Table of contents for this article

• • What is a virus
  • How does a virus spread?
  • The difference between Viruses and bacteria
  • Common viral infections

What is a virus?

Viruses are small groups of genetic code, such as DNA or RNA, enclosed within a shell of protein. A virus cannot survive or multiply on its own, nor can it obtain or store energy. It requires a living organism, or host, which it must inhabit to perform these functions that are basic to life. Hosts can be bacteria, plants, or animals,including human beings.

The incapability of a virus to survive without a host means that they are classed as non-living entities.

Some viruses, like the coronavirus SARS-CoV-2 behind COVID-19, infect the host for a number of days or weeks before being cleared from the system. Other viruses, like varicella-zoster that causes chickenpox, and the human immunodeficiency virus (HIV), can sit dormant in a host without causing an active infection for a number of years.

Read here to find out what happens when you’ve had a Covid test, from collection to results

How does a virus spread?

Most people are now aware that the SARS-CoV-2 virus can be spread through respiratory infection symptoms such as sneezing and coughing, and can also be spread through actions such as speaking or breathing.

There are four primary forms of transmission in which viruses spread:

1. Airborne transmission: Airborne transmission occurs when infected viral droplets in the air are inhaled by another living organism. Airborne transmission is how COVID-19 is commonly spread.

2. Vehicle transmission: Vehicle transmission occurs when food, water, body fluids, or inanimate objects passively carry the virus and transmit it when they come in contact with a potential host organism.

3. Direct transmission: Direct contact transmission occurs when viral particles are spread through physical contact between an infected and uninfected animal, plant, or human being. Examples include ingesting infected foodstuffs or transmission via kissing or sexual activity.

4. Indirect transmission: Indirect contact transmission occurs when the viral particles are spread via contact with contaminated materials such as unsterile medical equipment.

Difference between Viruses and bacteria

On the surface of it, viruses and bacteria may seem very similar. They are spread from human to human in very similar ways and can have similar ravaging effects on human bodies. However, there are in fact far more differences than similarities between them.

Viruses are much smaller than bacteria, and even the largest virus is tinier than the smallest bacterium.

A virus needs a living host to survive, thrive and multiply. This is not the case for bacteria, and they can live independently in almost any environment.

Treatment for bacterial infection is primarily via antibiotics. Antibiotics do not have an effect on viruses, which are generally treated with anti-viral agents where available.

Vaccines are an important preventive agent against viruses.

Common viral infections

• Coronavirus
• Influenza – causes ‘the ‘flu’
• Rhinoviruses – cause the ‘common cold’
• Human papillomavirus (HPV) – causes genital warts and cervical cancer
• Varicella-zoster – causes chickenpox
• Noroviruses – cause vomiting and diarrhoea
• Measles
• Mumps

What is the endgame of a virus?

From an evolutionary perspective, the ‘perfect’ virus is one that infects as many hosts as possible to replicate, without killing the host in the process, because the host is needed to aid transmission. The SARS-CoV-2 virus does this very well. Most infected people don’t die from the infection, and it has a relatively long incubation period, which is the time from infection to the point where symptoms are first displayed. This, and the highly effective manner in which it is transmitted through the air, make it a very successful virus.

The post What is a virus: How viruses spread, how they differ from bacteria, and common viral infections first appeared on Know Pathology Know Healthcare.

A recent study, published in the journal Nature npj Biofilms and Microbiomes, has demonstrated that gut bacteria can be used to determine whether a cancer drug will work for a certain individual and also if the patient is likely suffer side effects. The study was based on previous evidence that has shown people metabolize drugs in different ways depending on their microbiome.

Although still in the early stages, this research could potentially be the basis for future pathology tests which would help clinicians to better manage cancer treatments and possibly treatments for other diseases, too.

To see whether a person’s microbiome affected how they metabolized cancer drugs, researchers at the Albert Einstein College of Medicine in New York City collected faecal samples from 20 healthy individuals and treated the samples with irinotecan – a chemotherapy drug used to treat colorectal cancer.

When the researchers analysed the treated faecal samples they found that those containing a large amount of an enzyme called beta-glucuronidase, which is produced by gut bacteria, were less able to metabolise the drug. For a patient receiving irinotecan as treatment, this inability to metabolise the drug means they absorb the toxic substance rather than excrete it as waste, and this leads to side effects such as diarrhoea and dehydration.

Commenting on the study, lead researcher A/Professor Libusha Kelly explained the impact of side effects on patients: “Patients with colorectal cancer are already quite ill, so giving them a treatment that causes intestinal problems can be very dangerous. At the same time, irinotecan is an important weapon against this type of cancer.”

The research also demonstrated that beta-glucuronidase enzymes in the gut can interact with other more common drugs including ibuprofen and morphine. This interaction can “reactivate” the drugs in the liver, causing patients to absorb higher than intended doses.

According to Emily Balskus, a biochemist at Harvard University, pathology testing could one day be used to screen people’s microbiomes and determine whether a drug will work for them. If a person’s microbiome seems problematic, doctors could prescribe an enzyme inhibitor or put them on a diet that provides the bacteria with an alternate food source, which could stop beta-glucuronidase enzymes from interfering with the metabolism of the drug.

Dr Nick Musgrave, Pathology Awareness Australia ambassador is interested to see where this kind of research leads;

“Year by year we’re learning more about the impact of the microbiome on our health. The news that it impacts the metabolism of certain chemotherapeutic agents is further proof of this. It will be interesting to see if the microbiome also has an impact on other treatments. Of course these are very early days in our understanding of the effects of an individual’s microbiome and how to manage these effects.”

The post The surprising link between gut bacteria and cancer treatment first appeared on Know Pathology Know Healthcare.

The bug in question was Burkholderia cepacia, a type of bacteria that is usually found in soil, water or other liquids. It is not commonly found in blood samples sent to pathology labs but in this case, it had been found in patient blood samples. ¹

The patients in question were in the hospital’s intensive care unit (ICU) and were quite unwell. It was suspected that they had contracted an infection in the ICU, which is why the blood samples were sent for bacterial culture.

However, the characteristics of the B. cepacia organism and the fact that both patients were getting better on antibiotics that wouldn’t have usually treated this organism led to a suspicion that the blood samples had somehow been contaminated.

This is a rare occurrence in pathology labs and an investigation swiftly commenced to find the source of contamination, beginning with testing equipment and materials in the laboratory environment.

Dr Maloney returned from leave and was surprised to discover that despite extensive testing the cause had not been found but several more cases of B. cepacia in blood had arisen.

Professor Ramon Shaban is Clinical Chair in the Department of Infection Control at Gold Coast Health and says staff were working hard to find the cause.

“This is an environmental, water-based organism, so it’s unusual to see it as a bacteraemia (bacteria in the blood). We tested IV fluids and non-sterile gels that have been associated with outbreaks around the world, and were working our way through products to find the cause. We also contacted our peers and soon learned that other cases had been identified across Queensland and interstate, which supported our working hypothesis that this was a point source outbreak.”

A point source outbreak is where patients are exposed to a single source of the bacteria in a brief time period and there is no spread from person to person.

The search intensified and widened, and the culprit was quickly identified, Dr Maloney said:

“Ramon and I went to see a doctor who had been treating one of the patients and put in a central line the day before, when a blood sample was also taken. We asked the doctor to show us what equipment he used and where he had got it. We collected all these items including the ultrasound gel and took everything back to the lab to be tested. The next day I was surprised when Brian Gorman, a senior scientist let me know that we had a suspicious organism growing from the ultrasound gel that was labelled ‘sterile’. This was the gel that was used during ultrasound guided cannulation, and the suspicious organism turned out to be Burkholderia cepacia.”

A central line is a catheter inserted into the vein of a patient needing supply of medication or fluids over an extended period. The process is called cannulation and when ultrasound imaging guides the process a gel is used.

The fact that this product, which was supposed to be sterile but was not, was manufactured internationally was a serious concern to the team, who immediately issued a formal alert to other hospitals across the country.

In-depth microbiological testing was able to establish that the patients from GCUH and the other cases were all affected by the same bacteria and that the ultrasound gel was the common cause.

The Gold Coast Health team notified the Australian Therapeutic Goods Administration (TGA). Approximately 1400 kits containing the gel had been distributed to a dozen hospitals across Australia and within 36 hours the TGA had issued a recall for all these kits.

Ultimately, at least 12 patients tested positive for the bacteria but only one person had symptoms that were directly attributed to B. capacia and they have since recovered.

Dr Maloney said; “In cases like these the doctor is sending a blood sample to pathology because their patient is ill and they need to know why. With an unusual organism like this it is less clear if that is what is causing the illness, so you need to use all the pathology results as well as any other investigations that might be relevant such as diagnostic imaging, to build a full picture of what could be causing symptoms to ensure the patient gets the right treatment.”

Prof Shaban noted that the process was challenging with an unusual bug affecting a range of patients:

“The patients had few common clinical characteristics, which made it more difficult to track down the cause of the infection.”

The fast and systematic approach of the team at Gold Coast Health may well have saved lives. Bacteraemia (bacteria in the blood) is a serious condition and can be life-threatening. Had the contaminated gel not been recalled many more patients would have been affected.

Reference

1. Shaban RZ, Maloney S, Gerrard J, Collignon P, Macbeth D, Cruickshank M, Hume A, Jennison AV, Graham RMA, Bergh H, Wilson HL, Derrington P. (2017). Outbreak of healthcare-associated Burkholderia cenocepacia bacteraemia and infection attributed to contaminated ‘sterile’ gel used for central line insertion under ultrasound guidance and other procedures.  American Journal of Infection Control, Accepted 24 June, 2017.

The post A race against the clock for infection detectives in Queensland first appeared on Know Pathology Know Healthcare.

1. It may feel like collectors take a lot of blood when you have a blood test, don’t worry, 15 million blood cells are produced and destroyed in the human body every second!
2. Until the 1960s, pregnancy tests involved injecting a woman’s urine into a female African clawed frog!
3. The pap smear was developed by Georgios Papanicolaou. His wife, Mary, was his first subject – having a cervical smear every day for 21 years, all in the name of science!
4. Pathology is vital in the fight against antibiotic resistance as it tells doctors when to use antibiotics and which drug will be most effective. Milk from Tasmanian Devils could provide an effective antibiotic against superbugs. Peptides in the milk have been shown to kill the infamous ‘golden staph’ superbug. Go the Devils!
5. 17th Century Dutchman Antoni van Leeuwenhoek was the first to use a microscope to study tiny organisms. Widely known as ‘The Father of Microbiology’ he gave these organisms a name rarely used today, ‘animalcules’. This cute-sounding Latin name means ‘little animals’.
6. A technique developed in Queensland in 2014 uses venom from the Coastal Taipan or Eastern Brown Snakes to perform blood tests for patients on anticoagulant medications.
7. The average human body carries ten times more bacterial cells than human cells and scarily the strongest creatures on Earth are gonorrhoea bacteria. They can pull 100,000 times their own body weight.
8. Don’t worry though, most of the bacteria we carry are helpful. Bacteria produce chemicals that help us harness energy and nutrients from our food. Research has shown that germ-free rodents have to consume a third more calories than normal rodents to maintain body weight.
9. In Mesopotamia medical practitioners examined the livers of sacrificed sheep. At the time, the liver was thought to be the source of human blood. Clay models of sheep livers date back as far as 2050 B.C. Talk about medicine gone baaad!
10. In Medieval Europe, doctors often diagnosed their patients by observing the urine’s smell, consistency – and even its taste. Urine analysis was pioneered by Thomas Willis in the 1600s – he was the first to notice the characteristic sweet taste of urine from patients with diabetes.

What fantastic facts do you know about pathology? Post them at #IPD2016

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It has the mysterious name MALDI-TOF and to add to its futuristic feel it uses a laser inside a vacuum tube to perform tests on samples prepared with something known as “the matrix”.

(MALDI-TOF stands for Matrix-Assisted Laser Desorption & Ionisation- Time Of Flight.)

In order to operate this intriguing instrument, a scientist prepares a sample on a testing plate, firstly using Formic acid to assist in breaking down cell walls and exposing the proteins.

A liquid called the matrix is then applied and the proteins crystallize as it dries.

This plate of crystalline protein structures is then placed in a ‘well’ inside the large vacuum tube in the machine. A laser at the top of the tube is shot at the sample and measures the ‘peaks’ of the crystals.
This matches them with a database of organisms to determine what the bug in question is and how best to treat it.

So why is this important?

Before going in the machine, the scientist must use the sample to grow the organism.

Prior to the MALDI-TOF, scientists had to grow an organism for between 18 and 24 hours and sometimes up to 40 hours.

Once the organism had grown tests could then be set up but some of these could also take up to 18 hours, meaning the whole process could take days.

Now the MALDI-TOF can use growth 4 hours old to give a result, which only takes 30 seconds inside the machine.

In the case of life-threatening infections like septicaemia, this could save lives.

David Lorenz is a hospital scientist working in microbiology at the St Vincents Hospital pathology laboratory in Sydney.

“If something went wrong with the barrage of biochemical tests set up for the identification of an organism, you wouldn’t necessarily know of the problem until 24 hours later and then you’d have to start again. Although mistakes are rare, with the MALDI-TOF you can know within a minute if there is a problem with the sample and then you can run the test again.”

David says that not only has the MALDI-TOF improved lab turnaround times, which is clearly a benefit to patients and those treating them, it has improved workloads in labs too.

The machine can run up to 96 tests simultaneously every hour and is very accurate.

However, there are still some organisms that the MALDI-TOF cannot tell apart and results need to be interpreted by a skilled medical scientist. If the machine produces a result which is unclear or unusual a scientist can then choose to rerun tests or use alternative methods to identify bacteria.

MALDI-TOF can be used to identify all bacterial illnesses, including bacterial meningitis, E.coli and gonorrhoea. It can also be used on yeast and some fungi.

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