Paracoccus yeei is a rare gram-negative coccobacillus bacterium with notable clinical significance. While its epidemiology is not extensively studied, a growing body of literature reports infections caused by this microorganism. Most cases have been documented in the USA. Still, occurrences have also been reported in several other countries, including Mexico, Australia, France, India, Japan, Korea, Canada, China, Spain, and Taiwan.  

In terms of affected demographics, Paracoccus yeei infections have been identified in individuals spanning a wide age range, from as young as 6 weeks to as old as 77 years, with a noted male predominance. This bacterium tends to pose a greater risk to immunocompromised individuals or have a history of injury, including conditions such as diabetes mellitus, chronic kidney disease, malignancy, trauma, surgical procedures, or intravenous drug use.  

Three illustrative cases shed light on the clinical manifestations of Paracoccus yeei infections. In one instance, a 65-year-old male with a history of heroin dependence and a prior gasoline injury to his left eye suffered a traumatic injury to his right eye. It resulted in a central corneal ulcer, hazy pupil, eyelid swelling, periorbital edema, central vision loss, and conjunctival chemosis. The culture of the eye ulcer revealed Paracoccus yeei, which demonstrated sensitivity to beta-lactam antibiotics, ultimately leading to improved vision with treatment.  

In another case, a 67-year-old male with comorbid diabetes mellitus and chronic kidney disease developed fever, chills, and abdominal pain following peritoneal dialysis. His dialysate fluid exhibited cloudiness and a high white blood cell count, with Paracoccus yeei identified in the culture. This particular strain was resistant to cephalosporins and quinolones. Treatment with intraperitoneal cefepime and gentamicin over 14 days resulted in recovery.  

Lastly, a 6-week-old female with a congenital heart defect underwent cardiac surgery and subsequently developed postoperative meningitis. Clinical symptoms included headache, vomiting, and seizures, with cerebrospinal fluid analysis revealing pleocytosis and elevated protein levels. Cultures of the cerebrospinal fluid confirmed the presence of Paracoccus yeei, which was susceptible to aminoglycosides and carbapenems. Successful treatment was achieved with a 21-day course of intravenous meropenem and amikacin. 

Classification and Structure: 

Kingdom: Bacteria 

Phylum: Pseudomonadota 

Class: Alphaproteobacteria 

Order: Rhodobacterales 

Family: Rhodobacteraceae 

Genus: Paracoccus 

Species: Paracoccus yeei  

Paracoccus yeei is a gram-negative bacterium characterized by its coccobacillus or short rod-shaped morphology. Sometimes, it may also present as diplococci, appearing as pairs of spherical cells.

Paracoccus yeei can exhibit a distinctive feature where a visible vacuole is present in the central region, giving it an “O” shape. 

Genetically, P. yeei possesses a circular chromosome with an approximate size of 3.4 Mb. This bacterium also harbors eight extrachromosomal replicons, consisting of three chromids and five plasmids, varying in size. 

The genomic architecture of P. yeei is notably influenced by acquiring genomic islands, prophages, and insertion sequences. These elements contribute to the diversity and adaptability of the bacterium, allowing it to thrive and adapt to various environmental conditions. 

The presence of toxin-antitoxin (TA) systems was identified across all extrachromosomal replicas (ECRs) of the P. yeei CCUG 32053 strain. These systems play an essential role in plasmid stabilization by selectively removing plasmid-less cells on a post-segregational level. A member of the parDE superfamily of TA systems, designated as pYEE6, stands out among the identified loci.  

Furthermore, six loci encode toxins from the ParE/RelE class (pYEE8, two loci of pYEE5, pYEE4, pYEE7, pYEE3), while four more encode toxins from the VapC superfamily with a pilT N-terminal domain (pYEE6, two loci of pYEE4 & pYEE2). Surprisingly, these toxin proteins are coupled with antitoxins generally associated with toxins from several TA families. This fascinating arrangement represents the diverse and complicated structure of P. yeei’s TA systems.   

Notably, a study reported variations in antigenic reactions among P. yeei strains isolated from different clinical specimens when tested with antisera prepared from P. yeei ATCC BAA-599, the species’ type strain. These variations in antigenic properties suggest potential differences in the surface antigens or other immunogenic factors among P. yeei strains, which may have implications for diagnostics and host immune responses.   

The genomes of P. yeei strains TT13 and FDAARGOS_252 are characterized by a substantial presence of insertion sequences (ISs). In total, they carry 204 complete ISs and 152 partial elements. These IS elements can contribute to genome plasticity and may play a role in genomic rearrangements, gene expression regulation, or adaptation to different environmental niches.  

The phylogenetic tree based on the concatenated nucleotide alignments of 7 core genes namely- recA, atpD, dnaA, gyrB, dnaK, rpoB, and thrC, provides insights into the evolutionary relationships within the genus Paracoccus. This tree helps classify and relate different Paracoccus species based on their genetic similarities, shedding light on their evolutionary history and diversification. 

Paracoccus yeei exhibits several putative virulence factors that contribute to its pathogenic potential. These factors include genes responsible for adhesins, invasins, secretion systems, toxins, iron acquisition systems, stress response proteins, and antibiotic resistance mechanisms.

Among these, urease accessory proteins are crucial for the maturation of urease, a key enzyme for the bacterium—these accessory proteins aid in inserting two nickel ions at the enzyme’s active site. Nickel ion transport genes are found close to urease synthesis gene clusters in all known P. yeei genomes. 

 P. yeei is chromosomally encoded virulence factors, including superoxide dismutases. These enzymes may play a role in evading host defense mechanisms that employ reactive oxygen species. Additionally, putative sugar transferases, similar to undecaprenyl-phosphate galactose phosphotransferases of Haemophilus spp., are likely involved in lipopolysaccharide biosynthesis.

The clinical relevance of Paracoccus yeei is exemplified in cases of bacteremia, such as in patients with decompensated cirrhosis who present with variceal bleeding. Infections are relatively common among individuals with cirrhosis who experience gastrointestinal hemorrhage. Prophylactic antimicrobial therapy with third-generation cephalosporins is often recommended in such patients. However, it is noteworthy that in up to 50% of cases of cirrhosis-associated clinical sepsis, the infectious source remains unidentified, posing challenges in diagnosis and management. 

Like many bacterial infections, the human host’s defense against Paracoccus yeei relies on a multi-layered immune response that includes constitutive innate immune mechanisms and inducible immune responses. This intricate defense system is designed to prevent the establishment of infection and limit the activation of pattern recognition receptors (PRRs) by reducing the accumulation of pathogen-associated molecular patterns (PAMPs).   

Constitutive mechanisms also include the downregulation of PAMP signaling through PRRs. This downregulation helps prevent the overactivation of PRR-based inducible immune responses. By limiting PRR-induced expression of molecules like type I interferon and IL-1β, the immune system avoids excessive inflammation during the initial stages of infection.  If the level of PAMPs exceeds a certain threshold, PRR-based immunity is activated. This activation triggers inflammation and promotes the subsequent activation of the adaptive immune response, which involves T cells and antibodies.   

Complement-mediated phagocytosis is another crucial aspect of the immune response against bacterial infections like Paracoccus yeei. This process involves the specific recognition of complement components bound to the pathogen’s surface by complement receptors on phagocytes. Activation of the complement system, which can occur when the lectin pathway detects glycans, leads to the formation of C3 convertase & the generation of C3b. C3b then binds to complement receptors, initiating phagocytosis and facilitating the clearance of bacteria. 

Clinical manifestations of Paracoccus yeei infection can include ocular symptoms that affect the eyes and surrounding structures. These ocular manifestations may be conjunctivitis, uveitis, corneal ulcers, or even corneal transplant graft infections. For instance, a case report highlighted a 65-year-old male patient with a history of heroin dependence and a previous gasoline injury to the left eye.

This individual experienced a traumatic injury to the right eye, resulting in a central corneal ulcer. The clinical presentation included symptoms such as a hazy pupil, upper and lower eyelids swelling, periorbital edema, central vision loss, and conjunctival chemosis. 

Culture test: Paracoccus yeei can be cultured on agar plates, including Columbia sheep blood, chocolate, or MacConkey agar. Colonies typically appear nonhemolytic, whitish-gray, and convex, measuring 0.5 to 1 mm in diameter. These characteristic colonies may take approximately 48 hours to 3 days to develop.  

Gram Staining: Microscopic examination through Gram staining reveals that Paracoccus yeei is a gram-negative bacterium with a coccobacillus or short rod shape. It may occasionally appear as diplococci, consisting of pairs of spherical cells. Sometimes, a visible vacuole at the center may give it an “O” shape.  

Biochemical Tests: Paracoccus yeei is oxidase and catalase positive, characteristics that are significant for its differentiation from other bacteria. Its morphology and oxidase positivity may lead to potential confusion with Neisseria or Moraxella species. However, further biochemical tests, including nitrate reduction, glucose fermentation, and urease production, can help distinguish Paracoccus yeei from these genera.   

Molecular Identification: Molecular methods such as nucleic acid amplification tests (NAATs) are employed for accurate and rapid identification. These tests, including PCR or sequencing, target specific genes like 16S rRNA, gyrB, or recA, facilitating precise identification beyond phenotypic characteristics.  

Antimicrobial Susceptibility Testing: It is crucial to determine the most effective treatment. Paracoccus yeei typically displays sensitivity to beta-lactam antibiotics and aminoglycosides but resistance to cephalosporins and quinolones. However, susceptibility patterns may vary among strains and methods used. Conducting antimicrobial susceptibility testing is essential to guide appropriate therapy and prevent complications associated with resistant strains. 

• To reduce the risk of exposure, individuals should wear protective gloves and footwear when handling soil or water. After potential exposure, thorough handwashing is essential to remove any contaminants. 

• Paracoccus yeei is an opportunistic pathogen that poses a higher risk to individuals with compromised immunity or injuries. Therefore, maintaining overall health and immunity is essential for infection prevention. This includes adhering to a balanced diet, regular exercise, sufficient sleep, stress management, and considering preventive vaccines when available. 

First comprehensively documented case of Paracoccus yeei infection in a human – PubMed (nih.gov)  

Paracoccus yeei: a new unusual opportunistic bacterium in ambulatory peritoneal dialysis – ScienceDirect