Lecture 28 Applied Aspects of Microbial Evolution PDF

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SmoothPipeOrgan6770

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Cornell University

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microbial evolution antibiotic resistance viral evolution biology

Summary

This lecture covers applied aspects of microbial evolution, including evolution in action, antibiotic resistance, and viral evolution, focusing on influenza, HIV, and coronavirus. It details examples like MRSA and discusses the rapid evolution of these pathogens.

Full Transcript

ecture 28 Applied Aspects of Microbial Evolution ecture 28 Applied Aspects of Microbial Evolution 1)Evolution in Action 2)Evolution of Antibiotic Resistance 3)Viral Evolution - Influenza - HIV Coronavirus ) Evolution in Action Long Term Experiment...

ecture 28 Applied Aspects of Microbial Evolution ecture 28 Applied Aspects of Microbial Evolution 1)Evolution in Action 2)Evolution of Antibiotic Resistance 3)Viral Evolution - Influenza - HIV Coronavirus ) Evolution in Action Long Term Experimental Evolution of E. coli E. coli grown in a minimal glucose medium volution gives... ) Evolution in Action xperimental Evolution in Rhodobacter capsulatus R. capsulatus can use malate as e- donor to grow either: -by anoxygenic photosynthesis -or by fermentation. and it takes away. Evolution of Antibiotic Resistance The Problem of Antibiotic Resistance >30,000 tons/yr AB used in US (>100g/person) 60% of AB used in agricultural animal production ~70% of hospital acquired infections caused by AB resistant bacteria (changes in gene frequency are caused by selection and/or Evolution of Antibiotic Resistance The Problem of Antibiotic Resistance Evolution of Antibiotic Resistance Evolution of Antibiotic Resistance Evolution of Antibiotic Resistance Spontaneous mutation - modify existing genes -modify the target of the antibiotic -modify cell permeability to the antibiotic Horizontal Gene Transfer - acquire resistance genes for: -enzymes that inactivate an antibiotic -new proteins that compensate for loss of function Evolution of Antibiotic Resistance Example: MRSA - Methicillin Resistant Staphylococcus aureus more people in U.S die from MRSA than AIDS Staphylococcus aureus is common on skin MRSA is defined by presence of SCCmec gene cassette Evolution of Antibiotic Resistance SCCmec: staphylococcal chromosomal cassette containing mecA - mecA encodes a transpeptidase resistant to many beta-lactam antibiotics - SCCmec also has cassette chromosome recombinase (ccr) genes for integration and excision of the gene cassette into the bacterial chromosome 3) Viral Evolution Evolution and Influenza A Variants: classified by immune reaction H: Hemagglutinin, 18 known types (6 found in people) N: Neuraminidase, 11 known types (3 found in people) 3) Viral Evolution Evolution and Influenza A Antigenic Variation Antigenic drift: mutation (seasonal flu) change of 2-3 amino acids in H or N proteins can alter your immune response to the virus rendering you susceptible Reassortment: recombination (pandemic flu) recombination between human and zoonotic stains in a co- infected host can generate a 1. Would antigenic shift or drift have the most profound impact on our immune system? a). Antigenic shift (reassortment) b). Antigenic drift 1. Would antigenic shift or drift have the most profound impact on our immune system? Antigenic shift Antigenic drift 2. Why do we need a seasonal flu shot? 3) Viral Evolution 1918 Pandemic ~50 million deaths worldwide, ~675k in US 1957 Pandemic ~1.1 million deaths worldwide, ~116k in US 1968 Pandemic ~1 million deaths worldwide, ~100k in US Seasonal Flu ~250-500k deaths worldwide, ~30-50k in US 3) Viral Evolution Reassortment From 2009 within zoonotic H1N1 caused a pandemic in 2009 After the 1918 pandemic, antigenic drift has caused seasonal outbreaks of H1N1 Reassortment with an unknown zoonotic strain lead Current H5N1 Bird Flu Sit uation in Dairy Cows | Bir d Flu | CDC A multistate outbreak of HPAI A(H5N1) bird flu in dairy cows was first reported on March 25, 2024. This is the first time that these bird flu viruses had been found in cows. In the United States, since 2022, USDA APHIS has reported HPAI A(H5N1) virus detections in more than 200 mammals. A concerning development: H5N1 bird flu has infected a pig in Oregon, officials say – LA Times Oregon state and federal officials confirmed Wednesday that H5N1 bird flu was found in a pig living in Crook County — the first such swine infection reported in the current outbreak. The strain of bird flu virus in the pig is slightly different from the one that has been plaguing dairy cows in California and other states, which is known as B3.13. Instead, it is called D1 and probably originated in wild birds migrating along the Pacific flyway. Both strains are H5N1; they just followed slightly different evolutionary trajectories, which is reflected in their genetic sequence. Swine are considered by health officials to be Finding the flu virus in a pig, regardless of the efficient influenza mixing bowls: They are strain, is a concerning development, scientists say, susceptible to both avian and human flu viruses especially as human flu season begins. and can potentially provide an opportunity for different viruses to exchange genetic materials 3) Viral Evolution Evolution and HIV ~40 million infected worldwide, ~1M deaths/yr (~5k in USA) Genome: ssRNA (+) virus, 22k base pair genome (~22 genes) Host range: specific to primates Multiple independent origins (~1930s) HIV-1: chimp origin HIV-2: monkey origin Why do we still not have a good vaccine for HIV? 3) Viral Evolution SIV has jumped to humans at least twice, resulting in at least 5 different HIV groups Simian Immunodeficiency viruses (SIV) of apes Simian Immunodeficiency viruses (SIV) of monkeys 3) Viral Evolution Evolution and HIV Antigenic Variation - Rapid Mutation: mutates rapidly within host - Rapid Recombination: recombination between different variants in a host contributes to evolution Consequences of rapid evolution - Immune system evasion - Evolution of drug resistance 3) Viral Evolution HIV Evolution in 9 people over 10 years Virus: SARS-CoV-2 Disease: COVID-19 Transmission: airborne-aerosolized droplets Classification: Coronaviridae, Betacoronavirus Structure: enveloped virus Genome: +ssRNA, ~30 kb long, 27 genes Coronavirdiae: Viruses of bats that can jump species barriers. Seven are known to infect humans. Four cause mild respiratory ~5M deaths infections (“colds”), two: SARS-CoV and worldwide, ~750k in MERS-CoV cause severe respiratory US infections, and SARS-CoV-2 is the newest Phylogenetic tree of COVID-19 Lu et al 2020, Lancet, 395:56 COVID Variants Genomic Analysis of SARS-CoV-2 No evidence for reassortment w/ other viruses. Has a proofreading enzyme! Hence, the mutation rate is much slower than flu. SARS-CoV-2 strains are all highly similar (

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