Missing Microbes – a review of Martin Blaser’s book on changing dynamics between bacteria and man


A bitter pill? (Photo by Flickr user timsamoff under a CC BY-ND 2.0 licence)

A bitter pill? (Photo by Flickr user timsamoff under a CC BY-ND 2.0 licence)

By Jonas Waldenström

As a species, we humans have radically changed our way of life in the last hundred years. Through modern medicine, better nutrition and improved hygiene we not only live longer, but also with less disease and pain. We are also becoming taller and fatter than our ancestors.

However, at the same time we see new ailments arising, like increased asthmatic problems, allergies, certain cancer types, and obesity, to name a few. And of course, the looming threat of resistant bacteria, or emergence of novel zoonotic pathogens is always there, just a monkey or a palm civet cat away. Plenty to do for future generation of physicians and microbiologists.

And for ecologists, too. Personally, I would go so far as saying that the merging of evolutionary theory and medicine is one of the most urgent needs for modern society. We need to understand that every treatment targeting microbes will be answered by an evolutionary response. Sometimes the response is rapid, as when a plasmid encoding antibiotic resistance is transferred between bacteria, and sometimes more slowly in changing pathogenicity or selection of increased virulence. The awareness is already here, at least theoretically, albeit not in function at the hospital floor (or in the food animal industry).

This summer I read a book with the title ‘Missing microbes – how the overuse of antibiotics is fueling our modern plagues‘. The author is Martin J. Blaser, a prominent scientist that has worked with pathogenic bacteria for decades. He is actually one of the founding fathers in Campylobacter and Helicobacter research.

It is a very interesting book, where Dr Blaser put his own research on bacteria in connection to the increasing incidence of modern diseases, such as obesity and asthma. It is not yet another book on antibiotic resistance. No, it is a book on what the consequences of reduced microbiological diversity imposed by antibiotics may have for our health.

The central tenet is that the widespread use of antibiotics (to treat infections, to produce food, etc.) is drastically altering our microbiome. If you are not familiar with the term microbiome, this means the whole assemblage of microbes that live and thrive in and on our bodies. The problem with antibiotics is that they hit rather bluntly. If the target is a pathogenic bacterium in your urinary tract, say an E. coli infection, the drug that is delivered to knock it out will also run rampage through your systems and kill a lot of more friendly by-standers. Collateral damage, in gangster terms.

The microbiome is entangled bank of microorganisms, a rainforest of bacteria and viruses. But it is not static; it changes in responses to our diet, exposure, hormonal levels, competition etc. Several of its constituents are doing good deeds for its host, for instance helping us degrading food items. Many have also been there for a very long time, evolutionary times. Plenty of time to develop symbiotic relationships.

Think of it, what is the first present your parents gave you? Was it a teddy bear? No, it was the microbiome of your mother, as you (a little fetus) were passing through the birth canal, and later when you started sucking on your mother’s breasts, and was kissed by your proud parents and relatives. These bacteria are the starting point of the next generation’s microbiome, inherited across generations from parents to offspring. Dr Blaser argues that we are interrupting these long-term evolutionary relationships between microbes and man. Caesarian cuts mean that the baby is not exposed to all of the microbiome of the birth canal, and frequent use of antibiotics over the course of a lifetime (and especially in the early months) come as sweeping scythes that may knock out certain species of the microbiome.

Some of these passengers may be good for us in ways we cannot phantom. One example Dr Blaser writes about is Helicobacter pylori. This bug has been perceived as a real bad guy. It lives in your stomach and may give you peptic ulcers and is associated with certain gut cancers. The response we have launched is to whack it out with a cocktail of antibiotics. Kill it, and you will be better off (for instance see this post). However, Dr Blaser has gradually come to a different view. In a series of experiments, his team and others have linked the absence of H. pylori to other sets of illness and disease, such as efflux and cancer in upper parts of the gastrointestinal tract. Maybe the bad guy isn’t all bad, maybe it is sometimes even beneficial? And is health really the absence of bacteria, maybe the presence of certain bacteria has the benefit of keeping the immune system primed?

He has also investigated the effects of antibiotic treatments on the microbiome in mice, and shown that treatment in a certain time period in early life affects not only which microbes that make up the microbiome, but also obesity status later in life. Thus, the microbes in our gut could affect our phenotype, all other things being equal (for a good resume of this see here).

I really recommend you to read his book – it is a fascinating story, written by an active researcher (which we tend to do too seldom). He launches some very interesting hypothesis that can be tested by laboratory and field studies. Read it and make your own interpretations.



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Call of the wild: gulls as sentinels of antibiotic resistant bacteria

Gulls are our model species for antibiotic resistance dissemination. Picture from Wikimedia Commons.

Gulls are our model species for antibiotic resistance dissemination. Picture from Wikimedia Commons.

By Jonas Waldenström

What scare you the most, little one? Is it the monsters under your bed? Warfare, missiles and guns? Climate change? Spiders? Dogs with fangs? Yes, all of them are scary, and most are nasty. But if I have to choose among all the nastiness of this world I’d say antibiotic resistance scares me the most.

You have certainly heard about it, again and again. A researcher, or physician in a white lab coat saying that the situation is “worrisome” or even “alarming”. But it doesn’t really sink in. We don’t want to listen. We hurry, rush the kids to school and daycare, work dull hours in the office and dream about a better life. Or at least considers the substitutes for happiness:  a nicer car, a holiday in the sun, or a tight bum. But dreams sift like sand and we settle for a bottle of wine and a piece of beef on a Friday night. We are too occupied to ponder the grander questions, and leave the future for another day.

But if? Think about it.

What if antibiotics didn’t work? What kind of world would that be? We take these drugs for granted, but they are fairy stuff; twinkling wondrous inventions that can be gone in wink, rendered useless by evolution. You see, no one can escape evolution, and we have played the game wrong for as long as we have had antibiotics at our disposal. Instead of safeguarding, we have peppered the bacteria in animals, ourselves and the environment with antibiotics thereby increased the reward for resistance mutations to the point that they rapidly increase in frequency. In our hospitals and stables we have created environments were bacteria could mingle in antibiotic-cladded environments, promoting bacteria to share plasmid-borne resistance markers through horizontal transmission. Bad play, really bad play.

We talk misuse on an epic scale: an ever-accelerated prescription of drugs for any types of infections, even viral infections, where, of course, antibiotics do little good. We have used our drugs on food animals to treat infections, but also as growth promoters in chickens and swine; we have poured bucket loads of antibiotics in ponds to grow shrimps in clear-cut mangrove swamps; we have sprayed antibiotics on apple and fruits to keep them fresh until the retail level. But all this came with a cost, an interest rate we were not considering at the time. And soon it is time to settle the bill, but like Greece we have little means to pay.

When the magic bullets don’t hit their mark we will face a harsh reality. A post-antibiotic world. Science writer Maryn McKenna recently wrote an essay in Medium on how this brave new world would be. A world where simple infections could kill, a return to an era before the two world wars. No more knee implants and hip replacements, no more bowel surgery or nose jobs. A long kiss goodnight on our future health care.

But it can’t be that bad can it, you may ask yourself. They must exaggerate! Clearly, if things were so dire, the Government would do something about it! Well, truth is, we do far too little, governments included. We are standing with one foot leaning over the Pit of Doom (to use Fantasy jargon) and only a concerted action could take us out of it. Simply put, it is tragedy of the commons, where many small decisions end up in a big bad one.

To turn the tiller and set a new course we all need to chip in. Governments need to stimulate research in new drug developments. Global action needs to be taken for how to use antibiotics; these drugs are too potent to be sold over the counter without prescription. And antibiotics should not be used when they are not needed – and farm size and practices need to be addressed in the light of reducing consumption of antibiotics, not in the light of maximizing profit. And there need to be basic science. Our research group addresses the occurrence of resistance in the environment. Using gulls as model species we have travelled wide and far, from pole to pole, and sampled birds for antibiotic resistant bacteria. A few days ago we published our latest article on resistance dissemination in Europe. And it is a scary read.

Antibiotic resistance can attack you when you least expect it. Picture from Wikmedia Commons

Antibiotic resistance can attack you when you least expect it. Picture from Wikmedia Commons

A problem in most investigations, especially those conducted on wildlife, is that studies have been small – often a bunch of samples collected without proper sampling design or power calculation. Few studies have addressed larger spatial scales, beyond the country level. Graduate student Johan Stedt set out to change this, and his thesis – that he will defend in June – investigates the occurrence and frequency of resistance markers in gull Escherichia coli on a global scale. In the summer of 2009 (time flies fast in science between fieldwork and published articles) we sent out three teams of trained fieldworkers. In each car there was a liquid nitrogen dewar and sacks of sterile cotton wool swabs. Using our network of ornithologists across Europe, put in place by earlier flu virus studies, we were able to sample gull breeding colonies in nine European countries, from Spain and Portugal in the south, to Scandinavia in the north and the Baltic states in the east. All in all 3152 samples were collected during two weeks of fieldwork. This is by far the largest study conducted in wildlife across Europe.

In the lab, Johan spent months and months going through the samples. First, a primary isolation was done to get putative E. coli isolates. Then the identity of the bacterium needed to be validated with phenotypic test, and then the susceptibility of each isolate was tested with disc diffusion against a panel of 10 antibiotic agents. For the untrained ear they have strange, but beautiful names: ampicillin, cefadroxil, chloramphenicol, nalidixic acid, nitrofurantoin, mecillinam, tetracycline, tigecycline, streptomycin and trimethoprim/sulfamethoxazole. They are, however, commonly used in human and veterinary medicine.

But how is resistance quantified? It is actually rather simple. The isolate is inoculated onto an agar plate where little discs containing antibiotics are attached. The plate goes into a 37C heating cabinet for 24 hours and then one measure how close to the antibiotic discs the bacteria grow. A susceptible bacterium cannot grow close to the disc (where the antibiotic is leaked or ‘diffused’ into the agar), leaving a large zone devoid of growth called the inhibition zone. A resistant bug, on the other hand, can cope with the antibiotic compound and will therefore grow closer to the disc. Resistance is not always a black or white thing. Rather, there is a range of phenotypes with varying susceptibility to a compound. In clinical practice, breakpoints have been established for different bacteria and antibiotics by plotting the range of phenotypes for a large number of samples. This usually gives a normal distribution around the mean for susceptible bacteria, and a hump of isolates as outliers representing the resistant fraction.

Inhibition zones encircle the antibiotic discs in susceptible isolates. Picture from Wikimedia Commons

Inhibition zones encircle the antibiotic discs in susceptible isolates. Picture from Wikimedia Commons

Let’s return to the gulls. It pretty soon became apparent that resistant bacteria were common and widespread in European gulls. In fact, roughly a third of the isolates retrieved were resistant to at least one antibiotic compound, and a fair proportion was resistant to several. Looking at specific resistance profiles, the most frequently recovered phenotypes were resistant to tetracycline or ampicillin. These results are in concordance with other studies on gulls and may reflect the fact that these antibiotics have been commonly used in both veterinary and human medicine for decades. The occurrence of other resistance phenotypes, such as mecillinam and nalidixic acid resistance, was more surprising. Tigecycline was the only tested antibiotic that we did not find any resistance to; perhaps due to it being a relatively new antibiotic, used for skin-structure infections and complicated intra-abdominal infections.

A striking finding was the geographical variation in resistance levels. Have a look at the map above. Samples from the Iberian Peninsula were on average more often resistant than samples from gulls in more northern countries. This was true for all tested antibiotics (and also for ESBLs, but that is something that will be covered in another publication) and is also mirrored in similar data from humans and food animals in the EU. This south-to-north gradient can have many explanations, but likely reflects true differences in usage of antibiotic compounds across Europe.

Why gulls? What our research has indicated in this and other studies is that gulls are very convenient model species for dissemination of resistant bacteria in the environment. They are everywhere, especially where there is concentration of people, animals, and waste products. The twist in this study was to sample the birds during breeding times, when birds are most sedentary and where results therefore are more likely to depict the local situation.

Finally, what does this tell us? Should we worry about some resistant bugs in gull? The answer is yes, we should. You, me, we all should care – and we should act! Clearly there are no strict boundaries between the everyday lives of humans and the organisms that occur in the environment. The bugs we select for in our hospitals and in agriculture do not stay there – they leak, finding their way out into nature. The gull story shows that similar patterns occur across Europe, the situation in gulls is mirroring the situation in anthropogenic sources. They are our canaries for the antibiotic mines, our whistleblowers. And it is a vivid illustration of the magnitude of the resistance problem we are facing in the future.

Link to the paper:

Stedt, J., Bonnedahl, J., Hernandez, J., McMahon, B.J., Hasan, B., Olsen, B., Drobni, M. & Waldenström, J. 2014. Antibiotic resistance patterns in Escherichia coli from gulls in nine European countries. Infection Ecology and Epidemiology  4: 21565


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Travel the world – can antibiotic resistant bacteria hitchhike with migratory birds?

By Jonas Waldenström

800px-Seasons1.svgThe beauty of a planet rotating around a slightly tilted axis (23.5 % to the orbital plane, to be exact) is the variation this brings to the intensity of the sunlight that hits the ground. It gives rise to predictable seasonal changes, at our high latitudes equal to a blooming spring, a warm summer, a foggy and mild autumn, and a frosty winter. The tilted axis also means that when it is dark and cold Sweden, it is sunny and lovely on the other side of the globe. Or in other words: when my kids make snow angels in the yard, the penguins rear their chicks under the austral sun.

A large number of animals, in particular birds, but also bats, antelopes, and even insects, utilize the shifts in climate and migrate to make most of the boom of ephemeral resources made available during the warmer seasons. Go to the food, reproduce, raise the offspring, and then pull back to chill-out at lower latitudes during the non-breeding season. A related phenomenon has evolved in some human populations – it is now common that British, German and Swedish people undertake annual migratory movements to Spain. Unlike the other animals mention above, the human movements mainly involve the post-reproductive life-stages. Hordes of well-off elderly now bask in the sun and marinate their livers in cheap red wine. Senescence in the sun.

Basking in the sun

Basking in the sun

A reason why our elderly go to Spain, and not onwards to Morocco, or east to Turkey is the apparent similarities to home. It is different in Spain, yes, but still rather similar to Bavaria, Sussex or Jönköping – just warmer and more vibrant. But not too dangerous, or too vibrant. You can trust the water to be (moderately) clean, and you can eat the food without worrying too much about infections. A prophylactic intake of wine and a diet consisting of 50% canned foodstuffs from home and you are unlikely to succumb to nasty disease.

In epidemiology, we know for certain that travel brings you in contact with disease-causing organisms. When we travel we expose ourselves to pathogens to which our immune systems lack experience, and therefore fail to take swift actions. This is nothing new – this was the fait of the native Indians in South America facing the import of pathogens such as smallpox and whooping cough from invading conquistadores. And in tropical Africa, the Yellow Fever took a large toll of the missionaries sent to christen the heathens; and those fortunate to survive had to endure repeated spells of malaria fevers, and gastrointestinal unpleasantness. Today, prophylaxis and vaccines make us more prepared, but disease risks are a constant worry for the traveller even in our time. And when we get back from our travels we may carry bugs with us and cause secondary cases back at home. In the last weeks we have seen cases of MERS coronavirus associated with haji in Mecca in Arabic countries and Europe. In many gastrointestinal bacterial infections we see a higher degree of antibiotic resistance in travel-associated cases than in domestic cases. Simply, what goes around comes around – and travelling stirs the pot to a boil.

Furthermore, what we put in the pot – the meat and the apples – is highly important. Very little on your dinner plate was grown in your backyard, in fact the ingredients that make up the dish may have travelled half around the globe before being eaten by you. Our food animals are amplifying hosts for many pathogens that cause human infections. The shear numbers of animal involved, the transportation of animals and products, and the frequent use of antibiotics in the food production industry make an additional potent driving force for antibiotic resistance evolution.

On top of this, in the last decade a question whether wild birds can act as flying intercontinental carriers of resistant bacteria has emerged, again and again. The idea can be summarized as follows: If a bird picks up a resistant bug during the non-breeding period, and that bacterium becomes established in the gut, there is a chance that the bacterium could be disseminated along the migratory route all the way to the breeding grounds. Given the state of the world, where for instance there is a marked south-to-north gradient in bacterial resistance problems in Europe, and likewise between South and North America, bird migration can be associated with words like ‘risk’ and ‘threats’. Birds as flying missiles, or pathogen arks.

Did the pathogens fit on the Ark?

Did the pathogens fit on the Ark?

Seemingly elegant, this hypothesis suffers from a number of limitations. First, birds need to be colonized by the nasty bacteria in the first place. Then the bacteria need to be maintained in the gut of the bird for a considerable time, allowing the bird and the bug to move during migration. Once migrated, the bacteria need to be shed in such a manner that they find their way to humans, or more likely our domestic food animals, and then end up on our plate. A long way to go for a microorganism.

Our research group is addressing such questions. The first step is to thoroughly survey the occurrence of antibiotic resistant bacteria in wild birds. This process has going on for a few years, and although there is room for many, many more studies we do know something by now. First, antibiotic resistant bacteria are everywhere, literally everywhere – from the Arctic tundra to the vicinity of the Antarctic research bases. Wildlife is exposed to resistant bacteria and some birds, such as gulls and crows, tend to often carry resistant bugs. Second, we know from genotyping studies that the same types of resistance markers occur in bacteria both from human/food animals and in wild birds. Thus, there is an exchange between sources, likely heavily tilted towards a dissemination from anthropogenic sources to wildlife (rather than the opposite) and it seems most strongly occurring in specific bird species that are in close proximity to humans and food animals.

The most recent study from our group on this subject was published a few weeks ago. The study focused on a bird species that qualify for all of the check points that make a species a possible resistance disseminator culprit: the Franklin’s gull Leucophaeus pipixan. This species breeds in North America, in shallow lakes on the prairies between USA and Canada, but spend the non-breeding season all the way down in southern South America. In Peru and Chile it is common to see thousands of Franklin’s gulls at river mouths on the Pacific coast. And in these rivers the collected wastewater from millions of people are discharged. Thus the gulls find themselves in a habitat that potentially is full of unwanted antibiotic resistant microbes.

Gaviotas de Franclin at Con-con. Photo Jonas Bonnedahl

Gaviotas de Franclin at Con-con. Photo Jonas Bonnedahl

The team visited the Aconcagua and the Bio-Bio rivers in central Chile, where the water met the sea at Concón and Talcahuano, respectively. At these gorgeous sand beaches they sampled Franklin’s gulls. Samples were also collected from 49 healthy human volunteers from the city of San Antonio. Back in Sweden, the samples were cultivated for the presence of Escherichia coli, the most commonly used indicator bacterium in antibiotic research. Randomly collected isolates were then tested against a panel of 10 different antibiotics to measure the degree of acquired resistance. The original samples were also screened for a specific class of resistance mechanisms called extended spectrum beta-lactamases. Bacteria that produce these ESBL enzymes are resistant to a range of lactam antibiotics. ESBL resistance is an emerging problem all over the world, causing suffering and premature deaths.

The resistance profiles from the 267 avian E. coli were similar to that of human samples, with moderate resistance to ampicillin (10.1 %), tetracycline (8.2 %), and streptomycin (6.0 %). Only nitrofurantoin displayed full susceptibility in all samples; all others were in the range of 0.5 – 5 %. However, looking at ESBL in the samples, the gull sample had a prevalence of 30 %, compared to 12 % in the human sample. Not only were there loads of ESBL-positive birds, the ESBL variants were dominated by blaCTX-M-1 and blaCTX-M -15 genotypes that has been extensively described in E. coli causing human infections. Also a multilocus sequence typing of the bacteria showed connections to bacterial genotypes common in infections.

Thus, on the warm sands of Chile sits Franklin’s gulls and enjoy the austral summer. In their intestines they carry resistant bugs with the same genotypes that can cause  infections in humans. Remains to show if the birds can carry these bacteria to the US, or whether carriage is short-lived and more a product of the local environment.

Link to the article here:

Hernandez J, Johansson A, Stedt J, Bengtsson S, Porczak A, et al. (2013) Characterization and Comparison of Extended-Spectrum β-Lactamase (ESBL) Resistance Genotypes and Population Structure of Escherichia coli Isolated from Franklin’s Gulls (Leucophaeus pipixcan) and Humans in Chile. PLoS ONE 8(9): e76150. doi:10.1371/journal.pone.0076150


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Badrul Hasan presented his thesis on antimicrobial resistance in Bangladesh wildlife

I spent the day in Uppsala – the old student town where I once did my undergraduate studies in Biology. It was good to be back, to meet some great friends and collaborators, and – of course – to attend the thesis defense of Badrul Hasan!

A proud Dr Hasan!

A proud Dr Hasan!

Badrul came to Sweden from Bangladesh four years ago and have spent time both with us at Linnaeus University and at Uppsala University. It was great to see him present his thesis – calm, confident and skilled!

So what has Badrul done? The topic of the thesis is very timely – antimicrobial resistance in wildlife. By sampling wild birds, domestic poultry and humans in different areas of Bangladesh, Badrul tries to connect the various sources of resistance in an epidemiological framework.

Sometimes the thesis is akin to a horror-story! The situation in Bangladesh is alarming, to say the least – with widespread occurrence of multidrug resistance, beta-lactamase producing Escherichia coli more or less wherever you stick your sampling swab, and unrestricted use (or rather misuse) of antibiotics in agriculture and aquaculture. A ticking bomb.

Indian House Crows doing what they are best at - searching for food in waste

Indian House Crows doing what they are best at – searching for food in waste

In one of Badrul’s studies, he investigated the carriage of resistant bacteria in Indian House Crows at two hospital campuses. The crows were thriving, feeding on waste put out in the yard – a mixture of surgical leftovers, patient’s food and normal garbage. And the antibiotic resistant bacteria were thriving too. The close connection between humans and crows is evident, and there aren’t any closed doors between indoors and outdoors. What we select for in agriculture and in human medicine in terms of resistant bacteria are the very same infections that later will be close to impossible to treat when our children’s children get sick.

Or quoting Badrul:

“Every morning you wake up in bed, you hear a crow”

Some links to Badrul’s published papers:

The thesis as pdf

Antimicrobial Drug–Resistant Escherichia coli in Wild Birds and Free-range Poultry, Bangladesh

High prevalence of antibiotic resistance in pathogenic Escherichia coli from large- and small-scale poultry farms in Bangladesh.

Dissemination of NDM-1.