Microbiology #3

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Name: _________________________

Bio 351 Homework #3

Use the article: Relationship Between Maternal and Neonatal Staphylococcus aureus colonization

DUE: Monday January 29th at 11PM on Blackboard

1. What was the purpose, and justification for this research study (you will find this information after reading the introduction. You do not need to read the entire article)? If you include scientific jargon that the article uses, then I want you to explain to me in your own words the meaning of these terms. (2.5 points)

2. What were the results from Figure 1? (1.5 points)

Use your textbook, and lecture notes to answer the questions below (3 points each):

3. From your knowledge of Gram-positive and Gram-negative cell envelopes, why would penicillin be more effective in killing Gram-positive organisms than Gram-negative organisms?

4. Why is moist heat more efficient at killing microbes than dry heat? How does an autoclave kill microbes so efficiently?

5.7 Physical, Chemical, and Biological Control of Microbes

A variety of terms are used to describe antimicrobial control measures:

Sterilization: killing of all living organisms from inanimate objects

Disinfection: reduction of pathogens from inanimate objects (

1

0 minutes)

Antisepsis: killing or removal of pathogens from the surface of living tissues

Sanitation: reducing the microbial population to safe levels (30 seconds)

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1

Cells Die at a Logarithmic Rate

Microbes die according to a negative exponential curve, where cell numbers are reduced in equal fractions at constant intervals.

Decimal reduction time (D-value) is the length of time it takes an agent or a condition to kill 90% of the population.

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2
FIGURE 5.25 ■ The death curve and the determination of D-values.

Physical Agents That Kill Microbes – 1
High temperature
Moist heat is more effective than dry heat.
Boiling water (100oC) kills most cells.
Killing spores (resistant to adverse conditions) and thermophiles usually requires a combination of high pressure and temperature.
At high pressure, the boiling point of water rises to a temperature rarely experienced by microbes.
Even endospores quickly die under these conditions.

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3

Physical Agents That Kill Microbes – 2
Steam autoclave
121oC (250oF) at 15 psi for 20 minutes
Conditions produced in pressure cookers when canning vegetables

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4
FIGURE 5.26 ■ Steam autoclave.

Physical Agents That Kill Microbes – 3
Pasteurization
Many different time and temperature combinations can be used.
LTLT (low temperature/long time)
63oC for 30 minutes
HTST (high temperature/short time)
72oC for 15 seconds
Both processes kill Coxiella burnetii, the causative agent of Q fever.

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5

Physical Agents That Kill Microbes – 4
Cold
Low temperatures slow growth and preserve strains.
Refrigeration temperatures (4oC–8oC) are used for food preservation.
For long-term storage of cultures
Placing solutions in glycerol at –70oC
Lyophilization or freeze-drying

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6

Physical Agents That Kill Microbes – 5
Filtration
Micropore filters with pore sizes of 0.2 mm can remove microbial cells, but not viruses, from solutions.
Samples from 1 ml to several liters can be drawn through
a membrane filter by vacuum or can be forced through it using a syringe.

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7
FIGURE 5.27 ■ Membrane filtration devices.

Physical Agents That Kill Microbes – 6
Air can also be sterilized by filtration.
This process forms the basis of several personal protective devices.
Laminar flow biological safety cabinets force air through HEPA filters, which remove > 99.9% of airborne particulate material 0.3 μm in size or larger.
Biosafety cabinets are critical to protect individuals working with highly pathogenic material.
Newer technologies embed antimicrobial agents or enzymes directly into the fibers of the filter.

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8

Physical Agents That Kill Microbes – 7

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9
FIGURE 5.28 ■ Biological safety cabinet. CREDITS: A: A: Labconco Corporation; C: Nikki-Universal Co., Ltd., 2000

Physical Agents That Kill Microbes – 8
Irradiation
Ultraviolet light
Has poor penetrating power
Used only for surface sterilization
Gamma rays, electron beams, and X-rays
Have high penetrating power
Used to irradiate foods and other heat-sensitive items

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Some Bacteria Are Highly Resistant to Physical Control Measures
Deinococcus radiodurans
Nicknamed “Conan the bacterium”
Has the greatest ability to survive radiation of any known organism
Has exceptional capabilities
for repairing DNA damaged
by radiation
Was genetically engineered
for use in bioremediation

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11
FIGURE 5.29 ■ Deinococcus radiodurans. CREDITS: A: John R. Battista, Louisiana State University

Chemical Agents – 1
A number of factors influence the efficacy of a given chemical agent, including:
The presence of organic matter
The kinds of organisms present
Corrosiveness
Stability, odor, and surface tension

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12

Chemical Agents – 2
The phenol coefficient test compares the effectiveness of disinfectants.
Chemical agent Staphylococcus aureus Salmonella enterica
Phenol 1.0 1.0
Chloramine 133.0 100.0
Cresols 2.3 2.3
Ethanol 6.3 6.3
Formalin 0.3 0.7
Hydrogen peroxide Empty cell 0.001
Lysol 5.0 3.2
Mercury chloride 100.0 143.0
Tincture of iodine 6.3 5.8

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Table 5.3, Phenol Coefficients for Various Disinfectants.

Commercial Disinfectants and Antiseptics – 1
These include:
Ethanol
Iodine (Wescodyne and Betadine)
Chlorine
Ethylene oxide (a gas sterilant)
These damage proteins, lipids, and/or DNA.
Are used to reduce or eliminate microbial content from objects

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14

Commercial Disinfectants and Antiseptics – 2
Phenolics Alcohols Aldehydes Quaternary ammonium compounds Gases
The 2 dimensional structure of phenol. An alcohol group is attached to one of the carbons on a benzene ring. The 2 dimensional structure of ethanol. The carbon of a methyl group is bonded to another carbon, which is also bonded to two hydrogens and an alcohol group. The 2 dimensional structure for formaldehyde. A carbon atom is double bonded to an oxygen atom and single bonded to two hydrogen atoms. The 2 dimensional structure for cetylpyridinium chloride. The cetylpyridinium ion has a ring of 5 carbon atoms and 1 nitrogen atom. Every other bond in this ring is a double bond, totaling to 3 double bonds in the ring. The nitrogen atom is also bonded to a left parenthesis upper C upper H 2 right parenthesis 15 upper C upper H 3 group. This ion has a positive 1 charge. The chloride ion has a negative 1 charge. The 2 dimensional structure for ethylene oxide. The geometry for this structure is trigonal planar between the carbon atoms of two methyl groups and an oxygen atom.
The 2 dimensional structure of hexachlorophene. There are two benzene rings connected by an additional carbon atom. The carbon atom is also bonded to 2 hydrogens. The structure is symmetric with the plane of symmetry at the connecting carbon atom. The top carbon of each benzene ring is connected to an alcohol group. Three of the other four carbons not attached to groups are bonded to chlorine atoms. The 2 dimensional structure of isopropanol or also known as rubbing alcohol. There is a chain of three carbons. The central carbon is bonded above by a hydrogen and below by an alcohol group. The other two carbons are a part of methyl groups. The 2 dimensional structure for glutaraldehyde. There is a 5 carbon chain. The three carbon atoms in the middle are each bonded to 2 hydrogens. The carbon atoms on the end are double bonded to an oxygen and single bonded to a hydrogen. The left end carbon atom has the oxygen bonded above the hydrogen and the right end carbon atom has the oxygen bonded below the hydrogen. The 2 dimensional structure for benzalconium chloride or also known as mixture. This is an ionic complex whose cation has the following structure. A benzene ring on the left is attached to a carbon atom that is also bonded to two hydrogen atoms. This carbon atom is bonded to the right by a nitrogen atom. This nitrogen atom is bonded from the top and bottom by methyl groups and to the right by an R group. Below the structure, R equals an alkyl that is upper C 8 upper H 17 to upper C 18 to upper H 37. The anion for this compound is the chloride ion. The 2 dimensional structure for betapropiolactone. There is a rectangular structure between the carbon atoms of two methyl groups, an oxygen atom, and another carbon atom. The carbon atom is also double bonded to another oxygen atom.

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15
FIGURE 5.30 ■ Structures of some common disinfectants and antiseptics.

Bacteria Can Develop
Resistance to Disinfectants
This has been achieved via several mechanisms:
Altering the fatty acid synthesis protein normally targeted by triclosan
Producing membrane-
spanning, multidrug
efflux pumps
Forming multispecies
biofilms, which offer
collaborative protection

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16
FIGURE 5.31 ■ Mixed biofilm. CREDITS: A. Bridier et al. 2011. Biofouling 27:1017–1032

Antibiotics – 1
Antibiotics are chemical compounds synthesized by one microbe that kill or inhibit the growth of other microbial species.
Penicillin mimics part of the bacterial cell wall.
Prevents cell wall formation and is bactericidal
Other antibiotics target:
Protein synthesis
DNA replication
Cell membranes

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17

Antibiotics – 2
Penicillin
Produced by Penicillium notatum
Mimics a part of the cell wall
Prevents peptidoglycan synthesis and prevents cell wall formation

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18
FIGURE 5.32 ■ Penicillin. CREDITS: B: USPS; C: Christine L. Case/Skyline College

Antibiotics – 3
Penicillin
Is bactericidal because actively growing cells lyse without the support of the cell wall

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19
FIGURE 5.33 ■ Effect of ampicillin (a penicillin derivative) on E. coli. CREDITS: ART GIRARD, ANNE KLEIN, & A.J. MILICI, PFIZER GLOBAL RESEARCH AND DEVELOPMENT

Biological Control of Microbes
Biocontrol is the use of one microbe to control the growth of another.
Probiotics contain certain microbes that, when ingested, aim to restore balance to intestinal flora.
Lactobacillus and Bifidobacterium
Phage therapy aims to treat infectious diseases with a virus targeted to the pathogen.
Bacteriophages are a possible alternative to antibiotics in the face of rising antibiotic resistance.
Commercial phage products are now available to target a few food-borne pathogens.

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Relationship Between Maternal and Neonatal
Staphylococcus aureus Colonization

WHAT’S KNOWN ON THIS SUBJECT: Staphylococcus aureus is
a leading cause of infections in infants. Staphylococcal
colonization is a known risk factor for infection, but whether
maternal colonization plays a role in subsequent colonization in
the infant is unclear.

WHAT THIS STUDY ADDS: This prospective study found that
infants born to women colonized with S aureus either during their
third trimester of pregnancy or at the time of delivery are
more likely to harbor S aureus than are those born to
noncolonized women.

abstract
OBJECTIVE: The study aimed to assess whether maternal colonization
with Staphylococcus aureus during pregnancy or at delivery was
associated with infant staphylococcal colonization.

METHODS: For this prospective cohort study, women were enrolled at
34 to 37 weeks of gestation between 2007 and 2009. Nasal and vaginal
swabs for culture were obtained at enrollment; nasal swabs were
obtained from women and their infants at delivery and 2- and 4-month
postbirth visits. Logistic regression was used to determine whether
maternal colonization affected infant colonization.

RESULTS: Overall, 476 and 471 mother-infant dyads had complete
data for analysis at enrollment and delivery, respectively. Maternal
methicillin-resistant S aureus (MRSA) colonization occurred in 10%
to 17% of mothers, with the highest prevalence at enrollment. Infant
MRSA colonization peaked at 2 months of age, with 20.9% of infants
colonized. Maternal staphylococcal colonization at enrollment increased
the odds of infant staphylococcal colonization at birth (odds ratio; 95%
confidence interval: 4.8; 2.4–9.5), hospital discharge (2.6; 1.3–5.0), at 2
months of life (2.7; 1.6–4.3), and at 4 months of life (2.0; 1.1–3.5).
Similar results were observed for maternal staphylococcal
colonization at delivery. Fifty maternal-infant dyads had concurrent
MRSA colonization: 76% shared isolates of the same pulsed-field
type, and 30% shared USA300 isolates. Only 2 infants developed
staphylococcal disease.

CONCLUSIONS: S aureus colonization (including MRSA) was extremely
common in this cohort of maternal-infant pairs. Infants born to mothers
with staphylococcal colonization were more likely to be colonized, and
early postnatal acquisition appeared to be the primary mechanism.
Pediatrics 2012;129:e1252–e1259

AUTHORS: Natalia Jimenez-Truque, MQC, MSCI,a Sara
Tedeschi, MD,b Elizabeth J. Saye, BS,a Brian D. McKenna,
BS,a Weston Langdon, BS,a Jesse P. Wright, BS,a Andrew
Alsentzer, BS,a Sandra Arnold, MD, MS,c Benjamin R.
Saville, PhD,d Wenli Wang, MS,d Isaac Thomsen, MD,a and C.
Buddy Creech, MD, MPHa

aDivision of Pediatric Infectious Diseases, Vanderbilt University
Medical Center, Nashville, Tennessee; bDepartment of Medicine,
Brigham and Women’s Hospital, Boston, Massachusetts; cDivision
of Infectious Diseases, University of Tennessee Health Science
Center, Memphis, Tennessee; and dDepartment of Biostatistics,
Vanderbilt University School of Medicine, Nashville, Tennessee

KEY WORDS
Staphylococcus aureus, child, colonization, epidemiology,
pregnancy

ABBREVIATIONS
CA-MRSA—community-associated methicillin-resistant Staphylo-
coccus aureus
GBS—group B Streptococcus
GEE—generalized estimating equation
MRSA—methicillin-resistant Staphylococcus aureus
MSSA—methicillin-susceptible Staphylococcus aureus
PCR—polymerase chain reaction
PVL—Panton-Valentine leukocidin
SSTIs—skin and soft-tissue infections
VUMC—Vanderbilt University Medical Center

All authors have contributed appropriately to meet the criteria
to warrant authorship.

www.pediatrics.org/cgi/doi/10.1542/peds.2011-2308

doi:10.1542/peds.2011-2308

Accepted for publication Dec 15, 2011

Address correspondence to Natalia Jimenez-Truque, MQC, MSCI,
Epidemiology Graduate Student, Pediatric Infectious Diseases,
Vanderbilt University Medical Center, 1161 21st Ave South, D-7215
MCN, Nashville, TN 37232. E-mail: natalia.jimenez@vanderbilt.edu

PEDIATRICS (ISSN Numbers: Print, 0031-4005; Online, 1098-4275).

Copyright © 2012 by the American Academy of Pediatrics

FINANCIAL DISCLOSURE: The authors have indicated they have
no financial relationships relevant to this article to disclose.

FUNDING: This work was supported by the Fogarty International
Center at the National Institutes of Health (grant 1 R25
TW007697), the 2007 IDSA/SHEA Young Investigator Award in
MRSA Research (Dr Creech), the Monroe Carell, Jr. Children’s
Hospital Fund, and the National Center for Research Resources
at the National Institutes of Health (grant 1 UL1 RR024975).
Funded by the National Institutes of Health (NIH).

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Methicillin-resistant Staphylococcus au-
reus (MRSA) causes ∼100 000 inva-
sive infections and ∼20 000 deaths
per year in the United States; of these,
∼1000 infections and ∼100 deaths oc-
cur in children ,1 year of age.1 Further,
MRSA causes between 59% and 72%
of all skin and soft-tissue infections
(SSTIs),2,3 and up to 95% of all SSTIs in
children are caused by community-
associated MRSA (CA-MRSA).4 MRSA
now affects previously healthy individ-
uals without known risk factors,5,6 and
CA-MRSA has become the most frequent
clone of S aureus in many communities,
causing disease in neonatal intensive
care units (NICUs)7,8 and even among
healthy full-term babies.9,10

Approximately one-third of the gen-
eral population carries S aureus in
their nares,11 and staphylococcal col-
onization is a known risk factor for
subsequent infection.11 Previous data
suggest that the frequency of MRSA
colonization ranges from 1% to 4% in
infants and mothers,7–9,12–16 though
some areas of the US experience
higher rates of colonization.17–19 While
known risk factors for infant S aureus
colonization include breastfeeding,
number of household members,20,21

low birth weight, early gestational age
at birth, indwelling catheters, and du-
ration of antibiotic or ventilator days,7

it is not clear whether maternal nasal
and anogenital colonization plays a role
in infant colonization. Colonized moth-
ers can transmit MRSA to their
infants,10,12,13 but it remains unclear
whether there is real potential for sig-
nificant vertical maternal-infant trans-
mission of MRSA.

Our objective was to determine the
clinical and molecular epidemiology of
staphylococcal colonization in mothers
and their infants from the third tri-
mester of pregnancy to 4 months after
birth. By obtaining nasal swabs at each
time point, we estimated the frequency
of staphylococcal colonization and

analyzed the molecular characteristics
of these isolates. We also sought to
examine whether maternal MRSA nasal
and/or vaginal colonization is associ-
ated with subsequent colonization or
infection in the infant.

METHODS

Study Population

We conducted a prospective study
of MRSA colonization in a cohort of
maternal-infant pairs between June
2007andMarch2009.Weinvitedwomen
who were in their third trimester of
pregnancy (34–36 weeks of gestation)
and cared for at the Obstetrics Clinic of
Vanderbilt University Medical Center
(VUMC) in Nashville, Tennessee, or the
UT Medical Group Obstetrics Clinic
at the University of Tennessee Health
Science Center in Memphis, Tennessee,
to participate. Women had to be .18
years of age, willing to comply with
study-related procedures (including na-
sal swabs, enrollment of her child when
born, and willingnessto attend follow-up
visits), and capable of providing written
informed consent. The local institutional
review boards of VUMC and University
of Tennessee Health Science Center ap-
proved the study.

Study Procedures

An in-person interview questionnaire
was administered to determine risk
factors for staphylococcal exposure/
carriage, and a moistened nasal swab
was collected from the mother at the
time of enrollment and on the day of
delivery. Additionally, the group B
Streptococcus (GBS) culture collected
from the mother during her routine
prenatal care was sampled to detect
S aureus.

After the infant was born, the nursing
staff of the newborn nursery or NICU
alertedstudypersonnelwithin2hoursof
delivery. Cultures of nares and umbilicus
were obtained with a moistened cotton

swab before triple dye was applied to the
umbilicus. For newborns, cultures were
repeated immediately before discharge.

After discharge, infants and mothers
enrolled at VUMC were asked to return
to the Pediatric Clinical Research Cen-
terfornasalswabculturesamplestobe
taken at 2 and 4 months of age, while
samples from Memphis were collected
only if participants voluntarily returned.
Questionnaires were administered at
each visit to assess risk factors for
staphylococcal exposure and carriage,
history of maternal/infant staphylococ-
cal infection, history of hospitalization
or other medical illnesses/procedures,
and antibiotic use. Medical charts were
reviewed for clinically relevant illnesses
consistent with staphylococcal infec-
tions.Motherswereinstructedtoalert
study personnel if their infants devel-
opedSSTIsoriftheyor theirinfantswere
hospitalizedforany reason. This allowed
for additional cultures to be obtained,
where appropriate.

Cultures and Molecular
Laboratory Testing

All samples collected in this study were
processedatVUMC.Nasalandumbilical
swabs were placed in tryptic soy broth
with 6.5% NaCl and incubated for 24
hours at 37°C as an enrichment step.
Vaginal swabs were first processed at
the VUMC Microbiology Laboratory and
inoculated into Lim Broth (Becton,
Dickinson, and Co, Franklin Lakes, NJ)
for the detection of GBS. After broth
enrichment of all samples, a 10-mL in-
oculum was plated onto mannitol salt
agar plates with and without 4 mg/mL
oxacillin and incubated for 48 hours at
37°C. If yellow growth was observed,
colonies were plated onto tryptic soy
agar with 5% sheep blood and incu-
bated for 24 hours at 37°C. Latex ag-
glutination testing was performed
for the detection of clumping factor
(Staphaurex; Remel, Lenexa, KS), and
the presence of the nuc gene (specific

ARTICLE

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to S aureus) was confirmed by poly-
merase chain reaction (PCR). Isolates
confirmed to be MRSA by PCR detection
of the mecA gene were further char-
acterized by SCCmec typing, by using
the multiplex strategy of Oliveira and
de Lencastre.22 Nontypeable isolates by
the multiplex strategy underwent ccr
and mec class typing as previously
described.23 Detection of the Panton-
Valentine leukocidin (PVL) gene locus
was performed, as described else-
where.24 Genotyping of MRSA isolates
was performed by repetitive element
sequence–based PCR.25 Isolates with
.95% similarity were defined as in-
distinguishable.

Statistical Methods

Wilcoxon rank sum tests and Pearson
x2 tests were used to compare patient
characteristics between the 2 study
centers and between those with and
without infant colonization at birth.
Correlations between patient charac-
teristics were assessed by using
Spearman’s correlation coefficient, and
pairs of variables with a high correla-
tion were noted before proceeding to
modeling. Logistic regression models
with generalized estimating equations
(GEEs) were used to model child colo-
nization as a function of maternal colo-
nization at birth or enrollment and time
since birth (birth, discharge, 2 months,
4 months), adjusting for the following
potential confounders: number of pre-
vious births, gestational age at enroll-
ment, mode of delivery, race, and
admission to the NICU. The model also
included an interaction term between
maternal colonization at birth or en-
rollment and time. Due to potential col-
linearity, separate logistic regression
models were fitted with either maternal
colonization at birth or maternal colo-
nization at enrollment as predictors. A
sensitivity analysis was conducted in
which both GEE models were fitted by
using data from patients enrolled at
VUMC alone.

RESULTS

Overall, 629 mother-infant dyads were
enrolled. Demographic data and
clinical history are displayed in Table 1.
Infants colonized at birth were more
likely to have an African American
mother (75% vs 41%, P , .001) and to
have been born vaginally (86% vs 69%,
P = .018). No other patient character-
istics were associated with infant staph-
ylococcal colonization at birth (data not
shown). No preterm deliveries were en-
countered as we preferentially enrolled
women close to term and having GBS
screening performed. Thus, all infants
were born at or greater than 37 weeks’
gestation. The average time between
enrollment and delivery was 5 weeks,

corresponding to enrollment at 34 to 36
weeks and delivery at term.

Comparison Between the Two
Study Centers

To determine whether demographic
characteristics were similar between
the 2 study centers, we compared pa-
tient characteristics between the 2
sites. Women enrolled in the VUMC co-
hortwereolder(median,26vs23years;
P , .001), had higher median ges-
tational ages at enrollment (median,
36 vs 35 weeks; P , .001), were less
likely to undergo caesarean section
(27% vs 37%, P = .008), and were more
likely to have a history of mastitis or
staphylococcal infections previous to

TABLE 1 Demographic and Clinical Characteristics, by Enrollment Center

Na Vanderbilt
(N = 399)

Memphis
(N = 230)

Total
(N = 629)

P

Gestation, median wk
(interquartile range)

629 36 (36–36) 35 (35–36) 35 (35–36) ,.001b

Maternal race, n (%)

629 ,.001c

African American 132 (33) 203 (88) 335 (53)
Asian 4 (1) 0 (0) 4 (1)
Caucasian 228 (57) 22 (10) 250 (40)
Hispanic 12 (3) 5 (2) 17 (3)
Other 23 (6) 0 (0) 23 (4)

Maternal age, median y
(interquartile range)

620 26 (21–30) 23 (21–27) 24 (21–29) ,.001b

Previous births, median n
(interquartile range)

629 1 (0–2) 1 (0–2) 1 (0–2) .014b

Mode of delivery, n (%) 594 .008c

Cesarean section 101 (27) 79 (37) 180 (30)
Vaginal 279 (73) 135 (63) 414 (70)

Infant admitted to, n (%) 594 .15c

NICU 16 (4) 15 (7) 31 (5)
Nursery 362 (96) 201 (93) 563 (95)

History of mastitis, n (%) 627 .011c

No 383 (96) 228 (100) 611 (97)
Yes 15 (4) 1 (0) 16 (3)

Previous maternal
hospitalizations/
surgeries, n (%)d

629 ,.001c

No 169 (42) 67 (29) 236 (38)
Yes 230 (58) 163 (71) 393 (62)

Previous maternal
staphylococcal
infections, n (%)d

629 .016c

No 376 (94) 226 (98) 602 (96)
Yes 23 (6) 4 (2) 27 (4)

a N is the number of observations (missing values account for numerical differences between groups).
b Wilcoxon rank-sum test.
c Pearson x2.
d Within the past 12 mo before enrollment.

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enrollment (3.8% vs 0.4%, P = .011; 6%
vs 2%, P = .016), respectively (Table 1).

Colonization Prevalence Over Time

The proportions of staphylococcal col-
onizationinmothersandtheirinfantsat
each time point are shown in Fig 1.
Maternal MRSA colonization was high-
est at enrollment, with 225 (38.6%)
women colonized with S aureus and 97
(16.6%) colonized with MRSA (75 in the
nares alone, 15 with anogenital coloni-
zation alone, and 7 with both). At de-
livery, 136 and 53 women were colonized
with S aureus and MRSA, respectively.
At 2 and 4 months, 110 and 72 mothers
had S aureus, and 41 and 39 had MRSA,
respectively.

At birth, 44 (9.3%) infants were colo-
nized with S aureus and 12 (2.5%) with
MRSA; nasal and umbilical swabs were
cultured together. These frequencies
were 41 and 24 at discharge, respec-
tively. Infant staphylococcal coloniza-
tion peaked at 2 months of age, with
121 (38.9%) infants colonized with S
aureus and 65 (20.9%) with MRSA, but
decreased again by 4 months, to 65 and
31, respectively.

Association Between GBS and
S aureus Colonization

Of 616 women with GBS culture results,
171 (27.8%) were colonized with GBS. Of
these, 69 (40.3%) demonstrated vaginal
S aureus colonization (positive corre-
lation, Spearman’s correlation P = .026).
The majority of women without GBS
colonization also lacked S aureus vagi-
nal colonization (326 of 390 [83.6%]).
Thus, there was no inhibitory relation-
ship observed between GBS and vaginal
S aureus colonization at enrollment.
Among those colonized with GBS, the
proportions of women with nasal and
vaginal S aureus were not significantly
different (33.3% vs 25.6%, respectively;
P = .15), and there was a positive cor-
relation between vaginal and nasal col-
onization with S aureus at enrollment
(Spearman’s correlation P = .024).

Incidence of Infection

Only 2 staphylococcal infections were
observed during the study (0.42% of
infants). One infant developed a skin
abscess, while another infant developed
purulent conjunctivitis. Both infections
occurred near the 2-month visit, and
both were caused by USA300, SCCmec
IV CA-MRSA isolates; only 1 of these iso-
lates contained PVL.

Association Between Maternal
Colonization and Infant
Colonization

To determine whether maternal coloni-
zation correlated with future infant col-
onization, we fit 2 GEElogistic regression
models. The first evaluated maternal
colonizationatenrollment(34–37weeks’
gestation) as a predictor, while the
second evaluated maternal coloniza-
tion at delivery. The models included
476 and 471 maternal-infant dyads with
complete data, respectively (Table 2),
and both analyses demonstrated that
maternal staphylococcal colonization
significantly increased the odds of
infant staphylococcal colonization at
all time points, as shown in Table 2.

There was lack of evidence for associ-
ations between maternal character-
istics and infant colonization at any of
the time points. When performing the
same analyses with only the data from
the center with more complete follow-
up, results did not change materially
(data not shown). It should also be
noted that the odds ratios for infant
colonization are slightly different for
maternal colonization at enrollment

FIGURE 1
Proportionofcolonizationover time.PeakageofcolonizationwithSaureus(MSSAandMRSA),aswellas
MRSAspecifically,wasat2monthsofage,thoughsomeinfantswerecolonizedwithin2hoursofdelivery.
Maternal colonization was stable over time, although maternal swabs were not obtained on discharge
from the hospital (note nonconnecting lines).

TABLE 2 Odds of Infant Colonization With S
aureus (Both MSSA and MRSA at
Various Time Points), Based on
Maternal Colonization at
Enrollment or Delivery, Based on
GEE Logistic Regression Models

OR 95% CI P Value

Maternal
colonization at
enrollment (n = 476)
Birth 4.79 2.41–9.53 ,.001
Discharge 2.59 1.34–5.00 .005
2 mo 2.65 1.64–4.29 ,.001
4 mo 1.95 1.09–3.50 .025

Maternal
colonization at
delivery (n = 471)
Birth 3.77 2.00–7.11 ,.001
Discharge 2.76 1.43–5.33 .002
2 mo 3.09 1.80–5.32 ,.001
4 mo 3.53 1.87–6.68 ,.001

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versus maternal colonization at de-
livery. This may be due to transient
maternal carriage, which could differ
in the few weeks between enrollment
and delivery, or to different numbers of
available pairs for each analysis, which
would affect the precision of the odds
ratio estimate.

Giventhecorrelationbetweenmaternal
colonization and infant colonization, we
evaluated the characteristics of all
maternal-infant dyads with concurrent
colonization (Table 3). Twenty maternal-
infant pairs were identified in which
there was maternal colonization dur-
ing pregnancy (enrollment) and infant
colonization within 2 hours of birth.
Eight of these pairs demonstrated
maternal nasal S aureus colonization
at enrollment (of which, 3 were MRSA),
while 12 mothers exhibited vaginal
S aureus colonization at enrollment
(of which, 3 were MRSA); only 2 of the
latter had indistinguishable isolates,
suggesting vertical transmission. Next,
we identified additional maternal-infant

pairs in which there was maternal col-
onization at the time of delivery and in-
fant colonization within 2 hours of birth
or at discharge. Of women colonized
with S aureus at delivery, 20 (4.2%) had
infantswho were alsocolonizedatbirth,
and 14 (3.0%) had infants colonized at
discharge. MRSAwas present in 7 (35%)
of 20 and 8 (57%) of 14, respectively.
Concurrent colonization peaked at 2
months of age, with 51 maternal-infant
dyads (16.4%, MRSA present in 19 [37%]
of 51); however, concurrent colonization
decreased by 4 months of age, with
23 dyads exhibiting colonization (9.3%,
MRSA present in 10 [43%] of 23).

Molecular Characteristics of MRSA
Isolates

Overall, 369 MRSA isolates were re-
coveredfromthe cohort.SCCmec IVwas
present in 74.8% of isolates, consistent
with the largely community-based na-
ture of the cohort. SCCmec types II, III, I,
and V represented 8.1%, 7.3%, 5.4%, and
2.4% of the MRSA isolates, respectively.

Based on repetitive-element sequence-
based PCR, all isolates matched 1 of 11
distinct USA pulse types recognized. The
most common type was USA300, repre-
senting 34.2% of all MRSA isolates;
USA700 (14.4%) was also frequently
identified. Of all isolates, 111 (30%)
contained genes encoding PVL, an exo-
toxin found predominantly in CA-MRSA
strains within the USA300 pulse type;
82% of these were USA300. However,
27% of the USA300 isolates did not carry
PVL genes. Variants of PFGE pulse types
were not formally assessed, though
variants within each pulse-type were
appreciated based on rep-PCR patterns.

Of the 50 maternal-infant dyads with
concurrentMRSAcolonization,38(76%)
shared isolates of the same USA type
(Table 3); 28 pairs (56%) carried indis-
tinguishable isolates, while 15 (30%)
shared USA300 isolates. Of the 78 dyads
with concurrent MSSA colonization, 43
(55.1%) carried isolates of the same
USA type (Table 3); 27 (34.6%) of these
pairs had indistinguishable isolates,

TABLE 3 Concurrent Colonization With S aureus (MSSA and MRSA) in Maternal-Infant Pairs

Total Concurrent S. aureus (n = 128),
No. (%)

Concurrent MSSA (n = 78),
No. (%)

Concurrent MRSA (n = 50),
No. (%)

Concurrent
Colonization

Same USA
Typea

.95%
Similaritya

Concurrent
Colonization
Same USA
Typea
.95%
Similaritya
Concurrent
Colonization
Same USA
Typea
.95%
Similaritya

Enrollment
nasal (n = 473)b

8 (1.7) 4 (50.0) 2 (25.0) 5 (1.1) 3 (60.0)e 1 (20.0) 3 (0.6) 1 (33.3)k 1 (33.3)

Enrollment
vaginal (n = 473)c

12 (2.5) 5 (41.7) 2 (16.7) 9 (1.9) 3 (33.3)f 1 (11.1) 3 (0.6) 2 (66.7)l 1 (33.3)

Delivery (n = 473) 20 (4.2) 10 (50.0) 8 (40.0) 13 (2.7) 5 (38.5)g 4 (30.8) 7 (1.5) 4 (57.1)m 4 (57.1)
Discharge (n = 462)d 14 (3.0) 11 (78.6) 7 (50.0) 6 (1.3) 4 (66.7)h 3 (50.0) 8 (1.7) 7 (87.5)n 4 (50.0)
2 mo (n = 311) 51 (16.4) 37 (72.5) 22 (43.1) 32 (10.3) 21 (65.6)i 10 (31.2) 19 (6.1) 16 (84.2)o 12 (63.2)
4 mo (n = 246) 23 (9.3) 15 (65.2) 14 (60.9) 13 (5.3) 7 (53.8)j 8 (61.5) 10 (4.1) 8 (80.0)p 6 (60.0)
Total (N = 2438) 128 (5.2) 82 (64.1) 55 (43.0) 78 (3.2) 43 (55.1) 27 (34.6) 50 (2.0) 38 (76.0) 28 (56.0)
a Percentages in these columns refer to the numbers in the respective “Concurrent Colonization” columns.
b Pairs of maternal nasal colonization at enrollment and infant colonization at birth.
c Pairs of maternal vaginal colonization at enrollment and infant colonization at birth.
d Pairs of maternal colonization at delivery and infant colonization at discharge.
e USA400 (3).
f USA300 (2), USA700 (1).
g USA200 (1), USA400 (2), USA600 (1), USA700 (1).
h USA200 (2), USA400 (1), USA600 (1).
i USA200 (6), USA300 (3), USA400 (6), USA500 (1), USA600 (2), USA800 (1), USA900 (1), USA1000 (1).
j USA200 (3), USA400 (1), USA600 (1), USA700 (2).
k USA300 (1).
l USA100 (1), USA300 (1).
m USA100 (1), USA300 (3).
n USA200 (2), USA300 (2), USA400 (1), USA500 (1), USA800 (1).
o USA200 (1), USA300 (4), USA500 (5), USA600 (4), USA700 (1), USA800 (1).
p USA300 (4), USA400 (2), USA700 (2).

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and 5 (6.4%) were USA300. The propor-
tion of concurrently colonized maternal-
infant pairs did not differ significantly
between the 2 centers (P = .1447; data
not shown).

DISCUSSION

In this prospective study of women and
their newborn infants, we found that
infants born to women colonized with
S aureus during pregnancy or at the
time of delivery were more likely to be
colonized with Saureus in the immediate
newborn period. Though vertical trans-
mission occurred, based on concurrent
maternal vaginal colonization and early
infant colonization, horizontal trans-
mission in early neonatal life appeared
to be more common. MRSA colonization
was detected frequently in mothers,
ranging from 10% to 16% during preg-
nancy and the early postpartum period.
For infants, MRSA carriage peaked at 2
months of age (20%), and more than
one-third of all MRSA isolates belonged
to the current epidemic clone USA300.

The prevalence of colonization with
S aureus, and MRSA in particular, was
higher in our cohort than has been
shown in previous studies.12,14,16,26,27

Others have reported that ∼2% to 5% of
mothers12,14,16,26,27 and∼1%ofinfants26,27
are colonized with MRSA. In our cohort,
nearly 10% of mothers and 2.5% of
infants were colonized with MRSA at the
time of delivery (Fig 1). Previous studies
from our group have found similar col-
onization rates in mothers and chil-
dren,17 suggesting that colonization in
our target population may be higher
than in other populations or that the
method of detection (including broth
enrichment prior to primary plating28)
may increase yield.

This study represents the largest
prospective study of maternal-infant
staphylococcal colonization since the
emergenceofUSA300CA-MRSA.Peacock
et al, studying 100 mother-infant pairs
during the 6 months after delivery,

demonstrated that one of the major
determinants of infant staphylococcal
carriage is maternal colonization20; at
any time point, the odds of infant col-
onization were nearly 4 times greater
when mothers were also colonized than
when mothers were not colonized.
Studies from Lebon et al demonstrate
similar results,29 and extend these
findings to older children as well, by
using the powerful Generation R Study
cohort in the Netherlands to evaluate
the relationship between maternal and
child colonization with S aureus.30 At 24
months of age, children were twice as
likely to be colonized with S aureus
when the mother was also colonized.
Additionally, we found that 43% of con-
currently colonized dyads had indis-
tinguishable isolates. A previous study
by Huang et al (2009) found that at least
half of all S aureus isolates in their co-
hort were genetically indistinguishable,
though the number of concordant
maternal-infant pairs was very small.26

Taken together, these data demon-
strate the important role of horizontal
transmission in pediatric staphylococ-
cal colonization.

This study also begins to answer
a fundamental question of maternal-
infant health, Does vaginal coloni-
zation with S aureus during the third
trimester of pregnancy portend the
same risk of neonatal disease as other
pathogens (eg, group B Streptococ-
cus)? Our study suggests that vertical
transmission occurs, as infants born to
vaginally colonized mothers were 5
times more likely to be colonized within
2 hours of birth (data not shown); only
in a minority of cases, however, were
these strains indistinguishable. This
vertical transmission, occurring in only
2 neonates, is overshadowed by the
higher frequency of early horizontal
transmission in infants born to mothers
without vaginal colonization. The lack of
inhibition of vaginal S aureus growth by
GBS, as seen in other studies,13,15,16,18

did not explain the observed low rate
of vertical transmission of S aureus.
This implies that while hospital-based
screening and interventions may be
useful during staphylococcal outbreaks,8

it is horizontal spread within family
members, especially mother to child,
that may be a more appropriate target
of intervention.

Based on SCCmec typing, CA-MRSA
isolates were most prevalent (74.8%).
Given the prevalence of CA-MRSA in the
United States, this is not surprising;
however, only 30% of these strains
carried PVL, a bicomponent exotoxin
found predominantly in USA300 CA-
MRSA. This unexpected finding illus-
trates the heterogeneous nature of
staphylococci, since PVL was at one
point considered pathognomonic of
CA-MRSA. The identification of SCCmec
IV, PVL-negative MRSA is not unique to
this study; rather, previous studies
from our group and others17,26,31–33

have found similar strain types in the
community. This raises important ques-
tions regarding the link between colo-
nization and infection, generating the
hypothesis that only particular strain
types, containing a specific combination
of virulence determinants, are best
suited to cause disease in otherwise
healthy individuals. Whether this is due
to the independent effects of these
virulence determinants (eg, effect of
specific exotoxins on host cells), the
overexpression of these virulence fac-
tors, or a lack of host immunity to spe-
cific strain types is completely unclear.
The latter hypothesis is particularly in-
triguing for this cohort given the likely
presence of maternally derived staphy-
lococcal antibodies, which could poten-
tially abrogate the risk for infection in
this otherwise vulnerable population.
Future studies should focus on the mo-
lecular characteristics of colonization
strains and the prevalence of staphylo-
coccal antibodies in newborns to fur-
ther define this relationship.

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There are a few limitations that should
be discussed. Postdischarge follow-up
occurred at only 1 center, and loss to
follow-up occurred. However, this loss
to follow-up was nondifferential, mean-
ingitoccurredsimilarlyincolonizedand
noncolonized dyads, and thus is unlikely
tohavesubstantiallyaffectedtheresults.
Last, only nasal swabs were obtained
from mothers and their infants, except
at enrollment and delivery, respectively.
Ourgroupandothershavedemonstrated
thatstaphylococcalcarriage,particularly
USA300,34,35 may occur preferentially at
extranasal sites. Therefore, our data may
actually be an underrepresentation of
MRSA carriage in infants.

CONCLUSIONS

In this large, prospective cohort study,
we identified horizontal maternal-infant
transmissionastheprimarymechanism
for early infant staphylococcal coloniza-
tion. Vertical transmission occurs, but
the efficiency of transmission appeared
to be low given the relatively high fre-
quencyofcarriageinmotherscompared
withnewborns.Whileinfantcolonization
with MRSA was common, the frequency
of USA300, SCCmec IV, PVL-positive MRSA
colonization was less frequent. This
has important implications in disease
pathogenesis given that the rates of
infant staphylococcal disease in our

cohort (despite high carriage rates)
were extremely low. Taken together, it
would appear that prevention meas-
ures focused on controlling the spread
of specific strain types of MRSA (rather
than all MRSA) could be a more effective
strategy when outbreaks of staphylo-
coccal disease in newborns occur. Fu-
ture work should seek to elucidate the
potential role of maternally derived
antibodies in modifying staphylococcal
carriage/infection risk in infants.

ACKNOWLEDGMENTS
The authors are particularly grateful to
the nurses and clinical research staff of
theVanderbiltVaccineResearchProgram.

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Natalia Jimenez-Truque, Sara Tedeschi, Elizabeth J. Saye, Brian D. McKenna,
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6.

1

Viruses in Ecosystems

A virus is a noncellular particle that must infect a host cell, where it reproduces.

It typically subverts the cell’s machinery and directs it to produce viral particles.

The virus particle, or virion, consists of a single nucleic acid (DNA or RNA) contained within a protective protein capsid.

In more complex viruses, the protective protein may be called a head coat.

‹#›

1

Viruses Infect Cells – 1

Different types of viruses infect different specific host cells.

Usually, the hosts are limited to a particular host range of closely related strains or species.

Bacteriophage = Virus that infects bacteria

It forms a plaque of lysed cells on a lawn of bacteria.

An example of a human virus is the measles virus.

An example of a plant virus is the tobacco mosaic virus (TMV).

‹#›

2

Viruses Infect Cells – 2

‹#›
3
FIGURE 6.2 ■ Virus infections and disease. A. Bacteriophage T2 particles pack in a regular array within an E. coli cell (TEM). B. Bacteriophage infection forms plaques of lysed cells on a lawn of bacteria. C. Measles virions bud out of human cells in tissue culture (TEM). D. Child infected with measles shows a rash of red spots. E. Tobacco leaf section is packed with tobacco mosaic virus particles. F. Tomato leaf infected by tobacco mosaic virus shows mottled appearance.

Viruses Infect Cells – 3
But what happens after a virus infects a cell?
A remarkable view of viral replication emerges from fluorescence microscopy.
For an RNA virus, such as hepatitis C virus, virions are assembled within “virus factories,” virus-induced cell compartments called a replication complex.
The complexes move around within the cell.

‹#›
4
FIGURE 6.3 ■ Replication complexes of hepatitis C virus. Membranous replication complexes surround the nucleus of an infected liver cell in tissue culture. The virus expresses replication proteins fused to a fluorescent protein (GFP), shown pink.

Integrated Viral Genomes
Some viruses do more than replicate within a cell; they integrate their genomes into that of the host.
In effect, such viruses become a part of the host organism.
A virus that integrates its genome into the DNA of a bacterial genome is called a prophage.
Within a human cell, an integrated viral genome is called a provirus.
A permanently integrated provirus transmitted via the germ line is called an endogenous virus.

‹#›
5

Dynamic Nature of Viruses – 1
We now know that a virus may interconvert among three very different forms:
Virion, or virus particle – An inert particle that does not carry out any metabolism or energy conversion
Intracellular replication complex – Within a host cell, the viral gene products direct the cell’s enzymes to assemble progeny virions at “virus factories” called replication complexes.
Viral genome integrated within host DNA – This may be a permanent condition.

‹#›
6

Dynamic Nature of Viruses – 2

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FIGURE 6.4 ■ Virus as a subcellular organism. The virion, or virus particle, consists of a nucleic acid genome contained by a protein capsid. A virion may infect a host cell and cause the cell’s enzymes to synthesize progeny virions. Alternatively, infection may lead to integration of the viral genome within the host cell genome. Integration may last indefinitely, or else may lead to production of virions.

Viral Ecology – 1
While viruses are the tiniest of biological entities, they play starring roles in ecosystems.
Acute viruses (which rapidly kill their hosts) act as predators or parasites to limit host population density.
They also recycle nutrients from their host bodies.
Virus-associated mortality may increase the genetic diversity of host species.
Persistent viruses remain in hosts, where they may evolve traits that confer positive benefits in a virus-host mutualism.

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Viral Ecology – 2

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FIGURE 6.5 ■ The relationship of polydnaviruses, wasps, and caterpillars. Parasitoid wasps lay their eggs inside a living insect caterpillar. When a female wasp deposits her eggs inside the caterpillar, she also deposits her symbiogenic polydnavirus virions. The virions express wasp genes in the caterpillar, where they prevent the encapsulation process that would otherwise wall off the wasp egg and kill it.

Viral Disease
Each species of virus infects a particular group of host species, known as its host range.
Some viruses can infect only a single species; for example, HIV infects only humans.
By contrast, West Nile virus, transmitted by mosquitoes, infects many species of birds and mammals.
Chronic viral infections are more common than acute disease.
In contrast to our vast arsenal of antibiotics (effective against bacteria), the number of antiviral drugs remains small.

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6.2 Virus Structure
The structure of a virion keeps the viral genome intact, and it enables infection of the appropriate host cell.
The capsid packages the viral genome and delivers it into the host cell.
Different viruses make different capsid forms.
These can be divided into symmetrical and asymmetrical types.

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Symmetrical Virions – 1
Icosahedral viruses
Are polyhedral with 20 identical triangular faces
Have a structure that exhibits rotational symmetry

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FIGURE 6.7 ■ Herpes: icosahedral capsid symmetry. A. Icosahedral capsid of herpes simplex 1 (HSV-1), with envelope removed. Imaging of the capsid structure is based on computational analysis of cryo-TEM. Images of 146 virus particles were combined digitally to obtain this model of the capsid at 2 nm resolution. B. Icosahedral symmetry includes fivefold, threefold, and twofold axes of rotation. C. The icosahedral capsid contains spooled DNA. Source: A. C. Z. Hong Zhou et al. 1999. J. Virol. 73:3210.

Symmetrical Virions – 2
In some icosahedral viruses, the capsid is enclosed in an envelope, formed from the cell membrane.
The envelope contains glycoprotein spikes, which are encoded by the virus.
Between the envelope and capsid, tegument proteins may be found.

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FIGURE 6.8 ■ Envelope and tegument surround the herpes capsid. A. Section showing envelope and tegument proteins surrounding capsid (cryo-EM). B. Cutaway reconstruction of the herpes virion (cryo-EM tomography).

Symmetrical Virions – 3
Filamentous viruses
The capsid consists of a long tube of protein, with the genome coiled inside.
Vary in length, depending on genome size
Include bacteriophages as well as animal viruses

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FIGURE 6.9 ■ Filamentous viruses. A. Ebola virus filaments (SEM). B. The filamentous bacteriophage M13 has a relatively simple helical capsid that surrounds the genome coiled within (TEM).

Symmetrical Virions – 4
Filamentous viruses show helical symmetry.
The pattern of capsid monomers forms a helical tube around the genome, which usually winds helically within the tube.

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FIGURE 6.10 ■ Tobacco mosaic virus: helical symmetry. A. The helical filament of tobacco mosaic virus (TMV) contains a single-stranded RNA genome coiled inside. B. Components of the TMV virion.

Tailed Viruses
These have complex multipart structures.
T4 bacteriophages
Have an icosahedral “head” and helical “neck”

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FIGURE 6.11 ■ Bacteriophage T4 capsid. A. Phage T4 particle with protein capsid containing packaged double-stranded DNA genome. The capsid has a sheath with tail fibers that facilitate attachment to the surface of the host cell. After attachment, the sheath contracts and the core penetrates the cell surface, injecting the phage genome. B. E. coli infected by phage T4 (colorized blue, TEM).

Asymmetrical Virions – 1
Influenza viruses are RNA viruses that lack capsid symmetry.
Instead, the RNA segments are coated with nucleocapsid proteins.
Poxviruses
Their genome is surrounded by several layers.
A core envelope studded with spike proteins
An outer membrane
Also contain a large number of accessory proteins
These are needed early in viral infection.

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Asymmetrical Virions – 2
Large asymmetrical viruses contain so many enzymes that they appear to have evolved from degenerate cells.

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FIGURE 6.12 ■ Vaccinia poxvirus. A. Vaccinia virion observed in aqueous medium by atomic force microscopy (AFM). B. A pox virion includes an outer membrane and a core envelope membrane containing envelope proteins enclosing the double-stranded DNA genome and accessory proteins. The DNA is stabilized by a hairpin loop at each end.

Viroids
Viroids are RNA molecules that infect plants.
They have no protein capsid.
They are replicated by host RNA polymerase.
Some have catalytic ability.

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FIGURE 6.13 ■ Viroids: infective RNA. Potato spindle tuber viroid consists of a circular single stranded RNA (ssRNA) that hybridizes internally.

Prions
Prions are proteins that infect animals.
They have no nucleic acid component.
They have an abnormal structure that alters the conformation of other normal proteins.

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FIGURE 6.14 ■ Prion disease. A. The normal conformation of a prion, compared to the abnormal conformation. The abnormal form “recruits” normally folded proteins and changes their conformation into the abnormal form. (PDB code: 1AG2) B. Section of a human brain showing “spongiform” holes typical of Creutzfeldt-Jakob disease.

6.3 Viral Genomes and Classification
Viral genomes can be:
DNA or RNA
Single- or double-stranded (ss or ds)
Linear or circular
The form of the genome has key consequences for the mode of infection, and for the course of a viral disease.
Viral genomes are used as the basis of virus classification.

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Viral Genomes: Small
Small viruses commonly have a small genome, encoding under ten genes.
The genes may actually overlap in sequence.
Many small viral genomes consist of RNA.

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FIGURE 6.15 ■ Simple viral genomes. A. Cauliflower mosaic virus has a circular genome of double stranded DNA, whose strands are interrupted by nicks. The genome encodes seven overlapping genes. B. Avian leukosis virus, a single-stranded RNA retrovirus resembling eukaryotic mRNA. Three genes (gag, pol, and env) encode polypeptides that are eventually cleaved to form a total of nine functional products. LTR = long terminal repeat.

Viral Genomes: Large – 1
The “giant viruses” have genomes of double-stranded DNA comprising 500–2,500 genes.
The mimivirus, which infects amoebas, is as large as some bacteria.
It can actually become infected by smaller viruses called virophages.

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FIGURE 6.16 ■ Giant virus infecting an ameba. A. Mimivirus is larger than some bacteria (TEM). B. Sputnik virophage infects Mamavirus, a relative of Mimivirus (TEM).

Viral Genomes: Large – 2
A surprising source of giant viruses is the frozen environments of the Arctic and Antarctic regions.
The Siberian tundra reveals even more remarkable viruses.
Pithovirus
Mollivirus sibericum
Contains parts of a ribosome

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FIGURE 6.17 ■ Giant virus from Siberia. A. The Siberian tundra is melting. B. Pithovirus, a virus as large as E. coli, was isolated from tundra frozen for 30,000 years (TEM).

Viral Genomes: Large – 3
Giant viruses have genomes that specify so many enzymes with housekeeping cell functions.
Such large cell-like genomes suggest the likelihood that a virus evolved from a parasitic cell.

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FIGURE 6.18 ■ Genome of Mimivirus. The genome of this giant virus specifies numerous enzymes with cell functions.
Source: Didier Raoult, et al. Figure from “The 1.2-Megabase Genome Sequence of Mimivirus” Science, 19 Nov 2004: Vol. 306, Issue 5700, pp. 1344-1350. Copyright © 2004, The American Association for the Advancement of Science. Reprinted with permission from AAAS.

The International Committee on Taxonomy of Viruses
The International Committee on Taxonomy of Viruses (ICTV) has devised a classification system, based on several criteria:
Genome composition
Capsid symmetry
Envelope
Size of the virion
Host range

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The Baltimore Virus Classification – 1
In 1971, David Baltimore proposed that the main distinctions among classes of viruses be:
The genome composition (RNA or DNA)
The route used to express messenger RNA (mRNA)
Baltimore would go on to share the 1975 Nobel Prize in Physiology or Medicine for his work
on retroviruses.

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FIGURE 6.19 ■ Baltimore classification of viral genomes. B. David Baltimore (left), with a graduate student at the California Institute of Technology. Baltimore won the 1975 Nobel Prize in Physiology or Medicine for his work on retroviruses; co-winners were Renato Dulbecco and Howard Temin.

The Baltimore Virus Classification – 2
So far, the genome composition and mechanisms of replication and mRNA expression define seven fundamental groups of viral species:
Group I: Double-stranded DNA viruses
Group II: Single-stranded DNA viruses
Group III: Double-stranded RNA viruses
Group IV: (+) single-stranded RNA viruses
Group V: (–) single-stranded RNA viruses
Group VI: RNA retroviruses
Group VII: DNA pararetroviruses

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The Baltimore Virus Classification – 3

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FIGURE 6.19 ■ Baltimore classification of viral genomes. A. Seven categories of viral genome composition and replication mechanism.