Pathogen Infection in Wildlife 2.0

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Veterinary Microbiology".

Deadline for manuscript submissions: closed (31 July 2024) | Viewed by 15356

Special Issue Editor


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Guest Editor
Institute of Zoology, Slovak Academy of Sciences, Dúbravská Cesta 9, 84506 Bratislava, Slovakia
Interests: biodiversity; conservation biology; molecular biology; ecology and evolution; conservation; ecology; climate change; evolution; species diversity; wildlife conservation
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Special Issue Information

Dear Colleagues,

This Special Issue is a continuation of our previous Special Issue, “Pathogen Infection in Wildlife”.

Most emerging infectious diseases are caused by zoonotic pathogens associated with wildlife reservoirs. However, despite significant efforts to understand the spatiotemporal patterns of disease emergence, our knowledge of the geographical distribution and ecology of wildlife pathogens is largely limited to a few zoonoses. One of the key questions in disease ecology asks which factors drive pathogen occurrence in new hosts and host communities. While multiple evolutionary and ecological hypotheses have addressed this question, the results acquired thus far are complex and their implications are often only applicable to specific scenarios. The paucity of data and the complexity of the findings are particularly apparent for systems with vector-borne pathogens. We still do not sufficiently understand which factors affect host and vector competence and how these factors interact to affect pathogen emergence and persistence.

This Special Issue plans to address various topics on the ecology and evolution of different vector-borne wildlife pathogens, such as viruses, bacteria or protozoa, which can contribute to a better understanding of the processes of disease emergence in human and non-human animals.

Potential topics include, but are not limited to, the following:

  • The role of host and vector life history strategies and traits;
  • The role of host and vector community structure;
  • The role of habitat degradation and urbanization;
  • Host, vector and pathogen evolutionary histories;
  • Determinants of host and vector specificity;
  • Cryptic pathogen complexes;
  • Pathogen surveillance and detection techniques.

Dr. Radovan Václav
Guest Editor

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Published Papers (9 papers)

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Research

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12 pages, 4354 KiB  
Article
The Alligator and the Mosquito: North American Crocodilians as Amplifiers of West Nile Virus in Changing Climates
by Desiree Kirsten Andersen, Gracie Ann Fischer and Leigh Combrink
Microorganisms 2024, 12(9), 1898; https://doi.org/10.3390/microorganisms12091898 - 14 Sep 2024
Viewed by 1734
Abstract
In an age of emerging zoonoses, it is important to understand the intricate system of vectors and reservoirs, or hosts, and their relation to humans. West Nile Virus (WNV) has been detected in a myriad of nonhuman hosts. Transmission of the virus to [...] Read more.
In an age of emerging zoonoses, it is important to understand the intricate system of vectors and reservoirs, or hosts, and their relation to humans. West Nile Virus (WNV) has been detected in a myriad of nonhuman hosts. Transmission of the virus to humans is reliant on amplified seroprevalence within the host, which occurs primarily in birds. However, recent studies have found that other animal groups, including crocodilians, can obtain seroprevalence amplification to levels that make them competent hosts able to transmit WNV to mosquitoes, which can then transmit to humans. Climate change could exacerbate this transmission risk by shifting the distributions of mosquito vectors towards novel geographic ranges. Here, we use maximum entropy models to map the current and future distributions of three mosquito vector species and four crocodilian species in North America to determine the emerging risk of WNV outbreaks associated with changing climates and WNV associated with crocodilians in North America. From our models, we determined that one mosquito species in particular, Culex quinquefasciatus, will increase its distribution across the ranges of all crocodilian species in all tested climate change scenarios. This poses a potential risk to public health for people visiting and living near crocodilian farms and high-density natural crocodilian populations. Full article
(This article belongs to the Special Issue Pathogen Infection in Wildlife 2.0)
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16 pages, 3751 KiB  
Article
Exploring the Role of the Environment as a Reservoir of Antimicrobial-Resistant Campylobacter: Insights from Wild Birds and Surface Waters
by Louise Hock, Cécile Walczak, Juliette Mosser, Catherine Ragimbeau and Henry-Michel Cauchie
Microorganisms 2024, 12(8), 1621; https://doi.org/10.3390/microorganisms12081621 - 8 Aug 2024
Viewed by 1459
Abstract
Antimicrobial resistance (AMR) is a growing global health challenge, compromising bacterial infection treatments and necessitating robust surveillance and mitigation strategies. The overuse of antimicrobials in humans and farm animals has made them hotspots for AMR. However, the spread of AMR genes in wildlife [...] Read more.
Antimicrobial resistance (AMR) is a growing global health challenge, compromising bacterial infection treatments and necessitating robust surveillance and mitigation strategies. The overuse of antimicrobials in humans and farm animals has made them hotspots for AMR. However, the spread of AMR genes in wildlife and the environment represents an additional challenge, turning these areas into new AMR hotspots. Among the AMR bacteria considered to be of high concern for public health, Campylobacter has been the leading cause of foodborne infections in the European Union since 2005. This study examines the prevalence of AMR genes and virulence factors in Campylobacter isolates from wild birds and surface waters in Luxembourg. The findings reveal a significant prevalence of resistant Campylobacter strains, with 12% of C. jejuni from wild birds and 37% of C. coli from surface waters carrying resistance genes, mainly against key antibiotics like quinolones and tetracycline. This study underscores the crucial role of the environment in the spread of AMR bacteria and genes, highlighting the urgent need for enhanced surveillance and control measures to curb AMR in wildlife and environmental reservoirs and reduce transmission risks to humans. This research supports One Health approaches to tackling antimicrobial resistance and protecting human, animal, and environmental health. Full article
(This article belongs to the Special Issue Pathogen Infection in Wildlife 2.0)
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13 pages, 4766 KiB  
Article
Identification and Characterization of an Alphacoronavirus in Rhinolophus sinicus and a Betacoronavirus in Apodemus ilex in Yunnan, China
by Qian Liu, Dan-Shu Wang, Zhong-Hao Lian, Jie Fang, Pei-Yu Han, Ye Qiu, Jun-Ying Zhao, Li-Dong Zong, Yun-Zhi Zhang and Xing-Yi Ge
Microorganisms 2024, 12(7), 1490; https://doi.org/10.3390/microorganisms12071490 - 21 Jul 2024
Viewed by 1218
Abstract
Coronaviruses (CoVs), the largest positive-sense RNA viruses, have caused infections in both humans and animals. The cross-species transmission of CoVs poses a serious threat to public health. Rodents and bats, the two largest orders of mammals, serve as significant natural reservoirs for CoVs. [...] Read more.
Coronaviruses (CoVs), the largest positive-sense RNA viruses, have caused infections in both humans and animals. The cross-species transmission of CoVs poses a serious threat to public health. Rodents and bats, the two largest orders of mammals, serve as significant natural reservoirs for CoVs. It is important to monitor the CoVs carried by bats and rodents. In this study, we collected 410 fecal samples from bats and 74 intestinal samples from rats in Yunnan Province, China. Using RT-PCR, we identified one positive sample for alphacoronavirus (TC-14) from Rhinolophus sinicus (Chinese rufous horseshoe bat) and two positive samples for betacoronavirus (GS-53, GS-56) from Apodemus ilex (Rodentia: Muridae). We successfully characterized the complete genomes of TC-14 and GS-56. Phylogenetic analysis revealed that TC-14 clustered with bat CoV HKU2 and SADS-CoV, while GS-56 was closely related to rat CoV HKU24. The identification of positive selection sites and estimation of divergence dates further helped characterize the genetic evolution of TC-14 and GS-56. In summary, this research reveals the genetic evolution characteristics of TC-14 and GS-56, providing valuable references for the study of CoVs carried by bats and rodents in Yunnan Province. Full article
(This article belongs to the Special Issue Pathogen Infection in Wildlife 2.0)
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13 pages, 498 KiB  
Article
Characterising Eastern Grey Kangaroos (Macropus giganteus) as Hosts of Coxiella burnetii
by Anita Tolpinrud, Elizabeth Dobson, Catherine A. Herbert, Rachael Gray, John Stenos, Anne-Lise Chaber, Joanne M. Devlin and Mark A. Stevenson
Microorganisms 2024, 12(7), 1477; https://doi.org/10.3390/microorganisms12071477 - 19 Jul 2024
Cited by 1 | Viewed by 1283
Abstract
Macropods are often implicated as the main native Australian reservoir hosts of Coxiella burnetii (Q fever); however, the maintenance and transmission capacity of these species are poorly understood. The objective of this cross-sectional study was to describe the epidemiology of C. burnetii in [...] Read more.
Macropods are often implicated as the main native Australian reservoir hosts of Coxiella burnetii (Q fever); however, the maintenance and transmission capacity of these species are poorly understood. The objective of this cross-sectional study was to describe the epidemiology of C. burnetii in a high-density population of eastern grey kangaroos (Macropus giganteus) in a peri-urban coastal nature reserve in New South Wales, Australia. Blood, faeces and swabs were collected from forty kangaroos as part of a population health assessment. Frozen and formalin-fixed tissues were also collected from 12 kangaroos euthanised on welfare grounds. Specimens were tested for C. burnetii using PCR, serology, histopathology and immunohistochemistry. A total of 33/40 kangaroos were seropositive by immunofluorescence assay (estimated true seroprevalence 84%, 95% confidence interval [CI] 69% to 93%), with evidence of rising titres in two animals that had been tested four years earlier. The PCR prevalence was 65% (95% CI 48% to 79%), with positive detection in most sample types. There was no evidence of pathology consistent with C. burnetii, and immunohistochemistry of PCR-positive tissues was negative. These findings indicate that kangaroos are competent maintenance hosts of C. burnetii, likely forming a significant part of its animal reservoir at the study site. Full article
(This article belongs to the Special Issue Pathogen Infection in Wildlife 2.0)
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17 pages, 2718 KiB  
Article
Retrospective Detection of Ophidiomyces ophidiicola from Snake Moults Collected in Bieszczady Mountains, Poland
by Daniele Marini, Piotr Szczygieł, Katarzyna Kurek, Matteo Riccardo Di Nicola, Jean-Lou C. M. Dorne, Maria Luisa Marenzoni, Joëlle Rüegg, Stanisław Bury and Łukasz Kiraga
Microorganisms 2024, 12(7), 1467; https://doi.org/10.3390/microorganisms12071467 - 19 Jul 2024
Viewed by 1405
Abstract
Ophidiomyces ophidiicola, the causative agent of ophidiomycosis, poses a potential threat to wild snakes worldwide. This study aimed to retrospectively investigate the prevalence of O. ophidiicola in archived snake moults collected from the San River Valley in the Bieszczady Mountains, Poland, from [...] Read more.
Ophidiomyces ophidiicola, the causative agent of ophidiomycosis, poses a potential threat to wild snakes worldwide. This study aimed to retrospectively investigate the prevalence of O. ophidiicola in archived snake moults collected from the San River Valley in the Bieszczady Mountains, Poland, from 2010 to 2012. Using qPCR for O. ophidiicola detection and conventional PCR for clade characterisation, we analysed 58 moults and one road-killed specimen of Zamenis longissimus and Natrix natrix. A novel combination of primers (ITS2L) was used to simultaneously confirm SYBR Green-based qPCR results and perform genotyping. O. ophidiicola has been detected from two Z. longissimus and one N. natrix specimens. The identified clade (I-B) is consistent with those found in wild snakes of eastern Europe and San River Valley, indicating that O. ophidiicola has been present in this region for at least a decade. This study underscores the value of historical samples in understanding the long-term presence of pathogens and highlights the potential role of environmental reservoirs in the persistence of O. ophidiicola. Our findings are crucial for informing conservation strategies for the endangered Aesculapian snake populations in Poland, emphasising the need for ongoing monitoring and habitat management to mitigate the potential impact of ophidiomycosis. Full article
(This article belongs to the Special Issue Pathogen Infection in Wildlife 2.0)
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10 pages, 261 KiB  
Article
Escherichia coli Strains Isolated from American Bison (Bison bison) Showed Uncommon Virulent Gene Patterns and Antimicrobial Multi-Resistance
by Jonathan J. López-Islas, Daniel Martínez-Gómez, Wendy E. Ortiz-López, Tania Reyes-Cruz, Andrés M. López-Pérez, Carlos Eslava and Estela T. Méndez-Olvera
Microorganisms 2024, 12(7), 1367; https://doi.org/10.3390/microorganisms12071367 - 3 Jul 2024
Viewed by 1229
Abstract
E. coli is considered one of the most important zoonotic pathogens worldwide. Highly virulent and antimicrobial-resistant strains of E. coli have been reported in recent years, making it essential to understand their ecological origins. In this study, we analyzed the characteristics of E. [...] Read more.
E. coli is considered one of the most important zoonotic pathogens worldwide. Highly virulent and antimicrobial-resistant strains of E. coli have been reported in recent years, making it essential to understand their ecological origins. In this study, we analyzed the characteristics of E. coli strains present in the natural population of American bison (Bison bison) in Mexico. We sampled 123 individuals and determined the presence of E. coli using standard bacteriological methods. The isolated strains were characterized using molecular techniques based on PCR. To evaluate the diversity of E. coli strains in this population, we analyzed 108 suggestive colonies from each fecal sample. From a total of 13,284 suggestive colonies, we isolated 33 E. coli strains that contained at least one virulence gene. The virotypes of these strains were highly varied, including strains with atypical patterns or combinations compared to classical pathotypes, such as the presence of escV, eae, bfpB, and ial genes in E. coli strain LMA-26-6-6, or stx2, eae, and ial genes in E. coli strain LMA-16-1-32. Genotype analysis of these strains revealed a previously undescribed phylogenetic group. Serotyping of all strains showed that serogroups O26 and O22 were the most abundant. Interestingly, strains belonging to these groups exhibited different patterns of virulence genes. Finally, the isolated E. coli strains demonstrated broad resistance to antimicrobials, including various beta-lactam antibiotics. Full article
(This article belongs to the Special Issue Pathogen Infection in Wildlife 2.0)
18 pages, 8269 KiB  
Article
The Presence of Four Pathogenic Oral Bacterial Species in Six Wild Snake Species from Southern Taiwan: Associated Factors
by Wen-Hao Lin, Tein-Shun Tsai and Po-Chun Chuang
Microorganisms 2024, 12(2), 263; https://doi.org/10.3390/microorganisms12020263 - 26 Jan 2024
Cited by 1 | Viewed by 2255
Abstract
The oral cavity of snakes serves as a habitat for various microorganisms, some of which may include potential zoonotic pathogens posing risks to hosts and causing wound infections in snakebite victims. Clinical studies on snakebite cases in Taiwan have identified specific pathogens, such [...] Read more.
The oral cavity of snakes serves as a habitat for various microorganisms, some of which may include potential zoonotic pathogens posing risks to hosts and causing wound infections in snakebite victims. Clinical studies on snakebite cases in Taiwan have identified specific pathogens, such as Enterococcus faecalis (Gram-positive), Morganella morganii, Aeromonas hydrophila, and Pseudomonas aeruginosa (Gram-negative). However, the prevalence of these bacteria in the oral cavity of wild snakes remains largely unknown. This study investigated the occurrence of these bacteria in six wild snake species (Naja atra, Bungarus multicinctus, Trimeresurus stejnegeri, Protobothrops mucrosquamatus, Boiga kraepelini, and Elaphe taeniura friesi) from southern Taiwan, along with factors influencing their presence. Oropharyngeal swab samples were collected from a substantial number of wild-caught snakes (n = 1104), followed by DNA extraction, polymerase chain reaction, and gel electrophoresis. The band positions of samples were compared with positive and negative controls to determine the presence of target bacteria in each sample. The overall occurrence rates were 67.4% for E. faecalis, 31.5% for M. morganii, 8.2% for A. hydrophila, and 7.7% for P. aeruginosa. Among snake species, B. kraepelini exhibited dominance in E. faecalis (93.4%), A. hydrophila (17.1%), and P. aeruginosa (14.5%), while male N. atra showed dominance in M. morganii (51.3%). The occurrence of E. faecalis was lowest in winter. The results of multiple logistic regression analyses suggest that factors such as species, sex, temperature, season, and coexisting pathogens may have a significant impact on the occurrence of target bacteria. These findings have implications for wildlife medicine and snakebite management. Full article
(This article belongs to the Special Issue Pathogen Infection in Wildlife 2.0)
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17 pages, 2062 KiB  
Article
Comparison of Endogenous Alpharetroviruses (ALV-like) across Galliform Species: New Distant Proviruses
by Sergio Fandiño, Esperanza Gomez-Lucia, Laura Benítez and Ana Doménech
Microorganisms 2024, 12(1), 86; https://doi.org/10.3390/microorganisms12010086 - 31 Dec 2023
Viewed by 1576
Abstract
The Genus Alpharetrovirus contains viruses pathogenic mainly for chickens, forming the Avian Sarcoma and Leukosis Virus group (ASLV). Cells of most Galliform species, besides chickens, contain genetic elements (endogenous retroviruses, ERVs) that could recombine with other alpharetroviruses or express proteins, complementing defective ASLV, [...] Read more.
The Genus Alpharetrovirus contains viruses pathogenic mainly for chickens, forming the Avian Sarcoma and Leukosis Virus group (ASLV). Cells of most Galliform species, besides chickens, contain genetic elements (endogenous retroviruses, ERVs) that could recombine with other alpharetroviruses or express proteins, complementing defective ASLV, which may successfully replicate and cause disease. However, they are quite unknown, and only ALV-F, from ring-necked pheasants, has been partially published. Upon scrutiny of 53 genomes of different avian species, we found Alpharetrovirus-like sequences only in 12 different Galliformes, including six full-length (7.4–7.6 Kbp) and 27 partial sequences. Phylogenetic studies of the regions studied (LTR, gag, pol, and env) consistently resulted in five almost identical clades containing the same ERVs: Clade I (presently known ASLVs); Clade II (Callipepla spp. ERVs); Clade IIIa (Phasianus colchicus ERVs); Clade IIIb (Alectoris spp. ERVs); and Clade IV (Centrocercus spp. ERVs). The low pol identity scores suggested that each of these Clades may be considered a different species. ORF analysis revealed that putatively encoded proteins would be very similar in length and domains to those of other alpharetroviruses and thus potentially functional. This will undoubtedly contribute to better understanding the biology of defective viruses, especially in wild Galliformes, their evolution, and the danger they may represent for other wild species and the poultry industry. Full article
(This article belongs to the Special Issue Pathogen Infection in Wildlife 2.0)
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Review

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17 pages, 4174 KiB  
Review
Beyond the Wild MRSA: Genetic Features and Phylogenomic Review of mecC-Mediated Methicillin Resistance in Non-aureus Staphylococci and Mammaliicocci
by Idris Nasir Abdullahi, Javier Latorre-Fernández, Rine Christopher Reuben, Islem Trabelsi, Carmen González-Azcona, Ameni Arfaoui, Yahaya Usman, Carmen Lozano, Myriam Zarazaga and Carmen Torres
Microorganisms 2024, 12(1), 66; https://doi.org/10.3390/microorganisms12010066 - 29 Dec 2023
Cited by 4 | Viewed by 2227
Abstract
Methicillin resistance, mediated by the mecA gene in staphylococci and mammaliicocci, has caused tremendous setbacks in the use of antibiotics in human and veterinary medicine due to its high potential of presenting the multidrug resistance (MDR) phenotype. Three other mec analogs exist, of [...] Read more.
Methicillin resistance, mediated by the mecA gene in staphylococci and mammaliicocci, has caused tremendous setbacks in the use of antibiotics in human and veterinary medicine due to its high potential of presenting the multidrug resistance (MDR) phenotype. Three other mec analogs exist, of which the mecC has evolutionary been associated with methicillin-resistant Staphylococcus aureus (MRSA) in wild animals, thus loosely referred to as the wild MRSA. In this study, we present an epidemiological review and genomic analysis of non-aureus staphylococci and mammaliicocci that carry the mecC-mediated methicillin resistance trait and determine whether this trait has any relevant link with the One Health niches. All previous studies (2007 till 2023) that described the mecC gene in non-aureus staphylococci and mammaliicocci were obtained from bibliometric databases, reviewed, and systematically analyzed to obtain the antimicrobial resistance (AMR) and virulence determinants, mobilome, and other genetic contents. Moreover, core genome single-nucleotide polymorphism analysis was used to assess the relatedness of these strains. Of the 533 articles analyzed, only 16 studies (on livestock, environmental samples, milk bulk tanks, and wild animals) were eligible for inclusion, of which 17 genomes from 6 studies were used for various in silico genetic analyses. Findings from this systematic review show that all mecC-carrying non-aureus staphylococci were resistant to only beta-lactam antibiotics and associated with the classical SCCmec XI of S. aureus LGA251. Similarly, two studies on wild animals reported mecC-carrying Mammaliicoccus stepanovicii associated with SCCmec XI. Nevertheless, most of the mecC-carrying Mammaliicoccus species presented an MDR phenotype (including linezolid) and carried the SCCmec-mecC hybrid associated with mecA. The phylogenetic analysis of the 17 genomes revealed close relatedness (<20 SNPs) and potential transmission of M. sciuri and M. lentus strains in livestock farms in Algeria, Tunisia, and Brazil. Furthermore, closely related M. sciuri strains from Austria, Brazil, and Tunisia (<40 SNPs) were identified. This systematic review enhances our comprehension of the epidemiology and genetic organization of mecC within the non-aureus staphylococci and mammaliicocci. It could be hypothesized that the mecC-carrying non-aureus staphylococci are evolutionarily related to the wild MRSA-mecC. The potential implications of clonal development of a lineage of mecA/mecC carrying strains across multiple dairy farms in a vast geographical region with the dissemination of MDR phenotype is envisaged. It was observed that most mecC-carrying non-aureus staphylococci and mammaliicocci were reported in mastitis cases. Therefore, veterinarians and veterinary microbiology laboratories must remain vigilant regarding the potential existence of mecA/mecC strains originating from mastitis as a potential niche for this resistance trait. Full article
(This article belongs to the Special Issue Pathogen Infection in Wildlife 2.0)
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