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Identification of pathogens in culture-negative infective endocarditis cases by metagenomic analysis.

ABSTRACT: BACKGROUND:Pathogens identification is critical for the proper diagnosis and precise treatment of infective endocarditis (IE). Although blood and valve cultures are the gold standard for IE pathogens detection, many cases are culture-negative, especially in patients who had received long-term antibiotic treatment, and precise diagnosis has therefore become a major challenge in the clinic. Metagenomic sequencing can provide both information on the pathogenic strain and the antibiotic susceptibility profile of patient samples without culturing, offering a powerful method to deal with culture-negative cases. METHODS:To assess the feasibility of a metagenomic approach to detect the causative pathogens in resected valves from IE patients, we employed both next-generation sequencing and Oxford Nanopore Technologies MinION nanopore sequencing for pathogens and antimicrobial resistance detection in seven culture-negative IE patients. Using our in-house developed bioinformatics pipeline, we analyzed the sequencing results generated from both platforms for the direct identification of pathogens from the resected valves of seven clinically culture-negative IE patients according to the modified Duke criteria. RESULTS:Our results showed both metagenomics methods can be applied for the causative pathogen detection in all IE samples. Moreover, we were able to simultaneously characterize respective antimicrobial resistance features. CONCLUSION:Metagenomic methods for IE detection can provide clinicians with valuable information to diagnose and treat IE patients after valve replacement surgery. However, more efforts should be made to optimize protocols for sample processing, sequencing and bioinformatics analysis.

SUBMITTER: Cheng J

PROVIDER: S-EPMC6300891 | biostudies-literature | 2018 Dec

REPOSITORIES: biostudies-literature

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Identification of pathogens in culture-negative infective endocarditis cases by metagenomic analysis.

Cheng Jun J Hu Huan H Kang Yue Y Chen Weizhi W Fang Wei W Wang Kaijuan K Zhang Qian Q Fu Aisi A Zhou Shuilian S Cheng Chen C Cao Qingqing Q Wang Feiyan F Lee Shela S Zhou Zhou Z

Annals of clinical microbiology and antimicrobials 20181220 1

<h4>Background</h4>Pathogens identification is critical for the proper diagnosis and precise treatment of infective endocarditis (IE). Although blood and valve cultures are the gold standard for IE pathogens detection, many cases are culture-negative, especially in patients who had received long-term antibiotic treatment, and precise diagnosis has therefore become a major challenge in the clinic. Metagenomic sequencing can provide both information on the pathogenic strain and the antibiotic susc ...[more]

PMID: 30567558

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Project description:BackgroundCulture-negative endocarditis is uncommon, occurring in less than a third of all cases of infective endocarditis (IE). Culture-negative IE related to a cardiac device is an even greater diagnostic challenge due to its insidious presentation, with onset of symptoms ranging between 3 and 12 months after device implantation. Sensitivity of the modified Duke's criteria remains low in culture-negative and cardiac device-related IE (CDRIE) since classical signs and symptoms of IE are often absent. Small vessel vasculitis has been reported as an immune response to IE. Recognizing immunological phenomenon related to IE is of paramount clinical importance, prompting the search for an underlying infection and avoiding the use of immunosuppressive medications which would otherwise result in an adverse outcome.Case summaryAn 81-year-old Caucasian male presented to the ambulatory medical unit with a two-week history of a symmetrical, generalized purpuric rash. He had an indwelling permanent pacemaker following a transcatheter aortic valve implantation for severe aortic stenosis five years ago. Blood tests showed an iron deficiency anaemia, thrombocytopenia and normal renal function, both CRP and ESR were raised at 61 and 30 mm/hr, respectively. Skin biopsy demonstrated small vessel cutaneous vasculitis. Transthoracic echocardiography revealed a mobile mass measuring 0.9 × 1.7 cm, confirmed on transoesophageal echocardiogram as pacing lead endocarditis. Blood cultures were persistently negative. The patient underwent pacemaker lead extraction, following which the vasculitic rash improved.DiscussionBlood cultures in IE are more likely to be negative if there is a prior antibiotic administration or causative micro-organisms with limited proliferation which fail to grow in conventional media conditions. Transesophageal echocardiography (TOE) offers improved sensitivity and diagnostic yield when compared to transthoracic echocardiography (TTE) in patients with a high clinical suspicion of CDRIE. The evidence in the literature describing culture-negative IE associated with small vessel vasculitis is limited. However, it is recognized that cutaneous small vessel vasculitis may be associated with an underlying bacterial infection. IE produces an inflammatory response, resulting in the deposition of circulating immune complexes and cutaneous signs which are included in the modified Duke's criteria to aid diagnosis. Management of CDRIE requires a multi-disciplinary team approach with an 'Endocarditis Team.' Pacemaker lead infection requires transvenous lead extraction if it is a newly implanted lead. Locking stylets, extraction sheaths or snare retrieval are usually required in cases of older implanted leads. Surgical lead extraction remains the gold standard for larger vegetations (>20 mm) or associated valve endocarditis.

Project description:ObjectivesMetagenomic next-generation sequencing (mNGS) technology is helpful for the early diagnosis of infective endocarditis, especially culture-negative infective endocarditis, which may guide clinical treatment. The purpose of this study was to compare the presence of culture-negative infective endocarditis pathogens versus culture-positive ones, and whether mNGS test results could influence treatment regimens for patients with routine culture-negative infective endocarditis.MethodsThe present study enrolled patients diagnosed with infective endocarditis and tested for mNGS in the First Affiliated Hospital of Zhengzhou University from February 2019 to February 2022 continuously. According to the culture results, patients were divided into culture-negative group (Group CN, n=18) and culture-positive group (Group CP, n=32). The baseline characteristics, clinical data, pathogens, 30 day mortality and treatment regimen of 50 patients with infective endocarditis were recorded and analyzed.ResultsExcept for higher levels of PCT in the Group CN [0.33 (0.16-2.74) ng/ml vs. 0.23 (0.12-0.49) ng/ml, P=0.042], there were no significant differences in the basic clinical data and laboratory examinations between the two groups (all P>0.05). The aortic valve and mitral valve were the most involved valves in patients with infective endocarditis (aortic valve involved: Group CN 10, Group CP 16; mitral valve involved: Group CN 8, Group CP 21; P>0.05) while 9 patients had multiple valves involved (Group CN 2, Group CP 7; P>0.05). The detection rate of non-streptococci infections in the Group CN was significantly higher than that in the Group CP (9/18 vs. 3/32, P=0.004). There was no significant difference in patients with heart failure hospitalization and all-cause death at 30 days after discharge (3 in Group CN vs. 4 in Group CP, P>0.05). It is worth noting that 10 patients with culture-negative infective endocarditis had their antibiotic regimen optimized after the blood mNGS.ConclusionsCulture-negative infective endocarditis should be tested for mNGS for early diagnosis and to guide clinical antibiotic regimen.

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Identification of pathogens in culture-negative infective endocarditis cases by metagenomic analysis.

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Identification of pathogens in culture-negative infective endocarditis cases by metagenomic analysis.

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