New Sequence Types and Antimicrobial Drug-Resistant Strains of Streptococcus suis in Diseased Pigs, Italy, 2017-2019

Anatomo-pathological investigations in pigs of the Piedmont region (Northern Italy) for infectious diseases surveillance in an antimicrobial resistance perspective

Intensive breeding responds to the expanding market demand and animal health must be guaranteed to safeguard human and Public Health. Pig farming has grown in the last decades, leading to increased animal stress, pathogens dissemination, and the consequent use of antibiotics and the spread of antimicrobial-resistant bacteria. The present study aimed to describe the anatomopathological findings observed during necropsies performed from 2019 to 2021 on deceased pigs from five intensive breeding farms in northwestern Italy also reporting bacterial isolations, antimicrobial susceptibility testing, and virological results. Weaned pigs (WP) (N = 143) represented the majority of the carcasses, while the remaining part (N = 49) were fattening pigs (FP). Most of WP were affected by systemic disease (N = 79, 55.2 %), whereas 49 % of FP were affected by respiratory disease (N = 24). Streptococcus suis was the most frequently isolated microorganism in respiratory (around 20 % in both WP and FP) and systemic cases (25.3 % in WP and 33.3 % in FP). Enteric disorders were attributable to Brachyspira spp. and Escherichia coli in WP and FP (44.5 % and 55.5 %, respectively). Escherichia coli was considered to be the second causative agent of systemic disease (22.8 %) in WP. Streptococcus suis and monophasic Salmonella Typhimurium were isolated and demonstrated a high rate of multi-drug resistance (84 % and 100 %, respectively): the first showed resistance mainly against tetracyclines (100 %), lincosamides (88 %) and macrolides (84 %), whereas the latter to tetracyclines, sulfametox-trimethoprim, ampicillin, florfenicol, and enrofloxacin. Necropsy and microbiological assays are powerful tools for disease surveillance programs, highlighting potential risks for public health.

Streptococcus suis manganese transporter mutant as a live attenuated vaccine: Safety, efficacy, and virulence reversion mechanisms

Streptococcus suis is the leading cause of mortality in piglets and is responsible for severe economic losses in the global pork industry. Severe invasive diseases caused by S. suis include sepsis, meningitis, arthritis, and endocarditis. S. suis disease prevention is hampered by the lack of safe and efficacious vaccines. In this study, we constructed an S. suis live attenuated vaccine candidate lacking the major streptococcal manganese transporter, a known virulence determinant of this organism. The safety and efficacy of this live vaccine were evaluated in swine. Our clinical study results showed that when administered at a dose of 1010 CFU, the vaccine strain was safe and efficacious. However, a lower dose of 109 CFU failed to generate significant immune protection. To investigate if an adjuvant could enhance the efficacy of the vaccine at a lower dose, we spiked the vaccine with a polymeric adjuvant and evaluated its performance. Surprisingly, four pigs receiving the adjuvanted vaccine died during the vaccination phase. Pathology, microbiology, and genetic analyses suggested that the vaccine strain reverted to virulence in these animals. Functional genetic analysis found that the vaccine strain acquired compensatory mutations that upregulated the expression of a secondary manganese transporter, which in turn restored the virulence of the vaccine strain. Our results provide a new understanding of S. suis host adaptation mechanisms and useful information for the design of future live-attenuated vaccines.

Streptococcus suis serotypes 2, 1/2, 1, and 14 isolated from the brain of pigs dead with neurological symptoms or sudden death in Italian farms

The Streptococcus suis serotypes 2, and 14 are zoonotic pathogens in swine and present a capsular polysaccharide structure closely related to serotypes 1 and 1/2. Most molecular methods applied in veterinary diagnostic laboratories do not detect the single nucleotide polymorphism (SNP) that differentiates the serotypes 2 from 1/2, and 1 from 14. Consequently, epidemiological data is lacking. A collection of strains isolated between 2019 and 2024 from the brain of diseased pigs, and previously classified as 2-1/2 or 1-14, was analysed using three molecular methods able to detect of the SNP distinguishing the four serotypes. The study revealed that 57 % of those formerly classified as serotype 2-1/2 actually belong to serotype 1/2, while no serotype 14 was found among the strains classified as 1-14. The study also evaluates the feasibility of the routine application of these PCR-based methods for SNP detection, emphasizing the importance for accurate and rapid serotype identification to aid vaccine production and epidemiology.

Identification and characterization of Streptococcus suis strains isolated from eastern China Swine Farms, 2021-2023

The Streptococcus suis (S. suis) is an important zoonotic pathogen that causes streptococcal disease in pigs and poses a threat to humans. This study provides an understanding of the prevalence of  S.suis in eastern China and provides guidance for clinical prophylaxis. From 2021 to 2023, a total of 143 strains of S. suis were isolated from 1642 lung tissue and nasal swabs from healthy and suspected infected pigs in Shandong Province, China, using the Phenotypic tests and PCR technique. The isolates were then tested for serotype, virulence-related genes, and resistance genes. Among the 143 isolates, type 2 was the predominant serotype with 98 isolates (98/143, 68.5%), followed by type 5 with 22 isolates (22/143, 15.3%), type 4 with 6 isolates (6/143, 4.2%), type 19 with 4 isolates (4/143, 2.8%) and type 21 with 5 isolates (5/143, 3.5%), respectively. A minimum of 78.3% of the strains exhibited the presence of virulence-related genes including pgda, dlta, mann, fbps, orf2, and sspa, whereas the virulence-associated genes Sum, Sly, and Salkr are not widely prevalent. For the detection of resistance genes, it was found that the tetO gene had a high detection rate of 70.1% (101/143), whereas neither the pbp2b gene nor the cat1 and cat2 genes were detected. Antimicrobial susceptibility testing revealed that 96.5% (138/143) of the isolates exhibited multidrug resistance (MDR). And polypeptide B was found to be tolerated by 125 of the 143 strains (87.4%). Although we did not detect the β-lactam resistance gene in any of the 143 strains, an average of 39.2% of the strains were resistant to β-lactam antibiotics. The results of the current study is thought it may be help to understand the prevalence of S. suis and provide important insights into treatment and prevention.

New insights into the epidemiology of Streptococcus suis in pig production systems using whole genome sequencing

Streptococcus suis (S. suis) is a major pathogen for pigs, causing large economic losses to the swine industry. Moreover, this bacterium has a zoonotic potential, being capable of infecting humans in close contact with pigs or, less frequently, through contact with pork products. Given its importance in both veterinary and public health, S. suis remains a key topic of research. This study explores the genetic characteristics of 154 S. suis isolates obtained from clinical samples collected from pigs between 2018 and 2022. Whole genome sequencing (WGS) allowed a comprehensive analysis of the S. suis population in Spain, including detection of serotype, sequence type (ST), antimicrobial resistance genes, and virulence-associated genes. This approach also explored the vertical transmission of this pathogen through vertically integrated pyramids, as evidenced by associations between grandmother and mother sow farms, and phylogenetic groups, serotypes, and STs. Our analysis revealed that serotype 9 was the most prevalent in our strain collection, predominantly associated with ST123. Notably, the three most significant virulence genes, encoding the extracellular protein factor (EPF), the muramidase-release protein (MRP), and suilysin (SLY), were not consistently present in all clinical isolates. Regarding antimicrobial resistance, no phenotypic resistance was observed to ceftiofur or florfenicol, while observing low resistance to ampicillin (0.6 %) and enrofloxacin (2.6 %), intermediate resistance to penicillin (22.1 %), and high percentage of non-wild-type isolates to trimethoprim-sulfamethoxazole (57.1 %), and doxycycline (96.1 %). The most prevalent antimicrobial resistance genes (ARGs) were tet(O) (85.1 %) and erm(B) (86.4 %), conferring resistance to tetracyclines and macrolides, respectively, although macrolides were not included in the phenotypic testing. Overall, this study provides key epidemiological insights into this significant systemic pathogen within the Spanish swine population. The findings underscore the importance of understanding sample origins, such as grandmother and mother sow farms, to develop an effective antimicrobial stewardship program for managing S. suis-associated diseases.

Serotype distribution and antimicrobial susceptibility of Streptococcus suis isolates from porcine diagnostic samples in Hungary, 2020-2023

BACKGROUND

Streptococcus suis (S. suis) is a major swine pathogen and a significant zoonotic agent, causing substantial economic losses in the swine sector and having considerable public health importance. The control and management of S. suis-related conditions has become increasingly challenging due to the multitude of involved serotypes with varying antimicrobial resistance patterns. Here, we report the serological distribution and antimicrobial susceptibility of S. suis isolates isolated form clinical samples of Hungarian large-scale swine farms.

RESULTS

Between 2020 and 2023, altogether 296 S. suis isolates were obtained from diseased pigs of 64 Hungarian pig operations. Serotyping of the isolates was carried out by using molecular methods (cps-typing). The isolated strains belonged to 24 single cps-types. The most frequently detected cps-types during the four years of this passive survey were 9 (19.6%), 2 (19.3%), 1/2 (18.9%) and 7 (14.5%). The brain, spleen, endocardial valve thrombus and lung proved to be the most frequent site of S. suis strain isolation, and animals 29-75 days of age were affected in the highest proportion. Antimicrobial susceptibility testing of the isolates was performed by determining the minimal inhibitory concentration for 15 antimicrobial agents of veterinary and human importance using a commercial microdilution assay. More than 90% of the tested isolates proved to be susceptible to the examined beta-lactams, cephalosporins and florfenicol, as well as to rifampicin, trimethoprim/sulfamethoxazole and vancomycin. Phenotypic resistance profiles (resistotypes) of clindamycin-tetracyclin (3.8%), clindamycin-erythromycin-tetracyclin (8.4%) and clindamycin-erythromycin-tetracyclin-trimethoprim / sulfamethoxazole (3.8%) were most frequently detected. Vancomycin resistance was observed in the case of 1 S. suis strain.

CONCLUSIONS

The dominance of S. suis cps-types 9, 2, 1/2 and 7 in Hungary over the four years of this study aligns with previous reports from several countries worldwide. The presence of highly susceptible S. suis isolates suggests a prudent antibiotic usage and treatment practice in the surveyed Hungarian swine operations. In contrary, the presence of several resistotypes could indicate the problem of antibiotic resistance in the future.

Molecular characterization of Streptococcus suis isolates recovered from diseased pigs in Europe

Streptococcus suis is a major swine pathogen and zoonotic agent, causing important economic losses to the porcine industry. Here, we used genomics approaches to characterize 251 S. suis isolates recovered from diseased pigs across Belgium, France, Germany, Hungary, the Netherlands, Spain, and the United Kingdom. We identified 13 serotypes, being serotypes 9 and 2 the most prevalent, and 34 sequence types (STs), including 16 novel STs, although ST16 and ST1 dominated the strain population. Phylogenetic analysis revealed complex genetic relationships, notable geographic clustering, and potential differential capacity for capsular switching among serotype 9 isolates. We found antimicrobial resistance (AMR) genes in 85.3% of the isolates, with high frequencies of genes conferring resistance to tetracyclines and macrolides. Specifically, 49.4% of the isolates harbored the tetO gene, and 64.9% possessed the ermB gene. Additionally, we observed a diverse array of virulence-associated genes (VAGs), including the classical VAGs mrp, epf, and sly, with variable presence across different genotypes. The high genetic diversity among European S. suis isolates highlights the importance of targeted antimicrobial use and flexible vaccine strategies. Rapid strain characterization is crucial for optimizing swine health management, enabling tailored interventions like the development of autovaccines to mitigate S. suis infections.

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.

Antiviral Drug Candidate Repositioning for Streptococcus suis Infection in Non-Tumorigenic Cell Models

The increasing prevalence of antimicrobial resistance against zoonotic bacteria, including Streptococcus (S.) suis, highlights the need for new therapeutical strategies, including the repositioning of drugs. In this study, susceptibilities of bacterial isolates were tested toward ten different 3-amidinophenyalanine (Phe(3-Am)) derivatives via determination of minimum inhibitory concentration (MIC) values. Some of these protease inhibitors, like compounds MI-432, MI-471, and MI-476, showed excellent antibacterial effects against S. suis. Their drug interaction potential was investigated using human liver microsomal cytochrome P450 (CYP450) measurements. In our work, non-tumorigenic IPEC-J2 cells and primary porcine hepatocytes were infected with S. suis, and the putative beneficial impact of these inhibitors was investigated on cell viability (Neutral red assay), on interleukin (IL)-6 levels (ELISA technique), and on redox balance (Amplex red method). The antibacterial inhibitors prevented S. suis-induced cell death (except MI-432) and decreased proinflammatory IL-6 levels. It was also found that MI-432 and MI-476 had antioxidant effects in an intestinal cell model upon S. suis infection. Concentration-dependent suppression of CYP3A4 function was found via application of all three inhibitors. In conclusion, our study suggests that the potential antiviral Phe(3-Am) derivatives with 2',4' dichloro-biphenyl moieties can be considered as effective drug candidates against S. suis infection due to their antibacterial effects.

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.

Characterization of pig tonsils as niches for the generation of Streptococcus suis diversity

Streptococcus suis is a gram-positive bacterium that causes meningitis, septicemia, endocarditis, and other disorders in pigs and humans. We obtained 42 and 50 S. suis isolates from lesions of porcine endocarditis and palatine tonsils, respectively, of clinically healthy pigs in Japan; we then determined their sequence types (STs) by multilocus sequence typing (MLST), cps genotypes, serotypes, and presence of classical major virulence-associated marker genes (mrp, epf, and sly). The 42 isolates from endocarditis lesions were assigned to a limited number of STs and clonal complexes (CCs). On the other hand, the 50 isolates from tonsils were diverse in these traits and seemingly in the degree of virulence, suggesting that tonsils can accommodate a variety of S. suis isolates. The goeBURST full algorithm using tonsil isolates obtained in this study and those retrieved from the database showed that major CCs as well as many other clusters were composed of isolates originating from different countries, and some of the STs were very similar to each other despite the difference in country of origin. These findings indicate that S. suis with not only different but also similar mutations in the genome have survived in tonsils independently across different geographical locations. Therefore, unlike the lesions of endocarditis, the tonsils of pigs seemingly accommodate various S. suis lineages. The present study suggests that S. suis acquired its diversity by natural mutations during colonization and persistence in the tonsils of pigs.

Exogenous methionine contributes to reversing the resistance of Streptococcus suis to macrolides

Streptococcus suis (S. suis) has been increasingly recognized as a porcine zoonotic pathogen that threatens the health of both pigs and humans. Multidrug-resistant Streptococcus suis is becoming increasingly prevalent, and novel strategies to treat bacterial infections caused by these organisms are desperately needed. In the present study, an untargeted metabolomics analysis showed that the significant decrease in methionine content and the methionine biosynthetic pathway were significantly affected by the Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis in drug-resistant S. suis. The addition of L-methionine restored the bactericidal activity of macrolides, doxycycline, and ciprofloxacin on S. suis in vivo and in vitro. Further studies showed that the exogenous addition of methionine affects methionine metabolism by reducing S-adenosylmethionine synthetase activity and the contents of S-adenosylmethionine, S-adenosyl homocysteine, and S-ribose homocysteine. Methionine can decrease the total methylation level and methylesterase activity in multidrug resistant S. suis. The drug transport proteins and efflux pump genes were significantly downregulated in S. suis by exogenous L-methionine. Moreover, the exogenous addition of methionine can reduce the survival of S. suis by affecting oxidative stress and metal starvation in bacteria. Thus, L-methionine may influence the development of resistance in S. suis through methyl metabolism and metal starvation. This study provides a new perspective on the mitigation of drug resistance in S. suis.IMPORTANCEBacterial antibiotic resistance has become a severe threat to human and animal health. Increasing the efficacy of existing antibiotics is a promising strategy against antibiotic resistance. Here, we report that L-methionine enhances the efficacy of macrolides, doxycycline, and ciprofloxacin antibiotics in killing Streptococcus suis, including multidrug-resistant pathogens. We investigated the mechanism of action of exogenous methionine supplementation in restoring macrolides in Streptococcus suis and the role of the methionine cycle pathway on methylation levels, efflux pump genes, oxidative stress, and metal starvation in Streptococcus suis. It provides a theoretical basis for the rational use of macrolides in clinical practice and also identifies a possible target for restoring drug resistance in Streptococcus suis.

Streptococcus suis serotype 9 in Italy: genomic insights into high-risk clones with emerging resistance to penicillin

BACKGROUND

Streptococcus suis is an important pig pathogen and an emerging zoonotic agent. In a previous study, we described a high proportion of penicillin-resistant serotype 9 S. suis (SS9) isolates on pig farms in Italy.

OBJECTIVES

We hypothesized that resistance to penicillin emerged in some SS9 lineages characterized by substitutions at the PBPs, contributing to the successful spread of these lineages in the last 20 years.

METHODS

Sixty-six SS9 isolates from cases of streptococcosis in pigs were investigated for susceptibility to penicillin, ceftiofur and ampicillin. The isolates were characterized for ST, virulence profile, and antimicrobial resistance genes through WGS. Multiple linear regression models were employed to investigate the associations between STs, year of isolation, substitutions at the PBPs and an increase in MIC values to β-lactams.

RESULTS

MIC values to penicillin increased by 4% each year in the study period. Higher MIC values for penicillin were also positively associated with ST123, ST1540 and ST1953 compared with ST16. The PBP sequences presented a mosaic organization of blocks. Within the same ST, substitutions at the PBPs were generally more frequent in recent isolates. Resistance to penicillin was driven by substitutions at PBP2b, including K479T, D512E and K513E, and PBP2x, including T551S, while reduced susceptibility to ceftiofur and ampicillin were largely dependent on substitutions at PBP2x.

CONCLUSIONS

Here, we identify the STs and substitutions at the PBPs responsible for increased resistance of SS9 to penicillin on Italian pig farms. Our data highlight the need for monitoring the evolution of S. suis in the coming years.

Prevalence of Streptococcus suis serotype 2 isolated from pigs: A systematic review and meta-analysis

Background and Aim

Among Streptococcus suis serotypes, S. suis serotype 2 is the most significant serotype that causes serious diseases in pigs and humans worldwide. The present study aimed to estimate the global prevalence of S. suis serotype 2 isolated from pigs, determine its trend, and explore the factors associated with this serotype.

Materials and Methods

We retrieved relevant published studies from PubMed, Scopus, and the Web of Science. The retrieved citations were screened for possible inclusion. Relevant data were then extracted from the included studies. The random-effects model was used for all meta-analyses. A subgroup meta-analysis was used to assess the heterogeneity of the prevalence for four characteristics (continents, sampling organs, reporting unit, and pig's health status). A cumulative meta-analysis was performed to determine the cumulative prevalence over time. Meta-regression analysis was used to determine the trend of pooled prevalence of S. suis serotype 2 over time.

Results

Of 600 articles retrieved, 36 studies comprising a total sample size of 6939 isolates or samples from 16 countries of four continents were included for meta-analysis. The pooled prevalence of S. suis serotype 2 isolated from pigs was 13.6% (95% confidence interval [CI], 10.7%-17.1%), with high heterogeneity among the included studies (Cochran's Q, 431.6; p < 0.001; I2 = 91.9%; Table-1). No statistical significance was observed among subgroups of the four characteristics examined. However, the pooled prevalence of S. suis serotype 2 was as high as 16.0% (95% CI, 12.5%-20.3%; n = 16) in diseased pigs compared with 9.9% (95% CI, 5.6%-17.0%; n = 15) in healthy pigs. The pooled prevalence of S. suis serotype 2 isolated from pigs did not significantly decrease over time [regression coefficient = -0.020 (95% CI, 0.046-0.006, p = 0.139)]. The pooled prevalence of S. suis serotype 2 isolated from pigs fluctuated slightly between 13.2% and 17.8% from 2007 to 2023, although the pooled prevalence gradually decreased from 30.6% in 1987 to over 20% in 2003.

Conclusion

The global prevalence of S. suis serotype 2 isolated from pigs was estimated to be 13.6% (approximately 10% in healthy pigs and around 16% in diseased pigs). S. suis serotype 2 isolated from pigs did not change significantly over time. These results indicate that S. suis serotype 2 remains a problem for the pig industry and poses a threat to human health.

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.

Invasive Streptococcus suis isolated in Spain contain a highly promiscuous and dynamic resistome

Introduction

Streptococcus suis is a major pathogen for swine and human. Here we aimed to know the rates of antimicrobial resistance (AMR) in invasive S. suis isolates recovered along Spain between 2016 - 2021 and elucidate their genetic origin.

Methods

Antibiotic susceptibility testing was performed for 116 isolates of different genetic backgrounds and geographic origins against 18 antibiotics of 9 families. The association between AMR and genotypes and the origin of the isolates were statistically analyzed using Pearson´s chi-square test and the likelihood ratio. The antimicrobial resistant genes were identified by whole genome sequencing analysis and PCR screenings.

Results

High AMR rates (>80%) were detected for tetracyclines, spectinomycin, lincosamides, and marbofloxacin, medium (20-40%) for sulphonamides/trimethoprim, tiamulin, penicillin G, and enrofloxacin, and low (< 20%) for florfenicol, and four additional β-lactams. The occurrence of multidrug resistance was observed in 90% of isolates. For certain antibiotics (penicillin G, enrofloxacin, marbofloxacin, tilmicosin, and erythromycin), AMR was significantly associated with particular sequence types (STs), geographic regions, age of pigs, and time course. Whole genome sequencing comparisons and PCR screenings identified 23 AMR genes, of which 19 were previously reported in S. suis (aph(3')-IIIa, sat4, aadE, spw, aac(6')-Ie-aph(2'')-Ia, fexA, optrA, erm(B), mef(A/E), mrs(D), mph(C), lnu(B), lsa(E), vga(F), tet(M), tet(O), tet(O/W/32/O), tet(W)), and 4 were novel (aph(2'')-IIIa, apmA, erm(47), tet(T)). These AMR genes explained the AMR to spectinomycin, macrolides, lincosamides, tiamulin, and tetracyclines. Several genes were located on mobile genetic elements which showed a variable organization and composition. As AMR gene homologs were identified in many human and animal pathogens, the resistome of S. suis has a different phylogenetic origin. Moreover, AMR to penicillin G, fluoroquinolones, and trimethoprim related to mutations in genes coding for target enzymes (pbp1a, pbp2b, pbp2x, mraY, gyrA, parC, and dhfr). Bioinformatic analysis estimated traits of recombination on target genes, also indicative of gene transfer events.

Conclusions

Our work evidences that S. suis is a major contributor to AMR dissemination across veterinary and human pathogens. Therefore, control of AMR in S. suis should be considered from a One Health approach in regions with high pig production to properly tackle the issue of antimicrobial drug resistance.

A CRISPR-Cas12a-based platform facilitates the detection and serotyping of Streptococcus suis serotype 2

Streptococcus suis serotype 2 is an economically important zoonotic pathogen that causes septicemia, arthritis, and meningitis in pigs and humans. S. suis serotype 2 is responsible for substantial economic losses to the swine industry and poses a serious threat to public health, and accurate and rapid detection is important for the prevention and control of epidemic disease. In this study, we developed a high-fidelity detection and serotyping platform for S. suis serotype 2 based on recombinase polymerase amplification (RPA) and a clustered regularly interspaced short palindromic repeat (CRISPR)-Cas12a system called Cards-SSJ/K. Cards-SSJ had a detection limit of 10 CFU, takes <60 min, and no cross-reaction was found with other S. suis serotypes, closely related Streptococcus spp., or common pig pathogens, and Cards-SSK could differentiate serotype 2 from serotype 1/2. Results from Cards-SSJ and qPCR were equivalent in detecting S. suis serotype 2 in tissue samples. Analysis indicated that despite a relatively high reagent cost compared to PCR and qPCR, Cards-SSJ was less time-consuming and had low requirements for equipment and personnel. Thus, it is an excellent method for point-of-care detection for S. suis serotype 2.

Pharmacokinetics and Pharmacodynamics of Florfenicol in Plasma and Synovial Fluid of Pigs at a Dose of 30 mg/kgbw Following Intramuscular Administration

A major problem of our time is the ever-increasing resistance to antimicrobial agents in bacterial populations. One of the most effective ways to prevent these problems is to target antibacterial therapies for specific diseases. In this study, we investigated the in vitro effectiveness of florfenicol against S. suis, which can cause severe arthritis and septicemia in swine herds. The pharmacokinetic and pharmacodynamic properties of florfenicol in porcine plasma and synovial fluid were determined. After a single intramuscular administration of florfenicol at 30 mg/kg_bw, the AUC_0-∞ was 164.45 ± 34.18 µg/mL × h and the maximum plasma concentration was 8.15 ± 3.11 µg/mL, which was reached in 1.40 ± 0.66 h, whereas, in the synovial fluid, these values were 64.57 ± 30.37 µg/mL × h, 4.51 ± 1.16 µg/mL and 1.75 ± 1.16 h, respectively. Based on the MIC values of the 73 S. suis isolates tested, the MIC₅₀ and MIC₉₀ values were 2 µg/mL and 8 µg/mL, respectively. We successfully implemented a killing-time curve in pig synovial fluid as a matrix. Based on our findings, the PK/PD breakpoints of the bacteriostatic (E = 0), bactericidal (E = -3) and eradication (E = -4) effects of florfenicol were determined and MIC thresholds were calculated, which are the guiding indicators for the treatment of these diseases. The AUC_24h/MIC values for bacteriostatic, bactericidal and eradication effects were 22.22 h, 76.88 h and 141.74 h, respectively, in synovial fluid, and 22.42 h, 86.49 h and 161.76 h, respectively, in plasma. The critical MIC values of florfenicol against S. suis regarding bacteriostatic, bactericidal and eradication effects in pig synovial fluid were 2.91 ± 1.37 µg/mL, 0.84 ± 0.39 µg/mL and 0.46 ± 0.21 µg/mL, respectively. These values provide a basis for further studies on the use of florfenicol. Furthermore, our research highlights the importance of investigating the pharmacokinetic properties of antibacterial agents at the site of infection and the pharmacodynamic properties of these agents against different bacteria in different media.

Epidemiological and genomic analyses of human isolates of Streptococcus suis between 2005 and 2021 in Shenzhen, China

Streptococcus suis (S. suis) is an important food-borne zoonotic pathogen that causes swine streptococcosis, which threatens human health and brings economic loss to the swine industry. Three-quarters of human S. suis infections are caused by serotype 2. A retrospective analysis of human S. suis cases in Shenzhen, a megacity in China, with high pork consumption, between 2005 and 2021 was conducted to understand its genomic epidemiology, pathogen virulence, and drug resistance characteristics. The epidemiological investigation showed that human cases of S. suis in Shenzhen were mainly associated with people who had been in close contact with raw pork or other swine products. Whole-genome sequence analysis showed that 33 human isolates in Shenzhen were dominated by serotype 2 (75.76%), followed by serotype 14 (24.24%), and the most prevalent sequence types (STs) were ST7 (48.48%) and ST1 (39.40%). ST242 (9.09%) and ST25 (3.03%), which were rarely reported, were also found. Phylogenetic analysis showed that the Shenzhen human isolates had close genetic relatedness to isolates from Guangxi (China), Sichuan (China), and Vietnam. We found a new 82 KB pathogenicity island (PAI) in the serotype 2 isolate that may play a role in sepsis. Similarly, a serotype 14 isolate, containing 78 KB PAI, was isolated from a patient presenting with streptococcal toxic shock syndrome (STSLS) who subsequently died. Multi-drug resistance (MDR) was high in human isolates of S. suis from Shenzhen. Most human isolates were resistant to tetracycline, streptomycin, erythromycin, and clindamycin, and 13 isolates had intermediate resistance to penicillin. In conclusion, swine importation from Guangxi, Sichuan, and Vietnam should be more closely monitored, and the use of antibiotics limited to reduce the potential for antimicrobial resistance (AMR).

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.

Metabolomics and proteomics analyses revealed mechanistic insights on the antimicrobial activity of epigallocatechin gallate against Streptococcus suis

Streptococcus suis (S. suis) is a highly virulent zoonotic pathogen and causes severe economic losses to the swine industry worldwide. Public health security is also threatened by the rapidly growing antimicrobial resistance in S. suis. Therefore, there is an urgent need to develop new and safe antibacterial alternatives against S. suis. The green tea polyphenol epigallocatechin gallate (EGCG) with a number of potential health benefits is known for its antibacterial effect; however, the mechanism of its bactericidal action remains unclear. In the present, EGCG at minimal inhibitory concentration (MIC) showed significant inhibitory effects on S. suis growth, hemolytic activity, and biofilm formation, and caused damage to S. suis cells in vitro. EGCG also reduced S. suis pathogenicity in Galleria mellonella larvae in vivo. Metabolomics and proteomics analyses were performed to investigate the underlying mechanism of antibacterial activity of EGCG at MIC. Many differentially expressed proteins involved in DNA replication, synthesis of cell wall, and cell membrane, and virulence were down-regulated after the treatment of S. suis with EGCG. EGCG not only significantly reduced the hemolytic activity of S. suis but also down-regulated the expression of suilysin (Sly). The top three shared KEGG pathways between metabolomics and proteomics analysis were ABC transporters, glycolysis/gluconeogenesis, and aminoacyl-tRNA biosynthesis. Taken together, these data suggest that EGCG could be a potential phytochemical compound for treating S. suis infection.