Genetic analysis of Streptococcus suis isolates from wild rabbits

From Farm to Fork: Streptococcus suis as a Model for the Development of Novel Phage-Based Biocontrol Agents

Bacterial infections of livestock threaten the sustainability of agriculture and public health through production losses and contamination of food products. While prophylactic and therapeutic application of antibiotics has been successful in managing such infections, the evolution and spread of antibiotic-resistant strains along the food chain and in the environment necessitates the development of alternative or adjunct preventive and/or therapeutic strategies. Additionally, the growing consumer preference for “greener” antibiotic-free food products has reinforced the need for novel and safer approaches to controlling bacterial infections. The use of bacteriophages (phages), which can target and kill bacteria, are increasingly considered as a suitable measure to reduce bacterial infections and contamination in the food industry. This review primarily elaborates on the recent veterinary applications of phages and discusses their merits and limitations. Furthermore, using Streptococcus suis as a model, we describe the prevalence of prophages and the anti-viral defence arsenal in the genome of the pathogen as a means to define the genetic building blocks that are available for the (synthetic) development of phage-based treatments. The data and approach described herein may provide a framework for the development of therapeutics against an array of bacterial pathogens.

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.

Streptococcus suis in Brazil: Genotypic, Virulence, and Resistance Profiling of Strains Isolated from Pigs between 2001 and 2016

Streptococcus suis remains an important challenge for the worldwide swine industry. Considering that Brazil is a major pork producer and exporter, proper monitoring of the pathogen and resistance rates are required. We present here the characterization of Brazilian S. suis strains isolated over a 15 year period by pulsed-field gel electrophoresis (PFGE) typing, capsular, virulence, and antimicrobial resistance profiling. Serotype prevalence revealed a predominance of serotype 2/½ followed by 3, 7, 1/14, 6, 8, 18, 28, and 27; the latter had not yet been reported in Brazil. Resistance profiling enabled the differentiation of nine profiles presenting resistance to three and up to eight antimicrobial classes. Even though an association between the most resistant strains and isolation year starting from 2009 was observed, a high frequency of multidrug-resistant strains isolated from 2001 to 2003 was also detected. This suggests that despite the isolation period, S. suis strains already presented high resistance selection pressure. A slight association of serotype 2/½ with some virulence profiles and PFGE pulsotypes was also identified. Nevertheless, no clonal dispersion or persistency of clones over the analyzed years and herds was detected.

Antimicrobial Resistance in Streptococcus spp

The genus Streptococcus includes Gram-positive organisms shaped in cocci and organized in chains. They are commensals, pathogens, and opportunistic pathogens for humans and animals. Most Streptococcus species of veterinary relevance have a specific ecological niche, such as S. uberis, which is almost exclusively an environmental pathogen causing bovine mastitis. In contrast, S. suis can be considered as a true zoonotic pathogen, causing specific diseases in humans after contact with infected animals or derived food products. Finally, Streptococcus species such as S. agalactiae can be sporadically zoonotic, even though they are pathogens of both humans and animals independently. For clarification, a short taxonomical overview will be given here to highlight the diversity of streptococci that infect animals. Several families of antibiotics are used to treat animals for streptococcal infections. First-line treatments are penicillins (alone or in combination with aminoglycosides), macrolides and lincosamides, fluoroquinolones, and tetracyclines. Because of the selecting role of antibiotics, resistance phenotypes have been reported in streptococci isolated from animals worldwide. Globally, the dynamic of resistance acquisition in streptococci is slower than what is experienced in Enterobacteriaceae, probably due to the much more limited horizontal spread of resistance genes. Nonetheless, transposons or integrative and conjugative elements can disseminate resistance determinants among streptococci. Besides providing key elements on the prevalence of resistance in streptococci from animals, this article will also largely consider the mechanisms and molecular epidemiology of the major types of resistance to antimicrobials encountered in the most important streptococcal species in veterinary medicine.

Streptococcus suis - The "Two Faces" of a Pathobiont in the Porcine Respiratory Tract

Streptococcus (S.) suis is a frequent early colonizer of the upper respiratory tract of pigs. In fact, it is difficult to find S. suis-free animals under natural conditions, showing the successful adaptation of this pathogen to its porcine reservoir host. On the other hand, S. suis can cause life-threatening diseases and represents the most important bacterial cause of meningitis in pigs worldwide. Notably, S. suis can also cause zoonotic infections, such as meningitis, septicemia, endocarditis, and other diseases in humans. In Asia, it is classified as an emerging zoonotic pathogen and currently considered as one of the most important causes of bacterial meningitis in adults. The “two faces” of S. suis, one of a colonizing microbe and the other of a highly invasive pathogen, have raised many questions concerning the interpretation of diagnostic detection and the definition of virulence. Thus, one major research challenge is the identification of virulence-markers which allow differentiation of commensal and virulent strains. This is complicated by the high phenotypic and genotypic diversity of S. suis, as reflected by the occurrence of (at least) 33 capsular serotypes. In this review, we present current knowledge in the context of S. suis as a highly diverse pathobiont in the porcine respiratory tract that can exploit disrupted host homeostasis to flourish and promote inflammatory processes and invasive diseases in pigs and humans.

Genomic comparisons of Streptococcus suis serotype 9 strains recovered from diseased pigs in Spain and Canada

Streptococcus suis is one of the most important bacterial pathogens in the porcine industry and also a zoonotic agent. Serotype 9 is becoming one of the most prevalent serotypes within the S. suis population in certain European countries. In the present study, serotype 9 strains isolated from a country where infection due to this serotype is endemic (Spain), were compared to those recovered from Canada, where this serotype is rarely isolated from diseased pigs. For comparison purposes, strains from Brazil and the only strain isolated from a human case, in Thailand, were also incorporated. Firstly, sequence types (STs) were obtained followed by detection of putative virulence factors. Phylogenetic trees were constructed using the non-recombinant single nucleotide polymorphisms from core genomes of tested strains. Most Spanish strains were either ST123 or ST125, whereas Canadian strains were highly heterogeneous. However, the distribution of putative virulence factors was similar in both groups of strains. The fact that ST16 strains harbored more putative virulence genes and shared greater similarity with the genome of human serotype 2 strains suggests that they present a higher zoonotic and virulence potential than those from Canada and Spain. More than 80% of the strains included in this study carried genes associated with resistance to tetracycline, lincosamides and macrolides. Serotype 9 strains may be nearly 400 years old and have evolved in parallel into 2 lineages. The rapid population expansion of dominant lineage 1 occurred within the last 40 years probably due to the rapid development of the porcine industry.

Genotyping and investigating capsular polysaccharide synthesis gene loci of non-serotypeable Streptococcus suis isolated from diseased pigs in Canada

Streptococcus suis (S. suis) is an important swine pathogen and an emerging zoonotic agent. Most clinical S. suis strains express capsular polysaccharides (CPS), which can be typed by antisera using the coagglutination test. In this study, 79 S. suis strains recovered from diseased pigs in Canada and which could not be typed using antisera were further characterized by capsular gene typing and sequencing. Four patterns of cps locus were observed: (1) fifteen strains were grouped into previously reported serotypes but presented several mutations in their cps loci, when compared to available data from reference strains; (2) seven strains presented a complete deletion of the cps locus, which would result in an inability to synthesize capsule; (3) forty-seven strains were classified in recently described novel cps loci (NCLs); and (4) ten strains carried novel NCLs not previously described. Different virulence gene profiles (based on the presence of mrp, epf, and/or sly) were observed in these non-serotypeable strains. This study provides further insight in understanding the genetic characteristics of cps loci in non-serotypeable S. suis strains recovered from diseased animals. When using a combination of the previously described 35 serotypes and the complete NCL system, the number of untypeable strains recovered from diseased animals in Canada would be significantly reduced.

Novel Capsular Polysaccharide Loci and New Diagnostic Tools for High-Throughput Capsular Gene Typing in Streptococcus suis

Streptococcus suis is an important pathogen of pigs and may cause serious disease in humans. Serotyping is an important tool for detection and epidemiological studies of S. suis Thirty-three reference serotypes and nine novel cps loci (NCLs) are recognized in S. suis To gain a better understanding of the prevalence and genetic characteristics of NCLs, we investigated the serotype identity of 486 isolates isolated between 2013 and 2015 in China by capsular gene typing methods. Two hundred seventy-six isolates carried NCLs belonging to 16 groups, 8 of which appear to have not been reported previously. These isolates showed autoagglutination, polyagglutination, or nonagglutination with reference antisera and thus were nonserotypeable. Almost all isolates carrying the unknown NCLs were encapsulated, with various capsular thicknesses, indicating that they are most likely novel serotypes. To simultaneously identify the currently recognized 17 NCLs, an 18-plex detection system using the Luminex xTAG universal array technology was developed. Our data also provide valuable genetic information for monitoring the variations within NCLs by investigating the genetic characteristics of different subtypes within NCLs.

IMPORTANCE

Nonserotypeable Streptococcus suis isolates have been reported in many studies, and 9 novel cps loci (NCLs) have already been identified in nonserotypeable isolates. Moreover, novel cps loci are continually being found. The main purpose of this study was to investigate the prevalence and characteristics of NCLs in S. suis isolates recovered between 2013 and 2015 in China. This study provides valuable genetic information for monitoring the variations within NCLs. Meanwhile, a fast and cost-effective 18-plex detection system that can simultaneously identify the currently recognized 17 NCLs was developed in this study. This system will serve as a valuable tool for detecting known and identifying additional novel cps loci among nonserotypeable S. suis isolates.

Screening of virulence-associated genes as a molecular typing method for characterization of Streptococcus suis isolates recovered from wild boars and pigs

Streptococcus suis is an important zoonotic pathogen associated with a wide range of diseases in pigs, but has also been isolated from wild animals such as rabbits and wild boars. In the current study, 126 S. suis isolates recovered from pigs (n = 85) and wild boars (n = 41) were tested by polymerase chain reaction (PCR) for the presence of nine virulence-associated genes. S. suis isolates from wild boars were differentiated by the lower detection rates of the epf, sly, mrp, sao and dltA genes (0%, 2.4%, 2.4%, 4.8% and 21.9%, respectively) compared with the isolates from pigs (56.5%, 75.3%, 56.5%, 88.2.0% and 88.2%, respectively). The differences in the content of these virulence-associated genes were statistically significant (P < 0.05). There was a correlation between the variants saoM and saoL and serotypes 2 and 9, respectively (P < 0.05). Isolates were classified into 31 virulence-associated gene profiles (VPs). Ten VPs were detected among wild boar isolates and 22 VPs among pig isolates, with only two VPs common to wild boars and pigs. The predominant VPs among isolates from wild boars (VP1, VP7) were different from those observed in pig isolates (VP16 and VP26). VP16 was detected exclusively in clinical pig isolates of serotype 9 and VP26 was detected in 71.4% of the serotype 2 clinical pig isolates. Further multilocus sequence typing (MLST) analysis showed a significant correlation association between certain VPs and STs (VP16 and VP17 with ST123 and ST125 and VP26 with ST1). In conclusion, the current study showed that combination of virulence-associated gene profiling and MLST analysis may provide more information of the relatedness of the S. suis strains from different animal species that could be useful for epidemiological purposes.

Eight Novel Capsular Polysaccharide Synthesis Gene Loci Identified in Nontypeable Streptococcus suis Isolates

Streptococcus suis is an important pathogen of pigs and may cause serious disease in humans. Serotyping is one of the important diagnostic tools and is used for the epidemiological study of S. suis. Nontypeable S. suis strains have been reported in many studies; however, the capsular polysaccharide (CPS) synthesis cps loci of nontypeable strains have not been analyzed. In this study, we investigated the genetic characteristics of cps loci in 78 nontypeable strains isolated from healthy pigs. Eight novel cps loci (NCLs) were found, and all of them were located between the orfZ-orfX region and the glf gene. All NCLs possess the wzy and wzx genes, strongly suggesting that the CPSs of these NCLs were synthesized using the Wzx/Wzy-dependent pathway. The cps genes found in the 78 isolates were assigned to 96 homology groups (HGs), 55 of which were NCL specific. The encapsulation of the 78 isolates was also examined using transmission electron microscopy. Fifty-three isolates were found to have a capsule, and these were of varied thicknesses. Our data enhance our understanding of the cps gene cluster diversity of nontypeable S. suis strains and provide insight into the evolution of the S. suis capsular genes.

Characterization of multi-drug tolerant persister cells in Streptococcus suis

Background

Persister cells constitute a subpopulation of dormant cells within a microbial population which are genetically identical but phenotypically different to regular cells. Notably, persister cells show an elevated tolerance to antimicrobial agents. Thus, they are considered to represent a microbial ‘bet-hedging’ strategy and are of particular importance in pathogenic bacteria.

Results

We studied the ability of the zoonotic pathogen Streptococcus (S.) suis to form multi-drug tolerant variants and identified persister cells dependent on the initial bacterial growth phase. We observed lower numbers of persisters in exponential phase cultures than in stationary growth phase populations. S. suis persister cells showed a high tolerance to a variety of antibiotics, and the phenotype was not inherited as tested with four passages of S. suis populations. Furthermore, we provide evidence that the persister phenotype is related to expression of genes involved in general metabolic pathways since we found higher numbers of persister cells in a mutant strain defective in the catabolic arginine deiminase system as compared to its parental wild type strain. Finally, we observed persister cell formation also in other S. suis strains and pathogenic streptococcal species.

Conclusions

Taken together, this is the first study that reports multi-drug tolerant persister cells in the zoonotic pathogen S. suis.

Characterisation of Streptococcus suis isolates from wild boars (Sus scrofa)

Wild boar are widely distributed throughout the Iberian Peninsula and can carry potentially virulent strains of Streptococcus suis. The objective of this study was to determine the prevalence of S. suis in wild boars from two large geographical regions of Spain. Serotypes 1, 2, 7 and 9 identified were further genetically characterised by virulence-associated genotyping, pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) to determine the population structure of S. suis carried by these animals. Streptococcus suis was isolated from 39.1% of the wild boars examined: serotype 9 was the most frequently isolated (12.5%), followed by serotype 1 (2.5%). Serotype 2 was rarely isolated (0.3%). Eighteen additional serotypes were identified indicating wide diversity of this pathogen within the wild boar population. This heterogeneity was confirmed by PFGE and MLST analyses and the majority of isolates exhibited the virulence-associated genotype mrp-/epf-/sly-. The results of this study highlight that the carriage of S. suis by wild boars is commonplace. However, MLST data indicate that these isolates are not related to prevalent clonal complexes ST1, ST16, ST61 and ST87 typically associated with infection of pigs or humans in Europe.