Do humans spread zoonotic enteric bacteria in Antarctica?

Penguin-Driven Dissemination and High Enrichment of Antibiotic Resistance Genes in Lake Sediments across Antarctica

Numerous penguins can propagate pathogens with antibiotic resistance genes (ARGs) into Antarctica. However, the effects of penguin dissemination on the lake ARGs still have received little attention via guano deposition. Here, we have profiled ARGs in ornithogenic sediments subject to penguin guano (OLS) and nonornithogenic sediments (NOLS) from 16 lakes across Antarctica. A total of 191 ARGs were detected in all sediment samples, with a much higher abundance and diversity in OLS than in NOLS. Surprisingly, highly diverse and abundant ARGs were found in the OLS with a detection frequency of >40% and an absolute abundance of (2.34 × 109)-(4.98 × 109) copies g-1, comparable to those in coastal estuarine sediments and pig farms. The strong correlations of identified resistance genes with penguin guano input amount, environmental factors, mobile genetic elements, and bacterial community, in conjunction with network and redundancy analyses, all indicated that penguins were responsible for the dissemination and high enrichment of ARGs in lake sediments via the guano deposition, which might greatly outweigh local human-activity effects. Our results revealed that ARGs could be carried into lakes across the Antarctica through penguin migration, food chains, and guano deposition, which were closely connected with the widespread pollution of ARGs at the global scale.

Clustered Regularly Interspaced Short Palindromic Repeat-1 (CRISPR-1) Locus as a Tool for Tracing the Zoonotic History of Salmonella enterica Strains

Background Salmonella enterica is a significant foodborne pathogen that causes considerable illness and death in humans and animals. The clustered regularly interspaced short palindromic repeat (CRISPR)-CRISPR-associated protein (Cas) system in bacteria acts as an adaptive immune defense against invasive genetic elements by incorporating short intergenic spacers (IGSs) into CRISPR loci. These loci serve as molecular records of past interactions with phages and plasmids, providing insights into the transmission and evolution of bacterial strains across different hosts. Aim This study aimed to investigate the diversity of IGSs in the CRISPR-1 locus of S. enterica isolates from humans and camels. The objective was to assess the potential of IGSs to distinguish strains, track sources, and understand patterns of zoonotic transmission. Materials and methods Genomic DNA was extracted from multiple strains of S. enterica, and the CRISPR-1 locus was polymerase chain reaction (PCR) amplified and sequenced. The sequences were compared to identify distinct patterns of IGSs and potential host-specific characteristics. Sanger sequencing and bioinformatics tools were used to classify the IGSs and determine their similarity to known sequences in the National Center for Biotechnology Information (NCBI) database. Results Sequence analysis revealed five distinct CRISPR-1 types among S. enterica isolates from humans and three among camel isolates. The presence of shared IGSs between human and camel S. enterica isolates suggested zoonotic or reverse-zoonotic transmission events. Additionally, host-specific unknown IGSs (UIGS) were identified. Importantly, camel isolates initially identified as S. enterica subspecies enterica serovar Enteritidis based on rrnH gene sequencing were reclassified as S. enterica serovar Enteritidis based on CRISPR-1 profiling, demonstrating the higher resolution of CRISPR-based genotyping. Conclusion The diversity of IGSs in the CRISPR-1 locus effectively differentiated S. enterica strains and provided insights into their evolutionary origins and transmission dynamics. CRISPR-based genotyping proves to be a promising tool to complement traditional serotyping methods, enhancing the molecular epidemiology of salmonellosis and potentially leading to better management and control strategies for this pathogen.

Spread of antibiotic resistance genes to Antarctica by migratory birds

Recent studies have highlighted the presence of antibiotic resistance genes (ARGs) in Antarctica, which are typically indicative of human activity. However, these studies have concentrated in the Antarctic Peninsula region, and relatively less is known about ARG prevalence in East Antarctica, where human activity levels are lower compared to the Antarctic Peninsula. In addition, the mechanisms of ARG transmission to Antarctica through natural or anthropogenic pathways remain unclear. In this study, we analyzed the fecal samples of Adélie penguins and South polar skuas by using high-throughput sequencing and microfluidic quantitative PCR to detect potential pathogens and ARGs at their breeding colonies near Syowa Station in East Antarctica. These results revealed the presence of several potential pathogens in the fecal matter of both bird species. However, the HF183 marker, which indicates human fecal contamination, was absent in all samples, as well as seawater sampled near the breeding colonies. This suggests that the human fecal contamination was negligible in our study area. In addition to pathogens, we found a significant number of ARGs and metal resistance genes in the feces of both Adélie penguins and South polar skuas, with higher detection rates in skuas than in penguins. To better understand how these birds acquire and transmit these genes, we analyzed the migratory patterns of Adélie penguins and South polar skuas by geolocator tracking. We found that the skuas migrate to the tropical and subtropical regions of the Indian Ocean during the austral winter. On the other hand, Adélie penguins exhibited a more localized migration pattern, mainly staying within Antarctic waters. Because the Indian Ocean is considered one of the major reservoirs of ARGs, South polar skuas might be exposed to ARGs during their winter migration and transfer these genes to Antarctica.

Biodiversity of carbapenem-resistant bacteria in clinical samples from the Southwest Amazon region (Rondônia/Brazil)

Brazil is recognized for its biodiversity and the genetic variability of its organisms. This genetic variability becomes even more valuable when it is properly documented and accessible. Understanding bacterial diversity through molecular characterization is necessary as it can improve patient treatment, reduce the length of hospital stays and the selection of resistant bacteria, and generate data for health and epidemiological surveillance. In this sense, in this study, we aimed to understand the biodiversity and molecular epidemiology of carbapenem-resistant bacteria in clinical samples recovered in the state of Rondônia, located in the Southwest Amazon region. Retrospective data from the Central Public Health Laboratories (LACEN/RO) between 2018 and 2021 were analysed using the Laboratory Environment Manager Platform (GAL). Seventy-two species with carbapenem resistance profiles were identified, of which 25 species carried at least one gene encoding carbapenemases of classes A (blaKPC-like), B (blaNDM-like, blaSPM-like or blaVIM-like) and D (blaOXA-23-like, blaOXA-24-like, blaOXA-48-like, blaOXA-58-like or blaOXA-143-like), among which we will highlight Klebsiella pneumoniae, Pseudomonas aeruginosa, Acinetobacter baumannii, Serratia marcescens, and Providencia spp. With these results, we hope to contribute to the field by providing epidemiological molecular data for state surveillance on bacterial resistance and assisting in public policy decision-making.

Antibiotic resistance in wildlife from Antarctic Peninsula

Although considered one of the most pristine ecosystems, Antarctica has been largely influenced by human activities during the last 50 years, affecting its unique biodiversity. One of the major global threats to health is the emergence of antibiotic-resistant bacteria that may be actively transferred to wildlife. We cultured and tested for antibiotic resistance in 137 cloacal and fresh fecal samples of several avian and marine mammal species from the Antarctic Peninsula, the most impacted area in Antarctica. Alarmingly, 80 % of the isolates showed antibiotic resistance, either phenotypically or genotypically. Most of the resistant bacteria, such as Enterobacteriaceae and Enterococcus species, are part of local gastrointestinal microbiota. Penguins and pinnipeds harbored a great diversity of antibiotic resistance and must be eligible as sentinels for future studies. These results show that antibiotic resistance has rapidly transferred to bacteria in Antarctic wildlife, which is a global matter of concern.

Erysipelothrix amsterdamensis sp. nov., associated with mortalities among endangered seabirds

Infectious diseases threaten endangered species, particularly in small isolated populations. Seabird populations on the remote Amsterdam Island in the Indian Ocean have been in decline for the past three decades, with avian cholera caused by Pasteurella multocida proposed as the primary driver. However, Erysipelothrix species have also been sporadically detected from albatrosses on Amsterdam Island and may be contributing to some of the observed mortality. In this study, we genomically characterized 16 Erysipelothrix species isolates obtained from three Indian yellow-nosed albatross (Thalassarche carteri) chick carcasses in 2019. Histological analyses suggest that they died of bacterial septicaemia. Two isolates were sequenced using both Illumina short-read and MinION long-read approaches, which - following hybrid assembly - resulted in closed circular genomes. Mapping of Illumina reads from the remaining isolates to one of these new reference genomes revealed that all 16 isolates were closely related, with a maximum of 13 nucleotide differences distinguishing any pair of isolates. The nucleotide diversity of isolates obtained from the same or different carcasses was similar, suggesting all three chicks were likely infected from a common source. These genomes were compared with a global collection of genomes from Erysipelothrix rhusiopathiae and other species from the same genus. The isolates from albatrosses were phylogenetically distinct, sharing a most recent common ancestor with E. rhusiopathiae. Based on phylogenomic analysis and standard thresholds for average nucleotide identity and digital DNA-DNA hybridization, these isolates represent a novel Erysipelothrix species, for which we propose the name Erysipelothrix amsterdamensis sp. nov. The type strain is A18Y020dT (=CIP 112216T=DSM 115297T). The implications of this bacterium for albatross conservation will require further study.

Antimicrobial-Resistant Bacteria Carriage in Rodents According to Habitat Anthropization

It is increasingly suggested that the dynamics of antimicrobial-resistant bacteria in the wild are mostly anthropogenically driven, but the spatial and temporal scales at which these phenomena occur in landscapes are only partially understood. Here, we explore this topic by studying antimicrobial resistance in the commensal bacteria from micromammals sampled at 12 sites from a large heterogenous landscape (the Carmargue area, Rhone Delta) along a gradient of anthropization: natural reserves, rural areas, towns, and sewage-water treatment plants. There was a positive relationship between the frequency of antimicrobial-resistant bacteria and the level of habitat anthropization. Although low, antimicrobial resistance was also present in natural reserves, even in the oldest one, founded in 1954. This study is one of the first to support the idea that rodents in human-altered habitats are important components of the environmental pool of resistance to clinically relevant antimicrobials and also that a "One Health" approach is required to assess issues related to antimicrobial resistance dynamics in anthropized landscapes.

Integrative assessment of immunity, health-state, growth and survival of Magellanic penguin chicks in a colony exposed to ecotourism

Accumulating reports of negative impacts of tourist activities on wildlife emphasize the importance of closely monitoring focal populations. Although some effects are readily noticed, more subtle ones such as changes in physiological functions of individuals might go overlooked. Based on evidence of altered physiology associated with ecotourism on Magellanic penguins Spheniscus magellanicus, here we performed an integrated assessment using a diverse physiological toolkit together with more traditional fitness-related measures to better understand mechanisms and potential consequences. Chicks exposed to tourism showed altered immune parameters and elevated flea prevalence, reinforcing previous findings. Tourism-exposed female, but not male, chicks also showed relatively lower hematocrit and plasma protein levels, providing evidence consistent with a sex-specific response to tourist visitation. Physiological alterations detected in tourism-exposed young chicks (week 1-2) were maintained and the effect on flea infestation increased during the study period (week 4-5 of post-hatch). Despite the effects on physiology, these did not seem to translate into immediate fitness costs. No detectable tourism effects were found on brood sex ratios, chick growth and body condition, and survival until week 5-6 post-hatch. We detected no effects on reproductive output and only a marginal effect on nest survival during incubation despite previous reports of tourism-associated alterations in stress indices of adults. This disconnection could result if the physiological changes are not strong enough to impact fitness, if effects balance each other out, or if changes are part of a copying strategy. Alternatively, the physiological alterations might only show impacts later in the brooding cycle or even after chick emancipation from their parents. Our results suggest that integrative monitoring of potential anthropogenic impacts on wildlife should include evaluation of physiological mechanisms and individual-level responses in populations exposed to human activities.

Assessing evidence of a potential Salmonella transmission across the poultry food chain

Enhanced Salmonella surveillance programmes in poultry were implemented in all European Member States, with minimum prevalence targets for a list of targeted serotypes to safeguard food and public health. Based on the Belgian Salmonella surveillance programme and focusing on poultry, the overarching aim of this study was to highlight possible Salmonella transmissions across the food chain (FC). For this purpose, firstly, the prevalence patterns of Salmonella (targeted and the most prevalent non-targeted) serotypes along the FC were described over time. Secondly, the effectiveness of the control measures against vertical transmission (breeders to 1-day-old broiler and layer chicks) was indirectly assessed by looking into the odds of targeted serotypes detection. Thirdly, it was appraised if Salmonella prevalence can significantly increase during broilers and layers production. In addition, it was tested if being tested negative at the end of production in broilers when tested positive at the entrance is serotype dependent (targeted vs. non-targeted serotypes). Results showed that, firstly, the prevalence patterns of the listed serotypes were inconstant over time and across the FC. Secondly, the odds of Salmonella targeted serotype detection in 1-day-old broiler and in 1-day-old layer flocks were lower than in breeder flocks while, thirdly, infection during broiler and layer production can lead to significant increase in positivity in subsequent samples. Finally, being infected by a targeted or by non-targeted serotype at the entrance of the flock poorly reflects the Salmonella status at the end of production. Note that this study did not make a distinction between the different sources of contamination and the effects of sampling methods and isolation methods should be subject to further investigation.

Viral metagenomics reveals persistent as well as dietary acquired viruses in Antarctic fur seals

Viruses linked to animals inhabiting Antarctic latitudes remain poorly studied. Remote environments hosting large pinniped populations may be prone to exposure of immunologically naïve animals to new infectious agents due to increasing human presence or introduction of new animal species. Antarctic fur seals (Arctocephalus gazella) inhabiting the Western Antarctic Peninsula and the South Shetland Islands are challenged because of climate change and increased anthropogenic activity. In the present study, the fecal and serum virome of A. gazella was characterized by applying target enrichment next generation sequencing. The resulting viromes were dominated by CRESS-DNA sequences. Viruses known to infect vertebrate and invertebrate hosts were also observed in fecal samples. Fur seal picornavirus was present in all the fecal pools studied suggesting it is a prevalent virus in these species. Six different viruses presenting similarities with previously described A. gazella viruses or other otariids and mammal viruses were identified as potential new A. gazella viruses. Also, diet-derived viruses such as crustacean viruses were present in fecal content. Penguin viruses, but not fish viruses, were also detected. Obtained results contribute to a better understanding of the viral community present in these species, which is relevant for its conservation.

Eurasian griffon vultures carry widespread antimicrobial resistant Salmonella and Campylobacter of public health concern

The global emergence of antimicrobial-resistant (AMR) strains of Salmonella and Campylobacter is a serious public health concern. Both bacteria are leading causes of human gastrointestinal foodborne infections and the two most reported zoonoses in the European Union. By feeding on livestock carcasses, especially from intensive farming, as well as on landfill sites, obligate avian scavengers can become infected with zoonotic pathogens and AMR strains, and can be considered large-scale sentinels of the environmental burden. In this study, we assessed the occurrence and AMR of Salmonella spp. and Campylobacter spp. in 218 Eurasian griffon vultures (Gyps fulvus) captured in north-eastern Spain. We isolated Salmonella from 8.1 % of individuals and Campylobacter lari from 4.7 %. Among the 10 different Salmonella serovars found, monophasic S. Typhimurium was the most frequent. Genotyping analysis revealed same strains of monophasic S. Typhimurium shared by gulls, livestock and humans. Isolates from both bacterial species presented AMR to important antimicrobials (tetracyclines, fluoroquinolones and β-lactams). In conclusion, this study shows that Eurasian griffon vultures in north-eastern Spain are carriers of widespread AMR zoonotic Salmonella and Campylobacter. More comprehensive analyses are still needed to understand the potential risk of spill-over from those wild birds to humans.

Assessing the risk of human-to-wildlife pathogen transmission for conservation and public health

The SARS-CoV-2 pandemic has led to increased concern over transmission of pathogens from humans to animals, and its potential to threaten conservation and public health. To assess this threat, we reviewed published evidence of human-to-wildlife transmission events, with a focus on how such events could threaten animal and human health. We identified 97 verified examples, involving a wide range of pathogens; however, reported hosts were mostly non-human primates or large, long-lived captive animals. Relatively few documented examples resulted in morbidity and mortality, and very few led to maintenance of a human pathogen in a new reservoir or subsequent "secondary spillover" back into humans. We discuss limitations in the literature surrounding these phenomena, including strong evidence of sampling bias towards non-human primates and human-proximate mammals and the possibility of systematic bias against reporting human parasites in wildlife, both of which limit our ability to assess the risk of human-to-wildlife pathogen transmission. We outline how researchers can collect experimental and observational evidence that will expand our capacity for risk assessment for human-to-wildlife pathogen transmission.

Antimicrobial resistance in Antarctica: is it still a pristine environment?

Although the rapid spread of antimicrobial resistance (AMR), particularly in relation to clinical settings, is causing concern in many regions of the globe, remote, extreme environments, such as Antarctica, are thought to be relatively free from the negative impact of human activities. In fact, Antarctica is often perceived as the last pristine continent on Earth. Such remote regions, which are assumed to have very low levels of AMR due to limited human activity, represent potential model environments to understand the mechanisms and interactions underpinning the early stages of evolution, de novo development, acquisition and transmission of AMR. Antarctica, with its defined zones of human colonisation (centred around scientific research stations) and large populations of migratory birds and animals, also has great potential with regard to mapping and understanding the spread of early-stage zoonotic interactions. However, to date, studies of AMR in Antarctica are limited. Here, we survey the current literature focussing on the following: i) Dissection of human-introduced AMR versus naturally occurring AMR, based on the premise that multiple drug resistance and resistance to synthetic antibiotics not yet found in nature are the results of human contamination ii) The potential role of endemic wildlife in AMR spread There is clear evidence for greater concentrations of AMR around research stations, and although data show reverse zoonosis of the characteristic human gut bacteria to endemic wildlife, AMR within birds and seals appears to be very low, albeit on limited samplings. Furthermore, areas where there is little, to no, human activity still appear to be free from anthropogenically introduced AMR. However, a comprehensive assessment of AMR levels in Antarctica is virtually impossible on current data due to the wide variation in reporting standards and methodologies used and poor geographical coverage. Thus, future studies should engage directly with policymakers to promote the implementation of continent-wide AMR reporting standards. The development of such standards alongside a centralised reporting system would provide baseline data to feedback directly into wastewater treatment policies for the Antarctic Treaty Area to help preserve this relatively pristine environment. Video Abstract.

Dissemination of multidrug resistant bacteria to the polar environment - Role of the longest migratory bird Arctic tern (Sterna paradisaea)

The ever-increasing prevalence of antibiotic-resistant bacteria(ARB), primarily due to the frequent use and misuse of antibiotics, is an issue of serious global concern. Migratory birds have a significant role in dissemination of ARB, as they acquire resistant bacteria from reservoirs and transport them to other environments which are relatively less influenced by anthropogenically. We have investigated the prevalence of ARB in a long-distance migratory bird, the Arctic tern (Sterna paradisaea) captured from the Svalbard Archipelago. The birds were tagged with geolocators to track their extraordinary long migration, and the cloacal samples were collected before the migration and after the migration by recapturing the same birds. The tracking of 12 birds revealed that during the annual cycle they underwent a total of 166 stopovers (11-18, mean = 3.8) and recovery points along the Atlantic Ocean. Twelve major bacterial genera were identified from Arctic tern cloacal samples, which are dominated by Staphylococcus spp. and Aerococcus spp. The bacterial isolates showed resistance against 16 antibiotics (before migration) and 17 antibiotics (after migration) out of 17 antibiotics tested. Resistance to β-lactam and quinolone class of antibiotics were frequent among the bacteria. The study highlights the potential role of Arctic tern in the dissemination of multidrug resistant bacteria across far and wide destinations, especially to the polar environments.

Planetary Biosecurity: Applying Invasion Science to Prevent Biological Contamination from Space Travel

As plans for space exploration and commercial use expand rapidly, biosecurity measures and risk assessments that inform them must adapt. Sophisticated protocols are required to prevent biological contamination of extraterrestrial environments from Earth and vice versa. Such protocols should be informed by research on biological invasions—human-assisted spread of organisms into novel environments—which has revealed, inter alia, that (1) invasion risk is driven by the timing and frequency of introduction events, whose control requires addressing the least secure human activities associated with organismal transport; (2) invasions and their impacts are difficult to predict, because these phenomena are governed by context dependencies involving traits of the organism and the receiving environment; and (3) early detection and rapid response are crucial for prevention but undermined by taxonomic methods that fail to recognize what is “alien” versus what is native. Collaboration among astrobiologists, invasion biologists, and policymakers could greatly enhance planetary biosecurity protocols.

In-depth farm investigations and an exploratory risk factor analysis for the presence of Salmonella on broiler farms in Great Britain

Salmonella is a major cause of foodborne illness across Europe but there has been little recent research on its control in broiler production in Great Britain. Investigations of Salmonella presence on 20 broiler farms and a separate exploratory risk factor analysis involving 36 Salmonella-positive farms and 22 Salmonella-negative farms were carried out to investigate Salmonella contamination and control on broiler farms in Great Britain. Sources of Salmonella persistence on farm and potential risk factors for on-farm contamination were identified, enabling provision of up-to-date advice on Salmonella control to farmers. Twenty broiler farms across England and Wales were intensively sampled over time. Most farms were included in the study after routine testing as part of the Salmonella National Control Programmes (NCPs) identified regulated Salmonella serovars or potential associations with outbreak cases of significance for human health. Across all farms and visits, the highest proportion of Salmonella-positive samples were from areas exterior to broiler houses compared to anterooms or house interiors. Exterior Salmonella-positive samples were primarily collected from the immediate areas around the houses, with the highest proportions being from drainage, farm tracks/driveways, and pooled water. Elimination of Salmonella was variable but was most successful inside affected houses (compared to exterior areas) and for regulated Salmonella serovars under the Salmonella NCPs and high priority Salmonella strains with multi-drug resistances. It is likely that the financial and reputational concerns associated with regulated Salmonella serovars and those of greater public health significance underlie the reason that these serovars were more effectively controlled at farm level, as effective elimination of Salmonella can involve a considerable investment in infrastructure, time and resources. Without perceived direct benefits in eliminating non-regulated Salmonella serovars at farm level it can be challenging to maintain the required motivation and investment. A separate farm-level risk factor analysis was carried out using data collected from 58 broiler farms representing six GB broiler companies. Risk of testing positive for Salmonella via NCP sampling in the previous year was greater in the absence of house-specific anterooms and if at least some poultry houses were surrounded by soil/grass compared to if all were surrounded by concrete or a mixture of concrete and stones/gravel. Odds of testing positive for Salmonella in the previous year was also greater for farms whose maximum holding capacity was >100,000 birds, and farms where the usual number of visitors per day was 0-1 compared to 2-3. The analysis was exploratory and caution is required with interpretation, but results provide preliminary insight into aspects of farm management that may be important, practicable targets for Salmonella control on broiler farms in GB.

More-Than-Human and Deeply Human Perspectives on COVID-19

This multi-authored contribution explores what the COVID-19 pandemic demands of critical inquiry with a focus on the more-than-human. We show how COVID-19 is a complex series of multispecies encounters shaped by humans, non-human animals, and of course viruses. Central to these encounters is a politics of difference in which certain human lives are protected and helped to flourish while others, both human and animal, are forgotten if not sacrificed. Such difference encompasses practices of racialisation and racism, healthcare austerity, the circulation of capital, border-making, intervention into non-human nature, wildlife trade bans, anthropocentrism, and the exploitation of animal test subjects. The contributions highlight how COVID-19 provides a needed opportunity to unite new materialist and anti-racist, anti-colonial scholarship as well as reimagine more radically sustainable multispecies futures. This requires embracing anti-colonial humility, confronting debts owed to lab animal frontline workers, and rethinking economic systems that helped unleash COVID-19 and ensured it became a disaster.

Salmonella spp. profiles isolated from seabird samples from the Brazilian coast

In view of growing concerns, in a One Health context, regarding the transport and dissemination of pathogenic microorganisms among seabirds and other vertebrate animals, including humans, the aim of this study was to identify Salmonella spp. in stranded and non-stranded resident and migratory wild seabirds from the Brazilian coast. Antimicrobial susceptibility and molecular profiles, quinolone resistance genes and antigenic characterization of the isolates were also carried out. Fresh faeces and cloacal swabs were obtained totaling 122 seabirds sampled throughout different Brazilian coast regions. At the laboratory, sample culturing, Salmonella spp. isolation and biochemical identification were performed, followed by antigenic profile identification by serum agglutination, susceptibility profile characterization by the agar disc diffusion technique, detection of quinolone resistance genes (qnrA, qnrB, qnrS) using the multiplex polymerase chain reaction technique (multiplex PCR) and, finally, isolates profiles identification by pulsed field gel electrophoresis (PFGE). Salmonella enterica subsp. enterica was identified in 7% of the studied birds, comprising three different serovars: Panama (63 %), Typhimurium (25 %) and Newport (13 %). The most important findings reported herein are the first description of Salmonella panama in seabirds and the totality of isolates being resistant (or intermediate) to at least one tested antimicrobial, with emphasis on quinolone resistance. The molecular results suggest that the observed resistance cannot be explained by the presence of plasmid-mediated quinolone resistance genes. The PFGE suggests that the Panama and Newport profiles detected herein are not yet widespread in Brazil, unlike Typhimurium, which is already well distributed throughout the country. Considering this finding, we suggest that seabirds are an important link in the epidemiological chain of this serovar. The monitoring of these bacteria in seabirds, as well as of their susceptibility profiles to antimicrobials, must be continuous, strengthening the role of these animals as environmental health indicators and sentinels.

The ocular pyogranulomatous lesion in a Gentoo penguin (Pygoscelis papua) from the Antarctic Peninsula: evaluation of microbiological and histopathological analysis outcomes

In this study, it was aimed to present the results of microbiological, cytological, histopathological, and immunohistochemical analyses of ocular samples from an Antarctic (Ardley Island, King George Island) Gentoo penguin chick (Pygoscelis papua) with a pyogranulomatous lesion in the right eye. Samples were taken from both the healthy left eye and the lesion in the right eye. Conventional culture methods and phenotypic and molecular tests were used for bacterial isolation and identification, respectively. None of the isolates could be identified phenotypically. As a result, four of the five isolates obtained from the right eye were considered to belong to putative novel bacterial species and taxa as their similarity to GenBank data was below 98.75%. The isolates were considered to be Pasteurellaceae bacterium, Corynebacterium ciconiae, Cardiobacteriaceae bacterium, Actinomyces sp., and Dermabacteraceae bacterium. The only isolate from the left eye was identified as Psychrobacter pygoscelis. The cytological analysis demonstrated cell infiltrates composed mostly of degenerate heterophils, reactive macrophages, plasma cells, lymphocytes, and eosinophils. Based on histopathological findings, the lesion was defined as a typical pyogranulomatous lesion. Immunohistochemistry demonstrated that the granuloma was positive for TNF-α, IL-4, MMP-9, IL-1β, and IL-6. This is the first documented report of the unilateral pyogranulomatous ocular lesion in a Gentoo penguin chick, living in its natural habitat in Antarctica. This report also describes the isolation of four bacteria from the infected eye, which are considered to belong to novel Genus, species, or taxa. The primary bacterial pathogen that caused the ocular lesion was not able to be detected and remains unclear.

Multidrug-Resistant Phenotypes of Escherichia coli Isolates in Wild Canarian Egyptian Vultures (Neophron percnopterus majorensis)

Simple Summary

Increasing antimicrobial resistance is a global problem for both human and animal health. Escherichia coli is frequently used as a “sentinel” for antimicrobial resistance and as an indicator of faecal contamination of the environment. This study is a characterisation of the antimicrobial resistance phenotypes of E. coli isolates obtained from cloacal samples of Canarian Egyptian vultures. A total of 65 chickens and 38 adult and immature birds were studied. Antimicrobial susceptibility to 16 antibiotics of 12 different categories was determined in 103 E. coli isolates. We found a 39.8% prevalence of multidrug-resistant (MDR) E. coli. Almost all MDR phenotypes found included resistance to tetracycline, an antibiotic widely used in veterinary medicine. Resistance has also been found to chloramphenicol (13 MDR phenotypes), imipenem (5 MDR phenotypes) and others. Wild birds can act as reservoirs and disseminators of MDR E. coli, transferring them via faeces to the environment, feed or water. Our results highlight the need to minimise exposure of wild birds to antimicrobials from human activities to avoid the spread of antimicrobial resistance.

Abstract

The presence of multidrug-resistant (MDR) Escherichia coli in cloacal samples from Canarian Egyptian vultures was investigated. Samples were obtained from chicks (n = 65) and from adults and immature birds (n = 38). Antimicrobial susceptibility to 16 antibiotics included in 12 different categories was determined for 103 E. coli isolates. MDR was defined as acquired non-susceptibility to at least one agent in three or more antimicrobial categories. Forty-seven different resistance phenotypes were detected: 31 MDR (41 isolates) and 16 non-MDR (62 isolates). One isolate was resistant to all 12 antimicrobial categories and 2 phenotypes included resistance to 9 antimicrobial categories. Imipenem resistance was included in five MDR phenotypes, corresponding to five different isolates. Statistically significant differences in prevalence of MDR-phenotypes were found between chicks in nests and the rest of the animals, probably due to the shorter exposure time of chicks to antimicrobials. The main risk derived from MDR bacteria in scavengers is that it threatens the treatment of wild animals in rescue centres and could be transferred to other animals in the facilities. In addition to this, it could pose a health risk to veterinarians or other staff involved in wildlife protection programmes.

Antimicrobial Resistance in Pasteurellaceae Isolates from Pyrenean Chamois (Rupicapra pyrenaica) and Domestic Sheep in an Alpine Ecosystem

Antimicrobial resistance (AMR) has spread worldwide due to the inappropriate use of antimicrobial drugs in human and veterinary medicine, becoming a public health problem. However, little is known about its occurrence and maintenance in wild animals, and very few studies have been carried out in ecosystems subjected to low human pressure. In our study, nasal and lung swabs were collected from hunted Pyrenean chamois (Rupicapra pyrenaica), and nasal swabs from sympatric domestic sheep were also collected. The swabs were cultured in agar plates to obtain bacterial isolates from the Pasteurellaceae family. The presence of AMR was assessed in a total of 28 Pasteurellaceae isolates from 45 Pyrenean chamois, and 9 isolates from sympatric domestic sheep found in the National Hunting Reserve of Freser-Setcases (Northeastern Pyrenees, Spain). The isolates belonged to one of the following three species: Pasteurella multocida, Mannheimia haemolytica and Bibersteinia trehalosi. Some P. multocida and M. haemolytica isolates tested positive for AMR. The statistical analysis revealed no differences between the AMR levels from chamois and domestic sheep isolates. However, one P. multocida of chamois origin presented resistance to cephalosporins and fluoroquinolones, which are antibiotics of critical importance for human health. Further studies are required to elucidate potential routes of dissemination of AMR genes in natural environments and assess any significant persistence in wildlife to design risk mitigation actions.

Protected but not from Contamination: Antimicrobial Resistance Profiles of Bacteria from Birds in a Ghanaian Forest Protected Area

Resistance to antimicrobial agents is a growing concern in public health. It has been reported in wildlife from several places in the world though wild animals are not normally exposed to clinically used antimicrobial agents. Despite this, very little research has been done in Ghana to determine antimicrobial resistance in wild animals, particularly those in protected areas. In this study, the presence of colistin resistant and multidrug resistant (MDR) gram-negative bacteria in cloacal swabs of wild birds captured in a Ghanaian forest protected area were evaluated. A total of 195 isolates from 138 individual birds were obtained, identified and tested for resistance to colistin. The colistin-resistant isolates were subsequently tested for multidrug resistance to 4 other antimicrobial agents (Oxytetracycline, Streptomycin, Ampicillin and Ciprofloxacin). Colistin resistance was observed in 6.5% (9/138) of the birds and this was seen in only birds that were sampled close to the reception area of the protected area. About 50% of the colistin-resistant isolates were multidrug resistant. AMR isolates were obtained from birds that have been documented to show an insectivorous or omnivorous feeding preference. Data obtained from the study suggests that AMR and MDR occurred in wild birds from the Conservation Area and supports the claim that proximity to human impacted habitats (settlements/farmlands) increased the likelihood of carriage of AMR. Though the routes of transmission remain unclear, there is potential for spread from the wild birds to other wild/domestic animals and possibly back to humans.

Prokaryotic Diversity and Metabolically Active Communities in Brines from Two Perennially Ice-Covered Antarctic Lakes

The genomic diversity of bacteria and archaea in brines (BC1, BC2, and BC3) from two adjacent and perennially frozen Antarctic lakes (L16 and L-2) in the Boulder Clay (BC) area was investigated together with the metabolically active fraction of both communities, by analyzing the bulk rRNA as a general marker of metabolic activity. Although similar bacterial and archaeal assemblages were observed at phylum level, differences were encountered when considering the distribution in species. Overall, the total bacterial communities were dominated by Bacteroidetes. A massive occurrence of flavobacterial sequences was observed within the metabolically active bacterial communities of the BC1 brine, whereas the active fractions in BC2 and BC3 strongly differed from the bulk communities being dominated by Betaproteobacteria (mainly Hydrogenophaga members). The BC lakes also hosted sequences of the most thermally tolerant archaea, also related to well-known hyperthermophiles. Interestingly, RNA sequences of the hyperthermophilic genus Ferroglobus were retrieved in all brine samples. Finally, a high abundance of the strictly anaerobic methanogens (such as Methanosarcina members) within the active community suggests that anoxic conditions might occur in the lake brines. Our findings indicate perennially ice-covered Antarctic lakes as plausible terrestrial candidates for the study of the potential for extant life on different bodies of our solar system.

Assessing the role of livestock and sympatric wild ruminants in spreading antimicrobial resistant Campylobacter and Salmonella in alpine ecosystems

Background

Livestock play an important role as reservoir of enteric pathogens and antimicrobial resistance (AMR), a health and economic concern worldwide. However, little is known regarding the transmission and maintenance of these pathogens at the wildlife-livestock interface. In this study, we assessed the occurrence, genetic diversity and AMR of Campylobacter spp. and Salmonella spp. shed by sympatric free-ranging livestock and a wild herbivore in an alpine ecosystem.

Results

Campylobacter spp. was isolated from 23.3 % of cattle and 7.7 % of sheep but was not isolated from horses nor Pyrenean chamois (Rupicapra pyrenaica). Campylobacter jejuni was the most frequent species. A high genetic diversity and certain host specificity of C. jejuni isolates was observed. The main AMR detected in Campylobacter isolates was to nalidixic acid (88.2 %), ciprofloxacin (82.4 %) and tetracycline (82.4 %); only 11.7 % of the isolates were pan-susceptible and 17.6 % were multi-resistant. Salmonella ser. Newport was isolated only from one Pyrenean chamois and was pan-susceptible.

Conclusions

Results show that free-ranging cattle and sheep are spreaders of Campylobacter as well as their AMR strains in the alpine environment. Therefore, contaminated alpine pastures or streams may constitute a source for the dissemination of AMR enteropathogens. However, apparently, alpine wild ungulates such as Pyrenean chamois play a negligible role in the epidemiology of zoonotic enteropathogens and AMR, and are not potential bioindicators of the burden of alpine environments.

Risk assessment of SARS-CoV-2 in Antarctic wildlife

The coronavirus disease 2019 (COVID-19) pandemic is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This pathogen has spread rapidly across the world, causing high numbers of deaths and significant social and economic impacts. SARS-CoV-2 is a novel coronavirus with a suggested zoonotic origin with the potential for cross-species transmission among animals. Antarctica can be considered the only continent free of SARS-CoV-2. Therefore, concerns have been expressed regarding the potential human introduction of this virus to the continent through the activities of research or tourism to minimise the effects on human health, and the potential for virus transmission to Antarctic wildlife. We assess the reverse-zoonotic transmission risk to Antarctic wildlife by considering the available information on host susceptibility, dynamics of the infection in humans, and contact interactions between humans and Antarctic wildlife. The environmental conditions in Antarctica seem to be favourable for the virus stability. Indoor spaces such as those at research stations, research vessels or tourist cruise ships could allow for more transmission among humans and depending on their movements between different locations the virus could be spread across the continent. Among Antarctic wildlife previous in silico analyses suggested that cetaceans are at greater risk of infection whereas seals and birds appear to be at a low infection risk. However, caution needed until further research is carried out and consequently, the precautionary principle should be applied. Field researchers handling animals are identified as the human group posing the highest risk of transmission to animals while tourists and other personnel pose a significant risk only when in close proximity (< 5 m) to Antarctic fauna. We highlight measures to reduce the risk as well as identify of knowledge gaps related to this issue.

Gut microbiome is affected by inter-sexual and inter-seasonal variation in diet for thick-billed murres (Uria lomvia)

The role of the gut microbiome is increasingly being recognized by health scientists and veterinarians, yet its role in wild animals remains understudied. Variations in the gut microbiome could be the result of differential diets among individuals, such as variation between sexes, across seasons, or across reproductive stages. We evaluated the hypothesis that diet alters the avian gut microbiome using stable isotope analysis (SIA) and 16S rRNA gene sequencing. We present the first description of the thick-billed murre (Uria lomvia) fecal microbiome. The murre microbiome was dominated by bacteria from the genus Catellicoccus, ubiquitous in the guts of many seabirds. Microbiome variation was explained by murre diet in terms of proportion of littoral carbon, trophic position, and sulfur isotopes, especially for the classes Actinobacteria, Bacilli, Bacteroidia, Clostridia, Alphaproteobacteria, and Gammaproteobacteria. We also observed differences in the abundance of bacterial genera such as Catellicoccus and Cetobacterium between sexes and reproductive stages. These results are in accordance with behavioural observations of changes in diet between sexes and across the reproductive season. We concluded that the observed variation in the gut microbiome may be caused by individual prey specialization and may also be reinforced by sexual and reproductive stage differences in diet.

Occurrence and antibacterial resistance of culturable antibiotic-resistant bacteria in the Fildes Peninsula, Antarctica

Quantifying the occurrence of Antarctic antibiotic-resistant bacteria (ARB) is essential for assessing the level of pollution and assessing the "baseline" or background level of ARB in human uninhabited environments. Animal feces, soil, and sediments were sampled from Fildes Peninsula. The abundance of sulfamethazine- and ciprofloxacin-resistance bacteria and antibotic resistance genes (ARGs) within ARB were investigated. The results showed Ciprofloxacin- and Sulfamethazine-resistant bacteria isolated from samples accounted for the highest abundances of 30 CFU/g and 79.8 CFU/g, respectively. The dominant genus of Sulfamethazine-and quinolone-resistance bacteria was Pseudomonas and Arthrobacter, respectively. 106 ARGs were detected from ARB. Strong positive correlations between mobile genetic elements (MGEs) and ARGs were found, what is relatively novel observation that the mechanism is confirmed to also occur in the Antarctic. This study reveals the compositional characteristics of ARGs of strains in Antarctic, providing support for the source of Antarctic antibiotic resistance and drug resistance mechanisms.

Zoonotic Diseases: Etiology, Impact, and Control

Most humans are in contact with animals in a way or another. A zoonotic disease is a disease or infection that can be transmitted naturally from vertebrate animals to humans or from humans to vertebrate animals. More than 60% of human pathogens are zoonotic in origin. This includes a wide variety of bacteria, viruses, fungi, protozoa, parasites, and other pathogens. Factors such as climate change, urbanization, animal migration and trade, travel and tourism, vector biology, anthropogenic factors, and natural factors have greatly influenced the emergence, re-emergence, distribution, and patterns of zoonoses. As time goes on, there are more emerging and re-emerging zoonotic diseases. In this review, we reviewed the etiology of major zoonotic diseases, their impact on human health, and control measures for better management. We also highlighted COVID-19, a newly emerging zoonotic disease of likely bat origin that has affected millions of humans along with devastating global consequences. The implementation of One Health measures is highly recommended for the effective prevention and control of possible zoonosis.

International clones of extended-spectrum β-lactamase (CTX-M)-producing Escherichia coli in peri-urban wild animals, Brazil

CTX-M-type extended-spectrum β-lactamase (ESBL)-producing Escherichia coli clones have been increasingly reported worldwide. In this regard, although discussions of transmission routes of these bacteria are in evidence, molecular data are lacking to elucidate the epidemiological impacts of ESBL producers in wild animals. In this study, we have screened 90 wild animals living in a surrounding area of São Paulo, the largest metropolitan city in South America, to monitor the presence of multidrug-resistant (MDR) Gram-negative bacteria. Using a genomic approach, we have analysed eight ceftriaxone-resistant E. coli. Resistome analyses revealed that all E. coli strains carried blaCTX-M -type genes, prevalent in human infections, besides other clinically relevant resistance genes to aminoglycosides, β-lactams, phenicols, tetracyclines, sulphonamides, trimethoprim, fosfomycin and quinolones. Additionally, E. coli strains belonged to international sequence types (STs) ST38, ST58, ST212, ST744, ST1158 and ST1251, and carried several virulence-associated genes. Our findings suggest spread and adaptation of international clones of CTX-M-producing E. coli beyond urban settings, including wildlife from shared environments.

Evidence of Pathogen-Induced Immunogenetic Selection across the Large Geographic Range of a Wild Seabird

Over evolutionary time, pathogen challenge shapes the immune phenotype of the host to better respond to an incipient threat. The extent and direction of this selection pressure depend on the local pathogen composition, which is in turn determined by biotic and abiotic features of the environment. However, little is known about adaptation to local pathogen threats in wild animals. The Gentoo penguin (Pygoscelis papua) is a species complex that lends itself to the study of immune adaptation because of its circumpolar distribution over a large latitudinal range, with little or no admixture between different clades. In this study, we examine the diversity in a key family of innate immune genes-the Toll-like receptors (TLRs)-across the range of the Gentoo penguin. The three TLRs that we investigated present varying levels of diversity, with TLR4 and TLR5 greatly exceeding the diversity of TLR7. We present evidence of positive selection in TLR4 and TLR5, which points to pathogen-driven adaptation to the local pathogen milieu. Finally, we demonstrate that two positively selected cosegregating sites in TLR5 are sufficient to alter the responsiveness of the receptor to its bacterial ligand, flagellin. Taken together, these results suggest that Gentoo penguins have experienced distinct pathogen-driven selection pressures in different environments, which may be important given the role of the Gentoo penguin as a sentinel species in some of the world's most rapidly changing environments.

Applying science to pressing conservation needs for penguins

More than half of the world's 18 penguin species are declining. We, the Steering Committee of the International Union for Conservation of Nature Species Survival Commission Penguin Specialist Group, determined that the penguin species in most critical need of conservation action are African penguin (Spheniscus demersus), Galápagos penguin (Spheniscus mendiculus), and Yellow-eyed penguin (Megadyptes antipodes). Due to small or rapidly declining populations, these species require immediate scientific collaboration and policy intervention. We also used a pairwise-ranking approach to prioritize research and conservation needs for all penguins. Among the 12 cross-taxa research areas we identified, we ranked quantifying population trends, estimating demographic rates, forecasting environmental patterns of change, and improving the knowledge of fisheries interactions as the highest priorities. The highest ranked conservation needs were to enhance marine spatial planning, improve stakeholder engagement, and develop disaster-management and species-specific action plans. We concurred that, to improve the translation of science into effective conservation for penguins, the scientific community and funding bodies must recognize the importance of and support long-term research; research on and conservation of penguins must expand its focus to include the nonbreeding season and juvenile stage; marine reserves must be designed at ecologically appropriate spatial and temporal scales; and communication between scientists and decision makers must be improved with the help of individual scientists and interdisciplinary working groups.

Pathogen transmission risk by opportunistic gulls moving across human landscapes

Wildlife that exploit human-made habitats hosts and spreads bacterial pathogens. This shapes the epidemiology of infectious diseases and facilitates pathogen spill-over between wildlife and humans. This is a global problem, yet little is known about the dissemination potential of pathogen-infected animals. By combining molecular pathogen diagnosis with GPS tracking of pathogen-infected gulls, we show how this knowledge gap could be filled at regional scales. Specifically, we generated pathogen risk maps of Salmonella, Campylobacter and Chlamydia based on the spatial movements of pathogen-infected yellow-legged gulls (Larus michahellis) equipped with GPS recorders. Also, crossing this spatial information with habitat information, we identified critical habitats for the potential transmission of these bacteria in southern Europe. The use of human-made habitats by infected-gulls could potentially increase the potential risk of direct and indirect bidirectional transmission of pathogens between humans and wildlife. Our findings show that pathogen-infected wildlife equipped with GPS recorders can provide accurate information on the spatial spread risk for zoonotic bacteria. Integration of GPS-tracking with classical epidemiological approaches may help to improve zoonosis surveillance and control programs.

Meta-transcriptomics reveals a diverse antibiotic resistance gene pool in avian microbiomes

BACKGROUND

Antibiotic resistance is rendering common bacterial infections untreatable. Wildlife can incorporate and disperse antibiotic-resistant bacteria in the environment, such as water systems, which in turn serve as reservoirs of resistance genes for human pathogens. Anthropogenic activity may contribute to the spread of bacterial resistance cycling through natural environments, including through the release of human waste, as sewage treatment only partially removes antibiotic-resistant bacteria. However, empirical data supporting these effects are currently limited. Here we used bulk RNA-sequencing (meta-transcriptomics) to assess the diversity and expression levels of functionally viable resistance genes in the gut microbiome of birds with aquatic habits in diverse locations.

RESULTS

We found antibiotic resistance genes in birds from all localities, from penguins in Antarctica to ducks in a wastewater treatment plant in Australia. Comparative analysis revealed that birds feeding at the wastewater treatment plant carried the greatest resistance gene burden, including genes typically associated with multidrug resistance plasmids as the aac(6)-Ib-cr gene. Differences in resistance gene burden also reflected aspects of bird ecology, taxonomy, and microbial function. Notably, ducks, which feed by dabbling, carried a higher abundance and diversity of resistance genes than turnstones, avocets, and penguins, which usually prey on more pristine waters.

CONCLUSIONS

These transcriptome data suggest that human waste, even if it undergoes treatment, might contribute to the spread of antibiotic resistance genes to the wild. Differences in microbiome functioning across different bird lineages may also play a role in the antibiotic resistance burden carried by wild birds. In summary, we reveal the complex factors explaining the distribution of resistance genes and their exchange routes between humans and wildlife, and show that meta-transcriptomics is a valuable tool to access functional resistance genes in whole microbial communities.

Salmonella control in poultry flocks and its public health impact

An increase in confirmed human salmonellosis cases in the EU after 2014 triggered investigation of contributory factors and control options in poultry production. Reconsideration of the five current target serovars for breeding hens showed that there is justification for retaining Salmonella Enteritidis, Salmonella Typhimurium (including monophasic variants) and Salmonella Infantis, while Salmonella Virchow and Salmonella Hadar could be replaced by Salmonella Kentucky and either Salmonella Heidelberg, Salmonella Thompson or a variable serovar in national prevalence targets. However, a target that incorporates all serovars is expected to be more effective as the most relevant serovars in breeding flocks vary between Member State (MS) and over time. Achievement of a 1% target for the current target serovars in laying hen flocks is estimated to be reduced by 254,400 CrI95[98,540; 602,700] compared to the situation in 2016. This translates to a reduction of 53.4% CrI95[39.1; 65.7] considering the layer-associated human salmonellosis true cases and 6.2% considering the overall human salmonellosis true cases in the 23 MSs included in attribution modelling. A review of risk factors for Salmonella in laying hens revealed that overall evidence points to a lower occurrence in non-cage compared to cage systems. A conclusion on the effect of outdoor access or impact of the shift from conventional to enriched cages could not be reached. A similar review for broiler chickens concluded that the evidence that outdoor access affects the occurrence of Salmonella is inconclusive. There is conclusive evidence that an increased stocking density, larger farms and stress result in increased occurrence, persistence and spread of Salmonella in laying hen flocks. Based on scientific evidence, an impact of Salmonella control programmes, apart from general hygiene procedures, on the prevalence of Campylobacter in broiler flocks at the holding and on broiler meat at the end of the slaughter process is not expected.