Molecular Characterization of an Outbreak-involved Bacillus anthracis Strain Confirms the Spillover of Anthrax from West Africa

Abstract Background Anthrax, a zoonotic disease caused by the spore-forming bacterium Bacillus anthracis, remains a major global public health concern, especially in countries with limited resources. Sierra Leone, a West African country historically plagued by anthrax, has almost been out of report on this disease in recent decades, possibly due to limitations in diagnostic capabilities. In this study, we described a large-scale anthrax outbreak affecting both animals and humans and attempted to characterize the pathogen using molecular tools. Methods The causative agent of the animal outbreak was identified using the nanopore sequencing technique. Confirmation of suspected cases of cutaneous anthrax in humans, identified through active surveillance, was conducted using qPCR targeting both the chromosome and two virulent plasmids. Full-genome sequencing was accomplished by combining long-read and short-read sequencing methods. Subsequent phylogenetic analysis was performed based on the full-genome single nucleotide polymorphisms. Results The outbreak in Port Loko District, Sierra Leone, led to the death of 233 animals between March 26th and May 16th, 2022. We ruled out the initial suspicion of Anaplasma species and successfully identified B. anthracis as the causative agent of the outbreak. As a result of the government's prompt response, out of the 49 suspected human cases identified during the one-year active surveillance, only six human cases, all within the first month after the official declaration of the outbreak, were confirmed. The phylogenetic analysis indicated that the BaSL2022 isolate responsible for the outbreak was positioned in the A.Br.153 clade within the TransEuroAsian group of B. anthracis. Conclusions The anthrax outbreak identified in this study was unprecedented in scale in Sierra Leone. With regard to the shared predicament, the utilization of nanopore sequencing and molecular techniques to identify unknown diseases in Sierra Leone has provided valuable insights into emergency preparedness in similar nations. The A.Br.153 clade, where BaSL2022 was phylogenetically placed, is distinct from the existing West African lineages but may have been prevalent in a large area of West Africa for a long period and undergone evolutionary changes to adapt to novel geographical environments, as evidenced by the spillover of this strain to the United Kingdom and United States. Graphical Abstract