Detection of pathogens associated with early-onset neonatal sepsis in cord blood at birth using quantitative PCR

Background: Early onset neonatal sepsis (EONS) typically begins prior to, during or soon after birth and may be rapidly fatal. There is paucity of data on the aetiology of EONS in sub-Saharan Africa due to limited diagnostic capacity in this region, despite the associated significant mortality and long-term neurological impairment. Methods: We compared pathogens detected in cord blood samples between neonates admitted to hospital with possible serious bacterial infection (pSBI) in the first 48 hours of life (cases) and neonates remaining well (controls). Cord blood was systematically collected at Kilifi County Hospital (KCH) from 2011-2016, and later tested for 21 bacterial, viral and protozoal targets using multiplex PCR via TaqMan Array Cards (TAC). Results: Among 603 cases (101 [17%] of whom died), 179 (30%) tested positive for ≥1 target and 37 (6.1%) tested positive for multiple targets. Klebsiella oxytoca, Escherichia coli/Shigella spp., Pseudomonas aeruginosa, and Streptococcus pyogenes were commonest. Among 300 controls, 79 (26%) tested positive for ≥1 target, 11 (3.7%) were positive for multiple targets, and K. oxytoca and P. aeruginosa were most common. Cumulative odds ratios across controls: cases (survived): cases (died) were E. coli/Shigella spp. 2.6 (95%CI 1.6-4.4); E. faecalis 4.0 (95%CI 1.1-15); S. agalactiae 4.5 (95%CI 1.6-13); Ureaplasma spp. 2.9 (95%CI 1.3-6.4); Enterovirus 9.1 (95%CI 2.3-37); and Plasmodium spp. 2.9 (95%CI 1.4-6.2). Excluding K. oxytoca and P. aeruginosa as likely contaminants, aetiology was attributed in 9.4% (95%CI 5.1-13) cases using TAC. Leading pathogen attributions by TAC were E. coli/Shigella spp. (3.5% (95%CI 1.7-5.3)) and Ureaplasma spp. (1.7% (95%CI 0.5-3.0)). Conclusions: Cord blood sample may be useful in describing EONS pathogens at birth, but more specific tests are needed for individual diagnosis. Careful sampling of cord blood using aseptic techniques is crucial to minimize contamination. In addition to culturable bacteria, Ureaplasma and Enterovirus were causes of EONS.

Metal Contaminants Occurrence and Microbial Diversity From the Perspectives of Dual Tolerance by the Bacterial Isolates Along Altitudinal Zonation of River Teesta – a Pristine River System in Eastern Himalayas

The present study was conducted along River Teesta in Eastern Himalaya. Water and sediment samples were collected from six sampling points during the monsoon and winter seasons along the course of the river. The background information was collected by analysing physico-chemical parameters and the heavy metal concentrations. Culturable bacterial diversity using culture-based and molecular based 16S rRNA approaches characterized bacterial isolates to 5 major phyla, majority belonging Proteobacteria, Actinobacteria and Firmicutes followed by Bacteroidetes, Alpha-Proteobacteria, Beta-Proteobacteria, Gamma-Proteobacteria, Actinobacteria, Bacilli, Flavobacteriia, Deinococci, Sphingobacteriia and Cytophagia. The total of 245 characterized isolates belonged to 69 genera. Diversity indices were calculated for each site. There were variations in the community structure of culturable bacteria along the river stretch with some common and unique groups. Heavy metal tolerance and antibiotic resistance profiles showed some isolates to be tolerant to high levels of heavy metals and multiple antibiotic indicating a major concern. The antibiotic resistance diversified along the human impacted downstream sites. The present report on bacterial diversity and the associated metal and antibiotics tolerance is the first of its kind on Teesta river, the only major river system flowing through the state of Sikkim and parts of North Bengal.

Living in a bottle: Bacteria from sediment-associated Mediterranean waste and potential growth on polyethylene terephthalate (PET)

Ocean pollution is a worldwide environmental challenge that could be partially tackled through microbial applications. To shed light on the diversity and applications of the bacterial communities that inhabit the sediments trapped in artificial containers, we analyzed residues (Polyethylene terephthalate (PET) bottles and aluminum cans) collected from the Mediterranean Sea by scanning electron microscopy and Next Generation Sequencing. Moreover, we set a collection of culturable bacteria from the plastisphere that were screened for their ability to use PET as a carbon source. Our results reveal that Proteobacteria are the predominant phylum in all the samples and that Rhodobacteraceae, Woeseia, Actinomarinales, or Vibrio are also abundant in these residues. Moreover, we identified marine isolates with enhanced growth in the presence of PET: Aquimarina intermedia, Citricoccus spp., and Micrococcus spp. Our results suggest that the marine environment is a source of biotechnologically promising bacterial isolates that may use PET or PET additives as carbon sources.

A Round Trip to the Desert: In situ Nanopore Sequencing Informs Targeted Bioprospecting

Bioprospecting expeditions are often performed in remote locations, in order to access previously unexplored samples. Nevertheless, the actual potential of those samples is only assessed once scientists are back in the laboratory, where a time-consuming screening must take place. This work evaluates the suitability of using Nanopore sequencing during a journey to the Tabernas Desert (Spain) for forecasting the potential of specific samples in terms of bacterial diversity and prevalence of radiation- and desiccation-resistant taxa, which were the target of the bioprospecting activities. Samples collected during the first day were analyzed through 16S rRNA gene sequencing using a mobile laboratory. Results enabled the identification of locations showing the greatest and the least potential, and a second, informed sampling was performed focusing on those sites. After finishing the expedition, a culture collection of 166 strains belonging to 50 different genera was established. Overall, Nanopore and culturing data correlated well, since samples holding a greater potential at the microbiome level also yielded a more interesting set of microbial isolates, whereas samples showing less biodiversity resulted in a reduced (and redundant) set of culturable bacteria. Thus, we anticipate that portable sequencers hold potential as key, easy-to-use tools for in situ-informed bioprospecting strategies.

In Situ Investigation of Plastic-Associated Bacterial Communities in a Freshwater Lake of Hungary

Despite the great benefits of plastics in different aspects of life and due to the increase in plastic production and use, plastic wastes are becoming a major environmental concern. It is well known that inappropriate use and disposal lead to the accumulation of plastic litter in different aquatic environments. Microbial biofilm is able to develop on the surface of plastics (plastisphere) in aquatic environments over time. The aim of this study was to describe the bacterial communities associated with plastics in freshwater. Thus, in our first test, a total of six self-designed plastic colonizers were submerged under the surface of the water in Vácszentlászló lake, located in central Hungary, for a period of 3 months. Two plastic colonizers were cultivated monthly. Associated microbial communities were then analyzed as follows: (a) bacterial communities were studied by amplicon sequencing and (b) culturable bacteria were isolated from plastic surfaces and identified by 16S rRNA gene sequencing. Coinciding with these analyses of plastic colonizing communities, surface water samples from the lake were also taken, and in a second test, other materials (eg. wood, glass) associated bacterial communities were also investigated with the same methods. Amplicon sequencing showed notable differences between the plastic and other materials colonizing, and lake waterborne microbial community composition. Using the LB agar, no novel species were found; however, several known pathogenic species were identified. The self-designed plastic colonizer was successfully used during the winter over a 3-month period, suggesting that it could be an appropriate method of choice to study microplastic-associated microbes for longer periods and in variable environmental conditions.

Bioaerosol Emission from Biofilters: Impact of Bed Material Type and Waste Gas Origin

Three semi-technical scale biofilters were applied to treat waste gases at different industrial sites in Poland: a mechanical–biological treatment plant of municipal solid waste, a wastewater treatment plant and a food industry plant. Two types of materials were used as beds in the biofilters: stumpwood chips and pine bark, and stumpwood chips, pine bark and compost from green waste. Both bed materials supported the microbial growth and high numbers (106–108 cfu/g dry mass (DM)) of culturable bacteria, and fungi in beds were observed. There was no correlation between the number of microorganisms (cfu/g DM) and the respiratory activity in the biofilter beds. However, microbial respiration activity corresponded with microbial abundance expressed as microbial equivalents (ME), which was calculated based on adenosine triphosphate (ATP) determination. The biofilters either reduced or increased bioaerosol emissions from industrial plants, depending on the microbial content in the waste gases. A high microbial content in the waste gases made the effect of microbial emission from the biofilter bed negligible. The type of biofilter bed and number of microorganisms in the bed also influenced the final bioaerosol emission, but these factors were relevant for biofilters that treated waste gases with low microbial concentrations.

Prevalence and correlates of phenazine resistance in culturable bacteria from a dryland wheat field

Phenazines are a class of bacterially-produced redox-active natural antibiotics that have demonstrated potential as a sustainable alternative to traditional pesticides for the biocontrol of fungal crop diseases. However, the prevalence of bacterial resistance to agriculturally-relevant phenazines is poorly understood, limiting both the understanding of how these molecules might shape rhizosphere bacterial communities and the ability to perform risk assessment for off-target effects. Here, we describe profiles of susceptibility to the antifungal agent phenazine-1-carboxylic acid (PCA) across more than 100 bacterial strains isolated from a wheat field where PCA producers are indigenous and abundant. We find that Gram-positive bacteria are typically more sensitive to PCA than Gram-negative bacteria, but that there is also significant variability in susceptibility both within and across phyla. Phenazine-resistant strains are more likely to be isolated from the wheat rhizosphere, where PCA producers are also more abundant, compared to bulk soil. Furthermore, PCA toxicity is pH-dependent for most susceptible strains and broadly correlates with PCA reduction rates, suggesting that uptake and redox-cycling are important determinants of phenazine toxicity. Our results shed light on which classes of bacteria are most likely to be susceptible to phenazine toxicity in acidic or neutral soils. In addition, the taxonomic and phenotypic diversity of our strain collection represents a valuable resource for future studies on the role of natural antibiotics in shaping wheat rhizosphere communities.

Monoterpene Enrichments Have Positive Impacts on Soil Bacterial Communities and the Potential of Application in Bioremediation

We study here how soil bacterial communities of different ecosystems respond to disturbances caused by enrichments with monoterpenes that are common essential oil constituents. We used fenchone, 1,8-cineol and α-pinene, and soils from phrygana, a typical Mediterranean-type ecosystem where aromatic plants abound, and from another five ecosystem types, focusing on culturable bacteria. Patterns of response were common to all ecosystems, but responses themselves were not always as pronounced in phrygana as in the other ecosystems, suggesting that these enrichments are less of a disturbance there. More specifically, soil respiration and abundance of the bacterial communities increased, becoming from below two up to 16 times as high as in control soils (for both attributes) and remained at high levels as long as these compounds were present. Bacteria that can utilize these three compounds as substrates of growth became dominant members of the bacterial communities in the enriched soils. All changes were readily reversible once monoterpene addition stopped. Bacteria with the ability to utilize these monoterpenes as carbon sources were found in soils from all ecosystems, 15 strains in total, suggesting a rather universal presence; of these, six could also utilize the organic pollutants toluene or p-xylene. These results suggest also potential novel applications of monoterpenes in combating soil pollution.

The Isolation of Culturable Bacteria in Ixodes ricinus Ticks of a Belgian Peri-Urban Forest Uncovers Opportunistic Bacteria Potentially Important for Public Health

Most bacteria found in ticks are not pathogenic to humans but coexist as endosymbionts and may have effects on tick fitness and pathogen transmission. In this study, we cultured and isolated 78 bacteria from 954 Ixodes ricinus ticks collected in 7 sites of a Belgian peri-urban forest. Most isolated species were non-pathogenic environmental microorganisms, and were from the Firmicutes (69.23%), Actinobacteria (17.95%) and Proteobacteria (3.84%) phyla. One bacterium isolate was particularly noteworthy, Cedecea davisae, a rare opportunistic bacterium, naturally resistant to various antibiotics. It has never been isolated from ticks before and this isolated strain was resistant to ampicillin, cefoxitin and colistin. Although cultivable bacteria do not represent the complete tick microbiota, the sites presented variable bacterial compositions and diversities. This study is a first attempt to describe the culturable microbiota of ticks collected in Belgium. Further collections and analyses of ticks of different species, from various areas and using other bacterial identification methods would strengthen these results. However, they highlight the importance of ticks as potential sentinel for opportunistic bacteria of public health importance.