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

Case report: A case of widespread soft tissue infection and multiple abscesses secondary to hidradenitis suppurativa inducing septic shock caused by Lawsonella clevelandensis in China

Lawsonella clevelandensis is rare to associated with human infection, which may cause abscesses in abdominal cavity, liver, breast, and spine. Lawsonella clevelandensis is very difficult to be cultivated in regular manner; detection of 16S rRNA sequence is the main evidence for L. clevelandensis infection. The clinical manifestations of L. clevelandensis infection resemble other agents of Nocardia, Tuberculosis and non-tuberculous Mycobacterium (NTM) due to their morphologic similarities. Hidradenitis suppurativa (HS) is a chronic inflammatory disorder, which affects the intertriginous skin and is associated with numerous systemic comorbidities. HS eventually leads to severe pain, multiple abscesses, pus discharge, and irreversible tissue destruction. Lawsonella clevelandensis has not been reported to cause HS and systemic comorbidities. We presented the case of a 33-year-old male with widespread soft tissue infection and multiple abscesses secondary to HS (Hurley stage III) inducing septic shock caused by L. clevelandensis in China. He was diagnosed as HS and treated with intravenous antibiotic empirically. He developed multiple abscesses including lung and scrota. Bacterial and fungal cultures on blood and secretions from multiple skin lesions were all negative. Due to the misdiagnosis and progression of disease, the patient was transferred to intensive care unit, and he underwent drainage of the chest and right hemothorax removal under thoracoscopic. During the hospitalization, the patient developed septic shock and received mechanical ventilation. Computerized tomography (CT) scans revealed mediastinal emphysema, multiple subcutaneous emphysema, and severe pneumonia. Gene analysis of samples of incision and drainage of pus at the skin showed the rare infection of L. clevelandensis. Finally, the patients with recurrent soft tissue infections and multiple abscesses with negative microbiological culture results recovered after effective abscess drainage and antibiotic therapy. We suggested that NGS is a crucial supplementary diagnostic tool in individuals with recurrent skin infections and multiple abscesses, especially when conventional diagnostic methods are inconclusive.

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

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.

Exploring the interrelationship between the skin microbiome and skin volatiles: A pilot study

Unravelling the interplay between a human’s microbiome and physiology is a relevant task for understanding the principles underlying human health and disease. With regard to human chemical communication, it is of interest to elucidate the role of the microbiome in shaping or generating volatiles emitted from the human body. In this study, we characterized the microbiome and volatile organic compounds (VOCs) sampled from the neck and axilla of ten participants (five male, five female) on two sampling days, by applying different methodological approaches. Volatiles emitted from the respective skin site were collected for 20 min using textile sampling material and analyzed on two analytical columns with varying polarity of the stationary phase. Microbiome samples were analyzed by a culture approach coupled with MALDI-TOF-MS analysis and a 16S ribosomal RNA gene (16S RNA) sequencing approach. Statistical and advanced data analysis methods revealed that classification of body sites was possible by using VOC and microbiome data sets. Higher classification accuracy was achieved by combination of both data pools. Cutibacterium, Staphylococcus, Micrococcus, Streptococcus, Lawsonella, Anaerococcus, and Corynebacterium species were found to contribute to classification of the body sites by the microbiome. Alkanes, esters, ethers, ketones, aldehydes and cyclic structures were used by the classifier when VOC data were considered. The interdisciplinary methodological platform developed here will enable further investigations of skin microbiome and skin VOCs alterations in physiological and pathological conditions.

Microfiber-loaded bacterial community in indoor fallout and air-conditioner filter dust

Microfibers (MFs) are widely existed in indoor air; however, characteristic of microbiota on MFs is largely unknown. In this study, air-borne MFs were collected from fallout or air-conditioner (AC) filter dust in three types of indoor space including living room, dormitory and office. Both plastic and natural MFs were identified by Fourier transform infrared spectroscopy. Ultramicroscopic observation showed dense biofilms adhering on surfaces of MFs. Fallout MFs contained more bacteria but fewer fungi than MFs from AC filter dust. MFs-loaded bacteria were of highest abundance in living rooms, following dormitories and offices. Bacterial community and its diversity were further analyzed by 16S rRNA High-throughput sequencing. Up to 4540 of bacterium OTUs were shared in these MFs samples, unique OTUs in fallout and AC filter samples accounting for 26.3 % and 25.7 % of the total. Compared to MFs fallout, AC filter MFs contained more species of pathogenic bacteria, such as Betaproteobacteriales and Ralstonia, with obviously different β-diversity between two groups. Phenotypic analysis showed that fallout and AC filter MFs bacteria presented high index values of film formation, oxidative stress tolerance and potential pathogenicity. Overall, these results suggest that abundant bacteria including pathogen can be loaded on MFs, and would pose health risks through delivery of indoor MFs.

Lawsonella clevelandensis, a case series of vascular graft infections caused by a rare pathogen

Lawsonella clevelandensis is a fastidious Gram-positive, partially acid-fast, anaerobic, catalase positive bacterium that has been reported to be a rare cause of abdominal, breast, spinal, and liver abscesses. Here, three L. clevelandensis vascular graft infections (VGIs) and cardiac infections are reported.

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

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.

Diagnostic Value of 16S Ribosomal RNA Gene Polymerase Chain Reaction/Sanger Sequencing in Clinical Practice

BACKGROUND

Accurate microbiologic diagnosis is important for appropriate management of infectious diseases. Sequencing-based molecular diagnostics are increasingly used for precision diagnosis of infections. However, their clinical utility is unclear.

METHODS

We conducted a retrospective analysis of specimens that underwent 16S ribosomal RNA (rRNA) gene polymerase chain reaction (PCR) followed by Sanger sequencing at our institution from April 2017 through March 2019.

RESULTS

A total of 566 specimens obtained from 460 patients were studied. Patients were considered clinically infected or noninfected based on final diagnosis and management. In 17% of patients, 16S rRNA PCR/sequencing was positive and in 5% of patients, this test led to an impact on clinical care. In comparison, bacterial cultures were positive in 21% of patients. Specimens with a positive Gram stain had 12 times greater odds of having a positive molecular result than those with a negative Gram stain (95% confidence interval for odds ratio, 5.2-31.4). Overall, PCR positivity was higher in cardiovascular specimens (37%) obtained from clinically infected patients, with bacterial cultures being more likely to be positive for musculoskeletal specimens (P < .001). 16S rRNA PCR/sequencing identified a probable pathogen in 10% culture-negative specimens.

CONCLUSION

16S rRNA PCR/sequencing can play a role in the diagnostic evaluation of patients with culture-negative infections, especially those with cardiovascular infections.

Lawsonella clevelandensis: an emerging cause of vascular graft infection

Lawsonella clevelandensis, an emerging pathogen, was first described in 2016, and has been implicated in abdominal, breast and spinal abscesses in a limited number of cases. Being a fastidious organism, it is primarily identified with molecular methods. With the incorporation of broad-range PCR testing in clinical diagnostics, L. clevelandensis has been increasingly reported in the literature. We describe a case of a 65-year-old man who presented with bilateral psoas abscesses secondary to aorto-bi-iliac vascular graft infection with L. clevelandensis identified using 16S rRNA/PCR sequencing. The patient underwent surgical resection and replacement of infected graft, followed by 6 weeks of intravenous antibiotic therapy and then chronic suppression with doxycycline and cefadroxil. He was infection-free at last follow-up.