Clinical and microbiological features of Actinotignum bacteremia: a retrospective observational study of 57 cases

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.

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.

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.

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.

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.

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.

[Analysis of the diversity of Actinomyces/Actinotignum clinical isolates in a university hospital]

Actinomyces and related genera are grampositive bacilli, opportunistic pathogens, which have been mainly involved in endogenous infections. However, due to the complexity in identifying them for most clinical laboratories, there is scant knowledge about their real clinical significance. In this work, 166 isolates of 13 different species of Actinomyces/Actinotignum species recovered from clinical samples of patients treated in a university hospital were studied. The identification was performed by MALDI-TOF MS and molecular identification. MALDI-TOF MS identified 91.57% of the isolates (152/166) at the species level using a score ≥ 1.7 and 3.61% (6/166) of the isolates were identified only at the gender level with a score ≥ 1.5. MALDI-TOF MS did not yield reliable identification results for 4.82% (8/166) of the isolates. Actinomyces/Actinotignum species were isolated from: soft tissue (n: 47), urine samples (n: 35), head / neck abscesses (n: 19), genital abscesses (n: 11), blood samples (n: 10), breast abscesses (n: 8), osteoarticular samples (n: 6), abdominal/ascitic fluids (n: 3), abdominal abscesses (n: 5), sputum/BAL (n: 4), brain abscesses (n: 3), and others (n: 15). The results obtained from the statistical analysis showed a high differential frequency (> 2) for the location/species association: urine/A. schaalii/sanguinis; brain abscesses/A. europaeus; osteoarticular samples/A. urogenitalis; abdominal abscesses/ A. turicensis; respiratory samples/A. naeslundii/viscosus. This information provides a greater understanding of the clinical and epidemiological relevance of these species. The pathogenic role of Actinomyces spp. will be increasingly revealed as these microorganisms could be recognized thanks to prolonged culture and the advances in identification technology facilitated by MALDI-TOF MS.

Actinotignum schaalii and Aerococcus urinae as Etiology of Infected Kidney Cyst: A Diagnostic Challenge

The case presented here illustrates a sometimes complex disease presentation where interdisciplinary teamwork is essential. A 74-years-old woman with stable chronic obstructive pulmonary lung disease and a composite graft aortic valve implant was admitted to hospital with an episode of acute lower back pain combined with long-term fever. The final diagnoses of a left-sided, infected and radiologically evident kidney cyst caused by the urinary tract pathogens Actinotignum schaalii and Aerococcus urinae was established by the use of partial 16S/18S rRNA gene sequence analysis on kidney cyst drainage material taken after four weeks of relevant antibiotic therapy.

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.

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.

Development and Validation of a Reference Data Set for Assigning Staphylococcus Species Based on Next-Generation Sequencing of the 16S-23S rRNA Region

Many members of the Staphylococcus genus are clinically relevant opportunistic pathogens that warrant accurate and rapid identification for targeted therapy. The aim of this study was to develop a careful assignment scheme for staphylococcal species based on next-generation sequencing (NGS) of the 16S-23S rRNA region. All reference staphylococcal strains were identified at the species level using Sanger sequencing of the 16S rRNA, sodA, tuf, and rpoB genes and NGS of the 16S-23S rRNA region. To broaden the database, an additional 100 staphylococcal strains, including 29 species, were identified by routine diagnostic methods, 16S rRNA Sanger sequencing and NGS of the 16S-23S rRNA region. The results enabled development of reference sequences encompassing the 16S-23S rRNA region for 50 species (including one newly proposed species) and 6 subspecies of the Staphylococcus genus. This study showed sodA and rpoB targets were the most discriminative but NGS of the 16S-23S rRNA region was more discriminative than tuf gene sequencing and much more discriminative than 16S rRNA gene sequencing. Almost all Staphylococcus species could be distinguished when the max score was 99.0% or higher and the sequence similarity between the best and second best species was equal to or >0.2% (min. 9 nucleotides). This study allowed development of reference sequences for 21 staphylococcal species and enrichment for 29 species for which sequences were publicly available. We confirmed the usefulness of NGS of the 16S-23S rRNA region by identifying the whole species content in 45 clinical samples and comparing the results to those obtained using routine diagnostic methods. Based on the developed reference database, all staphylococcal species can be reliably detected based on the 16S-23S rRNA sequences in samples composed of both single species and more complex polymicrobial communities. This study will be useful for introduction of a novel diagnostic tool, which undoubtedly is an improvement for reliable species identification in polymicrobial samples. The introduction of this new method is hindered by a lack of reference sequences for the 16S-23S rRNA region for many bacterial species. The results will allow identification of all Staphylococcus species, which are clinically relevant pathogens.

Antibiotic resistance genes in the Actinobacteria phylum

The Actinobacteria phylum is one of the oldest bacterial phyla that have a significant role in medicine and biotechnology. There are a lot of genera in this phylum that are causing various types of infections in humans, animals, and plants. As well as antimicrobial agents that are used in medicine for infections treatment or prevention of infections, they have been discovered of various genera in this phylum. To date, resistance to antibiotics is rising in different regions of the world and this is a global health threat. The main purpose of this review is the molecular evolution of antibiotic resistance in the Actinobacteria phylum.

An Update on the Novel Genera and Species and Revised Taxonomic Status of Bacterial Organisms Described in 2016 and 2017

Recognition and acknowledgment of novel bacterial taxonomy and nomenclature revisions can impact clinical practice, disease epidemiology, and routine clinical microbiology laboratory operations. The Journal of Clinical Microbiology (JCM) herein presents its biannual report summarizing such changes published in the years 2016 and 2017, as published and added by the International Journal of Systematic and Evolutionary Microbiology Noteworthy discussion centers around descriptions of novel Corynebacteriaceae and an anaerobic mycolic acid-producing bacterium in the suborder Corynebacterineae; revisions within the Propionibacterium, Clostridium, Borrelia, and Enterobacter genera; and a major reorganization of the family Enterobacteriaceae. JCM intends to sustain this series of reports as advancements in molecular genetics, whole-genome sequencing, and studies of the human microbiome continue to produce novel taxa and clearer understandings of bacterial relatedness.

Treatment considerations for potential uropathogens detected by precision microbiological testing

PURPOSE

The clinical and microbiological data for urinary tract infections (UTIs) for 6 organisms detected by matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) at community health systems were examined.

SUMMARY

The use of precision microbiological diagnostic testing such as MALDI-TOF and real-time quantitative polymerase chain reaction has increased the ability to detect a wider spectrum of organisms. This has raised questions of the clinical relevance of infrequently encountered organisms, especially when cultured from urine. This article reviews clinical and microbiological data for UTIs for 6 organisms detected by MALDI-TOF at community health systems (Actinotignum schaalii, Chryseobacterium indologenes, Aerococcus urinae, Aerococcus sanguinicola, Corynebacterium riegelii, and Corynebacterium urealyticum). Since little information currently exists, most of the data associating the aforementioned organisms with UTIs were derived from case reports. Although these organisms are more readily identified using precision microbiological diagnostic testing methods, infection should not be assumed based on culture results alone since asymptomatic bacteriuria has been reported. Similar to more common urinary pathogens, clinical correlation is essential. To facilitate treatment, we provide a table of empirical options likely to achieve clinical success based on in vivo and in vitro data. If available, pathogen-specific susceptibility data should be used to direct therapy.

CONCLUSION

Clinical and microbiological data and potential treatment options were presented for 6 traditionally underrecognized organisms that are increasingly being found from urinary specimens. The treatment recommendations should be interpreted cautiously as they were devised through the use of very limited data.

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.

Actinotignum schaalii Infection: A Clandestine Cause of Sterile Pyuria?

Actinotignum schaalii is an underappreciated cause of urinary tract infections (UTIs) in older adults. The diagnosis may be missed due to difficulty isolating and identifying the organism. Complications can result because the organism is intrinsically resistant to 2 commonly used drugs to treat UTI, as illustrated by this case.

Propionimicrobium lymphophilum and Actinotignum schaalii bacteraemia: a case report

Propionimicrobium lymphophilum is an anaerobic Gram-positive bacillus that exists in human skin and urinary tract. The pathogenicity is, however, not well known. Only two cases of urinary tract infection have been described recently. In the case presented here, the bacterium was isolated, concomitant with Actinotignum schaalii, from blood culture of a patient with fever and difficulty of urination. The bacteria were identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and 16S rRNA sequencing. The case was successfully treated with ampicillin/sulbactam.