding of the etiology for the those causes of death is needed for sustainable progress in changing the trend from greater to lower mortality. Reducing sow mortality correlates well to greater productivity as measured by pigs per sow year. Deaths occur most commonly in the peri-parturient period. One path to improving pigs weaned per sow is to gain the needed understanding of the metabolic changes and stressors on the sow at farrowing. Retaining sows in the herd through lower mortality also promises to increase herd productivity through improving parity structure. Pigs from first parity sows have lighter birth weights and transfer less effective passive immunity compared with pigs from older sows but these differences have not been consistently shown. The pre-natal impacts of exposure to viral pathogens and altering nutrient supply also have been shown to affect the pig and needs additional research. Increasing the management, health, and nutrition of the sow to promote longevity is path forward to more pigs weaned and sustainable production.

Prevalence of hepatitis E virus genotype 4 of probable human origin in Tibetan pigs from the Qinghai-Tibetan Plateau, China.

Hepatitis E virus (HEV) is the most common cause of acute viral hepatitis worldwide. In 2018-2022, we investigated the presence of HEV RNA in 1233 stool samples collected in the Qinghai-Tibetan Plateau, including humans (16), Tibetan pigs (624), yaks (312), sheep (267), and dogs (14). HEV RNA was only detected in Tibetan pig faecal samples (18.27%, 114/624). To perform molecular characterization of HEV strains in Tibetan pigs, we obtained 21 complete HEV genome sequences between 2018 and 2022. Sequence comparisons showed that 21 HEV strains from Tibetan pigs shared the mean nucleotide identities with the reference HEV strains ranging between 82.9% and 94.9% and 89.3% and 92.1% similarities with human HEV strains. Phylogenetic analysis confirmed that all HEV strains were genotype 4, closely related to human HEV strains. Sequence recombinant analysis showed five potential recombinant strains identified in this study, of which SWU/D18/2018 (GenBank No. MK410044) was recombinant with human and swine HEV strains, located 6509-6878 nt from the recombination point. Based on the Bayesian evolutionary trees, we found that most HEV strains diverged later than human HEV (16 Tibetan pig HEV strains diverged later than 1979, and seven human HEV strains diverged earlier than 1979). Therefore, we speculated that the prevalence of HEV 4 in Tibetan pigs possibly originated from humans in the Qinghai-Tibetan Plateau.

Comparative Genetic Characterization of CTX-M-Producing Escherichia coli Isolated from Humans and Pigs with Diarrhea in Korea Using Next-Generation Sequencing.

Pathogenic E. coli causes intra- and extraintestinal diseases in humans and pigs and third-generation cephalosporins are the primary option for the treatment of these diseases. The objective of this study was to investigate the characteristics and correlation between CTX-M-producing E. coli from humans and pigs regarding CTX-M-producing E. coli using next-generation sequencing and bioinformatic tools. Among the 24 CTX-M-producing E. coli, three types of CTX-M genes (CTX-M-12, CTX-M-14, and CTX-M-15) were detected in humans and four types of CTX-M genes (CTX-M-14, CTX-M-15, CTX-M-55, and CTX-M-101) were detected in pigs. A total of 24 CTX-M-producing E. coli isolates also showed the following antimicrobial resistance genes: other B-Lactam resistance gene (75.0%); aminoglycoside resistance genes (75.0%); phenicol resistance genes (70.8%); tetracycline resistance genes (70.8%); sulfonamide resistance genes (66.7%); quinolone resistance genes (62.5%); trimethoprim resistance genes (54.2%); and fosfomycin resistance genes (8.3%). FII (92.3%) and FIB (90.9%) were the most common plasmid replicon in humans and pigs, respectively. A total of thirty-eight different genes associated with virulence 24 CTX-M-producing E. coli and all isolates contained at least more than one virulence gene. A total of 24 CTX-M-producing E. coli isolates showed 15 diverse sequence types (STs): thirteen isolates from human belonged to 6 different STs, and 11 isolates from pig belonged to 9 different STs. The presence of virulence genes in E. coli together with antimicrobial resistance genes (including CTX-M genes) emphasizes the necessity of comprehensive surveillance and persistent monitoring of the food chain to avoid all types of bacterial contamination, regardless of human or pig origin.

First report of whole genome sequence of septicemic Pasteurella multocida serovar B:2 'Soron' strain isolated from swine.

Pig pasteurellosis, caused by Pasteurella multocida, is an acute infection that also has economic implications for pig farmers. We report the complete genome sequence of a P. multocida, serovar B:2 'Soron' strain isolated from the blood of a pig that had died of pasteurellosis in India. The isolate was not found to be haemorrhagic septicaemia (HS) specific B:2 by the PCR assay. The genome of 'Soron' strain is a single circular chromosome of 2,272,124 base pairs in length and contains 2014 predicted coding regions, 4 ribosomal RNA operons, and 52 tRNAs. It has 1812 protein-coding genes that were also found in reference sequence PmP52Vac. Phylogenetic analysis revealed that Pm_P52VAc and P. multocida 'Soron' serovar B:2 were clustered in different clades. Pasteurella multocida 'Soron' serovar B:2 was found to cluster with the same ancestor of Pm70, which is of avian origin. The genome was found to contain regions that encode proteins which may confer resistance to various antibiotics including cephalosporin, which is used to treat pasteurellosis. The isolate was also found to harbour a phage region. This strain represents a novel multi-locus sequence type (MLST) that has not been previously identified, as all of the alleles used for MLST were found, but did not match any of the alleles in the database with 100% nucleotide identity. The most closely related ST was ST221. This is the first whole-genome sequence from P. multocida serovar B:2 of pig origin.

Public health implications of Yersinia enterocolitica investigation: an ecological modeling and molecular epidemiology study

BackgroundYersinia enterocolitica has been sporadically recovered from animals, foods, and human clinical samples in various regions of Ningxia, China. However, the ecological and molecular characteristics of Y. enterocolitica, as well as public health concerns about infection in the Ningxia Hui Autonomous Region, remain unclear. This study aims to analyze the ecological and molecular epidemiological characteristics of Y. enterocolitis in order to inform the public health intervention strategies for the contains of related diseases.MethodsA total of 270 samples were collected for isolation [animals (n = 208), food (n = 49), and patients (n = 13)], then suspect colonies were isolated and identified by the API20E biochemical identification system, serological tests, biotyping tests, and 16S rRNA-PCR. Then, we used an ecological epidemiological approach combined with machine learning algorithms (general linear model, random forest model, and eXtreme Gradient Boosting) to explore the associations between ecological factors and the pathogenicity of Y. enterocolitis. Furthermore, average nucleotide identity (ANI) estimation, single nucleotide polymorphism (SNP), and core gene multilocus sequence typing (cgMLST) were applied to characterize the molecular profile of isolates based on whole genome sequencing. The statistical test used single-factor analysis, Chi-square tests, t-tests/ANOVA-tests, Wilcoxon rank-sum tests, and Kruskal–Wallis tests.ResultsA total of 270 isolates of Yersinia were identified from poultry and livestock (n = 191), food (n = 49), diarrhoea patients (n = 13), rats (n = 15), and hamsters (n = 2). The detection rates of samples from different hosts were statistically different (χ2 = 22.636, P < 0.001). According to the relatedness clustering results, 270 isolates were divided into 12 species, and Y. enterocolitica (n = 187) is a predominated species. Pathogenic isolates made up 52.4% (98/187), while non-pathogenic isolates made up 47.6% (89/187). Temperature and precipitation were strongly associated with the pathogenicity of the isolates (P < 0.001). The random forest (RF) prediction model showed the best performance. The prediction result shows a high risk of pathogenicity Y. enterocolitica was located in the northern, northwestern, and southern of the Ningxia Hui Autonomous Region. The Y. enterocolitica isolates were classified into 54 sequence types (STs) and 125 cgMLST types (CTs), with 4/O:3 being the dominant bioserotype in Ningxia. The dominant STs and dominant CTs of pathogenic isolates in Ningxia were ST429 and HC100_2571, respectively.ConclusionsThe data indicated geographical variations in the distribution of STs and CTs of Y. enterocolitica isolates in Ningxia. Our work offered the first evidence that the pathogenicity of isolates was directly related to fluctuations in temperature and precipitation of the environment. CgMLST typing strategies showed that the isolates were transmitted to the population via pigs and food. Therefore, strengthening health surveillance on pig farms in high-risk areas and focusing on testing food of pig origin are optional strategies to prevent disease outbreaks.

Development of rapid and sensitive loop-mediated isothermal method for on-site visual identification of tissue origin of pig by using mitochondrial COI gene sequences

Context The loop-mediated isothermal amplification (LAMP) methods have great potential to identify the species origin of the tissue in meat and meat products at isothermal temperature and are also suitable for field conditions. Aim The present study aimed to develop a rapid, specific, and sensitive assay based on the LAMP technique for identification of tissue of pig origin. Methods The pig-specific primers were designed by targeting the mitochondrial COI gene. The amplification temperature and time for the LAMP reaction were optimised as 64°C and 45 min. The analysis of the amplified product was performed on the basis of the development of colour after the addition of intercalating SYBR Green I dye, and also by the ladder-like pattern on agarose-gel electrophoresis. Key results The assay was found to be highly specific for DNA templates of pig origin and showed no cross-reactivity with other food animals, viz. cattle, buffalo, sheep, and goats. The analytical sensitivities of the LAMP and PCR assays were recorded as up to 0.00001 ng and 0.1 ng respectively, of the absolute DNA content. The laboratory validation of the developed method was performed on blind samples and an admixture of meat from different food animals, viz. cattle, buffalo, sheep, goat and pig. The analysis could be performed in an hour by using supernatant from Phire Animal Tissue Direct PCR kit-treated tissue, excluding the complex process of nucleic acid extraction. Conclusion The LAMP assay was found to be cost-effective, easy to perform, and highly species-specific for pig tissue in meat and meat admixture. The result of the assay can be analysed with the naked eye without the need for sophisticated equipment. Compared with pre-standardised PCR assay, the developed LAMP method was quite sensitive and could be performed within 1 h, from sampling to analysis results. Implications The developed LAMP assay is low resource-based single-tube approach that could be exploited significantly in the fields of diagnostics, agriculture, and aquaculture.

Cotransfer of resistance to cephalosporins, colistin, and fosfomycin mediated by an IncHI2/pSH16G4928-like plasmid in ESBL-producing monophasic Salmonella Typhimurium strains of pig origin.

To assess the co-transmission risk of phenotypic and genetic resistance to cephalosporins, colistin, and fosfomycin in Salmonella strains collected along the whole pork production chain. From a total of 107 Salmonella isolates from samples collected in pig slaughterhouses and markets, 15 ESBL-producing Salmonella strains resistant to cefotaxime were identified by broth microdilution method and clavulanic acid inhibition test, including 14 monophasic Salmonella Typhimurium strains and one Salmonella Derby strain. Whole genome sequence analysis showed that nine monophasic S. Typhimurium strains coresistant to colistin and fosfomycin carried the resistance genes blaCTX-M-14, mcr-1, and fosA3. Conjugational transfer tests demonstrated that the phenotypic and genetic resistance to cephalosporins, colistin, and fosfomycin could cotransfer back and forth between Salmonella and Escherichia coli via an IncHI2/pSH16G4928-like plasmid. This study reports the cotransmission of phenotypic and genetic resistance to cephalosporins, colistin, and fosfomycin via an IncHI2/pSH16G4928-like plasmid in Salmonella strains of animal origin, giving an alarm for the prevention of the development and spread of bacterial multidrug resistance.

Genetic architecture and selection of Anhui autochthonous pig population revealed by whole genome resequencing.

The genetic resources among pigs in Anhui Province are diverse, but their value and potential have yet to be discovered. To illustrate the genetic diversity and population structure of the Anhui pigs population, we resequenced the genome of 150 pigs from six representative Anhui pigs populations and analyzed this data together with the sequencing data from 40 Asian wild boars and commercial pigs. Our results showed that Anhui pigs were divided into two distinct types based on ancestral descent: Wannan Spotted pig (WSP) and Wannan Black pig (WBP) origins from the same ancestor and the other four populations origins from another ancestor. We also identified several potential selective sweep regions associated with domestication characteristics among Anhui pigs, including reproduction-associated genes (CABS1, INSL6, MAP3K12, IGF1R, INSR, LIMK2, PATZ1, MAPK1), lipid- and meat-related genes (SNX19, MSTN, MC5R, PRKG1, CREBBP, ADCY9), and ear size genes (MSRB3 and SOX5). Therefore, these findings expand the catalogue and how these genetic differences among pigs and this newly generated data will be a valuable resource for future genetic studies and for improving genome-assisted breeding of pigs and other domesticated animals.

Genetic diversity of modern lines of hybrid pigs based on variations in mitochondrial DNA sequence

Genetic diversity of modern lines of hybrid pigs based on variations in mitochondrial DNA sequence

Origins of Polynesian Pigs Revealed by Mitochondrial Whole Genome Ancient DNA

Simple SummaryRetracing the ancient human migration routes in the remote islands of the Pacific relies on robust models of the origins and spread of animals that were commensal to long-distance ocean voyages. Domestic pigs (Sus scrofa) in Polynesia belong to a rare mitochondrial DNA group whose geographic origins are disputed. We report new complete genome ancient DNA that suggests all founding populations of pigs in Polynesia, first settled by people about 2800–700 years ago, can be traced back to northern peninsular Southeast Asia.Domestic pigs (Sus scrofa) were first transported to Polynesia through a series of long-distance voyages ultimately linked to the Neolithic expansion of Austronesian-speaking people out of Asia. The descendants of the founding pigs belong to a rare mtDNA group referred to as the “Pacific Clade” that may have originated in peninsular or island Southeast Asia. We report the first whole genome mtDNA from domestic pigs from any of the remote islands of the Pacific. In this brief report, we describe the close link we discovered between ancient mtDNA from archaeological specimens from across Polynesia and from that of modern pigs in northern peninsular Southeast Asia, specifically southern China’s Yunnan Province. More complete mtDNA coverage in commensal animals is necessary to improve our picture of the settlement of Polynesia (ca. 2800–700 years before the present) and specify the route, or routes, that pigs took from northern peninsular Southeast Asia.

Molecular epidemiology of methicillin-resistant Staphylococcus aureus isolated from pigs in Japan

Methicillin-resistant Staphylococcus aureus (MRSA) is the leading cause of infection in hospitalized patients and can be prevalent in humans and various animal species. In European countries, MRSA isolates belonging to clonal complex 398 have been detected at high rates in pigs. However, the prevalence of MRSA in pigs and farm environments in Japan remains unclear. MRSA isolates were obtained from pigs in slaughterhouses, diseased pigs on farms, imported breeding pigs, and farm dust. We conducted whole-genome sequencing (WGS) and analyzed the molecular epidemiological relationship between these MRSA isolates using core genome multilocus sequence typing (cgMLST). The prevalence rates of MRSA among pigs in slaughterhouses, diseased pigs on farms, imported breeding pigs, and farm dust were 5.2 %, 3.4 %, 28.8 %, and 0.06 %, respectively. ST 398 isolates that classified as ST398/t034 were isolated from pigs from all sources. The results of cgMLST showed that ST398/t034 isolates originating from domestic pigs clustered into the same cluster as the isolates from imported breeding pigs. However, some clusters only included isolates of domestic pig origin. Most MRSA isolates in this study carried resistance genes for aminoglycosides, β-lactams, macrolides, tetracyclines, and zinc. None of the MRSA isolates in this study harbored Panton-Valentine leukocidin toxin genes. Molecular epidemiological analysis suggested a relationship between isolates from slaughter pigs and imported breeding pigs and the presence of MRSA isolates of domestic origin. However, more data are needed for elucidation of the origin of these MRSA variants in the pig industry in Japan.