Section 10: Genetic Variation and Antibiotic Resistance that initiated this Small World Initiative...

12
Small World Initiative Instructor Guide Section 10: Genetic Variation and Antibiotic Resistance Section 10: Genetic Variation and Antibiotic Resistance TOPICS Genetic variation Antibiotic resistance mechanisms Natural selection Horizontal gene transfer SUMMARY This section is devoted to a discussion of antibiotic resistance which is, after all, the problem that initiated this Small World Initiative project. We dispel misconceptions about how resistance develops and use acquisition of antibiotic resistance within a population as an example of evolution in action. An important principle in evolution is that there is variation within a population; certain traits will be more advantageous and so organisms that harbor these traits survive and replicate. Distinction is made between the two main underlying molecular mechanisms for antibiotic resistance: 1) mutations that alter structure of the target molecule such that the antibiotic is no longer effective and 2) acquisition of gene cassettes through horizontal transfer from another organism. Instructors may wish to elaborate on the mechanisms of horizontal gene transfer in bacteria. We then describe why horizontal gene transfer often leads to acquisition of resistance to multiple antibiotics. LEARNING GOALS Indicate the common mechanisms of antibiotic resistance (what function is altered that leads to resistance). Compare the two main classes of genetic change that lead to antibiotic resistance in an individual cell. Explain why horizontal gene transfer can increase the rate of evolution of antibiotic resistance relative to spread of resistance gained through vertical transfer of mutation. Know what a plasmid is and what is required for it (or its genetic content) to be maintained within a population. Explain how selection pressure leads to antibiotic resistant populations of bacteria. Articulate the underlying molecular basis for variation within a population. Explain why resistance to one antibiotic often results in resistance to multiple antibiotics. PRE-CLASS PREPARATION Students should read Section 10 of the Laboratory Manual, Bacterial Antibiotic Resistance. Instructors may also wish to assign readings on horizontal gene transfer in bacteria (conjugation, transformation, and transduction).

Transcript of Section 10: Genetic Variation and Antibiotic Resistance that initiated this Small World Initiative...

Small  World  Initiative  Instructor  Guide   Section  10:  Genetic  Variation  and  Antibiotic  Resistance  

Section 10: Genetic Variation and Antibiotic Resistance

TOPICS Genetic variation Antibiotic resistance mechanisms Natural selection Horizontal gene transfer SUMMARY This section is devoted to a discussion of antibiotic resistance which is, after all, the problem that initiated this Small World Initiative project. We dispel misconceptions about how resistance develops and use acquisition of antibiotic resistance within a population as an example of evolution in action. An important principle in evolution is that there is variation within a population; certain traits will be more advantageous and so organisms that harbor these traits survive and replicate. Distinction is made between the two main underlying molecular mechanisms for antibiotic resistance: 1) mutations that alter structure of the target molecule such that the antibiotic is no longer effective and 2) acquisition of gene cassettes through horizontal transfer from another organism. Instructors may wish to elaborate on the mechanisms of horizontal gene transfer in bacteria. We then describe why horizontal gene transfer often leads to acquisition of resistance to multiple antibiotics. LEARNING GOALS

• Indicate the common mechanisms of antibiotic resistance (what function is altered that leads to resistance).

• Compare the two main classes of genetic change that lead to antibiotic resistance in an individual cell.

• Explain why horizontal gene transfer can increase the rate of evolution of antibiotic resistance relative to spread of resistance gained through vertical transfer of mutation.

• Know what a plasmid is and what is required for it (or its genetic content) to be maintained within a population.

• Explain how selection pressure leads to antibiotic resistant populations of bacteria. • Articulate the underlying molecular basis for variation within a population. • Explain why resistance to one antibiotic often results in resistance to multiple

antibiotics.

PRE-CLASS PREPARATION Students should read Section 10 of the Laboratory Manual, Bacterial Antibiotic Resistance. Instructors may also wish to assign readings on horizontal gene transfer in bacteria (conjugation, transformation, and transduction).

Small  World  Initiative  Instructor  Guide   Section  10:  Genetic  Variation  and  Antibiotic  Resistance  

PRE-CLASS ASSESSMENT 1. Defend or refute the following statements: A) People are becoming more immune to antibiotics as antibiotic use increases.

People don’t become immune to antibiotics; the bacterial cells that are resistant in a population have a selective advantage for survival in the presence of the antibiotic. As the prevalence of antibiotics in the environment increases, the selective pressure increases, leading to an increase in prevalence of antibiotic resistant strains.

B) Antibiotics are changing and becoming weaker. Antibiotics are a chemical with a precise molecular structure. They are not becoming weaker, they are simply not as effective against organisms that have acquired resistance

Note: Question 1 adapted from Juehner and Cloud-Hansen. 2. What are the two mechanisms by which antibiotic resistance can be acquired?

Through acquisition of a segment of DNA encoding genes for antibiotic resistance through horizontal gene transfer or through acquisition of a mutation in the antibiotic target that decreases binding affinity of the antibiotic.

GUIDE TO THE POWERPOINT SLIDES

Outline • Captivating story of antibiotic resistance • Variation within a population • Classes of genetic change that lead to antibiotic resistance

— Point mutation of a target molecule — Acquisition of function through horizontal gene transfer

• Horizontal gene transfer mechanisms • Plasmids • Selection pressure

Captivating story of antibiotic resistance We suggest shamelessly attracting the attention of students by opening this section with a story of an antibiotic-resistant infection of public health or personal concern. One suggestion is provided below (the reference can be found at the end of this section). In 1989, a woman in Denmark was diagnosed with Salmonella food infection after experiencing nine days of diarrhea. Doctors prescribed ciprofloxacin which, at the time, had very limited use and was considered a “big gun” antibiotic that should cure all strains. The patient did not recover. The bacteria destroyed colon tissue, allowing the organism and other microbes present in the colon to access the bloodstream. Doctors stitched her colon and administered heavy doses of two additional antibiotics. The Salmonella was killed, but the patient sustained septic shock due to the presence of the other colonic bacteria that had entered her bloodstream. Four days later she died.

Small  World  Initiative  Instructor  Guide   Section  10:  Genetic  Variation  and  Antibiotic  Resistance  

Pig farmers had been fighting Salmonella outbreaks with enrofloxacin, a quinolone class of antibiotic similar to ciprofloxacin. A Danish microbiologist traced the strain to contaminated pork from a single Danish herd. The herd strains were resistant to 7 different antibiotics, whereas up to that point, the most dangerous strains exhibited resistance to five antibiotics. Interestingly, the hogs had not been treated with quinolone, but others on nearby farms had. Eleven people were hospitalized due to contamination from this meat; two died. Natural variation within a population GUIDING QUESTIONS

• How does genetic variation arise? • How is antibiotic resistance acquired in an individual cell? • How is antibiotic resistance acquired by a population?

A central concept to convey is that natural selection acts on the genetic variation that already exists within a population. Presence of antibiotic doesn’t cause mutations to occur but rather selects for those resistant cells already present in the population.

Active Learning

Activity type: Electronic response and Independent problem solving

As a visual demonstration of natural selection and variation within a population, we begin with a photograph of a typical disk assay that assesses the antibiotic resistance pattern for a particular isolate that is spread as a lawn. Each disk is impregnated with antibiotic that diffuses through the medium, resulting in a zone of growth inhibition if the isolate is sensitive to the drug. One can see resistant colonies within most of the clearance zones.

Question: Some clearance zones contain isolated resistant colonies. Why? A. Some cells in the lawn population became resistant after exposure to the antibiotic. B. Some cells in the lawn population were already resistant to the antibiotic. Question: Design an experiment to distinguish between these two hypotheses: In our experience, students cannot come up with a viable experiment unless they are familiar with the classical experiments addressing this question (Lederberg and Lederberg (1952) or Luria and Delbruck (1943)). We will describe the Lederberg

•  Immediately*a+er*spreading*lawn*of*bacteria*onto*plate,*disks*are*placed*on*the*lawn.*

•  Each*disk*is*impregnated*with*a*different*an<bio<c*that*diffuses*through*the*medium.*

•  Zone*of*growth*inhibi<on*results*if*the*isolate*is*sensi<ve*to*the*drug.**

Small  World  Initiative  Instructor  Guide   Section  10:  Genetic  Variation  and  Antibiotic  Resistance  

experiment below. The problem arises when students realize that they do not have a way to rule out the possibility that the resistance arose as a result of exposure to antibiotic. Students should take comfort in the fact that this conundrum stumped many microbiologists for a long time. Joshua and Esther Lederberg designed a new technique to address this question.

Here we present a simplification of the classic Lederberg Experiment in which the replica plating technique was invented as a solution to address the problem of timing of antibiotic exposure. The Understanding Evolution website from Berkeley University (referenced below) provides a simplified explanation of the experiments. Additional details are provided in the notes section of the Powerpoint slide.

Briefly, cells were grown in culture with no antibiotic, then plated onto solid medium without antibiotic. A replica of the position of the colonies within the plate was made using the replica plating technique designed by the Lederbergs. A sterile piece of velvet is pressed onto the agar surface. Some cells from each colony are transferred to the velvet. The velvet is then pressed against two plates: a fresh plate without antibiotic and a fresh plate with antibiotic. Thus we have duplicate plates in

which colonies are positioned in identical locations. The two fresh plates are incubated. All colonies on the plate lacking antibiotics grow. A small percentage of colonies will grow on the plate containing antibiotics. These colonies represent cells that were resistant to the antibiotic prior to plating on the original plate. But how do we demonstrate that the mutation arose early rather than as the colony hit the plate with antibiotics? This is accomplished by examination of the corresponding colony imprint on the duplicate (antibiotic free) plate. Those cells have not been exposed to antibiotic. If resistance arose after exposure to antibiotic, we expect only a small percentage of the cells in that colony imprint to, again, acquire resistance. But, if the mutation existed early, then all of the cells in that colony should already be resistant. By re-plating cells from the unexposed colony onto antibiotic medium, we should see a large percentage of colonies growing, indicating the mutation was already present in the population. GUIDING QUESTION

• How is antibiotic resistance acquired in an individual cell?

The Lederberg Experiment helped to demonstrate that mutations are present within a population, not induced by the

environment

These%colonies%never%exposed%to%an2bio2c.%Are%they%resistant?%

h8p://evolu2on.berkeley.edu/evolibrary/ar2cle/muta2ons_07%

Modified%from:%

Small  World  Initiative  Instructor  Guide   Section  10:  Genetic  Variation  and  Antibiotic  Resistance  

Classes of genetic change that lead to antibiotic resistance Point mutation of a target molecule We refer back to our slides on the structure of the ribosome and how tetracycline interacts through non-covalent bonding interactions to bind to the small subunit, thus preventing mRNA access. A specific point mutation in one of the ribosomal proteins alters the site at which tetracycline binds, leading to tetracycline resistance but retaining function of the ribosome. Mutations in the rRNA could also lead to resistance. Mutations that lead to reduced uptake of the antibiotic may also occur (e.g. porin mutations that decrease β-lactam access to the cell).

Modifica(on*of*the*an(bio(c*target*through*point*muta(on*can*alter*structure*such*that*binding*affinity*

of*an(bio(c*is*decreased*

30S* 50S*

Ac(vity*of*the*target*must*be*retained*

The$an'bio'cs$shown$here$bind$to$the$16S$rRNA$of$the$30S$(small)$subunit$

From$Broderson$et$al.$(2000)$Cell$103:1143F1154$$

The$parts$of$the$16S$RNA$that$make$contact$with$any$of$the$an'bio'cs$are$colored$

Structure of Antibiotics in the 30S Subunit1145

Table 2. Refinement Statistics

Data Set Tetracycline Pactamycin Hygromycin B

Resolution (A) 99.0–3.4 99.0–3.4 99.0–3.3No. of reflections (working set) 172,608 166,337 178,509No. of reflections (free set) 9,128 8,776 9,454No. of atoms 51,941 51,917 51,913

protein 19,271 19,271 19,271RNA 32,508 32,508 32,508ligand 64 40 36metal ions 98 98 98

R factora (%) 22.2 (26.4) 23.2 (28.0) 21.8 (26.1)Coordinate errorb (A) 0.39 (0.46) 0.43 (0.51) 0.39 (0.46)Rms deviations

bond lengths (A) 0.0070 0.0070 0.0068bond angles (!) 1.26 1.25 1.25dihedrals (!) 28.4 28.4 28.5plane (!) 1.60 1.56 1.59

a Numbers in parentheses represent free R factor.b Estimated Luzzati coordinate error for reflections in the resolution range 5.0 A–3.4 A/3.4 A/3.3 A.Numbers in parentheses represent the cross-validated coordinate error.

one edge and either hydrophobic or stacking interac- the subunit. Throughout this paper, the binding site oftetracycline near the A site is termed the primary site,tions with the other side. We have found two binding

sites for Tc within the small ribosomal subunit. The bet- whereas the location in the body is called the secondarybinding site. The discovery of a second binding site ister occupied site is located near the acceptor site for

aminoacylated tRNA between the head and the body of not surprising since the drug is known to have second-ary, possibly nonspecific sites on both subunits (Pestka,the 30S (the A site), and the less occupied site is at the

interface between three RNA domains in the body of 1974; Vazquez, 1974).

Figure 1. Overview of Tetracycline, Pacta-mycin, and Hygromycin B in the 30S Subunit

Antibiotics are shown as space-filling mod-els, with tetracycline (blue), pactamycin(green), and hygromycin B (red). The parts of16S RNA that make contacts with any of thethree antibiotics are colored as in the follow-ing figures.

Tetracycline$

Pactamycin$

Hygromycin$B$

30S$(small)$subunit$

Green,&blue&and&cyan&represent&

relevant&helices&of&the&16S&rRNA&

tetracycline&

Cell1146

h<p://commons.wikimedia.org/wiki/File:Tetracycline_structure.svg&

The&primary&binding&site&of&tetracycline&(yellow)&is&to&

the&A&site&of&the&ribosome&&

From&Broderson&et&al.&(2000)&Cell&103:1143O1154&&

!!

Tetracycline!binding!likely!interferes!with!tRNA!(red)!and!mRNA!(yellow)!access!and!codon;an<codon!interac<on!

Cell1146

tetracycline!

From!Broderson!et!al.!(2000)!Cell!103:1143;1154!!

Small  World  Initiative  Instructor  Guide   Section  10:  Genetic  Variation  and  Antibiotic  Resistance  

The original data figure from Hu et al. (2005) shows the alignment of a ribosomal peptide from N. gonorrhoeae, B. subtilis, and T. thermophilus. Isolates from patients with N. gonorrhoeae infections resistant to treatment with tetracycline were found to have a DNA point mutation that resulted in a single amino acid change (valine to methionine at position 57) in the ribosomal protein S10. Evidence indicates that the affected amino acid is located in a loop proximal to the ‘A’ site of the 30S (small) ribosomal subunit and within 10 angstroms of the tetracycline binding site. The figure shows a model depicting the affected ribosomal protein (S10) in red, The model in the figure is from T. thermophiles depicting the amino acid corresponding to the N. gonorrhoeae Val-57 (Lys-55) as important for tetracycline binding and located near the aminoacyl-tRNA site. As another example, a mutation may lead to reduced uptake of antibiotic into the cell if a pore protein were mutated, for example.

Model&depic*ng&possible&tetracycline&binding&interac*ons&with&16S&rRNA&&

Cell1146

tetracycline&

Cell1146

The&point&here&is&not&to&memorize&this&specific&example,&but&to&use&it&as&context&to&understand:&•  The&role&of&nonDcovalent&bonding&interac*ons&in&biology&•  The&rela*onship&of&structure&to&func*on&•  How&the&ribosome&func*ons&at&the&molecular&level&

From&Broderson&et&al.&(2000)&Cell&103:1143D1154&&

Muta%on(in(ribosomal(protein(renders(bacteria(resistant(to(tetracycline(

Hu(et(al.((2005)(An%microb(Agents(Chemother.(49:4327D4334((

Muta%on(may(lead(to(reduced(uptake(of(an%bio%c(into(cell(

(

β6lactams(diffuse(through(the(outer(membrane(porins(and(would(be(sensi%ve(to(muta%ons(that(affect(porin(size.((Hydrophobic(an%bio%cs(such(as(fluoroquinolones(or(chloramphenicol(that(can(cross(the(lipid(bilayer(would(not(be(as(suscep%ble(to(a(porin(muta%on(

How$is$an)bio)c$resistance$acquired$By#an#individual#cell?#ANSWER:$$!  1.$When$a$muta)on$(o>en$a$point$muta)on)$alters$

structure$of$an)bio)c$target,$but$func)on$retained.$$

$##By$a$popula)on?$

Small  World  Initiative  Instructor  Guide   Section  10:  Genetic  Variation  and  Antibiotic  Resistance  

Acquisition of function through horizontal gene transfer In contrast to point mutations, antibiotic resistance can be acquired through horizontal transfer of a gene or cassette of genes that confer resistance to one or multiple antibiotics.

We provide some examples of gained functions that confer antibiotic resistance. For example, efflux pumps in the cytoplasmic membrane could pump antibiotics out, decreasing the effective concentration. Additionally, enzymes that inactivate the antibiotic could be produced

(e.g. β-lactamases as discussed in Section 3). In these cases, the function is gained through acquisition of a segment of DNA (usually a plasmid) large enough to encode the particular function(s) gained.

Horizontal gene transfer mechanisms Bacteria can transfer DNA horizontally (to non-progeny cells) via conjugation, transformation, and transduction. Genes for resistance to antibiotics are often clustered

together on the genome or on plasmids; therefore, horizontal transfer can result in transfer of resistance to many antibiotics. Antibiotic resistance gene clusters are often flanked by transposable elements that allow the DNA between the transposable elements

to be transferred to another plasmid or the genome. This is significant because not all plasmids are compatible with all species and some plasmids are not stably maintained. Again, our intent is not to reproduce content readily available in other sources and since the mechanisms of horizontal gene transfer are covered in all microbiology textbooks we leave it to individual instructors to develop sufficient materials to teach this topic.

2.#An&bio&c#resistance#can#occur#when#a#new#ac&vity#is#acquired#-  Usually#through#acquisi&on#of#a#large#

stretch#of#DNA#encoding#one#or#more#genes##

Example:)Efflux)pumps)in)the)cytoplasmic)membrane)pump)an6bio6cs)out,)decreasing)the)effec6ve)

concentra6on))

There%are%many%classes%of%efflux%pumps.%%

Journal)of)An6microbial)Chemotherapy)(2003))51,)1055G1065)(2003))

Example:)Enzymes)that)inac2vate)the)an2bio2c)

Penicillin)core)structure)

β:lactamase)cleavage)site)

β:lactamases)are)a)class)of)enzymes)that)inac2vate)β:lactams)by)cleaving)a)covalent)bond)that)is)cri2cal)for)structure/ac2vity)

Bacteria(can(transfer(DNA(horizontally((to(non5progeny(cells)(

•  Conjuga<on(•  Tranforma<on(•  Transduc<on(

Small  World  Initiative  Instructor  Guide   Section  10:  Genetic  Variation  and  Antibiotic  Resistance  

Plasmids We provide the minimum amount of information on plasmids that is required to understand the spread of resistance throughout populations of bacteria. Plasmids are made up of circular DNA and can replicate autonomously from the genome. It is important to stress here that resistance can spread throughout a population much more quickly if transferred through horizontal, rather than vertical means. Plasmids can be transferred to subsequent generations (heritable) and can be transferred horizontally to other bacteria, even to those of a different species.

At this point students should be able to meet the following goals:

ü Indicate the common mechanisms of antibiotic resistance (what function is altered that leads to resistance).

ü Compare the two main classes of genetic change that lead to antibiotic resistance in an individual cell.

ü Articulate the underlying molecular basis for variation within a population. ü Explain why horizontal gene transfer can increase the rate of evolution of

antibiotic resistance relative to spread of resistance gained through vertical transfer of mutation.

ü Know what a plasmid is and what is required for it (or its genetic content) to be maintained within a population.

Genes%for%resistance%to%an-bio-cs%are%o/en%clustered%together%on%the%genome%or%on%plasmids;%horizontal%transfer%can%result%in%transfer%of%resistance%to%many%an-bio-cs.%

genome%plasmid%

Plasmids%•  Circular%DNA%•  Replicate%autonomously%from%the%genome%•  Transferred%to%subsequent%genera-ons%(heritable)%•  Can%be%one%or%many%per%cell,%depending%on%the%plasmid%•  Can%be%transferred%to%other%bacteria,%even%of%different%species%%

An#bio#c(resistance(gene(clusters(are(o1en(flanked(by(transposable(elements(that(allow(the(DNA(between(the(transposable(elements(to(be(transferred(to(another(plasmid(or(the(genome.((

This(is(significant(because(not(all(plasmids(are(compa#ble(with(all(species(and(some(plasmids(are(not(stably(maintained.(((

Tn( Tn(An#bio#c(resistance(genes(

Horizontal*Transfer*

R"

R"R"

R" R"

R" R" R" R"

R"

R"

R"

R"

R" R"

R"

R"

R"

R"

R"

R"

Transfer*is*not*limited*to*organisms*of*the*same*species*

Small  World  Initiative  Instructor  Guide   Section  10:  Genetic  Variation  and  Antibiotic  Resistance  

Selection Pressure GUIDING QUESTION

• How is antibiotic resistance acquired by a population of cells?

Historically, we see the prevalence of antibiotic resistant clinical isolates increases after introduction of the antibiotic to the market. This is because the presence of the antibiotic causes selective pressure for the resistance trait to be maintained. For resistance to be maintained within a population, we generally consider three key events: 1. Acquisition of the resistant trait through either mutation or horizontal transfer 2. Selection 3. Replication of the resistant cells

The Lederberg Experiment helped to demonstrate that mutations are present within a population, not induced by

the environment These%colonies%never%exposed%to%an2bio2c.%Are%they%resistant?%

The%expecta2on,%based%on%our%hypothesis,%is%that%this%clonal%popula2on%of%cells%is%resistant%

An#bio#c(use(is(correlated(to(the(emergence(of(resistant(strains(

1942(First(therapeu#c(use(of(penicillin(

((((((1945(More(than(20%(of(S.#aureus#hospital(cases(are(penicillin(resistant(

1947((Streptomycin(approved(by(FDA(

1947(Streptomycin(resistance(observed(

1959(Methicillin(introduced(

1961(Methicillin(resistant(S.#aureus((MRSA)(observed((

1967(Gentamicin(approved(by(FDA(

1970(Gentamicin(resistance(observed(

Adapted(from(Science((2008)(321:356((

Penicillin'resistant'Staphylococci'(WHO,'1962)'

Figure'from'InternaAonal'BiodeterioraAon'and'BiodegradaAon'47:55'(2001)''

Within'a'few'years'of'introducing'penicillin,'resistant'strains'were'idenAfied'(e.g.'βMlactamases'acquired)' The$pharmaceu+cal$industry$responded$by$

producing$semi6synthe+c$deriva+ves$designed$to$be$resistant$to$β6lactamases$

Penicillin$G$

Methicillin$(Penicillin$deriva+ve)$

Small  World  Initiative  Instructor  Guide   Section  10:  Genetic  Variation  and  Antibiotic  Resistance  

This is an ideal place in which to discuss the recommended research paper for this section if desired. This paper highlights a clinical case in which resistance to vancomycin was transferred on a plasmid from a strain of Enterococcus faecalis to Staphylococcus aureus. The plasmid harbored a transposon with resistance genes not only for vancomycin but also many other antibacterials. At this point students should be able to meet the following goals:

ü Articulate the underlying molecular basis for variation within a population. ü Explain why resistance to one antibiotic often results in resistance to multiple

antibiotics.

Active Learning

Activity type: Shout out We end by repeating a question from the pre-class assessment. Defend or refute: People build up tolerance to antibiotics as antibiotic use increases.

People don’t become immune to antibiotics; the bacterial cells that are resistant in a population have a selective advantage for survival in the presence of the antibiotic. As the prevalence of antibiotics in the environment increases, the selective pressure increases, leading to an increase in prevalence of antibiotic resistant strains.

Hopefully the material presented clarified any misconceptions that may have existed. If not, the instructor can elaborate prior to moving on.

POST-CLASS ASSESSMENT 1. Your colleague has a collection of fecal bacteria isolated from patients with severe diarrhea. Each isolate is stored in pure culture. She tests each isolate for antibiotic resistance and notes that many of the organisms are resistant to ampicillin. She decides to use the sequence of the ampicillin resistance gene as a phylogenetic marker to determine relatedness of the collection of organisms. Provide an explanation for why this may not be the best approach.

This is not a good approach because the antibiotic resistance marker undergoes horizontal transfer. Horizontal transfer confounds the building and interpretation of phylogenetic trees because nothing can be inferred about evolutionary history from genes that undergo horizontal gene transfer.

S.#aureus#isolates(with(resistance(to(vancomycin(appeared(in(2002(

which President George W. Bush was expected to sign into law this week, says itapplies to military activity “or a scientific re-search activity [on marine mammals] con-ducted by or on behalf of the Federal Govern-ment.” But whether that encompasses anyscientist with federal funding is up to “agen-cies and lawyers” to decide, says KarenSteuer, a former House staffer who now ad-vises the National Environmental Trust inWashington, D.C. In any case, she notes, not

all marine mammal researchers receive feder-al funding. Nor does the law ease the rulesfor scientists doing ocean research that af-fects mammals incidentally, says PenelopeDalton of the Consortium for OceanographicResearch and Education in Washington, D.C.

Some critics also point to ambiguous lan-guage in a report accompanying the bill. Forexample, although the report discusses “bio-logically significant” impacts, a term scien-tists have pushed for, it defines altered behav-

ior as a “long-term” change in a “species orstock,” which could be impossible to deter-mine, Steuer says. The report and the final billare “inconsistent,” agrees Donna Wieting ofthe National Marine Fisheries Service, whichmust craft regulations to enforce the act.

Observers are hoping that the changeswill be revisited next year, when Congressresumes work on updating MMPA. Thosechanges “are going to be very important” toscientists, Ketten says. –JOCELYN KAISER

28 NOVEMBER 2003 VOL 302 SCIENCE www.sciencemag.org1488

ILLU

STRA

TIO

N:C

.SLA

YDEN

/SCIENCE;

SOU

RCE:

LIN

DA

WEI

GEL

The long-dreaded superbug surfaced on asummer Friday in 2002. The new strain ofStaphylococcus aureus, cultured from footulcers on a diabetes patient in a Detroit dial-ysis center, had developed resistance tovancomycin, one of the few antibiotics leftthat reliably kills staph. Doctors rushed thestrain to the Centers for Disease Control andPrevention in Atlanta, and nine local andCDC public health officials scoured the dial-ysis center and tested more than 300 peoplethe patient had come in contact with, col-

lecting samples to see if it had spread. Ithadn’t. “We dodged another bullet,” saysclinical microbiologist Donald Low of theUniversity of Toronto.

Now a study on page 1569 shows howthe microbe became a menace. Microbiolo-gists Linda Weigel and Fred Tenover ofCDC and colleagues found that the bug like-ly acquired the vancomycin-resistance traitfrom another microbe common in hospitalsettings, a dangerous alliance that health of-ficials had long feared. The new S. aureusstrain also resisted most common anti-

biotics, including penicillin, methicillin, andciprofloxacin, and it possessed the geneticmachinery to pass drug resistance on todrug-susceptible S. aureus strains.

S. aureus commonly lives on the skin andin the noses of healthy people, causing noth-ing worse than pimples and boils. But inhospitalized patients, it causes tens of thou-sands of infections each year, including seri-ous and sometimes fatal surgical-wound in-fections, bloodstream infections, and pneu-monia. Penicillin saved many patients, but

the microbe soonlearned to evade it,and over the pasthalf-century it hasdeveloped resist-ance to one antibi-otic after another.

By the late1980s, vancomycinwas the “drug oflast resor t” formultidrug-resistantstrains, Tenoversays. In 1992 re-searchers showedthat a vancomycin-resistant strain ofEnterococcus fae-calis, which alsoinfects hospitalizedpatients, couldtransfer its resist-ance genes to

S. aureus on the skin of a mouse. “We be-gan to anticipate that at some point we’dsee high-level resistance moving into S.aureus,” Tenover says.

When the Detroit vancomycin-resistant S. aureus (VRSA) strain appeared, the detec-tive work began. Doctors isolated two strainsfrom the patient. One resisted almost all avail-able antibiotics. The other, from the woman’sfoot ulcer, resisted the same drugs plus vanco-mycin. Doctors also cultured vancomycin-resistant E. faecalis from her foot ulcers.

The two S. aureus strains were otherwise

identical to each other and similar to a men-acing S. aureus strain that commonly infectshospital patients. Circular loops of DNAcalled plasmids from the VRSA and E. fae-calis strains, but not the susceptible S. au-reus strain, had a gene called vanA thatwards off vancomycin. That suggested thatthe drug-resistance gene had jumpedspecies, Weigel says.

To see how it made the jump, the re-searchers checked the plasmids for a mobilegenetic element called a transposon, a snip-pet of DNA that can jump out of one plas-mid and worm its way into another. As hasbeen found in other vancomycin-resistant E. faecalis strains, this one hosted a plasmidwith a transposon containing vanA. Thetransposon appeared in a plasmid in the newVRSA strain as well. Colleagues at The In-stitute for Genomic Research in Rockville,Maryland, sequenced the entire VRSA plas-mid, showing that the transposon was intactand ready to jump.

Together, the results suggest that E. fae-calis in the woman’s ulcer sidled up to S. au-reus and passed along its resistance plasmid.Enzymes in S. aureus seem to have de-stroyed the foreign E. faecalis plasmid, butbefore that happened, the transposonjumped, like a rat escaping a sinking ship,and infiltrated the S. aureus’s resident plas-mid to create a new hybrid. That created anasty new S. aureus strain that can spreadreadily in hospitals, resist almost all thedrugs available to kill it, and share itsweapons with S. aureus cousins that remainvulnerable to vancomycin. “What we’ve iso-lated is really the triple threat,” Tenover says.

In the clinic, says Low, “it’s critical forlaboratories to be on the lookout” for newVRSA strains and for doctors to work to keepthem in check. Two antibiotics, linezolid(Zyvox) and quinupristin/dalfopristin (Syner-cid), still stop VRSA, but it’s important thatdrug companies step up efforts to develop al-ternatives, he says: “Right now we’ve gotsomething in our back pocket, but that couldchange rapidly.” –DAN FERBER

Triple-Threat Microbe Gained Powers From Another BugM ICROB IO LOGY

N E W S O F T H E W E E K

S. aureus

Dangerous liaison. Vancomycin resistance probably jumped from E. fae-calis to S. aureus via a plasmid (black loop) carrying a transposon (red) thatthen infested the resident plasmid (blue).

on

Nov

embe

r 13,

201

2w

ww

.sci

ence

mag

.org

Dow

nloa

ded

from

•  VancomycinR(carried(on(plasmid(harboring(many(other(resistance(determinants(

•  Likely(transferred(horizontally(from(E.#faecalis#to(S.#aureus##

•  Once(inside(S.(aureus,(transposed(from#E.#faecalis#plasmid(to(resident(S.#aureus#plasmid( Ferber((2003)(Science(302:1488(

Small  World  Initiative  Instructor  Guide   Section  10:  Genetic  Variation  and  Antibiotic  Resistance  

2. Shigella sp. is a bacterial organism that can infect the gut, resulting in dysentery. In the 1950’s, Shigella outbreaks in Japan were treated with sulfonamide. Gradually, resistance was detected in patients . In some cases, sulfonamide resistant Shigella species were isolated from patients who had not been treated with sulfonamide. Sulfonamide sensitive and resistant E. coli cells were also detected in fecal samples of some of the same (untreated) patients.

A) Provide an explanation for why resistant Shigella species might be present in an individual in which there had been no selective pressure for the drug (no antibiotic usage).

Since other patients in the hospital had resistant infections, even the patients who hadn’t been treated were at risk for developing an infection due to exposure to the resistant cells within the hospital environment. This exposure can occur through contact with hospital surfaces, contact with clinical workers carrying the resistant organisms on gloves, etc.

B) Provide an explanation for why resistant E. coli cells would be present in an individual in which there had been no selective pressure for the drug (no antibiotic usage).

The antibiotic resistance determinant was probably transferred horizontally from the resistant Shigella species (described above) to the E. coli.

3. Defend or refute the following statement: Antibiotics have caused resistance by mutating bacteria.

Antibiotics don’t cause bacteria to mutate; antibiotics provide selective pressure such that those bacteria that already harbor resistance within a population will thrive while bacteria that do not harbor resistance will die.

ORIGINAL RESEARCH PAPERS FOR DISCUSSION The following article and accompanying review trace the fascinating path of horizontal gene transfer of a vancomycin-resistance determinant from a hospital strain of E. faecalis to S. aureus. This provides a real-world example of conjugation, transposition and clustering of antibiotic-resistance determinants. The article is short and relatively easy to comprehend. Weigel et al. (2003) Genetic Analysis of a High-Level Vancomycin-Resistant Isolate of Staphylococcus aureus. Science 302:1569-1571. Ferber (2003) Triple-Threat Microbe Gained Powers From Another Bug. Science 302:1488. The following short paper synthesizes information presented in Sections 6, 8 and 10 and provides insight into the mechanism of evolution described in Section 9. It provides students an opportunity to reinforce understanding of structure-function relationships, the effect of point mutations, and antibiotic resistance in the context of actual clinical cases of ciprofloxacin-resistant patient isolates. In brief, mutations in resistant clinical isolates were traced to a specific region of the gyrA or gyrB gene (subunits of DNA gyrase, the

Small  World  Initiative  Instructor  Guide   Section  10:  Genetic  Variation  and  Antibiotic  Resistance  

target of ciprofloxacin). All resistant isolates acquired mutations that altered a serine at position 83. A particularly prevalent change was serine (polar) to leucine (non-polar). Vila, J., Ruiz, J., Marco, F., Barcelo, A., Goñi, P., Giralt, E., and Jimenez de Anta, T. (1994) Association between double mutation in gyrA Gene of ciprofloxacin-resistant clinical isolates of Escherichia coli and MICs. Antimicrob Agents Chemother. 38:2477-2479. RESOURCES Understanding Evolution website of Berkeley University that contains easy to understand explanations of evolutionary concepts and includes a description of the Lederberg experiment discussed above: http://evolution.berkeley.edu http://evolution.berkeley.edu/evolibrary/article/mutations_07 REFERENCES Ferber (2000) Superbugs on the Hoof? Science 288:792-794. Description of the Salmonella food poisoning case in Denmark. Hu, M., Nandi, S., Davies, C., Nicholas, R. (2005) High-level chromosomally mediated tetracycline resistance in Neisseria gonorrhoeae results from a point mutation in the rpsJ gene encoding ribosomal protein S10 in combination with the mtrR and penB resistance determinants. Antimicrob Agents Chemother. 49:4327-4334. Source of original data presented in the slide set. Juehner, J., and Cloud-Hansen, K. Money, Sex, and Drugs: Exciting college freshman about Genetics available at the University of Wisconsin Institute for Biology Education: biology.wisc.edu/1329.htm Pre-Class assessment question number 1 Lederberg and Lederberg (1952) Replica plating and indirect selection of bacterial mutants. J. Bact. 63:399-406. Original paper on selection of resistant bacterial mutants showing that resistance is a trait present in the population prior to selective pressure. Luria, S. and Delbruck, M. (1943) Mutations of bacteria from virus sensitivity to virus resistance. Genetics 28:491-511. Often referred to as the fluctuation test, this experiment (like that of Lederberg and Lederberg) demonstrates that mutations (or variations) are present within a population rather than occurring in response to environmental change. Mølbak et al. (1999) An outbreak of multi-drug resistant, quinolone-resistant Salmonella enterica serotype typhimurium DT104. New England J. Med. 341:1420-1425. Report of the spread of quinolone-resistant Salmonella from food animals to humans in Denmark.