Previous Article | Next Article 
Infection and Immunity, April 2003, p. 2199-2207, Vol. 71, No. 4
0019-9567/03/$08.00+0 DOI: 10.1128/IAI.71.4.2199-2207.2003
Copyright © 2003, American Society for Microbiology. All Rights Reserved.
Group A Streptococcus Gene Expression in Humans and Cynomolgus Macaques with Acute Pharyngitis
Kimmo Virtaneva,1 Morag R. Graham,1 Stephen F. Porcella,1 Nancy P. Hoe,1 Hua Su,1 Edward A. Graviss,2 Tracie J. Gardner,2 James E. Allison,3 William J. Lemon,4 John R. Bailey,5 Michael J. Parnell,5 and James M. Musser1*
Laboratory of Human Bacterial Pathogenesis,1
Veterinary Branch, Rocky Mountain Laboratories, National Institute of AllergyInfectious Diseases, National Institutes of Health, Hamilton, Montana 59840,5
Department of Pathology, Baylor College of Medicine, Houston, Texas 77030,2
Pediatric Medical Group, Houston, Texas 77098,3
Division of Human Cancer Genetics, Ohio State University Comprehensive Cancer Center, Columbus, Ohio 432104
Received 14 October 2002/
Returned for modification 10 December 2002/
Accepted 9 January 2003

ABSTRACT
The molecular mechanisms used by group A
Streptococcus (GAS)
to survive on the host mucosal surface and cause acute pharyngitis
are poorly understood. To provide new information about GAS
host-pathogen interactions, we used real-time reverse transcription-PCR
(RT-PCR) to analyze transcripts of 17 GAS genes in throat swab
specimens taken from 18 pediatric patients with pharyngitis.
The expression of known and putative virulence genes and regulatory
genes (including genes in seven two-component regulatory systems)
was studied. Several known and previously uncharacterized GAS
virulence gene regulators were highly expressed compared to
the constitutively expressed control gene
proS. To examine in
vivo gene transcription in a controlled setting, three cynomolgus
macaques were infected with strain MGAS5005, an organism that
is genetically representative of most serotype M1 strains recovered
from pharyngitis and invasive disease episodes in North America
and Western Europe. These three animals developed clinical signs
and symptoms of GAS pharyngitis and seroconverted to several
GAS extracellular proteins. Real-time RT-PCR analysis of throat
swab material collected at intervals throughout a 12-day infection
protocol indicated that expression profiles of a subset of GAS
genes accurately reflected the profiles observed in the human
pediatric patients. The results of our study demonstrate that
analysis of in vivo GAS gene expression is feasible in throat
swab specimens obtained from infected human and nonhuman primates.
In addition, we conclude that the cynomolgus macaque is a useful
nonhuman primate model for the study of molecular events contributing
to acute pharyngitis caused by GAS.

INTRODUCTION
Group A
Streptococcus (GAS) is the most common cause of human
acute bacterial pharyngitis (
2,
39). Approximately 15 million
cases of streptococcal pharyngitis occur annually in the United
States, representing 15 to 30% of all childhood cases of acute
pharyngitis and 5 to 10% of adult cases (
2). The annual direct
health care costs associated with pharyngitis are approximately
2 billion dollars in the United States (
7). To colonize and
cause acute pharyngitis in a host, GAS must adapt to nutrient
conditions existing in the upper respiratory tract and respond
to innate and acquired host defense mechanisms. Many extracellular
products made by GAS have been implicated in attachment, colonization,
and the persistence of infection in the upper respiratory tract,
including adhesins and antiphagocytic molecules such as M protein,
hyaluronic acid capsule, fibronectin-binding proteins, lipoteichoic
acid, streptococcal Mac protein, and streptococcal inhibitor
of complement (
6,
20,
27). However, many of these molecules
have been studied mainly in the context of in vitro experiments
or in mouse models that are unlikely to recapitulate many aspects
of GAS-human molecular interactions. In addition, very little
is known about the in vivo gene transcription in GAS and other
microbial pathogens. Much of the available information derives
from an indirect assessment of gene expression inferred from
immunologic responses to cell surface components.
In vivo gene expression studies have been limited by technical problems associated with inability to obtain sufficient quantity of material from infection sites to yield interpretable results. However, we recently reported successful in vivo GAS gene transcript analysis after subcutaneous infection of mice (16), leading us to hypothesize that methods could be developed for analyzing GAS mRNA gene expression directly from human clinical material. We report here that GAS gene expression can be monitored in throat swab specimens obtained during acute pharyngitis in humans and experimentally infected nonhuman primates. Our data document the in vivo expression of (i) genes that are part of several two-component systems, (ii) other regulatory genes, and (iii) genes encoding proven and putative virulence factors.

MATERIALS AND METHODS
Bacterial strains and human clinical specimens.
Throat swab specimens from the posterior pharynx were collected
from 18 pediatric patients presenting with signs and symptoms
consistent with acute pharyngitis at a clinic in Houston, Tex.
The swabs were immediately cultured to confirm GAS pharyngitis
and frozen on dry ice. The GAS strains and throat swabs were
shipped on dry ice by commercial courier to Rocky Mountain Laboratories,
Hamilton, Mont. The
emm type of each GAS strain was determined
by methods described previously (
35). The 18 strains included
emm2 (
n = 1 strain),
emm4 (
n = 2 strains),
emm6 (
n = 2),
emm12 (
n = 3),
emm28 (
n = 2),
emm75 (
n = 3),
emm77 (
n = 2), and
emm89 (
n = 3). The study protocol was approved by the Human Subjects
Institutional Review Board at Baylor College of Medicine and
Affiliated Hospitals. Written informed consent was obtained
from all human subjects.
Strain MGAS5005 (serotype M1) was used for the nonhuman primate infection studies. This organism is genetically representative of serotype M1 isolates obtained from patients with pharyngitis and invasive infections in the United States, Canada, and western Europe (22). It has been characterized extensively genetically and used in mouse models of infections and in vitro studies (16, 20, 22, 27, 29, 42, 47).
Nonhuman primates and experimental inoculation.
The study protocol was approved by the Animal Care and Use Committee, Rocky Mountain Laboratories. Three cynomolgus macaques were used, including a juvenile female (15 months, 2.2 kg), an adult female (6 years, 8 months; 3.3 kg), and an adult male (9 years, 6 months; 7.1 kg). Two throat swabs and one venous blood specimen were collected from each animal on days 0, 2, 4, 7, 9, and 11 of the study. Day 0 samples were obtained immediately before inoculation with GAS. One swab was used to determine the level of GAS CFU by colony count measurement after overnight growth on blood agar plates, and a second swab was used to extract GAS RNA. Bacterial colonies with a morphology consistent with GAS were verified as such by sequencing of the emm gene. Plasma was separated from whole blood by centrifugation at 200 x g for 10 min.
Preinoculation throat swab specimens were collected by swabbing the tonsils vigorously with a sterile cotton applicator and culturing overnight on sheep blood agar plates. None of these specimens grew GAS. Strain MGAS5005 (serotype M1) used for experimental inoculation was cultured overnight on sheep blood agar plates at 37°C in 5% CO2, seeded into 11-ml of prewarmed Todd-Hewitt broth supplemented with 0.2% yeast extract (THY), and grown overnight at 37°C in 5% CO2. The overnight growth was subcultured to prewarmed THY broth and incubated for 5 h to late exponential phase (i.e., an optical density at 600 nm of 0.5). The culture was centrifuged, and the bacteria were suspended in pyrogen-free sterile phosphate-buffered saline (PBS) to a concentration of 107 CFU/ml. The viable bacterial cell count was verified by plating on sheep blood agar. Each monkey was anesthetized with ketamine and inoculated by dribbling 1 ml of the bacterial suspension slowly into the nares. GAS colony counts were obtained by culturing throat swabs taken on days 0, 2, 4, 7, 9, and 11. The swabs were immersed in 300 µl of sterile PBS, diluted serially in sterile PBS, plated onto sheep blood agar, and cultured overnight at 37°C in 5% CO2.
Clinical observations of nonhuman primates inoculated with GAS.
To investigate the cynomolgus macaque as a model of acute pharyngitis, clinical observations were made by one attending veterinarian. Pharyngeal erythema, tonsil size, presence of cervical lymphadenopathy, skin condition, weight, and eating behavior were evaluated. A grading scheme was used to estimate pharyngitis severity and tonsil size. Pharyngitis was scored as follows: mild erythema with hyperemic blood vessels (+1), more intense erythema and palatal petechiae (+2), and intense erythema with palatal petechiae and exudative tonsillitis (+3). Feinstein and Levitt (9) have established criteria for scoring tonsil enlargement during human GAS pharyngitis (0 to +4). The same criteria were used except cynomolgus macaque tonsils were scored from +1 to +4 since healthy macaque tonsils resemble slightly enlarged tonsils (+1) in humans.
Extraction of GAS RNA from throat swabs.
Total RNA was extracted from throat swabs with the FastPrep FP 120 kit (Qbiogene, Carlsbad, Calif.) by immersing the swab tips directly into the FastPrep Blue tubes containing 300 µl of 5 mM ammonium aurintricarboxylate, 500 µl of CRSR-Blue (Qbiogene), and 500 µl of acid phenol-chloroform (5:1, pH 4.5; Ambion, Austin, Tex.). The mixture was homogenized (80 s at speed 5), heated at 65°C for 20 min, and centrifuged at 16,000 x g for 15 min. The aqueous phase was collected, 250 µg of glycogen (Roche Applied Science, Indianapolis, Ind.) was added, and the mixture was concentrated to 100 µl with a vacuum concentrator (Eppendorf). The concentrate was purified by using the Qiagen RNeasy kit (Qiagen, Valencia, Calif.) according to the manufacturer's protocol (Qiagen). Contaminating DNA was removed by DNase I treatment (DNA-free; Ambion). To ensure that contaminating DNA was absent, an aliquot of RNA from each sample was subjected to 40 cycles TaqMan real-time PCR for the proS gene. All swabs analyzed yielded a PCR product for the proS gene when the proS primers were tested against cDNA synthesized from the purified swab RNAs, indicating that the proS gene primer sites were conserved in all GAS strains. The RNA was treated with DNase I (Ambion) until no signal was detected by TaqMan real-time reverse transcription-PCR (RT-PCR) by using the conserved proS gene as a target. None of the GAS primers (Table 1) cross-hybridized to cDNAs synthesized from RNA made from the oral flora present in the monkeys (data not shown).
TaqMan real-time PCR assay.
The sequences of the primers and probes used in the present
study are listed in Table
1. The Superscript II Choice system
(Invitrogen, Carlsbad, Calif.) was used for cDNA synthesis as
described by the manufacturer. RNA purified from each swab was
divided into four aliquots, to which 0.8 µg of bacteriophage
MS2 carrier RNA (Roche) was added to each aliquot, and reverse
transcribed with 1.5 µg of random hexamer primers at 42°C
for 1 h. The cDNA samples were treated with RNase H
- (Invitrogen)
for 1 h and diluted with water to 100 µl. TaqMan 5' nuclease
real-time PCR assays (Applied Biosystems, Foster City, Calif.)
were carried out in a 384-well format with an 7900HT instrument
(Applied Biosystems) in 10-µl reactions containing 1
x universal master mix, 100 nM 6-carboxy-4'5'-dichloro-2'7'-dimethylfluorescein
(JOE) and QSY-7 labeled putative prolyl-tRNA synthetase (
proS,
Spy1962; Table
2), 200 nM concentrations of target forward and
reverse primers, and 100 nM concentrations of the target TaqMan
oligonucleotide for 50°C for 2 min and 95°C for 10 min
and then for 40 cycles of 95°C for 15 s and 60°C for
1 min. All TaqMan oligonucleotide probes were labeled with 6-carboxyfluorescein
(6-FAM) at the 5' end and the quencher carboxytetramethylrhodamine
(TAMRA) at the 3' end. The comparative C
T method was used to
determine the ratio of target and endogenous control (Applied
Biosystems) as described previously (
16).
Measurement of antibody response by the nonhuman primates to GAS protein antigens.
Antibody titers to streptococcal inhibitor of complement (Sic;
Spy2016), a GAS homolog of
Listeria monocytogenes internalin
A (InlA; Spy1361), and streptolysin O (SLO; Spy0167) were measured
by enzyme-linked immunosorbent assay (ELISA). Sic and InlA were
purified at Rocky Mountain Laboratories, and SLO was purchased
from Sigma (St. Louis, Mo.). Sic and InlA were diluted to 2.5
µg/ml in buffer (0.05 M Tris, pH 7.5; 0.15 M NaCl), and
SLO was diluted to 10 µg/ml. Microtiter plates (Immulon-2;
Dynex Technologies, Inc., Chantilly, Va.) were coated (100 µl)
overnight at 4°C, washed with washing buffer (0.05 M Tris,
pH 7.5; 0.15 M NaCl; 0.5% Tween 20), and blocked with 2% bovine
serum albumin in washing buffer for 2 h at 37°C. After the
washing step, 100 µl of plasma was serially diluted in
washing buffer with 2% bovine serum albumin and added to the
wells, and the mixtures were incubated at 37°C for 1 h.
Plates were washed again, and a 1:500 dilution of 100 µl
of alkaline phosphatase-labeled goat anti-monkey immunoglobulin
G (Rockland, Gilbertsville, Pa.) was added to the wells, followed
by incubation for 1 h at 37°C, and 100 µl of substrate
(
p-nitrophenyl phosphate; Zymed, South San Francisco, Calif.)
was added. The absorbance at 405 nm was measured with an ELISA
reader (Dynex Technologies, Inc.). ELISA titers are expressed
as the reciprocal of plasma dilutions giving an absorbance threshold
value of

0.3. Preinoculation plasma was used as a negative control,
and the ELISA absorbance value of this sample was <0.1.

RESULTS
Expression of GAS two-component regulatory system genes in human pharyngitis.
Two-component signal transduction systems composed of a membrane-bound
sensor and a cytoplasmic response regulator are important mechanisms
used by pathogenic bacteria to sense and respond to environmental
stimuli during interactions with the host. Pathogenic bacteria
often use two-component systems to control expression of genes
encoding toxins, adhesions, and other virulence-associated cell
surface molecules that promote survival in vivo. The genome
of a serotype M1 GAS strain that has been sequenced (
10) contains
genes encoding 13 two-component systems, but little is known
about the function of most of these genes. Moreover, no information
is available about in vivo transcription of the genes in pharyngitis
episodes.
Given the importance of these genes in bacterial pathogenesis, we elected to begin our investigation by studying transcription of 6 of the 13 GAS two-component regulators (Table 2) by TaqMan real-time RT-PCR analysis of throat swab specimens obtained from 18 pediatric patients presenting with acute pharyngitis (Fig. 1). The median transcript levels of these genes were expressed as the fold difference relative to the internal normalizing gene proS. The proS gene was used as an internal reference because it is constitutively transcribed throughout the growth cycle of GAS (16). Although transcripts were detected for all six genes assayed, there was substantial variation in the relative level of transcript detected in our analysis. For example, five of the six genes (srtK, covS, zmpR, sycF, and ciaH) had a median level of relative expression that was less than the relative level of proS transcription (Fig. 1). Importantly, one gene (fasC) (25) was highly expressed, with relative transcripts being 5.8-fold higher than proS transcript levels (Fig. 1).
Expression of GAS transcriptional regulators in human pharyngitis.
We next studied the level of expression of four transcriptional
regulators (
rgg,
crgR,
perR, and
mga) in the throat swab specimens
(Fig.
1). These genes have been characterized previously in
GAS (
4,
24,
30-
32,
38,
44) and were selected for analysis on
the basis of their potential to regulate expression of genes
that may participate in host-pathogen interactions during pharyngitis.
In general, expression of the positive regulator
rgg was low
relative to the
proS gene (-13.4-fold) (Fig.
1). However, the
median relative expression of
rgg was 1.9-fold greater than
proS in swabs recovered from one patient each infected with
strains of serotype M75 and M77, a result suggesting strain-specific
differences in the level of transcript of this gene. The
perR gene was highly expressed (median transcript level 15.5-fold
relative to
proS), the recently identified cathelicidin resistance
gene regulator
crgR (
36) had a mean transcript level of 2.5-fold
relative to
proS, and the median relative transcript levels
of
mga was 2.0-fold relative to
proS (Fig.
1).
Expression of virulence genes in human GAS acute pharyngitis.
The expression level of genes encoding five proposed and two putative virulence factors was measured next (Fig. 1). Although the level of expression varied among the 18 patients, three of the genes (speB, grab, and mac) (27, 34, 41) had median relative expression levels that were less than that of proS, whereas the median relative expression level of four genes (scpA, bspA, edin, and sda) (5, 40, 42, 43, 57) exceeded the median expression level of proS. Of note, the most highly expressed gene among the 17 genes studied was sda (encoding a DNase), which had a median relative transcript level that was 61.6-fold higher than proS (Fig. 1).
Evaluation of experimental GAS pharyngitis in cynomolgus macaques.
The data presented above indicated that it was feasible to monitor transcripts of numerous GAS genes present in throat swab specimens obtained from hosts with pharyngitis. This observation, together with the lack of a small laboratory animal model that faithfully reproduces many aspects of GAS pharyngitis, led us to study gene transcript levels present in throat swabs obtained from experimentally infected nonhuman primates. An additional motivation for these studies was the capability of obtaining GAS gene transcript data during the very early phase of host-pathogen interactions in the upper respiratory tract, a goal currently not attainable in the human clinical setting.
To begin this analysis, three cynomolgus macaques were inoculated with GAS strain MGAS5005 in the nares and then studied for 12 days. This strain has been studied extensively and is genetically representative of serotype M1 strains commonly causing contemporary episodes of pharyngitis and invasive disease episodes in North America and western Europe (16, 20, 22, 27, 29, 42, 47). All three monkeys were colonized with GAS 48 h after inoculation (Fig. 2A). Pharyngitis with severe erythema and palatal petechiae were observed by day 4 in the adult macaques and by day 7 in the juvenile macaque (Fig. 2B). Tonsil enlargement was evident in the adult macaques on day 4 and in the juvenile animal on day 7 (Fig. 2C). The male monkey had severe tonsil enlargement by day 7, characterized by encroachment on the midline (+4 score). Taken together, these results indicated that the animals had developed acute GAS pharyngitis with clinical findings similar to those observed in many infected humans.
Consistent with the clinical observations, the monkeys had a
significant increase in antibody titer against SLO, Sic, and
the InlA homolog in serum obtained during convalescence (Fig.
3).
Analysis of gene expression in cynomolgus macaques.
To investigate the pattern of GAS gene expression in vivo over
the course of a 12-day infection, we isolated total RNA from
throat swabs obtained on days 2, 4, 7, 9, and 11 postinoculation.
Relative transcript levels for the GAS genes (Table
2) were
obtained by using the same techniques used for analysis of the
human throat swabs. A complex pattern of transcription of the
genes was detected in the three macaques (Fig.
4). For example,
transcription of three genes (
irr,
mac, and
edin) regulated
directly or indirectly by the CovRS two-component system (
8,
16,
17,
28), and one gene (
perR) not known to be influenced
by CovRS (
16) was detected on days 2, 4, 7, 9, and 11 of the
study in all monkeys except the day 2 sample from the juvenile
animal (Fig.
4). The relative transcript levels of two gene
regulators (
perR and
irr) varied from 1.0- to 15.6-fold and
from 5.4- to 27.5-fold, respectively. Transcription of two putative
virulence factors (
mac and
edin) also varied during the course
of infection (from 2.6- to 72.8-fold and from -1.3- to 4.5-fold,
respectively).

DISCUSSION
Analysis of GAS gene expression in human clinical specimens.
To gain new insight into GAS gene expression in vivo in human
patients with acute pharyngitis, we measured relative transcript
levels of 17 genes in throat swab specimens by quantitative
TaqMan real-time RT-PCR. Analysis of transcript levels of several
genes encoding known and putative extracellular virulence factors
was consistent with serological evidence that these GAS genes
are expressed during infection (
6,
21,
42,
43). For example,
SpeB, Mac, and BspA have been shown to be synthesized in vivo
in infected humans, as judged by analysis of antibody levels
present in acute- and convalescent-phase sera (
27,
34,
42,
43).
However, our study is the first to measure transcription of
GAS genes encoding two-component regulator systems and global
transcriptional activators during human infection (Fig.
1).
We found that the two-component regulatory system gene
fasC was highly expressed during acute pharyngitis (Fig.
1). The
fasBCA(X) genes have homology to
agr genes of
Staphylococcus aureus, a density-dependent quorum-sensing system that regulates
expression of several virulence factors. Kreikemeyer et al.
(
25) reported that
fasBCA(X) controls expression of fibronectin-binding
proteins (
fbp54,
mrp), streptolysin S-associated genes (
sagA/
pel),
superoxide dismutase (
sod), and streptokinase (
ska). The Fas
regulon is upregulated under amino acid starvation (
48,
49),
a condition that may occur in vivo in infected hosts. Recently,
Voyich et al. showed that another two-component system (
irr-ihk)
involved in evasion of innate immune system was also highly
expressed during human pharyngitis (
55).
Our studies also discovered that two regulators of gene expression (mga and perR) were highly expressed during acute pharyngitis (Fig. 1). Mga (multiple gene activator) has been studied extensively in GAS and is known to regulate several important virulence genes such as emm, scpA, mac, sic, streptococcal collagen-like protein 1 (scl1), and fibronectin-binding protein (fba), all of which have been reported to participate in adhesion to host cells or escape from host defenses (27, 29, 31, 32, 38, 51). Less is known about the role of perR in GAS gene regulation and host-pathogen interactions, although three recent studies are relevant (24, 44, 47). The GAS perR gene is homologous to the B. subtilis perR gene that is a negative regulator of response to hydrogen peroxide stress. King et al. (24) inactivated the perR gene in GAS and reported that the mutant strain was derepressed for the inducible peroxide resistance response and survived hydrogen peroxide challenge approximately 100 times better than the wild-type parental strain. More recently, Ricci et al. (44) reported that a GAS perR mutant strain was more sensitive to oxidative stress and was less virulent in a mouse air sac model than the wild-type isogenic strain. The transcript levels of perR are upregulated during growth in vitro under iron-restricted conditions (47). Hence, the identification of high levels of perR expression in vivo is consistent with the idea that this gene is highly expressed during acute pharyngitis, perhaps due to iron-restricted environmental conditions. Inasmuch as the three regulators fasBCA(X), mga, and perR were highly expressed in vivo, further studies are warranted to elucidate their contribution to human pharyngitis pathogenesis.
GAS acute pharyngitis in cynomolgus macaques.
Relevant animal models are essential to the development of a detailed understanding of the molecular interactions between pathogenic microbes and their host and to the development of new therapeutics, including vaccines. Mice can be colonized experimentally by GAS, but they do not develop an acute pharyngitis that mimics human disease (23, 29). On the basis of research conducted over decades, nonhuman primates are generally considered to be the most relevant animals for the study of experimental GAS pharyngitits (1, 12, 26, 50, 53, 56, 60). Although baboons (1) and rhesus macaques (53, 56) have been colonized successfully in the upper respiratory tract with GAS, these animals did not develop clinical signs of acute pharyngitis.
The three cynomolgus macaques inoculated with GAS developed acute pharyngitis signs similar to humans. All three monkeys were culture positive on day 2, had signs of tonsillitis and pharyngitis soon thereafter, and had an increase in serum antibody titers against the three GAS antigens tested, including SLO. The development of pharyngitis signs and increased antibody titers to extracellular secreted antigens paralled results described in earlier GAS pharyngitis studies conducted with chimpanzees, a species used previously to study GAS acute pharyngitis (12, 26, 60). In the aggregate, our results indicate that the cynomolgus macaque is a useful animal for experimental study of acute pharyngitis caused by GAS.
Use of monkeys to study the molecular processes contributing to GAS pharyngitis permits several types of analyses to be conducted that are not readily performed with human subjects. For example, GAS infection can be studied at precisely delineated times after inoculation, whereas human studies involve undefined time periods between exposure to the organism and presentation with clinical symptoms. Second, the monkey model permits analysis of infection pathogenesis with defined strains, including particular M protein serotypes of special interest in pharyngitis, and isogenic mutant strains. Third, inoculated monkeys are housed under controlled conditions; hence, they are subject to far less environmental variation than human patients. Despite reduction in the spectrum of confounding variables, significant variation was observed in GAS gene expression and the host clinical response between monkeys over the course of the infection. Variation in host response to GAS inoculation has been reported previously in a baboon model of GAS upper respiratory tract infection and was attributed to inconsistent development of opsonic antibodies and ineffectiveness in clearance of GAS (1). Expression differences in GAS transcript levels were also observed in cynomolgus macaques and humans (Fig. 1 and 4). The reasons for these differences are largely unknown; however, they may in part be due to variation in infecting GAS strains or the time of sampling.
Analysis of bacterial gene transcripts in vivo.
Analysis of quantitative bacterial gene transcript levels directly from clinical samples has been reported for relatively few pathogens (Table 3). Most studies have used real-time RT-PCR to measure transcript levels. Due to the detection limit with the real-time RT-PCR method (103 to 104 transcripts/sample) (14, 45), it has been not been possible to quantitate transcript levels of more than
20 genes by this method. Although the 384-well multiplexing format we used permitted us to achieve high throughput and quantitative RT-PCR results, expression microarray analysis of the complete bacterial transcriptome is clearly the preferred strategy for future experiments due to the comprehensive data set obtained. In this regard, we note that Merrell et al. (33) recently reported successful analysis of the Vibrio cholerae transcriptome by using 1 µg of RNA extracted from human stool. Studies of the complete in vivo transcriptome undoubtedly will provide many new insights into GAS host-pathogen interactions.

ACKNOWLEDGMENTS
We thank G. J. Adams and T. Downey for assistance with statistical
analysis; B. Lei and S. D. Reid for providing recombinant purified
GAS proteins; M. Gutacker for translating foreign journal articles;
M. Liu and D. E. Sturdevant for technical assistance; and W.
Sheets, R. Larson, and D. Dale for assistance with the animal
experiments. We are especially indebted to the physicians, support
staff, and the patients at the Pediatric Medical Group (an affiliate
of Texas Children's Pediatric Associates), Houston, Tex.
This work was supported in part by contract N01-AO-02738 from the National Institute of Allergy and Infectious Diseases.

FOOTNOTES
* Corresponding author. Mailing address: Laboratory of Human Bacterial Pathogenesis, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 903 South 4th St., Hamilton, MT 59840. Phone: (406) 363-9315. Fax: (406) 363-9427. E-mail:
jmusser{at}niaid.nih.gov.

Editor: D. L. Burns

REFERENCES
1 - Ashbaugh, C. D., T. J. Moser, M. H. Shearer, G. L. White, R. C. Kennedy, and M. R. Wessel. 2000. Bacterial determinants of persistent throat colonization and the associated immune response in a primate model of human group A streptococcal pharyngeal infection. Cell. Microbiol. 2:283-292.[CrossRef][Medline]
2 - Bisno, A. L. 2001. Acute pharyngitis. N. Engl. J. Med. 344:205-211.[Free Full Text]
3 - Blom, K., A.-M. Svennerholm, and I. Bolin. 2002. The expression of the Helicobacter pylori genes ureA and nap is higher in vivo than in vitro as measured by quantitative competitive reverse transcriptase-PCR. FEMS Microbiol. Med. Microbiol. 32:219-226.[CrossRef]
4 - Caparon, M. G., and J. R. Scott. 1987. Identification of a gene that regulates expression of M protein, the major virulence determinant of group A streptococci. Proc. Natl. Acad. Sci. USA 84:8677-8681.[Abstract/Free Full Text]
5 - Chen, C. C., and P. P. Cleary. 1990. Complete nucleotide sequence of the streptococcal C5a peptidase gene of Streptococcus pyogenes. J. Biol. Chem. 265:3161-3167.[Abstract/Free Full Text]
6 - Cunningham, M. W. 2000. Pathogenesis of group A streptococcal infections. Clin. Microbiol. Rev. 13:470-511.[Abstract/Free Full Text]
7 - Dale, J. B. 1999. Group A streptococcal vaccines. Infect. Dis. Clin. North Am. 13:227-243.[CrossRef][Medline]
8 - Federle, M. J., K. S. McIver, and J. R. Scott. 1999. A response regulator that represses transcription of several virulence operons in the group A streptococcus. J. Bacteriol. 181:3649-3657.[Abstract/Free Full Text]
9 - Feinstein, A. R., and M. Levitt. 1970. The role of tonsils in predisposing to streptococcal infections and recurrences of rheumatic fever. N. Engl. J. Med. 282:285-291.
10 - Ferretti, J. J., W. M. McShan, D. Ajdic, D. J. Savic, G. Savic, K. Lyon, C. Primeaux, S. Sezate, A. N. Suvorov, S. Kenton, H. S. Lai, S. P. Lin, Y. Qian, H. G. Jia, F. Z. Najar, Q. Ren, H. Zhu, L. Song, J. White, X. Yuan, S. W. Clifton, B. A. Roe, and R. McLaughlin. 2001. Complete genome sequence of an M1 strain of Streptococcus pyogenes. Proc. Natl. Acad. Sci. USA 98:4658-4663.[Abstract/Free Full Text]
11 - Fikrig, E., W. Feng, S. W. Barthold, S. R. Telford III, and R. A. Flavell. 2000. Arthropod- and host-specific Borrelia burgdorferi bbk32 expression and the inhibition of spriochete transmission. J. Immunol. 164:5344-5351.[Abstract/Free Full Text]
12 - Friou, G. J. 1950. Experimental infection of the upper respiratory tract of young chimpanzees with group A hemolytic streptococci. J. Infect. Dis. 86:264-274.[Medline]
13 - Gilmore, R. D., Jr., M. L. Mbow, and B. Stevenson. 2001. Analysis of Borrelia burgdorferi gene expression during life cycle phases of the tick vector Ixodes scapularis. Microbes Infect. 3:799-808.[CrossRef][Medline]
14 - Goerke, C., M. G. Bayer, and C. Wolz. 2001. Quantification of bacterial transcripts during infection using competitive reverse transcription-PCR (RT-PCR) and LightCycler RT-PCR. Clin. Diagn. Lab. Immunol. 8:279-282.[Abstract/Free Full Text]
15 - Goerke, C., U. Fluckiger, A. Steinhuber, W. Zimmerli, and C. Wolz. 2001. Impact of the regulatory loci agr, sarA and sae of Staphylococcus aureus on the induction of
-toxin during device-related infection resolved by direct quantitative transcript analysis. Mol. Microbiol. 40:1439-1447.[CrossRef][Medline]
16 - Graham, M. R., L. M. Smoot, C. A. Migliaccio, K. Virtaneva, D. E. Sturdevant, S. F. Porcella, M. J. Federle, G. J. Adams, J. R. Scott, and J. M. Musser. 2002. Virulence control in group A Streptococcus by a two-component gene regulatory system: global expression profiling and in vivo infection modeling. Proc. Natl. Acad. Sci. USA 99:13855-13860.[Abstract/Free Full Text]
17 - Heath, A., V. J. DiRita, N. L. Barg, and N. C. Engleberg. 1999. A two-component regulatory system, CsrR-CsrS, represses expression of three Streptococcus pyogenes virulence factors, hyaluronic acid capsule, streptolysin S, and pyrogenic exotoxin B. Infect. Immun. 67:5298-5305.[Abstract/Free Full Text]
18 - Hodzic, E., D. L. Borjesson, S. Feng, and S. W. Barthold. 2001. Acquisition dynamics of Borrelia burgdorferi and the agent of human granulocytic ehrlichiosis at the host-vector interface. Vector-Borne Zoonot. Dis. 1:149-158.
19 - Hodzic, E., S. Feng, K. J. Freet, D. L. Borjesson, and S. W. Barthold. 2002. Borrelia burgdorferi population kinetics and selected gene expression at the host-vector interface. Infect. Immun. 70:3382-3388.[Abstract/Free Full Text]
20 - Hoe, N. P., R. M. Ireland, F. R. DeLeo, B. B. Gowen, D. W. Dorward, J. M. Voyich, M. Liu, E. H. Burns, Jr., D. M. Culnan, A. Bretscher, and J. M. Musser. 2002. Insight into the molecular basis of pathogen abundance: group A Streptococcus inhibitor of complement inhibits bacterial adherence and internalization into human cells. Proc. Natl. Acad. Sci. USA 99:7646-7651.[Abstract/Free Full Text]
21 - Hoe, N. P., P. Kordari, R. Cole, M. Liu, T. Palzkill, W. Huang, D. McLellan, G. J. Adams, M. Hu, J. Vuopio-Varkila, T. R. Cate, M. E. Pichichero, K. M. Edwards, J. Eskola, D. E. Low, and J. M. Musser. 2000. Human immune response to streptococcal inhibitor of complement, a serotype M1 group A Streptococcus extracellular protein involved in epidemics. J. Infect. Dis. 182:1425-1436.[CrossRef][Medline]
22 - Hoe, N. P., K. Nakashima, S. Lukomski, D. Grigsby, M. Liu, P. Kordari, S. J. Dou, X. Pan, J. Vuopio-Varkila, S. Salmelinna, A. McGeer, D. E. Low, B. Schwartz, A. Schuchat, S. Naidich, D. De Lorenzo, Y. X. Fu, and J. M. Musser. 1999. Rapid selection of complement-inhibiting protein variants in group A Streptococcus epidemic waves. Nat. Med. 5:924-929.[CrossRef][Medline]
23 - Husmann, L. K., D. L. Dillehay, V. M. Jennings, and J. R. Scott. 1996. Streptococcus pyogenes infection in mice. Microb. Pathog. 20:213-224.[CrossRef][Medline]
24 - King, K. Y., J. A. Horenstein, and M. G. Caparon. 2000. Aerotolerance and peroxide resistance and PerR mutants of Streptococcus pyogenes. J. Bacteriol. 182:5290-5299.[Abstract/Free Full Text]
25 - Kreikemeyer, B., M. D. Boyle, B. A. Buttaro, M. Heinemann, and A. Podbielski. 2001. Group A streptococcal growth phase-associated virulence factor regulation by a novel operon (Fas) with homologies to two-component-type regulators requires a small RNA molecule. Mol. Microbiol. 39:392-406.[CrossRef][Medline]
26 - Krushak, D. H., R. A. Zimmerman, and B. L. Murphy. 1970. Induced group A beta-hemolytic streptococcic infection in chimpanzees. J. Am. Vet. Med. Assoc. 157:742-744.[Medline]
27 - Lei, B., F. R. DeLeo, N. P. Hoe, M. R. Graham, S. M. Mackie, R. L. Cole, M. Liu, H. R. Hill, D. E. Low, M. J. Federle, J. R. Scott, and J. M. Musser. 2001. Evasion of human innate and acquired immunity by a bacterial homolog of CD11b that inhibits opsonophagocytosis. Nat. Med. 7:1298-1305.[CrossRef][Medline]
28 - Levin, J. C., and M. R. Wessels. 1998. Identification of csrR/csrS, a genetic locus that regulates hyaluronic acid capsule synthesis in group A Streptococcus. Mol. Microbiol. 30:209-219.[CrossRef][Medline]
29 - Lukomski, S., K. Nakashima, I. Abdi, V. J. Cipriano, R. M. Ireland, S. D. Reid, G. G. Adams, and J. M. Musser. 2000. Identification and characterization of the scl gene encoding a group A Streptococcus extracellular protein virulence factor with similarity to human collagen. Infect. Immun. 68:6542-6553.[Abstract/Free Full Text]
30 - Lyon, W. R., C. M. Gibson, and M. G. Caparon. 1998. A role for trigger factor and an rgg-like regulator in the transcription, secretion and processing of the cysteine proteinase of Streptococcus pyogenes. EMBO J. 17:6263-6275.[CrossRef][Medline]
31 - McIver, K. S., and J. R. Scott. 1997. Role of mga in growth phase regulation of virulence genes of the group A Streptococcus. J. Bacteriol. 179:5178-5187.[Abstract/Free Full Text]
32 - McIver, K. S., A. S. Thurman, and J. R. Scott. 1999. Regulation of mga transcription in the group A Streptococcus: specific binding of Mga within its own promoter and evidence for a negative regulator. J. Bacteriol. 181:5373-5383.[Abstract/Free Full Text]
33 - Merrell, D. S., S. M. Butler, F. Qadri, N. A. Dolganov, A. Alam, M. B. Cohen, S. B. Calderwood, G. K. Schoolnik, and A. Camilli. 2002. Host-induced epidemic spread of the cholera bacterium. Nature 417:642-645.[CrossRef][Medline]
34 - Musser, J. M. 1997. Streptococcal superantigen, mitogenic factor, and pyrogenic exotoxin B expressed by Streptococcus pyogenes: structure and function. Prep. Biochem. Biotechnol. 27:143-172.[Medline]
35 - Musser, J. M., V. Kapur, J. Szeto, X. Pan, D. S. Swanson, and D. R. Martin. 1995. Genetic diversity and relationships among Streptococcus pyogenes strains expressing serotype M1 protein: recent intercontinental spread of a subclone causing episodes of invasive disease. Infect. Immun. 63:994-1003.[Abstract]
36 - Nizet, V., T. Ohtake, X. Lauth, J. Trowbridge, J. Rudisill, R. A. Dorschner, V. Pestonjamasp, J. Piraino, K. Huttner, and R. L. Gallo. 2001. Innate antimicrobial peptide protects the skin from invasive bacterial infection. Nature 414:454-457.[CrossRef][Medline]
37 - Ogunniyi, A. D., P. Giammarinaro, and J. C. Paton. 2002. The genes encoding virulence-associated proteins and the capsule of Streptococcus pneumoniae are upregulated and differentially expressed in vivo. Microbiology 148:2045-2053.[Abstract/Free Full Text]
38 - Perez-Casal, J. F., H. F. Dillon, L. K. Husmann, B. Graham, and J. R. Scott. 1993. Virulence of two Streptococcus pyogenes strains (types M1 and M3) associated with toxic-shock-like syndrome depends on an intact mry-like gene. Infect. Immun. 61:5426-5430.[Abstract/Free Full Text]
39 - Pichichero, M. E. 1998. Group A beta-hemolytic streptococcal infections. Pediatr. Rev. 19:291-302.[Free Full Text]
40 - Podbielski, A., I. Zarges, A. Flosdorff, and J. Weber-Heynemann. 1996. Molecular characterization of a major serotype M49 group A streptococcal DNase gene (sdaD). Infect. Immun. 64:5349-5356.[Abstract]
41 - Rasmussen, M., H. P. Müller, and L. Björck. 1999. Protein GRAB of Streptococcus pyogenes regulates proteolysis at the bacterial surface by binding
2-macroglobulin. J. Biol. Chem. 274:15336-15344.[Abstract/Free Full Text]
42 - Reid, S. D., N. M. Green, J. K. Buss, B. Lei, and J. M. Musser. 2001. Multilocus analysis of extracellular putative virulence proteins made by group A Streptococcus: population genetics, human serologic response, and gene transcription Proc. Natl. Acad. Sci. USA 98:7552-7557.[Abstract/Free Full Text]
43 - Reid, S. D., N. M. Green, G. L. Sylva, J. M. Voyich, E. T. Stenseth, F. R. DeLeo, T. Palzkill, D. E. Low, H. R. Hill, and J. M. Musser. 2002. Postgenomic analysis of four novel antigens of group A Streptococcus: growth-phase-dependent gene transcription and human serologic response. J. Bacteriol. 184:6316-6324.
44 - Ricci, S., R. Janulczyk, and L. Bjorck. 2002. The regulator PerR is involved in oxidative stress response and iron homeostasis and is necessary for full virulence of Streptococcus pyogenes. Infect. Immun. 70:4968-4976.[Abstract/Free Full Text]
45 - Rokbi, B., D. Seguin, B. Guy, V. Mazarin, E. Vidor, F. Mion, M. Cadoz, and M.-J. Quentin-Millet. 2001. Assessment of Helicobacter pylori gene expression within mouse and human gastric mucosae by real-time reverse transcriptase PCR. Infect. Immun. 69:4759-4766.[Abstract/Free Full Text]
46 - Shelburne, C. E., R. M. Gleason, G. R. Germaine, L. F. Wolff, B. H. Mullally, W. A. Coulter, and D. E. Lopatin. 2002. Quantitative reverse transcription polymerase chain reaction analysis of Porphyromonas gingivalis gene expression in vivo. J. Microbiol. Methods 49:147-156.[CrossRef][Medline]
47 - Smoot, L. M., J. C. Smoot, M. R. Graham, G. A. Somerville, D. E. Sturdevant, C. A. Migliaccio, G. L. Sylva, and J. M. Musser. 2001. Global differential gene expression in response to growth temperature alteration in group A Streptococcus. Proc. Natl. Acad. Sci. USA 98:10416-10421.[Abstract/Free Full Text]
48 - Steiner, K., and H. Malke. 2000. Life in protein-rich environments: the relA-independent response of Streptococcus pyogenes to amino acid starvation. Mol. Microbiol. 38:1004-1016.[CrossRef][Medline]
49 - Steiner, K., and H. Malke. 2001. relA-independent amino acid starvation response network of Streptococcus pyogenes. J. Bacteriol. 183:7354-7364.[Abstract/Free Full Text]
50 - Taranta, A., M. Spagnuolo, M. Davidson, G. Goldstein, and J. W. Uhr. 1969. Experimental streptococcal infections in baboons. Transplant. Proc. 1:992-993.[Medline]
51 - Terao, Y., S. Kawabata, E. Kunitomo, J. Murakami, I. Nakagawa, and S. Hamada. 2001. Fba, a novel fibronectin-binding protein from Streptococcus pyogenes, promotes bacterial entry into epithelial cells, and the fba gene is positively transcribed under the Mga regulator. Mol. Microbiol. 42:75-86.[CrossRef][Medline]
52 - Throup, J. P., K. K. Koretke, A. P. Bryant, K. A. Ingraham, A. F. Chalker, Y. Ge, A. Marra, N. G. Wallis, J. R. Brown, D. J. Holmes, M. Rosenberg, and M. K. Burnham. 2000. A genomic analysis of two-component signal transduction in Streptococcus pneumoniae. Mol. Microbiol. 35:566-576.[CrossRef][Medline]
53 - Vanace, P. W. 1960. Experimental streptococcal infection in the rhesus monkey. Ann. N. Y. Acad. Sci. 85:910-930.
54 - Vandecasteele, S. J., W. E. Peetermans, R. Merckx, M. van Ranst, and J. van Eldere. 2002. Use of gDNA as internal standard for gene expression in staphylococci in vitro and in vivo. Biochem. Biophys. Res. Commun. 291:528-534.[CrossRef][Medline]
55 - Voyich, J. M., D. E. Sturdevant, K. R. Braughton, S. D. Kobayashi, B. Lei, K. Virtaneva, D. W. Dorward, J. M. Musser, and F. R. DeLeo. 2003. Bacterial pathogen genome-wide protective response to human innate immunity: molecular strategies used by group A Streptococcus to evade destruction by human polymorphonuclear leukocytes. Proc. Natl. Acad. Sci. USA 100:1996-2001.
56 - Watson, R. F., S. Rothbard, and H. F. Swift. 1946. Type-specific protection and immunity following intranasal inoculation of monkeys with group A hemolytic streptococci. J. Exp. Med. 84:127-142.[Abstract]
57 - Yamaguchi, T., T. Hayashi, H. Takami, M. Ohnishi, T. Murata, K. Nakayama, K. Asakawa, M. Ohara, H. Komatsuzawa, and M. Sugai. 2001. Complete nucleotide sequence of a Staphylococcus aureus exfoliative toxin B plasmid and identification of a novel ADP-ribosyltransferase, EDIN-C. Infect. Immun. 69:7760-7771.[Abstract/Free Full Text]
58 - Yarwood, J. M., J. K. McCormick, M. L. Paustian, V. Kapur, and P. M. Schlievert. 2002. Repression of the Staphylococcus aureus accessory gene regulator in serum and in vivo. J. Bacteriol. 184:1095-1101.[Abstract/Free Full Text]
59 - Xiong, Y.-Q., W. van Wamel, C. C. Nast, M. R. Yeaman, A. L. Cheung, and A. S. Bayer. 2002. Activation and transcriptional interaction between agr RNAII and RNAIII in Staphylococcus aureus in vitro and in an experimental endocarditis model. J. Infect. Dis. 186:668-677.[CrossRef][Medline]
60 - Zimmerman, R. A., D. H. Krushak, E. Wilson, and J. D. Douglas. 1970. Human streptococcal disease syndrome compared with observations in chimpanzees. II. Immunologic responses to induced pharyngitis and the effect of treatment. J. Infect. Dis. 122:280-289.[Medline]
Infection and Immunity, April 2003, p. 2199-2207, Vol. 71, No. 4
0019-9567/03/$08.00+0 DOI: 10.1128/IAI.71.4.2199-2207.2003
Copyright © 2003, American Society for Microbiology. All Rights Reserved.
This article has been cited by other articles:
-
Loimaranta, V., Hytonen, J., Pulliainen, A. T., Sharma, A., Tenovuo, J., Stromberg, N., Finne, J.
(2009). Leucine-rich Repeats of Bacterial Surface Proteins Serve as Common Pattern Recognition Motifs of Human Scavenger Receptor gp340. J. Biol. Chem.
284: 18614-18623
[Abstract]
[Full Text]
-
Leday, T. V., Gold, K. M., Kinkel, T. L., Roberts, S. A., Scott, J. R., McIver, K. S.
(2008). TrxR, a New CovR-Repressed Response Regulator That Activates the Mga Virulence Regulon in Group A Streptococcus. Infect. Immun.
76: 4659-4668
[Abstract]
[Full Text]
-
Kinkel, T. L., McIver, K. S.
(2008). CcpA-Mediated Repression of Streptolysin S Expression and Virulence in the Group A Streptococcus. Infect. Immun.
76: 3451-3463
[Abstract]
[Full Text]
-
Shelburne, S. A. III, Okorafor, N., Sitkiewicz, I., Sumby, P., Keith, D., Patel, P., Austin, C., Graviss, E. A., Musser, J. M.
(2007). Regulation of Polysaccharide Utilization Contributes to the Persistence of Group A Streptococcus in the Oropharynx. Infect. Immun.
75: 2981-2990
[Abstract]
[Full Text]
-
Loughman, J. A., Caparon, M.
(2006). Regulation of SpeB in Streptococcus pyogenes by pH and NaCl: a Model for In Vivo Gene Expression. J. Bacteriol.
188: 399-408
[Abstract]
[Full Text]
-
Musser, J. M., DeLeo, F. R.
(2005). Toward a Genome-Wide Systems Biology Analysis of Host-Pathogen Interactions in Group A Streptococcus. Am. J. Pathol.
167: 1461-1472
[Abstract]
[Full Text]
-
Shelburne, S. A. III, Sumby, P., Sitkiewicz, I., Granville, C., DeLeo, F. R., Musser, J. M.
(2005). Central role of a bacterial two-component gene regulatory system of previously unknown function in pathogen persistence in human saliva. Proc. Natl. Acad. Sci. USA
102: 16037-16042
[Abstract]
[Full Text]
-
Shelburne, S. A. III, Granville, C., Tokuyama, M., Sitkiewicz, I., Patel, P., Musser, J. M.
(2005). Growth Characteristics of and Virulence Factor Production by Group A Streptococcus during Cultivation in Human Saliva. Infect. Immun.
73: 4723-4731
[Abstract]
[Full Text]
-
Virtaneva, K., Porcella, S. F., Graham, M. R., Ireland, R. M., Johnson, C. A., Ricklefs, S. M., Babar, I., Parkins, L. D., Romero, R. A., Corn, G. J., Gardner, D. J., Bailey, J. R., Parnell, M. J., Musser, J. M.
(2005). Longitudinal analysis of the group A Streptococcus transcriptome in experimental pharyngitis in cynomolgus macaques. Proc. Natl. Acad. Sci. USA
102: 9014-9019
[Abstract]
[Full Text]
-
Sumby, P., Barbian, K. D., Gardner, D. J., Whitney, A. R., Welty, D. M., Long, R. D., Bailey, J. R., Parnell, M. J., Hoe, N. P., Adams, G. G., DeLeo, F. R., Musser, J. M.
(2005). Extracellular deoxyribonuclease made by group A Streptococcus assists pathogenesis by enhancing evasion of the innate immune response. Proc. Natl. Acad. Sci. USA
102: 1679-1684
[Abstract]
[Full Text]
-
Brussow, H., Canchaya, C., Hardt, W.-D.
(2004). Phages and the Evolution of Bacterial Pathogens: from Genomic Rearrangements to Lysogenic Conversion. Microbiol. Mol. Biol. Rev.
68: 560-602
[Abstract]
[Full Text]
-
Lovenklev, M., Holst, E., Borch, E., Radstrom, P.
(2004). Relative Neurotoxin Gene Expression in Clostridium botulinum Type B, Determined Using Quantitative Reverse Transcription-PCR. Appl. Environ. Microbiol.
70: 2919-2927
[Abstract]
[Full Text]
-
Banks, D. J., Lei, B., Musser, J. M.
(2003). Prophage Induction and Expression of Prophage-Encoded Virulence Factors in Group A Streptococcus Serotype M3 Strain MGAS315. Infect. Immun.
71: 7079-7086
[Abstract]
[Full Text]