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Bacteriology of Ophthalmic Infections
Published in K. Balamurugan, U. Prithika, Pocket Guide to Bacterial Infections, 2019
Arumugam Priya, Shunmugiah Karutha Pandian
Perceptive features of the ocular microflora are fundamental in understanding the ocular diseases and infections. Axenfeld (1908) stated that the microbiota of eyelid and conjunctiva are similar to that of the skin and upper respiratory tract. Since then, microbial flora of the ocular surface has been subjected to numerous studies to investigate the indigenous flora of the healthy eyes, as a comparative analysis to interpret the microbial shift during diseased state, to assess the microbial community before intraocular surgeries, or to review the prophylactic strategies in postoperative infections. Axenfeld founds that Staphylococcus albus and Corynebacterium were frequently isolated organisms, whereas Staphylococcus aureus, Streptococcus spp., and few other gram-negative bacteria were found with least incidence. The classification of ocular microbiota based on the culture-dependent methods was alleged to be predominantly conquered by gram-positive species such as Staphylococcus, Streptococcus, Propionibacterium, and Corynebacterium; gram-negative species such as Neisseria, Haemophilus, and few fungal species (Miller and Iovieno, 2009). Culture-based characterization significantly surpassed cultivable and fastidious growing organisms. With the advent of molecular techniques, (Dong et al., 2011) instigated the genome based detection of ocular microbiota and revealed diverse microbial community including commensal, environmental, and opportunistic pathogens (Dong et al., 2011). The 12 genera, Pseudomonas, Propionibacterium, Bradyrhizobium, Corynebacterium, Acinetobacter, Brevundimonas, Staphylococci, Aquabacterium, Sphingomonas, Streptococcus, Streptophyta, and Methylobacterium, were represented as core microbiome of the conjunctiva. Based on the sequencing of 16S rDNA V3–V4 hypervariable segments of bacteria from conjunctival swab, Huang et al. (2016) linked additional genera such as Millisia, Anaerococcus, Finegoldia, Simonsellia, and Veillonella to the core conjunctival microbiota. Numerous studies have evidenced that the use of contact lenses (Hovding, 1981; Larkin and Leeming, 1991; Fleiszig and Efron, 1992; Iskeleli et al., 2005; Shin et al., 2016), the eyes that endured surgeries (Jabbarvand et al., 2016) and patients with prolonged hospital stays (Sahin et al., 2017) presented variations in the microbial diversity and abundance. Moreover, variation in the ocular microbiota between eyes of an individual and between individuals has also been affirmed (Hovding, 1981).
Drip irrigation biofouling with treated wastewater: bacterial selection revealed by high-throughput sequencing
Published in Biofouling, 2019
Kévin Lequette, Nassim Ait-Mouheb, Nathalie Wéry
For the first time, the bacterial communities associated with biofouling along a drip irrigation system fed by treated wastewater have been characterised. Differences in bacterial communities between pipe and dripper biofilms were highlighted and indicated that the bacteria involved in biofouling were not the same in pipes and in drippers. The main contributor to this divergence was the genus Aquabacterium. Material properties and changes in water dynamics could explain this divergence. The observed differences would need to be taken into account in the management of cleaning strategies, since they could modify the properties of the biofilms at a higher scale and thus the efficiency of cleaning treatments.
16S metagenomics for diagnosis of bloodstream infections: opportunities and pitfalls
Published in Expert Review of Molecular Diagnostics, 2018
Jean Pierre Rutanga, Sandra Van Puyvelde, Anne-Sophie Heroes, Claude Mambo Muvunyi, Jan Jacobs, Stijn Deborggraeve
Although the human blood is considered sterile, several studies have reported on the presence of bacteria in the blood of healthy individuals using 16S metagenomics. In 2001, Nikkari et al. [54] reported for the first time the presence of bacterial 16S rDNA in blood from four healthy individuals. In 2008, bacterial DNA detected in the blood of two healthy individuals was classified as Aquabacterium, Stenotrophomonas, Budvicia, Serratia, Bacillus and Flavobacteria genera by Moriyama and colleagues [55]. In a larger sample set of 60 healthy blood donors in Denmark, viable bacteria were grown in more than half of the blood donations. The majority of bacteria identified were facultative anaerobic (59.5%) or anaerobic (27.8%) species [56]. However, in 2016 Païssé et al. showed that the distribution of bacteria in the blood of healthy individuals is not homogeneous as significant differences in the proportions of bacterial classes between plasma, buffy coat, and red blood cell fractions were reported [27]. The authors hypothesized that this was due to either preferential localization of living bacteria, or to bacteria or their DNA being transported by immune cells or red blood cells. The majority of reported bacteria in healthy blood fell within the group of bacteria which are not likely to be detected by BC such as anaerobic and facultative anaerobic bacteria; and most of them were Proteobacteria and Actinobacteria [56]. The detection of bacteria from blood in healthy individuals can be explained by false positive results due to sample contamination or by transient asymptomatic bacteremia [57–59]. Possible causes of sample contamination are described below. Transient bacteremia, on the other hand, can be the result of bacterial translocation from various origins to the bloodstream, like bacteria translocating from the gut [60,61] or streptococci passing the oral mucosal barrier and leading to sub-acute endocarditis [62]. Constant aspiration of airborne soil bacteria has also been postulated as a possible source of bacteria in the bloodstream [55]. As it is the case for BCs, 16S metagenomics data should therefore always be interpreted together with clinical data.