Molecular epidemiology of panton valentine leukocidin-producing Staphylococcus aureus infections, Djibouti, 2018-2023

Abstract

Between 2018 and 2023, a genomic study was conducted in a military camp in Djibouti to investigate the molecular epidemiology of Panton-Valentine Leukocidin-producing Staphylococcus aureus. Among 43 isolates, Sequence Type 152 was predominant (72%), mainly associated with spa types t355 and t4235. Core-genome Multi-Locus Sequence Typing revealed two concurrent transmission dynamics: localized inter-human outbreaks and repeated introductions from external sources. Comparative genomics with other African Sequence Type 152 isolates showed similar levels of diversity, suggesting a widespread continental dissemination. These findings highlight the importance of genomic surveillance to better understand and control the spread of this virulent lineage in Africa.

Fig 1. ST152 PVL-producing S. aureus phylogenetic tree and allelic distances from the Djibouti outbreak.

The Djibouti ST152 S. aureus core-genome alignment-based phylogenetic tree is displayed on the left side of the figure, alongside the associated genomic metadata. The designation of the spa type is initially determined by the branch label, as indicated by the following colors: blue (t355), light blue (t4235), orange (t1299), and light orange (t4346). The isolation date of the bacterial strain is represented in the mm/dd/yyyy format. Stars labels represent patients status (red: soldier: white: civilian). The heatmap in the central panel illustrates cgMLST-based allelic distances, ranging from 1 to 159, represented by a color gradient from brown (25) to light blue (159). The black tiles represent distances below 24, which correspond to the hierCC24 affiliation. The short-period and the long-period hierCC24 assignments are represented by black squares and circles, respectively.

Fig 2. ST152 PVL-producing S. aureus molecular epidemiology in Africa.

The left side of the figure illustrates the distribution of genomes across the African continent. The colored circles indicate the countries from which the genomes were derived for the purpose of genomic comparison by cgMLST. The size of the circles is proportional to the number of genomes. On the right side, the corresponding minimum spanning tree is plotted. Dotted lines represent distances exceeding 50 alleles, and genomes are collapsed when distances are below 24 to represent hierCC24. The size of the circles is correlated with the number of genomes within hierCC24. The country of origin is depicted with the same colors as the map on the left side. The map was created using the rnaturalearth v1.0.1 and rnaturalearthdata v1.0.0 R packages with an open-source, copyright-free Africa map provided by Natural Earth (http://www.naturalearthdata.com).