Saturday, 3 December 2022

Malevolent Designer News - How Creationism's Favourite Sadist is Spreading Antimicrobial Resistance

Genomic analysis of sewage from 101 countries reveals global landscape of antimicrobial resistance | Nature Communications
 global map of antimicrobial resistance
During the COVID-19 pandemic, scientists realised the value of analysing the sewerage outflow from major population centres to monitor the prevalence of the virus and its variants in the population. This technique can also be used to monitor microbial prevalence and variants such as antimicrobial resistance.

Now a team of researchers at the Danish Technical University (DTU) has used data from these analyses to produce a map of microbial resistance at the level of resistance genes, rather than of resistant species.

From a Creationist perspective, what this is measuring is how well their pestilential malevolence is doing in its arms race against medical science to ensure its pathogens retain their ability to make us sick.

The results of the meta-analysis were surprising in that it showed the same genes were present in different species and in different places, indicating that exchange of genes between species is more frequent and extensive than was previously thought.

From the DTU News release:
There are large geographical differences in both how frequently resistant genes occur and in which types of bacteria the genes are found. This is shown by analyses of sewage from throughout the globe, thus underlining the importance of combating antimicrobial resistance based on data on local conditions.
collecting sereage sample for analysis in Ghana
Collection of sewage sample in Tamale, Ghana - one of 101 countries to have taken part in a global surveillance of infectious diseases and antimicrobial resistance via sewage.
Photo: Courage Kosi Setsoafia Saba
During the COVID-19 pandemic, the world has become aware of the value of using sewage analyses to monitor disease development in an area. However, at DTU National Food Institute, a group of researchers has been using sewage monitoring from throughout the world since 2016 as an effective and inexpensive tool for monitoring infectious diseases and antimicrobial resistance.

We’ve found similar resistance genes in highly different bacterial types. We find it worrying when genes can pass from a very broad group of bacteria to a completely different group with which there is no resemblance. It’s rare for these gene transmissions to occur over such long distances. It’s a bit like very different animal species producing offspring.

This makes it much more likely that the bacteria will actually kill people—for example in a hospital—because no treatment is available.

Assistant Professor Patrick Munk, senior author
Research Group for Genomic Epidemiology
Technical University of Denmark, Kgs, Lyngby, Denmark
By analysing sewage samples received by DTU from 243 cities in 101 countries between 2016 and 2019, the researchers have now mapped where in the world the occurrence of resistance genes is highest, how the genes are located, and in which types of bacteria they are found.

The results from the new metagenomic study—which have just been published in Nature Communications—have surprised the researchers. In fact, the study shows that the genes have appeared in many different genetic contexts and bacterial types, indicating greater transmission than the researchers had expected.

If the genes are in bacteria that don’t usually make people sick—such as lactic acid bacteria—it’s of less concern. However, if the resistance genes find their way into bacteria that are important to human health—such as salmonella—it’s a completely different story.


ABOUT THE METHOD

Like an intricate puzzle
The Research Group for Genomic Epidemiology at DTU National Food Institute has developed and maintains one of the world’s most comprehensive resistance databases. It currently includes 3,134 known resistance genes.

The researchers have used the database to map resistance genes in the sewage samples in the new study.

The samples contain a very large number of microorganisms from different sources, including human faeces. The frozen sewage samples have been sent to DTU, where laboratory technicians extract all the bacteria from the thawed samples.

The bacteria are then broken up and their collective DNA is broken into smaller pieces, which state-of-the-art DNA sequencing equipment can read all at once.

A supercomputer can then compare the billions of recorded DNA sequences with known genes and construct larger pieces of the original genomes contained in the samples.

This process provides insight into several areas such as in which bacteria and genetic neighbourhoods the resistance genes are located.

We interpret this to mean that we may be quite close to a transmission hotspot, where there is a gene transmission from one to another to a third bacterium. That’s why we’re seeing the gene in so many different contexts precisely there.

We risk overlooking important trends because we don’t have data. Right now, we have huge knowledge about how resistance behaves in the West and—based on that knowledge—we plan how to combat resistance. It now turns out that if we look at some new locations, the resistance genes may behave very differently—presumably because they have more favourable transmission conditions. Therefore, the way in which you combat resistance must also be adjusted and tailored to the local conditions.

There are many analogies with climate change, where what happens on the other side of the globe isn’t unimportant to you. One day or another, the problem will come back to bite us, as we’ve seen time and again.

Assistant Professor Patrick Munk
Hotspots for transmission of genes
In different places in Sub-Saharan Africa, the researchers have found the same resistance gene in a number of different bacteria.
[Professor Munk] adds that many of the surprising transmissions appear to occur in the Sub-Saharan Africa. These are also countries with the least developed programmes for monitoring resistance, which means that there is very little data on the resistance situation.

Successor
The global sewage project—which is supported by the Novo Nordisk Foundation and the VEO research project—concludes in 2023. The researchers find that it has proved to be a good supplement to existing monitoring initiatives, which mainly operate at national or regional level and measure resistance in bacteria from sick people.

They therefore hope that a successor to the project will appear, so that the world can continue to benefit from the important knowledge generated by the monitoring programme. This also applies to countries that have solid monitoring programmes and control strategies in place.


DATA SHARING

Reuseable data
Unlike data from conventional analysis methods, raw data from metagenomic studies can be reused to shed light on other problems. For example, the researchers in the sewage project have used their dataset to analyse the occurrence of other pathogenic microorganisms in the sewage.

The whole dataset from the sewage monitoring has been made freely available to researchers worldwide. For example, it has already been used to detect many new viruses globally and to map the ethnic composition of different populations.

As new resistance genes are discovered—even far into the future—researchers will be able to reuse raw data to quickly establish where they have first appeared and how they have spread.

RESEARCH

Behind the study
In the study, the researchers have analysed 757 sewage samples from 243 cities in 101 countries. The samples were collected and sent to DTU’s campus in Lyngby between 2016 and 2019.

Genomic analysis of wastewater is fast and fairly inexpensive relative to how many people you can cover. Wastewater analyses do not require ethical approval, as the sample material cannot be linked to individuals.

Read more about the results of the study in an article in Nature Communications: Genomic analysis of sewage from 101 countries reveals global landscape of antimicrobial resistance.
The following diagram, taken from the team's open access paper in Nature Communications, shows just how extensive gene-sharing via plasmids is, even between unrelated bacteria. As a Creationist would say, this shows how their favourite designer, having designed a way to help one bacteria make us sick despite medical science producing antibiotics to prevent it, makes sure the ability is spread as widely as possible, even, bizarrely, into harmless organisms such as lactobacilli.
sharing network between different bacteria
Fig. 4: Gene-sharing network between bacterial genera.
Edges link ARGs to the genera which their contigs were taxonomically assigned to. Only flanked, non-plasmidic contigs were used. The backbone algorithm was used to compute the graph layout. Color and thickness of edges denote the number of observed taxa-gene co-occurrences. Nodes are ARGs and genera which are visualized as grey boxes and colored circles respectively. Node size denote the centrality of the individual nodes to the overall network. Smaller subgraphs were manually moved for space efficiency, so relative distances between those mean nothing.

Copyright: © 2022 The authors.
Published by Springer Nature Ltd. Open access. (CC BY 4.0)
In the abstract to their paper, the scientists say:
Abstract
Antimicrobial resistance (AMR) is a major threat to global health. Understanding the emergence, evolution, and transmission of individual antibiotic resistance genes (ARGs) is essential to develop sustainable strategies combatting this threat. Here, we use metagenomic sequencing to analyse ARGs in 757 sewage samples from 243 cities in 101 countries, collected from 2016 to 2019. We find regional patterns in resistomes, and these differ between subsets corresponding to drug classes and are partly driven by taxonomic variation. The genetic environments of 49 common ARGs are highly diverse, with most common ARGs carried by multiple distinct genomic contexts globally and sometimes on plasmids. Analysis of flanking sequence revealed ARG-specific patterns of dispersal limitation and global transmission. Our data furthermore suggest certain geographies are more prone to transmission events and should receive additional attention.

There seem to be no lengths to which Creationism divine malevolence will not go in its determination to make us sick. Such fanatical zeal can only come from a deep and abiding hatred for its creation, or a deeply flawed, psychopathic personality that enjoys watching people and animals suffer in ever more inventive ways. For some reason, Creationists would rather that was our view of their putative intelligent designer rather than have people accept that there is no intelligence, malevolent, benevolent or indifferent, behind the evolution of species.

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