ABSTRACT
Here we report genome sequences of 12 Listeria ivanovii strains sent to the Centers for Disease Control and Prevention from 1987 to 2025. Four of these strains are of unknown origin; two are from food; one is from an animal; and five are of human origin, including two recently reported human cases.
KEYWORDS: Listeria, ivanovii, genome, foodborne, PacBio, Illumina
ANNOUNCEMENT
The Listeria genus comprises 27 species of Gram-positive, rod-shaped, facultative-anaerobic bacteria (1). L. monocytogenes and L. ivanovii have traditionally been recognized as the two pathogenic species capable of infecting humans, although sporadic cases of L. innocua and others have been documented (2). Listeria ivanovii, previously known as Listeria monocytogenes serovar 5, was first identified in aborted sheep in Bulgaria in 1955 (3) and reclassified as a novel species in 1984 (4). Since then, it has been found in various environments, foods, animals, and humans—both symptomatic and asymptomatic (5, 6)—although less so than L. monocytogenes (5, 7). Eleven human clinical cases have been reported in the literature since 1971. These cases mainly affect immunocompromised individuals and potentially foodborne vehicles of infection (8–17). L. ivanovii is a potentially underappreciated opportunistic pathogen important for public health surveillance with few available human or food-derived whole genome sequences. Here, we report 12 Listeria ivanovii isolates sent by state public health laboratories to the Centers for Disease Control and Prevention (CDC) through PulseNet, the nationwide surveillance network for enteric pathogens, and the National Listeria Reference Laboratory, between 1987 and 2025. Four were of unknown origin. Of the sequences with known origins, five were derived from humans (listeriosis), two from food (meat and camel milk), and one from sheep. While these isolations are sporadic, their sequences provide additional context for the diversity of this rare species and serve as resources for public health surveillance.
Organisms were isolated by a combination of traditional methods using biochemical tests and selective media (modified Oxford agar or polymyxin–acriflavine–lithium chloride–ceftazidime–aesculin–mannitol agar) in public health laboratories. They were sent to CDC as suspected Listeria ivanovii isolates. DNA was extracted with the DNeasy blood and tissue kit (Qiagen, USA) from single-colony isolates grown at 36°C on trypticase soy agar II with 5% sheep blood (BD, Germany) overnight. Genomic DNA libraries were produced from bacterial isolates for sequencing on the Pacific Biosciences (PacBio) RSII (n = 4) and Illumina MiSeq (n = 12) platforms. For PacBio single-molecule real-time (SMRT) sequencing, samples were sheared to 10 kb using g-TUBEs (Covaris, USA). Sample PNUSAL004272 was further size selected to 8 kb with the BluePippin system (Sage Science, USA). PacBio libraries were prepared with the SMRTbell template preparation kit v.1.0 (PacBio) and DNA/Polymerase Binding Kit P6 v.2 (PacBio) for sequencing with the C4v2 PacBio chemistry. For the Illumina MiSeq platform, paired-end 2 × 150 bp or 2 × 250 DNA libraries were prepared with the Illumina Nextera XT DNA Library Preparation Kit or the Illumina DNA prep kit.
Four genomes were sequenced with PacBio. Contigs were circularized without rotation, and default settings for the SMRT Analysis software were used, along with the hierarchical genome assembly process (HGAP v3) (18) assembler. The median genome length was 2,919,552 bp with 360,650 raw reads, 4,165 bp N50, 3,401 bp average read length, 37.15% GC content, and 291× coverage. For Illumina reads assembled with SKESA (19), sequence quality was evaluated using BioNumerics v.7.6.3 (Applied Maths, Belgium), and all passed standard quality metrics with Q scores of >34 in both reads and >99.65% bases aligned. The median genome length was 2,894,521 bp, with an N50 of 354,986 bp, 1,376,487 raw reads 184 bp long with 37.03% GC content and 91× coverage. Annotations were added by the National Center for Biotechnology Information (NCBI) Prokaryotic Genome Pipeline (PGAP) v.6.7 for PacBio and v.6.10 for Illumina with GeneMarkS-2+ (20, 21) upon submission to GenBank. Results are shown in Table 1 for Illumina and PacBio sequences.
TABLE 1.
Summary of genomic characteristics from Illumina and PacBio sequencing for the L. ivanovii isolates
| WGS ID (alt ID) |
Seq platform | Isolate host (source) | Year isolated (received), country (state) |
Depth of coverage (×) | No. of reads | Avg read length (bp) | No. of contigs | N50 (bp) |
GC content (%) | Total genome size (bp) | SRA accession no. | BioSample accession no. | Nucleotide accession no. |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| PNUSAL004272 (2019L-6001) | PacBio RSII | Human (pleural fluid) | 2018, USA (IL) | 299.49 | 327,281 | 3,778 | 1 | 4,911b | 37.15 | 2,919,242 | SRR32028211 | SAMN40742762 | CP165994 |
| PNUSAL004272 (2019L-6001) |
Illumina MiSeq | Human (pleural fluid) | 2018, USA (IL) | 86.9 | 1,081,518 | 235 | 15 | 377,747 | 37.03 | 2,894,062 | SRR28548437 | SAMN40742762 | JBNDYJ000000000 |
| PNUSAL001964 | PacBio RSII | Human (blood) | 2015, USA (CA) | 400.48 | 519,405 | 3,024 | 1 | 3,418b | 37.16 | 2,928,039 | SRR32028212 | SAMN04396061 | CP165993 |
| PNUSAL001964 | Illumina MiSeq | Human (blood) |
2015, USA (CA) | 53.5 | 1,059,984 | 147 | 31 | 213,242 | 37.05 | 2,897,853 | SRR3096904 | SAMN04396061 | JBNDYK000000000 |
| F5999 | PacBio RSII | Human | 1988, missing | 280.95 | 250,082 | 4,192 | 1 | 5,624b | 37.15 | 2,919,548 | SRR32028213 | SAMN13941783 | CP165991 |
| F5999 | Illumina MiSeq | Human | 1988, missing | 105.1 | 2,072,328 | 148 | 19 | 425,583 | 37.04 | 2,895,778 | SRR28548363 | SAMN13941783 | JBNDYM000000000 |
| F4081 (ATCC 19119)a |
PacBio RSII | Animal (sheep) | 1987, Bulgaria | 281.96 | 394,019 | 2,809 | 1 | 3,052b | 37.15 | 2,919,555 | SRR32028214 | SAMN40742705 | CP165992 |
| F4081 (ATCC 19119)a |
Illumina MiSeq | Animal (sheep) | 1987, Bulgaria | 53.9 | 1,061,390 | 148 | 17 | 549,535 | 37.02 | 2,890,168 | SRR28548361 | SAMN40742705 | JBNDYN000000000 |
| PNUSAL024131 | Illumina MiSeq |
Human (CSF) | 2024, USA (OR) | 156.3 | 1,894,318 | 241 | 25 | 325,982 | 36.9 | 3,051,281 | SRR31933685 | SAMN46166184 | JBNBNR000000000 |
| PNUSAL021079 (2024L-6004) |
Illumina MiSeq | Human (blood) | 2023, USA (TX) | 115.9 | 1,547,734 | 219 | 35 | 225,307 | 37.04 | 2,905,819 | SRR28548436 | SAMN40742764 | JBNBNS000000000 |
| 2022L-6226 | Illumina MiSeq | Food (meat) | 2022, USA (MA) | 97.8 | 1,226,042 | 233 | 15 | 425,615 | 37.03 | 2,894,980 | SRR28564828 | SAMN40759057 | JBNBNT000000000 |
| CDPHFDLB-F1607014-001 | Illumina MiSeq | Food (camel milk) | 2016, USA (CA) | 117.8 | 1,511,636 | 228 | 71 | 49,730 | 37.05 | 2,892,525 | SRR28548371 | SAMN40742733 | JBNBNU000000000 |
| J2188 | Illumina MiSeq | Missing | 2003, missing | 62.9 | 1,241,338 | 148 | 14 | 354,979 | 37.03 | 2,890,995 | SRR28548365 | SAMN40742708 | JBNBNV000000000 |
| H3291 | Illumina MiSeq | Missing | 1997, missing | 84.2 | 1,659,694 | 148 | 13 | 354,993 | 37.03 | 2,890,942 | SRR28548367 | SAMN13941784 | JBNDYL000000000 |
| F6000 | Illumina MiSeq | Missing | 1988, missing | 79.0 | 977,112 | 236 | 26 | 54,035 | 37.02 | 2,903,952 | SRR28548438 | SAMN40742766 | JBNBNW000000000 |
| F4084 | Illumina MiSeq | Missing | 1987, missing | 96.2 | 1,884,682 | 149 | 12 | 550,207 | 37.02 | 2,886,326 | SRR28548435 | SAMN40742765 | JBNBNX000000000 |
Type strain.
N50 of reads.
ACKNOWLEDGMENTS
We acknowledge the state public health laboratories that sent Listeria ivanovii isolates.
This project was supported in part by an appointment to the Research Participation Program at the Centers for Disease Control and Prevention administered by the Oak Ridge Institute for Science and Education through an interagency agreement between the U.S. Department of Energy and the Centers for Disease Control and Prevention.
The findings and conclusions in this report are those of the authors and do not necessarily represent the official position of the Centers for Disease Control and Prevention.
Contributor Information
Zuzana Kucerova, Email: zik0@cdc.gov.
Catherine Putonti, Loyola University Chicago, Chicago, Illinois, USA.
DATA AVAILABILITY
Table 1 contains available GenBank and Sequence Read Archive accession numbers for all strains. BioProject accession number PRJNA1128686 encompasses the PacBio sequences. Isolates are available by request.
ETHICS APPROVAL
This study has been conducted under surveillance and is therefore exempt from ethical review.
REFERENCES
- 1. Orsi RH, Liao J, Carlin CR, Wiedmann M. 2023. Taxonomy, ecology, and relevance to food safety of the genus Listeria with a particular consideration of new Listeria species described between 2010 and 2022. mBio. doi: 10.1128/mbio.00938-23:e0093823 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 2. McIntosh T, Kucerova Z, Katz LS, Lilley CM, Rowe LA, Unoarumhi Y, Batra D, Burnett E, Smikle M, Lee C. 2022. Genome sequences of hemolytic and nonhemolytic Listeria innocua strains from human, food, and environmental sources. Microbiol Resour Announc 11:e0072322. doi: 10.1128/mra.00723-22 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 3. Ivanov I. 1962. Untersuchungen über die Listeriose der Schafe in Bulgarien. Monatsh Veterinarmed 17:729–736. [Google Scholar]
- 4. Seeliger HPR, Rocourt J, Schrettenbrunner A, Grimont PAD, Jones D. 1984. Notes: Listeria ivanovii sp. nov. Int J Syst Bacteriol 34:336–337. doi: 10.1099/00207713-34-3-336 [DOI] [Google Scholar]
- 5. Hafner L, Pichon M, Burucoa C, Nusser SHA, Moura A, Garcia-Garcera M, Lecuit M. 2021. Listeria monocytogenes faecal carriage is common and depends on the gut microbiota. Nat Commun 12:6826. doi: 10.1038/s41467-021-27069-y [DOI] [PMC free article] [PubMed] [Google Scholar]
- 6. Rossi F, Giaccone V, Colavita G, Amadoro C, Pomilio F, Catellani P. 2022. Virulence characteristics and distribution of the pathogen Listeria ivanovii in the environment and in food. Microorganisms 10:1679. doi: 10.3390/microorganisms10081679 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 7. Scallan E, Hoekstra RM, Widdowson MA, Hall AJ, Griffin PM. 2011. Foodborne illness acquired in the United States (Reply). Emerg Infect Dis 17:1339–1340. doi: 10.3201/eid1707.110572 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 8. Blot M, Disson O, Leclercq A, Moura A, Bracq-Dieye H, Thouvenot P, Valès G, Burroni B, Lupo A, Lecuit M, Charlier C. 2022. Listeria-associated lymphadenitis: a series of 11 consecutive cases and review of the literature. Open Forum Infect Dis 9:ofab598. doi: 10.1093/ofid/ofab598 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 9. Busch LA. 1971. Human listeriosis in the United States, 1967-1969. J Infect Dis 123:328–332. doi: 10.1093/infdis/123.3.328 [DOI] [PubMed] [Google Scholar]
- 10. Cummins AJ, Fielding AK, McLauchlin J. 1994. Listeria ivanovii infection in a patient with AIDS. J Infect 28:89–91. doi: 10.1016/s0163-4453(94)94347-8 [DOI] [PubMed] [Google Scholar]
- 11. Elischerová K, Cupková E, Urgeová E, Lysý J, Sesevicková A. 1990. Isolation of Listeria ivanovii in Slovakia. Cesk Epidemiol Mikrobiol Imunol 39:228–236. [PubMed] [Google Scholar]
- 12. Guillet C, Join-Lambert O, Le Monnier A, Leclercq A, Mechaï F, Mamzer-Bruneel MF, Bielecka MK, Scortti M, Disson O, Berche P, Vazquez-Boland J, Lortholary O, Lecuit M. 2010. Human listeriosis caused by Listeria ivanovii. Emerg Infect Dis 16:136–138. doi: 10.3201/eid1601.091155 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 13. Rocourt J, Seeliger HP. 1985. Distribution of species of the genus Listeria. Zentralbl Bakteriol Mikrobiol Hyg A 259:317–330. [PubMed] [Google Scholar]
- 14. Snapir YM, Vaisbein E, Nassar F. 2006. Low virulence but potentially fatal outcome-Listeria ivanovii. Eur J Intern Med 17:286–287. doi: 10.1016/j.ejim.2005.12.006 [DOI] [PubMed] [Google Scholar]
- 15. Lessing MP, Curtis GD, Bowler IC. 1994. Listeria ivanovii infection. J Infect 29:230–231. doi: 10.1016/s0163-4453(94)90914-8 [DOI] [PubMed] [Google Scholar]
- 16. Beye M, Gouriet F, Michelle C, Casalta JP, Habib G, Raoult D, Fournier PE. 2016. Genome analysis of Listeria ivanovii strain G770 that caused a deadly aortic prosthesis infection. New Microbes New Infect 10:87–92. doi: 10.1016/j.nmni.2016.01.005 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 17. Mani S, Shanmugam L, Boppe A, G V. 2025. A rare case report of Listeria ivanovii bacteremia in an elderly patient with uncontrolled diabetes and chronic kidney disease from South India. Indian J Med Microbiol 53:100790. doi: 10.1016/j.ijmmb.2025.100790 [DOI] [PubMed] [Google Scholar]
- 18. Chin CS, Alexander DH, Marks P, Klammer AA, Drake J, Heiner C, Clum A, Copeland A, Huddleston J, Eichler EE, Turner SW, Korlach J. 2013. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods 10:563–569. doi: 10.1038/nmeth.2474 [DOI] [PubMed] [Google Scholar]
- 19. Souvorov A, Agarwala R, Lipman DJ. 2018. SKESA: strategic k-mer extension for scrupulous assemblies. Genome Biol 19:153. doi: 10.1186/s13059-018-1540-z [DOI] [PMC free article] [PubMed] [Google Scholar]
- 20. Zhao Y, Wu J, Yang J, Sun S, Xiao J, Yu J. 2012. PGAP: pan-genomes analysis pipeline. Bioinformatics 28:416–418. doi: 10.1093/bioinformatics/btr655 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 21. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP, Zaslavsky L, Lomsadze A, Pruitt KD, Borodovsky M, Ostell J. 2016. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 44:6614–6624. doi: 10.1093/nar/gkw569 [DOI] [PMC free article] [PubMed] [Google Scholar]
Associated Data
This section collects any data citations, data availability statements, or supplementary materials included in this article.
Data Availability Statement
Table 1 contains available GenBank and Sequence Read Archive accession numbers for all strains. BioProject accession number PRJNA1128686 encompasses the PacBio sequences. Isolates are available by request.