Emerging anaerobic and partially acid-fast Lawsonella clevelandensis: extended characterization by antimicrobial susceptibility testing and whole genome sequencing

Goldenberger, Daniel; Naegele, Matthias; Steffens, David L.; Eichenberger, Ramon M.; Egli, Adrian; Seth-Smith, Helena M. B.

doi:10.1016/j.cmi.2019.07.008

Cited by 11 publications

(7 citation statements)

References 7 publications

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“…We investigated the read coverage for detected microbes by aligning nonhuman reads to their genomes. As expected, for bacteria, most of the RNA-seq signals agree with the previous notion that most microbial reads are from rRNA, and for Lawsonella clevelandensis , a pathogen reported to induce abscess ( Goldenberger et al, 2019 ) as an example ( Figure 2E ). The RNA-seq signals for viruses are also consistent with their genome annotations.…”

Section: Resultssupporting

confidence: 89%

Cancer type classification using plasma cell-free RNAs derived from human and microbes

Chen

Jin

Wang

et al. 2022

eLife

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The utility of cell-free nucleic acids in monitoring cancer has been recognized by both scientists and clinicians. In addition to human transcripts, a fraction of cell-free nucleic acids in human plasma were proven to be derived from microbes and reported to have relevance to cancer. To obtain a better understanding of plasma cell-free RNAs (cfRNAs) in cancer patients, we profiled cfRNAs in ~300 plasma samples of 5 cancer types (colorectal cancer, stomach cancer, liver cancer, lung cancer, and esophageal cancer) and healthy donors (HDs) with RNA-seq. Microbe-derived cfRNAs were consistently detected by different computational methods when potential contaminations were carefully filtered. Clinically relevant signals were identified from human and microbial reads, and enriched Kyoto Encyclopedia of Genes and Genomes pathways of downregulated human genes and higher prevalence torque teno viruses both suggest that a fraction of cancer patients were immunosuppressed. Our data support the diagnostic value of human and microbe-derived plasma cfRNAs for cancer detection, as an area under the ROC curve of approximately 0.9 for distinguishing cancer patients from HDs was achieved. Moreover, human and microbial cfRNAs both have cancer type specificity, and combining two types of features could distinguish tumors of five different primary locations with an average recall of 60.4%. Compared to using human features alone, adding microbial features improved the average recall by approximately 8%. In summary, this work provides evidence for the clinical relevance of human and microbe-derived plasma cfRNAs and their potential utilities in cancer detection as well as the determination of tumor sites.

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Section: Resultssupporting

confidence: 89%

Cancer type classification using plasma cell-free RNAs derived from human and microbes

Chen

Jin

Wang

et al. 2022

eLife

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show abstract

“…We also investigated the read coverage for detected microbes by aligning non-human reads to their genomes. As expected, for bacteria, most of the RNA-seq signals agree with the previous notion that most microbial reads are from rRNA, as shown in Figure 2E for Lawsonella clevelandensis (a pathogen reported to induce abscess [52] ) as an example. The RNA-seq signals for viruses are also consistent with their genome annotations.…”

Section: Sequencing Of Cfrnas Captures Signals Of Various Long Rna Species In Plasmasupporting

confidence: 89%

Cancer Type Classification Using Plasma Cell Free RNAs Derived From Human and Microbes

Chen

Jin

Wang

et al. 2021

Preprint

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Background: The utilities of cell free nucleic acids in monitoring cancer have been recognized by both scientists and clinicians. In addition to human transcripts, a fraction of cell free nucleic acids in human plasma were proved to derived from microbes, and reported to have some relevance to cancer. Methods: To get a better understanding of plasma cell free RNAs (cfRNAs) in cancer patients, we profiled cfRNAs in ~300 plasma samples of five cancer types (colorectal cancer, stomach cancer, liver cancer, lung cancer, esophageal cancer) and healthy donors with RNA-seq. Results: Microbe derived cfRNAs were consistently detected by different computational methods when potential contaminations were carefully filtered. Clinically relevant signals can be identified from human and microbial reads, and alteration in human cfRNA expression and virus abundance both suggests some cancer patients were immunosuppressed, as indicated by enriched KEGG pathways of downregulated human genes and higher prevalence torque teno virus. Our data supports the diagnostic value of human and microbe derived plasma cfRNAs for cancer detection, as an area under receiver operating characteristic (ROC) curve of 0.931 for distinguishing cancer patients from healthy donors was achieved on validation set, using both human and microbial features. Moreover, these cfRNAs both have some cancer type specificity, and could distinguish tumors of different primary locations. Compared to using human feature alone, combining human and microbial features improves the average validation accuracy of between cancer type classification by 11.5%. Conclusions: In summary, this work provides evidence for the clinical relevance of human and microbe derived plasma cfRNAs, and their potential utilities in cancer detection, and determination of tumor sites.

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“…To our knowledge, there are only 12 cases of Lawsonella clevelandensis infection documented worldwildly as of now. Actually it is very difficult to be cultivated in regular manner, so determination of its infection is prone to be misdiagnosed [3,7], which could justify the rare condition of Lawsonella clevelandensis infection to some extent. Gene sequencing analysis is recommended to help diagnosis [3], of which detection of 16S rRNA sequence is the main evidence for Lawsonella clevelandensis infection determination d [9,[14][15][16].…”

Section: Discussionmentioning

confidence: 99%

“…Correspondingly, the antibiotics were adjusted to intravenous Cefoxitin (2.0 g, tid) and Ornidazole (500 mg, bid) following an adequate wound drainage and a thorough literature review [ 7 – 9 ]. Delightedly, her fever, white blood cells (WBC) and C-reactive protein (CRP) examination were significantly improved after therapy adjustment (Table 2 ).…”

Section: Case Presentationmentioning

confidence: 99%

“…Undisappointedly, the NGS results showed that Lawsonella clevelandensis infection was present in both pus and necrotic tissues, with the abundance being 96.60% Correspondingly, the antibiotics were adjusted to intravenous Cefoxitin (2.0 g, tid) and Ornidazole (500 mg, bid) following an adequate wound drainage and a thorough literature review [7][8][9]. Delightedly, her fever, white blood cells (WBC) and C-reactive protein (CRP) examination were significantly improved after therapy adjustment (Table 2).…”

Section: Case Presentationmentioning

confidence: 99%

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Infection caused by Lawsonella clevelandensis after breast augmentation with autologous fat grafting: a case report

et al. 2023

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Background Lawsonella clevelandensis is one recently documented anaerobic, which is partially acid-fast. Nevertheless, it is rarely found to be associated with human infections, especially in scope of plastic and cosmetic surgery before our patient who was performed breast augmentation with autologous fat grafting. Breast augmentation is becoming popular, the most common post-surgery complication of which is bacterial infection. Case presentation A 29-year-old female who was found swelling in her right breast and fever after breast augmentation surgery with autologous fat grafting was administered. Before administration, she had been treated with antibiotics (details unknown) for more than 1 month without any significant improvements. After administration, she was treated with intravenous antibiotic empirically and repeated debridement via Vaccuum Sealing Drainage (VSD). And samples of the necrotic tissues and pus collected in surgery were sent for microbiological testing. However, routine examination failed. Thus samples were further collected and sent to Genoxor Medical & Science Technology Inc. (Shanghai, China) to conduct Next-Generation Sequencing (NGS). Surprisingly Lawsonella clevelandensis was determined. Accordingly, sensitive antibiotic was applied in concert with thorough debridement and drainage and finally her condition was completely reversed with wound closure gradually. Conclusion Complications of breast augmentation with autologous fat graft are various, of which infection is most common. Rare pathogen such as Lawsonella clevelandensis infection in human is rare in clinical practice. Moreover, it is difficult to differentiate from non-tuberculous mycobacterium for its partial acid resistance, difficulty to culture and abscess formation. How to determine diagnosis of Lawsonella clevelandensis infection accurately come to be critical In our report, NGS is recommended as a useful method to identify the pathogen, which may provide us a novel tool for refractory wound.

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Emerging anaerobic and partially acid-fast Lawsonella clevelandensis: extended characterization by antimicrobial susceptibility testing and whole genome sequencing

Cited by 11 publications

References 7 publications

Cancer type classification using plasma cell-free RNAs derived from human and microbes

Cancer type classification using plasma cell-free RNAs derived from human and microbes

Cancer Type Classification Using Plasma Cell Free RNAs Derived From Human and Microbes

Infection caused by Lawsonella clevelandensis after breast augmentation with autologous fat grafting: a case report

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