Available online 17 September 2022, 102640

An increasingly diverse array of rare anaerobes cause invasive human infections.

Proteomics improves accurate identification of commonly encountered anaerobes.

VITEK® MS database versions from 2014-19 identified ∼50% of the rare anaerobes.

VITEK® MS database(s) should be updated with diverse spectra for rare anaerobes.

16S rRNA gene sequencing accurately identified anaerobes when proteomics failed.

Our large regional laboratory routinely provides a definitive identification (ID) for 800-1,200 anaerobic bacteria per annum that cause invasive human infections. An increasing number of isolates (i.e., 10–13%) recovered from clinical specimens from these cases were more unusual or rarely isolated genera and/or species (i.e., ≤5 individual cases/annum).

VITEK® MS (MALDI-TOF MS)is done initially on all anaerobic bacteria, but rare isolates undergo in-house PCR/sequencing when proteomics provides a wrong ID or no results despite repeat testing. A clinical microbiologist in consultation with the Infectious Diseases service approves molecular analyses. This multi-year comparison (2014-19) of the performance of MALDI-TOF MS and 16S rRNA gene sequencing using the IDNS Smart Gene bacterial dataset shows both method's abilities to provide a genus-level and/or species-level ID for rare isolates.

489 rare anaerobes were recovered from a variety of clinical specimens: 57% blood cultures, 19% other sterile fluids, 14% sterile tissues, 8% deep wounds/abscesses, and 2% prosthetic implants. 16S rRNA gene sequencing gave an accurate genus-vs. species level ID for 487/489 (99.6%) and 401/489 (82.0%) of isolates respectively. Accurate genus-vs species-level ID were obtained by MALDI-TOF MS for 269/489 (53.4%) and 187/489 (37.3%) of isolates respectively. MALDI-TOF MS gave wrong or no results for 35.1% of Gram-negative anaerobic cocci (GNAC), 62% of Gram-negative anaerobic bacilli (GNAB), 30.8% of Gram-positive anaerobic cocci (GPAC) and 46.3% of Gram-positive anaerobic bacilli (GPAB). Neither method gave an ID for one GNAB and one GPAC isolate. MALDI-TOF MS genus-level ID of GNAC and genus/species-level ID of GPAB improved during the study but its performance remained stable for genus- or species-level ID of other organism groups.

MALDI-TOF MS provides accurate ID for most common anaerobes, but molecular analyses need to be available for rare isolates. Large complex laboratories should have a workflow for sending rare isolates for 16S rRNA gene sequencing in invasive cases where a definitive ID is clinically required.

Anaerobes

VITEK® MS

MALDI-TOF MS

16S rRNA gene sequencing

Identification

© 2022 Published by Elsevier Ltd.