mBio

Journal: mBio

Publisher

American Society for Microbiology

ISSN

2150-7511, 2161-2129

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Publications 1 - 10 of 44

Gut Microbial Glycerol Metabolism as an Endogenous Acrolein Source
Zhang, Jianbo; Sturla, Shana; Lacroix, Christophe; et al. (2018)
mBio
Acrolein is a highly reactive electrophile causing toxic effects, such as DNA and protein adduction, oxidative stress, endoplasmic reticulum stress, immune dysfunction, and membrane damage. This Opinion/Hypothesis provides an overview of endogenous and exogenous acrolein sources, acrolein’s mode of action, and its metabolic fate. Recent reports underpin the finding that gut microbial glycerol metabolism leading to the formation of reuterin is an additional source of endogenous acrolein. Reuterin is an antimicrobial multicomponent system consisting of 3-hydroxypropionaldehyde, its dimer and hydrate, and also acrolein. The major conclusion is that gut microbes can metabolize glycerol to reuterin and that this transformation occurs in vivo. Given the known toxicity of acrolein, the observation that acrolein is formed in the gut necessitates further investigations on functional relevance for gut microbiota and the host.
Prophages and Growth Dynamics Confound Experimental Results with Antibiotic-Tolerant Persister Cells
Harms, Alexander; Fino, Cinzia; Sørensen, Michael A.; et al. (2017)
mBio
Bacterial persisters are phenotypic variants that survive antibiotic treatment in a dormant state and can be formed by multiple pathways. We recently proposed that the second messenger (p)ppGpp drives Escherichia coli persister formation through protease Lon and activation of toxin-antitoxin (TA) modules. This model found considerable support among researchers studying persisters but also generated controversy as part of recent debates in the field. In this study, we therefore used our previous work as a model to critically examine common experimental procedures to understand and overcome the inconsistencies often observed between results of different laboratories. Our results show that seemingly simple antibiotic killing assays are very sensitive to variations in culture conditions and bacterial growth phase. Additionally, we found that some assay conditions cause the killing of antibiotic-tolerant persisters via induction of cryptic prophages. Similarly, the inadvertent infection of mutant strains with bacteriophage ϕ80, a notorious laboratory contaminant, apparently caused several of the phenotypes that we reported in our previous studies. We therefore reconstructed all infected mutants and probed the validity of our model of persister formation in a refined assay setup that uses robust culture conditions and unravels the dynamics of persister cells through all bacterial growth stages. Our results confirm the importance of (p)ppGpp and Lon but no longer support a role of TA modules in E. coli persister formation under unstressed conditions. We anticipate that the results and approaches reported in our study will lay the ground for future work in the field.
Screening of Escherichia coli species biodiversity reveals new biofilm-associated antiadhesion polysaccharides
Rendueles, Olaya; Travier, Laetitia; Latour-Lambert, Patricia; et al. (2011)
mBio
Bacterial biofilms often form multispecies communities in which complex but ill-understood competition and coop-eration interactions occur. In light of the profound physiological modifications associated with this lifestyle, we hypothesizedthat the biofilm environment might represent an untapped source of natural bioactive molecules interfering with bacterial adhe-sion or biofilm formation. We produced cell-free solutions extracted fromin vitromature biofilms formed by 122 naturalEsche-richia coliisolates, and we screened these biofilm extracts for antiadhesion molecules active on a panel of Gram-positive andGram-negative bacteria. Using this approach, we showed that 20% of the tested biofilm extracts contained molecules that antag-onize bacterial growth or adhesion. We characterized a compound, produced by a commensal animalE. colistrain, for whichactivity is detected only in biofilm extract. Biochemical and genetic analyses showed that this compound corresponds to a newtype of released high-molecular-weight polysaccharide whose biofilm-associated production is regulated by the RfaH protein.We demonstrated that the antiadhesion activity of this polysaccharide was restricted to Gram-positive bacteria and that its pro-duction reduced susceptibility to invasion and provided rapid exclusion ofStaphylococcus aureusfrom mixedE. coliandS. au-reusbiofilms. Our results therefore demonstrate that biofilms contain molecules that contribute to the dynamics of mixed bacte-rial communities and that are not or only poorly detected in unconcentrated planktonic supernatants. Systematic identificationof these compounds could lead to strategies that limit pathogen surface colonization and reduce the burden associated with thedevelopment of bacterial biofilms on medical devices.
Genomic and geographic context for the evolution of high-risk carbapenem-resistant enterobacter cloacae complex clones ST171 and ST78
Gomez-Simmonds, Angela; Annavajhala, Medini K.; Wang, Zheng; et al. (2018)
mBio
Recent reports have established the escalating threat of carbapenem-resistant Enterobacter cloacae complex (CREC). Here, we demonstrate that CREC has evolved as a highly antibiotic-resistant rather than highly virulent nosocomial pathogen. Applying genomics and Bayesian phylogenetic analyses to a 7-year collection of CREC isolates from a northern Manhattan hospital system and to a large set of publicly available, geographically diverse genomes, we demonstrate clonal spread of a single clone, ST171. We estimate that two major clades of epidemic ST171 diverged prior to 1962, subsequently spreading in parallel from the Northeastern to the Mid-Atlantic and Midwestern United States and demonstrating links to international sites. Acquisition of carbapenem and fluoroquinolone resistance determinants by both clades preceded widespread use of these drugs in the mid-1980s, suggesting that antibiotic pressure contributed substantially to its spread. Despite a unique mobile repertoire, ST171 isolates showed decreased virulence in vitro. While a second clone, ST78, substantially contributed to the emergence of CREC, it encompasses diverse carbapenemase-harboring plasmids, including a potentially hypertransmissible IncN plasmid, also present in other sequence types. Rather than heightened virulence, CREC demonstrates lineage-specific, multifactorial adaptations to nosocomial environments coupled with a unique potential to acquire and disseminate carbapenem resistance genes. These findings indicate a need for robust surveillance efforts that are attentive to the potential for local and international spread of high-risk CREC clones.
Rapid and strain-specific resistance evolution of Staphylococcus aureus against inhibitory molecules secreted by Pseudomonas aeruginosa
Niggli, Selina; Schwyter, Lukas; Poveda, Lucy; et al. (2023)
mBio
Pseudomonas aeruginosa and Staphylococcus aureus frequently occur together in polymicrobial infections, and there is evidence that their interactions negatively affect disease outcome in patients. At the molecular level, interactions between the two bacterial species are well-described, with P. aeruginosa usually being the dominant species suppressing S. aureus through a variety of inhibitory molecules. However, in chronic infections the two species interact over prolonged periods of time, and S. aureus might be able to evolve resistance against inhibitory molecules deployed by P. aeruginosa. Here, we used experimental evolution to test this hypothesis by exposing three different S. aureus strains (Cowan I, 6850, and JE2) to the growth-inhibitory supernatant of P. aeruginosa PAO1 over 30 days. Prior to evolution, we found that S. aureus strains were inhibited by secreted compounds regulatorily controlled by the Pseudomonas quinolone signal quorum-sensing system. Following evolution, inhibitory effects were significantly attenuated, and we observed that adaptations were S. aureus strain specific and involved the upregulation of virulence traits such as staphyloxanthin production and the formation of small colony variants. At the genetic level, mutations in membrane transporters (known to be involved in antibacterial uptake) were the most frequent evolutionary targets. Our work indicates that adaptations of S. aureus to P. aeruginosa occurs rapidly and affect both virulence trait expression and membrane transporter functionality. Thus, pathogen evolution could promote species co-existence and complicate treatment options in infections.
Associations among wine grape microbiome, metabolome, and fermentation behavior suggest microbial contribution to regional wine characteristics
Bokulich, Nicholas; Collins, Thomas S.; Masarweh, Chad; et al. (2016)
mBio
Regionally distinct wine characteristics (terroir) are an important aspect of wine production and consumer appreciation. Microbial activity is an integral part of wine production, and grape and wine microbiota present regionally defined patterns associated with vineyard and climatic conditions, but the degree to which these microbial patterns associate with the chemical composition of wine is unclear. Through a longitudinal survey of over 200 commercial wine fermentations, we demonstrate that both grape microbiota and wine metabolite profiles distinguish viticultural area designations and individual vineyards within Napa and Sonoma Counties, California. Associations among wine microbiota and fermentation characteristics suggest new links between microbiota, fermentation performance, and wine properties. The bacterial and fungal consortia of wine fermentations, composed from vineyard and winery sources, correlate with the chemical composition of the finished wines and predict metabolite abundances in finished wines using machine learning models. The use of postharvest microbiota as an early predictor of wine chemical composition is unprecedented and potentially poses a new paradigm for quality control of agricultural products. These findings add further evidence that microbial activity is associated with wine terroir.
Barcoded Consortium Infections Resolve Cell Type-Dependent Salmonella enterica Serovar Typhimurium Entry Mechanisms
Di Martino, Maria L.; Ek, Viktor; Hardt, Wolf-Dietrich; et al. (2019)
mBio
Bacterial host cell invasion mechanisms depend on the bacterium’s virulence factors and the properties of the target cell. The enteropathogen Salmonella enterica serovar Typhimurium (S.Tm) invades epithelial cell types in the gut mucosa and a variety of immune cell types at later infection stages. The molecular mechanism(s) of host cell entry has, however, been studied predominantly in epithelial cell lines. S.Tm uses a type three secretion system (TTSS-1) to translocate effectors into the host cell cytosol, thereby sparking actin ruffle-dependent entry. The ruffles also fuel cooperative invasion by bystander bacteria. In addition, several TTSS-1-independent entry mechanisms exist, involving alternative S.Tm virulence factors, or the passive uptake of bacteria by phagocytosis. However, it remains ill-defined how S.Tm invasion mechanisms vary between host cells. Here, we developed an internally controlled and scalable method to map S.Tm invasion mechanisms across host cell types and conditions. The method relies on host cell infections with consortia of chromosomally tagged wild-type and mutant S.Tm strains, where the abundance of each strain can be quantified by qPCR or amplicon sequencing. Using this methodology, we quantified cooccurring TTSS-1-dependent, cooperative, and TTSS-1-independent invasion events in epithelial, monocyte, and macrophage cells. We found S.Tm invasion of epithelial cells and monocytes to proceed by a similar MOI-dependent mix of TTSS-1-dependent and cooperative mechanisms. TTSS-1-independent entry was more frequent in macrophages. Still, TTSS-1-dependent invasion dominated during the first minutes of interaction also with this cell type. Finally, the combined action of the SopB/SopE/SopE2 effectors was sufficient to explain TTSS-1-dependent invasion across both epithelial and phagocytic cells.
An Early Pandemic Analysis of SARS-CoV-2 Population Structure and Dynamics in Arizona
Ladner, Jason T.; Larsen, Brendan B.; Bowers, Jolene R.; et al. (2020)
mBio
In December of 2019, a novel coronavirus, SARS-CoV-2, emerged in the city of Wuhan, China, causing severe morbidity and mortality. Since then, the virus has swept across the globe, causing millions of confirmed infections and hundreds of thousands of deaths. To better understand the nature of the pandemic and the introduction and spread of the virus in Arizona, we sequenced viral genomes from clinical samples tested at the TGen North Clinical Laboratory, the Arizona Department of Health Services, and those collected as part of community surveillance projects at Arizona State University and the University of Arizona. Phylogenetic analysis of 84 genomes from across Arizona revealed a minimum of 11 distinct introductions inferred to have occurred during February and March. We show that >80% of our sequences descend from strains that were initially circulating widely in Europe but have since dominated the outbreak in the United States. In addition, we show that the first reported case of community transmission in Arizona descended from the Washington state outbreak that was discovered in late February. Notably, none of the observed transmission clusters are epidemiologically linked to the original travel-related case in the state, suggesting successful early isolation and quarantine. Finally, we use molecular clock analyses to demonstrate a lack of identifiable, widespread cryptic transmission in Arizona prior to the middle of February 2020.
Multi-omics profiling of cross-resistance between ceftazidime-avibactam and meropenem identifies common and strain-specific mechanisms in Pseudomonas aeruginosa clinical isolates
Bartmanski, Bartosz J.; Bösch, Anja; Schmitt, Steven; et al. (2025)
mBio
Pseudomonas aeruginosa is a highly versatile and resilient pathogen that can infect different tissues and rapidly develop resistance to multiple drugs. Ceftazidime-avibactam (CZA) is an antibiotic often used to treat multidrug-resistant infections; however, the knowledge on the CZA resistance mechanisms in P. aeruginosa is limited. Here, we performed laboratory evolution of eight clinical isolates of P. aeruginosa exposed to either CZA or meropenem (MEM) in sub-inhibitory concentrations and used multi-omics profiling to investigate emerging resistance mechanisms. The majority of strains exposed to MEM developed high resistance (83%, 20/24 strains from eight clinical isolates), with only 17% (4/24) acquiring cross-resistance to CZA. The rate of resistance evolution to CZA was substantially lower (21%, 5/24), while 38% (9/24) acquired cross-resistance to MEM. Whole-genome sequencing revealed strain heterogeneity and different evolutionary paths, with three genes mutated in three or more strains: dacB in CZA-treated strains and oprD and ftsI in MEM-treated strains. Transcriptomic and proteomic analysis underlined heterogeneous strain response to antibiotic treatment with few commonly regulated genes and proteins. To identify genes potentially associated with antibiotic resistance, we built a machine learning model that could separate CZA- and MEM-resistant from sensitive strains based on gene expression and protein abundances. To test some of the identified associations, we performed CRISPR-Cas9 genome editing that demonstrated that mutations in dacB, ampD, and, to a lesser extent, in mexR directly affected CZA resistance. Overall, this study provides novel insights into the strain-specific molecular mechanisms regulating CZA resistance in Pseudomonas aeruginosa.IMPORTANCEPseudomonas aeruginosa is one of the most difficult-to-treat pathogens in the hospital, which often acquires resistance to multiple antibiotics. Ceftazidime-avibactam (CZA) is an essential antibiotic used to treat multidrug-resistant infections, but its resistance mechanisms are not well understood. Here we investigated the evolution of resistance to CZA and meropenem (MEM) in eight clinical bacterial isolates from patients' blood, urine, and sputum. While the rate of resistance evolution to MEM was higher than to CZA, MEM-resistant strains rarely acquired cross-resistance toward CZA. To identify changes at the genome, transcriptome, and proteome levels during antibiotic exposure, we performed multi-omics profiling of the evolved strains and confirmed the effect of several genes on antibiotic resistance with genetic engineering. Altogether, our study provides insights into the molecular response of P. aeruginosa to CZA and MEM and informs therapeutic interventions, suggesting that CZA could still be effective for patients infected with MEM-resistant pathogens.
The Intestinal Microbiota Interferes with the microRNA Response upon Oral Listeria Infection
Archambaud, Cristel; Sismeiro, Odile; Toedling, Joern; et al. (2013)
mBio
The intestinal tract is the largest reservoir of microbes in the human body. The intestinal microbiota is thought to be able to modulate alterations of the gut induced by enteropathogens, thereby maintaining homeostasis. Listeria monocytogenes is the agent of listeriosis, an infection transmitted to humans upon ingestion of contaminated food. Crossing of the intestinal barrier is a critical step of the infection before dissemination into deeper organs. Here, we investigated the role of the intestinal microbiota in the regulation of host protein-coding genes and microRNA (miRNA or miR) expression during Listeria infection. We first established the intestinal miRNA signatures corresponding to the 10 most highly expressed miRNAs in the murine ileum of conventional and germfree mice, noninfected and infected with Listeria. Next, we identified 6 miRNAs whose expression decreased upon Listeria infection in conventional mice. Strikingly, five of these miRNA expression variations (in miR-143, miR- 148a, miR-200b, miR-200c, and miR-378) were dependent on the presence of the microbiota. In addition, as is already known, protein-coding genes were highly affected by infection in both conventional and germfree mice. By crossing bioinformatically the predicted targets of the miRNAs to our whole-genome transcriptomic data, we revealed an miRNA-mRNA network that suggested miRNA-mediated global regulation during intestinal infection. Other recent studies have revealed an miRNA response to either bacterial pathogens or commensal bacteria. In contrast, our work provides an unprecedented insight into the impact of the intestinal microbiota on host transcriptional reprogramming during infection by a human pathogen.

Publications 1 - 10 of 44

Journal: mBio

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