"Actinobaculum massiliae," a new species causing chronic urinary tract infection

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.

Advantage of precision metagenomics for urinary tract infection diagnostics

Background

Urinary tract infections (UTIs) remain a diagnostic challenge and often promote antibiotic overuse. Despite urine culture being the gold standard for UTI diagnosis, some uropathogens may lead to false-negative or inconclusive results. Although PCR testing is fast and highly sensitive, its diagnostic yield is limited to targeted microorganisms. Metagenomic next-generation sequencing (mNGS) is a hypothesis-free approach with potential of deciphering the urobiome. However, clinically relevant information is often buried in the enormous amount of sequencing data.

Methods

Precision metagenomics (PM) is a hybridization capture-based method with potential of enhanced discovery power and better diagnostic yield without diluting clinically relevant information. We collected 47 urine samples of clinically suspected UTI and in parallel tested each sample by microbial culture, PCR, and PM; then, we comparatively analyzed the results. Next, we phenotypically classified the cumulative microbial population using the Explify® data analysis platform for potential pathogenicity.

Results

Results revealed 100% positive predictive agreement (PPA) with culture results, which identified only 13 different microorganisms, compared to 19 and 62 organisms identified by PCR and PM, respectively. All identified organisms were classified into phenotypic groups (0-3) with increasing pathogenic potential and clinical relevance. This PM can simultaneously quantify and phenotypically classify the organisms readily through bioinformatic platforms like Explify®, essentially providing dissected and quantitative results for timely and accurate empiric UTI treatment.

Conclusion

PM offers potential for building effective diagnostic models beyond usual care testing in complex UTI diseases. Future studies should assess the impact of PM-guided UTI management on clinical outcomes.

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.

Judicial Opinions 103–111

In Opinion 103, the request to place the name Spirillum volutans Ehrenberg 1832 (Approved Lists 1980) on the list of rejected names is denied because a neotype may be designated. Similarly, because a neotype may be designated, in Opinion 104 the request to place the name Beijerinckia fluminensis Döbereiner and Ruschel 1958 (Approved Lists 1980) on the list of rejected names is denied. In Opinion 105, it is emphasized that the name Rhodoligotrophos Fukuda et al. 2012 does not contravene the Code. The request to orthographically correct Rhodoligotrophos Fukuda et al. 2012 to Rhodoligotrophus corrig. Fukuda et al. 2012 is denied. Opinion 106 addresses two Requests for an Opinion and results in the placement of the epithet hoagii in Corynebacterium hoagii (Morse 1912) Eberson 1918 (Approved Lists 1980) and Rhodococcus hoagii (Morse 1912) Kämpfer et al. 2014 on the list of rejected specific and subspecific epithets. Since this removes all known available earlier synonyms of Rhodococcus equi (Magnusson 1923) Goodfellow and Alderson 1977 (Approved Lists 1980), the request to conserve the epithet equi in this name is denied. In Opinion 107, Thermomicrobium fosteri Phillips and Perry 1976 (Approved Lists 1980) is placed on the list of rejected names as a nomen dubium et confusum. Opinion 108 denies the request to place Hyphomonas rosenbergii Weiner et al. 2000 on the list of rejected names because the information provided to the Judicial Commission is not sufficient to draw a conclusion on this matter. In Opinion 109, which addresses three Requests for an Opinion, the Judicial Commission denies the requests to place the names Bacillus aerius Shivaji et al. 2006, Bacillus aerophilus Shivaji et al. 2006 and Bacillus stratosphericus Shivaji et al. 2006 on the list of rejected names. Instead, it is concluded that these three names had not met the requirements for valid publication. Likewise, the Judicial Commission concludes in Opinion 110 that the name Actinobaculum massiliense corrig. Greub and Raoult 2006 had not met the requirements for valid publication. The Judicial Commission reaffirms in Opinion 111 that Methanocorpusculum parvum Zellner et al. 1988 is the nomenclatural type of Methanocorpusculum Zellner et al. 1988 and further emphasizes that the species was not in danger of losing this status. These Opinions were ratified by the voting members of the International Committee on Systematics of Prokaryotes.

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.

Phenotypic, molecular and genomic characterization of Actinobaculum suis isolated from swine in Brazil

Urinary tract infections (UTI) are considered one of the most important diseases of sows due to its close relationship with reproductive problems such as reduced litter size, increase in the rate of return to estrous, vulvar discharge, abortion, mastitis and anestrus. Actinobaculum suis is one of the main agents involved in porcine urinary tract infection and is responsible for the most severe and fatal cases in sows. In the present report, 23 A. suis strains isolated from a sow and boars in Brazil were identified by PCR and further characterized by broth microdilution, molecular typing by pulsed-field gel electrophoresis (PFGE), single-enzyme amplified fragment length polymorphism (SE-AFLP), and whole-genome sequencing. All strains were sensitive to ceftiofur, linezolid, nitrofurantoin, quinupristin-dalfopristin and vancomycin. Ciprofloxacin, daptomycin, lincomycin, erythromycin and tylosin resistance was observed in 100% of tested strains. Tetracycline and tigecycline also presented high resistance rates (87% and 30.4%, respectively). PFGE with eight different restriction enzymes and three programs did not enable strain characterization; however, all strains were typed by SE-AFLP that clustered strains according to their origin, thus proving an effective tool for A. suis genotyping. Whole-genome sequencing and comparative analysis enabled species differentiation from closely related genus. This is the first report of genomic characterization of A. suis.

Actinobaculum massiliense Proteome Profiled in Polymicrobial Urethral Catheter Biofilms

Actinobaculum massiliense, a Gram-positive anaerobic coccoid rod colonizing the human urinary tract, belongs to the taxonomic class of Actinobacteria. We identified A. massiliense as a cohabitant of urethral catheter biofilms (CB). The CBs also harbored more common uropathogens, such as Proteus mirabilis and Aerococcus urinae, supporting the notion that A. massiliense is adapted to a life style in polymicrobial biofilms. We isolated a clinical strain from a blood agar colony and used 16S rRNA gene sequencing and shotgun proteomics to confirm its identity as A. massiliense. We characterized this species by quantitatively comparing the bacterial proteome derived from in vitro growth with that of four clinical samples. The functional relevance of proteins with emphasis on nutrient import and the response to hostile host conditions, showing evidence of neutrophil infiltration, was analyzed. Two putative subtilisin-like proteases and a heme/oligopeptide transporter were abundant in vivo and are likely important for survival and fitness in the biofilm. Proteins facilitating uptake of xylose/glucuronate and oligopeptides, also highly expressed in vivo, may feed metabolites into mixed acid fermentation and peptidolysis pathways, respectively, to generate energy. A polyketide synthase predicted to generate a secondary metabolite that interacts with either the human host or co-colonizing microbes was also identified. The product of the PKS enzyme may contribute to A. massiliense fitness and persistence in the CBs.

The first reported case of pelvic inflammatory disease caused by Actinobaculum massiliense

We report the first case of pelvic inflammatory disease (PID) caused by Actinobaculum massiliense. A 53-year-old woman attended the emergency department with symptoms compatible with a PID episode, finally resolved by intramuscular antibiotic treatment. Actinobaculum sp. was isolated by culture, and A. massiliense was confirmed by matrix assisted laser desorption time-of-flight mass spectrometry and 16S rRNA gene sequencing. Only a few cases of A. massiliense infections have been reported, and the pathogenesis of infections by these bacteria is poorly understood. The introduction of new diagnostic methods into hospital routines will improve the detection of new and little-studied pathogens.

Actinomyces and Alimentary Tract Diseases: A Review of Its Biological Functions and Pathology

Actinomyces are nonmotile, filamentous, Gram-positive bacteria that cause actinomycosis in immunodeficiency patients. Although the prognosis of actinomycosis is good, the diagnosis of actinomycosis is quite difficult. Recent studies on actinomycosis have shown that Actinomyces play an important role in various biological and clinical processes, such as the formation of dental plaque and the degradation of organics in the gastrointestinal tract. Here, the distribution of Actinomyces in the digestive tract, and different biological effects of actinomycosis, and its clinical association with inflammatory diseases are discussed. Furthermore, an overview of the most commonly used treatment methods and drugs used to treat Actinomyces infected alimentary canal diseases is presented.

Cultivation of Peptidiphaga gingivicola from subgingival plaque: The first representative of a novel genus of Actinomycetaceae

A novel bacterium was isolated from the subgingival plaque of a patient with periodontal disease. Bacterial strain BA112^T is a facultative Gram-positive coccus. It metabolizes alanine, arginine, glycine, histidine, leucine, proline, serine and tyrosine, but does not appear to use carbohydrates. Urease, esculin, indole, catalase and nitrate reduction tests were all negative. Major cellular fatty acids were C_18:0 , C_12:0 , C_16:0 , C_18:1 w9c and C_20:0 . The genome was sequenced and is 2.4 Mbp in length and has 64% GC content. Based on phylogenetics of the 16S rRNA sequence and concatenated alignments of 37 conserved proteins, BA112^T belongs to the family Actinomycetaceae but is located on a branch of the tree without currently named members. Based on our phenotypic and phylogenetic studies, we propose that BA112^T is the first known representative of a new genus, for which the name Peptidiphaga gingivicola gen. nov., sp. nov. is proposed. The type strain is BA112^T .

Gram-Positive Uropathogens, Polymicrobial Urinary Tract Infection, and the Emerging Microbiota of the Urinary Tract

Gram-positive bacteria are a common cause of urinary-tract infection (UTI), particularly among individuals who are elderly, pregnant, or who have other risk factors for UTI. Here we review the epidemiology, virulence mechanisms, and host response to the most frequently isolated Gram-positive uropathogens: Staphylococcus saprophyticus, Enterococcus faecalis, and Streptococcus agalactiae. We also review several emerging, rare, misclassified, and otherwise underreported Gram-positive pathogens of the urinary tract including Aerococcus, Corynebacterium, Actinobaculum, and Gardnerella. The literature strongly suggests that urologic diseases involving Gram-positive bacteria may be easily overlooked due to limited culture-based assays typically utilized for urine in hospital microbiology laboratories. Some UTIs are polymicrobial in nature, often involving one or more Gram-positive bacteria. We herein review the risk factors and recent evidence for mechanisms of bacterial synergy in experimental models of polymicrobial UTI. Recent experimental data has demonstrated that, despite being cleared quickly from the bladder, some Gram-positive bacteria can impact pathogenic outcomes of co-infecting organisms. When taken together, the available evidence argues that Gram-positive bacteria are important uropathogens in their own right, but that some can be easily overlooked because they are missed by routine diagnostic methods. Finally, a growing body of evidence demonstrates that a surprising variety of fastidious Gram-positive bacteria may either reside in or be regularly exposed to the urinary tract and further suggests that their presence is widespread among women, as well as men. Experimental studies in this area are needed; however, there is a growing appreciation that the composition of bacteria found in the bladder could be a potentially important determinant in urologic disease, including susceptibility to UTI.

Modeling central metabolism and energy biosynthesis across microbial life

Background

Automatically generated bacterial metabolic models, and even some curated models, lack accuracy in predicting energy yields due to poor representation of key pathways in energy biosynthesis and the electron transport chain (ETC). Further compounding the problem, complex interlinking pathways in genome-scale metabolic models, and the need for extensive gapfilling to support complex biomass reactions, often results in predicting unrealistic yields or unrealistic physiological flux profiles.

Results

To overcome this challenge, we developed methods and tools (http://coremodels.mcs.anl.gov) to build high quality core metabolic models (CMM) representing accurate energy biosynthesis based on a well studied, phylogenetically diverse set of model organisms. We compare these models to explore the variability of core pathways across all microbial life, and by analyzing the ability of our core models to synthesize ATP and essential biomass precursors, we evaluate the extent to which the core metabolic pathways and functional ETCs are known for all microbes. 6,600 (80 %) of our models were found to have some type of aerobic ETC, whereas 5,100 (62 %) have an anaerobic ETC, and 1,279 (15 %) do not have any ETC. Using our manually curated ETC and energy biosynthesis pathways with no gapfilling at all, we predict accurate ATP yields for nearly 5586 (70 %) of the models under aerobic and anaerobic growth conditions. This study revealed gaps in our knowledge of the central pathways that result in 2,495 (30 %) CMMs being unable to produce ATP under any of the tested conditions. We then established a methodology for the systematic identification and correction of inconsistent annotations using core metabolic models coupled with phylogenetic analysis.

Conclusions

We predict accurate energy yields based on our improved annotations in energy biosynthesis pathways and the implementation of diverse ETC reactions across the microbial tree of life. We highlighted missing annotations that were essential to energy biosynthesis in our models. We examine the diversity of these pathways across all microbial life and enable the scientific community to explore the analyses generated from this large-scale analysis of over 8000 microbial genomes.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-2887-8) contains supplementary material, which is available to authorized users.

Description of strain FC3T as the neotype strain of Actinobaculum massiliense

Actinobaculum massiliense (Euzéby, 2006) was isolated from the urine of an elderly woman in 2001. Unfortunately, the strain deposited as the type strain was, by error, an Actinobaculum schaalii strain (Yassin et al., 2015). In 2015, we isolated a new strain of A. massiliense, FC3, from the urine of a 12-year-old patient with acute cystitis. We herein present the characteristics of strain FC3 (=CSUR P1982=DSM 100580) and formally propose it as the neotype strain of A. massiliense.

Actinotignum (formerly Actinobaculum) schaalii: a review of MALDI-TOF for identification of clinical isolates, and a proposed method for presumptive phenotypic identification

Actinotignum schaalii is a recognised cause of urinary tract infection. Following a case of urosepsis, 20 isolates of A. schaalii were collected over an initial 18 month period from urine and blood culture. An additional 25 isolates were collected over the following 13 months. Actinotignum schaalii had likely been overlooked or dismissed as a contaminant in our laboratory prior to this study period. It grows slowly on blood agar with supplemental CO2 or anaerobically. It may not grow on MacConkey agar or chromogenic agars used for routine urine culture. Repeated attempts at identification by matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF MS) may be required as the optimal age of cultures for testing is unclear. Utilising its characteristic antibiogram may assist phenotypic identification of this organism which is otherwise difficult to distinguish from other actinomycetes.

Draft Genome Sequence of Actinobaculum massiliense Strain FC3

Actinobaculum massiliense strain FC3 was isolated from the urine of a patient with acute cystitis. The 2.06-Mb genome of strain FC3 contains 17 toxin/antitoxin modules and 9 bacteriocin-encoding genes that may play a role in virulence. The genome also exhibits 693 genes acquired by lateral gene transfer.

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

The genus Actinotignum contains three species, Actinotignum schaalii (formerly Actinobaculum schaalii), Actinotignum urinale and Actinotignum sanguinis. A. schaalii is the species most frequently involved in human infections, with 172 cases, mostly urinary tract infections (UTIs), reported so far. Invasive infections have also been described. This facultative anaerobic Gram-positive rod is part of the urinary microbiota of healthy patients. It is responsible for UTIs, particularly in elderly men and young children. A. schaalii is an underestimated cause of UTIs because of its fastidious growth on usual media and difficulties associated with its identification using phenotypic methods. Indeed, this slow-growth bacterium requires blood-enriched media and an incubation time of 48 hours under anaerobic or 5% CO2 atmosphere. Furthermore, only matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF) or molecular-based methods allow the accurate identification of this bacteria. MALDI-TOF using Microflex LT with the Biotyper database (Bruker Daltonics, Bremen, Germany) is the most reliable technology for the routine identification of A. schaalii. The identification of this uropathogen is all the more important because it is resistant to trimethoprim/sulfamethoxazole and second-generation quinolones that are widely used in the treatment of UTIs. Antimicrobial therapy using β-lactams prolonged for up to 2 weeks is the most efficient treatment and should be recommended. Microbiologists should assess the presence of A. schaalii in urine using appropriate culture and identification methods in the case of a direct examination that is positive for small coccoid rods, a negative nitrite urinary stick associated with leukocyturia, treatment failure with trimethoprim/sulfamethoxazole or fluoroquinolones, or undocumented, repeated UTIs.

Actinomyces and related organisms in human infections

Actinomyces israelii has long been recognized as a causative agent of actinomycosis. During the past 3 decades, a large number of novel Actinomyces species have been described. Their detection and identification in clinical microbiology laboratories and recognition as pathogens in clinical settings can be challenging. With the introduction of advanced molecular methods, knowledge about their clinical relevance is gradually increasing, and the spectrum of diseases associated with Actinomyces and Actinomyces-like organisms is widening accordingly; for example, Actinomyces meyeri, Actinomyces neuii, and Actinomyces turicensis as well as Actinotignum (formerly Actinobaculum) schaalii are emerging as important causes of specific infections at various body sites. In the present review, we have gathered this information to provide a comprehensive and microbiologically consistent overview of the significance of Actinomyces and some closely related taxa in human infections.

Pathogens in Urine from a Female Patient with Overactive Bladder Syndrome Detected by Culture-independent High Throughput Sequencing: A Case Report

INTRODUCTION

Overactive bladder syndrome (OAB) is described as urgency, with or without urgency incontinence. A range of medical conditions shares the symptoms of OAB, however the diagnosis is contingent on the exclusion of urinary tract infection (UTI). Knowing that urine dipstick and routine culture of bacteria can miss UTI diagnosis caused by low-count bacteriuria or "difficult-to-culture" pathogens, we examined a case of OAB with a culture-independent approach.

CASE PRESENTATION

A 61-year-old Norwegian female with a long history of urinary symptoms and a diagnosis of OAB was selected as a suitable subject for a culture-independent 16S rDNA analysis on the patient´s urine. The patient's medical records showed no history of recurrent UTI, however, when the urine specimen was sent to routine culture at the time of study it showed a significant bacteriuria caused by a single bacterium, and the patient was prescribed antibiotics. The 16S rDNA analysis revealed not one, but many different bacteria, including a considerable amount of fastidious bacteria, indicating a polymicrobial state. One year later, the subject was still experiencing severe symptoms, and a follow-up analysis was performed. This time the urine-culture was negative, however, the 16S rDNA profile was quite similar to that of the first sample, again displaying a complex bacterial profile.

CONCLUSION

The use of 16S rDNA pyrosequencing and sequence analysis to uncover "difficult-to-culture" bacteria should be considered when examining patients with chronic urinary symptoms. These methods may contribute to further elucidation of the etiology of overactive bladder syndrome and other urinary syndromes.

The status of the species Actinobaculum massiliense (Greub and Raoult 2006). Request for an Opinion

A recent study on members of the genus Actinobaculum revealed that cultures of the species Actinobaculum massiliense CCUG 47753(T) ( = DSM 19118(T)) currently being distributed do not conform to the properties of the type strain of A. massiliense CIP 107404(T) given by Greub & Raoult [Greub, G. & Raoult, D. (2002). J Clin Microbiol 40, 3938-3941]. The original strain, CIP 107404(T) is no longer available from the Biological Resource Center of Institut Pasteur, Paris. Based on data currently available, the organism currently deposited as CCUG 47753(T) and DSM 19118(T) is a member of the species Actinobaculum schaalii. Clearly, the organism deposited as CCUG 47753(T) and DSM 19118(T) as the type strain of the species Actinobaculum massiliense does not have the properties given by Greub & Raoult. Based on the absence of an authentic type strain, the Judicial Commission is requested to examine the status of the name Actinobaculum massiliense Greub and Raoult 2006 and to issue an Opinion.

Dissection of the genus Actinobaculum: Reclassification of Actinobaculum schaalii Lawson et al. 1997 and Actinobaculum urinale Hall et al. 2003 as Actinotignum schaalii gen. nov., comb. nov. and Actinotignum urinale comb. nov., description of Actinotignum sanguinis sp. nov. and emended descriptions of the genus Actinobaculum and Actinobaculum suis; and re-examination of the culture deposited as Actinobaculum massiliense CCUG 47753T ( = DSM 19118T), revealing that it does not represent a strain of this species

The remarkable host specificity of the species of the genus Actinobaculum led us to recharacterize these species by a polyphasic approach. A comparative chemotaxonomic study including analysis of whole-cell sugars, amino acid composition of the peptidoglycan, fatty acid methyl esters, respiratory quinones and polar lipids revealed significant differences that, in combination with molecular data, support a dissection of the genus Actinobaculum. The proposals of this study include the reclassification of Actinobaculum schaalii and Actinobaculum urinale as Actinotignum schaalii gen. nov., comb. nov. (type strain DSM 15541(T) = CCUG 27420(T)) and Actinotignum urinale comb. nov. (type strain DSM 15805(T) = CCUG 46093(T)), respectively. Emended descriptions of the genus Actinobaculum and Actinomyces suis are also provided. The results of 16S rRNA gene sequence analysis and DNA-DNA hybridization also indicated that the type strain of Actinobaculum massiliense deposited as CCUG 47753(T) ( = DSM 19118(T)) should in fact be considered a member of the species Actinobaculum schaalii. In addition, comparative 16S rRNA gene sequencing and DNA-DNA relatedness studies of four strains recovered from clinical materials demonstrated that three of the isolates belonged to Actinotignum schaalii; the remaining strain represents a novel species, for which the name Actinotignum sanguinis sp. nov. is proposed. The type strain is IMMIB L-2199(T) ( = DSM 26039(T) = CCUG 64068(T)).

Actinobaculum schaalii causing epididymitis in an elderly patient

Actinobaculum schaalii is a Gram-positive coccoid rod that causes various infections in humans and is easily overlooked in cultures. A. schaalii has long been thought to be of low prevalence and limited invasive potential, causing benign cystitis in elderly patients with underlying urological conditions. Here, we report the first case of epididymitis caused by this bacterium.

Actinobaculum schaalii: An Emerging Uropathogen?

A. schaalii is a rare uropathogen. We report urosepsis with Actinobaculum schaalii detected serendipitously in blood and urine culture in a 79-year-old with urinary tract obstruction. This paper illuminates the flaws in our current system in detecting A. schaalii and raises awareness among clinicians and laboratory teams.

Actinobaculum schaalii: review of an emerging uropathogen

Actinobaculum schaalii is a facultative anaerobic, Gram-positive rod-shaped species phylogenetically related to Actinomyces that is likely part of the commensal flora of the human genitourinary tract. Because of its fastidious growth under aerobic conditions and its resemblance to bacteria of the resident flora, A. schaalii is frequently overlooked or considered as a contaminant. It is also difficult to identify phenotypically, still requiring molecular identification. Note that the recent technology of matrix-assisted laser desorption/ionisation time-of-flight-mass spectrometry could be a promising tool for its identification. Recent studies using sensitive PCR assays showed that its clinical significance was largely underestimated. Since its first description in 1997, A. schaalii has been responsible for numerous urinary tract infections (UTIs), mainly in elderly (usually >60 years) and patients with underlying urological conditions. Infected urines usually show many Gram-positive rods with significant leukocyturia and a negative test for nitrites. Numerous cases of severe infections have also been described, such as urosepsis, bacteremia, cellulitis, spondylodiscitis, and endocarditis. In vitro, A. schaalii is highly susceptible to β-lactams but it is resistant to ciprofloxacin and cotrimoxazole, first-choice antimicrobials for the oral treatment of UTIs. A penicillin (e.g. amoxicillin) or a cephalosporin (e.g. cefuroxime, ceftriaxone) should be the preferred treatment.

Assessing diversity of the female urine microbiota by high throughput sequencing of 16S rDNA amplicons

Background

Urine within the urinary tract is commonly regarded as "sterile" in cultivation terms. Here, we present a comprehensive in-depth study of bacterial 16S rDNA sequences associated with urine from healthy females by means of culture-independent high-throughput sequencing techniques.

Results

Sequencing of the V1V2 and V6 regions of the 16S ribosomal RNA gene using the 454 GS FLX system was performed to characterize the possible bacterial composition in 8 culture-negative (<100,000 CFU/ml) healthy female urine specimens. Sequences were compared to 16S rRNA databases and showed significant diversity, with the predominant genera detected being Lactobacillus, Prevotella and Gardnerella. The bacterial profiles in the female urine samples studied were complex; considerable variation between individuals was observed and a common microbial signature was not evident. Notably, a significant amount of sequences belonging to bacteria with a known pathogenic potential was observed. The number of operational taxonomic units (OTUs) for individual samples varied substantially and was in the range of 20 - 500.

Conclusions

Normal female urine displays a noticeable and variable bacterial 16S rDNA sequence richness, which includes fastidious and anaerobic bacteria previously shown to be associated with female urogenital pathology.

Actinobaculum bacteremia: a report of 12 cases

Actinobaculum species are anaerobic Gram-positive rods that have previously been associated with urinary tract infection (UTI) in the elderly. We report 12 patients with Actinobaculum bacteremia. Only 40% of blood cultures were clinically considered significant by the treating physicians, but most patients were treated for UTI, suggesting a possible urinary source of bacteremia. Clinicians should be aware of the pathogenic potential of Actinobaculum spp.

Actinobaculum schaalii causing Fournier's gangrene

Actinobaculum schaalii, which belongs to the group of Gram-positive rods, is difficult to culture. Using molecular genetics, Actinobaculum schaalii could be identified as a causing microorganism in a case of Fournier's gangrene.

Actinobaculum schaalii: clinical observation of 20 cases

Actinobaculum schaalii is a new species that has so far been isolated from human blood, urine and pus. Its importance has probably been underestimated and other Actinobaculum spp. may also have been underdiagnosed. This retrospective study comprises all known cases of A. schaalii infections identified since 2004 in the canton of Neuchâtel (170,000 inhabitants), Switzerland. Strains were cultivated and isolated in the bacteriology laboratory using its routine procedure. Identification included a Rapid ID 32 A strip (bioMérieux) and 16S rRNA gene sequencing. Twenty-one positive samples were found in 19 patients (11 male, 8 female) of all ages (range 16-91 years): 10 from urine (50%), six from blood (30%), one from both blood and urine (5%), and three from pus (15%). Thirteen out of 17 (76%) cases with either blood or urine specimens had underlying genitourinary tract pathologies. When urine cultures were positive for A. schaalii, leucocytes were found in all samples (10/10, 100%) but all nitrite tests were negative (10/10, 100%). The onset of appropriate treatment was delayed due to the diminished sensitivity of A. schaalii to the antibiotics commonly used for UTIs (i.e. ciprofloxacin and trimethoprim/sulfamethoxazole) and to the delay in microbiological diagnosis. A. schaalii should specifically be searched in all cases of leukocyturia with a negative nitrite test but with Gram-positive rods in the Gram stain, in patients with underlying genitourinary tract pathology, instead of dismissing these findings as clinically irrelevant colonization by coryneform bacteria. This infection may be much more common than previously thought.

Actinobaculum schaalii: a common cause of urinary tract infection in the elderly population. Bacteriological and clinical characteristics

To-date only 21 clinical cases of Actinobaculum schaalii infection have been published, and A. schaalii has been considered a rare cause of urinary tract infection (UTI) and urosepsis. Between y 2005 and 2008, we isolated A. schaalii from 55 predisposed elderly patients. In these cases, microscopic findings of coccoid rods in wet smears of urine gave rise to clinical suspicion and subsequently to its isolation from urine. Typically only scant growth of A. schaalii occurred after incubation of the urine for 24 h, but it became visible after 2 days of incubation in 5% CO(2). Preliminary biochemical identification was carried out by combining the API Coryne and Rapid ID32A test systems, and the identification was later confirmed by partial 16S rDNA gene sequencing. During the 4-y period, A. schaalii caused septicaemia, UTIs and asymptomatic bacteriuria. One patient was later infected with Actinobaculum massiliense. The incidence of A. schaalii infections is much higher than previously reported. We present numerous case reports and describe the bacteriological and clinical characteristics of this overlooked uropathogen.

Hidden pathogens uncovered: metagenomic analysis of urinary tract infections

Urinary tract infections (UTIs) are the most common kidney and urologic diseases in industrial nations and are usually caused through faecal contamination of the urinary tract. In this study, we have examined 1449 urine specimens both by culture and by PCR. The majority of UTIs examined were caused by Escherichia coli (35.15%), followed by miscellaneous bacteria (23.03%), and by Enterococcus faecalis (19.39%). A large fraction of fastidious and anaerobic bacteria (22.43%) was not detected under culture conditions but only by using PCR. This group of bacteria evade the standard culture conditions used in routine diagnostic laboratories examining urine specimens. The molecular approach used broad-range 16S rDNA PCR, denaturing high-performance liquid chromatography analysis, sequencing, and bioinformatic analysis to uncover these 'hidden' pathogens and is recommended in particular when examining leukocyte esterase-positive and culture-negative urinary tract specimens.

Actinomyces--gathering evidence of human colonization and infection

The roles of the 'classical'Actinomyces spp. as colonizers of oral cavities of man and animals, in development of intra-oral infections and as agents of actinomycosis have been well documented. This mini-review focuses on perceptions of human colonization and infection that have emerged in the past decade, largely as a result of advances in classification, identification and direct detection from clinical material. Arguably, of the greatest importance is the recognition of actinomycosis as a major factor and indicator of poor prognosis in both infected osteoradionecrosis and bisphosphonate-associated osteonecrosis of the jaws. Among recently described species, Actinomyces graevenitzii has been isolated almost exclusively from oral and respiratory sites and may be a causative agent of actinomycosis. Conversely, several other Actinomyces spp. are isolated commonly from superficial soft tissue infections. Members of the genus Actinobaculum, which is closely related to Actinomyces, are strongly associated with urosepsis. Isolation and identification of Actinomyces and related genera by conventional methods remain difficult. Diagnosis is commonly belated and based solely upon histological findings. Development of direct detection methods may aid patient management and further elucidate clinical associations.

Vertebral osteomyelitis caused by Actinobaculum schaalii: a difficult-to-diagnose and potentially invasive uropathogen

We report the first case of vertebral osteomyelitis caused by Actinobaculum schaalii and review all cases of A. schaalii identified at our institution between 2002 and 2005. A. schaalii causes urinary tract infections - especially in elderly people - occasionally with septic complications.

List of new names and new combinations previously effectively, but not validly, published

The purpose of this announcement is to effect the valid publication of the following new names and new combinations under the procedure described in the Bacteriological Code (1990 Revision). Authors and other individuals wishing to have new names and/or combinations included in future lists should send three copies of the pertinent reprint or photocopies thereof to the IJSEM Editorial Office for confirmation that all of the other requirements for valid publication have been met. It is also a requirement of IJSEM and the ICSP that authors of new species, new subspecies and new combinations provide evidence that types are deposited in two recognized culture collections in two different countries (i.e. documents certifying deposition and availability of type strains). It should be noted that the date of valid publication of these new names and combinations is the date of publication of this list, not the date of the original publication of the names and combinations. The authors of the new names and combinations are as given below, and these authors' names will be included in the author index of the present issue and in the volume author index. Inclusion of a name on these lists validates the publication of the name and thereby makes it available in bacteriological nomenclature. The inclusion of a name on this list is not to be construed as taxonomic acceptance of the taxon to which the name is applied. Indeed, some of these names may, in time, be shown to be synonyms, or the organisms may be transferred to another genus, thus necessitating the creation of a new combination.

Urosepsis with Actinobaculum schaalii and Aerococcus urinae

Actinobaculum was isolated from urine only after prolonged incubation in 5% CO(2) after discrepancy between urine Gram stain and initial culture results was observed. Additional patients were diagnosed using this method. The prevalence of Actinobaculum species in urinary tract infections is underestimated since it is not isolated by routine urine culture procedures.

Ten cases of Actinobaculum schaalii infection: clinical relevance, bacterial identification, and antibiotic susceptibility

Nine of 10 strains of Actinobaculum schaalii caused urinary tract infections in predisposed individuals. Identification included 16S rRNA gene sequence analysis and use of the API Coryne and Rapid ID 32 A test systems. A. schaalii is easily overlooked due to its slow growth in ambient air and its resemblance to the normal bacterial flora on skin and mucosa.

Isolation of Actinobaculum schaalii and Actinobaculum urinale from a patient with chronic renal failure

We report on the isolation of two species of Actinobaculum from blood culture of a patient with chronic renal failure. The two isolates were distinct with regard to their morphological and biochemical characteristics. Subsequent 16S rRNA gene sequencing classified the two species as Actinobaculum schaalii and A. urinale.

Diagnosis of infectious endocarditis in patients undergoing valve surgery

PURPOSE

Histologic examination of valve samples is considered as the gold standard for the diagnosis of infectious endocarditis. Molecular tools are also very promising for patients with negative-culture endocarditis. Thus, we studied the contribution of valvular histology, culture, and 16S rRNA PCR amplification plus sequencing to the diagnosis of infectious endocarditis in patients undergoing valve surgery.

SUBJECTS AND METHODS

We performed culture, histological examination, and broad-range PCR amplification plus sequencing on valve samples taken from 127 patients with infectious endocarditis and from 118 patients without endocarditis. The sensitivity and specificity of these tests for the diagnosis of endocarditis in patients undergoing valve surgery were studied.

RESULTS

The sensitivity of PCR was of 61% (64/105) whereas that of histological examination was of 63% (62/98) and that of valve culture was of only 13% (14/105). All 68 positive PCR results considered reliable according to an interpretation scheme were from patients with infectious endocarditis, resulting in a 100% (118/118) specificity of the interpreted molecular approach. The specificity of histology was also of 100% (118/118) when using stringent criteria (ie, presence of vegetation, microorganisms, and/or valvular inflammation with mainly polymorphonuclear cells). PCR identified an etiological agent in 38% (5/13) of definite blood culture-negative infectious endocarditis.

CONCLUSION

We show that valvular histology with stringent criteria is the gold standard for the diagnosis of infectious endocarditis. Broad-range amplification of 16S rRNA gene is indicated for infectious endocarditis of unknown etiology, whereas valve culture is of limited sensitivity.

PCR detection of bacteria on cardiac valves of patients with treated bacterial endocarditis

We used broad-range PCR amplification and sequencing to detect and identify bacterial DNA in 156 valves of patients treated for infective endocarditis (IE). Bacterial DNA was found more frequently in patients who underwent valve replacement while on antibiotic treatment for IE (60%) than in patients who had completed antibiotic treatment for IE (37%; P = 0.02). We found specific bacterial DNA in valves removed from 11 of 30 patients who had completed antibiotic treatment for IE. Six had no histological evidence of IE. The presence of DNA was significantly correlated with the presence of histologic lesions (P = 0.001) and with the presence of bacteria detected by Gram staining (P < 0.001). Bartonella and streptococci were detected for much longer after antibiotic treatment by PCR than other species (P = 0.047 and 0.04, respectively), and coagulase-negative staphylococci were detected for much shorter periods (P = 0.02). The finding that bacterial DNA was more likely to be detected in valves of patients with active IE than in patients who had completed antibiotic treatment for IE shows that bacterial DNA is cleared slowly. There was no significant correlation between the duration of antibiotic therapy and the presence of bacterial DNA in valves. Since the persistence of bacterial DNA in valves does not necessarily indicate the persistence of viable bacteria, the detection of bacterial DNA in valves from IE patients should be interpreted with caution, in particular in those patients with a past history of treated IE.

Systematic 16S rRNA gene sequencing of atypical clinical isolates identified 27 new bacterial species associated with humans

Clinical microorganisms isolated during a 5-year study in our hospital that could not be identified by conventional criteria were studied by 16S rRNA gene sequence analysis. Each isolate yielded a > or =1,400-bp sequence containing <5 ambiguities which was compared with the GenBank 16S rRNA gene library; 1,404 such isolates were tested, and 120 were considered unique (27 isolates) or rare (< or =10 cases reported in the literature) human pathogens. Eleven new species, "Actinobaculum massiliae," "Candidatus Actinobaculum timonae," Paenibacillus sanguinis, "Candidatus Bacteroides massiliae," Chryseobacterium massiliae, "Candidatus Chryseobacterium timonae," Paenibacillus massiliensis, "Candidatus Peptostreptococcus massiliae," "Candidatus Prevotella massiliensis," Rhodobacter massiliensis, and "Candidatus Veillonella atypica" were identified. Sixteen species were obtained from humans for the first time. Our results show the important role that 16S rRNA gene sequence-based bacterial identification currently plays in recognizing unusual and emerging bacterial diseases.

Rhodobacter massiliensis sp. nov., a new amoebae-resistant species isolated from the nose of a patient

From the nose of a patient with aspiration pneumonia, we isolated a new bacterium by amoebal co-culture using Acanthamoeba polyphaga. Based on phenotypic, 16S rRNA and phylogenetic analysis, we show that this isolate represents a new species within the genus Rhodobacter and and we have named it Rhodobacter massiliensis. The type strain has been deposited in the Collection de l'Institut Pasteur, Paris, France (CIP 107725), and in the Culture Collection of the University of Göteborg, Sweden (CCUG 47968), as strain Framboise.

Pyelonephritis caused by Actinobaculum schaalii in a child with pyeloureteral junction obstruction

Reported here is the case of a 5-year old boy with a pyeloureteral junction (PUJ) obstruction and pyelonephritis caused by Actinobaculum schaalii, an Actinomyces-like organism. Pyelonephritis or any other urinary tract infection caused by Actinobaculum schaalii has not been described in children before. The patient responded well to pyeloplasty in combination with antibiotic treatment.