Development of a multilocus sequence typing scheme for the pig pathogen Streptococcus suis: identification of virulent clones and potential capsular serotype exchange

Genetic diversity and antimicrobial susceptibility of Streptococcus suis from diseased Swiss pigs collected between 2019 - 2022

Streptococcus suis is an important pathogen causing severe disease in pigs and humans, giving rise to economic losses in the pig production industry. Out of 65 S. suis isolates collected from diseased pigs in Switzerland between 2019 and 2022, 57 isolates were thoroughly examined by phenotypic and whole genome sequence (WGS) based characterization. The isolates' genomes were sequenced allowing for a comprehensive analysis of their distribution in terms of serovar, sequence type (ST), clonal complex (CC), and classical virulence markers. Antimicrobial resistance (AMR) genes were screened, and phenotypic susceptibility to eight classes of antimicrobial agents was examined. Serovar 6, devoid of any resistance genes, was found to be most prevalent, followed by serovars 1, 3, 1/2, and 9. Thirty STs were identified, with ST1104 being the most prevalent. Serovar 2 and serovar 1/2 were associated with CC1, potentially containing the most virulent variants. Based on single nucleotide polymorphism (SNP) analyses, fifteen isolates belonged to one of seven putative transmission clusters each consisting of two or three isolates. High phenotypic AMR rates were detected for tetracyclines (80%) and macrolides (35%) and associated with the resistance genes tet(O) and erm(B), respectively. In contrast, susceptibility to β-lactam antibiotics and phenicols was high. Determination of phenotypic AMR profiling, including the minimum inhibitory concentrations (MICs) of the tested antimicrobial agents, sets a baseline for future studies. The study provides valuable insights into the genetic diversity and antimicrobial susceptibility of Swiss S. suis isolates, facilitating the identification of emerging clones relevant to public health concerns.

Isolation, Identification, Genomic Diversity, and Antimicrobial Resistance Analysis of Streptococcus suis in Hubei Province of China from 2021 to 2023

Streptococcus suis (S. suis) is a zoonotic pathogen capable of causing severe diseases in humans and pigs, including meningitis, sepsis, polyserositis, arthritis, and endocarditis. This study aimed to investigate the biological characteristics of 19 strains of S. suis isolated from diseased pigs in Hubei Province between 2021 and 2023. Through bioinformatics analysis, we investigated the serotype, MLST, pan-genome characteristics, SNP, AMR, and ICE of the 19 S. suis isolates. Among the 19 S. suis strains, ten serotypes were identified, and serotype 9 was the most prevalent (21.05%). Ten new alleles and nine new sequence types (STs) were discovered, with ST28 and ST243 emerging as the predominant STs. The results of the pan-genomic analysis of S. suis indicate that there are 943 core genes, 2259 shell genes, and 5663 cloud genes. Through SNP evolutionary analysis, we identified a strong genetic similarity between SS31 and the reference genome P1/7. The analysis of antibiotic resistance genes revealed widespread presence of erm(B) and tet(O) genes among 19 strains of S. suis. This association may be linked to the high resistance of S. suis to lincosamides, macrolides, and tetracyclines. Integrative and conjugative elements (ICEs) and integrative and mobilizable elements (IMEs) were identified in 16 strains, with a carriage rate of 84.21%, and resistance genes were identified within the ICE/IME elements of 8 strains. Antimicrobial susceptibility testing revealed that all strains showed sensitivity to vancomycin and lincomycin but resistance to tilmicosin, tiamulin, amoxicillin, and doxycycline. This study contributes to our understanding of the genomic diversity of S. suis in Hubei Province of China, providing essential data for the comprehensive prevention and control of S. suis infections in China.

Genomic epidemiology in Streptococcus suis: Moving beyond traditional typing techniques

Streptococcus suis is a bacterial gram-positive pathogen that causes invasive infections in swine and is also a zoonotic disease agent. Traditional molecular typing techniques such as ribotyping, multilocus sequence typing, pulse-field gel electrophoresis, or randomly amplified polymorphic DNA have been used to investigate S. suis population structure, evolution, and genetic relationships and support epidemiological and virulence investigations. However, these traditional typing techniques do not fully reveal the genetically heterogeneous nature of S. suis strains. The high-resolution provided by whole-genome sequencing (WGS), which is now more affordable and more commonly available in research and clinical settings, has unlocked the exploration of S. suis genetics at full resolution, permitting the determination of population structure, genetic diversity, identification of virulent clades, genetic markers, and other bacterial features of interest. This approach will likely become the new gold standard for S. suis strain typing as WGS instruments become more widely available and traditional typing techniques are gradually replaced.

Virulence genes, resistome and mobilome of Streptococcus suis strains isolated in France

Streptococcus suis is a leading cause of infection in pigs, causing extensive economic losses. In addition, it can also infect wild fauna, and can be responsible for severe infections in humans. Increasing antimicrobial resistance (AMR) has been described in S. suis worldwide and most of the AMR genes are carried by mobile genetic elements (MGEs). This contributes to their dissemination by horizontal gene transfer. A collection of 102 strains isolated from humans, pigs and wild boars in France was subjected to whole genome sequencing in order to: (i) study their genetic diversity, (ii) evaluate their content in virulence-associated genes, (iii) decipher the mechanisms responsible for their AMR and their association with MGEs, and (iv) study their ability to acquire extracellular DNA by natural transformation. Analysis by hierarchical clustering on principal components identified a few virulence-associated factors that distinguish invasive CC1 strains from the other strains. A plethora of AMR genes (n=217) was found in the genomes. Apart from the frequently reported erm(B) and tet(O) genes, more recently described AMR genes were identified [vga(F)/sprA, vat(D)]. Modifications in PBPs/MraY and GyrA/ParC were detected in the penicillin- and fluoroquinolone-resistant isolates respectively. New AMR gene-MGE associations were detected. The majority of the strains have the full set of genes required for competence, i.e for the acquisition of extracellular DNA (that could carry AMR genes) by natural transformation. Hence the risk of dissemination of these AMR genes should not be neglected.

Molecular Epidemiology of Underreported Emerging Zoonotic Pathogen Streptococcus suis in Europe

Streptococcus suis, a zoonotic bacterial pathogen circulated through swine, can cause severe infections in humans. Because human S. suis infections are not notifiable in most countries, incidence is underestimated. We aimed to increase insight into the molecular epidemiology of human S. suis infections in Europe. To procure data, we surveyed 7 reference laboratories and performed a systematic review of the scientific literature. We identified 236 cases of human S. suis infection from those sources and an additional 87 by scanning gray literature. We performed whole-genome sequencing to type 46 zoonotic S. suis isolates and combined them with 28 publicly available genomes in a core-genome phylogeny. Clonal complex (CC) 1 isolates accounted for 87% of typed human infections; CC20, CC25, CC87, and CC94 also caused infections. Emergence of diverse zoonotic clades and notable severity of illness in humans support classifying S. suis infection as a notifiable condition.

Comparative analysis of the interactions of different Streptococcus suis strains with monocytes, granulocytes and the complement system in porcine blood

Streptococcus suis (S. suis) is an important porcine pathogen causing meningitis, arthritis, and septicemia. Serotypes 2 and 14 are the most common zoonotic ones worldwide, whereas serotypes 2, 9, and 7 are very important in pigs in Europe. To cause invasive infections S. suis needs to enter the bloodstream. Consequently, the immune response in blood represents an important line of defense and bacteremia plays a key role in the pathogenesis of invasive S. suis infections. We investigated the working hypothesis that S. suis strains of the same serotype but different clonal complex (CC) might exhibit substantial differences in the interaction with components of the immune system in porcine blood. The experimental design of this study includes comparative analysis of 8 virulent strains belonging to 4 serotypes with strains of the same serotype being genetically not closely related. Significant differences between two strains of the same serotype but different clonal complex were recorded in the flow cytometric analysis of association with different leukocytes for serotype 9 and 14. Our results demonstrate that the serotype 9 strain of CC94 shows significantly increased association with monocytes and survival in porcine blood of conventional piglets as well as a tendency towards decreased composition of C3 in plasma of these piglets in comparison to the serotype 9 strain of CC16. Correlation analysis of C3 deposition on the bacterial surface and survival in respective blood samples of 8-week-old piglets demonstrated a negative correlation indicating that C3 deposition is a crucial step to limit bacterial survival and proliferation of different S. suis pathotypes in the blood of these piglets. In summary, our results indicate that the capsule composition of a S. suis strain is not alone sufficient to determine association with leukocytes, activation of complement, induction of proinflammatory cytokines, oxidative burst, and bacterial survival in porcine blood. In this study, substantial differences in these host-pathogen interactions were observed between strains of the same serotype. Therefore, a more comprehensive characterization of the field isolates, including at least MLST analysis to determine the sequence type/clonal complex, is recommended.

Genomic and phenotypic analysis of invasive Streptococcus suis isolated in Spain reveals genetic diversification and associated virulence traits

Streptococcus suis is a zoonotic pathogen that causes a major health problem in the pig production industry worldwide. Spain is one of the largest pig producers in the world. This work aimed to investigate the genetic and phenotypic features of invasive S. suis isolates recovered in Spain. A panel of 156 clinical isolates recovered from 13 Autonomous Communities, representing the major pig producers, were analysed. MLST and serotyping analysis revealed that most isolates (61.6%) were assigned to ST1 (26.3%), ST123 (18.6%), ST29 (9.6%), and ST3 (7.1%). Interestingly, 34 new STs were identified, indicating the emergence of novel genetic lineages. Serotypes 9 (27.6%) and 1 (21.8%) prevailed, followed by serotypes 7 (12.8%) and 2 (12.2%). Analysis of 13 virulence-associated genes showed significant associations between ST, serotype, virulence patterns, and clinical features, evidencing particular virulence traits associated with genetic clusters. The pangenome was generated, and the core genome was distributed in 7 Bayesian groups where each group included a variable set of over- and under-represented genes of different categories. The study provides comprehensive data and knowledge to improve the design of new vaccines, antimicrobial treatments, and bacterial typing approaches.

Laboratory Methods for Culture and Identification

This chapter addresses the cultivation, identification, and characterization of Streptococcus suis. Here, we describe in detail the most used methodologies and expected results.

Epidemiology and genetic diversity of Streptococcus suis in smallhold swine farms in the Philippines

This study aimed to determine the presence and characteristics of locally circulating strains of Streptococcus suis, the most important streptococcal pathogen in swine. Oral swab samples were collected from pigs from 664 representative smallhold farms across nine provinces in the Philippines. Isolates were identified and characterized using PCR assays. The study revealed an isolation rate of 15.8% (105/664, 95% CI: 13.0-18.6) among the sampled farms. Two hundred sixty-nine (269) S. suis isolates were recovered from 119 unique samples. Serotype 31 was the most prevalent (50/269, 95% CI: 13.9-23.2) among the other serotypes identified: 5, 6, 8, 9, 10, 11, 15, 16, 17, 21, 27, 28, and 29. The detection of the three 'classical' S. suis virulence-associated genes showed that 90.7% (244/269, 95% CI: 87.2-94.2) were mrp-/epf-/sly-. Multilocus sequence typing (MLST) analysis further revealed 70 novel sequence types (STs). Notably, several local isolates belonging to these novel STs formed clonal complexes (CC) with S. suis strains recovered from Spain and USA, which are major pork-exporting countries to the Philippines. This study functionally marks the national baseline knowledge of S. suis in Philippines.

Improvement of the mismatch amplification mutation assay-PCR for discrimination between Streptococcus suis serotypes 2 and 1/2

A mismatch amplification mutation assay (MAMA)-PCR, which detects a single-nucleotide polymorphism contributed to serological difference between Streptococcus suis serotypes 2 and 1/2, is used to discriminate between these serotypes. The present study reports unusual serotype 1/2 isolates untypable by the MAMA-PCR and improvement of the MAMA-PCR for typing such isolates.

Rapid Diagnostic of Streptococcus suis in Necropsy Samples of Pigs by thrA-Based Loop-Mediated Isothermal Amplification Assay

Streptococcus (S.) suis presents a serious threat to the pig industry as well as food safety and public health. Although several LAMP assays have been developed for the identification of S. suis, no universal assay is so far available for the field-suitable examination of clinical pig specimens. Based on the thrA housekeeping gene, a new loop-mediated isothermal amplification (LAMP) assay was developed and validated for the detection of S. suis in the brain and joints of pigs. For this LAMP assay, two different methods for the extraction of DNA from brain and joint swabs were compared. Using the LPTV boiling method, the detection limit of LAMP was 1.08 CFU/reaction, while the detection limit was 53.8 CFU/reaction using a commercial DNA extraction kit. The detection limits of thrA-LAMP in combination with the LPTV boiling method were 104-105 CFU/swab in the presence of brain tissue and 103-104 CFU/swab in the presence of joint tissue. The diagnostic quality criteria of LAMP were determined by the examination of 49 brain swabs and 34 joint swabs obtained during routine diagnostic necropsies. Applying the LPTV boiling method to brain swabs, the sensitivity, specificity, and positive and negative predictive values of thrA-LAMP were 88.0, 95.8, 95.7, and 88.5% using cultural investigation as a reference method, and 76.7, 100, 100, and 73.1% using real-time PCR as a reference method. Based on these results, the thrA-LAMP assay combined with the LPTV boiling method is suitable for rapid detection of S. suis from brain swabs.

Population structure and genetic diversity of Streptococcus suis isolates obtained from the United States

Diseases caused by the zoonotic pathogen Streptococcus suis are an extensive economic problem as well as an animal welfare concern for the global swine industry. Previous studies have evaluated the genomic diversity and population structure of S. suis isolates, however, the majority of these studies utilized isolates obtained from countries other than the U.S. This study applied whole genome sequencing and cgMLST-based typing to evaluate the population structure and genetic relatedness among S. suis isolates obtained within the U.S. The established high-resolution phylogenomic framework revealed extensive genomic variation and diversity among the sampled S. suis isolates, with isolates from the U.S. and from countries outside the U.S. found interspersed in the phylogeny. S. suis isolates obtained within the U.S. did not cluster by state or geographic location, however, isolates with similar serotypes, both obtained from within and outside the U.S., generally clustered together. Average nucleotide identity (ANI) values determined for the S. suis genomes were extensively broad, approaching the recommended species demarcation value, and correlated with the phylogenetic group distribution of the cgMLST-based tree. Numerous antimicrobial resistance (AMR) elements were identified among both U.S. and non-U.S. isolates with ble, tetO, and ermB genes identified as the most prevalent. The epf, mrp, and sly genes, historically used as markers for virulence potential, were also observed in the genomes of isolates that grouped together forming a subclade of clonal complex 1 (CC1) isolates. Collectively, the data in this report provides critical information needed to address potential biosurveillance needs and insights into the genetic diversity and population structure of S. suis isolates obtained within the U.S.

Genome characteristics related to the virulence of Streptococcus suis in Swedish pigs

The impact of S. suis on Swedish pig production has increased in recent years, and characterization of the strains present in the pig population is needed to aid in surveillance and prevention. Therefore, the aim of this study was to identify and characterize differences in the genomes between Swedish S. suis isolates associated with disease and isolates from healthy animals. Isolates categorized as being pathogenic (n = 100) or non-pathogenic (n = 117) were whole-genome sequenced, serotyped in silico, and sequence-typed using traditional MLST and core-genome MLST, and a genome-wide association study was performed to identify virulence-associated genes. In decreasing order, serotypes 2, 1, and 7 were the most common in the pathogenic group, and serotypes 15 and 12 were the most common in the non-pathogenic group. Among the commonly disease-associated sequence types, ST28 and ST25 were identified, whereas ST1 was scarcely found. The majority of isolates belonged to novel sequence types, revealing differences between Swedish isolates and those reported from other countries. The genomes of the pathogenic isolates were on average smaller and less heterogenic as compared to those of the non-pathogenic isolates. Although a majority of the previously published virulence-associated genes included in the study were found in the genomes of both pathogenic and non-pathogenic isolates, several new, significantly virulence-associated genes were identified.

Genomic characterization and virulence of Streptococcus suis serotype 4 clonal complex 94 recovered from human and swine samples

Streptococcus suis is a zoonotic pathogen that causes invasive infections in humans and pigs. Herein, we performed genomic analysis of seven S. suis serotype 4 strains belonging to clonal complex (CC) 94 that were recovered from a human patient or from diseased and clinically healthy pigs. Genomic exploration and comparisons, as well as in vitro cytotoxicity tests, indicated that S. suis CC94 serotype 4 strains are potentially virulent. Genomic analysis revealed that all seven strains clustered within minimum core genome group 3 (MCG-3) and had a high number of virulence-associated genes similar to those of virulent serotype 2 strains. Cytotoxicity assays showed that both the human lung adenocarcinoma cell line and HeLa cells rapidly lost viability following incubation for 4 h with the strains at a concentration of 106 bacterial cells. The human serotype 4 strain (ID36054) decreased cell viability profoundly and similarly to the control serotype 2 strain P1/7. In addition, strain ST1689 (ID34572), isolated from a clinically healthy pig, presented similar behaviour in an adenocarcinoma cell line and HeLa cells. The antimicrobial resistance genes tet(O) and ermB that confer resistance to tetracyclines, macrolides, and lincosamides were commonly found in the strains. However, aminoglycoside and streptothricin resistance genes were found only in certain strains in this study. Our results indicate that S. suis CC94 serotype 4 strains are potentially pathogenic and virulent and should be monitored.

Antibiotic Resistance Patterns and Molecular Characterization of Streptococcus suis Isolates from Swine and Humans in China

Streptococcus suis is a zoonotic pathogen that causes disease in humans after exposure to infected pigs or pig-derived food products. In this study, we examined the serotype distribution, antimicrobial resistance phenotypes and genotypes, integrative and conjugative elements (ICEs), and associated genomic environments of S. suis isolates from humans and pigs in China from 2008 to 2019. We identified isolates of 13 serotypes, predominated by serotype 2 (40/96; 41.7%), serotype 3 (10/96; 10.4%), and serotype 1 (6/96; 6.3%). Whole-genome sequencing analysis revealed that these isolates possessed 36 different sequence types (STs), and ST242 and ST117 were the most prevalent. Phylogenetic analysis revealed possible animal and human clonal transmission, while antimicrobial susceptibility testing indicated high-level resistance to macrolides, tetracyclines, and aminoglycosides. These isolates carried 24 antibiotic resistance genes (ARGs) that conferred resistance to 7 antibiotic classes. The antibiotic resistance genotypes were directly correlated with the observed phenotypes. We also identified ICEs in 10 isolates, which were present in 4 different genetic environments and possessed differing ARG combinations. We also predicted and confirmed by PCR analysis the existence of a translocatable unit (TU) in which the oxazolidinone resistance gene optrA was flanked by IS1216E elements. One-half (5/10) of the ICE-carrying strains could be mobilized by conjugation. A comparison of the parental recipient with an ICE-carrying transconjugant in a mouse in vivo thigh infection model indicated that the ICE strain could not be eliminated with tetracycline treatment. S. suis therefore poses a significant challenge to global public health and requires continuous monitoring, especially for the presence of ICEs and associated ARGs that can be transferred via conjugation. IMPORTANCE S. suis is a serious zoonotic pathogen. In this study, we investigated the epidemiological and molecular characteristics of 96 S. suis isolates from 10 different provinces of China from 2008 to 2019. A subset of these isolates (10) carried ICEs that were able to be horizontally transferred among isolates of different S. suis serotypes. A mouse thigh infection model revealed that ICE-facilitated ARG transfer promoted resistance development. S. suis requires continuous monitoring, especially for the presence of ICEs and associated ARGs that can be transferred via conjugation.

Serotype and multilocus sequence typing of Streptococcus suis from diseased pigs in Taiwan

Streptococcus suis (S. suis) infection can cause clinically severe meningitis, arthritis, pneumonia and septicemia in pigs. To date, studies on the serotypes, genotypes and antimicrobial susceptibility of S. suis in affected pigs in Taiwan are rare. In this study, we comprehensively characterized 388 S. suis isolates from 355 diseased pigs in Taiwan. The most prevalent serotypes of S. suis were serotypes 3, 7 and 8. Multilocus sequence typing (MLST) revealed 22 novel sequence types (STs) including ST1831-1852 and one new clonal complex (CC), CC1832. The identified genotypes mainly belonged to ST27, ST94 and ST1831, and CC27 and CC1832 were the main clusters. These clinical isolates were highly susceptible to ceftiofur, cefazolin, trimethoprim/sulfamethoxazole and gentamicin. The bacteria were prone to be isolated from cerebrospinal fluid and synovial fluid in suckling pigs with the majority belonging to serotype 1 and ST1. In contrast, ST28 strains that corresponded to serotypes 2 and 1/2 were more likely to exist in the lungs of growing-finishing pigs, which posted a higher risk for food safety and public health. This study provided the genetic characterization, serotyping and the most current epidemiological features of S. suis in Taiwan, which should afford a better preventative and treatment strategy of S. suis infection in pigs of different production stages.

Evaluation of pathotype marker genes in Streptococcus suis isolated from human and clinically healthy swine in Thailand

BACKGROUND

Streptococcus suis is a zoonotic pathogen that causes substantial economic losses in the pig industry and contributes to human infections worldwide, especially in Southeast Asia. Recently, a multiplex polymerase chain reaction (PCR) process was developed to distinguish disease-associated and non-disease-associated pathotypes of S. suis European strains. Herein, we evaluated the ability of this multiplex PCR approach to distinguish pathotypes of S. suis in Thailand.

RESULTS

This study was conducted on 278 human S. suis isolates and 173 clinically healthy pig S. suis isolates. PCR identified 99.3% of disease-associated strains in the human isolates and 11.6% of non-disease-associated strains in the clinically healthy pig isolates. Of the clinically healthy pig S. suis isolates, 71.1% were classified as disease-associated. We also detected undetermined pathotype forms in humans (0.7%) and pigs (17.3%). The PCR assay classified the disease-associated isolates into four types. Statistical analysis revealed that human S. suis clonal complex (CC) 1 isolates were significantly associated with the disease-associated type I, whereas CC104 and CC25 were significantly associated with the disease-associated type IV.

CONCLUSION

Multiplex PCR cannot differentiate non-disease-associated from disease-associated isolates in Thai clinically healthy pig S. suis strains, although the method works well for human S. suis strains. This assay should be applied to pig S. suis strains with caution. It is highly important that multiplex PCR be validated using more diverse S. suis strains from different geographic areas and origins of isolation.

Streptococcus suis outbreak caused by an emerging zoonotic strain with acquired multi-drug resistance in Thailand

Streptococcus suis is an emerging zoonotic swine pathogen which can cause severe infections in humans. In March 2021, an outbreak of S. suis infections with 19 confirmed cases of septicemia and meningitis leading to two deaths, occurred in Nakhon Ratchasima province, Thailand. We characterized the outbreak through an epidemiological investigation combined with Illumina and Nanopore whole genome sequencing (WGS). The source of the outbreak was traced back to a raw pork dish prepared from a single pig during a Buddhist ceremony attended by 241 people. WGS analysis revealed that a single S. suis serotype 2 strain belonging to a novel sequence type (ST) of the emergent Thai zoonotic clade CC233/379, was responsible for the infections. The outbreak clone grouped together with other Thai zoonotic strains from CC233/379 and CC104 in a global S. suis phylogeny and capsule switching events between serotype 2 zoonotic strains and serotype 7 porcine strains were identified. The outbreak strain showed reduced susceptibility to penicillin corresponding with mutations in key residues in the penicillin binding proteins (PBPs). Furthermore, the outbreak strain was resistant to tetracycline, erythromycin, clindamycin, linezolid and chloramphenicol, having acquired an integrative and conjugative element (ICE) carrying resistance genes tetO and ermB, as well as a transposon from the IS1216 family carrying optrA and ermA. This investigation demonstrates that multi-drug resistant zoonotic lineages of S. suis which pose a threat to human health continue to emerge.

Characterization of integrative and conjugative elements carrying antibiotic resistance genes of Streptococcus suis isolated in China

Streptococcus suis, an emerging zoonotic pathogen, is important reservoirs of antibiotic resistance genes that play critical roles in the horizontal transfer of corresponding resistances. In the present study, 656 antibiotic resistance (AR) genes were detected in 154 of 155 genomes of S. suis strains isolated from the nasopharynx of slaughtered pigs and the lungs of diseased pigs in China. The AR genes were clustered into 11 categories, consisting of tetracycline, macrolides, lincosamide, streptogramin, aminoglycoside, trimethoprim, amphenicols, nucleoside, quinupristin/dalfopristin, glycopeptide, and oxazolidinones resistance genes. In order to investigate the transmission patterns of the AR genes, AR genes-associated the mobile genetic elements (MGEs) were extracted and investigated. Twenty ICEs, one defective ICE, one tandem ICE, and ten prophages were found, which mainly carried tetracycline, macrolides/lincosamides/streptogramin (MLS), and aminoglycosides resistance genes. Three types of DNA cargo with AR genes were integrated into specific sites of ICEs: integrative mobilizable elements (IMEs), cis-IMEs (CIMEs), and transposon Tn916. Obvious differences in AR gene categories were found among the three cargo types. IMEs mainly harbored tetracycline and MLS resistance genes. CIMEs mainly carried aminoglycoside resistance genes, while transposon Tn916 carried only the tet (M) gene. Nearly all AR genes in ICEs were carried by IMEs and CIMEs. IMEs were prevalent and were also detected in additional 29 S. suis genomes. The horizontal transfer of IMEs and CIMEs may play critical role in ICE evolution and AR gene transmission in the S. suis population. Our findings provide novel insights into the transmission patterns of AR genes and the evolutionary mechanisms of ICEs in S. suis.

Characterisation of Streptococcus suis Isolates in the Czech Republic Collected from Diseased Pigs in the Years 2018-2022

As in other countries, in the Czech Republic, Streptococcus suis infection in pigs is considered an economically significant disease for the pig industry, though little is known about its population structure. We collected S. suis isolates from 144 farms in the years 2018-2022. All samples were taken from animals suffering from symptoms indicating possible S. suis infection. Serotyping revealed the presence of 23 different serotypes, and 18.94% were non-typable strains. The most common was S7 (14.96%), while other serotypes had frequencies of less than 10%. Sequence typing identified 56 different sequence types, including 31 newly assigned sequence types together with 41 new alleles in genes in the MLST schema. A large portion of isolates (25.70%) were of unknown sequence type. The most common sequence types were ST29 (14.77%) and ST28 (10.04%); the other sequence types had frequencies of less than 10%. In total, 100 different combinations of serotypes and sequence types were identified. Among them, S7ST29 was found in 72 isolates, representing 13.63% of all isolates, and was significantly associated with the central nervous system. Many other isolates of particular serotype and sequence type combinations were found in a few cases, and a number of isolates were non-typable.

Antibiotic resistance, virulence and genetic characteristics of Vibrio alginolyticus isolates from aquatic environment in costal mariculture areas in China

Vibrio alginolyticus has been the second most common Vibrio species in the world and mainly grows in the ocean or estuary environment, which can induce epidemics outbreaks under marine organisms, and causing serious economic losses in aquaculture industry. In this study, the genetic populations and evolutionary relationship analysis of V. alginolyticus isolated from different geographical locations in China with typical interannual differences were exhibited originally genetic diversity. Then the virulence genes prevalence, antibiotic resistance phenotype, and antimicrobial resistance genes risk diversity of V. alginolyticus were analyzed by phenotypic and molecular typing methods. And they were complex correlations among antibiotic phenotypes, resistance and virulence genes under different genotype of V. alginolyticus. The results provide a theoretical foundation for further understanding the genetic and metabolic diversity among V. alginolyticus in China, and lay a theoretical foundation for the transmission risk assessment and regional diagnosis of Vibrio in aquatic animals.

Comparative virulence and antimicrobial resistance distribution of Streptococcus suis isolates obtained from the United States

Streptococcus suis is a zoonotic bacterial swine pathogen causing substantial economic and health burdens to the pork industry worldwide. Most S. suis genome sequences available in public databases are from isolates obtained outside the United States. We sequenced the genomes of 106 S. suis isolates from the U.S. and analyzed them to identify their potential to function as zoonotic agents and/or reservoirs for antimicrobial resistance (AMR) dissemination. The objective of this study was to evaluate the genetic diversity of S. suis isolates obtained within the U.S., for the purpose of screening for genomic elements encoding AMR and any factors that could increase or contribute to the capacity of S. suis to transmit, colonize, and/or cause disease in humans. Forty-six sequence types (STs) were identified with ST28 observed as the most prevalent, followed by ST87. Of the 23 different serotypes identified, serotype 2 was the most prevalent, followed by serotype 8 and 3. Of the virulence genes analyzed, the highest nucleotide diversity was observed in sadP, mrp, and ofs. Tetracycline resistance was the most prevalent phenotypic antimicrobial resistance observed followed by macrolide-lincosamide-streptogramin B (MLSB) resistance. Numerous AMR elements were identified, many located within MGE sequences, with the highest frequency observed for ble, tetO and ermB. No genes encoding factors known to contribute to the transmission, colonization, and/or causation of disease in humans were identified in any of the S. suis genomes in this study. This includes the 89 K pathogenicity island carried by the virulent S. suis isolates responsible for human infections. Collectively, the data reported here provide a comprehensive evaluation of the genetic diversity among U.S. S. suis isolates. This study also serves as a baseline for determining any potential risks associated with occupational exposure to these bacteria, while also providing data needed to address public health concerns.

Genetic diversity and variation in antimicrobial-resistance determinants of non-serotype 2 Streptococcus suis isolates from healthy pigs

Streptococcus suis is a leading cause of bacterial meningitis in South-East Asia, with frequent zoonotic transfer to humans associated with close contact with pigs. A small number of invasive lineages are responsible for endemic infection in the swine industry, causing considerable global economic losses. A lack of surveillance and a rising trend in clinical treatment failure has raised concerns of growing antimicrobial resistance (AMR) among invasive S. suis. Gene flow between healthy and disease isolates is poorly understood and, in this study, we sample and sequence a collection of isolates predominantly from healthy pigs in Chiang Mai province, Northern Thailand. Pangenome characterization identified extensive genetic diversity and frequent AMR carriage in isolates from healthy pigs. Multiple AMR genes were identified, conferring resistance to aminoglycosides, lincosamides, tetracycline and macrolides. All isolates were non-susceptible to three or more different antimicrobial classes, and 75 % of non-serotype 2 isolates were non-susceptible to six or more classes (compared to 37.5 % of serotype 2 isolates). AMR genes were found on integrative and conjugative elements previously observed in other species, suggesting a mobile gene pool that can be accessed by invasive disease isolates. This article contains data hosted by Microreact.

Characterization of a Novel Linezolid Resistance Gene optrA and Bacitracin Resistance Locus-Carrying Multiple Antibiotic Resistant Integrative and Conjugative Element ICESsu1112S in Streptococccus Suis

Streptococcus suis strain 1112S was isolated from a diseased pig in a feedlot from Henan, China, in 2019. The isolate harbored a linezolid resistance gene optrA. WGS data revealed that the optrA gene was associated with a single copy ETAf ISS1S, in tandem with erm(B) and tet(O), located in a novel 72,587 bp integrative and conjugative element (ICE). Notably, this novel element, designated ICESsu1112S, also carried a novel bacitracin resistance locus. ICESsu1112S could be excised from chromosome and transferred to the recipient strain S. suis P1/7 with a frequency of 5.9 × 10⁻⁶ transconjugants per donor cell. This study provided the first description of the coexistence of optrA and a novel bacitracin locus on a multiple antibiotic resistant ICE and highlighted that ICE were major vehicle and contribute to the potential transfer of clinically relevant antibiotic resistance genes.

IMPORTANCE Antimicrobial resistance (AMR) caused by the imprudent use of antimicrobials has become a global problem, which poses a serious threat to treatment of S. suis infection in pigs and humans. Importantly, AMR genes can horizontally spread among commensal organisms and pathogenic microbiota, thereby accelerating the dissemination of AMR determinants. These transfers are mainly mediated by mobile genetic elements, including ICEs. In S. suis, ICEs are the major vehicles that contribute to the natural transfers of AMR genes among different bacterial pathogens. However, ICEs that carry optrA and bacitracin resistance locus are rarely investigated in S. suis isolates. Here, we investigated a S. suis isolate carrying an optrA and a novel bacitracin resistance locus, which were co-located on a novel multiple antibiotic resistant ICESsu1112S. Our study suggests that more research is needed to access the real significance of ICEs that horizontally spread clinical important resistance genes.

Distribution and characterization of Streptococcus suis serotypes isolated from January 2015 to June 2020 from diseased pigs in Québec, Canada

Streptococcus suis is one of the most important swine bacterial pathogens causing economic losses. This report presents the serotype distribution of S. suis recovered from diseased pigs in Québec from January 2015 to June 2020. Serotypes 1/2 and 2 predominated, followed by serotypes 7, 3, 5, 4, 9, 1, and 14. Compared to previously reported data, very few changes could be observed concerning the serotype distribution, indicating a relative stability. Half of the untypable isolates did not belong to the species S. suis sensu stricto, as determined by recN polymerase chain reaction. Less than 10% of "real S. suis" isolates were untypable. The genetic diversity of S. suis serotypes 1, 2, and 14, as analyzed by multilocus sequence typing, was mainly represented by sequence type (ST)1, ST28, ST25, and ST94. All ST1 isolates (considered highly virulent) belonged to either serotype 1 or 14.

Serotypes, Virulence-Associated Factors, and Antimicrobial Resistance of Streptococcus suis Isolates Recovered From Sick and Healthy Pigs Determined by Whole-Genome Sequencing

Streptococcus suis is ubiquitous in swine, and yet, only a small percentage of pigs become clinically ill. The objective of this study was to describe the distribution of serotypes, virulence-associated factor (VAF), and antimicrobial resistance (AMR) genes in S. suis isolates recovered from systemic (blood, meninges, spleen, and lymph node) and non-systemic (tonsil, nasal cavities, ileum, and rectum) sites of sick and healthy pigs using whole-genome sequencing. In total, 273 S. suis isolates recovered from 112 pigs (47 isolates from systemic and 136 from non-systemic sites of 65 sick pigs; 90 isolates from non-systemic sites of 47 healthy pigs) on 17 Ontario farms were subjected to whole-genome sequencing. Using in silico typing, 21 serotypes were identified with serotypes 9 (13.9%) and 2 (8.4%) as the most frequent serotypes, whereas 53 (19.4%) isolates remained untypable. The relative frequency of VAF genes in isolates from systemic (Kruskal–Wallis, p < 0.001) and non-systemic (Kruskal–Wallis, p < 0.001) sites in sick pigs was higher compared with isolates from non-systemic sites in healthy pigs. Although many VAF genes were abundant in all isolates, three genes, including dltA [Fisher's test (FT), p < 0.001], luxS (FT, p = 0.01), and troA (FT, p = 0.02), were more prevalent in isolates recovered from systemic sites compared with non-systemic sites of pigs. Among the isolates, 98% had at least one AMR gene, and 79% had genes associated with at least four drug classes. The most frequently detected AMR genes were tetO conferring resistance to tetracycline and ermB conferring resistance to macrolide, lincosamide, and streptogramin. The wide distribution of VAFs genes in S. suis isolates in this study suggests that other host and environmental factors may contribute to S. suis disease development.

Streptococcus suis Isolates-Serotypes and Susceptibility to Antimicrobials in Terms of Their Use on Selected Repopulated Czech Pig Farms

Streptococcus suis represents a primary health problem (such as meningitis, septicemia and arthritis in piglets and fatteners) in the swine industry worldwide and also an emerging zoonotic pathogen. In the Czech Republic, many pig farms repopulated their herds over the past decades to reduce morbidity and minimize treatment. The study analysed serotypes, sequence types and antimicrobial susceptibility in 39 S. suis isolates obtained from organs of diseased pigs from selected 16 repopulated farms with a history of S. suis-associated diseases and routine antimicrobial treatment with tulathromycin and/or amoxicillin. The analysis revealed diversity of collected isolates with regular occurrence of more than three serotypes per farm. The serotypes identified were 1/2 and 7, each in six isolates, followed by serotype 2 and 3 found in five isolates each, other serotypes were less frequent. Seven isolates were not typable by multiplex PCR and we also found sequence type of unknown type in thirteen isolates. The majority of S. suis isolates were resistant to clindamycin (n = 31), tetracycline (n = 29) and tilmicosin and tulathromycin (n = 28). On the other hand, with the exception of two isolates that were intermediately susceptible to penicillin and ampicillin, all isolates were susceptible to all three tested subgroups of beta-lactam antibiotics.

Identification and characterization of the cell division protein MapZ from Streptococcus suis

Streptococcus suis, an emerging zoonotic pathogen, causes invasive diseases in pigs, including sepsis, meningitis, endocarditis, pneumonia, and arthritis. Importantly, similar pathologies are reported in human S. suis infections. In previous work, the locus SSU0375 of S. suis strain P1.7 had been identified as a conditionally essential gene by intrathecal experimental infection of pigs with a transposon library of S. suis. This study aimed to identify the function of the corresponding gene product. Bioinformatics analysis and homology modeling revealed sequence and structural homologies with the Streptococcus pneumoniae mid-cell-anchored protein Z (MapZ) that is involved in cell division in different bacterial species. Indeed, depletion of this locus in S. suis strain 10 revealed a growth defect as compared to the wild type. Electron microscopy analysis of the corresponding mutant demonstrated morphological growth defects as compared to the wild-type strain, including an irregular cell shape and size as well as mispositioned division septa. Light microscopy and subsequent quantitative image analysis confirmed these morphological alterations. In the genetic rescue strain, the wild-type phenotype was completely restored. In summary, we proposed that SSU0375 or the corresponding locus in strain 10 encode for a S. suis MapZ homolog that guides septum positioning as evidenced for other members of the Streptococci family.

Emergence of a tet(M) Variant Conferring Resistance to Tigecycline in Streptococcus suis

The aim of this study was to gain insight into the resistance determinants conferring resistance to tigecycline in Streptococcus (S.) suis and to investigate the genetic elements involved in their horizontal transfer. A total of 31 tetracycline-resistant S. suis isolates were screened for tigecycline resistance by broth microdilution. S. suis isolate SC128 was subjected to whole genome sequencing with particular reference to resistance determinants involved in tigecycline resistance. Transferability of genomic island (GI) GISsuSC128 was investigated by transformation. The roles of tet(L) or tet(M) in contributing to tigecycline resistance in S. suis were confirmed by transformation using different tet(L)- or tet(M)-carrying constructs. Only S. suis SC128 showed a tigecycline resistance phenotype. A tet(L)-tet(M) and catA8 co-carrying GISsuSC128 was identified in this isolate. After transfer of the novel GI into a susceptible recipient, this recipient showed the same tigecycline resistance phenotype. Further transfer experiments with specific tet(L)- or tet(M)-carrying constructs confirmed that only tet(M), but not tet(L), contributes to resistance to tigecycline. Protein sequence analysis identified a Tet(M) variant, which is responsible for tigecycline resistance in S. suis SC128. It displayed 94.8% amino acid identity with the reference Tet(M) of Enterococcus faecium DO plasmid 1. To the best of our knowledge, this is the first time that a tet(M) variant conferring resistance to tigecycline was identified in S. suis. Its location on a GI will accelerate its transmission among the S. suis population.

Survival patterns of Streptococcus suis serotypes 1 and 14 in porcine blood indicate cross-reactive bactericidal antibodies in naturally infected pigs

Streptococcus suis serotype (cps) 1 and cps14 have been detected in association with severe diseases such as meningitis and polyarthritis in pigs. Though these two cps are very similar, only cps14 is an important zoonotic agent in Asia and only cps1 is described to be associated with diseases in suckling piglets rather than weaning piglets. The main objective of this study was to assess restriction of survival of cps14 and cps1 in porcine blood by IgG and IgM putatively cross-reacting with these two cps. Furthermore, we differentiate recent European cps1/14 strains by agglutination, cpsK sequencing, MLST and virulence-associated gene profiling. Our data confirmed cps1 of clonal complex 1 as an important pathotype causing polyarthritis in suckling piglets in Europe. The experimental design included also bactericidal assays with blood samples drawn at different ages of piglets naturally infected with different S. suis cps types including cps1 but not cps14. We report survival of a cps1 and a cps14 strain (both of sequence type 1) in blood of suckling piglets with high levels of maternal IgG binding to the bacterial surface. In contrast, killing of cps1 and cps14 was recorded in older piglets due to an increase of IgM as demonstrated by specific cleavage of IgM. Heterologous absorption of antibodies with cps1 or cps14 is sufficient to significantly increase the survival of the other cps. In conclusion, IgM elicited by natural S. suis infection is crucial for killing of S. suis cps1 and cps14 in older weaning piglets and has most likely the potential to cross-react between cps1 and cps14.

Comparative genetic analyses provide clues about capsule switching in Streptococcus suis 2 strains with different virulence levels and genetic backgrounds

Streptococcus suis (S. suis) is a major bacterial pathogen in the swine industry and an emerging zoonotic agent. S. suis produces an important extracellular component, capsular polysaccharide (CPS), based on which dozens of serotypes have been identified. Through virulence genotyping, we revealed the relatedness between subpopulations of S. suis serotype 2 (SS2), S. suis serotype 3 (SS3) and S. suis serotype 7 (SS7) strains despite their serotype differences. Multilocus sequence typing (MLST) was used to characterize the whole S. suis population and revealed capsule switching between S. suis strains. Importantly, capsule switching occurred in the SS2, SS3 and SS7 strains belonging to CC28 and CC29, which are phylogenetically distinct from the main CC1 SS2 lineage. To further explore capsule switching in S. suis, comparative genomic analyses were performed using available complete S. suis genomes. Phylogenetic analyses suggested that the SS2 strains could be divided into two clades (1 and 2), and those classified into clade 2 colocalized with SS3 and SS7 strains, in accordance with the above virulence genotyping and MLST analyses. Clade 2 SS2 strains presented high genetic similarity to SS3 and SS7 and shared common competence and defensive elements with them but were significantly different from Clade 1 SS2 strains. Notably, although the cps loci shared by Clade 1 and 2 SS2 strains were almost identical, a specific region of the cps locus of strain NSUI002 (Clade 2 SS2) could be found in the SS3 cps locus but not in the Clade 1 SS2 strain. These data indicated that the SS2 strains in CC28 and CC29 might have acquired the cps locus through capsule switching, which could explain the distinct genetic lineages within the SS2 population.

Interleukin-17A Contributes to Bacterial Clearance in a Mouse Model of Streptococcal Toxic Shock-Like Syndrome

Streptococcus suis (S. suis), an emerging zoonotic pathogen, can cause streptococcal toxic shock-like syndrome (STSLS) in humans with high mortality. STSLS is characterized by high bacterial burden, an inflammatory cytokine storm, multi-organ dysfunction, and ultimately acute host death. Although it has been found that a significantly high level of IL-17A was induced in an NLRP3-dependent manner during STSLS development, the role of IL-17A on S. suis STSLS remains to be elucidated. In this study, we found that the epidemic strain SC 19 caused a significantly higher level of IL-17A than the non-epidemic strain P1/7. In addition, higher bacterial burden was observed from SC 19-infected il17a−/− mice than il17a+/+ mice, although acute death, tissue injury and inflammatory cytokines storm were observed in both types of mice. Furthermore, compared with il17a+/+ mice, the level of neutrophils recruitment was lower in il17a−/− mice, and the levels of induced antimicrobial proteins, such as CRAMP, S100A8 and lipocalin-2, were also decreased in il17a−/− mice. In conclusion, this study demonstrated that IL-17A does not contribute to the severe inflammation, although it may play a minor role for bacterial clearance by inducing antimicrobial proteins and promoting neutrophil recruitment during STSLS.

Study of the relationship between untypable and typable isolates of Streptococcus suis recovered from clinically ill and healthy nursery pigs

Streptococcus suis naturally colonizes the upper respiratory tract of pigs and can lead to severe disease conditions. Although there are several serotypes associated with disease, untypable isolates have also been observed. The objective of this study was to investigate the relatedness of untypable S. suis isolates detected in clinical cases and healthy pigs in Ontario, Canada, and their relation to typing serotypes. One hundred fifty-six isolates obtained from 33 cases and 26 farm-and-pen-matched control pigs were sequenced using Illumina HiSeq sequencing. Protein sequences of the capsular polysaccharide genes (cps) were identified and analyzed using a maximum likelihood tree. Among the 27 untypable isolates, 3 were from systemic sites of cases and 13 and 11 were from upper respiratory sites of cases and controls, respectively. One hundred fifty-six isolates were grouped into 17 distinct groups based on the cps gene tree. Isolates from these 17 distinct individual cps groups were distributed among a minimum of one farm and maximum of eight farms. Untypable isolates were detected in 12 of those groups and each cps group had untypable isolates present amongst multiple farms. Interestingly, the three systemic untypable isolates not only coexisted with other serotypes found in the same location of the same pigs but were also found among different cps groups. These isolates are of interest and warrant further investigation. Overall, a wide diversity of S. suis among untypable isolates was observed in this study.

Acquiring high expression of suilysin enable non-epidemic Streptococccus suis to cause streptococcal toxic shock-like syndrome (STSLS) through NLRP3 inflammasome hyperactivation

The epidemic Streptococcus suis (S. suis) strain [Sequence type (ST) 7] was gradually evolving from the non-epidemic ST1 strain and got the ability for high expressing of suilysin (SLY). And the high expression of SLY was required for the epidemic strain to cause NLRP3 hyperactivation, which is essential for the induction of cytokines storm, dysfunction of multiple organs, and a high incidence of mortality, the characters of streptococcal toxic shock-like syndrome (STSLS). However, it remains to be elucidated whether acquiring high SLY expression due to genome evolution was sufficient for the non-epidemic strain to cause STSLS. Here, we found that the overexpression of SLY in ST1 strain (P1/7-SLY) could obviously increase the inflammasome activation, which was dependent on NLRP3 signalling. In contrast, the strain (P1/7-mSLY) overexpressing the mutant SLY (protein without hemolytic activity) could not significantly increase the inflammasome activation. Furthermore, similar to the epidemic strain, P1/7-SLY could cause STSLS in nlrp3^+/+ mice but not in nlrp3^−/− mice. In contrast, P1/7-mSLY could not cause STSLS in both nlrp3^+/+ mice and nlrp3^−/− mice. In summary, we demonstrate that genetic evolution enabling S. suis strain to express high level of SLY may be an essential and sufficient condition for NLRP3 inflammasome hyperactivation, which could further cause cytokines storm and STSLS.

Genetic analysis and pathogenicity of different sequence types of Streptococcus suis isolated from pigs in southern China

In this study, 52 Streptococcus suis isolates from pigs in southern China were divided into four known sequence types (STs) and six new STs, using multilocus sequence typing. Ten representative isolates were selected from 10 STs for the analysis of whole genome sequences. Virulence was assessed in 10 isolates, which were classified into three pathogenic groups. The prevalence of virulence-associated factors in the moderately pathogenic group was higher than that in the highly pathogenic group. The isolates from ST1 complex and serotype 2 were allocated to the moderately pathogenic group, while the isolates from the highly pathogenic group belonged to the non-ST1 complex and non-serotype 2. Three clusters were obtained based on multilocus sequence typing sequences: cluster III isolates from the nasal cavity of healthy pigs were classified into the highly pathogenic group and showed many peculiarities compared with cluster I and II isolates in virulence genotypes, genetic typing and pathogenesis, indicating a potential independent evolutionary line. Our results suggest that S. suis infections in China are becoming more complicated with constantly mutating isolates, which makes it difficult to distinguish their virulence by recognized typing methods. Thus, increased investigation and monitoring of these infections should be a priority for the swine industry in China.

Proposed virulence-associated genes of Streptococcus suis isolates from the United States serve as predictors of pathogenicity

BACKGROUND

There is limited information on the distribution of virulence-associated genes (VAGs) in U.S. Streptococcus suis isolates, resulting in little understanding of the pathogenic potential of these isolates. This lack also reduces our understanding of the epidemiology associated with S. suis in the United States and thus affects the efficiency of control and prevention strategies. In this study we applied whole genome sequencing (WGS)-based approaches for the characterization of S. suis and identification of VAGs.

RESULTS

Of 208 S. suis isolates classified as pathogenic, possibly opportunistic, and commensal pathotypes, the genotype based on the classical VAGs (epf, mrp, and sly encoding the extracellular protein factor, muramidase-release protein, and suilysin, respectively) was identified in 9% (epf+/mrp+/sly+) of the pathogenic pathotype. Using the chi-square test and LASSO regression model, the VAGs ofs (encoding the serum opacity factor) and srtF (encoding sortase F) were selected out of 71 published VAGs as having a significant association with pathotype, and both genes were found in 95% of the pathogenic pathotype. The ofs+/srtF+ genotype was also present in 74% of 'pathogenic' isolates from a separate validation set of isolates. Pan-genome clustering resulted in the differentiation of a group of isolates from five swine production companies into clusters corresponding to clonal complex (CC) and virulence-associated (VA) genotypes. The same CC-VA genotype patterns were identified in multiple production companies, suggesting a lack of association between production company, CC, or VA genotype.

CONCLUSIONS

The proposed ofs and srtF genes were stronger predictors for differentiating pathogenic and commensal S. suis isolates compared to the classical VAGs in two sets of U.S. isolates. Pan-genome analysis in combination with metadata (serotype, ST/CC, VA genotype) was illustrated to be a valuable subtyping tool to describe the genetic diversity of S. suis.

Strain Characterization of Streptococcus suis Serotypes 28 and 31, Which Harbor the Resistance Genes optrA and ant(6)-Ia

Streptococcus suis causes disease in pigs and is implicated increasingly in human disease worldwide. Although most clinical cases are associated with serotype 2, infections by other serotypes have sometimes been reported. Here, we sequenced the genome of a multidrug-resistant S. suis serotype 28 (strain 11313) and a multidrug-resistant S. suis serotype 31 (strain 11LB5). Strain 11313 was apathogenic in mouse infection models, whereas strain 11LB5 displayed ganglion demyelination, meningeal thickening, congestion, mononuclear cell infiltration, massive proliferation of cortical glial cells, and bacteria (>10⁴ CFU/g) in the spinal cord and ganglia in mice. Furthermore, immunohistochemistry found that the heavily infiltrated glial cells were astrocytes. Strain 11313 harbored the resistance genes ant(6)-Ia, erm(B), optrA, tet(l), tet(o), and strain 11LB5 harbored the resistance genes ant(6)-Ia, erm(B), tet(40), tet(o/w/32/o), aac(6′)-aph(2″). Mouse studies showed that strain 11LB5 exhibited a similar virulence to serotype 2 strain 700794, highlighting the need for surveillance of the other serotype S. suis isolates, in addition to serotype 2, in farms. This is the first report of the aminoglycoside resistance gene ant(6)-Ia in S. suis from animals. This suggests that S. suis might serve as an antibiotic resistance reservoir, which spreads the resistance gene ant(6)-Ia or optrA to other streptococcal pathogens on farms.

Comparative Virulence and Genomic Analysis of Streptococcus suis Isolates

Streptococcus suis is a zoonotic bacterial swine pathogen causing substantial economic and health burdens to the pork industry. Mechanisms used by S. suis to colonize and cause disease remain unknown and vaccines and/or intervention strategies currently do not exist. Studies addressing virulence mechanisms used by S. suis have been complicated because different isolates can cause a spectrum of disease outcomes ranging from lethal systemic disease to asymptomatic carriage. The objectives of this study were to evaluate the virulence capacity of nine United States S. suis isolates following intranasal challenge in swine and then perform comparative genomic analyses to identify genomic attributes associated with swine-virulent phenotypes. No correlation was found between the capacity to cause disease in swine and the functional characteristics of genome size, serotype, sequence type (ST), or in vitro virulence-associated phenotypes. A search for orthologs found in highly virulent isolates and not found in non-virulent isolates revealed numerous predicted protein coding sequences specific to each category. While none of these predicted protein coding sequences have been previously characterized as potential virulence factors, this analysis does provide a reliable one-to-one assignment of specific genes of interest that could prove useful in future allelic replacement and/or functional genomic studies. Collectively, this report provides a framework for future allelic replacement and/or functional genomic studies investigating genetic characteristics underlying the spectrum of disease outcomes caused by S. suis isolates.

Streptococcus suis: An Underestimated Emerging Pathogen in Hungary?

Streptococcus suis (S. suis) is an emerging zoonotic pathogen, demonstrated as an etiological agent in human infections in increasing frequency, including diseases like purulent meningitis, sepsis, uveitis-endophtalmitis and arthritis. Due to the increased availability and utility of novel diagnostic technologies in clinical microbiology, more studies have been published on the epidemiology of S. suis, both in veterinary and human medicine; however, there are no comprehensive data available regarding human S. suis infections from East-Central European countries. As a part of our study, data were collected from the National Bacteriological Surveillance (NBS) system on patients who had at least one positive microbiological result for S. suis, corresponding to an 18-year study period (2002-2019). n = 74 S. suis strains were isolated from invasive human infections, corresponding to 34 patients. The number of affected patients was 1.89 ± 1.53/year (range: 0-5). Most isolates originated from blood culture (63.5%) and cerebrospinal fluid (18.9%) samples. Additionally, we present detailed documentation of three instructive cases from three regions of the country and with three distinctly different outcomes. Hungary has traditional agriculture, the significant portion of which includes the production and consumption of pork meat, with characteristic preparation and consumption customs and unfavorable epidemiological characteristics (alcohol consumption, prevalence of malignant diseases or diabetes), which have all been described as important predisposing factors for the development of serious infections. Clinicians and microbiologist need to be vigilant even in nonendemic areas, especially if the patients have a history of occupational hazards or having close contact with infected pigs.

Pan-genome analysis of Streptococcus suis serotype 2 revealed genomic diversity among strains of different virulence

Streptococcus suis (SS) is an emerging zoonotic pathogen that causes severe infections in swine and humans. Among the 33 known serotypes, serotype 2 is most frequently associated with infections in pigs and humans. To better understand the virulence characterization of S. suis serotype 2 (SS2) and discriminate the difference between virulent and avirulent strains in SS2, characterization of the genomic features of strains with different virulence is required. The result showed that Streptococcus suis have an open pan-genome. The pan-genome shared by the 19 S. suis serotype 2 strains was composed of 1,239 core genes and 2,436 accessory genes. COG analysis indicated that core genes are involved in the basic physiological function, but accessory genes related to tachytely evolution. Comparative analysis between core genomes of virulent strains and 9 avirulent strains suggested that srtBCD pilus cluster was a significant discrepancy between virulent and avirulent strains. Analysis between high virulent and group B low virulent strains showed 53 and 58 genes specific to each other. Moreover, genomes of avirulent strains tend to be larger than virulent strains; avirulent strains tend to possess more prophages sequences than virulent strains. Our findings could be contributed to a better understanding of the genomics of S. suis serotype 2.

Population structure, genetic diversity and pathotypes of Streptococcus suis isolated during the last 13 years from diseased pigs in Switzerland

Streptococcus (S.) suis is a globally important swine pathogen, which comprises certain zoonotic serotypes. In this study, a detailed characterization of 88 porcine S. suis isolates was performed by analyzing capsular (cps) types, multilocus sequence typing (MLST) and investigation of the minimum core genome (MCG). In order to focus on the virulence potential of presumable invasive disease-associated S. suis isolates, virulence-associated gene profiles were assessed followed by screening a chosen subset of S. suis strains with a molecular pathotyping tool. Results showed a high genetic variability within this strain collection. In total, seventeen cps types were identified with a predominance of cps type 9 (15.9%) and 6 (14.8%). MLST revealed 48 sequence types (STs) including 41 novel ones. The population structure of S. suis was heterogenous and isolates belonged to eight different clonal complexes (CCs) including CC28 (9.1%), CC1109 (8%), CC13/149 (6.8%), CC1237 (5.7%), CC1 (3.4%), CC17 (3.4%), CC87 (2.3%), and CC1112 (1.1%), whereas a significant portion of isolates (60.2%) could not be assigned to any described CCs. Virulence-associated markers, namely extracellular protein factor (epf), muramidase-released protein (mrp), and suilysin (sly), showed a link with STs rather than with cps types. With this study an expanded knowledge about the population structure and the genetic diversity of S. suis could be achieved, which helps to contribute to an optimal public health surveillance system by promoting a focus on strains with an increased virulence and zoonotic potential.

Draft Genome Sequence of a Streptococcus suis Isolate from a Case of Cattle Meningitis

Streptococcus suis is primarily a pig pathogen and a zoonotic agent. Recently, the isolation of S. suis strain 10-36905 from a case of meningitis in cattle was reported. The draft genome sequence of this isolate demonstrates its divergent relationship with other S. suis strains.

Streptococcus suis is primarily a pig pathogen and a zoonotic agent. Recently, the isolation of S. suis strain 10-36905 from a case of meningitis in cattle was reported. The draft genome sequence of this isolate demonstrates its divergent relationship with other S. suis strains.

A critical review speculating on the protective efficacies of autogenous Streptococcus suis bacterins as used in Europe

Background

Streptococcus (S.) suis is a major porcine pathogen causing high morbidity worldwide. This includes well-managed herds with high hygiene standards. In Europe, no licensed vaccine is available. As practitioners are obliged to reduce the use of antibiotics, autogenous S. suis vaccines have become very popular in Europe.

Main body

Autogenous vaccines (AV) are generally neither tested for safety, immunogenicity nor protective efficacy, which leads to substantial uncertainties regarding control of disease and return on investment. Here, S. suis publications are reviewed that include important data on epidemiology, pathologies and bacterin vaccination relevant for the use of AV in the field. Differences between herds such as the porcine reproductive and respiratory syndrome virus infection status and the impact of specific S. suis pathotypes are probably highly relevant for the outcome of immunoprophylaxis using autogenous S. suis bacterins. Thus, a profound diagnosis of the herd status is crucial for management of expectations and successful implementation of AV as a tool to control S. suis disease. Induction of opsonizing antibodies is an in vitro correlate of protective immunity elicited by S. suis bacterins. However, opsonophagocytosis assays are difficult to include in the portfolio of diagnostic services.

Conclusion

Autogenous S. suis bacterins are associated with limitations and risks of failure, which can partly be managed through improvement of diagnostics.

Differential role of MyD88 signaling in Streptococcus suis serotype 2-induced systemic and central nervous system diseases

Streptococcus suis serotype 2 is an important porcine bacterial pathogen and a zoonotic agent responsible for sudden death, septic shock and meningitis, with exacerbated inflammation being a hallmark of the systemic and central nervous system (CNS) infections. However, S. suis serotype 2 strains are genetically and phenotypically heterogeneous, being composed of a multitude of sequence types (STs) whose virulence greatly varies. Yet, most studies have used 'classical' virulent Eurasian ST1 or ST7 strains, even though ST25 and ST28 strains account for most isolates in North America. While recognition of S. suis by innate immune cells has been associated with the myeloid differentiation primary response 88 (MyD88)-dependent Toll-like receptor (TLR) pathway in vitro, particularly surface-associated TLR2, little information is available regarding its role in vivo. This study demonstrates for the first time a differential role of MyD88 signaling in S. suis-induced systemic and CNS diseases, regardless of strain background diversity. The MyD88-dependent pathway is critical for the development of systemic disease via its role in inflammation, which subsequently controls bacterial burden. However, and differently from what has been described in vitro, TLR2 and TLR4 individually do not contribute to systemic disease, suggesting possible compensation in their absence and/or a collaborative role with other MyD88-dependent TLRs. On the other hand, CNS disease does not necessarily require MyD88 signaling and, consequently, neither TLR2 nor TLR4, suggesting a partial implication of other pathways. Finally, regardless of its notable heterogeneity, recognition of S. suis serotype 2 appears to be similar, indicating that recognized components are conserved motifs.

Specific bacteriophage of Bordetella bronchiseptica regulates B. bronchiseptica-induced microRNA expression profiles to decrease inflammation in swine nasal turbinate cells

Background

Respiratory diseases in pigs are the main health concerns for swine producers. Similar to the diseases in human and other animals, respiratory diseases are primary related to morbidity and are the result of infection with bacteria, viruses, or both. B. bronchiseptica causes serious respiratory diseases in the swine airway track. However, the B. bronchiseptica-specific bacteriophage has diverse advantages such as decreasing antibiotic overuse and possible therapeutic potential against bacteria.

Objective

The objects of this study were to investigate the therapeutic effect of specific B. bronchiseptica bacteriophages and to identify genes related to bacteriophage signaling utilizing RNA microarrays in swine nasal turbinate cells.

Methods

Bor-BRP-1 phages were applied 24 h prior to B.bronchiseptica infection (1 × 10⁷ cfu/ml) at several concentrations of bacterial infection. Cells were incubated to detect cytokines and 24 h to detect mucin production. And real-time quantitative PCR was performed to examine related genes expression. To determine the change of total gene expression based on B.bronchiseptica and Bor-BRP-1 treatment, we performed RNA sequencing experiments.

Results

The results showed that B. bronchiseptica induced increased expression of several inflammatory genes such as IL-1β, IL-6, and Muc1 in a dose-dependent manner. However, Bor-BRP-1 induced reduction of gene expression compared to the B. bronchiseptica induction group. In addition, microarrays detected Bor-BRP-1-altered inflammatory gene expression against B. bronchiseptica, reducing B. bronchiseptica-induced airway inflammation in swine epithelial cells.

Conclusion

These results suggest that the specific bacteriophage has a therapeutic potential to defend against B. bronchiseptica infection by altering inflammatory gene expression profiles.

Tools for Molecular Epidemiology of Streptococcus suis

Diseases caused by Streptococcus suis are a significant economic and welfare concern in pigs as well as in humans. Several molecular methods have been applied to investigate S. suis strain diversity and identify phylogenetic groups. Multilocus sequence typing (MLST), commonly used to differentiate between S. suis strains, has been instrumental in identifying that the species is genetically highly diverse. Recent advances in whole-genome analysis have resulted in schemes permitting the classification of S. suis populations as pathogenic or non-pathogenic, or disease-associated or non-disease associated. Here, we review these and other molecular approaches that can be used for surveillance, outbreak tracking, preventative health management, effective treatment and control, as well as vaccine development, including PCR based-assays that are easy to apply in modest diagnostic settings and which allow for the rapid screening of a large number of isolates at relatively low cost, granting the identification of several major clonal complexes of the S. suis population.

Rapid high resolution melting assay to differentiate Streptococcus suis serotypes 2, 1/2, 1, and 14

This rapid high resolution melting (HRM) assay allows distinguishing between Streptococcus suis serotype pairs 2 and 1/2 as well as 1 and 14, respectively, based on a single‐nucleotide polymorphism within capsular polysaccharide synthesis gene cluster K. This assay is easy to implement and identifies potential zoonotic serotypes.

Genotypic Comparison between Streptococcus suis Isolated from Pigs and Humans in Thailand

Streptococcus suis is a zoonotic pathogen of economic significance to the swine industry. The number of infected cases is increasing in humans worldwide. In this study, we determined the prevalence and diversity of S. suis carriage in slaughterhouse pigs in Phayao province, Thailand, where an outbreak occurred in 2007. The overall S. suis carriage rate was 35.2% among slaughterhouse pigs. The prevalence rates of serotypes 2 and 14 (the major serotypes infected in humans) were 6.7% and 2.6%, respectively. In both serotypes, 70.4% of isolates of serotypes 2 and 14 revealed sequence types and pulsotypes identical to human isolates in Thailand. It is suggested that pathogenic strains of S. suis are a risk factor for occupational exposure to pigs or the consumption of raw pork products. Food safety, hygiene, and health education should be encouraged to reduce the risk group.

Chromosomal Conjugative and Mobilizable Elements in Streptococcus suis: Major Actors in the Spreading of Antimicrobial Resistance and Bacteriocin Synthesis Genes

Streptococcus suis is a zoonotic pathogen suspected to be a reservoir of antimicrobial resistance (AMR) genes. The genomes of 214 strains of 27 serotypes were screened for AMR genes and chromosomal Mobile Genetic Elements (MGEs), in particular Integrative Conjugative Elements (ICEs) and Integrative Mobilizable Elements (IMEs). The functionality of two ICEs that host IMEs carrying AMR genes was investigated by excision tests and conjugation experiments. In silico search revealed 416 ICE-related and 457 IME-related elements. These MGEs exhibit an impressive diversity and plasticity with tandem accretions, integration of ICEs or IMEs inside ICEs and recombination between the elements. All of the detected 393 AMR genes are carried by MGEs. As previously described, ICEs are major vehicles of AMR genes in S. suis. Tn5252-related ICEs also appear to carry bacteriocin clusters. Furthermore, whereas the association of IME-AMR genes has never been described in S. suis, we found that most AMR genes are actually carried by IMEs. The autonomous transfer of an ICE to another bacterial species (Streptococcus thermophilus)-leading to the cis-mobilization of an IME carrying tet(O)-was obtained. These results show that besides ICEs, IMEs likely play a major role in the dissemination of AMR genes in S. suis.

MinION sequencing of Streptococcus suis allows for functional characterization of bacteria by multilocus sequence typing and antimicrobial resistance profiling

In recent years, high-throughput sequencing has revolutionized disease diagnosis by its powerful ability to provide high resolution genomic information. The Oxford Nanopore MinION sequencer has unparalleled potential as a rapid disease diagnostic tool due to its high mobility, accessibility, and short turnaround time. However, there is a lack of rigorous quality assessment and control processes standardizing the testing on the MinION, which is necessary for incorporation into a diagnostic workflow. Thus, our study examined the use of the MinION sequencer for bacterial whole genome generation and characterization. Using Streptococcus suis as a model, we optimized DNA isolation and treatments to be used for MinION sequencing and standardized de novo assembly to quickly generate a full-length consensus sequence achieving a 99.4% average accuracy. The consensus genomes from MinION sequencing were able to accurately predict the multilocus sequence type in 8 out of 10 samples and identified antimicrobial resistance profiles for 100% of the samples, despite the concern of a high error rate. The inability to unequivocally predict sequence types was due to difficulty in differentiating high identity alleles, which was overcome by applying additional error correction methods to increase consensus accuracy. This manuscript provides methods for the use of MinION sequencing for identification of S. suis genome sequence, sequence type, and antibiotic resistance profile that can be used as a framework for identification and classification of other pathogens.