Inguinal microbiome in patients undergoing an endovascular aneurysm repair: Application of next-generation sequencing of the 16S-23S rRNA regions

BACKGROUND

Surgical site infection (SSI) remains a hazardous complication after vascular surgery. In this pilot study we investigated the inguinal microbiome in skin biopsies using histology and 16S-23S rDNA Next Generation Sequencing (NGS). Our hypothesis was that causative microorganisms of SSI are present in the inguinal microbiome.

METHODS

Data on surgical site infections and skin samples from the Percutaneous in Endovascular Repair versus Open (PiERO) trail were evaluated. Two patients with SSI were matched for age and comorbidity to eight matching patients of the PiERO trial. All patients were treated for an abdominal aortic aneurysm with endovascular repair. Nasal and perineal cultures were taken preoperatively to detect Staphylococcus aureus carriage. After disinfection with chlorhexidine, groin biopsies were taken to identify bacteria in deeper skin layers. All samples were subjected to histological analysis and culture-free 16S-23S rDNA NGS.

RESULTS

Staphylococcus aureus species were cultured in 5 out of 20 preoperative nasal and perineal swaps. Histology detected only a few bacteria. NGS of the 16S-23S rRNA regions identified DNA of bacterial species in all biopsies (20/20). Most identified genera and species proved to be known skin flora bacteria. No relation was found between SSIs and the preoperative microbiome.

CONCLUSION

In this pilot study, an innovative analysis of the preoperative microbiome using 16S-23S rDNA NGS did not show a relation with the occurrence of a surgical site infection. No pathogenic bacterial species were present in the inguinal skin after disinfection with chlorhexidine.

Development and Validation of a Reference Data Set for Assigning Staphylococcus Species Based on Next-Generation Sequencing of the 16S-23S rRNA Region

Many members of the Staphylococcus genus are clinically relevant opportunistic pathogens that warrant accurate and rapid identification for targeted therapy. The aim of this study was to develop a careful assignment scheme for staphylococcal species based on next-generation sequencing (NGS) of the 16S-23S rRNA region. All reference staphylococcal strains were identified at the species level using Sanger sequencing of the 16S rRNA, sodA, tuf, and rpoB genes and NGS of the 16S-23S rRNA region. To broaden the database, an additional 100 staphylococcal strains, including 29 species, were identified by routine diagnostic methods, 16S rRNA Sanger sequencing and NGS of the 16S-23S rRNA region. The results enabled development of reference sequences encompassing the 16S-23S rRNA region for 50 species (including one newly proposed species) and 6 subspecies of the Staphylococcus genus. This study showed sodA and rpoB targets were the most discriminative but NGS of the 16S-23S rRNA region was more discriminative than tuf gene sequencing and much more discriminative than 16S rRNA gene sequencing. Almost all Staphylococcus species could be distinguished when the max score was 99.0% or higher and the sequence similarity between the best and second best species was equal to or >0.2% (min. 9 nucleotides). This study allowed development of reference sequences for 21 staphylococcal species and enrichment for 29 species for which sequences were publicly available. We confirmed the usefulness of NGS of the 16S-23S rRNA region by identifying the whole species content in 45 clinical samples and comparing the results to those obtained using routine diagnostic methods. Based on the developed reference database, all staphylococcal species can be reliably detected based on the 16S-23S rRNA sequences in samples composed of both single species and more complex polymicrobial communities. This study will be useful for introduction of a novel diagnostic tool, which undoubtedly is an improvement for reliable species identification in polymicrobial samples. The introduction of this new method is hindered by a lack of reference sequences for the 16S-23S rRNA region for many bacterial species. The results will allow identification of all Staphylococcus species, which are clinically relevant pathogens.

A Comparison of Three Different Bioinformatics Analyses of the 16S-23S rRNA Encoding Region for Bacterial Identification

Rapid and reliable identification of bacterial pathogens directly from patient samples is required for optimizing antimicrobial therapy. Although Sanger sequencing of the 16S ribosomal RNA (rRNA) gene is used as a molecular method, species identification and discrimination is not always achievable for bacteria as their 16S rRNA genes have sometimes high sequence homology. Recently, next generation sequencing (NGS) of the 16S–23S rRNA encoding region has been proposed for reliable identification of pathogens directly from patient samples. However, data analysis is laborious and time-consuming and a database for the complete 16S–23S rRNA encoding region is not available. Therefore, a better, faster, and stronger approach is needed for NGS data analysis of the 16S–23S rRNA encoding region. We compared speed and diagnostic accuracy of different data analysis approaches: de novo assembly followed by Basic Local Alignment Search Tool (BLAST), operational taxonomic unit (OTU) clustering, or mapping using an in-house developed 16S–23S rRNA encoding region database for the identification of bacterial species. De novo assembly followed by BLAST using the in-house database was superior to the other methods, resulting in the shortest turnaround time (2 h and 5 min), approximately 2 h less than OTU clustering and 4.5 h less than mapping, and a sensitivity of 80%. Mapping was the slowest and most laborious data analysis approach with a sensitivity of 60%, whereas OTU clustering was the least laborious approach with 70% sensitivity. Although the in-house database requires more sequence entries to improve the sensitivity, the combination of de novo assembly and BLAST currently appears to be the optimal approach for data analysis.

[Fatal encephalitis caused by a parasite]

BACKGROUND

Encephalitis caused by a free-living amoeba is relatively rare and usually fatal. This is because the diagnosis is often made late and treatment is difficult.

CASE DESCRIPTION

A 41-year-old patient with a previous history including kidney transplant was admitted with clinical symptoms of encephalitis. Brain imaging showed a number of hypodense regions, which were possibly abscesses. Although an infectious cause seemed probable, even the most extensive antimicrobial treatment was ineffective. The cause was not found until 2 months after the patient's death: infection with Balamuthia mandrillaris. A PCR test was used to detect this amoeba.

CONCLUSION

This case study describes the first patient in the Netherlands to be diagnosed with granulomatous amoebic encephalitis caused by B. mandrillaris. An amoeba may be the cause of encephalitis with either a fulminant course or with a gradual increase of symptoms, without conventional anti-infective therapy being effective.