KEYWORDS: Emerging pathogen, opportunistic infection, limitations of automated systems, MALDI-TOF MS

BACKGROUND

Sphingomonas paucimobilis is an emerging opportunistic, nil-fermenter implicated in a wide range of healthcare-associated infections, including bacteremia, pneumonia, urinary tract infections, and other pyogenic infections. It exhibits low virulence ascribed to a distinct glycosphingolipid structure in the cell wall, lack of lipopolysaccharide components, and endotoxic activity.1 Consequently, human infections are uncommon and are primarily reported in immunocompromised patients or in association with medical devices.

S. paucimobilis is ubiquitous in nature, most abundantly found in water and soil.2 The water distribution infrastructure, particularly through biofilm formation, may serve as a potential source of infection.3 Being a rare, emerging pathogen, S. paucimobilis is not routinely identified by clinical microbiology laboratories. Conventional phenotypic methods for the identification of this organism remain relevant, particularly in resource-limited settings. Nevertheless, conventional biochemical tests often fail to provide species-level resolution, and misidentification is not uncommon. The slow-growing nature of S. paucimobilis and difficulty in demonstrating its motility due to temperature sensitivity may delay diagnosis and affect therapeutic decision-making. Although advanced automated technologies like matrix-assisted laser desorption/ionisation time of flight mass spectroscopy (MALDI-TOF MS) offer greater precision and lower turnaround time, they may face limitations due to under-representation of rare/emerging species in databases. Therefore, enhancing awareness of conventional morphological and biochemical characteristics, alongside refining diagnostic algorithms, remains essential for timely and accurate identification.

Owing to chromosomally encoded β-lactamases, the majority of strains of S. paucimobilis are resistant to penicillin and first-generation cephalosporins.4 However, most are susceptible to tetracycline, chloramphenicol, cotrimoxazole, and aminoglycosides.5 This makes its identification imperative for guiding appropriate therapeutic management.

Here, we report a case of S. paucimobilis UTI from a patient with kidney impairment and discuss the challenges pertaining to its identification.

CASE PRESENTATION

A 42-year-old male patient presented with a low-grade fever and thrombocytopenia for a one-month duration. Laboratory investigations on admission showed a raised creatinine level of 8.63 mg/dL and urea 179 mg/dL. However, urine output was found normal, and other parameters in the kidney function test were within normal limits. Furthermore, other investigations, including complete blood count, peripheral smear, liver function tests, and viral markers, did not reveal any significant findings. The patient had an unremarkable medical history. The patient’s urine sample showed 8-10 RBCs and 15-20 WBCs per high-power field. However, blood culture was sterile. Haemodialysis was commenced in view of worsening kidney function.

Subsequently, the urine sample showed pure growth of 105 CFU/mL (significant bacteriuria) of non-lactose fermenting (NLF) colonies on cysteine lactose electrolyte deficient (CLED) agar. The colonies were 1-2 mm in size and pale yellow in colour after 24 hours of incubation on CLED agar. Identification of the isolate was attempted using MALDI-TOF MS (VITEK®MS, bioMérieux, Marcy-I’Étoile, France), although it failed to yield a reliable result. Identification by MALDI-TOF MS was re-attempted; however, the isolate could not be reliably identified. Simultaneously, identification was carried out using both conventional microbiological methods and the Vitek-2 automated system for confirmation. Gram’s stain revealed Gram-negative rods. The organism was catalase-positive, oxidase-weak positive, and non-motile on hanging drop preparation. A subculture on blood agar medium showed yellow pigmented colonies after 24 hours of incubation. The isolate was identified as Sphingomonas paucimobilis by the Vitek-2 system. Furthermore, the isolate was susceptible to amikacin, cotrimoxazole, chloramphenicol, netilmicin and gentamicin and resistant to ciprofloxacin and tetracycline on antibiotic susceptibility testing by the Vitek-2 system. A follow-up urine sample was requested to isolate the same organism and to confirm its role as the true pathogen of urinary tract infection (UTI). The repeat sample demonstrated similar growth characteristics and antimicrobial susceptibility patterns.

Significant diagnostic challenges arose due to the organism’s phenotypic similarities with other non-fermenting oxidase-positive Gram-negative bacilli such as Burkholderia spp. (gray, chartreuse, yellow), Pseudomonas stutzeri (Gray or slight yellow), Chryseobacterium spp. (yellow- orange), Stenotrophomonas maltophilia (lavender, gray, slight yellow) as given in Table 1. 

Table 1. Differentiating features between Sphingomonas paucimobilis and its differential diagnoses.5

The sample was reported as S. paucimobilis UTI (105 CFU/mL), and the patient was advised oral cotrimoxazole (160/800 mg) BD for 7 days. Follow-up urine sample collected after three days yielded 0-2 RBCs and 3-4 WBCs per high-power field on routine microscopy and an insignificant bacterial count on culture. Fever subsided. The patient undergoes haemodialysis every 15-20 days at a local hospital for the kidney dysfunction and was prescribed corticosteroids.

DISCUSSION

Sphingomonas paucimobilis is an emerging, rare pathogen implicated in healthcare-associated infections.1 It is known to cause opportunistic infections in immunocompromised patients or device-associated infections. In the present case, the patient had kidney impairment and was started on corticosteroids, but was not catheterised at the time of sample collection. Pure growth of significant bacteriuria was observed in urine samples from a patient with clinical features and laboratory investigations suggesting impaired kidney function. The organism has been reported from a wide variety of nosocomial as well as community-acquired infections. Community-acquired infections of this organism are more common than nosocomial ones.7

As observed in our case, MALDI-TOF MS failed to yield an accurate identification of the organism, despite having isolated colonies. With the increasing recognition of the pathogenic potential of emerging organisms in various clinical scenarios, identification through MALDI-TOF MS may be hindered in some cases by the limited inclusion of rare organisms in standard spectral libraries. In addition, the presence of a mixture of organisms in clinical samples can further complicate the identification of these bacteria. In poly-microbial cultures, the subtle growth characteristics of S. paucimobilis may be overshadowed by more rapidly growing organisms. Moreover, close relatedness of species of interest may interfere with reliable identification.6

Sphingomonas paucimobilis is a Gram-negative, motile rod with a polar flagellum. Albeit the organism demonstrates temperature-sensitive motility, motility occurs at 18-22°C, but not at 37°C. Due to difficulty in demonstrating motility, it is known as ‘paucimobilis’.7 Colonies grown on blood agar are yellow pigmented, without any visible hemolysis, after 24 hours of incubation at ambient temperature. Oxidase reaction is weak positive or negative, aiding in narrowing down the differential.5 This underscores the continued relevance of conventional identification methods when automated techniques fall short. In the absence of standardised guidelines, antibiotic sensitivity-guided case-to-case therapy is warranted with prompt initiation to prevent complications.5

Given its rarity, non-specific clinical presentation and morphological similarities, S. paucimobilis may be easily misidentified for more commonly encountered Gram-negative non-fermenters, which include Pseudomonas aeruginosa, Acinetobacter baumannii, and Burkholderia cepacia, including other uncommon differential diagnoses as discussed above. However, a few key microbiological features aid in their differentiation (Table 1). Erroneous identification of S. paucimobilis can lead to suboptimal treatment choices due to the atypical resistance patterns among the nil-fermenters and further correlation with its pathogenic potential. 

CONCLUSIONS
S. paucimobilis is an emerging opportunistic pathogen capable of causing clinically significant infections. This case highlights the limitations of MALDI-TOF MS in accurately identifying uncommon organisms, reaffirming the importance of conventional microbiological techniques for a definite diagnosis. Early recognition and targeted antimicrobial therapy are essential for optimal patient outcomes in such atypical infections.

INFORMED CONSENT

Patient consent was duly obtained.

CONFLICT OF INTERESTS STATEMENT

The authors declare no conflict of interest.

SOURCE OF FUNDING 

This research received no specific grant from any funding agency in the public, commercial, or not-for-profit sectors. 

AUTHOR’S CONTRIBUTIONS

K: Contributed to data curation, investigation, formal analysis, draft writing and editing.
SM: Conceptualized the study and contributed to formal analysis, resources, supervision, reviewing and editing.
BKD: Contributed to supervision, resources and reviewing.

REFERENCES 

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2. Toh HS, Tay HT, Kuar WK, Weng TC, Tang HJ, Tan CK. Risk factors associated with Sphingomonas paucimobilis infection. J Microbiol Immunol Infect. 2011;44(4):289-95.

3. Gulati P, Ghosh M. Biofilm forming ability of Sphingomonas paucimobilis isolated from community drinking water systems on plumbing materials used in water distribution.  J Water Health.  2017;15(6):942-54.

4. Pascale R, Russo E, Esposito I, Leone S, Esposito S. Sphingomonas paucimobilis osteomyelitis in an immunocompetent patient. A rare case report and literature review. New Microbiol. 2013;36(4):423-6.

5. Washington CW, Stephen DA, Koneman EW, Allen SD, Janda WM, Schreckenberger PC, et al. Koneman’s color atlas and textbook of diagnostic microbiology. 7th ed. Philadelphia: Wolters Kluwer; 2017.

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7. Sagar D. Community Acquired Sphingomonas paucimobilis: Instigator or an Innocent Bystander. Indian J Med Microbiol. 2024;48:100524.