Dr. Anna Smielewska, a consultant virologist in the UK, spoke at ESCMID Global about 16S rRNA sequencing in healthcare settings. The title of the session was “Implementing portable, real-time 16S rRNA sequencing in the healthcare sector enhances antimicrobial stewardship.” Smielewska works with the Liverpool University Hospitals, several hospitals with a broad range of cases. The first clinical case was about an asylum seeker with three years in the UK and three in Germany. The patient presented with swelling and itching of skin that was generalized followed by swelling of hands and feet a year later. After that, the person had swelling and rash on lips and face, then torso, hands, and feet. Smielewska explained that 16S sequencing can help with “precise, timely and specific diagnostics.” A massive robot or susceptibility disks can be used to determine antibiotic resistance. MALDI-TOF can be used for identification. The biopsy suggested acid fast bacillus. 16S sequencing identified Mycobacterium lepromatosis, the second most common cause of Hansen’s disease! When comparing Sanger DNA sequencing of the 16S to Oxford Nanopore Technologies (ONT), ONT is faster, easier, and sensitive.
Smielewska described a second case of a twelve-year-old with limb weakness, urinary incontinence, headache, altered cognition. MRI was normal and microbiology was culture negative. High sensitivity/low specificity Fusobacterium nucleatum was identified. The child had already completed a course of antibiotics. Nevertheless, this organism is important to track because of its emerging pathogenicity.
The third case Smielewska described was that of a fifteen year old with two week history of new onset swellings of their left arm. The patient had no fever, no vomiting, no diarrhea, no cough, and no weight loss. The pain started in the elbow and moved up to the axila. The teen has two old cats, a dog, and a fish. The results came back with Bartonella sp. Smielewska then explained that Bartonella can be Bartonella henselae, Bartonella quintana, or Bartonella bacilliformis. With 16S sequencing on ONT, the result was B. henselae from a catch scratch two months prior.
After running 16S sequencing with ONT for nine months, Smielewska and team analyzed data and in approximately two thirds there wasn’t a difference or it reassured the clinicians decision. However, in a third, there was an impact on patient outcome with sooner discharge dates. I’ve always enjoyed case studies and clinical microbiology. I enjoyed this session, and it reinforced my interest in the use of ONT for public health surveillance work!
