Whole-genome resequencing of Hu sheep identifies candidate genes associated with agronomic traits.

The phenotypic diversity resulting from artificial or natural selection of sheep has made a significant contribution to human civilization. Hu sheep are a local sheep breed unique to China with high reproductive rates and rapid growth. Genome selection signatures have been widely used to investigate the genetic mechanisms underlying phenotypic variation in livestock. Here, we conduct whole-genome sequencing of 207 Hu sheep and compare them with the wild ancestors of domestic sheep (Asiatic mouflon) to investigate the genetic characteristics and selection signatures of Hu sheep. Based on six signatures of selection approaches, we detect genomic regions containing genes related to reproduction (BMPR1B, BMP2, PGFS, CYP19, CAMK4, GGT5, and GNAQ), vision (ALDH1A2, SAG, and PDE6B), nervous system (NAV1), and immune response (GPR35, SH2B2, PIK3R3, and HRAS). Association analysis with a population of 1299 Hu sheep reveal those missense mutations in the GPR35 (GPR35 g.952651 A>G; GPR35 g.952496 C>T) and NAV1 (NAV1 g.84216190 C>T; NAV1 g.84227412 G>A) genes are significantly associated (P < 0.05) with immune and growth traits in Hu sheep, respectively. This research offers unique insights into the selection characteristics of Hu sheep and facilitates further genetic improvement and molecular investigations.

Heritability and recursive influence of host genetics on the rumen microbiota drive body weight variance in male Hu sheep lambs.

BACKGROUND: Heritable rumen microbiota is an important modulator of ruminant growth performance. However, no information exists to date on host genetics-rumen microbiota interactions and their association with phenotype in sheep. To solve this, we curated and analyzed whole-genome resequencing genotypes, 16S rumen-microbiota data, and longitudinal body weight (BW) phenotypes from 1150 sheep. RESULTS: A variance component model indicated significant heritability of rumen microbial community diversity. Genome-wide association studies (GWAS) using microbial features as traits identified 411 loci-taxon significant associations (P < 10-8). We found a heritability of 39% for 180-day-old BW, while also the rumen microbiota likely played a significant role, explaining that 20% of the phenotypic variation. Microbiota-wide association studies (MWAS) and GWAS identified four marker genera (Bonferroni corrected P < 0.05) and five novel genetic variants (P < 10-8) that were significantly associated with BW. Integrative analysis identified the mediating role of marker genera in genotype influencing phenotype and unravelled that the same genetic markers have direct and indirect effects on sheep weight. CONCLUSIONS: This study reveals a reciprocal interplay among host genetic variations, the rumen microbiota and the body weight traits of sheep. The information obtained provide insights into the diverse microbiota characteristics of rumen and may help in designing precision microbiota management strategies for controlling and manipulating sheep rumen microbiota to increase productivity. Video Abstract.

Ultrashort lipo-tetrapeptide with potent antibacterial activity and local therapeutic effect against Staphylococcus aureus.

OBJECTIVES: Mastitis in dairy cows is a common infectious disease on dairy farms and a major danger to the dairy industry. The harmful bacteria with the greatest clinical isolation rate are Staphylococcus aureus. As a result, bacterial mastitis in dairy cows can lead to decreased milk output, quality, and costs. Traditional antibiotics are currently used to treat mastitis in dairy cows. Nonetheless, long-term usage of high doses of antibiotics increases the risk of the establishment of drug-resistant strains, and the problem of drug residues is becoming more prevalent. We investigated the antibacterial effects of varying molecular side chain length lipopeptides on Staphylococcus aureus ATCC25923 and GS1311 using five tetrapeptide ultrashort lipopeptides developed and synthesised in this study. METHODS: To evaluate the application value of the synthesized lipopeptides in the prevention and treatment of mastitis, the lipopeptides with the best antibacterial action were chosen for safety testing and a mouse mastitis model treatment test. RESULTS: Three of the lipopeptides produced have strong antibacterial properties. Within the drug's safe concentration range, C16KGGK has an excellent antibacterial action and can have a therapeutic influence on mastitis induced by Staphylococcus aureus infection in mice. CONCLUSION: The findings of this study can be used to develop new antibacterial medications and their therapeutic application in the treatment of mastitis in dairy cows.

Phylogenetic and pathogenic characterization of lumpy skin disease virus circulating in China.

The genomic characterization of emerging pathogens is critical for unraveling their origin and tracking their dissemination. Lumpy skin disease virus (LSDV) is a rapidly emerging pathogen in Asia including China. Although the first Lumpy skin disease (LSD) outbreak was reported in 2019, the origin, transmission, and evolutionary trajectory of LSDV in China have remained obscure. The viral genome of a circulating LSDV strain in China, abbreviated LSDV/FJ/CHA/2021, was sequenced using the next-generation sequencing technique. The morphology and cytoplasmic viral factory of these LSDV isolates were observed using transmission electron microscopy. Subsequently, the genomic characterization of this LSDV isolate was systematically analyzed for the first time using the bioinformatics software. The current study revealed that several mutations in the genome of LSDV isolates circulating in China were identified using single nucleotide polymorphisms (SNPs) analysis, an instrument to evaluate for continuous adaptive evaluation of a virus. Furthermore, phylogenomic analysis was used to identify the lineage using the whole genome sequences of 44 LSDV isolates. The result revealed that the isolates from China were closely similar to that of the LSDV isolates from Vietnam, which are divided into a monophyletic lineage sub-group I. The SNPs and Simplot analysis indicate no significant occurrence of the recombinant event on the genome of LSDV isolates in China. Notably, the live virus challenge experiment demonstrated that the pathogenic characterization of this LSDV isolate belongs to a virulent strain. Collectively, we gain the first insight into the evolutionary trajectory, spatiotemporal transmission, and pathogenic characterization of circulating LSDV in China. This study provides a unique reference for risk assessment, guiding diagnostics, and prevention in epizootic and non-epizootic areas.

Synthetic Cationic Lipopeptide Can Effectively Treat Mouse Mastitis Caused by Staphylococcus aureus.

Mastitis caused by Staphylococcus aureus (S. aureus) in dairy cows is one of the most common clinical diseases in dairy cattle. Unfortunately, traditional antibiotic treatment has resulted in the emergence of drug-resistant strains of bacteria, making this disease more difficult to treat. Therefore, novel lipopeptide antibiotics are becoming increasingly important in treating bacterial diseases, and developing novel antibiotics is critical in controlling mastitis in dairy cows. We designed and synthesized three cationic lipopeptides with palmitic acid, all with two positive charges and dextral amino acids. The lipopeptides' antibacterial activity against S. aureus was determined using MIC and scanning electron microscopy. The safety concentration range of lipopeptides for clinical usage was then estimated using the mouse erythrocyte hemolysis assay and CCK8 cytotoxicity. Finally, lipopeptides with high antibacterial activity and minimal cytotoxicity were selected for the treatment experiments regarding mastitis in mice. The observation of histopathological changes, bacterial tissue load and expression of inflammatory factors determined the therapeutic effects of lipopeptides on mastitis in mice. The results showed that all three lipopeptides displayed some antibacterial activity against S. aureus, with C16dKdK having a strong antibacterial impact and being able to treat the mastitis induced by S. aureus infection in mice within a safe concentration range. The findings of this study can be used as a starting point for the development of new medications for the treatment of mastitis in dairy cows.

Effect of feed efficiency on growth performance, body composition, and fat deposition in growing Hu lambs.

The present study aimed to investigate the relationship between growth performance, body composition, and fat deposition factors, and feed efficiency in growing lambs. We measured average daily feed intake (ADFI) and body weight (BW) from 653 Hu sheep that were fed a pellet diet. The residual feed intake (RFI) not significantly genetic and phenotypic correlated with the metabolic body weight (MBW) and average daily gain (ADG), but it was significantly genetic and phenotypic correlated with ADFI and the feed conversion ratio (FCR) (p < 0.01). However, the FCR was significantly associated with growth traits (p < 0.01). With the same ADG, body fat deposition was greater in animals with low feed efficiency compared with high feed efficiency. Therefore, excessive fat deposition can affect the feed efficiency of the body, and organ weight and gut-weight have a greater impact on the feed efficiency of lambs. The reticulum stomach and jejunum of lambs with a low RFI were smaller compared with that in the high RFI, indicating that lambs with a low RFI have less intake and a higher absorption rate. Small organs, such as the liver, of lambs with high FE might be associated with low energy expenditure and slow metabolism. This study provides a new perspective to study the biological processes responsible for feed efficiency variation in lambs.

Whole genome re-sequencing reveals artificial and natural selection for milk traits in East Friesian sheep.

The East Friesian sheep is one of the important high-yielding dairy sheep breeds, but still little is known about their genetic and genomic variation during domestication. Therefore, we analyzed the genomic data of 46 sheep with the aim of identifying candidate genes that are closely related to milk production traits. Our genomic data consisted of 20 East Friesian sheep and 26 Asian Mouflon wild sheep. Finally, a total of 32590241 SNPs were identified, of which 0.61% (198277) SNPs were located in exonic regions. After further screening, 122 shared genomic regions in the top 1% of F ST and top 1% of Nucleotide diversity ratio were obtained. After genome annotation, these 122 candidate genomic regions were found to contain a total of 184 candidate genes. Finally, the results of KEGG enrichment analysis showed four significantly enriched pathways (P < 0.05): beta-Alanine metabolism (SMOX, HIBCH), Pathways in cancer (GLI2, AR, TXNRD3, TRAF3, FGF16), Non-homologous end-joining (MRE11), Epstein-Barr virus infection (TRAF3, PSMD13, SIN3A). Finally, we identified four important KEGG enrichment pathways and 10 candidate genes that are closely related to milk production in East Friesian sheep. These results provide valuable candidate genes for the study of milk production traits in East Friesian sheep and lay an important foundation for the study of milk production traits.

Specific Monoclonal Antibodies Targeting Unique HA Epitopes Block H7N9 Influenza A Viral Replication.

The H7N9 subtype influenza A viruses pose a serious threat to public health, and there is still a lack of vaccines or drugs for humans against H7N9 influenza viruses. In this study, we screened two monoclonal antibodies (MAbs), 4H1E8 and 7H9A6, that specifically recognize the hemagglutinin (HA) protein of H7N9 influenza virus and display highly neutralizing activity against H7N9 virus. The epitopes recognized by two MAbs are nearly all conserved within all known H7 subtypes. Characteristic identification showed that two MAbs have high avidity for the HA protein but no hemagglutinin inhibition activity or antibody-dependent cellular cytotoxicity. Mechanistically, the 4H1E8 and 7H9A6 antibodies inhibit the pH-dependent conformational change of HA and block the HA-mediated membrane fusion. More importantly, 4H1E8 and 7H9A6 exhibit promising prophylactic and therapeutic effects against lethal challenge with H7N9 virus. Moreover, 4H1E8- and 7H9A6-treated mice displayed inhibition of pulmonary viral replication and reduced lung lesions after viral challenge. Together, these findings indicate that antibodies 4H1E8 and 7H9A6 recognize unique epitopes in the HA protein and possess the neutralizing activity and protective efficacy against the H7N9 influenza A viruses. IMPORTANCE In 2013, H7N9 influenza viruses appeared in China and other countries resulting in more than 1,500 individual infections or death. There are still limited studies on vaccines or drugs for humans against H7N9 influenza viruses. Alternative approaches against H7N9 virus infection need to be developed. Here, we identified two monoclonal antibodies (4H1E8 and 7H9A6) that possess neutralizing activity by blocking the pH-dependent HA-mediated membrane fusion. Additionally, the two monoclonal antibodies protect mice against the H7N9 virus challenge prophylactically or therapeutically. Therefore, our study demonstrates that 4H1E8 and 7H9A6 could be used for the prevention and treatment of the H7N9 influenza virus, and the conserved epitopes we identified may contribute to the development of a broad H7N9 vaccine and provide insights into unique antiviral approaches.

Whole-genome resequencing reveals molecular imprints of anthropogenic and natural selection in wild and domesticated sheep.

The abundance of domesticated sheep varieties and phenotypes is largely the result of long-term natural and artificial selection. However, there is limited information regarding the genetic mechanisms underlying phenotypic variation induced by the domestication and improvement of sheep. In this study, to explore genomic diversity and selective regions at the genome level, we sequenced the genomes of 100 sheep across 10 breeds and combined these results with publicly available genomic data from 225 individuals, including improved breeds, Chinese indigenous breeds, African indigenous breeds, and their Asian mouflon ancestor. Based on population structure, the domesticated sheep formed a monophyletic group, while the Chinese indigenous sheep showed a clear geographical distribution trend. Comparative genomic analysis of domestication identified several selective signatures, including IFI44 and IFI44L genes and PANK2 and RNF24 genes, associated with immune response and visual function. Population genomic analysis of improvement demonstrated that candidate genes of selected regions were mainly associated with pigmentation, energy metabolism, and growth development. Furthermore, the IFI44 and IFI44L genes showed a common selection signature in the genomes of 30 domesticated sheep breeds. The IFI44 c. 54413058 C>G mutation was selected for genotyping and population genetic validation. Results showed that the IFI44 polymorphism was significantly associated with partial immune traits. Our findings identified the population genetic basis of domesticated sheep at the whole-genome level, providing theoretical insights into the molecular mechanism underlying breed characteristics and phenotypic changes during sheep domestication and improvement.

Antibacterial effect of synthetic ultra-short lipopeptide on Streptococcus agalactiae and its active on bacterial mastitis in mice.

Streptococcus agalactiae mastitis is one of the significant threats to the milk industry. The traditional antibiotic treatment method is easy to cause the emergence of resistant strains, and the problem of drug residue is increasingly severe. In this study, we designed and synthesized five lipopeptides. The antibacterial activity of different molecular structure lipopeptides against Streptococcus agalactiae was detected. Furthermore, the mouse mastitis model was established using Streptococcus agalactiae. The lipopeptides with better antibacterial effect were selected for the treatment experiment to evaluate the application value in the treatment of mastitis. The results showed that 4 of the synthesized lipopeptides had specific antibacterial activity. SLP3 and SLP4 have an excellent antibacterial effect and can treat murine mastitis caused by Streptococcus agalactiae infection within the safe concentration range. The results of this study can provide an excellent experimental basis for new antibiotics and clinical application in the treatment of dairy cow mastitis.

Ovine ELOVL5 and FASN genes polymorphisms and their correlations with sheep tail fat deposition.

Reducing tail fat deposition can increase the economic value of a carcass and improve feed efficiency. This study aimed to explore ELOVL5 and FASN polymorphisms associated with tail fat deposition and their expression levels of sheep. Association analysis showed that ELOVL5 synonymous mutation g.62534 C > T was associated with tail width, tail fat weight, and relative tail fat weight (P < 0.05). FASN synonymous mutation g.12694 A > G was associated with tail length and width (P < 0.05). Combined effect analyses indicated significant differences between the combined genotypes and tail fat deposition. Quantitative real-time reverse transcription PCR indicated that the ELOVL5 and FASN expression levels were significantly higher in tail fat than in other tissues (P < 0.05). ELOVL5 expression levels in tail-fat tissue of big-tail sheep was significantly higher than that in small-tail sheep (P < 0.01). FASN expression levels were significantly higher in tail-fat tissue of small-tail sheep than in that of big-tail sheep (P < 0.05). During development, ELOVL5 tail fat expression increased significantly from 0 to 6 months old (P < 0.05), and FASN expression at 3 months old was significantly higher than that at 0 (minimum) and 6 months old (P < 0.05). Therefore, ELOVL5 and FASN polymorphisms could represent new candidate molecular markers and targets to reduce tail fat deposition in sheep.

Expression of ovine CTNNA3 and CAP2 genes and their association with growth traits.

Growth traits is a critical economic trait for animal husbandry. In this study, the SNPs of CTNNA3 and CAP2 genes were investigated to check whether they are associated with growth traits (body weight, body height, body length and chest circumference) in Hu sheep. The result of the association analysis indicated that the mutation in CTNNA3 (g.2018018 A > G) were associated significantly with body weight, body height, body length and chest circumference (P < 0.05), the mutation in CAP2 (g.8588 T > C) were associated significantly with body height at 140, 160, 180 days (P < 0.05), AA and CC of CTNNA3 and CAP2 were the dominant genotypes associated with growth traits in Hu sheep. Moreover, combined effect analyses indicated that the growth traits with combined genotypes AACTNNA3-CCCAP2 and AACTNNA3-CTCAP2 were higher than those with genotype GGCTNNA3-CTCAP2. RT-qPCR indicated that CTNNA3 expression levels were significantly higher in liver and lung than in other nine tissues (P < 0.05), CAP2 expression levels were significantly higher in bone, heart, liver, lung and duodenum than in other six tissues (P < 0.05). In conclusion, CTNNA3 and CAP2 polymorphisms could be used as genetic markers for improving growth traits in Hu sheep husbandry.

Detecting Single Nucleotide Polymorphisms in MEF2B and UCP3 and Elucidating Their Association with Sheep Growth Traits.

Herein we detected single nucleotide polymorphisms in MEF2B and UCP3 by DNA sequencing and the KASPar technology and analyzed their association with sheep growth traits. Two synonymous mutations, g.1826 C > T and g.10266 G > C, were detected, respectively, and they were found to be significantly associated with sheep growth traits (p < 0.05). In case of MEF2B g.1826 C > T, the average body weight and chest and cannon circumference of sheep with the CC genotype were significantly higher than those of sheep with the CT and TT genotypes (p < 0.05). Moreover, in case of UCP3 g.10266 G > C, the average body weight and chest and cannon circumference of sheep with the GG genotype were significantly higher than those of sheep with the GC and CC genotypes (p < 0.05). Moreover, the average body weight of sheep with the CC/GG genotype was higher compared with those of other genotype combinations. We also assessed MEF2B and UCP3 expression in different sheep tissues, confirming their expression in all examined tissues. To summarize, we believe that the polymorphisms identified in MEF2B and UCP3 can serve as molecular markers for sheep growth traits.

Whole-genome resequencing identified candidate genes associated with the number of ribs in Hu sheep.

The number of ribs is an important economic trait in the sheep industry when the sheep are raised for mutton. However, in sheep, the genetic mechanisms regulating rib number are poorly understood. In the present study, we aimed to identify important candidate genes that affect the increase in rib number in sheep. Whole-genome resequencing of 36 Hu sheep with an increased number of ribs (R14) and 36 sheep with normal (R13) rib numbers was carried out. Analysis using three methods (fixation index (FST), Fisher's exact test, and Chi-squared test) showed that 219 single nucleotide polymorphism sites overlapped among the results of the three methods, which represented 206 genes. Gene ontology and Kyoto Encyclopedia of Genes and Genomes analyses indicated that the genes were mainly associated with regulation of developmental process, inorganic anion transport, cellular biosynthetic process, tight junction, the oxytocin signaling pathway, and arrhythmogenic right ventricular cardiomyopathy. Four mutations were selected according to the significantly selected genomic regions and important pathways for genotyping and association analysis. The result demonstrated that three synonymous mutations correlated significantly with the rib number. Importantly, we revealed that the CPOX (encoding coproporphyrinogen oxidase), KCNH1 (encoding potassium voltage-gated channel subfamily H member 1), and CPQ (encoding carboxypeptidase Q) genes have a combined effect on rib number in Hu sheep. Our results identified candidate molecular markers for rib number in sheep breeding.

Polymorphisms in ovine ME1 and CA1 genes and their association with feed efficiency in Hu sheep.

Improving feed efficiency would increase profitability for producers. The objective of this study was to detect the expression levels of ME1 and CA1 and the polymorphisms of ME1 and CA1 associated with the feed conversion ratio (FCR) and residual feed intake (RFI) of Hu sheep by using qRT-PCR, pooled DNA sequencing and KASPar assay. The qRT-PCR results indicated that the expression levels of ME1 and CA1 were significantly higher in the liver tissues of low-RFI sheep than in those of the high-RFI sheep (p <.01). Association analysis demonstrated that the polymorphism ME1 g.453 C > T was significantly associated with FCR and RFI (p <.05). The polymorphism CA1 g.199 C > T had a significantly associated with FCR (p <.05) and no association with RFI (p >.05). Significant differences were observed between the combined genotypes and FCR and RFI at different measurement periods (p <.05). Thus, we propose the use of these two polymorphisms as new candidate molecular markers for improving feed efficiency in sheep populations.

Synthetic surfactin analogues have improved anti-PEDV properties.

Surfactin has antiviral activity against various enveloped viruses by inhibiting viral membrane fusion. However, the potential utility of surfactin as an antiviral drug is limited by its cytotoxicity. In this study, 10 surfactin analogues were obtained by chemical synthesis and evaluated to determine their anti-PEDV activities, hemolytic activities, and critical micelle concentrations. The main goal of our study was to develop a safer drug; a surfactin analogue with high anti-PEDV activity and low hemolytic activity. Compared with surfactin, one of the analogues we developed, SLP5, has lower hemolytic activity, with the same antiviral activity. The selectivity index of SLP5 is 52, while the SI for surfactin is 4, in other words, the safe and effective concentration range of SLP5 is 12 times greater than that of surfactin. Like surfactin, SLP5 has a direct antiviral effect on PEDV. Structurally, SLP5 is a linear lipopeptide with three carboxyl groups. Surfactin derivatives similar to SLP5 could be obtained by lactone bond hydrolyzation of surfactin, as well as total synthesis.

Transferrin receptor 1 is a supplementary receptor that assists transmissible gastroenteritis virus entry into porcine intestinal epithelium.

BACKGROUND: Transmissible gastroenteritis virus (TGEV), the etiologic agent of transmissible gastroenteritis, infects swine of all ages causing vomiting and diarrhea, in newborn piglets the mortality rate is near 100%. Intestinal epithelial cells are the primary target cells of TGEV. Transferrin receptor 1 (TfR1), which is highly expressed in piglets with anemia, may play a role in TGEV infection. However, the underlying mechanism of TGEV invasion remains largely unknown. RESULTS: Our study investigated the possibility that TfR1 can serve as a receptor for TGEV infection and enables the invasion and replication of TGEV. We observed that TGEV infection promoted TfR1 internalization, clustering, and co-localization with TfR1 early in infection, while TfR1 expression was significantly down-regulated as TGEV infection proceeded. TGEV infection and replication were inhibited by occluding TfR1 with antibodies or by decreasing TfR1 expression. TGEV infection increased in TGEV-susceptible ST or IPEC-J2 cell lines and TGEV-resistant Caco-2 cells when porcine TfR1 was over-expressed. Finally, we found that the TGEV S1 protein interacts with the extracellular region of TfR1, and that pre-incubating TGEV with a protein fragment containing the extracellular region of TfR1 blocked viral infection. CONCLUSIONS: Our results support the hypothesis that TfR1 is an additional receptor for TGEV and assists TGEV invasion and replication.

Surfactin Inhibits Membrane Fusion during Invasion of Epithelial Cells by Enveloped Viruses.

Because membrane fusion is a crucial step in the process by which enveloped viruses invade host cells, membrane fusion inhibitors can be effective drugs against enveloped viruses. We found that surfactin from Bacillus subtilis can suppress the proliferation of porcine epidemic diarrhea virus (PEDV) and transmissible gastroenteritis virus (TGEV) in epithelial cells at a relatively low concentration range (15 to 50 µg/ml), without cytotoxicity or viral membrane disruption. Membrane fusion inhibition experiments demonstrate that surfactin treatment significantly reduces the rate at which the virus fuses to the cell membrane. Thermodynamic experiments show that the incorporation of small amounts of surfactin hinders the formation of negative curvature by lamellar-phase lipids, suggesting that surfactin acts a membrane fusion inhibitor. A fluorescent lipopeptide similar to surfactin was synthesized, and its ability to insert into the viral membrane was confirmed by spectroscopy. In vivo experiments have shown that oral administration of surfactin to piglets protects against PEDV infection. In conclusion, our study indicates that surfactin is a membrane fusion inhibitor with activity against enveloped viruses. As the first reported naturally occurring wedge lipid membrane fusion inhibitor, surfactin is likely to be a prototype for the development of a broad range of novel antiviral drugs.IMPORTANCE Membrane fusion inhibitors are a rapidly emerging class of antiviral drugs that inhibit the infection process of enveloped viruses. They can be classified, on the basis of the viral components targeted, as fusion protein targeting or membrane lipid targeting. Lipid-targeting membrane fusion inhibitors have a broader antiviral spectrum and are less likely to select for drug-resistant mutations. Here we show that surfactin is a membrane fusion inhibitor and has a strong antiviral effect. The insertion of surfactin into the viral envelope lipids reduces the probability of viral fusion. We also demonstrate that oral administration of surfactin protects piglets from PEDV infection. Surfactin is the first naturally occurring wedge lipid membrane fusion inhibitor that has been identified and may be effective against many viruses beyond the scope of this study. Understanding its mechanism of action provides a foundation for the development of novel antiviral agents.

Multilocus sequence typing and virulence genotyping of Streptococcus suis serotype 9 isolates revealed high genetic and virulence diversity.

Streptococcus suis is an important swine pathogen that can cause a variety of diseases. Streptococcus suis serotype 9 (SS9) is a prevalent serotype, but limited information is available. Here, we studied and compared 30 SS9 isolates, including 24 isolates from China between year 2004 and 2013, 5 isolates from Vietnam and a serotype reference isolate from Denmark. A multilocus sequence typing (MLST) analysis was performed to exploit the genetic relationships between those isolates. The phylogenetic tree based on the MLST data divides those isolates into two clades (I and II), revealing different evolutionary paths of collected strains. A virulence genotyping analysis was performed by detecting 23 virulence-related genes; the clustering result also revealed two clusters (I and II), highly in accordance with MLST analysis result, showing that phylogenetic relatedness led to the presence of similar virulence genotypes. Murine model infection experiment was performed to assess the virulence of those strains in cluster I and cluster II, which displayed high virulence diversity even within a same cluster/ST. Notably, ST 243 could be regarded as an ST with high virulence potential in SS9. In conclusion, this study has revealed high genetic and virulence diversity in SS9 isolates.

Characterization and virulence clustering analysis of extraintestinal pathogenic Escherichia coli isolated from swine in China.

BACKGROUND: Swine extraintestinal pathogenic Escherichia coli (ExPEC) is an important pathogen that leads to economic and welfare costs in the swine industry worldwide, and is occurring with increasing frequency in China. By far, various virulence factors have been recognized in ExPEC. Here, we investigated the virulence genotypes and clonal structure of collected strains to improve the knowledge of phylogenetic traits of porcine ExPECs in China. RESULTS: We isolated 64 Chinese porcine ExPEC strains from 2013 to 14 in China. By multiplex PCR, the distribution of isolates belonging to phylogenetic groups B1, B2, A and D was 9.4%, 10.9%, 57.8% and 21.9%, respectively. Nineteen virulence-related genes were detected by PCR assay; ompA, fimH, vat, traT and iutA were highly prevalent. Virulence-related genes were remarkably more prevalent in group B2 than in groups A, B1 and D; notably, usp, cnf1, hlyD, papA and ibeA were only found in group B2 strains. Genotyping analysis was performed and four clusters of strains (named I to IV) were identified. Cluster IV contained all isolates from group B2 and Cluster IV isolates had the strongest pathogenicity in a mouse infection model. As phylogenetic group B2 and D ExPEC isolates are generally considered virulent, multilocus sequence typing (MLST) analysis was performed for these isolates to further investigate genetic relationships. Two novel sequence types, ST5170 and ST5171, were discovered. Among the nine clonal complexes identified among our group B2 and D isolates, CC12 and CC95 have been indicated to have high zoonotic pathogenicity. The distinction between group B2 and non-B2 isolates in virulence and genotype accorded with MLST analysis. CONCLUSION: This study reveals significant genetic diversity among ExPEC isolates and helps us to better understand their pathogenesis. Importantly, our data suggest group B2 (Cluster IV) strains have the highest risk of causing animal disease and illustrate the correlation between genotype and virulence.