Whole‐genome sequencing reveals Listeria monocytogenes diversity and allows identification of long‐term persistent strains in Brazil

Anderson C Camargo (1) , Alexandra Moura (2) , Johannetsy Avillan (3) , Nicole Herman (4) , Adelle P Mcfarland (5) , Srinand Sreevatsan (6) , Douglas R Call (3) , Joshua J Woodward (5) , Marc Lecuit (2, 7, 8, 9, 10) , Luís A Nero (1)

1 UFV - Universidade Federal de Viçosa = Federal University of Viçosa
2 Biologie des Infections - Biology of Infection
3 Paul G. Allen School for Global Animal Health [WSU, USA]
4 UMN - University of Minnesota [Twin Cities]
5 University of Washington [Seattle]
6 Michigan State University [East Lansing]
7 UPD5 - Université Paris Descartes - Paris 5
8 CHU Necker - Enfants Malades [AP-HP]
9 Service des Maladies infectieuses et tropicales [CHU Necker]
10 Imagine - U1163 - Imagine - Institut des maladies génétiques (IHU)

Advances in whole-genome sequencing (WGS) technologies have documented genetic diversity and epidemiology of the major foodborne pathogen Listeria monocytogenes (Lm) in Europe and North America, but data concerning South America are scarce. Here, we examined the population structure and genetic diversity of this major foodborne pathogen collected in Brazil. Based on core genome multilocus sequence typing (cgMLST), isolates from lineages I (n = 22; 63%) and II (n = 13; 37%) were distributed into 10 different sublineages (SLs) and represented 31 new cgMLST types (CTs). The most prevalent SLs were SL9 (n = 9; 26%), SL3 (n = 6; 17%) and SL2 and SL218 (n = 5; 14%). Isolates belonging to CTs L2-SL9-ST9-CT4420 and L1-SL315-ST520-CT4429 were collected 3 and 9 years apart, respectively, revealing long-term persistence of Lm in Brazil. Genetic elements associated with stress survival were present in 60% of isolates (57% SSI-1 and 3% SSI-2). Pathogenic islands were present in 100% (LIPI-1), 43% (LIPI-3) and 6% (LIPI-4) of the isolates. Mutations leading to premature stop codons were detected in the prfA and inlA virulence genes. This study is an important contribution to understanding the genomic diversity and epidemiology of Lm in South America. In addition, the results highlight the importance of using WGS to reveal Lm long-term persistence.

Keywords: Listeria monocytogenes; whole genome sequencing; molecular typing; virulence; resistance; persistence

Domains: Life Sciences [q-bio]; Human health and pathology; Life Sciences [q-bio]; Human health and pathology; Emerging diseases; Life Sciences [q-bio]; Human health and pathology; Infectious diseases; Life Sciences [q-bio]; Microbiology and Parasitology; Life Sciences [q-bio]; Microbiology and Parasitology; Bacteriology

Anderson C Camargo, Alexandra Moura, Johannetsy Avillan, Nicole Herman, Adelle P Mcfarland, et al.. Whole‐genome sequencing reveals Listeria monocytogenes diversity and allows identification of long‐term persistent strains in Brazil. Environmental Microbiology, 2019, 21 (12), pp.4478-4487. ⟨10.1111/1462-2920.14726⟩. ⟨pasteur-02562190⟩