Where does antibiotic resistance come from?

Where does antibiotic resistance come from?

The world has finally woken up to the grave fact that we face the imminent collapse of our first-line medical protection against pathogenic microorganisms – antibiotics. The pharmaceutical industry churns out over 100,000 tons of antibiotics every year, and much of that tonnage is inexpertly over- or mis-prescribed and has led to a plethora of multiply antibiotic-resistant superbugs. But where do these pathogens acquire the genes for antibiotic resistance? There seem to be three answers: overuse of antibiotics either selects for pre-existent resistance mutations lying in bacterial genomes, or fortuitous de novo mutations that occur in the face of the intense selection pressure of antibiotic treatment. And there is a third way. For over 30 years, microbiologists have suspected that pathogenic bacteria obtain their resistance genes from the very organisms that supply our antibiotics in the first place – actinobacteria, otherwise known as actinomycetes, which look like fine filamentous fungal hyphae and inhabit soils.

One single genus of actinobacteria, Streptomyces, has made a gigantic contribution, from the days of Alexander Fleming to the present, to the production of our antibiotic arsenal. Over 80% of our antibiotics have been sourced from them. From streptomycin, in the 1940s, to the cephalosporins, chloramphenicol, neomycin and the tetracyclines and on to erythromycin, vancomycin and gentomycin in more recent years – and many others.

Actinobacteria produce all these toxic antibacterials in order to attack and destroy competing species in the soil around them, and, to make sure that they do not succumb to their own poison, they contain a suite of protective antibiotic resistance genes. On top of that, actinobacteria collect resistance genes from each other so that they are an equally rich source of antibiotics, and antibiotic resistance, at the same time. In an open-access paper published June 7th in Nature Communications, titled “Dissemination of antibiotic resistance genes from antibiotic producers to pathogens”, Xinglin Jiang et al have painstakingly proved the microbiologists suspicion that pathogens purloin resistance genes from actinobacteria by tracking a route they call “carry-back” – horizontal gene transfer in both directions – by which the resistance genes get transferred.

Their suspicions were alerted by the discovery that many of the resistance genes in important gram-negative pathogens like E. coli and Pseudomonas aeruginosa bore remarkable sequence similarity to antibiotic resistance genes from actinobacteria. So, if pathogens import their resistance from the actinobacteria resistance factories, how do they do it? The team provide evidence that pathogens encounter actinobacteria in places like farmyard soil or clinical waste, and conjugate with them – a form of bacterial “sex” that transfers pathogen DNA into the actinobacteria. Once there, the pathogen DNA recombines with actinobacterial DNA to form a sandwich of actinobacterial DNA – rich in resistance genes – flanked by pathogen DNA. When the actinobacterial cell dies this DNA sandwich lives on, quite viable, in the soil where it can eventually be picked up by transport through the cell membranes of other pathogens, a process called natural transformation, and reincorporated into their genomes – a loaded gun ready to cause medical havoc.

 

 

 

 

 

Evolution trades lifetime reproductive success for susceptibility to heart disease

Evolution trades lifetime reproductive success for susceptibility to heart disease

Coronary artery disease (CAD) perennially tops the league for killer diseases. It’s estimated that over 600,000 Americans die from a heart attack every year and CAD is the leading cause of death for both men and women. Furthermore, arterial plaque formation can be detected as early as adolescence and progressively afflicts us throughout our reproductive years into old age. If CAD is not simply a disease of post-reproductive age, you might therefore expect that selection would have operated to ameliorate these fitness-reducing effects of CAD but it appears that it has not. Now an international collaboration of scientists, including Stephen Stearns from Yale University and lead researcher on the famous Framingham Heart Study, claims to have part of the answer. CAD is maintained in human populations, they say, by the classic evolutionary trade-off of antagonistic pleiotropy. Gene variants shown to confer risk of CAD are also involved in fertility. Evolution may have traded lifetime reproductive success for susceptibility to heart disease in later age.

In a paper this week in PLoS Genetics titled “Genetic loci associated with coronary artery disease harbor evidence of selection and antagonistic pleiotropy” Byars et al point out that there are two popular misconceptions about CAD. Firstly, that it only occurs in older people and, secondly, that it is a disease that has mainly afflicted modern humans. If either were true, they say, selection might not have had either the opportunity or sufficient time to affect the genetic variation that is associated with CAD. However, CAD takes root as early as adolescence where disease origins can be detected through atherosclerosis and myocardial infarction, and manifests during reproductive age. CAD is also a product of many heritable risk factors (cholesterol, weight, blood pressure) whose variation is expressed during the reproductive period, when CAD could drive selection directly or indirectly. Furthermore, CAD is no modern self-inflicted disease of the Western lifestyle. It has impacted human populations for thousands of years at least – as evidence of arterial plaque from Egyptian mummies and mummified remains from Peru and elsewhere has shown. Plenty of time for evolutionary responses to CAD to have occurred which have left their signatures in the genomes of modern humans.

Their study has identified many adaptive signals among CAD loci and for highly-ranked CAD genes there was a consistent overlap between selection and genetic risk of CAD. Thus many of these genes must have been modified by CAD-linked selection pressures. This confirms not only that CAD has indeed been present for an evolutionarily-relevant period of thousands of years but that selection has occurred in young adults partly through direct pathology of CAD, like a heart attack, or via selection on CAD risk factors. But, by dipping into data from the Framingham Heart Study, they also found that CAD-disposing genes were disproportionately linked to female lifetime reproductive success relative to genes in the rest of the genome. Out of 76 CAD genes, 51 genes contained point mutations that were significantly nominally associated with lifetime reproductive success. Some, they say, directly affected fitness by influencing offspring number or age at menarche and menopause, while others correlated with traits involving ability to fertilise eggs or successfully conceive babies, or factors influencing fetal growth, development or survival.

Specifically, out of the 40 top-ranked CAD genes they found that PPAP2B was associated with reproductive capacity, SMAD3 with twinning, and KIAA1462 and SLC22A5 on numbers of offspring produced. While PHACTR1, LPL, SMAD3, ABO and SLC22A5 seem to contribute to the timing of reproductive lifespan through influencing menarche and menopause and expression of PHACTR1, KCNK5, MRAS and ADAMST7 appear to regulate lactation capacity. Some of these genes are highly expressed during embryogenesis and may also influence female receptiveness to implantation.

So much for female fertility. What about men, who are slightly more susceptible than women for CAD? They found many genes that affected male fertility and 13 that affected fertility in both men and women. For instance, the gene SLC22A5 causes both cardiomyopathy and male infertility due to an altered ability to break down lipids.

They conclude: “Our study provides new evidence that genes underlying CAD have recently been modified by natural selection and that these same genes uniquely and extensively contribute to human reproduction, which suggests that natural selection may have maintained genetic variation contributing to CAD because of its beneficial effects on fitness. This study provides novel evidence that CAD has been maintained in modern humans as a by-product of the fitness advantages those genes provide early in human life-cycles.”

Prebiotics cut down body fat in obese children

Prebiotics cut down body fat in obese children

This post is the third of a recent trilogy on links between the microbiome and health. Researchers from the University of Calgary have carried out a trial on 7 to 12 year old children who were classified as overweight or obese for their age. Although the total number of children in the trial was fairly small – 42 individuals – the trial was double-blinded and placebo controlled. The children were assigned into groups which were either given a readily available prebiotic fibrous product, oligofructose-enriched inulin, or a placebo, for 16 weeks. The experiment is reported in an open access uncorrected proof in the journal Gastroenterology.

Over the 16 weeks, the researchers measured fat mass and lean mass; height, weight and waist circumference; and analysed blood samples for lipids, cytokines, lipopolysaccharide, and insulin. They also took stool samples to check for changes to the resident gut microbiota. They noted changes between the prebiotic-treated group and the controls at a number of levels. There was a decrease in serum triglycerides of 19% in the prebiotic group, while there were significant increases in species of Bifidobacterium – a direct result of filling the gut with fiber – and decreases in Bacteroides vulgatus. The prebiotic treatment palpably slowed weight gain: the placebo group recorded a 2.4 fold increase in body weight over the prebiotic group over 16 weeks and while the prebiotic group held Body Mass Index stable over this period it was significantly increased in the placebo group. Percentage total body fat was also clearly lower in the prebiotic group by the end of the experimental period. While the duration of the experiment and the young age of the children meant that indicators of widespread inflammation were not noticed they did see a higher level of circulating inflammatory cytokine interleukin-6 in the placebo group and they are now planning bigger trials of this very simple dietary intervention to provide more evidence of cheap and efficient control of childhood obesity. This looks like a group of significantly overweight children rescued from two forms of evolutionary mis-match: a couch-potato life-style rich in fats and refined carbs, and an unhealthy gut microbiota incapable of regulating inflammation and adiposity.

Can the gut microbiota slow the progression of Alzheimer’s disease?

Can the gut microbiota slow the progression of Alzheimer’s disease?

In a current paper in Scientific Reports, Bonfilli et al describe research on a mouse model of Alzheimer’s disease that provides strong and detailed evidence for multiple changes in the diseased brain that appear to lead to an amelioration of neurodegeneration. The AD mice were treated with a probiotic formulation called SLAB51, rich in lactic acid bacteria and bifidobacteria, and the assumption is that the modulation of the gut microbiota this causes affects the brain and behaviour through the gut-brain axis.

On a behavioural level, treated mice out-performed controls on several tests of memory including the novel-object recognition (NOR) test which is used to evaluate recognition memory and is based on the spontaneous tendency of rodents to spend more time exploring a novel object than a familiar one. The amount of time the rodent spends exploring each novel object over a 10 minute test period provides a powerful measurement of memory integrity and attention. Treated mice also out-performed controls on a passive avoidance test which relies on memory of punishment.

In terms of brain anatomy there were notable differences in cortical thickness between probiotic treated and un-treated AD mice, particularly in the hippocampus, and ventricular enlargement in the untreated individuals. They then measured the plasma concentration of the gut peptide hormones ghrelin, leptin, GLP-1 and GIP because of their neuroprotective effects and potential as therapeutic targets and found them elevated in the treated AD mice. With respect to the main culprit in Alzheimer’s disease – ß amyloid, they noted that the load of the more toxic peptide, ß-amyloid-42, was decreased in treated mice, together with amyloid oligomers. They saw a significant reduction of extracellular amyloid deposits. They also recorded a restoration of proteolytic pathways and autophagy in the brains of probiotic-treated AD mice. In particular, they noted a strong increase in the apoptotic p53 in untreated AD mice which was held in check in treated mice. The SLAB51 probiotic was able to restore cathepsin L activity in 18- and 24-week-old mice compared with controls which was of particular interest considering the ability of this enzyme to increase α-secretase activity, thereby suppressing Aβ levels.

All in all, their results suggest a restoration of hippocampal function in probiotic treated AD mice. Improvement of cognitive function seems supported by increased plasma concentration of gut hormones such as ghrelin, leptin, GLP1 and GIP( these are lowered in AD patients which is important because there is evidence that ghrelin reduces synaptic degeneration and leptin is neuroprotective against ß-amyloid at least in vitro and directly affects the gamma-secretase amyloidogenic pathway). They showed that the probiotics counteracted the typical morphological alterations of AD, including reduction in brain weight, decline of cortical areas, and general brain damage and shrinkage. Furthermore, SLAB51 contributed to a consistent reduction in the amount of cerebral Aβ, both in the form of peptides and oligomers. Consequently, a decreased number and size of amyloid plaques were observed upon treatment. All this adds up, they say, to a convincing display of the delaying action of probiotic gut microbiota modulation on Alzheimer’s progression.

Lactobacillus parafarraginis from yoghurt fights gram-negative bacterial pathogens

Lactobacillus parafarraginis from yoghurt fights gram-negative bacterial pathogens

Here’s an interesting little story from the annual American Society for Microbiology meeting that was held in New Orleans this past week. Scientists from Broderick Eribo’s lab at Howard University have isolated a species of Lactobacillus from yoghurt that has widespread ability to impede the growth of a spectrum of important gram-negative bacterial pathogens. Bacterial species are known to impede each other’s growth but, usually, gram-positive bacteria are only effective against other gram-positives, and likewise for gram-negative bugs. This is the first finding of such widespread impedance of a gram-positive bug (Lactobacillus) against many gram-negative species.

In this current work, briefly explained in a conference presentation, 68 species of Lactobacillus were isolated from yoghurt and tested against 3 standard indicator organisms: Staphylococcus aureus, Listeria monocytogenes and Escherichia coli. Although all had some effect, Lactobacillus parafarraginis was selected for further tests which demonstrated that it was capable of limiting the growth of 14 multi-drug resistant pathogens that had been obtained from patients. These comprised 5 isolates of Escherichia coli, 2 isolates of Pseudomonas aeruginosa, and isolates of Acinetobacter baumannii/haemolyticus, Enterobacter aerogenes, Proteus mirabilis and Klebsiella pneumonia. Fast perfusion liquid chromatography and PCR suggested that the inhibitory agent is a bacteriocin. Good evidence for the potential rewards in protection, inside our guts, from pathogens that can be obtained from common probiotics and incorporated into a healthy gut microbiota.