Imperial College London

Professor José R Penadés

Faculty of MedicineDepartment of Infectious Disease

Director MRC Centre for Molecular Bacteriology & Infection



+44 (0)20 7594 8533j.penades Website




Mrs Anna Lee +44 (0)20 7594 2954




Flowers buildingSouth Kensington Campus





Publication Type

110 results found

Ibarra-Chávez R, Brady A, Chen J, Penadés JR, Haag AFet al., 2022, Phage-inducible chromosomal islands promote genetic variability by blocking phage reproduction and protecting transductants from phage lysis, PLoS Genetics, Vol: 18, ISSN: 1553-7390

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.

Journal article

Brady A, Quiles-Puchalt, Gallego del Sol F, Zamora-Caballero S, Felipe-Ruíz A, Val-Calvo J, Meijer WJJ, Marina A, Penades Jet al., 2021, The arbitrium system controls prophage induction, Current Biology, Vol: 31, Pages: 5037-5045, ISSN: 0960-9822

Some Bacillus-infecting bacteriophages use a peptide-based communication system, termed arbitrium, to coordinate the lysis-lysogeny decision. In this system the phage produces AimP peptide during the lytic cycle. Once internalised by the host cell, AimP binds to the transcription factor AimR, reducing aimX expression and promoting lysogeny. Although these systems are present in a variety of mobile genetic elements, their role in the phage life cycle has only been characterised in phage phi3T during phage infection. Here, using the B. subtilis SPb prophage, we show that the arbitrium system is also required for normal prophage induction. Deletion of the aimP gene increased phage reproduction, while the aimR deletion significantly reduced the number of phage particles produced after prophage induction. Moreover, our results indicated that AimR is involved in a complex network of regulation and brought forward two new players in the SPb lysis-lysogeny decision system, YopN and the phage repressor YopR. Importantly, these proteins are encoded in an operon, the function of which is conserved across all SPb-like phages encoding the arbitrium system. Finally, we obtained mutant phages in the arbitrium system, which behaved almost identically to the wt phage, indicating that the arbitrium system is not essential in the laboratory but is likely beneficial for phage fitness in nature. In support of this, by possessing a functional arbitrium system the SPb phage can optimise production of infective particles whilst also preserving the number of cells that survive after prophage induction, a strategy that increases phage persistence in nature.

Journal article

Fillol-Salom A, Bacigalupe R, Humphrey S, Chiang YN, Chen J, Penades Jet al., 2021, Lateral transduction is inherent to the life cycle of the archetypical Salmonella phage P22, Nature Communications, Vol: 12, Pages: 1-11, ISSN: 2041-1723

Lysogenic induction ends the stable association between a bacteriophage and its host, andthe transition to the lytic cycle begins with early prophage excision followed by DNA replication and packaging (ERP). This temporal program is considered universal for P22-liketemperate phages, though there is no direct evidence to support the timing and sequence ofthese events. Here we report that the long-standing ERP program is an observation of theexperimentally favored Salmonella phage P22 tsc229 heat-inducible mutant, and that wildtype P22 actually follows the replication-packaging-excision (RPE) program. We find that P22tsc229 excises early after induction, but P22 delays excision to just before it is detrimental tophage production. This allows P22 to engage in lateral transduction. Thus, at minimalexpense to itself, P22 has tuned the timing of excision to balance propagation with lateraltransduction, powering the evolution of its host through gene transfer in the interest of selfpreservation.

Journal article

Humphrey S, Fillol-Salom A, Quiles-Puchalt N, Ibarra-Chávez R, Haag A, Chen J, Penades Jet al., 2021, Bacterial chromosomal mobility via lateral transduction exceeds that of classical mobile genetic elements, Nature Communications, Vol: 12, Pages: 1-12, ISSN: 2041-1723

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 chromosomalregions 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.

Journal article

Hawkins NC, Kizziah JL, Penades JR, Dokland Tet al., 2021, Shape shifter: redirection of prolate phage capsid assembly by staphylococcal pathogenicity islands, NATURE COMMUNICATIONS, Vol: 12

Journal article

Humphrey S, San Millan A, Toll-Riera M, Connolly J, Flor-Duro A, Chen J, Ubeda C, MacLean RC, Penades Jet al., 2021, Staphylococcal phages and pathogenicity islands drive plasmid evolution, Nature Communications, Vol: 12, Pages: 1-15, ISSN: 2041-1723

Conjugation has classically been considered the main mechanism driving plasmid transfer in nature. Yet bacteria frequently carry so-called non-transmissible plasmids, raising questions about how these plasmids spread. Interestingly, the size of many mobilizable and non transmissible plasmids coincides with the average size of phages (~40kb) or that of a family of pathogenicity islands, the phage-inducible chromosomal islands (PICIs, ~11 kb). Here, we show that phages and PICIs from Staphylococcus aureus can mediate intra- and inter-species plasmid transfer via generalised transduction, potentially contributing to non-transmissible plasmid spread in nature. Further, staphylococcal PICIs enhance plasmid packaging efficiency, and phages and PICIs exert selective pressures on plasmids via the physical capacity of their capsids, explaining the bimodal size distribution observed for non-conjugative plasmids. Our results highlight that transducing agents (phages, PICIs) have important roles in bacterial plasmid evolution and, potentially, in antimicrobial resistance transmission.

Journal article

Haag AF, Podkowik M, Ibarra-Chavez R, Gallego del Sol F, Ram G, Chen J, Marina A, Novick RP, Penades JRet al., 2021, A regulatory cascade controls Staphylococcus aureus pathogenicity island activation, NATURE MICROBIOLOGY, Vol: 6, Pages: 1300-+, ISSN: 2058-5276

Journal article

Miguel-Romero L, Alqasmi M, Bacarizo J, Tan JA, Cogdell RJ, Chen J, Byron O, Christie GE, Marina A, Penadés JRet al., 2021, Non-canonical <i>Staphylococcus aureus</i> pathogenicity island repression

<jats:title>ABSTRACT</jats:title><jats:p>Mobile genetic elements (MGEs) control their life cycles by the expression of a master repressor, whose function must be disabled to allow the spread of these elements in nature. Here we describe an unprecedented repression-derepression mechanism involved in the transfer of the <jats:italic>Staphylococcus aureus</jats:italic> pathogenicity islands (SaPIs). Contrary to the classical phage and SaPI repressors, which are dimers, the SaPI1 repressor Stl<jats:sup>SaPI1</jats:sup> presents a unique tetrameric conformation, never seen before. Importantly, not just one but two tetramers are required for SaPI1 repression, which increases the novelty of the system. To derepress SaPI1, the phage-encoded protein Sri binds to and induces a conformational change in the DNA binding domains of Stl<jats:sup>SaPI1</jats:sup>, preventing the binding of the repressor to its cognate Stl<jats:sup>SaPI1</jats:sup> sites. Finally, our findings demonstrate that this system is not exclusive to SaPI1 but widespread in nature. Overall, our results characterise a novel repression-induction system involved in the transfer of MGE-encoded virulence factors in nature.</jats:p><jats:sec><jats:title>Significance</jats:title><jats:p>While most repressors controlling the transfer of mobile genetic elements are dimers, we demonstrate here that the Staphylococcal pathogenicity island 1 (SaPI1) is repressed by two tetramers, which have a novel structural fold in their body that has never been seen before in other proteins. Moreover, by solving the structure of the SaPI1 repressor in complex with its inducing protein Sri, we have demonstrated that Sri forces the SaPI1 repressor to adopt a conformation that is incompatible with DNA binding, explaining how SaPI1 is induced. Finally, our results demonstrate that this repression system is not exclusive of the SaPIs but widesp

Journal article

Fillol-Salom A, Bacigalupe R, Humphrey S, Chiang YN, Chen J, Penadés JRet al., 2021, The secret life (cycle) of temperate bacteriophages

<jats:title>Abstract</jats:title><jats:p>Lysogenic induction ends the stable association between a bacteriophage and its host, and the transition to the lytic cycle begins with prophage <jats:underline>e</jats:underline>xcision followed by DNA <jats:underline>r</jats:underline>eplication and <jats:underline>p</jats:underline>ackaging (ERP) – a temporal program that is considered universal for most temperate phages. Here we report that the long-standing ERP program is an artefact of the experimentally favoured <jats:italic>Salmonella</jats:italic> phage P22 ts<jats:italic>c<jats:sub>2</jats:sub>29</jats:italic> heat-inducible mutant, and that wildtype P22 actually follows a replication-packaging-excision (RPE) program. We found that unlike P22 ts<jats:italic>c<jats:sub>2</jats:sub>29</jats:italic>, P22 delayed excision to just before it was detrimental to phage production. Thus, at minimal expense to itself, P22 has tuned the timing of excision to balance propagation with lateral transduction, powering the evolution of its host through gene transfer in the interest of self-preservation.</jats:p><jats:sec><jats:title>One Sentence Summary</jats:title><jats:p>Genetic analyses propose a new life cycle for temperate bacteriophages.</jats:p></jats:sec>

Journal article

Brady A, Felipe-Ruiz A, Gallego Del Sol F, Marina A, Quiles-Puchalt N, Penadés JRet al., 2021, Molecular basis of lysis-lysogeny decisions in gram-positive phages., Annual Review of Microbiology, Vol: 10, Pages: 1-19, ISSN: 0066-4227

Temperate bacteriophages (phages) are viruses of bacteria. Upon infection of a susceptible host, a temperate phage can establish either a lytic cycle that kills the host or a lysogenic cycle as a stable prophage. The life cycle pursued by an infecting temperate phage can have a significant impact not only on the individual host bacterium at the cellular level but also on bacterial communities and evolution in the ecosystem. Thus, understanding the decision processes of temperate phages is crucial. This review delves into the molecular mechanisms behind lysis-lysogeny decision-making in Gram-positive phages. We discuss a variety of molecular mechanisms and the genetic organization of these well-understood systems. By elucidating the strategies used by phages to make lysis-lysogeny decisions, we can improve our understanding of phage-host interactions, which is crucial for a variety of studies including bacterial evolution, community and ecosystem diversification, and phage therapeutics. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see for revised estimates.

Journal article

Yebra G, Haag AF, Neamah MM, Wee BA, Richardson EJ, Horcajo P, Granneman S, Angeles Tormo-Mas M, de la Fuente R, Fitzgerald JR, Penades JRet al., 2021, Radical genome remodelling accompanied the emergence of a novel host-restricted bacterial pathogen, PLoS Pathogens, Vol: 17, Pages: 1-23, ISSN: 1553-7366

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 aureus is a multi-host bacterial species associated with human and livestock infections. A microaerophilic subspecies, Staphylococcus aureus subsp. anaerobius, is responsible for Morel’s disease, a lymphadenitis restricted to sheep and goats. However, the evolutionary history of S. aureus subsp. anaerobius and its relatedness to S. aureus are unknown. Population genomic analyses of clinical S. aureus subsp. anaerobius isolates revealed a highly conserved clone that descended from a S. aureus progenitor about 1000 years ago before differentiating into distinct lineages that contain African and European isolates. S. aureus subsp. anaerobius has undergone limited clonal expansion, with a restricted population size, and an evolutionary rate 10-fold slower than S. 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 the S. aureus genome through an array of diverse mechanisms in parallel.

Journal article

Prieto JM, Rapún-Araiz B, Gil C, Penadés JR, Lasa I, Latasa Cet al., 2020, Inhibiting the two-component system GraXRS with verteporfin to combat Staphylococcus aureus infections, Scientific Reports, Vol: 10, ISSN: 2045-2322

Infections caused by Staphylococcus aureus pose a serious and sometimes fatal health issue. With the aim of exploring a novel therapeutic approach, we chose GraXRS, a Two-Component System (TCS) that determines bacterial resilience against host innate immune barriers, as an alternative target to disarm S. aureus. Following a drug repurposing methodology, and taking advantage of a singular staphylococcal strain that lacks the whole TCS machinery but the target one, we screened 1.280 off-patent FDA-approved drug for GraXRS inhibition. Reinforcing the connection between this signaling pathway and redox sensing, we found that antioxidant and redox-active molecules were capable of reducing the expression of the GraXRS regulon. Among all the compounds, verteporfin (VER) was really efficient in enhancing PMN-mediated bacterial killing, while topical administration of such drug in a murine model of surgical wound infection significantly reduced the bacterial load. Experiments relying on the chemical mimicry existing between VER and heme group suggest that redox active residue C227 of GraS participates in the inhibition exerted by this FDA-approved drug. Based on these results, we propose VER as a promising candidate for sensitizing S. aureus that could be helpful to combat persistent or antibiotic-resistant infections.

Journal article

Yebra G, Haag AF, Neamah MM, Wee BA, Richardson EJ, Horcajo P, Granneman S, Tormo-Más MÁ, de la Fuente R, Fitzgerald JR, Penadés JRet al., 2020, Massive genome decay and insertion sequence expansion drive the evolution of a novel host-restricted bacterial pathogen

<jats:title>Abstract</jats:title><jats:sec><jats:title>Background</jats:title><jats:p>The emergence of new pathogens is a major threat to public and veterinary health. Changes in bacterial habitat such as those associated with a switch in host or disease tropism are often accompanied by genetic adaptation. <jats:italic>Staphylococcus aureus</jats:italic> is a multi-host bacterial species comprising strains with distinct tropisms for human and livestock species. A microaerophilic subspecies, <jats:italic>Staphylococcus aureus</jats:italic> subsp. <jats:italic>anaerobius</jats:italic>, is responsible for outbreaks of Morel’s disease, a lymphadenitis in small ruminants. However, the evolutionary history of <jats:italic>S. aureus</jats:italic> subsp. <jats:italic>anaerobius</jats:italic> and its relatedness to <jats:italic>S. aureus</jats:italic> are unknown.</jats:p></jats:sec><jats:sec><jats:title>Results</jats:title><jats:p>Evolutionary genomic analyses of clinical <jats:italic>S. aureus</jats:italic> subsp. <jats:italic>anaerobius</jats:italic> isolates revealed a highly conserved clone that descended from a <jats:italic>S. aureus</jats:italic> progenitor about 1000 years ago before differentiating into distinct lineages representing African and European isolates. <jats:italic>S. aureus</jats:italic> subsp. <jats:italic>anaerobius</jats:italic> has undergone limited clonal expansion, with a restricted population size, and an evolutionary rate 10-fold slower than <jats:italic>S. aureus</jats:italic>. The transition to its current restricted ecological niche involved acquisition of a pathogenicity island encoding a ruminant host-specific effector of abscess formation, several large chromosomal re-arrangements, and the accumulation of at least 205 pse

Journal article

Rapun-Araiz B, Haag AF, De Cesare V, Gil C, Dorado-Morales P, Penades JR, Lasa Iet al., 2020, Systematic reconstruction of the complete two-component sensorial network in staphylococcus aureus., mSystems, Vol: 5, Pages: 1-16, ISSN: 2379-5077

In bacteria, adaptation to changes in the environment is mainly controlled through two-component signal transduction systems (TCSs). Most bacteria contain dozens of TCSs, each of them responsible for sensing a different range of signals and controlling the expression of a repertoire of target genes (regulon). Over the years, identification of the regulon controlled by each individual TCS in different bacteria has been a recurrent question. However, limitations associated with the classical approaches used have left our knowledge far from complete. In this report, using a pioneering approach in which a strain devoid of the complete nonessential TCS network was systematically complemented with the constitutively active form of each response regulator, we have reconstituted the regulon of each TCS of S. aureus in the absence of interference between members of the family. Transcriptome sequencing (RNA-Seq) and proteomics allowed us to determine the size, complexity, and insulation of each regulon and to identify the genes regulated exclusively by one or many TCSs. This gain-of-function strategy provides the first description of the complete TCS regulon in a living cell, which we expect will be useful to understand the pathobiology of this important pathogen.IMPORTANCE 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 wit

Journal article

Kiga K, Tan X-E, Ibarra-Chávez R, Watanabe S, Aiba Y, Sato'o Y, Li F-Y, Sasahara T, Cui B, Kawauchi M, Boonsiri T, Thitiananpakorn K, Taki Y, Azam AH, Suzuki M, Penadés JR, Cui Let al., 2020, Development of CRISPR-Cas13a-based antimicrobials capable of sequence-specific killing of target bacteria, Nature Communications, Vol: 11, ISSN: 2041-1723

The emergence of antimicrobial-resistant bacteria is an increasingly serious threat to global health, necessitating the development of innovative antimicrobials. Here we report the development of a series of CRISPR-Cas13a-based antibacterial nucleocapsids, termed CapsidCas13a(s), capable of sequence-specific killing of carbapenem-resistant Escherichia coli and methicillin-resistant Staphylococcus aureus by recognizing corresponding antimicrobial resistance genes. CapsidCas13a constructs are generated by packaging programmed CRISPR-Cas13a into a bacteriophage capsid to target antimicrobial resistance genes. Contrary to Cas9-based antimicrobials that lack bacterial killing capacity when the target genes are located on a plasmid, the CapsidCas13a(s) exhibit strong bacterial killing activities upon recognizing target genes regardless of their location. Moreover, we also demonstrate that the CapsidCas13a(s) can be applied to detect bacterial genes through gene-specific depletion of bacteria without employing nucleic acid manipulation and optical visualization devices. Our data underscore the potential of CapsidCas13a(s) as both therapeutic agents against antimicrobial-resistant bacteria and nonchemical agents for detection of bacterial genes.

Journal article

Ibarra-Chávez R, Haag AF, Dorado-Morales P, Lasa I, Penadés JRet al., 2020, Rebooting synthetic phage-inducible chromosomal islands: one method to forge them all, BioDesign Research, Vol: 2020, Pages: 1-14

Phage-inducible chromosomal islands (PICIs) are a widespread family of mobile genetic elements, which have an important role in bacterial pathogenesis. These elements mobilize among bacterial species at extremely high frequencies, representing an attractive tool for the delivery of synthetic genes. However, tools for their genetic manipulation are limited and timing consuming. Here, we have adapted a synthetic biology approach for rapidly editing of PICIs in Saccharomyces cerevisiae based on their ability to excise and integrate into the bacterial chromosome of their cognate host species. As proof of concept, we engineered several PICIs from Staphylococcus aureus and Escherichia coli and validated this methodology for the study of the biology of these elements by generating multiple and simultaneous mutations in different PICI genes. For biotechnological purposes, we also synthetically constructed PICIs as Trojan horses to deliver different CRISPR-Cas9 systems designed to either cure plasmids or eliminate cells carrying the targeted genes. Our results demonstrate that the strategy developed here can be employed universally to study PICIs and enable new approaches for diagnosis and treatment of bacterial diseases.

Journal article

Fillol-Salom A, Miguel-Romero L, Marina A, Chen J, Penades JRet al., 2020, Beyond the CRISPR-Cas safeguard: PICI-encoded innate immune systems protect bacteria from bacteriophage predation, CURRENT OPINION IN MICROBIOLOGY, Vol: 56, Pages: 52-58, ISSN: 1369-5274

Journal article

Bacigalupe R, Angeles Tormo-Mas M, Penades JR, Fitzgerald JRet al., 2019, A multihost bacterial pathogen overcomes continuous population bottlenecks to adapt to new host species, Science Advances, Vol: 5, ISSN: 2375-2548

While many bacterial pathogens are restricted to single host species, some have the capacity to undergo host switches, leading to the emergence of new clones that are a threat to human and animal health. However, the bacterial traits that underpin a multihost ecology are not well understood. Following transmission to a new host, bacterial populations are influenced by powerful forces such as genetic drift that reduce the fixation rate of beneficial mutations, limiting the capacity for host adaptation. Here, we implement a novel experimental model of bacterial host switching to investigate the ability of the multihost pathogen Staphylococcus aureus to adapt to new species under continuous population bottlenecks. We demonstrate that beneficial mutations accumulated during infection can overcome genetic drift and sweep through the population, leading to host adaptation. Our findings highlight the remarkable capacity of some bacteria to adapt to distinct host niches in the face of powerful antagonistic population forces.

Journal article

Kiga K, Tan X-E, Ibarra-Chávez R, Watanabe S, Aiba Y, Satoo Y, Li F-Y, Sasahara T, Cui B, Kawauchi M, Boonsiri T, Thitiananpakorn K, Taki Y, Azam AH, Suzuki M, Penadés JR, Cui Let al., 2019, Development of CRSIPR-Cas13a-based antimicrobials capable of sequence-specific killing of target bacteria, Publisher: Cold Spring Harbor Laboratory

<jats:title>Abstract</jats:title><jats:p>Emergence of antimicrobial-resistant bacteria is an increasingly serious threat to global health, necessitating the development of innovative antimicrobials. We established a series of CRISPR-Cas13a-based antibacterial nucleocapsid, termed CapsidCas13a(s), capable of sequence-specific killing of carbapenem-resistant <jats:italic>Escherichia coli</jats:italic> and methicillin-resistant <jats:italic>Staphylococcus aureus</jats:italic> through promiscuous RNA cleavage after recognizing corresponding antimicrobial resistance genes. CapsidCas13a constructs were generated by packaging CRISPR-Cas13a into a bacteriophage capsid to target antimicrobial resistance genes. Contrary to Cas9-based antimicrobials that lack bacterial killing capacity when the target genes are located on a plasmid, the CapsidCas13a(s) exhibited strong bacterial killing activities upon recognizing target genes regardless of their location. The antimicrobials’ treatment efficacy was confirmed using a <jats:italic>Galleria mellonella</jats:italic> larvae model. Further, we demonstrated that the CapsidCas13a(s) can assist in bacterial gene detection without employing nucleic acid amplification and optical devices.</jats:p>

Working paper

Fillol-Salom A, Bacarizo J, Alqasmi M, Rafael Ciges-Tomas J, Martinez-Rubio R, Roszak AW, Cogdell RJ, Chen J, Marina A, Penades JRet al., 2019, Hijacking the hijackers: escherichia coli pathogenicity islands redirect helper phage packaging for their own benefit, Molecular Cell, Vol: 75, Pages: 1020-1030.e4, ISSN: 1097-2765

Phage-inducible chromosomal islands (PICIs) represent a novel and universal class of mobile genetic elements, which have broad impact on bacterial virulence. In spite of their relevance, how the Gram-negative PICIs hijack the phage machinery for their own specific packaging and how they block phage reproduction remains to be determined. Using genetic and structural analyses, we solve the mystery here by showing that the Gram-negative PICIs encode a protein that simultaneously performs these processes. This protein, which we have named Rpp (for redirecting phage packaging), interacts with the phage terminase small subunit, forming a heterocomplex. This complex is unable to recognize the phage DNA, blocking phage packaging, but specifically binds to the PICI genome, promoting PICI packaging. Our studies reveal the mechanism of action that allows PICI dissemination in nature, introducing a new paradigm in the understanding of the biology of pathogenicity islands and therefore of bacterial pathogen evolution.

Journal article

Ciges-Tomas JR, Alite C, Humphrey S, Donderisl J, Bowring J, Salvatella X, Penades JR, Marina Aet al., 2019, The structure of a polygamous repressor reveals how phage-inducible chromosomal islands spread in nature, Nature Communications, Vol: 10, ISSN: 2041-1723

Stl is a master repressor encoded by Staphylococcus aureus pathogenicity islands (SaPIs) that maintains integration of these elements in the bacterial chromosome. After infection or induction of a resident helper phage, SaPIs are de-repressed by specific interactions of phage proteins with Stl. SaPIs have evolved a fascinating mechanism to ensure their promiscuous transfer by targeting structurally unrelated proteins performing identically conserved functions for the phage. Here we decipher the molecular mechanism of this elegant strategy by determining the structure of SaPIbov1 Stl alone and in complex with two structurally unrelated dUTPases from different S. aureus phages. Remarkably, SaPIbov1 Stl has evolved different domains implicated in DNA and partner recognition specificity. This work presents the solved structure of a SaPI repressor protein and the discovery of a modular repressor that acquires multispecificity through domain recruiting. Our results establish the mechanism that allows widespread dissemination of SaPIs in nature.

Journal article

Chiang YN, Penades JR, Chen J, 2019, Genetic transduction by phages and chromosomal islands: The new and noncanonical, PLoS Pathogens, Vol: 15, Pages: 1-7, ISSN: 1553-7366

Journal article

Fillol-Salom A, Alsaadi A, de Sousa JAM, Zhong L, Foster KR, Rocha EPC, Penades JR, Ingmer H, Haaber Jet al., 2019, Bacteriophages benefit from generalized transduction, PLoS Pathogens, Vol: 15, ISSN: 1553-7366

Temperate phages are bacterial viruses that as part of their life cycle reside in the bacterial genome as prophages. They are found in many species including most clinical strains of the human pathogens, Staphylococcus aureus and Salmonella enterica serovar Typhimurium. Previously, temperate phages were considered as only bacterial predators, but mounting evidence point to both antagonistic and mutualistic interactions with for example some temperate phages contributing to virulence by encoding virulence factors. Here we show that generalized transduction, one type of bacterial DNA transfer by phages, can create conditions where not only the recipient host but also the transducing phage benefit. With antibiotic resistance as a model trait we used individual-based models and experimental approaches to show that antibiotic susceptible cells become resistant to both antibiotics and phage by i) integrating the generalized transducing temperate phages and ii) acquiring transducing phage particles carrying antibiotic resistance genes obtained from resistant cells in the environment. This is not observed for non-generalized transducing temperate phages, which are unable to package bacterial DNA, nor for generalized transducing virulent phages that do not form lysogens. Once established, the lysogenic host and the prophage benefit from the existence of transducing particles that can shuffle bacterial genes between lysogens and for example disseminate resistance to antibiotics, a trait not encoded by the phage. This facilitates bacterial survival and leads to phage population growth. We propose that generalized transduction can function as a mutualistic trait where temperate phages cooperate with their hosts to survive in rapidly-changing environments. This implies that generalized transduction is not just an error in DNA packaging but is selected for by phages to ensure their survival.

Journal article

Haag AF, Fitzgerald JR, Penades JR, 2019, Staphylococcus aureus in Animals, Microbiology Spectrum, Vol: 7, Pages: 1-19, ISSN: 2165-0497

Staphylococcus aureus is a mammalian commensal and opportunistic pathogen that colonizes niches such as skin, nares and diverse mucosal membranes of about 20-30% of the human population. S. aureus can cause a wide spectrum of diseases in humans and both methicillin-sensitive and methicillin-resistant strains are common causes of nosocomial- and community-acquired infections. Despite the prevalence of literature characterising staphylococcal pathogenesis in humans, S. aureus is a major cause of infection and disease in a plethora of animal hosts leading to a significant impact on public health and agriculture. Infections in animals are deleterious to animal health, and animals can act as a reservoir for staphylococcal transmission to humans.Host-switching events between humans and animals and amongst animals are frequent and have been accentuated with the domestication and/or commercialisation of specific animal species. Host-switching is typically followed by subsequent adaptation through acquisition and/or loss of mobile genetic elements such as phages, pathogenicity islands and plasmids as well as further host-specific mutations allowing it to expand into new host populations.In this chapter, we will be giving an overview of S. aureus in animals, how this bacterial species was, and is, being transferred to new host species and the key elements thought to be involved in its adaptation to new ecological host niches. We will also highlight animal hosts as a reservoir for the development and transfer of antimicrobial resistance determinants.

Journal article

Gallego del Sol F, Penades JR, Marina A, 2019, Deciphering the molecular mechanism underpinning phage arbitrium communication systems, Molecular Cell, Vol: 74, Pages: 59-72.e3, ISSN: 1097-2765

Bacillus phages use a communication system, termed “arbitrium,” to coordinate lysis-lysogeny decisions. Arbitrium communication is mediated by the production and secretion of a hexapeptide (AimP) during lytic cycle. Once internalized, AimP reduces the expression of the negative regulator of lysogeny, AimX, by binding to the transcription factor, AimR, promoting lysogeny. We have elucidated the crystal structures of AimR from the Bacillus subtilis SPbeta phage in its apo form, bound to its DNA operator and in complex with AimP. AimR presents intrinsic plasticity, sharing structural features with the RRNPP quorum-sensing family. Remarkably, AimR binds to an unusual operator with a long spacer that interacts nonspecifically with the receptor TPR domain, while the HTH domain canonically recognizes two inverted repeats. AimP stabilizes a compact conformation of AimR that approximates the DNA-recognition helices, preventing AimR binding to the aimX promoter region. Our results establish the molecular basis of the arbitrium communication system.

Journal article

Haag AF, Ross Fitzgerald J, Penadés JR, 2019, Staphylococcus aureus in animals, Gram-Positive Pathogens, Pages: 731-746, ISBN: 9781683670124

The genus Staphylococcus currently comprises 81 species and subspecies (, and most members of the genus are mammalian commensals or opportunistic pathogens that colonize niches such as skin, nares, and diverse mucosal membranes. Several species are of significant medical or veterinary importance. Staphylococcus pseudintermedius (1) is a leading cause of pyoderma in dogs and is considered to be a significant reservoir of antimicrobial resistance factors for the genus (2, 3). S. pseudintermedius is very similar to Staphylococcus intermedius and can be distinguished from other coagulase-positive staphylococci by positive arginine dihydrolase and acid production from β-gentiobiose and d-mannitol (4) or by using a multiplex-PCR approach targeting the nuclease gene nuc (5). Staphylococcus saprophyticus is the second leading cause of uncomplicated urinary tract infections (6). While Staphylococcus epidermidis is a normal component of the epidermal microbiota, it is a leading cause of biofilm contamination of medical devices (7). The most promiscuous and most significant human pathogenic staphylococcal species is Staphylococcus aureus, which is the causal agent of a variety of disease symptoms that can range from cosmetic to lethal manifestations. S. aureus is distinguished from most members of the genus by its abundant production of secreted coagulase, an enzyme which converts serum fibrinogen to fibrin and promotes clotting. However, the S. intermedius group and some strains of Staphylococcus lugdunensis have coagulase activity (5, 8, 9).

Book chapter

Manning KA, Quiles-Puchalt N, Penades JR, Dokland Tet al., 2018, A novel ejection protein from bacteriophage 80 alpha that promotes lytic growth, VIROLOGY, Vol: 525, Pages: 237-247, ISSN: 0042-6822

Journal article

Chen J, Quiles-Puchalt N, Chiang YN, Bacigalupe R, Fillol-Salom A, Chee MSJ, Fitzgerald JR, Penades JRet al., 2018, Genome hypermobility by lateral transduction, Science, Vol: 362, Pages: 207-212, ISSN: 0036-8075

Genetic transduction is a major evolutionary force that underlies bacterial adaptation. Here we report that the temperate bacteriophages of Staphylococcus aureus engage in a distinct form of transduction we term lateral transduction. Staphylococcal prophages do not follow the previously described excision-replication-packaging pathway but instead excise late in their lytic program. Here, DNA packaging initiates in situ from integrated prophages, and large metameric spans including several hundred kilobases of the S. aureus genome are packaged in phage heads at very high frequency. In situ replication before DNA packaging creates multiple prophage genomes so that lateral-transducing particles form during normal phage maturation, transforming parts of the S. aureus chromosome into hypermobile regions of gene transfer.

Journal article

Fillol-Salom A, Martinez-Rubio R, Abdulrahman RF, Chen J, Davies R, Penades JRet al., 2018, Phage-inducible chromosomal islands are ubiquitous within the bacterial universe, The ISME Journal: multidisciplinary journal of microbial ecology, Vol: 12, Pages: 2114-2128, ISSN: 1751-7362

Phage-inducible chromosomal islands (PICIs) are a recently discovered family of pathogenicity islands that contribute substantively to horizontal gene transfer, host adaptation and virulence in Gram-positive cocci. Here we report that similar elements also occur widely in Gram-negative bacteria. As with the PICIs from Gram-positive cocci, their uniqueness is defined by a constellation of features: unique and specific attachment sites, exclusive PICI genes, a phage-dependent mechanism of induction, conserved replication origin organization, convergent mechanisms of phage interference, and specific packaging of PICI DNA into phage-like infectious particles, resulting in very high transfer frequencies. We suggest that the PICIs represent two or more distinct lineages, have spread widely throughout the bacterial world, and have diverged much more slowly than their host organisms or their prophage cousins. Overall, these findings represent the discovery of a universal class of mobile genetic elements.

Journal article

Fernandez L, Gonzalez S, Quiles-Puchalt N, Gutierrez D, Penades JR, Garcia P, Rodriguez Aet al., 2018, Lysogenization of Staphylococcus aureus RN450 by phages phi 11 and phi 80 alpha leads to the activation of the SigB regulon, Scientific Reports, Vol: 8, ISSN: 2045-2322

Staphylococcus aureus is a major opportunistic pathogen that commonly forms biofilms on various biotic and abiotic surfaces. Also, most isolates are known to carry prophages in their genomes. With this in mind, it seems that acquiring a better knowledge of the impact of prophages on the physiology of S. aureus biofilm cells would be useful for developing strategies to eliminate this pathogen. Here, we performed RNA-seq analysis of biofilm cells formed by S. aureus RN450 and two derived strains carrying prophages ϕ11 and ϕ80α. The lysogenic strains displayed increased biofilm formation and production of the carotenoid pigment staphyloxanthin. These phenotypes could be partly explained by the differences in gene expression displayed by prophage-harboring strains, namely an activation of the alternative sigma factor (SigB) regulon and downregulation of genes controlled by the Agr quorum-sensing system, especially the decreased transcription of genes encoding dispersion factors like proteases. Nonetheless, spontaneous lysis of part of the population could also contribute to the increased attached biomass. Interestingly, it appears that the phage CI protein plays a role in orchestrating these phage-host interactions, although more research is needed to confirm this possibility. Likewise, future studies should examine the impact of these two prophages during the infection.

Journal article

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