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

Abstract

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.

Keywords: 16S rRNA gene sequencing; Actinobaculum schaalii; Actinotignum schaalii; MALDI-TOF MS; anaerobic infection; bloodstream infection; emerging infection; phylogenetic analysis; skin and soft tissue infection; urine culture; uropathogen.

FIG 1

Distribution of Actinotignum schaalii clinical specimens by source. There were 86 A. schaalii isolates recovered from clinical specimens between 2012 and 2019. All samples were identified using 16S rRNA gene sequencing or MALDI-TOF MS. The sunburst chart is color-coded according to the clinical specimen source; pink represents blood specimens, blue represents skin and soft tissue abscess specimens, green represents intra-abdominal abscess specimens, yellow represents urine samples, gray represents implanted device specimens, and brown represents bone specimens.

FIG 2

Phylogenetic tree of Actinotignum schaalii 16S rRNA gene-sequenced partial sequences. The neighbor-joining tree illustrates the phylogenetic relatedness of the sequences. The phylogenetic tree tips are labeled with the GenBank accession number and the clinical infection diagnosis. The clinical outcomes are illustrated by shape (star, outpatient; circle, inpatient) and are color-coded based on the source of infection, as in Fig. 1. The reference strains are bolded, and the red taxons represent death within 90 days. The scale bar represents the number of nucleotide substitutions per site.