Article
Microbiology
Hanka Brangsch, Anatolii Golovko, Nataliia Pinchuk, Oleg Deriabin, Tetiana Kyselova, Joerg Linde, Falk Melzer, Mandy Carolina Elschner
Summary: This study investigates the genetic diversity of Bacillus anthracis strains in Ukraine and highlights the importance of surveillance and prevention methods for anthrax outbreaks. The results provide insights into the global distribution of B. anthracis genotypes.
Article
Microbiology
Mostafa Y. Abdel-Glil, Alexandra Chiaverini, Giuliano Garofolo, Antonio Fasanella, Antonio Parisi, Dag Harmsen, Keith A. Jolley, Mandy C. Elschner, Herbert Tomaso, Jorg Linde, Domenico Galante
Summary: A novel cgMLST scheme for Bacillus anthracis has been developed, providing high-resolution strain genotyping. The scheme has been evaluated on 584 genomes from 50 countries and confirmed the genetic distances and clades of B. anthracis. It can be used for rapid and harmonized interlaboratory comparisons, essential for global surveillance and outbreak analysis.
JOURNAL OF CLINICAL MICROBIOLOGY
(2021)
Article
Microbiology
Li Maria Ma, Nicolas Lopez, Guodong Zhang
Summary: This article reports the draft whole-genome sequences of four Bacillus strains selected as potential probiotics for poultry. These genome sequences will provide a foundation for further characterization and understanding of their probiotic attributes.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2023)
Article
Microbiology
Olga Bassy, Markus Antwerpen, Maria Victoria Ortega-Garcia, Maria Jesus Ortega-Sanchez, Jose Antonio Bouzada, Juan Carlos Cabria-Ramos, Gregor Grass
Summary: In this study, researchers sequenced and characterized 29 new B. anthracis isolates from outbreaks in west central and central Spain in 2021. They identified a new sub-clade, A.Br.11/ESPc, which is a sister group of the American A.Br.WNA lineage. The diversity of Spanish B. anthracis and its phylogenetic links to European or American relatives remain poorly understood.
Article
Microbiology
Laura M. Carroll, Chung K. Marston, Cari B. Kolton, Christopher A. Gulvik, Jay E. Gee, Zachary P. Weiner, Jasna Kovac
Summary: This study characterized three B. cereus s.l. isolates associated with two anthrax cases in welders in the United States in 2020. The genomes of these isolates belonged to different species, with two being closely related to B. tropicus and one being most similar to B. anthracis.
Article
Multidisciplinary Sciences
Chunyu Liu, Jessica L. Fetterman, Xianbang Sun, Kaiyu Yan, Poching Liu, Yan Luo, Jun Ding, Jun Zhu, Daniel Levy
Summary: This study compared mtDNA sequence variants between LCL and whole blood samples. The results showed that most homoplasmic variants were present in both LCL and blood samples, while most heteroplasmic variants were unique to either LCL or blood samples. LCL samples had a higher number of heteroplasmic variants compared to whole blood samples, but a similar number of homoplasmic variants. Additionally, LCL samples tended to have lower levels of heteroplasmy.
SCIENTIFIC REPORTS
(2022)
Article
Microbiology
Noah Bryan, Rebecca Anderson, Opeyemi U. Lawal, Valeria R. Parreira, Lawrence Goodridge
Summary: In this study, we report the draft genome sequence of Bacillus anthracis strain N1, which was isolated from a recreational freshwater lake and found to carry multiple antibiotic resistance genes and biosynthetic gene clusters.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2023)
Article
Biotechnology & Applied Microbiology
Yanchun Wang, Shuli Sang, Xin Zhang, Haoxia Tao, Qing Guan, Chunjie Liu
Summary: Researchers have developed a new method to edit the genome of Bacillus anthracis using the AsCas12f1 nuclease from Acidibacillus sulfuroxidans. The method shows high efficiency and is capable of large-fragment deletion. The length of the homologous arms of the donor DNA is closely related to the editing efficiency. A two-plasmid system was also constructed for potential multi-gene modification.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
Article
Biochemical Research Methods
Na Lu, Yi Qiao, Pengfei An, Jiajian Luo, Changwei Bi, Musheng Li, Zuhong Lu, Jing Tu
Summary: Multiple displacement amplification (MDA) is widely used for whole genome amplification, but the formation of chimeric sequences in MDA interferes with bioinformatics analysis. This study developed a pipeline for recognizing and restoring chimeras in long-read sequencing data, which can reduce the influence of chimeras and improve the analysis of structural variation.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Biotechnology & Applied Microbiology
Joerg Linde, Hanka Brangsch, Martin Hoelzer, Christine Thomas, Mandy C. Elschner, Falk Melzer, Herbert Tomaso
Summary: This study evaluated the application of Oxford Nanopore Technology (ONT) long-read sequencing in highly pathogenic bacteria and found that combining data from ONT and Illumina can be used for high-resolution genotyping, but further improvement is needed for certain bacteria.
Article
Biotechnology & Applied Microbiology
Ahmer Bin Hafeez, Karolina Pelka, Kamila Buzun, Randy Worobo, Piotr Szweda
Summary: This study aimed to analyze the whole genome and assess the antimicrobial potential of bacterial isolates from honey in northern Poland. A total of 132 strains were obtained from three honey samples, and the antimicrobial activity of CFAM was used to select strains for detailed genomic investigation. Two isolates were classified as Bacillus paralicheniformis and one isolate as Bacillus subtilis, and all three isolates showed potential as producers of antimicrobial compounds.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2023)
Article
Multidisciplinary Sciences
Lauren A. Choate, Gilad Barshad, Pierce W. McMahon, Iskander Said, Edward J. Rice, Paul R. Munn, James J. Lewis, Charles G. Danko
Summary: The study reveals potential human genome adaptation to anthrax disease and genetic signatures indicating recent positive selection on European-specific decrease in ANTXR2 expression. This suggests that humans adapted to anthrax disease due to early ecological changes associated with hunting and scavenging, and a second period of adaptation after the rise of modern agriculture.
NATURE COMMUNICATIONS
(2021)
Article
Environmental Sciences
Huichun Xiang, Yanhui He, Xiaobo Wang, Jianwen Wang, Tao Li, Shuangxi Zhu, Ziyan Zhang, Xiaolin Xu, Zhansheng Wu
Summary: Using rhizobacteria as biological fertilizer is expanding in agriculture as substitutes for chemical fertilizers. Bacillus subtilis SL-44 can produce beneficial secondary metabolites and secrete antifungal substances, effectively controlling plant diseases. Genome-wide analysis of SL-44 revealed potential to produce bioantagonistic natural products and growth-promoting metabolites, which may facilitate further research into effective therapies for harmful diseases.
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
(2023)
Article
Microbiology
Gregor Fiedler, Anna-Delia Herbstmann, Etienne Doll, Mareike Wenning, Erik Brinks, Jan Kabisch, Franziska Breitenwieser, Martin Lappann, Christina Boehnlein, Charles M. A. P. Franz
Summary: Genetic heterogeneity of Heyndrickxia sporothermodurans was evaluated using whole genome sequencing. Results showed that Heyndrickxia vini should be reclassified as Heyndrickxia sporothermodurans, with the genome containing numerous mobile elements presumably related to spore heat tolerance.
Article
Biochemistry & Molecular Biology
Sergey Pisarenko, Eugene Eremenko, Dmitry A. Kovalev, Alla G. Ryazanova, Anna Yu Evchenko, Lyudmila Yu Aksenova, Zorigma F. Dugarzhapova, Elena Kravets, Olga Semenova, Olga Bobrysheva, Sergei Balakhonov, Alexander N. Kulichenko
Summary: This research conducted whole genome SNP analysis on 15 strains of Bacillus anthracis isolated from Eastern Siberia and the Far East from 1956 to 2018. The study identified 6400 chromosomal SNPs, allowing for differentiation of the strains and establishing genetic diversity among them. The strains from this region were classified into 5 genetic groups, with the greatest diversity observed in the southern regions of Eastern Siberia.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2021)
Article
Microbiology
Abraham G. Moller, Kyle Winston, Shiyu Ji, Junting Wang, Michelle N. Hargita Davis, Claudia R. Solis-Lemus, Timothy D. Read
Summary: This study investigated the genetic basis of strain-to-strain variation in sensitivity to phages in Staphylococcus aureus, identifying putative loci that affect host range and discovering previously unreported genes influencing bacterial growth during phage infection. Predictive models were developed based on the host range matrix data, suggesting the complexity of phage susceptibility in S. aureus but also the potential for targeted phage therapy.
Article
Chemistry, Multidisciplinary
E. Randal Hofmann, Charles Davidson, Hsiu Chen, Melody Zacharko, Jay E. Dorton, Gary K. Kilper, Carcie Graves, Aleksandr E. Miklos, Katherine Rhea, Joe Ma, Bruce G. Goodwin, Shanmuga Sozhamannan
Summary: Lateral flow immunoassays are simple diagnostic devices used for detecting biological agents or other analytes of interest. There is a need for multiplex LFI devices that can differentiate between pathogens, especially in situations where reducing assay time and costs is critical. Developing a sensor-based multiplex LFI device could improve accuracy in interpreting ambiguous test results, especially at lower antigen concentrations and when there are imperfections in the strips.
Article
Microbiology
Vishnu Raghuram, Ashley M. Alexander, Hui Qi Loo, Robert A. Petit, Joanna B. Goldberg, Timothy D. Read
Summary: This study investigates the mutations in the agr operon of Staphylococcus aureus and their impact on strain characteristics. The study shows a close association between agr type and S. aureus clonal complex, and a strong linkage between agrBDC alleles. More than 5% of the genomes analyzed have frameshift mutations in the agr operon. The recurring mutations in different clonal lineages suggest that strains with agr frameshifts are short-lived in evolution.
MICROBIOLOGY SPECTRUM
(2022)
Article
Microbiology
Concerta L. Holley, Vijaya Dhulipala, Jacqueline T. Balthazar, Adriana Le Van, Afrin A. Begum, Shao-Chun Chen, Timothy D. Read, Mitch Matoga, Irving F. Hoffman, Daniel Golparian, Magnus Unemo, Ann E. Jerse, William M. Shafer
Summary: A new drug-resistant mutation, fusA2, has been identified, which increases resistance of gonococci to gentamicin, but may result in fitness defects during experimental infection. Furthermore, analysis of whole-genome sequences revealed that other fusA alleles do not possess the same ability to decrease gentamicin susceptibility.
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
(2022)
Article
Microbiology
Sankhya Bommana, Gracie Richards, Mike Kama, Reshma Kodimerla, Kenan Jijakli, Timothy D. Read, Deborah Dean
Summary: Chlamydia trachomatis is the primary cause of bacterial sexually transmitted infections worldwide. This study investigates the microbial composition and function in the vagina, endocervix, and rectum of Fijian women with and without C. trachomatis infections. The results show unique microbial profiles in C. trachomatis-infected women, with more complex microbial pathways in the endocervix compared to the vagina. In addition, some women showed similarities in microbiome composition across different sites, suggesting potential intragenitorectal transmission. This study highlights the importance of understanding genitorectal microbiomes in promoting C. trachomatis infection and calls for larger prospective studies to better define the microbiomes of Pacific Islanders.
MICROBIOLOGY SPECTRUM
(2022)
Article
Virology
Catherine E. Arnold, Logan J. Voegtly, Emily K. Stefanov, Matthew R. Lueder, Andrea E. Luquette, Robin H. Miller, Haven L. Miner, Andrew J. Bennett, Lindsay Glang, Tara N. McGinnis, Kristie E. Reisinger, Jae W. Dugan, Michael A. Mangat, Daniel J. Silberger, Rebecca L. Pavlicek, Chaselynn M. Watters, Gregory K. Rice, Francisco Malagon, Regina Z. Cer, Stephen M. Eggan, Kimberly A. Bishop-Lilly
Summary: This study contributes to the knowledge base of circulating SARS-CoV-2 lineages in the under-sampled country of Djibouti, and reveals circulating variants of concern, mutations of interest, and emerging spike mutations.
Article
Genetics & Heredity
Robert Player, Kathleen Verratti, Andrea Staab, Ellen Forsyth, Amanda Ernlund, Mihir S. Joshi, Rebecca Dunning, David Rozak, Sarah Grady, Bruce Goodwin, Shanmuga Sozhamannan
Summary: An optimized targeted genomic sequencing method using Oxford Nanopore Technology (ONT) was developed and compared with PCR for biodefense and biosurveillance applications. The study identified the best ONT library preparation method and integrated it into a real-time amplicon sequence analysis workflow. The results showed that the ONT method provided faster and more accurate detection of target organisms compared to PCR-based methods.
Article
Microbiology
Abraham G. Moller, Robert A. Petit III, Michelle H. Davis, Timothy D. Read
Summary: This study developed a method for rapid detection of vancomycin-intermediate resistance in Staphylococcus aureus through long-read genomic sequencing. The method can identify VISA genotypes and incorporate a comprehensive database of VISA genetic determinants.
MICROBIOLOGY SPECTRUM
(2023)
Article
Microbiology
Samantha L. L. Sholes, Sarah Harrison, Samantha Forrest, Sarah Ton, Sarah L. L. Grady, Kathleen Verratti, Roger D. D. Plaut, Bruce G. G. Goodwin, Shanmuga Sozhamannan
Summary: We report the draft genome assemblies of mutants of the attenuated Bacillus anthracis (Sterne) strain 7702 that are resistant to phage AP50c, including the parent strain, several phage-resistant derivatives, and mutants of genes in the pathways for synthesis and assembly of the S-layer.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2023)
Article
Chemistry, Analytical
Ishi Keenum, Robert Player, Jason Kralj, Stephanie Servetas, Michael D. Sussman, Joseph A. Russell, Jennifer Stone, Sailaja Chandrapati, Shanmuga Sozhamannan
Summary: This study presents the minimum information requirements for AS in biodetection applications, which were developed under the auspices of the AOAC INTERNATIONAL Stakeholder Program. The guidelines aim to improve data quality, track workflow performance, and enhance the trustworthiness of AS results for decision makers.
JOURNAL OF AOAC INTERNATIONAL
(2023)
Article
Virology
Moushimi Amaya, Randy Yin, Lianying Yan, Viktoriya Borisevich, Bishwo N. Adhikari, Andrew Bennett, Francisco Malagon, Regina Z. Cer, Kimberly A. Bishop-Lilly, Antony S. Dimitrov, Robert W. Cross, Thomas W. Geisbert, Christopher C. Broder
Summary: Using a recombinant Cedar virus (rCedV) reverse genetics platform, chimeric viruses (rCedV-NiV-B and rCedV-HeV) were generated with the fusion (F) and attachment (G) glycoprotein genes of Nipah virus (NiV-Bangladesh) or Hendra virus in place of those of rCedV. These chimeras induced an interferon response and utilized specific entry receptors compared to rCedV. Neutralization tests with monoclonal antibodies showed a high correlation between the chimeras and authentic NiV-B and HeV. A high-throughput fluorescence reduction neutralization test (FRNT) using the chimeras was established and showed highly correlated results with plaque reduction neutralization tests (PRNT). The FRNT assay also measured serum neutralization titers from henipavirus G glycoprotein immunized animals. These rCedV chimeras provide a rapid and cost-effective henipavirus-based surrogate neutralization assay.
Article
Virology
Adrian C. Paskey, Xiao Fang Lim, Justin H. J. Ng, Gregory K. Rice, Wan Ni Chia, Casandra W. Philipson, Randy Foo, Regina Z. Cer, Kyle A. Long, Matthew R. Lueder, Lindsay Glang, Kenneth G. Frey, Theron Hamilton, Ian H. Mendenhall, Gavin J. Smith, Danielle E. Anderson, Lin-Fa Wang, Kimberly A. Bishop-Lilly
Summary: This study reports the discovery of a new bat-borne mumps virus in a captive colony of lesser dawn bats in Southeast Asia. The analysis of the RNA sequences reveals that this new virus shares only 86% amino acid identity with its closest relative, the African bat-borne mumps virus. While there is no immediate cause for concern, it is crucial to further investigate and monitor bat-borne mumps viruses to determine the risk of human infection.
Article
Virology
Celeste Huaman, Adrian C. Paskey, Caitlyn Clouse, Austin Feasley, Madeline Rader, Gregory K. Rice, Andrea E. Luquette, Maren C. Fitzpatrick, Hannah M. Drumm, Lianying Yan, Regina Z. Cer, Marina Donduashvili, Tamar Buchukuri, Anna Nanava, Christine E. Hulseberg, Michael A. Washington, Eric D. Laing, Francisco Malagon, Christopher C. Broder, Kimberly A. Bishop-Lilly, Brian C. Schaefer
Summary: Rabies is still present worldwide, but dog rabies has been mostly eliminated in the Americas and Europe through vaccination programs. However, sporadic cases of dog rabies still occur in Eastern Europe, including Georgia. Recent genetic diversity assessment of rabies strains in Georgia showed that they are closely related to local strains, and current human rabies vaccines can protect against Georgian dog rabies.
Article
Microbiology
Concerta L. L. Holley, Vijaya Dhulipala, Stavaros A. A. Maurakis, Ashley Nicole Greenawalt, Timothy D. D. Read, Cynthia N. N. Cornelissen, William M. M. Shafer
Summary: The expression of the vaccine candidate gene ompA in Neisseria gonorrhoeae is regulated by iron ions and a new transcription factor called NceR. This study reveals the complexity of gene regulation for vaccine candidates and improves our understanding of their availability during infection.
Article
Microbiology
Abraham G. Moller, Robert A. Petit, Timothy D. Read
Summary: Phage therapy is a potential alternative treatment for Staphylococcus aureus infections. The study found that phage adsorption genes are highly conserved in the S. aureus species, but horizontal gene transfer may play an important role in the strain-specific evolution of host range patterns.