Novel Organism Verification and Analysis (NOVA) study: identification of 35 clinical isolates representing potentially novel bacterial taxa using a pipeline based on whole genome sequencing

Veronika Muigg^#¹, Helena M B Seth-Smith^#^{1

2

3

4}, Kai-Manuel Adam⁵, Maja Weisser⁵, Vladimira Hinić^{1

4}, Annette Blaich¹, Tim Roloff^{1

2

3

4}, Ulrich Heininger⁶, Hanna Schmid⁶, Maurus Kohler⁷, Lukas Graf⁸, Dylan M Winterflood¹, Pascal Schlaepfer⁹, Daniel Goldenberger¹⁰

Affiliations

¹ Clinical Bacteriology and Mycology, University Hospital Basel and University of Basel, Petersgraben 4, Basel, 4031, Switzerland.
² Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland.
³ Swiss Institute of Bioinformatics, Basel, Switzerland.
⁴ Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland.
⁵ Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland.
⁶ Infectious Diseases and Vaccinology, University of Basel Children's Hospital, Basel, Switzerland.
⁷ Kantonsspital Baselland (Bruderholz, Liestal, Laufen), Bruderholz, Switzerland.
⁸ Ear, Nose and Throat Department, University Hospital Basel, Basel, Switzerland.
⁹ Laboratory Medicine, University Hospital Basel and University of Basel, Basel, Switzerland.
¹⁰ Clinical Bacteriology and Mycology, University Hospital Basel and University of Basel, Petersgraben 4, Basel, 4031, Switzerland. daniel.goldenberger@usb.ch.

^# Contributed equally.

PMID: 38178003
PMCID: PMC10768270
DOI: 10.1186/s12866-023-03163-7

Novel Organism Verification and Analysis (NOVA) study: identification of 35 clinical isolates representing potentially novel bacterial taxa using a pipeline based on whole genome sequencing

Veronika Muigg et al. BMC Microbiol. 2024.

. 2024 Jan 5;24(1):14.

doi: 10.1186/s12866-023-03163-7.

Authors

Affiliations

¹ Clinical Bacteriology and Mycology, University Hospital Basel and University of Basel, Petersgraben 4, Basel, 4031, Switzerland.
² Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland.
³ Swiss Institute of Bioinformatics, Basel, Switzerland.
⁴ Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland.
⁵ Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland.
⁶ Infectious Diseases and Vaccinology, University of Basel Children's Hospital, Basel, Switzerland.
⁷ Kantonsspital Baselland (Bruderholz, Liestal, Laufen), Bruderholz, Switzerland.
⁸ Ear, Nose and Throat Department, University Hospital Basel, Basel, Switzerland.
⁹ Laboratory Medicine, University Hospital Basel and University of Basel, Basel, Switzerland.
¹⁰ Clinical Bacteriology and Mycology, University Hospital Basel and University of Basel, Petersgraben 4, Basel, 4031, Switzerland. daniel.goldenberger@usb.ch.

^# Contributed equally.

PMID: 38178003
PMCID: PMC10768270
DOI: 10.1186/s12866-023-03163-7

Abstract

Background: Reliable species identification of cultured isolates is essential in clinical bacteriology. We established a new study algorithm named NOVA - Novel Organism Verification and Analysis to systematically analyze bacterial isolates that cannot be characterized by conventional identification procedures MALDI-TOF MS and partial 16 S rRNA gene sequencing using Whole Genome Sequencing (WGS).

Results: We identified a total of 35 bacterial strains that represent potentially novel species. Corynebacterium sp. (n = 6) and Schaalia sp. (n = 5) were the predominant genera. Two strains each were identified within the genera Anaerococcus, Clostridium, Desulfovibrio, and Peptoniphilus, and one new species was detected within Citrobacter, Dermabacter, Helcococcus, Lancefieldella, Neisseria, Ochrobactrum (Brucella), Paenibacillus, Pantoea, Porphyromonas, Pseudoclavibacter, Pseudomonas, Psychrobacter, Pusillimonas, Rothia, Sneathia, and Tessaracoccus. Twenty-seven of 35 strains were isolated from deep tissue specimens or blood cultures. Seven out of 35 isolated strains identified were clinically relevant. In addition, 26 bacterial strains that could only be identified at the species level using WGS analysis, were mainly organisms that have been identified/classified very recently.

Conclusion: Our new algorithm proved to be a powerful tool for detection and identification of novel bacterial organisms. Publicly available clinical and genomic data may help to better understand their clinical and ecological role. Our identification of 35 novel strains, 7 of which appear to be clinically relevant, shows the wide range of undescribed pathogens yet to define.

Keywords: Clinical isolates; Clinical significance; Difficult to identify strains; Novel bacteria; Type (strain) genome server (TYGS); Whole genome sequencing (WGS).

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Conflict of interest statement

Competing interests. The authors declare no competing interests.

Figures

**Fig. 1**
Algorithm for identification of clinical isolates suitable for the NOVA study

**Fig. 2**
TYGS GBDP tree showing relationships between *Corynebacterium* genomes and references. Figure was generated by TYGS (10.1038/s41467-019-10210-3), with 11 genomes sequenced for this publication shown in blue colour. Species clusters are defined by dDDH with a 70% cutoff shown in the first metadatacolumn. Isolates USB_NOVA_40 and USB_NOVA_41 represent *C. pseudogenitalium*, isolates USB_NOVA_47, USB_NOVA_57, and USB_NOVA_60 cluster with species *C. hindlerae*, “*C. provencense”*, and “*C. phoceense”*, respectively; the other 6 genomes do not form clusters with any sequenced type strains

See this image and copyright information in PMC

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Novel Organism Verification and Analysis (NOVA) study: identification of 35 clinical isolates representing potentially novel bacterial taxa using a pipeline based on whole genome sequencing

Affiliations

Novel Organism Verification and Analysis (NOVA) study: identification of 35 clinical isolates representing potentially novel bacterial taxa using a pipeline based on whole genome sequencing

Authors

Affiliations

Abstract

Conflict of interest statement

Figures

References

MeSH terms

Substances