“I have a 3 year old patient with an infected ulcer on their leg which is proving particularly difficult to treat” was the opening statement from the Surgeon.
 
“What antibiotic are you giving?” asked the Microbiologist in a surly tone, thinking this was going to be a simple case of wrong antibiotic.
 
“I’ve been using Co-amoxiclav, but it doesn’t seem to be getting better” was the reply.
 
“Have you sent any samples to the lab?”
 
“I swabbed the wound and the result has come back showing a Coagulase-positive Staphylococcus; I wonder if this might be Staphylococcus pseudintermedius or possibly Staphylococcus aureus” said the Surgeon.
 
“Staphylococcus aureus is the most common bacterium we see in this situation” answered the Microbiologist, “why do you think it might be Staphylococcus pseudintermedius?”
 
“In our patients Staphylococcus pseudintermedius is often grown from these types of samples…oh, I forgot to mention, I’m a Veterinary Surgeon and the 3 year old patient is a Husky” was the reply…. “I should say too that the bacterium is resistant to beta-lactams… according to the report…

Looking down the blood cultures list whilst prioritising what needed phoning out first the Microbiologist noticed a blood culture positive on day 3 with a Gram-positive bacillus in the aerobic bottle only. Normally this wouldn’t provoke much interest as most pathogens grow within 12-24 hours and most Gram-positive bacilli are skin contaminants (Corynebacterium spp. and Cutibacterium spp.). However these were unlikely in this case: Corynebacterium spp. normally grow faster than this and would be in both bottles whereas Cutibacterium spp. although anaerobes tend to grow much slower. The clinical details just said “fever” (not overly helpful!) and considering the sample was 3 days old already, it didn’t seem that urgent, so the Microbiologist put it to the bottom of the list and got on busily calling out all of the Gram-negative bacilli and Gram-positive cocci, as these were more likely to be significant.

​Having cleared all the other positive blood cultures the Microbiologist came back to the Gram-positive bacillus. Looking up where the patient had been on this admission showed the blood culture had been taken in the Emergency Department, the patient had then briefly gone to the medical admissions unit before being discharged later the same day. Not much to go on there then. Maybe it wasn’t going to be significant after all.
 
Out of curiosity the Microbiologist then decided to check if the patient had been in before. This threw up something unexpected. The patient had had multiple attendances to the haematology ward as well as the outpatient clinic. Pulling up the clinic letters showed that the patient actually had chronic lymphoblastic leukaemia (CLL) and would therefore be immunosuppressed. This changed the situation; the blood culture could be an opportunistic pathogen and not a contaminant at all, muttering to himself, “chronic lymphoblastic anaemia is significant info for the specimen request card, when will they learn!” the Microbiologist decided to phone out the result straight away.
 
Still cursing healthcare staff who don’t fill out request forms with adequate clinical details, the Microbiologist bleeped the Haematology Registrar to find out more…
 
It turned out that the patient had presented to the Emergency Department with a fever and shortness of breath. The fever settled and the blood tests showed the patient wasn’t neutropaenic. The blood cultures had been taken before the blood test results came back. A dose of Piptazobactam had also been given in case the patient had febrile neutropaenia but this had been stopped when the neutrophil count was shown to be in the normal range. “As the patient was feeling better they were allowed to go home”, the Registrar said a little sheepishly knowing something was amiss if the Microbiologist was “showing concern”.
 
“Mmmmm…” said the Microbiologist to himself, “a blood culture positive on day 3 with a Gram-positive bacillus in the aerobic bottle only”… “Mmmmm…” he said again “this could be Nocardia”. The Microbiologist suggested getting the patient back in for a review whilst the laboratory tried to identify the microorganism. By the time the patient had been reassessed the organism had a name, Nocardia farcinica.

​What are the Nocardia spp.?
Nocardia spp. are a group of aerobic Gram-positive bacilli which do not take up Gram’s stain very well and so appear as long beaded Gram-positive bacilli. They have some mycolic acid in their cell wall, as a result they can be stained using a modified Ziehl-Neelsen (ZN) stain. The modified ZN stain uses 0.5-1% acid-alcohol as a decolouriser rather than the normal 3% used for Mycobacterium spp.  
 
Nocardia spp. live ubiquitously in soil, water and organic material within the environment. They are found worldwide.
 
On culture Nocardia spp. are slow growing, taking 2-3 days to produce typical colonies which look a bit like small fungi with hyphae. In fact early Microbiologists thought they were fungi and hence named all of the similar organisms to Nocardia spp. the Actinomycetes (a mycete is a fungus). They are bacteria though.
 
There are over 80 species within the Nocardia genus but the most common causing human disease include:

• Nocardia asteroides
• Nocardia farcinica
• Nocardia nova
• Nocardia camea
• Nocardia braziliensis
• Nocardia otitidiscaviarum
• Nocardia cyriacigeorgica
• Nocardia abscessus

 
How does infection with Nocardia spp. present?
The most common presentation of infection with Nocardia spp., known as nocardiosis, is with pneumonia, lung abscesses and lung cavitation. This is because the bacteria are most commonly acquired by inhalation. People with a normal immune system usually clear the bacteria but immunosuppression, especially defective cell mediated immunity, predisposes to this opportunistic pathogen. The most common immune problems include prolonged steroid use, haematological cancer, chemotherapy, organ transplantation and Human Immunodeficiency Virus infection.
 
Occasional infections occur in skin and soft tissue following contamination of wounds e.g. soil inoculation of a thorn injury or an animal or insect bite. In this case cellulitis or superficial abscesses are the most common presentations.
 
With pulmonary infections, infection spreads from the lungs via the blood stream to any body organ, but especially the brain where the bacteria cause abscesses; this is more common with N. farcinica than other species. Untreated pulmonary infections sometimes erode through the tissues of the thorax to discharge onto the chest wall through sinuses.

How is nocardiosis diagnosed?
Nocardiosis is diagnosed through the culture of Nocardia spp. from normally sterile sites. Identification of the bacterium used to be a bit of a nightmare and was based upon colonial appearance on agar, Gram appearance, modified ZN and unreliable biochemical methods. Nowadays MaldiTOF and PCR are excellent and reliable ways of identifying this bacterium.
 
If someone is suspected of having nocardiosis then further imaging is required, especially of the thorax. It is worth talking directly to the Radiologists to find the best modality for investigating. In my experience CT is often useful but I’m not a Radiologist. Confirmation of infection usually requires sticking a needle into the suspected site and aspirating pus for further laboratory testing; again this is often conducted by Radiologists.
 
Any immunocompromised patient with cutaneous or pulmonary infection should also have a brain scan to look for dissemination.
 
How is nocardiosis treated?
The treatment of nocardiosis can be difficult. It is important to test the individual bacteria for antimicrobial sensitivity as they are not always predictable. There is no national or international standard method for doing this but both Etests and broth dilution are suitable.
 
The species of bacterium is also important as some are more resistant than others e.g. N. farcinica is usually resistant to 3rd generation cephalosporins such as Ceftriaxone as well as Imipenem. Source control is also important, including drainage of abscesses and debridement of infected tissue wherever possible.
 
Trimethoprim-Sulfamethoxazole (Septrin) is the usual first line treatment with other agents added as required. Empirical first line treatments include:

Duration:

• Pulmonary 6-12 months
• Immunocompromised or disseminated ≥ 12 months
• For severe infection or disseminated disease IV antimicrobials should be continued for at least 6 weeks at which stage the patient can be converted to orals
• Cutaneous 3-6 months

 
Once sensitivities are known patients on three agent regimens can be converted to two agent regimens.
 
If there is no improvement within 2 weeks of starting treatment then the patient should be reviewed, further source control undertaken and consideration given to changing the antibiotics to alternative agents. Other antibiotics shown to have activity against some Nocardia spp. include: Co-amoxiclav, Ceftriaxone, Ciprofloxacin, Clarithromycin, Linezolid, Minocycline, Doxycycline and Tobramycin.
 
Monitoring
It is important to keep a close eye on these patients to look for disease progression as well as treatment toxicity. The most important toxicity is bone marrow suppression from the prolonged Trimethoprim-Sulfamethoxazole treatment. At least fortnightly full blood count, Urea and electrolytes and liver function tests should be checked. In addition further imaging is often required; some experts repeat imaging at 1, 3, 6 and 12 months of treatment and then 6 and 12 months after treatment to ensure there is no relapse.
 
With early diagnosis and targeted antimicrobial treatment the long term survival is 90%.
 
So our patient was brought back into hospital and reassessed. A CT scan of their chest showed a number of cavities however the scan of their head was normal. They were started on IV antimicrobials and by two weeks had started to improve. The patient was advised it was going to be a long course of treatment, the Microbiologist returned to the list of blood cultures to see if he could “intervene”, or more accurately “meddle”, with any other patient and their unsuspecting Registrar!

While sat in the cystic fibrosis multidisciplinary team (MDT) meeting a tricky clinical question was asked…
 
“We have a patient with an infective exacerbation of their cystic fibrosis with Burkholderia multivorans but she is allergic to Ceftazidime and Meropenem and gets bad gastrointestinal symptoms with tetracyclines. What do you think?” asked the Respiratory Consultant.
 
I really like these types of MDTs when I have to scratch my head and try to work out a solution but this one was a bit of a puzzler. I know Ceftazidime and Meropenem are often used to treat infections with Burkholderia spp. and that Minocycline is also an option, but what to do when these can’t be used? I had to admit I didn’t know for sure and that I would have to go and look at the literature and get back to them. So off I went to consultant the “Interweb”.

“Happy birthday to us, happy birthday to us, happy birthday dear Bug Blog, happy birthday to ussss…”
The Bug Blog is 5 years old! You may not realise it but we have been doing this together for 5 years. In that time we have written over 190 blogs on various microbiology related subjects as diverse as Proteus mirabilis (which Penny thinks smells like chocolate!), necrotising fasciitis and even Poldark’s Putrid Throat. It can be quite a challenge to find the time to write a blog every week but we strive to keep it up (on average we have managed about 40 per year). What makes it worthwhile is all of you out there taking the trouble to read what we have to say. So thank you for staying with us and reading all of our microbiological rambles…

A recent conversation got me thinking… a rare occurrence some would say… about the identification of bacteria. The patient I was discussing had two bacteria growing in his blood cultures and we weren’t sure if both were genuine or whether one was a skin contaminant. There was both a Staphylococcus spp. and a Proteus mirabilis growing, but the P. mirabilis was growing all over the Staphylococcus spp. preventing its further identification. I suggested putting up a CLED agar plate (see later in the blog) and a number of people looked at me like I was crazy… and whilst I do occasionally come up with some crazy ideas this really wasn’t one of the them. To understand my logic you have to know a bit about P. mirabilis, especially its laboratory identification. Let me explain further…

Last week saw an event of great celebration and much excitement and even made it onto the national TV news… No, I’m not talking about the marriage of Prince Harry and Megan Merkel... I’m talking about the birth of a little baby boy who turned up unexpectedly 3 months post-term!
 
Okay, so clearly 3 months post-term is not going to be a human baby. This baby weighed somewhere between 90-120 kg and took over 22 months to “cook” in his 35-year-old mum Thi-Hi-Way. Yep, he’s an elephant calf, and his keepers at Chester Zoo were caught completely by surprise when they came in to work on Friday morning to find a new-born elephant calf amongst their herd of Asian elephants. Wow what a job! They had thought his mum had miscarried as she had gone long past her due date, but low-and-behold they were wrong… I hope they call him Harry for obvious reasons!
http://www.chesterstandard.co.uk/news/16239014.Surprise_baby_elephant_birth_at_Chester_Zoo_astonishes_keepers/ 

In 1941 John Rex Whinfield and James Tennant Dickson of Calico Printers' Association of Manchester, England, patented a new compound that changed the way foods are packaged, the clothes we wear and many other manufacturing processes. The compound was poly(ethylene terephthalate) (PET), and is the most widely used polyester plastic worldwide. About 60% of the world’s PET is used to produce polyester often in the context of clothing production, with about 30% being used to produce plastic drinks bottles.

The Microbiology Consultant was waiting for the new Microbiology Registrar to finish the authorisation before going through any problems or questions they had. They started with their first question, a urine isolate which was identified as Pseudomonas aeruginosa but the antibiotic sensitivities didn’t make sense. The bacterium was sensitive to Co-amoxiclav and Ceftriaxone but resistant to Gentamicin and Amikacin. Pseudomonas aeruginosa is normally resistant to Co-amoxiclav and Ceftriaxone and sensitive to Gentamicin and Amikacin. A “nonsensical” or “incorrect” result like this should normally prompt further investigation as to what might be wrong before it is authorised or released.

The patient’s mother was at her wits end. Her little boy’s head was covered in scaly skin. At first she thought his scaly hair was dandruff so she had washed his hair in medicated shampoo but this was met with screams and tears. She thought he was being a bit extreme “it’s only dandruff” but guessed kids can be funny about having soap in their eyes. He just kept saying “mummy my head is really sore”. Tonight he had refused to have his hair washed and while trying to get him into bed, she noticed he was going bald! She was so alarmed that she brought him in to the Emergency Department for help.

Gosh nearly 2,000 of you read last weeks’ blog on cholera (that’s a record) and it sparked a couple of really good questions to Nuts & Bolts.
 
One from Virginia related to the use of TCBS agar to grow Vibrio cholerae, so I thought that this week I would cover some “old fashioned” microbiology and talk about agar. Really! I hear you cry “that’s not very interesting”! Well, as “interesting” is banned when discussing microbiology, I’ll use “actually very clever” to describe the reasons why we use different types of agar in the laboratory… here goes…