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Overall, I enjoyed this project and was intrigued about the information I obtained on these organisms. In regards to the microbiome, I believe research on this topic can further enhance our understanding of microbiology and lead to innovation in medicine, science, and technology. I like the padlet's made by: https://padlet.com/sbotkin96/nvrzx7od2jya and https://padlet.com/humphje/fca31vlzga4i.

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The closest two organism present on this tree are Veillonella and Erysipelothrix. These two species are related to their most recent ancestor and do not have subdivisions of ancestors. The most distant organisms are Lactobacillus and Aggregatibacter.

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New research/Emerging Threats from the literature

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New research/Emerging Threats from the literature

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In a specific study, researchers observed the interaction of Treponema Pallidum with human platelets. The results of the study concluded that when the human body is infected with T. Pallidum, the species may exploit the platelet function with host cells to aid in establishment of disseminated (spread throughout organ or body) infection.

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Interaction of Treponema pallidum, the syphilis spirochete, with human platelets.

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PLoS One. 2019 Jan 18;14(1):e0210902. doi: 10.1371/journal.pone.0210902. eCollection 2019. Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't

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Treponema Pallidum are species that cause diseases such as syphilis, bejel, and yaws. Treponema Pallidum is aquired by close sexual contact resulting in syphilis. This organism can gain access to a host's blood and lymph systems through tissue and mucous membranes.

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Kingdom: Bacteria
Phylum: Spirochaetae
Class: Spirochaetes
Order: Spirochaetales
Family: Spirochaetaceae
Genus: Treponema
Species: T. Pallidum

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Treponema Pallidum are spirochaete bacterium that are gram-negative. This bacterium is responsible for many human transmitted diseases.

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Treponema pallidum is a spirochaete bacterium with various subspecies that cause the diseases syphilis, bejel, and yaws. It is transmitted only amongst humans. It is a helically coiled microorganism usually 6-15 μm long and 0.1-0.2 μm wide. T. pallidum's lack of metabolic pathways ( tricarboxylic acid cycle, oxidative phosphorylation) results in minimal metabolic activity. The treponemes have a cytoplasmic and an outer membrane. Using light microscopy, treponemes are visible only by using dark field illumination. Treponema pallidum consists of 3 species, T. p. pallidum, T. p. endemicum, and T. p. pertenue, each of these subspecies has a distinct disease associated with them.

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Treponema pallidum pallidum, which causes syphilis

T. p. endemicum, which causes bejel or endemic syphilis

T. p. pertenue, which causes yaws

The three subspecies causing yaws, pinta, and syphilis are morphologically and serologically indistinguishable. These bacteria were originally classified as members of separate species, but DNA hybridization analysis indicates they are members of the same species. Treponema carateum, the cause of pinta, remains a separate species because no isolate is available for DNA analysis. Subspecies T. p. endemicum and T. p. pertenue, disease transmittance is considered non-venereal. T. p. pallidum is the most invasive pathogenic subspecies while T. p. carateum is the least invasive of the subspecies. T. p. endemicum and T. p. pertenue are intermediately invasive.

Ultrastructure

Treponema pallidum is a helically shaped bacteria comprised of an outer membrane, peptidoglycan layer, inner membrane, protoplasmic cylinder, and periplasmic space.[citation needed ] It is often described as Gram negative, but its outer membrane lacks lipopolysaccharide, which is found in the outer membrane of other Gram-negative bacteria. It has an endoflagella (periplasmic flagella) comprised of 4 main polypeptides, a core structure, and a sheath.[citation needed ] The flagella is located within the periplasmic space and wraps around the protoplasmic cylinder. T. pallidum's outer membrane has the most contact with host cells and contains few transmembrane proteins, limiting antigenicity while its cytoplasmic membrane is covered in lipoproteins. The outer membrane's treponemal ligands main function is attachment to host cells, with functional and antigenic relatedness between ligands. The genus Treponema has ribbons of cytoskeletal cytoplasmic filaments that run the length of the cell just underneath the cytoplasmic membrane. They are composed of the intermediate filament-like protein CfpA (cytoplasmic filament protein A). Although the filaments may be involved in chromosome structure and segregation or cell division, their precise function is unknown.

Successful long-term cultivation of T. pallidum subspecies pallidum in a tissue culture system has been reported in 2018.

The chromosomes of the T. pallidum subspecies are small, about 1.14 Mbp. Their DNA sequences are more than 99.7% identical. T. pallidum subspecies pallidum was sequenced in 1998. This sequencing is significant due to T. pallidum not being capable of growing in a pure culture, meaning that this sequencing played an important role in understanding the microbe's functions. It revealed that T. pallidum relies on its host for many molecules provided by biosynthetic pathways, as well as it is missing genes responsible for encoding key enzymes in oxidative phosphorylation and the tricarboxylic acid cycle. It was found that this is due to 5% of T. pallidum's genes code for transport genes. The recent sequencing of the genomes of several spirochetes permits a thorough analysis of the similarities and differences within this bacterial phylum and within the species. T. p. pallidum has one of the smallest bacterial genomes at 1.14 million base pairs, and has limited metabolic capabilities, reflecting its adaptation through genome reduction to the rich environment of mammalian tissue. The shape of T. pallidum is flat and wavy. In order to avoid antibodies attacking, the cell has few proteins exposed on the outer membrane sheath. Its chromosome of about 1000 kilo base pairs is circular with a 52.8% G + C average. Sequencing has revealed a bundle of 12 proteins and some putative hemolysins are potential virulence factors of T. pallidum. 92.9% of DNA was determined to be ORF's, 55% of which had predicted biological functions.

The clinical features of syphilis, yaws, and bejel occur in multiple stages that affect the skin. The skin lesions observed in the early stage last for weeks or months. The skin lesions are highly infectious, and the spirochetes in the lesions are transmitted by direct contact. The lesions regress as the immune response develops against T. pallidum. The latent stage that results lasts a lifetime in many cases. In a minority of cases, the disease exits latency and enters a tertiary phase, in which destructive lesions of skin, bone, and cartilage ensue. Unlike yaws and bejels, syphilis in its tertiary stage often affects the heart, eyes, and nervous system as well.

T. p. pallidum is a motile spirochaete that is generally acquired by close sexual contact, entering the host via breaches in squamous or columnar epithelium. The organism can also be transmitted to a fetus by transplacental passage during the later stages of pregnancy, giving rise to congenital syphilis. The helical structure of T. p. pallidum allows it to move in a corkscrew motion through mucous membranes or enter minuscule breaks in the skin. In women the initial lesion is usually on the labia, the walls of the vagina, or the cervix; in men it is on the shaft or glans of the penis. It gains access to the host's blood and lymph systems through tissue and mucous membranes. In more severe cases, it may gain access to the host by infecting the skeletal bones and central nervous system of the body.

The incubation period for a T. p. pallidum infection is usually around 21 days, but can range from 10 days to 90 days.

T. pallidum was first microscopically identified in syphilitic chancres by Fritz Schaudinn and Erich Hoffmann at the Charité in Berlin in 1905. This bacterium can be detected with special stains, such as the Dieterle stain. T. pallidum is also detected by serology, including nontreponemal VDRL, rapid plasma reagin, treponemal antibody tests ( FTA-ABS), T. pallidum immobilization reaction, and syphilis TPHA test.

During the early 1940s rabbit models in combination with the drug penicillin allowed for a long term drug treatment. These experiments establish the ground work that modern scientists use for syphilis therapy. Penicillin can inhibit T. pallidum in 6-8 hours though the cells still remain in lymph nodes and regenerate. Though penicillin is not the only drug that can be used to inhibit T. pallidum, it has also been found that any β-lactam antibiotics or macrolides can also be used. The T. pallidum strain 14 has built resistance to some macrolides, including erythromycin and azithromycin. Resistance to macrolides in T. Pallidum strain 14 is believed to derive from a single point mutation that increased the organisms livability. Many of the syphilis treatment therapies only lead to bacteriostatic results, unless larger concentrations of penicillin are used for bactericidal effects. Penicillin overall is the most recommended antibiotic by the CDC as it shows the best results with prolonged usage, it can inhibit and may even kill T. Pallidum at low to high doses with each increase in concentration being more effective.

No vaccine for syphilis is available as of 2017. The outer membrane of T. pallidum has too few surface proteins for an antibody to be effective. Efforts to develop a safe and effective syphilis vaccine have been hindered by uncertainty about the relative importance of humoral and cellular mechanisms to protective immunity, and because T. pallidum outer membrane proteins have not been unambiguously identified. In contrast, some of the known antigens are intracellular and antibody against them are ineffective to clear the infection.

"Syphilis- CDC Fact Sheet." Centers for Disease Control and Prevention. May. 2004. Centers for Disease Control and Prevention. 7 February 2006

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Treponema pallidum is a spirochaete bacterium with various subspecies that cause the diseases syphilis, bejel, and yaws. It is transmitted only amongst humans. It is a helically coiled microorganism usually 6-15 μm long and 0.1-0.2 μm wide. T. pallidum's lack of metabolic pathways ( tricarboxylic acid cycle, oxidative phosphorylation) results in minimal metabolic activity.

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New research/Emerging Threats from the literature

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New research/Emerging Threats from the literature

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A 50 year old man presented to the emergency department was complaining of symptomatic large volume ascites. In this present study, researchers observed that Granulicatella spp. can cause bacteremia and infective endocarditis of prosthetic valves, ultimately the leading cause of the patient's symptoms.

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Abstract

Granulicatella adiacens is a Gram-positive coccus, formerly grouped with nutritionally variant Streptococcus, often found as commensal bacteria of the human oral cavity, urogenital tract, and gastrointestinal tract. Prior case reports have demonstrated Granulicatella spp. as a pathogen that can cause bacteremia and infective endocarditis particularly of prosthetic valves and pacemaker leads. Here, we report on a unique case of Granulicatella adiacens bacterascites in a 50-year-old male.

1. Introduction

Granulicatella adiacens is a Gram-positive coccus that is nonmotile, nonsporulating, catalase-negative, oxidase-negative, and facultatively anaerobic. G. adiacens often grows on agar as satellite colonies adjacent to another organism that provides nutrients such as Staphylococcus aureus or Staphylococcus epidermidis [ 1, 2]. G. adiacens colonies are alpha-hemolytic on sheep-blood agar [ 1]. The organism has been found to be resistant to optochin and susceptible to vancomycin [ 1]. The genus Granulicatella has three species, G. adiacens, G. elegans, and G. balaenopterae, with only the former two having been isolated from human samples [ 2]. Granulicatella species are an uncommon cause of infection. To date, there have been no described cases of Granulicatella adiacens as a cause of spontaneous bacterial peritonitis or as an isolate of ascites fluid.

2. Case Report

2.1. History

A 50-year-old man presented to the emergency department (ED) complaining of symptomatic large volume ascites. The patient and his ascites had been followed by his PCP, who had been adjusting diuretics. However, the patient was failing diuretic management and so was referred to our hospital for a therapeutic paracentesis. The patient's past medical history was significant for a complicated course of gallstone pancreatitis that occurred eight months prior to his current presentation. Chart review revealed several prolonged hospital courses, totaling 53 hospital days, with multiple complications, including necrotizing pancreatitis status after necrosectomy and cholecystectomy, interval placement and subsequent removal of a percutaneous endoscopic gastrostomy tube with jejunal arm (PEG-J) for enteral feeding, Clostridium difficile diarrheal infection for which he had received fourteen days of treatment with oral metronidazole, and a new diagnosis of diabetes mellitus. Additionally, he had been found to have new portal vein and splenic vein thromboses during that hospitalization and had since completed six months of therapeutic anticoagulation, originally with Apixaban, which was later switched to Rivaroxaban.

At the time of the patient's current presentation for ascites, most of the above medical problems had resolved. He was tolerating a regular diet and was being followed by his PCP for management of recurrent ascites felt to be due to the above-mentioned portal vein thrombosis.

The patient reported no symptoms other than decreased appetite secondary to bloating and pain in his right groin likely from nonincarcerated hernia. He had no fever, shortness of breath, nausea, vomiting, diarrhea, or significant constipation.

Upon presentation to the ED, computed tomography (CT) of the abdomen showed large volume ascites with no propagation of the portal vein or splenic vein thromboses with interim development of collaterals.

2.2. Physical Examination

On exam, the patient's heart rate was normal with a regular rhythm, his lungs were clear, and there was no lower extremity edema. His abdomen was significantly distended, with bulging flanks and a palpable fluid wave. There was a well-healed midline surgical scar with a distal keloid and easily reducible umbilical hernia. Aside from the ascites, the patient had no other sequelae of chronic liver dysfunction; he exhibited no jaundice, no palmar erythema, no spider angiomata, no venous distention, and no asterixis.

2.3. Laboratory and Radiological Investigations

In the ED, the patient underwent paracentesis by the gastroenterology (GI) team under normal sterile technique with removal of approximately 4.5 L of clear, yellow fluid. Initial Gram stain of the ascites fluid revealed white blood cells and no bacteria. Pertinent fluid analyses revealed glucose 100 mg/dL, amylase 52 U/L, WBC 372/UL with 48% polymorphonuclear cells (PMNs) and 24% lymphocytes, total protein 4.2 g/dL, and albumin 2.1 g/dL giving a serum albumin ascites gradient of 1.5, consistent with portal hypertension or congestive heart failure. Blood work revealed a peripheral white blood cell count of 6.85 k/ μL with a normal differential, platelet count of 326 k/ μ L, and a lactic acid of 1.3 mmol/L. Ultrasound of the abdomen confirmed that there was no interim propagation of the portal vein thrombosis as well as presence of patent collaterals.

2.4. Hospital Course

The patient was discharged from the ED with a follow-up outpatient appointment with a GI physician for further evaluation and management of recurrent ascites. The following day, the GI team was contacted by the Clinical Microbiology Laboratory that Gram-positive cocci in chains were growing in the ascites sample. The GI team contacted the patient's wife who reported that the patient had experienced no clinical status change since the procedure, specifically no fevers or abdominal pain.

The GI team felt that the laboratory result likely represented a contaminant in the sample, and they decided to await speciation before asking the patient to return to the hospital. The following day, the Clinical Microbiology Laboratory reported Granulicatella adiacens (not a common laboratory contaminant), so the patient was asked to return to the hospital to be admitted for further monitoring and evaluation.

Upon return to the hospital, the patient reported interval improvement in his abdominal bloating and appetite, and he denied any new symptoms, including fever, abdominal pain, nausea, or diarrhea. His exam was unchanged from prior exam aside from a decrease in his abdominal distention. The GI team performed a diagnostic paracentesis, which revealed glucose of 135 mg/dL, WBC of 813/UL with 72% lymphocytes, 1% PMNs, and 2% atypical lymphocytes, total protein of 4.3 g/dL, and albumin of 2.1 g/dL. Ascites fluid again showed 3+ white blood cells and the bacterial culture again grew Granulicatella adiacens. Peripheral blood cultures from two separate peripheral sites were collected and showed no growth after 72 hours. Blood work was not significantly changed from the first presentation.

The patient underwent a transthoracic echocardiogram that showed no evidence of structural cardiac defect and no evidence of endocarditis. His previous CT was reexamined and a large fluid collection was seen with a possible rim of residual pancreatic tissue. Based on this, a magnetic resonance cholangiopancreatography (MRCP) was performed that revealed a fluid collection with possible communication to the left colon. The GI team consulted the general surgery team, who, on review of the imaging and patient status, felt that the risks associated with any surgical intervention outweighed the potential benefits of source control.

Due to the patient having a penicillin allergy, he received intravenous vancomycin for his course of therapy. The five-day antibiotic course was initially complicated by an infusion-related "red man" reaction requiring pretreatment with diphenhydramine and slower infusion times. On hospital day 3, a peripherally inserted central venous catheter (PICC) line was placed, and the patient was discharged home in stable condition. The patient underwent colonoscopy one month later and was found to have three hyperplastic polyps without evidence of malignancy. There was no apparent communication between the colon and the fluid pocket that had been visualized on MRCP. No further blood or ascites cultures were collected in the immediate period after his hospitalization.

3. Discussion

Granulicatella adiacens is an uncommon cause of infection, but when present, it is most commonly found in the bloodstream. Review of the English literature shows that bacteremia is usually related to device/graft infection or endocarditis (). Cargill et al. described 17 cases of Granulicatella spp. endocarditis between 1997 and 2012 including infections of prosthetic valves and a pacemaker lead [ 2]. It is suspected that cases of Granulicatella spp. infective endocarditis are underreported and that some cases may be a cause of reported culture-negative endocarditis. Bacteremia with Granulicatella spp.without endocarditis has been reported, including a single case of infection of aortic atheroma with associated dissection [ 2]. Other infections have included seeding by prosthetic material or surgery with isolates from brain abscess, CSF, joint space, vertebrae, and breast implant [ 2].

Table 1

To our knowledge, we are the first to report a case of G. adiacens as a cause of monomicrobial nonneutrocytic bacterascites. Bacterascites is thought to represent colonization of ascites fluid and may progress to the life threatening complication of spontaneous bacterial peritonitis (SBP). The pathogens related to bacterascites are similar to SBP; however the diagnosis of SBP requires the presence of >/= 250 PMN cells/mm ³ in addition to a positive Gram stain and/or culture of the ascitic fluid [ 24, 25]. The pathogenesis of SBP is thought to be directly related to hepatic dysfunction, with portal hypertension and local intestinal immunodeficiency leading to intestinal bacterial overgrowth and intestinal mucosal edema leading to breakdown of the epithelial barrier and increased permeability, which can allow for bacterial translocation to other tissues. In patients with ascites fluid that contains protein levels <1 g/dL and/or C3 levels < 13 mg/dL, there is a predisposition for infection [ 24].

Notably, Altay et al. described a case of G. adiacens bacterial peritonitis in a 55-year-old woman, but this was thought to be a peritoneal dialysis-related infection [ 13]. In that case, the patient was being treated empirically with intraperitoneal cefazolin and gentamicin when repeat cultures of the dialysate grew a single colony of G. adiacens susceptible to the empiric regimen. The patient completed 14 days of antibiotic therapy and showed clinical improvement after 2 days with concomitant decrease in ascites leukocytosis [ 13].

The origin of G. adiacens in our patient remains unclear. The possibility of an occult colon cancer leading to bacterial translocation, akin to Streptococcus bovis, was considered, but as colonoscopy was unrevealing for malignancy, this is unlikely. As discussed above, CT and MRCP of the abdomen demonstrated a fluid collection near the tail of the pancreas that may have communicated with the wall of the descending colon. Although subsequent colonoscopy did not show evidence of a direct communication, such an area of weakness in the gut wall may have been susceptible to earlier bacterial translocation.

Granulicatella spp., when not seen as a causative agent in infective endocarditis or other endovascular infections or bacteremia, have been associated with surgical intervention or seeding from a prosthesis [ 2]. As this patient had prior extensive abdominal surgery, it is possible that the original introduction of G. adiacens occurred during surgery and simply went undetected due to his lack of symptoms. This possibility seems less likely given that the patient had undergone one previous paracentesis several months earlier that grew no organism; however G. adiacens is not easily detected and has been found in peritoneal fluid previously documented as culture-negative [ 13]. It remains questionable whether the presence of Granulicatella spp. bacterascites was clinically significant, given the patient's failure to develop peritonitis.

The question of asymptomatic bacterascites is controversial as to whether it may be an incidental finding in patients without laboratory diagnosis of spontaneous bacterial peritonitis. The tendency is to err on the side of treatment in these cases. Older data show that, in patients with nonneutrocytic monomicrobial bacterascites, 62% (65/105) became sterile without antimicrobial intervention. The remaining 38% progressed to SBP [ 24]. The current recommendations for antibiotic treatment of and prophylaxis against SBP are targeted toward patients with cirrhosis and low ascites protein levels, neither of which describes this patient [ 25]. With respect to Granulicatella spp. as a causative agent, more data would be necessary to draw conclusions regarding the pathogenicity of this particular organism in ascites fluid. Limitations of earlier data are subject to the nutritionally variable nature of this organism, as its prior eponym suggests. Fortunately, 16s rRNA sequencing and mass spectrometry are becoming increasingly more common diagnostic tools, in some cases replacing traditional culture, which often confused this organism with poorly growing Streptococcus.

Our patient was treated with a 5-day course of intravenous vancomycin although Granulicatella adiacens infections have most commonly been treated with a beta-lactam antibiotic (). Intravenous vancomycin was chosen in this case because the patient had a penicillin allergy. Additionally, antibiotic susceptibility testing could not be performed for this isolate so beta-lactam antibiotic susceptibility or resistance could not be assessed. A limitation of our report is that successful eradication was not definitively demonstrated, as repeat paracentesis was not performed because the patient was doing well clinically, and our patient was asymptomatic prior to initiation of microbial therapy. Contamination is not suspected, as the organism grew from two separate cultures, obtained two days apart. If our patient manifests symptoms or if future blood or ascites fluid cultures grow Granulicatella spp., further evaluation is warranted with blood cultures and a repeat echocardiogram as well as additional abdominal/pelvis imaging. Repeat paracentesis with positive culture could indicate a complication such as an abscess formation or continued reinfection via translocation. At the current time, the patient has been out of the hospital for more than six months, and he has experienced no apparent complications.

This case presents an interesting finding of Granulicatella spp. as an infectious agent involved in bacterascites with potential to progress to spontaneous bacterial peritonitis that has not been previously described in the literature. Clinical suspicion and testing for Granulicatella spp. in peritoneal fluid may help us to learn more about this commensal organism of the GI tract and its pathogenicity and response to therapy. We would recommend serial paracenteses with monitoring for clearance of the organism from the fluid and/or development of laboratory confirmed neutrocytic SBP for future cases prior to initiation of therapy.

Conflict of Interests

The authors declare that there is no conflict of interests regarding the publication of this paper.

References

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13. Altay M., Akay H., Yildiz E., Duranay M. A novel agent of peritoneal dialysis-related peritonitis: [ Granulicatella adiacens . [ PubMed] Google Scholar]

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17. Fukuda R., Oki M., Ueda A., et al. Vertebral osteomyelitis associated with [ Granulicatella adiacens . [ PubMed] Google Scholar]

25. Runyon B. A. [ AASLD Practice Guideline. AASLD; 2012. Management of adult patients with ascites due to cirrhosis: an update 2012. [ PubMed] Google Scholar]

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Case Report of Granulicatella adiacens as a Cause of Bacterascites

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Granulicatella adiacens is a Gram-positive coccus, formerly grouped with nutritionally variant Streptococcus, often found as commensal bacteria of the human oral cavity, urogenital tract, and gastrointestinal tract. Prior case reports have demonstrated Granulicatella spp. as a pathogen that can cause bacteremia and infective endocarditis particularly of prosthetic valves and pacemaker leads.

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Granulicatella species are a normal component of the oral flora, found in dental plaque, endodontic infection, and dental abscesses, along with causes of a variety of serious infections. Bloodstream infections such as endocarditis have been reported. In addition, studies have shown that this microorganism can cause infection of the central nervous system.

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Kingdom: Bacteria
Phylum: Firmicutes
Class: Bacilli
Order: Lactobacillales
Family: Carnobacteriaceae
Genus: Granulicatella
Species: G. Adjacens

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Granulicatella adjacens are catalase-negative and oxidase-negative, facultatively, anaeorbic, Gram-positive cocci that are normal components of oral flora. (Below is the image of Granulicatella Adjacens)