Characterization of Streptococcus pluranimalium from a cattle with mastitis by whole genome sequencing and functional validation

Copper homeostasis in Streptococcus and Neisseria: Known knowns and unknown knowns

Our research group studies copper (Cu) homeostasis in Streptococcus and Neisseria, with a current focus on species that colonise the human oral cavity. Our early ventures into this field very quickly revealed major differences between well-characterised Cu homeostasis systems in species with well-known pathogenic potential and the uncharacterised systems in species that are considered as components of the normal healthy human microflora. In this article, we summarise the known and predicted mechanisms of Cu homeostasis in Streptococcus and Neisseria. We focus exclusively on proteins that directly sense and change (increase or decrease) cellular Cu availability. Where relevant, we make comparisons with examples from species isolated from outside the human oral cavity and from animal hosts. The emerging picture depicts diverse cellular strategies for handling Cu, even among closely related bacterial species.

Respiratory pathogens carriage in guinea pigs raised as livestock in Ecuador: A proxy to study a neglected reservoir for zoonotic transmission in the Andean Region

In the Andean region of South America, guinea pigs (Cavia porcellus) are raised as livestock in close contact with other domestic animals and humans. Although the susceptibility of guinea pigs to being affected by a wide range of diseases is well known as a laboratory animal model, there are a few reports about the potential role of zoonotic pathogens in livestock guinea pigs. In this work, we analyzed the nasopharyngeal carriage of respiratory pathogenic viruses and bacteria in guinea pigs from farms in Ecuador. We isolated streptococci and aerococci cultures that were analyzed for species identification by MALDI-TOF MS. Several species, including Streptococcus pneumoniae, S. pseudopneumoniae, S. oralies, and S. mitis were found. Moreover, strains resistant to antibiotics like levofloxacin, erythromycin, and sulfamethoxazole-trimethoprim were also found. Our results suggest the role of guinea pigs as a zoonotic reservoir for occupational exposure to respiratory pathogens in the Andean region of South America, where guinea pig farming is an important industry.

Recent development and fighting strategies for lincosamide antibiotic resistance

SUMMARYLincosamides constitute an important class of antibiotics used against a wide range of pathogens, including methicillin-resistant Staphylococcus aureus. However, due to the misuse of lincosamide and co-selection pressure, the resistance to lincosamide has become a serious concern. It is urgently needed to carefully understand the phenomenon and mechanism of lincosamide resistance to effectively prevent and control lincosamide resistance. To date, six mobile lincosamide resistance classes, including lnu, cfr, erm, vga, lsa, and sal, have been identified. These lincosamide resistance genes are frequently found on mobile genetic elements (MGEs), such as plasmids, transposons, integrative and conjugative elements, genomic islands, and prophages. Additionally, MGEs harbor the genes that confer resistance not only to antimicrobial agents of other classes but also to metals and biocides. The ultimate purpose of discovering and summarizing bacterial resistance is to prevent, control, and combat resistance effectively. This review highlights four promising strategies, including chemical modification of antibiotics, the development of antimicrobial peptides, the initiation of bacterial self-destruct program, and antimicrobial stewardship, to fight against resistance and safeguard global health.

Comparative study of the bacterial community of organic and conventional cow's milk

Agricultural practises such as conventional and organic farming can potentially affect the microbial communities in milk. In the present study, the bacterial diversity of milk was investigated using high-throughput sequencing on ten organic and ten conventional farms in the Azores, a region where milk production is largely based on year-round grazing systems. The microbiota of milk from both production systems was dominated by Bacillota, Pseudomonadota, Actinomycetota and Bacteroidota. The organic milk showed greater heterogeneity between farms, as reflected in the dispersion of diversity indices and the large variation in the relative abundances of the dominant genera. In contrast, conventionally produced milk showed a high degree of similarity within each season. In the conventional production system, the season also had a strong influence on the bacterial community, but this effect was not observed in the organic milk. The LEfSe analysis identified the genus Iamia as significantly (p < 0.05) more abundant in organic milk, but depending on the season, several other genera were identified that distinguished organic milk from conventionally produced milk. Of these, Bacillus, Iamia and Nocardioides were associated with the soil microbiota in organic farming.

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.

The pseudokinase MLKL contributes to host defense against Streptococcus pluranimalium infection by mediating NLRP3 inflammasome activation and extracellular trap formation

Host innate immunity plays a pivotal role in the early detection and neutralization of invading pathogens. Here, we show that pseudokinase mixed lineage kinase-like protein (MLKL) is required for host defence against Streptococcus pluranimalium infection by enhancing NLRP3 inflammasome activation and extracellular trap formation. Notably, Mlkl deficiency leads to increased mortality, increased bacterial colonization, severe destruction of organ architecture, and elevated inflammatory cell infiltration in murine models of S. pluranimalium pulmonary and systemic infection. In vivo and in vitro data provided evidence that potassium efflux-dependent NLRP3 inflammasome signalling downstream of active MLKL confers host protection against S. pluranimalium infection and initiates bacterial killing and clearance. Moreover, Mlkl deficiency results in defects in extracellular trap-mediated bactericidal activity. In summary, this study revealed that MLKL mediates the host defence response to S. pluranimalium, and suggests that MLKL is a potential drug target for preventing and controlling pathogen infection.

Whole genome sequence of Streptococcus pluranimalium SP21-2, a porcine strain harbouring optrA and lsa(E) with chromosomal location

OBJECTIVES

The aim of this study was to characterise the whole genome sequence of multidrug-resistant Streptococcus pluranimalium strain SP21-2 of swine origin in China.

METHODS

Illumina Miseq (200X coverage) and Nanopore PromethION platform (100X coverage) were used for genome sequencing. Rapid Annotation using Subsystem Technology (RAST) was used to annotate the genome of SP21-2. The antimicrobial resistance genes (ARGs) were identified using ResFinder-4.1.

RESULTS

The assembled circular genome of S. pluranimalium SP21-2 was 1,987,058 bp in length with a GC content of 39.54%, and no plasmid sequence was detected. A total of 2086 coding sequences were predicted by RAST. Oxazolidinone-phenicol resistance gene, optrA, and pleuromutilin-lincosamide-streptogramin A resistance gene, lsa(E), are both located on chromosomes, associated with IS1216 and ISS1S, respectively. In addition, SP21-2 harbours lnu(B) (lincosamide), ant (6)-Ia and aac(6')-aph(2") (aminoglycoside), erm(B) (macrolide), and tet(O) (tetracycline).

CONCLUSION

We firstly report the oxazolidinone-phenicol gene, optrA, and pleuromutilin-lincosamide-streptogramin A resistance gene, lsa(E), in S. pluranimalium. In this strain, we firstly identified ISS1S and IS1216 carrying ARGs in S. pluranimalium, which will provide a valuable reference to understanding potential transfer mechanisms of ARGs in S. pluranimalium.

Biological Properties of Streptococcus pluranimalium as the New Human Pathogen

BACKGROUND: The limited amount of information available today does not fully reflect the biological properties of Streptococcus pluranimalium as a pathogen new to humans, its pathogenicity factors, and, as a consequence, the pathogenesis of diseases, which is causes AIM: The aim of this research was to study the biological properties of S. pluranimalium, its sensitivity to antibiotics and antiseptics, as well as its adhesive properties. METHODS: Two hundred samples were collected from the coronal pockets in patients with acute purulent pericoronitis during 2019–2021 years. Among them, five clinical strains of S. pluranimalium were isolated. Final identification was carried out using a Vitec-2compact bioMérieux automatic bacteriological analyzer. The sensitivity of the studied microbial strains to antibiotics of various groups was determined by the disk diffusion method. The adhesive properties of S. pluranimalium were determined according to the standard Brilis method. RESULTS: It possesses typical morphological and cultural properties characteristics of the genus Streptococcus representatives. This microorganism virtually does not break down carbohydrates, but it produces arylamidases that enables it to be differentiated from other streptococci. S. pluranimalium demonstrates variable sensitivity to antibiotics; the lowest sensitivity has been found out to the second-generation fluoroquinolones. In addition, the clinical isolates studied show high adhesive properties to human red blood cells. CONCLUSIONS: S. pluranimalium is increasingly acting as the causative agent of human infectious diseases. The information available today fully reflects the biological properties of a pathogen new to humans, its pathogenicity factors.

Streptococcus oriscaviae sp. nov. Infection Associated with Guinea Pigs

Pet bite-related infections are commonly caused by the pet's oral flora transmitted to the animal handlers through the bite wounds. In this study, we isolated a streptococcus, HKU75T, in pure culture from the purulent discharge collected from a guinea pig bite wound in a previously healthy young patient. HKU75T was alpha-hemolytic on sheep blood agar and agglutinated with Lancefield group D and group G antisera. API 20 STREP showed that the most likely identity for HKU75T was S. suis I with 85.4% confidence while Vitek 2 showed that HKU75T was unidentifiable. MALDI-TOF MS identified HKU75T as Streptococcus suis (score of 1.86 only). 16S rRNA gene sequencing showed that HKU75T was most closely related to S. parasuis (98.3% nucleotide identity), whereas partial groEL and rpoB gene sequencing showed that it was most closely related to S. suis (81.8% and 89.8% nucleotide identity respectively). Whole genome sequencing and intergenomic distance determined by ANI revealed that there was <85% identity between the genome of HKU75T and those of all other known Streptococcus species. Genome classification using concatenated sequences of 92 bacterial core genes showed that HKU75T belonged to the Suis group. groEL gene sequences identical to that of HKU75T could be directly amplified from the oral cavities of the two guinea pigs owned by the patient. HKU75T is a novel Streptococcus species, which we propose to be named S. oriscaviae. The oral cavity of guinea pigs is presumably a reservoir of S. oriscaviae. Some of the reported S. suis strains isolated from clinical specimens may be S. oriscaviae. IMPORTANCE We reported the discovery of a novel Streptococcus species, propose to be named Streptococcus oriscaviae, from the pus collected from a guinea pig bite wound in a healthy young patient. The bacterium was initially misidentified as S. suis/S. parasuis by biochemical tests, mass spectrometry. and housekeeping genes sequencing. Its novelty was confirmed by whole genome sequencing. Comparative genomic studies showed that S. oriscaviae belongs to the Suis group. S. oriscaviae sequences were detected in the oral cavities of the two guinea pigs owned by the patient, suggesting that the oral cavity of guinea pigs could be a reservoir of S. oriscaviae. Some of the reported S. suis strains may be S. oriscaviae. Further studies are warranted to refine our knowledge on this novel Streptococcus species.

Distribution, Diversity and Roles of CRISPR-Cas Systems in Human and Animal Pathogenic Streptococci

Streptococci form a wide group of bacteria and are involved in both human and animal pathologies. Among pathogenic isolates, differences have been highlighted especially concerning their adaptation and virulence profiles. CRISPR-Cas systems have been identified in bacteria and many streptococci harbor one or more systems, particularly subtypes I-C, II-A, and III-A. Since the demonstration that CRISPR-Cas act as an adaptive immune system in Streptococcus thermophilus, a lactic bacteria, the diversity and role of CRISPR-Cas were extended to many germs and functions were enlarged. Among those, the genome editing tool based on the properties of Cas endonucleases is used worldwide, and the recent attribution of the Nobel Prize illustrates the importance of this tool in the scientific world. Another application is CRISPR loci analysis, which allows to easily characterize isolates in order to understand the interactions of bacteria with their environment and visualize species evolution. In this review, we focused on the distribution, diversity and roles of CRISPR-Cas systems in the main pathogenic streptococci.

Streptococcus pluranimalium meningoencephalitis in a horse

A 3-y-old, female Quarter Horse with a history of acute neurologic signs was found dead and was submitted for postmortem examination. Areas of petechial and ecchymotic hemorrhage were present on cross-sections of the cerebrum, cerebellum, and brainstem. Histologic examination of the brain revealed severe, purulent meningoencephalitis and vasculitis with a myriad of intralesional gram-positive cocci. Streptococcus pluranimalium was identified from formalin-fixed, paraffin-embedded tissue obtained from sites with active lesions by PCR and nucleotide sequencing of bacterial 16S ribosomal RNA. S. pluranimalium should be considered as a cause of meningoencephalitis in a horse.

Microbial Communities of Meat and Meat Products: An Exploratory Analysis of the Product Quality and Safety at Selected Enterprises in South Africa

Consumption of food that is contaminated by microorganisms, chemicals, and toxins may lead to significant morbidity and mortality, which has negative socioeconomic and public health implications. Monitoring and surveillance of microbial diversity along the food value chain is a key component for hazard identification and evaluation of potential pathogen risks from farm to the consumer. The aim of this study was to determine the microbial diversity in meat and meat products from different enterprises and meat types in South Africa. Samples (n = 2017) were analyzed for Yersinia enterocolitica, Salmonella species, Listeria monocytogenes, Campylobacter jejuni, Campylobacter coli, Staphylococcus aureus, Clostridium perfringens, Bacillus cereus, and Clostridium botulinum using culture-based methods. PCR was used for confirmation of selected pathogens. Of the 2017 samples analyzed, microbial ecology was assessed for selected subsamples where next generation sequencing had been conducted, followed by the application of computational methods to reconstruct individual genomes from the respective sample (metagenomics). With the exception of Clostridium botulinum, selective culture-dependent methods revealed that samples were contaminated with at least one of the tested foodborne pathogens. The data from metagenomics analysis revealed the presence of diverse bacteria, viruses, and fungi. The analyses provide evidence of diverse and highly variable microbial communities in products of animal origin, which is important for food safety, food labeling, biosecurity, and shelf life limiting spoilage by microorganisms.

Characterization of intrauterine cultivable aerobic microbiota at the time of insemination in dairy cows with and without mild endometritis

It is generally accepted that postpartum uterine infections decrease conception rates in dairy cows. Whereas clinical endometritis (CE) has been studied intensively, only little information about CE at the time of artificial insemination (AI) is available. The aim of this study was to characterize the intrauterine cultivable aerobic microbiota in healthy cows and in cows with mild CE at AI and to investigate its effect on the subsequent insemination success. The vaginal discharge score (VDS) of 120 Holstein Frisian dairy cows was assessed shortly after AI using the Metricheck device and pregnancy diagnosis was performed 39 days after AI. On average, cows received their second insemination (2.0 ± 1.2 standard deviation (SD)) and were 120.5 ± 40.2 days in milk. Intrauterine cytobrush samples were taken from cows with clear mucus (VDS 0, n = 58) and from cows with flecks of pus (VDS 1, n = 62), which was regarded as mild CE. Bacteria collected with the cytobrush were cultivated aerobically and identified by matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). A total of 358 bacterial isolates were recovered, comprising 49 bacterial genera and 116 species. Bacillus, Staphylococcus, Corynebacterium and Streptococcus were the most prevalent genera with relative abundances of 19.6%, 14.2%, 10.1% and 8.1%, whereas common uterine pathogens, such as Trueperella pyogenes and Escherichia coli, were rarely detected. Bacillus spp. were more frequently detected in group VDS 0 (51.7%) than in VDS 1 (22.6%; P = 0.001) and there was a higher prevalence of Corynebacterium spp. in VDS 0 than in VDS 1 (37.9% vs 19.3%; P = 0.03). Cows with VDS 1 at the time of AI harbored neither Bacillus licheniformis nor Bacillus subtilis, while these species were detected in 27.6% and 8.6% of VDS 0 (P < 0.001 and P = 0.024 respectively). The insemination success in VDS 0 and 1 was 43.1 and 25.8% (P = 0.046). The diagnosis of mild CE at AI and the total bacterial load decreased the chance of pregnancy (P = 0.03) but no significant correlation between a distinctive bacterial species and insemination success was observed. In summary, cultivable uterine bacteria at AI presumably represent a part of the physiological microbiota, which is not directly linked to impaired fertility. These findings question intrauterine antimicrobial treatment shortly after AI and could represent the basis for the development of future treatment strategies.

The first report of Streptococcus pluranimalium infection from Iran: A case report and literature review

The Streptococcus pluranimalium was isolated from both of animals and human infection. There is limited information about pathogenicity of S pluranimalium. As fastidious bacteria, S pluranimalium is not isolated in the routinely culture media and easily misidentified with other streptococci species with conventional microbiology test. According to review of the literatures, the cephalosporins, aminoglycosides, vancomycin, and linezolid are the first choice agents for treatment of infection caused by S pluranimalium.