Epidemiological and phylogenetic analysis of anthrax in Kazakhstan in 2024

Anthrax remains an important zoonotic disease in Kazakhstan due to the persistence of environmental reservoirs and long-standing endemic foci. Despite ongoing surveillance, the epidemiological characteristics and genetic diversity of circulating Bacillus anthracis strains in the country remain incompletely understood.

A retrospective epidemiological and phylogenetic investigation of anthrax outbreaks reported in Kazakhstan during 2024 was conducted. Epidemiological data were collected for all laboratory-confirmed human cases and associated outbreak foci. Confirmation of infection was performed by PCR, and B. anthracis isolates were obtained from clinical, environmental and animal-associated samples. Whole-genome sequencing and core-genome single nucleotide polymorphism (cgSNP) analysis were used to characterize the genetic relationships among isolates and to determine their phylogenetic placement.

Nine anthrax outbreaks were identified across four regions of Kazakhstan (Almaty, Zhambyl, Atyrau, and West Kazakhstan), resulting in 20 confirmed human cases. All patients were male, with the highest proportion occurring among individuals aged 36-55 years (45%). The mean patient age was 43.9 years (range: 16-64 years). Most infections were associated with slaughtering infected livestock (65%), followed by handling contaminated meat (15%). PCR confirmed infection in all 20 human cases. Culture yielded 17 human-derived B. anthracis isolates from 14 patients and 17 environmental/animal-derived isolates, resulting in 34 isolates in total. Of these, 22 representative isolates underwent whole-genome sequencing. Phylogenetic analysis revealed the circulation of two major lineages. Isolates from Atyrau and West Kazakhstan clustered within the Trans-Eurasian (TEA/STI) lineage. Atyrau isolates formed a tight cluster differing by only 21-32 cgSNPs, consistent with a shared epidemiolocal source, whereas the West Kazakhstan isolate was highly divergent. Zhambyl and Almaty region belonged to the A.Br.Ames lineage but diverged into two distinct sublineages. Zhambyl region isolates demonstrated minimal divergence from the global reference genome Ames Ancestor, differing by only 16-31 SNPs. Almaty region isolates formed an endemic subclone, separated from the reference group by approximately 114 SNPs. Comparison with the Ames Ancestor and Sterne reference strains demonstrated substantial genetic divergence.

Anthrax outbreaks in Kazakhstan during 2024 were primarily associated with livestock exposure and occurred within established endemic regions. Whole-genome sequencing revealed the coexistence of distinct TEA and Ames lineages, including evidence of persistent local transmission and long-term evolutionary stability of endemic B. anthracis populations. These findings enhance understanding of anthrax epidemiology in Central Asia and support the integration of genomic surveillance into national outbreak investigation programs.