Genome characterization and population genetic structure of the zoonotic pathogen, Streptococcus canis

Antimicrobial resistance of Streptococcus dysgalactiae, Streptococcus agalactiae, and Streptococcus canis in quarter milk samples from Bavaria, Southern Germany, between 2012 and 2022

The objective of this study was to analyze the in vitro antimicrobial resistance (AMR) of Streptococcus (Sc.) dysgalactiae, Sc. agalactiae, and Sc. canis over a 10-year period from 2012 to 2022 against the most commonly used antimicrobial agents. For this purpose, all quarter milk samples (QMS) submitted to the milk laboratory of the Bavarian Animal Health Service (TGD) were analyzed. Each QMS was tested using the California Mastitis Test (CMT) and categorized as negative (N), subclinical (S), or clinical (C) mastitis if the milk character was abnormal. Samples with Sc. dysgalactiae, Sc. agalactiae, or Sc. canis were included and a subset of isolates were further tested for in vitro antimicrobial resistance by breakpoint analysis with broth microdilution. Sc. dysgalactiae (61%, n = 65,750) was the most abundant pathogen among those 3 species, followed by Sc. agalactiae (28%, n = 30,486), and Sc. canis (11%, n = 11,336). All 3 species showed the highest resistance to the same 4 antimicrobial agents: erythromycin, marbofloxacin, pirlimycin, and cefalexin/kanamycin with varying degrees of resistance. Throughout the study period, Sc. dysgalactiae, Sc. agalactiae, and Sc. canis were largely susceptible to the remaining antimicrobial agents tested (penicillin, amoxicillin-clavulanate, oxacillin, cefazolin, cefoperazone, cefquinome). Only less than 14% of isolates of Sc. dysgalactiae and Sc. canis were resistant against any of the antimicrobials tested. Sc. agalactiae was the species with the highest percentage of resistant isolates. While the percentage of resistant isolates from Sc. canis and Sc. dysgalactiae decreased, the percentage of resistant Sc. agalactiae isolates increased since 2017. In summary, most isolates were not resistant to the most commonly used antimicrobial agents for mastitis therapy, including β-lactam antibiotics and penicillin should remain the first-choice therapy against streptococcal mastitis.

Acute Haematogenous Revision Total Knee Arthroplasty Infection by Streptococcus canis Treated by Debridement, Antibiotics, and Implant Retention: A Case Report

Prosthetic joint infections (PJIs) are one of the most feared complications by orthopaedic surgeons. Haematogenous PJI represents an important part of PJI cases. Streptococcus canis is an extremely rare cause of haematogenous PJI and its medical and surgical treatment and prognosis are not well established. We present a 79-year-old female patient who had a revision total knee arthroplasty (rTKA) surgery three years before. She was admitted to the hospital referring to three days of knee pain, restricted range of motion, and fever. Blood tests demonstrated leukocyte and C-reactive protein elevation. Joint fluid aspiration showed elevated white blood cell count with a high neutrophil differential and its conventional culture was positive for Streptococcus canis. She did not have pets but she took care of her daughter's dog. An acute haematogenous infection of the rTKA was diagnosed and treated with debridement, antibiotics (eight weeks of IV ceftriaxone), and implant retention (DAIR). After one year, the patient remains clinically asymptomatic without changes on X-rays and with normal serum levels of inflammatory blood markers. Streptococcus canis has to be kept in mind as a possible cause of haematogenous TKA infection in patients who have contact with domestic pets and patients should be asked for this contact. We recommend DAIR as a viable treatment option for this type of infection, which may show excellent results.

Multiple Drug Resistant Streptococcus Strains-An Actual Problem in Pig Farms in Western Romania

Streptococci are a type of bacteria that can cause severe illnesses in humans and animals. Some typical species like S. suis, or atypical species like S. porcinus and, S. dysgalactiae subsp. dysgalactiae, can cause infections like septicemia, meningitis, endocarditis, arthritis, and septic shock. S. suis is considered a newly emerging zoonotic pathogen. Although human streptococcal infection outbreaks are rare, it is appropriate to review the main streptococcal species isolated in pig farms in western Romania, due to the high degree of antibiotic resistance among most isolates commonly used in human treatment. This study examines the resistance patterns of these isolates over 5 years (2018-2023). The research investigated the antimicrobial susceptibility of 267 strains of Streptococcus spp. isolated from pigs, primarily from lung and brain tissues. This report is the first to describe the distribution of atypical Streptococcus species (SDSE, S. porcinus, S. hyovaginalis, S. pluranimalium, S. canis) in Romania, as well as the antibiotic resistance profile of these potentially zoonotic species. It is important to re-evaluate and consider the high rates of resistance of S. suis to tetracyclines, lincosamides, macrolides, and aminoglycosides, as well as the high recovery rates of S. suis from the lungs and brain when treating swine diseases.

New variant strain of Streptococcus canis with Lancefield group C isolated from canine otitis externa

Every basic course in microbiology teaches us, Streptococcus canis always tests positive for Lancefield group G. Surprisingly, we identified a strain of S. canis with Lancefield group C, cultured from a dog with otitis externa after lateral ear canal resection. Whole genome sequencing data and analysis points towards a horizontal gene transfer event between S. canis and S. dysgalactiae. Although these species are closely related, gene transfer in this region of the genome of S. canis has not been described before. The value of technologies as MALDI-TOF MS and sequencing in microbiological diagnostics will grow as more diverse streptococci arise that do not always conform anymore to the classical Lancefield group typing.

Bacteriophage Therapy to Control Bovine Mastitis: A Review

Bovine mastitis is a polymicrobial disease characterised by inflammation of the udders of dairy and beef cattle. The infection has huge implications to health and welfare of animals, impacting milk and beef production and costing up to EUR 32 billion annually to the dairy industry, globally. Bacterial communities associated with the disease include representative species from Staphylococcus, Streptococcus, Enterococcus, Actinomyces, Aerococcus, Escherichia, Klebsiella and Proteus. Conventional treatment relies on antibiotics, but antimicrobial resistance, declining antibiotic innovations and biofilm production negatively impact therapeutic efficacy. Bacteriophages (phages) are viruses which effectively target and lyse bacteria with extreme specificity and can be a valuable supplement or replacement to antibiotics for bovine mastitis. In this review, we provide an overview of the etiology of bovine mastitis, the advantages of phage therapy over chemical antibiotics for the strains and research work conducted in the area in various model systems to support phage deployment in the dairy industry. We emphasise work on phage isolation procedures from samples obtained from mastitic and non-mastitic sources, characterisation and efficacy testing of single and multiple phages as standalone treatments or adjuncts to probiotics in various in vitro, ex vivo and in vivo bovine mastitis infection models. Furthermore, we highlight the areas where improvements can be made with focus on phage cocktail optimisation, formulation, and genetic engineering to improve delivery, stability, efficacy, and safety in cattle. Phage therapy is becoming more attractive in clinical medicine and agriculture and thus, could mitigate the impending catastrophe of antimicrobial resistance in the dairy sector.

Streptococcus canis prevalence on the normal and abnormal ocular surface of dogs referred for ophthalmic disease in Canada

Streptococcus canis is a beta-haemolytic, Gram-positive cocci commonly identified on the canine ocular surface under both healthy and diseased conditions. The objective of the study was to determine the prevalence of S. canis on the normal and abnormal ocular surface of a canine ophthalmology referral population in Canada, and to investigate potential clinical aspects that may be associated with its presence. Included were 59 dogs (118 eyes) with unilateral or bilateral ocular disease diagnosed at the time of conjunctival sampling. A real-time PCR specific for S. canis was standardized for use with conjunctival swabs. Total DNA was extracted from 118 samples and used as template for the diagnostic assay. Samples were considered positive if amplification was detected and dissociation temperature matched a positive control. Signalment and other clinical data were also collected at the time of sampling. Of the 118 eyes sampled, 8 tested positive for S. canis (6.8%). No association between the detection of S. canis and breed, cephalic conformation, sex, age, use of ophthalmic antibiotics or other topical medications, ophthalmic diagnosis, use of systemic antibiotics or other systemic medications, or systemic diagnosis was identified. In conclusion, S. canis may be present on the ocular surface of dogs at a higher rate than previously reported. It is suggested that this may be linked to the use of PCR for pathogen detection instead of culture.

New Insights on Streptococcus dysgalactiae subsp. dysgalactiae Isolates

Streptococcus dysgalactiae subsp. dysgalactiae (SDSD) has been considered a strict animal pathogen. Nevertheless, the recent reports of human infections suggest a niche expansion for this subspecies, which may be a consequence of the virulence gene acquisition that increases its pathogenicity. Previous studies reported the presence of virulence genes of Streptococcus pyogenes phages among bovine SDSD (collected in 2002-2003); however, the identity of these mobile genetic elements remains to be clarified. Thus, this study aimed to characterize the SDSD isolates collected in 2011-2013 and compare them with SDSD isolates collected in 2002-2003 and pyogenic streptococcus genomes available at the National Center for Biotechnology Information (NCBI) database, including human SDSD and S. dysgalactiae subsp. equisimilis (SDSE) strains to track temporal shifts on bovine SDSD genotypes. The very close genetic relationships between humans SDSD and SDSE were evident from the analysis of housekeeping genes, while bovine SDSD isolates seem more divergent. The results showed that all bovine SDSD harbor Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas IIA system. The widespread presence of this system among bovine SDSD isolates, high conservation of repeat sequences, and the polymorphism observed in spacer can be considered indicators of the system activity. Overall, comparative analysis shows that bovine SDSD isolates carry speK, speC, speL, speM, spd1, and sdn virulence genes of S. pyogenes prophages. Our data suggest that these genes are maintained over time and seem to be exclusively a property of bovine SDSD strains. Although the bovine SDSD genomes characterized in the present study were not sequenced, the data set, including the high homology of superantigens (SAgs) genes between bovine SDSD and S. pyogenes strains, may indicate that events of horizontal genetic transfer occurred before habitat separation. All bovine SDSD isolates were negative for genes of operon encoding streptolysin S, except for sagA gene, while the presence of this operon was detected in all SDSE and human SDSD strains. The data set of this study suggests that the separation between the subspecies "dysgalactiae" and "equisimilis" should be reconsidered. However, a study including the most comprehensive collection of strains from different environments would be required for definitive conclusions regarding the two taxa.

A Comparative Study on Changes in Total and Differential Milk Cell Counts, Activity, and Expression of Milk Phagocytes of Healthy and Mastitic Indigenous Sahiwal Cows

Milk somatic cell counts (SCCs) have been used as a gold standard to monitor mammary health as well as an indicator of raw milk quality. The present work was undertaken to compare the changes in the milk SCC, milk differential leukocyte counts (DLCs), phagocytic activity (PA) of milk neutrophils and macrophages (by nitroblue tetrazolium assay), extracellular trap formation (PicoGreen assay) and mRNA expression of various genes in milk neutrophils and macrophages (reverse transcription–polymerase chain reaction), and milk plasma cortisol concentration (enzyme-linked immunosorbent assay) in healthy, subclinical mastitis (SCM), and clinical mastitis (CM) cows. Milk was collected from healthy, SCM, and CM cows grouped based on their SCCs and California mastitis test with eight cows in each group. Milk SCC was estimated by SCC counter, and DLC was done after staining the milk slide under a microscope at 100×. Total SCCs in healthy, SCM, and CM cows were on an average of 128.30, 300.3, and 694.40 × 10³ cells/mL, respectively. Milk DLCs indicated a lower percentage of macrophage and lymphocytes and a higher (p < 0.05) percentage of neutrophils in SCM and CM compared to healthy milk. The percentage of mature segmented neutrophils was lower, whereas immature band neutrophils were higher (p < 0.05) in the SCM and CM groups as compared to healthy cows. The viability, in vitro PA, and extracellular trap formation of neutrophils were lower (p < 0.05) in SCM and CM milk samples as compared to healthy samples. However, the PA of macrophage remained unchanged in all the studied groups. The relative mRNA expression of Toll-like receptors (TLR2, TLR4), myeloperoxidase, and interleukin 2α (IL-2α) receptor (CD25) were minimum in healthy samples and increased (p < 0.05) with the progress of mammary inflammation. However, CD44 decreased (p < 0.05), and CD62L remained unchanged in mastitis as compared to healthy cows. Plasma cortisol concentrations were higher (p < 0.05) in mastitis as compared to healthy cows and were negatively correlated with the number of milk macrophages and the functions of milk phagocytes. Estimation of total SCC, milk DLC, and activity of milk phagocytes is essential for effective control and prevention of incidence of mastitis in dairy cows.

An Outbreak of Subclinical Mastitis in a Dairy Herd Caused by a Novel Streptococcus canis Sequence Type (ST55)

Simple Summary

Although Streptococcus (S). canis is mainly isolated from carnivores, intramammary infection in dairy cows caused by this bacterium have been reported. Cats and dogs with access to the barn have been considered as the main source of these infections. Here, we report subclinical mastitis and substantially increased bulk milk somatic cell counts in a dairy herd. During a herd visit, management and hygiene practices were evaluated and data from the milk quality control program were retrieved. Furthermore, quarter milk samples, mucosal swabs from farm cats and a dog, and swabs from the milking unit were aseptically collected. The samples were examined bacteriologically, and S. canis was identified using conventional phenotypic methods and matrix-assisted laser desorption ionization time-of-flight mass spectrometry. Genetic relationships between S. canis isolates were determined by multilocus sequence typing, revealing that all S. canis isolates shared the same sequence type, presenting a new combination of alleles for which a new number (ST55) was assigned. As the most likely source of intramammary infection, a farmyard cat was identified. The concurrent treatment of all positive cows and the improvement of management (no further access of carnivores to the barn) lead to positive results, including a decreased somatic cell count.

Abstract

The present case report provides data on the phenotypic and genotypic properties of S. canis isolated from nine dairy cows with subclinical mastitis (SCC greater than 200,000 cells/mL in the quarter milk sample, no clinical signs) and from a cat living in the barn and reports the eradication of the pathogen from the herd with an automatic milking system. The isolates were identified using conventional bacteriology, matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) and genetic relationships were investigated by multilocus sequence typing (MLST). Udder health management and hygiene instructions comprised the removal of the carnivores from the barn, strict monitoring of milking hygiene and techniques to avoid new infections via the milking robot, with simultaneous therapy for all infected cows. Phenotypic and genotypic properties of all isolates were identical. MLST revealed a unique sequence type (ST55) and a farmyard cat was identified as the most likely source of the S. canis infection in cows. The simultaneous treatment of all infected cows and management and hygiene improvements lead to a decreased SCC within four weeks.

Streptococcal Infections in Marine Mammals

Marine mammals are sentinels for the marine ecosystem and threatened by numerous factors including infectious diseases. One of the most frequently isolated bacteria are beta-hemolytic streptococci. However, knowledge on ecology and epidemiology of streptococcal species in marine mammals is very limited. This review summarizes published reports on streptococcal species, which have been detected in marine mammals. Furthermore, we discuss streptococcal transmission between and adaptation to their marine mammalian hosts. We conclude that streptococci colonize and/or infect marine mammals very frequently, but in many cases, streptococci isolated from marine mammals have not been further identified. How these bacteria disseminate and adapt to their specific niches can only be speculated due to the lack of respective research. Considering the relevance of pathogenic streptococci for marine mammals as part of the marine ecosystem, it seems that they have been neglected and should receive scientific interest in the future.

Tackling Multidrug Resistance in Streptococci - From Novel Biotherapeutic Strategies to Nanomedicines

The pyogenic streptococci group includes pathogenic species for humans and other animals and has been associated with enduring morbidity and high mortality. The main reason for the treatment failure of streptococcal infections is the increased resistance to antibiotics. In recent years, infectious diseases caused by pyogenic streptococci resistant to multiple antibiotics have been raising with a significant impact to public health and veterinary industry. The rise of antibiotic-resistant streptococci has been associated to diverse mechanisms, such as efflux pumps and modifications of the antimicrobial target. Among streptococci, antibiotic resistance emerges from previously sensitive populations as result of horizontal gene transfer or chromosomal point mutations due to excessive use of antimicrobials. Streptococci strains are also recognized as biofilm producers. The increased resistance of biofilms to antibiotics among streptococci promote persistent infection, which comprise circa 80% of microbial infections in humans. Therefore, to overcome drug resistance, new strategies, including new antibacterial and antibiofilm agents, have been studied. Interestingly, the use of systems based on nanoparticles have been applied to tackle infection and reduce the emergence of drug resistance. Herein, we present a synopsis of mechanisms associated to drug resistance in (pyogenic) streptococci and discuss some innovative strategies as alternative to conventional antibiotics, such as bacteriocins, bacteriophage, and phage lysins, and metal nanoparticles. We shall provide focused discussion on the advantages and limitations of agents considering application, efficacy and safety in the context of impact to the host and evolution of bacterial resistance.

Streptococcus halichoeri: Comparative Genomics of an Emerging Pathogen

Streptococcus halichoeri is an emerging pathogen with a variety of host species and zoonotic potential. It has been isolated from grey seals and other marine mammals as well as from human infections. Beginning in 2010, two concurrent epidemics were identified in Finland, in fur animals and domestic dogs, respectively. The fur animals suffered from a new disease fur animal epidemic necrotic pyoderma (FENP) and the dogs presented with ear infections with poor treatment response. S. halichoeri was isolated in both studies, albeit among other pathogens, indicating a possible role in the disease etiologies. The aim was to find a possible common origin of the fur animal and dog isolates and study the virulence factors to assess pathogenic potential. Isolates from seal, human, dogs, and fur animals were obtained for comparison. The whole genomes were sequenced from 20 different strains using the Illumina MiSeq platform and annotated using an automatic annotation pipeline RAST. The core and pangenomes were formed by comparing the genomes against each other in an all-against-all comparison. A phylogenetic tree was constructed using the genes of the core genome. Virulence factors were assessed using the Virulence Factor Database (VFDB) concentrating on the previously confirmed streptococcal factors. A core genome was formed which encompassed approximately half of the genes in Streptococcus halichoeri. The resulting core was nearly saturated and would not change significantly by adding more genomes. The remaining genes formed the pangenome which was highly variable and would still evolve after additional genomes. The results highlight the great adaptability of this bacterium possibly explaining the ease at which it switches hosts and environments. Virulence factors were also analyzed and were found primarily in the core genome. They represented many classes and functions, but the largest single category was adhesins which again supports the marine origin of this species.

Immunodetection of Streptococcus uberis pathogen in raw milk

Streptococcus uberis is a major mastitis-causing environmental pathogen, which rapid immunodetection has not been possible due to the absence of specific anti-Str. uberis antibodies. Recently, a specific antibody against the Str. uberis adhesion molecule (SUAM) has been designed. In the present study, the specificity and affinity of this antibody towards SUAM antigenic region SAPVYLGVSTE and Str. uberis cells are characterized, using experimental and in silico bioinformatic methods. The selectivity studies and bioinformatic analyses revealed high specificity of the antibody towards Str. uberis. The K_d value of SAPVYLGVSTE/anti-Str. uberis antibody complex was 27 ± 6 nM, indicating the applicability of this antibody for the detection of Str. uberis. The anti-Str. uberis antibody was used as a specific biorecognition element of a biosensor for the detection of Str. uberis bacteria in phosphate buffer and in milk and these analyses took less than 20 min. The Str. uberis biosensor was also tested in the milk of cows suffering from mastitis and the obtained results were in good agreement with the conventional identification of this pathogen by microbiological plating.

Streptococcus canis Are a Single Population Infecting Multiple Animal Hosts Despite the Diversity of the Universally Present M-Like Protein SCM

Streptococcus canis is an animal pathogen which occasionally causes infections in humans. The S. canis M-like protein (SCM) encoded by the scm gene, is its best characterized virulence factor but previous studies suggested it could be absent in a substantial fraction of isolates. We studied the distribution and variability of the scm gene in 188 S. canis isolates recovered from companion animals (n = 152), wild animal species (n = 20), and humans (n = 14). Multilocus sequence typing, including the first characterization of wildlife isolates, showed that the same lineages are present in all animal hosts, raising the possibility of extensive circulation between species. Whole-genome analysis revealed that emm-like genes found previously in S. canis correspond to divergent scm genes, indicating that what was previously believed to correspond to two genes is in fact the same scm locus. We designed primers allowing for the first time the successful amplification of the scm gene in all isolates. Analysis of the scm sequences identified 12 distinct types, which could be divided into two clusters: group I (76%, n = 142) and group II (24%, n = 46) sharing little sequence similarity. The predicted group I SCM showed extensive similarity with each other outside of the N-terminal hypervariable region and a conserved IgG binding domain. This domain was absent from group II SCM variants found in isolates previously thought to lack the scm gene, which also showed greater amino acid variability. Further studies are necessary to elucidate the possible host interacting partners of the group II SCM variants and their role in virulence.

Analysis of the Type II-A CRISPR-Cas System in Streptococcus canis Isolated from Diseased Companion Animals and One Human Patient in Japan

We determined the whole-genome sequence (WGS) of Streptococcus canis strain TA4 harboring the M-like protein gene (scm); the strain was isolated from a human patient presenting with bacteremia. The potential of type II-A clustered regularly interspaced short palindromic repeats (CRISPR) array-based typing was evaluated, and the genetic relation was elucidated between spacer genogroups and scm prevalence and/or polymorphisms among the isolates from 19 diseased companion animals and the human patient. CRISPRFinder and CRISPRCasFinder detected the type II-A locus with the same repeat sequences in strain TA4 and another WGS of S. canis strain, isolated from a cow with mastitis. An optimized PCR-based amplification method was used to sequence the region covering the locus around the leader and terminal repeat sequences. Among the 20 isolates sequenced, 16 strains (including TA4) were identified with the CRISPR array. We conducted comparative analysis of the homologous spacer sequences and performed grouping based on the successive common ancestral spacer types. These 16 isolates were assigned to five genogroups (A to E) with scm being absent in genogroup A. We found a relationship between genogroups C and E and allele type 1 of the deduced M-like protein. These preliminary findings suggest the feasibility of CRISPR array-based typing and a genetic relation between the spacer genogroups and scm prevalence and/or polymorphisms in the isolates.

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.

Minimal PAM specificity of a highly similar SpCas9 ortholog

RNA-guided DNA endonucleases of the CRISPR-Cas system are widely used for genome engineering and thus have numerous applications in a wide variety of fields. CRISPR endonucleases, however, require a specific protospacer adjacent motif (PAM) flanking the target site, thus constraining their targetable sequence space. In this study, we demonstrate the natural PAM plasticity of a highly similar, yet previously uncharacterized, Cas9 from Streptococcus canis (ScCas9) through rational manipulation of distinguishing motif insertions. To this end, we report affinity to minimal 5'-NNG-3' PAM sequences and demonstrate the accurate editing capabilities of the ortholog in both bacterial and human cells. Last, we build an automated bioinformatics pipeline, the Search for PAMs by ALignment Of Targets (SPAMALOT), which further explores the microbial PAM diversity of otherwise overlooked Streptococcus Cas9 orthologs. Our results establish that ScCas9 can be used both as an alternative genome editing tool and as a functional platform to discover novel Streptococcus PAM specificities.

Prevalence and diversity of M-like protein (SCM) gene in Streptococcus canis isolates from diseased companion animals in Japan: Implication of SCM allele

Streptococcus canis (Sc)-origin M-like protein (SCM) binds to plasminogen and immunoglobulin G and facilitates anti-phagocytic properties. We aimed to determine the prevalence and diversity of the scm gene in Sc isolates from diseased companion animals in Japan and to propose potential SCM alleles of amino acid (AA) sequences. We collected β-hemolytic streptococci from diseased animals with host information nationwide in 2015 and 2017. After Sc identification and scm gene amplification and sequencing, the gene's prevalence and relationship between its presence and host information were determined. Furthermore, phylogenetic trees of AA sequences were constructed, and classification and distribution of SCM alleles based on variations of AA sequences were conducted. The scm detection rates were 70.6% (n = 48, 2015) and 82.9% (n = 97, 2017). There was a relationship between scm presence and Tokyo in 2015 and 2017. We found an association between scm detection and dogs in 2017 alone. Major sequence sizes were 1311 bp, 1308 bp, and 1305 bp. Using the phylogenetic trees of AA sequences, we confirmed shared positions of five identical sequence patterns in both periods. Nine SCM alleles were determined with six signal-peptide types. Most prevalent alleles were type 1, type 2, and type 4 in both periods. Our observations suggest prevalence and diversity of scm in animal-origin Sc isolates in Japan.

Draft Genome Sequence of Streptococcus canis Clinical Strain TA4, Harboring the M-Like Protein Gene and Isolated in Japan from a Patient with Bacteremia

Streptococcus canis is an animal-origin β-hemolytic bacterium that can cause severe infections in animals and occasionally infects humans. Here, we report a draft genome sequence of an S. canis strain harboring the M-like protein gene. This strain was isolated from a patient with bacteremia (reported by Taniyama et al. [D. Taniyama, Y. Abe, T. Sakai, T. Kikuchi, and T. Takahashi, IDCases 7:48–52, 2017, https://doi.org/10.1016/j.idcr.2017.01.002]). The draft genome comprises 2,129,080 bp in 60 contigs.

An update on environmental mastitis: Challenging perceptions

Environmental mastitis is the most common and costly form of mastitis in modern dairy herds where contagious transmission of intramammary pathogens is controlled through implementation of standard mastitis prevention programmes. Environmental mastitis can be caused by a wide range of bacterial species, and binary classification of species as contagious or environmental is misleading, particularly for Staphylococcus aureus, Streptococcus uberis and other streptococcal species, including Streptococcus agalactiae. Bovine faeces, the indoor environment and used pasture are major sources of mastitis pathogens, including Escherichia coli and S. uberis. A faeco-oral transmission cycle may perpetuate and amplify the presence of such pathogens, including Klebsiella pneumoniae and S. agalactiae. Because of societal pressure to reduce reliance on antimicrobials as tools for mastitis control, management of environmental mastitis will increasingly need to be based on prevention. This requires a reduction in environmental exposure through bedding, pasture and pre-milking management and enhancement of the host response to bacterial challenge. Efficacious vaccines are available to reduce the impact of coliform mastitis, but vaccine development for gram-positive mastitis has not progressed beyond the "promising" stage for decades. Improved diagnostic tools to identify causative agents and transmission patterns may contribute to targeted use of antimicrobials and intervention measures. The most important tool for improved uptake of known mastitis prevention measures is communication. Development of better technical or biological tools for management of environmental mastitis must be accompanied by development of appropriate incentives and communication strategies for farmers and veterinarians, who may be confronted with government-mandated antimicrobial use targets if voluntary reduction is not implemented.

Human case of bacteremia caused by Streptococcus canis sequence type 9 harboring the scm gene

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This is the first reported human case of bacteremia caused by Streptococcus canis having scm gene encoding M-like protein.

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The identity was based on similarity of its 16S rRNA and detection of the specific cfg gene encoding a co-hemolysin.

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This isolate was confirmed to be sequence type 9.

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This strain didn’t have the erm(A), erm(B), or mef(A), macrolide resistance genes, but was not susceptible to azithromycin.

Streptococcus canis (Sc) is a zoonotic pathogen that is transferred mainly from companion animals to humans. One of the major virulence factors in Sc is the M-like protein encoded by the scm gene, which is involved in anti-phagocytic activities, as well as the recruitment of plasminogen to the bacterial surface in cooperation with enolase, and the consequent enhancement of bacterial transmigration and survival. This is the first reported human case of uncomplicated bacteremia following a dog bite, caused by Streptococcus canis harboring the scm gene. The similarity of the 16S rRNA from the infecting species to that of the Sc type strain, as well as the amplification of the species-specific cfg gene, encoding a co-hemolysin, was used to confirm the species identity. Furthermore, the isolate was confirmed as sequence type 9. The partial scm gene sequence harbored by the isolate was closely related to those of other two Sc strains. While this isolate did not possess the erm(A), erm(B), or mef(A), macrolide/lincosamide resistance genes, it was not susceptible to azithromycin: its susceptibility was intermediate. Even though human Sc bacteremia is rare, clinicians should be aware of this microorganism, as well as Pasteurella sp., Prevotella sp., and Capnocytophaga sp., when examining and treating patients with fever who maintain close contact with companion animals.

Biotypes and ScM types of isolates of Streptococcus canis from diseased and healthy cats

Lancefield group G Streptococcus canis is a component of the normal urogenital and pharyngeal flora of the cat. It is also frequently implicated in epizootics of severe disease in closed cat colonies and animal shelters. Given the importance of S canis as a feline pathogen and relative lack of published information on characteristics potentially associated with virulence, the authors have compared isolates from healthy and diseased cats in New York and California using fermentation profiles (biotype) and ScM sequences. With few exceptions, isolates associated with disease were biotype 1. Four alleles of scm were identified of which type 1 dominated in diseased cats. Type 4 allelic variants were found only in healthy cats and all but one were biotype 2. Type 2 and 3 alleles showed extensive N-terminal variation suggesting a plasminogen-binding site as found on the type 1 allele was absent. Cat antisera to ScM were opsonobactericidal, and these potentially protective antibodies increased during convalescence.

Streptococcal toxins: role in pathogenesis and disease

Group A Streptococcus (Streptococcus pyogenes), group B Streptococcus (Streptococcus agalactiae) and Streptococcus pneumoniae (pneumococcus) are host-adapted bacterial pathogens among the leading infectious causes of human morbidity and mortality. These microbes and related members of the genus Streptococcus produce an array of toxins that act against human cells or tissues, resulting in impaired immune responses and subversion of host physiological processes to benefit the invading microorganism. This toxin repertoire includes haemolysins, proteases, superantigens and other agents that ultimately enhance colonization and survival within the host and promote dissemination of the pathogen.

Molecular epidemiology and genomics of group A Streptococcus

Streptococcus pyogenes (group A Streptococcus; GAS) is a strict human pathogen with a very high prevalence worldwide. This review highlights the genetic organization of the species and the important ecological considerations that impact its evolution. Recent advances are presented on the topics of molecular epidemiology, population biology, molecular basis for genetic change, genome structure and genetic flux, phylogenomics and closely related streptococcal species, and the long- and short-term evolution of GAS. The application of whole genome sequence data to addressing key biological questions is discussed.

Phylogenomics and the dynamic genome evolution of the genus Streptococcus

The genus Streptococcus comprises important pathogens that have a severe impact on human health and are responsible for substantial economic losses to agriculture. Here, we utilize 46 Streptococcus genome sequences (44 species), including eight species sequenced here, to provide the first genomic level insight into the evolutionary history and genetic basis underlying the functional diversity of all major groups of this genus. Gene gain/loss analysis revealed a dynamic pattern of genome evolution characterized by an initial period of gene gain followed by a period of loss, as the major groups within the genus diversified. This was followed by a period of genome expansion associated with the origins of the present extant species. The pattern is concordant with an emerging view that genomes evolve through a dynamic process of expansion and streamlining. A large proportion of the pan-genome has experienced lateral gene transfer (LGT) with causative factors, such as relatedness and shared environment, operating over different evolutionary scales. Multiple gene ontology terms were significantly enriched for each group, and mapping terms onto the phylogeny showed that those corresponding to genes born on branches leading to the major groups represented approximately one-fifth of those enriched. Furthermore, despite the extensive LGT, several biochemical characteristics have been retained since group formation, suggesting genomic cohesiveness through time, and that these characteristics may be fundamental to each group. For example, proteolysis: mitis group; urea metabolism: salivarius group; carbohydrate metabolism: pyogenic group; and transcription regulation: bovis group.

First reported human case of native mitral infective endocarditis caused by Streptococcus canis

A 65 year-old woman was admitted for acute heart failure and severe sepsis revealing definite mitral infective endocarditis with severe regurgitation, complicated by multiple embolisms. Three blood cultures yielded a group G Streptococcus canis strain. Urgent surgery was performed with bioprosthetic valve replacement. Polymerase chain reaction analysis of the valve found S canis DNA. Amoxicillin and gentamicin were given for 2 weeks followed by 4 weeks of amoxicillin alone. She reported contact with a dog without bite. S canis has been reported to cause zoonotic septicemia but to our knowledge, this is the first human case of native valve infective endocarditis.

Transcriptomic and genomic evidence for Streptococcus agalactiae adaptation to the bovine environment

Background

Streptococcus agalactiae is a major cause of bovine mastitis, which is the dominant health disorder affecting milk production within the dairy industry and is responsible for substantial financial losses to the industry worldwide. However, there is considerable evidence for host adaptation (ecotypes) within S. agalactiae, with both bovine and human sourced isolates showing a high degree of distinctiveness, suggesting differing ability to cause mastitis. Here, we (i) generate RNAseq data from three S. agalactiae isolates (two putative bovine adapted and one human) and (ii) compare publicly available whole genome shotgun sequence data from an additional 202 isolates, obtained from six host species, to elucidate possible genetic factors/adaptations likely important for S. agalactiae growth and survival in the bovine mammary gland.

Results

Tests for differential expression showed distinct expression profiles for the three isolates when grown in bovine milk. A key finding for the two putatively bovine adapted isolates was the up regulation of a lactose metabolism operon (Lac.2) that was strongly correlated with the bovine environment (all 36 bovine sourced isolates on GenBank possessed the operon, in contrast to only 8/151 human sourced isolates). Multi locus sequence typing of all genome sequences and phylogenetic analysis using conserved operon genes from 44 S. agalactiae isolates and 16 additional Streptococcus species provided strong evidence for acquisition of the operon via multiple lateral gene transfer events, with all Streptococcus species known to be major causes of mastitis, identified as possible donors. Furthermore, lactose fermentation tests were only positive for isolates possessing Lac.2. Combined, these findings suggest that lactose metabolism is likely an important adaptation to the bovine environment. Additional up regulation in the bovine adapted isolates included genes involved in copper homeostasis, metabolism of purine, pyrimidine, glycerol and glucose, and possibly aminoglycoside antibiotic resistance.

Conclusion

We detected several genetic factors likely important in S. agalactiae’s adaptation to the bovine environment, in particular lactose metabolism. Of concern is the up regulation of a putative antibiotic resistance gene (GCN5-related N-acetyltransferase) that might reflect an adaptation to the use of aminoglycoside antibiotics within this environment.

Horizontally Transferred Genetic Elements and Their Role in Pathogenesis of Bacterial Disease

This article reviews the roles that laterally transferred genes (LTG) play in the virulence of bacterial pathogens. The features of LTG that allow them to be recognized in bacterial genomes are described, and the mechanisms by which LTG are transferred between and within bacteria are reviewed. Genes on plasmids, integrative and conjugative elements, prophages, and pathogenicity islands are highlighted. Virulence genes that are frequently laterally transferred include genes for bacterial adherence to host cells, type 3 secretion systems, toxins, iron acquisition, and antimicrobial resistance. The specific roles of LTG in pathogenesis are illustrated by specific reference to Escherichia coli, Salmonella, pyogenic streptococci, and Clostridium perfringens.