Analysis of the Listeria monocytogenes Population Structure among Isolates from 1931 to 2015 in Australia

Abstract

Listeriosis remains among the most important bacterial illnesses, with a high associated mortality rate. Efforts to control listeriosis require detailed knowledge of the epidemiology of the disease itself, and its etiological bacterium, Listeria monocytogenes. In this study we provide an in-depth analysis of the epidemiology of 224 L. monocytogenes isolates from Australian clinical and non-clinical sources. Non-human sources included meat, dairy, seafood, fruit, and vegetables, along with animal and environmental isolates. Serotyping, Multi-Locus Sequence Typing, and analysis of inlA gene sequence were performed. Serogroups IIA, IIB, and IVB comprised 94% of all isolates, with IVB over-represented among clinical isolates. Serogroup IIA was the most common among dairy and meat isolates. Lineage I isolates were most common among clinical isolates, and 52% of clinical isolates belonged to ST1. Overall 39 STs were identified in this study, with ST1 and ST3 containing the largest numbers of L. monocytogenes isolates. These STs comprised 40% of the total isolates (n = 90), and both harbored isolates from clinical and non-clinical sources. ST204 was the third most common ST. The high prevalence of this group among L. monocytogenes populations has not been reported outside Australia. Twenty-seven percent of the STs in this study contained exclusively clinical isolates. Analysis of the virulence protein InlA among isolates in this study identified a truncated form of the protein among isolates from ST121 and ST325. The ST325 group contained a previously unreported novel mutation leading to production of a 93 amino acid protein. This study provides insights in the population structure of L. monocytogenes isolated in Australia, which will contribute to public health knowledge relating to this important human pathogen.

Keywords: Listeria monocytogenes; MLST; SNP typing; inlA; serotype.

FIGURE 1

Distribution of different serogroups among isolates from: (A) all sources; (B) human clinical; (C) dairy; (D) meat; (E) animal; and (F) vegetable sources. Numbers of isolates are marked for each serogroup segment.

FIGURE 2

Distribution of STs identified from each source, with increasing circle size representing a larger number of isolates of that ST. Clonal complexes are partitioned (gray shading, and indicated by gray text). Connecting lines infer phylogenetic relatedness in terms of number of allelic differences (thick solid, 1; thin solid in partition, 2; thin solid outside partition, 3; broken, 4–6; dotted, no allelic matches). ST202 is lineage III.

FIGURE 3

Distribution of STs across the main categories included in this study (i.e., C, clinical; NC, non-clinical; D, dairy; M, meat). Numbers represent the number of different STs unique to, or shared by, the relevant categories. (A) Clinical versus non-clinical ST distributions. (B) Clinical versus dairy versus meat ST distributions.

FIGURE 4

Phylogenetic analysis of inlA gene sequences among isolates in this study. Lineage I STs are labeled in blue, lineage II STs are labeled in black, and lineage III in green. Red coloring in pie charts indicates the proportion of clinical isolates among all isolates of that ST. ¹ST121 isolates contained a PMSC at AA⁴⁹²; ²ST325 isolates contained a PMSC at AA⁹³.

FIGURE 5

Phylogenetic analysis of serogroup IIA core genome SNPs. CCs and STs containing multiple isolates are indicated by labeled rounded rectangles (the CC or ST is labeled on the outside right, and the number of SNPs is indicated by the number on the inside right of the rectangle). Isolates linked by colored shading have a known epidemiological linkage, with the number indicating the highest number of SNPs when comparing isolates in that subset.

FIGURE 6

Phylogenetic analysis of serogroup IIB core genome SNPs. CCs and STs containing multiple isolates are indicated by labeled rounded rectangles (the CC or ST is labeled on the outside right, and the number of SNPs is indicated by the number on the inside right of the rectangle). Isolates linked by colored shading are epidemiologically linked, with the number indicating the highest number of SNPs when comparing isolates in that subset.

FIGURE 7

Phylogenetic analysis of serogroup IIC core genome SNPs. STs containing multiple isolates are indicated by labeled rounded rectangles (the CC or ST is labeled on the outside right, and the number of SNPs is indicated by the number on the inside right of the rectangle).

FIGURE 8

Phylogenetic analysis of serogroup IVB core genome SNPs. CCs and STs containing multiple isolates are indicated by labeled rounded rectangles (the CC or ST is labeled on the outside right, and the number of SNPs is indicated by the number on the inside right of the rectangle). Isolates linked by colored shading are epidemiologically linked, with the number indicating the highest number of SNPs when comparing isolates in that subset.