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Microbiology Australia Microbiology Australia
Issue 3

Vertical Transmission, September 2010

After a very successful scientific meeting in Sydney, it is good to reflect that the world of microbes is anything but dull and boring! The quality and diversity of the speakers and the material presented is a credit to the National Scientific Advisory Committee and the Local Organising Committee. You may have noticed (in a way we hope you didn’t) but we went into the meeting without our in-house conference organiser, Janette Sofronidis. Sadly for us, Janette left the ASM in May after 10 years of outstanding service. The Society would like to t...

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Diagnostic microbiology in the 21st century – a quiet revolution

It is a very exciting time to be a microbiologist. In the early 21st century we are seeing a maturation of molecular biology methods and their translation into the clinical microbiology laboratory, in combination with improvements in existing methods and substantial increases in the power of information technology.

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Rapid sequencing and analysis for pathogen confirmation

Genetic amplification methods and especially those based on the polymerase chain reaction (PCR) are revolutionising diagnostic microbiology. Genetic amplification is rapidly becoming the method of choice to detect viruses, ‘single pathogen’ infections such as Chlamydia and Gonorrhoea, slow growing or difficult-to-grow bacteria such as mycobacteria and legionella, or toxigenic bacteria such as Shigatoxigenic Escherichia coli and Clostridium difficile. This trend has been accelerated with the use of fluorescent, probe-based, real-time PCR, high-t...

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A pragmatic approach to screening for transmissible resistance in the Enterobacteriaceae

Determining the origin, spread and characteristics of important resistance genes and plasmids in Gram-negative bacteria may be more informative than determining the epidemiology of bacteria themselves. Infection control resistance surveillance and containment efforts should focus on the transmission characteristics of the resistance rather than those of the index organism at the point of recognition.

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Rapid microbial identifications by MALDI-TOF – Viva la revolution!

Although the application of mass spectrometry to bacterial identification was proposed as far back as 1975 by John Anhalt, it was not until 1987 when Professor Franz Hillenkamp and Dr Michael Karas first pioneered Matrix Assisted Laser Desorption/Ionisation Time-of-Flight mass spectrometry (MALDI-TOF MS) for truly rapid microbial identification in diagnostic microbiology laboratories. Conventional phenotypic methods of identifying isolates of bacteria, yeasts and filamentous fungi require hours to several days to complete, depending on the type...

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Diagnosis of herpesviruses and approaches to difficult diagnoses

Herpesviruses are a ubiquitous family of DNA viruses, with 40–60% of the adult population seropositive for cytomegalovirus (CMV), and more than 90% for Epstein-Barr virus (EBV) and varicella zoster virus (VZV). Following primary infection, herpesviruses become latent in the host and may reactivate during periods of immunosuppression, such as in transplant recipients, HIV-positive patients and pregnant women. The clinical course following reactivation presents a screening and diagnostic challenge, particularly as reactivation in immunosuppressed...

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Pitfalls of viral load testing

Viral load testing is the quantitative measurement of viral nucleic acid in body fluids or tissues. In medical practice, viral load assays are commonly performed for HIV, Hepatitis B and Hepatitis C viruses. These assays are funded under the Medicare Benefits Schedule (MBS) system (Item numbers 69378/81/82, 69482/3 and 69488 respectively).

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Diagnosis of influenza following the first wave of pandemic (H1N1) 2009 influenza

Aetiological confirmation of respiratory tract infections in individual patients facilitates appropriate antimicrobial use and infection control procedures. From a public health perspective, influenza confirmation allows assessment of community attack rates and the efficacy of vaccination programs, while assisting in modelling for pandemic preparedness planning. Rapid antigen and immunofluorescent antigen tests are relatively insensitive in detecting pandemic (H1N1) 2009 influenza, and influenza subtype-specific nucleic acid amplification tests...

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Detection and diagnosis of new pathogens

Molecular laboratory techniques are widely used to detect new or previously unrecognised agents which are implicated in infectious disease. In many cases, the traditional microbiology techniques are inadequate and commonly fail to uncover the aetiologic agent, particularly new viruses that continue to challenge the human population. Metagenomics-based tools, such as microarrays and high-throughput deep sequencing are increasingly applied and are ideal for the identification of new human pathogens, particularly viruses.

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Applications and integration of chromogenic culture media in clinical microbiology

The ability to rapidly detect and identify micro-organisms is of paramount importance for many microbiology laboratories. The application of new classes of enzymatic-based chromogenic compounds has revolutionised traditional culture media, leading to the developments of a new generation of chromogenic media. Many studies have shown that the chromogenic agar has become more than an isolation media when compared to conventional culture media. A newer, faster, more cost-effective means in the presumptive identification or screening of microorganis...

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Rapid detection of bacteraemia

Bacteraemic sepsis has a high mortality that can be reduced by early diagnosis and initiation of appropriate antimicrobial therapy 1. Rapid confirmation of the diagnosis and identification of the causal agent provide guidance on the adequacy and duration of antimicrobial therapy and on the need for source investigation. Clinical microbiology laboratories have rightly placed great emphasis on this aspect of their practice. As causal organisms are usually present in low titre, direct microscopy is impractical and laboratories have generally relie...

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‘Swabs’ then and now: cotton to flocked nylon

Microbiological sample collections using cotton-tipped swabs (with or without serum), Dacron™, rayon and calcium alginate, with shafts of wood, plastic and various thicknesses and types of metal have all been used over the years. The swabs have been contained in glass or plastic tubes with and without various types of transport media. Swabs are an easy and popular method of sample collection, although microbiology laboratories traditionally prefer tissue, body fluids or aspirates ahead of swabs. As microbiology laboratories increasingly adopt n...

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Recent advances in molecular and non-PCR-based platforms for the rapid diagnosis of invasive candidasis in the ICU

Invasive candidasis (IC) accounts for 15–30% of all nosocomial intensive care unit (ICU) infections. Two-thirds of infections are due to candidemia, a rate 5–10 times higher compared with that in the general hospital population. Crude mortality rates and associated health costs remain high, despite advances in antifungal therapy. Candida albicans remains the most frequently isolated species (45%) although there has been a slow but definite shift towards non-C. albicans species (especially Candida glabrata) infections, which has been attributed ...

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New approaches to enterovirus identification

The human enteroviruses (HEVs) are members of the Picornaviridae family and cause a diverse range of diseases from respiratory illness to paralysis. Historically, HEVs were isolated in cell culture and subtype identification was by neutralisation using specific antisera. Currently, diagnostic virology laboratories use nucleic-acid-based tests to detect and identify HEVs in clinical specimens.

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DNA sequencing of fungi in a microbiology laboratory

The identification of fungi in a general microbiology laboratory using traditional techniques has always been problematic for several reasons. These include the requirement for trained personnel to identify the fungi, as well as the fact that many fungi take much longer than bacteria to grow, making identification of these organisms in a timely fashion difficult. An additional complication is that some fungi do not show characteristic structures, making identification by traditional techniques difficult, if not impossible. DNA sequencing for th...

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ASM Affairs, September 2010

Vale - Kevin Marshall 1932-2010; Report of the ASM Scientific Meeting, Sydney, 4-8 July 2010; From the Conference, ASM 2010 Sydney; 2010 ASM Awards; Q & A for Glen Ulett, FASM; Jeff Butler – Burnet-Hayes award; Jackie Mahar – Millis-Colwell award

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Book Review

Australian Anti-Infection Handbook; PCR for Clinical Microbiology

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