Bio303 laboratory diagnosis of infection
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In this Bio303 module talk, I provide an overview of how infections are diagnosed in the clinical microbiology lab, focusing on technologies, old and new, and also on practical issues and workflows crucial to optimal use of the lab.
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Bio303 laboratory diagnosis of infection
- 1. Laboratory Diagnosis of Infectious Disease: From Gram-stain to Genomes Professor Mark Pallen
- 6. A proper clinical assessment is essential for optimal use of laboratory services!
- 9. Laboratory Diagnosis of Infection culture on plates or in broth identification by biochemical or serological tests on pure growth from single colony microscopy Decolorise Counterstain Stain unstained or stained with e.g. Gram stain sensitivities Serodiagnosis DNA technologies by disc diffusion methods, breakpoints or MICs
- 11. The Gram Stain Crystal violet Gram's iodine Decolorise with acetone Counterstain with e.g. methyl red Gram-positives appear purple Gram-negatives appear pink
- 12. The Gram Stain Gram-positive rods Gram-negative rods Gram-positive cocci Gram-negative cocci
- 21. The E Test
- 36. The Birth of Genomic Epidemiology for Bacteria
- 37. The Birth of Genomic Epidemiology for Bacteria
- 41. Results: Outbreak Isolates Are Distinguishable At Only Three Loci SNP 1 SNP 2 SNP 3 AB0057 C A G M1 C A G M2 T A G M3 T A T M4 T A G C1 T T G C2 T A G
- 46. 19 th Century 21 st Century 20 th Century
Editor's Notes
- 95 & 63 strains
- 95 & 63 strains
- Change shading Ultimately, we detected three SNP loci which allowed us to distinguish between isolates in the outbreak. These are presented with reference to an unrelated Acinetobacter reference, AB57 which we consider has the “ancestral” state at these loci.
- Referring back to the outbreak diagram we can plot these consequent genotypes onto each isolate. So when considering C1 it can be seen that it has a unique genotype compared with the others thus making it hard to make a compelling case for transmission from any of the military patients. But when we consider the case of C2 it can be seen that it shares the same genotype as M2 and M4. Given that M2 and C2 were in neighboring beds around week 4 but M4 did not come into contact with C2 at any point, we believe we can make a strong case for transmission from M2 and C2.
- You can read the full story of these study in the Journal of Hospital Infection where it is available as an online pre-print. Our analyses support transmission of MDR-Aci from the wound of a military patient M2 to the respiratory tract of a civilian patient C2. As MDR-Aci was not isolated from C2 until several weeks after M2 left the adjacent bed, however, we cannot determine when and how transmission occurred. One possibility is that C2 became colonised when the two patients were nursed together, but that colonisation did not reach detectable levels in the sputum until much later. Another possibility is that M2 contaminated the local environment and C2 acquired the organism from the environment only after M2 had left the ward. This latter option would be consistent with a significant role of the environment.