A clade of Listeria monocytogenes serotype 4b variant strains linked to recent listeriosis outbreaks associated with produce from a defined geographic region in the US

Abstract

Four listeriosis incidences/outbreaks, spanning 19 months, have been linked to Listeria monocytogenes serotype 4b variant (4bV) strains. Three of these incidents can be linked to a defined geographical region, while the fourth is likely to be linked. In this study, whole genome sequencing (WGS) of strains from these incidents was used for genomic comparisons using two approached. The first was JSpecies tetramer, which analyzed tetranucleotide frequency to assess relatedness. The second, the CFSAN SNP Pipeline, was used to perform WGS SNP analyses against three different reference genomes to evaluate relatedness by SNP distances. In each case, unrelated strains were included as controls. The analyses showed that strains from these incidents form a highly related clade with SNP differences of ≤101 within the clade and >9000 against other strains. Multi-Virulence-Locus Sequence Typing, a third standardized approach for evaluation relatedness, was used to assess the genetic drift in six conserved, known virulence loci and showed a different clustering pattern indicating possible differences in selection pressure experienced by these genes. These data suggest a high degree of relatedness among these 4bV strains linked to a defined geographic region and also highlight the possibility of alterations related to adaptation and virulence.

Antimicrobial Susceptibility and Multilocus Sequence Typing ofListeria monocytogenesIsolated Over 11 Years from Food, Humans, and the Environment in Italy

“…On the contrary, other authors found that serotype 1/2a isolates were more frequently resistant to ciprofloxacin compared to serotype 4b (Safdar and Armstrong, 2003;Kovacevic et al, 2013). Besides, the association of antimicrobial resistance or reduced susceptibility to serotype 4b is of concern, since strains belonging to this serotype were associated to outbreaks (Althaus et al, 2017;Buchanan et al, 2017;Burall et al, 2017).…”

Current Trends in Foodborne Human Listeriosis

“…This was very unusual given the demographics of listeriosis cases are comprised mostly of elderly and immunocompromised patients 15) . A series of WGS analysis of the 4bV isolates from these outbreaks by JSpecies, Center for Food Safety and Nutrition (CFSAN) WGS Pipeline and Basic Local Alignment Search Tool (BLAST) analysis also revealed that these isolates belonged to a distinct clade and were genetically well separated from 4b and 4bV strains reported from other outbreaks, including 4b isolates recovered from the caramel apple-associated outbreak 21) . All three different analytical tools resulted in a very similar conclusion although the Single Nucleotide Polymorphism (SNP) analyses provided much more resolution in the analysis.…”

“…It is interesting to note that with the implementation of PFGE-and WGSbased typing systems, we are discovering more outbreaks and discovering them earlier, resulting in fewer cases than the outbreaks before the PulseNet era. Recently, Burall et al 21) described a series of outbreaks involving caramel apple, cheese, stone fruit and bagged salad and showed that all these outbreaks/incidents were caused by serotype 4bV, though the caramel apple outbreak also involved cases caused by serotype 4b strains. The most interesting is the caramel apple outbreak 22) , which caused 35 illnesses and seven deaths encompassing 12 states ( Table 3).…”

“…All three different analytical tools resulted in a very similar conclusion although the Single Nucleotide Polymorphism (SNP) analyses provided much more resolution in the analysis. Another significant finding from that work 21) was the observation with Multi Virulence Loci Sequence Typing (MVLST) analysis, utilizing a limited set of defined virulence gene sequences, that selective pressures on a subset of genes may have played a significant role in our ability to understand the strain-to-strain variability and thus the evolution of newer traits. Furthermore, the analysis reported by Burall et al 21) clearly showed that these highly related 4bV strains may have originated from a small geographical region in the USA.…”

“…Another significant finding from that work 21) was the observation with Multi Virulence Loci Sequence Typing (MVLST) analysis, utilizing a limited set of defined virulence gene sequences, that selective pressures on a subset of genes may have played a significant role in our ability to understand the strain-to-strain variability and thus the evolution of newer traits. Furthermore, the analysis reported by Burall et al 21) clearly showed that these highly related 4bV strains may have originated from a small geographical region in the USA. Whether this was due to shared agricultural practices, supplies, and/or equipment leading to cross-contamination or due to the natural presence of this strain throughout this geographical region is not clear at this point.…”