The puzzle of the evolutionary natural history of tuberculosis.

Several pieces of the puzzle of the natural history of tuberculosis are assembled in this review to illustrate the potential reservoirs and sources of the Mycobacterium tuberculosis complex (MTBC) mycobacteria, their transmission to animals and humans, and their fate in populations, in a co-evolutionary perspective. Millennia-old companions of mammalian and human populations, MTBC are detected in the soil, in which they infect and survive within vegetative amoebae and cysts, except for Mycobacterium canettii. Never detected in the sphere of plants, they are transmissible by transcutaneous, digestive and respiratory routes and cause an infection of the lymphatic system with secondary dissemination in most tissues, in which they determine a specific and non-pathognomonic granulomatous inflammatory reaction; in which MTBC survives in dormant form irrespective of MTBC species and mammalian species; indicating that the current epidemiology in mammalian populations is essentially governed by the probabilities of contact between mammalian species and MTBC species. Individual variabilities in clinical expression of tuberculosis are related to MTBC species, strain and inoculum; host genetic factors; acquired modulations of the inflammatory response; and probably human microbiota. This review of the literature suggests an evolutionary natural history of telluric environmental mycobacteria, satellites of unicellular eukaryotes, transmissible to mammals via the digestive and then respiratory tracts, in which they determine a fatal contagious infection that is primarily lymphatic and a quiescence-mimicking encysted form. This review opens perspectives for microbiological and translational medical research.

Yersinia pestis: the Natural History of Plague.

The Gram-negative bacterium Yersinia pestis is responsible for deadly plague, a zoonotic disease established in stable foci in the Americas, Africa, and Eurasia. Its persistence in the environment relies on the subtle balance between Y. pestis-contaminated soils, burrowing and nonburrowing mammals exhibiting variable degrees of plague susceptibility, and their associated fleas. Transmission from one host to another relies mainly on infected flea bites, inducing typical painful, enlarged lymph nodes referred to as buboes, followed by septicemic dissemination of the pathogen. In contrast, droplet inhalation after close contact with infected mammals induces primary pneumonic plague. Finally, the rarely reported consumption of contaminated raw meat causes pharyngeal and gastrointestinal plague. Point-of-care diagnosis, early antibiotic treatment, and confinement measures contribute to outbreak control despite residual mortality. Mandatory primary prevention relies on the active surveillance of established plague foci and ectoparasite control. Plague is acknowledged to have infected human populations for at least 5,000 years in Eurasia. Y. pestis genomes recovered from affected archaeological sites have suggested clonal evolution from a common ancestor shared with the closely related enteric pathogen Yersinia pseudotuberculosis and have indicated that ymt gene acquisition during the Bronze Age conferred Y. pestis with ectoparasite transmissibility while maintaining its enteric transmissibility. Three historic pandemics, starting in 541 AD and continuing until today, have been described. At present, the third pandemic has become largely quiescent, with hundreds of human cases being reported mainly in a few impoverished African countries, where zoonotic plague is mostly transmitted to people by rodent-associated flea bites.

Digestive tract methanodrome: Physiological roles of human microbiota-associated methanogens.

Methanogens are the archaea most commonly found in humans, in particular in the digestive tract and are an integral part of the digestive microbiota. They are present in humans from the earliest moments of life and represent the only known source of methane production to date. They are notably detected in humans by microscopy, fluorescent in situ hybridization, molecular biology including PCR-sequencing, metagenomics, matrix-assisted laser desorption ionization time-of-flight mass spectrometry and culture. Methanogens present in the human digestive tract play major roles, in particular the use of hydrogen from the fermentation products of bacteria, thus promoting digestion. They are also involved in the transformation of heavy metals and in the use of trimethylamine produced by intestinal bacteria, thus preventing major health problems, in particular cardiovascular diseases. Several pieces of evidence suggest their close physical contacts with bacteria support symbiotic metabolism. Their imbalance during dysbiosis is associated with many pathologies in humans, particularly digestive tract diseases such as Crohn's disease, ulcerative colitis, diverticulosis, inflammatory bowel disease, irritable bowel syndrome, colonic polyposis, and colorectal cancer. There is a huge deficit of knowledge and partially contradictory information concerning human methanogens, so much remains to be done to fully understand their physiological role in humans. It is necessary to develop new methods for the identification and culture of methanogens from clinical samples. This will permit to isolate new methanogens species as well as their phenotypic characterization, to explore their genome by sequencing and to study the population dynamics of methanogens by specifying in particular their exact role within the complex flora associated with the mucous microbiota of human.

The diversity of mycolactone-producing mycobacteria.

Mycolactone-producing mycobacteria (MPM) form an intriguing group of environmental opportunistic pathogens of mammals and human patients in whom they cause cutaneous and subcutaneous ulcers known as "Buruli ulcer" when they occur in humans. We reviewed whole genome sequence data and ecological and phenotypic characteristics from 44 MPMs and closely related Mycobacterium marinum. This analysis indicated that all the 24 M. marinum isolates were delineated into seven taxa and our comprehensive, polyphasic taxonomic approach led to the proposal of delineating M. marinum genomospecies, 01-07. Likewise, 20 MPMs isolates were delineated into seven additional M. ulcerans genomospecies, 01-07. A taxonomic card explaining the ecology, hosts of isolation and the plasmid harboured is provided for each taxon.

Methanogens as emerging pathogens in anaerobic abscesses.

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.

Methanobrevibacter smithii, a methanogen consistently colonising the newborn stomach.

Methanobrevibacter smithii is the main human methanogen almost always found in the digestive tract of adults. Yet, the age at which M. smithii establishes itself as part of the developing intestinal microflora remains unknown. In order to gain insight into this, we developed a polyphasic approach, including microscopic observation by fluorescence in situ hybridisation, polymerase chain reaction (PCR) sequencing detection, identification and culture, to isolate and genotype M. smithii in one-day-old newborns' gastric juice specimens. In the presence of negative controls, 50/50 (100%) prospectively analysed newborn gastric juice specimens were PCR-positive for methanogens, all identified as M. smithii by sequencing. We succeeded in cultivating M. smithii in 35/50 (70%) newborn gastric juice specimens, while 15/50 specimens remained sterile. Further, M. smithii was observed by direct microscopic investigation using fluorescence in situ hybridisation. Multispacer sequence typing found one of seven different genotypes per specimen, these genotypes having all been previously described in adult human stools. Methanobrevibacter smithii is an early inhabitant of the human stomach, colonising the gastric mucosa just after birth, and the mother's gut microbiota is a probable source of colonisation.

Staphylococcus caprae bone and joint infections: a re-emerging infection?

Staphylococcus caprae has been recently classified as a human pathogen, but the incidence of S. caprae in human bone and joint infections (BJIs) is under-reported. In this study, we report 25 cases of S. caprae BJI, and we review the 31 cases published in the literature. Molecular techniques and matrix-assisted laser desorption ionization time-of-flight mass spectrometry improved the identification of clinically relevant S. caprae strains. In this study, 96% of S. caprae BJIs were localized to the lower limbs, and 88% of the cases involved orthopaedic device infections. S. caprae joint prosthesis infections (JPIs), internal osteosynthesis device infections (I-ODIs) and BJIs without orthopaedic device infections were recorded in 60%, 28% and 12% of cases, respectively. Ten (40%) S. caprae BJIs were polymicrobial infections. These infections were associated with past histories of malignancy (p 0.024). Of the 14 bacterial species related to S. caprae BJI, 57% were staphylococci. I-ODIs were significantly associated with polymicrobial infections (p 0.0068), unlike JPIs, which were monomicrobial infections (p 0.0344). Treatment with rifampicin and fluoroquinolone was recorded in 40% of cases. Surgical treatment was performed in 76% of cases, e.g. prosthesis removal (36%), osteosynthesis device removal (24%), and surgical debridement (16%). Thirty per cent of cases were not treated. Relapses were observed mainly in the patients treated by surgical debridement only (p 0.033). In summary, S. caprae BJI is an underestimated hospital-acquired emerging infection. S. caprae BJI is correlated with infections in orthopaedic devices, which must be removed to control the infection.

Potential changes to French recommendations about peri-prosthetic infections based on the international consensus meeting (ICMPJI).

BACKGROUND: Despite the large volume of studies on the prevention, diagnosis, and treatment of peri-prosthetic infections, surgical practice often rests on limited scientific evidence in this field. The vast International Consensus Meeting on Peri-prosthetic Joint Infection (ICMPJI) held in 2013 produced robust recommendations. HYPOTHESIS: French consensus conference recommendations show no major differences with ICMPJI recommendations. MATERIALS AND METHODS: The 207 recommendations developed by 300 experts at the ICMPJI were translated, and the translation was then examined by four reviewers, including 2 having participated in the consensus conference. The reviewers looked for any differences with French practices and recommendations. RESULTS: Twenty-three major differences or innovations were identified compared to French recommendations and standard practice. Among them, pre-operative screening for nasal or urinary micro-organisms is performed routinely in France but should be reserved according to the ICMPJI for symptomatic patients and/or patients at high risk for infection. The ICMPJI emphasizes the role for the operating room environment as a vector for infection; more specifically, the operating lamp handle and suction cannula deserve close attention. A wound discharge persisting longer than 5-7 days requires irrigation and debridement. This procedure is effective only within the first 3 post-operative months and/or the first 3 weeks after symptom onset and must include exchange of all modular implants. The ICMPJI warns against both irrigation-debridement in fungal infections (suggesting two-stage prosthesis replacement) and one-stage replacement in patients with sinus tracts. The use of spacers (articulating at the knee) is recommended in the event of two-stage prosthesis replacement. DISCUSSION: The ICMPJI recommendations differed in many ways with French recommendations and standard practice. They can be expected to impact practices in France, although a point worth noting is that only 1 of the 207 recommendations received unanimous agreement by the conference experts (keeping operating room traffic to a minimum).

Looking in amoebae as a source of mycobacteria.

Mycobacteria exhibit various relationships with amoebae, ranging from the killing of one partner by the other one, to amoebae hosting mycobacteria in trophozoites and cysts. This observation indicates that poorly described biological factors affect the relationships, including mycobacterial cell-wall glycolipids and the size of the mycobacteria. Experimental observations indicate that a majority of environmental, opportunistic mycobacteria but also obligate pathogens including Mycobacterium tuberculosis, Mycobacterium leprae and Mycobacterium ulcerans are inter-amoebal organisms. Amoebae may give opportunities for genetic exchanges between mycobacteria, sympatric intra-amoebal organisms and the amoebae themselves. Amoebae clearly protect opportunistic mycobacterial pathogens during their environmental life but their role for obligate mycobacterial infection remains to be established. Accordingly, water was the source for emerging, community-acquired and health care-associated infection with amoeba-resisting mycobacteria of the Mycobacterium avium, Mycobacterium abscessus and Mycobacterium fortuitum groups, among others. Amoebae are organisms where mycobacteria can be found and, accordingly, amoeba co-culture can be used for the isolation of mycobacteria from environmental and clinical specimens. Looking in amoebae may help recovering new species of mycobacteria.

Planctomycetes DNA in febrile aplastic patients with leukemia, rash, diarrhea, and micronodular pneumonia.

We found Planctomycetes DNA in 2 out of 100 blood samples from patients suffering from leukemia with neutropenia induced by chemotherapy, as well as fever, rash, pneumonia, and diarrhea. Antibiotic-resisting Planctomycetes may be pathogenic in these patients.

Disseminated Mycobacterium lentiflavum responsible for hemophagocytic lymphohistocytosis in a man with a history of heart transplantation.

Mycobacterium lentiflavum is a nontuberculous, slowly growing mycobacterium usually recognized as a contaminant. Here, we report a case of disseminated M. lentiflavum infection responsible for hemophagocytic lymphohistocytosis in a heart-transplanted man.

Relation between nasal carriage of Staphylococcus aureus and surgical site infection in orthopedic surgery: the role of nasal contamination. A systematic literature review and meta-analysis.

UNLABELLED: Staphylococcus aureus is the pathogen most frequently implicated in infection on orthopedic hardware; various strategies are deployed to limit the risk of transmission and surgical infection. OBJECTIVES: The present study is based on a meta-analysis assessing firstly the relationship between nasal carriage of S. aureus and the development of osteo-articular infection and secondly current methods of decolonization. RESULTS: The meta-analysis showed increased risk of surgical site infection in case of nasal carriage of S. aureus: OR=5.92, 95% CI [1.15-30.39]; P=0.033. For cross-transmission, a scientifically proven reduction in surgical site S. aureus levels is ensured by associated mupirocin and 2% chlorhexidine antiseptic solution in subjects with positive nasal screening results for all surgical procedures taken together; the reduction was not, however, significant in the orthopedic surgery subgroup. The meta-analysis confirmed these findings: OR=0.60, 95% CI [0.34-1.06]; P=0.08. CONCLUSION: The literature review confirmed that nasal carriage of S. aureus is a major risk factor for surgical site infection. The efficacy of eradication could not be demonstrated for orthopedic surgery as samples were too small. The positive trend found, however, should encourage further studies with sufficient power and risk/benefit should meanwhile be assessed on a case-by-case basis. LEVEL OF EVIDENCE: Level 2. Meta-analysis.

Free-living amoebae, a training field for macrophage resistance of mycobacteria.

Mycobacterium species evolved from an environmental recent common ancestor by reductive evolution and lateral gene transfer. Strategies selected through evolution and developed by mycobacteria resulted in resistance to predation by environmental unicellular protists, including free-living amoebae. Indeed, mycobacteria are isolated from the same soil and water environments as are amoebae, and experimental models using Acanthamoeba spp. and Dictyostelium discoideum were exploited to analyse the mechanisms for intracellular survival. Most of these mechanisms have been further reproduced in macrophages for mycobacteria regarded as opportunistic and obligate pathogens. Amoebal cysts may protect intracellular mycobacteria against adverse conditions and may act as a vector for mycobacteria. The latter hypothesis warrants further environmental and clinical studies to better assess the role of free-living amoebae in the epidemiology of infections caused by mycobacteria.

Interactions between Mycobacterium xenopi, amoeba and human cells.

Outbreaks due to Mycobacterium xenopi have been linked with contaminated water. M. xenopi has been shown to interact with the biofilm formed in water distribution systems and to be hosted by free-living Acanthamoeba. The present study investigated the interaction between M. xenopi and A. polyphaga amoeba, and between M. xenopi and human fibroblast HEL cells. Examination using the light microscopy together with electronic and confocal microscopy demonstrated that M. xenopi was located within the amoeba and in HEL cells. The Light Cycler measurement of the M. xenopi:A. polyphaga DNA ratio and the M. xenopi:HEL cell DNA ratio demonstrated intra-amoebal and intracellular growth of M. xenopi with doubling-times of five-days and 10 days, respectively. Intra-amoebal M. xenopi survived protozoan encystment and germination. These data demonstrate that M. xenopi is a facultative intra-amoebal and intracellular pathogen. Testing intra-amoebal M. xenopi might be necessary to properly evaluate decontamination procedures for hospital water supply systems in order to achieve eradication.

Nosocomial influenza in children.

Influenza is the most important cause of acute respiratory illness leading to hospitalization among children during community epidemics. This illness can cause extensive nosocomial outbreaks with serious morbidity and mortality among specific groups of children. Paediatric patients with community-acquired influenza and healthcare workers are the main reservoir for the nosocomial spread of the virus. During epidemics in the community, testing for influenza should be requested in all children with compatible symptoms admitted in the hospital, and measures should be introduced for the prevention or early control of an outbreak. Recent advances in the management of influenza include rapid diagnoses based on antigen detection and the identification of the new neuraminidase inhibitors zanamivir and oseltamivir. Annual vaccination against influenza of children with high-risk conditions, their family members and healthcare workers is the principle measure for the prevention of nosocomial outbreaks. Although vaccination against influenza appears to be cost-effective at all ages in terms of prevention of illness, related hospitalizations, deaths, reduction of healthcare costs and productivity loss, vaccination coverage among target groups is limited.

rpoB sequence analysis of cultured Tropheryma whippelii.

Until recently no isolate of Tropheryma whippelii was available, and therefore genetic studies were limited to those based on PCR amplification of conserved genes. In this study we determined the nucleotide sequence of rpoB (encoding the beta-subunit of RNA polymerase) from a cultured strain of T. whippelii using degenerate consensus PCR and genome walking. The T. whippelii rpoB consists of 3,657 bp with a 50.4% GC content and encodes 1,218 amino acids with a calculated molecular mass of 138 kDa. Comparison of T. whippelii RpoB with other eubacterial RpoB proteins indicated sequence similarity ranging from 57.19 (Mycoplasma pneumoniae) to 74.63% (Mycobacterium tuberculosis). Phylogenetic analysis of T. whippelii based on comparison of its RpoB sequence with sequences available for other bacteria was consistent with that previously derived from the 16S ribosomal DNA (rDNA) sequence, indicating that it belongs to the actinomyces clade. The sequence comparison allowed the design of a primer pair, TwrpoB.F and TwrpoB.R, specific for T. whippelii rpoB. When incorporated into a PCR, this primer pair allowed the detection of T. whippelii rpoB in three of three 16S rDNA PCR-positive biopsy specimens and zero of seven negative controls. rpoB could therefore be targeted in PCR-mediated detection and identification of this emerging bacterial species. This approach has previously been shown useful for the identification of related mycobacteria. This study underscores that a method involving isolation and then propagation of emerging bacteria is a useful way to quickly achieve extensive molecular knowledge of these pathogens.

Molecular identification of a Dietzia maris hip prosthesis infection isolate.

Dietzia maris, an environmental actinomycete, has been implicated only once in human disease. We herein report the first D. maris isolate from a bone biopsy specimen in a patient hospitalized for a total hip prosthesis replacement. Cell wall fatty acid analysis and 16S ribosomal DNA gene sequencing were utilized to achieve its definite identification. This case report illustrates the usefulness of such methods for the accurate identification of actinomycetes.