On the origin of the treponematoses: a phylogenetic approach

Redefining the treponemal history through pre-Columbian genomes from Brazil

The origins of treponemal diseases have long remained unknown, especially considering the sudden onset of the first syphilis epidemic in the late 15th century in Europe and its hypothesized arrival from the Americas with Columbus' expeditions1,2. Recently, ancient DNA evidence has revealed various treponemal infections circulating in early modern Europe and colonial-era Mexico3-6. However, there has been to our knowledge no genomic evidence of treponematosis recovered from either the Americas or the Old World that can be reliably dated to the time before the first trans-Atlantic contacts. Here, we present treponemal genomes from nearly 2,000-year-old human remains from Brazil. We reconstruct four ancient genomes of a prehistoric treponemal pathogen, most closely related to the bejel-causing agent Treponema pallidum endemicum. Contradicting the modern day geographical niche of bejel in the arid regions of the world, the results call into question the previous palaeopathological characterization of treponeme subspecies and showcase their adaptive potential. A high-coverage genome is used to improve molecular clock date estimations, placing the divergence of modern T. pallidum subspecies firmly in pre-Columbian times. Overall, our study demonstrates the opportunities within archaeogenetics to uncover key events in pathogen evolution and emergence, paving the way to new hypotheses on the origin and spread of treponematoses.

Monkeypox (Mpox): Evolution of Transmission and Comprehensive Review

The human monkeypox (mpox) virus is an orthopox virus that can be transmitted to humans. Though the disease has been endemic in Africa, the recent mpox outbreak since May 2022. We attempted to examine differences between the endemic form of mpox and the current outbreak. Review of electronic medical database with relevant keywords. The current outbreak of mpox has disproportionately impacted the gay, bisexual and other men who have sex with men (MSM) community. This is also the first time that widespread semen testing has turned up evidence of mpox viral deoxyribonucleic acid (DNA). Cases in the present outbreak are more likely to affect adults, involve the genitalia, and have no prodrome. Close diagnostic differentials include varicella and hand-foot-mouth disease. The disease is usually self-limiting; though secondary infections, anorectal pain, pharyngitis, ocular lesions and rarely, renal injury and myocarditis may occur. This review focuses primarily on the novel clinical characteristics and emerging sexual transmission route of the mpox virus, which, although unconfirmed, appears extremely likely as the route of spread. Dermatologists have an important role in this health emergency, as early diagnosis can cause a significant reduction in disease transmission.

Performance of Molecular Tests in the Diagnosis of Syphilis From 2009 to 2019: A Systematic Review and Meta-Analysis

BACKGROUND

Syphilis continues to be a public health problem, and its diagnosis still has limitations. Molecular diagnosis provides an alternative for rapid and effective management. The objective is to determine the accuracy of tests in the molecular diagnosis of syphilis.

METHODS

We searched PubMed and Web of Sciences for articles related to molecular detection of syphilis from January 1, 2009, to December 31, 2019. The bivariate Reitsma model and the hierarchical receiver operating characteristic curve model were used to evaluate the diagnostic performance of molecular tests at a 95% confidence interval. A subgroup meta-analysis was performed to explore sources of heterogeneity.

RESULTS

Forty-seven articles were identified for qualitative synthesis, of which 23 met the inclusion criteria for meta-analysis. The pooled sensitivities in conventional polymerase chain reaction (PCR) and real-time PCR were 77.52 (59.50-89.01) and 68.43 (54.96-79.39), respectively. The pooled specificities were 98.00 (90.73-99.59) and 98.84 (97.55-99.46), respectively. Ulcer samples had a better performance (sensitivity of 79.88 [69.00-87.62] and specificity of 98.58 [97.25-99.27]), and the major target genes were the polymerase A gene and tpp47 gene.

CONCLUSIONS

Our work showed that conventional PCR was more widely used than real-time PCR in the diagnosis of syphilis, and ulcers were the best specimens. Sample types and target genes are factors that may influence the quality of the different tests. These results could provide evidence for further work in the direction of providing a more efficient diagnostic test.

Metagenomic Research of Infectious Diseases in Archaeological Contexts: Evidence from the Hospital Real de Todos-os-Santos (Portugal)

Syphilis is one of the most exciting diseases explored in paleopathology and, therefore, tracing back its origin and development has provided a prolific debate. The combination of paleopathological data with historical sources, iconography, and archaeological contexts were the primary sources used to reconstruct its historical path. However, there are some limitations to paleopathological diagnosis due to the nature of bone reaction to stimuli. In addition, historical sources are subjected to a bias of social and cultural nature and the knowledge of those who wrote them. Hence, ancient DNA analysis offers the possibility of acquiring proof of cause by identifying pathogens in an organism. We undertook a metagenomic study of a skeleton exhumed from the Royal Hospital of All Saints (Portugal), renowned for treating syphilis from the 16th century onwards. The skeleton had previously been diagnosed with syphilis according to paleopathological analysis. However, the metagenomics analysis showed no presence of the pathogen associated with syphilis (i.e., Treponema pallidum) but revealed pathogenic microorganisms related to respiratory diseases (pneumonia), nonspecific bone infections (osteomyelitis), and oral bacterial pathologies as well as Hansen’s disease (also known as leprosy). The results are exciting and demand a reappraisal of the observed bone changes, recontextualizing their characterization as syphilis related. They prove that past reconstruction of health and disease diagnoses based on assessing human osteological remains of known context (such as a syphilitic hospital) may bias interpretations and, therefore, caution is recommended, not forgetting that the absence of evidence is not evidence of absence (in this case of syphilis) in life.

Evolutionary processes in the emergence and recent spread of the syphilis agent, Treponema pallidum

The incidence of syphilis has risen worldwide in the last decade in spite of being an easily treated infection. The causative agent of this sexually transmitted disease is the bacterium Treponema pallidum subspecies pallidum (TPA), very closely related to subsp. pertenue (TPE) and endemicum (TEN), responsible for the human treponematoses yaws and bejel, respectively. Although much focus has been placed on the question of the spatial and temporary origins of TPA, the processes driving the evolution and epidemiological spread of TPA since its divergence from TPE and TEN are not well understood. Here, we investigate the effects of recombination and selection as forces of genetic diversity and differentiation acting during the evolution of T. pallidum subspecies. Using a custom-tailored procedure, named phylogenetic incongruence method, with 75 complete genome sequences, we found strong evidence for recombination among the T. pallidum subspecies, involving 12 genes and 21 events. In most cases, only one recombination event per gene was detected and all but one event corresponded to intersubspecies transfers, from TPE/TEN to TPA. We found a clear signal of natural selection acting on the recombinant genes, which is more intense in their recombinant regions. The phylogenetic location of the recombination events detected and the functional role of the genes with signals of positive selection suggest that these evolutionary processes had a key role in the evolution and recent expansion of the syphilis bacteria and significant implications for the selection of vaccine candidates and the design of a broadly protective syphilis vaccine.

King Charles VIII of France's Death: From an Unsubstantiated Traumatic Brain Injury to More Realistic Hypotheses

On April 7, 1498, Charles VIII, King of France, attended a game of palm in the ditches of the Château d'Amboise. The 27-year-old King suddenly collapsed and became comatose. He laid down, almost on his own, on a straw mat that was hastily arranged, and he died 9 hours later. His contemporaries perceived his death as a perfect reminder of fatality: a king could die alone in a miserable gallery. All who looked into this curious death had dwelled on the frontal blow to head that the king had sustained right before his demise and had not considered alternative scenarios. The present study, still with limited available evidence, aimed to reexamine the historical account of his death in light of modern medical knowledge. It is virtually impossible that a minor bump with low kinetic energy could kill a 27-year-old man. Many historical accounts of Charles VIII's life and death, including Italian ambassadors' letters, led us to reconsider the commonly held version and to propose an alternative hypothesis. We have concluded that Charles VIII had experienced an acute consciousness disorder with language impairment that could have been related to an epileptic condition secondary to neurosyphilis. We have discussed whether a more accurate diagnosis for the cause of death could be obtained by a pathological analysis of the King's remains.

Continental-scale genomic analysis suggests shared post-admixture adaptation in the Americas

American populations are one of the most interesting examples of recently admixed groups, where ancestral components from three major continental human groups (Africans, Eurasians and Native Americans) have admixed within the last 15 generations. Recently, several genetic surveys focusing on thousands of individuals shed light on the geography, chronology and relevance of these events. However, even though gene flow could drive adaptive evolution, it is unclear whether and how natural selection acted on the resulting genetic variation in the Americas.

In this study, we analysed the patterns of local ancestry of genomic fragments in genome-wide data for ~ 6000 admixed individuals from 10 American countries. In doing so, we identified regions characterized by a divergent ancestry profile (DAP), in which a significant over or under ancestral representation is evident.

Our results highlighted a series of genomic regions with DAPs associated with immune system response and relevant medical traits, with the longest DAP region encompassing the human leukocyte antigen locus. Furthermore, we found that DAP regions are enriched in genes linked to cancer-related traits and autoimmune diseases. Then, analysing the biological impact of these regions, we showed that natural selection could have acted preferentially towards variants located in coding and non-coding transcripts and characterized by a high deleteriousness score.

Taken together, our analyses suggest that shared patterns of post admixture adaptation occurred at a continental scale in the Americas, affecting more often functional and impactful genomic variants.

Penicillin Treatment Failure in Rabbit Syphilis Due to the Persistence of Treponemes (Treponema paraluisleporidarum Ecovar Cuniculus) in the Focus of Infection

Rabbit venereal spirochetosis, a disease caused by Treponema paraluisleporidarum ecovar Cuniculus (TPeC), affects both wild and pet rabbits, and is transmitted sexually and via direct contact among animals. Treatment of syphilis in pet rabbits requires administration of antibiotics, including penicillin G, chloramphenicol, or fluoroquinolones. The aim of this work was to elucidate the cause of penicillin treatment failure in rabbit syphilis in a pet rabbit treated in Brno, Czech Republic, and to assess the phylogenetic relatedness of the agent to previously characterized pathogenic treponemes. Following amputation of the infected digits, the second round of penicillin treatment using the same dosage and application route resulted in the disappearance of clinical symptoms within a period of two weeks. The bacterium was successfully isolated from the claws, propagated in three experimental rabbits, and the resulting TPeC strain was designated as Cz-2020. Analysis of four genetic loci revealed that the Cz-2020 strain was similar but also clearly distinct from the only TPeC strain, which had been characterized in detail to date, i.e., the Cuniculi A strain, which was isolated in North America. The strain Cz-2020 represents the first available viable TPeC strain of European origin. DNA sequences encoding five penicillin-binding proteins of the strain Cz-2020 were compared to those of Cuniculi A, which is known to be sensitive to penicillin. The sequences differed in six nucleotides resulting in single amino acid changes in Penicillin-binding protein 1, 2, and 3. Since the second round of treatment was successful, we conclude that the penicillin treatment failure in the first round resulted from the presence of infection foci in claws where treponemes persisted.

Hannibal’s Ophthalmia—A New Answer to An Ancient Question

In the spring of 217 bce, shortly after Hannibal’s famous elephantborne crossing of the Alps, the general was afflicted by an acute, painful eye condition that has never been adequately explained and that led to permanent unilateral loss of vision in 1 eye. In modern times, scant attention has been given to understanding this condition. We review the historical and geographic evidence and consider possible infective explanations for Hannibal's condition, including elephant-associated zoonoses. Ultimately, we suggest that a keratitis from waterborne organisms, such as Pseudomonas spp. or Acanthamoeba spp., might provide the best answer to this ancient enigma.

A treponemal genome from an historic plague victim supports a recent emergence of yaws and its presence in 15th century Europe

Developments in techniques for identification of pathogen DNA in archaeological samples can expand our resolution of disease detection. Our application of a non-targeted molecular screening tool for the parallel detection of pathogens in historical plague victims from post-medieval Lithuania revealed the presence of more than one active disease in one individual. In addition to Yersinia pestis, we detected and genomically characterized a septic infection of Treponema pallidum pertenue, a subtype of the treponemal disease family recognised as the cause of the tropical disease yaws. Our finding in northern Europe of a disease that is currently restricted to equatorial regions is interpreted within an historical framework of intercontinental trade and potential disease movements. Through this we offer an alternative hypothesis for the history and evolution of the treponemal diseases, and posit that yaws be considered an important contributor to the sudden epidemic of late 15^th century Europe that is widely ascribed to syphilis.

Covid-19: End of the beginning?

The limited case cluster of atypical pneumonia detected in central China in December 2019, now known as Coronavirus Disease 2019 (Covid-19), converted into a million confirmed cases worldwide in only 10 weeks. Declared a pandemic by the World Health Organization (WHO) on 11 March 2020 (WHO, 2020) and passing the 3 million mark on 27 April, the world is under formidable strain with respect to public health, economy and personal life. Time and again we are alerted about unforeseen, new effects of this disease, which brings to mind the terms "known unknowns" and "unknown unknowns" used by former U.S. Secretary of Defense Donald Rumsfield when referring to the lack of evidence of weapons of mass destruction in Iraq ahead of the second Gulf war, a fitting vocabulary as we again are faced with mass destruction, though this time of a different kind.

Advancing the understanding of treponemal disease in the past and present

Syphilis was perceived to be a new disease in Europe in the late 15th century, igniting a debate about its origin that continues today in anthropological, historical, and medical circles. We move beyond this age-old debate using an interdisciplinary approach that tackles broader questions to advance the understanding of treponemal infection (syphilis, yaws, bejel, and pinta). How did the causative organism(s) and humans co-evolve? How did the related diseases caused by Treponema pallidum emerge in different parts of the world and affect people across both time and space? How are T. pallidum subspecies related to the treponeme causing pinta? The current state of scholarship in specific areas is reviewed with recommendations made to stimulate future work. Understanding treponemal biology, genetic relationships, epidemiology, and clinical manifestations is crucial for vaccine development today and for investigating the distribution of infection in both modern and past populations. Paleopathologists must improve diagnostic criteria and use a standard approach for recording skeletal lesions on archaeological human remains. Adequate contextualization of cultural and environmental conditions is necessary, including site dating and justification for any corrections made for marine or freshwater reservoir effects. Biogeochemical analyses may assess aquatic contributions to diet, physiological changes arising from treponemal disease and its treatments (e.g., mercury), or residential mobility of those affected. Shifting the focus from point of origin to investigating who is affected (e.g., by age/sex or socioeconomic status) and disease distribution (e.g., coastal/ inland, rural/urban) will advance our understanding of the treponemal disease and its impact on people through time.

Directly Sequenced Genomes of Contemporary Strains of Syphilis Reveal Recombination-Driven Diversity in Genes Encoding Predicted Surface-Exposed Antigens

Syphilis, caused by Treponema pallidum subsp. pallidum (TPA), remains an important public health problem with an increasing worldwide prevalence. Despite recent advances in in vitro cultivation, genetic variability of this pathogen during infection is poorly understood. Here, we present contemporary and geographically diverse complete treponemal genome sequences isolated directly from patients using a methyl-directed enrichment prior to sequencing. This approach reveals that approximately 50% of the genetic diversity found in TPA is driven by inter- and/or intra-strain recombination events, particularly in strains belonging to one of the defined genetic groups of syphilis treponemes: Nichols-like strains. Recombinant loci were found to encode putative outer-membrane proteins and the recombination variability was almost exclusively found in regions predicted to be at the host-pathogen interface. Genetic recombination has been considered to be a rare event in treponemes, yet our study unexpectedly showed that it occurs at a significant level and may have important impacts in the biology of this pathogen, especially as these events occur primarily in the outer membrane proteins. This study reveals the existence of strains with different repertoires of surface-exposed antigens circulating in the current human population, which should be taken into account during syphilis vaccine development.

Tropical rainforest flies carrying pathogens form stable associations with social nonhuman primates

Living in groups provides benefits but also incurs costs such as attracting disease vectors. For example, synanthropic flies associate with human settlements, and higher fly densities increase pathogen transmission. We investigated whether such associations also exist in highly mobile nonhuman primate (NHP) Groups. We studied flies in a group of wild sooty mangabeys (Cercocebus atys atys) and three communities of wild chimpanzees (Pan troglodytes verus) in Taï National Park, Côte d'Ivoire. We observed markedly higher fly densities within both mangabey and chimpanzee groups. Using a mark-recapture experiment, we showed that flies stayed with the sooty mangabey group for up to 12 days and for up to 1.3 km. We also tested mangabey-associated flies for pathogens infecting mangabeys in this ecosystem, Bacillus cereus biovar anthracis (Bcbva), causing sylvatic anthrax, and Treponema pallidum pertenue, causing yaws. Flies contained treponemal (6/103) and Bcbva (7/103) DNA. We cultured Bcbva from all PCR-positive flies, confirming bacterial viability and suggesting that this bacterium might be transmitted and disseminated by flies. Whole genome sequences of Bcbva isolates revealed a diversity of Bcbva, probably derived from several sources. We conclude that flies actively track mangabeys and carry infectious bacterial pathogens; these associations represent an understudied cost of sociality and potentially expose many social animals to a diversity of pathogens.

Identification of positively selected genes in human pathogenic treponemes: Syphilis-, yaws-, and bejel-causing strains differ in sets of genes showing adaptive evolution

BACKGROUND

Pathogenic treponemes related to Treponema pallidum are both human (causing syphilis, yaws, bejel) and animal pathogens (infections of primates, venereal spirochetosis in rabbits). A set of 11 treponemal genome sequences including those of five Treponema pallidum ssp. pallidum (TPA) strains (Nichols, DAL-1, Mexico A, SS14, Chicago), four T. p. ssp. pertenue (TPE) strains (CDC-2, Gauthier, Samoa D, Fribourg-Blanc), one T. p. ssp. endemicum (TEN) strain (Bosnia A) and one strain (Cuniculi A) of Treponema paraluisleporidarum ecovar Cuniculus (TPeC) were tested for the presence of positively selected genes.

METHODOLOGY/PRINCIPAL FINDINGS

A total of 1068 orthologous genes annotated in all 11 genomes were tested for the presence of positively selected genes using both site and branch-site models with CODEML (PAML package). Subsequent analyses with sequences obtained from 62 treponemal draft genomes were used for the identification of positively selected amino acid positions. Synthetic biotinylated peptides were designed to cover positively selected protein regions and these peptides were tested for reactivity with the patient's syphilis sera. Altogether, 22 positively selected genes were identified in the TP genomes and TPA sets of positively selected genes differed from TPE genes. While genetic variability among TPA strains was predominantly present in a number of genetic loci, genetic variability within TPE and TEN strains was distributed more equally along the chromosome. Several syphilitic sera were shown to react with some peptides derived from the protein sequences evolving under positive selection.

CONCLUSIONS/SIGNIFICANCE

The syphilis-, yaws-, and bejel-causing strains differed relative to sets of positively selected genes. Most of the positively selected chromosomal loci were identified among the TPA treponemes. The local accumulation of genetic variability suggests that the diversification of TPA strains took place predominantly in a limited number of genomic regions compared to the more dispersed genetic diversity differentiating TPE and TEN strains. The identification of positively selected sites in tpr genes and genes encoding outer membrane proteins suggests their role during infection of human and animal hosts. The driving force for adaptive evolution at these loci thus appears to be the host immune response as supported by observed reactivity of syphilitic sera with some peptides derived from protein sequences showing adaptive evolution.

A Case of Syphilis with High Bone Arsenic Concentration from Early Modern Cemetery (Wroclaw, Poland)

Venereal syphilis is a sexually transmitted disease caused by Treponema pallidum - Gram-negative, slowly growing bacteria. The spread of the disease in the Old World was due to increased birth rate, urban population growth, migration and lack of knowledge concerning the epidemiology. In the past, the treatment was mainly symptomatic and included application of mercury compounds. The goal of the study was to present the case of advanced venereal syphilis found in early modern (16th-18thc) graveyard localized in Wroclaw, Poland. The object of the study is a cranium of a male whose age at death has been estimated to be over 55. In order to observe the morphological and paleopathological characteristics of the examined material, anthropometrics, computed tomography, spectrometry and microscopic methods were incorporated. Microscopic analysis revealed the presence of the extensive inflammatory lesions. Analyses indicate tertiary stage of venereal syphilis as the most probable cause of the observed lesions. Concentration of arsenic (16.17±0.58 μg/g) in examined bone samples was about hundred times bigger than average arsenic concentration in bones reported in other studies. Advanced stage of observed lesions along with high arsenic level may suggest long-lasting palliative care and usage of arsenic compound in therapeutic treatment of this chronic disease.

The Bioarchaeology of Health Crisis: Infectious Disease in the Past

Beginning some 10,000 years ago, humans began a dramatic alteration in living conditions relating especially to the shift in lifeway from foraging to farming. In addition to the initiation of and increasing focus on the production and consumption of domesticated plant carbohydrates, this revolutionary transformation in diet occasioned a decline in mobility and an increased size and agglomeration of populations in semipermanent or permanent settlements. These changes in life conditions presented an opportunity for increased transmission of pathogenic microbes from host to host, such as those that cause major health threats affecting most of the 7.5 billion members of our species today. This article discusses the bioarchaeology of infectious disease, focusing on tuberculosis, treponematosis, dental caries, and periodontitis, all of which continue to contribute to high levels of morbidity and mortality among the world's populations today.

Historic Treponema pallidum genomes from Colonial Mexico retrieved from archaeological remains

Treponema pallidum infections occur worldwide causing, among other diseases, syphilis and yaws. In particular sexually transmitted syphilis is regarded as a re-emerging infectious disease with millions of new infections annually. Here we present three historic T. pallidum genomes (two from T. pallidum ssp. pallidum and one from T. pallidum ssp. pertenue) that have been reconstructed from skeletons recovered from the Convent of Santa Isabel in Mexico City, operational between the 17th and 19th century. Our analyses indicate that different T. pallidum subspecies caused similar diagnostic presentations that are normally associated with syphilis in infants, and potential evidence of a congenital infection of T. pallidum ssp. pertenue, the causative agent of yaws. This first reconstruction of T. pallidum genomes from archaeological material opens the possibility of studying its evolutionary history at a resolution previously assumed to be out of reach.

Reanalysis of Chinese Treponema pallidum samples: all Chinese samples cluster with SS14-like group of syphilis-causing treponemes

OBJECTIVE

Treponema pallidum subsp. pallidum (TPA) is the causative agent of syphilis. Genetic analyses of TPA reference strains and human clinical isolates have revealed two genetically distinct groups of syphilis-causing treponemes, called Nichols-like and SS14-like groups. So far, no genetic intermediates, i.e. strains containing a mixed pattern of Nichols-like and SS14-like genomic sequences, have been identified. Recently, Sun et al. (Oncotarget 2016. https://doi.org/10.18632/oncotarget.10154 ) described a new "phylogenetic group" (called Lineage 2) among Chinese TPA strains. This lineage exhibited a "mosaic genomic structure" of Nichols-like and SS14-like lineages.

RESULTS

We reanalyzed the primary sequencing data (Project Number PRJNA305961) from the Sun et al. publication with respect to the molecular basis of Lineage 2. While Sun et al. based the analysis on several selected genomic single nucleotide variants (SNVs) and a subset of highly variable but phylogenetically poorly informative genes, which may confound the phylogenetic analysis, our reanalysis primarily focused on a complete set of whole genomic SNVs. Based on our reanalysis, only two separate TPA clusters were identified: one consisted of Nichols-like TPA strains, the other was formed by the SS14-like TPA strains, including all Chinese strains.

Tracing the origin of Treponema pallidum in China using next-generation sequencing

Syphilis is a systemic sexually transmitted disease caused by Treponema pallidum ssp. pallidum (TPA). The origin and genetic background of Chinese TPA strains remain unclear. We identified a total of 329 single-nucleotide variants (SNVs) in eight Chinese TPA strains using next-generation sequencing. All of the TPA strains were clustered into three lineages, and Chinese TPA strains were grouped in Lineage 2 based on phylogenetic analysis. The phylogeographical data showed that TPA strains originated earlier than did T. pallidum ssp. pertenue (TPE) and T. pallidum ssp. endemicum (TPN) strains and that Chinese TPA strains might be derived from recombination between Lineage 1 and Lineage 3. Moreover, we found through a homology modeling analysis that a nonsynonymous substitution (I415F) in the PBP3 protein might affect the structural flexibility of PBP3 and the binding constant for substrates based on its possible association with penicillin resistance in T. pallidum. Our findings provide new insight into the molecular foundation of the evolutionary origin of TPA and support the development of novel diagnostic/therapeutic technology for syphilis.

Complete genome sequences of two strains of Treponema pallidum subsp. pertenue from Ghana, Africa: Identical genome sequences in samples isolated more than 7 years apart

BACKGROUND

Treponema pallidum subsp. pertenue (TPE) is the causative agent of yaws, a multi-stage disease, endemic in tropical regions of Africa, Asia, Oceania, and South America. To date, four TPE strains have been completely sequenced including three TPE strains of human origin (Samoa D, CDC-2, and Gauthier) and one TPE strain (Fribourg-Blanc) isolated from a baboon. All TPE strains are highly similar to T. pallidum subsp. pallidum (TPA) strains. The mutation rate in syphilis and related treponemes has not been experimentally determined yet.

METHODOLOGY/PRINCIPAL FINDINGS

Complete genomes of two TPE strains, CDC 2575 and Ghana-051, that infected patients in Ghana and were isolated in 1980 and 1988, respectively, were sequenced and analyzed. Both strains had identical consensus genome nucleotide sequences raising the question whether TPE CDC 2575 and Ghana-051 represent two different strains. Several lines of evidence support the fact that both strains represent independent samples including regions showing intrastrain heterogeneity (13 and 5 intrastrain heterogeneous sites in TPE Ghana-051 and TPE CDC 2575, respectively). Four of these heterogeneous sites were found in both genomes but the frequency of alternative alleles differed. The identical consensus genome sequences were used to estimate the upper limit of the yaws treponeme evolution rate, which was 4.1 x 10-10 nucleotide changes per site per generation.

CONCLUSIONS/SIGNIFICANCE

The estimated upper limit for the mutation rate of TPE was slightly lower than the mutation rate of E. coli, which was determined during a long-term experiment. Given the known diversity between TPA and TPE genomes and the assumption that both TPA and TPE have a similar mutation rate, the most recent common ancestor of syphilis and yaws treponemes appears to be more than ten thousand years old and likely even older.

[Nonviral sexually transmitted infections-epidemiology, clinical manifestations, diagnostic workup, therapy : Part 3: Treponemes, Gardnerella and trichomonads]

In Germany, the reported syphilis prevalence has increased continuously since 2010, with a total of 6834 syphilis cases being reported in 2015. The largest increase of reported syphilis occurred in men who have sex with men (MSM). The antibiotic agent of choice for treatment of syphilis is still penicillin. There are no penicillin-resistant Treponema pallidum strains. Alternatives are ceftriaxone and doxycycline. In Germany, azithromycin is not approved for treatment of syphilis; however, therapy failures are increasingly reported. Bacterial vaginosis is accompanied by vaginal discharge. The vaginal secretion exhibits an increased pH value higher than 4.5. Clinical symptoms are pruritus, burning, and the characteristic amine odor. The probability for bacterial vaginosis is highest in women with higher numbers of sexual partners, unmarried women, early first sexual intercourse, in commercial female sex workers, and those women who regularly apply vaginal douches. The main pathogen of bacterial vaginosis is Gardnerella vaginalis. For oral therapy metronidazole is given, alternatively clindamycin; the latter should be applied additionally as topical agent. Trichomoniasis is considered as the nonviral sexually transmitted infection with the highest prevalence worldwide. Other than direct microscopic detection of the protozoa (trophozoites) in vaginal secretion or urine, PCR has been approved as the diagnostic method with the highest sensitivity. Oral metronidazole represents the therapy of choice in trichomoniasis.

Human Treponema pallidum 11q/j isolate belongs to subsp. endemicum but contains two loci with a sequence in TP0548 and TP0488 similar to subsp. pertenue and subsp. pallidum, respectively

Background

Treponema pallidum subsp. endemicum (TEN) is the causative agent of endemic syphilis (bejel). An unusual human TEN 11q/j isolate was obtained from a syphilis-like primary genital lesion from a patient that returned to France from Pakistan.

Methodology/Principal findings

The TEN 11q/j isolate was characterized using nested PCR followed by Sanger sequencing and/or direct Illumina sequencing. Altogether, 44 chromosomal regions were analyzed. Overall, the 11q/j isolate clustered with TEN strains Bosnia A and Iraq B as expected from previous TEN classification of the 11q/j isolate. However, the 11q/j sequence in a 505 bp-long region at the TP0488 locus was similar to Treponema pallidum subsp. pallidum (TPA) strains, but not to TEN Bosnia A and Iraq B sequences, suggesting a recombination event at this locus. Similarly, the 11q/j sequence in a 613 bp-long region at the TP0548 locus was similar to Treponema pallidum subsp. pertenue (TPE) strains, but not to TEN sequences.

Conclusions/Significance

A detailed analysis of two recombinant loci found in the 11q/j clinical isolate revealed that the recombination event occurred just once, in the TP0488, with the donor sequence originating from a TPA strain. Since TEN Bosnia A and Iraq B were found to contain TPA-like sequences at the TP0548 locus, the recombination at TP0548 took place in a treponeme that was an ancestor to both TEN Bosnia A and Iraq B. The sequence of 11q/j isolate in TP0548 represents an ancestral TEN sequence that is similar to yaws-causing treponemes. In addition to the importance of the 11q/j isolate for reconstruction of the TEN phylogeny, this case emphasizes the possible role of TEN strains in development of syphilis-like lesions.

Treponema pallidum subsp. endemicum (TEN) is an uncultivable pathogenic treponeme that causes bejel (endemic syphilis), a chronic human infection mostly affecting children under 15 years of age, occurring mainly in several African and Middle East countries. In this work, we characterized a TEN 11q/j isolate from France that was obtained from an adult male with genital lesions, who was suspected of having syphilis and who received benzathine penicillin G. DNA sequencing of the isolate revealed two loci that were, rather than to TEN, related either to T. pallidum subsp. pertenue or to T. pallidum subsp. pallidum and likely resulted from recombination events. The recombination event in TP0488 as well as the recombination in TP0548, of the 11q/j, helped clarify the phylogeny of the TEN strains indicating that the recombination in TP0548 took place in a treponeme that was ancestral of Bosnia A and Iraq B, but was not an ancestor of the 11q/j isolate. In contrast, a recombination event in TP0488 appeared in the ancestor of the 11q/j isolate after separation of the ancestral treponeme of Bosnia A and Iraq B. This case also points to a possible role of TEN strains in development of syphilis-like lesions in countries with endemic syphilis.

Metabolic competition as a driver of bacterial population structure

Understanding the processes whereby diversity arises and is maintained in pathogen populations is pivotal for designing disease control interventions. A particular problem is the maintenance of strain structure in bacterial pathogen populations despite frequent genetic exchange. Although several theoretical frameworks have been put forward to explain this widespread phenomenon, few have focused on the role of genes encoding metabolic functions, despite an increasing recognition of their importance in pathogenesis and transmission. In this article, we review the literature for evidence of metabolic niches within the host and discuss theoretical frameworks which examine ecological interactions between metabolic genes. We contend that metabolic competition is an important phenomenon which contributes to the maintenance of population structure and diversity of many bacterial pathogens.

Microbial Genomics of Ancient Plagues and Outbreaks

The recent use of next-generation sequencing methods to investigate historical disease outbreaks has provided us with an unprecedented ability to address important and long-standing questions in epidemiology, pathogen evolution, and human history. In this review, we present major findings that illustrate how microbial genomics has provided new insights into the nature and etiology of infectious diseases of historical importance, such as plague, tuberculosis, and leprosy. Sequenced isolates collected from archaeological remains also provide evidence for the timing of historical evolutionary events as well as geographic spread of these pathogens. Elucidating the genomic basis of virulence in historical diseases can provide relevant information on how we can effectively understand the emergence and re-emergence of infectious diseases today and in the future.

Sexually transmitted infections: old foes on the rise

Sexually transmitted infections (STIs) are commonly spread via sexual contact. It is estimated that one million STIs are acquired every day worldwide. Besides their impact on sexual, reproductive and neonatal health, they can cause disastrous and life-threatening complications if left untreated. In addition to this personal burden, STIs also represent a socioeconomic problem, deriving in treatment costs of tremendous proportions. Despite a substantial progress in diagnosis, treatment and prevention, the incidence of many common STIs is increasing, and STIs continue to represent a global public health problem and a major cause for morbidity and mortality. With this Special Issue, Microbial Cell provides an in-depth overview of the eight major STIs, covering all relevant features of each infection.

Comparative Microbial Genomics and Forensics

Forensic science concerns the application of scientific techniques to questions of a legal nature and may also be used to address questions of historical importance. Forensic techniques are often used in legal cases that involve crimes against persons or property, and they increasingly may involve cases of bioterrorism, crimes against nature, medical negligence, or tracing the origin of food- and crop-borne disease. Given the rapid advance of genome sequencing and comparative genomics techniques, we ask how these might be used to address cases of a forensic nature, focusing on the use of microbial genome sequence analysis. Such analyses rely on the increasingly large numbers of microbial genomes present in public databases, the ability of individual investigators to rapidly sequence whole microbial genomes, and an increasing depth of understanding of their evolution and function. Suggestions are made as to how comparative microbial genomics might be applied forensically and may represent possibilities for the future development of forensic techniques. A particular emphasis is on the nascent field of genomic epidemiology, which utilizes rapid whole-genome sequencing to identify the source and spread of infectious outbreaks. Also discussed is the application of comparative microbial genomics to the study of historical epidemics and deaths and how the approaches developed may also be applicable to more recent and actionable cases.

Tools for opening new chapters in the book of Treponema pallidum evolutionary history

Treponema pallidum infections causing yaws disease and venereal syphilis are globally widespread in human populations, infecting hundreds of thousands and millions annually respectively; endemic syphilis is much less common, and pinta has not been observed in decades. We discuss controversy surrounding the origin, evolution and history of these pathogens in light of available molecular and anthropological evidence. These bacteria (or close relatives) seem to affect many wild African nonhuman primate (NHP) species, though to date only a single NHP Treponema pallidum genome has been published, hindering detection of spillover events and our understanding of potential wildlife reservoirs. Similarly, only ten genomes of Treponema pallidum infecting humans have been published, impeding a full understanding of their diversity and evolutionary history. Research efforts have been hampered by the difficulty of culturing and propagating Treponema pallidum. Here we highlight avenues of research recently opened by the coupling of hybridization capture and next-generation sequencing. We present data generated with such an approach suggesting that asymptomatic bones from NHP occasionally contain enough treponemal DNA to recover large fractions of their genomes. We expect that these methods, which naturally can be applied to modern biopsy samples and ancient human bones, will soon considerably improve our understanding of these enigmatic pathogens and lay rest to old yet unresolved controversies.

Quarantine as a public health measure against an emerging infectious disease: syphilis in Zurich at the dawn of the modern era (1496-1585)

Syphilis is considered as one of the most devastating sexually transmitted diseases in human history. Based on historical records, the "Böse Blattern" (German for "Evil Pocks") spread through Europe after 1495 and shared symptoms with what we know today as syphilis. Many cities took measures to protect their population. Here, transliterations of archival documents from the 15(th) and 16(th) century (provided in the appendix) are used to trace the steps taken by the governing authorities in Zurich to deal with this emerging infectious disease. One of the central measures taken by the city was to establish a quarantine facility referred to as the "Blatternhaus". The city doctors, including the well-known physician and naturalist Conrad Gessner, oversaw the obligatory quarantine and treatment of patients with symptoms. Treatment could range from better nutrition, herbal remedies and skin ointments to aggressive heat therapy and "smoking". Furthermore, the affliction was suspected as a sexually acquired disease, hence prostitutes and infected foreigners were extradited from the city. Meanwhile, the church used its social influence to promote a more "Christian" behavior. In several respects, the public health measures taken in the 16(th) century against a new and menacing epidemic do not diverge in their basic rationale from approaches used during the 20(th) century and today.

The Columbian Exchange as a source of adaptive introgression in human populations

BACKGROUND

The term "Columbian Exchange" refers to the massive transfer of life between the Afro-Eurasian and American hemispheres that was precipitated by Columbus' voyage to the New World. The Columbian Exchange is widely appreciated by historians, social scientists and economists as a major turning point that had profound and lasting effects on the trajectory of human history and development.

PRESENTATION OF THE HYPOTHESIS

I propose that the Columbian Exchange should also be appreciated by biologists for its role in the creation of novel human genomes that have been shaped by rapid adaptive evolution. Specifically, I hypothesize that the process of human genome evolution stimulated by the Columbian Exchange was based in part on selective sweeps of introgressed haplotypes from ancestral populations, many of which possessed pre-evolved adaptive utility based on regional-specific fitness and health effects.

TESTING THE HYPOTHESIS

Testing of this hypothesis will require comparative analysis of genome sequences from putative ancestral source populations, with genomes from modern admixed populations, in order to identify ancestry-specific introgressed haplotypes that exist at higher frequencies in admixed populations than can be expected by chance alone. Investigation of such ancestry-enriched genomic regions can be used to provide clues as to the functional roles of the genes therein and the selective forces that have acted to increase their frequency in the population.

IMPLICATIONS OF THE HYPOTHESIS

Critical interrogation of this hypothesis could serve to underscore the important role of introgression as a source of adaptive alleles and as a driver of evolutionary change, and it would highlight the role of admixture in facilitating rapid human evolution.

A Retrospective Study on Genetic Heterogeneity within Treponema Strains: Subpopulations Are Genetically Distinct in a Limited Number of Positions

BACKGROUND

Pathogenic uncultivable treponemes comprise human and animal pathogens including agents of syphilis, yaws, bejel, pinta, and venereal spirochetosis in rabbits and hares. A set of 10 treponemal genome sequences including those of 4 Treponema pallidum ssp. pallidum (TPA) strains (Nichols, DAL-1, Mexico A, SS14), 4 T. p. ssp. pertenue (TPE) strains (CDC-2, Gauthier, Samoa D, Fribourg-Blanc), 1 T. p. ssp. endemicum (TEN) strain (Bosnia A) and one strain (Cuniculi A) of Treponema paraluisleporidarum ecovar Cuniculus (TPLC) were examined with respect to the presence of nucleotide intrastrain heterogeneous sites.

METHODOLOGY/PRINCIPAL FINDINGS

The number of identified intrastrain heterogeneous sites in individual genomes ranged between 0 and 7. Altogether, 23 intrastrain heterogeneous sites (in 17 genes) were found in 5 out of 10 investigated treponemal genomes including TPA strains Nichols (n = 5), DAL-1 (n = 4), and SS14 (n = 7), TPE strain Samoa D (n = 1), and TEN strain Bosnia A (n = 5). Although only one heterogeneous site was identified among 4 tested TPE strains, 16 such sites were identified among 4 TPA strains. Heterogeneous sites were mostly strain-specific and were identified in four tpr genes (tprC, GI, I, K), in genes involved in bacterial motility and chemotaxis (fliI, cheC-fliY), in genes involved in cell structure (murC), translation (prfA), general and DNA metabolism (putative SAM dependent methyltransferase, topA), and in seven hypothetical genes.

CONCLUSIONS/SIGNIFICANCE

Heterogeneous sites likely represent both the selection of adaptive changes during infection of the host as well as an ongoing diversifying evolutionary process.

Palaeoparasitology - Human Parasites in Ancient Material

Parasite finds in ancient material launched a new field of science: palaeoparasitology. Ever since the pioneering studies, parasites were identified in archaeological and palaeontological remains, some preserved for millions of years by fossilization. However, the palaeoparasitological record consists mainly of parasites found specifically in human archaeological material, preserved in ancient occupation sites, from prehistory until closer to 2015. The results include some helminth intestinal parasites still commonly found in 2015, such as Ascaris lumbricoides, Trichuris trichiura and hookworms, besides others such as Amoebidae and Giardia intestinalis, as well as viruses, bacteria, fungi and arthropods. These parasites as a whole provide important data on health, diet, climate and living conditions among ancient populations. This chapter describes the principal findings and their importance for knowledge on the origin and dispersal of infectious diseases.

The molecular epidemiology of Treponema pallidum subspecies pallidum

Pathogens adapt and evolve in response to pressures exerted by host environments, leading to generation of genetically diverse variants. Treponema pallidum subspecies pallidum displays a substantial amount of interstrain diversity. These variants have been identified in various parts of the world, indicating transmission linkage between geographical regions. Genotyping is based on molecular characterisation of various loci in the syphilis treponeme genome, but still require further development and continued research, as new bacterial types are continually being detected. The goal for studying the molecular epidemiology of Treponema pallidum variants is the global monitoring of the transmission of genetically distinct organisms with different drug sensitivities and, potentially, different virulence proprieties.

Yaws Prevalence, Lessons from the Field and the Way Forward towards Yaws Eradication in Ghana

Despite past WHO/UNICEF led global yaws eradication efforts, the disease seems to persist. The true burden is however not known for comprehensive action. Ghana's data showed significant increase in notified cases since the 1970s. Recognizing limitations in routine data, we carried out a yaws treatment survey in 2008 in three purposively selected districts to establish the prevalence and learn lessons for renewed action. Of 208,413 school children examined, 4,006 were suspected yaws cases (prevalence 1.92 (95% CI: 1.86–1.98) percent). Of 547 schools surveyed, 13% had prevalence between 5% and 10% while 3% had prevalence above 10%. The highest school prevalence was 19.5%. Half of the schools had cases. The large sample allowed aggregating the school results by administrative levels. The lowest aggregated prevalences of 0.23%, 0.40%, and 0.64% were in the urban sub-districts of Asamankese, Oda, and Achiase, respectively, while the highest of 8.61%, 3.69%, and 1.4% were in rural Akroso, Mepom, and Aperade, respectively. In conclusion, the prevalence of yaws is high in some schools in rural, hard-to-reach areas of Ghana. Considering past global eradication efforts, our findings suggest yaws may be resurging for which programmatic action is needed.

Ancient pathogen genomics: insights into timing and adaptation

Disease is a major cause of natural selection affecting human evolution, whether through a sudden pandemic or persistent morbidity and mortality. Recent contributions in the field of ancient pathogen genomics have advanced our understanding of the antiquity and nature of human-pathogen interactions through time. Technical advancements have facilitated the recovery, enrichment, and high-throughput sequencing of pathogen and parasite DNA from archived and archaeological remains. These time-stamped genomes are crucial for calibrating molecular clocks to infer the timing of evolutionary events, while providing finer-grain resolution to phylogenetic reconstructions and complex biogeographical patterns. Additionally, genome scale data allow better identification of substitutions linked to adaptations of the pathogen to their human hosts. As methodology continues to improve, ancient genomes of humans and their diverse microbiomes from a range of eras and archaeological contexts will enable population-level ancient analyses in the near future and a better understanding of their co-evolutionary history.

Syphilis in the United States

Syphilis gained notoriety in the 1500s, when it became widespread throughout Europe. While the origins of syphilis are not certain, recent data have shown that it may have originated in the Americas from a close relative that causes Yaws (Treponema pallidum pertenue).(1) For the past 500years, the disease has shown its various faces all over the world. The 19th century saw an entire medical subspecialty-syphilology (sometimes known as syphilography)-devoted to the study of the great disease, then known as "the great imitator." Syphilis has an entire textbook of presentations and can mimic many other infections and immune-mediated processes. At the beginning of the 20th century, the many faces of the disease led to Sir William Osler's well-known aphorism, "The physician who knows syphilis knows medicine."(2) When penicillin was discovered, and used to treat syphilis in 1943, some thought that syphilis would go by the wayside, but syphilis continued what it has been doing for so many years . . . inconspicuously infecting humans. The United States has seen the incidence of syphilis increase numerous times throughout the past 70years. Every decrease in the incidence of syphilis is followed shortly by an increase. A marked shift in the epidemiology occurred from 1990 to 2000. In the 1990s, syphilis primarily occurred in heterosexual minority groups. In the new millennium, a majority of cases of syphilis are now transmitted among men who have sex with men (MSM).(3) This contribution discusses the incidence of syphilis in the United States and the reasons these trends continue.

Whole genome sequence of the Treponema pallidum subsp. endemicum strain Bosnia A: the genome is related to yaws treponemes but contains few loci similar to syphilis treponemes

Background

T. pallidum subsp. endemicum (TEN) is the causative agent of bejel (also known as endemic syphilis). Clinical symptoms of syphilis and bejel are overlapping and the epidemiological context is important for correct diagnosis of both diseases. In contrast to syphilis, caused by T. pallidum subsp. pallidum (TPA), TEN infections are usually spread by direct contact or contaminated utensils rather than by sexual contact. Bejel is most often seen in western Africa and in the Middle East. The strain Bosnia A was isolated in 1950 in Bosnia, southern Europe.

Methodology/Principal Findings

The complete genome of the Bosnia A strain was amplified and sequenced using the pooled segment genome sequencing (PSGS) method and a combination of three next-generation sequencing techniques (SOLiD, Roche 454, and Illumina). Using this approach, a total combined average genome coverage of 513× was achieved. The size of the Bosnia A genome was found to be 1,137,653 bp, i.e. 1.6–2.8 kbp shorter than any previously published genomes of uncultivable pathogenic treponemes. Conserved gene synteny was found in the Bosnia A genome compared to other sequenced syphilis and yaws treponemes. The TEN Bosnia A genome was distinct but very similar to the genome of yaws-causing T. pallidum subsp. pertenue (TPE) strains. Interestingly, the TEN Bosnia A genome was found to contain several sequences, which so far, have been uniquely identified only in syphilis treponemes.

Conclusions/Significance

The genome of TEN Bosnia A contains several sequences thought to be unique to TPA strains; these sequences very likely represent remnants of recombination events during the evolution of TEN treponemes. This finding emphasizes a possible role of repeated horizontal gene transfer between treponemal subspecies in shaping the Bosnia A genome.

Uncultivable treponemes represent bacterial species and subspecies that are obligate pathogens of humans and animals causing diseases with distinct clinical manifestations. Treponema pallidum subsp. pallidum causes sexually transmitted syphilis, a multistage disease characterized in humans by localized, disseminated, and chronic forms of infection, whereas Treponema pallidum subsp. pertenue (agent of yaws) and Treponema pallidum subsp. endemicum (agent of bejel) cause milder, non-venereally transmitted diseases affecting skin, bones and joints. The genetic basis of the pathogenesis and evolution of these microorganisms are still unknown. In this study, a high quality whole genome sequence of the T. pallidum subsp. endemicum Bosnia A strain was obtained using a combination of next-generation sequencing approaches and compared to the genomes of available uncultivable pathogenic treponemes. Relative to all known genomes of Treponema pallidum subspecies, no major genome rearrangements were found in the Bosnia A. The Bosnia A strain clustered with other yaws-causing strains, while syphilis-causing strains clustered separately. In general, the Bosnia A genome showed similar genetic characteristics to yaws treponemes but also contained several sequences thought to be unique to syphilis-causing strains. This finding suggests a possible role of repeated horizontal gene transfer between treponemal subspecies in shaping the Bosnia A genome.

Endemic treponemal diseases

The endemic treponemal diseases, consisting of yaws, bejel (endemic syphilis) and pinta, are non-venereal infections closely related to syphilis, and are recognized by WHO as neglected tropical diseases (NTDs). Despite previous worldwide eradication efforts the prevalence of yaws has rebounded in recent years and the disease is now a major public health problem in 14 countries. Adequate data on the epidemiology of bejel and pinta is lacking. Each disease is restricted to a specific ecological niche but all predominantly affect poor, rural communities. As with venereal syphilis, the clinical manifestations of the endemic treponemal diseases are variable and can be broken down in to early stage and late stage disease. Current diagnostic techniques are unable to distinguish the different causative species but newer molecular techniques are now making this possible. Penicillin has long been considered the mainstay of treatment for the endemic treponemal diseases but the recent discovery that azithromycin is effective in the treatment of yaws has renewed interest in these most neglected of the NTDs, and raised hopes that global eradication may finally be possible.

The endemic treponematoses

The agents of human treponematoses include four closely related members of the genus Treponema: three subspecies of Treponema pallidum plus Treponema carateum. T. pallidum subsp. pallidum causes venereal syphilis, while T. pallidum subsp. pertenue, T. pallidum subsp. endemicum, and T. carateum are the agents of the endemic treponematoses yaws, bejel (or endemic syphilis), and pinta, respectively. All human treponematoses share remarkable similarities in pathogenesis and clinical manifestations, consistent with the high genetic and antigenic relatedness of their etiological agents. Distinctive features have been identified in terms of age of acquisition, most common mode of transmission, and capacity for invasion of the central nervous system and fetus, although the accuracy of these purported differences is debated among investigators and no biological basis for these differences has been identified to date. In 2012, the World Health Organization (WHO) officially set a goal for yaws eradication by 2020. This challenging but potentially feasible endeavor is favored by the adoption of oral azithromycin for mass treatment and the currently focused distribution of yaws and endemic treponematoses and has revived global interest in these fascinating diseases and their causative agents.