16S rRNA deep sequencing identifies Actinotignum schaalii as the major component of a polymicrobial intra-abdominal infection and implicates a urinary source

Abstract

Introduction. It can be difficult to catalogue the individual organisms comprising polymicrobial patient infections, both because conventional clinical microbiological culture does not facilitate the isolation and enumeration of all members of a complex microbial community, and because fastidious organisms may be mixed with organisms that grow rapidly in vitro. Empiric antimicrobial treatment is frequently employed based on the anatomical site and the suspected source of the infection, especially when an appropriately collected surgical specimen is not obtained. Case presentation. We present a case of an intra-abdominal infection in a patient with complex anatomy and recurrent urinary tract infections. Imaging did not reveal a clear source of infection, no growth was obtained from urine cultures and initial abdominal fluid cultures were also negative. In contrast, 16S rRNA deep sequencing of abdominal fluid samples revealed mixed bacterial populations with abundant anaerobes, including Actinotignum schaalii (Actinobaculum schaalii). Ultimately, only Enterobacter cloacae complex and meticillin-resistant Staphylococcus aureus, both of which were identified by sequencing, were recovered by culture. Conclusion. The clinical application of 16S rRNA deep sequencing can more comprehensively and accurately define the organisms present in an individual patient's polymicrobial infection than conventional microbiological culture, detecting species that are not recovered under standard culture conditions or that are otherwise unexpected. These results can facilitate effective antimicrobial stewardship and help elucidate the possible origins of infections.

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

“…The significant difference between As+ and As − samples’ β-diversity indicates that there are bacteria mutually exclusive/co-occurring to A. schaalii , as proved by many reports of poly-bacterial infections [ 5 , 6 , 7 , 8 , 9 , 10 ]. We identified P. lymphophilum and Fusobacterium nucleatum both separately and combined with Alcaligenes faecalis and Streptococcus spp.…”

“…Actinotignum schaalii is typically present in the urogenital tract and has not been detected in stool [3]. It has been recognized as an emerging, opportunistic pathogen and co-agent of various, typically polymicrobial infections [1,[4][5][6][7][8][9][10][11][12][13][14], easily overlooked due to its…”

“…Actinotignum schaalii is typically present in the urogenital tract and has not been detected in stool [ 3 ]. It has been recognized as an emerging, opportunistic pathogen and co-agent of various, typically polymicrobial infections [ 1 , 4 , 5 , 6 , 7 , 8 , 9 , 10 , 11 , 12 , 13 , 14 ], easily overlooked due to its slow growth and capnophilic nature using routine culture techniques [ 1 , 9 , 10 , 15 , 16 , 17 , 18 , 19 ]. A. schaalii has been identified in urine from patients with UTI or urosepsis, together with Gram-negative rods ( Citrobacter sp., Pseudomonas aeruginosa , Escherichia coli , Klebsiella sp., Proteus sp.…”

“…A. schaalii was one of the most prevalent bacteria in a large cohort of urinary tract catheter samples, in earlier published observational study [ 30 ]. Kotaskova et al [ 30 ], and others [ 10 , 16 , 19 , 33 ] were able to identify A. schaalii exclusively by broad-range molecular techniques. Concurrently, catheter presence was defined as a risk factor for A. schaalii caused UTI [ 6 , 9 , 19 , 34 ], possibly leading to bacteriemia [ 9 , 35 ] or even urosepsis [ 6 , 9 , 11 , 12 ].…”