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Drug-resistant germs found to help their brethren through the attack

Sept. 1, 2010
Courtesy of Howard Hughes Medical Institute
and World Science staff

Confronting at­tack by an­ti­bi­otics, some bac­te­ria help each oth­er out—and un­for­tu­nately for us, they’re bet­ter off for it, re­search­ers have found. 

Though a small frac­tion of pathogens in a col­o­ny may have evolved the abil­ity to re­sist a drug or class of drugs, these “su­per bugs” were found to help their more vul­ner­a­ble peers by over-pro­duc­ing a drug-fighting sub­stance.

Pre­vail­ing wis­dom held that an­ti­bi­ot­ic re­sistance works only on an in­di­vid­ual lev­el: a bac­te­ri­um ac­quires a muta­t­ion that con­fers pro­tec­tion against a drug, al­low­ing it to sur­vive and re­pro­duce. Even­tu­al­ly, as vul­ner­a­ble bac­te­ria die, the mu­tan­t's stronger prog­e­ny re­pop­u­late the col­o­ny. This basically reflects how evolution is believed to work in all species: mem­bers that are “fit­ter” or bet­ter adapt­ed to pre­vail­ing con­di­tions spread their genes through the po­pu­lation at the ex­pense of other mem­bers. 

But the new stu­dy, to ap­pear in the Sept. 2 is­sue of the re­search jour­nal Na­ture, in­di­cates there are al­so popula­t­ion-wide changes in the bac­te­ri­al com­mun­ity at work. Faced with an on­slaught of an­ti­bi­otics, re­sistant Esch­e­rich­i­chia coli mi­crobes pro­duce—at an en­er­gy cost to them­selves—a pro­tein mol­e­cule that seeps in­to the com­munal broth and trig­gers a slew of pro­tec­tive mech­a­nisms in their non-re­sistant neigh­bors.

The study comes from re­search­ers at the How­ard Hughes Med­i­cal In­sti­tute in Chevy Chase, Md.

In the past few years, the rise of “su­per bugs” such as me­thi­cillin-re­sistant Staph­y­lo­coc­cus au­re­us, or MRSA, has had hos­pi­tals and med­i­cal pro­fes­sion­als scram­bling to fend off a pub­lic health dis­as­ter. The new find­ings could help ex­plain why re­sistance has been so hard to curb, the re­search­ers say.

The in­sti­tute's James J. Col­lins and col­leagues at Bos­ton Uni­vers­ity grew bac­te­ria in a biore­ac­tor—a large, capped glass ves­sel with many ex­tend­ed arms that al­low re­search­ers pre­cise con­trol over what the bugs are ex­posed to. “It kind of looks like a com­po­nent of a moon­shine fac­to­ry out in the back­woods,” Col­lins said.

In­ter­est­ed in how ge­net­ic­ally iden­ti­cal E. coli ac­quire muta­t­ions that con­fer re­sistance, the re­search­ers trick­led the an­ti­bi­ot­ic nor­floxacin in­to the biore­ac­tor. As they upped the bugs' ex­po­sure, the sci­en­tists per­i­od­ic­ally re­moved sam­ples of bac­te­ria and meas­ured the min­i­mum strength of drug that stops growth of the bug.

“That's when we were stopped in our tracks,” Col­lins said. To their sur­prise, the re­search­ers found that the popula­t­ion as a whole was much more drug-re­sistant than in­di­vid­ual sam­ples. Less than one in a hun­dred in­di­vid­uals were typ­ic­ally drug-re­sistant.

The team then an­a­lyzed the pro­teins made by re­sistant bac­te­ria in the pres­ence of nor­floxacin, and found that a com­pound called tryp­to­phanase was par­tic­u­larly abun­dant. Tryp­to­phanase breaks down a bi­o­log­i­cal mol­e­cule, the ami­no ac­id tryp­to­phan, in­to smaller bits. One of the prod­ucts of this re­ac­tion is in­dole, a sig­nal­ing mol­e­cule that E. coli pro­duces un­der cer­tain stress­ful con­di­tions.

In­dole turns out to of­fer bac­te­ria two kinds of pro­tec­tion against nor­floxacin, ac­cord­ing to Col­lins' group. One is to turn on cel­lu­lar machines that pump the an­ti­bi­ot­ic out of the cell, as if ex­pel­ling a poi­son. In­dole al­so turns on chem­i­cal pro­cesses that pro­tect the cell from ox­i­da­tive stress, a chem­i­cal im­bal­ance that leads to the build up tox­ic mol­e­cules called free rad­i­cals. A few years ago, Col­lins's team re­ported that an­ti­bi­otics tend to work by pum­mel­ing bugs with free rad­i­cals. “Here we're see­ing that in­dole is damp­en­ing that—turn­ing on the sprin­klers for the fire re­sult­ing from the an­ti­bi­otics,” he said.

By com­par­ing the growth of bac­te­ria, the re­search­ers found that the mu­tants pro­duce in­dole at a sig­nif­i­cant cost to them­selves. “They don't grow as well as they could, be­cause they're pro­duc­ing in­dole for eve­ry­body else,” Col­lins said.

Such al­tru­is­tic be­hav­ior—which ap­pears in spe­cies through­out the an­i­mal king­dom, in­clud­ing hu­man­s—p­re­sents a well-known par­a­dox for ev­o­lu­tion­ary bi­ol­o­gists: if ev­o­lu­tion fa­vors the fit­test, why would an in­di­vid­ual sac­ri­fice its own fit­ness for the rest of the group?

Col­lins said his find­ings bol­ster the “kin se­lec­tion” the­o­ry—for­malized in the 1960s by the Brit­ish ev­o­lu­tion­ary bi­ol­o­gist W.D. Hamil­ton—that said that or­gan­isms may be­have al­tru­is­tic­ally to­ward oth­ers that share their genes. By protecting their own gene pool, they promote the spread of their genes indirectly, even if they them­selves suffer or die in the pro­cess. This prin­ciple could have been at work in the “chari­table” E. coli, since they were helping mem­bers of their own popula­t­ion.

“We are plan­ning to ex­plore wheth­er si­m­i­lar strate­gies are used by oth­er bac­te­ri­al spe­cies,” Col­lins added.

Col­lins thinks the study is most di­rectly per­ti­nent to pub­lic health. The re­search­ers found that the same popula­t­ion-wide pro­tec­tion oc­curs when bugs are ex­posed to oth­er kinds of an­ti­bi­otics. What's more, many types of bac­te­ria pro­duce in­dole, sug­gest­ing that a si­m­i­lar co­op­er­a­tive pro­cess may hap­pen in a host of bac­te­ri­al spe­cies.

Fu­ture re­search on an­ti­bi­otics might well fo­cus on tar­get­ing the in­dole path­way as a means to block bugs' abil­ity to share re­sistance, Col­lins said. More broad­ly, the work high­lights the press­ing need for in­vest­ment in new an­ti­bi­ot­ic de­vel­op­ment. “The chance that we'll have new and dan­ger­ous su­per bugs emerg­ing is quite high, and I'm wor­ried that our ar­se­nal of an­ti­bi­otics is dwindling,” Col­lins said. “We have time to re­spond now, but we need a move­ment backed by po­lit­i­cal will to ex­pand an­ti­bi­ot­ic re­search and de­vel­op­ment.”

* * *

Faced with attack by human-made antibiotics, bacteria help each other out—and unfortunately for us, are better off for it, researchers have found. Though a small fraction of pathogens in a colony may have evolved the ability to resist a drug or class of drugs, these “super bugs“ were found to help their more vulnerable peers by over-producing a drug-fighting substance. Prevailing wisdom held that antibiotic resistance works only on an individual level: a bacterium acquires a mutation that confers protection against a drug, allowing it to survive and reproduce. Eventually, as vulnerable bacteria die, the mutant's stronger progeny repopulate the colony. But the new study, to appear in the Sept. 2 issue of the research journal Nature, indicates there are also population-wide changes in the bacterial community at work. Faced with an onslaught of antibiotics, resistant Escherichia coli produce—at an energy cost to themselves—a protein molecule that seeps into the communal broth and triggers a slew of protective mechanisms in their non-resistant neighbors. The study comes from researchers at the Howard Hughes Medical Institute in Chevy Chase, Md. In the past few years, the rise of “super bugs“ such as methicillin-resistant Staphylococcus aureus, or MRSA, has had hospitals and medical professionals scrambling to fend off a public health disaster. The new findings could help explain why resistance has been so hard to curb, the researchers say. The institute's James J. Collins and colleagues at Boston University grew bacteria in a bioreactor—a large, capped glass vessel with many extended arms that allow researchers precise control over what the bugs are exposed to. “It kind of looks like a component of a moonshine factory out in the backwoods,“ Collins said. Interested in how genetically identical E. coli acquire mutations that confer resistance, the researchers trickled the antibiotic norfloxacin into the bioreactor. As they upped the bugs' exposure, the scientists periodically removed samples of bacteria and measured the minimum strength of drug that stops growth of the bug. “That's when we were stopped in our tracks,“ Collins said. To their surprise, the researchers found that the population as a whole was much more drug-resistant than individual samples. Less than one in a hundred individuals were typically drug-resistant. The team then analyzed the proteins made by resistant bacteria in the presence of norfloxacin, and found that a compound called tryptophanase was particularly abundant. Tryptophanase breaks down a biological molecule, the amino acid tryptophan, into smaller bits. One of the products of this reaction is indole, a signaling molecule that E. coli produces under certain stressful conditions. Indole turns out to offer bacteria two kinds of protection against norfloxacin, according to Collins' group. One is to turn on cellular machines that pump the antibiotic out of the cell, as if expelling a poison. Indole also turns on chemical processes that protect the cell from oxidative stress, a chemical imbalance that leads to the build up toxic molecules called free radicals. A few years ago, Collins's team reported that antibiotics tend to work by pummeling bugs with free radicals. “Here we're seeing that indole is dampening that—turning on the sprinklers for the fire resulting from the antibiotics,“ he said. By comparing the growth of bacteria, the researchers found that the mutants produce indole at a significant cost to themselves. “They don't grow as well as they could, because they're producing indole for everybody else,“ Collins said. Such altruistic behavior—which appears in species throughout the animal kingdom, including humans—presents a well-known paradox for evolutionary biologists: if evolution favors the fittest, why would an individual sacrifice its own fitness for the rest of the group? Collins said his findings bolster the “kin selection“ theory—formalized in the 1960s by the British evolutionary biologist W.D. Hamilton—that said that organisms may behave altruistically toward others that share their genes. So even if altruistic behavior prevents an individual from surviving to pass its own genes on to future generations, others in the population can fulfill that evolutionary role. In this case, the E. coli were from the same population, so by producing indole, the resistant mutants were protecting their own gene pool. “We are planning to explore whether similar strategies are used by other bacterial species,“ Collins added. Collins thinks the study is most directly pertinent to public health. The researchers found that the same population-wide protection occurs when bugs are exposed to other kinds of antibiotics. What's more, many types of bacteria produce indole, suggesting that a similar cooperative process may happen in a host of bacterial species. Future research on antibiotics might well focus on targeting the indole pathway as a means to block bugs' ability to share resistance, Collins said. More broadly, the work highlights the pressing need for investment in new antibiotic development. “The chance that we'll have new and dangerous super bugs emerging is quite high, and I'm worried that our arsenal of antibiotics is dwindling,“ Collins said. “We have time to respond now, but we need a movement backed by political will to expand antibiotic research and development.“