Skip directly to site content Skip directly to page options Skip directly to A-Z link Skip directly to A-Z link Skip directly to A-Z link

Disclaimer: Early release articles are not considered as final versions. Any changes will be reflected in the online version in the month the article is officially released.

Volume 32, Number 9—September 2026

Research

Clustering and Source Association of Clinical and Nonclinical Listeria monocytogenes Isolates, New York, USA, 2000–20211

Hilal Samut, Damaris V. Mendez-Vallellanes, Hannah Hoyt, Samantha E. Wirth, Lisa Mingle, Brian D. Sauders, Gregory A. Deiulio, Alyssa W. Dickey, Maria L. Ishida, William J. Wolfgang, Kimberlee A. Musser, Martin Wiedmann, and Renato H. OrsiComments to Author 
Author affiliation: Cornell University, Ithaca, New York, USA (H. Samut, M. Wiedmann, R.H. Orsi); New York State Department of Health, Wadsworth Center, Albany, New York, USA (D.V. Mendez-Vallellanes, H. Hoyt, S.E. Wirth, L. Mingle, W.J. Wolfgang, K.A. Musser); New York State Department of Agriculture and Markets, Albany (B.D. Sauders, G.A. Deiulio, A.W. Dickey, M.L. Ishida)

Main Article

Table 3

Summary of detected inlA premature stop codons in study of clustering and source association of clinical and nonclinical Listeria monocytogenes isolates, New York, USA, 2000–2021*

CCs with respective inlA allele inlA allele IDs with detected PMSCs† PMSC type (length of truncated protein)‡ No. observed clinical and nonclinical isolates with respective inlA allele   Sources of nonclinical isolates with respective inlA allele
CC5
 138
 1 (605 aa)
 6 clinical isolates and 18 nonclinical isolates
   Raw meat, n = 6; processed meat, n = 4; sandwich, n = 1; salad, n = 1; retail, n = 6
CC9
 43
 8 (459 aa)
 5 nonclinical isolates
   Processed meat, n = 3; retail, n = 2
CC9
 44
 11 (684 aa)
 1 nonclinical isolate
   Processed fish, n = 1
CC9
 47
 12 (576 aa)
 5 nonclinical isolates
   Processed meat, n = 1; retail, n = 4
CC9
 48
 4 (8 aa)
 2 clinical isolates and 39 nonclinical isolates
   Processed meat, n = 26; processed fish, n = 1; retail, n = 10; farm, n = 2
CC9
 69
 19 (326 aa)
 1 nonclinical isolate
   Processed meat, n = 1
CC121
 49
 6 (491 aa)
 3 clinical isolates and 17 nonclinical isolates
   Processed fish, n = 12; processed meat, n = 1; processing environment, n = 4
CC121
 438
 5 (188 aa)
 2 clinical isolates and 6 nonclinical isolates
   Raw meat, n = 1; processed meat, n = 1; raw fish, n = 1; retail, n = 1
CC193
 41
 25 (25 aa)
 1 nonclinical isolate
   Processed fish, n = 1
CC199
 28
 4 (8 aa)
 1 clinical isolate and 40 nonclinical isolates
   Processed fish, n = 5; raw fish, n = 3; processed meat, n = 3; produce, n = 1; nuts, n = 1; retail, n = 26; processing environment, n = 1
CC224
 125
 2 (655 aa)
 1 clinical isolate and 2 nonclinical isolates
   Processed fish, n = 1; salad, n = 1
CC321
 91
 3 (699 aa)
 17 clinical isolates and 78 nonclinical isolates
   Processed meat, n = 16; processed fish, n = 10; sandwiches, n = 3; processed dairy, n = 1; raw fish, n = 1; salad, n = 1; processing environment, n = 20; retail, n = 26
CC635
 439
 7 (561 aa)
 5 nonclinical isolates
   Processing environment, n = 5
ST13 35 15 (76 aa) 1 nonclinical isolate   Processed meat, n = 1

*CC, clonal complex; ID, identification number; PMSC, premature stop codon. †These allele IDs refer to IDs listed at https://bigsdb.pasteur.fr. ‡The classification of inlA PMSC types is based on Maury et al. (4) and Van Stelten et al. (13).

Main Article

References
  1. Scallan Walter  EJ, Cui  Z, Tierney  R, Griffin  PM, Hoekstra  RM, Payne  DC, et al. Foodborne illness acquired in the United States—major pathogens, 2019. Emerg Infect Dis. 2025;31:669–77.PubMedGoogle Scholar
  2. Ferreira  V, Wiedmann  M, Teixeira  P, Stasiewicz  MJ. Listeria monocytogenes persistence in food-associated environments: epidemiology, strain characteristics, and implications for public health. J Food Prot. 2014;77:150–70. DOIPubMedGoogle Scholar
  3. Maury  MM, Tsai  YH, Charlier  C, Touchon  M, Chenal-Francisque  V, Leclercq  A, et al. Uncovering Listeria monocytogenes hypervirulence by harnessing its biodiversity. Nat Genet. 2016;48:308–13. DOIPubMedGoogle Scholar
  4. Maury  MM, Bracq-Dieye  H, Huang  L, Vales  G, Lavina  M, Thouvenot  P, et al. Hypervirulent Listeria monocytogenes clones’ adaption to mammalian gut accounts for their association with dairy products. Nat Commun. 2019;10:2488. DOIPubMedGoogle Scholar
  5. Daeschel  D, Pettengill  JB, Wang  Y, Chen  Y, Allard  M, Snyder  AB. Genomic analysis of Listeria monocytogenes from US food processing environments reveals a high prevalence of QAC efflux genes but limited evidence of their contribution to environmental persistence. BMC Genomics. 2022;23:488. DOIPubMedGoogle Scholar
  6. He  Y, Xu  T, Li  S, Mann  DA, Britton  B, Oliver  HF, et al. Integrative assessment of reduced Listeria monocytogenes susceptibility to benzalkonium chloride in produce processing environments. Appl Environ Microbiol. 2022;88:e0126922. DOIPubMedGoogle Scholar
  7. Stout  A, Van Stelten-Carlson  A, Marquis  H, Ballou  M, Reilly  B, Loneragan  GH, et al. Public health impact of foodborne exposure to naturally occurring virulence-attenuated Listeria monocytogenes: inference from mouse and mathematical models. Interface Focus. 2020;10:20190046. DOIPubMedGoogle Scholar
  8. Samut  H, Mendez-Vallellanes  DV, Hoyt  H, Wirth  SE, Mingle  L, Sauders  BD, et al. Retrospective analysis of historical Listeria monocytogenes clinical isolates, New York, USA, 2000–2021. Emerg Infect Dis. 2025;31:1883–92. DOIPubMedGoogle Scholar
  9. Pightling  AW, Pettengill  JB, Luo  Y, Baugher  JD, Rand  H, Strain  E. Interpreting whole-genome sequence analyses of foodborne bacteria for regulatory applications and outbreak investigations. Front Microbiol. 2018;9:1482. DOIPubMedGoogle Scholar
  10. Jackson  KA, Gould  LH, Hunter  JC, Kucerova  Z, Jackson  B. Listeriosis outbreaks associated with soft cheeses, United States, 1998–2014. Emerg Infect Dis. 2018;24:1116–8. DOIPubMedGoogle Scholar
  11. Chen  Y, Gonzalez-Escalona  N, Hammack  TS, Allard  MW, Strain  EA, Brown  EW. Core genome multilocus sequence typing for identification of globally distributed clonal groups and differentiation of outbreak strains of Listeria monocytogenes. Appl Environ Microbiol. 2016;82:6258–72. DOIPubMedGoogle Scholar
  12. Pettengill  JB, Rand  H, Wang  SS, Kautter  D, Pightling  A, Wang  Y. Transient and resident pathogens: Intra-facility genetic diversity of Listeria monocytogenes and Salmonella from food production environments. PLoS One. 2022;17:e0268470.PubMedGoogle Scholar
  13. Van Stelten  A, Simpson  JM, Ward  TJ, Nightingale  KK. Revelation by single-nucleotide polymorphism genotyping that mutations leading to a premature stop codon in inlA are common among Listeria monocytogenes isolates from ready-to-eat foods but not human listeriosis cases. Appl Environ Microbiol. 2010;76:2783–90. DOIPubMedGoogle Scholar
  14. Moura  A, Lefrancq  N, Wirth  T, Leclercq  A, Borges  V, Gilpin  B, et al. Listeria CC1 Study Group. Emergence and global spread of Listeria monocytogenes main clinical clonal complex. Sci Adv. 2021;7:eabj9805. DOIPubMedGoogle Scholar
  15. Fotopoulou  ET, Jenkins  C, Barker  CR, Painset  A, Didelot  X, Simbo  A, et al. Genomic epidemiology of the clinically dominant clonal complex 1 in the Listeria monocytogenes population in the UK. Microb Genom. 2024;10:001155. DOIPubMedGoogle Scholar
  16. Ikhimiukor  OO, Mingle  L, Wirth  SE, Mendez-Vallellanes  DV, Hoyt  H, Musser  KA, et al. Long-term persistence of diverse clones shapes the transmission landscape of invasive Listeria monocytogenes. Genome Med. 2024;16:109. DOIPubMedGoogle Scholar
  17. Chen  Y, Gonzalez-Escalona  N, Hammack  TS, Allard  MW, Strain  EA, Brown  EW. Core genome multilocus sequence typing for identification of globally distributed clonal groups and differentiation of outbreak strains of Listeria monocytogenes. Appl Environ Microbiol. 2016;82:6258–72. DOIPubMedGoogle Scholar
  18. Coipan  CE, Friesema  IHM, van Hoek  AHAM, van den Bosch  T, van den Beld  M, Kuiling  S, et al. New insights into the epidemiology of Listeria monocytogenes—a cross-sectoral retrospective genomic analysis in the Netherlands (2010–2020). Front Microbiol. 2023;14:1147137. DOIPubMedGoogle Scholar
  19. Nightingale  KK, Windham  K, Martin  KE, Yeung  M, Wiedmann  M. Select Listeria monocytogenes subtypes commonly found in foods carry distinct nonsense mutations in inlA, leading to expression of truncated and secreted internalin A, and are associated with a reduced invasion phenotype for human intestinal epithelial cells. Appl Environ Microbiol. 2005;71:8764–72. DOIPubMedGoogle Scholar
  20. Magagna  G, Gori  M, Russini  V, De Angelis  V, Spinelli  E, Filipello  V, et al. Evaluation of the virulence potential of Listeria monocytogenes through the characterization of the truncated forms of Internalin A. Int J Mol Sci. 2023;24:10141. DOIPubMedGoogle Scholar
  21. Manuel  CS, Van Stelten  A, Wiedmann  M, Nightingale  KK, Orsi  RH. Prevalence and distribution of Listeria monocytogenes inlA alleles prone to phase variation and inlA alleles with premature stop codon mutations among human, food, animal, and environmental isolates. Appl Environ Microbiol. 2015;81:8339–45. DOIPubMedGoogle Scholar
  22. Fagerlund  A, Wagner  E, Møretrø  T, Heir  E, Moen  B, Rychli  K, et al. Pervasive Listeria monocytogenes is common in the Norwegian food system and is associated with increased prevalence of stress survival and resistance determinants. Appl Environ Microbiol. 2022;88:e0086122. DOIPubMedGoogle Scholar
  23. Wu  J, NicAogáin  K, McAuliffe  O, Jordan  K, O’Byrne  C. NicAogáin K, McAuliffe O, Jordan K, O’Byrne C. NicAogáin K, McAuliffe O, Jordan K, O’Byrne C. Phylogenetic and phenotypic analyses of a collection of food and clinical Listeria monocytogenes isolates reveal loss of function of sigma B from several clonal complexes. Appl Environ Microbiol. 2022;88:e0005122. DOIPubMedGoogle Scholar
  24. Pérez-Baltar  A, Pérez-Boto  D, Medina  M, Montiel  R. Genomic diversity and characterization of Listeria monocytogenes from dry-cured ham processing plants. Food Microbiol. 2021;99:103779. DOIPubMedGoogle Scholar
  25. Wagner  E, Fagerlund  A, Thalguter  S, Jensen  MR, Heir  E, Møretrø  T, et al. Deciphering the virulence potential of Listeria monocytogenes in the Norwegian meat and salmon processing industry by combining whole genome sequencing and in vitro data. Int J Food Microbiol. 2022;383:109962. DOIPubMedGoogle Scholar
  26. Amarasekara  NR, Swamy  AS, Paudel  SK, Jiang  W, Li  K, Shen  C, et al. Hypervirulent clonal complex (CC) of Listeria monocytogenes in fresh produce from urban communities. Front Microbiol. 2024;15:1307610. DOIPubMedGoogle Scholar
  27. Smith  A, Hearn  J, Taylor  C, Wheelhouse  N, Kaczmarek  M, Moorhouse  E, et al. Listeria monocytogenes isolates from ready to eat plant produce are diverse and have virulence potential. Int J Food Microbiol. 2019;299:23–32. DOIPubMedGoogle Scholar
  28. Chen  M, Cheng  J, Wu  Q, Zhang  J, Chen  Y, Zeng  H, et al. Prevalence, potential virulence, and genetic diversity of Listeria monocytogenes isolates from edible mushrooms in Chinese markets. Front Microbiol. 2018;9:1711. DOIPubMedGoogle Scholar
  29. Belias  A, Sullivan  G, Wiedmann  M, Ivanek  R. Factors that contribute to persistent Listeria in food processing facilities and relevant interventions: a rapid review. Food Control. 2022;133:133. DOIGoogle Scholar
  30. Sullivan  G, Orsi  RH, Estrada  E, Strawn  L, Wiedmann  M. Whole-genome sequencing-based characterization of Listeria isolates from produce packinghouses and fresh-cut facilities suggests both persistence and reintroduction of fully virulent L. monocytogenes. Appl Environ Microbiol. 2022;88:e0117722. DOIPubMedGoogle Scholar
  31. Estrada  EM, Hamilton  AM, Sullivan  GB, Wiedmann  M, Critzer  FJ, Strawn  LK. Prevalence, persistence, and diversity of Listeria monocytogenes and Listeria species in produce packinghouses in three U.S. states. J Food Prot. 2020;83:277–86. DOIPubMedGoogle Scholar
  32. Murugesan  L, Kucerova  Z, Knabel  SJ, LaBorde  LF. Predominance and distribution of a persistent Listeria monocytogenes clone in a commercial fresh mushroom processing environment. J Food Prot. 2015;78:1988–98. DOIPubMedGoogle Scholar
  33. Chen  Y, Simonetti  T, Peter  K, Jin  Q, Brown  E, LaBorde  LF, et al. Genetic diversity of Listeria monocytogenes isolated from three commercial tree fruit packinghouses and evidence of persistent and transient contamination. Front Microbiol. 2022;12:756688. DOIPubMedGoogle Scholar
  34. Simonetti  T, Peter  K, Chen  Y, Jin  Q, Zhang  G, LaBorde  LF, et al. Prevalence and distribution of Listeria monocytogenes in three commercial tree fruit packinghouses. Front Microbiol. 2021;12:652708. DOIPubMedGoogle Scholar
  35. Palacios  A, Vasser  M, Madad  A, Ivory  S, Edwards  L, Donovan  D, et al. Two concurrent outbreaks of Listeria monocytogenes infections linked to packaged salads, United States, 2014–2022. Emerg Infect Dis. 2025;31:2216–24. DOIPubMedGoogle Scholar

Main Article

1Preliminary results from this study were presented at the 2025 International Association for Food Protection Conference; July 27–30, 2025; Cleveland, Ohio, USA.

Page created: July 30, 2026
Page updated: August 17, 2026
Page reviewed: August 17, 2026
The conclusions, findings, and opinions expressed by authors contributing to this journal do not necessarily reflect the official position of the U.S. Department of Health and Human Services, the Public Health Service, the Centers for Disease Control and Prevention, or the authors' affiliated institutions. Use of trade names is for identification only and does not imply endorsement by any of the groups named above.
file_external