Draft genome sequence of a non-tuberculous Mycobacterium strain isolated from a clinical urine sample Joanna E. Rivas Ramos, Paul R. Johnston, Robert J. H. Hammond, Matthew T. G. Holden, Derek J. Sloan, Andreas F. Haag Access Microbiology, 2026 Here, we report the draft sequence of a rapid-growing nontuberculous Mycobacterium isolated from a urine sample at the Scottish Mycobacteria Reference Laboratory, Royal Infirmary of Edinburgh, UK. The reported genome has a length of 6,749,454 bp, a G+C content of 67.2 mol% and 6,336 protein CDSs. Average nucleotide identity (ANI) analysis identified Mycobacterium vanbaalenii PYR-1 as the closest relative (83.32% ANI), indicating that this isolate likely represents a novel species within the genus. Notably, phenotypic characterization revealed a distinct antimicrobial resistance (AMR) profile. This assembly provides a valuable resource for studying the evolution of AMR mechanisms in nontuberculous mycobacteria and offers insight into resistance phenotypes observed in clinical isolates.
The ClpX protease is essential for inactivating the CI master repressor and completing prophage induction in Staphylococcus aureus Mohammed A. Thabet, José R. Penadés, Andreas F. Haag Nature Communications, 2023 Bacteriophages (phages) are the most abundant biological entities on Earth, exerting a significant influence on the dissemination of bacterial virulence, pathogenicity, and antimicrobial resistance. Temperate phages integrate into the bacterial chromosome in a dormant state through intricate regulatory mechanisms. These mechanisms repress lytic genes while facilitating the expression of integrase and the CI master repressor. Upon bacterial SOS response activation, the CI repressor undergoes auto-cleavage, producing two fragments with the N-terminal domain (NTD) retaining significant DNA-binding ability. The process of relieving CI NTD repression, essential for prophage induction, remains unknown. Here we show a specific interaction between the ClpX protease and CI NTD repressor fragment of phages Ф11 and 80α in Staphylococcus aureus. This interaction is necessary and sufficient for prophage activation after SOS-mediated CI auto-cleavage, defining the final stage in the prophage induction cascade. Our findings unveil unexpected roles of bacterial protease ClpX in phage biology.
Multilayer Regulation of Neisseria meningitidis NHBA at Physiologically Relevant Temperatures Sara Borghi, Ana Antunes, Andreas F. Haag, Marco Spinsanti, Tarcisio Brignoli, Enea Ndoni, Vincenzo Scarlato, Isabel Delany Microorganisms, 2022 Neisseria meningitidis colonizes the nasopharynx of humans, and pathogenic strains can disseminate into the bloodstream, causing septicemia and meningitis. NHBA is a surface-exposed lipoprotein expressed by all N. meningitidis strains in different isoforms. Diverse roles have been reported for NHBA in heparin-mediated serum resistance, biofilm formation, and adherence to host tissues. We determined that temperature controls the expression of NHBA in all strains tested, with increased levels at 30–32 °C compared to 37 °C. Higher NHBA expression at lower temperatures was measurable both at mRNA and protein levels, resulting in higher surface exposure. Detailed molecular analysis indicated that multiple molecular mechanisms are responsible for the thermoregulated NHBA expression. The comparison of mRNA steady-state levels and half-lives at 30 °C and 37 °C demonstrated an increased mRNA stability/translatability at lower temperatures. Protein stability was also impacted, resulting in higher NHBA stability at lower temperatures. Ultimately, increased NHBA expression resulted in higher susceptibility to complement-mediated killing. We propose that NHBA regulation in response to temperature downshift might be physiologically relevant during transmission and the initial step(s) of interaction within the host nasopharynx. Together these data describe the importance of NHBA both as a virulence factor and as a vaccine antigen during neisserial colonization and invasion.
Phage-inducible chromosomal islands promote genetic variability by blocking phage reproduction and protecting transductants from phage lysis Rodrigo Ibarra-Chávez, Aisling Brady, John Chen, José R. Penadés, Andreas F. Haag Plos Genetics, 2022 Phage-inducible chromosomal islands (PICIs) are a widespread family of highly mobile genetic elements that disseminate virulence and toxin genes among bacterial populations. Since their life cycle involves induction by helper phages, they are important players in phage evolution and ecology. PICIs can interfere with the lifecycle of their helper phages at different stages resulting frequently in reduced phage production after infection of a PICI-containing strain. Since phage defense systems have been recently shown to be beneficial for the acquisition of exogenous DNA via horizontal gene transfer, we hypothesized that PICIs could provide a similar benefit to their hosts and tested the impact of PICIs in recipient strains on host cell viability, phage propagation and transfer of genetic material. Here we report an important role for PICIs in bacterial evolution by promoting the survival of phage-mediated transductants of chromosomal or plasmid DNA. The presence of PICIs generates favorable conditions for population diversification and the inheritance of genetic material being transferred, such as antibiotic resistance and virulence genes. Our results show that by interfering with phage reproduction, PICIs can protect the bacterial population from phage attack, increasing the overall survival of the bacterial population as well as the transduced cells. Moreover, our results also demonstrate that PICIs reduce the frequency of lysogenization after temperate phage infection, creating a more genetically diverse bacterial population with increased bet-hedging opportunities to adapt to new niches. In summary, our results identify a new role for the PICIs and highlight them as important drivers of bacterial evolution.
Staphylococcus Amy C. Pickering, Andreas F. Haag, José R. Penades, J. Ross Fitzgerald Pathogenesis of Bacterial Infections in Animals Fifth Edition, 2022
Bacterial chromosomal mobility via lateral transduction exceeds that of classical mobile genetic elements Suzanne Humphrey, Alfred Fillol-Salom, Nuria Quiles-Puchalt, Rodrigo Ibarra-Chávez, Andreas F. Haag, John Chen, José R. Penadés Nature Communications, 2021 It is commonly assumed that the horizontal transfer of most bacterial chromosomal genes is limited, in contrast to the frequent transfer observed for typical mobile genetic elements. However, this view has been recently challenged by the discovery of lateral transduction in Staphylococcus aureus, where temperate phages can drive the transfer of large chromosomal regions at extremely high frequencies. Here, we analyse previously published as well as new datasets to compare horizontal gene transfer rates mediated by different mechanisms in S. aureus and Salmonella enterica. We find that the horizontal transfer of core chromosomal genes via lateral transduction can be more efficient than the transfer of classical mobile genetic elements via conjugation or generalized transduction. These results raise questions about our definition of mobile genetic elements, and the potential roles played by lateral transduction in bacterial evolution.
Radical genome remodelling accompanied the emergence of a novel host-restricted bacterial pathogen Gonzalo Yebra, Andreas F. Haag, Maan M. Neamah, Bryan A. Wee, Emily J. Richardson, Pilar Horcajo, Sander Granneman, María Ángeles Tormo-Más, Ricardo de la Fuente, J. Ross Fitzgerald, José R. Penadés Plos Pathogens, 2021 The emergence of new pathogens is a major threat to public and veterinary health. Changes in bacterial habitat such as a switch in host or disease tropism are typically accompanied by genetic diversification.Staphylococcus aureusis a multi-host bacterial species associated with human and livestock infections. A microaerophilic subspecies,Staphylococcus aureussubsp.anaerobius, is responsible for Morel’s disease, a lymphadenitis restricted to sheep and goats. However, the evolutionary history ofS.aureussubsp.anaerobiusand its relatedness toS.aureusare unknown. Population genomic analyses of clinicalS.aureussubsp.anaerobiusisolates revealed a highly conserved clone that descended from aS.aureusprogenitor about 1000 years ago before differentiating into distinct lineages that contain African and European isolates.S.aureussubsp.anaerobiushas undergone limited clonal expansion, with a restricted population size, and an evolutionary rate 10-fold slower thanS.aureus. The transition to its current restricted ecological niche involved acquisition of a pathogenicity island encoding a ruminant host-specific effector of abscess formation, large chromosomal re-arrangements, and the accumulation of at least 205 pseudogenes, resulting in a highly fastidious metabolism. Importantly, expansion of ~87 insertion sequences (IS) located largely in intergenic regions provided distinct mechanisms for the control of expression of flanking genes, including a novel mechanism associated with IS-mediated anti-anti-sense decoupling of ancestral gene repression. Our findings reveal the remarkable evolutionary trajectory of a host-restricted bacterial pathogen that resulted from extensive remodelling of theS.aureusgenome through an array of diverse mechanisms in parallel.
Systematic reconstruction of the complete two-component sensorial network in staphylococcus aureus B. Rapun-Araiz, A. F. Haag, V. De Cesare, C. Gil, P. Dorado-Morales, J. R. Penades, I. Lasa Msystems, 2020 Bacteria are able to sense environmental conditions and respond accordingly. Their sensorial system relies on pairs of sensory and regulatory proteins, known as two-component systems (TCSs). The majority of bacteria contain dozens of TCSs, each of them responsible for sensing and responding to a different range of signals. Traditionally, the function of each TCS has been determined by analyzing the changes in gene expression caused by the absence of individual TCSs. Here, we used a bacterial strain deprived of the complete TC sensorial system to introduce, one by one, the active form of every TCS. This gain-of-function strategy allowed us to identify the changes in gene expression conferred by each TCS without interference of other members of the family.
Draft genome sequence of a non-tuberculous Mycobacterium strain isolated from a clinical urine sample JER Ramos, PR Johnston, RJH Hammond, MTG Holden, DJ Sloan, ... Access Microbiology 8 (1), 001110. v3 , 2026 2026 Citations: 1
Draft Genome Sequence of a non-tuberculous Mycobacterium Strain Isolated from a Clinical Urine Sample. RR JE, PR Johnston, RJH Hammond, MTG Holden, DJ Sloan, AF Haag 2025
Quorum-sensing agr system of Staphylococcus aureus primes gene expression for protection from lethal oxidative stress M Podkowik, AI Perault, G Putzel, A Pountain, J Kim, AL DuMont, ... Elife 12, RP89098 , 2024 2024 Citations: 46
The ClpX protease is essential for inactivating the CI master repressor and completing prophage induction in Staphylococcus aureus MA Thabet, JR Penadés, AF Haag Nature Communications 14 (1), 6599 , 2023 2023 Citations: 11
In Vivo Gene Expression Profiling of Staphylococcus aureus during Infection Informs Design of Stemless Leukocidins LukE and -D as Detoxified Vaccine Candidates AF Haag, L Liljeroos, P Donato, C Pozzi, T Brignoli, MJ Bottomley, ... Microbiology spectrum 11 (1), e02574-22 , 2023 2023 Citations: 6
S. aureus antigens and compositions thereof F Bagnoli, A Haag, L LILJEROOS US Patent App. 17/783,725 , 2023 2023
S. aureus antigens and compositions thereof F Bagnoli, A Haag, L Liljeroos 2023
Staphylococcus AC Pickering, AF Haag, JR Penades, JR Fitzgerald Pathogenesis of bacterial infections in animals, 543-564 , 2022 2022 Citations: 6
The ClpX protease is essential for removing the CI master repressor and completing prophage induction in Staphylococcus aureus MA Thabet, JR Penadés, AF Haag bioRxiv, 2022.09. 18.507959 , 2022 2022 Citations: 2
Regulatory cascade in Staphylococcus aureus pathogenicity island activation AF Haag, M Podkowik, R Ibarra-Chávez, FG del Sol, G Ram, J Chen, ... Microbiology Society Annual Conference 2021 , 2022 2022
Systematic Reconstruction of the Complete Two-Component Sensorial Network in Staphylococcus aureus A Haag, B Rapun-Araiz, VD Cesare, P Dorado-Morales, J Penadés, ... Access Microbiology 4 (5), po0644 , 2022 2022
Regulatory cascade in SaPI activation A Haag, M Podkowik, R Ibarra-Chávez, FG del Sol, G Ram, J Chen, ... Access Microbiology 4 (5), po0626 , 2022 2022
Multilayer Regulation of Neisseria meningitidis NHBA at Physiologically Relevant Temperatures S Borghi, A Antunes, AF Haag, M Spinsanti, T Brignoli, E Ndoni, ... Microorganisms 10 (4), 834 , 2022 2022 Citations: 5
Phage-inducible chromosomal islands promote genetic variability by blocking phage reproduction and protecting transductants from phage lysis R Ibarra-Chavez, A Brady, J Chen, JR Penades, AF Haag PLoS Genetics 18 (3), e1010146 , 2022 2022 Citations: 26
Bacterial chromosomal mobility via lateral transduction exceeds that of classical mobile genetic elements S Humphrey, A Fillol-Salom, N Quiles-Puchalt, R Ibarra-Chávez, AF Haag, ... Nature communications 12 (1), 6509 , 2021 2021 Citations: 113
A regulatory cascade controls Staphylococcus aureus pathogenicity island activation AF Haag, M Podkowik, R Ibarra-Chávez, F Gallego del Sol, G Ram, ... Nature microbiology 6 (10), 1300-1308 , 2021 2021 Citations: 40
Radical genome remodelling accompanied the emergence of a novel host-restricted bacterial pathogen G Yebra, AF Haag, MM Neamah, BA Wee, EJ Richardson, P Horcajo, ... PLoS Pathogens 17 (5), e1009606 , 2021 2021 Citations: 19
Massive genome decay and insertion sequence expansion drive the evolution of a novel host-restricted bacterial pathogen G Yebra, AF Haag, MM Neamah, BA Wee, EJ Richardson, P Horcajo, ... bioRxiv, 2020.10. 13.331058 , 2020 2020
Systematic reconstruction of the complete two-component sensorial network in Staphylococcus aureus B Rapun-Araiz, AF Haag, V De Cesare, C Gil, P Dorado-Morales, ... Msystems 5 (4), 10.1128/msystems. 00511-20 , 2020 2020 Citations: 57
The impact of two-component sensorial network in staphylococcal speciation B Rapun-Araiz, AF Haag, C Solano, I Lasa 2020 Citations: 33
MOST CITED SCHOLAR PUBLICATIONS
Staphylococcus aureus in Animals AF Haag, JR Fitzgerald, JR Penadés Microbiology spectrum 7 (3), 10.1128/microbiolspec. gpp3-0060-2019 , 2019 2019 Citations: 406
Protection of Sinorhizobium against Host Cysteine-Rich Antimicrobial Peptides Is Critical for Symbiosis AF Haag, M Baloban, M Sani, B Kerscher, O Pierre, A Farkas, R Longhi, ... PLoS biology 9 (10), e1001169 , 2011 2011 Citations: 235
Molecular insights into bacteroid development during Rhizobium– legume symbiosis AF Haag, MFF Arnold, KK Myka, B Kerscher, S Dall'Angelo, M Zanda, ... FEMS microbiology reviews 37 (3), 364-383 , 2013 2013 Citations: 213
The Role of Two-Component Signal Transduction Systems in Staphylococcus aureus Virulence Regulation AF Haag, F Bagnoli Staphylococcus aureus: Microbiology, Pathology, Immunology, Therapy and … , 2016 2016 Citations: 142
Role of cysteine residues and disulfide bonds in the activity of a legume root nodule-specific, cysteine-rich peptide AF Haag, B Kerscher, S Dall'Angelo, M Sani, R Longhi, M Baloban, ... Journal of Biological Chemistry 287 (14), 10791-10798 , 2012 2012 Citations: 115
Bacterial chromosomal mobility via lateral transduction exceeds that of classical mobile genetic elements S Humphrey, A Fillol-Salom, N Quiles-Puchalt, R Ibarra-Chávez, AF Haag, ... Nature communications 12 (1), 6509 , 2021 2021 Citations: 113
Importance of Lipopolysaccharide and Cyclic β ‐1,2‐Glucans in Brucella ‐Mammalian Infections AF Haag, KK Myka, MFF Arnold, P Caro-Hernández, GP Ferguson International journal of microbiology 2010 (1), 124509 , 2010 2010 Citations: 106
Essential Role for the BacA Protein in the Uptake of a Truncated Eukaryotic Peptide in Sinorhizobium meliloti VL Marlow, AF Haag, H Kobayashi, V Fletcher, M Scocchi, GC Walker, ... Journal of bacteriology 191 (5), 1519-1527 , 2009 2009 Citations: 98
BacA is essential for bacteroid development in nodules of galegoid, but not phaseoloid, legumes R Karunakaran, AF Haag, AK East, VK Ramachandran, J Prell, EK James, ... Journal of bacteriology 192 (11), 2920-2928 , 2010 2010 Citations: 94
Systematic reconstruction of the complete two-component sensorial network in Staphylococcus aureus B Rapun-Araiz, AF Haag, V De Cesare, C Gil, P Dorado-Morales, ... Msystems 5 (4), 10.1128/msystems. 00511-20 , 2020 2020 Citations: 57
The Sinorhizobium meliloti LpxXL and AcpXL Proteins Play Important Roles in Bacteroid Development within Alfalfa AF Haag, S Wehmeier, S Beck, VL Marlow, V Fletcher, EK James, ... Journal of Bacteriology 191 (14), 4681-4686 , 2009 2009 Citations: 51
Quorum-sensing agr system of Staphylococcus aureus primes gene expression for protection from lethal oxidative stress M Podkowik, AI Perault, G Putzel, A Pountain, J Kim, AL DuMont, ... Elife 12, RP89098 , 2024 2024 Citations: 46
A regulatory cascade controls Staphylococcus aureus pathogenicity island activation AF Haag, M Podkowik, R Ibarra-Chávez, F Gallego del Sol, G Ram, ... Nature microbiology 6 (10), 1300-1308 , 2021 2021 Citations: 40
The impact of two-component sensorial network in staphylococcal speciation B Rapun-Araiz, AF Haag, C Solano, I Lasa 2020 Citations: 33
Partial complementation of Sinorhizobium meliloti bacA mutant phenotypes by the Mycobacterium tuberculosis BacA protein MFF Arnold, AF Haag, S Capewell, HI Boshoff, EK James, R McDonald, ... Journal of bacteriology 195 (2), 389-398 , 2013 2013 Citations: 33
Exploring host-pathogen interactions through genome wide protein microarray analysis L Scietti, K Sampieri, I Pinzuti, E Bartolini, B Benucci, A Liguori, AF Haag, ... Scientific reports 6 (1), 27996 , 2016 2016 Citations: 31
Sak and Sak4 recombinases are required for bacteriophage replication in Staphylococcus aureus MM Neamah, I Mir-Sanchis, M López-Sanz, S Acosta, I Baquedano, ... Nucleic Acids Research 45 (11), 6507-6519 , 2017 2017 Citations: 29
Molecular basis of ligand-dependent regulation of NadR, the transcriptional repressor of meningococcal virulence factor NadA A Liguori, E Malito, P Lo Surdo, L Fagnocchi, F Cantini, AF Haag, S Brier, ... PLoS pathogens 12 (4), e1005557 , 2016 2016 Citations: 29
Biochemical characterization of Sinorhizobium meliloti mutants reveals gene products involved in the biosynthesis of the unusual lipid A very long-chain fatty acid AF Haag, S Wehmeier, A Muszyński, B Kerscher, V Fletcher, SH Berry, ... Journal of Biological Chemistry 286 (20), 17455-17466 , 2011 2011 Citations: 29
Phage-inducible chromosomal islands promote genetic variability by blocking phage reproduction and protecting transductants from phage lysis R Ibarra-Chavez, A Brady, J Chen, JR Penades, AF Haag PLoS Genetics 18 (3), e1010146 , 2022 2022 Citations: 26