Actinobaculum schaalii, a commensal of the urogenital area
Correspondence: Anne Buchhave Olsen, Department of Urology, Viborg Hospital, Heibergs Allé 4, 8800 Viborg, Denmark.
What's known on the subject? and What does the study add?
- Actinobaculum schaalii is considered to be a part of the normai flora in the genital and urinary tract area. It has been associated to urinary tract infection (UTI), sepsis, osteomyelitis, endocarditis and Foumier's gangrene. So far it has mainly been isolated from urine, blood and pus, and predominantly in elderly patients.
- This study examined the habitat of A. schaalii by collecting samples from skin and urine in patients with kidney or ureter stones before and after treatment with Extracorporeal Shock Wave Lithotripsy (ESWL). Additionally faeces and vaginal swabs from routine specimen in patients not undergoing ESWL and without known urinary calculi were also analysed.
- The study does not find A. schaalii in faeces but shows it to be presents on skin and mucosa in the genital area. A. schaalii is also shown a possible pathogen in the stone-patient group undergoing ESWL.
- To study the habitat of Actinobaculum schaalii by examing groin swabs, faeces samples and vaginal swabs, and to determine whether it is a common uropathogen in patients with kidney or ureter stones.
Patients and Methods
- A quantitative real-time PCR assay was used to analyse all samples, which were collected between 2010 and 2011.
- A total of 38 patients (24 men and 14 women), with kidney or ureter stones and undergoing extracorporeal shock wave lithotripsy (ESWL), provided urine samples and had groin swabs taken. In addition, 30 faecal samples and 19 vaginal swabs that had been sent for routine microbiological examinations from patients outside the ESWL group were analysed.
- A chi-squared test was used to analyse the differences between patient groups, studying samples from urine, faeces samples, groin swabs and vaginal swabs.
- Actinobaculum schaalii was found in the urine samples from 14 (37%) patients undergoing ESWL, and in both urine and groin swabs from seven (18%) patients.
- Actinobaculum schaalii was not found in faeces samples but it was found in six (32%) of the vaginal swabs, predominantly in patients >50 years (P = 0.06).
- The study indicates that A. schaalii is a commensal found on skin, urine and vaginal mucosa in the human urogenital area and supports other investigations in its finding that the elderly are at greatest risk of being colonized with A. schaalii.
Actinobaculum schaalii is a Gram-positive, facultative anaerobic rod that requires 5% CO2 and is unable to reduce nitrate to nitrite [1-4]. The bacterium is considered to be a part of the normal flora in the genital and urinary tract area . Since 1997, when A. schaalii was first named, it has been associated with UTI, sepsis, osteomyelitis, endocarditis and Fournier's gangrene [3, 5-9]. So far it has mainly been isolated from urine, blood and pus [2, 3, 7, 10], and predominantly in elderly patients [1, 2, 4, 8, 11], but has also been found on the skin in small children [12, 13].
A species-specific TaqMan real-time quantitative PCR has been developed at Viborg Hospital which is more sensitive and makes detection faster than culture .
Nearly all strains of A. schaalii have been found to be resistant to ciprofloxacin and trimethoprim but sensitive to β-lactam antibiotics [3, 11, 14].
The present study aimed to determine the habitat of A. schaalii by collecting samples from skin and urine in patients with kidney or ureter stones before and after treatment with ESWL. Faeces and vaginal swabs from routine specimens in patients not undergoing ESWL and without known urinary calculi were also analysed.
Materials and Methods
A total of 38 consecutive patients undergoing ESWL in the period from February to May 2011, were included in the study. The patients had no previous ESWL treatment and no clinical UTI. The patients submitted urine samples before and immediately after ESWL treatment. A groin swab was also taken immediately before ESWL treatment. In addition to the samples from patients undergoing ESWL, vaginal swabs and faeces samples sent for routine examination were analysed.
Urine Samples and Groin Swabs
Groin swabs (ESWAB, Copan Diagnostics inc., Murrieta, CA, USA) and urine samples were consecutively collected from 24 men and 14 women with kidney or ureter stones before and after ESWL treatment. The median (range) age of the patients was 54 (26–82) years. All the patients were selected from the ESWL treatment centre at the Department of Urology, Viborg Hospital. Catheterized patients and patients with nitrite-stix-positive urine were not included in the study.
Cultivation of Urine Samples
Urine samples were examined using a combined leukocyte esterase and nitrite stix (Combur-test, Roche Diagnostics Ltd, Lewes, East Sussex, UK) and real-time PCR, and were cultured on 5% Columbia sheep blood agar (Becton Dickinson, Heidelberg, Germany) in an aerobic atmosphere of 5% CO2 at 35 °C for 2 days. All colonizations with ≥104 colony-forming units (CFU)/mL were reported.
Vaginal Swabs and Faeces Samples
The 19 vaginal swabs sent for routine cultivation were examined using real-time PCR. The women from whom the swabs were taken had a median (range) age of 47 (22–93) years. In addition, 30 faeces samples from 11 men and 19 women with a median (range) age of 74 (42–88) years were sent for routine examination for pathogenic bacteria examined by real-time PCR.
Real-time PCR and DNA Extraction
DNA was extracted, using an Arrow Bugs'n Beads kit (NorDiag, Oslo, Norway), from 700 μL urine according to the manufacturer's instructions, eluted in 50 μL elution buffer, and stored at 4 °C until use. Vaginal and groin swabs were transferred to 1 mL saline and 1 mL buffer (ESWAB), respectively, were vortexed and DNA was extracted from 700 μL as described above. Approximately 50 mg of faeces was suspended in 1 mL saline, was vortexed and DNA was extracted from 700 μL as described above. A known final concentration of 104 A. schaalii CCUG 2740 was added to 50 mg faeces and suspended in 1 mL saline and was used to examine if faeces inhibited DNA extractions or the real-time PCR reaction. Furthermore, an internal control was added to all real-time PCR samples to examine if the real-time PCR reaction was inhibited. Real-time PCR was performed as described by Bank et al. . A tenfold serial dilution of known concentrations (104 to 106 CFU/mL) of A. schaalii CCUG 27420 was used to quantify the concentration in the urine samples.
The study was approved by The National Committee on Health Research Ethics. All patients who met the demands for participation were sent written information explaining the project and a consent form for signing before the ESWL treatment. On the day on which the patient underwent ESWL the consent form was collected and the patient was once again introduced to the project by a physician from the Department of Urology. The kidney and ureter stone patients answered questions on stone location, stone number, previous infections and comorbidities. Further information about the patients was collected using the hospital's electronic patient records and from previous CT scans.
A chi-squared test was used to analyse the differences between patient groups and a Mann–Whitney U-test was used to analyses differences in patients' age (Table 1).
Table 1. Demographic, clinical and microbiological data from 38 consecutive urine samples from patients with kidney or ureter stones collected before ESWL treatment and screened using real-time PCR and culture.
|Total no. of patients (%)||14 (37)||24 (63)||–|
|Median (range) age, years||59 (37–77)||53 (26–82)||0.04|
|Groin swab PCR ≤ 104 CFU/mL, n (%)||7 (18)||0||–|
|Ureter stone, n||1||1||1.00|
|Kidney stone, n|| || || |
|Conventional uropathogens ≥104 CFU/mL found by culture, n||5||8||1.00|
Using real-time PCR analyses of the urine samples taken before ESWL treatment, A. schaalii was found in quantities equivalent to >104–106 CFU/mL in 14 (37%) of the patients with kidney or ureter stones. Of the urine samples collected after ESWL, 11 (29%) were found to contain A. schaalii. Of the urine samples collected before ESWL treatment leukocytes were found in five (36%) of those harbouring A. schaalii and in only two (8%) of those where A. schaalii was not found (P = 0.08).
Twelve (86%) of the patients with A. schaalii in the urine were >50 years of age. A. schaalii was found in the urine collected before ESWL treatment in eight of the men and in six of the women (P = 0.73). There were no differences in the finding of A. schaalii (P = 0.88) or other uropathogens (P = 0.19) in the urine samples collected before or after ESWL treatment.
Neither the location (kidney or ureter) nor the number of stones increased the frequency of finding A. schaalii (>0.19; Table 1). Patients were questioned on comorbidities such as heart disease, diabetes and renal insufficiency and none were found to affect the results.
Actinobaculum schaalii was found in seven (18%) of the groin swabs in quantities equivalent to ≤104 CFU/mL and in these seven patients A. schaalii was found to be colonized in the urine. A. schaalii was found in groin swabs from five (36%) of the women and from two (8%) of the men (P = 0.08). Age was not associated with the presence of A. schaalii in the groin swabs (P = 0.84).
Of the 19 vaginal swabs sent for routine bacteriological examination, A. schaalii was found in six (32%). A. schaalii was identified in one of the vaginal swabs from patients ≤50 years and in five from patients >50 years (P = 0.06).
Actinobaculum schaalii was not identified in any of the 30 faeces samples. No inhibition of the real-time PCR was observed.
The present study found that A. schaalii was present as a commensal on skin and mucosa in the genital area, although the number of patients tested was relatively small. The study focused on determining the habitat of A. schaalii and its importance in patients with kidney or ureter stones. This bacterium has been suggested to be a part of the normal flora in the human genitourinary tract [2, 8, 11]. It was not found in any of the faeces samples but in a third of the vaginal swabs and predominantly in those from patients >50 years of age.
Half of the patients with A. schaalii in the urine sample also had positive groin swabs. The swabs containing A. schaalii were mainly from women, but no difference was found regarding the patient's age. The urine samples showed that the majority of patients with A. schaalii were >50 years of age which is consistent with other studies [4, 8].
Real-time PCR from urine samples showed that A. schaalii were found in quantities equivalent to >104–106 CFU/mL in 37% of the patients with kidney or ureter stones. The CO2 growth demands of A. schaalii probably mean that most of the patients with A. schaalii infection would not normally be diagnosed in routine practice, which supports the hypothesis that A. schaalii infections are underdiagnosed [3, 4, 7, 8, 10, 11]. Underdiagnosis is a problem if antibiotics such as ciprofloxacin or trimethoprim are chosen as the initial treatment because A. schaalii is not susceptible to these antibiotics [1, 3, 8, 11]; therefore, at our Department of Urology, patients who present a leukocyte-positive and nitrite-negative urine stix are prescribed pivmecillinam before ESWL treatment, to reduce the risk of infection after treatment.
In conclusion, the present study indicates that A. schaalii is a commensal found on skin, urine and vaginal mucosa in the human urogenital area. The study supports other investigations in that the elderly are at greatest risk of being colonized with A. schaalii. A. schaalii only rarely causes UTI, but it should be taken into consideration, especially if the patient shows clinical signs of urinary infection with leukocytes in the urine but no visible growth by culture after 1 day of incubation on agar plates.
We thank Anders Brøndums Velgørende Fond for funding.
Conflict of Interest