Rectal Chlamydia trachomatis infection: a narrative review of the state of the science and research priorities

Abstract

Chlamydia trachomatis (CT) is the most commonly reported infection in the United States (US). Most chlamydial research to date has focused on urogenital infection, but a growing body of research has demonstrated that rectal chlamydia is a relatively common infection among clinic-attending men and women. We know that the majority of rectal CT infections are asymptomatic, but the health implications of these infections, particularly for women, are unclear. Additionally, there are key knowledge gaps related to the epidemiologic parameters of rectal chlamydia, the routes of acquisition, the duration of infection, and the clinical significance of a positive rectal CT test. This lack of information has led to a blind spot in the potential role of rectal chlamydia in sustaining high levels of CT transmission in the US. Further, recent findings from animal models suggest that the immune response generated from gastrointestinal chlamydial infection can protect against urogenital infection; however, it remains to be determined whether rectal chlamydia similarly modulates anti-CT immunity in humans. This is a critical question in the context of ongoing efforts to develop a CT vaccine. In this narrative review, we summarize the state of the science for rectal chlamydia and discuss the key outstanding questions and research priorities in this neglected area of sexual health research.

SHORT SUMMARY

Rectal Chlamydia trachomatis is a commonly diagnosed infection but there are key gaps in our understanding of the clinical, epidemiologic, and biologic aspects of infection.

INTRODUCTION

Chlamydia trachomatis (CT) is the most common bacterial sexually transmitted infection (STI) in the world.¹ In the United States (US), there were an estimated 4 million cases of chlamydia in 2018,² making it the most commonly reported condition nationally. Despite longstanding public health chlamydia control programs, rates of reported chlamydia in the US have persistently increased over the past 20 years and are now at an all-time high.³ Chlamydial infections disproportionately impact young women (<25 years of age), particularly Black, Hispanic, and Native American women, and men who have sex with men (MSM).

CT infects epithelial cells of the oropharynx, urogenital tract (UT), and gastrointestinal tract (GIT). In veterinary contexts (e.g., cattle, pigs, goats, sheep), Chlamydia spp. are considered to be members of the ‘normal’ GIT microflora, colonizing these animal hosts without consequent inflammation.⁴ Until recently, the contemporary human CT literature has focused predominantly on UT chlamydia, due to the adverse health outcomes in the female reproductive tract. However, the rectum is increasingly recognized as a common anatomic site of CT infection in humans, and among MSM is associated with proctitis and HIV acquisition.⁵ Among MSM in sexual health clinics, 10-15% test positive for rectal chlamydia.³ Among cisgender women, the prevalence of rectal CT among clinic patients is 8-9%,^6-9 comparable to the prevalence of UT chlamydia.⁶ The US Centers for Disease Control and Prevention (CDC) recommends at least annual screening for rectal chlamydia among MSM who have receptive anal sex and more frequent screening for MSM at higher risk for infection. Routine screening for rectal chlamydia is not recommended for cisgender women, but may be appropriate in some situations in the context of shared decision-making between the clinician and patient based on the patient’s reported sexual behavior and exposures.⁵

Despite the high prevalence of rectal chlamydia, there are critical knowledge gaps in our understanding of the biologic, epidemiologic, and clinical aspects of these infections. In this narrative review, we present four emerging topics in rectal chlamydia that span the translational science continuum, and we discuss current states of knowledge, key outstanding questions, and the most critical research priorities for each topic area (summarized in Table 1). Throughout this review, the sex and gender terms we use reflect the published literature, in which binary gender has typically been used to indicate sex at birth and current genitalia. We specify cisgender when findings specifically reported sex at birth and gender.

Table 1.

Summary of key outstanding research questions for rectal C. trachomatis (CT)

Topic	Key Outstanding Research Questions
Health implications	What are the health implications of rectal CT among cisgender women?
Transmission and natural history	What behaviors, other than receptive anal intercourse, are associated with rectal CT acquisition? What are the unique microbiologic features of CT strains that have an affinity for the rectum? What is the role of CT persistence in rectal infections? What is the true duration of infection of rectal CT, particularly among women? What proportion of rectal CT positive NAAT tests represent true infections versus detection of cell-free CT nucleic acid or nonviable, extracellular CT developmental forms? Are there circulating rectal CT strains that cannot be detected by currently available diagnostic tests?
Rectal CT treatment	Why is azithromycin a suboptimal therapy for rectal CT and what are the mechanisms of azithromycin treatment failure? What is the minimally effective dose of doxycycline to cure rectal CT infection?
Immune response	Does the presence of rectal CT modify or enhance anti-CT immunity? Does rectal CT infection in humans induce immune responses that could protect from subsequent urogenital infection?

NAAT, nucleic acid amplification test

HEALTH IMPLICATIONS OF RECTAL CT

The majority (>85%) of rectal CT infections are asymptomatic,¹⁰ but rectal infection can lead to proctitis.⁵ Infection with CT biovars L1, L2, or L3 can cause the clinical syndrome of lymphogranuloma venereum (LGV). The most common manifestation of rectal LGV is proctocolitis, and the most common manifestation of UT LGV is tender inguinal or femoral lymphadenopathy.⁵ Despite reports of increasing L-biovar CT prevalence among MSM,^11-13 25-50% of these infections may actually be asymptomatic.^11,14,15 Among MSM, rectal chlamydia has been associated with an increased risk of HIV acquisition and transmission independent of reported sexual behavior.^16,17

Although the high prevalence of rectal chlamydia among women in sexual health clinics is established, the clinical relevance is not. CT colonization of the UT can lead to pelvic inflammatory disease, chronic pelvic pain, ectopic pregnancy, and tubal factor infertility.⁵ However, it is not clear whether rectal chlamydia can result in these sequelae because we do not know if and how often CT is auto-inoculated from the rectum to the genital tract. This proposed route of auto-inoculation – which is analogous to bacterial urinary tract infections in women – has been hypothesized by several investigators and demonstrated in animal models of CT infection,^4,18,19 but has not been formally proven to occur in humans. However, several epidemiologic studies in women support the hypothesis, albeit indirectly, that undiagnosed and/or inadequately treated rectal chlamydia may be a source of recurrent UT chlamydia in women.^20-25

Understanding the frequency of auto-inoculation from the rectum to the vagina is key to characterizing the health implications of rectal chlamydia in women, which will in turn determine whether a positive rectal CT test in a woman is a clinically important finding and will inform decisions about whether or not routine rectal screening in women should be implemented. Beyond the individual health implications of rectal chlamydia, the contribution of rectal CT infection on transmission is an important scientific question because these infections have the potential to act as a reservoir that could sustain transmission in a population.

TRANSMISSION AND NATURAL HISTORY

Rectal CT Transmission

Although many routes of rectal CT acquisition have been elucidated, the relative contribution of each route to infection, particularly for women, is unknown. Among MSM, the primary route of rectal CT acquisition is via receptive anal sex, though several studies have also demonstrated an association between rectal CT and other sexual practices such as oral-anal sex, fingering or fisting, use of sex toys, and use of saliva as lubricant.^26-29 In contrast, in women, anal sex is unlikely to be the primary route of rectal CT acquisition given that the prevalence of rectal chlamydia in women is similar among those who do and do not report anal sex.^7,9 Many women may acquire rectal chlamydia from preceding UT infections, given the close proximity of the vagina and anus, female toileting hygiene practices, and the fact that most women (approximately 70%) with UT CT also test positive for rectal chlamydia.⁷ Indeed, “cross-over” infections (i.e., cervical to rectal) in macaque models have been observed,³⁰ and modeling data suggest that up to 87% of rectal CT infections in women are acquired from UT infections.^31s Some women probably acquire rectal chlamydia via sexual practices such as oral-anal sex, but data to describe the frequency of these practices among women are virtually non-existent. Several investigators^4,32s,33s have put forth the hypothesis that oral acquisition of CT (i.e., via penile-oral sex) leads to rectal chlamydia, which requires that CT survives transit through the upper GI tract to ultimately colonize the colon. This has been demonstrated in animal models^34s-36s and is supported by some epidemiologic evidence in humans,^37s,38s but has not been experimentally demonstrated in humans. To improve our ability to detect rectal CT infections, more data are needed to better understand the association between rectal chlamydia and behaviors other than receptive anal sex among all populations.

CT Tissue Tropism

A major unanswered question regarding the natural history of rectal CT infection is whether specific strains of CT exhibit greater tropism for rectal versus urogenital tissues. In a 1987 study that compared the serotypes of MSM rectal isolates against cervical isolates,^39s Walter Stamm and colleagues found that CT serovars D/ D’ and G were the most prevalent serovar in rectal isolates, whereas serovars E and F were predominant in cervical samples. Although less prevalent, four additional serovars were isolated from cervical samples but not rectal samples. The affinity of particular serovars for rectal versus UT tissues suggests either an adaptation and/or enhanced tropism of these strains for rectal or UT tissues. More recent genomic comparisons of circulating CT strains have revealed the presence of unique polymorphisms that are enriched in rectal-associated serovars.^40s,41s A major research priority is therefore to develop a better understanding of the CT strains that have tropism for rectal versus UT infections, and their distinctive genetic differences. These strains may exhibit unique microbiological features that impact their infectivity, growth rates, persistence, dissemination, transmission, and interactions with the immune system. All of the latter are outstanding questions in the context of rectal chlamydia.

Rectal CT Persistence

The microbiologic concept of CT persistence may have important implications for health outcomes, but at present, the relationship between persistence and clinical treatment failure is not well understood. In vitro, CT enters a quiescent state when faced with metabolic or environmental stresses, temporarily halting replication, known as the aberrant or persistent state.^42s This defining feature of all Chlamydia species is well-documented in tissue culture models and has been observed in vivo in at least one study of endocervical infection.^43s While this phenomenon has long been hypothesized as a potential strategy for establishing long-term, persistent CT infections in vivo and evasion from host immune responses, the relationship between the microbiologic state of persistence and clinical outcomes such as treatment failure or reinfection, has not been studied.

Duration of Rectal CT Infection

The relatively long duration of rectal CT infections may contribute to sustained high levels of CT transmission at the population level. Empiric data from a natural history study of rectal chlamydia in MSM by Barbee and colleagues suggests that the median duration is approximately 13 weeks.^44s However, 38% of participants with rectal chlamydia in that study were censored due to antibiotic use, so the true duration of rectal chlamydia in the absence of treatment remains unknown. It is possible that the duration may actually be closer to that estimated from modeling studies, which suggest that rectal chlamydia may persist for nearly two years.^45s Interestingly, in other empiric studies, approximately 13-20% of MSM with rectal chlamydia clear their infection in the time between an original positive test and returning for treatment (usually approximately 1-2 weeks later).^24,46s-48s It is unclear if these individuals had infections of short duration or if the infections were identified near the end of their duration. Elucidating the duration of infection – including among cisgender women, in whom the duration of infection has never been measured – has important implications for our understanding of rectal chlamydia’s role in population-level CT transmission. If many of these infections go undiagnosed and untreated and they are indeed long-duration infections, this may contribute to the high levels of reported chlamydia in the US.

Viability of CT in the Rectum

Another area of ongoing uncertainty is how often detection of CT nucleic acid via nucleic acid amplification testing (NAAT) – the diagnostic standard – represents a true infection with viable, replicating bacteria that have infected cells, as opposed to detection of cell-free CT nucleic acid or nonviable, extracellular CT developmental forms. This question is less relevant in the context of anal sex-acquired infections, where introduction of CT likely occurs in the rectum (via ejaculation), and more relevant for oral-anal sex or auto-inoculation from the vagina, which involves more superficial introduction of CT at the peri-anal region. In cohort studies of women in the US and Europe, 50-60% of rectal CT specimens that were positive by NAAT were also positive by culture^38s or viability assay.^49s Notably, this is nearly identical to the proportion of vaginal specimens (64%) deemed ‘viable’ using the same assay.^50s Some studies have used the CT bacterial load as a proxy for true cellular infection, assuming that a high bacterial load is more likely to represent a true infection. In these studies, rectal CT bacterial load was found to be similar for men and women,^51s and the same or higher than the UT CT load for 67% of women.^52s These findings suggest that rectal CT infections indicate cellular infections as often as UT infections, and argue for the clinical relevance of positive rectal NAAT results. However, this remains a highly debated topic.

Emergence of CT Strains that are Undetectable by Diagnostic Tests

The widespread reliance on NAAT for clinical diagnosis of CT raises concern for the emergence of CT strains that may evade detection, diagnosis, and treatment. Because the practice of primary CT culture from swabs has been largely abandoned and no genomic CT surveillance exists, this is a problem of unknown magnitude and represents a major blind spot in CT epidemiology. On multiple occasions, CT variants have arisen with polymorphisms in the genetic targets of the NAAT assays used at the time. The 2006 Swedish new variant contained a 377 bp deletion in a CT plasmid target that was used by the Roche and Abbott diagnostic platforms, and this mutation likely resulted in thousands of missed diagnoses.^53s In 2019, a series of UT CT strains were identified in Finland and England with polymorphisms in the 23S rRNA gene which is the target of the widely used Aptima Combo 2 NAAT assay.^54s,55s The prevalence of the Finnish and English CT variants, and their broader geographic distribution, are outstanding questions that have not been addressed. A credible hypothesis is that similar variants may be in circulation for rectal chlamydia; however, this question cannot be investigated until genome sequencing of CT isolates becomes more commonplace.

RECTAL CT TREATMENT

Doxycycline and azithromycin are both commonly used to treat rectal chlamydia. Prior to 2020,^56s the CDC STI Treatment Guidelines recommended either doxycycline (100 mg twice daily for one week) or azithromycin (1 g single dose) for the treatment of both rectal and UT chlamydia. Due to the relative ease of a single dose treatment and possibility for directly observed therapy in some settings, many clinicians prefer to use azithromycin. The revised gonorrhea treatment guidelines published in 2020 recommended doxycycline as the preferred treatment when CT co-infection has not been excluded^56s and the 2021 STI Treatment Guidelines also presented a revised recommendation for doxycycline as the preferred treatment for chlamydia.⁵ However, the extent to which this recommendation will be translated into practice remains to be seen. Evidence of doxycycline’s superiority in the treatment of UT chlamydia accumulated through multiple studies^20,57s,58s; no single study was sufficient to prompt a widespread change in practice or guidelines. Treatment recommendations for rectal chlamydia have long been extrapolated from studies of UT chlamydia, but many observational studies suggested that azithromycin was inferior to doxycycline and that the difference in effectiveness at the rectum was greater than at the urogenital site.^59s,60s Two recent randomized, controlled trials of rectal chlamydia treatment among MSM definitively demonstrated the inferiority of azithromycin compared to doxycycline, with microbiologic cure proportions of 74-76% for azithromycin compared to 97-100% for doxycycline.^24,61s Among cisgender women, recent evidence suggests that azithromycin is inferior to doxycycline for the treatment of rectal chlamydia.^62s

The reasons for the poor performance of azithromycin at the rectal site are unknown, although several theories have been considered and ruled out. First, since azithromycin is a single-dose treatment, inadequate patient adherence is not a concern. Second, azithromycin resistance among CT isolates has never been conclusively demonstrated. Although one prior report^63s described a resistant strain, upon further analysis, the strain was determined not to have true (homotypic) antibiotic resistance but rather a heterotypic resistance pattern.^64s That is, some organisms survived in the presence of azithromycin and others did not, but there was no difference in the minimum inhibitory concentration (MIC) to azithromycin between surviving and non-surviving strains. Third, treatment failure does not appear to be due to inadequate tissue penetration or dosing of azithromycin. A pharmacokinetic study demonstrated that drug concentrations of azithromycin in rectal tissue after a single oral dose of azithromycin remain above the minimum inhibitory concentration for azithromycin in CT for at least 14 days.^65s Animal studies have also shown comparable levels of azithromycin in the GIT and UT despite the poorer efficacy of treatment in the GIT.^66s However, intracellular penetration of azithromycin varies by cell type, and may be different in GIT cells compared to UT cells.^67s,68s Furthermore, some evidence suggests that the MIC for azithromycin may be higher in GIT cells than UT cells.^69s Finally, undetected LGV-biovar CT infections do not account for the inferior efficacy of azithromycin. In the recent randomized, controlled trial of rectal CT treatment,²⁴ only ~5% of participants had LGV-biovar CT, and azithromycin performed equally poorly among LGV-biovar and non-LGV-biovar CT.

Several research priorities in the area of rectal chlamydia treatment remain to be addressed. Understanding the mechanism of azithromycin treatment failure in rectal chlamydia may yield insights into the natural history and immunology of CT infections. Although not yet observed, evolution of azithromycin resistance among CT remains a possibility that would be difficult to detect without concerted research effort in the absence of public health surveillance. To our knowledge this has not been well-studied among contemporary CT specimens nor in specimens from rectal CT infections. Antimicrobial susceptibility in CT is difficult to assess or monitor because in vitro testing does not correlate well with clinical persistence.^70s,71s Furthermore, although it is generally assumed not to represent true resistance, the relationship between heterotypic resistance among CT in vitro, CT growth in vivo, and clinical outcomes has not been fully examined. Additionally, appropriate treatment for LGV-biovar CT infections remains uncertain. Some evidence suggests that asymptomatic or minimally symptomatic infections do not require prolonged treatment,^72s though this has not been studied in a sufficiently large prospective trial. Since LGV testing is not routinely available for clinical use in the US and the clinical significance of LGV-biovar infections in the absence of LGV syndrome is uncertain, the approach to LGV treatment in the US currently relies on presumptive treatment for LGV in patients who have symptoms or signs of proctocolitis.⁵ We do not know the minimally effective dose of doxycycline. Although clinicians often have concerns about patient adherence to doxycycline, complete adherence is probably not necessary for effective treatment. Studies of chlamydial treatment with less frequent doxycycline dosing (e.g. 200 mg on day 1 followed by 100 mg daily for 6-9 days) have shown high efficacy^73s and with a half-life of 18 hours, it is plausible that incomplete adherence to doxycycline could still achieve cure. Finally, if doxycycline post-exposure prophylaxis is found to be effective in preventing bacterial STIs, the impact of widespread intermittent doxycycline on rectal CT infections will be an important area of future work.

IMMUNE RESPONSE TO RECTAL CT

There is no clear data in humans describing the immune response to rectal CT infection in either the rectum or UT or the risk of CT reinfection. In mice, Chlamydia inoculation of the lungs, eye, UT, and GIT elicits strong mucosal immunity, and induces marked inflammation with rapid chlamydial clearance at all sites except the GIT.^74s GIT infection in mice results in long-lasting non-pathogenic colonization, conferred protection against reinfection of the GIT, and provides trans-mucosal protection against UT challenge.^75s,76s Comparable evidence in humans is lacking. Men with rectal chlamydia have elevations in systemic CD8+ T cell activation^77s but have reduced rectal cytokine concentration.^78s Adaptive immune responses to rectal CT infection have not been well-studied.

Why Chlamydia is able to persist in the GIT without pathology is still unclear. The GIT, which must tolerate a high concentration of commensal microorganisms, has evolved unique characteristics marked by enhanced tolerogenic/suppressive immune signatures.^79s,80s. The lack of pathology in the GIT could result from tolerance to CT in this site or maintenance of CT in a persistent/latent state that do not invoke a strong immune response. Further study is needed to clarify this point. Another intriguing possibility is that the gut microbiome contributes to CT persistence via production of metabolites that drive CT into persistent forms. A link between bacterial vaginosis and risk of CT infection supports the hypothesis that the local microbiome has a strong role in CT pathogenesis, ^80s-82s but whether this occurs in the GIT remains to be investigated.

Most human data on anti-CT immunity comes from studies of UT chlamydia. However, given the high prevalence of rectal chlamydia among women with UT chlamydia, these data undoubtedly reflect a mixture of individuals with concurrent UT/rectal infection and those with UT infection alone. It is important to consider previous studies of chlamydia immunity through this lens. Among individuals with UT chlamydia, secretion of interferon gamma (IFN-γ) by CD4⁺ T cells correlates most strongly with resolution of infection and protection from reinfection.^83s-86s Cytotoxic CD8⁺ T cells on the other hand appear to play a limited role in resolving CT infection.^87s The role for antibodies is less clear. Some human studies support anti-CT antibodies protecting from reinfection^88s but more evidence indicates that antibodies do not correlate with protection.^89s,90s On the other hand, animal studies strongly support a role for antibodies in protection from secondary infections.^87s,91s,92s In human UT chlamydia, there is evidence that natural clearance of CT offers some protection from reinfection. The arrested immunity hypothesis posits that routine screening and early treatment may actually interfere with the development of effective natural immunity.^93s-95s In untreated women, it may take many months to clear UT chlamydia,^96s,97s but those women who clear infection are less likely to be subsequently re-infected compared to those who were treated with antibiotics.^98s In mice, early treatment interferes with the development of protective immunity against reinfection.^99s However, we do not know whether or not infection with rectal chlamydia provides robust natural immunity.

A primary research priority is understanding the role of rectal chlamydia in modifying or enhancing anti-CT immunity and determining whether or not rectal chlamydia protects from re-infection in the UT. Given the existing data from murine models suggesting that GIT CT confers trans-mucosal protection against UT challenge,^75s,76s it is an intriguing hypothesis to consider that the presence of chlamydia in the GIT could result in protection from UT chlamydia in humans, or could lead to a greater magnitude and duration of immune responses against chlamydia as compared to UT infection alone. Longitudinal studies designed to examine the immune response to rectal chlamydia and subsequent risk of re-infection are key. Such studies in humans are challenging, since it is nearly impossible to align the timing of specimen collection with acquisition of infection. However, the use of non-human primates, which are readily translatable to the human experience and can be rectally infected with chlamydia,^100s-103s may be an ideal model in which to examine this question. If GIT infection induces protective immune responses against CT, oral or rectal immunization has the potential to enhance immune responses at systemic and mucosal sites and protect from UT infection.^104s

SUMMARY

Rectal chlamydia is a relatively common infection in both men and women. Although we have effective antibiotics to treat rectal chlamydia, screening for rectal chlamydia is focused on men who report penile-anal sex, which means that many infections – particularly among women – go undiagnosed and untreated. However, the health implications of rectal chlamydia in women are unclear, and we do not know if under-detected rectal chlamydia is a key contributor to sustained level of chlamydia transmission in the population. The clinical importance of rectal chlamydia may lie in the capacity for these infections to serve as a reservoir for recurrent UT infection in women and/or to modulate host immunity in a manner which leads to subsequent protection from UT infection. These high priority questions need to be experimentally pursued by clinical, translational, and basic researchers to define the extent of the impact rectal chlamydia infections have on human health.