Impact of international travel and diarrhea on gut microbiome and resistome dynamics

International travel contributes to the global spread of antimicrobial resistance. Travelers\u27 diarrhea exacerbates the risk of acquiring multidrug-resistant organisms and can lead to persistent gastrointestinal disturbance post-travel. However, little is known about the impact of diarrhea on travelers\u27 gut microbiomes, and the dynamics of these changes throughout travel. Here, we assembled a cohort of 159 international students visiting the Andean city of Cusco, Peru and applied next-generation sequencing techniques to 718 longitudinally-collected stool samples. We find that gut microbiome composition changed significantly throughout travel, but taxonomic diversity remained stable. However, diarrhea disrupted this stability and resulted in an increased abundance of antimicrobial resistance genes that can remain high for weeks. We also identified taxa differentially abundant between diarrheal and non-diarrheal samples, which were used to develop a classification model that distinguishes between these disease states. Additionally, we sequenced the genomes of 212 diarrheagenic Escherichia coli isolates and found those from travelers who experienced diarrhea encoded more antimicrobial resistance genes than those who did not. In this work, we find the gut microbiomes of international travelers\u27 are resilient to dysbiosis; however, they are also susceptible to colonization by multidrug-resistant bacteria, a risk that is more pronounced in travelers with diarrhea

A site assessment tool for inpatient controlled human infection models for enteric disease pathogens

The use of the controlled human infection model to facilitate product development and to advance understanding of host-pathogen interactions is of increasing interest. While administering a virulent (or infective) organism to a susceptible host necessitates an ongoing evaluation of safety and ethical considerations, a central theme in conducting these studies in a safe and ethical manner that yields actionable data is their conduct in facilities well-suited to address their unique attributes. To that end, we have developed a framework for evaluating potential sites in which to conduct inpatient enteric controlled human infection model to ensure consistency and increase the likelihood of success.publishedVersio

Human papillomavirus (HPV) screening and cervical cancer burden. A Brazilian perspective

This review tackles the issues related to disease burden caused by cervical cancer (CC) and its precursor (CIN) lesions in Brazil. A special focus is given to new technologies with potential to interfere with the development of CC by reducing the high-risk human papillomavirus (hr-HPV)-induced lesions that remain a major public health burden in all developing countries where organized screening programs do not exist. Globally, 85 % of all incident CC and 50 % of CC deaths occur in the developing countries. Unfortunately, most regions of Brazil still demonstrate high mortality rates, ranking CC as the second most common cancer among Brazilian women. Recently, CC screening programs have been tailored in the country to enable early detection of CC precursor lesions and thereby reduce cancer mortality. A combination of HPV testing with liquid-based cytology (LBC) seems to be a promising new approach in CC screening, with high expectation to offer an adequate control of CC burden in this country

Eurogin Roadmap 2017: triage strategies for the management of HPV-positive women in cervical screening programmes

Cervical cancer screening will rely, increasingly, on HPV testing as a primary screen. The requirement for triage tests which can delineate clinically significant infection is thus prescient. In this EUROGIN 2017 roadmap, justification behind the most evidenced triages is outlined, as are challenges for implementation. Cytology is the triage with the most follow-up data; the existence of an HR-HPV-positive, cytology-negative group presents a challenge and retesting intervals for this group (and choice of retest) require careful consideration. Furthermore, cytology relies on subjective skills and while adjunctive dual-staining with p16/Ki67 can mitigate inter-operator/-site disparities, clinician-taken samples are required. Comparatively, genotyping and methylation markers are objective and are applicable to self-taken samples, offering logistical advantages including in low and middle income settings. However, genotyping may have diminishing returns in immunised populations and type(s) included must balance absolute risk for disease to avoid low specificity. While viral and cellular methylation markers show promise, more prospective data are needed in addition to refinements in automation. Looking forward, systems that detect multiple targets concurrently such as next generation sequencing platforms will inform the development of triage tools. Additionally, multistep triage strategies may be beneficial provided they do not create complex, unmanageable pathways. Inevitably, the balance of risk to cost(s) will be key in decision making, although defining an acceptable risk will likely differ between settings. Finally, given the significant changes to cervical screening and the variety of triage strategies, appropriate education of both health care providers and the public is essential

Epidemiologic investigation of the value of human papillomavirus (HPV) testing and genotyping in cervical cancer screening in Canada

Papanicolaou (Pap) cytology-based cervical cancer screening was introduced in Canada decades ago, and has since led to substantial reductions in cervical cancer incidence and mortality rates. These rates have leveled off over the past decade, however, indicating that further gains under this screening paradigm are unlikely. The low sensitivity of Pap cytology, alongside costly infrastructure and personnel requirements needed to maintain effective cytology-based cervical screening programs, have also remained important limitations associated with this ongoing screening strategy. The understanding that virtually all cervical cancers are caused by persistent infection with oncogenic genotypes of human papillomavirus (HPV), referred to as high-risk HPV (HR-HPV), has led to major advances in cervical cancer prevention, and a renewed focus on maximizing the effectiveness and efficiency of screening strategies in Canada and elsewhere.The overall aim of this doctoral research was to examine the clinical value of HR-HPV testing and genotyping among women undergoing routine primary cervical cancer screening in Canada. Data from the Canadian Cervical Cancer Screening Trial (CCCaST; n=10,154) were used to accomplish the following objectives: (i) evaluate the short-term (up to 36 months) ability of HPV DNA testing and Pap testing (individually and jointly) to detect high-grade cervical lesions and cervical cancer; (ii) assess the long-term (up to 120 months) prognostic value of HPV DNA testing and Pap testing (individually and jointly) to detect high-grade cervical lesions and cervical cancer; (iii) examine to what extent the separate detection of HPV genotypes in cervical samples provides additional risk stratification for detecting high-grade cervical lesions and cervical cancer among HPV+ women.Within this dissertation, the predictive abilities of enrollment HR-HPV testing (to include genotyping) and Pap cytology results to detect CIN2+ were assessed and compared using the Kaplan-Meier method, the log-rank test, and multivariable Cox proportional hazards (PH) regression during each of two follow-up periods (protocol-defined and extended). A flexible generalization of the Cox PH model allowed for simultaneous testing of the following important assumptions imposed a priori by a conventional Cox PH model: proportionality of hazards (PH assumption), and linearity of the relationship between continuous predictors and the logarithm of the hazard (linearity assumption). If one or both of these assumptions were rejected, non-proportional (i.e., time-dependent (TD)) and/or non-linear (NL) covariate effects were modeled. The performance of various HR-HPV and Pap cytology screening strategies to triage HR-HPV+ women to colposcopy were also compared.Work within this dissertation indicates that cervical cancer screening incorporating HR-HPV testing for women aged ≥30 years may allow for greater disease detection than cytology-based screening, and permit safe extensions of screening intervals. HR-HPV genotype-specific testing could provide further improvement in the positive predictive value of such screening. Primary HR-HPV testing also provided a similar or greater level of reassurance against disease risks as currently recommended screening strategies. Concerns surrounding primary HR-HPV screening (namely, its reduced specificity) may be effectively mitigated via triage of HR-HPV+ women to colposcopy and further follow-up. Finally, due to violations of the PH assumption, conventional Cox PH model estimates considerably underestimated adjusted hazard ratios associated with positive HR-HPV testing results, either alone or in conjunction with cytology results, early on in the follow-up periods.Le dépistage du cancer du col de l’utérus par analyse de frottis cytologique ou test de Papanicolaou, communément appelé test Pap, a été introduit au Canada il y a de cela plusieurs décennies. Cette mesure a permis de réduire de façon considérable tant le taux d’incidence que le taux de mortalité de ce cancer. Ces taux se sont toutefois stabilisés au cours des dernières années; des gains importants reliés à ce type de dépistage sont donc peu probables. La faible sensibilité du test Pap de même que les coûts élevés des infrastructures et du personnel nécessaires au maintien de ce programme demeurent des limites bien réelles. Depuis que l’on sait que tous les cancers du col sont causés par une infection au virus du papillome humain (VPH) de type oncogène, des avancées spectaculaires ont été réalisées en matière de prévention, à un point tel que l’utilité et l’efficacité des stratégies déjà en place au Canada et ailleurs dans le monde sont maintenant remises en question.L’objectif général de la présente recherche doctorale est de déterminer la valeur clinique du test de détection de VPH oncogène chez des femmes canadiennes testées pour le cancer du col de l’utérus de façon régulière. Les données provenant de l’étude Canadian Cervical Cancer Screening Trial (CCCaST; n = 10,154) ont été utilisées afin de répondre aux objectifs suivants : 1) évaluer au cours d’une période de 36 mois les habiletés du test VPH et du test Pap (de façon séparée et conjointe) à détecter les néoplasies cervicales intraépithéliales (CIN) de haut grade et le cancer du col; 2) déterminer la valeur pronostique du test VPH et du test Pap (de façon séparée et conjointe) pour détecter les CIN de haut grade et le cancer du col sur une période de 120 mois; 3) examiner dans quelle mesure la détection de différents types de VPH pourrait améliorer la stratification des risques pour la détection des CIN de haut grade et du cancer du col chez les femmes dont le test VPH est positif.Dans cette thèse, les habiletés prédictives du test VPH et du test Pap pour détecter les CIN ont été comparées avec la méthode de Kaplan-Meier, le test du log-rank, et un modèle de Cox multivarié, et ce pour deux périodes distinctes, soit celle définie par le protocole et celle incluant un suivi prolongé. Une version plus flexible du modèle de Cox permet de tester simultanément les hypothèses à confirmer imposées par l’utilisation d’un modèle conventionnel : la proportionnalité des taux de survie (hazard ratio/HR), et la linéarité entre les prédicteurs continus et le logarithme du taux de survie. Si au moins une de ces hypothèses se révélait fausse, des modèles tenant compte de la non-proportionnalité ou de la non-linéarité étaient utilisés. Les performances de différentes stratégies de dépistage basées sur le test VPH, le test Pap, et la référence en colposcopie des femmes ayant un test positif au VPH ont également été comparées.Le travail effectué dans le cadre de cette dissertation démontre que le dépistage du cancer du col incorporant le test VPH permet une meilleure détection de ce cancer que le test Pap utilisé seul chez les femmes ≥30 ans, ce qui réduit ainsi la fréquence de dépistage. L’introduction du test VPH augmenterait la valeur prédictive positive de ce dépistage. Le test VPH comme mesure de prévention primaire donne des résultats comparables et rassure davantage sur les risques de développement du cancer que les stratégies de dépistage du moment. Les inquiétudes face au test VPH comme mesure de prévention primaire, en particulier sa spécificité, peuvent être atténuées en faisant un tri des femmes ayant un test positif au VPH, et en leur réservant l’analyse cytologique et un suivi plus accru. Finalement, en raison de la violation des hypothèses de la proportionnalité des HR, les estimations du modèle de Cox conventionnel sous-estiment considérablement les HR ajustés associés à un test VPH oncogène positif, utilisé seul ou avec le test Pap, et ce dès le début du suivi

A systematic review of experimental infections with enterotoxigenic \u3ci\u3eEscherichia coli\u3c/i\u3e (ETEC)

Volunteer challenge with enterotoxigenic Escherichia coli (ETEC) has been used for four decades to elucidate the pathogenesis and immune responses and assess efficacy of various interventions. We performed a systematic review of these studies and a meta-analysis of individual patient-level data (IPD) from a subset of studies using standard methodology. We identified 27 studies of 11 ETEC strains administered to 443 naive subjects at doses from 1 × 106 to 1 × 1010 colony forming units (cfu). Diarrhea attack rates varied by strain, dose and enterotoxin. Similar rates were seen at doses of 5 × 108 to 1 × 1010 cfu with the three most commonly used strains B7A, E24377A, H10407. In IPD analysis, the highest diarrhea attack rates were seen with strains B7A, H10407 and E24377A. The H10407 induced significantly higher stool output than the other strains. Additionally, the rate of output was different across strains. The risk of diarrhea, abdominal cramps, nausea and headaches differed significantly by ETEC strain. An increased risk of nausea, abdominal cramps and headaches was seen for females. Baseline anti-LT IgG titers appeared to be associated with a decrease risk of diarrhea outcomes, a trend not seen with anti-LT IgA or seen consistently with anti-colonization factor antibodies. Neither early antibiotic treatment nor diarrhea duration significantly affected the frequency or magnitude of serologic responses. These studies have served as an invaluable tool in understanding disease course, pathogenicity, innate immune responses and an early assessment of product efficacy. When designing and planning experimental ETEC infection studies in this age of increased ethical scrutiny and growing appreciation of post-infectious sequelae, better understanding of available data is essential