Identification of Anthrax as the Cause of a Cluster of Unexplained Deaths, Uganda, 2023: The Role of Metagenomic Next-Generation Sequencing and Postmortem Specimens

Abstract

Between April and November 2023, 27 unexplained human deaths that presented with swelling of the arms, skin sores with black centers, difficulty in breathing, obstructed swallowing, headaches, and other body aches were reported in Kyotera District, Uganda by the Public Health Emergency Operations Center. Subsequently, the death of cattle on farms and the consumption of carcass meat by some residents were also reported. Field response teams collected clinical/epidemiological data and autopsy samples to determine the cause of deaths. Metagenomic next-generation sequencing (mNGS) and target enrichment sequencing conducted on postmortem samples confirmed Bacillus anthracis, the etiological agent of anthrax disease, as the cause of the deaths. Applying mNGS to autopsy specimens is useful as a retrospective tool for identifying high-consequence pathogens during suspected outbreaks of unknown etiology.

Figure 1.

Map showing Kyotera District, where anthrax was recently confirmed by metagenomic next-generation sequencing on postmortem samples in 2023. Other districts where anthrax outbreaks have previously been reported over the years are also highlighted. These include Arua, Kween, Kiruhura, Sheema, and that districts that cover Queen Elizabeth National Park (QENP) (Kasese, Kamwenge, Rubirizi, and Rukungiri).

Figure 2.

(A) Mapping and coverage plot for first sample deep sequenced in August 2023 and confirmed positive for Bacillus anthracis. The graph shows reads mapped to a B. anthracis reference genome (accession no. CP066168.1). (B) Skin ulcer or sore on the hand/arm with a black coloration or center was a common sign in most affected individuals before death. Other signs/symptoms included fever, vomiting, diarrhea, chest discomfort, difficulty in breathing, profuse sweating, and body aches. (C) Postmortem findings showed brain hemorrhage in some of the suspected cases that were later confirmed by metagenomic next-generation sequencing to have died of anthrax. Common to both cases was brain hemorrhage with increased intracranial pressure. (D) Mapping and coverage plots for additional samples deep sequenced in November 2023 and confirmed positive for B. anthracis. The graph shows reads mapped to a B. anthracis reference genome (accession no. CP066168.1) as in (A).