2014 molecular microbiology meeting

Molecular Microbiology Meeting, Waterview, Sydney, 5-6th March, 2014.

As is often the case with specialist national conferences, the recent Molecular Microbiology Meeting was an exceptional opportunity to share ideas and learn from others working in the same field.  The choice of which four talks to review was a difficult one, particularly for the MicroGnome, who took notes from dawn to dusk on both conference days. Topics covered by the speakers ranged across all the main categories of infective agent, through diagnosis, antimicrobial resistance and molecular epidemiology, to emerging biotechnology and clinical pathology lab administration. With a tight timetable, speakers were notably disciplined in keeping to schedule, which allowed plenty of time for questions.


Here is a taste of what you missed:

Whole genome sequencing for bacteriology, S Bentley, Cambridge

Molecular microbiology methods are being used increasingly in laboratory diagnosis, detection of antimicrobial resistance, in outbreak investigation and to investigate vaccine escape. The impact of bacterial whole genome sequencing (WGS) is being felt in analysis of mutations, single nucleotide polymorphisms, and of gene presence/absence. WGS applications in bacteriology include identification, assessment of virulence, antimicrobial resistance, potential vaccine coverage and phylogenetic relationships. Challenges of translation of WGS into clinical applications include integration into the clinical laboratory, infection control practice which requires, in turn data interpretation, reporting and database management, linked to what the physician user wants. Notable examples include:

  • MRSA transmission pathway mapping, which is more discriminating by WGS than by MLST. Potential cost savings by application of WGS to infection control.
  • XDRTB where continued spread may occur due to the length of time required to culture then analyse the bacteria. Faster detection of XDRTB can inform treatment decisions.

Carbapenemase-producing Enterobacteriaceae, GM Rossoline, Siena

Several distinct families of carbapenemases have emerged. These are transferable, in high risk bacterial lineages that retain their virulence. They include three main types; KPC, OXO-48-like and the metallobetalactamases (MBL), IMP, VIM & NDM. The KPC form of resistance arrived in Italy in 2008 and has since spread widely so that it was common by later 2013. It is also widespread in Greece. Treatment options are limited and suboptimal, so that there is increased risk of treatment failure. There is newly emergent Colistin resistance in these bacteria, which removes one of the last remaining effective antibiotics. Selection of stable Colistin resistance in the absence of the antibiotic has occurred, with stepwise increase in resistance. Colistin should therefore not be used alone for treatment of KPC+ Klebsiella pneumoniae infections. CPE remain in the intestine for prolonged periods and thus remain a risk to the patient and their contacts. New antimicrobial agents are being assessed including combinations with betalactamases inhibitors. But for the meantime, we will have to rely on combination antimicrobial therapy, infection control and antibiotic stewardship.

Vancomycin resistant Staphylococci, B Howden, Melbourne

MRSA first came to attention in 1961 and has since become a recognised cause of high mortality infection. In 1991 an ability to form a Vancomycin high MIC subpopulation was noted, and subsequently referred to as heteroresistance. The evolution of high MIC Vancomycin resistant S. aureus (VRSA) was demonstrated in 2009 as a result of a chimeric plasmid containing elements of enterococcal origin. Transcriptional analysis demonstrates key differences in bacterial capsule, protein A and aspartate synthesis. Changes in a two component system affect bacterial cell wall metabolism and are associated with increased cell wall thickness. In a hollow fibre infection model run over 10 days, variable vancomycin doseage was associated with changes in the genes coding for the two component system. Serial passage of the bacteria showed reduced fitness. Tracking the evolution of S.aureus during the course of prolonged systemic infection, small colony variants were seen to emerge with time. These observations may explain why rifampicin resistance emerges quickly when given simultaneously with Vancomycin.

Bacterial detection and dynamics in sepsis, Westmead group, Sydney

The key problem for the clinical laboratory in sepsis is that culture takes 24-48 hours to generate useful results and nucleic cid amplification tests still take 12-18 hours, when critical results are needed within 5 hours. In a study that used 16s DNA targets to identify the bacteria responsible for DNAaemia in sepsis, results were available in a few hours. Satisfactory explanations were available for the few initially discordant results. For Gram negative species, DNA positive results persisted for up to 3 days, but Gram positive cocci subsided in most cases by 24 hours. Although there are hundreds of Gram negative antibiotic resistance genes, a much smaller selection can be used to predict the majority of clinically important resistance types. Optimal choice of anticoagulant is needed for the blood sample tube. Higher bacterial counts in severe sepsis and septic shock make detection easier in these patients.



  1. Very good and comprehensive post. Enjoyed it. There has to be a solution for the duration of the tests.
    Best regards

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