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Year : 2020  |  Volume : 38  |  Issue : 2  |  Page : 216--218

Community-acquired infection caused by small-colony variant of Staphylococcus aureus

Sumit Rai1, Pramod Kumar Sharma2, Nirpex Tyagi1, Sugandh Agarwal1,  
1 Department of Clinical Microbiology, Super Specialty Paediatric Hospital, Postgraduate Teaching Institute, Noida, Uttar Pradesh, India
2 Department of Paediatric Surgery, Super Specialty Paediatric Hospital, Postgraduate Teaching Institute, Noida, Uttar Pradesh, India

Correspondence Address:
Dr. Sumit Rai
Department of Clinical Microbiology, Super Specialty Paediatric Hospital, Postgraduate Teaching Institute, Sector 30, Noida, Uttar Pradesh


Staphylococcus aureus and other Gram negative bacteria produce small colony variants (SCV) which usually emerge after exposure to antimicrobials. They cause repeated infections, treatment failures and often pass unnoticed during cultures due to unusual appearance and incomplete incubation. This infectious disease grand round highlights a similar clinical case with atypical history and appearance of a SCV of S. aureus and why prolonged incubation is necessary for aspirates from patients with recurrent infections like abscesses.

How to cite this article:
Rai S, Sharma PK, Tyagi N, Agarwal S. Community-acquired infection caused by small-colony variant of Staphylococcus aureus.Indian J Med Microbiol 2020;38:216-218

How to cite this URL:
Rai S, Sharma PK, Tyagi N, Agarwal S. Community-acquired infection caused by small-colony variant of Staphylococcus aureus. Indian J Med Microbiol [serial online] 2020 [cited 2020 Dec 1 ];38:216-218
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Small colony variants (SCV) among Staphylococcus aureus are easily missed mutant strains which are known to cause recurrent infections and harbor atypical phenotypic and resistance patterns. Their uncharacteristic appearance on sheep blood agar and slow growth makes them prone to be overlooked as contaminants. They are known emerge after exposure to multiple antibiotics and cause persistent infections. However, we present a case which presented as community acquired infection caused by a small colony variant of Staphylococcus aureus in an infant never exposed to antimicrobials previously.

 Case Report

An 11-month-old infant was brought to the paediatric surgery outpatient department with complaints of a small abscess and pain in the right axilla with surrounding swelling for the past 7 days and fever for 3 days. There was no suppuration and the patient was initially managed at some health-care facility with magnesium sulphate dressing. The general condition of the child was fair and his vitals were stable. The swelling was approximately 4 cm × 3 cm in the right axilla. The skin over the swelling was red and warm fluctuant and tender. Laboratory investigations revealed leucocyte counts of 24,800/mm 3, with a differential count of neutrophils 58%, lymphocytes 34%, eosinophils 3% and monocytes 5% and adequate platelet count. Ultrasonography of the right axilla detected well-defined heterogeneously hypoechoic lesion with liquefied contents and subcutaneous oedema associated with multiple smaller satellite lesions. Incision and drainage of the abscess was done under general anaesthesia and approximately 20 mL of aspirated pus was sent for microbiological investigations.

Differential diagnosis

This is a case of an infant presenting with an erythematous, warm, tender and fluctuant axillary swelling; the provisional diagnosis most likely appears to be a pyogenic abscess. However, had the abscess been and non-tender with suppuration at the intradermal injection site on the lateral aspect of the upper arm, one would suspect Bacillus Calmette–Guérin abscess. Other differential diagnoses would include infective lymphadenopathy or secondary infection of a tubercular lymph node which would have been matted and presented with other systemic constitutional symptoms like fever of unknown origin. Lymphoma and metastatic lymphadenopathy are rare for this age, for the location and if present, these are usually seen in patients of breast carcinomas which also is not suspected here. Fungal abscess is another possibility but extremely rare. The patient did not have any contact with animals or arthropod bites to include zoonotic infections in the differential diagnosis like cat-scratch disease and ulceroglandular infections like tularaemia. Absence of epitrochlear lymphadenopathy ruled out congenital syphilis. However, ultrasonography, which is the gave the impression of diagnostic modality for children under 14 years, favoured pyogenic abscess.

Additional investigations

Microscopy of the aspirate in Gram's stain revealed numerous pus cells and no organisms, while no acid-fast bacilli were observed in Ziehl–Neelsen staining. Culture was done as per the standard protocol. After 24 h of aerobic incubation, pure growth of tiny, approximately 0.2 mm pinpoint, slightly pigmented, non-hemolytic colonies were observed on sheep blood agar (SBA) and no growth was observed on MacConkey agar. Staining revealed Gram-positive cocci in clusters, which gave a positive catalase reaction. Tube coagulase performed with rabbit plasma (HiMedia) with Staphylococcus aureus ATCC 25923 as a positive control was negative after 6 h but turned positive after overnight incubation at 37°C. The isolate was put up for identification and susceptibility in Vitek2 Compact (BioMerieux, France). Manual susceptibility was put up for S. aureus as per the Clinical and Laboratory Standards Institute protocol. After further incubation for 24 h (total 48 h), the colony size grew larger with still no haemolysis or pigmentation. After further aerobic incubation for 1 more day (total 72 h), the SBA plate demonstrated a typical 'fried egg appearance' as described for small-colony variant (SCV) of S. aureus with central raised and flat peripheral parts [

[Figure 1]a, [Figure 1]b, [Figure 1]c, [Figure 1]d.[1],[2] Vitek2 identified the isolate as S. aureus but failed to detect growth in the susceptibility card. The manual antibiotic susceptibility testing on Mueller-Hinton agar plate demonstrated very fine growth with susceptibility to amikacin, tetracycline, teicoplanin and linezolid and resistance to cefoxitin, gentamicin and erythromycin and positive for inducible clindamycin resistance (D-test). Vancomycin minimum inhibitory concentration using E-test (AB BioMerieux) was 2 μg/mL.{Figure 1}


The patient was started on vancomycin in the 'meningitis dose' of 60 mg/kg/day and amikacin in conventional paediatric doses. The therapy was continued for 7 days and based on the clinical judgement, the patient was discharged on oral linezolid for another 1 week and was advised follow-up in the outpatient department. After completion of 1 week of the oral linezolid treatment, the patient returned with the infection resolved. There were no relapses in follow-up.

Learning pearls

Microbiological perspective

SCVs among Staphylococcus spp are usually auxotrophic variants that arise out of chronic exposure to antibiotics and cause infections with chronic and relapsing courses based on their adaptive intracellular lifestyle. They are characterized by small colony size, slow growth and downregulated virulence genes, while the genes for biofilm formation and adhesion are usually upregulated. SCVs have been characterized based on auxotrophism, toward specific substrates such ase haemin, Vitamin K (menadione) or thymidine, which support the growth of these SCVs or give enhanced growth under capnophilic conditions.[1],[3] Genetic mutants develop based on what antibiotics have been used to treat the patient. Long-term aminoglycoside therapy is associated with the development of menadione or haemin-dependent SCVs, while co-trimoxazole has been associated with the emergence of thymidine-dependent SCVs.[4],[5] This strain was negative for mannitol fermentation and failed to show any augmentation when attempted to grow around a plain disc impregnated with 15 μl menadione (Vitamin K).

Clinical perspective

In community-acquired methicillin-resistant S. aureus infections, conventional paediatric doses of vancomycin 40 mg/kg/day are unsuccessful. Instead, the 'meningitis dose' of 60 mg/kg/day achieves serum trough levels of 15–20 μg/mL that successfully eliminates the infection without causing nephrotoxicity in children compared to adults.[6] Despite appropriate treatment, the fact that SCVs can cause chronic, recurrent infections, the patient may be lost to follow-up, as such patients tend to move from various hospitals citing inappropriate treatment at the previous health-care facility. Patients with localized axillary swelling should be evaluated for aetiologies classically associated with the region involved according to the lymphatic drainage patterns. The management must include a complete haemogram, imaging like ultrasonography in children <14 years and computed tomography scan for more than 14 years, and biopsy depending on clinical presentation, location of the swelling and underlying risk factors. Biopsy options include fine-needle aspiration, core needle or open excisional biopsy. Antibiotics may be used empirically to treat acute unilateral axillary swellings, based on hospital antibiogram, especially in children with systemic symptoms. Corticosteroids have limited use in the management of such cases and should not be used without an appropriate diagnosis.

Take home points

For the diagnostician, one must examine growth from all aspirates from usually sterile sites very cautiously to not to miss out on SCVs and ensure that all purulent aspirates are enriched for a prolonged duration, if possible by automated methods. If a patient cites a history of recurrent purulent infections, besides ruling out causes such as diabetes mellitus, primary immunodeficiencies, cystic fibrosis or autoimmune disorders, one should keep SCVs in the differential diagnosis especially if there is a history of chronic treatment with multiple antibiotics and send aspirates for prolonged culture and incubation.

Declaration of patient consent

The authors certify that they have obtained all appropriate patient consent forms. In the form the patient(s) has/have given his/her/their consent for his/her/their images and other clinical information to be reported in the journal. The patients understand that their names and initials will not be published and due efforts will be made to conceal their identity, but anonymity cannot be guaranteed.

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Conflicts of interest

There are no conflicts of interest.


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