Brian Coombes

Brian Coombes
McMaster University | McMaster · Department of Biochemistry and Biomedical Sciences

PhD

About

182
Publications
22,433
Reads
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6,844
Citations
Citations since 2017
70 Research Items
3571 Citations
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20172018201920202021202220230200400600
20172018201920202021202220230200400600
20172018201920202021202220230200400600
Introduction
Brian Coombes is a microbial biochemist studying the role of microbes in acute and chronic diseases.
Additional affiliations
July 2016 - present
McMaster University
Position
  • Professor and University Scholar
March 2006 - April 2009
Public Health Agency of Canada
Position
  • Researcher
February 2006 - June 2016
McMaster University
Position
  • Professor (Associate)
Education
August 2002 - February 2006
University of British Columbia - Vancouver
Field of study
  • Postdoctoral Fellowship
September 1997 - May 2002
McMaster University
Field of study
  • PhD, Medical Sciences

Publications

Publications (182)
Article
Full-text available
The emergence and spread of carbapenem-resistant Gram-negative pathogens is a global public health problem. The acquisition of metallo-β-lactamases (MBLs) such as NDM-1 is a principle contributor to the emergence of carbapenem-resistant Gram-negative pathogens that threatens the use of penicillin, cephalosporin and carbapenem antibiotics to treat i...
Article
Full-text available
Crohn's disease is a chronic inflammatory condition of the gastrointestinal tract in which alterations to the bacterial community contribute to disease. Adherent-invasive Escherichia coli are associated with human Crohn's disease; however, their role in intestinal immunopathology is unclear because of the lack of an animal model compatible with chr...
Article
Full-text available
The acquisition of DNA by horizontal gene transfer enables bacteria to adapt to previously unexploited ecological niches. Although horizontal gene transfer and mutation of protein-coding sequences are well-recognized forms of pathogen evolution, the evolutionary significance of cis-regulatory mutations in creating phenotypic diversity through alter...
Article
The increasing use of polymyxins1 in addition to the dissemination of plasmid-borne colistin resistance threatens to cause a serious breach in our last line of defence against multidrug-resistant Gram-negative pathogens, and heralds the emergence of truly pan-resistant infections. Colistin resistance often arises through covalent modification of li...
Article
Full-text available
Author Summary Western societies have a disproportionately high rate of inflammatory bowel disease (IBD), with growing incidence especially in the adolescent population. A large body of evidence supports the view that bacteria in the gut participate in the pathophysiology of human bowel diseases. The unifying concept is chronic inflammation that is...
Article
The NleGs are the largest family of type 3 secreted effectors in attaching and effacing (A/E) pathogens, such as enterohemorrhagic Escherichia coli (EHEC), enteropathogenic E. coli, and Citrobacter rodentium. NleG effectors contain a conserved C-terminal U-box domain acting as a ubiquitin protein ligase and target host proteins via a variable N-ter...
Preprint
Full-text available
Bloodstream infections caused by invasive, non-typhoidal salmonellae (iNTS) are a major global health concern. These infections are especially problematic in sub-Saharan Africa, where the sequence type (ST) 313 of invasive non-typhoidal Salmonella Typhimurium (iNTS) is dominant. Unlike S. Typhimurium strains that cause mild gastroenteritis, iNTS st...
Article
Full-text available
Gram-negative bacteria are intrinsically resistant to a plethora of antibiotics that effectively inhibit the growth of Gram-positive bacteria. The intrinsic resistance of Gram-negative bacteria to classes of antibiotics, including rifamycins, aminocoumarins, macrolides, glycopeptides, and oxazolidinones, has largely been attributed to their lack of...
Article
Full-text available
Crohn’s disease is an inflammatory disease of the gastrointestinal tract characterized by an aberrant response to microbial and environmental triggers. This includes an altered microbiome dominated by Enterobacteriaceae and in particular adherent-invasive E. coli (AIEC). Clinical evidence implicates periods of psychological stress in Crohn’s diseas...
Article
Full-text available
Bacteria inhabit diverse environmental niches and consequently must modulate their metabolism to adapt to stress. The nucleotide second messengers guanosine tetraphosphate (ppGpp) and guanosine pentaphosphate (pppGpp) (collectively referred to as (p)ppGpp) are essential for survival during nutrient starvation. (p)ppGpp is synthesized by the RelA-Sp...
Article
Full-text available
Adherent-invasive Escherichia coli (AIEC) are pathogenic bacteria frequently isolated from patients who have Crohn’s disease (CD). Despite the phenotypic differences between AIEC and commensal E. coli, comparative genomic approaches have been unable to differentiate these two groups, making the identification of key virulence factors a challenge. H...
Article
Mapping the emergence of a highly invasive lineage reveals a crucial step in the evolution of Salmonella strains.
Article
Full-text available
The stringent response is an essential mechanism of metabolic reprogramming during environmental stress that is mediated by the nucleotide alarmones, guanosine tetraphosphate and pentaphosphate ((p)ppGpp). In addition to physiological adaptations, (p)ppGpp also regulates virulence programs in pathogenic bacteria including Salmonella enterica serova...
Article
Full-text available
Antibiotics halt the growth of bacteria by targeting core, essential physiology that is required for life on standard microbiological media. Many more biochemical and virulence processes, however, are required for bacteria to cause infection in a host. Indeed, chemical inhibitors of the latter processes are overlooked using conventional antibiotic...
Article
Full-text available
Anti-virulence therapies are under active investigation as antibiotic alternatives; however, their identification from large-scale chemical libraries poses a unique challenge. The dispensability of virulence factors for growth in vitro precludes conventional, optical density-based screening methods. Here, we provide a protocol for high-throughput s...
Article
Salmonella serovars are leading causes of gastrointestinal disease and have become increasingly resistant to fluoroquinolone and cephalosporin antibiotics. Overcoming this healthcare crisis requires new approaches in antibiotic discovery and the identification of unique bacterial targets. In this work, we describe a chemical genomics approach to id...
Article
Full-text available
Addressing the ongoing antibiotic crisis requires the discovery of compounds with novel mechanisms of action that are capable of treating drug-resistant infections¹. Many antibiotics are sourced from specialized metabolites produced by bacteria, particularly those of the Actinomycetes family². Although actinomycete extracts have traditionally been...
Article
Full-text available
To revitalize the antibiotic pipeline, it is critical to identify and validate new antimicrobial targets¹. In Mycobacteria tuberculosis and Francisella tularensis, biotin biosynthesis is a key fitness determinant during infection2,3,4,5, making it a high-priority target. However, biotin biosynthesis has been overlooked for priority pathogens such a...
Article
Full-text available
Citrobacter rodentium strain DBS100 causes an infection of the intestines in mice. It provides an important model for human gastrointestinal pathogens, such as enteropathogenic and enterohemorrhagic Escherichia coli , which cause life-threatening infections. To identify the genetic determinants that are common across the enteropathogenic bacteria,...
Article
Escherichia coli is one of the most genetically and phenotypically diverse species of bacteria. This remarkable diversity produces a plethora of clinical outcomes following infection and has informed much of what we currently know about host–pathogen interactions for a wide range of bacteria–host relationships. In studying the role of microbes in d...
Article
Full-text available
Microbe-host interactions are generally homeostatic, but when dysfunctional, they can incite food sensitivities and chronic diseases. Celiac disease (CeD) is a food sensitivity characterized by a breakdown of oral tolerance to gluten proteins in genetically predisposed individuals, although the underlying mechanisms are incompletely understood. Her...
Article
Full-text available
Commensal bacteria influence host physiology, without invading host tissues. We show that proteins from segmented filamentous bacteria (SFB) are transferred into intestinal epithelial cells (IECs) through adhesion-directed endocytosis that is distinct from the clathrin-dependent endocytosis of invasive pathogens. This process transfers microbial ce...
Article
Crohn's disease (CD) is an inflammatory bowel disease influenced by bacteria. Adherent-invasive E. coli (AIEC) is associated with CD, yet the adaptations facilitating AIEC gut colonization are unknown. AIEC isolates exhibit high genetic diversity, suggesting strains evolve independently across different gut environments. We tracked the adaptive evo...
Article
The complex infection environment within hosts exerts unique stresses across tissues and cell types, selecting for phenotypic heterogeneity in bacterial populations. Pathogens maintain variability during infection as a strategy to cope with fluctuating host immune conditions, leading to diversification of virulence phenotypes. Recent improvements i...
Article
Full-text available
Salmonella Typhimurium (S. Tm) establishes systemic infection in susceptible hosts by evading the innate immune response and replicating within host phagocytes. Here, we sought to identify inhibitors of intracellular S. Tm replication by conducting parallel chemical screens against S. Tm growing in macrophage-mimicking media and within macrophages....
Article
Background: Crohn's disease (CD) is an inflammatory bowel disease with a complex etiology. Paradoxically, CD is associated with the use of antibiotics and with an increased abundance of an unusual phenotypic group of Escherichia coli known as adherent-invasive E. coli (AIEC). However, the impact of antibiotics on AIEC infection has not been well s...
Article
Full-text available
Bacterial two-component regulatory systems (TCS) couple the detection of niche-specific cues with adaptive gene expression to optimize fitness. In Salmonella Typhimurium (STM), the SsrA-SsrB TCS regulates virulence genes needed for survival within host cells, yet the impact of this TCS on regulatory evolution in this pathogen remains incompletely u...
Article
The pathogenic strategy of Escherichia coli and many other gram-negative pathogens relies on the translocation of a specific set of proteins, called effectors, into the eukaryotic host cell during infection. These effectors act in concert to modulate host cell processes in favor of the invading pathogen. Injected by the type III secretion system (T...
Article
Full-text available
Enteropathogenic Escherichia coli (EPEC) use a needle-like injection apparatus known as the type III secretion system (T3SS) to deliver protein effectors into host cells. Effector translocation is highly stratified in EPEC with the translocated intimin receptor (Tir) being the first effector delivered into the host. CesT is a multi-cargo chaperone...
Data
SDS-PAGE analysis of the Tir peptide-CesT complexes. SDS-PAGE analysis of His6-Tir peptides co-expressed and purified with (A) CesT and (B) CesT138. The resolved samples represent elution fractions from Ni-affinity pull-downs, with Tir residues labeled on top of the corresponding lanes. (TIF)
Data
Table A and B containing the strains, plasmids, and primers used in this study. (DOCX)
Data
Structural comparison of Tir32-80-CesT138 and EHEC CesT dimers. Cartoon representation of the (A) Tir32-80-CesT138 dimer present along the crystallographic 2-fold axis of symmetry, and superposition with (B) EHEC CesT dimer, and (C) crystallographic symmetry mates of EHEC CesT whose domain swapped region superimposes with the Tir binding site. The...
Data
SDS-PAGE analysis of in vitro T3SS assays for the various Tir mutagenesis and domain mutants. EPEC strains grown in T3SS inducing conditions were analyzed for total secreted protein by SDS-PAGE for the (A) Tir β-motif variants, (B) Tir chromosomal truncation mutants, and (C) Tir CesT-extension motif variants. The gels were stained with coomassie br...
Data
Gel filtration chromatography of the purified Tir-CesT complexes. The Tir23-550-CesT (black) and Tir81-550-CesT (green) complexes elutes at ~180–200 kDa. The Tir23-80-CesT (pink), Tir32-80-CesT (red), Tir35-77-CesT (purple), and Tir490-550-CesT (orange) complexes elute at ~50 kDa. CesT (blue) and CesT138 (cyan) are shown for reference and elute as...
Preprint
Full-text available
Salmonella Typhimurium (S. Tm) evades the innate immune response by residing within host phagocytes. To identify inhibitors of intracellular S. Tm growth, we performed parallel chemical screens against S. Tm growing in macrophage-mimicking media and within macrophages. These screens identified novel antibacterials, and revealed that antibiotics wit...
Article
Background Crohn’s disease (CD) is an immune-mediated intestinal illness that is a significant health concern in many developed countries. CD is believed to have a complex etiology consisting of both host susceptibility factors and environmental insults. Multiple epidemiological studies have linked antibiotics with subsequent CD diagnosis. CD is al...
Article
Background Prior exposure to foodborne pathogens causing acute gastroenteritis can have long lasting consequences, including an increased risk of Crohn’s disease (CD). However, the underlying pathologic connection between the inciting event and CD, a chronic inflammatory condition, is not known. Adherent-invasive E. coli (AIEC) are enriched in the...
Article
Full-text available
Plasmid-borne colistin resistance mediated by mcr-1 may contribute to the dissemination of pan-resistant Gram-negative bacteria. Here, we show that mcr-1 confers resistance to colistin-induced lysis and bacterial cell death, but provides minimal protection from the ability of colistin to disrupt the Gram-negative outer membrane. Indeed, for colisti...
Article
Full-text available
The human gut is home to trillions of bacteria and provides the scaffold for one of the most complex microbial ecosystems in nature. Inflammatory bowel diseases, such as Crohn's disease, involve a compositional shift in the microbial constituents of this ecosystem with a marked expansion of Enterobacteriaceae, particularly Escherichia coli. Adheren...
Article
Full-text available
Salmonella Typhimurium has a broad arsenal of genes that are tightly regulated and coordinated to facilitate adaptation to the various host environments it colonizes. The genome of Salmonella Typhimurium has undergone multiple gene acquisition events and has accrued changes in non-coding DNA that have undergone selection by regulatory evolution. To...
Article
Full-text available
The evolution of bacterial pathogenicity, heavily influenced by horizontal gene transfer, provides new virulence factors and regulatory connections that alter bacterial phenotypes. Salmonella pathogenicity islands 1 and 2 (SPI-1 and SPI-2) are chromosomal regions that were acquired at different evolutionary times and are essential for Salmonella vi...
Data
Negative controls for cat reporter assays and EMSAs. Expression of the transcriptional fusions sirA-cat (A) and csrA-cat (B) was determined in the WT S. Typhimurium strain containing the vector pMPM-K3, or the plasmid pK3-SsrB, which expresses SsrB from a constitutive promoter. The CAT-specific activity was determined from bacterial cultures grown...
Data
Growth rates of the WT S. Typhimurium strain and its isogenic ΔSPI-2 mutant inside macrophages. Fold-replication represents the CFUs recovered at the different post-infection times relative to the CFUs at 1 h post-infection for each strain. The dashed line is used to distinguish between increased and decreased replication levels. Data represents th...
Data
Expression of hns in macrophages is not affected by the absence of SsrB. The intracellular expression of the hns-lux transcriptional fusion was examined in the WT S. Typhimurium strain and its derivative ΔSPI-2 mutant (lacking SsrB) in RAW264.7 murine macrophage-like cells. Luminescence was quantified and normalized to CFU counts at 1, 4, 8, 12, an...
Data
Comparison of the promoter sequences contained in the hilD-cat-37+6 and hilA-cat-35+6 transcriptional fusions. Common nucleotides are indicated by shading. The two predicted SsrB binding sites in hilD are shown by red letters. The transcriptional start site (+1) and the -35 and -10 promoter sequences are underlined. (TIFF)
Data
SsrA and SsrB repress the expression of invF inside macrophages. Expression of the invF-lux (A) and hns-lux (B) transcriptional fusion was analyzed in the WT S. Typhimurium strain and its isogenic ΔssrA and ΔssrB mutants inside RAW264.7 murine macrophage-like cells. Monolayers of macrophages were infected with an equal number of bacteria of the res...
Data
Repression of hilA by SsrB requires the DNA sequence located upstream of the hilA promoter. Expression of the hilA-lux-740+350 (full length) (A) and hilA-lux-36+446 (truncated) (B) transcriptional fusions was determined in the WT S. Typhimurium strain and its isogenic ΔssrB mutant containing or not the pWSK129 vector, or the pPssrA-ssrB (D56E) plas...
Data
Mutations in hilA affecting repression by SsrB also affect activation by HilD. Expression of the hilA-cat-100+6 WT (WT SsrB binding site) (A) and hilA-cat-100+6 Mut (mutated SsrB binding site) (B) fusions was determined in the WT S. Typhimurium strain and its isogenic ΔhilD mutant. The CAT-specific activity was determined from bacterial cultures gr...
Data
invF is not de-repressed in the absence of SsrB during in vitro growth conditions. (A) The expression of InvF-FLAG was analyzed by Western blot in the WT S. Typhimurium strain and in a ΔssrB mutant, using monoclonal anti-FLAG antibodies. As a loading control, the expression of DnaK was also determined using monoclonal anti-DnaK antibodies. Expressi...
Article
Intestinal dysbiosis contributes to obesity and insulin resistance, but intervening with antibiotics, prebiotics, or probiotics can be limited by specificity or sustained changes in microbial composition. Postbiotics include bacterial components such as lipopolysaccharides, which have been shown to promote insulin resistance during metabolic endoto...
Article
Genomic analysis of Salmonella Enteritidis isolates taken from a single individual with a chronic and relapsing infection reveals how these bacteria have adapted to their host surroundings. Increased within-host fitness comes at the expense of ancillary traits such as virulence.
Article
Full-text available
Crohn’s disease (CD) is an immune-mediated intestinal illness that significantly compromises health in many developed countries. Although definitive causes remain elusive, the required contribution of microbes in the progression of disease has become an accepted concept. Known CD risk factors, such as antibiotic use and acute infectious gastroenter...
Article
Full-text available
Importance: Salmonella enterica infections other than typhoid and paratyphoid fever are a major global health burden, as they cause high morbidity and mortality worldwide. Strategies that prevent Salmonella-related diseases are greatly needed, and there is a significant push for the development of vaccines against nontyphoidal Salmonella enterica...
Article
The widespread emergence of antibiotic drug resistance has resulted in a worldwide healthcare crisis. In particular, the extensive use of β-lactams, a highly effective class of antibiotics, has been a driver for pervasive β-lactam resistance. Among the most important resistance determinants are the metallo-β-lactamases (MBL), which are zinc-requiri...