J. Microbiol. Infect. Dis., (2026), Vol. 16(3): 145–149

Case Report

10.5455/JMID.2026.v16.i3.2

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A rare case of Citrobacter youngae co-infection in a diabetic foot ulcer: Importance of deep tissue culture in a Tertiary Care Hospital

Arokiamary Ramaraj, Karthika Jayakumar^*, Jaison Jayakaran and Sandeep Kadali

Department of Microbiology, Shri Sathya Sai Medical College & Research Institute, Sri BalajiVidyapeeth (Deemed to be University), Puducherry, India

*Corresponding Author: Karthi Jayakumar. Professor and Head, Department of Microbiology, Shri Sathya Sai Medical College and Research Institute, Tamil Nadu, India. Email: jayakumarkarthika900 [at] gmail.com

Submitted: 10/02/2026 Revised: 20/05/2026 Accepted: 31/05/2026 Published: 07/07/2026

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ABSTRACT

Background: Diabetic foot infections (DFIs) are often polymicrobial and require accurate microbiological diagnosis for effective management. Superficial cultures may fail to detect deeper pathogens, leading to inadequate therapy. This study aims to highlight the role of deep tissue culture in identifying uncommon pathogens.

Case Description: We report a single case study of an 82-year-old male with long-standing diabetes mellitus presenting with a non-healing left foot ulcer following a thorn prick injury. Initial pus culture yielded Klebsiella pneumoniae, and empirical therapy failed to produce clinical improvement. Deep tissue culture obtained during surgical debridement revealed polymicrobial infection with K. pneumoniae and Citrobacter youngae. Identification was confirmed using the VITEK 2 automated system. Antibiotic therapy was modified based on susceptibility testing, resulting in significant clinical recovery.

Conclusion: This case emphasizes that deep tissue sampling is crucial in non-responding DFIs for accurate pathogen identification and targeted therapy. Detection of rare organisms such as C. youngae can significantly alter clinical management and improve outcomes.

Keywords: Antimicrobial susceptibility, Citrobacter youngae, Deep tissue culture, Diabetic foot ulcer, Vitek identification.

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Introduction

Diabetic foot infections are a major cause of morbidity and are frequently polymicrobial, involving both aerobic and anaerobic organisms (Lipsky, 2012). Gram-negative bacilli are commonly implicated in chronic infections, particularly in immunocompromised patients (Koneman et al., 2017).

Members of the genus Citrobacter are facultative anaerobic Gram-negative bacilli belonging to the family Enterobacteriaceae and are widely distributed in the environment and human gut (Samonis et al., 2009). While Citrobacter freundii and Citrobacter koseri are commonly reported pathogens, Citrobacter youngae remains a rare clinical isolate (Gupta et al., 2013).

Recent advances in automated identification systems such as VITEK and MALDI-TOF have improved detection of uncommon organisms (Liu et al., 2018). This case highlights the diagnostic importance of deep tissue culture in identifying rare pathogens contributing to persistent diabetic foot infections.

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Case Details

This is a single case report conducted in a tertiary care hospital between January and March 2026.

Patient presentation

One patient with a clinically diagnosed diabetic foot infection not responding to empirical therapy was investigated.

Clinical findings

Non-healing ulcer with purulent discharge.

Sample collection

Following surgical debridement, pus aspirate and deep tissue samples (~1 g) were collected under sterile conditions.

Transport procedure

Samples were transported within 30 minutes in sterile containers without transport media as per IDSA guidelines (Lipsky, 2012).

Culture method

Samples were inoculated onto Blood agar and MacConkey agar and incubated at 37°C for 18–24 hours under aerobic conditions.

Identification

Preliminary identification was done using biochemical tests. Final confirmation was performed using the VITEK 2 automated system (bioMérieux) (Farmer et al., 1985).

Advanced methods such as MALDI-TOF were recommended but not available in this setting.

Antimicrobial sensitivity test

Performed using the VITEK 2 system and interpreted according to CLSI guidelines (2024).

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Results

Gram stain from pus and tissue samples showed abundant pus cells and Gram-negative bacilli. Pus culture yielded K. pneumoniae alone. deep tissue culture using VITEK-2 demonstrated rare pathogen citrobacter youngae alone. Biochemical characteristics included motility, citrate positivity, H₂S production, and glucose fermentation. Definitive identification was achieved using VITEK 2 with high confidence.

Microbiological findings

Microbiological findings are seen in Table 1.

Antimicrobial sensitivity

The K. pneumoniae isolate was sensitive to ceftriaxone, amikacin, ciprofloxacin, and piperacillin–tazobactam.

The C. youngae isolate demonstrated resistance to multiple beta-lactams but remained susceptible to meropenem, aminoglycosides, trimethoprim–sulfamethoxazole, and tigecycline.

Treatment modification

Based on susceptibility results, therapy was modified to cotrimoxazole, resulting in clinical improvement.

Outcome

Ulcer started healing well.

Biochemical tests are shown in Figure 1. Gram stain showing Gram-negative bacilli from the tissue sample is shown in Figure 2. VITEK report screenshot is shown in Figure 3. Wound images are shown in Figure 4.

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Discussion

Deep tissue cultures provide several advantages over superficial swabs, including more accurate identification of true pathogens, reduced contamination from skin flora, and better detection of anaerobic and deep-seated organisms (Janda and Abbott, 2006).

Table 1. Microbiological findings.

Fig. 1. Biochemical testing.

Fig. 2. Gram stain showing Gram-negative bacilli from tissue sample.

Fig. 3. VITEK report screenshot.

Fig. 4. Wound images (Before and After).

Citrobacter youngae remains a rare isolate, accounting for approximately 3%–4% of clinical Citrobacter isolates in hospital-based studies (Chow et al., 1991).

Its identification in deep tissue suggests a true pathogenic role rather than colonization.

Advanced identification methods such as MALDI-TOF or molecular sequencing could further improve epidemiological understanding (Murray et al., 2020).

Additional clinical details include the duration of diabetes: >15 years, HbA1c: 8.6%, and wound classification was Wagner Grade III.

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Conclusion

This case demonstrates that deep tissue culture is essential in non-responsive diabetic foot infections. Identification of rare pathogens such as C. youngae significantly impacts antimicrobial therapy and clinical outcome (Radice, 2001; Gupta et al., 2013; Fonton et al., 2024; Lee, 2024).

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Acknowledgment

The authors express their sincere gratitude to the Management of Sri Balaji Vidyapeeth and Shri Sathya Sai Medical College & Research Institute for providing the necessary infrastructure and institutional support to carry out this work. We are deeply thankful to the faculty and technical staff of the Department of Microbiology for their valuable guidance, continuous encouragement, and laboratory assistance throughout the study. The authors also extend special thanks to the Department of Microbiology for facilitating sample processing, microbiological analysis, and technical support essential for the successful completion of this work. Finally, we acknowledge all contributors involved directly and indirectly in the preparation and presentation of this manuscript.

Funding

None.

Authors’ contributions

Dr. Arokiamary: Conceptualization of the study, data collection, microbiological analysis, literature review, manuscript drafting, and preparation of the final manuscript. Dr. Karthi Jayakumar: Study supervision, critical review of the manuscript, guidance in study design, interpretation of microbiological findings, and final approval of the manuscript. Dr. Jaison Jayakaran: Data interpretation, manuscript editing, technical guidance in laboratory procedures, and critical revision of the manuscript for important intellectual content. Mr. Sandeep: sample processing assistance, data compilation, and technical assistance during microbiological investigations.

Conflict of interest

The authors declare that there is no conflict of interest.

Data availability

The data supporting the findings of this study are available within the article. Additional data related to this study are available from the corresponding author upon reasonable request.

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