IHU Méditerranée Infection, UMR MEPHI, 19-21, Bd. Jean Moulin, 13005, Marseille, France.
Aix-Marseille Université, MEPHI, IRD, IHU Méditerranée Infection, Marseille, France.
Eur J Clin Microbiol Infect Dis. 2019 May;38(5):811-818. doi: 10.1007/s10096-019-03510-5. Epub 2019 Feb 22.
Methanogens are strictly anaerobic archaea metabolising by-products of bacterial fermentation into methane by using three known metabolic pathways, i.e. the reduction of carbon dioxide, the fermentation of acetate or the dismutation of methanol or methylamines. Methanogens described in human microbiota include only Euryarchaeota, i.e. Methanobrevibacter smithii, Methanobrevibacter oralis, Methanobrevibacter arbophilus, Methanobrevibacter massiliensis, Methanomassiliicoccus luminyensis, Methanosphaera stadtmanae and Ca. Methanomethylophilus alvus and Ca. Methanomassiliicoccus intestinalis. Methanogens are emerging pathogens associated with brain and muscular abscesses. They have been implicated in dysbiosis of the oral microbiota, periodontitis and peri-implantitis. They have also been associated with dysbiosis of the digestive tract microbiota linked to metabolic disorders (anorexia, malnutrition and obesity) and with lesions of the digestive tract (colon cancer). Their detection in anaerobic pus specimens and oral and digestive tract specimens relies on microscopic examination by fluorescence in situ hybridisation, specific DNA extraction followed by polymerase chain reaction (PCR)-based amplification of the 16S rRNA and mcrA gene fragments and isolation and culture in the supporting presence of hydrogen-producing bacteria. Diagnostic identification can be performed by matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF MS) and can be further completed by genotyping through multi-spacer sequencing and, ultimately, whole genome sequencing (WGS). Ornidazole derivatives, fusidic acid and rifampicin are the compounds to be included in in vitro susceptibility testing to complete the clinical workflow. Clinical microbiology laboratories should work toward developing cheap and easy protocols for the routine detection and identification of methanogens in selected specimens in order to refine the diagnosis of infections, as well as to expand the knowledge about this group of intriguing microorganisms.
产甲烷菌是严格厌氧的古菌，通过三种已知的代谢途径将细菌发酵的副产物转化为甲烷，即二氧化碳还原、乙酸发酵或甲醇或甲胺歧化。人类微生物组中描述的产甲烷菌仅包括广古菌，即史密斯甲烷短杆菌、口腔甲烷八叠球菌、甲烷鬃毛菌、马赛甲烷球菌、吕米尼甲烷球菌、斯塔特曼甲烷球菌和 Ca. 甲烷甲基杆菌和 Ca. 甲烷甲烷球菌。产甲烷菌是与脑和肌肉脓肿相关的新兴病原体。它们与口腔微生物群落的失调、牙周炎和种植体周围炎有关。它们还与与代谢紊乱（厌食、营养不良和肥胖）相关的消化道微生物群落失调以及与消化道病变（结肠癌）有关。在厌氧脓标本以及口腔和消化道标本中检测它们依赖于荧光原位杂交的显微镜检查、特定的 DNA 提取，然后是聚合酶链反应（PCR）扩增 16S rRNA 和 mcrA 基因片段以及在产氢细菌存在下的分离和培养。诊断鉴定可以通过基质辅助激光解吸/电离飞行时间质谱（MALDI-TOF MS）进行，通过多间隔序列基因分型进一步完成，最终通过全基因组测序（WGS）完成。奥硝唑衍生物、夫西地酸和利福平是体外药敏试验中要包含的化合物，以完成临床工作流程。临床微生物学实验室应努力开发廉价且易于常规检测和鉴定选定标本中产甲烷菌的方案，以完善感染的诊断，并扩展对这群有趣微生物的了解。
