Abstract
Recently developed nanopore sequencing technologies offer a unique opportunity to rapidly close the genome and to identify complete sequences of mobile genetic elements (MGEs). In this study, 17 isolates of Listeria monocytogenes (Lm) epidemic clone II (ECII) from seven ready-to-eat meat or poultry processing facilities, not known to be associated with outbreaks, were shotgun sequenced, and among them, five isolates were further subjected to long-read sequencing. Additionally, 26 genomes of Lm ECII isolates associated with three listeriosis outbreaks in the U.S. and South Africa were obtained from the National Center for Biotechnology Information (NCBI) database and analyzed to evaluate if MGEs may be used as a high-resolution genetic marker for identifying and sourcing the origin of Lm. The analyses identified four comK prophages in 11 non-outbreak isolates from four facilities and three comK prophages in 20 isolates associated with two outbreaks that occurred in the U.S. In addition, three different plasmids were identified among 10 non-outbreak isolates and 14 outbreak isolates. Each comK prophage and plasmid was conserved among the isolates sharing it. Different prophages from different facilities or outbreaks had significant genetic variations, possibly due to horizontal gene transfer. Phylogenetic analysis showed that isolates from the same facility or the same outbreak always closely clustered. The time of most recent common ancestor of the Lm ECII isolates was estimated to be in March 1816 with the average nucleotide substitution rate of 3.1 × 10−7 substitutions per site per year. This study showed that complete MGE sequences provide a good signal to determine the genetic relatedness of Lm isolates, to identify persistence or repeated contamination that occurred within food processing environment, and to study the evolutionary history among closely related isolates.
Highlights
Listeriosis, a foodborne illness caused by Listeria monocytogenes (Lm), is a rare disease but can be severe
Seventeen isolates of Lm epidemic clone II (ECII) recovered from seven RTE meat or poultry processing facilities (A, B, C, D, E, F, and G) in the U.S between 2002 and 2009 (Table 1) were sequenced by Illumina MiSeq using the whole genome shotgun strategy; these isolates are not known to be associated with any outbreaks and were referred to as non-outbreak isolates hereinafter
Two “intact” prophages of 62.2 Kb and 31 Kb were predicted in the middle of relatively large shotgun contigs (141 Kb and 148 Kb) from YA00079283 and we likely identified the complete region of each prophage
Summary
Listeriosis, a foodborne illness caused by Listeria monocytogenes (Lm), is a rare disease but can be severe. Meningitis, encephalitis, among other conditions and in severe cases, die. Among the most common foodborne illnesses, listeriosis exhibits the highest mortality rate approaching 30%, with pregnant women, newborn infants, and the immunocompromised population at the highest risk [1]. Even though invasive listeriosis infections are not common in healthy individuals, it is important to understand the potential public health impact of Lm contamination [1]. Strains from many listeriosis outbreaks belong to a small number of clones, designated as epidemic clones (ECs) or clonal complexes (CCs) [3]. Among the ECs, epidemic clone II (ECII), known as clonal complex
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