DNA barcoding of sigmodontine rodents: identifying wildlife reservoirs of zoonoses

A review of emerging health threats from zoonotic New World mammarenaviruses

Despite repeated spillover transmission and their potential to cause significant morbidity and mortality in human hosts, the New World mammarenaviruses remain largely understudied. These viruses are endemic to South America, with animal reservoir hosts covering large geographic areas and whose transmission ecology and spillover potential are driven in part by land use change and agriculture that put humans in regular contact with zoonotic hosts.We compiled published studies about Guanarito virus, Junin virus, Machupo virus, Chapare virus, Sabia virus, and Lymphocytic Choriomeningitis virus to review the state of knowledge about the viral hemorrhagic fevers caused by New World mammarenaviruses. We summarize what is known about rodent reservoirs, the conditions of spillover transmission for each of these pathogens, and the characteristics of human populations at greatest risk for hemorrhagic fever diseases. We also review the implications of repeated outbreaks and biosecurity concerns where these diseases are endemic, and steps that countries can take to strengthen surveillance and increase capacity of local healthcare systems. While there are unique risks posed by each of these six viruses, their ecological and epidemiological similarities suggest common steps to mitigate spillover transmission and better contain future outbreaks.

Utility of cytochrome c oxidase I for the deciphering of unstable phylogeny and taxonomy of gorals, genus Nemorhaedus Hamilton Smith, 1827 (Bovidae, Ovibovina)

Gorals represent ungulate mammals of the Palearctic and Indo-Malayan realms that face habitat destruction and intense hunting pressure. Their classification has been the subject of various (mainly genetic) assessments in the last decade, but some results are conflicting, hampering some conservation-based decisions. Genetic sampling of gorals has increased considerably in recent years, at least for mitochondrial (mt) DNA. Results based on two mt genes (cytochrome b and the D-loop) are currently available. Still, the utility of cytochrome oxidase subunit I remains unanalysed, even though it belongs among the gene markers that enable a correct species identification in mammals. This study examines phylogenetic relationships and species delimitation in gorals using all currently available cytochrome oxidase subunit I sequences, including the not yet analysed goral population from Pakistan. Our results of various phylogenetic approaches, such as maximum parsimony, likelihood and Bayesian inference, and exploration of species boundaries via species delimitation support the validity of six species of goral, namely N.baileyi, N.caudatus, N.cranbrooki, N.evansi, N.goral, and N.griseus. This result accords well with results based on other mt genes, especially the cytochrome b from the highly exhaustive data sampling. Our study also summarises common sources of errors in the assessment of goral phylogeny and taxonomy and highlights future priorities in understanding goral diversification.

Breathing can be dangerous: Opportunistic fungal pathogens and the diverse community of the small mammal lung mycobiome

Human lung mycobiome studies typically sample bronchoalveolar lavage or sputum, potentially overlooking fungi embedded in tissues. Employing ultra-frozen lung tissues from biorepositories, we obtained fungal ribosomal RNA ITS2 sequences from 199 small mammals across 39 species. We documented diverse fungi, including common environmental fungi such as Penicillium and Aspergillus, associates of the human mycobiome such as Malassezia and Candida, and others specifically adapted for lungs (Coccidioides, Blastomyces, and Pneumocystis). Pneumocystis sequences were detected in 83% of the samples and generally exhibited phylogenetic congruence with hosts. Among sequences from diverse opportunistic pathogens in the Onygenales, species of Coccidioides occurred in 12% of samples and species of Blastomyces in 85% of samples. Coccidioides sequences occurred in 14 mammalian species. The presence of neither Coccidioides nor Aspergillus fumigatus correlated with substantial shifts in the overall mycobiome, although there was some indication that fungal communities might be influenced by high levels of A. fumigatus. Although members of the Onygenales were common in lung samples (92%), they are not common in environmental surveys. Our results indicate that Pneumocystis and certain Onygenales are common commensal members of the lung mycobiome. These results provide new insights into the biology of lung-inhabiting fungi and flag small mammals as potential reservoirs for emerging fungal pathogens.

DNA barcodes highlight genetic diversity patterns in rodents from lowland desert and andean areas in argentina

Rodents are an important component of South America fauna. Their high diversity has motivated researchers to continually review their taxonomy, genetic diversity, species limits, and phylogenetic relationships. We apply DNA-barcodes for assessing the taxonomic and genetic diversity in the two major lineages of South American rodents: caviomorphs and sigmodontines. We analyzed 335 COI barcodes in 34 morphologically determined species from 39 localities along central Andes and arid lands of Argentina. Neighbor Joining and Maximum Likelihood reconstruction provided clear separation between species. The Barcode Index Number and Bayesian Poisson Tree Processes were used to confirm concordance between sequence clusters and species designations by taxonomy. We found deep divergence within the Phyllotis xanthopygus species complex, with distances up to 13.0% between geographically separated lineages. Minor divergences (3.30% and 2.52%) were found within Abrothrix hirta, and Tympanoctomys barrerae, respectively, with differentiation in their genetic lineages. Also, we documented geographically separated clusters for Akodon spegazzinii and A.oenos with up to 2.3% divergence, but clustering methods failed to distinguish them as different species. Sequence results show a clear barcode gap with a mean intraspecific divergence (0.56%) vs. a minimum nearest-neighbor distance averaging (10.1%). Distances between congeneric species varied from 4.1 to 14%, with the exception of two related forms within Euneomys and the sister species Akodon spegazzinii and A. oenos. This study constitutes a substantial contribution to the global barcode reference library. It provides insights into the complex phylogeographic patterns and speciation scenarios in rodents, while highlighting areas that require in-depth taxonomic and integrative research.

The spleen bacteriome of wild rodents and shrews from Marigat, Baringo County, Kenya

BACKGROUND

There is a global increase in reports of emerging diseases, some of which have emerged as spillover events from wild animals. The spleen is a major phagocytic organ and can therefore be probed for systemic microbiome. This study assessed bacterial diversity in the spleen of wild caught small mammals so as to evaluate their utility as surveillance tools for monitoring bacteria in an ecosystem shared with humans.

METHODS

Fifty-four small mammals (rodents and shrews) were trapped from different sites in Marigat, Baringo County, Kenya. To characterize their bacteriome, DNA was extracted from their spleens and the V3-V4 regions of the 16S rRNA amplified and then sequenced on Illumina MiSeq. A non-target control sample was used to track laboratory contaminants. Sequence data was analyzed with Mothur v1.35, and taxomy determined using the SILVA database. The Shannon diversity index was used to estimate bacterial diversity in each animal and then aggregated to genus level before computing the means. Animal species within the rodents and shrews were identified by amplification of mitochondrial cytochrome b (cytb) gene followed by Sanger sequencing. CLC workbench was used to assemble the cytb gene sequences, after which their phylogenetic placements were determined by querying them against the GenBank nucleotide database.

RESULTS

cytb gene sequences were generated for 49/54 mammalian samples: 38 rodents (Rodentia) and 11 shrews (Eulipotyphyla). Within the order Rodentia, 21 Acomys, eight Mastomys, six Arvicanthis and three Rattus were identified. In the order Eulipotyphyla, 11 Crucidura were identified. Bacteria characterization revealed 17 phyla that grouped into 182 genera. Of the phyla, Proteobacteria was the most abundant (67.9%). Other phyla included Actinobacteria (16.5%), Firmicutes (5.5%), Chlamydiae (3.8%), Chloroflexi (2.6%) and Bacteroidetes (1.3%) among others. Of the potentially pathogenic bacteria, Bartonella was the most abundant (45.6%), followed by Anaplasma (8.0%), Methylobacterium (3.5%), Delftia (3.8%), Coxiella (2.6%), Bradyrhizobium (1.6%) and Acinetobacter (1.1%). Other less abundant (<1%) and potentially pathogenic included Ehrlichia, Rickettsia, Leptospira, Borrelia, Brucella, Chlamydia and Streptococcus. By Shannon diversity index, Acomys spleens carried more diverse bacteria (mean Shannon diversity index of 2.86, p = 0.008) compared to 1.77 for Crocidura, 1.44 for Rattus, 1.40 for Arvicathis and 0.60 for Mastomys.

CONCLUSION

This study examined systemic bacteria that are filtered by the spleen and the findings underscore the utility of 16S rRNA deep sequencing in characterizing complex microbiota that are potentially relevant to one health issues. An inherent problem with the V3-V4 region of 16S rRNA is the inability to classify bacteria reliably beyond the genera. Future studies should utilize the newer long read methods of 16S rRNA analysis that can delimit the species composition.

In vitro Evaluation of Medihoney Antibacterial Wound Gel as an Anti-biofilm Agent Against Ventricular Assist Device Driveline Infections

Objectives: In adult ventricular assist device (VAD) programs in Australian hospitals, Medihoney Antibacterial Wound Gel (MAWG) is routinely used at the skin exit-site of VAD drivelines to prevent infections; however, its effectiveness remains unclear. Our aim was to assess antimicrobial activity of Medihoney wound gel, using in vitro models that mimic clinical biofilms grown at the driveline exit-site. Methods: Antimicrobial susceptibility testing of MAWG was performed for 24 clinical isolates grown under planktonic conditions, and four representative strains grown as biofilms. Different antimicrobial mechanisms of MAWG were assessed respectively for their relative contribution to its anti-biofilm activity. A colony biofilm assay and a drip-flow biofilm reactor assay mimicking the driveline exit-site environment were used to evaluate the activity of MAWG against biofilm growth at the driveline exit-site. Results: MAWG demonstrated species-specific activity against planktonic cultures [minimum inhibitory concentrations (MICs), 5-20% weight/volume (W/V) for Staphylococcus species, 20->40% (W/V) for Pseudomonas aeruginosa and Candida species]. Higher concentrations [MICs, 30->80% (W/V)] were able to inhibit biofilm growth, but failed to eradicate pre-established biofilms. The anti-biofilm properties of MAWG were multi-faceted, with the often-advertised "active" ingredient methylglyoxal (MGO) playing a less important role. The colony biofilm assay and the drip-flow biofilm reactor assay suggested that MAWG was unable to kill biofilms pre-established in a driveline exit-site environment, or effectively prevent planktonic cells from forming adherent monolayers and further developing mature biofilms. Conclusion: Our work suggests a suboptimal effectiveness of MAWG in preventing driveline infections due to biofilm development.

Hantavirus host assemblages and human disease in the Atlantic Forest

Several viruses from the genus Orthohantavirus are known to cause lethal disease in humans. Sigmodontinae rodents are the main hosts responsible for hantavirus transmission in the tropical forests, savannas, and wetlands of South America. These rodents can shed different hantaviruses, such as the lethal and emerging Araraquara orthohantavirus. Factors that drive variation in host populations may influence hantavirus transmission dynamics within and between populations. Landscape structure, and particularly areas with a predominance of agricultural land and forest remnants, is expected to influence the proportion of hantavirus rodent hosts in the Atlantic Forest rodent community. Here, we tested this using 283 Atlantic Forest rodent capture records and geographically weighted models that allow us to test if predictors vary spatially. We also assessed the correspondence between proportions of hantavirus hosts in rodent communities and a human vulnerability to hantavirus infection index across the entire Atlantic Forest biome. We found that hantavirus host proportions were more positively influenced by landscape diversity than by a particular habitat or agricultural matrix type. Local small mammal diversity also positively influenced known pathogenic hantavirus host proportions, indicating that a plasticity to habitat quality may be more important for these hosts than competition with native forest dwelling species. We found a consistent positive effect of sugarcane and tree plantation on the proportion of rodent hosts, whereas defaunation intensity did not correlate with the proportion of hosts of potentially pathogenic hantavirus genotypes in the community, indicating that non-defaunated areas can also be hotspots for hantavirus disease outbreaks. The spatial match between host hotspots and human disease vulnerability was 17%, while coldspots matched 20%. Overall, we discovered strong spatial and land use change influences on hantavirus hosts at the landscape level across the Atlantic Forest. Our findings suggest disease surveillance must be reinforced in the southern and southeastern regions of the biome where the highest predicted hantavirus host proportion and levels of vulnerability spatially match. Importantly, our analyses suggest there may be more complex rodent community dynamics and interactions with human disease than currently hypothesized.

DNA barcoding of the rodent genus Oligoryzomys (Cricetidae: Sigmodontinae): mitogenomic-anchored database and identification of nuclear mitochondrial translocations (Numts)

DNA barcoding has become a standard method for species identification in taxonomically complex groups. An important step of the barcoding process is the construction of a library of voucher-based material that was properly identified by independent methods, free of inaccurate identification, and paralogs. We provide here a cytochrome oxidase I (mt-Co1) DNA barcode database for species of the genus Oligoryzomys, based on type material and karyotyped specimens, and anchored on the mitochondrial genome of one species of Oligoryzomys, O. stramineus. To evaluate the taxonomic determination of new COI sequences, we assessed species intra/interspecific genetic distances (barcode gap), performed the General Mixed Yule Coalescent method (GMYC) for lineages' delimitation, and identified diagnostic nucleotides for each species of Oligoryzomys. Phylogenetic analyses of Oligoryzomys were performed on 2 datasets including 14 of the 23 recognized species of this genus: a mt-Co1 only matrix, and a concatenated matrix including mt-Co1, cytochrome b (mt-Cytb), and intron 7 of the nuclear fibrinogen beta chain gene (i7Fgb). We recovered nuclear-mitochondrial translocated (Numts) pseudogenes on our samples and identified several published sequences that are cases of Numts. We analyzed the rate of non-synonymous and synonymous substitution, which were higher in Numts in comparison to mtDNA sequences. GMYC delimitations and DNA barcode gap results highlight the need for further work that integrate molecular, karyotypic, and morphological analyses, as well as additional sampling, to tackle persistent problems in the taxonomy of Oligoryzomys.

Does the widely distributed rodent Calomys tener (Cricetidae: Sigmodontinae) constitute a single evolutionary unit?

The nominal species Calomystener (Winge, 1887) ranges broadly in open lands of the Caatinga, Cerrado, Pantanal and Mata Atlântica of Brazil, and was recently reported from the Pampas of southern Brazil, and in the Selva Paranaense of eastern Paraguay and northeastern Argentina. This rodent can be infected with the pathogenic Araraquara hantavirus in Brazil. Given that most epidemiological studies have not taken into account updated taxonomic findings of their rodent hosts, in this study, we obtained sequence data of the Cyt-b and COI genes of specimens of C.tener from 22 different geographical localities from throughout the currently known distribution of the species (including individuals from Argentina, Paraguay, Bolivia, and Brazil) to test if it constitutes a single genetic unit or if it presents genetic discontinuities that may represent different evolutionary lineages. Phylogenetic analyses including several species of Calomys recovered several clades with strong support. Regarding C.tener, it is recovered as sister to the node that cluster C.laucha (Fischer, 1814) sensu lato, C.expulsus (Lund, 1841) and species in the C.callosus (Rengger, 1830) species complex. At the intraspecific level there are no genetic gaps among haplotypes of C.tener that could suggest more than one species. The recent captures in the Pampas of southern Brazil and in the Selva Paranaense suggest that the species may be colonizing new geographic areas.

Genetic variability of populations of the white-eared opossum, Didelphis albiventris Lund 1840 (Didelphimorphia; Didelphidae) in Brazil

Didelphis albiventris are found throughout Northeast and Central Brazil to central-southern Uruguay and it was subject of few studies in a population level. Given this, the present study investigated the genetic variability of the species using the mitochondrial molecular marker cytochrome oxidase c subunit I. We analyzed samples from the different biomes within three Brazilian regions: Northeast (Caatinga , Cerrado, and Atlantic Forest), Southeast (Cerrado , Atlantic Forest, Cerrado/Atlantic Forest, and Cerrado/Caatinga ecotones) and South (Pampa and Atlantic Forest). Software BAPs retrieved five distinct demes: dm 1, dm 2, and dm 5 that occurs in South, Northeast and Southeast regions respectively and the dm 3 and dm 4 are wide distributed in Northeast and Southeast. Population analysis performed with AMOVA, haplotype network and Mantel test estimated the veracity of the demes. The FST shows structuring for the five demes, with dm 1 (South region) isolated from the others, however the other analysis showed the Northeast/Southeast demes (dm 2-5) united, diagnosing gene flow between them, mainly at the transitional zones, in areas as far away as areas with similar latitude interval (Southeast vs South) that was not detected gene flow. In the haplotype network, the mutational steps was conclusive in split dm1 from dm 2-5 with 15 mutational steps and the Mantel test was moderated, which is explained by genetic similarity despite the great geographic distances (Northeast/Southeast). Thus, our analysis recognized two different lineages (South and Northeast/Southeast) and indicate that the biomes were not decisive in their isolation. The sharing of demes at the transitional zones and in areas with high latitudinal intervals reflects a recent ancestral polymorphism for D. albiventris. The plasticity in the occupation of the space by this species contributes in its wide dispersion capability, that is, geographical distribution. Our results revealed important implications for the management of D. albiventris in these transitional zones areas where demes were shared.

A new species of Eimeria Schneider, 1875 from the Serra dos Órgãos National Park, Rio de Janeiro, Brazil, with notes on its endogenous development in the montane grass mouse, Akodon montensis Thomas, 1913 (Rodentia: Sigmodontinae)

A total of 53 specimens of the montane grass mouse, Akodon montensis Thomas, 1913 were collected in the Serra dos Órgãos National Park (SONP) in November 2014 and July 2015. The fecal material was analyzed, and a prevalence of 7.5% was recorded for a new coccidian species of the genus Eimeria Schneider, 1875, with part of its endogenous development recorded in the small intestine. The oocysts of a new coccidian species of genus Eimeria are ellipsoidal to subspherical. The wall is bi-layered, c. 1.5 μm (1.3–1.6 μm) thick, outer layer rough. Oocyst (n = 126) mean length is 25.3 μm (21.0–28.0 μm), with a width of 20.2 μm (17.0–22.0 μm) and mean length/width (L:W) ratio of 1.3 (1.2–1.4). Polar granule is present, with the oocyst residuum as a large spherical to subspherical globule. Sporocyst shape (n = 126) is ellipsoidal, with a mean length of 11.8 μm (9.3–14.4 μm), width of 7.9 μm (6.7–9.3 μm), and mean L:W ratio of 1.5 (1.4–1.7). Sporocysts with nipple-like Stieda body and sub-Stieda body are absent. A sporocyst residuum formed by several globules, usually along the sporocyst wall. This is the first record of Eimeria in the montane grass mouse from Brazil.

Multivariate discrimination among cryptic mites of the genus Androlaelaps (Acari: Mesostigmata: Laelapidae) parasitic of sympatric akodontine rodents (Cricetidae: Sigmodontinae) in northeastern Argentina: possible evidence of host switch followed by speciation, with the description of two new species

Laelapids are among the most common ectoparasites of rodents. Currently, it is under discussion whether there is a single polixenous species that parasites a variety of hosts, or whether there are cryptic species highly host specific. Herein, multivariate morphometric analyses of cryptic sympatric laelapids of the genus Androlaelaps allowed us to identify different species. These species are specific of their akodontine hosts, Akodon montensis and Thaptomys nigrita, in localities situated in northeastern Argentina. In addition, we analyzed similar laelapids associated with the akodontines Deltamys kempi and Akodon cursor. Using principle component analyses we differentiated four laelapid species, each one host specific, independent of sympatry of the hosts, and without geographical variation. From these four species, we described two new species (Androlaelaps navonae n. sp. and Androlaelaps wingei n. sp.). We determined the four species based on a range of variations in several characters, mainly size. These four laelapid species belong to the Androlaelaps rotundus species group, specific to akodontines. These species are very similar among them but differ from the remainder species of the group by their small size, distance between j6 setae similar to the distance between the z5 setae, strong ventral setae, opisthogaster with 13 pairs of strong setae (one close to the distal margin of epigynal shield), and anal shield wider than long. Further studies will elucidate whether they constitute a new laelapid genus. Phylogenetic and ecological factors influencing host-specificity are discussed, and we propose that host colonization could have taken place by host switching of a single laelapid species among rodent species, followed by speciation.

Status and prospects of DNA barcoding in medically important parasites and vectors

For over 10 years, DNA barcoding has been used to identify specimens and discern species. Its potential benefits in parasitology were recognized early, but its utility and uptake remain unclear. Here we review studies using DNA barcoding in parasites and vectors affecting humans and find that the technique is accurate (accords with author identifications based on morphology or other markers) in 94-95% of cases, although aspects of DNA barcoding (vouchering, marker implicated) have often been misunderstood. In a newly compiled checklist of parasites, vectors, and hazards, barcodes are available for 43% of all 1403 species and for more than half of 429 species of greater medical importance. This is encouraging coverage that would improve with an active campaign targeting parasites and vectors.

Three new cecidogenous species of Palaeomystella Fletcher (Lepidoptera, Momphidae) from the Brazilian Atlantic Rain Forest

Three new cecidogenous species of Palaeomystella Fletcher (Lepidoptera, Momphidae) from the Brazilian Atlantic Rain Forest are described. Larvae of P. fernandesi Moreira & Becker, sp. n., P. rosaemariae Moreira & Becker, sp. n. and P. tavaresi Becker & Moreira, sp. n. induce galls, respectively, on Tibouchina sellowiana (Cham.) Cogn., T. asperior (Cham.) Cogn. and T. fissinervia (Schrank & Mart. ex DC.) Cogn. (Melastomataceae). Adults, immature stages and galls are illustrated, and data on life history and a preliminary analysis of mitochondrial DNA sequences, including related species, are also provided.

DNA barcoding of Murinae (Rodentia: Muridae) and Arvicolinae (Rodentia: Cricetidae) distributed in China

Identification of rodents is very difficult mainly due to high similarities in morphology and controversial taxonomy. In this study, mitochondrial cytochrome oxidase subunit I (COI) was used as DNA barcode to identify the Murinae and Arvicolinae species distributed in China and to facilitate the systematics studies of Rodentia. In total, 242 sequences (31 species, 11 genera) from Murinae and 130 sequences (23 species, 6 genera) from Arvicolinae were investigated, of which 90 individuals were novel. Genetic distance, threshold method, tree-based method, online BLAST and BLOG were employed to analyse the data sets. There was no obvious barcode gap. The average K2P distance within species and genera was 2.10% and 12.61% in Murinae, and 2.86% and 11.80% in Arvicolinae, respectively. The optimal threshold was 5.62% for Murinae and 3.34% for Arvicolinae. All phylogenetic trees exhibited similar topology and could distinguish 90.32% of surveyed species in Murinae and 82.60% in Arvicolinae with high support values. BLAST analyses yielded similar results with identification success rates of 92.15% and 93.85% for Murinae and Arvicolinae, respectively. BLOG successfully authenticated 100% of detected species except Leopoldamys edwardsi based on the latest taxonomic revision. Our results support the species status of recently recognized Micromys erythrotis, Eothenomys tarquinius and E. hintoni and confirm the important roles of comprehensive taxonomy and accurate morphological identification in DNA barcoding studies. We believe that, when proper analytic methods are applied or combined, DNA barcoding could serve as an accurate and effective species identification approach for Murinae and Arvicolinae based on a proper taxonomic framework.

The role of sigmodontine rodents as sylvatic hosts of Trypanosoma cruzi in the Argentinean Chaco

The role of rodents in the sylvatic transmission of Trypanosoma cruzi has seldom been investigated using parasitological and molecular methods. We assessed the occurrence of T. cruzi in wild small rodents from Pampa del Indio, in the Argentinean Chaco, and identified the taxonomic status of positive rodents by sequencing a fragment of cytochrome b gene (cytb) and performing BLAST searches and phylogenetic analyses. A total of 176 Sigmodontinae rodents was captured in six surveys using 5425 trap-nights in a wide range of sylvatic habitats between 2009 and 2011. Host infection was determined by xenodiagnosis and by polymerase chain reaction amplification of the hyper-variable region of kinetoplast DNA minicircles of T. cruzi (kDNA-PCR) from blood samples. None of the 176 rodents examined was xenodiagnosis-positive. The prevalence of infection determined by kDNA-PCR from blood samples was 16.2% (95% confidence interval, 10.1-21.9%). Half of the infections detected by kDNA-PCR were confirmed by nuclear satellite DNA-PCR or by kDNA-PCR of the rectal contents of xenodiagnostic bugs. The 24 positive specimens were assigned to eight species, providing the first records of T. cruzi in Akodon montensis, Akodon toba, Graomys chacoensis, and Oligoryzomys chacoensis. The occurrence of T. cruzi infection in Oligoryzomys nigripes, Calomys callosus, Necromys lasiurus and Oecomys sp. (most probably Oecomys mamorae) from the Gran Chaco is also reported for the first time. Although sigmodontine rodents were frequently infected, the intensity of bug rectal infection with T. cruzi was below the detection limit of xenodiagnosis (subpatent infectiousness to bugs), indicating they had a low reservoir host competence.