Obligate anaerobes are abundant in human necrotizing soft tissue infection samples - a metagenomics analysis

Abstract

Necrotizing soft tissue infections (NSTIs) are associated with high morbidity and mortality and are increasing in incidence. Proper identification of the microbial causes of NSTIs is a crucial step in diagnosis and treatment, but the majority of data collected are culture based, which is biased against fastidious organisms, including obligate anaerobes. The goal of this study was to address this gap in knowledge by characterizing NSTI microbial communities through molecular diagnostics. We performed 16S rRNA sequencing on human NSTI samples and identified five genera most commonly found in NSTIs (Prevotella, Bacteroides, Peptoniphilus, Porphyromonas, and Enterococcus). We found that a >70% contribution of obligate anaerobes to the bacterial population distribution was associated with NSTI mortality, and that NSTI samples, from both survivors and non-survivors, had an increased relative abundance of gram negative bacteria compared to those of abscess patients. Based on our data, we conclude that obligate anaerobes are abundant in NSTIs and a high relative abundance of anaerobes is associated with a worse outcome. We recommend increasing anaerobe antibiotic coverage during the treatment of NSTIs even when anaerobes are not found by traditional clinical microbiology methods, and especially when there is a clinical suspicion for anaerobe involvement.

Keywords: 16S rRNA sequencing; Molecular diagnostics; Necrotizing soft tissue infection (NSTI); Obligate anaerobes; Skin and soft tissue infection (SSTI).

Figure 1

Visual representation of wounds by sex and location. Each number is associated with our study participant code number. For both NSTI and abscess patients, the wound location was widespread and evenly distributed among men and women. (A) NSTI wounds. Square around the number indicates mortality due to the NSTI, diamond indicates an amputation, and circle indicates mortality not due to the NSTI. (B) Abscess wounds. All abscess patients survived with no notable morbidities.

Figure 2

Percentage of patients with the specified genus who were NSTI non‐survivors or survivors. Arrow indicates the 20% mark of the population with each genus of bacteria (20% of our NSTI patients were non‐survivors).

Figure 3

Shannon and Chao indices of wound diversity.

Figure 4

Aerotolerance of NSTI survivors, NSTI non‐survivors, and abscess patients. (A) Mean percent distribution of bacteria based on aerotolerance and on patient populations. (B) Proportions of patients in each group with wound microbiota composed of >70% obligate anaerobes. p‐value = 0.028 comparing wounds NSTI non‐survivors to abscess patients. p‐values were calculated using Fisher's exact test.

Figure 5

Gram designation of NSTI survivors, NSTI non‐survivors, and abscess patients. *P < 0.05 should be sufficient.