Assessing the genome level diversity of Listeria monocytogenes from contaminated ice cream and environmental samples linked to a listeriosis outbreak in the United States

Abstract

A listeriosis outbreak in the United States implicated contaminated ice cream produced by one company, which operated 3 facilities. We performed single nucleotide polymorphism (SNP)-based whole genome sequencing (WGS) analysis on Listeria monocytogenes from food, environmental and clinical sources, identifying two clusters and a single branch, belonging to PCR serogroup IIb and genetic lineage I. WGS Cluster I, representing one outbreak strain, contained 82 food and environmental isolates from Facility I and 4 clinical isolates. These isolates differed by up to 29 SNPs, exhibited 9 pulsed-field gel electrophoresis (PFGE) profiles and multilocus sequence typing (MLST) sequence type (ST) 5 of clonal complex 5 (CC5). WGS Cluster II contained 51 food and environmental isolates from Facility II, 4 food isolates from Facility I and 5 clinical isolates. Among them the isolates from Facility II and clinical isolates formed a clade and represented another outbreak strain. Isolates in this clade differed by up to 29 SNPs, exhibited 3 PFGE profiles and ST5. The only isolate collected from Facility III belonged to singleton ST489, which was in a single branch separate from Clusters I and II, and was not associated with the outbreak. WGS analyses clustered together outbreak-associated isolates exhibiting multiple PFGE profiles, while differentiating them from epidemiologically unrelated isolates that exhibited outbreak PFGE profiles. The complete genome of a Cluster I isolate allowed the identification and analyses of putative prophages, revealing that Cluster I isolates differed by the gain or loss of three putative prophages, causing the banding pattern differences among all 3 AscI-PFGE profiles observed in Cluster I isolates. WGS data suggested that certain ice cream varieties and/or production lines might have contamination sources unique to them. The SNP-based analysis was able to distinguish CC5 as a group from non-CC5 isolates and differentiate among CC5 isolates from different outbreaks/incidents.

Fig 1. Maximum likelihood tree of Cluster I isolates.

Isolates were obtained from Group I illnesses, food samples produced on Production line A of Facility I, and environmental samples from Facility I. The SNP matrix was generated using CFSAN029793 as the reference and contained 152 polymorphic loci. The tree uses midpoint rooting. Isolate identifier is followed by sample type, abbreviation of production date of the food samples, and available PFGE profile in the parenthesis. Isolates of the same PFGE profile are in the same color and isolates without PFGE information are in black. The 36 isolates without PFGE profiles were obtained from L. monocytogenes enumeration and growth kinetics studies [5, 25] and the method of isolation (direct plating (DP) or most probable number (MPN)) is listed in the parenthesis after each isolate ID. The 4 clinical isolates are highlighted in boxes. Blue arrows denote isolates from sandwiches produced in December 2014. Brown arrows denote isolates from scoops produced in March 2015. The bootstrap values for major clades are listed on top of the root of each clade. The AscI-PFGE profiles, the minimum and maximum numbers of SNPs with the medians in the parenthesis are listed near the root of each clade.)

Fig 2. AscI-PFGE banding pattern changes due to the gain/loss of prophages 2 and 3.

The AscI-PFGE profile and corresponding brief two-enzyme PFGE profiles are listed on the right of the gel images. The corresponding prophage gain/loss profiles are listed to the right. + indicates the gain of a prophage and–indicates the loss of a prophage. Isolates exhibiting GX6A16.0061 contained both prophages 2 and 3. The loss of prophage 3 resulted in the change of a ~275 Kbp fragment in the gel pattern of GX6A16.0061 to ~237 Kbp in the gel patterns of GX6A16.0026 and GX6A16.0020, and this ~237 Kbp fragment and a ~240 Kbp fragment formed a duplet. The loss of prophage 2 resulted in the change of a ~392 Kbp fragment in the gel patterns of GX6A16.0061 and GX6A16.0026 to ~352 Kbp in the gel pattern of GX6A16.0020. The loss of both prophages 2 and 3 resulted in the pattern change from GX6A16.0061 to GX6A16.0020.

Fig 3. Maximum likelihood tree of Cluster II isolates.

Isolates were collected from ice cream produced in Production line B of Facility I (Clade IIa), ice cream/environment from Facility II and Group II illnesses (Clade IIb). The SNP matrix was generated using CFSAN030683 as the reference and contained 169 polymorphic loci. The tree uses midpoint rooting. Isolate identifier is followed by sample type and abbreviation of collection date. Isolates from environmental samples are followed by the sample ID in the parenthesis. Environmental sample IDs ending with A and B indicate two colonies from the same sample. Purple color for an environmental sample ID indicates that for that sample one colony is inside Sub-clade IIb.1 and the other colony is outside Sub-clade IIb.1. Blue color for an environmental sample ID indicates that for that sample both colonies are either inside or outside Sub-clade IIb.1. Only one colony was picked from each of the two environmental samples (024 and 64) and their sample IDs are in blue. Isolates exhibiting PFGE profiles P10, P11, P12 and P13 are printed in blue, red, green and purple, respectively. The clinical isolates, all placed inside Sub-clade IIb.1, are highlighted in boxes. The bootstrap values of major clades are listed on top of the root of each clade. The minimum and maximum numbers of SNPs with median in the parenthesis are listed near the root of major clades.

Fig 4. Phylogenetic analysis of Clonal complex (CC) 5 strains from several outbreaks/incidents and other serogroup IIb isolates.

The tree uses midpoint rooting. Bootstrap values of major clades are listed near the root of each clade. Serogroup IIb strains differing from CC5 strains by two or more multilocus sequence typing (MLST) alleles were used for comparison. CC5 isolates formed a cluster, within which isolates from each of the cantaloupe, cheese, stone fruit, and ice cream outbreak/incident were all sequence type (ST) 5 and formed distinct clades. The PFGE-matched, epidemiologically unrelated isolates for Clusters I and II of the ice cream outbreak were distinguished from Cluster I and II isolates. The non-ST5 CC5 strain (CFSAN028312, ST745) is placed outside clades representing all other incidents. Within the CC5 cluster, ST5 isolates do not form a distinct clade to be separated from the ST745 strain.