Efficacy of an anaerobic swab transport system to maintain aerobic and anaerobic microorganism viability after storage at -80 degrees C

Culturing and Molecular Approaches for Identifying Microbiota Taxa Impacting Children's Obesogenic Phenotypes Related to Xenobiotic Dietary Exposure

Integrated data from molecular and improved culturomics studies might offer holistic insights on gut microbiome dysbiosis triggered by xenobiotics, such as obesity and metabolic disorders. Bisphenol A (BPA), a dietary xenobiotic obesogen, was chosen for a directed culturing approach using microbiota specimens from 46 children with obesity and normal-weight profiles. In parallel, a complementary molecular analysis was carried out to estimate the BPA metabolising capacities. Firstly, catalogues of 237 BPA directed-cultured microorganisms were isolated using five selected media and several BPA treatments and conditions. Taxa from Firmicutes, Proteobacteria, and Actinobacteria were the most abundant in normal-weight and overweight/obese children, with species belonging to the genera Enterococcus, Escherichia, Staphylococcus, Bacillus, and Clostridium. Secondly, the representative isolated taxa from normal-weight vs. overweight/obese were grouped as BPA biodegrader, tolerant, or resistant bacteria, according to the presence of genes encoding BPA enzymes in their whole genome sequences. Remarkably, the presence of sporobiota and concretely Bacillus spp. showed the higher BPA biodegradation potential in overweight/obese group compared to normal-weight, which could drive a relevant role in obesity and metabolic dysbiosis triggered by these xenobiotics.

Recovery of aerobic gram-negative bacteria from the Copan Eswab transport system after long-term storage

We evaluated the Copan Eswab transport system for the quantitative recovery of Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa after 1, 2, 3, 5, and 7 days of storage at room and refrigerator temperatures, and 7 and 30 days of storage at -80 °C and -20 °C using mono- and polymicrobial samples. The study was based on Clinical and Laboratory Standards Institute (CLSI) M40-A2 standard procedures on the quality control of microbiological transport systems. Eswab met the CLSI standards at room and refrigerator temperatures for all (combinations of) bacterial strains tested. At room temperature, after 24 h, bacterial growth was observed. At -80 °C, bacterial viability was maintained in monomicrobial samples; however, in polymicrobial samples, P. aeruginosa recovery was compromised. Storage at -20 °C was unsuitable. We conclude that specimens collected using Eswab should be transported to the laboratory as soon as possible. If transport or processing is delayed, specimens should preferably be stored at refrigerator temperatures.

Cross-country transport and isolation and identification of Streptococcus pneumoniae by use of alternate sources of blood supplemented media among laboratories in India

Background

The isolation of S. pneumoniae (Sp) depends on specimen integrity / transport, media and expertise. The non-availability of sheep blood agar poses a challenge in identification of colonial morphology and identification in India.

Methods

Laboratories processed swabs containing either pure Sp or Sp in mixed cultures with a second (confounding) bacterium shipped across the country in cold conditions. Duplicate set of swabs was shipped back to the central laboratory to assess the impact of shipping on culture viability. The identical swab was cultured on sheep, human blood and one additional agar plate used in the laboratory.

Results

46/60(77%) of cultures containing only Sp were correctly identified. In specimens where Sp was present in mixed culture, the proportion of isolates in which Sp was correctly identified varied, with most variability attributed to the particular confounding organism rather than the media. There was no discernible impact of temperature-controlled (4-6°C) transport on the isolation of Sp from culture swabs.

Conclusions

The study clearly elucidates the ability of laboratories for isolation of S. pneumoniae on human blood agar in resource limited settings. The results highlight the difficulties inherent in correctly identifying pathogens in mixed cultures in needs improvement using standardized tests across the study centers. The study also reaffirms the ability to transport biological specimens over long geographical distances without loss.

The gut microbiota of nonalcoholic fatty liver disease: current methods and their interpretation

The role of intestinal bacteria in the pathogenesis of nonalcoholic fatty liver disease is increasingly acknowledged. Recently developed microbial profiling techniques are beginning to shed light on the nature of gut microbiota alterations in nonalcoholic fatty liver disease. In this review, we summarize the gut microbiota composition changes that have been reported during different stages of human nonalcoholic fatty liver disease, and highlight the relation between bile acids and gut bacteria in this context. In addition, we discuss the different methodologies used in microbiota analyses as well as the interpretation of microbiota data. Whereas the currently available studies have provided useful information, future large-scale prospective studies with carefully phenotyped subjects and sequential sampling will be required to demonstrate a causal role of gut microbiota changes in the etiology of nonalcoholic fatty liver disease.

Current and past strategies for bacterial culture in clinical microbiology

A pure bacterial culture remains essential for the study of its virulence, its antibiotic susceptibility, and its genome sequence in order to facilitate the understanding and treatment of caused diseases. The first culture conditions empirically varied incubation time, nutrients, atmosphere, and temperature; culture was then gradually abandoned in favor of molecular methods. The rebirth of culture in clinical microbiology was prompted by microbiologists specializing in intracellular bacteria. The shell vial procedure allowed the culture of new species of Rickettsia. The design of axenic media for growing fastidious bacteria such as Tropheryma whipplei and Coxiella burnetii and the ability of amoebal coculture to discover new bacteria constituted major advances. Strong efforts associating optimized culture media, detection methods, and a microaerophilic atmosphere allowed a dramatic decrease of the time of Mycobacterium tuberculosis culture. The use of a new versatile medium allowed an extension of the repertoire of archaea. Finally, to optimize the culture of anaerobes in routine bacteriology laboratories, the addition of antioxidants in culture media under an aerobic atmosphere allowed the growth of strictly anaerobic species. Nevertheless, among usual bacterial pathogens, the development of axenic media for the culture of Treponema pallidum or Mycobacterium leprae remains an important challenge that the patience and innovations of cultivators will enable them to overcome.

The effect of sampling and storage on the fecal microbiota composition in healthy and diseased subjects

Large-scale cohort studies are currently being designed to investigate the human microbiome in health and disease. Adequate sampling strategies are required to limit bias due to shifts in microbial communities during sampling and storage. Therefore, we examined the impact of different sampling and storage conditions on the stability of fecal microbial communities in healthy and diseased subjects. Fecal samples from 10 healthy controls, 10 irritable bowel syndrome and 8 inflammatory bowel disease patients were collected on site, aliquoted immediately after defecation and stored at -80°C, -20°C for 1 week, at +4°C or room temperature for 24 hours. Fecal transport swabs (FecalSwab, Copan) were collected and stored for 48-72 hours at room temperature. We used pyrosequencing of the 16S gene to investigate the stability of microbial communities. Alpha diversity did not differ between all storage methods and -80°C, except for the fecal swabs. UPGMA clustering and principal coordinate analysis showed significant clustering by test subject (p<0.001) but not by storage method. Bray-Curtis dissimilarity and (un)weighted UniFrac showed a significant higher distance between fecal swabs and -80°C versus the other methods and -80°C samples (p<0.009). The relative abundance of Ruminococcus and Enterobacteriaceae did not differ between the storage methods versus -80°C, but was higher in fecal swabs (p<0.05). Storage up to 24 hours (at +4°C or room temperature) or freezing at -20°C did not significantly alter the fecal microbial community structure compared to direct freezing of samples from healthy subjects and patients with gastrointestinal disorders.

Relationship between bacteriological findings in the second and fourth weeks postpartum and uterine infection in dairy cows considering bacteriological results

The uterine lumen in early postpartum dairy cows is contaminated with different bacteria. The most relevant uterine pathogens are Escherichia coli and Trueperella pyogenes. Prevalence of α-hemolytic streptococci and coagulase-negative staphylococci (CNS) is also high; however, these pathogens are considered opportunistic. The overall objective of this study was to investigate effects of the intrauterine presence of E. coli, T. pyogenes, α-hemolytic streptococci, or CNS at 10±1 d in milk (DIM) on the type of bacteria 2 wk later and their influence on uterine infections and subsequent reproductive performance. Furthermore, we set out to quantify 2 relevant methodological factors (i.e., laboratory and sampling instrument). Bacteriological samples were collected at 10±1 and 24±1 DIM from the uterine lumen using a cytobrush (CB). Vaginal mucus was classified by vaginoscopy. In a subsample, bacteriological results of 3 different laboratories and of CB and cotton swabs (CS) were compared. Samples of uterine discharge were collected at 10±1 DIM and bacteriological samples were taken using CB and CS. Bacteria were identified and bacterial growth quantified on a 4-point scale. Animals infected with E. coli or T. pyogenes at 10±1 DIM had a higher risk for an infection with the same bacterial species at 24±1 DIM [E. coli relative risk (RR)=3.7 and T. pyogenes RR=2.9]. Moreover, the risk of being diagnosed with abnormal vaginal discharge at 24±1 DIM increased in cows with E. coli (RR=1.7) or T. pyogenes (RR=1.7) at 10±1 DIM. Uterine infection with α-hemolytic streptococci or CNS did not increase the risk of an infection with T. pyogenes or E. coli or abnormal vaginal discharge 2 wk later. Cows with E. coli at 10±1 DIM or T. pyogenes at 24±1 DIM had greater days to first artificial insemination than cows positive for the 3 remaining bacterial species. Cows with T. pyogenes at 10±1 DIM had more days to pregnancy and more cows were culled when positive for E. coli at 10±1 DIM. Agreement of bacteriological results of 3 different laboratories were significant for laboratory A + B and A + C for the CB and CS. The highest agreement considering the bacterial species was for E. coli. All results for laboratory A + B and A + C for the CB and CS were significant. The results generated from samples collected with CB agreed nicely with those from CS from each laboratory (laboratory A: 250/272; laboratory B: 264/272; laboratory C: 253/272).

Anaerobic oral flora in the North American black bear (Ursus americanus) in eastern North Carolina

Microbial flora can provide insight into the ecology and natural history of wildlife in addition to improving understanding of health risks. This study examines the anaerobic oral flora of hunter killed black bears (Ursus americanus) in eastern North Carolina. Oral swabs from the buccal and lingual supragingival tooth surfaces of the first and second mandibular and maxillary molars of 22 black bears were inoculated onto Brucella Blood Agar plates supplemented with hemin and vitamin K after transport from the field using reduced oxoid nutrient broth. Sixteen anaerobic bacterial species, representing nine genera were identified using the RapID ANA II Micromethod Kit system and a number of organisms grown that could not be identified with the system. The most frequently identified anaerobes were Peptostreptococcus prevotii, Streptococcus constellatus, and Porphyromonas gingivalis. The diversity in the anaerobic oral flora of black bear in eastern North Carolina suggests the importance of including these organisms in basic health risk assessment protocols and suggests a potential tool for assessment of bear/habitat interactions.