The Impact of Molecular Technology on STD Control A Historical Perspective P. Frederick Sparling 1. Introduction 1.1. The Way it Was Sexually transmitted diseasesh ave afflicted humankind for millennia, based on references to apparent gonorrhea or nongonococcal urethritis in the Old Testament (Levtttcus). For most of history there has been no means of specific diagnosis, and clinical diagnosis of syndromes was fraught with error. Usually, this made no difference because there was no specific therapy and no means of prevention other than abstinence or monogamy, which was slightly effective at best (witness the very high prevalence of syphilis m much of Europe and the USA before advent of specific therapy, approaching 10% in many populations and 25% m some). Occasionally, syndromic diagnosis did cause serious conse- quences. If we could talk with John Hunter today, he certainly would bemoan the absence m his time of specific diagnostic tests for gonorrhea and syphilis. Had he had accesst o such tests,h e certainly would not have maculated himself with urethral exudate from a patient with gonorrhea and subclmical syphihs, resulting m the acqutsition of both gonorrhea and syphilis (I)! Not only did he suffer from both diseases,b ut he also understandably but incorrectly concluded that both diseases had the same etiology, which held back the entire field until the discovery that Neisseria gonorrhoeae and Treponema pallidum were sepa- rate causes of the very distinctive diseases. The understanding of specific etiologies of STDs and all infectious diseases required new technology. First was the visualizatton of bacteria by Gram’s stain, and then culture of bacteria m vitro. Thus, in 1879 Neisser was able to vtsuahze the organism that carries his name and correctly identified it as the From Methods m Molecular Medune, Vol 20 Sexually Transmrtted Diseases Methods and Protocols Edlted by R W Peelmg and P F Sparlmg 0 Humana Press Inc. Totowa, NJ 3 4 Spading cause of gonorrhea. Shortly thereafter, in 1882, it was cultured in vitro by Leistikow and Loeffler. Roughly concurrent were the discovertes of virulent T pallzdum by maculation of chimpanzees, visualization of T. pallidurn m lesions by dark field mtcroscopy, and development of useful if not specific serologic tests for syphilis (by Metchnikoff, Schaudinn, and Wassermann respectively). These late 19th century discoveries were revolutionary, and paved the way to our modern understanding of the epidemiology, transmis- sion, and accurate diagnosis of these classic STDs. Once effective therapy became available about half a century later (discounting the arsenicals which were not effective enough to have a major impact on syphilis prevalence), rea- sonably accurate diagnostic tests helped mmreasurably in finding and then treating asymptomatic cases of both gonorrhea and syphilis. This lead to dra- matic declines in incidence and prevalence of both diseases after World War II m most of the world, and even more dramatic declines m the late complications of syphilis m particular. Relative control of the two major STDs (gonorrhea and syphilis) had been achieved in the USA by the 1950s. Curiously absent, however, was discussion or concern over other STDs that we now recognize as of equal or greater srg- nificance. The problem was that the technological revolution had stalled, and had not gone far enough. There were bacteria that were very common indeed that did not grow on usual agar media, and did not stain by Gram’s stain: the chlamydia. There were viruses to be discovered that were either clmically unknown or msuffciently appreciated on climcal grounds alone: human gem- tal wart vn-uses, genital herpes viruses and many more. Discovery of then importance was only possible with development of cell culture technology for viruses and obligate mtracellular bacteria such as the chlamydia. Development of electron microscopy, and especially in the 1980s of multiple molecular biol- ogy techniques as well as the expanded deployment of the still new technology of monocional antibody production, created a second and still ongoing revolu- tion in our ability to detect, and therefore to understand, a variety of old and “new” STDs. Understanding how far we have come in the past few decades may be illus- trated by recollectton of a formative experience m thts author’s traming. Dur- mg a three week course on venereology for new US Public Health Service officers assigned to the Venereal Disease Research Laboratorres m 1964, there was little mention of Herpes simplex mfections, and only the briefest discus- sion of “venereal” warts, which were discussed prmcipally in terms of their differentiation from the secondary lesions of mucosal syphilis. There was actu- ally more dtscussion about staphylococcal infections than there was about the comphcattons of human papilloma virus infections, for the simple reason that there was yet no evidence that these common sexually transmitted agents are Impact of Molecular Technology on STD Control 5 the leading cause of cervtcal cancer. There was also scant, if any, discussion about asymptomatic carriers of gonococci, and no discussion at all about Chlurnydiu trachomatu. Rather, there was considerable discussion about the three principal “minor STDs”: granuloma ingumale, chancroid, and lym- phogranuloma venereum (LGV). All three were understood as clinical entities, but diagnostic tools were few and poor. It took the deployment of modern microbtology (culture m eggs, and later in cell culture) and good clinical infer- ence before chlamydia were dtscovered to be common causes of cervtcitis, urethritis, and salpmgitis. It also took the development of molecular diagnostic tests for typing particular variants of human papilloma viruses (HPV) before it was realized that some but not all HPV were able to trigger the path to cervical cancer. Discovery of the rather astounding prevalence of HPV awaited discov- ery and deployment of the polymerase chain reaction (PCR). In 1964, when I entered the field as a novice, testing for STDs was limited to the classic serologic tests for syphilis, updated by then to include the first generation of specific treponemal tests, as well as the still extant TPI immobi- lization test; dark field microscopy and rare animal inoculation to recover T pallidurn; culture and mtcroscopy for N. gonorrhoeae; group serology for LGV antigen; biopsy for granuloma mguinale; and Tzanck preparations and occasional culture for Herpes simplex virus. Nonspecific vagmitis (bacterial vagmosis) was diagnosed by examining for vaginal secretions for clue cells. There were no tests for either genital chlamydia or HPV, and of course none for HIV, which had not been recognized yet although the first human mfec- tions had already occurred. No one suspected sexual transmission of hepatitis viruses. Nongonococcal urethritis was simply defined as urethritis (in men, since the urethral syndrome in women had yet to be defined) m whom there was no evidence of gonococct. Trichomonas was recognized as a problem in women, but no one took seriously the possibility that men might harbor the organism, and some might have symptoms from it. Genital mycoplasmas were not yet on the scene. The vaginal microbial flora was virtually totally unknown; certainly, there was no thought that certain lactobacilli might be protective against infection by various pathogens. We live in a much more sophisticated world now, only a little over thirty years from that course on STDs at the Communicable Disease Center (CDC). We are aware of the dangers of silent infection by HPV m some persons, and the complications of asymptomatic or oligosymptomatic genital chlamydia infections. We actually understand a great deal about the molecular events that lead to cancer, in the case of HPV, or fallopian tube scarring and infertility, or Reiter’s syndrome, m the case of genital chlamydra. Application of modern 6 Spading microbiology techniques has clarified the roles of various organisms in bacte- rial vaginosis, and has helped to elucidate the role that bacterial vagmosis seems to play in more serious diseases such as salpingitis. We are on the verge of being able to rapidly and specifically diagnose the cause of syndromes such as genital ulcer syndrome that may have multiple etrologres. Now that we have effective therapy for genital herpes virus infections, it 1sh elpful to have a mul- tiplicity of diagnostic tests including culture so that we can know certainly who has herpetic mfection. Much of the practice of genitourinary medicme, or STD control, as venereology has come to be known, now depends on mcreas- mgly effective and raped diagnostic tests. And then of course, there is HIV. This is such a big development that it threatens to dwarf other STDs in the public mind, and it has become a specialty within a specialty as new treatments and tests rapidly evolve. Here we are almost completely dependent on serologic tests,s ophtstlcated molecular analy- ses of the state of the mnnune system, and the extent of the “viral load” to guide our diagnosis, prognosis, and treatment. It is safe to say that had this infection evolved in another era, like the one described in 1964 at the CDC course mentioned above, it would have taken much longer at best to discover the cause,a nd we might still be groping for useful testsa nd therapies.B ecause HIV occurred m the era of “molecular medlcme,” we have collecttvely made amaz- ing strides in understanding the disease and m beginning to control it. The point is, we depend on really good tests, and are fortunate to have more and increasingly better tests at our disposal for all the STDs, including HIV. This book is an attempt to capture this rapidly moving field, in a form that will be useful to practitioners in the laboratory, and to chmcians who desire deeper understanding of the basis of the new tests that are rapidly entering practice. 2. What Will Be the Impact of the New Tests? There are so many new tests that it is difficult to try to predict then impact Because many are relatively expensive, then deployment will be somewhat lim- ited, certainly excluding much of the developing world where the STD problems are worst. New inexpensive testsa re needed that can be used in the field. Develop- ment of reliable, stable simple sensitive and specific antigen detection tests for virtually all of the major STDs, would have a huge impact, because much of the world still relies on syndromic diagnosis through algorithms. This need is exempli- fied by the announcement by the Rockefeller Foundatton of a prize of one mrlhon US dollars for development of a simple nonculture testf or gonorrhea and chlamy- dia, suitable for use m the developing world. At the time of this writing there are attempts to create such a test, but certainly there has been no announcement of a winner. Thus, despite our excttement about the plethora of useful new molecu- lar tests for a variety of STDs, there is still much work to be done. Impact of Molecular Technology on STD Control 7 Putting these cautionary comments aside, there is room for real optimism about what has been accomplished m recent years. The new tools at our disposal are already making a difference in many ways. I will illustrate the power of the new tests, and also what we still need, by focusing on a few of the areas that are covered in detail in later chapters of this book (see Chapters 2,3,5,8, 11, 12, 13). 2.1. Gonococcal Infection The advent of PCR and the related ligase chain reaction (LCR) tests has made it possible to detect current or very recent infection by amplifying gono- coccal DNA m patient secretions, including urine and vaginal secretions (2,3). The revolutionary impact of these tests is based on their abtlity to detect infec- tion in women without doing an invasive pelvic exam, which is slow and some- thing most women would rather avoid. This is possible because screening urine or vaginal fluids is at least as sensitive as screening cervical secretions. Some argue that DNA-based tests might be a problem because they do not allow testing of isolates for antimicrobial sensitivity, and there IS no means for strain typing as can be done by several techniques with live isolates. However, there are new technologies on the horizon including chip-based DNA sequencing (41 that will allow detection of genes such as beta lactamase, directly from patient secretions, and simtlar methods almost certainly can be used to perform molecular strain typing based on the DNA sequence of porm or other genes. The DNA-based diagnostic tests are a real advance in our ability to diagnose gonorrhea, particularly m screening high prevalence populations for infection, especially in women. Curiously, we still do not have an effective serological test for gonorrhea, and no one is working on this problem to the best of my knowledge. 2.2. Genital Chlamydia Infection Virtually the same comments apply as were made about gonococcal infec- tions, but the impact here is even greater because culture tests for chlamydia are so much more difficult and expensive than they are for gonorrhea. Antigen detection tests for chlamydia (5) were developed that were quite sensitive and specific, but the new nucleic acid based tests are clearly more sensttive than any previous tests,a nd there is good evidence that they are specific as well (6). DNA remains detectable for many days in patient secretions after effective treatment, so DNA-based amphfication tests cannot be used as a test of cure (7). This undoubtedly applies to all infectious diseases. Screening for genital chlamydta infections appears to have an impact on community prevalence (8), and wider use of the DNA-based tests will hasten the decline of chlamydia in societtes that can afford to use these tests. Of course, cost is an issue, even in rich countries such as the USA. Cost effectiveness analyses will be needed 8 Spading before managed care companies or health departments can fully commit to using these excellent tests( 9). As with gonococcal infection, we lack a useful serologi- cal test for genital chlamydia. There is exciting evidence that correlates serum antibody responses to certain antigens (especially the heat shock protein of approx 60 kDa) with increased likelihood of late complications of disease, par- ticularly salpmgitis, ectopic pregnancy, and tubal mfertility (10, II), but the tests are not sufficient at present for mdtvidual diagnostic use. Interesting as the sero- logical results are, they remain in the province of research laboratories. 2.3. Syphilis Development of DNA-based technologies for syphilis diagnosis will help in a couple of ways: detection of the etiologic agent in genital ulcers, through use of multiplex panels, and detection of T pallzdum m tissues especially cere- brospmal fluid (CSF), m order to help make more accurate diagnosis of neuro- syphilis. A charitable assessmento f the present state of the art of diagnosis of neurosyphilis is that it is problematic (12). PCR tests of CSF will hopefully allow differentration between the many causes of CNS pleocytosis in AIDS patients, and will help determine whether patients with serological evidence of syphilis have active mfection of the central nervous system. Clinicians are in great need of help in both of these arenas. Unlike the casesw ith gonorrhea and chlamydia, we lack good data at present to determine the role of these tests m management of possible neurosyphilis; hope is high but data are needed. The DNA sequence of T pallidurn was completed very recently. One hopes that analysis of the genomic sequence will lead to insights about the physiol- ogy of the organism, and therefore to solutions of the very old problem of in vitro cultivation outside of animals. Availability of the DNA sequence will predictably enable the development of molecular strain typing tools, which has been entirely lacking m syphilis research until now. One envisions the PCR- based sequencing from patient materials of genes that are known to be variable in different isolates, as a means of better understanding the evolution of the organism within an mdividual, and as it moves between individuals. There is no reason that this cannot be done as effectively for T pallidurn as it can now be done for C trachomatis and iV. gonorrhoeae, and HPV and HIV. Develop- ment of better serological tests based on knowledge of the DNA sequence of pathogenic and nonpathogenic treponemes is another development that can be anticipated with reasonable confidence. 2.4. HPV infection Nearly all of our current understanding about the epidemiology and patho- genesis of HPV disease 1so wing to the development of molecular methods for typing isolates, and detecting the virus in patient materials in the absence of Impact of Molecular Technology on STD Control 9 culture (13,14). A most interesting recent development is the creation of serologi- cal testsb ased on artificial pseudovirus particles, the result of expressing particular genes as recombinant proteins in vitro. These tests,w hich are discussedi n Chapter 11 of this book, are effective tools for epidemiologic studies of diseasep revalence (15) in the same manner that specific serological tests for herpes virus infection have allowed estimations of the true prevalence of genital herpes infections. 2.5. HIV Infection We are dependent to a large measure on molecular methods to assessw ho has very early HIV disease, the extent of disease in virtually everyone who is being considered for treatment, and for following the response to treatment (16). Availability of chip-based sequencing technology is beginning to be deployed already as a tool to determine the sensitivity of HIV to particular antiviral agents, and we can look forward to much more widespread use of these techniques. Indeed, the state of the art is so dependent on viral load test- mg by molecular methods that the absence of these tests in developing coun- tries is a real dilemma for clinicians trying to deploy the new but expensive antiviral therapies for HIV wisely. Assays for infectious amounts of virus in secretions, based on quantttative assays for HIV RNA in patient samples, has shown that other “minor” STDs, such as gonorrhea, have important effects on increasing the shedding of HIV in secretions, and therefore presumably increasing the risk of sexual transmission of HIV (17). 3. Conclusion I have made no attempt to be encyclopedic about the history of testing for STDs. However, this brief appraisal makes it clear that there has been a revolu- tion in our ability to apply sensitive and specific tests for diagnosis, and as an aid to therapy in a variety of STDs. Indeed, the development of such tests has been directly linked to improved understanding of the epidemiology and natu- ral history of many STDs, as for instance HPV and HIV. We have come a very long way from the mttial (successful) effort to make a serological test for syphi- lis based on crude extracts of syphilitic liver tissue. In retrospect, it is not sur- prising that Wassermann’s original serological test for syphilis actually discovered increased serum antibody responses to what we now understand is a normal tissue antigen:diphosphatidyl glycerol. If the original tests for STDs sometimes depended as much on serendipity as the prepared mind and good scientific reasoning, we certainly have now moved to a time and place where hard science forms the basis for most of the new tests that are being developed at a nearly breathtaking pace. New tests as well as a more open acceptance of the importance of STDs have transformed the entire field. What we knew just 34 years ago pales in comparison to what we now know. 10 Sparling The challenge is to deploy these tests and those that will follow in the most cost effective manner, and to try to use them as adjuncts not only to treat, but also to help in prevention. Perhaps the next generation of molecular tests will include very inexpensive tests that are suitable for use in the whole world. References 1. Denhie, C. C. (1962) A History of Syphilis, Springfield, IL. 2. Chmg, S., Lee, H., Hook, E. W , Jacobs, M. R , Zemlman, J., et al (1995) Ltgase chain reaction for detection of Nezsseria gonorrhoeae for urogenital swabs. J Clan Mcroblol. 33,3 11 l-3 114 3. Mahoney, J. B, Luinstra, K. E., Tyndall, M., et al. (I 995) Multtple PCR for detec- tion of Chlamydla trachomatls and Nelsseria gonorrhoeae m gemtourinary speci- mens. J Clan Mcroblol 33,3049-3053 4. Check, W. (1998) Clinical mlcrobtology eyes nucleic acid-based technologies MM News 64(2), 84-88 5. Beebe, J. L, Masters, H , Jungkind, D., Heltzel, D M , Wemberg, A. (1996) Con- tirmatton of the Syva mtcrotrak enzyme mnnunoassay for Chlamydra trachomatzs by Syva direct fluorescent antibody test. Sex Trans Du 23(6), 465-470. 6. Gaydos, C. A. and Quinn, T. (1995) DNA amplificatton assays: a new standard for dtagnosts of Chlamydia trachomatis infecttons. Venereology 4, 164-169. 7. Gaydos, C. A., Crotchfeld, K. A., Howell, M. R., Krahan, S., Hauptman, P., Quinn, T. C. (1998) Molecular amphfication assays to detect chlamydial infec- tions m urme specimens from htgh school female students and to momtor the persistence of chlamydtal DNA after therapy. J Znf Dzs 177,4 17-424 8. Mertz, K. J , Levme, W. C , Mosure, D. J., Berman, S. M., Dortan, K. J. (1997) Trends in the prevalence of chlamydial infections, the impact of commumty-wide testing. Sex Trans Dv 24(3), 169-175 9 Marrazzo, J M., Celum, C. L., Hillis, S D., Fine, D., DeLtsle, S., Handsfield, H. H (1997) Performance and cost-effectiveness of selecttve screening criteria for Chlamydla trachomatzs mfectton m women, tmplicatlons for a national chlamydia control strategy. Sex Trans Dw. 24(3), 13 l-140. 10. Domeika, M., Komeika, K., Paavonen, J., Mardh, P. A., Witkin, S. S. (1998) Humoral immune response to conserved epitopes of Chlamydia trachomatu and human 60-kDa heat-shock protein m women with pelvic inflammatory disease. J. Znf Dzs 177,714-719. 11 Peeling, R. W., Kimani, J., Plummer, F , Maclean, I., Cheang, M., Bwayo, J., Bnmham, R. C. (1997) Antibody to chlamydial hsp60 predicts an increased rusk for chlamydtal pelvic inflammatory disease J Znf Dzs 175, 1153-l 158. 12. Flood, J. M., Weinstock, H. S , Guroy, M. E., Bayne, L., Stmon, R P., Bolan, G. (1998) Neurosyphlhs durmg the AIDS epidemic, San Franctsco, 1985- 1992 J, Znf Dls. 177,93 l-940. 13. Ho, G. Y., Bierman, R., Beardsley, L., Chang, C. J., Burk, R. D. (1998) Natural history of cervicovaginal papillomavirus infection in young women. NIL04 338(7), 423-428 impact of Molecular Technology on STD Control 11 14. Burk, R. D., Kadish, A. S., Calderin, S., Romney, S. L. (1986) Humanpapillomavuus mfectton of the cervix detected by cervicovaginal lavage and molecular hybrid- ization: correlation with biopsy results and Papanicolaou smear. Am J Obstet Gynecol 154,982-989 15. Carter, J. J., Koutsky, L. A., Wipf, G. C., Christensen, N. D., Lee, S. K., Kuypers, J., Kiviat, N., Galloway, D. A. The natural history of human papillomavuus type 16 capstd antibodies among a cohort of university women. 16. FISCUS, S. A , Hughes, M D., Lathey, J. L., Pi, T., Jackson, B , Rasheed, S , et al. (1998) Changes m virologic markers as predictors of CD4 cell decline and pro- gression of disease in human immunodeficiency virus type l-infected adults treated with nucleosides J Inf: Du. 177,625-633 17. Cohen, M. S., Hoffman, I. F , Royce, R. A., Kazembe, P., Dyer, J. R., Daly, C. C , et al (1997) Reduction of concentration of HIV-l m semen after treatment of urethrms; implications for sexual transmission of HIV- 1 Lancet 349(9069), 1868-1873 2 Neisseria gonorrhoeae Detection and Typing by Probe Hybridization, LCR, and PCR Charlotte A. Gaydos and Thomas C. Quinn 1. Introduction 7.1. Taxonomy Neisseria gonorrhoeae, first described by Neisser in 1879, 1s a Gram-nega- tive, nonmottle, nonspore-forming diplococcus, belonging to the family Neisseriaceae. It is the etiologic agent of gonorrhea. The other pathogemc spe- cies is Neisseria meningitzdis, to which N. gonorrhoeae is genetically closely related. Although N. meningitidzs is not usually considered to be a sexually trans- mitted disease, it may infect the mucous membranes of the anogenital area of homosexual men (2). The other members of the genus, which include Neisseria lactamica, Nelsseria polysaccharea, Neissena cinerea, and Neissenaf2avescens, which are related to Neisseria gonorrhoeae, and saccharolytic strams, such as Neisserza subjlava, Neisseria swca, and Nelsseria mucosa, which are less genetically related to the aforementioned, are considered to be nonpathogenic, being normal flora of the nasopharyngeal mucous membranes (2). 1.2. Clinical Significance Gonococcal infection may be either symptomatic or asymptomatic, and can cause urethritis, cervicms, proctitis, Bartholinitis, or conjunctivitis. Gonorrhea is the most frequently reported bacterial infection in the US. In males, compli- cations may include: epididymitis, prostatitis, and seminal vesiculitis. In homosexuals, rectal infection and pharyngitis can occur. In females, most cases are asymptomatic, and Infections of the urethra and rectum often coexist with cervical mfection. Comphcattons can include pelvic inflammatory dis- ease, pelvic pain, ectopic pregnancy, infertility, Fitz-Hugh Curtis syndrome, From Methods m Molecular Medlone. Vol 20 Sexually TransmItted Diseases Methods and Protocols Edlted by R W Peehg and P F Sparllng 0 Humana Press Inc , Totowa, NJ 15