2024 ESKAPE Pathogens Lecture 1 PDF

Professor Christopher McDevitt Email: http://mcdevittlab.org Department of Microbiology & Immunology Peter Doherty Institute for Infection and Immunity  Learn the bacteria that make up the ESKAPE pathogens Understand the key virulence, genomic Learning...

Professor Christopher McDevitt Email: http://mcdevittlab.org Department of Microbiology & Immunology Peter Doherty Institute for Infection and Immunity  Learn the bacteria that make up the ESKAPE pathogens Understand the key virulence, genomic Learning and evolutionary factors that have led to the rise of MRSA and VRE Objectives Know the molecular mechanisms for vancomycin and methicillin resistance in VRE and MRSA, respectively  “Resistance to antibiotics could bring the end of modern medicine as we know it” Margaret Chan, 2012 Director-General, WHO  Common opportunistic and nosocomial pathogens with high levels of antibiotic resistance from multiple mechanisms E Enterococcus faecium S Staphylococcus aureus K Klebsiella pneumoniae A Acinetobacter baumannii P Pseudomonas aeruginosa E Enterobacter spp.  Enterococcus faecium Staphylococcus Klebsiella pneumoniae aureus Acinetobacter baumannii Pseudomonas aeruginosa Enterobacter sp.  World Health Organization (WHO) priority pathogens for development on new antibiotic therapeutics Medium Priority High Priority Critical Priority 1. Streptococcus pneumoniae 1. Enterococcus faecium 1. Acinetobacter baumannii 2. Haemophilus influenzae 2. Staphylococcus aureus 2. Pseudomonas aeruginosa 3. Shigella spp. 3. Helicobacter pylori 3. Enterobacteriaceae 4. Campylobacter 5. Salmonella spp. 6. Neisseria gonorrhoeae  Gram-positive, cocci shaped bacterium Also known as ‘Golden Staph’ Discovered in 1884 by Friedrich Rosenbach Non-motile and non-spore forming Catalase positive β-haemolytic on blood-agar plates ⍺-toxin lyses red blood cells Common component of microbial flora Major cause of healthcare associated infections (HAI) >500,000 infections per year in US hospitals >50,000 deaths each year in USA  Skin infections Minor skin infections such as pimples, impetigo and boils Invasive soft-tissue infections, such as cellulitis Food poisoning Enterotoxigenic strains Life threatening serious infections Endocarditis (heart valve infections), bacteraemia, pneumonia, osteomyelitis, implant infections Transmission Contact an infected object or tissue (e.g. pus) Nosocomial infections – often from colonised healthcare workers Community acquired/hospital acquired infections have increased over the past 20 years  Bacterial capsule Adhesins Microbial surface components that recognize adhesive matrix molecules (MSCRAMMs) Enable initial attachment of bacteria to host tissue. Biofilm formation Enzymes Coagulase, hyaluronidase, DNases, and lipases Toxins Superantigens – e.g. TSST-1 Enterotoxins α-toxin, β-toxin, etc  S. aureus genome Average genome size is ~2.8 Mbp Clinical isolates range from 2.5 – 3.0 Mbp Genomes encode between 2,500 and 2,800 open reading frames (strain dependent) Core genome is only 1,441 genes Accessory genome and unique genes make up about 80% (5,970 genes) of the pan-genomic content Pan-genome is heavily enriched for genes associated with mobile genetic elements Transposons Bacteriophages Staphylococcal cassette chromosome (SCC) elements  Methicillin Semi-synthetic β-lactamase resistant penicillin introduced in 1959 Methicillin resistant S. aureus emerged in 1960 MRSA remained rare until the 1980s Resistance due to mecA gene – alternate PBP (PBP2a) Confers resistance to almost all β-lactam antibiotics Unlike penicillin resistance, methicillin resistance is not by plasmid-borne β-lactamase Spread to many staphylococcal species On mobile genetic elements  Mobile genetic element transmission of methicillin resistance SCCmec Mobile 21-60 Kb element Multiple SCCmec types Similar genetic structure Resistance acquired from environmental staphylococci Genomic analysis show regions from environmental and animal staphylococcal species with high levels of similarity to MRSA SCCmec Species include Staphylococcus sciuri, Staphylococcus fleurettii and Staphylococcus vitulinus  Gram-positive, cocci shaped bacterium Occurs as pairs or as chains Catalase negative Associated with healthcare associated infections (HAI) Gamma-haemolytic (i.e. non-haemolytic) No apparent haemolysis on blood agar, but there can be a slight discolouration Other enterococci can show haemolysis Commensal bacterium, but can also be a pathogen Gastrointestinal (GI) tract of humans and animals Outbreak-related enterococci have acquired tailored gene repertoires not present in commensal organisms  E. faecium genome Average genome size is ~2.85 Mbp Animal and clinical isolates range from 2.4 – 3.4 Mbp Genomes encode between 2,300 and 3,300 open reading frames (strain dependent) Core genome is only 1,013 genes Accessory genome and unique genes make up about two-thirds of the pan-genomic content Pan-genome is heavily enriched for genes involved in carbohydrate transport and metabolism  MSCRAMMs (microbial surface components recognizing adhesive matrix molecules)  Worldwide transmission and spread of HAIs In E. faecium: HAIs associated with clade A, while clade B represents commensal bacteria Clade A features: Altered cell wall and capsule Missing CRISPR system Unique phosphotransfer system Prominent starvation tolerance Overall better adapted to hospital environment  HAI-related E. faecium primarily emerged by gaining genes through horizontal gene transfer (HGT) HGT is a prominent driver of E. faecium strain diversity E. faecium genome is highly dynamic Constant flux of accessory genes through HGT events Acquisition of new genetic material mainly via conjugation Not known to be naturally transformable (i.e. not naturally competent) Acquisition of genes related to antimicrobial resistance  E. faecium genomes contain a total of 34 unique antibiotic resistance genes Penicillin Average of 9 antibiotic resistance genes per genome Significant isolate to isolate variation in resistance complement Intrinsic resistance to most β-lactam antibiotics Attributable to a low affinity for PBP5 b-lactam ring Ampicillin can be used for treatment Monotherapy for endocarditis treatment has a relatively poor cure rate (< 40%). Kanamycin Intrinsic resistance to aminoglycoside antibiotics Poor penetration into cells limits efficacy Acquired resistance HGT events facilitating the acquisition of new or enhancing resistance mechanisms  Vancomycin Vancomycin is a glycopeptide antibiotic used to treat Gram-positive bacterial infections Vancomycin Resistant Enterococci (VRE) Resistance emerged in 1980s Leading cause of MDR infections ~80% of device associated infections such as catheter, central line, ventilators Limited treatment options for VRE infections VRE colonized individuals are more likely to transmit the pathogen to other patients  Vancomycin inhibits cell wall synthesis in Gram-positive bacteria Prevents D-ala D-ala moieties from interacting with the cell wall cross-linking enzyme Vancomycin resistance Change of the D-ala D-ala moiety to D-ala D-lac reduces vancomycin binding affinity by ~1000-fold Other stem peptide variations have also been observed (D-ala D-ser) Cell wall synthesis no longer blocked  Vancomycin is made by the soil bacterium Amycolatopsis orientalis Resistance mechanisms may have been acquired from this or a related organism Expression of an enzyme alters the terminal residue VanA – High level resistance to vancomycin and teicoplanin; inducible upon exposure to antibiotic VanB – Low level resistance to vancomycin; inducible upon exposure  vanA operon carried on Tn1546 Predominantly occurs within an Inc18 family plasmid Can also occur in a plasmid independent manner Vancomycin intermediate S. aureus (VISA) VISA arises from mutations that result in thicker cell wall via increased D-Ala-D-Ala production Vancomycin resistant S. aureus (VRSA) Vancomycin susceptible S. aureus (VSSA) acquires resistance vanA genes move from VRE to Tn1546 moved from VRE to MRSA on conjugative plasmid Tn1546 then transposed to a plasmid resident in VSSA Vancomycin resistance not yet widespread in S. aureus  vanB operon on Tn1549 Tn1549 carried by commensal anaerobic gut bacteria Mobilised via HGT within the GI tract to E. faecium De novo evolution of vanB-mediated resistance also observed in patients  Key Learning Concepts S. aureus Highly significant bacterial pathogen that can cause a range of acute and invasive infections Genome is enriched for mobile genetic elements which permits transmission of virulence factors, such as antibiotic resistance Methicillin resistance arises from mecA, which is on SSCmec, a mobile genetic element E. faecium A GI tract commensal, but also associated with outbreak as a HAI Genomics of HAI strains reveal tailored genetic repertoires comprised of genes for capsule formation, adherence to biotic and abiotic surfaces and biofilm formation Vancomycin resistance in VRE is carried on mobile genetic elements, which can be transmitted to other bacteria