Commonly asked microbiology questions about uncommon pathogens

Microbiology is constantly changing – we rename pathogens, discover new ones and subdivide others. As molecular technology takes over traditional culture, microbiology interpretation will only become more complex. For this reason, microbiology can be confusing, particularly when a new organism pops up that you can barely pronounce, let alone understand the significance of.

A 52-year-old woman with a background of well-controlled type 2 diabetes presents with left lower-lobe pneumonia and a CURB-65 score of 1. You give her a form for a sputum sample and empirically treat with a course of oral amoxicillin 500mg three times a day.

Three days later, the following laboratory report for her sputum sample appears in your inbox:

Microbiology – moderate numbers of leucocytes, large numbers of mixed organisms, and small numbers of epithelial cells.

Culture – a moderate growth of respiratory flora, with growth of Aspergillus fumigatus (see photo).

Is the Aspergillus significant?

This is a common question I get from GPs. Aspergillus spores are ubiquitous, and we inhale them regularly. These often find their way into the respiratory tract and, when cultured from sputum samples, usually represent colonisation. On occasion, Aspergillus grown from sputum may indicate invasive infection (but the vast majority of people won’t have this). Thus, culture results need to be interpreted in conjunction with clinical information and risk factors for each patient.

Laboratory findings that may suggest infection over colonisation include the presence of fungal hyphae in sputum microscopy and the isolation of Aspergillus from repeated sputum samples. In cases of invasive disease, a diagnosis should generally be made in conjunction with a respiratory specialist as treatment is lengthy and expert guidance is needed if the infection does not respond to treatment.

Aerococcus urinae is an emerging urinary pathogen in older adults, particularly those with comorbidities. This pathogen is usually susceptible to amoxicillin and nitrofurantoin, and often resistant to ciprofloxacin and trimethoprim.

Actinotignum schaalii is another organism you may not have heard of. It is more common in older adults and those with urinary tract abnormalities. Treatment should consist of two weeks of beta-lactam antibiotics. Again, ciprofloxacin and trimethoprim are not reliable.

As always, treating urinary tract infections requires clinical suspicion of infection (eg, lower urinary symptoms) as asymptomatic bacteriuria is common.

Arcanobacterium haemolyticum causes pharyngitis/tonsilitis in adolescents and may cause a rash in up to 50 per cent of patients. Erythromycin is the drug of choice. Penicillin and amoxicillin are good alternatives, but the occasional treatment failure has been documented. Occasionally, this organism can cause skin/soft tissue infections, but will respond to the same treatments.

Plesiomonas is a freshwater organism that causes a range of diarrhoeal illness, from mild secretory diarrhoea to a more invasive dysenteric illness

Blastocystis hominis and Dientamoeba fragilis are both protozoan organisms of disputed pathogenicity. They are found in both symptomatic and asymptomatic individuals. Although some reports have found their presence associated with diarrhoea, abdominal pain, nausea and vomiting, other studies have found no association between the presence of these organisms and gastrointestinal disease. They should only be considered as a possible cause of gastrointestinal symptoms after exclusion of other causes. Treatment for both (if warranted) is metronidazole – seven days for B. hominis and 10 days for D. fragilis.

The role of Aeromonas (spp.) as a gastrointestinal pathogen is also uncertain. Isolation of this freshwater organism from the stool of asymptomatic individuals is common, but it seems to be isolated more commonly from patients with diarrhoea. It has been implicated as a cause of acute secretory diarrhoea, acute dysentery (with blood), chronic diarrhoea (lasting >10 days) and traveller’s diarrhoea. Treatment is usually self-limiting, but most local isolates are susceptible to cotrimoxazole. For invasive infections (severe skin/soft tissue infection, bacteraemia), discuss treatment with an infection specialist.

Less common, but similar to Aeromonas, Plesiomonas (spp.) is a freshwater organism that causes a range of diarrhoeal illness, from mild secretory diarrhoea to a more invasive dysenteric illness. Gastrointestinal infection is usually self-limiting, but this organism can cause invasive infection, particularly skin/soft tissue infection. If considering treatment, discussion with an infection specialist is advised.

With many labs now using PCR to detect faecal pathogens, a number of GPs will regularly find shiga toxin-producing Escherichia coli (eg, E.coli O157:H7) in their laboratory reports. Shiga toxin-producing E. coli may cause painful diarrhoea that often becomes bloody. The most important complication of this infection is haemolytic uraemic syndrome, which is reported in 6 to 9 per cent of infections. Although relatively uncommon, the highest incidence is in children under age 10.

Laboratory findings of HUS include haemolytic anaemia with red blood cell fragments, thrombocytopenia and acute kidney injury. Onset is typically between days five and 10 of illness. Antimicrobial treatment is not recommended. If HUS develops, a prompt hospital referral is required for supportive treatment of acute kidney injury and anaemia.

Aaron Keene is a clinical microbiologist at Southern Community Laboratories in Christchurch