The roles of antimicrobial resistance, phage diversity, isolation source and selection in shaping the genomic architecture of Bacillus anthracis

Abstract

Bacillus anthracis, the causative agent of anthrax disease, is a worldwide threat to livestock, wildlife and public health. While analyses of genetic data from across the globe have increased our understanding of this bacterium’s population genomic structure, the influence of selective pressures on this successful pathogen is not well understood. In this study, we investigate the effects of antimicrobial resistance, phage diversity, geography and isolation source in shaping population genomic structure. We also identify a suite of candidate genes potentially under selection, driving patterns of diversity across 356 globally extant B. anthracis genomes. We report ten antimicrobial resistance genes and 11 different prophage sequences, resulting in the first large-scale documentation of these genetic anomalies for this pathogen. Results of random forest classification suggest genomic structure may be driven by a combination of antimicrobial resistance, geography and isolation source, specific to the population cluster examined. We found strong evidence that a recombination event linked to a gene involved in protein synthesis may be responsible for phenotypic differences between comparatively disparate populations. We also offer a list of genes for further examination of B. anthracis evolution, based on high-impact single nucleotide polymorphisms (SNPs) and clustered mutations. The information presented here sheds new light on the factors driving genomic structure in this notorious pathogen and may act as a road map for future studies aimed at understanding functional differences in terms of B. anthracis biogeography, virulence and evolution.

Interactions between commensal Enterococcus faecium and Enterococcus lactis and clinical isolates of Enterococcus faecium

“…S3 ). Out of the other nine strains which showed at least one grade one inhibition after proteinase K treatment, three strains did not contain prophage regions (51269068, K59-55 and K60-14), four contained one prophage region each (51269070: Entero_phiFL1A, 51269769: Lister_2389 (Pope et al 2007 ), K59-50: Lister_2389, K60-13: Entero_IME_EFm5 (Gong et al 2016 )) and two contained multiple prophage regions (K59-27: Entero_IME_EFm5 (Gong et al 2016 ); Entero_phiFL1A (Yasmin et al 2010 ), 51270828: Bacill_phBC6A52 (Bruce et al 2021 ); Entero_IME_EFm5; Staphy_SPbeta_like (Oliveira et al 2019 )). Since we suspected that phages could be involved in the phenotype of the supernatants of 51276488, K59-36 and K60-7, we expected that single plaques would be visible upon dilution of the native concentrated supernatants.…”

Lysins as a powerful alternative to combat Bacillus anthracis

“…Recently, a large-scale analysis of a global collection of 356 B. anthracis genomes has revealed the presence of ten AMR genes with five of them being notably widespread across the majority of examined isolates (Bruce et al 2021 ). Although the presence of such genes does not always translate to actual resistance (Bruce et al 2021 ), it underscores the importance of alerting medical professionals to the potential emergence of a significant treatment challenge.…”

“…Recently, a large-scale analysis of a global collection of 356 B. anthracis genomes has revealed the presence of ten AMR genes with five of them being notably widespread across the majority of examined isolates (Bruce et al 2021 ). Although the presence of such genes does not always translate to actual resistance (Bruce et al 2021 ), it underscores the importance of alerting medical professionals to the potential emergence of a significant treatment challenge. Monitoring the occurrence of rare B. anthracis AMR genes in specific regions is crucial for pinpointing areas where the situation is particularly problematic and may necessitate more concerted efforts in treatment protocols (Bruce et al 2021 ).…”

“…Although the presence of such genes does not always translate to actual resistance (Bruce et al 2021 ), it underscores the importance of alerting medical professionals to the potential emergence of a significant treatment challenge. Monitoring the occurrence of rare B. anthracis AMR genes in specific regions is crucial for pinpointing areas where the situation is particularly problematic and may necessitate more concerted efforts in treatment protocols (Bruce et al 2021 ). Interestingly, it was observed that the use of a chemical mutagen substantially increased the frequency of antibiotic resistance in B. cereus RSVF1.…”

One Health: a holistic approach for food safety in livestock

“…Limited surveillance in resource-poor countries further complicates epidemiological data collection. Additionally, antibiotic resistance in B. anthracis is concerning [ 29 ], with 10 antimicrobial-resistant genes identified in a global genome-wide dataset [ 30 ]. The One Health concept emphasizes collaboration between experts in clinical and veterinary medicine, epidemiology, microbiology, genetics, immunology and ecology to develop interdisciplinary plans to combat this challenging, multi-host and deadly zoonotic pathogen [ 31 ].…”