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Biology subjects

Cocker, D.

Publications and source records attributed to Cocker, D..

3 recordsLinked to original sources

Lung microbiomes variable responses to dust exposure

Inhalation of dust is significant and relevant to health effects. As pollution and climate change worsen in dryland regions, wind currents entrain loose sediment and dust. This potentially disperses toxic geochemical and microbial burdens throughout the region. When inhaled environmental dust and host-associated microbiomes mingle, they pose exposure risks to host respiratory health. The Salton Sea, Californias largest lake, is shrinking thus exposing nearby communities to playa dust. Therefore, we analyze the effect of Salton Sea dust exposure in murine models to relate lung microbial communities and respiratory health. We used an environmental chamber to expose mice to dust filtrate or ambient air and examined the effects of those exposures on lung microbiomes. We found that lung microbial composition varied by dust exposure. Furthermore, dust elicited neutrophil recruitment and immune responses more than mice exposed to ambient air. Sources of dust differentially affected the composition of the lung core microbiome. Lung microbial diversity correlated with neutrophil recruitment as lungs associated with inflammatory responses harbored more diverse microbiomes. Although Salton Sea dust influences dust microbiomes and prevalent taxa, these responses were variable. The composition of lungs exposed to dust collected further from the Sea was more similar to lungs from ambient air exposures; in contrast, dust collected near the Sea yielded lung microbiomes that clustered further from lungs exposed to ambient air. As lakes continue to dry out, we expect greater public health risks in proximal dryland regions, which may correlate with dust microbial dispersal-related changes to lung microbiomes. ImportanceDust inhalation can lead to health effects, especially when toxic chemicals and microbes mix in with the dust particles. As Californias Salton Sea dries up, it exposes lake bottom sediments to wind, which disperses the dried sediments. To mimic the effect of inhaling Salton Sea dust, we collected and filtered airborne dust to use in exposure experiments with mice in environmental chambers. We predicted that inhaling small dust particles, chemicals, and microbial residues found in this dust would affect mouse respiratory health, or change the microbes found inside their lungs. We found that inhaling dust led to lung inflammation and the dust source influenced the type of microbes found inside mouse lungs. As lakes continue to dry out, we expect greater health risks and changes to lung microbiomes. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=95 SRC="FIGDIR/small/648223v1_ufig1.gif" ALT="Figure 1"> View larger version (21K): org.highwire.dtl.DTLVardef@11e791eorg.highwire.dtl.DTLVardef@1a1a853org.highwire.dtl.DTLVardef@31ee4aorg.highwire.dtl.DTLVardef@135f40_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

One Health in Eastern Africa: No barriers for ESBL producing E. coli transmission or independent antimicrobial resistance gene flow across ecological compartments

The One Health paradigm considers the interdependence of human, animal and environmental health. In high-income countries, limited evidence has been found from recent studies to support the importance of a One Health approach to addressing spread of antimicrobial resistance (AMR). Given AMR is a global threat, and we are all interconnected it would be important to know if closer interaction of humans with animals and the environment in low-income present a contrasting picture. We used whole genome sequencing to investigate the genomic diversity and to infer transmission of extended spectrum beta-lactamase producing Escherichia coli (ESBL-Ec) between different ecological niches (humans, animals and the environment). We found high diversity of ESBL-Ec with 172 genomic clusters and 167 sequence types identified from 2,344 genomes. Common ESBL genes, blaCTX-M-15 (67.6%) and blaCTX-M-27 (14.2%) were carried on a complex network of different plasmids, presenting multiple pathways for dissemination and revealing the high force of selection. Using fine-scale genomic clustering across multiple thresholds ranging from 0 to 20 single nucleotide polymorphisms, we found that genomes isolated from humans, animals and the environment formed overlapping clusters, indicating recent ESBL-Ec transmission and co-circulation both within and between ecological compartments. These findings demonstrate that the One Health approach is highly relevant to tackling AMR in low-income settings, and therefore critical to consider if we are to address the rise of AMR globally.

genomics↗

MagnaExtract, a novel magnetic bead-based extraction method for the molecular detection of antimicrobial resistance genes in fresh water.

BackgroundThe environmental is increasingly recognised as an important reservoir of antimicrobial resistance (AMR) genes. Polymerase chain reaction (PCR) and whole genome sequencing (WGS) have great potential in the surveillance of AMR genes. However, molecular methods are dependent upon the isolation of high-quality DNA yields. Currently, there is no consensus for the optimum DNA extraction strategies from complex environmental matrices for downstream molecular applications. MethodsWe present a novel magnetic bead-based method for the isolation of antimicrobial resistance genes (ARGs) from river water in Malawi, named MagnaExtract. We present this with analytic limit of detection (LOD) as well as a case study in Southern Malawi. Here we compare the DNA yield and subsequent PCR output from MagnaExtract with commercially available QIAGEN kits and the crude boil and spin method, utilising a high-resolution melt analysis (HRM) PCR panel designed for the detection of third generation cephalosporin and carbapenem resistant genes. ResultsOf the 98 water samples evaluated we found the MagnaExtract method to be comparable, and in some instances superior to commercially available kits for the isolation of ARGs from river water samples. In addition, we found overnight incubation to promote the recovery of extended spectrum beta-lactamase (ESBL) genes and simultaneous reduction in the detection of carbapenemase genes. ConclusionThe MagnaExtract approach offers a simple, affordable, high yielding extraction method that could be used for the detection of ARGs isolated from river water samples in environmental surveillance campaigns in East Africa.

molecular biology↗