The genus Aerococcus consists of several species, the majority of which are associated with the urogenital tracts of livestock and humans. The most prevalent and threatening species, however, is Aerococcus urinae. Table 1 shows enrichment in adult females diagnosed with UTI or UUI relative to asymptomatic controls (detected in 11%, 34%, and 4%, respectively). Thus, A. urinae is implicated with urine, especially in adult females with LUTS. However, the circumstances and implications of how it ends up there remains a mystery. The natural reservoir of the bacterium is poorly described and the circumstances in which it becomes pathogenic are uncharacterized. Currently, there is a demonstrative need for greater investigation into the involvement of A. urinae in urinary tract disorders such as UTI and UUI, as well as invasive tissue infections. With increasing antibiotic resistance observed in clinical isolates, A. urinae poses a growing threat to the undiagnosed (and misdiagnosed) patient.

The first isolates of A. urinae came from the urine of patients diagnosed with UTI (117). Originally thought of as a rare cause of human infection, the bacterium has since seen a clear rise in diagnoses and case reports alongside improvements in culture techniques and identification technologies (118–121). While lethal cases are rare, A. urinae has been identified in a variety of severe disease complications, such as soft tissue infections and bacteremia, all traced to a urological origin (120, 122–124). Non-invasive infections are associated with UTI and UUI in women ( Table 1 ) (9, 21). However, enhanced culturing of urine from asymptomatic participants also detects this species, complicating characterization of A. urinae’s status, and suggesting that it is an opportunistic pathogen (125).

Monoculture of A. urinae from urine is uncommon; instead, it is often identified alongside several other species, contributing to its dismissal as a contaminant. In cases of bacteremia, however, the majority of infections are monomicrobial with significant risk for endocarditis and septic embolization (126, 127). Thus, it remains unclear whether this bacterium works in concert with others or on its own.

Risk factors for invasive infections include older age and comorbid genitourinary diseases (121, 124, 128). In pediatric settings, A. urinae has been reported as a cause for extraordinary malodorous urine in boys with comorbid urogenital disorders as a risk factor (129, 130). Malodorous urine has been documented in adult patients as well, having been described as ammoniacal and “socially disabling” (120, 131).

In all severe cases of infection, misidentification and lack of resistance testing can lead to fatality (132, 133). Currently, the criterion standard for rapid identification in the clinical setting is via MALDI-TOF MS (125). However, A. urinae is easily missed on routine urine culture and other bacteriological tests and, when isolated, is often misidentified as streptococci, staphylococci, or enterococci because they share many characteristics.

Whole genome sequencing and phenotypic characterization of the organism has revealed substantial diversity within the A. urinae species designation such that subdivision has been suggested (134–136), although the clinical relevance of such divisions remains unknown. Like other invasive uropathogens, A. urinae demonstrates the ability to form biofilms on catheters and heart tissue, as well as the ability to aggregate platelets (137–139). The first UTI mouse model for A. urinae demonstrated a tropism for the kidney, indicating a route for ascending infection despite the bacterium being non-motile (140). Analysis for virulence factors revealed genes predicted to be associated with adhesion and anti-phagocytosis (135). Proteomic studies have supported this finding, revealing an abundance of adhesive surface proteins expressed on the bacterium’s surface (138, 141). Unfortunately, no genetic model currently exists to allow mechanistic studies into these virulence factors.

With proper identification and susceptibility testing, antibiotic therapy is generally effective for A. urinae infection. Isolates from several studies have demonstrated susceptibilities to most antibiotics used against Gram-positive organisms; however, resistances have been indicated to fluoroquinolones, cephalosporins, trimethoprim-sulfamethoxazole, and tetracycline (142–146). There is concern that antibiotic resistance may be increasing; rising resistance has been detected in wastewater samples (147). As with the related streptococci, staphylococci, and enterococci, the possibility of horizontal gene transfer of resistance genes may pose a significant future risk. Another member of this genus, A. urinaeequi, has been found to harbor a plasmid with tetracycline resistance and a transposable element with vancomycin resistance (148, 149). As such, prudent stewardship based on careful microbial identification is foundational for the diagnosis and treatment of A. urinae infections.

Facklamia species are challenging to accurately identify with current microbiologic systems; they are often confused with hemolytic streptococci (150). Thus, F. hominis is an underrecognized pathogen that has been isolated from a variety of clinical specimens, including bacteremia associated with brain and soft tissue abscesses, endocarditis, necrotizing gangrene, and ischemic stroke symptoms (151). It also has been associated with pediatric pyelonephritis (152), acute cystitis and urosepsis (152), as well as bacteremia associated with transurethral resection of the prostate (153). Despite isolation from vaginal specimens and urine, especially in adult females with UUI ( Table 1 ), the role of F. hominis as a commensal and the transition to opportunistic pathogen has yet to be explored (151). Antibiotic resistances have been demonstrated towards cephalosporins, erythromycin, clindamycin, and trimethoprim-sulfamethoxazole (150, 151). More studies are needed to investigate mechanisms of virulence, predisposing risk factors, and rates of infection.

G. sanguinis was first isolated from human blood in 1978; more recently it was proposed to be its own novel genus (154). Globicatella infections have been associated with bacteremia, septicemia, meningitis, infective endocarditis, wound infections, and UTIs in humans on a sporadic basis (154–156). Isolates have been detected in catheter-associated biofilms along with A. urinae (138). As such, G. sanguinis is now considered to be an emerging pathogen with an expanding disease spectrum, recently identified from patients with endophthalmitis and osteomyelitis (157, 158). Since this species also has been considered to be a commensal bacterium (159), it likely should be considered an opportunistic uropathogen. Because of its close resemblance to streptococci and aerococci under microscopic examination and morphologically on blood agar, G. sanguinis is often misidentified. As a result, it can be easily underestimated in clinical settings (160).

This genus of facultatively anaerobic Gram-positive rods consists of 4 species: Actinotignum schaalii, Actinotignum urinale, Actinotignum sanguinis, and Actinotignum timonense (192–195). A. schaalii and A. urinale were first described under the basonyms Actinobaculum schaalii and Actinobaculum urinale, respectively (192, 193). However, based on the 16S rRNA gene sequence, a remote relationship with the Actinobaculum suis type strain was found (Soltys 50052), resulting in reclassification to the Actinotignum genus (194, 196).

Although first isolated from blood, both A. schaalii, A. sanguinis, and A. urinale have since been isolated from urine. A. schaalii has most often been reported in the context of UTI (197). For example, it is reported to be an emerging uropathogen of elderly people suffering from UTI with comorbidities (198, 199). It also has been detected in children with urinary tract disorders (200, 201). The genus as a whole has been reported to be significantly more common in adult women with UUI than in unaffected controls (9, 21) ( Table 1 ), but the species A. schaalii specifically has been found at significantly higher mean abundances in adult women with UUI compared to unaffected controls (202).

Other species have been associated with infections. A. urinale was first isolated from human urine of patients with UTI (194); however, it also has been isolated from human blood cultures (203). A. sanguinis was first isolated from a human blood culture of a patient with septicemia and has been co-isolated with Trueperella bernardiae from breast abscesses in women (204). The first report of A. timonense concerned an isolate from the urine of a 59-year-old man with end-stage renal disease (195).

Like many of the species reviewed here, Actinotignum species grow slowly under ambient atmospheric conditions typically used by clinical microbiology laboratories; thus, they are often overgrown by faster-growing bacteria. Furthermore, because these species resemble commensal skin and mucosal species, they are often mistakenly identified as contaminants (205). Also, until recently, Actinotignum species were difficult to identify after cultivation. However, the advent of molecular techniques has resulted in increasing reports of A. schaalii in the context of human infection (198, 199). Further research is essential to determine whether these Actinotignum species are uropathogens.

Formerly belonging to the Actinomyces genus, the new Gleimia genus consists of three members: G. europea, G. hominis, and G. coleocanis. The first two have been isolated in humans and the latter in dogs. Human isolates have been implicated in UTIs (182, 206) and have been suggested as a bladder cancer marker (207). They can present clinically with persistent ear infections and recurrent soft tissue infections (208–211), as well as abscesses of the neck, back, feet, brain, and genital area in both men and women of various ages (182, 185, 187, 206, 208, 212–214). Recent cases have linked G. europaea with necrotizing fasciitis (210, 211) with a recent case report of rapid infection progression and Fournier’s Gangrene (215). Due to ineffective identification techniques, taxon reclassification, and inadequate research, Gleimia species remain misunderstood with few reports concerning their pathophysiology.

Like Gleimia, a former member of the Actinomyces genus, S. turicensis and S. radingae are Gram-positive, catalase- and urease-negative, anaerobic, filamentous bacilli (182, 216) that have both been isolated from catheterized urine. Originally isolated from a perianal abscess, they were originally classed as CDC Coryneform Group E, from which A. radingae and A. turicensis were purified and characterized (216). After reassessment of phylogenetic positioning and chemotaxonomic characteristics, these species were reassigned to Schaalia along with eleven other species (191), including S. meyeri and S. odontolytica, all part of the human commensal urinary bladder microbiome.

S. turicensis is a commensal of the skin, gut, oral cavity, and female urogenital tract (182) but is also an opportunistic pathogen. Clinical isolates have been reported in bacteremia (217), purent mastoiditis and meningitis (218), infection following rotator cuff repair (219), gonococcal urethritis (220), and a perianal abscess (216). The circumstances and conditions that transform S. turicensis from commensal to pathogen remain to be elucidated.

T. bernardiae is an emerging opportunistic pathogen in both humans (204, 221–229) and animals (230, 231). In the 1980s, isolates recovered from blood cultures, wounds, abscesses, and skin infections were found to be similar by biochemical testing and described using the provisional name CDC fermentative Coryneform group 2 (CDC group 2) (230). CDC group 2 was formally assigned to the species Actinomyces bernardiae based on 16S rRNA gene sequencing and other features for strains recovered from infections in the United States, Canada, and Switzerland (226). In 1997, following reanalysis of the 16S rRNA gene sequences and after comparison with species in the genus Actinomyces, A. bernardiae was assigned to the genus Arcanobacterium (232). After reassessment of phylogenetic positioning and chemotaxonomic characteristics, this species was reassigned to Trueperella, along with A. abortisuis, A. bialowiezensis, A. bonasi and A. pyogenes (233). Of these five organisms, only T. bernardiae and T. pyrogenes have been reported in humans, all associated with mild to severe infections and abscesses. As all 5 species have been reported as pathogens in animals, it has yet to be established if T. bernardiae and T. pyrogenes are commensals in skin, oropharynx, and urinary tract or are opportunistic zoonotic pathogens of humans (225, 231, 233). The occurrence of T. bernardiae in polymicrobial infections may reflect dependence of this organism on nutrients provided by other species. Immunosuppressed patients appear to be more at risk for infection by T. bernardiae (94).

The first member of this anaerobic, diphtheroid, Gram-positive genus was initially characterized as a distinct species with resemblance to the genus Actinomyces in 2003 (234). Case reports have associated V. cambriensis in polymicrobial, anaerobic human abscess infections (235). The source of these infections remains unknown, and it is unclear if this microbe depends on one or more partner species for survival or infection. Before the advent of MALDI-TOF MS, accurate identification of V. cambriense in routine clinical microbiology laboratories was difficult (233). Thus, in the past, this species may have been dismissed as contamination (97). Indeed, the use of more modern detection methods have identified members of the genus Varibaculum in human urine, as well as prostate and bladder cancer (236–238). Whereas metaculturomic methods rarely detect this anaerobe, it is frequently detected by metagenomic approaches. How Varibaculum species cause disease remains poorly understood.

Actinomyces neuii was discovered in 1994 (239). Recently, it was given its own genus Winkia (191). This catalase-positive coccobacillus has been found in asymptomatic women (240) but may be an opportunistic emerging pathogen in humans. Infections include abscesses and infected atheromas (241), cellulitis (242), endophthalmitis, and UTIs (185), as well as bacteremia, including endocarditis (243). Isolates have also been implicated in neonatal sepsis (244–246) and bacterial vaginosis (247). In all cases, how W. neuii is mechanistically involved in these diseases is poorly described. Antibiotic resistance to fluoroquinolones has been observed (248), but wider studies into urinary isolate resistances are needed. Like other Gram-positive rods, it is often dismissed as a contaminant (249). We have found it to be highly enriched in adult females with UUI relative to asymptomatic controls (28% and 3%, respectively) (21) ( Table 1 ).

is a facultative anaerobic fermenter that is non-lipophilic (250, 251). It is unusual, as it lacks mycolic acid, which is common in other coryneforms. Although a commensal of skin and mucous membranes, C. amycolatum can be an opportunistic pathogen, especially in immunosuppressed patents and nosocomial environments. It has been isolated from blood cultures, cellulitis, wounds, endocarditis, and peritonitis (250, 253). A recent pan-genomic study of drug resistant and commensal isolates of C. amycolatum gave insight into the core genome and the transition from commensal to pathogenic phenotype (262).

is an asaccharolytic, lipophilic coryneform that expresses lipase and strong urease activity (250, 261, 263). C. urealyticum is an opportunistic nosocomial pathogen that can cause acute cystitis, pyelonephritis, alkaline-encrusted cystitis, and encrusted pyelitis (250). It has been associated with bacteremia, mainly in patients with chronic urological diseases and its strong urease activity is a major factor in urinary stone formation (260). Painful and persistent pathologies occur associated with encrustations in the kidney, ureters, and urethra due to alkalinization of urine from metabolism of urea (261). It tends to be multi-drug resistant. In a study of C. urealyticum infections in kidney transplant recipients, between 40 to 85% of the isolates tested were resistant to azithromycin, cefotaxime, chloramphenicol, ciprofloxacin, clindamycin, erythromycin, gentamycin, norfloxacin, penicillin G, or tetracycline (261) One non-antibiotic treatment relies on oral L-methionine, which when metabolized acidifies urine (264, 265). It is unclear if this treatment is bactericidal or bacteriostatic, as in the original report removing methionine resulted in return of the uropathogens (264). C. urealyticum is also a zoonotic pathogen associated with UTIs in dogs, cats and other animals (250).

The Dermabacter genus contains three species: D. hominis, D. jinjuensis, and D. vaginalis, of which only D. hominis has been found in human catheterized urine ( Table 1 ). First described in 1988 (266), this Gram-positive, non-spore forming, non-acid fast, facultative anaerobic short rod is considered to be a commensal of human skin (267). However, D. hominis has been reported in diverse clinically relevant scenarios, almost always as part of polymicrobial communities in patients that are immunocompromised or suffering with significant comorbidities, most often cardiovascular disease, diabetes mellitus, and chronic kidney disease (267). Other reports exist of its isolation from biopsies of bone and joint infections and swabs of soft tissue infection (267), a case of trichobacteriosis axillaris (268), a neck sebaceous cyst (269), blood cultures of patients with bacteremia (270), peritoneal fluid from a patient with end stage renal disease (271), recurrent abscesses (272), bone deposits from a patient with chronic osteomyelitis (273), breast implant infections (274), and cerebral abscess of a renal transplant patient (275). In one report, D. hominis isolated from human semen was found to be capable of forming a strong biofilm, which could potentially be a cause of prostatitis (276). Thus, in immunocompromised patients or those with comorbidities, D. hominis may be pathogenic. Although we have detected it in the bladder urine of adult females with UTI and UUI ( Table 1 ), the relationship between this microbe and the urinary tract remains unclear.

Originally assigned to Centers for Disease Control and Prevention coryneform group B-1 and B-3 (277) and later the genus Arthrobacter (278), the recently established genus Pseudoglutamicibacter contains two species: P. cumminsii and P. albus (279). It is unknown whether these species are commensal microbes or opportunistic pathogens, and we have detected both species in the bladder urine of both asymptomatic and affected adult females (1% and 11%, respectively) ( Table 1 ). However, most samples collected from humans have been associated with severe infections and abscesses, including infected amniotic fluid, chronic cervicitis, chronic otorrhea, external otitis, calcaneus osteomyelitis, sepsis, and UTI (277, 280). Isolation sites have included blood, bone, amniotic fluid, leg wounds, and urine (277, 280).

Both P. cumminsii and P. albus are Gram-positive, mesophilic, catalase-positive, obligate aerobe coccobacilli (278, 279). P. cumminisii is the most frequently encountered member of the genus in human clinical specimens (280). A recent case study identified P. cumminsii in the urine culture of a woman with UTI (281). The first clinical specimen of P. albus was isolated from a blood culture of a surgical patient with severe phlebitis (278). The 16S rRNA genes of P. cumminsii and P. albus share a high degree of homology. This makes distinguishing these two organisms difficult (279). Better differentiation will require whole genome sequencing of isolates and better defined MALDI-TOF profiles.

Several species belong to the genus Alloscardovia, but only A. omnicolens has been described in human urine, especially from UUI patients ( Table 1 ). It is a Gram-positive, oxidase and catalase-negative, non-spore-forming, anaerobic rod (283, 284). While originally considered to be a commensal of the gastrointestinal tract and oral cavity, there is evidence that this microbe is clinically significant and should not be ignored if found in clinical specimens, especially if isolated from the urinary tract (285). The Alloscardovia genus was first described in 2007 by Huys and co-authors after sampling various clinical sites, including the urethra, urine, blood, abscesses of the lung and aorta, and tonsils (286). A. omnicolens has been identified in urine cultures of bladder cancer patients with concurrent UTI (285). It also has been considered the probable cause of infection for at least one UTI (283) and a case of bacteremia due to a UTI in a 70-year-old woman with advanced uterine cancer (287). Therefore, A. omnicolens appears to be an opportunistic pathogen. Antibiotic resistance to metronidazole and moxifloxacin has been described (288, 289).

Is a Gram-positive obligate anaerobic bacillus with the ability to hydrolyze esculin (290, 293–297). As such, it is rarely cultured, even by EQUC, but it is observed by metagenomic approaches.

Discovered in 1898, it was named Bacillus ramosum then renamed Ramibacterium ramosum (295, 297). The demonstration of sporulation led to its reclassification as Clostridium ramosum (294, 297). Further dissections of the genus Clostridium, using a combination of genetic markers, led to another name change, this time to Erysipelatoclostridium ramosum and most recently to Thomasclavelia ramosum (290, 293, 296).

While found as part of the commensal flora in the gastrointestinal and urinary tracts, this organism has been documented in infections, such as appendicitis, blood, brain abscess, bacteremia, joint infections, and pulmonary gangrene (295, 297, 298). It also is one of the few sporulating bacteria detected in the urinary microbiome. Further study is warranted to understand how this commensal becomes an opportunistic and potent pathogen.

Originally described in 1936, the genus Peptostreptococcus consists of four species, P. anaerobius, P. canis, P. russellii, and P. stomatis (40, 292, 299). These are Gram-positive anaerobic cocci; thus, they are rarely cultured but are frequently detected by metagenomic approaches. They have weak fermentative and proteolytic metabolisms. Consequently, it may be symbiotic with other organisms from which it derives nutrients (300). Indeed, P. anaerobius has been isolated most often from polymicrobial infections of soft tissue, bone, brain, implant-related and respiratory tract infections (40, 292, 299). P. anaerobius is also one of the most common Gram-positive, anaerobic cocci isolated from infections of the female urogenital tract and the abdominal cavity (292). Thus, while P. anaerobius is probably a commensal of the gastrointestinal, vaginal, and urinary tracts, it can be an opportunistic pathogen, particularly within polymicrobial infections.

The genus Prevotella consists of 55 distinct species of Gram-negative coccobacilli anaerobes that are commonly found in the oral, gastrointestinal, and urogenital tracts of humans and animals. It was originally proposed to characterize the moderately saccharolytic, oral Bacteroides species (302). Until recently, the lack of characteristic phenotypic and biochemical traits had hampered identification at the species level among this group of obligatory anaerobes. They are rarely cultured, but the availability of 16S rRNA sequence analysis has improved detection, and thus the number of recognized Prevotella species has increased over the last few years (303). Recently, a genomic and functional analysis of the 55 phenotypically, ecologically and functionally diverse species comprising Prevotella identified 7 distinct clades and thus reassignment across 7 genera, with 4 of them being new genera: Segatella, Hoylesella, Leyella and Palleniella (304). Below, we review Prevotella bivia and Hoylesella timonensis.

Previously classified as Bacteroides bivius, P. bivia is commonly found in the human vaginal microbiome (305). Though normally a commensal, P. bivia has pathogenic potential to trigger severe infection and induce tissue destruction, especially when there is excess estrogen and with the synergistic cooperation of other species (306). P. bivia is one of the most frequently isolated anaerobic bacteria in cases of bacterial vaginosis. The presence of P. bivia creates an environment that facilitates growth of Peptostreptococcus anerobius (300) and Gardnerella vaginalis (307). P. anaerobius growth is enhanced with production of certain amino acids by P. bivia. Likewise, G. vaginalis growth is enhanced with production of ammonia by P. bivia.

P. bivia is one of the most frequently isolated bacteria in women with pelvic inflammatory disease, as noted in a retrospective, cross-sectional study (308), It has also been implicated in cases of recurrent UTIs, osteomyelitis (309), osteitis (310), endocarditis (311), necrobacillosis (312), sinusitis (313), wound infections from animal bites (314, 315), intracranial abscesses (316), periodontal and tubo-ovarian abscesses (317), and adverse pregnancy outcomes such as preterm labor (318). The virulence factors of P. bivia are not fully understood, but research suggests that they may include adhesins that allow the bacteria to attach to host cells, enzymes that degrade host tissue, and toxins that damage host cells and stimulate inflammation. As with other members of the genus Prevotella, antibiotic resistance is becoming an increasing concern; the most common are amoxicillin-clavinate, clindamycin, and moxifloxacin (319). Thus, further research into P. bivia is warranted.

Prevotella timonensis was first isolated from a human breast abscess (320). After reassessment of phylogenetic positioning and chemotaxonomic characteristics, this species was reassigned to Hoylesella (304). Like the previously described anaerobes, H. timonensis is rarely cultured but detected often by metagenomics. The breast abscess isolate mentioned above ferments glucose, maltose, and lactose. It also hydrolyzes esculin but is urease and catalase negative. Although the species has most often been isolated from cutaneous/soft tissue abscesses and bone infections, it is also prevalent in human genitourinary samples, including from urine (304, 321). While H. timonensis may be a commensal organism in the genitourinary tract, it has been associated with bacterial vaginosis (322). Thus, some evidence supports its role as an emerging opportunistic pathogen (321, 322).