Improving the sensitivity of gastrointestinal helminth detection using the Mini-FLOTAC technique in wild birds.

High-performance-validated tests are essential for successful epidemiological monitoring, surveillance of parasitic infections, and comparative studies in wildlife populations. The Mini-FLOTAC is a novel flotation-based technique for the sensitive detection and quantification of gastrointestinal parasites that is recently being explored for use in wildlife. A limitation of any flotation-based copromicroscopic method is the selection of the flotation solution (FS), which might influence the performance of the test. However, no study has compared the influence of using different FS in the Mini-FLOTAC technique for parasite detection in wild birds. Here, we evaluated the diagnostic performance of the Mini-FLOTAC in three waterbird host species using two widely used FS: saturated salt (NaCl; specific gravity 1.20) and saturated zinc sulfate (ZnSO4; specific gravity 1.35). One hundred fresh fecal samples were analyzed for parasite fecal egg counts (FEC). Regardless of the host species, fecal samples evaluated with the Mini-FLOTAC method using ZnSO4 resulted in a significantly higher detection rate and higher FEC of strongylid, capillarid, cestode, and trematode parasites, than samples analyzed with the NaCl solution. Our concise study demonstrated the importance of using an appropriate FS for the identification of parasite eggs in wildlife species, especially in hosts with an expected aggregated distribution and low parasite load such as waterbird hosts. The higher analytical sensitivity of the Mini-FLOTAC technique achieved with ZnSO4, and its applicability to fieldwork, highlights this method as a promising tool for the quantitative surveillance of parasite infections in wild bird populations.

Molecular identification and morphological variations of Dermacentor albipictus collected from two deer species in northern Mexico.

In total, 57 ticks were collected from six white-tailed deer (Odocoileus virginianus) and three mule deer (O. hemionus) in northern Mexico during the 2017, 2018 and 2019 hunting seasons. Morphological features of adult male and female ticks were observed and photographed using a stereo-microscope and scanning electron micrography. The ticks were identified as Dermacentor albipictus based on taxonomic keys. Molecular analysis using DNA amplification of the 16S rDNA and cytochrome oxidase 1 (COI) genes was employed to resolve the phylogenetic relationships from 18 strains of Dermacentor species. Bayesian phylogenetic analysis was performed in order to obtain a phylogenetic tree based on the concatenated sequence in the D. albipictus clade. The geometric morphometric analysis compared the body shape of ticks collected from specimens of two deer species by analyzing nine dorsal and ventral landmarks from both males and females. The results suggest that body shape variation in dorsal structures might be related to the host.

Novel Avulaviruses in Penguins, Antarctica.

We identified 3 novel and distinct avulaviruses from Gentoo penguins sampled in Antarctica. We isolated these viruses and sequenced their complete genomes; serologic assays demonstrated that the viruses do not have cross-reactivity between them. Our findings suggest that these 3 new viruses represent members of 3 novel avulavirus species.

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.

Abundance and associated factors of Amblyomma tigrinum (Acari: Ixodidae) infesting wild foxes in north-central Chile.

The tick Amblyomma tigrinum inhabits areas with diverse climatic conditions, with adult stages parasitizing wild canids, such as chilla (Lycalopex griseus) and culpeo (Lycalopex culpaeus) foxes. We described the infestation loads in wild foxes captured at three sites (periurban, rural and wild) through an anthropization gradient in north-central Chile. We tested whether local-scale environmental and/or individual host factors can predict tick abundance by using negative binomial models. During 2018-2020 (spring and summer), we captured 116 foxes (44 chillas and 72 culpeos), and 102 of them were infested with ticks (87.9%, CI=80.6-93.2%). We collected 996 A. tigrinum adult ticks, estimating a total mean abundance of 8.6±0.8 ticks/host. Periurban and rural foxes harbored greater tick loads than foxes from the wild site (2.34 and 1.71 greater, respectively) while tick abundance in summer decreased by up to 57% compared to spring. Tempered, more humid climate conditions of the periurban site could favor the development and survival of adults A. tigrinum; and ticks may have adopted a quiescent stage or similar survival mechanisms to cope with summer temperature increases related to the ongoing megadrought. Further studies are warranted to understand the underlying factors determining the life cycle of A. tigrinum at larger spatiotemporal scales.

Gastrointestinal parasites in wild rodents in Chiloé Island-Chile.

Gastrointestinal parasites are well-documented in small mammals from north-central Chile, but little is known about endoparasites of rodents in southern Chile. A survey was conducted between January and February 2018 to evaluate gastrointestinal parasites and risk factors of wild rodents that live in rural areas in Northern Chiloé Island, Chile. A total of 174 fecal samples from rodents of six native and one introduced species were collected and examined using the Mini-FLOTAC method. Also, 41 individuals of four native wild rodent species were examined furtherly to determinate adult parasites from gastrointestinal tracts. The overall prevalence of endoparasites was 89.65% (156). Helminth egg types included: Rodentolepis spp., Capillariidae, Trichuris sp., Syphacia sp., oxyurid-type eggs, Strongyloides sp., Spirurid-type eggs, Strongilid-type eggs, Moniliformis sp., and an unidentified nematode egg and larvae. Protozoa comprised coccidia, amoeba, and unidentified cysts. From necropsies, adult parasites involved Syphacia sp. Trichuris sp., Protospirura sp. and Physaloptera sp. In Abrothrix olivacea, individuals with low-body-mass index exhibited reduced infection probability for Spirurid-type and Strongilid-type eggs. Some parasites in this study may affect human health. In rural settings where environmental conditions are changing, more research should be undertaken to understand parasitic infections in wildlife and implications for public health and conservation.

Performance estimation of two in-house ELISA assays for COVID-19 surveillance through the combined detection of anti-SARS-CoV-2 IgA, IgM, and IgG immunoglobulin isotypes.

The main objective of this study was to estimate the performance, under local epidemiological conditions, of two in-house ELISA assays for the combined detection of anti-SARS-CoV-2 IgA, IgM, and IgG immunoglobulins. A total of 94 serum samples were used for the assessment, where 44 corresponded to sera collected before the pandemic (free of SARS-CoV-2 antibodies), and 50 sera were collected from confirmed COVID-19 patients admitted to the main public hospital in the city of Valdivia, southern Chile. The Nucleocapsid (Np) and the receptor-binding domain (RBD) proteins were separately used as antigens (Np and RBD ELISA, respectively) to assess their diagnostic performance. A receiver operating characteristic (ROC) analysis was performed to estimate the optical density (OD) cut-off that maximized the sensitivity (Se) and specificity (Sp) of the ELISA assays. Np ELISA had a mean Se of 94% (95% CI = 83.5-98.8%) and a mean Sp of 100% (95% CI = 92.0-100%), with an OD 450 nm positive cut-off value of 0.88. On the other hand, RBD ELISA presented a mean Se of 96% (95% CI = 86.3-99.5%) and a mean Sp of 90% (95% CI = 78.3-97.5%), with an OD 450 nm positive cut off value of 0.996. Non-significant differences were observed between the Se distributions of Np and RBD ELISAs, but the latter presented a significant lower Sp than Np ELISA. In parallel, collected sera were also analyzed using a commercial lateral flow chromatographic immunoassay (LFCI), to compare the performance of the in-house ELISA assays against a commercial test. The LFCI had a mean sensitivity of 94% (95% CI = 87.4-100%) and a mean specificity of 100% (95% CI = 100-100%). When compared to Np ELISA, non-significant differences were observed on the performance distributions. Conversely, RBD ELISA had a significant lower Sp than the LFCI. Although, Np ELISA presented a similar performance to the commercial test, this was 2.5 times cheaper than the LFCI assay (labor cost not considered). Thus, the in-house Np ELISA could be a suitable alternative tool, in resource limited environments, for the surveillance of SARS-CoV-2 infection, supporting further epidemiological studies.

Upraising a silent pollution: Antibiotic resistance at coastal environments and transference to long-distance migratory shorebirds.

Large amounts of antibiotics from different sources have been released into coastal environments, especially in high human-populated areas, but comprehensive studies of antibiotic footprint in wildlife are scarce. Here we assess occurrence of antibiotic resistant bacteria (ARB) and antibiotic resistance gene (ARG) both in sediments and gut microbiota of a long-distance migratory shorebird species in two coastal wetlands at a sparsely-populated area in Pacific Patagonian coasts with contrasting potential antibiotic sources, especially from aquaculture. We found 62% of sediment samples showing ARB, and ARGs similarly occurring in sediments at both bays. However multi-resistant ARB were found only at sediments in the bay surrounding aquaculture operations. An 87% of cloacal bird samples showed at least one ARB, with 63% being multi-resistant and some of them with a high potential pathogenicity. ARGs were present in 46% of the samples from birds, with similar multi-resistant frequencies among bays. Besides specific differences mainly associated to antibiotics used in salmon aquaculture that boosted ARB in sediments, ARB and ARGs occurrence was overall similar at two bays with contrasting main human activities, in spite of being a comparatively low human-populated area. Therefore, our results reinforce the idea that the antibiotic footprint may be widespread at a global scale and can extend beyond the geographical influence of antibiotic sources, especially at coastal environments where migratory shorebirds act both as reservoirs and potential spreaders of antibiotic resistance.

Circulation patterns of human seasonal Influenza A viruses in Chile before H1N1pdm09 pandemic.

Understanding the diversity and circulation dynamics of seasonal influenza viruses is key to public health decision-making. The limited genetic information of pre-pandemic seasonal IAVs in Chile has made it difficult to accurately reconstruct the phylogenetic relationships of these viruses within the country. The objective of this study was to determine the genetic diversity of pre-pandemic human seasonal IAVs in Chile. We sequenced the complete genome of 42 historic IAV obtained between 1996 and 2007. The phylogeny was determined using HA sequences and complemented using other segments. Time-scale phylogenetic analyses revealed that the diversity of pre-pandemic human seasonal IAVs in Chile was influenced by continuous introductions of new A/H1N1 and A/H3N2 lineages and constant viral exchange between Chile and other countries every year. These results provide important knowledge about genetic diversity and evolutionary patterns of pre-pandemic human seasonal IAVs in Chile, which can help design optimal surveillance systems and prevention strategies. However, future studies with current sequences should be conducted.

Case Report: First Report and Phylogenetic Analysis of Porcine Astroviruses in Chile.

Porcine Astrovirus (PoAstV) causes mild diarrhea in young pigs and is considered an emerging virus in the swine industry worldwide. PoAstV has high genetic diversity and has been classified into five genetic lineages, PoAstV1-5. In Chile, only human astroviruses have been reported. This study aimed to determine the presence and genetic diversity of PoAstV circulating in intensive pig farms in Chile. Seventeen Chilean intensive swine farms from Valparaíso, Metropolitana, O'Higgins, Ñuble and Araucanía regions were sampled. A selection of oral fluid and fecal material samples from 1-80 days-old pigs were collected and analyzed using next-generation sequencing. The circulation of PoAstV was confirmed in all studied farms. We obtained complete or partial sequences of PoAstV-2 (n = 3), PoAstV-4 (n = 2), and PoAstV-5 (n = 7). In 15 out of 17 farms, we detected more than one lineage co-circulating. Phylogenetic analyses grouped the seven PoAstV-5 strains in a monophyletic cluster, closely related to the United States PoAstV-5 strains. The three PoAstV-2 were located into two separate sub-clusters. PoAstV-4 sequences are also grouped in two different clusters, all related to Japanese strains. Thus, our results indicate that PoAstV circulates in Chile with high frequency and diversity. However, the lack of reference sequences impairs local evolution patterns establishment and regional comparisons. This is the first contribution of PoAstV genomes in Latin America; more studies are needed to understand the diversity and impact of PoAstV on swine health.

The mitochondrial genome of two long-distance migratory shorebirds: the Hudsonian godwit (Limosa haemastica) and the Red knot (Calidris canutus).

We report the mitochondrial genome sequences of two migratory shorebirds, the Hudsonian godwit (Limosa haemastica) and the Red knot (Calidris canutus) obtained through shotgun sequencing. The mitogenome is of 16.445 bp for the godwit and 15.609 bp for the knot containing thirteen protein-coding genes, two rRNAs, twenty-two tRNAs, and a control region. The ATP8 and tRNA-Glu were not found in the knot. Bayesian phylogenetic analysis supported the position of both species in the clade of the Scolopacidae Family.

Role of wastewater treatment plants on environmental abundance of Antimicrobial Resistance Genes in Chilean rivers.

BACKGROUND: Point sources such as wastewater treatment plants (WWTPs) commonly discharge their effluent into rivers. Their waste may include antibiotic residues, disinfectants, antibiotic resistant bacteria (ARB), and Antimicrobial Resistance Genes (ARG). There is evidence that ARG can be found in the natural environment, but attribution to specific point sources is lacking. OBJECTIVES: The goal of this study was to assess the release and dissemination of ARG from three WWTPs in southern Chile via two pathways: through the river systems, and through wild birds. METHODS: A longitudinal study was conducted, collecting river sediment samples at different distances both upstream and downstream from each WWTP. Wild birds were sampled from around one of the WWTPs once a month for 13 months. A microfluidic q-PCR approach was used to quantify 48 genes covering different molecular mechanisms of resistance, and data was analyzed using ordination methods and linear mixed regression models. RESULTS: There was a statistically significant increase downstream from the WWTPs (p < 0.05) for 17 ARG, but the downstream dissemination through the rivers was not clear. Beta-lactamase genes blaKPC, blaTEM, and blaSHV were the most abundant in birds, with higher abundance of blaSHV in migratory species compared to resident species (p < 0.05). The gene profile was more similar between the migratory and resident bird groups compared to the WWTP gene profile. CONCLUSIONS: While results from this study indicate an influence of WWTPs on ARG abundance in the rivers, the biological significance of this increase and the extent of the WWTPs influence are unclear. In addition, wild birds were found to play a role in disseminating ARG, although association to the specific WWTP could not be ascertained.

MOLECULAR IDENTIFICATION OF AVIAN VIRUSES IN NEOTROPIC CORMORANTS ( PHALACROCORAX BRASILIANUS) IN CHILE.

We identified two RNA (paramyxovirus and coronavirus) and two DNA (adenovirus and herpesvirus) viruses in a common aquatic bird, the Neotropic Cormorant ( Phalacrocorax brasilianus), and determined their phylogenetic relationships to other global circulating variants. We analyzed 104 cloacal swabs from individuals collected at locations in Central Chile. Sequences were obtained from amplicons using consensus primers targeting conserved genes of the virus families Paramyxoviridae, Coronaviridae, Adenoviridae, and Herpesviridae. A total of 20.2% of the samples was positive for coronavirus, 8.7% for adenovirus, and 3.8% for herpesvirus. No paramyxoviruses were detected. All coronaviruses were identified as viruses of the Gammacoronavirus genus, closely related to the infectious bronchitis virus clade (bootstrap clade support=75%). All adenovirus samples were identified as Aviadenovirus, related to a gull and falcon adenovirus (Bayesian posterior probability=0.86). The herpesviruses identified were related to the infectious laryngotracheitis virus ( Gallid herpesvirus 1) of the genus Iltovirus (bootstrap clade support=99%). We provide information about the diversity of viruses circulating among apparently healthy Neotropic Cormorants.

Echinococcus Granulosus in the Endangered Patagonian Huemul (Hippocamelus bisulcus).

Cystic echinococcosis (CE) is a zoonotic parasitic disease associated with Echinococcus granulosus. The parasite is maintained by domestic and wild canids as definitive hosts with several ungulate species as intermediate hosts in domestic and peridomestic transmission cycles. In Chile, CE is endemic, and the role of livestock and dogs (Canis lupus familiaris) in the cycle and the accidental infection of humans are widely documented at rural sites. However, the role of wild herbivores in wild cycles or the potential transmission of CE from livestock is still unknown in Chile and the rest of South America. We used molecular techniques to describe CE infecting a Patagonian huemul (Hippocamelus bisulcus) in Cerro Castillo National Reserve (Aysén region, Chile). We make inferences about the risk of disease spillover from sympatric domestic and wild species. The DNA-based molecular analysis revealed that the huemul was infected with E. granulosus G1 genotype, sharing haplotypes with other G1 samples collected from sheep (Ovis aries) and cattle (Bos taurus) worldwide. Geographic overlap between sheep and huemul populations in the reserve likely facilitates parasite spillover into wild deer populations, with shepherd or stray dogs and wild foxes (Lycalopex culpaeus) potentially acting as bridging hosts between livestock and the endangered huemul. Further studies are warranted to understand the implications of E. granulosus for huemul conservation throughout the Chilean Patagonia.

Assessing the effects of human activities on the foraging opportunities of migratory shorebirds in Austral high-latitude bays.

Human presence at intertidal areas could impact coastal biodiversity, including migratory waterbird species and the ecosystem services they provide. Assessing this impact is therefore essential to develop management measures compatible with migratory processes and associated biodiversity. Here, we assess the effects of human presence on the foraging opportunities of Hudsonian godwits (Limosa haemastica, a trans-hemispheric migratory shorebird) during their non-breeding season on Chiloé Island, southern Chile. We compared bird density and time spent foraging in two similar bays with contrasting disturbance levels: human presence (mostly seaweed harvesters accompanied by dogs) was on average 0.9±0.4 people per 10 ha in the disturbed bay, whereas it was negligible (95% days absent) in the non-disturbed bay. Although overall abundances were similar between bays, godwit density was higher in the non-disturbed bay throughout the low tide period. Both days after the start of the non-breeding season and tidal height significantly affected godwit density, with different effects in either bay. Time spent foraging was significantly higher in the non-disturbed bay (86.5±1.1%) than in the disturbed one (81.3±1.4%). As expected, godwit density significantly decreased with the number of people and accompanying dogs in the disturbed bay. Our results indicate that even a low density of people and dogs can significantly reduce the foraging opportunities of shorebirds. These constraints, coupled with additional flushing costs, may negatively affect godwits' pre-migratory fattening. Hence, as a first step we suggest limiting human presence within bays on Chiloé to 1 person per 10 ha and banning the presence of accompanying dogs in sensitive conservation areas.

Short-term thermoregulatory adjustments in a South American anseriform, the black-necked swan (Cygnus melanocoryphus).

Avian bioenergetic studies suggest that, compared with other vertebrates, birds are efficient thermoregulators. However, most avian physiological studies have been performed in species of small body masses (less than 1 kg). In contrast to what might be anticipated, thermoregulatory abilities of large, flying birds are scarcely studied, especially in temperate zones and aquatic systems. In order to determine short-term metabolic adjustment after thermal challenge, we studied the bioenergetics of a South American anseriform, the black-necked swan (Cygnus melanocoryphus). Our results suggest that this swan species exhibits lower resting metabolic rate compared with other anseriforms, and some hetherothermia. In addition, the black-necked swans in our study changed "wet" thermal conductance at different ambient temperatures. At our working Ta range (5, 10, 15, 20 and 25 degrees C) calculated values were considerably higher than expected (23%, 26%, 39% and 51% higher than expected, respectively). Our results differ considerably from the only two previous reports in swan species, suggesting that C. melanocoryphus, perhaps due to its temperate distribution, is more sensitive to changes in environmental temperature.

Respiratory Mites ( Orthohalarachne diminuata) and ß-hemolytic Streptococci-Associated Bronchopneumonia Outbreak in South American Fur Seal Pups ( Arctocephalus australis).

Although mites of the Orthohalarachne genus are common parasites of otariids, their role as agents of disease and in causing population-level mortality is unknown. In the austral summer of 2016, there was an increase in mortality among South American fur seal ( Arctocephalus australis) pups at Guafo Island, Northern Chilean Patagonia. Pups found dead or terminally ill had moderate to marked, multifocal, mucopurulent bronchopneumonia associated with large numbers of respiratory mites ( Orthohalarachne diminuata) and rare Gram-positive cocci. In lung areas less affected by bronchopneumonia, acute interstitial pneumonia with marked congestion and scant hemorrhage was evident. Bacteria from pups dying of bronchopneumonia were isolated and identified as Streptococcus marimammalium and Streptococcus canis. Respiratory mites obstructed airflow, disrupted airway epithelial lining, and likely facilitated the proliferation of pathogenic ß-hemolytic streptococci, leading to severe bronchopneumonia and death of fur seal pups. An abrupt increase in sea surface temperature in Guafo Island corresponded to the timing of the bronchopneumonia outbreak. The potential role of environmental factors in the fur seal pup mortality warrants further study.

Abundance and associated factors of Amblyomma tigrinum (Acari: Ixodidae) infesting wild foxes in north-central Chile / Abundância e fatores associados do Amblyomma tigrinum (Acari: Ixodidae) infestando raposas silvestres no centro-norte do Chile

Abstract The tick Amblyomma tigrinum inhabits areas with diverse climatic conditions, with adult stages parasitizing wild canids, such as chilla (Lycalopex griseus) and culpeo (Lycalopex culpaeus) foxes. We described the infestation loads in wild foxes captured at three sites (periurban, rural and wild) through an anthropization gradient in north-central Chile. We tested whether local-scale environmental and/or individual host factors can predict tick abundance by using negative binomial models. During 2018-2020 (spring and summer), we captured 116 foxes (44 chillas and 72 culpeos), and 102 of them were infested with ticks (87.9%, CI=80.6-93.2%). We collected 996 A. tigrinum adult ticks, estimating a total mean abundance of 8.6±0.8 ticks/host. Periurban and rural foxes harbored greater tick loads than foxes from the wild site (2.34 and 1.71 greater, respectively) while tick abundance in summer decreased by up to 57% compared to spring. Tempered, more humid climate conditions of the periurban site could favor the development and survival of adults A. tigrinum; and ticks may have adopted a quiescent stage or similar survival mechanisms to cope with summer temperature increases related to the ongoing megadrought. Further studies are warranted to understand the underlying factors determining the life cycle of A. tigrinum at larger spatiotemporal scales.

Resumo Amblyomma tigrinum habita em áreas com diversas condições climáticas, com estágios adultos, geralmente, parasitando canídeos silvestres, como chilla (Lycalopex griseus) e culpeo (Lycalopex culpaeus). Neste trabalho, são descritas as cargas de infestação de A. tigrinum em raposas silvestres, capturadas em três locais (periurbano, rural e silvestre) no centro-norte do Chile. Foi testado se os fatores ambientais e/ou individuais do hospedeiro, em escala local, podem prever a abundância de carrapatos, usando-se modelos binomiais negativos. Durante 2018-2020 (primavera e verão), foram capturadas 116 raposas (44 chillas e 72 culpeos), e 102 delas estavam infestadas por carrapatos (87,9%, IC=80,6-93,2%). Foram coletados 996 carrapatos adultos de A. tigrinum, estimando-se uma abundância média total de 8,6±0,8 carrapatos/hospedeiro. As raposas periurbanas e rurais abrigaram cargas de carrapatos maiores do que as raposas do local silvestre (2,34 e 1,71 maior, respectivamente), enquanto a abundância de carrapatos, no verão, diminuiu até 57% em comparação com a primavera. As condições climáticas temperadas e mais úmidas do sítio periurbano podem favorecer o desenvolvimento e a sobrevivência dos adultos de A. tigrinum; e os carrapatos podem ter adotado um estágio quiescente ou mecanismos de sobrevivência semelhantes, para lidar com os aumentos de temperatura no verão, relacionados à mega seca em andamento.

Complete mitochondrial genome of the Neotropic cormorant (Phalacrocorax brasilianus).

The complete sequence of the Neotropic cormorant (Phalacrocorax brasilianus) mitochondrial DNA was obtained by the shotgun sequencing approach. The mitogenome is 19 042 bp in length and includes 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNA genes, a control region and a duplicated region of 2418 bp. The base composition is 32.1% for C, 31.8% for A, 22.6% for T and 13.4% for G, with an overall GC content of 45.5%. This is the first mitogenome of the P. brasilianus described and will be a useful tool for further phylogenetic and population genetic studies.

Complete mitochondrial genome of the South American fur seal (Arctocephalus australis).

The complete mitochondrial DNA sequence of the South America fur seal (Arctocephalus australis) was obtained by a shotgun sequencing approach. The mitogenome is 16,372 bp in length and includes the genes coding for the two rRNA species (12S and 16S), 13 protein-coding genes, 22 transfer RNA genes, and a control region. The base composition is 33.0% for A, 26.7% for C, 26.1 for T and 14.2% for G, with an overall GC content of 40.9%. The description of this mitogenome will be useful for further phylogeny and genetic studies on Pinnipeds.