The genetic secrets of a misnamed microbe could help ease a lung condition that affects hundreds of millions of people, says microbiologist Timothy Murphy

You study Haemophilus influenzae or H. flu. This bacterium’s name suggests it causes flu, a viral illness. How did this come about?
It was named during the 1918 influenza epidemic. When pathologists looked at the lungs of patients, they saw a bacterium and named it Haemophilus influenzae, mistakenly thinking it caused influenza. But it was a secondary infection that people contracted as a result of the flu.

Why is this misnamed microbe so important?
I work with people who have chronic obstructive pulmonary disease (COPD) – an umbrella term for lung diseases including emphysema and chronic bronchitis. It affects more than 300 million people worldwide. This bacterium has a special relationship with COPD because those with the condition simply can’t clear the bacteria. It gets into their lower airways and can cause infection that leads to serious complications.

You lead the longest running clinical study of COPD in the US, with a huge collection of H. flu samples. How did it all start?
We enrolled our first patient in 1994. At that time the role of bacteria and bacterial infection in COPD wasn’t well understood. We wanted to enroll people over time and study them and their bacteria to better understand this factor.

Why is gathering many samples over such a long period important?
COPD behaves very differently in different people. Some will have shortness of breath while others will cough a lot but have no shortness of breath. In any study you need large numbers to account for that range. It’s similar for the bacterium. There are tremendous differences among the different H. flu strains and so we need a large collection to make meaningful observations and to find the genes important for causing infection. Now we are beginning to sequence the genomes of these strains and we can see that one strain can differ from another by as much as 20 per cent.

You brought about a major shift in clinical understanding of COPD. Tell me about it.
People with COPD might acquire a new strain of H. flu every month, even if it doesn’t cause symptoms. We have learned that it’s when people acquire new strains that they are most likely to see flare-ups in their symptoms. Before that, there was this idea that it simply took a certain amount of bacteria to cause an infection.

What do you hope to learn by sequencing the various genomes in your H. flu collection?
We have three goals. The first is to understand why some strains persist in the airways and others are cleared. The second is to contribute to current efforts to develop a vaccine. And the third is to understand how the bacteria manage to persist in spite of repeated antibiotic treatments.

Examining sputum samples for two decades doesn’t sound like a barrel of laughs

One time I asked a patient to tell me about the colour of his sputum. He said: “Well doc, don’t take this the wrong way, but it’s almost exactly the colour of your shirt.” Sometimes you get to laugh.

This article appeared in print under the headline “H. flu ŽÚŸ±Č”łółÙ±đ°ù”

A prehistoric shark species is the earliest animal known to migrate, over 300 million years ago. The sharks lived in rivers but swam down to the sea to breed and care for their young.

Bandringa were primitive sharks that lived about 310 million years ago. They did not look much like typical modern sharks, having long spoon-shaped snouts.

Until recently scientists thought there had been two species of Bandringa, one that lived in fresh water and one that lived in the sea. But according to of the University of Michigan in Ann Arbor, there was only one species. The sharks migrated from their freshwater habitat to a saltwater nursery to reproduce.

Sallan and her team examined Bandringa remains from three sites in the Mazon Creek deposit in Illinois, including egg casings, bones, and soft tissue from juveniles and hatchlings. One site was originally on the coast but the others were inland. They found no evidence that fossils from the different sites belonged to different species.

Instead, Sallan says, “the three sites are segregated by age”. Juveniles and hatchlings were found alongside the eggs in the coastal site, while the bodies of adults were found inland. “That’s what lets us see the migration.” The coastal site is the oldest known example of a shark nursery.

Journey of the shark

Sallan says the Bandringa are far and away the oldest known example of a migrating animal. In 2011, palaeontologists found the first solid evidence that sauropod dinosaurs migrated seasonally, about 150 million years ago.

It certainly seems to be the earliest evidence of migration in a vertebrate, says of the University of Nebraska at Omaha. But migration may have an even longer history. “I could readily entertain the possibility that earlier vertebrates were making migrations between fresh water and salt,” he says. “It may go back quite a ways before this.”

Most modern sharks migrate from the open ocean to near shore to lay eggs or give birth. They do so to protect their young from predators, including other sharks. The Bandringa sharks switched from a marine habitat to a freshwater one, but continued to return to saltwater to breed and lay their eggs.

In theory, the Bandringa‘s young might have been perfectly safe in their freshwater environment, but Sallan suggests that they were locked into their ancestors’ behaviour of breeding in the sea. Recent genetic evidence has shown that sharks return to where they were born to breed, and palaeontologists have long suspected that prehistoric sharks also migrated.

The Bandringa must have had sufficient memory capacity to return to the same location every time they bred. They would also have needed processes to control their salt levels as they moved from fresh water to saltwater and back again. Modern sharks do regulate their salt levels, but most are only ever in saltwater. “Because they made the switch from saltwater to fresh, the Bandringa would have required a system to control their salinity levels in fresh water as well as saltwater,” says Sallan.

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