Linköping University Medical Dissertations
No. 1049
Lactobacillus iners
and the normal vaginal flora
Tell Jakobsson
MD
Clinical Microbiology
Department of Clinical and Experimental Medicine
Faculty of Health Sciences
Linköping University
Sweden
Linköping 2008
Tell Jakobsson, 2008
Published articles have been reprinted with permission from the respective copyright holders: Journal of Clinical
Microbiology (Paper I 2002 and paper IV 2007), APMIS/Wiley-Blackwell Publishing Ltd (Paper II and III
2002)
Printed in Sweden by LiUTryck, Linköping, Sweden 2008
ISBN 978-91-7393-953-9
ISSN 0345-0082
3
Abstract
The ecological niche of the vagina contains a large number of different microbes that are
constantly interacting with each other and the host. Culture methods have not been sufficient
in order to resolve the complexity of the normal vaginal flora. Further, the methods for
delineating normal flora from not normal flora are not easily handled and are traditionally not
based on culture but on microscopy of elements of the vaginal fluid. In the work presented in
this thesis, an international collaboration was established that pin-pointed some of the
difficulties in classifying vaginal floras, including staining, sampling, and discordance when
lactobacilli are few in number, and that emphasized the importance of the size of the vision
field in microscopes. As lactobacilli are prominent members of the normal vaginal flora they
need to be carefully classified if further work towards more robust scoring tools is to be
achieved.
Phenotypic methods have not been able to separate the closely related Lactobacillus species
of the vagina. Progress in molecular biology has provided possibilities to characterize these
lactobacilli, which are mainly from the Lactobacillus acidophilus group. In this work a large
number of strains collected by true random sampling were subjected to RAPD-PCR, TTGE
and multiplex PCR for species identification. The major species found were L. crispatus, L.
gasseri and L. jensenii and the recently described L. iners. The presence of L. iners has not
been detected in previous studies due to its special nutrient requirements. Development of
pyrosequencing technology also made it possible to match signatures of the two variable
regions V1 and V3 of the 16S rRNA gene of the vaginal lactobacilli and identify them to the
species level in a high throughput manner. The study confirmed that the dominating flora in
women with normal vaginal flora comprises the four species mentioned previously.
Repetitive sampling during IVF-treatment with highly varying oestrogen levels demonstrates
changes that possibly occur during changes in the natural life cycle. Furthermore, L. iners was
found to be the first species to be established after spontaneously resolved or treated Bacterial
Vaginosis.
These findings can be of help in developing new strategies for regaining and retaining the
normal vaginal flora.
4
5
List of papers
This dissertation is based on the following papers:
I. Forsum U, Jakobsson T, Larsson PG, Schmidt H, Beverly, A Bjørnerem, A Carlsson, B
Csango P, Donders G, Hay P, Ison C, Keane F, McDonald H, Moi H, Platz-Christensen J-J,
Schwebke J, An international study of the inter-observer variation between the interpretations
of vaginal smear criteria of Bacterial Vaginosis. APMIS 2002;110:811-8.
II. Vásquez A, Jakobsson T, Ahrné S, Forsum U, Molin G, The vaginal Lactobacillus flora
of healthy Swedish women, J Clin Microbiol. 2002;40:2746-9.
III. Tärnberg M.E, Jakobsson T, Jonasson J, Forsum U, Identification of randomly selected
colonies of Lactobacilli from normal vaginal fluid by pyrosequencing of the 16S rDNA
Variable V1 and V3 Regions, APMIS 2002;110:802-10.
IV. Jakobsson T, Forsum U. Lactobacillus iners: a marker of changes in the vaginal flora? J
Clin Microbiol. 2007;45:3145.
V. Jakobsson T and Forsum U. The predominant Human vaginal Lactobacillus flora during
IVF treatment, 2008 submitted to J Clin Microbiol.
Related publications by the author
VI. Larsson PG, Fåhraeus L, Carlsson B, Jakobsson T, Forsum U; Premature study group of
the Southeast Health Care Region of Sweden. Late miscarriage and preterm birth after
treatment with clindamycin: a randomised consent design study according to Zelen. BJOG.
2006;113:629-37.
VII. Forsum U, Holst E, Larsson PG, Vasquez A, Jakobsson T, Mattsby-Baltzer I. Bacterial
vaginosis--a microbiological and immunological enigma. APMIS. 2005;113:81-90.
VIII. Suhonen S, Haukkamaa M, Jakobsson T, Rauramo I. Clinical performance of a
levonorgestrel-releasing intrauterine system and oral contraceptives in young nulliparous
women: a comparative study. Contraception. 2004;69:407-12.
IX. Larsson PG, Carlsson B, Fåhraeus L, Jakobsson T, Forsum U. Diagnosis of bacterial
vaginosis: need for validation of microscopic image area used for scoring bacterial
morphotypes. Sex Transm Infect. 2004;80:63-7.
X. Larsson PG, Fåhraeus L, Carlsson B, Jakobsson T, Forsum U. Predisposing factors for
bacterial vaginosis, treatment efficacy and pregnancy outcome among term deliveries; results
from a preterm delivery study. BMC Women's Health 2007, 7:20, doi:10.1186/1472-6874-720.
XII: Jakobsson T as participant in the workshop Scoring vaginal fluid smears for diagnosis
of bacterial vaginosis: need for quality specifications. APMIS 2008;116:156-159.
6
Abbreviations
AMP
Adenosine monophosphate
ATP
Adenosine triphosphate
BV
Bacterial vaginosis
DNA
Deoxyribonucleic acid
IL1ra
Interleukin-1 receptor antagonist
IVF
In vitro fertilization
GnRH
Gonadotropin-releasing hormone
FISH
Fluorescence in situ hybridisation
FSH
Follicle-stimulating hormone
MBL
Mannose-binding lecithin
PAP smear Papanicolaou smear
PCR
Polymerase chain reaction
RAPD
Randomly amplified polymorphic DNA
RNA
Ribonucleic acid
TLR
Toll-like receptor
TTGE
Temporal temperature gradient gel electrophoresis
7
Table of contents
Abstract
3
List of papers
5
Abbreviations
6
Table of contents
7
INTRODUCTION
9
Vaginal lactobacilli
10
Bacterial Vaginosis
14
Diagnosis of Bacterial Vaginosis
15
MATERIAL AND METHODS
18
Microbiology in vaginal secretions as observed in the microscope (I) 18
Collection of samples
Wet smear composite clinical criteria of Amsel
Nugent’s scoring system of Gram-stained smears
Statistics
Characterization of the dominating flora in healthy women with
normal vaginal flora (II and III)
Study population
Collection of samples
Nucleic acid based techniques
Randomly Amplified Polymorphic DNA-PCR
Temporal Temperature Gradient gel Electrophoresis
Multiplex PCR
20
8
16S rDNA sequencing
Pyrosequencing
Characterization of the dominating flora in women
during IVF treatment (IV and V)
24
Study population
Hormonal assessment
Collection of samples
Bioinformatics
RESULTS AND DISCUSSION
26
Microbiology in vaginal secretions as observed in the microscope
26
Dominating normal vaginal flora in healthy Swedish women.
30
Dominating normal vaginal flora in patients during IVF treatment.
32
GENERAL SUMMARY
35
ACKNOWLEDGEMENTS
36
REFERENCES
39
Papers I-V
47
9
INTRODUCTION
The orifices of the human body are covered by mucous membranes that are physiological
barriers to intrusion from foreign organisms, chemicals and other objects. To ensure proper
protection it is generally assumed that an intact bacterial flora is required. One example of this
is the vaginal bacterial flora that constitutes a normal part of female physiology from foetal
life until death. The flora changes in a typical manner during the female life cycle. At birth,
the vagina is sterile. After only a few days, when oestrogen from the mother has led to an
increase of the glycogen content in the vaginal epithelial cells, colonization by lactobacilli
from the mother occurs concomitantly(38). With oestrogen levels slowly diminishing,
glycogen disappears, and thereby the prerequisite for the dominance of the lactobacilli(63).
During childhood, skin commensals and bowel bacteria colonize and dominate the microbial
content of the vagina. At the time of menarche, the rise in oestrogen increases glycogen
deposition in the vaginal epithelial cells, which is a prerequisite for the development of the
adult vaginal microflora. This flora is predominant until menopause, when it is replaced with
a flora similar to the flora found prior to the menarche, unless hormonal replacement therapy
is started(10).
The facts related above are part of the medical knowledge acquired over the years, but the
finer details of the composition and role of the vaginal flora are still a matter of debate. This is
mainly due to the fact that studies of microbial ecology in the vagina have been hampered by
a lack of discriminating tools for the study of the flora itself, as well as not completely
resolved questions relating to the categorization of physiological and abnormal states of the
flora as normal healthy flora, bacterial vaginosis, other abnormal flora types, etc.(16). In the
10
present studies more detailed descriptions are given of the kinds of lactobacilli that form part
of the normal flora in healthy women of childbearing age. The studies also seek to define how
the dominant lactobacilli flora changes over time in women undergoing IVF-treatment in
order to further define the co-variability of the flora and oestrogen levels.
Vaginal lactobacilli
The first microbiological study of the female vagina was mainly descriptive(18), and the
vaginal Gram-positive non-motile rods were known as “Döderlein’s bacilli” for almost a
century. Orla-Jensen laid the foundations for a classification based on four genera of lactic
acid bacteria: Lactobacillus, Leuconostoc, Pediococcus and Streptococcus(69). In 1928
Thomas first described Döderlein’s bacilli as Lactobacillus acidophilus(88).
The traditional phenotypic methods that were available, and which are still very important in
current classifications, are: morphology, mode of glucose fermentation, growth at certain
“cardinal” temperatures (e.g. 10°C and 45°C), and range of sugar utilisation(4). These and
other characteristics have not been useful for discriminating the closely related bacteria in the
ecological niche of the normal human vagina, which mainly belong to the L. acidophilus
group(9).
Other earlier studies using the classic phenotypic identification methods demonstrated
heterogeneity of the flora, for reviews see Redondo-Lopez and Zhong(76, 96). The most
frequently occurring species were L. acidophilus, L. brevis, L. casei, L. catenaforme L.
fermentum, L. jensenii, L. plantarum, L. rhamnosus and L. salivarius. This reflects the
unreliability of the phenotypic methods, especially within the genetically close L. acidophilus
group. One taxonomy of the L. acidophilus group was based on DNA homology studies(31,
47).
11
Modern phylogeny of lactobacilli presents six or seven different groups based on 16S rDNA
sequences: L. buchneri group, L. casei and L. sakei group, L. delbrüeckii or acidophilus
group, L. plantarum group, L. reuteri group and finally L. salivarius group(41). DNA-DNA
hybridisation as well as phenotypic characters was used by Giorgio (36) for the study of
vaginal lactobacilli isolated from asymptomatic women, and these were identified as L.
gasseri, L. jensenii and L. crispatus. One not identified group of heterofermentative
lactobacilli was found, as well as one isolate of L. fermentum.
Antonio et al, using whole-chromosomal probes in a material of 215 American women, found
L. crispatus, L. jensenii, a previously not described species, and L gasseri as the dominating
species(2). Song found mainly L. crispatus and L. gasseri in 49 Japanese women using DNADNA hybridisation(82). Kilic et al, in a material of 209 women from the US and Turkey,
identified most lactobacilli as L crispatus, L gasseri and L jensenii(48).
Since 2000, development of new methods for nucleic acid based comparisons has been rapid.
Kullen described a DNA-sequence based comparison of the first third of the 16S rRNA gene
for rapid and valid identification of lactobacilli from various human sources belonging to the
L. acidophilus group(50). In addition, Vasquez et al described TTGE as a useful method for
handling identification of large amounts of isolates in studies of the taxonomy of
lactobacilli(90). The early results on classification of lactobacilli have later been confirmed by
the use of new nucleic acid based techniques targeting the 16S rRNA gene. In a worldwide
study of 35 strains from 7 countries, most women harboured L crispatus, L jensenii and L
gasseri(71).
There are some important issues that have to be addressed concerning the selection of strains
in these studies. Several of the studies were performed on laboratory strains or with the origin
of the sample not stated, or without indicating the age, health or hormonal status of the host.
Most studies do not define the vaginal samples as normal according to Amsel or Nugent, so it
12
is not known whether the women had a normal vaginal status or not(1, 66). In most of the
studies the colonies were selected by morphology, and in none of the studies was there any
discussion of randomisation in the selection of the colonies cultured. All of these factors must
have influenced the results, but since all of the studies show almost identical results
concerning the species, we must conclude in any case that these three species obviously
dominate the normal vaginal microflora.
The recent introduction of techniques for studying the bacterial nucleic acids without previous
culture has further expanded our knowledge of the vaginal flora. This provides an option for
studying the vaginal flora, including many cases of BV, and, in fact, the focus of the studies
pertains to the syndrome of BV. Fredricks analysed some of the first studies using cultivationindependent methods to study the vaginal flora(30). In two studies the flora was characterized
with Gram-stained smears, and if normal the dominant species were L. crispatus, L. jensenii
and/or L. gasseri(22, 92). In studies with less well characterized flora, L. iners was found as
well(44, 97), and as the only lactobacilli in patients with BV according to Amsel(28). A
number of uncultivable, previously unknown species in the niche were found and are
commented on in the following section on BV.
In an African study using Nugent’s scoring of Gram-stained smears from healthy women
attending a reproductive healthcare service, 51% were scored intermediate, 35% normal, and
14% BV. Among the patients without BV, sequencing of a part of the 16S rRNA gene
revealed that 65% of the patients harboured L. iners(3). These results are consistent with a
Japanese study where L. iners was found in 40% of women with a normal flora, in 48% with
an intermediary flora and in 46% of women with BV according to Nugent’s score(86). In a
recent American study of women without signs of vaginal infection, 52% of the patients were
dominated by L. iners(98).
13
When trying to delineate normal flora vs. abnormal flora, the patophysiology of the normal
microflora and its role in safeguarding against other organisms and overt infection must also
be considered. Previously, competitive exclusion of pathogens was considered to be a major
task for the normal vaginal flora(5). The acidic milieu that is hostile to many pathogens has
also been attributed to the lactobacilli(6, 7). Another major issue has so far concerned the
question of whether vaginal lactobacilli are hydrogen peroxide producers or not, stemming
from the idea that a hydrogen peroxide producing lactobacillus could be the “normal” and
thus a protective lactobacillus(19). Bacteriocins synthesized by the ribosomes to inhibit
growth of other bacteria are frequent in lactobacilli(59). In the L. acidophilus group they have
so far been found only in L. acidophilus, which is not frequently found in the normal vaginal
flora(70).
Recent papers have introduced new hypotheses on proinflammatory changes in BV(94, 95):
1. The innate immunity seems to be most important. Studies of the normal flora in other
niches indicate that TLR of many different types, MBL, and certain heat-shock
proteins might be of major importance in normal vaginal flora as well(33). This
remains to be studied.
2. The adaptive immune regulation should also be important for protection vaginally.
This includes locally produced proinflammatory cytokines, interleukins and other
immune modulators(27, 60).
3. The presence of locally produced enzymes like secretory leukocyte protease inhibitor
(27), prolidase and sialidase(11).
There is reason to believe that continued studies of host-microorganism interactions will
follow these general hypotheses and, in fact, gene polymorphisms in human genes coding
for MBL, IL1ra and TLR4 have already been found and the allelic variations are
suspected to be of importance for the development of BV(34, 35, 37, 65).
14
Bacterial Vaginosis
Apart from lactobacilli, the vagina harbours many other bacterial species in varying amounts
in conditions that are not considered healthy. In certain conditions the lactobacilli in fertile
women are far outnumbered, mainly by anaerobes. The most frequent disturbance is the
syndrome of Bacterial Vaginosis (BV)(83). The lactobacilli in BV are overgrown by large
amounts of Gardnerella vaginalis and anaerobes, mainly Bacteroides spp and Mobiluncus;
for reviews see Hillier and Forsum(25, 43). In the present decade a number of fastidious
species have been found in large amounts in the vaginal secretions of women with BV. These
include Atopobium vaginae(78, 92); Eggerthella species, Leptotrichia species, Megasphera
species and a newly discovered species of the Clostridiales order(29, 86, 87, 97).
The prevalence of BV varies widely in different populations. In cervical PAP smear screening
programs and in antenatal care units the prevalence is below 10 %(52, 53). In women
undergoing termination of pregnancy in Sweden the incidence was found to be 20 %(57), in a
recent national survey in the US it was 29%(49) and in rural Uganda over 50%(72).
Just as little is known about how to delineate the healthy vaginal flora from the abnormal
vaginal flora, studies have long been hampered by the lack of common understanding of how
to recognize and categorize bacterial species that comprise normal and various abnormal
vaginal states. This has been troublesome, since the main field of BV research primarily
concerns studies comparing randomised controlled treatment of healthy vs. non-healthy
groups. When it is impossible to delimit the healthy and non-healthy groups based on proper
identification of bacterial types relating to established bacterial species, the conclusions based
on the results will be doubtful.
The effects of loss of the normal microflora in BV are associated with several severe
reproductive and genitourinary complications in women(55, 67). Preterm delivery is the
15
leading cause of perinatal mortality and morbidity in the developed world(39, 89).There may
be a clinical association between BV and preterm delivery(56, 67, 85), and if treatment of BV
could prevent only a few cases of premature births, much pain and high costs could be
prevented (VI).
BV has also been associated with an increased risk of postoperative infections after
hysterectomy(73) and abortion(54) and may enhance the transmission of HIV(79).
During the last two decades numerous studies have been presented in which different
Lactobacillus spp have been introduced into the vagina for the purpose of normalizing the
vaginal flora. Maggi used a mixture of L. brevis, L. salivarius and L gasseri(61). McLean
suggested L. acidophilus(64) and Ocana L. crispatus(68). Falagas presented a summary of
randomised clinical trials with L. acidophilus; L. fermentum and L. rhamnosus administered
orally and L. gasseri administered vaginally(20). In a recent study from Norway, patients with
BV who had received vaginal treatment with clindamycin thereafter were given
supplementary vaginal treatment with L. gasseri and L. fermentum for three cycles of 10 days
each. The time to relapse was marginally prolonged(58).
By and large, no effects or only marginal effects of lactobacillus instillation are documented
in these studies and no study has so far been published where the treatment strains have been
proven to adhere to and colonize the vagina.
Diagnosis of Bacterial Vaginosis
The diagnostic tools for BV are also a matter of controversy. Following the initial discovery
of the mixed bacterial overgrowth of mainly anaerobes(32), different scoring systems have
been developed. Since BV is not a simple infection caused by a single agent, the aim of using
a cultural technique for diagnosis of BV is not achievable in clinical practice due to the
16
required workload and costs. The strong association between the many newly discovered
uncultivable species and BV further illustrates this. The development of PCR probes for
detection of the microbes present in the vaginal fluid has made it possible to construct DNA
libraries of the microbiology with several microbes that were previously undetected.
The lack of knowledge of the microbiology of BV resulted in development of several scoring
systems during the final decades of the 20th century. In the early 1980s the composite criteria
of Amsel were established as the gold standard for diagnosis of BV. The disadvantages are
several. Firstly, practically all of the tests are subjective, i.e. they can differ from time to time
even with the same investigator. The pH is not always unequivocal and can be falsely
elevated by mixture of the vaginal and cervical secretions. Likewise, the sensitivity for the
amines differs depending on whether or not the investigator ate garlic for lunch or, even
worse, whether he or she smokes. Some individuals cannot sense the unpleasant odour of trimethylamine due to a genetic aberration (Forsum, U. personal comm.). The microscopic
analysis of clue cells is sometimes difficult, and the discharge of a woman with BV can vary
considerably. In the US, the clue cell criterion is applied differently, from mere existence to
occurrence on 20% of the epithelial cells. For a review see Forsum et al(26). Amsel’s criteria
are, however, the gold standard that research in BV has had to put up with for almost 20
years.
In the light of these difficulties, there has been a search for different and hopefully more
robust scoring systems. Spiegel et al.(84) defined a scoring system for bacterial morphotypes,
which can be seen in Gram-stained smears made from vaginal secretion of women undergoing
examination for BV. Nugent et al. (66) later refined the system, and the revised system has
gained wide acceptance as the scoring system of choice for research, but not in routine
laboratories as it is time-consuming. Other scoring systems, based on similar principles(42,
93) or using wet mounts of vaginal secretion observed in phase contrast microscopy(80), have
17
also gained acceptance in some parts of the world. A similar system has been proposed for use
with PAP-stained vaginal (but not cervical) smears(74). As mentioned above, a key issue is
definition of the normal vaginal status. In my studies I have chosen to define the vaginal flora
of the patients according to the composite criteria of Amsel(1) and with a smear Gram-stained
and analysed according to Nugent’s criteria(66). Only patients who were normal according to
Amsel’s criteria and to Nugent’s criteria, i.e. with a score of 1-3, were included in studies II,
III and IV.
18
MATERIAL AND METHODS
Microbiology in vaginal secretions as observed in the microscope
(paper I)
This paper was organized as a workshop for collaborative validation of robust concepts and
their dimensions expressed as vaginal smear scores. The workshop was undertaken on the
assumption that the concepts (i.e. morphotypes of bacteria, cells or other concepts) that form
the best basis of a scoring system are not known with certainty. Specific purposes of the
workshop were to evaluate the deviance between participants’ interpretations of each of some
selected criteria of BV and to evaluate the agreement between the different criteria assessed
as the mean of the different interpretations.
Collection of samples
An invitation to take part in the workshop was sent by the organizers to known
researchers and practitioners in the field. Participants collected a total of at least 20 slides of
vaginal smears including smears from at least seven patients with BV. The samples were
collected from patients seeking care for lower genital tract complaints using the local standard
method. A total of 258 slides thus collected were circulated among participants from the US,
Europe and Australia.
Amsel’s wet smear composite clinical criteria
The diagnosis is carried out in any clinical setting with access to a microscope and is based on
the following four criteria:
1.
Typical, thin, milky, homogenous fluor.
19
2.
pH>4.5
3.
Clue cells seen under the microscope in a wet smear
4.
Positive sniff test, i.e. an odour like rotten fish immediately after adding a drop
of 10% potassium hydroxide to the fluor.
Amsel’s criteria are positive for BV when three of the four criteria are fulfilled(1).
Nugent’s scoring system for Gram-stained smears
Score
0
Lactobacillus
morphotype
/vision field(x1000)
>30
Gardnerella
morphotype
/vision field(x1000)
0
Curved bacteria
morphotype
/vision field(x1000)
0
1
5-30
<1
1-5
2
1-4
1-4
>5
3
<1
5-30
4
0
>30
In the Nugent scoring system scores of 0-3 = normal flora, scores of 4-6 are intermediary
scores, and scores of 7-10 are BV(66).
Statistics
The results of different participants were compared using the kappa coefficient. Intra-observer
reliability of quantitative ratings was compared to agreement beyond chance. A value above
0.75 represents excellent agreement beyond chance(24).
20
Characterization of the dominating flora in healthy women with
normal vaginal flora (papers II and III)
Study population
In paper II, 23 healthy women scheduled for their regular cervical PAP smear at the antenatal
care unit at the University Hospital in Linköping, Sweden, were examined concerning their
vaginal microbiological status. In paper III, the dominating vaginal lactobacilli of 23 healthy
women were studied. Of the women in the first study, 12 returned three years later for their
scheduled PAP-smear check-up and thus took part in both studies.
Collection of samples
One sample of vaginal fluid was collected for culture, one for wet smear and composite
criteria of Amsel, and one was air dried for later Gram staining.
A sterile cotton swab was rolled over the upper third of the vaginal wall and placed in Copan
transport medium. After dilution the specimens were cultured for 42-72 h on horse blood agar
and Rogosa agar in 10% CO2 and 5% O2 at 37ºC.
Colonies from each kind of agar were randomly selected by marking colony positions in a
random fashion with a fine-point felt-tip pen on the bottom of each plate. After the plate was
inverted, the colony closest to the felt-tip pen mark, regardless of colour or size, was picked
for propagation and Gram staining. Colonies with Gram-positive bacteria with a Lactobacillus
like morphology were chosen for further investigation.
In paper II, the samples were spread with a rubber policeman on three different agar plates,
and three colonies were randomly selected from each plate for reculture. The first five
samples were cultivated in duplex. For paper III, 10 colonies from Rogosa agar and 10
colonies from blood agar were randomly selected for repropagation.
21
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Citation and related information available at http://www.rna.ccbb.utexas.edu/
AC
B-V3.as
V3
pJBS-V3.se
V1
pBR-V1.as
Lactobacillus acidophilus
(M58802)
1.cellular organisms 2.Bacteria 3.Firmicutes
4.Bacillus/Clostridium group 5.Bacillus/Lactobacillus/Streptococcus group
6.Lactobacillaceae 7.Lactobacillus
July 2001
Figure 1
22
Nucleic acid based techniques
Two different types of molecular biology methods were used to group and identify the strains
to the species level.
RAPD-PCR is a fingerprinting method targeting the whole bacterial genome.
The other methods all target the 16S rRNA gene, constituting around 1500 nucleotides. The
gene has extremely conserved regions, which are suitable targets for primers, mixed with
highly variable regions. Most endogenous bacteria as well as most pathogens are possible to
characterize with different polymerase chain reaction (PCR) methods. The gene from
Lactobacillus acidophilus is illustrated in figure 1(8).
Randomly Amplified Polymorphic DNA-PCR
Randomly amplified polymorphic DNA (RAPD) -PCR analysis was used to group the isolates
in the first study. An arbitrary primer of 9 nucleotides was used to amplify the DNA at a low
stringency annealing temperature. The number and the location of the random annealing sites
vary for different strains of a bacterial species. After separation of the amplified products with
agarose gel electrophoresis a pattern of bands characteristic of the particular bacterial strain is
produced.. Photographic negatives of the gels were scanned, analysed and grouped by
GelCompar 4.2 software.(46, 75, 91)
Temporal Temperature Gradient gel Electrophoresis
A PCR-product from the first 350 nucelotides of the 16S rDNA is analysed by TTGE on a
polyacrylamide gel plate with the temperature gradually rising from 61 to 71ºC, expanding the
separation range and thus increasing the sensitivity.(90)
23
Multiplex PCR
Multiplex PCR targeting the intergenic spacer region between the 16S and the 23S rDNAs
and the 23S rRNA gene is used in order first to group the strains to one of four groups. The
strains are then characterized with a multiplex-PCR II with species-specific primers for L.
acidophilus and L. jensenii and for L. crispatus and L. gasseri(81). The amplicons are
identified with agarose gel electrophoresis.
16S rDNA sequencing
The target for identification was the first 900 nucleotides from the 5’ end. After purification
the PCR products are used in sequence reactions with the Thermo Sequenas Cy5 Die
Terminator Kit with biotinylated primer. After purification, sequences are determinated in an
ALFexpressII instrument.
Pyrosequencing
Pyrosequencing is a real time sequence analysis technique. Pyrophosphate is detected upon
nucleotide incorporation.
Broad-range PCR amplification of 16S rDNA variable regions V1 and V3 is performed with
one of the primers in each pair being biotinylated (Figure 1). The biotinylated PCR products
are prepared with streptavidin coated Dynabeads followed by denaturation with sodium
hydroxide.
1. The sequencing primer is hybridized to the single stranded DNA template and
incubated with DNA polymerase, ATP sulphurylase, Luciferase, Apyrase, Adenosine
5’ phosphosulphate (APS) and Luciferin.
2. The first deoxynucleotide is added, incorporated by DNA polymerase. Pyrophosphate
(PPi) is released in equimolar quantity to the incorporated nucleotides.
24
3. PPi + APS
ATP sulphurylase ATP
4. Luciferin + ATP + O2
luciferase
oxyluciferin + AMP + PPi + CO2 + light
5. A CCD-camera detects light which generates a peak on a printer in proportion to the
number of incorporated nucleotides. Unincorporated nucleotides and ATP are
degraded by apyrase.
6. Back to step 2, with addition of the next nucleotide, and the process starts over again.
The signatures are then classified by alignment with NCBI catalogued sequences.
Characterization of the dominating flora in women during IVF
treatment (papers IV and V)
Study population
The study population started with 34 women following the protocol for IVF- treatment with
FSH-stimulation and ovum pickup. Five patients who did not show normal vaginal status
according to Amsel or Nugent were excluded. Twelve of the patients returned only once and
were likewise excluded from the study. Four of these patients with lactobacilli growing only
on blood agar are presented separately in paper V. Study IV comprises the vaginal secretions
of the remaining 17 women cultured at 62 occasions, three to five times per patient.
Hormonal assessment
Patients were treated according to the national guidelines for hyper ovulation in IVF
treatment. After downregulation with a GnRH- analogue, buserelin 0.15 mgx4 nasal
inhalation, FSH-stimulation was added (follitropin alfa or beta) with a typical subcutaneous
25
start dose of 150 IE daily.
The level of oestradiol in plasma was measured two weeks after start of the GnRH-analogue,
within one week from start of FSH-stimulation, and at each following visit with an ultrasound
check of follicular growth, and finally at ovum pick up. The patients who established a
pregnancy returned for an ultrasound check six weeks later and plasma was then also obtained
for determination of oestradiol.
Collection of samples of vaginal secretion
Samples were collected and cultured in the same manner as described above for studies II and
III. The selection of strains was done as described earlier. When growth on Rogosa agar was
successful, no colonies were collected from the horse blood agar plates. If colonies grew only
on horse blood agar, they were collected.
Bioinformatics
PCR and pyrosequencing was performed on the V1 and V3 regions of the 16S rRNA gene in
the same way as described above.
Reference 16S rRNA gene sequences of vaginal origin were aligned and arranged in
BioEdit(40) with Clustal W and with the Mega3(51) software. The signatures of the V1 and
V3 regions were checked for their ability to discriminate to the species level.
26
RESULTS AND DISCUSSION
Microbiology in vaginal secretions as observed in the microscope
Although Amsel's criteria are the accepted "gold standard" for the clinical diagnosis of BV,
the numerical score devised by Nugent et al. has gained wide acceptance as the scoring
system of choice. The Nugent scoring system is based on Spiegel’s bacterial morphotypes in
Gram-stained smears. The use of Gram-stained vaginal smears has also been validated against
Amsel's criteria in several different contexts, i.e. studies in the areas of obstetrics and
gynaecology. Agreement between the Amsel and Nugent criteria can vary, but by and large
the Gram stain appears to be the more accurate method(45). In treatment studies the more
reproducible Gram stain scoring methods are thus favoured. It is, however, important to
ensure that scoring systems meet the quality assessment requirements for procedures used in
daily diagnostic work. From this perspective, the robustness of scoring procedures must be
assessed when they are performed in different settings and populations around the world and
by different observers. The scoring systems have been criticized for having variables that are
not independent of each other and for including variables with low sensitivity and specificity.
Furthermore, the Nugent scoring system was originally set up to be used for BV diagnosis in
pregnancy.
In the international workshop on BV scoring (I) that is the starting point for this thesis, the
results were generally encouraging in that good concordance was observed among most
observers when valuated against each other with kappa statistics. However, many
disagreements arose as to the relation of scoring systems to diagnostic concepts not related to
BV (e.g. altered vaginal flora and intermediate flora), indicating a great need for further
27
studies on how to standardize and validate the scoring systems used. Specific technical and
interpretive items that were pinpointed by the workshop results include:
1. In general, there were major discrepancies when the lactobacilli were few in number. This
is of importance since the score intervals are narrow.
2. Disagreement on how to delineate between Gram-positive rods and small type bacteria (i e
Gardnerella and Bacteroides morphotypes).
3a. Further difficulties included preparation of specimens. Collecting techniques and tools
varied: speculums, wooden tools for PAP smears, cotton swabs and pH testers - resulting in
different thicknesses of the slides.
3b. Staining procedures varied - decolourization is the critical step.
4. Variations in vision fields among microscopes. The variation is estimated at a factor of two
or three in some microscopes (IX).
In addition, a recent publication pointed out the presence of sub-categories of slides from BVfree women that pinpoint, in particular, a distinct morphotype related to L. crispatus and a
subcategory possibly related to Bifidobacterium spp(98). There is also a lingering feeling
among researchers and practitioners using various scoring systems in microscopic slides for
the diagnosis of BV that the scores obtained do not always correspond to the perceived
condition of the women who are examined, and that this might be due to a variety of
interpretational problems.
To the best of our knowledge, no work has previously been published, apart from an initial
report by Dunkelberg, in which parameters pertaining to the scoring situation itself, and
validation of the scoring of the actual object seen, have been discussed in detail(17).
There has been disagreement on which morphotypes should be considered gram-positive rods
and thus scored as the lactobacillus morphotype (XII). A frequently occurring staining
phenomenon is the tendency of old lactobacilli to lose their gram-positivity. The staining
28
procedures vary; small bacteria morphotypes (Gardnerella and Prevotella morphotypes) may
vary in size and exist as round to more elongated forms where there is no defined border to
separate them from the lactobacillus morphotypes. No definite criteria exist for distinguishing
different Lactobacillus morphotypes and for demarcating them from the Gardnerella and
Prevotella morphotypes. Morphotypes suggestive of gram-positive cocci, which are not
accounted for in the scoring system, might in some cases be difficult to distinguish from the
Gardnerella and Prevotella morphotypes.
There is hence a need to study the effects of the above stated problems on scoring results.
Digital images of samples would offer a possibility to score exactly the same bacterial cells
and thus evaluate how various investigators score the different bacterial morphologies and
other specimen components. In a new workshop (XII), the participants were presented with
digital images at approximately the magnification obtained in a microscope and asked to
identify objects.
The workshop organizers identified 22 categories of microbial morphotypes and cellular
elements of importance for BV scoring, and selected digital images taken to represent
morphotypes and cellular elements that might be identified with low interobserver variation
by participants assigning the images to the predetermined classes.
Some morphotypes and cellular elements were deemed simple and others more difficult,
depending on the backgrounds of the 11 participants.
The other 10 participants and I categorized objects into the 22 predetermined categories listed
below. The results clearly indicated that most participants categorized various Lactobacillus
morphotypes similarly, but disagreed regarding the kind of Lactobacillus it was (wide vs.
thin). Prevotella and G. vaginalis morphotypes were surprisingly often categorized
incorrectly. Results at the more finely grained category level were even more discordant.
29
The conclusion is that the robustness of categorization of the included objects must be
considered doubtful, despite the fact that the categorization follows well-established
principles and is in common use all over the world. Categories of microbial morphotypes and
cellular elements of importance for BV scoring.
Lactobacillus
overdecolourized Gram-positive rod
thin Lactobacillus
curved rod-shaped bacterium
wide Lactobacillus
yeast
Enterobacteriacae
sperm
Fusobacterium
leucocyte
G. vaginalis
cervical epithelial cell
Mobiluncus
squamous epithelial cell
Prevotella
unknown object
coccus morphotypes
artefact
coccobacillus morphotypes
other object
Gram-positive rod
stain deposit
In the BV 00 workshop (I), mutual agreement on the three morphotype criteria (Lactobacillus,
Gardnerella/Prevotella and Mobiluncus) was lower than agreement on the quantity of any
given organism. This finding suggests that there is a smaller factual difference between the
criteria. The study also showed excellent interobserver agreements for the weighted kappa
statistics for scoring of so-called intermediate flora. Hillier et al. suggested that a higher
Nugent score is a sign of aggravation of BV. The data of Verhelst et al. point to the possibility
of identifiable subgroups of Lactobacillus morphotypes that correlate to Lactobacillus species
present in the slides. However, it has not been adequately determined if the Nugent
intermediate score truly represents another clinical group. Further, the relationship to disease
30
concepts other than BV, such as aerobic vaginitis and altered vaginal flora, has not been
explored in detail. Clearly, more studies are needed to elucidate these relationships. Our
findings indicate that the basic categorization of morphotypes is a key problem that needs
validation if concordance between scoring systems and individuals assigning scores is to be
achieved. This would be facilitated if Gram-stained smears were analysed in detail with
digital images, which is now technically possible with an excellent image quality, and the
respective morphotypes were correlated to individual libraries of DNA sequences of strains in
the vaginal fluid by using the FISH technique(28).
For a mutually agreed upon study of FISH-based DNA probes correlating morphotypes with
DNA sequence differences to be accepted, some basic categorization principles have to be
adhered to: observations in the microscope can be registered using a nominal scale, and
ranked on an ordinal scale(12, 13). The perceived morphotypes can be subjected to
comparative scrutiny, and robustness can be assessed in a comparison of how observations are
made by individuals(14). Definitions of analytical quality specifications are essential.
Dominating normal vaginal flora in healthy Swedish women.
Study II showed that L. crispatus, L. gasseri, L. iners, and L. jensenii were the most
frequently occurring species in the healthy vaginas of 23 Swedish women. Twenty of the
women were dominated by one species, and none by more than two.
RAPD analysis directly identified the isolates that could only grow on blood agar as L. iners.
L. iners is a newly described species(21). The absence of L. iners in other studies searching
for lactobacilli might be explained by the use of selective Lactobacillus media such as Rogosa
and MRS agar where these lactobacilli do not grow. The reasons for using the selective media
31
have traditionally been of a practical nature. Since there are at least 50 different species
present in the vaginal fluid, mostly in minute amounts, overgrowth of some of these has made
isolation of lactobacilli on routine agars extremely difficult.
Species such as L. rhamnosus, L. fermentum, L. plantarum, and L. acidophilus have also
frequently been recovered from the vagina(76, 96). The differences in Lactobacillus flora
between different studies may be attributed to a number of factors. The most likely
explanations are variations in the way that samples are taken and treated, the vaginal status,
and the fact that identification has previously often been based on phenotypic methods(64,
77).
To summarise, it is necessary to focus on true random sampling of non-selected colonies on
non-selective media in healthy vaginal fluid in order to describe the normal flora.
An important new finding of this study is the possibility that L. iners is one of the normally
occurring lactobacilli in the human vagina.
In study III, 17 women were found to be colonized with one species, four by two species and
one woman, aged 53 years, by four different species. The species identified were the same as
in study II.
Study III has introduced a new, fast, accurate technology that can, at a reasonable cost,
provide the tools for a more versatile numerical taxonomy for vaginal lactobacilli. With these
new tools the scope of Lactobacillus studies can be broadened to include the study of
geographical distribution, age, parity, diagnosis, treatment and so on. In such further studies it
is also important to define the vaginal status (i.e. normal Nugent and/or Amsel criteria) of the
study subjects in order to create a body of knowledge about normal Lactobacilli in fertile
women without interference from subjects in the study population with altered microflora
such as BV. Further typing of Lactobacillus species is also needed if studies of the
epidemiology of the various species in the vagina are to be successful. A possible tool for
32
identification of subtypes is multilocus sequence typing (MLST)(15, 62). Such a technique
might be necessary in order to trace colonization of administered probiotic strains in the
future.
Table I.
Study II+ study III
Woman
Study II
No of
strains
6
27
22
12
18
21
23
19
4
5
15
24
9
9
18
9
8
11
18
3
5
9
9
6
Species II
Species III
Study III
No of
strains
G
G
J
J
C
C
C
I
C
G
G
I
G
G
J
J10I4G1V1
C
C12J7
C11J2
I
G19C1
C
J
C
19
10
19
16
4
19
13
10
20
10
20
20
Table I presents a comparison of the results of studies II and III. Most of the women retained
the same dominating species when returning after three years. Four patients changed to one of
the other three dominating species. The main results were more or less the same with the two
different methods and different numbers of studied strains. The diversity in woman no. 12
might be due to a lower oestrogen level since she was 53 years of age at the time.
Dominating normal vaginal flora in patients during IVF treatment.
My thesis work provides more detailed descriptions of the species of lactobacilli that form
part of the normal flora in healthy women of childbearing age. The studies also seek to define
how the dominant lactobacilli flora changes over time. Women undergoing IVF-treatment can
33
be used as a suitable model for such studies in that the oestrogen levels of the women are
manipulated for the sake of the treatment. Studies on the co-variability of the flora and
oestrogen levels are thus possible in these women.
A total of 184 out of 186 lactobacillus isolates were subjected to PCR and pyrosequencing of
the 16S rRNA gene regions V1 and V3. Three sequences were obtained for each strain
subjected to PCR and pyrosequencing, one for the V1 region and two complementary
sequences for the V3 region. All were categorized separately and matched with the reference
strain of each species (for L. jensenii also two subtypes). Of a possible 552 sequences, 519
were suitable for sequence analysis.
Ten of 17 patients continued to exhibit L. crispatus, L. gasseri and/or L. jensenii with little
variation throughout the study period. The flora of three patients was dominated by L.
delbrüeckii, L. rhamnosus or L. vaginalis. One patient had a dominance of L. iners. The
remaining three had an initial flora dominated by L. rhamnosus or L. reuteri. With rising
oestrogen levels, the make-up of the flora changed and became dominated by one of the three
species of normal vaginal flora.
Paper V briefly describes four of the patients originally meant to be accepted for the paper IV
study. One patient presented with abnormal vaginal flora. At check-up eight days later she
presented with normal flora and was thus accepted for the paper IV study. This is patient no.
17, who presented with Lactobacillus iners throughout the study period. The other four
women, for different reasons, only returned once or twice and were therefore excluded from
the paper IV study. Since these patients all had lactobacilli growing only on blood agar, we
still found it worthwhile to analyse these strains too, in the same way as the strains in paper
IV.
One of the patients showed Lactobacillus iners and normal flora in both samples that were
taken. Two of the patients presented with Bacterial Vaginosis, were treated with
34
metronidazole 2g, and returned one week later with normal vaginal flora. The fifth patient
presented with abnormal flora and presented with normal vaginal flora at check-up thirteen
days later.
When these patients had normal vaginal flora according to Amsel and Nugent, the strains
were recultured and three colonies were randomly selected in the same way as described
earlier. One of these strains from each sample occasion was analysed with PCR and
pyrosequencing as in papers III and IV and was found to be Lactobacillus iners in all cases.
These findings are in concordance with the results of Ferris et al.(23).
The results from studies IV and V clearly indicate that by using molecular biology tools we
are now on the brink of finding ways of mapping the important changes in the vaginal flora
that could be the basis for further studies.
35
General summary
The diagnostic tools available to delineate healthy vaginal flora from non-healthy vaginal
flora need to be further developed. Poorly defined vaginal status is at least in part responsible
for the discordance of results in studies on the vaginal flora and is furthermore a key issue in
treatment studies of Bacterial Vaginosis.
Molecular biology techniques, especially sequencing of variable regions of the wellcharacterized 16S rRNA gene, are accurate in identifying the previously inseparable species
of the genus Lactobacillus. Pyrosequencing is suitable and accurate for high throughput
identification of vaginal lactobacilli.
The dominant species in healthy Swedish women and in Swedish women during IVF
treatment are L. crispatus, L. gasseri and L. jensenii. This is in concordance with studies in
very different settings around the world.
L. iners can be the dominating species in a healthy flora during the different phases of IVF
treatment, and initially after spontaneously resolved or medically treated Bacterial Vaginosis.
L. iners does not grow on media selective for Lactobacilli and thus it has not been identified
in many studies. To the best of my knowledge it has not previously been reported as
dominating the flora of women with normal vaginal flora.
During IVF-treatment at low oestrogen levels, other species of Lactobacilli, normally found in
the gut, can be dominant in the vaginal flora. At rising oestrogen levels the flora progressively
changes and becomes dominated by one of the three species found in normal vaginal flora.
36
Acknowledgements
I would like to express my thanks to:
All the women who contributed with small drops of vaginal fluid and without whom this
work would not have been possible.
Professor Urban Forsum, my main supervisor, for bringing me back to focus over and over
again, for introducing me into the fascinating world of the microbes, and for supporting me in
continuing this work and completing my thesis.
Assistant professors Lars Fåhraeus and Per-Göran Larsson, my co-supervisors, for pleasure,
friendship, and refreshing, wild, and crazy scientific ideas that finally produced quite a few
articles.
My co-authors in Lund and Linköping for excellent guidance, co-operation and skilful
production of manuscripts.
My colleagues and all the staff both at the Division of Obstetrics and Gynaecology and the
Department of Obstetrics and Gynaecology especially the Antenatal Care Unit, Outpatients
Clinic and Reproductive Medicine Centre as well as at the Division of Clinical Microbiology
and the Department of Clinical Microbiology in Linköping.
Special thanks to laboratory engineer Maud Nilsson and laboratory technicians Bodil Carlsson
and Anita Johansson for support and education in laboratory practice and for answering my
never-ending microbiological questions.
37
My relatives and friends for being there when I needed you.
My beloved wife Evy and our children Frida, Gustav and Arvid for giving me the fighting
spirit and for your eternal love.
The study was supported by grants from the Medical Research Council of Southeast Sweden
and by the ALF project at the University Hospital Linköping, Sweden.
38
39
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