PMC9550235_01
The timeline of this patient. Bedside chest x-rays on 10 and 11 April revealed patchy high-density shadows with localized consolidation in the right lung field. Chest computed tomography (CT) showed the infection was continuously absorbed.
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F1
The bedside chest x-ray showed infectious lesions and pleural effusion in the right lung (Figure 1, Supplementary Figure S1). On 11 April 2021, the bedside chest x-ray was repeated, and the symptoms improved (Figure 1, Supplementary Figure S1). Chest CT was performed on the same day, indicating a right lung abscess with cavitation (Figure 1, Supplementary Figure S1). On 23 April 2021, the re-examination of chest CT showed that the lesion was continuously absorbed (Figure 1). On 24 May 2021 and 9 July 2021 (Figure 1, Supplementary Figure S1), the re-examination of chest CT showed further absorption of the lesion.
The microbiology laboratory reported positive Gram-negative bacteria and preliminarily considered Eikenella at the genus level. (A) smear Gram staining; (B) bacterial colony morphology on blood plate after 72 h.
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F2
Direct smear staining showed elongated Gram-negative bacteria (Figure 2A). We observed a typical straw cap colony on the plate, which was flat, with central convex and smooth round (Figure 2B).
The metagenomic next-generation sequencing (mNGS) results of this patient. The coverages of Eikenella corrodens by the first mNGS and Eikenella halliae by the second mNGS are shown in (A,B) respectively. The detected specific read numbers and the percentages of E. corrodens and E. halliae are shown in (C,D), respectively.
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F3
China), identifying the pathogens as E. halliae (82 specific reads, Figures 3B,D). Considering the rarity of the pathogen in this patient, the previously negative mNGS data were reanalyzed, and E. corrodens (91 unique reads, Figures 3A,C) were found in the background microorganisms.
The detected NGS results of the isolate mapped to the reference genome of Eikenella halliae (GCF_001648475.1). Reads with >70% identity to the reference genome of E. halliae are marked in dark red; Reads with 50 ~ 70% identity to the reference genome of E. halliae are marked in light red; Reads with < 50% identity to the reference genome of E. halliae are marked in gray.
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F4
So, high-throughput whole genome sequencing (WGS) was finally applied, of which the result showed that the isolate had the best concordance with E. halliae (Figure 4).