Severe lower limb infection by Kerstersia gyiorum: clinical and genomic insights into an underestimated pathogen

Abstract

Since Kerstersia gyiorum was first described and named in 2003, reports of human infections caused by this organism have gradually increased. Here, we present a detailed report of a severe case of lower right limb infection caused by K. gyiorum that was characterized by rapid disease progression and multidrug resistance. We also present the complete genome sequence of the isolate, WCHKG1. A systematic analysis of the clinical features of our case patient and previous K. gyiorum-infected patients revealed that the most common site of infection was the lungs (48%), and that the organism showed the lowest sensitivity to commonly used quinolones among the major antibiotic classes. Clinical infections caused by K. gyiorum may be underestimated, thus the use of quinolones in treating such infections should be avoided. Genomic and phylogenetic analyses of K. gyiorum identified conservation of antibiotic efflux pump systems and virulence factors, which may play critical roles in its antibiotic resistance and pathogenicity. Furthermore, evidence of clonal transmission in animals suggests a need for vigilance regarding potential clonal spread in clinical settings. Our study contributes to the current understanding of K. gyiorum and offers useful insights to support its clinical management and infection control.

1 Introduction

Kerstersia gyiorum, a Gram-negative coccobacillus belonging to the genus Kerstersia within the family Alcaligenaceae, was first described and named by Coenye et al. (1). The species name gyiorum, meaning “from the limbs,” was chosen because the organism was initially primarily isolated from lower-extremity wounds (1). However, K. gyiorum has since been detected in a variety of environments, including the intestines of brown-throated sloths (2), the blowholes of Yangtze finless porpoises (3), and boar semen (4), indicating a broad ecological distribution. For nearly a decade after its initial identification, there were no reports of K. gyiorum causing human clinical infections. Almuzara et al. (5) reported a case of cholesteatomatous chronic otitis media caused by K. gyiorum, followed an increasing number of studies documenting infections involving the ear (6), lower limbs (6), lungs (7), urinary tract (8), appendix (9), and bloodstream (10) in a human. Importantly, K. gyiorum is difficult to distinguish from other microorganisms using conventional methods, including biochemical tests and automated identification systems. This is primarily due to its biochemical phenotype being similar to other pathogens (such as Alcaligenes faecalis) (11), as well as its delayed inclusion in automated biochemical identification system databases (e.g., Vitek2) (5), leading to past misidentification or oversight in clinical laboratories (10, 12, 13). Consequently, its clinical significance may have been overlooked or underestimated. Previous studies have reported that K. gyiorum may be misidentified as Alcaligenes faecalis (5), Aeromonas salmonicida (14), or Lautropia mirabilis (10), which can delay accurate species identification and impact the timely implementation of appropriate treatment strategies. With the advancement of techniques such as matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI–TOF MS) and 16S rRNA gene sequencing, K. gyiorum can now be identified more accurately in clinical laboratories (15, 16). Furthermore, the maturation and widespread use of next-generation sequencing (NGS) have facilitated the acquisition of complete genome sequences for K. gyiorum isolates (2, 17, 18). However, a systematic analysis of the clinical and genomic characteristics of K. gyiorum is urgently needed to improve our understanding of this organism and establish a reliable foundation for infection prevention and treatment. In this study, we report a case of severe lower limb infection caused by K. gyiorum that was successfully treated. Additionally, we conducted a comprehensive analysis of the clinical and genomic features of K. gyiorum to help fill the current knowledge gap regarding this emerging pathogen.

2 Materials and methods

2.1 Bacterial isolation, culture, and identification

Colombian blood agar and MacConkey agar plates (Pangtong Medical Devices, Chongqing, China) were inoculated with wound exudate specimens and incubated at 37°C for 24 h in a 5% CO_₂ incubator. The species of the isolated strains were identified using MALDI–TOF MS. The K. gyiorum strain WCHKG1 was further purified, and its colony morphology was observed. Species identification was confirmed via 16S rRNA gene sequencing, as previously described (11).

2.2 Morphological characterization

Gram staining was performed using a commercial staining kit (Bomei Biotechnology, Hefei, China). Bacterial morphology and the Gram reaction were observed under a light microscope (Olympus, Tokyo, Japan) using oil immersion. Negative staining of WCHKG1 was performed using 2.0% (w/v) uranyl acetate, and its fine morphological features were observed under a transmission electron microscope (Hitachi, Japan) at an accelerating voltage of 80 kV.

2.3 Antimicrobial susceptibility testing

The minimum inhibitory concentrations (MICs) of antibiotics against WCHKG1 were determined using the broth microdilution method, in accordance with the Clinical and Laboratory Standards Institute (CLSI) guidelines (19). Escherichia coli ATCC 25922 was used as the quality control strain, and all tests were conducted in triplicate. Except for tigecycline, whose breakpoint was defined by the European Committee on Antimicrobial Susceptibility Testing (20), breakpoints for all other antibiotics were interpreted in accordance with CLSI criteria (19). Antimicrobial susceptibility testing for additional isolates was performed using the Vitek2-Compact analysis system (bioMérieux, France) and the Kirby-Bauer disk diffusion method.

2.4 Whole-genome sequencing

Genomic DNA of strain WCHKG1 was extracted using the QIAamp DNA Mini Kit (Qiagen, Hilden, Germany) and sequenced using the HiSeq X Ten platform (Illumina, San Diego, CA, United States), in accordance with the manufacturers’ protocols. For long-read sequencing, DNA from the same batch was prepared using the Rapid Sequencing Kit V14 (Oxford Nanopore Technologies, Oxford, United Kingdom), and sequencing was conducted on the MinION platform using an R10.4.1 flow cell. Paired-end 150-bp reads were trimmed to remove adapters using Trimmomatic v0.39 (21) and assembled into contigs using SPAdes v3.15.3 (22). For complete genome assembly, reads shorter than 1,000 bp or with an average quality score < Q8 were filtered out using NanoFilt v2.8.0 (23). To obtain the complete genome, a hybrid assembly of short and long reads was performed using Unicycler v0.4.3 (24). Default parameters were used for all bioinformatic tools unless otherwise specified.

2.5 Patients and clinical data

Clinical data collected from the patient reported in this study included comprehensive demographic information, background conditions, comorbidities, infection site, specimen type, diagnostic methods, identified pathogens, antimicrobial susceptibility results, antibiotic treatments, and clinical outcomes. In addition, we conducted literature searches of the PubMed, Web of Science, Embase, Ovid MEDLINE, Cochrane, bioRxiv, and medRxiv databases to identify all studies reporting human infections caused by K. gyiorum that had been published up to March 15, 2025. The search terms used were “Kerstersia gyiorum” and “K. gyiorum.” We also reviewed the reference lists of the retrieved articles. Studies published in both English and non-English languages were included, and Google Translate was used for translations of studies in languages other than English or Chinese. Relevant patient characteristics and infection-related information were extracted from all eligible reports and analyzed.

2.6 Genomic analysis

Whole-genome sequences of K. gyiorum available in the GenBank database as of March 15, 2025, were retrieved and analyzed alongside our genome sequence of WCHKG1. Quality control of the assembled genomes was performed using QUAST v5.3.0 (25) and CheckM2 v1.1.0 (26). Species identification was based on average nucleotide identity (ANI) analysis using fastANI v1.34 (27). Plasmid replicons, antimicrobial resistance genes, and virulence factors were identified using ABRicate¹ in conjunction with the PlasmidFinder (28), ResFinder (29), and VFDB (30) databases. Given the limited characterization of plasmids, resistance genes, and virulence factors in K. gyiorum, we applied relaxed thresholds of 60% for both percent identity and subject coverage. Single-nucleotide polymorphisms (SNPs) in the K. gyiorum genomes were identified using Snippy v4.6.0.²

2.7 Phylogenetic analysis

Core genes across the K. gyiorum genome sequences were identified and aligned using PIRATE v1.0.5.³ Homologous regions were identified and removed using Gubbins v3.4 (31). A maximum-likelihood phylogenetic tree was then constructed based on the genomic sequences with homologous recombination regions removed, using the GTRGAMMA model with 1,000 bootstrap replicates. The tree was visualized using iTOL.⁴

3 Results

3.1 Case overview

A 69-year-old female patient was admitted to the hospital with a 2-year history of swelling and pain, a 1-month history of ulceration in the right lower limb, and intermittent low-grade fever for 1 week. Upon admission, her highest recorded body temperature was 38.0 °C, without accompanying chills or rigors. She was a farmer by occupation, with no history of smoking or alcohol consumption. At admission, her comorbidities included varicose veins of the right lower limb, renal insufficiency, hyperuricemia, malnutrition, and anemia. On physical examination, the patient’s vital signs were as follows: respiratory rate 21 breaths/min, heart rate 82 beats/min, blood pressure 122/68 mmHg, and oxygen saturation (SpO_₂) 98% without supplemental oxygen. Examination of the right lower limb revealed swelling and tenderness, extensive erythema, localized skin ulceration with purulent discharge, partial epidermal desquamation, and a foul odor (Figure 1A). By 1 week post admission, the skin necrosis on the right lower limb had progressed rapidly, with peeling of the necrotic tissue and exposure of the underlying muscle. Wound debridement was performed to remove necrotic epidermis and purulent exudate from the affected leg (Figure 1B). Laboratory tests revealed elevated inflammatory markers: white blood cells (14.96 × 10⁹/L), neutrophils (11.73 × 10⁹/L), procalcitonin (0.45 ng/mL), C-reactive protein (98.90 mg/L), and interleukin-6 (117 pg./mL). Additionally, liver and kidney function tests showed normal total serum bilirubin, alanine aminotransferase, and aspartate aminotransferase levels, but elevated serum creatinine (99.00 μmol/L) and reduced estimated glomerular filtration rate (eGFR) at 48.64 mL/min/1.73 m². Abdominal venous Doppler ultrasound showed no abnormalities in the inferior vena cava, bilateral common iliac veins, or external iliac veins. The patient was initially treated empirically with intravenous broad-spectrum antibiotic imipenem (1.0 g every 12 h) for 1 week prior to confirmation of the causative organism.

Figure 1

Wound exudate from the patient’s right leg was collected and used to inoculate Colombian blood agar and MacConkey agar plates. Four distinct colony morphologies were observed. MALDI-TOF MS identified the bacteria from these colonies as K. gyiorum, Proteus mirabilis, Pseudomonas aeruginosa, and Providencia stuartii. In three subsequent cultures of wound secretions collected on non-consecutive days, only K. gyiorum was isolated, suggesting that K. gyiorum was the primary and persistent pathogen responsible for the lower limb wound infection. K. gyiorum was further purified and designated as strain WCHKG1. After a 24-h culture on Colombian blood agar and MacConkey agar, WCHKG1 formed flat, gray-white, slightly dry colonies with an irregular surface and relatively regular edges (Supplementary Figure S1). Light microscopic examination and staining revealed that the strain was Gram-negative, displaying single, paired, or bead-like chain arrangements (Supplementary Figure S2). Under transmission electron microscopy, WCHKG1 cells measured approximately 1 μm in length and 0.8 μm in width; no flagella were observed, but surface folds were present (Supplementary Figure S3). A 1,395-bp 16S rRNA gene sequence was obtained for WCHKG1. BLAST analysis against the NCBI core nucleotide database identified K. gyiorum as the closest match, with 99.93% identity to the type strain LMG 5906 (GenBank accession number NR_025669.1).

Antimicrobial susceptibility testing of K. gyiorum WCHKG1 showed the following: susceptible (S) to amikacin, ampicillin, aztreonam, cefazolin, cefepime, cefotaxime, ceftazidime, ceftriaxone, gentamicin, imipenem, meropenem, minocycline, piperacillin, piperacillin–tazobactam, tigecycline, tobramycin, and trimethoprim–sulfamethoxazole; intermediate (I) to chloramphenicol and colistin; and resistant (R) to cefuroxime, ciprofloxacin, levofloxacin, and tetracycline (Table 1). P. mirabilis, P. aeruginosa, and P. stuartii were susceptible to amikacin, aztreonam, meropenem, piperacillin–tazobactam, and ceftazidime. P. mirabilis and P. stuartii were resistant to trimethoprim–sulfamethoxazole, ciprofloxacin, moxifloxacin, and levofloxacin. Based on the susceptibility profile, the patient’s antibiotic regimen was adjusted to intravenous infusion of piperacillin–tazobactam (4.5 g every 8 h) for 4 weeks. She received anti-infective treatment, along with meticulous wound care and nutritional support. As a result, the right lower limb wound infection was brought under control, purulent discharge was reduced, and the patient’s body temperature returned to normal. The patient subsequently underwent skin grafting on the granulating wound of the right lower limb (Figure 1C). Following intensive treatment, inflammatory markers normalized, the skin graft survived, and she was discharged with an improved condition. Six months after discharge, the patient returned to normal daily life (Figure 1D). A 3-year follow-up showed that the patient did not experience recurrent infection, although a residual limp remained (Supplementary Figure S4).

3.2 Clinical characteristics of patients with Kerstersia gyiorum infection

A total of 158 articles were initially retrieved from the literature. After removal of duplicates, 43 articles were screened by title and abstract. Studies were included in the subsequent analysis if they clearly identified K. gyiorum as the causative pathogen and reported infections in human patients. Ultimately, 22 articles met the eligibility criteria. These studies collectively reported a total of 39 cases of K. gyiorum infection (5–14, 16, 17, 32–41) (Supplementary Table S1), which were analyzed alongside our case to summarize the clinical characteristics. Among these 40 patients, the median age was 68 years (range: 13–95 years) and 68% (n = 27) were male. The most common country of origin was China (52.5%, n = 21), followed by Turkey (15%, n = 6) and the United States (12.5%, n = 5) (Supplementary Table S1). The majority of patients (53%, n = 21) had comorbidities associated with K. gyiorum infection (Supplementary Table S1).

Analysis of infection sources revealed that the most common site of infection was the lungs (48%, n = 19), followed by the ears (28%, n = 11), and lower limbs (18%, n = 7) (Supplementary Table S1). The most frequently collected specimen types were wound secretions (45%) and sputum (45%) (Supplementary Table S1). Thirty-seven (93%) of the patients were diagnosed with K. gyiorum infection using MALDI-TOF MS, while three (7%) were identified via 16S rRNA gene sequencing. In 12 studies involving 14 patients, the VITEK system was reportedly unable to accurately identify K. gyiorum (Supplementary Table S1). More than half (68%, n = 27) of the cases involved polymicrobial infections, which included our case. The most commonly co-isolated pathogen was P. aeruginosa, found in 37% (10/27) of the mixed-infection cases (Supplementary Table S1). Treatment and clinical outcomes were documented in 22 patients, of whom 16 (73%) received monotherapy with antibiotics as initial treatment, and six (27%) received combination antibiotic therapy. Quinolones were the most common initial antibiotics (50%). The total duration of antibiotic therapy ranged from 4 to 70 days. Most of these patients (91%, 20/22) recovered, with one patient experiencing residual sequelae (Supplementary Table S1).

3.3 Antibiotic susceptibility of Kerstersia gyiorum

A total of 35 K. gyiorum isolates from 18 previous studies underwent antimicrobial susceptibility testing (5–14, 16, 18, 34, 36–40). These results were integrated with the susceptibility profile of WCHKG1 (Table 2). K. gyiorum demonstrated high susceptibility to the following antibiotics: imipenem (100%, 29/29), meropenem (100%, 30/30), ceftazidime (94%, 31/33), amikacin (94%, 29/31), piperacillin–tazobactam (92%, 22/24), cefepime (90%, 18/20), tobramycin (86%, 19/22), gentamicin (82%, 18/22), and aztreonam (83%, 19/23). In contrast, resistance was frequently observed to ciprofloxacin (71%, 25/35), levofloxacin (48%, 12/25), and trimethoprim–sulfamethoxazole (21%, 6/29) (Table 2).

3.4 Genomic characteristics of Kerstersia gyiorum

The complete genome of K. gyiorum strain WCHKG1 contains 3,884,372 bp, with a sequencing coverage of 845 × and a GC content of 62.41%. This strain shares 98.85% ANI with the type strain K. gyiorum DSM 16618^T (NCBI assembly accession no. GCA_004216755.1), exceeding the commonly accepted species demarcation threshold of 95–96% (42), thereby confirming its species identity. The complete genome sequence and Sequence Read Archive (SRA) data have been submitted to the GenBank database.

We retrieved 22 K. gyiorum whole-genome sequences from the GenBank database.⁵ Among them, GCA_004216755.1 (strain DSM 16618), GCA_008801725.1 (strain CCUG 47000), and GCA_965138795.1 (strain CIP108214) represent the genome of the K. gyiorum type strain. Given the superior assembly quality of GCA_004216755.1 (strain DSM 16618), which has fewer contigs, it was selected for subsequent analyses. Ultimately, 20 K. gyiorum genomes were included in the final analysis. These genomes, obtained between 2014 and 2024, originated from five countries, with Brazil contributing the most (60%, 12/20). Thirteen of the 20 genomes were isolated from animal feces, five from humans (including four clinical isolates), and two from environmental sources (Supplementary Table S2; Figure 2). The genome sequence of WCHKG1 was analyzed in combination with these publicly available genomes.

Figure 2

All 21 genomes exhibited high completeness (> 93%) and low contamination (< 2.5%). Compared with the type strain DSM 16618^T, the ANI values ranged from 97.93 to 100.00%, confirming that all of the genomes belong to the K. gyiorum species. Genome sizes ranged from 3.57 to 3.98 Mbp (average: 3.83 Mbp) and GC content varied between 62.36 and 62.69% (Supplementary Table S2). Plasmid replicons IncN2, IncQ1, and IncQ2 were detected among these genomes. IncN2 and IncQ2 were present in most (92%, 12/13) of the animal-derived isolates, but were absent in human- and environment-derived isolates. Conversely, IncQ1 was detected in 33% (2/6) of the human-derived isolates and 100% (2/2) of the environment-derived isolates, but was not found in animal-derived isolates (Supplementary Table S2; Figure 2).

Using the ResFinder database, 19 genes associated with antimicrobial resistance were identified (Supplementary Table S2; Figure 2). These included the following: genes encoding efflux pumps, such as CeoAB-OpcM, which are associated with reduced susceptibility to aminoglycosides and fluoroquinolones (43); MexGHI-OpmD, affecting resistance to fluoroquinolones and tetracyclines (44); MuxABC-OpmB, impacting resistance to aztreonam, macrolides, tetracycline, and novobiocin (45); and the smeABC complex, which influences fluoroquinolone susceptibility (46). These resistance determinants were relatively well conserved across the K. gyiorum genomes (Supplementary Table S2; Figure 2).

Using the VFDB database, 18 putative virulence factors were identified (Supplementary Table S2; Figure 2). These included genes related to capsule formation, flagella, lipopolysaccharide (LPS), and siderophore systems, such as enterobactin and yersiniabactin. Notably, genes involved in flagellar biosynthesis (cheW, cheY, flgG, flgI, flhA, fliG, fliP), enterobactin-related transport (fepC), and yersiniabactin biosynthesis (ybtP) were highly conserved and detected in all of the analyzed K. gyiorum genomes (Supplementary Table S2; Figure 2).

3.5 Phylogenetic characteristics

A maximum-likelihood phylogenetic tree was constructed based on genomic sequences from 21 K. gyiorum strains, with homologous recombination regions excluded (Figure 2). Phylogenetic analysis revealed a host-associated clustering pattern, with genomes from humans, animals, and environmental sources forming relatively distinct clades (Figure 2). Next, we analyzed the SNPs between isolates. Among K. gyiorum genomes derived from humans (minimum pairwise SNPs > 1,800) and environmental sources (minimum pairwise SNPs > 300), no evidence of clonal clustering was observed (Figure 2; Table 3). By contrast, three clonal clusters were identified among the animal-derived K. gyiorum genomes, each characterized by < 25 SNPs between strains within the cluster and by > 500 SNPs separating them from strains outside the cluster (Figure 2; Table 3).

4 Discussion

Here, we have presented a case of severe right lower limb infection caused by K. gyiorum, distinguishable from typical presentations of Vibrio vulnificus-associated necrotizing fasciitis (47) by the patient’s full-thickness skin necrosis with intact underlying muscle tissue. The atypical pattern of tissue damage may indicate a unique pathogenic mechanism, warranting further investigation. Although previous studies reported chronic lower limb infections due to K. gyiorum (6, 11, 32), to our knowledge, this is the most severe acute manifestation to be documented.

Strain WCHKG1, isolated from the wound exudate, was identified as K. gyiorum using MALDI-TOF MS and confirmed by 16S rRNA gene sequencing, consistent with previously reported diagnostic approaches (12, 13, 34). WCHKG1 exhibited resistance to multiple antibiotics, including cefuroxime, ciprofloxacin, levofloxacin, and tetracycline. Notably, earlier studies (39) also reported K. gyiorum strains resistant to ciprofloxacin, levofloxacin, and tetracycline, highlighting the emerging concern of antibiotic resistance in this species. Our patient was treated with a combination of antimicrobial therapy and skin grafting, and was followed for 3 years. Although she returned to her normal daily life, a persistent limp remained. This is the first reported case of K. gyiorum infection resulting in a long-term sequela, underscoring the potential severity of such infections and the importance of timely and aggressive management.

Our analysis of 40 K. gyiorum cases revealed that more than half of the patients (53%) had comorbidities and 68% had polymicrobial infections—findings consistent with previous reports (14, 36). While earlier reports suggested that K. gyiorum primarily causes infections of the limbs and ears (1, 14), we found that the lungs were the most common site (48%), followed by the ears (28%) and lower limbs (18%). This shift may reflect the results of two recent studies from China (39, 40), as well as the increasing use of MALDI-TOF MS, which has improved diagnostic sensitivity (48). The VITEK system has been shown to misidentify K. gyiorum (10, 12, 13), whereas MALDI-TOF MS offers more accurate identification (13, 33, 39), reducing the risk of misdiagnosis or underdiagnosis. In most reported cases, quinolones were used as the first-line treatment. However, our analysis of susceptibility test results indicated that K. gyiorum strains exhibit the lowest susceptibility to quinolones among major antibiotic classes. Thus, quinolones may not be the optimal empirical choice for treating K. gyiorum infections.

The plasmid replicons identified among 21 K. gyiorum whole-genome sequences revealed differences between animal- and human-derived strains. This observation has been previously reported (2), but was not explored in depth here because of the draft quality of most genomes, which limits the accuracy of plasmid structure analysis.

Analysis of antibiotic resistance genes in K. gyiorum revealed the presence of multiple conserved efflux pump systems, including CeoAB-OpcM, MexGHI-OpmD, MuxABC-OpmB, and smeABC. These systems are known to reduce susceptibility to fluoroquinolones and tetracycline, providing a genomic basis for the observed resistance patterns.

Virulence factor analysis revealed that several virulence-associated genes are highly conserved in K. gyiorum, including those involved in flagellar biosynthesis (cheW, cheY, flgG, flgI, flhA, fliG, fliP), the enterobactin siderophore system (fepC), and the yersiniabactin siderophore system (ybtP). These findings are consistent with previous studies that broadly identified flagellar and iron acquisition-related genes in K. gyiorum genomes (2, 35). Flagella are known to play a key role in bacterial pathogenesis (49), and both enterobactin and yersiniabactin are essential for bacterial iron uptake and virulence (50, 51). However, transmission electron microscopy of K. gyiorum strain WCHKG1 showed that the bacterium lacked visible flagella. Similarly, another species within the Kerstersia genus, K. similis, also exhibits aflagellar morphology (52). The functional role of these conserved flagellar biosynthesis genes in K. gyiorum pathogenicity remains unclear, warranting further investigation.

Phylogenetic analysis revealed three clonal clusters (SNPs < 25) among animal-derived K. gyiorum isolates, suggesting clonal transmission in animals. Although no clonal clustering (SNPs > 1,800) was observed among human-derived isolates, the potential for clonal spread in clinical settings cannot be ruled out and should be monitored closely.

5 Conclusion

This case of acute, severe right lower limb infection caused by an isolate of K. gyiorum was characterized by rapid progression and multidrug resistance, providing valuable clinical insights into the treatment of K. gyiorum infections. Our clinical and genomic analyses indicated that K. gyiorum can infect multiple anatomical sites, and that quinolones may not be the most suitable first-line treatment. The K. gyiorum genome exhibits conservation of antibiotic efflux pump systems and virulence factors, which may play important roles in its antibiotic resistance and pathogenicity. Additionally, we observed evidence of clonal transmission among animal-derived isolates, highlighting the potential for similar clonal spread in clinical settings and underscoring the need for increased vigilance. These findings contribute to addressing current knowledge gaps regarding this emerging pathogen, supporting future efforts in infection prevention and management. However, our findings are limited by the relatively small number of reported K. gyiorum infections and available genome sequences. Further research with larger sample sizes is needed to validate these observations.

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