Summary Background Madagascar accounts for 75% of global plague cases reported to WHO, with an annual incidence of 200–700 suspected cases (mainly bubonic plague). In 2017, a pneumonic plague epidemic of unusual size occurred. The extent of this epidemic provides a unique opportunity to better understand the epidemiology of pneumonic plagues, particularly in urban settings. Methods Clinically suspected plague cases were notified to the Central Laboratory for Plague at Institut Pasteur de Madagascar (Antananarivo, Madagascar), where biological samples were tested. Based on cases recorded between Aug 1, and Nov 26, 2017, we assessed the epidemiological characteristics of this epidemic. Cases were classified as suspected, probable, or confirmed based on the results of three types of diagnostic tests (rapid diagnostic test, molecular methods, and culture) according to 2006 WHO recommendations. Findings 2414 clinically suspected plague cases were reported, including 1878 (78%) pneumonic plague cases, 395 (16%) bubonic plague cases, one (<1%) septicaemic case, and 140 (6%) cases with unspecified clinical form. 386 (21%) of 1878 notified pneumonic plague cases were probable and 32 (2%) were confirmed. 73 (18%) of 395 notified bubonic plague cases were probable and 66 (17%) were confirmed. The case fatality ratio was higher among confirmed cases (eight [25%] of 32 cases) than probable (27 [8%] of 360 cases) or suspected pneumonic plague cases (74 [5%] of 1358 cases) and a similar trend was seen for bubonic plague cases (16 [24%] of 66 confirmed cases, four [6%] of 68 probable cases, and six [2%] of 243 suspected cases). 351 (84%) of 418 confirmed or probable pneumonic plague cases were concentrated in Antananarivo, the capital city, and Toamasina, the main seaport. All 50 isolated Yersinia pestis strains were susceptible to the tested antibiotics. Interpretation This predominantly urban plague epidemic was characterised by a large number of notifications in two major urban areas and an unusually high proportion of pneumonic forms, with only 23% having one or more positive laboratory tests. Lessons about clinical and biological diagnosis, case definition, surveillance, and the logistical management of the response identified in this epidemic are crucial to improve the response to future plague outbreaks. Funding US Agency for International Development, WHO, Institut Pasteur, US Department of Health and Human Services, Laboratoire d'Excellence Integrative Biology of Emerging Infectious Diseases, Models of Infectious Disease Agent Study of the National Institute of General Medical Sciences, AXA Research Fund, and the INCEPTION programme.

Bats are reservoirs for several zoonotic pathogens of medical importance; however, infection dynamics of pathogens in wild bat populations remain poorly understood. Here, we examine the influence of host crowding and population age structure on pathogen transmission and diversity in bat populations. Focusing on two pathogen taxa of medical importance, Leptospira bacteria and paramyxoviruses, we monitored host population and pathogen shedding dynamics within a maternity colony of the tropical bat species Mormopterus francoismoutoui, endemic to Réunion Island. Our data reveal astonishingly similar infection dynamics for Leptospira and paramyxoviruses, with infection peaks during late pregnancy and 2 months after the initial birth pulse. Furthermore, although co-infection occurs frequently during the peaks of transmission, the patterns do not suggest any interaction between the two pathogens. Partial sequencing reveals a unique bat-specific Leptospira strain contrasting with the co-circulation of four separate paramyxovirus lineages along the whole breeding period. Patterns of infection highlight the importance of host crowding in pathogen transmission and suggest that most bats developed immune response and stop excreting pathogens. Our results support that bat maternity colonies may represent hot spots of transmission for bacterial and viral infectious agents, and highlight how seasonality can be an important determinant of host-parasite interactions and disease emergence.

The Nycteribiidae are obligate blood-sucking Diptera (Hippoboscoidea) flies that parasitize bats. Depending on species, these wingless flies exhibit either high specialism or generalism toward their hosts, which may in turn have important consequences in terms of their associated microbial community structure. Bats have been hypothesized to be reservoirs of numerous infectious agents, some of which have recently emerged in human populations. Thus, bat flies may be important in the epidemiology and transmission of some of these bat-borne infectious diseases, acting either directly as arthropod vectors or indirectly by shaping pathogen communities among bat populations. In addition, bat flies commonly have associations with heritable bacterial endosymbionts that inhabit insect cells and depend on maternal transmission through egg cytoplasm to ensure their transmission. Some of these heritable bacteria are likely obligate mutualists required to support bat fly development, but others are facultative symbionts with unknown effects. Here, we present bacterial community profiles that were obtained from seven bat fly species, representing five genera, parasitizing bats from the Malagasy region. The observed bacterial diversity includes Rickettsia, Wolbachia, and several Arsenophonus-like organisms, as well as other members of the Enterobacteriales and a widespread association of Bartonella bacteria from bat flies of all five genera. Using the well-described host specificity of these flies and data on community structure from selected bacterial taxa with either vertical or horizontal transmission, we show that host/vector specificity and transmission mode are important drivers of bacterial community structure. Bats are increasingly recognized as natural reservoirs of a large number of emerging infectious agents (1-4). It is thus implicit that vectors of bat-borne disease will play important roles in the epidemiology and dynamics of infectious agents that can eventually emerge in human populations. Further, bats are hosts to different ectoparasites, including mites, fleas, ticks, and bat flies (5, 6). Bat flies (Diptera: Hippoboscoidea) are obligate blood-sucking parasites that are classically divided into two families-the Streblidae and the Nycteribiidae (7). Together, the Hippoboscidae (louse or ked flies), Streblidae, and Nycteribiidae are referred to as the Pupipara sensu stricto due to their adenotrophic viviparity, where all larval developmental stages occur within the adult female's body and the larva are nourished by milk glands until they are ready to pupate. This particularity of the Pupipara sensu stricto is thought to promote vertical parasite transmission, thus influencing the epidemiological role of these vectors in disease transmission.To date, studies of microorganisms associated with nycteribiids have mainly focused on two groups of bacteria-Bartonella spp. (8-11) and Arsenophonus-like organisms (referred to here as ALOs) (12-15). These bacterial genera offer contrasting model systems for investigating t...