Early Release – Two Cases of Posttraumatic Kosakonia Infection, Argentina, 2023 – Volume 32, Number 3—March 2026 – Emerging Infectious Diseases journal

Medical literature recognized the genus Kosakonia in 2013, after the systematic reorganization of Enterobacter genus (1). Largely known as plant growth–promoting bacteria, or phytopathogens (2), the species included in this genus are rapidly gaining relevance as opportunistic human pathogens. However, because of the bacteria’s phenotypic similarities with Enterobacter and Pantoea, clinicians frequently misidentify Kosakonia infections, leading to an underestimation of their true clinical incidence (3–5). We describe 2 cases of osteomyelitis in Argentina caused by Kosakonia species associated with environmental trauma.

Case 1 involved a 12-year-old girl with an open supracondylar elbow fracture sustained falling from a horse and involving soil contamination. Despite surgical fixation and cephalosporin prophylaxis, she sought treatment 10 days later for purulent discharge. Cultures yielded a gram-negative rod (isolate CMVA41). We treated the suspected osteomyelitis with intravenous piperacillin/tazobactam and clindamycin, followed by oral ciprofloxacin and clindamycin for 6 weeks, resulting in complete resolution.

Case 2 involved a 20-year-old man with chronic posttraumatic knee osteomyelitis following a puncture with a tree thorn. We cultured a gram-negative rod (isolate CMVA47) from surgical samples. We administered vancomycin and piperacillin/tazobactam, followed by a course of oral amoxicillin and ciprofloxacin for 6 weeks, achieving clinical cure.

We performed a polyphasic identification approach for both cases. Colonies were yellow and lactose-fermenting on eosin methylene blue (Levine) agar. Initial phenotypic identification using conventional biochemical tests failed to provide reliable genus-level identification (Appendix Table). We subsequently performed matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (Bruker Biotyper, library v13.0; https://www.bruker.com). We identified isolate CMVA47 as Kosakonia cowanii with a secure species-level score (2.052). In contrast, we initially misidentified isolate CMVA41 as K. radicincitans with a low confidence score (1.717), indicating probable genus-level identification but species uncertainty. This result highlighted a limitation: the spectral library lacked a reference profile for K. oryzae, leading to potential misclassification (6).

To resolve those uncertainties, we performed whole-genome sequencing (WGS) using the Illumina NovaSeq6000 platform (https://www.illumina.com). For strain CMVA41, the 16S rRNA gene sequence showed 100% identity with the reference K. oryzae sequence Ola 51. Relative to the same reference, we noted an average nucleotide identity value of 98.83% and a digital DNA-DNA hybridization value of 91.6%, with ribosomal multilocus sequence typing identifying the strain as the same species with 94% support. Those results differed from MALDI-TOF mass spectrometry identification and indicated K. oryzae as a clinically relevant human pathogen. For strain CMVA47, although the 16S rRNA gene (99.77% identity) and average nucleotide identity (95.94%) supported identification as K. cowanii, the digital DNA-DNA hybridization value (65.1%) fell below the 70% threshold typically used for species delineation.

Figure

Figure. Data from a study of 2 cases of posttraumatic Kosakoniainfection, Argentina, 2023. Maximum-likelihood phylogeny calculated using 1,214,977 single-nucleotide variants from a core-gene alignment of 3,232 genes from genomes…

We produced a core genome phylogeny analysis based on concatenated sequences of 3,232 core genes that shared >50% sequence identity and were present in >80% of the included genomes (1 reference genome of each Kosakonia species, if present, downloaded from the National Center for Biotechnology Information RefSeq database [https://www.ncbi.nlm.nih.gov/refseq]). CVMA41 clustered with K. oryzae and CVMA47 clustered with K. cowanii, with 100% bootstrap support (Figure). The genomic divergence observed in CMVA47 suggested that revisiting genomic thresholds within the Kosakonia genus might be necessary, as seen in other genera (7).

Antimicrobial susceptibility testing revealed that both isolates were susceptible to aminoglycosides, fluoroquinolones, trimethoprim/sulfamethoxazole, extended-spectrum cephalosporins, and carbapenems. Of note, although CMVA41 was susceptible to all tested agents, CVMA47 exhibited resistance to ampicillin and intermediate susceptibility to cefazolin. This phenotypic profile serves as a marker distinguishing Kosakonia spp. from Enterobacter cloacae complex. Enterobacter cloacae complex typically exhibits intrinsic resistance to ampicillin/sulbactam and carries an inducible chromosomal ampC β-lactamase that can lead to third-generation cephalosporin resistance upon derepression, but both Kosakonia isolates remained susceptible to these agents. Genomic analysis confirmed the absence of ampC and its regulator ampR in both strains. This distinction is clinically relevant, supporting the use of ampicillin/sulbactam or cephalosporins as therapeutic options, sparing carbapenems. Consequently, we theorized that the ampicillin resistance in CVMA47 was likely attributable to the putative chromosomic β-lactamase KSA-1, which was identified in Kosakonia sacchari, showing 78.6% similarity to this class A extended-spectrum β-lactamase, rather than an AmpC-type enzyme (8). Our results further support that genomic divergence in CVMA47 is biologically meaningful. Researchers noted similar findings regarding Kluyvera spp., where the presence of intrinsic β-lactamases were linked to species differentiation and the proposal of refined taxonomic thresholds (9).

Identifying Kosakonia isolates in this study illustrates the challenges that clinical laboratories face with emerging pathogens. The cases we describe contribute to the growing evidence that Kosakonia infections are strongly associated with traumatic inoculation of plant material, although reports have described endogenous infections (3,10). The identification of K. oryzae as a human pathogen expands the spectrum of Kosakonia species with clinical relevance. MALDI-TOF mass spectrometry represents a considerable improvement over biochemical tests, but the reliability of such analysis is contingent on updated databases (6). WGS thus stands as the standard for accurate identification of such environmental pathogens, essential for defining their epidemiology and guiding antimicrobial stewardship.

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