https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1469-0691.2008.02070.x

Then and now: use of 16S rDNA gene sequencing for bacterial identification and discovery of novel bacteria in clinical microbiology laboratories

Defensins of vertebrate animals.

In adult individuals, the intestinal microbiota comprises several hundred, mostly anaerobic, bacterial species. This complex ecosystem is formed through the successive establishment of different bacteria in infancy and early childhood. Facultative and aerotolerant bacteria establish first, followed by more and more strict anaerobes. The bacteria derive from different sources and the colonization pattern is influenced by delivery mode and environmental factors. Commensal microbes provide the major drive for maturation of the immune system. Increased hygiene appears to have changed the gut flora of Western infants, which may affect the risk of developing immune mediated diseases. Conclusion: It is clear that the process of infant colonization needs to be studied further, since composition of the microbiota may impact on child health.

Establishment of the gut microbiota in Western infants

Antibiotics are chemotherapeutic agents, which have been a very powerful tool in the clinical management of bacterial diseases since the 1940s. However, benefits offered by these magic bullets have been substantially lost in subsequent days following the widespread emergence and dissemination of antibiotic resistant strains. While it is obvious that excessive and imprudent use of antibiotics significantly contributes to the emergence of resistant strains, antibiotic-resistance is also observed in natural bacteria of remote places unlikely to be impacted by human intervention. Both antibiotic biosynthetic genes and resistance-conferring genes have been known to evolve billions of years ago, long before clinical use of antibiotics. Hence it appears that antibiotics and antibiotics resistance determinants have some other roles in nature, which often elude our attention because of overemphasis on the therapeutic importance of antibiotics and the crisis imposed by the antibiotic-resistance in pathogens. In the natural milieu, antibiotics are often found to be present in subinhibitory concentrations acting as signalling molecules supporting quorum sensing and biofilm formation. They also play an important role in the production of virulence factors and influence host-parasite interactions (e.g., phagocytosis, adherence to the target cell and so on). The evolutionary and ecological aspects of antibiotics and antibiotic-resistance in the naturally occurring microbial community are little understood. Therefore, the actual role of antibiotics in nature warrants in-depth investigations. Studies on such an intriguing behaviour of the microorganisms promise insight into the intricacies of the microbial physiology and are likely to provide some lead in controlling the emergence and subsequent dissemination of antibiotic resistance. This article highlights some of the recent findings on the role of antibiotics and genes that confer resistance to antibiotics in nature.

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The multifaceted roles of antibiotics and antibiotic resistance in nature.

Background Previous reports on molecular rapid diagnostic testing (mRDT) do not consistently demonstrate improved clinical outcomes in bloodstream infections (BSIs). This meta-analysis seeks to evaluate the impact of mRDT in improving clinical outcomes in BSIs. Methods We searched PubMed, CINAHL, Web of Science, and EMBASE through May 2016 for BSI studies comparing clinical outcomes between mRDT and conventional microbiology methods. Results Thirty-one studies were included with 5920 patients. The mortality risk was significantly lower with mRDT than with conventional microbiology methods (odds ratio [OR], 0.66; 95% confidence interval [CI], .54-.80), yielding a number needed to treat of 20. The mortality risk was slightly lower with mRDT in studies with antimicrobial stewardship programs (ASPs) (OR, 0.64; 95% CI, .51-.79), and non-ASP studies failed to demonstrate a significant decrease in mortality risk (0.72; .46-1.12). Significant decreases in mortality risk were observed with both gram-positive (OR, 0.73; 95% CI, .55-.97) and gram-negative organisms (0.51; .33-.78) but not yeast (0.90; .49-1.67). Time to effective therapy decreased by a weighted mean difference of -5.03 hours (95% CI, -8.60 to -1.45 hours), and length of stay decreased by -2.48 days (-3.90 to -1.06 days). Conclusions For BSIs, mRDT was associated with significant decreases in mortality risk in the presence of a ASP, but not in its absence. mRDT also decreased the time to effective therapy and the length of stay. mRDT should be considered as part of the standard of care in patients with BSIs.

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The Effect of Molecular Rapid Diagnostic Testing on Clinical Outcomes in Bloodstream Infections: A Systematic Review and Meta-analysis

Prospective intervention study with a microarray-based, multiplexed, automated molecular diagnosis instrument (Verigene system) for the rapid diagnosis of bloodstream infections, and its impact on the clinical outcomes

The authors have investigated Staphylococcus aureus transmission between healthy, lactating mothers without mastitis and their infants by breastfeeding using both bacteriological and molecular-epidemiological methods. They studied 8 healthy, lactating mothers without clinical signs of mastitis and their infants who were less than 3 months old. They collected samples of breast milk, swabs of the mothers' nipples, the infants' nares, and the infants' oral cavities. There was a 50% transmission rate between the pairs. As the result of 12 antibiotics' susceptibility, Methicillin-resistant S. aureus was isolated from 2 of the 4 pairs. Using pulsed-field gel electrophoresis, the authors determined chromosomal DNA restriction patterns of the S. aureus isolated from 4 mother-infant pairs. The DNA fragment patterns of the organism within a given mother-infant pair were indistinguishable or closely related. The results suggest that methicillin-resistant S. aureus or methicillin-sensitive S. aureus may be transmitted between healthy, lactating mothers without mastitis and their infants by breastfeeding.

Transmission of Staphylococcus aureus between healthy, lactating mothers and their infants by breastfeeding.

A Novel Mouse β-Defensin, mBD-6, Predominantly Expressed in Skeletal Muscle

Prevalence of toxin A-nonproducing/toxin-B-producing Clostridium difficile in the Tsukuba-Tsuchiura district, Japan.

Leptotrichia amnionii is an organism that rarely causes female genital tract infection. We describe a case of a male patient with arthritis on the left knee joint due to this organism.

Shigemi Hitomi

Papers

Prospective intervention study with a microarray-based, multiplexed, automated molecular diagnosis instrument (Verigene system) for the rapid diagnosis of bloodstream infections, and its impact on the clinical outcomes

Transmission of Staphylococcus aureus between healthy, lactating mothers and their infants by breastfeeding.

A Novel Mouse β-Defensin, mBD-6, Predominantly Expressed in Skeletal Muscle

Prevalence of toxin A-nonproducing/toxin-B-producing Clostridium difficile in the Tsukuba-Tsuchiura district, Japan.

Bacterial Arthritis Caused by Leptotrichia amnionii