Staphylococcus intermedius
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1. Classification
a. Higher order taxa
Cellular organisms; Bacteria; Terrabacteria group; Bacillota; Bacilli; Bacillales; Staphylococcaceae; Staphylococcus; Staphylococcus intermedius group[1].
2. Description and significance
Staphylococcus intermedius (S. intermedius) is a Gram-positive, coagulase-positive cocci[2,3] that is found over the skin and mucus of animals like dogs, pigeons, minks, cats, horses, foxes, raccoons, goats, and gray squirrels[4,5]. S. intermedius has veterinary importance, as it’s the predominant cause of skin and soft tissue infections in dogs[6,7,8,9,10]. Although S. intermedius is pathogenic to animals and rare in humans, it can transfer from animal to human and cause infections[3,5]. The number of case reports of serious invasive infections of S. intermedius in humans is rising[11]. Additionally, in 1991, there was an outbreak of S. intermedius-related food intoxication of over 265 in western United States[12]. However, even with the rise of infections, there is still a lack of useful tools to accurately clinically diagnose S. intermedius[3]. Before its description, S. intermedius had been grouped together with Staphylococcus aureus[13]. It wasn’t until 1976 when S. intermedius could be separated from S. aureus using its cell wall structure and guanine-cytosine content[3]. It also wasn’t until 2005 when researchers, using more advanced molecular technologies, were able to reclassify S. intermedius into the Staphylococcus Intermedius Group (SIG), which include the three bacterial species S. intermedius, Staphylococcus pseudintermedius, and Staphylococcus delphini[3,4,14]. There is no distinction between the SIG cell morphology or phenotypes[3,4]. Recently, modern molecular sequencing approaches have been developed to differentiate between the SIG species[3,15,16].
3. Genome structure
Whole genome sequencing of S. intermedius NCTC11048, isolated from the nares of a Pigeon,2 was carried out and compared with the genomes of S. pseudintermedius ED99 and S. delphini 8086, as well as other Staphylococcal species[17]. The draft genome of S. intermedius was ~2,780,000 base pairs, significantly larger than S. pseudintermedius and S. delphini. Average G+C content of the three Staphylococcus Intermedius Group species (37.4% to 38.3%) is higher than other Staphylococcal species[17]. Analysis revealed a high level of conservation and synteny between the Staphylococcus Intermedius Group and S. aureus Mu50, S. epidermidis RP62A, S. haemolyticus JCSC1435, S. saprophyticus ATCC15305, and S. carnosus TM300, sharing a core genome of 1214 genes. However, they differ in the oriC environ, a chromosomal region among Staphylococci that has many species-specific coding sequences (CDS)[17,18]. Occurrences of CRISPR are rare among Staphylococci, but S. intermedius contain a CRISPR locus of the Nmeni and Mtube subtype,[17] which is associated exclusively with vertebrate pathogens and commensals[19]. The presence of CRISPR in S. intermedius correlates with an absence of plasmids and prophages[20,21].
S. intermedius genes code for the exoenzymes staphylocoagulase, serine protease HtrA, glutamyl-endopeptidase, thermonuclease, thermolysin, zinc metalloproteinase aureolysin, lipases, and protease ClpX. Unlike S. pseudintermedius and S. delphini, S. intermedius genes do not code for putative sialidase and neuraminidase[17].
Toxins have been found to be important for staphylococcal survival and pathogenesis[22]. S. intermedius contains genes coding for several toxins, such as β-hemolysin, δ hemolysin, hemolysin III, bi-component leukotoxin Luk-I, leukocidins Luk F-1 and Luk S-1, enterotoxin Se-int, and several exfoliative toxins[17]. S. intermedius genes also code for proteins with ~42% identity to the Von Willebrand-binding protein found in S. aureus[17]. These proteins are involved in the formation of abscesses[23]. Genes encoding for putative cell wall-associated proteins were found in S. intermedius, which may be relevant to its canine host tropism[17].
4. Phylogenetics
The nomenclature and the phylogenetic relationships among staphylococci species are categorized by their metabolism mechanisms, pathogenicity, and clinical significance[24]. Based on Bayesian Estimation of Species Trees (BEST) analysis and Individual Gene Trees analysis, the Staphylococcus genus into 15 cluster groups and 6 species groups. It identified two major clades within Staphylococci: oxidase-positive and oxidase-negative species[24]. S. intermedius, S. delphini, and S. pseudintermedius belong to the same clade, forming the Staphylococcus Intermedius Group. As part of the same clade, members of the SIG share a common trait as pathogens in animal mucus, but rarely cause infection in healthy individuals[24]. Additionally, average nucleotide identity value (ANIs) of 93.61% confirmed the genetic similarity among SIG, compared to other Staphylococci[17].
5. Cell structure
S. intermedius appear as Gram-positive, irregular clumps of pairs or individual cocci ranging from 0.8 to 1.50 μm. Cells are non-motile, non-spore forming, and grow well at 45°C[2]. Colonies appear as white, circular, glistening colonies[2]. Cell walls do not contain protein A or polysaccharide Aβ (β-N-acetylglucosaminyl ribitol teichoic acid). The peptidoglycan of the cell wall is of the L-LysGly4_5,L-Ser0,.2-10 type[2]. A high content of serine in the peptidoglycan causes resistance to the bacteriocin lysostaphin[2]. S. intermedius contains genes coding for adhesins that help mediate binding to extracellular matrix proteins. Adhesins include elastin-binding protein, intercellular adhesion proteins, and several putative cell surface proteins identified in S. pseudintermedius (SpsA, B, C, E, H, N, and R)[17].
6. Metabolic processes
S. intermedius is a chemoorganotrophic, facultatively anaerobic bacteria that is catalase and coagulase positive[2]. It does not produce acid from maltose, arabinose, and xylose, nor use anaerobic respiration with mannitol. However, it produces acid from glucose, galactose, fructose, mannose, sucrose, trehalose, glycerol, mannitol, and lactose[2]. S. Intermedius does not utilize a metabolic pathway to produce acetylmethylcarbinol during the fermentation of sugar[25]. S. intermedius does not produce arginine dihydrolase and caseinase[2]. In contrast to S. aureus, S intermedius is positive for pyrrolidonyl arylamidase and β-galactosidase positive[26]. Positive results in the urease test showed that S. intermedius has urease to produce ammonia and carbon dioxide to raise the pH in the environment[15].
S. intermedius has several mechanisms for iron acquisition, including the use of siderophores to transport staphyloferrin A and heme,[27] as well as the production of staphylobactin A and ABC transporters for ferrichrome, iron-manganese, and ferrous iron[17].
7. Ecology
S. intermedius had been historically identified to be predominantly found in animals, particularly in dogs and other domesticated species, but they can also be found in cow’s milk[28]. S. intermedius’ prevalence in dogs is 39%[6]. However, more recent research identified its dominant presence in pigeons, rather than domesticated animals[4]. S. intermedius typically resides in the skin and mucous membranes of individuals, which can cause infection. However, this mainly occurs in non-human mammals,[29] as S. intermedius’ prevalence–based on saliva cultures and anti-DNase antibodies–in humans is less than 20%[30,31,32,33,34]. There is the potential for bacteria to be transferred indirectly from household items, for recolonization purpose and as a source for recurring infections within the community[29].
S. intermedius contains a diverse set of genes coding for proteins that may be involved in osmo-protection and resistance to oxidative stress that allow it to survive in distinct host-dependent environments, such as putative nitroreductase and several sodium/salt transporters[17]. S. Intermedius also produces a heat-stable nuclease capable of cleaving nucleic acids under high-temperatures[35].
8. Pathology
Global regulation of the production of virulence factors in S. aureus involves the genes sar (staphylococcal accessory regulator) and agr (accessory gene regulator)[36]. Similarly, S. intermedius contains sarA, R, and Z, which are genes found to control S. aureus virulence[17]. Real time quantitative PCR confirmed that S. intermedius expression of RNAIII (an effector of the agr system) and several toxins is initiated by an environmental signal during growth, involving the use of quorum sensing to adjust virulence around other cells[37].
S. intermedius is a bacterium commonly found in the skin and mouths of dogs, but it could be transmitted through animal contact. Exposure to dogs is the most consistent and preventable risk factor for S. intermedius infection[38]. Case reports show S. intermedius causing a variety of infections, including infected dog bite wounds,[6] bacteremia,[5] brain abscess,[38] sinusitis,[39] otitis externa,[40] nail bed infection,[41] mastoiditis,[42] and skin abscess[43]. For example, a 73-year-old woman's left elbow joint replacement led to a S. intermedius wound infection from her pet dog[44]. Another case was a 46-year-old man with type I diabetes who presented with a persistent ulcer on his left big toe. He had not been consistently monitoring his blood glucose levels or using insulin as prescribed, while also living alone with his two dogs[15]. Diabetes mellitus has also been identified as a possible risk factor for SIG infection[3].
Although S. intermedius is a rare cause of infections in humans, the true incidence is unknown because S. intermedius was historically often mistaken for S. aureus[11]. S. intermedius has more limited clinical importance when compared to S. pseudintermedius[17]. Current clinical methods of testing for β-galactosidase can differentiate the Staphylococcus Intermedius Group (SIG) from S. aureus, but not all labs are capable of conducting this test, leading to misdiagnosis[3]. The traditional method of using phenotypic characteristics to differentiate among the SIG is ineffective[4]. In terms of treatment, S. intermedius is sensitive to the antibiotics tetracycline, macrolides, lincosamides, streptogramins, aminoglycosides, aminocyclitols, fluoroquinolones, erythromycin, trimethoprim, ampicillin, and methicillin[17]. Comparatively, S. pseudintermedius often has multi-resistance to all antibiotics mentioned[17].
9. Current Research
Isolated cases involving human infection have revealed that early diagnosis is crucial for proper treatment of S. intermedius infections[45]. The incidence of S. intermedius infections is now known to be low, due to its historical misidentification as S. aureus[11]. However, case studies have shown S. intermedius to be an opportunistic pathogen that is capable of infecting humans[11,15,43]. The rarity of infections demonstrates a lack of knowledge of S. intermedius[43] and the difficulty in identifying S. intermedius makes it likely that human infection cases of S. intermedius have been underestimated[38].
Future research aims to better understand the zoonotic and pathogenic potential of S. intermedius, as its identification, molecular mechanism of adaptation to different hosts, infection doses, and the mechanisms and factors of pathogen transmission are poorly understood[46]. Most S. intermedius cases of infection have been associated with animal exposure[43]. However, recent research has shown that S. intermedius can cause infection even among healthy individuals without exposure to animals[43]. While coagulase-positive S. intermedius infections are secondary to S. aureus, clinicians should be aware of S. intermedius’ pathogenic potential and conduct a detailed history of their patients to ensure an accurate diagnosis[43].
The variance of S. intermedius strains has led researchers to believe that there are species or subspecies that could be discovered from strains that were phenotypically identified as S. intermedius[14]. Phenotypic and biochemical similarity among the Staphylococcus Intermedius Group (SIG), which contains S. intermedius, S. pseudintermedius, and S. delphini, complicates the development of reliable and affordable molecular genetic techniques to differentiate between them[46]. Modern genomic or molecular approaches, such as MALDI-TOF mass spectrometry, PCR-RFLP, and Rep-PCR, have been developed as efficient tools to tell them apart[15,16].
10. References
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