Microbiology

Major genetic discontinuity and novel toxigenic species in Clostridioides difficile taxonomy

1. Daniel R Knight
2. Korakrit Imwattana
3. Brian Kullin
4. Enzo Guerrero-Araya
5. Daniel Paredes-Sabja
6. Xavier Didelot
7. Kate E Dingle
8. David W Eyre
9. César Rodríguez
10. Thomas V Riley

• Curated by eLife

  Summary: We appreciate this study and find that the conclusions that reclassify Clostridiodes are largely justified by the data/analysis. The major concern is that the work represents the application of standard approaches to refine species classification, as opposed to either proposing a novel approach to classify species or defining a split that might be more surprising and/or clinically significant (e.g. Kumar et al. Nature Genetics, 2019). Consequently, despite being a useful contribution to the literature we believe it is more suitable for a specialized audience.

  Reviewer #1 opted to reveal their name to the authors in the decision letter after review.

Reviewed by eLife

High-resolution mapping of the neutralizing and binding specificities of polyclonal rabbit serum elicited by HIV Env trimer immunization

1. Adam S. Dingens
2. Payal Pratap
3. Keara Malone
4. Sarah K. Hilton
5. Thomas Ketas
6. Christopher A. Cottrell
7. Julie Overbaugh
8. John P. Moore
9. P.J. Klasse
10. Andrew B. Ward
11. Jesse D. Bloom

Reviewed by eLife

Faster Cryptococcus Melanization Increases Virulence in Experimental and Human Cryptococcosis

1. Herdson Renney de Sousa
2. Getúlio Pereira de Oliveira
3. Stefânia de Oliveira Frazão
4. Kaio César de Melo Gorgonha
5. Camila Pereira Rosa
6. Emãnuella Melgaço Garcez
7. Joaquim Lucas
8. Amabel Fernandes Correia
9. Waleriano Ferreira de Freitas
10. Higor Matos Borges
11. Lucas Gomes de Brito Alves
12. Hugo Costa Paes
13. Luciana Trilles
14. Márcia dos Santos Lazera
15. Marcus de Melo Teixeira
16. Vitor Laerte Pinto
17. Maria Sueli Soares Felipe
18. Arturo Casadevall
19. Ildinete Silva-Pereira
20. Patrícia Albuquerque
21. André Moraes Nicola

• Curated by eLife

  Summary: The description of how faster melanization is associated with LC3-mediated phagocytosis evasion, virulence and outcomes in humans is interesting and does provide some new information. In general, the study has been executed well, with clear articulation of the results and appending conclusions. However, the work falls short of investigating any substantive mechanistic basis for the observations and how they relate to the broader metabolism in Cryptococcus. .

Reviewed by eLife

Glycine acylation and trafficking of a new class of bacterial lipoprotein by a composite secretion system

1. Christopher Icke
2. Freya J Hodges
3. Karthik Pullela
4. Samantha A McKeand
5. Jack Alfred Bryant
6. Adam F Cunningham
7. Jeff A Cole
8. Ian R Henderson

• Curated by eLife

  Summary: All three reviewers were enthusiastic about the identification and characterization of a hybrid secretion system involved in lipoprotein acylation and trafficking. We were impressed by the strength and extent of the data and the clever use of genetic, biochemical and bioinformatic approaches. At the same time, there was agreement that the conclusion that acylation is involved in CexE secretion is not fully supported. There was also consensus that overlap between this study and the 2020 PLOS Pathogen paper from Belmont-Monroy, necessitates more direct acknowledgement.

Reviewed by eLife

Evolutionary dynamics and geographic dispersal of beta coronaviruses in African bats

1. Babatunde O. Motayo
2. Olukunle Oluwapamilerin Oluwasemowo
3. Paul A. Akinduti

Reviewed by PeerJ, ScreenIT

Integron activity accelerates the evolution of antibiotic resistance

1. Célia Souque
2. José Antonio Escudero
3. R Craig MacLean

• Curated by eLife

  Summary: In this manuscript, the authors test the long-standing "evolution-on-demand" hypothesis of integrons. Using a combination of genetic construction work, experimental evolution, and WGS the authors present a convincing body of work favoring the presented hypothesis. They introduce three antibiotic gene cassettes into an integron and use an "evolutionary ramp" approach with gentamicin and demonstrate that the gentamicin resistance cassette shuffles towards the start of the integron. This provides compelling evidence favoring the evolutionary effects of an active class 1 integrase.

  The paper is clear, well written and demonstrates neatly the benefits of integron shuffling. The authors should also be given credit for including experimental data from an integron containing a clinical plasmid including resistance cassettes to the last resort antibiotics carbapenems. This is largely missing in the field.

  Our overall assessment of the manuscript is positive. However, a number of questions have been raised regarding the mechanistic aspects and conclusions of the paper. We are therefore suggesting additional assays to measure phenotypic effects of evolved integrons, and possibly data analyses on the negative controls. If these are not possible to perform, the main conclusions could be slightly altered instead to focus more on the genomics. Finally, we provide some suggestions on making the discussion more balanced and in clarifying the role of chromosomal mutations in the integron-facilitated evolution.

Reviewed by eLife

Redefining De Novo Gammaherpesvirus Infection Through High-Dimensional, Single-Cell Analysis of Virus and Host

1. Jennifer N. Berger
2. Bridget Sanford
3. Abigail K. Kimball
4. Lauren M. Oko
5. Rachael E. Kaspar
6. Brian F. Niemeyer
7. Kenneth L. Jones
8. Eric T. Clambey
9. Linda F. van Dyk

Reviewed by eLife

Freshwater monitoring by nanopore sequencing

1. Lara Urban
2. Andre Holzer
3. J Jotautas Baronas
4. Michael B Hall
5. Philipp Braeuninger-Weimer
6. Michael J Scherm
7. Daniel J Kunz
8. Surangi N Perera
9. Daniel E Martin-Herranz
10. Edward T Tipper
11. Susannah J Salter
12. Maximilian R Stammnitz

Reviewed by eLife

A pentameric protein ring with novel architecture is required for herpesviral packaging

1. Allison L Didychuk
2. Stephanie N Gates
3. Matthew R Gardner
4. Lisa M Strong
5. Andreas Martin
6. Britt A Glaunsinger

Reviewed by eLife

Mycobacterium tuberculosis SufR Responds to Nitric oxide via its 4Fe-4S cluster and Regulates Fe-S cluster Biogenesis for Persistence in Mice

1. Kushi Anand
2. Ashutosh Tripathi
3. Kaustubh Shukla
4. Nitish Malhotra
5. Anil Kumar Jamithireddy
6. Rajiv Kumar Jha
7. Susmit Narayan Chaudhury
8. Raju S Rajmani
9. Arati Ramesh
10. Valakunja Nagaraja
11. Balasubramanian Gopal
12. Ganesh Nagaraju
13. Aswin Sai Narain Seshayee
14. Amit Singh

Reviewed by eLife