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Identification of Raoultella terrigena as a rare causative agent of subungual abscess based on 16S rRNA and housekeeping gene sequencing.

1. Introduction

Raoultella terrigena is a Gram-negative, oxidase-negative, aerobic, nonmotile, capsulated, non-spore-forming bacterium. It was primarily recovered from soil and considered as a nonpathogenic species, although it harbours numerous virulence factors found in Klebsiella pneumoniae [1]. Very few reports of clinical infections caused by this species are available so far, and its clinical significance is still unclear [1]. A previous study showed that the carriage rate of R. terrigena in healthy people was 0.9% by analyzing 5,377 different stool specimens [2]. The incidence of R. terrigena among clinical Klebsiella isolates was 0.4%, and most of these isolates were obtained from respiratory secretions [2]. We here reported a case of a 63-year-old man who developed a subungual abscess caused by R. terrigena. We further performed a literature review on R. terrigena infections.

2. Case History

In March 2015, a 63-year-old man was admitted to the surgery department of a university hospital with the complaint of a painful abscess on his right thumb lasting for 3 days. The patient is a farmer and had no prior medical and surgical history. Eight days before his admission, the patient experienced an accidental injury on his thumb during working in the field and later washed the wound by river water As shown by physical examination, the abscess was at the lateral nail edge, and finger pad was tense and pus presented. No other skin lesions were detected. The patient was consequently diagnosed as the subungual abscess. A longitudinal incision and drainage were thus performed with expression of purulent fluid, and a culture of the fluid was performed. The relief of pain immediately after this treatment was reported by the patient. 500 mg of imipenem twice a day for 10 days was prescribed to the patient, and he recovered after this treatment.

The pus from the incision was inoculated onto sheep blood agar plates and incubated at 37[degrees]C in a CO2-enriched (5%) atmosphere for 24 h. Incubation yielded single colonies of Gram-negative rod-shaped bacterium identified by Gram staining (Figure 1(a)). Colonies of isolate Z38 were circular, smooth, glistening, light yellow, and nonhemolysis after 48 h of incubation on sheep blood agar plates at 37[degrees]C (Figure 1(b)). The samples were analyzed by MALDI-TOF mass spectrometry (Autoflex III, Bruker, Germany) and were identified as Raoultella terrigena with a similarity rate of 99.9%.

As Raoultella terrigena is rarely identified in clinical samples, identification was subsequently redone by VITEK 2 system with panel AST-GN-13 (BioMerieux, France). The isolate was identified as Raoultella planticola by the VITEK 2 system. Antimicrobial susceptibility testing was also performed by VITEK 2 system with panel AST-GN-13, and Escherichia coli ATCC 25922 and Pseudomonas aeruginosa ATCC 27853 were as controls. The result interpretation was performed as described in CLSI guidelines. The isolate was susceptible to all antibiotics tested except ampicillin (Table 1).

To get a reliable identification, 16S rRNA and the housekeeping gene sequencing were further used to accurately identify and discriminate. PCR amplification of the 16S rRNA was performed with the universal bacterial primers 27f (5'-AGAGTTTGATCCTGGCTCAG-3') and 1492r (5'TACCTTGTTACGACTT-3'). The 1.4 kb PCR product was sequenced and blasted in GenBank to identify the species. Alignments of 16S rRNA sequences of the isolate Z38 and type strains of close related species collected from EzTaxon-e database were generated by ClustalW program. A neighbor-joining phylogenetic tree based on the Tamura-Nei model was constructed by MAGA6.06. The phylogeny indicated the strain Z38 (KT276326) sharing 99% identity with the type strain Raoultella terrigena NBRC [12941.sup.T] (Y17658) (Figure S1A in Supplementary Material available online at http://dx

Housekeeping genes rpoB, gyrA, and parC were sequenced to demonstrate the taxonomic identification as described previously [3]. The sequence similarity of gyrA, parC, and rpoB between pus isolate Z38 and the most closely related type strain (R. terrigena NBRC [12941.sup.T]) was 99%, 99%, 98%, respectively (Table 2 and Figures S2, S3, and S4). The phylogenetic tree constructed by concatenating sequences of the 3 housekeeping genes showed that strain Z38 formed a distinct lineage with R. terrigena NBRC [12941.sup.T] (Figure S1B). Together with the typing result of 16S rRNA, the pus isolate Z38 was identified as R. terrigena.

3. Discussion

R. terrigena is a soil microorganism with only two reports of clinical infection. Goegele et al. described the first case of human infection in a liver transplant recipient who developed fatal endocarditis due to R. terrigena in 2007 [4]. The association between R. terrigena and sepsis was reported in 2011, which represents the second case of human infection [5]. We speculated that the pathogen in our case may originate from environment, since the patient injured in the farmland and had the risk of infection by soil bacterium.

Accurate identification of Raoultella spp. is a challenge by routine work as this genus shares highly similar phenotypes with other genera of Enterobacteriaceae, especially Klebsiella spp. [5]. In 2001, Raoultella spp. as a novel species was separated from Klebsiella spp. on the basis of 16S rDNA and rpoB typing results [6]. Phylogenetic analysis of gyrB sequences showed that K. terrigena (R. terrigena) and K. pneumoniae belong to two separate lineages [7]. Difficulties in correct identification of Raoultella spp. may have led to an underestimation of its incidence and uncertainty on its pathogenic role [8]. Currently, the identification of Raoultella species from clinical specimens mainly relied on phenotypic methods. A study has validated that MALDI-TOF MS increases the accuracy of Raoultella identifications to the genus level [9]. However, the three species of Raoultella genus shared very close genetic relationship and can only be distinguished by a very few biochemical characters. In our study, a discrepancy was caused by MALDI-TOF mass spectrometry and VITEK 2 identification. Thus, molecular techniques are highly recommended to discriminate the three species [5].

However, no molecular markers are available for this purpose from the literature due to the rarity of the pathogen. A study showed that rpoB was demonstrated on the correct identifications of all Raoultella isolates [8]. Furthermore, three housekeeping genes gyrA (383bp), rpoB (512bp), and parC (319 bp) were used for species-level identification of members of the Klebsiella/Raoultella complex [3]. Therefore, in our study three housekeeping genes (gyrA, rpoB, and parC) were chosen for the identification of R. terrigena. The phylogenetic analysis by concatenating the 3 housekeeping genes showed that strain Z38 was clustered with R. terrigena. This result is consistent with the results of MALDI-TOF and 16S rRNA sequencing (Figure S1). We therefore concluded that VITEK 2 system is not suitable for R. terrigena identification. Our study further implies that human infections by R. terrigena maybe underestimated due to the difficulties in correctly identifying this bacterium during routine diagnosis in clinical microbiology laboratories.

The clinical features and outcomes of human infections caused by R. terrigena have been rarely reported. The first R. terrigena infection case was reported in 2007, and a 45year-old patient developed endocarditis due to R. terrigena after liver transplant [4]. Another infection case occurred in a patient who underwent pancreatic resection for pancreatic cancer [5]. However, the pathogenic role of Raoultella spp. in human infection is still difficult to elucidate. Notably, some species of Raoultella spp., for example, Raoultella ornithinolytica, have been suggested as opportunistic pathogens that mainly infect elderly patients with immunosuppression or comorbidities, particularly solid tumours [8].

In conclusion, this report describes the first case of subungual abscess caused by R. terrigena infection. Our finding highlights that the soil microflora enables causing severe infections. Additionally, molecular identification enables us to accurately identify fastidious organisms from clinical specimens when phenotypic identification fails.

Competing Interests

The authors declare that they have no competing interests.

Authors' Contributions

Yu Wang and Xiawei Jiang are equal contributors.


The authors thank Dr. Kai Zhou for his critical review of this paper.


[1] R. Podschun, A. Fischer, and U. Ullmann, "Characterization of Klebsiella terrigena strains from humans: haemagglutinins, serum resistance, siderophore synthesis, and serotypes," Epidemiology and Infection, vol. 125, no. 1, pp. 71-78, 2000.

[2] R. Podschun and U. Ullmann, "Isolation of Klebsiella terrigena from clinical specimens," European Journal of Clinical Microbiology & Infectious Diseases, vol. 11, no. 4, pp. 349-352, 1992.

[3] Z.-I. Kimura, K. M. Chung, H. Itoh, A. Hiraishi, and S. Okabe, "Raoultella electrica sp. nov., isolated from anodic biofilms of a glucose-fed microbial fuel cell," International Journal of Systematic and Evolutionary Microbiology, vol. 64, no. 4, Article ID 058826, pp. 1384-1388, 2014.

[4] H. Goegele, E. Ruttmann, J. Aranda-Michel et al., "Fatal endocarditis due to extended spectrum betalactamase producing Klebsiella terrigena in a liver transplant recipient," Wiener Klinische Wochenschrift, vol. 119, no. 11-12, pp. 385-386, 2007

[5] M. M. Shaikh and M. Morgan, "Sepsis caused by Raoultella terrigena" JRSM Short Reports, vol. 2, no. 6, pp. 49-49, 2011.

[6] M. Drancourt, C. Bollet, A. Carta, and P. Rousselier, "Phylogenetic analyses of Klebsiella species delineate Klebsiella and Raoultella gen. nov., with description of Raoultella ornithinolytica comb. nov., Raoultella terrigena comb. nov. and Raoultella planticola comb. nov.," International Journal of Systematic and Evolutionary Microbiology, vol. 51, no. 3, pp. 925-932, 2001.

[7] C. Dauga, "Evolution of the gyrB gene and the molecular phylogeny of Enterobacteriaceae: a model molecule for molecular systematic studies," International Journal of Systematic and Evolutionary Microbiology, vol. 52, no. 2, pp. 531-547, 2002.

[8] M. Ponce-Alonso, L. Rodriguez-Rojas, R. del Campo, R. Canton, and M. Morosini, "Comparison of different methods for identification of species of the genus Raoultella: report of 11 cases of Raoultella causing bacteraemia and literature review," Clinical Microbiology and Infection, vol. 22, no. 3, pp. 252-257, 2016.

[9] E. De Jong, A. S. De Jong, N. Smidts-van den Berg, and R. J. Rentenaar, "Differentiation of Raoultella ornithinolytica/ planticola and Klebsiella oxytoca clinical isolates by matrix-assisted laser desorption/ionization-time of flight mass spectrometry," Diagnostic Microbiology and Infectious Disease, vol. 75, no. 4, pp. 431-433, 2013.

Yu Wang, (1) Xiawei Jiang, (1) Zemin Xu, (2) Chaoqun Ying, (1) Wei Yu, (1) and Yonghong Xiao (1)

(1) State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China

(2) Ningbo Institute of Microcirculation and Henbane, Ningbo, China

Correspondence should be addressed to Yonghong Xiao;

Received 8 October 2015; Revised 28 April 2016; Accepted 15 May 2016

Academic Editor: Maurizio Sanguinetti

Caption: FIGURE 1: Gram staining and morphology of R. terrigena Z38 colony. (a) Gram-negative, short-rod-shaped bacterium was observed (magnification, x100). (b) Shown are circular, smooth, glistening, light yellow, and nonhemolysis colonies after a 48-hour culture on sheep blood agar under aerobic conditions.
TABLE 1: Antibiotic resistance profiles of Raoultella terrigena Z38.

Antibiotics               MIC ([micro]g/mL) (a)       Susceptibility

Ampicillin                          16                      R
Amikacin                [less than or equal to] 2           S
Ciprofloxacin          [less than or equal to] 0.25         S
Levofloxacin           [less than or equal to] 0.25         S
Cefoperazone            [less than or equal to] 1           S
Imipenem                [less than or equal to] 1           S
Trimethoprim-           [less than or equal to] 20          S
Tobramycin              [less than or equal to] 1           S
Piperacillin-           [less than or equal to] 4           S
Ampicillin-sulbactam    [less than or equal to] 2           S
Aztreonam               [less than or equal to] 1           S
Cefotetan               [less than or equal to] 4           S
Cefazolin               [less than or equal to] 4           S
Gentamicin              [less than or equal to] 1           S
Ceftazidime             [less than or equal to] 1           S
Cefepime                [less than or equal to] 1           S
Ertapenem              [less than or equal to] 0.5          S

(a) MICs were determined using the Vitek 2 GN and AST cards,
following the manufacturer's instructions. The susceptibility
breakpoints of MICs followed those recommend by the Clinical and
Laboratory Standards Institute.

TABLE 2: The list of gene sequences used for phylogenetic
tree construction.

Species                                    16S rRNA      gyrA

Raoultella terrigena NBRC [12941.sup.T]     Y17658     AF303617
Raoultella planticola NBRC [12939.sup.T]   AF129443    AF303621
Raoultella ornithinolytica NBRC            AF129441    AF303618
Raoultella electrica [1GB.sup.T]           AB762091    AB828204
Klebsiella oxytoca ATCC [13182.sup.T]       U78183     AF052257
Klebsiella oxytoca KCTC 1686               NR_102982   CP003218
Klebsiella michiganensis [W14.sup.T]       JQ070300    JQ990329
Klebsiella variicola At-22                 NR_074729   NC013850
Klebsiella pneumoniae subsp. Pneumonia      Y17656     DQ673325
  ATCC [13883.sup.T]
Klebsiella pneumoniae subsp.               NR_114507   FO203501
  rhinoscleromatis ATCC [13884.sup.T]
Klebsiella pneumoniae subsp. Ozaenae       AF130982    AF303619
  ATCC 11297
Serratia liquefaciens ATCC [27592.sup.T]   NR_121703   CP006252

Species                                        rpoB           parC

Raoultella terrigena NBRC [12941.sup.T]      AY367362       AF303651
Raoultella planticola NBRC [12939.sup.T]     AY367361       AF303655
Raoultella ornithinolytica NBRC              AF129447       AF303652
Raoultella electrica [1GB.sup.T]             AB828205       AB828206
Klebsiella oxytoca ATCC [13182.sup.T]        AY367363          --
Klebsiella oxytoca KCTC 1686                 CP003218       CP003218
Klebsiella michiganensis [W14.sup.T]         JQ269337          --
Klebsiella variicola At-22                  NC_013850       CP001891
Klebsiella pneumoniae subsp. Pneumonia       DQ673324       AF303641
  ATCC [13883.sup.T]
Klebsiella pneumoniae subsp.               ACZD01000183   ACZD01000120
  rhinoscleromatis ATCC [13884.sup.T]
Klebsiella pneumoniae subsp. Ozaenae         AF129445       AF303653
  ATCC 11297
Serratia liquefaciens ATCC [27592.sup.T]    NC.021742       CP006252
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Title Annotation:Case Report
Author:Wang, Yu; Jiang, Xiawei; Xu, Zemin; Ying, Chaoqun; Yu, Wei; Xiao, Yonghong
Publication:Canadian Journal of Infectious Diseases and Medical Microbiology
Article Type:Case study
Date:Jan 1, 2016
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