Zoonotic pathogens, those transmitted from animals to humans, constitute a major public health risk with high associated global economic costs. Diseases associated with these pathogens represent more than 60% of emerging infectious diseases and predominantly originate in wildlife (1). Over the last decades, the emergence and re-emergence of zoonotic pathogens have led to an increasing number of epidemics, as illustrated by the current Covid-19 pandemic. There is ample evidence that human impact on native ecosystems such as deforestation, agricultural development, and urbanization, is linked to spillover of pathogens from animals to humans (2). However, research and calls to action have mainly focused on the importance of surveillance and prevention of zoonotic emergences along landscape interfaces, with special emphasis on tropical forests and agroecosystems, and studies and reviews pointing out the zoonotic risk associated with cities are scarce.  Additionally, cities are sometimes wrongly seen as one homogeneous ecosystem, almost exclusively human, with a Northern hemisphere-biased perception of what a city is, which fails to take into account the ecological and socio-economic diversities that can constitute an urban area.

Here, Dobigny and Morand (3) aim to draw attention to the importance of urban ecosystems in zoonotic risk and advocate that further attention should be paid to urban, peri-urban and suburban areas. In this well-organized and well-documented review, the authors show, using updated literature, that cities are places where massive contacts occur between wildlife, domestic animals, and human inhabitants (thus constituting spillover opportunities), and that it is even likely that human and wildlife contact in urban centers is more prevalent than in wild areas, perhaps contrary to intuition. Indeed, cities currently constitute the most important environment of human life and are places for millions of close interactions between humans and animals, including pets and domestic animals, wild animals through the intrusion of wild urban-adapted species (e.g., some bat, rodent, or bird species among others), manipulation and consumption of wildlife meat, and the existence of wildlife meat markets, which all constitute a major risk for zoonotic spillover. In cities, lab escapees of zoonotic pathogens also exist, and trends of adaptation to urban ecological conditions of many vectors of primary health importance is also a concern. The authors further argue that cities are predominant places for both epidemic amplification of human-human transmitted pathogens, because they are places with high human densities and population growth, and for dissemination of reservoirs, vectors and pathogens, as they are transport hubs. Dobigny & Morand further predict, likely correctly, that cities may be important places for pathogen evolution.  Finally, they propose actions and recommendations to limit the risk of zoonotic spillover events from urban ecosystems and future directions for research aiming at assessing this risk. 

The reviewers found the manuscript well-organized and presented, timely, and bringing novel contributions to the field of zoonotic emergence. I strongly recommend this article, which should benefit a large audience, particularly in the context of the current Covid-19 pandemics and the ongoing One Health initiatives aiming at preventing future zoonotic disease emergence (4). 

References

(1) Jones KE, Patel NG, Levy MA, Storeygard A, Balk D, Gittleman JL, Daszak P (2008) Global trends in emerging infectious diseases. Nature, 451, 990–993. https://doi.org/10.1038/nature06536

(2) White RJ, Razgour O (2020) Emerging zoonotic diseases originating in mammals: a systematic review of effects of anthropogenic land-use change. Mammal Review, 50, 336–352. https://doi.org/10.1111/mam.12201

(3) Dobigny G, Morand S (2022) Zoonotic emergence at the animal-environment-human interface: the forgotten urban socio-ecosystems. Zenodo, 6444776, ver. 3 peer-reviewed and recommended by Peer Community in Infections. https://doi.org/10.5281/zenodo.6444776

(4) Morand S, Lajaunie C (2021) Biodiversity and COVID-19: A report and a long road ahead to avoid another pandemic. One Earth, 4, 920–923. https://doi.org/10.1016/j.oneear.2021.06.007

Mycobacterium bovis, also called M. tuberculosis var. bovis, is a bacterium belonging to the M. tuberculosis complex (i.e., MTBC) and which can cause through zoonotic transmission another form of human tuberculosis (Tb). It is above all the agent of bovine tuberculosis (i.e., bTb) which affects not only cattle (wild or farmed) but also a large diversity of other wild mammals worldwide. An increasing number of infected animal cases are being discovered in many regions of the world, thus raising the problem of tuberculosis transmission, including to humans, more complex than previously thought. Efforts have been made in terms of vaccination or culling of populations of host carrier species, such as the badger for example, however leading to consequences of greater dispersion of the infectious agent. M. bovis shows a more or less significant capacity to persist outside its hosts, particularly in the environment under certain abiotic and biotic conditions. This bacillus can be transmitted and spread in many ways, including through aerosol, mucus and sputum, urine and feces, by direct contact with infected animals, their dead bodies or rather via their excreta or by inhalation of aerosols, depending on the host species concerned.

In this paper, Calenge and his collaborators (Callenge et al. 2024) benefited from a national surveillance program on M. bovis cases in wild species, set up in 2011 in France, i.e., Sylvatub, for detecting and monitoring M. bovis infection in European badger (Meles meles) populations. Sylvatub is a participatory program involving both national and local stakeholder systems in order to determine changes in bTb infection levels in domestic and wild animal species. This original work had two aims: to describe spatial disease dynamics in the three clusters under scrutiny using a complex Bayesian model; and to develop indicators for the monitoring of the M. bovis infection by stakeholders and decision-makers of the program. This paper is timely and very comprehensive.

In this cogent study, the authors illustrate this point by using epidemiological surveillance to obtain large amounts of data (which is generally lacking in human epidemiology, but more dramatically lacking in animal epidemiology) and a highly sophisticated biostatistical analysis (Callenge et al. 2024). It is in itself a demonstration of the current capabilities of population dynamics applied to infectious disease situations, in this case animal, in the rapidly developing discipline of disease ecology and evolution. One of the aims of the study is to propose statistical models that can be used by the different stakeholders in charge, for instance, of wildlife conservation or the regional or State veterinary services to assess disease risk in the most affected regions.

References

Assel AKHMETOVA​, Jimena GUERRERO​, Paul McADAM, Liliana CM SALVADOR​, Joseph CRISPELL​, John LAVERY​, Eleanor PRESHO​, Rowland R KAO​, Roman BIEK​, Fraser MENZIES​, Nigel TRIMBLE​, Roland HARWOOD​, P Theo PEPLER, Katarina ORAVCOVA​, Jordon GRAHAM​, Robin SKUCE​, Louis DU PLESSIS​, Suzan THOMPSON​, Lorraine WRIGHT​, Andrew W BYRNE​, Adrian R ALLEN. 2023. Genomic epidemiology of Mycobacterium bovis infection in sympatric badger and cattle populations in Northern Ireland. Microbial Genomics 9: mgen001023. https://doi.org/10.1099/mgen.0.001023

Roman BIEK, Anthony O’HARE, David WRIGHT, Tom MALLON, Carl McCORMICK, Richard J ORTON, Stanley McDOWELL, Hannah TREWBY, Robin A SKUCE, Rowland R KAO. 2012. Whole genome sequencing reveals local transmission patterns of Mycobacterium bovis in sympatric cattle and badger populations. PLoS Pathogens 8: e1003008. https://doi.org/10.1371/journal.ppat.1003008

Clément CALENGE, Ariane PAYNE, Edouard REVEILLAUD, Céline RICHOMME, Sébastien GIRARD, Stephanie DESVAUX. 2024. Assessing the dynamics of Mycobacterium bovis infection in three French badger populations. bioRxiv, ver. 3 peer-reviewed and recommended by Peer Community In Infections. https://doi.org/10.1101/2023.05.31.543041

Marc CHOISY, Pejman ROHANI. 2006. Harvesting can increase severity of wildlife disease epidemics. Proceedings of the Royal Society, London, Ser. B 273: 2025-2034. https://doi.org/10.1098/rspb.2006.3554

Shannon C DUFFY, Sreenidhi SRINIVASAN, Megan A SCHILLING, Tod STUBER, Sarah N DANCHUK, Joy S MICHAEL, Manigandan VENKATESAN, Nitish BANSAL, Sushila MAAN, Naresh JINDAL, Deepika CHAUDHARY, Premanshu DANDAPAT, Robab KATANI, Shubhada CHOTHE, Maroudam VEERASAMI, Suelee ROBBE-AUSTERMAN, Nicholas JULEFF, Vivek KAPUR, Marcel A BEHR. 2020. Reconsidering Mycobacterium bovis as a proxy for zoonotic tuberculosis: a molecular epidemiological surveillance study. Lancet Microbe 1: e66-e73. https://doi.org/10.1016/S2666-5247(20)30038-0

Jean-François GUEGAN. 2019. The nature of ecology of infectious disease. The Lancet Infectious Diseases 19. https://doi.org/10.1016/s1473-3099(19)30529-8

Brandon H HAYES, Timothée VERGNE, Mathieu ANDRAUD, Nicolas ROSE. 2023. Mathematical modeling at the livestock-wildlife interface: scoping review of drivers of disease transmission between species. Frontiers in Veterinary Science 10: 1225446. https://doi.org/10.3389/fvets.2023.1225446

David KING, Tim ROPER, Douglas YOUNG, Mark EJ WOOLHOUSE, Dan COLLINS, Paul WOOD. 2007. Bovine tuberculosis in cattle and badgers. Report to Secretary of State about tuberculosis in cattle and badgers. London, UK. https://www.bovinetb.info/docs/RBCT_david_%20king_report.pdf  

Robert MM SMITH , Francis DROBNIEWSKI, Andrea GIBSON, John DE MONTAGUE, Margaret N LOGAN, David HUNT, Glyn HEWINSON, Roland L SALMON, Brian O’NEILL. 2004. Mycobacterium bovis Infection, United Kingdom. Emerging Infectious Diseases 10: 539-541. https://doi.org/10.3201/eid1003.020819 

Despite decades of advances and understanding of the indiscriminate nature of human immunodeficiency virus (HIV), it remains shrouded in stigma that makes it difficult to reach some key populations at risk of transmission. The advent of self-testing technology for HIV (HIVST) has opened much-needed potential for bringing privacy to prevention that is crucial for curtailing its continued spread (Johnson et al., 2014). The HIV Self-Testing in Africa (STAR) Initiative (https://www.psi.org/fr/project/star/), carried out in Eastern and Southern Africa between 2015 and 2020 (Simwinga et al., 2022), demonstrated the market and public health operational potential of HIVST of different distribution methods. From 2019 to 2022, the “AutoTest de dépistage du VIH : Libre d’Accéder à la connaissance de son Statut" (ATLAS, translating to “HIVST: Freedom to know your status”) program built on these findings to quantify the public health value of HIVST for reaching key populations in West Africa (specifically, Mali, Senegal and Côte d’Ivoire) (Ky-Zerbo et al., 2022).

The innovative secondary distribution methods these studies employed, where the primary targeted populations were also encouraged to take and provide tests to their contacts, helped widen the reach of HIVST within key population networks beyond those relying on access to HIV testing facilities.

The tricky part of the self-testing model lies in assessing its reach and impact while maintaining the privacy of self-testers that is central to its success. Following voluntary phone survey methods that previously were able to show expanded reach of HIVST to first-time testers in key populations in West Africa and high rates of confirmatory testing and treatment seeking (Kra et al., 2022), Kra et al. (Kra et al., 2024) quantified how many of these self-tests led to a positive result – allowing wider assessment of follow-up behaviors and positivity rates among the hard-to-reach populations the program had targeted. 

While the numbers were low, the results were informative. Among respondents who reported a positive (“reactive”) HIVST, just 44% proceeded to confirmatory testing. This is lower than in other populations where HIVST follow-up has been assessed (Thirumurthy et al., 2016). The main reasons given for not confirming a reactive self-test was misinterpretation of HIVST results and not understanding that confirmatory testing was needed. The result thus highlighted a need for improved communication on how to correctly interpret HIVST results, and the authors provided ranges for how this misinterpretation could have affected their positivity estimates. However, the majority of those who sought confirmatory testing did so within 3 months, and nearly all of those with confirmed infection started on treatment. HIV positivity rates in the three countries were all higher than other published HIV positivity estimates (Giguère et al., 2021; Maheu-Giroux et al., 2019), suggesting that HIVST methods were highly effective at reaching the targeted communities. 

Finally, while the authors demonstrated their methods as an effective way of assessing the utility of HIVST campaigns and identifying ways to improve them, the follow-up surveys are likely too costly to replace current passive surveillance methods for assessing community disease burden. That said, these precious data should be taken as validation of the public health value of HIV self-testing in key populations across communities in West Africa. With improvements in communicating instructions for use and follow-up, there is little doubt that the innovation of HIVST primary and secondary distribution could become a widely useful addition to the fight against HIV. 

References

Giguère, K., Eaton, J. W., Marsh, K., Johnson, L. F., Johnson, C. C., Ehui, E., Jahn, A., Wanyeki, I., Mbofana, F., Bakiono, F., Mahy, M., & Maheu-Giroux, M. (2021). Trends in knowledge of HIV status and efficiency of HIV testing services in sub-Saharan Africa, 2000–20: a modelling study using survey and HIV testing programme data. The Lancet HIV, 8(5), e284–e293. https://doi.org/10.1016/S2352-3018(20)30315-5

Johnson, C., Baggaley, R., Forsythe, S., Van Rooyen, H., Ford, N., Napierala Mavedzenge, S., Corbett, E., Natarajan, P., & Taegtmeyer, M. (2014). Realizing the potential for HIV self-testing. In AIDS and Behavior (Vol. 18, Issue SUPPL. 4). Springer New York LLC. https://doi.org/10.1007/s10461-014-0832-x

Kra, A. K., Fosto, A. S., N’guessan, K. N., Geoffroy, O., Younoussa, S., Kabemba, O. K., Gueye, P. A., Ndeye, P. D., Rouveau, N., Boily, M. C., Silhol, R., d’Elbée, M., Maheu-Giroux, M., Vautier, A., & Larmarange, J. (2022). Can HIV self-testing reach first-time testers? A telephone survey among self-test end users in Côte d’Ivoire, Mali, and Senegal. BMC Infectious Diseases, 22. https://doi.org/10.1186/s12879-023-08626-w

Kra, A. K., Fotso, A. S., Rouveau, N., Maheu-Giroux, M., Boily, M.-C., Silhol, R., d’Elbée, M., Vautier, A., Lamarange, J., & the Atlas team. (2024). HIV self-testing positivity rate and linkage to confirmatory testing and care: a telephone survey in Côte d’Ivoire, Mali, and Senegal. MedRxiv, Ver. 4 Peer-Reviewed and Recommended by Peer Community in Infections, 2023.06.10.23291206. https://doi.org/https://doi.org/10.1101/2023.06.10.23291206

Ky-Zerbo, O., Desclaux, A., Boye, S., Maheu-Giroux, M., Rouveau, N., Vautier, A., Camara, C. S., Kouadio, B. A., Sow, S., Doumenc-Aidara, C., Gueye, P. A., Geoffroy, O., Kamemba, O. K., Ehui, E., Ndour, C. T., Keita, A., & Larmarange, J. (2022). “I take it and give it to my partners who will give it to their partners”: Secondary distribution of HIV self-tests by key populations in Côte d’Ivoire, Mali, and Senegal. BMC Infectious Diseases, 22. https://doi.org/10.1186/s12879-023-08319-4

Maheu-Giroux, M., Marsh, K., Doyle, C. M., Godin, A., Lanièce Delaunay, C., Johnson, L. F., Jahn, A., Abo, K., Mbofana, F., Boily, M. C., Buckeridge, D. L., Hankins, C. A., & Eaton, J. W. (2019). National HIV testing and diagnosis coverage in sub-Saharan Africa: A new modeling tool for estimating the “first 90” from program and survey data. AIDS, 33, S255–S269. https://doi.org/10.1097/QAD.0000000000002386

Simwinga, M., Gwanu, L., Hensen, B., Sigande, L., Mainga, M., Phiri, T., Mwanza, E., Kabumbu, M., Mulubwa, C., Mwenge, L., Bwalya, C., Kumwenda, M., Mubanga, E., Mee, P., Johnson, C. C., Corbett, E. L., Hatzold, K., Neuman, M., Ayles, H., & Taegtmeyer, M. (2022). Lessons learned from implementation of four HIV self-testing (HIVST) distribution models in Zambia: applying the Consolidated Framework for Implementation Research to understand impact of contextual factors on implementation. BMC Infectious Diseases, 22(Suppl 1). https://doi.org/10.1186/s12879-024-09168-5

Thirumurthy, H., Masters, S. H., Mavedzenge, S. N., Maman, S., Omanga, E., & Agot, K. (2016). Promoting male partner HIV testing and safer sexual decision making through secondary distribution of self-tests by HIV-negative female sex workers and women receiving antenatal and post-partum care in Kenya: a cohort study. The Lancet HIV, 3(6), e266–e274. https://doi.org/10.1016/S2352-3018(16)00041-2

High-throughput sequencing (HTS) has revealed an incredible diversity of microorganisms in ecosystems and is also changing the monitoring of macroorganism biodiversity (Deiner et al. 2017; Piper et al. 2019).  

The diagnostic of plant pathogens and the identification of pests is gradually integrating the use of these techniques, but there are still obstacles. Most of them are related to the reliability of these analyses, which have long been considered insufficient because of their dependence on a succession of sophisticated operations involving parameters that are sometimes difficult to adapt to complex matrices or certain diagnostic contexts. The need to validate HTS approaches is gradually being highlighted in recent work but remains poorly documented (Bester et al. 2022).

In this paper, a large community of experts presents and discusses the key steps for optimal control of HTS performance and reliability in a diagnostic context (Massart et al. 2022). It also addresses the issue of costs. The article provides recommendations that closely combine the quality control requirements commonly used in conventional diagnostics with newer or HTS-specific control elements and concepts that are not yet widely used. It discusses the value of these for the use of the various techniques currently covered by the terms "High Throughput Sequencing" in diagnostic activities. The elements presented are intended to limit false positive or false negative results but will also optimise the interpretation of contentious results close to the limits of analytical sensitivity or unexpected results, both of which appear to be frequent when using HTS.

Furthermore, the need for risk analysis, verification and validation of methods is well illustrated with numerous examples for each of the steps considered crucial to ensure reliable use of HTS. The clear contextualisation of the proposals made by the authors complements and clarifies the need for user expertise according to the experimental objectives. Some unanswered questions that will require further development and validation are also presented.

This article should benefit a large audience including researchers with some level of expertise in HTS but unfamiliar with the recent concepts of controls common in the diagnostic world as well as scientists with strong diagnostic expertise but less at ease with the numerous and complex procedures associated with HTS.

References

Bester R, Steyn C, Breytenbach JHJ, de Bruyn R, Cook G, Maree HJ (2022) Reproducibility and Sensitivity of High-Throughput Sequencing (HTS)-Based Detection of Citrus Tristeza Virus and Three Citrus Viroids. Plants, 11, 1939. https://doi.org/10.3390/plants11151939

Deiner K, Bik HM, Mächler E, Seymour M, Lacoursière-Roussel A, Altermatt F, Creer S, Bista I, Lodge DM, de Vere N, Pfrender ME, Bernatchez L (2017) Environmental DNA metabarcoding: Transforming how we survey animal and plant communities. Molecular Ecology, 26, 5872–5895. https://doi.org/10.1111/mec.14350

Massart, S et al. (2022) Guidelines for the reliable use of high throughput sequencing technologies to detect plant pathogens and pests. Zenodo, 6637519, ver. 3  peer-reviewed and recommended by Peer Community in Infections. https://doi.org/10.5281/zenodo.6637519

Piper AM, Batovska J, Cogan NOI, Weiss J, Cunningham JP, Rodoni BC, Blacket MJ (2019) Prospects and challenges of implementing DNA metabarcoding for high-throughput insect surveillance. GigaScience, 8, giz092. https://doi.org/10.1093/gigascience/giz092

One of the greatest achievements of health sciences is the eradication of infectious diseases such as smallpox that in the past imposed a severe burden on humankind, through global vaccination campaigns. Moreover, progress towards the eradication of others such as poliomyelitis, dracunculiasis, and yaws is being made.

In contrast, other infections that were previously contained are reemerging, due to several factors, including lack of access to vaccines due to geopolitical reasons, the rise of anti-vaccine movements, and the constant mobility of infected persons from the endemic sites.

One of such disease is diphtheria, caused by Corynebacterium diphtheriae and a few other related species such as C. ulcerans and C. pseudotuberculosis. Importantly, in France, diphtheria cases reported in 2022 increased 7-fold from the average of previously recorded cases per year in the previous 4 years and the situation in other European countries is similar.

Hence, as reported here, Hennart et al. (2023) developed DIPHTOSCAN, a free access bioinformatics tool with user-friendly interphase, aimed to easily identify, extract and interpret important genomic features such as the sublineage of the strain, the presence of the tox gene (as a string predictor for toxigenic disease) as well as genes coding other virulence factors such as fimbriae, and the presence of know resistant mechanisms towards antibiotics like penicillin and erythromycin currently used in the clinic to treat this infection.

The authors validated the performance of their tool with a large collection of genomes, including those obtained from the isolates of the 2022 outbreak in France, more than 1,200 other genomes isolated from France, Algeria, and Yemen, and more than 500 genomes from several countries from Europe, America, Africa, Asia, and Oceania that are available through the NCBI site.

DIPHTOSCAN will allow the rapid identification and surveillance of potentially dangerous strains such as those being tox-positive isolates and resistant to multiple drugs and/or first-line treatments and a better understanding of the epidemiology and evolution of this important reemerging disease.

Reference

Hennart M., Crestani C., Bridel S., Armatys N., Brémont S., Carmi-Leroy A., Landier A., Passet V., Fonteneau L., Vaux S., Toubiana J., Badell E. and Brisse S. (2023). A global Corynebacterium diphtheriae genomic framework sheds light on current diphtheria reemergence. bioRxiv, 2023.02.20.529124, ver 3 peer-reviewed and recommended by PCI Infections. https://doi.org/10.1101/2023.02.20.529124