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Metatranscriptomic Analysis Reveals Active Bacterial Communities in Diabetic Foot Infections.

ABSTRACT: Despite the extended view of the composition of diabetic foot infections (DFIs), little is known about which transcriptionally active bacterial communities are pertinent to infection, and if any differences are associated with increased infection severity. We applied a RNA sequencing approach to analyze the composition, function, and pathogenicity of the active bacterial communities in DFIs. Taxonomic profiling of bacterial transcripts revealed the presence of 14 bacterial phyla in DFIs. The abundance of the Spiroplasma, Vibrio, and Mycoplasma were significantly different in different infection severities (P < 0.05). Mild and severe stages of infections were dominated by Staphylococcus aureus and Porphyromonas asaccharolytica, respectively. A total of 132 metabolic pathways were identified of which ribosome and thiamin being among the most highly transcribed pathways. Moreover, a total of 131 antibiotic resistance genes, primarily involved in the multidrug efflux pumps/exporters, were identified. Furthermore, iron acquisition systems (synthesize and regulation of siderophores) and pathways involved in the synthesis and regulation of cell-surface components associated with adhesion, colonization, and movement of bacterial cells were the most common virulence factors. These virulence factors may help bacteria compete for scares resources and survive the host wound proteases. Characterization of transcriptionally active bacterial communities can help to provide an understanding of the role of key pathogens in the development of DFIs. Such information can be clinically useful allowing replacement of DFIs empirical therapy with targeted treatment.

SUBMITTER: Heravi FS

PROVIDER: S-EPMC7387423 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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Metatranscriptomic Analysis Reveals Active Bacterial Communities in Diabetic Foot Infections.

Heravi Fatemah Sadeghpour FS Zakrzewski Martha M Vickery Karen K Malone Matthew M Hu Honghua H

Frontiers in microbiology 20200722

Despite the extended view of the composition of diabetic foot infections (DFIs), little is known about which transcriptionally active bacterial communities are pertinent to infection, and if any differences are associated with increased infection severity. We applied a RNA sequencing approach to analyze the composition, function, and pathogenicity of the active bacterial communities in DFIs. Taxonomic profiling of bacterial transcripts revealed the presence of 14 bacterial phyla in DFIs. The abu ...[more]

PMID: 32793159

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Project description:The use of natural marine bacteria as "oil sensors" for the detection of pollution events can be suggested as a novel way of monitoring oil occurrence at sea. Nucleic acid-based devices generically called genosensors are emerging as potentially promising tools for in situ detection of specific microbial marker genes suited for that purpose. Functional marker genes are particularly interesting as targets for oil-related genosensing but their identification remains a challenge. Here, seawater samples, collected in tanks with oil addition mimicking a realistic oil spill scenario, were filtered and archived by the Environmental Sample Processor (ESP), a fully robotized genosensor, and the samples were then used for post-retrieval metatranscriptomic analysis. After extraction, RNA from ESP-archived samples at start, Day 4 and Day 7 of the experiment was used for sequencing. Metatranscriptomics revealed that several KEGG pathways were significantly enriched in samples exposed to oil. However, these pathways were highly expressed also in the non-oil-exposed water samples, most likely as a result of the release of natural organic matter from decaying phytoplankton. Temporary peaks of aliphatic alcohol and aldehyde dehydrogenases and monoaromatic ring-degrading enzymes (e.g., ben, box, and dmp clusters) were observed on Day 4 in both control and oil-exposed and non-exposed tanks. Few alkane 1-monooxygenase genes were upregulated on oil, mostly transcribed by families Porticoccaceae and Rhodobacteraceae, together with aromatic ring-hydroxylating dioxygenases, mostly transcribed by Rhodobacteraceae. Few transcripts from obligate hydrocarbonoclastic genera of Alcanivorax, Oleispira and Cycloclasticus were significantly enriched in the oil-treated exposed tank in comparison to control the non-exposed tank, and these were mostly transporters and genes involved in nitrogen and phosphorous acquisition. This study highlights the importance of seasonality, i.e., phytoplankton occurrence and senescence leading to organic compound release which can be used preferentially by bacteria over oil compounds, delaying the latter process. As a result, such seasonal effect can reduce the sensitivity of genosensing tools employing bacterial functional genes to sense oil. A better understanding of the use of natural organic matter by bacteria involved in oil-biodegradation is needed to develop an array of functional markers enabling the rapid and specific in situ detection of anthropogenic pollution.

Project description:Diabetic foot infection has become one of the most important public health concerns and is a growing problem. Pseudomonas aeruginosa is an important opportunistic multidrug-resistant bacterium in diabetic foot infections. In the absence of antibiotics active against MDR strains of P. aeruginosa, phage therapy becomes a key way to deal with P. aeruginosa infections. Out of 185 samples collected from diabetic foot ulcers, 50 (27.02%) isolates were identified as P. aeruginosa. The incidence increases with older ages, and males (n=34, 68%) predominated in all age groups. The tested isolates showed maximum susceptibility towards colistin (80%), imipenem (72%), amikacin (66%), and piperacillin/tazobactam (62%), while these isolates showed moderate susceptibility towards ceftazidime (58%), cefepime (52%) and gentamicin (46%). However, it showed complete resistance (100%) to ampicillin, cefaclor, and sulphamethoxazole/trimethoprim and highly resistance to clindamycin (90%) and amoxicillin/clavulanic acid (84%). Two bacteriophages (ϕPAE1 and ϕPAE2) isolated from sewage samples showed a broad host range against P. aeruginosaa clinical strains. ϕPAE2 infected 74% (37/50) and ϕPAE2 58% (29/50). Furthermore, both phages were host-specific, infecting only P. aeruginosa strains and could not infect other bacterial species in the cross-infectivity studies. Both phages were found to be relatively heat stable as over a period of 1 h, after exposure to a temperature range of 37-50°C, no significant loss in phage activity was observed. On the other hand, the lowest activity was observed at 70°C (39.15%) for ϕPAE1 whereas it was inactivated at 75°C while the lowest activity was observed at 75°C (38.01%) for ϕPAE2 whereas it was inactivated at 80°C. Isolated phages were able to survive and lyse host bacteria over a wide pH range. The optimum pH range for infection was from 6 to 8. Furthermore, ϕPAE1 lost its ability to lyses at pH 2, 3, 11 and 12, whereas; ϕPAE2 lost its infectivity at pH 2, 3 and 12. Chloroform was the most effective solvent that reduced the infectivity of ϕPAE1 and ϕPAE2 to 63.27% and 77.88%, respectively. On the other hand, petroleum ether showed the lowest effect on the infectivity of ϕPAE1 and ϕPAE2; it was reduced to 96.4% and 97.48%, respectively, followed by acetone and ethyl alcohol. The ability of P. aeruginosa phages to form plaques after different storage temperatures (4°C, 30°C, 37°C and 44°C) for a month was slightly affected. The storage of ϕPAE1 and ϕPAE2 at 4ºC showed the least effect on its infectivity, and the storage at 44ºC showed the highest reduction in its infectivity. Moreover, Phage counts were slightly decreased by increasing storage period and temperature.

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Metatranscriptomic Analysis Reveals Active Bacterial Communities in Diabetic Foot Infections.

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Metatranscriptomic Analysis Reveals Active Bacterial Communities in Diabetic Foot Infections.

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