Let's not beat around the bush. This is an extraordinary book. David Quammen has woven a story of incredible complexity; a detective story with a difference, with a host of murderers  all of them real. They are viruses, bacteria and single-celled organisms which infect other animals, but every now and then make the jump  spill over  to our own species. Each chapter follows the quest to track down a new villain. An international team of detectives works on the cases, and Quammen follows them as they uncover the traces which will lead them to the killers.

After an opening chapter about a horrific virus which lays low horses and humans, the Ebola virus emerges through a dark tale, with piles of dead gorillas in the forest, consumption of rotting bushmeat, sorcery and Rosicrucianism. The story is grim enough without the usually exaggerated descriptions of Ebola: sufferers crying blood and melting from the inside out. Quammen doesn't sensationalise his material (you could argue he doesn't need to  it's quite dreadful enough). He's much more interested in demystifying these outbreaks, finding out what we know about them and how this might help us to anticipate future emergent diseases and limit their impact. He promises to tell us the "complicated story", not the dramatic one. But this is such a consummate piece of science writing that you're likely to imbibe some extremely complex concepts without realising it. There's no "here's the science bit"; lessons in virology, epidemiology and genetics are woven seamlessly into the story.

In each chapter a disease gradually comes into focus, starting with rumours, a few seemingly unconnected, mysterious deaths. The history of the investigation unfolds until we come face to face with the killer. In the process we learn the myriad ways in which a germ can move from one host to another  through excrement, excretions, mucus and blood  and uncover the dangerous activities that may have led to exposure: climbing trees? touching or eating dead animals? drinking date-palm sap? Quammen also hunts down the unwitting accomplices: the animals who carry these diseases before they jump into humans: pigs, birds, monkeys, apes and bats.

The real heroes of the piece are the detectives  the scientists working tirelessly out in the field and in their labs to solve the crimes committed by those microscopic murderers. As brilliant as Quammen is at describing the workings of viruses, he's also a masterful portrait painter, a close observer of people. These range from the molecular scientist working on Sars "with the instincts of an epidemiologist and the balls of a brass macaque" to the ecologist who relishes eating his way through the exotic biota on offer on Chinese menus to the expert in veterinary diseases who is a "sturdy fellow looking like a former high school quarterback grown fortyish and serious."

The historical details are fascinating: in the 19th century scientists looked down light microscopes to discover minute creatures in the blood cells of malaria patients, while viruses remained mysterious and invisible until the invention of the electron microscope in the 1930s. There are historical landmarks: President Hoover banning the import of parrots into the US; an outbreak of inflamed joints and spreading rashes becoming linked to deer ticks in the Connecticut town of Lyme; a flurry of "harmless" infections proving fatal in male patients in the States in the 1980s.

Quammen takes us on a global journey, visiting orderly labs but also getting out into the field with researchers  trapping bats in China and monkeys in Bangladesh, travelling deep into the Cameroon forest to hear tales of initiation ceremonies requiring bushmeat in the form of chimpanzee arms.

Towards the end of the book he loses touch with reality and goes off on a fictional flight of fancy about the origin of HIV, mixed up with his own journey along the Congo river. It all gets a bit Apocalypse Now in this diverting but incongruous departure from the unwavering attention to evidence in the rest of the book.

The emergence of zoonotic diseases  these afflictions which jump from other species to us  is not a new phenomenon but they do seem to be on the increase, and Quammen explores the reasons behind this in his final chapter: a huge global human population, a huge global population of livestock, destruction of natural habitats, disrupted ecosystems  it could easily become a diatribe about nature's revenge on humankind. But Quammen isn't a romantic, sentimental environmentalist. He is careful to emphasise that humans are part of the natural world, not separate from it  and there lies the problem.

My advice, having read Spillover: buy the book, be sure to get your flu jab this winter (if you need one), and remember: "The duck is the Trojan horse."

Human beings are restless, nosey and aggressive. These characteristics have made us one of the most invasive species our planet has ever encountered and allowed us to colonise nearly every terrestrial environment. During this progress, humans have made many acquisitions, several of them unwanted. Our constant movement between vast, populous cities and novel environments makes us easy prey for opportunistic pathogens that replicate fast, and transmit by sneezes and dirty hands before sickness even begins to show. These pathogens can spread around the world in hours by aeroplane to infect the unsuspecting on another continent. That's how "swine flu" spread in 2009; it was already unstoppable by the time we noticed it. We were lucky it wasn't particularly virulent.

David Quammen's Spillover is a collection of stories about the sources of diseases called zoonoses. These are the infections that humans acquire from other animals; the most notorious recent example is HIV/Aids, but they encompass a huge range of viruses, bacteria and parasites, including Ebola, some malarias and Q fever. It seems that zoonoses are increasing, at least reports of them are. In 2012 alone, hantavirus (a Sars-like virus), E coli O157 and legionnaires' disease have hit the headlines  all originated in other animals.

Quammen tells us we don't have far to look for blame when weird infectious diseases spring up: they usually result from humans moving into wild ecosystems or from forcing encounters with other species. Bats are at the centre of many of his stories; they seem to be a reservoir for a number of the nastier viruses  Marburg, probably Ebola, Nipah and Hendra viruses  as well as a source of bacterial and fungal infections. Bats are excellent crucibles for pathogens because they often live in huge numbers at high densities, roost in tight proximity and, in part because of habitat loss, congregate around human settlements. Bats could have provided cavemen and women with measles and mumps too. Another particularly acquisitive period in human evolution was probably livestock domestication about 10,000 years ago. This seems to have been the major trigger not just for human civilisation, but also for the accumulation of the familiar repertoire of communicable human diseases.

If they are not made locally extinct by our activities, other animal species either hang on at the fringes of human settlements, or take to suburban living. In the US, homes in woodland idylls are aspirational dwellings, but the human invasion has made Lyme disease a widespread problem. Having lost their own space, the wild reservoir hosts of this bacterial infection  mice and deer, with their tick vectors  are forced to colonise the newly made backyards and come into contact with humans. Likewise, intimate living with rats in chaotic medieval cities allowed plague to spread worldwide, and as rat populations thrive in modern cities too, it wouldn't take much of a drop in living standards to give plague a new foothold.

Smaller, highly mobile creatures also bring unwanted pathogens into human spaces. Mosquitoes can make the transition from forest to city living strikingly easily. They ride in planes and have taken with them terrible afflictions, such as West Nile virus to the US, and have spread dengue virus in Asia and South America. Mosquitoes breed fast, are genetically flexible, and can adapt rapidly to change their feeding and flying behaviour, tolerate climate shifts and develop insecticide resistance. Some are adept at breeding in almost any drop of uncovered water, for instance in an old tin can, a discarded tyre, or a hollow plant stem. This way, Asian tiger mosquitoes have spread to Europe, where they now breed and are known to have transmitted chikungunya virus to Italy.

Quammen has not considered  perhaps because we have only recently had the technology to witness it  the extraordinary amount of gene swapping among pathogens. Some of the most mobile of these genes supply components for antibiotic resistance and virulence, and may help a pathogen to change its host. This genetic movement, in combination with the profligate use of antibiotics, has now rendered a large armamentarium of once life-saving drugs useless.

Zoonosis is a topic that, like the pathogens themselves, is hard to keep under control, and Quammen's treatment is rather uneven. Perhaps unsurprisingly, he veers from inflamed alarmism to cold, sober mathematics. I started off feeling irritated by asides such as "Here's what you have to come to understand " But he is terrific when on a quest to uncover the circumstances that led to a particular spillover event. The stories of the victims and the scientists are told in astonishing detail. He has named nearly all the local heroes of epidemiology and made several forays into west Africa in the process. He's at his best towards the end of the book in the section devoted to HIV, although soon afterwards he becomes so impassioned he inserts long flights of fictional fancy about the "Voyager" who brings HIV into the wider world. The book needed fiercer editing.

Like bats, humans now live together in huge numbers, tightly packed and forever flitting from place to place. We are prime candidates for, as Quammen puts it, the Next Big One. What will it be? Perhaps an RNA virus, like the one portrayed in Steven Soderbergh's film Contagion, but probably one more banal  influenza. Again though, we can teeter from the routine consideration of seasonal influenza (which still kills thousands of people each year) to scaremongering about bird flu (which has so far killed only a few hundred  though more than half of those infected died).

The problem is that, for all its apparent simplicity, the flu virus hides its secrets well. It is constantly changing to acquire and shed mutations, at the same time gaining and losing virulence and shifting host adaptability. Making the annual vaccine for seasonal flu is an industrial-scale challenge of diplomacy and logistics, masterminded by the World Health Organisation. Influenza drugs are poor and resistance to them builds up quickly during an epidemic. So although we know a lot about flu, there is a lot more we don't know. We can't predict with much accuracy when the next spillover from birds will happen, whether or not it will spawn a devastating pandemic killing tens of millions, or where, how and what subtype it will be. We only know we still don't have the surveillance systems in place to stop it in time.