Plant-associated microorganisms: a view from the scope of microbiology

Microorganisms interact with plants because plants offer a wide diversity of habitats including the phyllosphere (aerial plant part), the rhizosphere (zone of influence of the root system), and the endosphere (internal transport system). Interactions of epiphytes, rhizophytes or endophytes may be detrimental or beneficial for either the microorganism or the plant and may be classified as neutralism, commensalism, synergism, mutualism, amensalism, competition or parasitism

Applications of MALDI-TOF mass spectrometry in clinical diagnostic microbiology.

Until recently, microbial identification in clinical diagnostic laboratories has mainly relied on conventional phenotypic and gene sequencing identification techniques. The development of matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) devices has revolutionized the routine identification of microorganisms in clinical microbiology laboratories by introducing an easy, rapid, high throughput, low-cost, and efficient identification technique. This technology has been adapted to the constraint of clinical diagnostic laboratories and has the potential to replace and/or complement conventional identification techniques for both bacterial and fungal strains. Using standardized procedures, the resolution of MALDI-TOF MS allows accurate identification at the species level of most Gram-positive and Gram-negative bacterial strains with the exception of a few difficult strains that require more attention and further development of the method. Similarly, the routine identification by MALDI-TOF MS of yeast isolates is reliable and much quicker than conventional techniques. Recent studies have shown that MALDI-TOF MS has also the potential to accurately identify filamentous fungi and dermatophytes, providing that specific standardized procedures are established for these microorganisms. Moreover, MALDI-TOF MS has been used successfully for microbial typing and identification at the subspecies level, demonstrating that this technology is a potential efficient tool for epidemiological studies and for taxonomical classification.

Postmortem angiography using femoral cannulation and postmortem microbiology.

Despite the undeniable advantages of postmortem angiography, numerous questions have arisen concerning the influence that the injected contrast media may exercise on biological fluids and tissues collected for toxicological and biochemical investigations. Moreover, cardiac blood for microbiological investigations cannot be obtained post-angiography. In this study, we examined whether the peripheral blood collected prior to postmortem angiography, using percutaneous access to femoral vessels after skin surface disinfection, could be suitable for microbiological investigations when postmortem angiography with femoral vessel cannulation is also performed. A total of 66 cases were included in the study and were divided into two subgroups (angiography and bacteriology group, 33 cases and control group, 33 cases). Autopsies, histology, toxicology, bacteriology, and biochemical investigations (procalcitonin, C-reactive protein, interleukin-6, and soluble triggering receptors expressed on myeloid cells type 1) were performed in all cases. No statistically significant differences between the two groups were noted, and identified category distribution (death unrelated to infection, true infection, false positive, and undetermined) was rather similar in both studied populations. These preliminary results suggest that postmortem angiography using a femoral approach does not constitute an impediment to the collection of peripheral blood for microbiology and vice versa. Moreover, the use of femoral blood for microbiology does not lead to an increased risk of doubtful results.

A descriptive study on the surgery and the microbiology of Gustilo type III fractures in an university hospital in Switzerland.

OBJECTIVE: To describe the epidemiology, the surgical treatment, the microbiology, the antibiotic prophylaxis and the outcome of patients with the most severe type of open fractures. METHODS: Retrospective chart reviews of patients with Gustilo type III open fracture admitted to an university hospital in Switzerland between January 2007 and December 2011. The patient's and fracture's characteristics, surgery, antibiotic prophylaxis, and microbiology findings at the initial and at the revision surgery were described. RESULTS: Thirty patients were included (83% male, mean age 41 years). More than half of the patients had polytrauma. In all patients, debridement and stabilization surgery (70% using external fixation) were performed at admission. Soft tissue reconstruction was performed in 87% and in 23% immediate bone graft was performed. Antibiotic prophylaxis were given in all patients for a median duration of 9 days (60% received amoxicillin/clavulanic acid). Positive bacterial culture was found in 53% of the patients at initial surgery and in 88% at revision surgery. At initial and revision surgery, 47% and 88% of the pathogens were amoxicillin/clavulanic acid-resistant. Treatment outcome was favorable in 24 of 30 patients (80%) and in six cases (20%) an amputation had to be performed. None of the patients had chronic bone infection. CONCLUSIONS: Positive cultures were found often in open fractures. Amoxicillin/clavulanic acid which is often mentioned in many guidelines as prophylaxis in open fractures does not cover the most common isolated organisms. The combination of surgery and antibiotic prophylaxis leads to good outcome in Gustilo type III fracture.

Legume rotation effects on early growth and rhizosphere microbiology of sorghum in West African soils

Cereal yield increases in legume rotations on west African soils were the subject of much recent research aiming at the development of more productive cropping systems for the mainly subsistence-oriented agriculture in this region. However, little has been done to elucidate the possible contribution of soil microbiological factors to these rotation effects. Therefore a pot trial was conducted using legume rotation and continuous cereal soils each from one site in Burkina Faso and two sites in Togo where cropping system experiments had been conducted over 4 yrs. All soils were planted with seedlings of sorghum (Sorghum bicolor L. Moench). From 21 days after sowing onwards relative growth rates in rotation soils were higher than in the continuous cereal soils, resulting in between 69 and 500% higher shoot dry matter of rotation sorghum compared to sorghum growing in continuous cereal soils. Across sites rotation soils were characterized by higher pH, higher microbial N and a lower microbial biomass C/N ratio and, with the exception of one site, a higher fungal biomass in the rhizosphere. The bacterial and eukaryal community structure in the soil, assessed by denaturing gradient gel electrophoresis (DGGE), differed between sites. However, only at one site differed the bacterial and the eukaryal community structure in the rotation soil significantly from that in the continuous cereal soil. Although the results of this study confirmed the marked plantgrowth differences between sub-Saharan legume-rotation soils and their continuous cereal counterparts they also showed the difficulties to differentiate possible microbiological causes from their effects.

Intestinal microbiology in Crohn's disease: a study of Escherichia coli as a potential etiologic agent

La malaltia de Crohn és una malaltia inflamatòria intestinal crònica d'etiologia encara desconeguda. Actualment es pensa que hi participen factors genètics i immunològics que confereixen una susceptibilitat a l'hoste, i factors externs o ambientals, com serien els microorganismes i/o l'estil de vida. L'objectiu principal d'aquest treball ha estat descriure les poblacions bacterianes associades especialment als malalts de Crohn, amb la intenció d'identificar possibles agents etiològics. Els resultats d'aquest treball coincideixen amb investigacions prèvies que descriuen l'alteració bacteriana present en els malalts de Crohn (disbiosi) i recolzen la hipòtesi que implica el recentment descrit patovar "Adherent- Invasive Escherichia coli" (AIEC) en l'etiologia d'aquesta malaltia inflamatòria intestinal. A més, contribuïm a la descripció de les poblacions d'E. coli associades a la mucosa intestinal aportant dades sobre aspectes ecològics i patogènics. Finalment, descrivim nous aspectes fenotípics d'AIEC que podrien estar relacionats amb la seva patogènia, com seria la capacitat de formar biofilms.

Microbiology of the human intestinal tract and approaches for its dietary modulation

Gut bacteria can be categorised as being either beneficial or potentially pathogenic due to their metabolic activities and fermentation end-products. Health-promoting effects of the microflora may include immunostimulation, improved digestion and absorption, vitamin synthesis, inhibition of the growth of potential pathogens and lowering of gas distension. Detrimental effects are carcinogen production, intestinal putrefaction, toxin production, diarrhoea/constipation and intestinal infections. Certain indigenous bacteria such as bifidobacteria and lactobacilli are considered to be examples of health-promoting constituents of the microflora. They may aid digestion of lactose in lactose-intolerant individuals, reduce diarrhoea, help resist infections and assist in inflammatory conditions. Probiotics, prebiotics and synbiotics are functional foods that fortify the lactate producing microflora of the human or animal gut.