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The aim of this paper is to review the most significant livestock-associated zoonoses. Human and animal health are intimately connected. This idea has been known for more than a century but now it has gained special importance because of the increasing threat from zoonoses. Zoonosis is defined as any infection naturally transmissible from vertebrate animals to humans. As the frequency and prevalence of zoonotic diseases increase worldwide, they become a real threat to public health. In addition, many of the newly discovered diseases have a zoonotic origin. Due to globalization and urbanization, some of these diseases have already spread all over the world, caused by the international flow of goods, people, and animals. However, special attention should be paid to farm animals since, apart from the direct contact, humans consume their products, such as meat, eggs, and milk. Therefore, zoonoses such as salmonellosis, campylobacteriosis, tuberculosis, swine and avian influenza, Q fever, brucellosis, STEC infections, and listeriosis are crucial for both veterinary and human medicine. Consequently, in the suspicion of any zoonoses outbreak, the medical and veterinary services should closely cooperate to protect the public health.

Streptococcus suis is one of the important emerging zoonotic pathogens. Serotype 2 is most prevalent in patients worldwide. In the present study, we first isolated one S. suis serotype 7 strain GX69 from the blood culture of a patient with septicemia complicated with pneumonia in China. In order to deepen the understanding of S. suis serotype 7 population characteristics, we investigated the phylogenetic structure, genomic features, and virulence of S. suis serotype 7 population, including 35 strains and 79 genomes. Significant diversities were revealed in S. suis serotype 7 population, which were clustered into 22 sequence types (STs), five minimum core genome (MCG) groups, and six lineages. Lineages 1, 3a, and 6 were mainly constituted by genomes from Asia. Genomes of Lineages 2, 3b, and 5a were mainly from Northern America. Most of genomes from Europe (41/48) were clustered into Lineage 5b. In addition to strain GX69, 13 of 21 S. suis serotype 7 representative strains were classified as virulent strains using the C57BL/6 mouse model. Virulence-associated genes preferentially present in highly pathogenic S. suis serotype 2 strains were not suitable as virulence indicators for S. suis serotype 7 strains. Integrative mobilizable elements were widespread and may play a critical role in disseminating antibiotic resistance genes of S. suis serotype 7 strains. Our study confirmed S. suis serotype 7 is a non-negligible pathotype and deepened the understanding of the population structure of S. suis serotype 7, which provided valuable information for the improved surveillance of this serotype.

CAPES - Coordenação de Aperfeiçoamento de Pessoal de Nível Superior As doenças transmitidas por alimentos consistem em um dos principais problemas de saúde pública em todo o mundo. Os produtos de origem animal são capazes de causar doenças em humanos ao potencializar as chances de transmissão de patógenos zoonóticos a partir da ingestão de alimentos contaminados. Este estudo foi dividido em dois capítulos. O Capítulo 1 traz um referencial teórico acerca das doenças transmitidas por alimentos, e inclui uma contextualização sobre o tema e uma discussão acerca dos principais desafios e progressos em relação à problemática das doenças de origem alimentar no Brasil. O Capítulo 2 consiste em um estudo descritivo e epidemiológico que avalia a situação atual (2015­2020) do país em relação à essas doenças, e como o consumo de produtos de origem animal impacta esse cenário. O estudo foi realizado a partir de dados secundários do Ministério da Saúde do Brasil, obtidos por meio da plataforma e­SIC. O processo de investigação epidemiológica das doenças transmitidas por alimentos no Brasil progrediu ao longo dos anos, mas ainda enfrenta desafios, principalmente relacionados ao fortalecimento do Sistema Nacional de Vigilância Epidemiológica das Doenças Transmitidas por Alimentos. Quanto ao cenário dessas doenças no país, a maior parte dos surtos entre 2015­2020 envolveu alimentos ignorados (n = 2259; 66,66%), e entre as de origem declarada 311 (27,52%) envolveram produtos de origem animal. Esses alimentos apresentaram ainda aumento de 0,40% de chance de envolvimento em casos de indivíduos doentes por ingestão de alimentos contaminados (OR = 1,004; p = 0,001). Ovos e carne bovina, por sua vez, foram os mais frequentemente incriminados nos surtos no período avaliado (n = 131; 42,13% e n = 58; 18,65%, respectivamente), e nas regiões Sul e Sudeste do Brasil o número de doentes em detrimento da ingestão de produtos de origem animal foi maior (n = 2191; 29,46% e n = 2369; 31,85%, nessa ordem). Verão e primavera apresentaram, respectivamente, os maiores valores de notificações relacionadas a essa categoria de alimentos, e a presença conjunta de fatores de transmissão em produtos de origem animal elevou os valores de notificações (n = 104; 55,92%), doentes (n= 3036; 62,78%) e hospitalizados (n = 333; 53,54%). Os resultados demonstram o potencial dos produtos de origem animal como vias de transmissão de patógenos zoonóticos, e que ações para o controle e prevenção das doenças de origem alimentar podem de fato reduzir esse risco. Foodborne diseases are one of the main public health problems worldwide. Animal source foods are capable of causing disease in humans by increasing the chances of transmission of zoonotic pathogens from the ingestion of contaminated food. This study was divided into two chapters. Chapter 1 provides a theoretical framework about foodborne diseases, and includes a contextualization on the subject and a discussion of the main challenges and progress related to the problem of foodborne diseases in Brazil. Chapter 2 consists in a descriptive and epidemiological study that assesses the current situation (2015­2020) of the country in relation to these diseases, and how the consumption of animal source foods impacts this overview. The study was carried out using secondary data from the Brazilian Ministry of Health, obtained through the e ­SIC platform. The process of epidemiological investigation of foodborne diseases in Brazil has progressed over the years, but it still faces challenges, mainly related to the strengthening of the National System for Epidemiological Surveillance of Foodborne Diseases. Regarding the situation of these diseases in the country, most of the outbreaks between 2015­2020 involved ignored foods (n = 2259; 66.66%), and among those of declared origin, 311 (27.52%) involved animal source foods. These foods also showed a 0.40% increase in the chance of involvement in cases of sick individuals due to ingestion of contaminated food (OR = 1.004; p = 0.001). Eggs and beef, in turn, were the most frequently incriminated in outbreaks in the period evaluated (n = 131; 42.13% and n = 58; 18.65%, respectively), and in the South and Southeast regions of Brazil the number of sick individuals to the detriment of the intake of products of animal origin was higher (n = 2191; 29.46% and n = 2369; 31.85%, in that order). Summer and spring presented, respectively, the highest values of notifications related to this category of food, and the joint presence of transmission factors in animal source foods increased the values of notifications (n = 104; 55.92%), sick individuals (n=3036; 62.78%) and hospitalized (n=333; 53.54%). The results demonstrate the potential of animal products as a means of transmitting zoonotic pathogens, and that actions for the control and prevention of foodborne diseases can actually reduce this risk. Dissertação (Mestrado)

Psittacine birds are commonly kept as companion birds and the maintenance of these birds in captivity may represent a zoonotic risk and contribute to the propagation of multidrug-resistant and β-lactamase extended-spectrum (ESBLs)-producing pathogens. This study aimed to identify and characterize strains of the Klebsiella pneumoniae complex isolated from diseased psittacine birds, determining virulence and resistance profiles. K. pneumoniae strains were isolated from 16 birds (16/46). All strains carried more than three virulence genes, with a high frequency of fimH and kpn (93.75%), uge (87.52%), and irp-2 (81.25%) genes. The antimicrobial susceptibility revealed that 3/16 strains were ESBL producers. Genomic analysis revealed that CTX-M-15-positive strains belonged to sequence types (STs) ST15, ST147, and ST307, characterized as international clones associated with outbreaks of healthcare-associated infections (HAIs) worldwide.

H-index is the most commonly applied tool to evaluate scientific productivity. In this study, the use of the H-index to evaluate scientific production in swine veterinary medicine was explored. A database of 137 pig infectious agents was constructed, including its taxonomic division, zoonotic potential, status as emerging pathogen and whether it was OIE-listed. The H-index and the total number of citations were calculated for those pathogens, the location of the affiliation of the first author of each paper included in the H-index core was registered and, for the ten pathogens with the highest H-index, evolution over time was measured. H-index values were compared to the M quotient, A-index, G-index, HG-index and the G/H ratio. H-indices were found to be severely affected by search accuracy and the database was hand curated. Swine pathogen H-indexes were highly dispersed ranging from 0 to 106 and were generally higher for pathogens causing endemic diseases in large pig producing countries. Indeed, the three top pathogens were Escherichia coli, Porcine reproductive and respiratory syndrome virus and Porcine circovirus type 2 with H-indices 106, 95 and 85, respectively. H-indices of viruses and bacteria were significantly higher (P 0.001) than other pathogen types. Also, non-zoonotic pathogens had higher H-indices than zoonotic pathogens (p 0.009) while no differences could be found for being listed by the OIE. For emerging diseases, only non-emerging viruses had higher H-index (p = 0.02). The study of H-indexes over time revealed three general patterns and that they had increased mainly after the 1980's. As expected, there were strong geographic patterns in terms of authorship and North America (38%) and Europe (46%) coped the majority of the papers. Finally, in order to quantify the contribution of a subject to a specific field, a new index "Deciphering Citations Organized by Subject" (Dcos) is proposed.

Hepatitis E virus (HEV) is an important enteric agent that can circulate in swine; it is excreted in manure, and of zoonotic interest. The present study investigated, by RT-qPCR, the circulation of HEV in swine manure from different types of pig farms (maternity, nursery, and grow-finish farms) in Santa Catarina State, the major pig production area of Brazil, and also evaluated the HEV removal efficiency of psychrophilic anaerobic biodigesters (PABs). While HEV was consistently detected in manure from grow-finish pig farms (>4 log HEV genome copies (GC) L−1), the virus was not detected in manure from maternity and nursery farms. These findings suggest a potential high biosafety status during primary-swine production, with a subsequent contamination in grow-finish production. The anaerobic biodigestion process reduced more than 2 log10 HEV GC in the processed swine manure. However, the virus concentration in final effluent remained high, with an average value of 3.85 log10 HEV GC L−1. Consequently, our results demonstrate that PABs can be a robust tool for effective inactivation of HEV, while reinforcing the need for sanitary surveillance and legislation of swine manure-derived biofertilizers, to avoid the spread of zoonotic enteric pathogens such as HEV.

Shiga toxin-producing Escherichia coli (STEC) and Listeria monocytogenes are worldwide recognized zoonotic pathogens. Recent reports have emerged about the circulation of antimicrobial-resistant STEC and L. monocytogenes isolates. To assess the frequency of antimicrobial resistance and related genes in these pathogens, we studied 45 STEC and 50 L. monocytogenes isolates locally recovered from different sources. Antimicrobial susceptibility testing was performed by disk-diffusion method, and the genomic sequences of three selected STEC and from all 50 L. monocytogenes isolates were analyzed for antibiotic resistance genes. Four STEC and three L. monocytogenes isolates were phenotypically resistant to at least one of the antibiotics tested. Resistance genes aph(3″)-Ib, aph(3')-Ia, aph(6)-Id, bla T EM-1B, sul2, mef (A), and tet(A) were found in a human STEC ampicillin-resistant isolate. All L. monocytogenes isolates harbored fosX, lin, mdrL, lde fepA, and norB. Overall resistance in L. monocytogenes and STEC was low or middle. However, the high load of resistance genes found, even in susceptible isolates, suggests that these pathogens could contribute to the burden of antimicrobial resistance.

Bushmeat harvesting and consumption represents a potential risk for the spillover of endemic zoonotic pathogens, yet remains a common practice in many parts of the world. Given that the harvesting and selling of bushmeat is illegal in Tanzania and other parts of Africa, the supply chain is informal and may include hunters, whole-sellers, retailers, and individual resellers who typically sell bushmeat in small pieces. These pieces are often further processed, obscuring species-identifying morphological characteristics, contributing to incomplete or mistaken knowledge of species of origin and potentially confounding assessments of pathogen spillover risk and bushmeat offtake. The current investigation sought to identify the species of origin and assess the concordance between seller-reported and laboratory-confirmed species of origin of bushmeat harvested from in and around the Serengeti National Park in Tanzania. After obtaining necessary permits, the species of origin of a total of 151 bushmeat samples purchased from known intermediaries from 2016 to 2018 were characterized by PCR and sequence analysis of the cytochrome B (CytB) gene. Based on these sequence analyses, 30%, 95% Confidence Interval (CI: 24.4-38.6) of bushmeat samples were misidentified by sellers. Misreporting amongst the top five source species (wildebeest, buffalo, impala, zebra, and giraffe) ranged from 20% (CI: 11.4-33.2) for samples reported as wildebeest to 47% (CI: 22.2-72.7) for samples reported as zebra although there was no systematic bias in reporting. Our findings suggest that while misreporting errors are unlikely to confound wildlife offtake estimates for bushmeat consumption within the Serengeti ecosystem, the role of misreporting bias on the risk of spillover events of endemic zoonotic infections from bushmeat requires further investigation.

Leptospirosis is a worldwide emerging zoonotic disease caused by Leptospira species, that in some patients develop severe forms with high mortality. In France, Corsica is the area where the highest incidences have been reported. The present study was focused on the analysis of pathogenic Leptospira species in rodents of Corsica, as these micromammals are the main natural reservoirs of the bacteria, in order to identify the circulating species and to locate possible risk focuses of transmission, as no previous study on the presence of Leptospira species has been carried out in the island. Rattus rattus, Rattus norvegicus, Apodemus sylvaticus and Mus musculus domesticus were captured in the proximity of water sources along Corsica, the detection of pathogenic Leptospira species was carried out by amplification of the LipL32 gene. The bacteria were found in all the rodent species analyzed and widely. The general prevalence was 10.4%, reaching the maximum value in Bastia (45%). Leptospira interrogans and Leptospira borgpetersenii were identified by phylogenetic analysis, but also two sequences which corresponded to an unnamed Leptospira species, only previously found in rodents of New Caledonia. The high incidence of human leptospirosis in Corsica could be partially explained by the wide distribution of pathogenic Leptospira species identified in this study. Also, the presence of an unknown pathogenic species of Leptospira in an area with high prevalence, may be involved in the higher incidence of Leptospirosis in this island, however, the zoonotic capacity of this species remains unknown. The results obtained are interesting for public health since all positive samples were found near water sources and one of the routes of transmission of leptospirosis is contact with contaminated water. This information could help the competent entities to take preventive measures, reducing the incidence of human leptospirosis in Corsica.

Acute febrile illnesses occur frequently in Guinea. Acute fever itself is not a unique, hallmark indication (pathognomonic sign) of any one illness or disease. In the infectious disease context, fever’s underlying cause can be a wide range of viral or bacterial pathogens, including the Ebola virus. In this study, molecular and serological methods were used to analyze samples from patients hospitalized with acute febrile illness in various regions of Guinea. This analysis was undertaken with the goal of accomplishing differential diagnosis (determination of causative pathogen) in such cases. As a result, a number of pathogens, both viral and bacterial, were identified in Guinea as causative agents behind acute febrile illness. In approximately 60% of the studied samples, however, a definitive determination could not be made.

The majority of emerging and reemerging zoonotic viral pathogens are RNA viruses. Pathogen discovery programs of emerging infectious diseases (EIDs) in wildlife have implicated rodents and shrews as hosts of diverse human pathogens, such as hantaviruses, arenaviruses, paramyxoviruses, etc. Despite these threats, little is known about the diversity of viruses circulating among rodents and shrews in Kenya, meaning the risk of infectious disease outbreak from these small mammals could be oblivious. This study reports the first surveillance toward understanding the diversity of RNA viruses carried by rodents and shrews in areas of high-potential contact with humans in Kenya through molecular detection. A total of 617 samples comprising fecal, urine, and tissues from 138 rodents and 5 shrews were screened for eight different families of viruses using RT-PCR assays. The results highlight the presence of diverse astroviruses, paramyxoviruses, hepeviruses, and arenavirus, circulating in both wild and synanthropic Kenyan rodents and shrews. Most of the viruses detected in this study are novel strains and some belong to the families that contain important human viral pathogens. Notably, a novel arenavirus was detected in Grammomys macmillani, a rodent species newly identified to harbor arenavirus, and it potentially represent a novel arenavirus species. Our findings demonstrate the need for continued pathogen surveillance among these small mammals as well as among the vulnerable and exposed livestock and humans. This would help in development and implementation of effective preventive and control strategies on EIDs in countries with rich wildlife biodiversity like Kenya.

Els recursos disponibles al medi urbà poden ser aprofitats per diverses espècies de fauna salvatge. El porc senglar (Sus scrofa) porta temps explorant àrees urbanes i peri-urbanes, però això causa problemes i riscs per a la seguretat i la salut de les persones. Les interaccions entre persones i porcs senglars van en augment, paral·lelament a les tendències creixents de les seves poblacions, especialment a les àrees urbanitzades d’Europa. Aquesta tesi identifica els factors que determinen la presència de porcs senglars a l’àrea urbana de Barcelona, descriu els canvis fenotípics dels porcs senglars urbans respecte als no urbans, i posa de manifest l’existència de riscs sanitaris derivats de dita presència a un àrea urbana. La presència de porcs senglars a la ciutat de Barcelona va ser més freqüent en punts pròxims a les rieres que baixen del massís de Collserola cap a la ciutat, en paisatges fragmentats i amb major presència de zones verdes i colònies de gats de carrer. Així mateix, també va ser més abundant durant la primavera i l’estiu, possiblement degut a la major grandària dels grups familiars després dels parts, a la dispersió de juvenils i subadults, i a la menor disponibilitat d’aliment durant l’estiu a les regions mediterrànies. A més, els porcs senglars urbans van consumir més aliment d’origen antropogènic, van tenir un creixement més accelerat, assolint una major massa corporal que els no urbans. Les femelles d’origen urbà també començaren a reproduir-se abans que les d’origen no urbà, probablement perquè arribaren abans al pes requerit. No obstant això, l’esperança de vida es va veure minvada en els porcs senglars urbans, assenyalant una possible conseqüència negativa derivada d’explorar Barcelona. Aquesta tesi també descriu la presència de patògens zoonòsics al porc senglar i a les seves paparres. Els porcs senglars de l’Àrea Metropolitana de Barcelona (AMB) es trobaren parasitats per les paparres Hyalomma lusitanicum, Dermacentor marginatus, Rhipicephalus sanguineus sensu lato i, de forma anecdòtica, Rhipicephalus bursa. Alhora, les paparres analitzades foren portadores de tres espècies zoonòsiques i emergents de Rickettsia (R. massiliae, R. slovaca i R. raoultii), tot i que les mostres de melsa de porc senglar foren negatives. Per tant, malgrat que els porcs senglars no semblen actuar com a reservoris de Rickettsia spp. a l’AMB, sí que podrien afavorir la dispersió de les paparres, així com la circulació de Rickettsia spp. entre elles en promoure la seva abundància. També podrien facilitar la transmissió de Rickettsia spp. entre paparres mitjançant l’alimentació simultània del mateix hoste. Tanmateix, els porcs senglars de l’AMB també van ser portadors de dues espècies de Campylobacter, essent C. lanienae més prevalent que C. coli, i diversos serotips de Salmonella enterica subsp. enterica. Els aïllats de Campylobacter mostraren una gran diversitat genètica, i alguns exhibiren un gran potencial de virulència. Tots els aïllats de Campylobacter foren resistents com a mínim a un dels antimicrobians analitzats, i prop del 60% dels aïllats de C. coli i un aïllat de Salmonella mostraren multirresistència. Aquest aïllat de Salmonella és la variant monofàsica del serotip Thyphimurium i s’ha relacionat amb problemes de salut pública a Europa. Aquests resultats confirmen la importància del porc senglar com a reservori d’espècies de Campylobacter zoonòsiques i termòfiles, i posen de manifest que els porcs senglars poden ser portadors i propagadors d’aquests bacteris a zones urbanes i peri-urbanes de l’AMB. Els resultats d’aquesta tesi són rellevants tant per a la gestió del porc senglar a zones urbanes, com per a la protecció de la salut pública a l’AMB. Diverses mesures de gestió derivades dels resultats d’aquesta tesi ja s’estan aplicant i avaluant a la ciutat de Barcelona. Aquesta tesi contribueix a la millora del coneixement sobre el porc senglar urbà amb una perspectiva ecològica, epidemiològica i de gestió. There are wildlife species able to exploit the resources offered by urban environments. Wild boars can explore urban and peri-urban areas, but their presence in these areas is a nuisance and poses a risk for public health and safety. Interactions between wild boars and people are expected to continue rising in Europe owing to increasing wild boar and human population trends, particularly in urban settings. This thesis determines the drivers of wild boar presence in the urban area of Barcelona, addresses the phenotypic changes shown by urban individuals with respect to non-urban ones, and identifies wild boar related public health concerns in an urban environment. Wild boar presence in the city of Barcelona was positively correlated to proximity to streams in the bordering Collserola natural space, higher landscape fragmentation and the presence of both urban green areas and stray cat colonies. The presence was also more frequent in spring and summer, which could be related to births leading to a higher group size and increased energetic needs, juvenile and yearling dispersal and lower availability of food resources in the warm seasons in Mediterranean regions. Moreover, urban wild boars used more anthropogenic food resources, showed higher body mass and grew faster than non-urban ones. Urban female wild boars started reproducing earlier than non-urban ones, probably as a result of achieving the required body mass earlier. However, urban wild boars died at a younger age than non-urban wild boars, indicating a possible cost of exploring the urban area for the wild boar in Barcelona. This thesis also describes the presence of zoonotic tick-borne and foodborne pathogens carried by ticks parasitizing wild boars and wild boars, respectively. Wild boars in the Metropolitan Area of Barcelona (MAB) carried ticks belonging to species Hyalomma lusitanicum, Dermacentor marginatus, Rhipicephalus sanguineus sensu lato and, anecdotally, Rhipicephalus bursa. Screening of tick pools revealed the presence of three emerging zoonotic Rickettsia species (R. massiliae, R. slovaca and R. raoultii), whereas wild boar spleen samples yielded negative results. Therefore, despite wild boars do not seem to act as reservoirs of Rickettsia spp. in the MAB, they could be favouring tick dispersion and promoting Rickettsia spp. circulation among ticks by sustaining abundant tick populations and facilitating the transmission via co-feeding. Wild boars in the MAB also carried Campylobacter spp., C. lanienae being more prevalent than C. coli, and different serovars of Salmonella enterica subsp. enterica. There was a high genetic diversity among Campylobacter isolates, some of which showed a high virulence potential. None of the Campylobacter isolates were susceptible to all the antimicrobials tested, and nearly 60% of C. coli isolates and one Salmonella isolate were multiresistant, the latter being a monophasic S. Typhimurium clone of public health concern in Europe. These results provide further evidence on the role of wild boars as reservoirs of zoonotic thermophilic Campylobacter species, and show that they can carry and spread these foodborne zoonotic bacteria into urban and peri-urban areas in the MAB. Results from this thesis have management and public health implications, and several management measures derived from these results are currently being applied and scientifically evaluated in Barcelona. This thesis contributes to improve the incipient knowledge of wild boars in urban and peri-urban areas from an ecological, epidemiological and applied management approach.

Streptococcus suis, particularly S. suis serotype 2 (SS2), is an important zoonotic pathogen causing meningitis in humans worldwide. Although the proper classification of the causative and pathogenic serotype is salutary for the clinical diagnosis, cross-reactions leading to the indistinguishability of serotypes by the current serotyping methods are significant limitations. In the present study, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) analysis of extracted peptides was developed to improve the classification of serotype of S. suis. The peptide mass fingerprint (PMFs) database of S. suis was generated from the whole-cell peptides of 32 reference strains of S. suis isolates obtained from pigs. Thirty-two human S. suis isolates from clinical cases in Thailand were used to validate this alternative serotyping method in direct comparison to the multiplex (m)PCR approach. All reference strains, representing 32 serotypes of S. suis, exhibited their individual PMFs patterns, thus allowing differentiation from one another. Highly pathogenic SS2 and SS14 were clearly differentiated from the otherwise serologically closely related SS1/2 and SS1, respectively. The developed MALDI-TOF-MS serotyping method correctly classified the serotype in 68.8% (22/32) of the same serotype isolates generated from the PMFs database; while the validity for the clinical human isolates was 62.5% (20/32). The agreement between the MALDI-TOF-MS and mPCR serotyping was moderate with a Kappa score of 0.522, considering that mPCR could correctly serotype up to 75%. The present study demonstrated that PMFs from the developed MALDI-TOF-MS-based method could successfully discriminate the previously indistinguishable highly pathogenic SS2 and SS14 from SS1/2 and SS1, respectively. Moreover, this serotyping method distinguished pathogenic SS6, and so is an alternative approach of choice to rapidly and reliably serotype clinically pathogenic S. suis isolates.

Camels are increasingly becoming the livestock of choice for pastoralists reeling from effects of climate change in semi-arid and arid parts of Kenya. As the population of camels rises, better understanding of their role in the epidemiology of zoonotic diseases in Kenya is a public health priority. Rift Valley fever (RVF), brucellosis and Q fever are three of the top priority diseases in the country but the involvement of camels in the transmission dynamics of these diseases is poorly understood. We analyzed 120 camel serum samples from northern Kenya to establish seropositivity rates of the three pathogens and to characterize the infecting Brucella species using molecular assays. We found seropositivity of 24.2% (95% confidence interval [CI]: 16.5–31.8%) for Brucella, 20.8% (95% CI: 13.6–28.1%) and 14.2% (95% CI: 7.9–20.4%) for Coxiella burnetii and Rift valley fever virus respectively. We found 27.5% (95% CI: 19.5–35.5%) of the animals were seropositive for at least one pathogen and 13.3% (95% CI: 7.2–19.4%) were seropositive for at least two pathogens. B. melitensis was the only Brucella spp. detected. The high sero-positivity rates are indicative of the endemicity of these pathogens among camel populations and the possible role the species has in the epidemiology of zoonotic diseases. Considering the strong association between human infection and contact with livestock for most zoonotic infections in Kenya, there is immediate need to conduct further research to determine the role of camels in transmission of these zoonoses to other livestock species and humans. This information will be useful for designing more effective surveillance systems and intervention measures., Author summary Dromedary camels are well adapted to the arid and semi-arid environment that makes up about 80% of Kenya’s landmass. As such, camels play an important role in the socio-economic wellbeing and food security of pastoralists in the country. However, the species remains relatively neglected in scientific research, one of the main reasons being camels are mostly found in remote, low-income, arid regions of Africa and Asia. We carried out a study to determine the levels of exposure of camels in northern Kenya to Brucella spp., Coxiella burnetii and Rift Valley fever virus, three priority zoonotic pathogens in the country. We found high levels of exposure to the three pathogens, indicating the important role camels might play in the epidemiology of the zoonotic diseases in humans and other livestock. Based on the study findings, we argue for the immediate need for investments in disease surveillance and control strategies for priority zoonotic disease in camels in Kenya.

Hepatitis E virus (HEV) is an important enteric agent that can circulate in swine; it is excreted in manure, and of zoonotic interest. The present study investigated, by RT-qPCR, the circulation of HEV in swine manure from different types of pig farms (maternity, nursery, and grow-finish farms) in Santa Catarina State, the major pig production area of Brazil, and also evaluated the HEV removal efficiency of psychrophilic anaerobic biodigesters (PABs). While HEV was consistently detected in manure from grow-finish pig farms (>4 log HEV genome copies (GC) L−1), the virus was not detected in manure from maternity and nursery farms. These findings suggest a potential high biosafety status during primary-swine production, with a subsequent contamination in grow-finish production. The anaerobic biodigestion process reduced more than 2 log10 HEV GC in the processed swine manure. However, the virus concentration in final effluent remained high, with an average value of 3.85 log10 HEV GC L−1. Consequently, our results demonstrate that PABs can be a robust tool for effective inactivation of HEV, while reinforcing the need for sanitary surveillance and legislation of swine manure-derived biofertilizers, to avoid the spread of zoonotic enteric pathogens such as HEV.

Pathogens originating from wildlife (zoonoses) pose a significant public health burden, comprising the majority of emerging infectious diseases. Efforts to control and prevent zoonotic disease have traditionally focused on animal-to-human transmission, or "spillover." However, in the modern era, increasing international mobility and commerce facilitate the spread of infected humans, nonhuman animals (hereafter animals), and their products worldwide, thereby increasing the risk that zoonoses will be introduced to new geographic areas. Imported zoonoses can potentially "spill back" to infect local wildlife-a danger magnified by urbanization and other anthropogenic pressures that increase contacts between human and wildlife populations. In this way, humans can function as vectors, dispersing zoonoses from their ancestral enzootic systems to establish reservoirs elsewhere in novel animal host populations. Once established, these enzootic cycles are largely unassailable by standard control measures and have the potential to feed human epidemics. Understanding when and why translocated zoonoses establish novel enzootic cycles requires disentangling ecologically complex and stochastic interactions between the zoonosis, the human population, and the natural ecosystem. In this Review, we address this challenge by delineating potential ecological mechanisms affecting each stage of enzootic establishment-wildlife exposure, enzootic infection, and persistence-applying existing ecological concepts from epidemiology, invasion biology, and population ecology. We ground our discussion in the neotropics, where four arthropod-borne viruses (arboviruses) of zoonotic origin-yellow fever, dengue, chikungunya, and Zika viruses-have separately been introduced into the human population. This paper is a step towards developing a framework for predicting and preventing novel enzootic cycles in the face of zoonotic translocations.

Environmental persistence of zoonotic pathogens is a key trait that influences the probability of zoonotic spillover. Pathogen survival outside of the host determines the window available for contact with the new recipient host species and the dose of pathogen available to that host. The longer a pathogen survives in the environment, the more disconnected the reservoir and recipient hosts can be in space and time, and the more likely that an infective dose will be available to recipient hosts. Therefore, environmental persistence is a key parameter for mechanistic models needed to predict pathogen spillover. Avian influenza can be transmitted from wildlife to poultry and people in part due to its ability to persist in the environment. Considerable work has been done to quantify trends in avian influenza persistence across environmental conditions, often published in separate studies with separate datasets. In this paper, we quantify the trends and variability of avian influenza viral persistence across environmental conditions by collating disjoint experimental data on viral particle persistence in water across many studies and a range of environmental conditions. The collated data represent 120 estimates from three different studies of the decay rates of highly pathogenic avian influenza H5N1 (90 estimates from Asia and 30 from Europe) in response to temperature, pH, and salinity. We analyzed these data with a Bayesian model to control for biases with random effects and used experimental replicates and R2 estimates of the publication's regression procedures as statistical weights. We found temperature significantly decreases persistence of H5N1 virus in water, and this effect is stronger than that of salinity alone. Salinity interacts with temperature and probably drives the most contrasting persistence scenarios between cold-saline and warm-saline water bodies, where highest and lowest persistence times could occur respectively. Our work provides needed parameters for models that examine the risk of spillover of avian influenza viruses.

Background Diarrheal disease remains among the leading causes of global mortality in children younger than 5 years. Exposure to domestic animals may be a risk factor for diarrheal disease. The objectives of this study were to identify animal-related exposures associated with cases of moderate-to-severe diarrhea (MSD) in children in rural western Kenya, and to identify the major zoonotic enteric pathogens present in domestic animals residing in the homesteads of case and control children. Methodology/Principal findings We characterized animal-related exposures in a subset of case and control children (n = 73 pairs matched on age, sex and location) with reported animal presence at home enrolled in the Global Enteric Multicenter Study in western Kenya, and analysed these for an association with MSD. We identified potentially zoonotic enteric pathogens in pooled fecal specimens collected from domestic animals resident at children’s homesteads. Variables that were associated with decreased risk of MSD were washing hands after animal contact (matched odds ratio [MOR] = 0.2; 95% CI 0.08–0.7), and presence of adult sheep that were not confined in a pen overnight (MOR = 0.1; 0.02–0.5). Variables that were associated with increased risk of MSD were increasing number of sheep owned (MOR = 1.2; 1.0–1.5), frequent observation of fresh rodent excreta (feces/urine) outside the house (MOR = 7.5; 1.5–37.2), and participation of the child in providing water to chickens (MOR = 3.8; 1.2–12.2). Of 691 pooled specimens collected from 2,174 domestic animals, 159 pools (23%) tested positive for one or more potentially zoonotic enteric pathogens (Campylobacter jejuni, C. coli, non-typhoidal Salmonella, diarrheagenic E. coli, Giardia, Cryptosporidium, or rotavirus). We did not find any association between the presence of particular pathogens in household animals, and MSD in children. Conclusions and significance Public health agencies should continue to promote frequent hand washing, including after animal contact, to reduce the risk of MSD. Future studies should address specific causal relations of MSD with sheep and chicken husbandry practices, and with the presence of rodents., Author summary Diarrheal disease is one of the leading causes of death worldwide in children younger than 5 years. Exposure to animals in homes may be a risk factor for diarrhea in children. To test this, we studied a subset of children in the Global Enteric Multicenter Study (GEMS) in rural western Kenya, whose caretakers reported the presence of animals in the children’s homesteads. In GEMS, children with moderate-to-severe diarrhea (MSD) were matched with children without MSD, who were of the same sex, similar age and who lived in the same area. We asked questions about the presence and management of animals in the children’s homesteads. We also collected fecal specimens from domestic animals present at homesteads and tested these for microbes that could cause diarrheal disease in children. We found that children who reportedly washed their hands after animal contact, and who lived in a homestead with adult sheep that were not confined to a pen overnight, had a lower risk of MSD. Children who lived in homesteads that owned more adult sheep, or in which fresh rodent droppings were observed frequently, had a higher risk of MSD, as did children who reportedly participated in providing water to chickens in the homestead. We did not find any association between the presence of particular pathogens in household animals, and MSD in children.

Background Cryptosporidium spp., Giardia duodenalis and Enterocytozoon bieneusi are the main causal pathogens of gastrointestinal disease. However, there are limited reports about the prevalence of these organisms in captive Eurasian wild boars worldwide. Therefore, we examined the occurrence and identified the species/assemblages/genotypes of these pathogens in captive Eurasian wild boars, and estimated the zoonotic potential. Findings Of 357 fecal samples collected from captive Eurasian wild boars in China, 155 (43.4%) were infected with Cryptosporidium, G. duodenalis and/or E. bieneusi. The infection rates significantly differed in different areas, but did not differ between wild boars kept indoors and outdoors. Three (0.8%), 11 (3.1%) and 147 (41.2%) fecal samples were positive for Cryptosporidium, G. duodenalis and E. bieneusi, respectively. Sequence analysis of SSU rRNA gene revealed that all of the Cryptosporidium strains belonged to C. scrofarum. Based on the sequence analysis of the β-giardia gene of G. duodenalis, assemblages E and A were characterized. Fourteen E. bieneusi genotypes comprising five novel (WildBoar 7–11) and eight known (EbpC, F, CHG19, CHC5, PigEBITS5, D, RWSH4, SC02) genotypes were identified by ITS sequencing. EbpC was the most frequent genotype, detected in 85 specimens. Phylogenetic analysis revealed that all 14 genotypes belonged to Group 1. Conclusions This first report on the occurrence of Cryptosporidium, G. duodenalis and E. bieneusi in captive wild boars in China indicates that the presence of zoonotic species/assemblages/genotypes poses a threat to public health. The findings suggest that wild boars could be a significant source of human infection and water pollution.

Pathogens that spill over between species cause a significant human and animal health burden. Here, we describe characteristics of animal reservoirs that are required for pathogen spillover. We assembled and analyzed a database of 330 disease systems in which a pathogen spills over from a reservoir of one or more species. Three-quarters of reservoirs included wildlife, and 84% included mammals. Further, 65% of pathogens depended on a community of reservoir hosts, rather than a single species, for persistence. Among mammals, the most frequently identified reservoir hosts were rodents, artiodactyls, and carnivores. The distribution among orders of mammalian species identified as reservoirs did not differ from that expected by chance. Among disease systems with high priority pathogens and epidemic potential, we found birds, primates, and bats to be overrepresented. We also analyzed the life history traits of mammalian reservoir hosts and compared them to mammals as a whole. Reservoir species had faster life history characteristics than mammals overall, exhibiting traits associated with greater reproductive output rather than long-term survival. Thus, we find that in many respects, reservoirs of spillover pathogens are indeed special. The described patterns provide a useful resource for studying and managing emerging infectious diseases.

Pearls: Host population dynamics are the key of wildlife zoonotic risk; Aquatic and terrestrial agents of tularemia coexist in nature; Irrigation has provided aquatic reservoirs and a grass-loving amplification agent for tularemia in Spain; Fluctuating mammalian populations shape tularemia epidemiology; Tularemia surveillance must target unstable mammalian host populations., This work was funded by Programa Estatal de I+D+i Orientada a los Retos de la Sociedad; Ministerio de Economía y Competitividad, Gobierno de España (Spain). This publication is part of the project ECOTULA (reference: CGL2015-66962-C2-1-R).

Zoonotic pathogens such as Ebola and rabies pose a major health risk to humans. One proven approach to minimizing the impact of a pathogen relies on reducing its prevalence within animal reservoir populations using mass vaccination. However, two major challenges remain for vaccination programs that target free-ranging animal populations. First, limited or challenging access to wild hosts, and second, expenses associated with purchasing and distributing the vaccine. Together, these challenges constrain a campaign’s ability to maintain adequate levels of immunity in the host population for an extended period of time. Transmissible vaccines could lessen these constraints, improving our ability to both establish and maintain herd immunity in free-ranging animal populations. Because the extent to which vaccine transmission could augment current wildlife vaccination campaigns is unknown, we develop and parameterize a mathematical model that describes long-term mass vaccination campaigns in the US that target rabies in wildlife. The model is used to investigate the ability of a weakly transmissible vaccine to (1) increase vaccine coverage in campaigns that fail to immunize at levels required for herd immunity, and (2) decrease the expense of campaigns that achieve herd immunity. When parameterized to efforts that target rabies in raccoons using vaccine baits, our model indicates that, with current vaccination efforts, a vaccine that transmits to even one additional host per vaccinated individual could sufficiently augment US efforts to preempt the spread of the rabies virus. Higher levels of transmission are needed, however, when spatial heterogeneities associated with flight-line vaccination are incorporated into the model. In addition to augmenting deficient campaigns, our results show that weak vaccine transmission can reduce the costs of vaccination campaigns that are successful in attaining herd immunity., Author summary Zoonotic pathogens pose a significant health risk to humans. Mass vaccination programs have shown promise for controlling zoonoses in reservoir populations and, in turn, lessening the health burden posed to neighboring human populations. Despite some significant successes, major logistical challenges remain for programs that seek to establish and maintain herd immunity in free-ranging animal populations. Specifically, limited host access and costs associated with vaccine distribution may hinder efforts to vaccinate a host population and preempt spillover of a zoonotic pathogen. We use mathematical models, parameterized with data from campaigns in the US that target rabies in wildlife, to illustrate how transmissible vaccines can overcome these challenges. Specifically, we find levels of vaccine transmission necessary to boost vaccination efforts that seek to preempt the spread of rabies, and also predict the cost savings that could be realized with a transmissible vaccine.

SUMMARYEchinococcus granulosusis the causative agent of cystic echinococcosis. The disease is a significant global public health concern and human infections are most commonly associated withE. granulosussensu stricto (s. s.) genotype G1. The objectives of this study were to: (i) analyse the genetic variation and phylogeography ofE. granulosuss. s. G1 in part of its main distribution range in Europe using 8274 bp of mtDNA; (ii) compare the results with those derived from previously used shorter mtDNA sequences and highlight the major differences. We sequenced a total of 91E. granulosuss. s. G1 isolates from six different intermediate host species, including humans. The isolates originated from seven countries representing primarily Turkey, Italy and Spain. Few samples were also from Albania, Greece, Romania and from a patient originating from Algeria, but diagnosed in Finland. The analysed 91 sequences were divided into 83 haplotypes, revealing complex phylogeography and high genetic variation ofE. granulosuss. s. G1 in Europe, particularly in the high-diversity domestication centre of western Asia. Comparisons with shorter mtDNA datasets revealed that 8274 bp sequences provided significantly higher phylogenetic resolution and thus more power to reveal the genetic relations between different haplotypes.

A considerable amount of disease is transmitted from animals to humans and many of these zoonoses are neglected tropical diseases. As outbreaks of SARS, avian influenza and Ebola have demonstrated, however, zoonotic diseases are serious threats to global public health and are not just problems confined to remote regions. There are two fundamental, and poorly studied, stages of zoonotic disease emergence: ‘spillover’, i.e. transmission of pathogens from animals to humans, and ‘stuttering transmission’, i.e. when limited human-to-human infections occur, leading to self-limiting chains of transmission. We developed a transparent, theoretical framework, based on a generalization of Poisson processes with memory of past human infections, that unifies these stages. Once we have quantified pathogen dynamics in the reservoir, with some knowledge of the mechanism of contact, the approach provides a tool to estimate the likelihood of spillover events. Comparisons with independent agent-based models demonstrates the ability of the framework to correctly estimate the relative contributions of human-to-human vs animal transmission. As an illustrative example, we applied our model to Lassa fever, a rodent-borne, viral haemorrhagic disease common in West Africa, for which data on human outbreaks were available. The approach developed here is general and applicable to a range of zoonoses. This kind of methodology is of crucial importance for the scientific, medical and public health communities working at the interface between animal and human diseases to assess the risk associated with the disease and to plan intervention and appropriate control measures. The Lassa case study revealed important knowledge gaps, and opportunities, arising from limited knowledge of the temporal patterns in reporting, abundance of and infection prevalence in, the host reservoir., Author Summary Many dangerous diseases emerge via spillover from animals, with limited human-to-human infection (stuttering-transmission) often being the first stage of human disease spread. Understanding the conditions (biological, environmental and socio-economic factors) that regulate spillover and disease spread is key to its mitigation. Here we are interested in questions such as: If we have quantified pathogen dynamics in the reservoir, with some knowledge of the mechanism of contact, can we estimate the likelihood of spillover events? Can we tease apart how much the disease is transmitted by animals and how much by humans? We developed a unified mathematical framework, based on Poisson processes with memory of past events, to understand the dynamics of spillover and stuttering-transmission. This framework, which can be applied across the disease transmission spectrum, allows the teasing apart of the disease burden attributed to animal-human and human-human transmission. Using this model, we can infer human disease risk based on knowledge of infection patterns in the animal reservoir host and the contact mechanisms required for transmission to humans.

Although the majority of emerging infectious diseases can be linked to wildlife sources, most pathogen spillover events to people could likely be avoided if transmission was better understood and practices adjusted to mitigate risk. Wildlife trade can facilitate zoonotic disease transmission and represents a threat to human health and economies in Asia, highlighted by the 2003 SARS coronavirus outbreak, where a Chinese wildlife market facilitated pathogen transmission. Additionally, wildlife trade poses a serious threat to biodiversity. Therefore, the combined impacts of Asian wildlife trade, sometimes termed bush meat trade, on public health and biodiversity need assessing. From 2010 to 2013, observational data were collected in Lao PDR from markets selling wildlife, including information on volume, form, species and price of wildlife; market biosafety and visitor origin. The potential for traded wildlife to host zoonotic diseases that pose a serious threat to human health was then evaluated at seven markets identified as having high volumes of trade. At the seven markets, during 21 observational surveys, 1,937 alive or fresh dead mammals (approximately 1,009 kg) were observed for sale, including mammals from 12 taxonomic families previously documented to be capable of hosting 36 zoonotic pathogens. In these seven markets, the combination of high wildlife volumes, high risk taxa for zoonoses and poor biosafety increases the potential for pathogen presence and transmission. To examine the potential conservation impact of trade in markets, we assessed the status of 33,752 animals observed during 375 visits to 93 markets, under the Lao PDR Wildlife and Aquatic Law. We observed 6,452 animals listed by Lao PDR as near extinct or threatened with extinction. The combined risks of wildlife trade in Lao PDR to human health and biodiversity highlight the need for a multi-sector approach to effectively protect public health, economic interests and biodiversity.

Аvian mobility and migration are crucial epizootological factors for the spread of several zoonoses. Their causative agents can be transmitted between species at breeding, wintering and stop-over places. The true impact of birds’ migration on the geographical distribution of important bacterial and viral pathogens is still not well established and subject of intensive interdisciplinary studies. Migratory birds may act as conveyers and could be involved in carriage of microbial pathogens by three mechanisms: 1) as biological carriers; 2) as mechanical carriers e.g. through their excreta (cloacal mixture of feces and urine); and 3) as hosts and carriers (transporters) by transporting infected hematophagous ectoparasites as vectors of diseases through long distances. In tick-borne infections, larval or nymphal ticks are known to remain attached to the host for several days and then to drop off in a new geographic area during bird migration. In food- and waterborne infections, the agent can be shed by infected migrating birds, resulting in contamination of soil and environment. The available data about bird species, seasonality, geographic regions of occurrence and European migratory flyways are presented and discussed with a focus on migratory birds as hosts and carriers of the most frequent zoonotic bacterial (campylobacteriosis, salmonellosis, Lyme borreliosis, etc.) and viral (avian influenza, paramyxoviruses, etc.) diseases. A better understanding of avian migration patterns and birds’ potential role in the geographic expansion of infectious diseases would help predicting, and may be preventing future outbreaks of infections among other birds, farm and wild animals, and humans. Sufficient knowledge on this spectacular phenomenon could elucidate the complex interrelationships that exist between the emerging infection diseases of humans, animals and wildlife, e.g. the impact of wild birds on transmission of drug-resistant bacterial species., BG; bg; EFSAfocalpoint@mzh.government.bg

Dairy cattle manure serves as a potential source of contamination and infection of animals, humans and the environment. Manure samples withdrawn from a balloon-type digester during anaerobic digestion were evaluated for the presence of antibiotic-resistant bacterial pathogens. The bacterial load of the samples was determined via a viable plate count method and the recovered isolates were subjected to characterisation and identification. These isolates were employed in antibiotic susceptibility testing using a disc diffusion method against a suite of 10 conventional antibiotics. The multiple antibiotic resistance (MAR) index was calculated and MAR phenotypes were generated. Although all the bacterial pathogens showed a certain degree of resistance to the studied antibiotics, a marked resistance was demonstrated by Campylobacter sp. to co-trimoxazole (87.5%) and nalidixic acid (81.5%). Remarkably, a high resistance (82.42%) was demonstrated against the antibiotic class, macrolide, followed by beta-lactams (40.44%), suggesting that bacterial resistance depended on the chemical structure of the antibiotics. However, individual bacterial isolates varied in resistance to particular antibiotics. Of the 83 bacterial isolates, 40(48.19%) observed MAR &gt, 0.2 and, thus, were described as multidrug-resistant isolates. A total of 28 MAR phenotypes were revealed with the highest frequency of MAR phenotypes (37.5%) expressed against 3 antibiotics. Results indicated a high risk of exposure to various antibiotics and wide diversity of antibiotic resistance.

Food-producing animals are the primary reservoir of zoonotic pathogens, and the detection of extended spectrum β-lactamase (ESBL) producers among Escherichia coli and Salmonella strains has increased in recent years. ESBLs are widely detected in various human medical institutions but they are not so frequently reported in the bacterial population circulating in animals. This could indicate that these enzymes are less prevalent in animals than in humans, but also that they have not been extensively sought. The increasing occurrence of ESBL producers in animals is highlighted and discussed in this review with respect to the circulation of these resistance traits also among human pathogens.

Infectious disease metagenomics is driven by the question: "what is causing the disease'?" in contrast to classical metagenome studies which are guided by "what is out there'?" In case of a novel virus, a first step to eventually establishing etiology can be to recover a full-length viral genome from a metagenomic sample. However, retrieval of a full-length genome of a divergent virus is technically challenging and can be time-consuming and costly. Here we discuss different assembly and fragment linkage strategies such as iterative assembly, motif searches, k-mer frequency profiling, coverage profile binning, and other strategies used to recover genomes of potential viral pathogens in a timely and cost-effective manner.

To investigate the effects of irrigation on land cover changes and the risk of selected zoonotic pathogens, we carried out a study in irrigated, pastoral and riverine areas in the eastern Kenya. Activities implemented included secondary data analyses to determine land use and land cover (LULC) changes as well as human, livestock and wildlife population trends; entomological surveys to characterize mosquitoes population densities and species distribution by habitat and season; and serological surveys in people to determine the risk of Rift Valley fever virus (RVFV), West Nile fever virus (WNV), dengue fever virus (DFV), Leptospira spp. and Brucella spp. Results demonstrate a drastic decline in vegetation cover over R approximate to 25 years particularly in the irrigated areas where cropland increased by about 1,400% and non-farm land (under closed trees, open to closed herbaceous vegetation, bushlands and open trees) reduced by 30-100%. The irrigated areas had high densities of Aedes mcintoshi, Culexspp. and Mansonia spp. (important vectors for multiple arboviruses) during the wet and dry season while pastoral areas had high densities of Ae. tricholabis specifically in the wet season. The seroprevalences of RVFV, WNV and DFV were higher in the irrigated compared to the pastoral areas while those for Leptospira spp and Brucella spp. were higher in the pastoral compared to the irrigated areas. It is likely that people in the pastoral areas get exposed to Leptospira spp by using water fetched from reservoirs that are shared with livestock and wildlife, and to Brucella spp. by consuming raw or partially cooked animal source foods such as milk and meat. This study suggests that irrigation increases the risk of mosquito-borne infections while at the same time providing a protective effect against zoonotic pathogens that thrive in areas with high livestock population densities.

Streptococcus gallolyticus subsp. gallolyticus was identified in humans and animals as commensal of the gut and can act as a causative agent of endocarditis and septicemia. A case-control study was performed to identify yet unknown risk factors for the transmission of this facultative pathogen. The prevalence in the gut of 99 healthy volunteers was determined using real-time polymerase chain reaction resulting in 62.5% S. gallolyticus subsp. gallolyticus positive excrements. Subsequent cultivation offered three isolates and epidemiological analysis based on MLST revealed sequence type (ST) 3 and ST 7, previously detected from bovine and endocarditis patients. These results support the hypotheses of the zoonotic potential of this bacterium. Participant questionnaires were evaluated concerning personal characteristics, nutritional habits and animal contact. Specifically, closer contact between participants and animals influenced the colonization of the human gut significantly and was further affected if volunteers used excrement for the fertilization of plants.

Suggested citation for this article: Bloom S, Levitt A. Seeing things differently. Emerg Infect Dis [Internet]. 2014 Feb [date cited]. http://dx.doi.org/10.3201/eid2002.AC2002

Background Hotspot detection and characterization has played an increasing role in understanding the maintenance and transmission of zoonotic pathogens. Identifying the specific environmental factors (or their correlates) that influence reservoir host abundance help increase understanding of how pathogens are maintained in natural systems and are crucial to identifying disease risk. However, most recent studies are performed at macro-scale and describe broad temporal patterns of population abundances. Few have been conducted at a microscale over short time periods that better capture the dynamical patterns of key populations. These finer resolution studies may better define the likelihood of local pathogen persistence. This study characterizes the landscape distribution and spatio-temporal dynamics of Oligoryzomys fulvescens (O. fulvescens), an important mammalian reservoir in Central America. Methods Information collected in a longitudinal study of rodent populations in the community of Agua Buena in Tonosí, Panama, between April 2006 and December 2009 was analyzed using non-spatial analyses (box plots) and explicit spatial statistical tests (correlograms, SADIE and LISA). A 90 node grid was built (raster format) to design a base map. The area between the nodes was 0.09 km2 and the total study area was 6.43 km2 (2.39 x 2.69 km). The temporal assessment dataset was divided into four periods for each year studied: the dry season, rainy season, and two months-long transitions between seasons (the months of April and December). Results There were heterogeneous patterns in the population densities and degrees of dispersion of O. fulvescens that varied across seasons and among years. The species typically was locally absent during the late transitional months of the season, and re-established locally in subsequent years. These populations re-occurred in the same area during the first three years but subsequently re-established further south in the final year of the study. Spatial autocorrelation analyses indicated local populations encompassed approximately 300–600 m. The borders between suitable and unsuitable habitats were sharply demarcated over short distances. Conclusion Oligoryzomys fulvescens showed a well-defined spatial pattern that evolved over time, and led to a pattern of changing aggregation. Thus, hot spots of abundance showed a general shifting pattern that helps explain the intermittent risk from pathogens transmitted by this species. This variation was associated with seasonality, as well as anthropogenic pressures that occurred with agricultural activities. These factors help define the characteristics of the occurrence, timing, intensity and duration of synanthropic populations affected by human populations and, consequently, possible exposure that local human populations experience., Author Summary In Panama, hantavirus pulmonary syndrome (HPS) is due to infection with the Choclo virus, which is transmitted by the rice rat (Oligoryzomys fulvescens). Hantavirus infection is endemic in rural, Central-West Panama, an area characterized by a very dynamic combination of subsistence and industrial agriculture. This region contains one of the highest hantavirus antibody prevalence (16–62%) in humans on the continent, but with low mortality (17%) in the affected population. People become infected in and around the household area. Evidence points to the increase in and dynamic nature of agricultural activity in this region as the primary causes of increased hantavirus infection in humans in Panama. This study was conducted on a high spatio-temporal resolution that better captures how rapidly the abundances of reservoir populations shift—altering this aspect of zoonotic spillover of pathogens. Practically, the results demonstrate an important challenge in monitoring or predicting zoonotic disease outbreaks at the level of reservoir populations. These populations are subject to fluctuations over time (both within and among years). The populations themselves are geographically restricted, even within their broader range. Suitable habitats for rodents may change but are poorly understood. Our results are valuable to understand hantavirus dynamics in Panama and the many other countries from North to South America in which hantaviruses are endemic in host populations.

To explore geographic and host-taxonomic patterns of hantaviruses in Paraguay, we established sampling sites in the Mbaracayu Biosphere Reserve. We detected Jabora virus and Itapua37/Juquitiba-related virus in locations approximately 20 m apart in different years, which suggested sympatry of 2 distinct hantaviruses.

Understanding the dynamics of zoonotic pathogens in their reservoir host populations is a prerequisite for predicting and preventing human disease epidemics. The human infection risk of Puumala hantavirus (PUUV) is highest in northern Europe, where populations of the rodent host (bank vole, Myodes glareolus) undergo cyclic fluctuations. We conducted a 7-year capture-mark-recapture study to monitor seasonal and multiannual patterns of the PUUV infection rate in bank vole populations exhibiting a 3-year density cycle. Infected bank voles were most abundant in mid-winter months during years of increasing or peak host density. Prevalence of PUUV infection in bank voles exhibited a regular, seasonal pattern reflecting the annual population turnover and accumulation of infections within each year cohort. In autumn, the PUUV transmission rate tracked increasing host abundance, suggesting a density-dependent transmission. However, prevalence of PUUV infection was similar during the increase and peak years of the density cycle despite a twofold difference in host density. This may result from the high proportion of individuals carrying maternal antibodies constraining transmission during the cycle peak years. Our exceptionally intensive and long-term dataset provides a solid basis on which to develop models to predict the dynamic public health threat posed by PUUV in northern Europe.