Clonal Lineages of Erysipelothrix rhusiopathiae Responsible for Acute Swine Erysipelas in Japan Identified by Using Genome-Wide Single-Nucleotide Polymorphism Analysis

An Update in Knowledge of Pigs as the Source of Zoonotic Pathogens

The available data indicate that the human world population will constantly grow in the subsequent decades. This constant increase in the number of people on the Earth will lead to growth in food demand, especially in food of high nutritional value. Therefore, it is expected that the world livestock population will also increase. Such a phenomenon enhances the risk of transmitting pathogens to humans. As pig production is one of the most significant branches of the world's livestock production, zoonoses of porcine origins seem to be of particular importance. Therefore, in this review, we aim to introduce the latest data concerning, among other things, epidemiology and available preventive measures to control the most significant porcine zoonoses of viral, bacterial, and parasitic origin.

Population Structure and Genomic Characteristics of Australian Erysipelothrix rhusiopathiae Reveals Unobserved Diversity in the Australian Pig Industry

Erysipelothrix rhusiopathiae is a bacterial pathogen that is the causative agent of erysipelas in a variety of animals, including swine, emus, turkeys, muskox, caribou, moose, and humans. This study aims to investigate the population structure and genomic features of Australian isolates of E. rhusiopathiae in the Australian pig industry and compare them to the broader scope of isolates worldwide. A total of 178 isolates (154 Australian, seven vaccine isolates, six international isolates, and 11 of unknown origin) in this study were screened against an MLST scheme and publicly available reference isolates, identifying 59 new alleles, with isolates separating into two main single locus variant groups. Investigation with BLASTn revealed the presence of the spaA gene in 171 (96%) of the isolates, with three main groups of SpaA protein sequences observed amongst the isolates. Novel SpaA protein sequences, categorised here as group 3 sequences, consisted of two sequence types forming separate clades to groups 1 and 2, with amino acid variants at positions 195 (D/A), 303 (G/E) and 323(P/L). In addition to the newly identified groups, five new variant positions were identified, 124 (S/N), 307 (Q/R), 323 (P/L), 379 (M/I), and 400 (V/I). Resistance screening identified genes related to lincomycin, streptomycin, erythromycin, and tetracycline resistance. Of the 29 isolates carrying these resistance genes, 82% belonged to SpaA group 2-N101S (n = 22) or 2-N101S-I257L (n = 2). In addition, 79% (n = 23) of these 29 isolates belonged to MLST group ST 5. Our results illustrate that Australia appears to have a unique diversity of E. rhusiopathiae isolates in pig production industries within the wider global context of isolates.

A PCR assay to specifically detect serovar 1a strains of Erysipelothrix rhusiopathiae and differentiate them from serovar 2 strains possessing an intact ERH_1440 gene

The Erysipelothrix rhusiopathiae ERH_1440 gene, which encodes CDP-glycerol:poly (glycerophosphate) glycerophosphotransferase, is conserved in serovar 1a strains. The gene is usually missing or truncated in other serovar strains and therefore has been used for PCR detection of serovar 1a strains. We have previously reported a rare case of an E. rhusiopathiae serovar 2 strain possessing an intact ERH_1440. In this study, we analyzed three additional serovar 2 strains with an intact ERH_1440 and developed a new PCR assay for the specific detection and differentiation of serovar 1a strains from these serovar 2 strains. PCR with primers designed based on serovar 1a-specific gene sequences upstream of ERH_1440 showed 100% specificity for four hundred thirty Erysipelothrix strains isolated from extensive origins.

Comparative genomics of a novel clade shed light on the evolution of the genus Erysipelothrix and characterise an emerging species

Erysipelothrix sp. isolates obtained from a deadly outbreak in farmed turkeys were sequenced and compared to representatives of the genus. Phylogenetic trees—supported by digital DNA:DNA hybridization and Average Nucleotide Identity—revealed a novel monophyletic clade comprising isolates from pigs, turkeys, and fish, including isolates previously described as E. sp. Strain 2. Genes coding for the SpaC protein, typically found in E. sp. Strain 2, were detected in all isolates of the clade. Therefore, we confirm E. sp. Strain 2 represents a unique species, that despite its official name “Erysipelothrix piscisicarius” (meaning a killer of fish), may be isolated from a broad host range. Core genome analysis showed that the pathogenic species of this genus, E. rhusiopathiae and the clade E. sp. Strain 2, are enriched in core functionalities related to nutrient uptake and transport, but not necessarily homologous pathways. For instance, whereas the aerobic DctA transporter may uptake C₄-dicarboxylates in both species, the anaerobic DcuC transporter is exclusive of the E. sp. Strain 2. Remarkably, the pan-genome analysis uncovered that genes related to transport and metabolism, recombination and repair, translation and transcription in the fish isolate, within the novel clade, have undergone a genomic reduction through pseudogenization. This reflects distinct selective pressures shaping the genome of species and strains within the genus Erysipelothrix while adapting to their respective niches.

Serovars and SpaA Types of Erysipelothrix rhusiopathiae Isolated from Pigs in Japan from 2012 to 2019

Erysipelothrix rhusiopathiae causes swine erysipelas (SE), which results in considerable economic loss on pig farms. During SE outbreaks that occurred sporadically from 2008 to 2011 in Japan, new E. rhusiopathiae strains were isolated with a specific surface protective antigen (Spa)A protein characterized by methionine at position 203 and isoleucine at position 257 (M203/I257 SpaA type). To determine whether strains with the M203/I257 SpaA type are still prevalent in Japan, we collected 79 strains of E. rhusiopathiae from pigs showing various SE symptoms from 2012 to 2019 and classified them based on serovar typing, spaA gene sequence analysis, and lineage typing. We found that the majority of recent E. rhusiopathiae strains (59/79) belonged to the serovar 1a strain, and that the M203/I257 SpaA type (56/59) was predominant continuing from 2008 to 2011. Furthermore, serovar 1a strains with IVb-1 and IVb-2 lineages that had been isolated in specific regions of Japan were no longer local but were found across Japan. The pathogenicity of recent isolates tested in mice was not significantly changed when compared to that of previously isolated strains. Our results suggest that recent SE outbreaks were not due to changes in the SpaA protein or to altered virulence of E. rhusiopathiae but were rather caused by the persistent presence of E. rhusiopathiae with the M203/I257 SpaA type.

Comparative genome analysis of Erysipelothrix rhusiopathiae isolated from domestic pigs and wild boars suggests host adaptation and selective pressure from the use of antibiotics

The disease erysipelas caused by Erysipelothrix rhusiopathiae (ER) is a major concern in pig production. In the present study the genomes of ER from pigs (n=87), wild boars (n=71) and other sources (n=85) were compared in terms of whole-genome SNP variation, accessory genome content and the presence of genetic antibiotic resistance determinants. The aim was to investigate if genetic features among ER were associated with isolate origin in order to better estimate the risk of transmission of porcine-adapted strains from wild boars to free-range pigs and to increase our understanding of the evolution of ER. Pigs and wild boars carried isolates representing all ER clades, but clade one only occurred in healthy wild boars and healthy pigs. Several accessory genes or gene variants were found to be significantly associated with the pig and wild boar hosts, with genes predicted to encode cell wall-associated or extracellular proteins overrepresented. Gene variants associated with serovar determination and capsule production in serovars known to be pathogenic for pigs were found to be significantly associated with pigs as hosts. In total, 30 % of investigated pig isolates but only 6 % of wild boar isolates carried resistance genes, most commonly tetM (tetracycline) and lsa(E) together with lnu(B) (lincosamides, pleuromutilin and streptogramin A). The incidence of variably present genes including resistance determinants was weakly linked to phylogeny, indicating that host adaptation in ER has evolved multiple times in diverse lineages mediated by recombination and the acquisition of mobile genetic elements. The presented results support the occurrence of host-adapted ER strains, but they do not indicate frequent transmission between wild boars and domestic pigs. This article contains data hosted by Microreact.

Development of a Multiplex PCR-Based Assay for Rapid Serotyping of Erysipelothrix Species

The Gram-positive bacterium Erysipelothrix rhusiopathiae is a zoonotic pathogen that causes erysipelas in a wide range of mammalian and avian species. Historically, E. rhusiopathiae has been differentiated from other Erysipelothrix species by serotyping. Among 28 serovars of Erysipelothrix species, specific serovars, namely, 1a, 1b, and 2 of E. rhusiopathiae, are associated mainly with the disease in pigs, poultry, and humans; however, other serovar strains are often simultaneously isolated from diseased and healthy animals, indicating the importance of isolate serotyping for epidemiology. The traditional serotyping protocol, which uses heat-stable peptidoglycan antigens and type-specific rabbit antisera in an agar-gel precipitation test, is time-consuming and labor-intensive. To develop a rapid serotyping scheme, we analyzed sequences of the 12- to 22-kb chromosomal region, which corresponds to the genetic region responsible for virulence of serovar 1a and 2 strains of E. rhusiopathiae, of the 28 serovars of Erysipelothrix species. We confirmed that the serovar 13 strain lacks the genomic region and that some serovar strains possess very similar or the same genetic structure, prohibiting differentiation of the serovars. We created 4 multiplex PCR sets allowing the simultaneous detection and differentiation of the majority of Erysipelothrix serovars. Together with a previously reported multiplex PCR that can differentiate serovars 1a, 1b, 2, and 5, the multiplex PCR-based assay developed in this study covers all but one (serovar 13) of the reported serovars of Erysipelothrix species and should be a valuable tool for etiological as well as epidemiological studies of Erysipelothrix infections.

Erysipelothrix Spp.: Past, Present, and Future Directions in Vaccine Research

Erysipelothrix spp. comprise a group of small Gram-positive bacteria that can infect a variety of hosts including mammals, fish, birds, reptiles and insects. Among the eight Erysipelothrix species that have been described to date, only Erysipelothrix rhusiopathiae plays a major role in farmed livestock where it is the causative agent of erysipelas. E. rhusiopathiae also has zoonotic potential and can cause erysipeloid in humans with a clear occupational link to meat and fish industries. While there are 28 known Erysipelothrix serovars, over 80% of identified isolates belong to serovars 1 or 2. Vaccines to protect pigs against E. rhusiopathiae first became available in 1883 as a response to an epizootic of swine erysipelas in southern France. The overall vaccine repertoire was notably enlarged between the 1940s and 1960s following major outbreaks of swine erysipelas in the Midwest USA and has changed little since. Traditionally, E. rhusiopathiae serovar 1a or 2 isolates were inactivated (bacterins) or attenuated and these types of vaccines are still used today on a global basis. E. rhusiopathiae vaccines are most commonly used in pigs, poultry, and sheep where the bacterium can cause considerable economic losses. In addition, erysipelas vaccination is also utilized in selected vulnerable susceptible populations, such as marine mammals in aquariums, which are commonly vaccinated at regular intervals. While commercially produced erysipelas vaccines appear to provide good protection against clinical disease, in recent years there has been an increase in perceived vaccine failures in farmed animals, especially in organic outdoor operations. Moreover, clinical erysipelas outbreaks have been reported in animal populations not previously considered at risk. This has raised concerns over a possible lack of vaccine protection across various production species. This review focuses on summarizing the history and the present status of E. rhusiopathiae vaccines, the current knowledge on protection including surface antigens, and also provides an outlook into future directions for vaccine development.

Genomic and Immunogenic Protein Diversity of Erysipelothrix rhusiopathiae Isolated From Pigs in Great Britain: Implications for Vaccine Protection

Erysipelas, caused by the bacterium Erysipelothrix rhusiopathiae, is re-emerging in swine and poultry production systems worldwide. While the global genomic diversity of this species has been characterized, how much of this genomic and functional diversity is maintained at smaller scales is unclear. Specifically, while several key immunogenic surface proteins have been identified for E. rhusiopathiae, little is known about their presence among field strains and their divergence from vaccines, which could result in vaccine failure. Here, a comparative genomics approach was taken to determine the diversity of E. rhusiopathiae strains in pigs in Great Britain over nearly three decades, as well as to assess the field strains’ divergence from the vaccine strain most commonly used in British pigs. In addition, the presence/absence and variability of 13 previously described immunogenic surface proteins was determined, including SpaA which is considered a key immunogen. We found a high diversity of E. rhusiopathiae strains in British pigs, similar to the situation described in European poultry but in contrast to swine production systems in Asia. Of the four clades of E. rhusiopathiae found globally, three were represented among British pig isolates, with Clade 2 being the most common. All British pig isolates had one amino acid difference in the immunoprotective domain of the SpaA protein compared to the vaccine strain. However, we were able to confirm using in silico structural protein analyses that this difference is unlikely to compromise vaccine protection. Of 12 other known immunogenic surface proteins of E. rhusiopathiae examined, 11 were found to be present in all British pig isolates and the vaccine strain, but with highly variable degrees of conservation at the amino acid sequence level, ranging from 0.3 to 27% variant positions. Moreover, the phylogenetic incongruence of these proteins suggests that horizontal transfer of genes encoding for antigens is commonplace for this bacterium. We hypothesize that the sequence variants in these proteins could be responsible for differences in the efficacy of the immune response. Our results provide the necessary basis for testing this hypothesis through in vitro and in vivo studies.

Genome-Wide Identification of Virulence Genes in Erysipelothrix rhusiopathiae: Use of a Mutant Deficient in a tagF Homolog as a Safe Oral Vaccine against Swine Erysipelas

Swine erysipelas is caused by the Gram-positive pathogen Erysipelothrix rhusiopathiae The swine erysipelas live vaccine in Japan, the E. rhusiopathiae Koganei 65-0.15 strain (Koganei), has been reported to cause arthritis and endocarditis. To develop a vaccine with increased safety, we used a virulent Fujisawa strain to construct transposon mutants for a total of 651 genes, which covered 38% of the coding sequence of the genome. We screened the mutants for attenuation by inoculating mice with 108 CFU of each mutant and subsequently assessed protective capability by challenging the surviving mice with 103 CFU (102 times the 50% lethal dose) of the Fujisawa strain. Of the 23 attenuated mutants obtained, 6 mutants were selected and evaluated for protective capability in pigs by comparison to that of the Koganei strain. A mutant in the ERH_0432 (tagF) gene encoding a putative CDP-glycerol glycerophosphotransferase was found to be highly attenuated and to induce humoral and cell-mediated immune responses in conventional pigs. An in-frame deletion mutant of the gene, the Δ432 mutant, was constructed, and attenuation was further confirmed in germfree piglets; three of four piglets subcutaneously inoculated with 109 CFU of the Δ432 mutant showed no apparent clinical symptoms, whereas all four of the Koganei-inoculated piglets died 3 days after inoculation. It was confirmed that conventional pigs inoculated orally or subcutaneously with the Δ432 strain were almost completely protected against lethal challenge infection. Thus, the tagF homolog mutant of E. rhusiopathiae represents a safe vaccine candidate that can be administered via the oral and subcutaneous routes.

A putative transcription regulator involved in the virulence attenuation of an acriflavine-resistant vaccine strain of Erysipelothrix rhusiopathiae, the causative agent of swine erysipelas

Acriflavine, an acridine dye that causes frameshift mutations, has been used to attenuate various veterinary pathogens for the development of live vaccines. Erysipelothrix rhusiopathiae Koganei 65-0.15 strain (Koganei) (serovar 1a) is the acriflavine-resistant live vaccine currently used in Japan for the control of swine erysipelas. To investigate the attenuation mechanisms of the Koganei strain, we analyzed the draft genome sequence of the Koganei strain against the reference genome sequence of the E. rhusiopathiae Fujisawa strain (serovar 1a). The sequence analysis revealed a high degree of sequence similarity between the two strains and identified a total of 98 sequence differences within 80 protein-coding sequences. Among them, insertions/deletions (indels) were identified in 9 genes, of which 7 resulted in frameshift and premature termination. To investigate whether these mutations resulted in the attenuation of the Koganei strain, we focused on the indel mutation identified in ERH_0661, an XRE family transcriptional regulator. We introduced the mutation into ERH_0661 of the Fujisawa strain and restored the mutation of the Koganei strain. Animal experiments using the recombinant strains showed that mice survived inoculation with 10³ colony forming units (CFUs) (equivalent to approximately 100 50% lethal doses [LD50] of the wild-type Fujisawa) of the recombinant Fujisawa strain, and the mice became ill after inoculation with 10⁸ CFUs of the recombinant Koganei strain. These results suggest that the transcriptional regulator ERH_0661 is involved in the virulence of E. rhusiopathiae and that the ERH_0661 mutation is partially responsible for the attenuation of the Koganei strain.

Wild boars: A potential source of Erysipelothrix rhusiopathiae infection in Japan

The potential role of wild boars as a source of erysipelas infection was investigated. An ELISA test of wild boar serum samples from 41 prefectures in Japan revealed that proportions of the Erysipelothrix rhusiopathiae-positive samples were very high in all the prefectures, and the mean positive rate was 95.6% (1312/1372). Serovars of E. rhusiopathiae isolates from wild boars were similar to those of previously reported swine isolates, and all serovar isolates tested were found to be pathogenic to mice. These results suggest that wild boars in Japan constitute a reservoir of E. rhusiopathiae and may pose risks to other animals.

Identification of serovar 1a, 1b, 2, and 5 strains of Erysipelothrix rhusiopathiae by a conventional gel-based PCR

Among the four species of the genus Erysipelothrix, Erysipelothrix rhusiopathiae is the main species that causes disease in swine and poultry and has also been isolated from human patients. Recently, E. rhusiopathiae infections in domesticated animals have increased in many countries and are also the cause of emerging wildlife disease in arctic and boreal ecosystems. Historically, E. rhusiopathiae has been differentiated from other Erysipelothrix species by their serovars, which are determined based on cell wall antigens. Serotyping of Erysipelothrix is important, as specific E. rhusiopathiae serovars (1a, 1b, and 2) are associated with disease in pigs, poultry, and humans. However, serotyping is laborious and time-consuming and requires a full set of serovar reference strains and strain-specific antiserum. In this study, to develop a conventional gel-based PCR assay that can detect the main disease-associated serovars of E. rhusiopathiae, the draft genome sequences of E. rhusiopathiae strains of serovars 1a, 1b, 2, and 5, the last of which is often isolated from wild animals, were analyzed. Primers were designed based on the serovar-specific sequences of the strains and tested for field strains isolated from extensive origins. Among two hundred and ninety-seven isolates of various serovar strains of E. rhusiopathiae and other Erysipelothrix species, the PCR assay identified serovar 1a, 1b, 2, and 5 strains of E. rhusiopathiae. This conventional gel-based PCR assay should be useful for serovar surveillance of E. rhusiopathiae isolates in domesticated and wild animals as well as in humans.

Draft Genome Sequences of Lawsonia intracellularis Swine Strains Causing Proliferative Enteropathy in Japan

The draft genome sequences of three strains of Lawsonia intracellularis, an obligate intracellular animal pathogen responsible for causing proliferative enteropathy, obtained from swine in different prefectures in Japan revealed the absence of a genomic island previously reported to be linked to host adaptation and to high genomic diversity, despite geographical proximity.

The draft genome sequences of three strains of Lawsonia intracellularis, an obligate intracellular animal pathogen responsible for causing proliferative enteropathy, obtained from swine in different prefectures in Japan revealed the absence of a genomic island previously reported to be linked to host adaptation and to high genomic diversity, despite geographical proximity.

Identification of the Chromosomal Region Essential for Serovar-Specific Antigen and Virulence of Serovar 1 and 2 Strains of Erysipelothrix rhusiopathiae

Erysipelothrix rhusiopathiae causes swine erysipelas, an infection characterized by acute septicemia or chronic endocarditis and polyarthritis. Among 17 E. rhusiopathiae serovars, determined based on heat-stable peptidoglycan antigens, serovars 1 and 2 are most commonly associated with the disease; however, the molecular basis for the association between these serovars and virulence is unknown. To search for the genetic region defining serovar 1a (Fujisawa) strain antigenicity, we examined the 15-kb chromosomal region encompassing a putative pathway for polysaccharide biosynthesis, which was previously identified in the E. rhusiopathiae Fujisawa strain. Six transposon mutants of Fujisawa strain possessing a mutation in this region lost antigenic reactivity with serovar 1a-specific rabbit serum. Sequence analysis of this region in wild-type strains of serovars 1a, 1b, and 2 and serovar N, which lacks serovar-specific antigens, revealed that gene organization was similar among the strains and that serovar 2 strains showed variation. Serovar N strains displayed the same gene organization as the serovar 1a, 1b, or 2 strain and possessed certain mutations in this region. In two of the analyzed serovar N strains, restoration of the mutations via complementation with sequences derived from serovar 1a and 2 strains recovered antigenic reactivity with 1a- and 2-specific rabbit serum, respectively. Several gene mutations in this region resulted in altered capsule expression and attenuation of virulence in mice. These results indicate a functional connection between the biosynthetic pathways for the capsular polysaccharide and peptidoglycan antigens used for serotyping, which may explain variation in virulence among strains of different serovars.

Multiplex PCR assay for the simultaneous detection and differentiation of clonal lineages of Erysipelothrix rhusiopathiae serovar 1a strains currently circulating in Japan

The species Erysipelothrix rhusiopathiae displays genetic heterogeneity; however, E. rhusiopathiae serovar 1a strains currently circulating in Japan exhibit remarkably low levels of genetic diversity and group into clonal sublineages of Lineage IVb (IVb-1 and IVb-2). In the present study, based on whole genome sequencing data, we designed primers for a multiplex PCR assay to simultaneously detect and differentiate the sublineages of E. rhusiopathiae strains. Among the one hundred and twenty-seven isolates of various serovar strains, including isolates from a wide range of hosts and geographic origins, the PCR assay could successfully detect and differentiate the serovar 1a strains belonging to the sublineages.