In January, a previously healthy 39-year-old man was brought to our emergency department with a 1-week history of pain and ulceration in his left calf. He developed a sudden pain in the left lower extremity after exercise a week ago, followed by a high fever (40.0  C) with dizziness, nausea, and shortness of breath. Lower limb pain increased gradually, accompanied by swelling and skin lesions. Twenty-four hours before the visit, the patient showed anuria. Physical examination in the emergency room detected tachycardia (112 bpm) and hypotension (72/39 mmHg). The patient was rapidly admitted to the ICU at the midnight. He was an ex-tobacco smoker for 3 years and drank a little beer sometimes. No other history was recorded, including tumors, organ transplants, immunodeficiency, diabetes, toxic exposure, insect stings, or trauma. Arterial blood gas indicated metabolic acidosis with respiratory alkalosis with a pH of 7.404, and lactic acid of 7.1. His initial blood test results were as follows: white blood cells, 21.33*109/L; hemoglobin, 134 g/L; platelets, 44*109/L; laboratory studies also showed elevated plasma C-reactive protein levels (541.0 mg/l), while procalcitonin and interleukin-6 (IL-6) levels exceeded the limit of detection (>100 ng/mL and >5000 pg/mL, respectively). Other laboratory tests showed low albumin (20.2 g/L), high serum creatinine (219 mumol/L), elevated serum creatine kinase (1813 U/L), dysfunction of coagulation (INR1.33, PT16.6 s, APTT 66.8 s), and elevated D-dimer (3.7 mg/L). On physical examination, moderate swelling, hemorrhagic blisters and bullae, marked pain with movement, and overlying erythema of his left lower limb were found (Figure 1). Computed tomography (CT) showed diffuse subcutaneous soft tissue lesions in the lower leg and pneumonia. Transthoracic echocardiography demonstrated normal left ventricular function. No abscess was found.
The patient was diagnosed with septic shock due to necrosis of the skin and deep soft tissue of the left extremity. He immediately received meropenem and daptomycin treatment empirically, fluid resuscitation, and noradrenaline via an internal jugular central venous catheter. Continuous hemodiafiltration was also implied. Although sepsis was diagnosed, the pathogen of the initial infection was unclear. Before the use of antibiotics, cultures, as well as the rapid pathogen detection by metagenomic next-generation sequencing (mNGS), were drawn from the pustule, deep soft tissue (lower limb), and two-site blood samples (both aerobic and anaerobic bottles) at least twice. Cultures were performed by experienced laboratory operators in a standard manner and the mNGS tests were performed following the manufacturer's instructions. Generally, standard samples were handled with quality-filtered, elimination of duplicate readings, removal of low-quality sequences that match human genome sequences. Libraries for mNGS were prepared using the Illumina  DNA Prep, (M) Tagmentation (20018705, Illumina) according to the manufacturer's recommendation. Pooled libraries were sequenced on NextSeq  550Dx system using a 75 bp, single-end sequencing kit (Illumina), and at least 20 milslion sequencing reads were acquired for each sample. A negative control sample was processed and sequenced in parallel in each sequencing run for quality control. The data was processed using PIseqTM (Pathogen Identification Sequencing) Metagenomic Sequencing Data Management System V2.0 (WillingMed) simultaneously to draw the conclusion. However, although the patient's hemodynamics was gradually improving after the antibiotic treatment, the area of redness and swelling of the left lower limb gradually spread to the root of the thigh and perineum (Figure 1). Moreover, the patient developed moderate acute respiratory distress syndrome (ARDS) with a PaO2/FiO2 ratio of 152.5 mmHg and high-flow nasal oxygen (HFNO) was used to improve hypoxemia. There's also liver function damage with total bilirubin levels (TBIL) significantly increased. On the third day after admission, the mNGS results showed GAS both in pustule and deep soft tissue (Table 1). The pustule mNGS report detected a total of 132 unique GAS sequence reads, representing 96.3% of microbial reads and 0.49% of the nucleotide sequence coverage. The soft tissue mNGS report identified a total of 142474 unique GAS sequence reads, representing 100% of microbial reads. The virulence profiling and antimicrobial genes report were also presented (Supplementary Table 1). Thus, we diagnosed this patient as having streptococcal toxic shock syndrome based on the criteria (shown in Supplementary Table 2) and necrotizing fasciitis. Other tests for pathogens such as parasites, epidemic hemorrhagic fever, leptospirosis, tuberculosis were all negative. Therefore, antibiotic therapy comprising piperacillin/tazobactam (4.5g Q6H/day) and clindamycin (900mg Q8H/day) instead of meropenem was given immediately. Because of the low platelet count and disorder of coagulation, the surgeon had to postpone the surgical debridement while observing the tension of the wound closely. Meanwhile, he received intravenous immunoglobulin (IVIG) 0.5g/kg/day for 5 days. Over the next 5 days, his kidney function and coagulation were recovered and the general condition was improved subsequently. The temperature dropped to the normal range, too. Ten days after admission, as the PaO2/FiO2 ratio increased to 311 mmHg, HFNO could be stopped. At this time, magnetic resonance imaging (MRI) was taken and showed diffuse swelling in bilateral buttock, erector spinal muscle, left thigh root, left lower limb muscle, and muscle space (Figure 2). Three days later, he received the first surgical debridement and then was transferred to the general ward. The patient underwent another debridement surgery and the following skin grafting during the hospitalization. After the operations and rehabilitation exercises, he is now recovering well and ready to be discharged from the hospital. During the patient's stay in the ICU, the results of the cultures were all negative in the blood, pustule, and deep soft tissue. The clinical course with laboratory results and treatments was concluded in Figure 3.