Retrospective Analysis of Historical Listeria monocytogenes Clinical Isolates, New York, USA, 2000-20211

Abstract

We used whole-genome sequencing data to investigate historical Listeria monocytogenes clinical (n = 1,046) and nonclinical (n = 1,325) isolates from New York, USA. Applying a threshold of <20 single-nucleotide polymorphism differences for single-linkage clustering, 321 clinical isolates clustered into 85 clusters ranging from 2-33 isolates per cluster. Fourteen clusters included isolates with outbreak codes (4 clusters with New York codes and 10 with multistate codes). Three New York outbreak codes were assigned to isolates that were genetically highly related and from cases <2 months apart. Fifteen clusters included isolates that were obtained >10 years apart; 33 clusters included isolates from the same or contiguous counties. Seventeen clusters included food and environmental isolates highly related to clinical isolates. These findings suggest that some listeriosis clusters can be local and span a long period, demonstrating the importance of investigating small, localized listeriosis cases with closely related isolates, even over long timeframes.

Keywords: Listeria monocytogenes; New York; REP strains; United States; bacteria; cgMLST; cluster; enteric infections; epidemiology; food safety; foodborne; listeriosis; outbreak; persistence; surveillance.

Figure 1

Distribution of timespan, number of clinical isolates, and number of counties among clusters in retrospective analysis of historical Listeria monocytogenes clinical isolates, New York, USA, 2000–2021. Clinical isolates that show a single-nucleotide polymorphism (SNP) distance of <20 SNPs to >1 of the other clinical isolates were grouped into a cluster; therefore, each cluster contains >2 clinical isolates. Each circle represents between 1 and 6 clusters, and the size of the circle is proportional to the number of clusters represented. Circles are color-coded according to the number of counties in each cluster. Timespan represents the interval between the first and the last collected clinical isolates in a cluster, measured in years with a month (1/12 of a year) as the minimum measurable unit. If the first and last collected clinical isolates in a cluster were obtained within the same month of the same year, the timespan for the cluster is zero.

Figure 2

Distribution of clinical isolates within clusters (i.e., the isolates with pairwise SNP distance ≤20) in retrospective analysis of historical Listeria monocytogenes clinical isolates, New York, USA, 2000–2021. A) Distribution of isolates by New York county during 2000–2021 (except for the New York City [NYC] area); B) distribute of isolates in NYC during 2000–2004. The boroughs of NYC (Manhattan, Brooklyn, Queens, the Bronx, and Staten Island) were separated from New York counties outside NYC because of the limited number of isolates available for these regions.

Figure 3

Maximum SNP distances observed in clusters in retrospective analysis of historical Listeria monocytogenes clinical isolates, New York, USA, 2000–2021. Timespan corresponds to the interval in years between an isolate pair where the maximum number of SNPs was observed among closely related isolates (i.e., SNPs <20). If the clinical isolates in a NY-cluster were collected within the same month of the same year, the timespan for the NY-cluster is 0. SNP, single-nucleotide polymorphism.

Figure 4

Pairwise SNP distances observed among 321 clinical isolates in clusters in retrospective analysis of historical Listeria monocytogenes clinical isolates, New York, USA, 2000–2021. Each data point represents a pair of isolates from the same county (A), contiguous counties (B), or noncontiguous counties (C). The timespan corresponds to the interval between each isolate pair within clusters in years with a month (1/12 of a year) as the minimum measurable unit. If the clinical isolates in a cluster were collected within the same month of the same year, the timespan for the cluster is 0. SNP, single-nucleotide polymorphism.

Figure 5

Number of food isolates obtained by food category in retrospective analysis of historical Listeria monocytogenes clinical isolates, New York, USA, 2000–2021. Some categories reflect limited metadata detail: food indicates unspecified food products, spread includes unspecified spreadable foods (e.g., cheese or other dips), and seafood dish includes prepared seafood dishes, whereas seafood indicates raw or unspecified seafood items.