Actinotignum schaalii (formerly Actinobaculum schaalii): a newly recognized pathogen-review of the literature

The performance of a Fully Automated Urine Particle Analyzer, Sysmex UF-5000, in detecting fastidious bacteria in urine samples

Several types of fastidious bacteria can cause tract infections. We evaluated the performance of counting fastidious bacteria using a Fully Automated Urine Particle Analyzer UF-5000. The results showed that UF-5000 counts fastidious bacteria in urine without the need for culture using measurement principles based on flow cytometry.

Fannyhessea vaginae causing bacteraemia and vertebral osteomyelitis: first report of invasive disease in a male

Introduction.Fannyhessea vaginae (formerly Atopobium vaginae) is an anaerobic organism commonly associated with female genital flora, with rare cases of invasive disease reported in females. Case report. We discuss the case of an 81-year-old male who presented with an acute history of back pain and signs of urinary tract infection in the context of intermittent self-urinary catheterisation. Multiple blood cultures grew Fannyhessea vaginae with a later finding of lumbar vertebral osteomyelitis as the cause of back pain. Treatment was commenced with ampicillin, later switched to ceftriaxone, with improvement of acute signs of infection. Conclusion. Gram-positive anaerobic organisms including Fannyhessea vaginae are possibly under-recognised causes of urinary tract particularly in older males. These bacteria may prove challenging to grow in standard protocols for urine culture; anaerobic or extended incubation could be considered particularly in complicated cases of urinary tract infection without an identifiable pathogen.

Preanalytical, Analytical and Postanalytical Analyses on Corynebacterium spp. and Actinomycetaceae in Urine Samples of Patients with Suspected Urinary Tract Infection-A Hypothesis-Forming Observational Study

A hypothesis-forming exploratory cross-sectional assessment was conducted to assess the occurrence and relevance of Gram-positive rod-shaped bacteria like Corynebacterium spp. and Actinomycetaceae in human urine samples. In total, 1170 urine samples from 1031 inpatients with suspected urinary tract infection were assessed for culture-based growth of Gram-positive rod-shaped bacteria applying API Coryne assays, matrix-assisted laser desorption-ionization time-of-flight mass spectrometry (MALDI-TOF-MS), and in-house 16S rRNA gene sequencing. Overall, 502 different bacterial colonies from 346 urine samples taken from 324 inpatients were observed. The three quantitatively most abundant genera or genus clusters were Corynebacterium (254 isolates, 62%), Actinomyces/Winkia (79 isolates, 19%), and Actinotignum/Actinobaculum (29 isolates, 7%). Compared to sequencing, the diagnostic accuracy of all assessed competitor assays from the diagnostic routine was <80% for differentiation on the genus level and <30% for differentiation on the species level. Prolongated incubation for 4 days compared to 2 days resulted in additional detection of 15% of the totally recorded Gram-positive rod-shaped bacteria. An approximately 5-fold increased detection rate in mid-stream urine compared to urine acquired applying alternative sampling strategies was observed. In conclusion, in the rare event of the suspected clinical relevance of such findings, confirmatory testing with invasively sampled urine should be considered due to the high contamination rate observed in mid-stream urine. Confirmatory testing by DNA-sequencing methods should be considered if an exact identification of genus or species is regarded as relevant for the individual choice of the therapeutic strategy.

Case report: A rare case of skin abscess caused by coinfection of Actinobaculum schaalii and Actinomyces turicensis

Skin abscess is one of the most common infections of the skin and soft tissues. However, anaerobic bacteria are infrequently identified as the causative agents of this particular form of abscess. In this case, a 34-year-old pregnant woman was diagnosed with a skin abscess with the use of ultrasonography. The microbiological analysis results of the purulent fluid revealed the coinfection of Actinobaculum schaalii and Actinomyces turicensis. The patient was first treated empirically with 3 days of cefathiamidine, which resulted in no symptom improvement. Subsequently, a surgical procedure involving incision and draining was performed, with the administration of ceftriaxone. After 7 days of antibiotic intervention, the patient exhibited a satisfactory recovery. Clinicians need to be aware of other types of infections that might be attributed to Actinobaculum schaalii and Actinomyces turicensis, in addition to urinary tract infections.

Resistance to first-line antibiotic therapy among patients with uncomplicated acute cystitis in Melbourne, Australia: prevalence, predictors and clinical impact

Background

Australian guidelines recommend trimethoprim or nitrofurantoin as first-line agents for uncomplicated urinary tract infections (UTIs). Laboratory surveillance indicates high rates of trimethoprim resistance among urinary bacterial isolates, but there are scant local clinical data about risk factors and impact of trimethoprim resistance.

Objectives

To determine the prevalence, risk factors, mechanism and impact of resistance to first-line antibiotic therapy for uncomplicated UTIs in the community setting.

Methods

A prospective observational study from October 2019 to November 2021 in four general practices in Melbourne, Australia. Female adult patients prescribed an antibiotic for suspected or confirmed uncomplicated acute cystitis were eligible. Primary outcome was urine isolates with resistance to trimethoprim and/or nitrofurantoin.

Results

We recruited 87 participants across 102 UTI episodes with median (IQR) age of 63 (47-76) years. Escherichia coli was the most common uropathogen cultured (48/62; 77%); 27% (13/48) were resistant to trimethoprim (mediated by a dfrA gene) and none were resistant to nitrofurantoin. Isolates with resistance to a first-line therapy were more common among patients reporting a history of recurrent UTIs [risk ratio (RR): 2.08 (95% CI: 1.24-3.51)] and antibiotic use in the previous 6 months [RR: 1.89 (95% CI: 1.36-2.62)]. Uropathogen resistance to empirical therapy was not associated with worse clinical outcomes.

Conclusions

Resistance to trimethoprim is common in uncomplicated UTIs in Australia but may not impact clinical outcomes. Further research is warranted on the appropriateness of trimethoprim as empirical therapy, particularly for patients with antimicrobial resistance risk factors.

Emerging and Fastidious Uropathogens Were Detected by M-PCR with Similar Prevalence and Cell Density in Catheter and Midstream Voided Urine Indicating the Importance of These Microbes in Causing UTIs

Introduction

This study compared microbial compositions of midstream and catheter urine specimens from patients with suspected complicated urinary tract infections to determine if emerging and fastidious uropathogens are infecting the bladder or are contaminants.

Methods

Urine was collected by in-and-out catheter (n = 1000) or midstream voiding (n = 1000) from 2000 adult patients (≥60 years of age) at 17 DispatchHealth sites across 11 states. The two groups were matched by age (mean 81 years), sex (62.1% female, 37.9% male), and ICD-10-CM codes. Microbial detection was performed with multiplex polymerase chain reaction (M-PCR) with a threshold for "positive detection" ≥ 10,000 cells/mL for bacteria or any detection for yeast. Results were divided by sex.

Results

In females, 28 of 30 microorganisms/groups were found by both collection methods, while in males 26 of 30 were found by both. There were significant overlaps in the detection and densities of classical uropathogens including Escherichia coli, Enterococcus faecalis, and Klebsiella pneumoniae, as well as emerging uropathogens including Actinotignum schaalii and Aerococcus urinae. In females, detection rates were slightly higher in midstream voided compared to catheter-collected (p = 0.0005) urine samples, while males showed the opposite trend (p < 0.0001). More polymicrobial infections were detected in midstream voided compared to catheter-collected samples (64.4% vs 45.7%, p < 0.0001) in females but the opposite in males (35.6% vs 47.0%, p = 0.002).

Discussion

In-and-out catheter-collected and midstream voided urine specimens shared significant similarities in microbial detections by M-PCR, with some differences found for a small subset of organisms and between sexes.

Conclusion

Non-invasive midstream voided collection of urine specimens for microbial detection and identification in cases of presumed UTI does not result in significantly more contamination compared to in-and-out catheter-collected specimens. Additionally, organisms long regarded as contaminants should be reconsidered as potential uropathogens.

Acute Pyelonephritis with Bacteremia in an 89-Year-Old Woman Caused by Two Slow-Growing Bacteria: Aerococcus urinae and Actinotignum schaalii

Aerococcus urinae is an aerobic Gram-positive coccus that grows as tiny alpha-hemolytic colonies. Actinotignum schaalii is a slow-growing facultative anaerobic Gram-positive rod. These bacteria are part of the urogenital microbiota of healthy patients, but can also be involved in urinary tract infections (UTIs), particularly in elderly men and young children. Because A. urinae and A. schaalii are fastidious and are difficult to identify with phenotypic methods, they are underestimated causes of UTIs. Their growth is slow and requires a blood-enriched medium incubated under an anaerobic or 5% CO2 atmosphere for 48 h and from 24 to 48 h for A. schaalii and A. urinae, respectively. Furthermore, accurate identification is only possible using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) or molecular-based methods. In rare cases, these bacteria can be responsible for invasive infections. We describe, here, an unusual case of bacteremic UTI caused by both A. schaalii and A. urinae in an 89-year-old woman. She presented with dyspnea, and bacteriuria was noted. This challenging clinical and microbiological diagnosis was made in our laboratory by Gram staining urine with a leucocyte count >50/μL and/or a bacterial count >14/μL urinary culture on a blood agar plate. After 10 days of antimicrobial treatment consisting of 2 g amoxicillin PO t.i.d., the patient was discharged with a complete clinical and biological recovery. A. schaalii and A. urinae are probably still underestimated causes of UTIs. Microbiologists could consider the presence of these two bacteria using appropriate culture and identification methods in cases where a positive direct examination of urine reveals small Gram-positive rods or cocci, where undocumented UTIs are present in elderly patients, but also where a urinary dipstick is negative for nitrites and is associated with leukocyturia.

Comparison Shows that Multiplex Polymerase Chain Reaction Identifies Infection-associated Urinary Biomarker-positive Urinary Tract Infections That Are Missed by Standard Urine Culture

Background

Multiplex polymerase chain reaction (M-PCR) has increased sensitivity for microbial detection compared with standard urine culture (SUC) in cases diagnosed as urinary tract infections (UTIs), leading to questions whether detected microbes are likely causative of UTIs or are incidental findings.

Objective

To compare infection-associated biomarker levels against M-PCR and SUC results in symptomatic cases with a presumptive diagnosis of a UTI by a urologist.

Design setting and participants

Participants were ≥60 yr old and presented to urology clinics between January and April 2023 with symptoms of UTIs (n = 583). Urine microbial detection was by M-PCR and SUC. Three infection-associated biomarkers (neutrophil gelatinase-associated lipocalin, interleukin-8, and interleukin-1β) were measured by enzyme-linked immunosorbent assay. Symptomatic cases with elevated biomarkers, detection of uropathogens, and a specialist clinical diagnosis of a UTI were considered definitive UTI cases.

Outcome measurements and statistical analysis

Distributions were compared using two-sample Wilcoxon rank sum test, with two-tailed p values of <0.05 considered statistically significant.

Results and limitations

In cases with M-PCR-positive/SUC-negative results (n = 80), all median biomarker levels were significantly higher (p < 0.0001) than in cases with M-PCR-negative/SUC-negative results (n = 107). Two or more biomarkers were positive in 76% of M-PCR-positive/SUC-negative specimens. Limitation was an inability to examine associations between each individual organism and inflammation.

Conclusions

A significant number of M-PCR-positive/SUC-negative cases had elevated levels of infection-related urinary biomarkers, especially when infection was caused by organisms other than Escherichia coli. This is a strong indication that microbes detected by M-PCR, which would be missed by SUC, are associated with UTIs.

Patient summary

We compared infection-associated biomarkers in patients diagnosed with urinary tract infections (UTIs) against the detection of microorganisms by standard urine culture (SUC) and multiplex polymerase chain reaction (M-PCR). We found that most patients with microorganisms detected by M-PCR, which were missed by SUC, had elevated markers of inflammation, indicating that these organisms were likely causative of UTIs.

Survey of the infant male urobiome and genomic analysis of Actinotignum spp

The urinary bladder harbors a community of microbes termed the urobiome, which remains understudied. In this study, we present the urobiome of healthy infant males from samples collected by transurethral catheterization. Using a combination of enhanced culture and amplicon sequencing, we identify several common bacterial genera that can be further investigated for their effects on urinary health across the lifespan. Many genera were shared between all samples suggesting a consistent urobiome composition among this cohort. We note that, for this cohort, early life exposures including mode of birth (vaginal vs. Cesarean section), or prior antibiotic exposure did not influence urobiome composition. In addition, we report the isolation of culturable bacteria from the bladders of these infant males, including Actinotignum spp., a bacterial genus that has been associated with urinary tract infections in older male adults. Herein, we isolate and sequence 9 distinct strains of Actinotignum spp. enhancing the genomic knowledge surrounding this genus and opening avenues for delineating the microbiology of this urobiome constituent. Furthermore, we present a framework for using the combination of culture-dependent and sequencing methodologies for uncovering mechanisms in the urobiome.

Impact of microbiota and host immunologic response on the efficacy of anticholinergic treatment for urgency urinary incontinence

INTRODUCTION AND HYPOTHESIS

Studies within the past decade have suggested associations among composition of the urinary microbiota, local immune responses, and urinary incontinence symptoms. To investigate these relationships, we evaluated the structure of the urinary microbiome, local inflammatory markers, and patient responses prior to and at 6-weeks after treatment with anticholinergic medication for urgency urinary incontinence (UUI).

METHODS

Using a prospective pilot study, we enrolled women who presented with UUI symptoms and were prescribed treatment with anticholinergics. Catheterized urine samples were collected from participants at their baseline and 6-week follow-up visits for microbiological (standard and 16S rRNA gene phylotyping analyses) and cytokine analysis along with the UDI-6 questionnaire and 2-day bladder diary.

RESULTS

Patients were Caucasian, post- menopausal, with a median age of 64 and median BMI of 30.1 kg/m2. Among the patients, 75% had UUI symptoms for less than 2 years, but with a frequency of at least a few times a week or every day. Most women were prescribed 10 mg oxybutynin ER daily at enrollment. Patients had varied urinary microbiota by culture and 16S phylotyping, with species of Lactobacillus being the most common, in six samples, in addition to taxa associated with Enterococcus, Staphylococcus, and mixed flora. Cytokine levels showed no differences before and after treatment with anticholinergics, nor correlation with urinary bacteria or microbiome composition.

CONCLUSIONS

Our pilot study suggests factors in addition to the urinary microbiome and local immune responses may be involved in patients' response to anticholinergics for UUI.

A test combining multiplex-PCR with pooled antibiotic susceptibility testing has high correlation with expanded urine culture for detection of live bacteria in urine samples of suspected UTI patients

We evaluated whether multiplex polymerase chain reaction (M-PCR) detects viable micro-organisms by comparing micro-organism identification with standard urine culture (SUC) and expanded quantitative urine culture (EQUC). Of the 395 organisms detected by M-PCR, EQUC detected 89.1% (p = 0.10), whereas SUC detected 27.3% (p < 0.0001 vs. M-PCR and p < 0.0001 vs EQUC). M-PCR identified 260 nonfastidious bacteria, EQUC detected 96.5% (p = 0.68), whereas SUC detected 41.5% (p < 0.0001). Common nonfastidious bacteria missed by SUC included Escherichia coli (72.5% detected), Klebsiella pneumoniae (66.7% detected), Enterococcus faecalis (34.6% detected) and Enterococcus faecium (0% detected). M-PCR identified 135 fastidious bacteria and EQUC 101 (74.8%, p = 0.01), whereas SUC failed to detect any (0%, p < 0.0001). Clinical samples evaluated using EQUC and M-PCR yielded very similar findings, indicating that most microbes identified by M-PCR represented viable organisms, and validating M-PCR as a diagnostic tool for UTIs.

Elevated UTI Biomarkers in Symptomatic Patients with Urine Microbial Densities of 10,000 CFU/mL Indicate a Lower Threshold for Diagnosing UTIs

The literature lacks consensus on the minimum microbial density required for diagnosing urinary tract infections (UTIs). This study categorized the microbial densities of urine specimens from symptomatic UTI patients aged ≥ 60 years and correlated them with detected levels of the immune response biomarkers neutrophil gelatinase-associated lipocalin (NGAL), interleukin-8 (IL-8), and interleukin-1-beta (IL-1β). The objective was to identify the microbial densities associated with significant elevation of these biomarkers in order to determine an optimal threshold for diagnosing symptomatic UTIs. Biobanked midstream voided urine samples were analyzed for microbial identification and quantification using standard urine culture (SUC) and multiplex-polymerase chain reaction (M-PCR) testing, while NGAL, IL-8, and IL-1β levels were measured via enzyme-linked immunosorbent assay (ELISA). NGAL, IL-8, and IL-1β levels were all significantly elevated at microbial densities ≥ 10,000 cells/mL when measured via M-PCR (p < 0.0069) or equivalent colony-forming units (CFUs)/mL via SUC (p < 0.0104) compared to samples with no detectable microbes. With both PCR and SUC, a consensus of two or more elevated biomarkers correlated well with microbial densities > 10,000 cells/mL or CFU/mL, respectively. The association between ≥10,000 cells and CFU per mL with elevated biomarkers in symptomatic patients suggests that this lower threshold may be more suitable than 100,000 CFU/mL for diagnosing UTIs.

The role of Actinomyces spp. and related organisms in cervicofacial infections: Pathomechanism, diagnosis and therapeutic aspects

Members of the Actinomyces genus and Actinomyces-like organisms (ALOs; namely Actinotignum, Arcanobacterium, Schaalia and Varibaculum) are Gram-positive, non-spore-forming rods that are commensal members of the human oral cavity, gastrointestinal tract, female genital tract and skin microbiota. Cervicofacial actinomycosis or "lumpy jaw syndrome" - the chronic, suppurative granulomatous disease caused by Actinomyces spp. And ALOs - is characterized by an initially slow and unspecific disease-presentation, which often mimics other pathologies, followed by the formation of painful abscesses and severe tissue destruction. Actinomycosis has been described as a rare disease, however, reliable epidemiological data are lacking. In addition, there is increasing awareness regarding the role of Actinomyces spp. in the development of osteoradionecrosis and medication-related osteonecrosis of the jaw. The aim of this narrative review is to succinctly summarize the current advances regarding the microbiological, clinical, diagnostic and therapeutic aspects of cervicofacial actinomycosis, in addition to the roles of Actinomyces species and ALOs as members of the oral microbiota and in dental biofilm, in other dental infections (caries, root canal infection, periapical infection, periodontitis) and osteonecrosis of the jaw, in the context of recent taxonomic changes affecting the genus. Our paper aims to be a blueprint for dentists, other physicians, microbiologists and researchers regarding the multifaceted field of cervicofacial actinomycosis.

Presence and Relevance of Emerging Microorganisms in Clinical Genitourinary Samples

Microorganisms responsible for genitourinary infections increasingly include species other than conventional etiological agents that are of clinical and pathogenic relevance and therapeutic interest. This cross-sectional descriptive study selected samples from clinical genitourinary episodes between January 2016 and December 2019 in which emerging microbiological agents were detected. The patients’ epidemiological characteristics, clinical presentation, antibiotic treatment, and outcome were studied to identify their pathogenic role. The emerging microorganisms most frequently detected in urinary tract infections were Streptococcus bovis (58.5%) and Gardnerella spp. (23.6%) in females and S. bovis (32.3%), Aerococcus urinae (18.6%), and Corynebacterium spp. (16.9%) in males, while the most frequently detected in genital infections were S. viridans (36.4%) in females and C. glucuronolyticum (32.2%) and Gardnerella spp. (35.6%) in males. All cases in female children were produced by S. bovis. Symptomatic episodes were more frequent with Aerococcus spp. and S. bovis and the presence of leukocytosis more frequent with Aerococcus spp. Quinolones and doxycycline were most often prescribed antibiotics for genital infections and quinolones and amoxicillin-clavulanic acid for urinary infections. Urinary infection by Aerococcus spp. was more frequent in males of advanced age, Corynebacterium spp. was more frequent in permanent vesical catheter carriers, and episodes of asymptomatic bacteriuria by Gardnerella spp. were more frequent in patients with kidney transplant and chronic consumers of corticosteroid therapy. Lactobacillus spp. should be considered in urinary infections of patients of advanced age and with a previous antibiotic load. Genital infection by Gardnerella spp. was significantly associated with a history of risky sexual relations.

Microbiological Characterization of Actinotignum schaalii Strains Causing Invasive Infections during a Multiyear Period in a Large Canadian Health Care Region

Actinotignum schaalii is an underrecognized Gram-positive bacillus that is associated with urinary tract infections and cutaneous abscesses. The role of A. schaalii in invasive infections continues to be unappreciated because the bacteria can be isolated from a diverse spectrum of clinical specimens, ranging from being a single pathogen in urine and blood cultures to being deemed a colonizer in polymicrobial anaerobic cultures of sterile fluids and tissues. We conducted a microbiological analysis of clinical isolates obtained from 2012 through 2019. A total of 86 isolates were analyzed; 37 (43%) were from blood cultures, 35 (41%) were from deep wounds and abscesses, 6 (7%) were from urine samples, and the rest were recovered from peritoneal, kidney, and scrotal fluid samples. Urinary tract infections were clinically identified as the source of most cases of bacteremia, although no simultaneous urine cultures yielded positive results. The 16S rRNA gene sequences were available for 32 isolates (37%). Phylogenetic analysis revealed that AS.1/AS.2 strains caused a larger proportion of bloodstream infections (BSIs) (100% versus 52% [P = 0.01]) and trended toward a higher rate of hospitalization (91% versus 76% [P = 0.18]) but had a lower clindamycin MIC90 (0.12 versus >256 μg/mL). Our study emphasizes the emergence of A. schaalii as a pathogen in human urine samples, BSIs, and skin and soft tissue infections. It highlights the pitfalls of current laboratory methods in recovering and identifying this organism from clinical specimens, particularly urine samples. Phylogenetic analysis showed unique genotypic sequences for A. schaalii AS.1/AS.2 strains causing urosepsis, which requires further study to identify potential virulence factors. IMPORTANCE Actinotignum schaalii is an underrecognized Gram-positive bacillus due to its special growth requirements and prior phenotypic identification methods, and it is often mistaken as a contaminant. It has been associated with various clinical syndromes, from urinary tract infections to cutaneous infections. The widespread use of molecular diagnostic methods allowed for improved detection. However, its role in invasive infections remains underappreciated. We conducted a detailed microbiological analysis to improve our understanding of this organism's genotypic and phenotypic characteristics. Our results highlight the pitfalls of clinical laboratory recovery, particularly from urine cultures. Although most BSIs were caused by urinary tract infections, no simultaneous urine cultures identified A. schaalii, largely due to the failure of phenotypic methods to reliably isolate and identify this organism. Additionally, this is the first study demonstrating A. schaalii strains with differences in clinical and microbiological characteristics, raising the possibility of potential bacterial virulence factors contributing to invasive infections.

Fournier's Gangrene Mimicking Acute Epididymo-Orchitis in an Undiagnosed Diabetic Patient

Fournier's gangrene (FG) is an infectious disease characterized by necrotizing fasciitis of the perineal, perianal, or genital area associated with aging, male gender, diabetes mellitus (DM), alcoholism, trauma, and immunosuppression states. It can rapidly evolve into sepsis, septic shock, and multiorgan failure with a high mortality rate. We present the case of a 55-year-old man who developed a severe FG, initially assumed as an epididymo-orchitis with new-onset DM. The early identification and treatment resulted in a favorable outcome, being discharged from the hospital after 21 days. Diabetic patients are more susceptible to having severe infections such as FG, hence the importance of adequate metabolic control and increased suspicion to prevent fatal complications.

Urinary microbiota and bladder cancer: A systematic review and a focus on uropathogens

The higher incidence of bladder cancer in men has long been attributed to environmental factors, including smoking. The fact that the sex ratio of bladder cancer remains consistently weighted toward men despite the remarkable increase in the prevalence of smoking among women suggests that other risk factors influence the incidence rates of bladder cancer. These factors may include the urinary microbiota. In this study, we provide a review of recent literature regarding the association between bladder cancer and changes in the urinary microbiota, with a focus on the potential role of uropathogens in the microbiota and sex in bladder cancer. Four databases were systematically searched up to 31 March 2021 to identify human case-controlled studies that evaluated the relationship between urinary microbiota and bladder cancer. We combined bacterial taxa that were significantly higher or lower in the bladder cancer group in each study in the urine (voided and catheterized) and tissue samples. Findings from sixteen eligible studies were analyzed. The total sample size of the included studies was 708 participants, including 449 (63.4 %) bladder cancer patients and 259 (36.6 %) participants in the control group. When considering only the taxa that have been reported in at least two different studies, we observed that with regards to neoplastic tissues, no increased taxa were reported, while Lactobacillus (2/5 of the studies on tissue samples) was increased in nonneoplastic-tissue compared to neoplastic-tissues at the genus level. In catheterized urine, Veillonella (2/3 of the studies on catheterized urine) was increased in bladder cancer patients compared to the control groups at the genus level. In voided urine, Acinetobacter, Actinomyces, Aeromonas, Anaerococcus, Pseudomonas, and Tepidomonas were increased in the bladder cancer patients, while Lactobacillus, Roseomonas, Veillonella were increased in the control groups. Regarding gender, the genus Actinotignum was increased in female participants while Streptococcus was increased in male participants at the genus level. Regarding potential uropathogens in the urinary microbiota, Escherichia-Shigella provided conflicting results, with both showing higher and lower levels in the bladder cancer groups. However, the family Enterobacteriaceae was lower in the bladder cancer groups than in the control groups. In conclusion, there is no consensus on what taxa of the urinary microbiota are associated with bladder cancer according to the sample type. Findings on the potential role of uropathogens in the urinary microbiota in bladder cancer remain inconsistent. Due to the limited number of studies, further studies on urinary microbiota and bladder cancer are needed to address this issue. Given that all publications concerning the urinary microbiota and bladder cancer have been performed using 16S rRNA gene sequencing, we propose that polyphasic approaches, including culture-dependent techniques, may allow for a more comprehensive investigation of the urinary microbiota associated with bladder cancer.

Characterizing Actinotignum schaalii infections in a large Canadian healthcare region

Aims: We characterize the epidemiology of Actinotignum schaalii within a large Canadian region after implementation of improved identification methods. Patients & methods: Positive cultures for A. schaalii from a centralized microbiology laboratory in Canada were analyzed. Clinical data were retrieved through administrative databases and chart reviews. Primary outcome was incidence of A. schaalii infections; secondary outcomes included mortality, hospital admission and length of stay. Results & conclusions: 86 unique isolates were studied, 37 bloodstream infections (BSI) and 49 non-BSIs. Patients with BSIs were older with more comorbidities, with urinary tract infections implicated as the most frequent source; skin abscesses caused the most non-BSIs. Hospitalization and 90-day mortality was higher in the BSI group. A. schaalii is an important community-acquired pathogen with the potential to cause invasive infections.

Semen dysbiosis—just a male problem?

Seminal microflora is crucial to male fertility. Dysbiosis—disturbance of quantitative ratios of individual bacteria or appearance of pathogenic species—rarely results in symptomatic disease. Inflammation results in decreased sperm production, lower motility, or morphological changes and, in the long term, can cause ejaculatory duct obstruction, leading to infertility. Moreover, it may cause infection of the partner’s female genital tract. Dysbiosis in both partners results in fertility problems, disorders in embryo implantation, or miscarriages. In addition, chronic inflammation of the male genitourinary system may accelerate the appearance of antisperm antibodies. A comprehensive examination of seminal microflora can clarify the causes of infertility or prevent pathological conditions that affect seminal parameters. Seminal microflora as a direct impact on fertility problems as well as a decrease in the effectiveness of assisted reproduction methods, insemination, or in vitro procedures.

A 2-Year Retrospective Case Series on Isolates of the Emerging Pathogen Actinotignum schaalii from a Canadian Tertiary Care Hospital

(1) Background: Actinotignum schaalii is an emerging, opportunistic pathogen often linked with UTIs but can extend beyond the urogenital system. Data on the clinical significance of A. schaalii are still emerging. (2) Methods: A retrospective review of A. schaalii isolates in a Canadian tertiary care hospital was conducted. The clinical data of patients that grew A. schaalii from January 2020 to 2022 were documented. Demographics, site, management, and microbiological parameters surrounding culture and sensitivities were recorded. (3) Results: A total of 43 cases of A. schaalii were identified. Actinotignum schaalii was primarily involved in UTIs (n = 17), abscesses (n = 9), bacteremia (n = 6), septic arthritis (n = 5), and ulcers (n = 5). A. schaalii had a slight predilection for polymicrobial infections (51.1%, n = 22 out of 43), with Aerococcus urinae (n = 5) being the most common coisolate. Susceptibility testing was only performed in two cases that showed sensitivity to beta-lactam antibiotics and resistance to metronidazole and ciprofloxacin. Amoxicillin–clavulanate (n = 5) is the most frequently prescribed antibiotic. (4) Conclusions: The non-urogenic clinical significance of A. schaalii remains undervalued. The management of A. schaalii infection is multimodal, consisting predominantly of antimicrobials and surgical procedures specific to the etiology. Clinicians should request sensitivities for A. schaalii so that appropriate antimicrobial coverage can be provided.

Infectious hematogenous lumbar spondylodiscitis caused by Actinotignum schaalii in a 74-year-old man: A case report

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Haematogenous bacterial spondylodiscitis due to infection with a well-treatable but easily overlooked and often underdiagnosed pathogen.

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An argument against short pedicle screw instrumentation, when urgent surgical therapy of the infected spine is required, in patients with PD and poor general condition.

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Especially in cases where a bacterial infection is suspected clinically and by imaging, the detection of germs must be forced by all means in order to be able to treat the patients well.

Emerging Presence of Culturable Microorganisms in Clinical Samples of the Genitourinary System: Systematic Review and Experience in Specialized Care of a Regional Hospital

The detection of emerging pathogens responsible for genitourinary infections has increased with technological advances. We conducted a systematic review of publications on the involvement of these microorganisms in genitourinary samples, and we also investigated their presence and antibiotic susceptibility in samples from patients at our regional hospital (Granada, Spain). The MEDLINE database was searched up to 31 December 2020, and a cross-sectional descriptive study was performed of results obtained in urine samples and genital exudates from January 2016 through December 2019. The review highlighted the frequent involvement of Neisseria meningitidis in genital infections, while the data on other microorganisms were consistent with findings in our patient series. The emerging microorganisms most often responsible for urinary tract infections were Streptococcus bovis (58.5%) and Gardnerella vaginalis (23.6%) in females, and S. bovis (32.3%), Aerococcus urinae (18.6%), and Corynebacterium spp. (16.9%) in males; those most frequently reported in genital infections were S. viridans (36.4%) in females and C. glucuronolyticum (32.2%) and G. vaginalis (35.6%) in males. In general, emerging pathogens are resistant to conventional antibiotics such as penicillin. However, there has also been an increase in beta-lactam resistance by the S. bovis group and Corynebacterium spp. The systematic review showed that emerging microorganisms are responsible for only a small percentage of genitourinary infections but are of major clinical interest, with a predominance of the S. bovis group, G. vaginalis, Lactobacillus spp., Aerococcus spp., and Corynebacterium spp. in urine samples and of G. vaginalis and C. glucuronolyticum in genital samples. Given the increasing resistance to antibiotics empirically prescribed in patients with genitourinary infections, it is recommended to create an antibiogram in all cases.

Distribution and Evolutionary History of Sialic Acid Catabolism in the Phylum Actinobacteria

Sialic acids are present in humans and other metazoans, playing essential roles in physiological and pathological processes. Commensal and pathogenic bacteria have evolved the capacity to utilize sialic acids as nutrient and energy sources. However, in some actinobacteria, sialic acid catabolism (SAC) is associated with free-living populations. To unravel the distribution and evolutionary history of SAC in the phylum Actinobacteria, we analyzed the presence and diversity of the putative SAC gene cluster (nan) in 7,180 high-quality, nonredundant actinobacterial genomes that covered 1,969 species. The results showed that ∼13% of actinobacterial species had the potential to utilize sialic acids, with 45 species capable of anhydro-SAC, all except two of them through the canonical pathway. These species belonged to 20 orders and 81 genera, with ∼36% of them from four genera, Actinomyces, Bifidobacterium, Corynebacterium, and Streptomyces. Moreover, ∼40% of the nan-positive species are free living. Phylogenetic analysis of the key nan genes, nanA, nanK, and nanE, revealed a strong signal of horizontal gene transfer (HGT), accompanied with vertical inheritance and gene loss. This evolutionary pattern led to high diversity and differential distribution of nan among actinobacterial taxa and might cause the cluster to spread to some free-living species while losing in some host-associated species. The evolution of SAC in actinobacteria probably represents the evolution of certain kinds of noncore bacterial functions for environmental adaptation and lifestyle switch, in which HGT plays a dominant role. IMPORTANCE Sialic acids play essential roles in the physiology of humans and other metazoan animals, and microbial sialic acid catabolism (SAC) is one of the processes critical for pathogenesis. To date, microbial SAC is studied mainly in commensals and pathogens, while its distribution in free-living microbes and evolutionary pathway remain largely unexplored. Here, by examining all actinobacterial genomes available, we demonstrate that putative SAC is present in a small proportion of actinobacterial species, of which, however, ∼40% are free-living species. We also reveal remarkable difference in the distribution of SAC among actinobacterial taxa and high diversity of the putative SAC gene clusters. HGT plays a significant role in the evolution of SAC, accompanied with vertical inheritance and gene loss. Our results provide a comprehensive and systematic picture of the distribution and evolutionary history of SAC in actinobacteria, expanding the current knowledge on bacterial adaptation and diversification.

[Actinotignum schaalii: Report of two cases of bacteremia in Argentina]

Actinotignum schaalii is an emerging pathogen in elderly patients with urinary tract pathologies. Two cases of A. schaalii bacteremia are described. Case 1: 79-year-old patient with a history of benign prostatic hyperplasia. He was admitted to the ward for febrile syndrome, abdominal pain, and dysuria. Case 2: 95-year-old patient with prostatic adenomectomy, urethrostomy due to urethral stricture, and benign prostatic hyperplasia. He was admitted due to febrile syndrome, productive cough, bilateral infiltrates with right paracardiac image, and pleural effusion. In both patients, A. schaalii was isolated in blood cultures, identified by MALDITOF-MS mass spectrometry. Only in case 1 was it confirmed that the focus of bacteremia was urinary. It is important to suspect this emerging pathogen in urinary infections with pathological sediment without developing in traditional culture media to ensure adequate empirical treatment. Since most of the isolates show resistance to ciprofloxacin and trimethoprim-sulfamethoxazole.

Microbial community networks across body sites are associated with susceptibility to respiratory infections in infants

Respiratory tract infections are a major cause of morbidity and mortality worldwide in young children. Concepts such as the gut-lung axis have highlighted the impact of microbial communities at distal sites in mediating disease locally. However, little is known about the extent to which microbial communities from multiple body sites are linked, and how this relates to disease susceptibility. Here, we combine 16S-based rRNA sequencing data from 112 healthy, term born infants, spanning three body sites (oral cavity, nasopharynx, gut) and the first six months of life. Using a cross-niche microbial network approach, we show that, already from the first week of life on, there is a strong association between both network structure and species essential to these structures (hub species), and consecutive susceptibility to respiratory tract infections in this cohort. Our findings underline the crucial role of cross-niche microbial connections in respiratory health.

Presumed Septic Shock Caused by Actinotignum schaalii Bacteremia

We herein report a case of presumed septic shock due to Actinotignum schaalii bacteremia with urinary tract infection. A 65-year-old Japanese man suffering from a fever was diagnosed with septic shock due to urinary tract infection. A urine sample was additionally incubated under 5% CO₂ and anaerobic conditions after A. schaalii was identified in a blood culture, but A. schaalii was not detected in the urine culture. If Gram-positive rods are observed on Gram staining of a urine sample in symptomatic patients with a predisposing urogenital condition, 5% CO₂ and an anaerobic culture of a urine sample should be performed immediately.

Actinotignum schaalii: Relation to Concomitants and Connection to Patients' Conditions in Polymicrobial Biofilms of Urinary Tract Catheters and Urines

Actinotignum schaalii is an emerging, opportunistic pathogen and its connection to non-infectious diseases and conditions, such as prostate or bladder cancer, or chronic inflammation has been proposed. Here, we analyzed 297 urine, ureteral and urinary catheter samples from 128 patients by Polymerase Chain Reaction followed by Denaturing Gradient Gel Electrophoresis and Sequencing (PCR-DGGE-S), and culture, and 29 of these samples also by 16S rRNA Illumina sequencing, to establish A. schaalii’s prevalence in urinary tract-related samples, its relation to other bacteria, and its potential association with patients’ conditions and samples’ characteristics. A. schaalii-positive samples were significantly more diverse than A. schaalii negative and between-group diversity was higher than intra-group. Propionimicrobium lymphophilum, Fusobacterium nucleatum, Veillonella sp., Morganella sp., and Aerococcus sp. were significantly more often present in A. schaalii-positive samples; thus, we suggest these species are A. schaalii’s concomitants, while Enterobacter and Staphylococcaceae were more often identified in A. schaalii-negative samples; therefore, we propose A. schaalii and these species are mutually exclusive. Additionally, a significantly higher A. schaalii prevalence in patients with ureter stricture associated hydronephrosis (p = 0.020) was noted. We suggest that A. schaalii could be an early polybacterial biofilm colonizer, together with concomitant species, known for pro-inflammatory features.

Actinotignum schaalii Caught for the Second Time in Fournier's Gangrene!

Actinotignum schaalii, a Gram-positive rod residing in the urinary tract, is responsible for urinary tract infections and their complications including but not limited to bacteremia and sepsis. A. schaalii is increasingly being detected in body fluid specimens owing to advancements in PCR techniques. This report describes an interesting case of an adult diabetic patient managed for Fournier's gangrene. A. schaalii was detected in the PCR of his wound cultures. To the best of our knowledge, this is the second case of A. schaalii as the causative agent for Fournier's gangrene.

Case Report: Emphysematous Pyelonephritis With a Congenital Giant Ureterocele

A 14-year-old girl noticed malodorous urine and experienced left flank pain. The patient was presented to our hospital with gradually increasing pain. She had no underlying disease but had a history of pain on micturition for several days. Hematologic examination indicated low white blood cell and platelet counts and a high serum lactate level. Computed tomography showed that a part of the parenchyma of the left kidney had poor contrast and was deteriorated, with fluid and gas retention from the perirenal region to the retroperitoneal cavity. A left hydroureter and large ureterocele were observed in the bladder. She was diagnosed with emphysematous pyelonephritis (EPN) with a giant congenital ureterocele. Vasopressors and blood transfusion failed to maintain normal circulatory dynamics, and an open left nephrectomy and transurethral ureterocele fenestration were performed. The excised outer portion of the left kidney was dissolved by the infection and replaced with blood clots and necrotic tissue. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry identified the inflammatory, gas-producing bacteria Actinotignum schaalii, Peptoniphilus asaccharolyticus, and Actinomyces odontolyticus. Meropenem was administered for 4 days postoperatively and then de-escalated to sulbactam/ampicillin for another 10 days. The patient was discharged on day 17 of hospitalization, and the postoperative course remained favorable. EPN is extremely rare in pediatric patients, and it is believed that nephrectomy is sometimes necessary if the patient does not have normal circulatory dynamics despite the use of catecholamines.

Performance and Application of 16S rRNA Gene Cycle Sequencing for Routine Identification of Bacteria in the Clinical Microbiology Laboratory

This review provides a state-of-the-art description of the performance of Sanger cycle sequencing of the 16S rRNA gene for routine identification of bacteria in the clinical microbiology laboratory. A detailed description of the technology and current methodology is outlined with a major focus on proper data analyses and interpretation of sequences. The remainder of the article is focused on a comprehensive evaluation of the application of this method for identification of bacterial pathogens based on analyses of 16S multialignment sequences. In particular, the existing limitations of similarity within 16S for genus- and species-level differentiation of clinically relevant pathogens and the lack of sequence data currently available in public databases is highlighted. A multiyear experience is described of a large regional clinical microbiology service with direct 16S broad-range PCR followed by cycle sequencing for direct detection of pathogens in appropriate clinical samples. The ability of proteomics (matrix-assisted desorption ionization-time of flight) versus 16S sequencing for bacterial identification and genotyping is compared. Finally, the potential for whole-genome analysis by next-generation sequencing (NGS) to replace 16S sequencing for routine diagnostic use is presented for several applications, including the barriers that must be overcome to fully implement newer genomic methods in clinical microbiology. A future challenge for large clinical, reference, and research laboratories, as well as for industry, will be the translation of vast amounts of accrued NGS microbial data into convenient algorithm testing schemes for various applications (i.e., microbial identification, genotyping, and metagenomics and microbiome analyses) so that clinically relevant information can be reported to physicians in a format that is understood and actionable. These challenges will not be faced by clinical microbiologists alone but by every scientist involved in a domain where natural diversity of genes and gene sequences plays a critical role in disease, health, pathogenicity, epidemiology, and other aspects of life-forms. Overcoming these challenges will require global multidisciplinary efforts across fields that do not normally interact with the clinical arena to make vast amounts of sequencing data clinically interpretable and actionable at the bedside.

The Pathogenic Role of Actinomyces spp. and Related Organisms in Genitourinary Infections: Discoveries in the New, Modern Diagnostic Era

Actinomycosis is a chronic, suppurative, granulomatous infectious disease, caused by different species of Actinomyces bacteria. To date, 26 validly published Actinomyces species have been described as part of a normal human microbiota or from human clinical specimens. Due to the rapid spread of new, modern diagnostic procedures, 13 of 26 of these species have been described in this century and the Actinomycetaceae family has undergone several taxonomic revisions, including the introduction of many novel species termed Actinomyces-like organisms (ALOs). There is scarce data available on the role of these novel bacterial species in various infectious processes in human medicine. The aim of this review is to provide a comprehensive overview of Actinomyces and closely related organisms involved in human diseases-with a special focus on newly described species-in particular their role in genitourinary tract infections in females and males.

Actinotignum schaalii Abscess in a Patient with Common Variable Immunodeficiency

Actinotignum schaalii is an anaerobic, gram-positive commensal organism of the urogenital tract. A. schaalii typically causes urinary tract infections, predominantly in the elderly. Here, we describe the first case of A. schaalii infection presenting as cellulitis and abscess in a patient with common variable immunodeficiency. The patient was successfully treated with an incision and drainage and a prolonged antibiotic course. A. schaalii infection should be considered in sterile abscesses, and anaerobic cultures should be requested in the absence of positive routine cultures.

Acute Esophageal Necrosis in a Patient With Prostate Cancer Postchemotherapy

Acute esophageal necrosis (AEN) describes a potentially irreversible injury to esophageal mucosa secondary to vascular hypoperfusion. An 84-year-old man was admitted for the correction of a displaced nephrostomy tube and management of acute kidney injury. During his stay, the patient developed odynophagia and acute gastrointestinal hemorrhage. Despite mild initial symptoms, diffuse circumferential black esophageal mucosa was visualized on endoscopy, and a diagnosis of AEN was made. This unique case highlights the association between AEN and leukopenia, vascular disease, hypercoagulability, and infection. Presentations such as this patient should prompt the physicians' consideration of this differential earlier.

The Role of Gram-Negative Bacteria in Urinary Tract Infections: Current Concepts and Therapeutic Options

Urinary tract infections (UTIs) are some of the most common infections in human medicine worldwide, recognized as an important public health concern to healthcare systems around the globe. In addition, urine specimens are one of the most frequently submitted samples for culture to the clinical microbiology laboratory, exceeding the number of most of the other sample types. The epidemiology, species-distribution and susceptibility-patterns of uropathogens vary greatly in a geographical and time-dependent manner and it also strongly correlated with the reported patient population studied. Nevertheless, many studies highlight the fact that the etiological agents in UTIs have changed considerably, both in nosocomial and community settings, with a shift towards "less common" microorganisms having more pronounced roles. There is increasing demand for further research to advance diagnostics and treatment options, and to improve care of the patients. The aim of this review paper was to summarize current developments in the global burden of UTI, the diagnostic aspects of these infectious pathologies, the possible etiological agents and their virulence determinants (with a special focus on the members of the Enterobacterales order), current guidelines and quality indicators in the therapy of UTIs and the emergence of multidrug resistance in urinary pathogens.

A case report of necrotizing fasciitis with growth of Actinomyces europaeus and Actinotignum schaalii

Actinomyces europeaeus and Actinotignum schaalii are two facultative anaerobes that are common contaminants of human flora; namely the urinary tract, the female genital tract and the gastrointestinal tract. A. europeaeus has been linked with abscesses, decubitus ulcers and purulent urethritis, while A. schaalii has been associated with urinary tract infections, bacteremia and Fournier's gangrene. Here we present a case report of an 84-year-old female patient found to have a necrotizing soft tissue infection caused by A. europeaeus and A. schaalii. To our knowledge, this is the first case report that documents A. europeaeus as a causal agent of a necrotizing infection.

How MALDI-TOF mass spectrometry can aid the diagnosis of hard-to-identify pathogenic bacteria - the rare and the unknown

Introduction: Ten years after its introduction into clinical microbiology, MALDI-TOF mass spectrometry has become the standard routine identification tool for bacteria in most laboratories. The technology has accelerated analyses and improved the quality of results. The greatest significance has been observed for bacteria that were challenging to be identified by traditional methods. Areas covered: We searched in existing literature (Pubmed) for reports how MALDI-TOF MS has contributed to identification of rare and unknown bacteria from different groups. We describe how this has improved the diagnostics in different groups of bacteria. Reference patterns for strains which yet cannot be assigned to a known species even enable the search for related bacteria in studies as well as in routine diagnostics. MALDI-TOF MS can help to discover and investigate new species and their clinical relevance. It is a powerful tool in the elucidation of the bacterial composition of complex microbiota in culturomics studies. Expert opinion: MALDI-TOF MS has improved the diagnosis of bacterial infections. It also enables knowledge generation for prospective diagnostics. The term 'hard-to-identify' might only be rarely attributed to bacteria in the future. Novel applications are being developed, e.g. subspecies differentiation, typing, and antibiotic resistance testing which may further contribute to improved microbial diagnostics.

Native aortic endocarditis due to an unusual pathogen: Actinotignum schaalii

We report a case of aortic native valve endocarditis due to Actinotignum schaalii in an 89-year-old man with prostatism history but no signs of urinary infection. Actinotignum schaalii was isolated not only from positive blood culture but also from cardiac valve culture using mass spectrometry and 16S rDNA sequencing. Actinotignum schaalii is recognized as commensal of genitourinary tract, but it was underdiagnosed. The advances in bacterial identification such as MALDI-TOF MS probably explain the increasing described cases of infections due to A. schaalii these last years.

New Bugs and New Drugs: Updates in Clinical Microbiology

BACKGROUND

The landscape of clinical microbiology laboratories is changing. As new technologies are introduced, we are better able to detect and identify pathogens and to recognize and characterize emerging antimicrobial resistance mechanisms.

CONTENT

In this review, a selected cross-section of current hot topics in clinical microbiology is discussed. These topics include (a) diagnostics for urinary tract and sexually transmitted infections; (b) phenotypic and genotypic methods of detecting carbapenem resistance and discussion of newly approved anti-infective agents for these multi-drug resistant organisms; and (c) the significance, epidemiology, and identification of the emerging pathogens Mycobacterium chimaera and Candida auris.

SUMMARY

Communication between clinical microbiologists and their clinical colleagues is imperative to convey the significance of emerging pathogens and resistance determinants, as well as the performance characteristics of new diagnostic methods. Additionally, as antimicrobial resistance is surging, it is important to comprehensively evaluate the resistance profiles of clinical isolates to facilitate antimicrobial stewardship and inform infection prevention measures. Although antimicrobial resistance is a global public health crisis, it is encouraging that new anti-infective agents are in the pipeline and being approved for use in patients.

Significant increase in cultivation of Gardnerella vaginalis, Alloscardovia omnicolens, Actinotignum schaalii, and Actinomyces spp. in urine samples with total laboratory automation

While total laboratory automation (TLA) is well established in laboratory medicine, only a few microbiological laboratories are using TLA systems. Especially in terms of speed and accuracy, working with TLA is expected to be superior to conventional microbiology. We compared in total 35,564 microbiological urine cultures with and without incubation and processing with BD Kiestra TLA for a 6-month period each retrospectively. Sixteen thousand three hundred thirty-eight urine samples were analyzed in the pre-TLA period and 19,226 with TLA. Sixty-two percent (n = 10,101/16338) of the cultures processed without TLA and 68% (n = 13,102/19226) of the cultures processed with TLA showed growth. There were significantly more samples with two or more species per sample and with low numbers of colony forming units (CFU) after incubation with TLA. Regarding the type of bacteria, there were comparable amounts of Enterobacteriaceae in the samples, slightly less non-fermenting Gram-negative bacteria, but significantly more Gram-positive cocci, and Gram-positive rods. Especially Alloscardivia omnicolens, Gardnerella vaginalis, Actinomyces spp., and Actinotignum schaalii were significantly more abundant in the samples incubated and processed with TLA. The time to report was significantly lower in the TLA processed samples by 1.5 h. We provide the first report in Europe of a large number of urine samples processed with TLA. TLA showed enhanced growth of non-classical and rarely cultured bacteria from urine samples. Our findings suggest that previously underestimated bacteria may be relevant pathogens for urinary tract infections. Further studies are needed to confirm our findings.