Methanobrevibacter smithii Archaemia in Febrile Patients With Bacteremia, Including Those With Endocarditis

Abstract

Background The spectrum of infections caused by the emerging opportunistic pathogens methanogens which escape routine detection remains to be described. To determine the prevalence of archaemia, we searched for methanogens in the blood of febrile patients using specific tools. Methods We conducted a prospective study at Institut Hospitalier Universitaire Méditerranée Infection, Marseille, France, September 2018 - April 2020, enrolling 7,716 blood culture samples routinely collected in patients with fever. Blood samples were screened by specific PCR assays for the presence of methanogens. Positive samples were observed by autofluorescence and electron microscopy, analyzed by metagenomics and cultured using previously developed methods. Blood culture bottles experimentally inoculated were used as controls. The presence of methanogens in vascular and cardiac tissues was assessed by indirect immunofluorescence, fluorescent in situ hybridization and PCR-based investigations. Results PCR detection attempted in 7,716 blood samples, was negative in all 1,312 aerobic bottles and 810 bacterial culture-negative anaerobic bottles. PCRs were positive in 27/5,594 (0.5%) bacterial culture-positive anaerobic bottles that contained cultures collected from 26 patients. Sequencing confirmed Methanobrevibacter smithii associated with staphylococci in 14 patients, fermentative Enterobacteriaceae in nine patients and streptococci in three patients. Metagenomics confirmed M. smithii in five blood samples, and M. smithii was isolated via culture in broth from two samples; the genomes of these two isolates were sequenced. Blood cultures experimentally inoculated with Enterobacteriaceae, Staphylococcus epidermidis or Staphylococcus hominis yielded hydrogen, but no methane, authentifying observational data.Three patients, all diagnosed with infectious mitral endocarditis, were diagnosed by microscopy, PCR-based detections and culture: we showed M. smithii microscopically and by a specific PCR followed by sequencing method in two of three cardiovascular tissues. Conclusions Using appropriate methods of detection, M. smithii is demonstrated as causing archaemia and endocarditis in febrile patients who are coinfected by bacteria.

Methanobrevibacter smithii tonsillar phlegmon: a case report

“…In this patient, M. smithii was detected in a pus sample also containing eight different bacterial species, and such an association of M. smithii with bacteria, chiefly anaerobes, is constant in all the previous descriptions of M. smithii coinfections [ [11] , [12] , [13] , [14] ]. These bacteria essentially belong to the enterobacterial and bacteroidal orders comprising hydrogen producers [ 26 , 27 ].…”

“…For molecular detection of methanogens, DNA was extracted from the pus sample using the automated extractor EZ1 advanced XL with the EZ1 DNA Tissue kit (Qiagen, Courtaboeuf, France) after 20-minute sonication. Amplification of the archaeal 16S rRNA gene was performed as previously described by Drancourt et al [ 14 ]. Sequencing the amplicon yielded 100% sequence similarity with the reference M. smithii ATCC 35061 homologous sequence (GenBank accession number: NC_009515 ).…”

“…In this situation of bacterial tonsillar phlegmon, detection of methanogenic archaea, mainly represented by Methanobrevibacter smithii , the most abundant methanogenic archaea species in the human gut [ 10 ] and which are recently emerging as a copathogen in various disease situations [ [11] , [12] , [13] , [14] ], would require specific laboratory methods.…”

Diversity of Methanogens in Animals’ Gut

“…Moreover, methanogens have been associated with dysbiosis such as in the case of vaginosis [9], urinary tract infections [10], and anaerobe abscesses of the brain [11,12], the muscle [13], the oral cavity in the case of periodontitis, and periimplantitis [14,15] in the case of refractory sinusitis [16]. Recently, we observed blood-borne methanogens associated with endocarditis [17]. In all these situations, anaerobe bacteria were associated in the methanogendisease process, and this observation was probably reflecting methanogen specificities, The sources, modes of acquisition, and dynamics of digestive-tract methanogens remain poorly investigated.…”

Stool methanogens in intestine mammal species

“…Moreover, methanogens have been associated with dysbiosis such as in the case of vaginosis (5), urinary tract infections (6) and anaerobe abscesses of the oral cavity in the case of periodontitis and periimplantitis (7,8), in the case of refractory sinusitis (9), brain (10,11) and muscle (12). Recently, we observed blood-borne methanogens associated with endocarditis (13). In all these situations, anaerobe bacteria were associated in the methanogen disease process and this observation was probably reflecting methanogen specificities including the absolute oxygen intolerance and the necessity of a hydrogen source to produce methane (14,15).…”