Lab Med Online.  2017 Oct;7(4):201-205. 10.3343/lmo.2017.7.4.201.

Five Cases of the Gram Variable Bacterium Paenibacillus urinalis Isolated from Clinical Specimens and its Clinical Significance

  • 1Department of Laboratory Medicine, School of Medicine, Kyung Hee University, Seoul, Korea.


Paenibacillus urinalis was first isolated from the urine of a woman in 2008, and was reported to be a contaminant. Here, we report 5 cases of P. urinalis isolated over 5 months at a tertiary hospital. Using an API kit, 4 cases were classified as Cellulomonas species. Owing to the low reliability of API kit results and Gram stain results indicating gram variable bacilli for few specimens, MALDI-TOF MS and 16S rRNA gene sequencing were performed for identification. The last case showed Gram variable bacilli, and therefore, based on previous experience, 16S rRNA gene base sequence analysis was carried out without an additional API kit. All isolated strains were confirmed to be P. urinalis, and were judged to be contaminants. As for Gram variable bacteria, the use of current biochemical identification systems may lead to misidentification as other bacteria, which may cause unnecessary or improper use of antibiotics. Moreover, whereas most of the Paenibacillus species are reported to be contaminants, some of them are being reported as sources of infection. Therefore, more accurate identification will be necessary in the future. Accordingly, it is expected that accurate identification of this genus will help clinical physicians make decisions regarding appropriate treatment and use of antibiotics.


Paenibacillus urinalis; Paenibacillus species; Gram variable organism; MALDI-TOF MS; 16S rRNA sequencing

MeSH Terms

Anti-Bacterial Agents
Base Sequence
Genes, rRNA
Tertiary Care Centers
Anti-Bacterial Agents


  • Fig. 1 (A) Blood agar plate after a 24-hour incubation at 37℃, 5% CO2; Colonies are non-hemolytic, circular, greyish, smooth and 1–3 mm in diameter, (B) Gram stain of the clinical isolate shows Gram variable rods.

  • Fig. 2 The neighbor-joining phylogenetic tree based on 16S rRNA sequences showing the phylogenetic position of the isolates from the studied cases and related Paenibacillus species. Bootstrap tests (1000 replicates) are shown adjacent to the branches. The scale bar length of 0.01 indicates 1% sequence distance.


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