High-resolution typing of Chlamydia trachomatis: epidemiological and clinical uses

Genetic characterization of the Entamoeba moshkovskii population based on different potential genetic markers

Entamoeba moshkovskii, according to recent studies, appears to exert a more significant impact on diarrhoeal infections than previously believed. The efficient identification and genetic characterization of E. moshkovskii isolates from endemic areas worldwide are crucial for understanding the impact of parasite genomes on amoebic infections. In this study, we employed a multilocus sequence typing system to characterize E. moshkovskii isolates, with the aim of assessing the role of genetic variation in the pathogenic potential of E. moshkovskii. We incorporated 3 potential genetic markers: KERP1, a protein rich in lysine and glutamic acid; amoebapore C (apc) and chitinase. Sequencing was attempted for all target loci in 68 positive E. moshkovskii samples, and successfully sequenced a total of 33 samples for all 3 loci. The analysis revealed 17 distinct genotypes, labelled M1–M17, across the tested samples when combining all loci. Notably, genotype M1 demonstrated a statistically significant association with diarrhoeal incidence within E. moshkovskii infection (P = 0.0394). This suggests that M1 may represent a pathogenic strain with the highest potential for causing diarrhoeal symptoms. Additionally, we have identified a few single-nucleotide polymorphisms in the studied loci that can be utilized as genetic markers for recognizing the most potentially pathogenic E. moshkovskii isolates. In our genetic diversity study, the apc locus demonstrated the highest Hd value and π value, indicating its pivotal role in reflecting the evolutionary history and adaptation of the E. moshkovskii population. Furthermore, analyses of linkage disequilibrium and recombination within the E. moshkovskii population suggested that the apc locus could play a crucial role in determining the virulence of E. moshkovskii.

Evaluation of Chlamydia trachomatis Genotypes in Endocervical Specimens by Sequence Analysis of ompA Gene among Women in Tehran

Tehran's actual prevalence of Chlamydia trachomatis (CT) and its genotypes are still unclear. Molecular typing of CT strains can provide essential epidemiological knowledge and contribute to improved control measures. In this study, we aimed to determine the prevalence of CT and its genotypes in the endocervical infections of females who attended the gynecology and infertility clinics in Tehran. A total of 291 women were tested for chlamydial infection by in-house PCR using specific primers for the CT cryptic plasmid. Nested PCR for amplification of the ompA gene in positive samples was carried out, genotyping was performed by sequencing this gene, and further phylogenetic analysis was conducted. Sexual infection by CT was observed in 10.3% (30/291) of the subjects, and the mean age of patients was 30.4. The ompA gene was sequenced in 27 samples, revealing E genotypes 40.7%, (n = 11), F 25.9%, (n = 7), G 18.5%, (n = 5), D 11.1%, (n = 3), and K 3.7%, (n = 1). This study emphasizes the importance of the diversity among CT genotypes in our studied population and the need for wide-screening the neglected bacterial infection among women in Tehran.

Specific high-resolution scheme to improve understanding of the spatio-temporal dispersion of lymphogranuloma venereum epidemic

Introduction

Lymphogranuloma venereum (LGV) is already endemic in vulnerable populations in several European countries; however, molecular epidemiology data with improved accuracy are necessary to better understand LGV epidemic in these countries. Current strategies to study the molecular epidemiology of LGV cases involve schemes based on a few genetic fragments of Chlamydia trachomatis, which have demonstrated limited discriminatory power for LGV. Therefore, this study aimed to propose a new combination of molecular markers based on the most variable genes of L-genotype genomes to improve the characterization of the current LGV epidemic in Madrid, Spain.

Methods

Four genes were selected according to their diversity index (CTLon_0054, CTLon_0087, CTLon_0243 and CTLon_0301) for use in combination with ompA. In silico and experimental studies were performed to compare the previously described multilocus sequence typing (MLST) schemes with our proposal. Moreover, the proposed scheme was applied (n = 68) to analyze the spatio-temporal spread of the LGV cases.

Results

Our proposal demonstrated higher diversity allowing the identification of three main groups compared to the previously published MLST based on hypervariable genes wherein only a single sequence type was identified. The temporal analysis showed that the major cluster was progressively diversifying, revealing a very active transmission chain. Furthermore, an L2b genome identical to that of the origin of the epidemic was detected, suggesting reintroductions or a low screening rate in vulnerable populations. The spatial distribution suggests that the selection and spread of new variants occurs from the central district to the peripheral regions.

Discussion

The scheme proposed in this study has proven to be useful for appropriate discrimination of LGV strains. This study, to our knowledge for the first time, demonstrates a spatio-temporal spread that increases our understanding and identifies areas with special susceptibility for maintenance of the endemic situation of LGV.

Genomic Analysis of MSM Rectal Chlamydia trachomatis Isolates Identifies Predicted Tissue-Tropic Lineages Generated by Intraspecies Lateral Gene Transfer-Mediated Evolution

Chlamydia trachomatis is an obligate intracellular bacterium that causes serious diseases in humans. Rectal infection and disease caused by this pathogen are important yet understudied aspects of C. trachomatis natural history. The University of Washington Chlamydia Repository has a large collection of male-rectal-sourced strains (MSM rectal strains) isolated in Seattle, USA and Lima, Peru. Initial characterization of strains collected over 30 years in both Seattle and Lima led to an association of serovars G and J with male rectal infections. Serovar D, E, and F strains were also collected from MSM patients. Genome sequence analysis of a subset of MSM rectal strains identified a clade of serovar G and J strains that had high overall genomic identity. A genome-wide association study was then used to identify genomic loci that were correlated with tissue tropism in a collection of serovar-matched male rectal and female cervical strains. The polymorphic membrane protein PmpE had the strongest correlation, and amino acid sequence alignments identified a set of PmpE variable regions (VRs) that were correlated with host or tissue tropism. Examination of the positions of VRs by the protein structure-predicting Alphafold2 algorithm demonstrated that the VRs were often present in predicted surface-exposed loops in both PmpE and PmpH protein structure. Collectively, these studies identify possible tropism-predictive loci for MSM rectal C. trachomatis infections and identify predicted surface-exposed variable regions of Pmp proteins that may function in MSM rectal versus cervical tropism differences.

Chlamydia trachomatis as a Current Health Problem: Challenges and Opportunities

Chlamydia is one of the most common sexually transmitted bacterial infections (STIs) worldwide. It is caused by Chlamydia trachomatis (CT), which is an obligate intracellular bacterium. In some cases, it can occur in coinfection with other parasites, increasing the pathologic potential of the infection. The treatment is based on antibiotic prescription; notwithstanding, the infection is mostly asymptomatic, which increases the risk of transmission. Therefore, some countries have implemented Chlamydia Screening Programs in order to detect undiagnosed infections. However, in Portugal, there is no CT screening plan within the National Health Service. There is no awareness in the general healthcare about the true magnitude of this issue because most of the methods used are not Nucleic Acid Amplification Technology-based and, therefore, lack sensitivity, resulting in underreporting infection cases. CT infections are also associated with possible long-term severe injuries. In detail, persistent infection triggers an inflammatory milieu and can be related to severe sequels, such as infertility. This infection could also trigger gynecologic tumors in women, evidencing the urgent need for cost-effective screening programs worldwide in order to detect and treat these individuals adequately. In this review, we have focused on the success of an implemented screening program that has been reported in the literature, the efforts made concerning the vaccine discovery, and what is known regarding CT infection. This review supports the need for further fundamental studies in this area in order to eradicate this infection and we also suggest the implementation of a Chlamydia Screening Program in Portugal.

Diagnosis of Chlamydia trachomatis genital infections in the era of genomic medicine

PURPOSE

Chlamydial genital infections constitute significant sexually transmitted infections worldwide. The often asymptomatic status of C. trachomatis (CT) infections leads to an increased burden on human reproductive health, especially in middle- and low-income settings. Early detection and management of these infections could play a decisive role in controlling this public health burden. The objective of this review is to provide an insight into the evolution of diagnostic methods for CT infections through the development of new molecular technologies, emphasizing on -omics' technologies and their significance as diagnostic tools both for effective patient management and control of disease transmission.

METHODS

Narrative review of the diagnostic methodologies of CT infections and the impact of the introduction of -omics' technologies on their diagnosis by review of the literature.

RESULTS

Various methodologies are discussed with respect to working principles, required specifications, advantages, and disadvantages. Implementing the most accurate methods in diagnosis is highlighted as the cornerstone in managing CT infections.

CONCLUSION

Diagnostics based on -omics' technologies are considered to be the most pertinent modalities in CT testing when compared to other available methods. There is a need to modify these effective and accurate diagnostic tools in order to render them more available and feasible in all settings, especially aiming on turning them to rapid point-of-care tests for effective patient management and disease control.

Evaluation of 2 Commercial Assays for the Detection of Lymphogranuloma Venereum in Rectal Samples

BACKGROUND

The early identification of the Chlamydia trachomatis variants that cause lymphogranuloma venereum (LGV) is very important to establish an adequate antibiotic treatment. This identification should be made with molecular techniques that are easy to perform and accessible to most microbiology laboratories. The objective of this study was to evaluate 2 real-time polymerase chain reaction (PCR)-based assay (VIASURE Haemophilus ducreyi + C. trachomatis (LGV) real-time PCR detection kit and the Allplex Genital ulcer Assay) for the detection of LGV in rectal samples.

MATERIALS AND METHODS

Prospective study on positive rectal samples for C. trachomatis. All samples were processed in parallel by both tests. As a molecular reference method and to solve possible discrepancies between both assays, a PCR-based restriction fragment length polymorphism analysis of the major outer membrane protein gene (omp1) was used.

RESULTS

In total, we detected 157 positive rectal samples for C. trachomatis, of which 36 were identified as LGV by PCR-based restriction fragment length polymorphism analysis. The positive percent agreement, negative percent agreement, and overall percent agreement were 88.9%, 100%, and 97.3%, respectively, for the Allplex Genital ulcer assay and 91.6%, 100%, and 97.1%, respectively, for the VIASURE assay. In the direct comparison between the Seegene assay and the VIASURE assay, we obtained a kappa concordance index of 0.98 between both tests.

CONCLUSIONS

According to the results obtained, both tests could be used for the detection of LGV in rectal samples.

High-resolution multilocus sequence typing for Chlamydia trachomatis: improved results for clinical samples with low amounts of C. trachomatis DNA

BACKGROUND

Several Multilocus Sequence Typing (MLST) schemes have been developed for Chlamydia trachomatis. Bom's MLST scheme for MLST is based on nested PCR amplification and sequencing of five hypervariable genes and ompA. In contrast to other Chlamydia MLST schemes, Bom's MLST scheme gives higher resolution and phylogenetic trees that are comparable to those from whole genome sequencing. However, poor results have been obtained with Bom's MLST scheme in clinical samples with low concentrations of Chlamydia DNA.

RESULTS

In this work, we present an improved version of the scheme that is based on the same genes and MLST database as Bom's MLST scheme, but with newly designed primers for nested-1 and nested-2 steps under stringent conditions. Furthermore, we introduce a third primer set for the sequencing step, which considerably improves the performance of the assay. The improved primers were tested in-silico using a dataset of 141 Whole Genome Sequences (WGS) and in a comparative analysis of 32 clinical samples. Based on cycle threshold and melting curve analysis values obtained during Real-Time PCR of nested-1 & 2 steps, we developed a simple scoring scheme and flow chart that allow identification of reaction inhibitors as well as to predict with high accuracy amplification success. The improved MLST version was used to obtain a genovars distribution in patients attending an STI clinic in Tel Aviv.

CONCLUSIONS

The newly developed MLST version showed great improvement of assay results for samples with very low concentrations of Chlamydia DNA. A similar concept could be applicable to other MLST schemes.

Reduction of non-typeable results using a plasmid oriented Lymfogranuloma venereum PCR for typing of Chlamydia trachomatis positive samples

Objectives

Typing of Chlamydia trachomatis (CT) is traditionally performed by characterising the ompA gene, resulting in more than a dozen different genovars, A to L. Type L is associated with Lymphogranuloma venereum (LGV) and commonly screened for using PCR, targeting the chromosomal pmpH gene. We aimed to develop and validate a new CT/LGV plasmid-based typing assay targeting the pgp3 gene, to increase sensitivity and thus reduce the number of non-typeable results.

Methods

The new pgp3 PCR assay using LNA probes to detect point mutations was analytically and prospectively validated in a routine diagnostic laboratory setting. For the analytical tests, quantified nucleotide constructs (gBlocks) were used to perform limit of detection analyses. Quality control panel samples from 2018 and 2019 for CT were also tested. For the clinical study patient samples which were collected in two months in 2018 were tested simultaneously using the pmpH PCR and the pgp3 PCR.

Results

Analytically, the assay proved to be 100% specific relative to the previously used LGV typing assay targeting the single copy pmpH gene but it was much more sensitive to detect non-LGV CT. In the quality control panel 2 nonLGV samples and 7 LGV samples were solely positive with the pgp3 PCR and not with the pmpH PCR. None of the samples from analytical specificity panels were positive, indicating 100% specificity. In a prospective panel of 152 clinical samples, 142 (93%) were successfully typed with the pgp3 PCR compared to 78% with the pmpH PCR. The pgp3 PCR was fully concordant with the pmpH PCR to identify all LGV subtypes and detected an increased number of clinical samples of non-LGV subtype.

Conclusion

We developed and validated a sensitive and specific plasmid-based typing assay to discriminate LGV from non-LGV CT subtypes. This is useful in a clinical setting to quickly determine the optimal treatment for Chlamydia trachomatis infections.

Chlamydiae from Down Under: The Curious Cases of Chlamydial Infections in Australia

In Australia, the most researched and perhaps the most successful chlamydial species are the human pathogen Chlamydia trachomatis, animal pathogens Chlamydia pecorum and Chlamydia psittaci. C. trachomatis remains the leading cause of sexually transmitted infections in Australians and trachoma in Australian Indigenous populations. C. pecorum is globally recognised as the infamous koala and widespread livestock pathogen, whilst the avian C. psittaci is emerging as a horse pathogen posing zoonotic risks to humans. Certainly not innocuous, the human infections with Chlamydia pneumoniae seem to be less prevalent that other human chlamydial pathogens (namely C. trachomatis). Interestingly, the complete host range for C. pecorum and C. psittaci remains unknown, and infections by other chlamydial organisms in Australian domesticated and wildlife animals are understudied. Considering that chlamydial organisms can be encountered by either host at the human/animal interface, I review the most recent findings of chlamydial organisms infecting Australians, domesticated animals and native wildlife. Furthermore, I also provide commentary from leading Australian Chlamydia experts on challenges and future directions in the Chlamydia research field.

2019 European guideline on the management of lymphogranuloma venereum

New or important issues in this updated version of the 2013 European guideline on the management of lymphogranuloma venereum (LGV): EPIDEMIOLOGY: Lymphogranuloma venereum continues to be endemic among European men who have sex with men (MSM) since 2003. Lymphogranuloma venereum infections in heterosexuals are extremely rare in Europe, and there is no evidence of transmission of LGV in the European heterosexual population.

AETIOLOGY AND TRANSMISSION

Chlamydia trachomatis serovars/genovars L2b and L2 are the causative strains in the majority of cases in Europe.

CLINICAL FEATURES

Among MSM, about 25% of the anorectal LGV infections are asymptomatic. Genital infections among MSM are rare; the ratio of genital vs. anorectal LGV infections is 1 in 15.

DIAGNOSIS

To diagnose LGV, a sample tested C. trachomatis positive with a commercial nucleic acid amplification test (NAAT) platform should be confirmed with an LGV discriminatory NAAT.

TREATMENT

Doxycycline 100 mg twice a day orally for 21 days is the recommended treatment for LGV. This same treatment is recommended also in asymptomatic patients and contacts of LGV patients. If another regimen is used, a test of cure (TOC) must be performed.

Unveiling the Multilocus Sequence Typing (MLST) Schemes and Core Genome Phylogenies for Genotyping Chlamydia trachomatis

Multilocus sequence typing (MLST) has become a useful tool for studying the genetic diversity of important public health pathogens, such as Chlamydia trachomatis (Ct). Four MLST schemes have been proposed for Ct (data available from Chlamydiales MLST databases). However, the lack of a sole standardized scheme represents the greatest limitation regarding typing this species. This study was thus aimed at evaluating the usefulness of the four MLST schemes available for Ct, describing each molecular marker's pattern and its contribution toward a description of intra-specific genetic diversity and population structure. The markers for each scheme, showed a variable power of dicrimination, exhibiting in some cases over estimation in the determination of Sequence Types (STs). However, individual analysis of each locus's typing efficiency and discrimination power led to identifying 8 markers as having a suitable pattern for intra-specific typing. analyzing the 8 candidate markers gave a combination of 3 of these loci as an optimal scheme for identifying a large amount of STs, maximizing discrimination power whilst maintaining suitable typing efficiency. One scheme was compared against core genome phylogenies, finding a higher typing resolution through the last approach. These results confirm once again that although complete genome data, in particular from core genome MLST (cgMLST) allow a high resolution clustering for Ct isolates. There are combinations of molecular markers that could generate equivalent results, with the advantage of representing an easy implementation strategy and lower costs leading to contribute to the monitoring and molecular epidemiology of Ct.

Discovery of Human-Specific Immunodominant Chlamydia trachomatis B Cell Epitopes

Current serological assays for species-specific detection of anti-Chlamydia species antibodies suffer from well-known shortcomings in specificity and ease of use. Due to the high prevalences of both anti-C. trachomatis and anti-C. pneumoniae antibodies in human populations, species-specific serology is unreliable. Therefore, novel specific and simple assays for chlamydial serology are urgently needed. Conventional antigens are problematic due to extensive cross-reactivity within Chlamydia spp. Using accurate B cell epitope prediction and a robust peptide ELISA methodology developed in our laboratory, we identified immunodominant C. trachomatis B cell epitopes by screening performed with sera from C. trachomatis-infected women. We discovered 38 novel human host-dependent antigens from 20 immunodominant C. trachomatis proteins, in addition to confirming 10 host-independent mouse serum peptide antigens that had been identified previously. This extended set of highly specific C. trachomatis peptide antigens can be used in simple ELISA or multiplexed microarray formats and will provide high specificity and sensitivity to human C. trachomatis serodiagnosis.

Chlamydia species-specific serology is compromised by cross-reactivity of the gold standard microimmunofluorescence (MIF) or commercial enzyme-linked immunosorbent assays (ELISAs). This study was conducted to discover novel C. trachomatis-specific peptide antigens that were recognized only by the antibody response of the natural human host. We evaluated a library of 271 peptide antigens from immunodominant C. trachomatis proteins by reactivity with 125 C. trachomatis antibody-positive sera from women with PCR-confirmed C. trachomatis infection and 17 C. trachomatis antibody-negative sera from low-risk women never diagnosed with C. trachomatis infection. These C. trachomatis peptide antigens had been predicted in silico to contain B cell epitopes but had been nonreactive with mouse hyperimmune sera against C. trachomatis. We discovered 38 novel human host-dependent antigens from 20 immunodominant C. trachomatis proteins (PmpD, IncE, IncG, CT529, CT618, CT442, TarP, CT143, CT813, CT795, CT223, PmpC, CT875, CT579, LcrE, IncA, CT226, CT694, Hsp60, and pGP3). Using these human sera, we also confirmed 10 C. trachomatis B cell epitopes from 6 immunodominant C. trachomatis proteins (OmpA, PmpD, IncE, IncG, CT529, and CT618) as host species-independent epitopes that had been previously identified by their reactivity with mouse hyperimmune sera against C. trachomatis. ELISA reactivities against these peptides correlated strongly with the C. trachomatis microimmunofluorescence (MIF) text results (Pearson’s correlation coefficient [R] = 0.80; P < 10⁻⁶). These C. trachomatis peptide antigens do not cross-react with antibodies against other Chlamydia species and are therefore suitable for species-specific detection of antibodies against C. trachomatis. This study identified an extended set of peptide antigens for simple C. trachomatis-specific ELISA serology.

IMPORTANCE Current serological assays for species-specific detection of anti-Chlamydia species antibodies suffer from well-known shortcomings in specificity and ease of use. Due to the high prevalences of both anti-C. trachomatis and anti-C. pneumoniae antibodies in human populations, species-specific serology is unreliable. Therefore, novel specific and simple assays for chlamydial serology are urgently needed. Conventional antigens are problematic due to extensive cross-reactivity within Chlamydia spp. Using accurate B cell epitope prediction and a robust peptide ELISA methodology developed in our laboratory, we identified immunodominant C. trachomatis B cell epitopes by screening performed with sera from C. trachomatis-infected women. We discovered 38 novel human host-dependent antigens from 20 immunodominant C. trachomatis proteins, in addition to confirming 10 host-independent mouse serum peptide antigens that had been identified previously. This extended set of highly specific C. trachomatis peptide antigens can be used in simple ELISA or multiplexed microarray formats and will provide high specificity and sensitivity to human C. trachomatis serodiagnosis.

Laboratory Processes for Confirmation of Lymphogranuloma Venereum Infection During a 2015 Investigation of a Cluster of Cases in the United States

In September 2015, the Centers for Disease Control and Prevention were notified of a suspected outbreak investigation of lymphogranuloma venereum (LGV) cases by the Michigan Department of Health and Human Services. The Centers for Disease Control and Prevention offered support with a laboratory-developed polymerase chain reaction test for LGV. This note describes the laboratory workflow and procedures used for the laboratory confirmation of LGV infection.

Comparison of reverse hybridization and ompA sequencing methods applied on Chlamydia trachomatis strains from Tunisia

Two techniques based on ompA amplification of Chlamydia trachomatis were compared, being reverse hybridization (RHM) and ompA sequencing (OSA), to investigate the concordance between them and to study the epidemiological relevance of each method. In addition, phylogenetic analysis was performed on the ompA sequences. One hundred and seven C. trachomatis positive samples from Tunisian patients and female sex workers were analyzed using both the RHM and ompA sequencing. The overall genovar distribution obtained with both techniques was very similar. The RHM identified nine genovars, being B, D, E, F, G, H, I, J and K, where B, I, J, and K were only found in mixed infections versus 7 types for the OSA being D, E, F, G, H, I, and K. The agreement between both typing techniques was 87.8%. Both methods showed that genovar E was the most predominant type. In 24.3% of the analyzed samples, mixed infections were detected. In 96.1% of these, the genovar identified by OSA was also detected using the RHM. OmpA sequencing allowed determination of six genovar types that could not be typed using RHM. The analyses of ompA nucleotide variation in the 107 clinical specimens detected ompA genovar variants with distinct ompA mutational patterns for types D2, G1, G2, and H1. In conclusion, RHM and OSA showed a high agreement in C. trachomatis genotyping results with each having their specific benefits.

Anorectal Lymphogranuloma Venereum in Madrid: A Persistent Emerging Problem in Men Who Have Sex With Men

BACKGROUND

Since 2003, outbreaks of lymphogranuloma venereum (LGV) with anorectal syndrome have been increasingly recognized in many Western countries. All of them have been classified as LGV serovar L2b, mainly occurring in human immunodeficiency virus (HIV)-infected men who have had sex with men (MSM). We describe a series of 26 diagnosed cases of LGV proctitis in downtown Madrid, Spain, in 2014, after implementing routine diagnostic procedures for this disease in symptomatic MSM.

METHODS

We conducted an observational study of patients with symptomatic proctitis attending an outpatient infectious diseases clinic in Madrid, Spain during calendar year 2014. Clinical, epidemiological, laboratory, and therapeutic data were gathered and analyzed.

RESULTS

Twenty-six patients were included in the analysis. All were MSM, and 24 of them were HIV-positive. All patients reported having acute proctitis symptoms including tenesmus (85%), pain (88%), constipation (62%), or anal discharge (96%). Proctoscopy showed mucopurulent exudate (25 patients [96%]), and rectal bleeding, with mucosal erythema and/or oedema in all cases. Rectal swabs were obtained from all patients, and LGV serovar L2 was confirmed in all of them. The cure rate was 100% after standard treatments with doxycycline 100 mg twice per day for 3 weeks. Simultaneous rectal infections with other sexually transmitted pathogens (gonorrhoea, herpes simplex virus, Mycoplasma genitalium) and systemic sexually transmitted diseases (STDs) (syphilis, acute HIV, and hepatitis C infections) were also documented in 12 patients (46%), but these co-infections did not appear to influence the clinical manifestations of LGV.

CONCLUSIONS

Anorectal LGV is a common cause of acute proctitis and proctocolitis among HIV-infected MSM who practice unprotected anal sex, and it is frequently associated with other rectal STDs. The implementation of routine screening and prompt diagnosis of these rectal infections should be mandatory in all clinical settings attended by HIV and STD patients.

Azithromycin Treatment Failure for Chlamydia trachomatis Among Heterosexual Men With Nongonococcal Urethritis

BACKGROUND

Three recent prospective studies have suggested that the 1-g dose of azithromycin for Chlamydia trachomatis (Ct) was less effective than expected, reporting a wide range of treatment failure rates (5.8%-22.6%). Reasons for the disparate results could be attributed to geographic or methodological differences. The purpose of this study was to reexamine the studies and attempt to harmonize methodologies to reduce misclassification as a result of false positives from early test-of-cure (TOC) or reinfection as a result of sexual exposure rather than treatment failure.

METHODS

Men who had sex with women, who received 1-g azithromycin under directly observed therapy for presumptive treatment of nongonococcal urethritis with confirmed Ct were included. Baseline screening was performed on urethral swabs or urine, and TOC screening was performed on urine using nucleic acid amplification tests. Posttreatment vaginal sexual exposure was elicited at TOC. Data from the 3 studies were obtained and reanalyzed. Rates of Ct retest positive were examined for all cases, and a sensitivity analysis was conducted to either reclassify potential false positives/reinfections as negative or remove them from the analysis.

RESULTS

The crude treatment failure rate was 12.8% (31/242). The rate when potential false positives/reinfections were reclassified as negative was 6.2% (15/242) or when these were excluded from analysis was 10.9% (15/138).

CONCLUSIONS

In these samples of men who have sex with women with Ct-related nongonococcal urethritis, azithromycin treatment failure was between 6.2% and 12.8%. This range of failure is lower than previously published but higher than the desired World Health Organization's target chlamydia treatment failure rate of < 5%.

Bacterial genome sequencing in clinical microbiology: a pathogen-oriented review

In recent years, whole-genome sequencing (WGS) has been perceived as a technology with the potential to revolutionise clinical microbiology. Herein, we reviewed the literature on the use of WGS for the most commonly encountered pathogens in clinical microbiology laboratories: Escherichia coli and other Enterobacteriaceae, Staphylococcus aureus and coagulase-negative staphylococci, streptococci and enterococci, mycobacteria and Chlamydia trachomatis. For each pathogen group, we focused on five different aspects: the genome characteristics, the most common genomic approaches and the clinical uses of WGS for (i) typing and outbreak analysis, (ii) virulence investigation and (iii) in silico antimicrobial susceptibility testing. Of all the clinical usages, the most frequent and straightforward usage was to type bacteria and to trace outbreaks back. A next step toward standardisation was made thanks to the development of several new genome-wide multi-locus sequence typing systems based on WGS data. Although virulence characterisation could help in various particular clinical settings, it was done mainly to describe outbreak strains. An increasing number of studies compared genotypic to phenotypic antibiotic susceptibility testing, with mostly promising results. However, routine implementation will preferentially be done in the workflow of particular pathogens, such as mycobacteria, rather than as a broadly applicable generic tool. Overall, concrete uses of WGS in routine clinical microbiology or infection control laboratories were done, but the next big challenges will be the standardisation and validation of the procedures and bioinformatics pipelines in order to reach clinical standards.

Detailed molecular epidemiology of Chlamydia trachomatis in the population of Southampton attending the genitourinary medicine clinic in 2012-13 reveals the presence of long established genotypes and transitory sexual networks

Chlamydia trachomatis is the most common sexually transmitted infection (STI) in England. Our objective was to perform a detailed survey of the molecular epidemiology of C. trachomatis in the population of Southampton UK attending the genitourinary medicine clinic (GUM) to seek evidence of sexual network activity. Our hypothesis was that certain genotypes can be associated with specific demographic determinants. 380 positive samples were collected from 375 C. trachomatis positive GUM attendees out of the 3118 who consented to be part of the survey. 302 of the positive samples were fully genotyped. All six of the predominant genotypes possessed ompA locus type E. One ward of Southampton known to contain a large proportion of students had a different profile of genotypes compared to other areas of the city. Some genotypes appeared embedded in the city population whilst others appeared transient. Predominant circulating genotypes remain stable within a city population whereas others are sporadic. Sexual networks could be inferred but not conclusively identified using the data from this survey.

Rapid detection and strain typing of Chlamydia trachomatis using a highly multiplexed microfluidic PCR assay

Nucleic acid amplification tests (NAATs) are recommended by the CDC for detection of Chlamydia trachomatis (Ct) urogenital infections. Current commercial NAATs require technical expertise and sophisticated laboratory infrastructure, are time-consuming and expensive, and do not differentiate the lymphogranuloma venereum (LGV) strains that require a longer duration of treatment than non-LGV strains. The multiplexed microfluidic PCR-based assay presented in this work simultaneously interrogates 13 loci to detect Ct and identify LGV and non-LGV strain-types. Based on amplified fragment length polymorphisms, the assay differentiates LGV, ocular, urogenital, and proctocolitis clades, and also serovars L1, L2, and L3 within the LGV group. The assay was evaluated in a blinded fashion using 95 clinical swabs, with 76 previously reported as urogenital Ct-positive samples and typed by ompA genotyping and/or Multi-Locus Sequence Typing. Results of the 13-plex assay showed that 51 samples fell within urogenital clade 2 or 4, 24 samples showed both clade 2 and 4 signatures, indicating possible mixed infection, gene rearrangement, or inter-clade recombination, and one sample was a noninvasive trachoma biovar (either a clade 3 or 4). The remaining 19 blinded samples were correctly identified as LGV clade 1 (3), ocular clade 3 (4), or as negatives (12). To date, no NAAT assay can provide a point-of-care applicable turnaround time for Ct detection while identifying clinically significant Ct strain types to inform appropriate treatment. Coupled with rapid DNA processing of clinical swabs (approximately 60 minutes from swab-in to result-out), the assay has significant potential as a rapid POC diagnostic for Ct infections.

Systematic Review and Meta-Analysis of Doxycycline Efficacy for Rectal Lymphogranuloma Venereum in Men Who Have Sex with Men

A high microbial cure rate was shown with 100 mg doxycycline twice daily for 21 days.

Rectal lymphogranuloma venereum (LGV) has reemerged as a sexually transmitted infection among men who have sex with men (MSM), particularly those who are HIV-positive. We undertook a systematic review and meta-analysis to determine the efficacy of doxycycline (100 mg 2×/d for 21 days) for rectal LGV in MSM. Nine studies were included: 4 prospective, 4 retrospective, and 1 combined retrospective and prospective. In total, 282 MSM with rectal LGV were included in the studies. All studies reported using nucleic acid amplification tests to assess microbial cure. Most patients (>80%) had symptomatic rectal infection. The fixed-effects pooled efficacy for doxycycline was 98.5% (95% CI 96.3%–100%, I² = 0%; p = 0.993). Doxycycline at 100 mg twice daily for 21 days demonstrated a high microbial cure rate. These data support doxycycline at this dosage and duration as first-line therapy for rectal LGV in MSM.

Does typing of Chlamydia trachomatis using housekeeping multilocus sequence typing reveal different sexual networks among heterosexuals and men who have sex with men?

Background

Chlamydia trachomatis infections remain the most common bacterial sexually transmitted infection worldwide. To gain more insight into the epidemiology and transmission of C. trachomatis, several schemes of multilocus sequence typing (MLST) have been developed. We investigated the clustering of C. trachomatis strains derived from men who have sex with men (MSM) and heterosexuals using the MLST scheme based on 7 housekeeping genes (MLST-7) adapted for clinical specimens and a high-resolution MLST scheme based on 6 polymorphic genes, including ompA (hr-MLST-6).

Methods

Specimens from 100 C. trachomatis infected men who have sex with men (MSM) and 100 heterosexual women were randomly selected from previous studies and sequenced. We adapted the MLST-7 scheme to a nested assay to be suitable for direct typing of clinical specimens. All selected specimens were typed using both the adapted MLST-7 scheme and the hr-MLST-6 scheme. Clustering of C. trachomatis strains derived from MSM and heterosexuals was assessed using minimum spanning tree analysis.

Results

Sufficient chlamydial DNA was present in 188 of the 200 (94 %) selected samples. Using the adapted MLST-7 scheme, full MLST profiles were obtained for 187 of 188 tested specimens resulting in a high success rate of 99.5 %. Of these 187 specimens, 91 (48.7 %) were from MSM and 96 (51.3 %) from heterosexuals. We detected 21 sequence types (STs) using the adapted MLST-7 and 79 STs using the hr-MLST-6 scheme. Minimum spanning tree analyses was used to examine the clustering of MLST-7 data, which showed no reflection of separate transmission in MSM and heterosexual hosts. Moreover, typing using the hr-MLST-6 scheme identified genetically related clusters within each of clusters that were identified by using the MLST-7 scheme.

Conclusion

No distinct transmission of C. trachomatis could be observed in MSM and heterosexuals using the adapted MLST-7 scheme in contrast to using the hr-MLST-6. In addition, we compared clustering of both MLST schemes and demonstrated that typing using the hr-MLST-6 scheme is able to identify genetically related clusters of C. trachomatis strains within each of the clusters that were identified by using the MLST-7 scheme.

Electronic supplementary material

The online version of this article (doi:10.1186/s12879-016-1486-2) contains supplementary material, which is available to authorized users.

Chlamydia trachomatis infection prevalence and serovar distribution in a high-density urban area in the north of Italy

The aim of this study was to assess Chlamydia trachomatis (CT) infection prevalence and serovar distribution in a high-density urban area in the north of Italy, by comparing different groups of subjects divided on the basis of the type of care provider they referred to (STI Clinic, gynaecologists or general practitioners). From January 2011 to May 2014, all the specimens submitted to the Microbiology Laboratory of St Orsola Hospital in Bologna for CT detection were tested by PCR assay. For positive specimens, molecular genotyping based on RFLP analysis was performed. Total prevalence of CT infection was 8.1 %, with significant differences between subgroups (P<0.01) but stable during the study period. The STI Clinic was mainly responsible for CT diagnosis, whereas the lowest infection prevalence was detected in gynaecological clinics, despite the high number of tests performed. Extra-genital samples were almost exclusively collected from males at the STI Clinic. Interestingly, 13.3 % of patients providing extra-genital specimens were positive for CT on rectal and/or pharyngeal swabs, and 4.4 % of cases would have been missed if extra-genital sites had not been tested. The most common serovar was E, and serovar distribution was influenced by gender (P<0.01), age (P<0.01), care provider (P=0.01) and anatomical site (P<0.01). The L2 serovar was detected only in extra-genital samples from males at the STI Clinic. Knowledge about care providers' contributions in CT testing and diagnosis is essential for infection control. CT typing is crucial for appropriate management of specific infections, such as lymphogranuloma venereum in extra-genital samples of high-risk populations.

Chlamydia trachomatis Frequency in a Cohort of HPV-Infected Colombian Women

Background

Chlamydia trachomatis (C. trachomatis), an obligate intracellular bacterium, is the commonest infectious bacterial agent of sexual transmission throughout the world. It has been shown that the presence of this bacteria in the cervix represents a risk regarding HPV persistence and, thereafter, in developing cervical cancer (CC). Prevalence rates may vary from 2% to 17% in asymptomatic females, depending on the population being analysed. This study reports the identification of C. trachomatis in a cohort of 219 HPV-infected Colombian females.

Methods

C. trachomatis infection frequency was determined during each of the study’s follow-up visits; it was detected by amplifying the cryptic plasmid sequence by polymerase chain reaction (PCR) using two sets of primers: KL5/KL6 and KL1/KL2.

Infection was defined as a positive PCR result using either set of primers at any time during the study. Cox proportional risk models were used for evaluating the association between the appearance of infection and a group of independent variables.

Results

Base line C. trachomatis infection frequency was 28% (n = 61). Most females infected by C. trachomatis were infected by multiple types of HPV (77.42%), greater prevalence occurring in females infected with HPV-16 (19.18%), followed by HPV-58 (17.81%). It was observed that females having had the most sexual partners (HR = 6.44: 1.59–26.05 95%CI) or infection with multiple types of HPV (HR = 2.85: 1.22–6.63 95%CI) had the greatest risk of developing C. trachomatis.

Conclusions

The study provides data regarding the epidemiology of C. trachomatis /HPV coinfection in different population groups of Colombian females and contributes towards understanding the natural history of C. trachomatis infection.

Highly diverse MLVA-ompA genotypes of rectal Chlamydia trachomatis among men who have sex with men in Brighton, UK and evidence for an HIV-related sexual network

OBJECTIVES

In this prospective study, we aimed to determine the distribution of genotypes by multilocus variable number tandem repeat (VNTR) analysis plus analysis of the ompA gene (MLVA-ompA) of rectal Chlamydia trachomatis among men who have sex with men (MSM) attending Brighton Genitourinary Medicine (GUM) Clinic and to examine any correlations with clinical variables, including HIV status, and to isolate rectal C. trachomatis cultures maximising the possibility of obtaining complete genotyping data.

METHODS

Samples were assigned genotypes by PCR and sequencing of the markers of the MLVA-ompA genotyping system. Rectal C. trachomatis was isolated in cell culture using McCoy cells. Data regarding demographics, HIV status, rectal symptoms and history of sexually transmitted infections, including C. trachomatis, were collected.

RESULTS

1809 MSM attending the clinic between October 2011 and January 2013 took part in the study, 112 (6.2%) of whom had rectal samples that tested positive for C. trachomatis. 85/112 (75.9%) C. trachomatis-positive rectal samples were assigned 66 different genotypes. Two distinct genotype subclusters were identified: subcluster 1 consisted of more HIV-negative men than subcluster 2 (p=0.025), and the MLVA-ompA genotypes in these subclusters reflected this. Isolates were successfully cultured from 37 of the 112 specimens, from which 27 otherwise unobtainable (from direct PCR) MLVA-ompA genotypes were gained.

CONCLUSIONS

The most prevalent genotypes were G, E and D representing some overlap with the heterosexual distribution in UK. Subcluster 1 consisted of more 'heterosexual genotypes' and significantly more HIV-negative men than subcluster 2, associated with 'MSM genotypes'. There was a higher diversity of C. trachomatis strains among MSM in Brighton than observed in other cities.

Global Multilocus Sequence Type Analysis of Chlamydia trachomatis Strains from 16 Countries

The Uppsala University Chlamydia trachomatis multilocus sequence type (MLST) database (http://mlstdb.bmc.uu.se) is based on five target regions (non-housekeeping genes) and the ompA gene. Each target has various numbers of alleles-hctB, 89; CT058, 51; CT144, 30; CT172, 38; and pbpB, 35-derived from 13 studies. Our aims were to perform an overall analysis of all C. trachomatis MLST sequence types (STs) in the database, examine STs with global spread, and evaluate the phylogenetic capability by using the five targets. A total of 415 STs were recognized from 2,089 specimens. The addition of 49 ompA gene variants created 459 profiles. ST variation and their geographical distribution were characterized using eBURST and minimum spanning tree analyses. There were 609 samples from men having sex with men (MSM), with 4 predominating STs detected in this group, comprising 63% of MSM cases. Four other STs predominated among 1,383 heterosexual cases comprising, 31% of this group. The diversity index in ocular trachoma cases was significantly lower than in sexually transmitted chlamydia infections. Predominating STs were identified in 12 available C. trachomatis whole genomes which were compared to 22 C. trachomatis full genomes without predominating STs. No specific gene in the 12 genomes with predominating STs could be linked to successful spread of certain STs. Phylogenetic analysis showed that MLST targets provide a tree similar to trees based on whole-genome analysis. The presented MLST scheme identified C. trachomatis strains with global spread. It provides a tool for epidemiological investigations and is useful for phylogenetic analyses.