Oak Tree Bacterium Identified in Human Infection for the First Time

A bacterium until now known almost exclusively as a culprit in tree disease has been recovered from a human patient for the first time. Researchers in Hamburg, Germany, report the isolation of Gibbsiella quercinecans, a species first described in 2010 in association with Acute Oak Decline in the United Kingdom and Spain, from a deep intraoperative specimen taken from a man with a phlegmonous soft tissue infection of the thumb. The case, published in the journal New Microbes and New Infections, marks the first time any member of the genus Gibbsiella has been linked to a human infection, and it raises questions about how often environmental organisms slip through routine diagnostic nets unrecognized.

The patient, a 60-year-old man with no relevant medical history, fell from his bicycle onto paving stones in Northern Germany, close to oak trees (Quercus robur). He sustained lacerations to the scalp and left thumb. Both wounds looked superficial at first assessment and were debrided, irrigated and sutured before he was discharged in stable condition. Two days later, however, the thumb wound had become increasingly painful, red and purulent, while the scalp wound remained uninfected. He never developed fever, and when he was referred to hospital, laboratory tests showed only a mild inflammatory response: a C-reactive protein level of 16.2 mg/L and a leukocyte count of 7.77 × 10⁹/L, without leukocytosis.

Surgical exploration of the thumb became necessary. Preoperative x-rays in two planes showed no bony lesions or signs of osteitis. Intraoperatively, the surgeons encountered purulent wound exudate accompanied by localized inflammation of the extensor tendon sheath. At the level of the interphalangeal joint, the long extensor tendon was partially transected, with roughly 30 percent of its diameter affected, and the joint capsule was damaged, exposing the joint cartilage. The joint itself contained clear synovial fluid and the cartilage appeared intact, with no evidence of joint empyema. The team took sterile samples of infected subcutaneous and tenosynovial tissue for microbiological analysis, then performed radical debridement, irrigated the joint with diluted gentamicin solution, reconstructed the tendon and closed the wound. The patient spent five days in hospital receiving intravenous cefazolin, after which oral amoxicillin/clavulanic acid was continued for five more days. Inflammatory markers declined and local findings improved, although reduced tendon function required physiotherapy.

The microbiological work-up proved unusually challenging. Specimens were processed by routine methods and inoculated onto chocolate agar and Columbia blood agar, with aerobic incubation at 37 °C in 5 percent CO₂, alongside anaerobic culture on Schaedler agar. After 24 hours, medium-sized, grey, smooth, moist, non-haemolytic colonies with entire margins appeared on chocolate agar, and no other aerobic or anaerobic growth was detected. The colonies were colourless on MacConkey agar, indicating a non-lactose-fermenting phenotype, and the organism also grew at room temperature and at 27 °C. Crucially, the isolate grew in pure culture from a deep surgical specimen, with no alternative pathogens present, a finding that, together with the favourable response to surgery and antibiotics, supports a genuine etiological role for the bacterium rather than incidental contamination.

Initial identification attempts failed in instructive ways. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS), the workhorse of modern clinical microbiology, produced spectra of adequate quality but could not name the organism, because G. quercinecans was simply absent from the reference library. The closest matches were various Serratia species, all with identification scores below the reliable threshold of 1.7. An automated biochemical system, the VITEK 2, went further and misidentified the isolate as Serratia plymuthica with a probability of 88 to 92 percent, despite phenotypic characteristics that did not fit. Partial sequencing of the 16S ribosomal DNA gene narrowed the affiliation to the genus Gibbsiella but could not resolve the species.

Definitive identification came from whole-genome sequencing on the Oxford Nanopore Technologies platform. The resulting long reads were assembled with Unicycler v0.5.0 into a complete, circular chromosome of 5,672,081 base pairs, with no plasmids detected. Average nucleotide identity analysis using OrthoANIu against reference strains of G. quercinecans returned values of 98.32 percent for both strains tested, well above the roughly 95 to 96 percent threshold used to delineate bacterial species. A core-genome maximum-likelihood phylogeny, inferred from 60,736 core-genome SNPs with Roary and RAxML-NG, placed the clinical isolate squarely within the G. quercinecans cluster and clearly separated it from other Gibbsiella species and from the biochemically similar genus Serratia, confirming the species-level classification beyond doubt.

Genomic analysis also offered reassurance about the organism’s threat potential. Screening against the MEGARes and CARD resistance databases identified only three chromosomally encoded, efflux-associated elements: CRP, a global regulator that represses expression of the MdtEF pump, and two RND-type efflux pumps, SDEX and SDEY, linked to multi-compound drug and biocide resistance. No known acquired antimicrobial resistance determinants were found, and a search of the Virulence Factor Database returned no matches to known virulence genes. Susceptibility testing by disc diffusion and VITEK 2 against EUCAST breakpoints for Enterobacterales confirmed the isolate was susceptible to ampicillin, ampicillin/sulbactam, piperacillin/tazobactam, cefotaxime, ceftazidime, ertapenem, imipenem, meropenem, ciprofloxacin and trimethoprim/sulfamethoxazole. The ampicillin minimum inhibitory concentration, verified by gradient diffusion, sat at 8 mg/L, close to the clinical breakpoint but still within the susceptible range.

The ecological backdrop makes the case biologically plausible. Since its original description as one of the bacterial species associated with Acute Oak Decline, G. quercinecans has been detected in additional settings, including Acute Oak Decline in south-west Poland and bacterial canker of Russian olive, suggesting a broader geographic and ecological distribution than initially appreciated. The organism has been shown to persist in forest soil and rainwater, and it can grow across a relatively broad temperature range, including at 37 °C, a tolerance compatible with both environmental persistence and growth in a human host. In plant disease settings it is typically found as part of polymicrobial communities rather than as a sole pathogen, whereas this case yielded monomicrobial growth from deep tissue. The authors suggest that environmental inoculation at the time of trauma, facilitated by the disruption of skin integrity, is the most likely explanation, with primary wound closure possibly hindering local clearance of the inoculated bacteria. Comparable trauma-associated infections caused by other plant-associated Enterobacterales, such as Pantoea agglomerans and Kosakonia cowanii, follow a similar pattern.

The case carries broader implications for diagnostics and for how clinicians think about infection after outdoor injuries. Primary skin and soft tissue infections are usually attributed to a small set of well-characterized pathogens, but secondary infections following trauma are often polymicrobial and can include environmental bacteria. Here, both MALDI-TOF MS and automated biochemical systems failed to deliver a reliable species-level identification, and only molecular and genomic analysis succeeded. The authors caution that resistance and virulence screens are limited to determinants represented in current reference databases, so novel mechanisms in G. quercinecans cannot be excluded, and that the absence of molecular confirmation directly from the primary specimen and of histopathological correlation are limitations of the report. Whether environmental and climate-related stressors might expand the distribution of Acute Oak Decline and its bacterial communities, and thereby increase human exposure, remains unknown. The isolate has been deposited at the German Collection of Microorganisms and Cell Cultures (DSMZ) under submission number DSM 121826, and its genome is publicly available, giving clinicians and researchers a reference point the next time an unremarkable-looking wound culture turns out to be anything but ordinary.

Subject of Research: First human isolation of the oak-associated bacterium Gibbsiella quercinecans from a soft tissue infection

Article Title: First human isolation of Gibbsiella quercinecans associated with infection – significance and relevance

Article References: Lübbe, J., Schaudig, L., Huang, J., Tanida, K., Christner, M., Aepfelbacher, M., Rein, S., Rohde, H., & Berinson, B. (2026). First human isolation of Gibbsiella quercinecans associated with infection – significance and relevance. New Microbes and New Infections, Article 101867. https://doi.org/10.1016/j.nmni.2026.101867

Image Credits: AI Generated

DOI: Not provided

Keywords: Gibbsiella quercinecans, Acute Oak Decline, soft tissue infection, whole-genome sequencing, MALDI-TOF MS, antimicrobial susceptibility, environmental bacteria, Enterobacterales, trauma, diagnostic microbiology, phylogenetics, emerging pathogens