ABSTRACT
Background
Phytobacter spp., a recently recognized human pathogen, presents significant diagnostic challenges. Conventional biochemical and automated identification methods often fail to distinguish Phytobacter from other Enterobacterales, which hinders accurate diagnosis and may potentially delay appropriate treatment. Since 2018, our state public health laboratory (LACEN-PR) has adopted a polyphasic identification strategy, integrating matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, API 20E, targeted quantitative PCR, and whole-genome sequencing to investigate closely related Enterobacterales isolates that were initially misidentified and subsequently confirmed as Phytobacter spp. This study reports three cases of Phytobacter-associated sepsis, including a putative novel Phytobacter species and the first documented case of blaNDM-positive Phytobacter ursingii.
Case Summary
Case 1: A 31-year-old man living with HIV developed sepsis following respiratory failure. Initial testing misidentified the isolate as Leclercia adecarboxylata, but the polyphasic approach revealed the potential for a novel Phytobacter species. The patient showed clinical improvement following targeted antimicrobial therapy. Case 2: A 50-year-old trauma patient developed sepsis caused by a Phytobacter spp. The isolate was closely related to that of Case 1. Despite treatment, he succumbed to the infection. Case 3: A 68-year-old woman with multiple comorbidities who developed septic shock. Blood cultures identified blaNDM-positive Phytobacter ursingii. The patient did not survive.
Conclusion
These cases underscore the clinical significance of Phytobacter spp. as an emerging pathogen and highlight the challenges posed by their misidentification. The discovery of a novel species and multidrug-resistant P. ursingii highlights the need for improved diagnostic accuracy and effective treatment to enhance surveillance and improve patient outcomes.
KEYWORDS: polyphasic identification, Phytobacter, new species, emerging pathogen, sepsis
INTRODUCTION
Although Phytobacter spp. were isolated as early as the 1970s (1–3), they have only recently been recognized as human pathogens. Retrospective analyses suggest multiple strains previously assigned to other genera now fall within the Phytobacter clade (4–7). Some bloodstream isolates have been associated with high mortality (4, 8–10). Given the frequency of misidentification, it is likely that Phytobacter spp. have been involved in many unrecognized clinical infections and outbreaks worldwide.
Phytobacter spp. have been implicated in a range of infections, including sepsis, catheter-associated, pulmonary, and urinary tract infections (4, 11–13), as well as outbreaks in Brazil, the USA, Singapore, and Japan (5, 8, 11–13). Since then, leading authorities have emphasized the importance of accurate identification and surveillance of this genus (14–17).
Conventional identification methods, including biochemical tests (e.g., API 20E), automated systems (e.g., VITEK, Phoenix, and Microscan), and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), often misclassify Phytobacter spp. as other Enterobacterales species (4–6, 11, 12). Due to inaccurate database entries, even advanced sequencing techniques can produce erroneous results, complicating diagnosis and species assignment (4, 7, 18). Due to phenotypic similarities and outdated databases, Phytobacter isolates are frequently misidentified as other members of the order Enterobacterales (such as Pantoea agglomerans, Kluyvera intermedia, Leclercia adecarboxylata, Kosakonia spp., Cronobacter spp., and Citrobacter spp.) (4, 6, 8, 13). These limitations compromise both clinical care and epidemiological investigations, emphasizing the need for polyphasic identification strategies and updated reference databases.
Here, we describe three cases of bloodstream infection caused by Phytobacter spp. in southern Brazil between 2020 and 2024. In addition to clinical summaries, we present a detailed microbiological investigation, including the discovery of a potentially novel species and the first report of blaNDM-positive Phytobacter ursingii.
CASE PRESENTATION
Before presenting the clinical cases, we first summarize the Microbiological Characterization Workflow adopted in this study. Additionally, clinical cases are described and summarized in Table 1, which outlines the progression and key events of each case, and Table 2, which presents a comparative overview of microbiological and diagnostic test results.
TABLE 1.
Chronological overview of clinical and laboratory findings in three Phytobacter sepsis casesb
| Events | Case 1 | Case 2 | Case 3 |
|---|---|---|---|
| Patient | 31-year-old man | 50-year-old man | 68-year-old woman |
| Comorbidities | HIV infection | None reported | Hypertension, diabetes mellitus, and heart failure |
| Hospitalizationa | March 2020 | March 2020 | January 2024 |
| Antibiotic therapiesa | Ceftriaxone 2 g IV q24h (day 0–7) | Cefazolin 2 g IV q8h (day 0–2) | Ceftriaxone 2 g IV q24h + Metronidazole 500 mg IV q8h (day 0–1) |
| Azithromycin 500 mg PO q24h (day 0–5) | Piperacillin/Tazobactam 4.5 g IV q6h (day 0–3), then 2.25 g IV q8h (day 4–8) | ||
| Oseltamivir 75 mg PO q12h (day 0–7) | Vancomycin 1.5 g IV q8h (day 0–1) | Micafungin 100 mg IV q24h (day 0–12) | |
| Sulfamethoxazole/Trimethoprim 1,600 mg/320 mg PO q6h (day 2–22), then 400 mg/80 mg PO q24h (day 23–25) | Acyclovir 400 mg PO q24h (day 0–9) | ||
| Meropenem 1 g IV q8h (day 9–18) | Meropenem 2 g IV q8h (day 0–1) | Meropenem 1 g IV q8h (day 0–3), then 0.5 g IV q12h (day 4–5) | |
| Linezolid 600 mg IV q12h (day 9–11) | Linezolid 600 mg IV q12h (day 0–1) | ||
| Polymyxin B 1,000,000 IU IV q12h (day 13–25) | Polymyxin B 1,000,000 IU IV q12h (day 0 only) | Polymyxin B 1,000,000 IU IV q12h (day 0–5) | |
| Fluconazole 200 mg IV q24h (day 18–20), then 150 mg IV q24h (day 21–28) | |||
| Sample obtaineda | Blood cultures (day 7) | Blood cultures (day 6) | Rectal swab collected during routine intensive care unit surveillance (day 4) and blood cultures (day 13) |
| Hospital lab resultsa |
Leclercia adecarboxylata (day 9) AST (day 10) |
Leclercia adecarboxylata (day 7) AST (day 7) |
NDM-producing Citrobacter freundii for rectal swab (day 5) and carbapenem-resistant “Pantoea agglomerans” from blood culture (day 14) |
| LACEN-PR identification conclusion | Phytobacter sp. | Phytobacter sp. | Phytobacter ursingii |
| Clinical outcomea | Discharge (day 30) | Death (day 7) | Death (day 19) |
The three hospitalizations occurred in the same institution.
“Day X” refers to the days of hospitalization. IV, intravenous; PO, per os; q24h, every 24 h; q12h, every 12 h; q8h, every 8 h.
TABLE 2.
Identification workflow and results for Phytobacter isolates from the three clinical casesd
| Test results | Case 1 | Case 2 | Case 3 | |
|---|---|---|---|---|
| LACEN-PR ID | 27808 RM | 27653 RM | 50337 RM | |
| Culture | MacConkey agar lactose positive | MacConkey agar lactose positive | MacConkey agar lactose positive | |
| API 20E | 1-2-0-4-7-3-3-7 | 1-2-0-4-7-3-3-7 | 1-2-0-4-5-3-3-7 | |
| Pantoea spp. 2 (30.9%) | Pantoea spp. 2 (30.9%) | Pantoea spp. 2 (57.1%) | ||
| VITEK-2 AST-N panels (µg/mL) | Amoxicillin/clavulanic acid | ND | ND | ND |
| Ampicillin | ≥32 (R) | ≥32 (R) | ND | |
| Ampicillin/sulbactam | ≥32 (R) | ≥32 (R) | ND | |
| Piperacillin/tazobactam | ≤4 (S) | ≤4 (S) | ND | |
| Ceftazidime | 4 (I) | 4 (I) | ≥64 (R) | |
| Ceftriaxone | ≥64 (R) | ≥64 (R) | ≥64 (R) | |
| Ceftazidime/avibactam | ND | ND | ≥16 (R) | |
| Ceftolozane/tazobactam | ND | ND | 16 (R) | |
| Cefepime | 8 (R) | 2 (I) | 8 (R) | |
| Aztreonam | ND | ND | ≤1 (S) | |
| Ertapenem | ≤0.5 (S) | ≤0.5 (S) | ≥8 (R) | |
| Imipenem | ≤0.25 (S) | ≤0.25 (S) | ND | |
| Meropenem | ≤0.25 (S) | ≤0.25 (S) | ≥16 (R) | |
| Amikacin | ≤2 (S) | ≤2 (S) | ≥64 (R) | |
| Gentamicin | ≤1 (S) | ≤1 (S) | ≥16 (R) | |
| Ciprofloxacin | ≤0.25 (S) | ≤0.25 (S) | ≤0.06 (S) | |
| Gradient concentration testa (µg/mL) | Ceftazidime = 2 (I) | Ceftazidime R; Cefepime R; |
ND | |
| MALDI-TOF MS (VITEK-MS, IVD Myla database v4) | Leclercia adecarboxylata (99.9%) | Leclercia adecarboxylata (99.6%) | No identification | |
| MALDI-TOF MS (VITEK-MS, RUO Saramis database v4.16; System v4.1.0.9, year 2010) | Phytobacter spp. (84.7%) | Phytobacter spp. (77.5%) | Phytobacter spp. (81.4%) | |
| Full 16S rRNA geneb - BLASTN and leBIBI (identical results) | Pseudescherichia vulneris | Pseudescherichia vulneris | Phytobacter ursingii | |
| bla CTX-M-2 b | Positive | Positive | Not detected | |
| blaNDM gene (in-house qPCR)c | Negative | Negative | Positive | |
| nifL gene (in-house qPCR) | Positive | Positive | Positive | |
| WGS and Type Strain Genome Server | Phytobacter sp. nov. | Phytobacter sp. nov. | Phytobacter ursingii | |
E-test (bioMérieux). This method was used as a complementary approach when VITEK-2 results were inconclusive.
The blaCTX-M-2 gene and the 16S rRNA were analyzed based on whole-genome sequencing (WGS) results.
The blaNDM-1 gene was detected by quantitative PCR (qPCR) and confirmed by WGS.
R, resistant; S, susceptible; I, susceptible, increased exposure (when applicable); N/A, not available; ND, not determined. Interpretive breakpoints for antibiotics were based on the BrCAST 2020 (case 01 and 02) and 2024 (case 03) guidelines (https://brcast.org.br/).
In 2020, the Paraná State Central Laboratory (LACEN-PR) issued a technical note highlighting the emergence of Phytobacter spp. and offering extended molecular identification and resistance screening for voluntarily submitted clinical isolates. A polyphasic identification strategy was adopted to clarify cases initially reported as Leclercia, Pantoea, or other rare taxa.
Isolates are typically received after the patient’s clinical course has ended; thus, LACEN-PR’s analyses are intended for epidemiological and scientific purposes rather than clinical decisions.
The identification workflow combined phenotypic and molecular methods. Initial screening was performed using MALDI-TOF MS (VITEK-MS) with both IVD (Myla software) and RUO (Saramis) databases, according to Mazzetti et al. (19), and API 20E (bioMérieux) for biochemical profiling. While Phytobacter is not included in the API 20E database, the system reliably excludes common Enterobacterales and remains a useful, low-cost preliminary tool. Alternate databases (https://bacdive.dsmz.de/api-test-finder; https://enteroplus.app.achillescdss.com.br) have recently included Phytobacter spp. phenotypes. A detailed characterization of Phytobacter’s biochemical traits, as determined using API 20E, is available in Smits et al. (4).
A Phytobacter genus-specific quantitative PCR (qPCR) assay targeting the nifL gene was previously proposed and validated. Briefly, this gene, which is part of the nitrogen fixation operon, was selected through comparative genomic analysis as a conserved and specific marker for the genus, due to its consistent presence in Phytobacter spp. and absence in closely related Enterobacterales (20).
Molecular confirmation involved genus-specific qPCR targeting the nifL gene, followed by 16S rRNA gene sequencing (MicroSEQ kit) and phylogenomic placement via whole-genome sequencing (WGS) (Illumina MiSeq), analyzed through TYGS (Type Strain Genome Server; https://tygs.dsmz.de/). The full-length 16S rRNA gene sequence was confirmed by WGS. Antimicrobial resistance genes, including blaCTX-M and blaNDM, were identified via in silico analysis of WGS data. Antimicrobial susceptibility testing was performed using the VITEK-2 system (AST-N panel; bioMérieux) and interpreted according to the 2022 guidelines of the Brazilian Committee on Antimicrobial Susceptibility Testing (BrCAST).
This retrospective study focused on the microbiological characterization of emerging Phytobacter species. No patient intervention or prospective data collection was involved, and formal ethical approval was not required under local regulations. All data were fully anonymized, and only essential clinical and microbiological details are reported, without risk of patient identification.
Case 1
A 31-year-old man with newly diagnosed HIV (CD4+ = 9 cells/µL; reference: 540-1731 cells/µL (21); HIV viral load = 149,858 copies/mL) was admitted with acute respiratory failure in March 2020. Empirical therapy for community-acquired pneumonia was initiated with ceftriaxone and azithromycin (day 1), followed by trimethoprim-sulfamethoxazole (day 6) for suspected pneumocystosis. On day 7, hemodynamic instability prompted the collection of peripheral blood cultures, which yielded a gram-negative bacillus.
On day 9, the hospital laboratory reported that the isolate was identified as Leclercia adecarboxylata by MALDI-TOF MS (VITEK-MS, using IVD database). Given ongoing clinical severity, therapy was escalated on day 10 to meropenem + linezolid, and polymyxin B was added on day 14 (for complete posology see Table 1).
Reanalysis using the RUO database yielded an 84.7% probability of Phytobacter spp. The API 20E biochemical profile was compatible with previously described Phytobacter phenotypes. A genus-specific qPCR targeting the nifL gene tested positive.
The full 16S rRNA gene sequencing identified Pseudescherichia vulneris as the closest match in both BLASTN and leBIBI analyses. WGS, analyzed via TYGS, confirmed it as a Phytobacter genus but did not correspond to any described species, supporting its classification as a putative novel species. WGS also revealed the presence of blaCTX-M-2, correlating with phenotypic resistance to cefazolin, cefuroxime, ceftriaxone, and cefepime. The isolate remained susceptible to ceftazidime, carbapenems, amikacin, and polymyxin. The patient improved and was discharged after 30 days.
Case 2
A 50-year-old man was admitted to the intensive care unit (ICU) in March 2020 after polytrauma from a high-impact accident, including brain injury requiring decompression. On day 6, with signs of sepsis, empirical meropenem and vancomycin were initiated (for complete posology see Table 1), and blood culture was collected via peripheral venipuncture. Despite initial treatment, he died 7 days after admission.
Blood cultures yielded a gram-negative bacillus initially identified as Leclercia adecarboxylata by MALDI-TOF MS (VITEK-MS). Further analysis using the RUO database indicated Phytobacter spp. The API 20E biochemical profile was consistent with that of Phytobacter, and the nifL-targeted qPCR tested positive.
The full 16S rRNA sequencing provided inconclusive species-level resolution; however, WGS confirmed the isolate as a Phytobacter species closely related to that from Case 1 and also identified the blaCTX-M-2 gene, in agreement with phenotypic resistance to all tested cephalosporins, except ceftazidime. The isolate remained susceptible to carbapenems, amikacin, and polymyxin.
Case 3
A 68-year-old woman with a history of hypertension, diabetes mellitus, and heart failure was admitted to the ICU in January 2024 with septic shock of presumed abdominal origin, associated with acute kidney injury requiring dialysis. Empirical ceftriaxone and metronidazole were initiated on day 1. Despite supportive care, her condition remained critical, leading to escalation to meropenem, polymyxin B, and linezolid. On day 5, a rectal swab (collected during routine ICU surveillance) tested positive for Citrobacter freundii harboring blaNDM.
On day 13, due to persistent critical illness, peripheral blood cultures (collected via peripheral venipuncture) were obtained.
The blood cultures yielded a carbapenem-resistant gram-negative bacillus, initially identified as Pantoea agglomerans by VITEK-2 (GN panel), while MALDI-TOF MS using the IVD database returned a “no identification” result. Analysis with the RUO gave an 81.4% chance of Phytobacter spp. The API 20E biochemical profile aligned with previously described Phytobacter patterns, and qPCR targeting the nifL and blaNDM genes was positive. The 16S rRNA and WGS confirmed Phytobacter ursingii harboring blaNDM-1. Despite treatment, the patient died on hospitalization day 19.
DISCUSSION
We report three cases of sepsis caused by two different Phytobacter species, including two attributed to a newly identified species pending validation and, to our knowledge, the first documented case of blaNDM-positive P. ursingii. These findings highlight the pathogenic potential of this emerging genus.
The two novel species isolates, recovered from ICU patients within 25 days, were closely related by WGS, suggesting nosocomial transmission (M. Pillonetto, L. N. V. S. Arend, D. O. Kulek, A. Mazzetti, S. Jordan, L. Fenske, J. Blom, M. T. Mira, T. H. M. Smits, F. Rezzonico, unpublished data). Their detection highlights the need for precise identification to support the recognition of outbreaks and public health responses.
In the third case, a P. ursingii bloodstream isolate carrying blaNDM-1 was detected. To our knowledge, carbapenemase production mediated by blaNDM has never been reported in this species. Phytobacter spp. isolates are known to harbor a range of beta-lactamase genes, including blaCTX-M, blaKPC, blaIMP-1, blaIMP-4, blaIMP-6, blaTEM, blaGES-5, and blaNDM, further complicating antimicrobial treatment (4–7, 12, 22, 23) and reinforcing the importance of routine susceptibility testing.
Clinicians and microbiologists should be aware of the diagnostic challenges associated with Phytobacter spp. Its colonies on MacConkey agar strongly resemble other common species such as E. coli and C. freundii (Fig. 1) or even K. pneumoniae (Fig. 2). Conventional methods, including MALDI-TOF MS, may fail to correctly identify isolates due to incomplete or outdated database entries for this genus, leading to misidentification as other Enterobacterales (24). Although RUO MALDI-TOF MS scores >80% may suggest Phytobacter, this alone is not sufficiently reliable. As described by Dubois et al. (25), scores between 60% and 99.8% qualify as “good ID” and may support presumptive identification; however, they are insufficient for accurate genus-level classification in clinical or epidemiological contexts. Until validated, Phytobacter spectra are incorporated into clinical databases; confirmation with genus-specific qPCR or WGS remains necessary.
Fig 1.
Growth of Phytobacter sp. nov. on MacConkey agar. Representative culture of Phytobacter sp. nov. showing strong lactose-positive colonies, surrounded by bile-precipitation on MacConkey agar after 24 h of incubation at 35°C, consistent with vigorous lactose fermentation. Colonies appear large, dry, and pink colored, with irregular margins. Morphology resembles Escherichia coli and/or Citrobacter freundii on MacConkey agar.
Fig 2.
Growth of Phytobacter ursingii on MacConkey Agar. Representative culture of Phytobacter ursingii showing lactose-positive colonies on MacConkey agar after 24 h of incubation at 35°C. Colonies appear slightly mucoid, with regular margins and pink-colored, surrounded by bile-precipitation, consistent with strong lactose fermentation.
Similarly, biochemical tests, such as API 20E, may also yield inconclusive or ambiguous results. Therefore, a polyphasic approach, combining phenotypic and genotypic methods, is essential for accurate identification. Specifically, the 16S rRNA gene sequencing, targeted qPCR assays for the genus Phytobacter (20), and WGS should be considered, especially in cases of severe infections or suspected outbreaks. WGS also enables the detection of resistance genes and virulence factors.
Conclusion
In this case series, two of the three patients died during hospitalization. However, given their underlying conditions, critical clinical status, and comorbidities, it is not possible to directly attribute these deaths to a Phytobacter sepsis. Misidentification likely obscures the true burden of these infections. The genetic proximity of two ICU isolates supports Phytobacter as a potential opportunistic nosocomial pathogen, underscoring the need for accurate diagnostics and increased clinical awareness.
Contributor Information
Marcelo Pillonetto, Email: m.pilonetto@pucpr.br.
Nicholas M. Moore, Rush University Medical Center, Chicago, Illinois, USA
DATA AVAILABILITY
The associated BioSamples and raw sequencing reads are publicly available under BioProject PRJNA1336074.
REFERENCES
- 1. Ewing WH, Fife MA. 1972. Enterobacter agglomerans (Beijerinck) comb. nov. (the Herbicola-Lathyri Bacteria). Int J Syst Bacteriol 22:4–11. doi: 10.1099/00207713-22-1-4 [DOI] [Google Scholar]
- 2. Maki DG, Rhame FS, Mackel DC, Bennett JV. 1976. Nationwide epidemic of septicemia caused by contaminated intravenous products. Am J Med 60:471–485. doi: 10.1016/0002-9343(76)90713-0 [DOI] [PubMed] [Google Scholar]
- 3. Felts SK, Schaffner W, Melly MA, Koenig MG. 1972. Sepsis caused by contaminated intravenous fluids: epidemiologic, clinical, and laboratory investigation of an outbreak in one hospital. Ann Intern Med 77:881–890. doi: 10.7326/0003-4819-77-6-881 [DOI] [PubMed] [Google Scholar]
- 4. Smits THM, Arend L, Cardew S, Tång-Hallbäck E, Mira MT, Moore ERB, Sampaio JLM, Rezzonico F, Pillonetto M. 2022. Resolving taxonomic confusion: establishing the genus Phytobacter on the list of clinically relevant Enterobacteriaceae. Eur J Clin Microbiol Infect Dis 41:547–558. doi: 10.1007/s10096-022-04413-8 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 5. Pillonetto M, Arend LN, Faoro H, D’Espindula HRS, Blom J, Smits THM, Mira MT, Rezzonico F. 2018. Emended description of the genus Phytobacter, its type species Phytobacter diazotrophicus. Int J Syst Evol Microbiol 68:176–184. doi: 10.1099/ijsem.0.002477 [DOI] [PubMed] [Google Scholar]
- 6. Ma Y, Yao R, Li Y, Wu X, Li S, An Q. 2020. Proposal for Unification of the genus Metakosakonia and the genus Phytobacter to a single genus Phytobacter and reclassification of Metakosakonia massiliensis as Phytobacter massiliensis comb. nov. Curr Microbiol 77:1945–1954. doi: 10.1007/s00284-020-02004-4 [DOI] [PubMed] [Google Scholar]
- 7. Huang Z, Zhang G, Zheng Z, Lou X, Cao F, Zeng L, Wang D, Yu K, Li J. 2024. Genomic insights into the evolution, pathogenicity, and extensively drug-resistance of emerging pathogens Kluyvera and Phytobacter Front Cell Infect Microbiol 14:1376289. doi: 10.3389/fcimb.2024.1376289 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 8. Pillonetto M, Arend L, Gomes SMT, Oliveira MAA, Timm LN, Martins AF, Barth AL, Mazzetti A, Hersemann L, Smits THM, Mira MT, Rezzonico F. 2018. Molecular investigation of isolates from a multistate polymicrobial outbreak associated with contaminated total parenteral nutrition in Brazil. BMC Infect Dis 18:397. doi: 10.1186/s12879-018-3287-2 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 9. Centers for Disease Control and Prevention (CDC) . 1997. Nosocomial bacteremias associated with intravenous fluid therapy--USA. MMWR Morb Mortal Wkly Rep 46:1227–1233. [PubMed] [Google Scholar]
- 10. Habsah H, Zeehaida M, Van Rostenberghe H, Noraida R, Wan Pauzi WI, Fatimah I, Rosliza AR, Nik Sharimah NY, Maimunah H. 2005. An outbreak of Pantoea spp. in a neonatal intensive care unit secondary to contaminated parenteral nutrition. J Hosp Infect 61:213–218. doi: 10.1016/j.jhin.2005.01.004 [DOI] [PubMed] [Google Scholar]
- 11. Hon P, Ko KKK, Zhong JCW, De PP, Smits THM, Low J, Vasoo S, Tsui CKM. 2023. Genomic identification of two Phytobacter diazotrophicus isolates from a neonatal intensive care unit in Singapore. Microbiol Resour Announc 12:e0016723. doi: 10.1128/mra.00167-23 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 12. Kubota H, Nakayama T, Ariyoshi T, Uehara S, Uchitani Y, Tsuchida S, Nishiyama H, Morioka I, Koshinaga T, Kusabuka A, Nakatsubo N, Yamagishi T, Tabuchi Y, Okuno R, Kobayashi K, Mitobe M, Yokoyama K, Shinkai T, Suzuki J, Sadamasu K. 2023. Emergence of Phytobacter diazotrophicus carrying an IncA/C2 plasmid harboring blaNDM-1 in Tokyo, Japan. mSphere:e00147–23. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 13. Choice S, Sherman A, Holder K, Harrington E. 2024. Gram-negative sepsis caused by a rare pathogen Phytobacter ursingii BMJ Case Rep 17:e258384. doi: 10.1136/bcr-2023-258384 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 14. Janda JM, Abbott SL. 2021. The changing face of the family Enterobacteriaceae (Order: “Enterobacterales”): new members, taxonomic issues, geographic expansion, and new diseases and disease syndromes. Clin Microbiol Rev 34:e00174-20. doi: 10.1128/CMR.00174-20 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 15. Munson E, Carroll KC. 2021. Summary of novel bacterial isolates derived from human clinical specimens and nomenclature revisions published in 2018 and 2019. J Clin Microbiol 59:e01309-20. doi: 10.1128/JCM.01309-20 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 16. Carroll KC. 2023. Manual of Clinical Microbiology. Vol. 4. ASM Press, Newark. [Google Scholar]
- 17. Carella A, Carroll KC, Munson E. 2024. Update on novel validly published and included bacterial taxa derived from human clinical specimens and taxonomic revisions published in 2023. J Clin Microbiol 62:e0100424. doi: 10.1128/jcm.01004-24 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 18. Liu L, Feng Y, Wei L, Qiao F, Zong Z. 2020. Precise species identification and taxonomy update for the genus Kluyvera with reporting Kluyvera sichuanensis sp. nov. Front Microbiol 11:579306. doi: 10.3389/fmicb.2020.579306 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 19. Mazzetti A, D’Espindula HRS, Kulek DO, Jones KL, Kraft L, Smits THM, Rezzonico F, Mira MT, Pillonetto M. 2026. Construction of a superspectrum for rapid identification of opportunistic human pathogens belonging to the genus Phytobacter using whole-cell MALDI-TOF MS. Diagn Microbiol Infect Dis 115:117275. doi: 10.1016/j.diagmicrobio.2026.117275 [DOI] [PubMed] [Google Scholar]
- 20. Michel IR, Kulek D, Arend L, Pillonetto M, Smits THM, Rezzonico F. 2024. Development of two quantitative PCR assays for the detection of emerging opportunistic human pathogens belonging to the genus Phytobacter in routine diagnostics. Diagn Microbiol Infect Dis 110:116556. doi: 10.1016/j.diagmicrobio.2024.116556 [DOI] [PubMed] [Google Scholar]
- 21. Torres AJL, Angelo ALD, Silva MO, Bastos M de C, Souza DF de, Inocencio LA, Lemos JAR de, S. Junior R, Castro AC de, Palma PVB, Ceci L, Netto EM, Brites C. 2013. Establishing the reference range for t lymphocytes Subpopulations in adults and children from Brazil. Rev Inst Med trop S Paulo 55:323–328. doi: 10.1590/S0036-46652013000500005 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 22. Tsuji S, et al. 2026. Draft genome sequence of bla IMP-1-carrying Phytobacter ursingii OUH-01, isolated from the feces of an acute lymphoblastic leukemia patient. Microbiology Resource Announcements:e00876–25. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 23. Tumeo A, Kovarova A, McDonagh F, Ryan K, Clarke C, Miliotis G. 2026. Human colonization with Phytobacter co-harboring blaIMP-4 and mcr-9.1 highlights its potential as emerging human pathogen. bioRxiv:202510.09.681365. doi: 10.1101/2025.10.09.681365 [DOI] [PubMed]
- 24. Dal Lin A, Kulek DO, Gonçalves GA, Kraft L, Neto JFC, Vizentainer G, Pillonetto M. 2024. Building of a new spectra for the identification of Phytobacter spp., an emerging Enterobacterales, using MALDI Biotyper. Microbiol Spectr 12:e0110724. doi: 10.1128/spectrum.01107-24 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 25. Dubois D, Grare M, Prere M-F, Segonds C, Marty N, Oswald E. 2012. Performances of the Vitek MS matrix-assisted laser desorption ionization-time of flight mass spectrometry system for rapid identification of bacteria in routine clinical microbiology. J Clin Microbiol 50:2568–2576. doi: 10.1128/JCM.00343-12 [DOI] [PMC free article] [PubMed] [Google Scholar]
Associated Data
This section collects any data citations, data availability statements, or supplementary materials included in this article.
Data Availability Statement
The associated BioSamples and raw sequencing reads are publicly available under BioProject PRJNA1336074.