Ali Kilic - Academia.edu (original) (raw)
Papers by Ali Kilic
Gazi Medical Journal, 1999
Mikrobiyoloji bülteni, 2002
The aim of this study was to identify the vaginal lactobacilli in the species level and to invest... more The aim of this study was to identify the vaginal lactobacilli in the species level and to investigate the concordance between classical methods and polymerase chain reaction (PCR) for the typing of these isolates. Vaginal swab samples which have been collected from women who were admitted to the outpatient clinics of Gynecology Department of our hospital, were examined by standard microbiological methods and additionally were inoculated into selective lactobacilli media. Of 200 subjects, 59.5% have had normal vaginal flora, 31% were diagnosed as bacterial vaginosis and 9.5% as vaginal candidiasis. The lactobacilli isolation rates of these groups were found 76.5%, 45.2% and 78.9%, respectively. A total of 160 facultative anaerobic Lactobacillus strains were isolated from 134 (67%) of the swab samples. Of these, 90.6% were identified into species level by classical methods, and the most frequently isolated species in our study was found as L. gasseri (40%), followed by L. delbrueckii...
Mikrobiyoloji bülteni, 2007
As Gardnerella vaginalis is accepted as a member of normal vaginal flora, it is one of the domina... more As Gardnerella vaginalis is accepted as a member of normal vaginal flora, it is one of the dominant species which has been related to bacterial vaginosis (BV). The aim of this study was to determine the isolation rate, biotypes and antibiotic resistance patterns of G.vaginalis from the vaginal swab samples of 408 women who were admitted to the outpatient clinics of Family Planning Center. Hippurate hydrolysis, lipase and beta-galactosidase tests were performed for biotyping the isolates, and agar dilution (for metronidazole) and disk diffusion (for clindamycin) tests were used for the detection of antibiotic resistance patterns. As a result, by Nugent's BV scoring protocol, 122 (29.9%), 20 (29.4%), 137 (33.6%), and 18 (4.4%) of the women were diagnosed as BV, intermediate form, normal vaginal flora (NVF) and mycotic vaginosis, respectively. The overall isolation rate of G.vaginalis was found as 23% (94/408). Of them, 56.4% (53/94) and 8.5% (8/94) were isolated from samples of BV...
Clinical Microbiology and Infection, 2004
The occurrence of cagA and vacA alleles among Helicobacter pylori isolates from Turkish patients ... more The occurrence of cagA and vacA alleles among Helicobacter pylori isolates from Turkish patients and their relationship with ulcer disease outcome was investigated. Among isolates from 47 patients with peptic ulcer disease and 51 patients with non-ulcer dyspepsia, 72.3% and 44.4%, respectively, were cagA-positive (p 0.019). Most (88.8%) isolates were typed as vacA s1, and all of these were subtype s1a. The commonest (51.0%) vacA genotype was s1a m1. The results of multivariate analysis indicated that infection with cagA-positive H. pylori was the only variable associated with an increased risk of peptic ulcer disease (odds ratio, 3.01; 95% confidence interval, 1.27-7.10; p 0.012).
Cardiovascular Pathology, 2006
It has been suggested that chronic infections may have a role in both the initiation and progress... more It has been suggested that chronic infections may have a role in both the initiation and progression of atherosclerosis. While the majority of available data are focused on coronary artery disease, our aim was to investigate the presence of Chlamydia pneumoniae and Helicobacter pylori in samples from aortoiliac occlusive disease. Aorta-iliac atherectomy specimens were collected under sterile conditions from 21 patients (19 male, 2 female) undergoing surgery for aortoiliac occlusive disease. Seventeen macroscopically healthy vessels (12 internal mammary arteries, 3 radial arteries, prepared for coronary artery bypass graft, and 2 traumatic artery specimens, one of which was a superficial femoral artery and the other was a radial artery) were used as control. Blood samples for serological assays were obtained immediately before surgery. The polymerase chain reaction (PCR) was employed to search for H. pylori and C. pneumoniae DNA in atherosclerotic plaques and healthy vessel samples. Group-specific chlamydial lipopolysaccharide (LPS) antigens in atherosclerotic plaques and in healthy vessel samples and serum IgG antibodies to chlamydial LPS were determined by using a commercially available enzyme-linked immunosorbent assay (ELISA). Antibodies to H. pylori were also tested in all cases by means of an in-house ELISA. Chlamydial LPS and DNA were detected in 6 of 21 (28.57%) atherosclerotic lesions using ELISA or PCR, respectively. There was no evidence of H. pylori DNA in any plaque specimens. All cases in which C. pneumoniae DNA was positive were also seropositive for antichlamydial LPS. Neither C. pneumoniae DNA nor antigen nor H. pylori DNA was found in the macroscopically healthy samples. Our results suggest that C. pneumoniae but not, as proposed, H. pylori may be involved in the pathogenesis of aortoiliac atherosclerosis.
Brazilian Journal of Microbiology, 2008
The extended-spectrum β-lactamase (ESBL)-producing bacteria have been isolated at increasing freq... more The extended-spectrum β-lactamase (ESBL)-producing bacteria have been isolated at increasing frequency worldwide. Expression of ESBL is often associated with multidrug resistance and dissemination by resistance plasmids. During a two-month period in 2000, 133 clinical isolates of enterobacterial strains were randomly collected from outpatients and inpatients at a university hospital in Turkey. The ESBL producing strains were determined by double-disk synergy (DDS) testing. Twenty ESBL producing strains (15%) including Escherichia coli (n = 9), Klebsiella pneumoniae (n = 7), Klebsiella oxytoca (n = 2) and Enterobacter aerogenes (n = 2) were detected and further analyzed for their resistance transfer features, plasmid profile and nature of the resistance genes. Plasmid transfer assays were performed using broth mating techniques. TEM-and SHV-genes were analyzed by polymerase chain reaction (PCR) and hybridization using specific probes. EcoRI restriction enzyme analyses of R plasmids were used in the detection of epidemic plasmids. Fourteen plasmid profiles (A, B1, B2, C1, and C2 to L) were obtained with EcoRI restriction enzyme analysis. Most of these plasmids were detected to carry both TEM-and SHV-derived genes by PCR, and confirmed by localizing each gene by hybridization assay. Epidemiological evidence indicated that there was an apparent horizontal dissemination of conjugative R plasmids among multidrug-resistant enterobacterial genera and species in this hospital.
Sugar metabolism by Streptococcus mutans is associated with tooth decay. The most abundant sugars... more Sugar metabolism by Streptococcus mutans is associated with tooth decay. The most abundant sugars in the human diet are sucrose and maltose, a derivative of starch. Previously, we reported a binding protein-dependent transport system (msm) in S. mutans that transports sucrose and maltose, but its associated enzymes do not metabolize maltose. By searching the S. mutans genomic sequence for a maltose system (mal), we found a gene cluster encoding proteins with homology to those of msm and the Escherichia coli maltose system. Mutants were constructed by deleting msm or mal, or both, and tested for sugar utilization. Deletion of the mal system diminished the ability of S. mutans to ferment maltose, but deletion of only the mal transporter genes or msm showed reduced utilization of chromogenic maltosides. Maltose, sucrose, glucose, fructose, mannose, and N-acetyl glucosamine inhibited utilization of chromogenic maltosides by the wild-type strain and mutants. In conclusion, the two bindin...
Developments in biological standardization, 1995
Anaerobe, 2001
Anaerobes contribute to the severity and chronicity of infections that occur in and around the or... more Anaerobes contribute to the severity and chronicity of infections that occur in and around the oral cavity. One of the factors involved in the pathogenesis of otitis media with effusion (OME) is the retrograde movement of bacteria from the oropharynx into the middle ear cavity. OME is one of the most common causes of hearing loss in children. We have used a PCR-based method to identify Actinobacillus actinomycetemcomitans, Porphyromonas gingivalis, Treponema denticola and Fusobacterium nucleatum in 65 middle ear effusion (MEE) samples obtained from paediatric patients seen for myringotomy and tube placement. DNA was extracted from MEE samples and PCR was initially done with DNA extracts by using the universal primers within the 16S rRNA gene sequence common to all bacterial species. The positive samples were further assessed with four species-specific primers. With the universal primers, 27 of 65 samples (41.5%) showed positive reaction indicating the presence of bacterial DNA. F. nucleatum was present in 10 out of 27 PCR-positive samples (37%) while one sample was positive for both T. denticola and F. nucleatum (3.7%). A. actinomycetemcomitans and P. gingivalis were not detected in any of the samples. The results of this study suggest that oral bacterial species may also play a role in the aetiopathogenesis of paediatric MEE.
Plasmid, 2002
Lactobacillus fermentum KC5b, a strain originally isolated from the human vagina, contains a cryp... more Lactobacillus fermentum KC5b, a strain originally isolated from the human vagina, contains a cryptic plasmid pKC5b. The sequence and genetic organization of the 4392-bp plasmid were determined. It contains two convergently oriented replicons, which are homologous to each other and to the stable replicon of the Enterococcus faecium plasmid pMBB1. The two replicons of pKC5b were used either individually or together to construct Lactobacillus-Escherichia coli shuttle plasmids. Only the plasmid pSP1 that carried both replicons transformed lactobacilli, suggesting a complementary function between the two replicons. Since the replicons had a high homology to those of other plasmids that replicate via a theta-like mechanism and no detectable single-stranded intermediates were found for the plasmid, it is possible that pKC5b may replicate via a theta-like mechanism. The new shuttle plasmid pSP1 has been transformed and stably maintained in several Lactobacillus strains. As an initial application, pSP1 was used to clone the S-layer protein gene (slpA) of Lactobacillus acidophilus ATCC 4356 into a heterologous vaginal Lactobacillus strain and achieved surface-bound expression of the protein.
Plasmid, 1997
Tn5252 is a promiscuous streptococcal element capable of madiating horizontal spread of multiple ... more Tn5252 is a promiscuous streptococcal element capable of madiating horizontal spread of multiple antibiotic resistance. To begin understanding the functional role of a transfer-related region in Tn5252, its nucleotide sequence was determined. Sequence of this 3.3-kb DNA segment revealed the presence of six open reading frames. The predicted amino acid sequence of one of the open reading frames, ORF9, showed similarity to a predicted protein product of the lactococcal conjugative plasmid, pC1528. The deduced primary protein sequence of another, ORF4, showed strong structural similarity to conserved regions of various prokaryotic DNA relaxases that initiate conjugal transfer by strand-and site-specific cleavage at the transfer origin. A hybrid protein containing the ORF4 protein fused to the carboxyl terminal end of maltose binding protein was purified from Escherichia coli and found to specifically nick plasmids carrying a 2-kb DNA segment derived from the transposon. The nicking reaction is protein concentration-dependent. These results imply that the conjugative transposition of Tn5252 may involve rolling circle replication and transfer of a unique DNA strand.
Journal of Applied Microbiology, 2002
Lactobacilli are widely distributed in food and the environment, and some colonize the human body... more Lactobacilli are widely distributed in food and the environment, and some colonize the human body as commensal bacteria. The aim of this study was to determine the species of lactobacilli that colonize the vagina and compare them with those found in food and the environment. Methods and Results: Thirty-®ve Lactobacillus strains from women from seven countries were isolated, and sequences from 16S rRNA genes were determined and compared with existing data in GenBank. A phylogenetic tree was achieved using the Neighbour-Joining method based on the analysis of 1465 nucleotides. The results showed that most vaginal isolates were L. crispatus, L. jensenii and L. gasseri. Some were L. vaginalis, L. fermentum, L. mucosae, L. paracasei and L. rhamnosus. Two isolates from a native American woman displayed distinct branches, indicating novel phylotypes. Few vaginal isolates matched food or environmental Lactobacillus species. Conclusions: Most women worldwide were colonized by three common Lactobacillus species: L. crispatus, L. jensenii and L. gasseri. Signi®cance and Impact of Study: Knowledge of vaginal Lactobacillus species richness and distribution in women worldwide may lead to the design of better probiotic products as bacterial replacement therapy.
Infectious Diseases in Obstetrics and Gynecology, 1997
Objective: During bacterial vaginosis, an unexplained decrease of vaginal lactobacilli occurs. To... more Objective: During bacterial vaginosis, an unexplained decrease of vaginal lactobacilli occurs. To identify whether these lactobacilli could be infected by phages, we isolated phages from vaginal lactobacilli and analyzed their potential virulence in attacking vaginal lactobacilli in vitro. Methods: Vaginal samples were obtained from 39 reproductive-aged women. The selective Rogosa SL agar was used to isolate lactobacilli, from which phages induced by mitomycin C or released spontaneoulsy were analyzed by the agar spot method. Results: Of 20 samples from women with vaginal infections, 12 did not have lactobacilli. From the remaining 8 infection samples and the 19 samples from healthy women, 37 Lactobacillus strains were isolated, from which 7 temperate phages were identified. Upon analysis, all 7 phages infected vaginal lactobacilli from the same and/or different women in vitro. Two phages, (bkc005 and (bkc007, had a broad host range, infecting 7 of 8 species tested. A control intestinal Lactobacillus phage also lysed several vaginal strains. One vaginal phage, (bkc039, was apparently lytic against vaginal lactobacilli from 7 other women. This phage was characterized as follows: plaque morphology, small and clear; burst size, 300 phages per cell; spontaneous induction rate, 1 per 106 cells; DNA, double-stranded and linear, 41 kb; and shape, a hexogonal head and a non-contractile tail. Conclusions: Bacteriophages were isolated from vaginal lactobacilli of some women and were shown in vitro to lyse vaginal Lactobacillus strains from the same and/or different women. It was suggested that vaginal lactobacilli might be suppressed by phages. Infect.
Infectious Diseases in Obstetrics and Gynecology, 1997
Objective: Bacterial vaginosis is associated with an unexplained loss of vaginal lactobacilli. Pr... more Objective: Bacterial vaginosis is associated with an unexplained loss of vaginal lactobacilli. Previously, we have identified certain vaginal lactobacilli-released phages that can inhibit in vitro other vaginal lactobacilli. However, there is no apparent route for phages to be transmitted among women. The purpose of this study was to identify whether certain Lactobacillus products commonly used by women release phages or bacteriocins that can inhibit vaginal lactobacilli. Methods: From 26 Lactobacillus products (2 acidophilus milks, 20 yogurts, 3 Lactobacillus pills, and 1 vaginal douche mix), lactobacilli were isolated with Rogosa SL agar (Difco, Detroit, MI). From these lactobacilli, phages and bacteriocins were induced with mitomycin C and tested against a collection of vaginal Lactobacillus strains. Results: From the 26 products, 43 Lactobacillus strains were isolated. Strains from 11 yogurts released phages, among which 7 inhibited vaginal lactobacilli. Eleven strains released bacteriocins that inhibited vaginal lactobacilli. While about one-half of the vaginal strains were lysed by bacteriocins, less than 20% were lysed by phages. Conclusions: Some vaginal lactobacilli were inhibited in vitro by phages or bacteriocins released from Lactobacillus products used by women, implying that vaginal lactobacilli may be reduced naturally due to phages or bacteriocins from the environment.
FEMS Microbiology Letters, 2007
Sugar metabolism by Streptococcus mutans is associated with tooth decay. The most abundant sugars... more Sugar metabolism by Streptococcus mutans is associated with tooth decay. The most abundant sugars in the human diet are sucrose and maltose, a derivative of starch. Previously, we reported a binding protein-dependent transport system (msm) in S. mutans that transports sucrose and maltose, but its associated enzymes do not metabolize maltose. By searching the S. mutans genomic sequence for a maltose system (mal), we found a gene cluster encoding proteins with homology to those of msm and the Escherichia coli maltose system. Mutants were constructed by deleting msm or mal, or both, and tested for sugar utilization. Deletion of the mal system diminished the ability of S. mutans to ferment maltose, but deletion of only the mal transporter genes or msm showed reduced utilization of chromogenic maltosides. Maltose, sucrose, glucose, fructose, mannose, and N-acetyl glucosamine inhibited utilization of chromogenic maltosides by the wild-type strain and mutants. In conclusion, the two binding protein-dependent systems in S. mutans appear to transport collaboratively their common substrate sugars, notably sucrose and maltose.
Clinical Diagnostic Laboratory Immunology, 2001
Lactobacilli play an important role in maintaining vaginal health. However, during bacterial vagi... more Lactobacilli play an important role in maintaining vaginal health. However, during bacterial vaginosis lactobacilli decrease for unknown reasons. Our preliminary study showed that phages could infect vaginal lactobacilli. Therefore, the aim of this study was to analyze the distribution, virulence, and types of vaginal Lactobacillus phages isolated from women of two countries: the United States and Turkey. A total of 209 vaginal lactobacilli were isolated from reproductive-aged women in the United States ( n = 107) and Turkey ( n = 102). By analysis of 16S rRNA gene sequence and by comparison of protein profiles, most lactobacilli were identified as L. crispatus , L. gasseri , and L. jensenii . After mitomycin C induction, 28% of American lactobacilli and 36% of Turkish lactobacilli released phages. A total of 67 phages were isolated and further characterized by their host range, electron microscopy, and DNA homology. All 67 phages were infective against lactobacilli from both collec...
The Eurasian Journal of Medicine
Gazi Medical Journal, 1999
Mikrobiyoloji bülteni, 2002
The aim of this study was to identify the vaginal lactobacilli in the species level and to invest... more The aim of this study was to identify the vaginal lactobacilli in the species level and to investigate the concordance between classical methods and polymerase chain reaction (PCR) for the typing of these isolates. Vaginal swab samples which have been collected from women who were admitted to the outpatient clinics of Gynecology Department of our hospital, were examined by standard microbiological methods and additionally were inoculated into selective lactobacilli media. Of 200 subjects, 59.5% have had normal vaginal flora, 31% were diagnosed as bacterial vaginosis and 9.5% as vaginal candidiasis. The lactobacilli isolation rates of these groups were found 76.5%, 45.2% and 78.9%, respectively. A total of 160 facultative anaerobic Lactobacillus strains were isolated from 134 (67%) of the swab samples. Of these, 90.6% were identified into species level by classical methods, and the most frequently isolated species in our study was found as L. gasseri (40%), followed by L. delbrueckii...
Mikrobiyoloji bülteni, 2007
As Gardnerella vaginalis is accepted as a member of normal vaginal flora, it is one of the domina... more As Gardnerella vaginalis is accepted as a member of normal vaginal flora, it is one of the dominant species which has been related to bacterial vaginosis (BV). The aim of this study was to determine the isolation rate, biotypes and antibiotic resistance patterns of G.vaginalis from the vaginal swab samples of 408 women who were admitted to the outpatient clinics of Family Planning Center. Hippurate hydrolysis, lipase and beta-galactosidase tests were performed for biotyping the isolates, and agar dilution (for metronidazole) and disk diffusion (for clindamycin) tests were used for the detection of antibiotic resistance patterns. As a result, by Nugent's BV scoring protocol, 122 (29.9%), 20 (29.4%), 137 (33.6%), and 18 (4.4%) of the women were diagnosed as BV, intermediate form, normal vaginal flora (NVF) and mycotic vaginosis, respectively. The overall isolation rate of G.vaginalis was found as 23% (94/408). Of them, 56.4% (53/94) and 8.5% (8/94) were isolated from samples of BV...
Clinical Microbiology and Infection, 2004
The occurrence of cagA and vacA alleles among Helicobacter pylori isolates from Turkish patients ... more The occurrence of cagA and vacA alleles among Helicobacter pylori isolates from Turkish patients and their relationship with ulcer disease outcome was investigated. Among isolates from 47 patients with peptic ulcer disease and 51 patients with non-ulcer dyspepsia, 72.3% and 44.4%, respectively, were cagA-positive (p 0.019). Most (88.8%) isolates were typed as vacA s1, and all of these were subtype s1a. The commonest (51.0%) vacA genotype was s1a m1. The results of multivariate analysis indicated that infection with cagA-positive H. pylori was the only variable associated with an increased risk of peptic ulcer disease (odds ratio, 3.01; 95% confidence interval, 1.27-7.10; p 0.012).
Cardiovascular Pathology, 2006
It has been suggested that chronic infections may have a role in both the initiation and progress... more It has been suggested that chronic infections may have a role in both the initiation and progression of atherosclerosis. While the majority of available data are focused on coronary artery disease, our aim was to investigate the presence of Chlamydia pneumoniae and Helicobacter pylori in samples from aortoiliac occlusive disease. Aorta-iliac atherectomy specimens were collected under sterile conditions from 21 patients (19 male, 2 female) undergoing surgery for aortoiliac occlusive disease. Seventeen macroscopically healthy vessels (12 internal mammary arteries, 3 radial arteries, prepared for coronary artery bypass graft, and 2 traumatic artery specimens, one of which was a superficial femoral artery and the other was a radial artery) were used as control. Blood samples for serological assays were obtained immediately before surgery. The polymerase chain reaction (PCR) was employed to search for H. pylori and C. pneumoniae DNA in atherosclerotic plaques and healthy vessel samples. Group-specific chlamydial lipopolysaccharide (LPS) antigens in atherosclerotic plaques and in healthy vessel samples and serum IgG antibodies to chlamydial LPS were determined by using a commercially available enzyme-linked immunosorbent assay (ELISA). Antibodies to H. pylori were also tested in all cases by means of an in-house ELISA. Chlamydial LPS and DNA were detected in 6 of 21 (28.57%) atherosclerotic lesions using ELISA or PCR, respectively. There was no evidence of H. pylori DNA in any plaque specimens. All cases in which C. pneumoniae DNA was positive were also seropositive for antichlamydial LPS. Neither C. pneumoniae DNA nor antigen nor H. pylori DNA was found in the macroscopically healthy samples. Our results suggest that C. pneumoniae but not, as proposed, H. pylori may be involved in the pathogenesis of aortoiliac atherosclerosis.
Brazilian Journal of Microbiology, 2008
The extended-spectrum β-lactamase (ESBL)-producing bacteria have been isolated at increasing freq... more The extended-spectrum β-lactamase (ESBL)-producing bacteria have been isolated at increasing frequency worldwide. Expression of ESBL is often associated with multidrug resistance and dissemination by resistance plasmids. During a two-month period in 2000, 133 clinical isolates of enterobacterial strains were randomly collected from outpatients and inpatients at a university hospital in Turkey. The ESBL producing strains were determined by double-disk synergy (DDS) testing. Twenty ESBL producing strains (15%) including Escherichia coli (n = 9), Klebsiella pneumoniae (n = 7), Klebsiella oxytoca (n = 2) and Enterobacter aerogenes (n = 2) were detected and further analyzed for their resistance transfer features, plasmid profile and nature of the resistance genes. Plasmid transfer assays were performed using broth mating techniques. TEM-and SHV-genes were analyzed by polymerase chain reaction (PCR) and hybridization using specific probes. EcoRI restriction enzyme analyses of R plasmids were used in the detection of epidemic plasmids. Fourteen plasmid profiles (A, B1, B2, C1, and C2 to L) were obtained with EcoRI restriction enzyme analysis. Most of these plasmids were detected to carry both TEM-and SHV-derived genes by PCR, and confirmed by localizing each gene by hybridization assay. Epidemiological evidence indicated that there was an apparent horizontal dissemination of conjugative R plasmids among multidrug-resistant enterobacterial genera and species in this hospital.
Sugar metabolism by Streptococcus mutans is associated with tooth decay. The most abundant sugars... more Sugar metabolism by Streptococcus mutans is associated with tooth decay. The most abundant sugars in the human diet are sucrose and maltose, a derivative of starch. Previously, we reported a binding protein-dependent transport system (msm) in S. mutans that transports sucrose and maltose, but its associated enzymes do not metabolize maltose. By searching the S. mutans genomic sequence for a maltose system (mal), we found a gene cluster encoding proteins with homology to those of msm and the Escherichia coli maltose system. Mutants were constructed by deleting msm or mal, or both, and tested for sugar utilization. Deletion of the mal system diminished the ability of S. mutans to ferment maltose, but deletion of only the mal transporter genes or msm showed reduced utilization of chromogenic maltosides. Maltose, sucrose, glucose, fructose, mannose, and N-acetyl glucosamine inhibited utilization of chromogenic maltosides by the wild-type strain and mutants. In conclusion, the two bindin...
Developments in biological standardization, 1995
Anaerobe, 2001
Anaerobes contribute to the severity and chronicity of infections that occur in and around the or... more Anaerobes contribute to the severity and chronicity of infections that occur in and around the oral cavity. One of the factors involved in the pathogenesis of otitis media with effusion (OME) is the retrograde movement of bacteria from the oropharynx into the middle ear cavity. OME is one of the most common causes of hearing loss in children. We have used a PCR-based method to identify Actinobacillus actinomycetemcomitans, Porphyromonas gingivalis, Treponema denticola and Fusobacterium nucleatum in 65 middle ear effusion (MEE) samples obtained from paediatric patients seen for myringotomy and tube placement. DNA was extracted from MEE samples and PCR was initially done with DNA extracts by using the universal primers within the 16S rRNA gene sequence common to all bacterial species. The positive samples were further assessed with four species-specific primers. With the universal primers, 27 of 65 samples (41.5%) showed positive reaction indicating the presence of bacterial DNA. F. nucleatum was present in 10 out of 27 PCR-positive samples (37%) while one sample was positive for both T. denticola and F. nucleatum (3.7%). A. actinomycetemcomitans and P. gingivalis were not detected in any of the samples. The results of this study suggest that oral bacterial species may also play a role in the aetiopathogenesis of paediatric MEE.
Plasmid, 2002
Lactobacillus fermentum KC5b, a strain originally isolated from the human vagina, contains a cryp... more Lactobacillus fermentum KC5b, a strain originally isolated from the human vagina, contains a cryptic plasmid pKC5b. The sequence and genetic organization of the 4392-bp plasmid were determined. It contains two convergently oriented replicons, which are homologous to each other and to the stable replicon of the Enterococcus faecium plasmid pMBB1. The two replicons of pKC5b were used either individually or together to construct Lactobacillus-Escherichia coli shuttle plasmids. Only the plasmid pSP1 that carried both replicons transformed lactobacilli, suggesting a complementary function between the two replicons. Since the replicons had a high homology to those of other plasmids that replicate via a theta-like mechanism and no detectable single-stranded intermediates were found for the plasmid, it is possible that pKC5b may replicate via a theta-like mechanism. The new shuttle plasmid pSP1 has been transformed and stably maintained in several Lactobacillus strains. As an initial application, pSP1 was used to clone the S-layer protein gene (slpA) of Lactobacillus acidophilus ATCC 4356 into a heterologous vaginal Lactobacillus strain and achieved surface-bound expression of the protein.
Plasmid, 1997
Tn5252 is a promiscuous streptococcal element capable of madiating horizontal spread of multiple ... more Tn5252 is a promiscuous streptococcal element capable of madiating horizontal spread of multiple antibiotic resistance. To begin understanding the functional role of a transfer-related region in Tn5252, its nucleotide sequence was determined. Sequence of this 3.3-kb DNA segment revealed the presence of six open reading frames. The predicted amino acid sequence of one of the open reading frames, ORF9, showed similarity to a predicted protein product of the lactococcal conjugative plasmid, pC1528. The deduced primary protein sequence of another, ORF4, showed strong structural similarity to conserved regions of various prokaryotic DNA relaxases that initiate conjugal transfer by strand-and site-specific cleavage at the transfer origin. A hybrid protein containing the ORF4 protein fused to the carboxyl terminal end of maltose binding protein was purified from Escherichia coli and found to specifically nick plasmids carrying a 2-kb DNA segment derived from the transposon. The nicking reaction is protein concentration-dependent. These results imply that the conjugative transposition of Tn5252 may involve rolling circle replication and transfer of a unique DNA strand.
Journal of Applied Microbiology, 2002
Lactobacilli are widely distributed in food and the environment, and some colonize the human body... more Lactobacilli are widely distributed in food and the environment, and some colonize the human body as commensal bacteria. The aim of this study was to determine the species of lactobacilli that colonize the vagina and compare them with those found in food and the environment. Methods and Results: Thirty-®ve Lactobacillus strains from women from seven countries were isolated, and sequences from 16S rRNA genes were determined and compared with existing data in GenBank. A phylogenetic tree was achieved using the Neighbour-Joining method based on the analysis of 1465 nucleotides. The results showed that most vaginal isolates were L. crispatus, L. jensenii and L. gasseri. Some were L. vaginalis, L. fermentum, L. mucosae, L. paracasei and L. rhamnosus. Two isolates from a native American woman displayed distinct branches, indicating novel phylotypes. Few vaginal isolates matched food or environmental Lactobacillus species. Conclusions: Most women worldwide were colonized by three common Lactobacillus species: L. crispatus, L. jensenii and L. gasseri. Signi®cance and Impact of Study: Knowledge of vaginal Lactobacillus species richness and distribution in women worldwide may lead to the design of better probiotic products as bacterial replacement therapy.
Infectious Diseases in Obstetrics and Gynecology, 1997
Objective: During bacterial vaginosis, an unexplained decrease of vaginal lactobacilli occurs. To... more Objective: During bacterial vaginosis, an unexplained decrease of vaginal lactobacilli occurs. To identify whether these lactobacilli could be infected by phages, we isolated phages from vaginal lactobacilli and analyzed their potential virulence in attacking vaginal lactobacilli in vitro. Methods: Vaginal samples were obtained from 39 reproductive-aged women. The selective Rogosa SL agar was used to isolate lactobacilli, from which phages induced by mitomycin C or released spontaneoulsy were analyzed by the agar spot method. Results: Of 20 samples from women with vaginal infections, 12 did not have lactobacilli. From the remaining 8 infection samples and the 19 samples from healthy women, 37 Lactobacillus strains were isolated, from which 7 temperate phages were identified. Upon analysis, all 7 phages infected vaginal lactobacilli from the same and/or different women in vitro. Two phages, (bkc005 and (bkc007, had a broad host range, infecting 7 of 8 species tested. A control intestinal Lactobacillus phage also lysed several vaginal strains. One vaginal phage, (bkc039, was apparently lytic against vaginal lactobacilli from 7 other women. This phage was characterized as follows: plaque morphology, small and clear; burst size, 300 phages per cell; spontaneous induction rate, 1 per 106 cells; DNA, double-stranded and linear, 41 kb; and shape, a hexogonal head and a non-contractile tail. Conclusions: Bacteriophages were isolated from vaginal lactobacilli of some women and were shown in vitro to lyse vaginal Lactobacillus strains from the same and/or different women. It was suggested that vaginal lactobacilli might be suppressed by phages. Infect.
Infectious Diseases in Obstetrics and Gynecology, 1997
Objective: Bacterial vaginosis is associated with an unexplained loss of vaginal lactobacilli. Pr... more Objective: Bacterial vaginosis is associated with an unexplained loss of vaginal lactobacilli. Previously, we have identified certain vaginal lactobacilli-released phages that can inhibit in vitro other vaginal lactobacilli. However, there is no apparent route for phages to be transmitted among women. The purpose of this study was to identify whether certain Lactobacillus products commonly used by women release phages or bacteriocins that can inhibit vaginal lactobacilli. Methods: From 26 Lactobacillus products (2 acidophilus milks, 20 yogurts, 3 Lactobacillus pills, and 1 vaginal douche mix), lactobacilli were isolated with Rogosa SL agar (Difco, Detroit, MI). From these lactobacilli, phages and bacteriocins were induced with mitomycin C and tested against a collection of vaginal Lactobacillus strains. Results: From the 26 products, 43 Lactobacillus strains were isolated. Strains from 11 yogurts released phages, among which 7 inhibited vaginal lactobacilli. Eleven strains released bacteriocins that inhibited vaginal lactobacilli. While about one-half of the vaginal strains were lysed by bacteriocins, less than 20% were lysed by phages. Conclusions: Some vaginal lactobacilli were inhibited in vitro by phages or bacteriocins released from Lactobacillus products used by women, implying that vaginal lactobacilli may be reduced naturally due to phages or bacteriocins from the environment.
FEMS Microbiology Letters, 2007
Sugar metabolism by Streptococcus mutans is associated with tooth decay. The most abundant sugars... more Sugar metabolism by Streptococcus mutans is associated with tooth decay. The most abundant sugars in the human diet are sucrose and maltose, a derivative of starch. Previously, we reported a binding protein-dependent transport system (msm) in S. mutans that transports sucrose and maltose, but its associated enzymes do not metabolize maltose. By searching the S. mutans genomic sequence for a maltose system (mal), we found a gene cluster encoding proteins with homology to those of msm and the Escherichia coli maltose system. Mutants were constructed by deleting msm or mal, or both, and tested for sugar utilization. Deletion of the mal system diminished the ability of S. mutans to ferment maltose, but deletion of only the mal transporter genes or msm showed reduced utilization of chromogenic maltosides. Maltose, sucrose, glucose, fructose, mannose, and N-acetyl glucosamine inhibited utilization of chromogenic maltosides by the wild-type strain and mutants. In conclusion, the two binding protein-dependent systems in S. mutans appear to transport collaboratively their common substrate sugars, notably sucrose and maltose.
Clinical Diagnostic Laboratory Immunology, 2001
Lactobacilli play an important role in maintaining vaginal health. However, during bacterial vagi... more Lactobacilli play an important role in maintaining vaginal health. However, during bacterial vaginosis lactobacilli decrease for unknown reasons. Our preliminary study showed that phages could infect vaginal lactobacilli. Therefore, the aim of this study was to analyze the distribution, virulence, and types of vaginal Lactobacillus phages isolated from women of two countries: the United States and Turkey. A total of 209 vaginal lactobacilli were isolated from reproductive-aged women in the United States ( n = 107) and Turkey ( n = 102). By analysis of 16S rRNA gene sequence and by comparison of protein profiles, most lactobacilli were identified as L. crispatus , L. gasseri , and L. jensenii . After mitomycin C induction, 28% of American lactobacilli and 36% of Turkish lactobacilli released phages. A total of 67 phages were isolated and further characterized by their host range, electron microscopy, and DNA homology. All 67 phages were infective against lactobacilli from both collec...
The Eurasian Journal of Medicine