Wild rodents serve as reservoirs for Cryptosporidium and are overpopulated globally. However, genetic data regarding Cryptosporidium in these animals from China are limited. Here, we have determined the prevalence and genetic characteristics of Cryptosporidium among 370 wild rodents captured from three distinct locations in the southern region of Zhejiang Province, China. Fresh feces were collected from the rectum of each rodent, and DNA was extracted from them. The rodent species was identified by PCR amplifying the vertebrate cytochrome b gene. Cryptosporidium was detected by PCR amplification and amplicon sequencing the small subunit of ribosomal RNA gene. Positive samples of C. viatorum and C. parvum were further subtyped by analyzing the 60-kDa glycoprotein gene. A positive Cryptosporidium result was found in 7% (26/370) of samples, involving five rodent species: Apodemus agrarius (36), Niviventer niviventer (75), Rattus losea (18), R. norvegicus (155), and R. tanezumi (86). Their respective Cryptosporidium positive rates were 8.3%, 5.3%, 11.1%, 7.1%, and 7.0%. Sequence analysis confirmed the presence of three Cryptosporidium species: C. parvum (4), C. viatorum (1), and C. muris (1), and two genotypes: Cryptosporidium rat genotype IV (16) and C. mortiferum-like (4). Additionally, two subtypes of C. parvum (IIdA15G1 and IIpA19) and one subtype of C. viatorum (XVdA3) were detected. These results demonstrate that various wild rodent species in Zhejiang were concurrently infected with rodent-adapted and zoonotic species/genotypes of Cryptosporidium, indicating that these rodents can play a role in maintaining and dispersing this parasite into the environment and other hosts, including humans.
UNASSIGNED: Transmission interspécifique de Cryptosporidium chez les rongeurs sauvages de la région sud de la province chinoise du Zhejiang et son impact possible sur la santé publique.
UNASSIGNED: Les rongeurs sauvages servent de réservoirs à Cryptosporidium et ont des grandes populations à l’échelle mondiale. Cependant, les données génétiques concernant Cryptosporidium chez ces animaux en Chine sont limitées. Ici, nous avons déterminé la prévalence et les caractéristiques génétiques de Cryptosporidium parmi 370 rongeurs sauvages capturés dans trois endroits distincts de la région sud de la province du Zhejiang, en Chine. Des excréments frais ont été collectés dans le rectum de chaque rongeur et l’ADN en a été extrait. L’espèce de rongeur a été identifiée par amplification par PCR du gène du cytochrome b des vertébrés. Cryptosporidium a été détecté par amplification PCR et séquençage d’amplicons de la petite sous-unité du gène de l’ARN ribosomal. Les échantillons positifs de C. viatorum et C. parvum ont ensuite été sous-typés en analysant le gène de la glycoprotéine de 60 kDa. Un résultat positif pour Cryptosporidium a été trouvé dans 7 % (26/370) des échantillons, impliquant cinq espèces de rongeurs : Apodemus agrarius (36), Niviventer niviventer (75), Rattus losea (18), R. norvegicus (155) et R. tanezumi (86). Leurs taux respectifs de positivité pour Cryptosporidium étaient de 8,3 %, 5,3 %, 11,1 %, 7,1 % et 7,0 %. L’analyse des séquences a confirmé la présence de trois espèces de Cryptosporidium : C. parvum (4), C. viatorum (1) et C. muris (1), et de deux génotypes : Cryptosporidium génotype IV de rat (16) et C. mortiferum-like (4). De plus, deux sous-types de C. parvum (IIdA15G1 et IIpA19) et un sous-type de C. viatorum (XVdA3) ont été détectés. Ces résultats démontrent que diverses espèces de rongeurs sauvages du Zhejiang sont simultanément infectées par des espèces/génotypes de Cryptosporidium zoonotiques et adaptés aux rongeurs, ce qui indique que ces rongeurs peuvent jouer un rôle dans le maintien et la dispersion de ce parasite dans l’environnement et d’autres hôtes, y compris les humains.

We first sequenced and characterised the complete mitochondrial genome of Toxocara apodeme, then studied the evolutionary relationship of the species within Toxocaridae. The complete mitochondrial genome was amplified using PCR with 14 specific primers. The mitogenome length was 14303 bp in size, including 12 PCGs (encoding 3,423 amino acids), 22 tRNAs, 2 rRNAs, and 2 NCRs, with 68.38% A+T contents. The mt genomes of T. apodemi had relatively compact structures with 11 intergenic spacers and 5 overlaps. Comparative analyses of the nucleotide sequences of complete mt genomes showed that T. apodemi had higher identities with T. canis than other congeners. A sliding window analysis of 12 PCGs among 5 Toxocara species indicated that nad4 had the highest sequence divergence, and cox1 was the least variable gene. Relative synonymous codon usage showed that UUG, ACU, CCU, CGU, and UCU most frequently occurred in the complete genomes of T. apodemi. The Ka/Ks ratio showed that all Toxocara mt genes were subject to purification selection. The largest genetic distance between T. apodemi and the other 4 congeneric species was found in nad2, and the smallest was found in cox2. Phylogenetic analyses based on the concatenated amino acid sequences of 12 PCGs demonstrated that T. apodemi formed a distinct branch and was always a sister taxon to other congeneric species. The present study determined the complete mt genome sequences of T. apodemi, which provide novel genetic markers for further studies of the taxonomy, population genetics, and systematics of the Toxocaridae nematodes.

Antibiotic resistance genes (ARGs) have attracted widespread attention as a new global pollutant, mainly due to the abuse of antibiotics. To investigate the diversity of ARGs in three rodent species, we used metagenomic sequencing analysis to analyze the diversity of antibiotic resistance genes of 17 individuals of Apodemus peninsulae and 17 individuals of Myodes rufocanus collected from Mudanfeng, and nine individuals of Apodemus agrarius collected from Sandaoguan. A total of 19 types and 248 subclasses of ARGs were detected in the three rodent species. Seven ARGs showed significant difference and five ARGs showed extremely significant difference between M. rufocanus and A. agrarius. Seven ARGs showed significant difference and four ARGs showed extremely significant difference between A. peninsulae and A. agrarius. Four ARGs showed significant difference and five ARGs showed extremely significant difference between M. rufocanus and A. peninsulae. ARGs showing high abundance in three rodents were macrolides, lincoamides, tetracyclines, and β-lactams. ARGs were widely distributed in the three rodent species. The significant differences in ARGs among different species might be due to the different distribution areas and their diet differentiation. The study could provide a basis for further studies of ARGs in mice and improve the understanding of the harm of ARGs transmission.
抗生素抗性基因(ARGs)作为全球新型污染物受到广泛关注,其产生的原因主要是抗生素的滥用。为探究大林姬鼠、棕背鼠平和黑线姬鼠的抗生素抗性基因多样性,采用宏基因组测序分析来自黑龙江牡丹峰的17只大林姬鼠、17只棕背鼠平和三道关的9只黑线姬鼠的抗生素抗性基因多样性。从3种啮齿动物中共检测到19种类型及248个亚类的ARGs。棕背鼠平和黑线姬鼠差异显著的ARGs有7个,差异极显著的有5个;大林姬鼠和黑线姬鼠差异显著的ARGs有7个,差异极显著的有4个;棕背鼠平和大林姬鼠差异显著的ARGs有4个,差异极显著的有5个。3种啮齿动物丰度较高的抗生素抗性基因大类为大环内酯类、林可酰胺类、四环素类、β-内酰胺类。ARGs已广泛存在于3种啮齿动物体内,不同物种之间抗生素抗性基因的多样性存在显著差异,产生差异的原因可能是由于3种啮齿动物的分布区不同并存在食性分化。本研究可以为啮齿动物抗生素抗性基因的后续研究提供依据,并加深对ARGs传播危害的认识。.

BACKGROUND: The geographic distribution and host-parasite interaction networks of Sarcocystis spp. in small mammals in eastern Asia remain incompletely known.
METHODS: Experimental infections, morphological and molecular characterizations were used for discrimination of a new Sarcocystis species isolated from colubrid snakes and small mammals collected in Thailand, Borneo and China.
RESULTS: We identified a new species, Sarcocystis muricoelognathis sp. nov., that features a relatively wide geographic distribution and infects both commensal and forest-inhabiting intermediate hosts. Sarcocystis sporocysts collected from rat snakes (Coelognathus radiatus, C. flavolineatus) in Thailand induced development of sarcocysts in experimental SD rats showing a type 10a cyst wall ultrastructure that was identical with those found in Rattus norvegicus from China and the forest rat Maxomys whiteheadi in Borneo. Its cystozoites had equal sizes in all intermediate hosts and locations, while sporocysts and cystozoites were distinct from other Sarcocystis species. Partial 28S rRNA sequences of S. muricoelognathis from M. whiteheadi were largely identical to those from R. norvegicus in China but distinct from newly sequenced Sarcocystis zuoi. The phylogeny of the nuclear 18S rRNA gene placed S. muricoelognathis within the so-called S. zuoi complex, including Sarcocystis attenuati, S. kani, S. scandentiborneensis and S. zuoi, while the latter clustered with the new species. However, the phylogeny of the ITS1-region confirmed the distinction between S. muricoelognathis and S. zuoi. Moreover, all three gene trees suggested that an isolate previously addressed as S. zuoi from Thailand (KU341120) is conspecific with S. muricoelognathis. Partial mitochondrial cox1 sequences of S. muricoelognathis were almost identical with those from other members of the group suggesting a shared, recent ancestry. Additionally, we isolated two partial 28S rRNA Sarcocystis sequences from Low\'s squirrel Sundasciurus lowii that clustered with those of S. scandentiborneensis from treeshews.
CONCLUSIONS: Our results provide strong evidence of broad geographic distributions of rodent-associated Sarcocystis and host shifts between commensal and forest small mammal species, even if the known host associations remain likely only snapshots of the true associations.

In mammalian research, it has been debated what can initiate an evolutionary tradeoff between different senses, and the phenomenon of sensory tradeoff in rodents, the most abundant mammalian clade, is not evident. The Nile rat (Arvicanthis niloticus), a murid rodent, recently adapted to a diurnal niche through an evolutionary acquisition of daylight vision with enhanced visual acuity. As such, this model provides an opportunity for a cross-species investigation where comparative morphological and multi-omic analyses of the Nile rat are made with its closely related nocturnal species, e.g. the mouse (Mus musculus) and the rat (Rattus norvegicus). Thus, morphological examinations were performed, and evolutionary reductions in relative sizes of turbinal bone surfaces, the cribriform plate, and the olfactory bulb were discovered in Nile rats. Subsequently, we compared multiple murid genomes, and profiled olfactory epithelium transcriptomes of mice and Nile rats at various ages with RNA sequencing. The results further demonstrate that, in comparison with mouse olfactory receptor (OR) genes, Nile rat OR genes have experienced less frequent gain, more frequent loss, and more frequent expression reduction during their evolution. Furthermore, functional degeneration of coding sequences in the Nile rat lineage was found in OR genes, yet not in other genes. Taken together, these results suggest that acquisition of improved vision in the Nile rat has been accompanied by degeneration of both olfaction-related anatomical structures and OR gene repertoires, consistent with the hypothesis of an olfaction-vision tradeoff initiated by the switch from a nocturnal to a diurnal lifestyle in mammals.

Mining can significantly alter landscapes, impacting wildlife and ecosystem functionality. Natural recovery in open-pit mines is vital for habitat restoration and ecosystem re-establishment, although few empirical studies have examined this process. Here, we assessed temporal and spatial responses of small rodents at the community, population, and individual levels during natural mine recovery. We examined the abundance, reproductive potential, and individual health of small rodents at active mines and at former mine sites left to recover naturally for approx. 10 and 20 years. We also assessed the effects of disturbance on rodent recovery processes at three distances from the mine boundary. Rodent numbers peaked after 10-13 years of recovery and exhibited the strongest male bias in the sex ratio. The Chinese white-bellied rat (Niviventer confucianus) was the most abundant species, achieving its highest population abundance at sites abandoned for 10-13 years and thriving at locations closer to the mine boundary. Only Chevrier\'s field mouse exhibited morphological responses to the mine recovery category. Ectoparasite load was unaffected by mine or distance-disturbance categories. Both Chevrier\'s field mouse (Apodemus chevrieri) and the South China field mouse (Apodemus draco) were affected significantly by vegetation layer cover during recovery succession. Our study highlights the complexities of ecological succession, with a peak in abundance as pioneer communities transition toward a climax seral stage. Careful prior planning and active site management are necessary to optimize abandoned mine recovery. Efforts to accelerate mine recovery through technical restoration should promote conditions that initiate and perpetuate the establishment and succession of wildlife assemblages.

Hemorrhagic fever with renal syndrome (HFRS) is caused by hantaviruses (HVs) and is endemic in Zhejiang Province, China. In this study, we aimed to explore the changing epidemiology of HFRS cases and the dynamics of hantavirus hosts in Zhejiang Province. Joinpoint regression was used to analyze long-term trends in the incidence of HFRS. The comparison of animal density at different stages was conducted using the Mann-Whitney Test. A comparison of HV carriage rates between stages and species was performed using the chi-square test. The incidence of HFRS shows a continuous downward trend. Cases are widely distributed in all counties of Zhejiang Province except Shengsi County. There was a high incidence belt from west to east, with low incidence in the south and north. The HFRS epidemic showed two seasonal peaks in Zhejiang Province, which were winter and summer. It showed a marked increase in the age of the incidence population. A total of 23,073 minibeasts from 21 species were captured. Positive results were detected in the lung tissues of 14 rodent species and 1 shrew species. A total of 80% of the positive results were from striped field mice and brown rats. No difference in HV carriage rates between striped field mice and brown rats was observed (χ2 = 0.258, p = 0.611).

The Rocahepevirus ratti hepatitis E virus genotype C1 (HEV-C1) has been documented to infect humans. However, the understanding of HEV-C1 remains constrained. This study aims to determine the prevalence and genomic characteristics of HEV-C1 in small animals in Yunnan province of southwestern China. A total of 444 liver tissues were collected from animals covering the orders Rodentia, Soricomorpha, Scandentia and Erinaceomorpha in three regions in Yunnan. Then Paslahepevirus balayani and Rocahepevirus were examined using RT-qPCR. The detection rate of Rocahepevirus was 12.95 % (36/278) in animals of order Rodentia, with 14.77 % (35/237) in Rattus tanezumi and 33.33 % (1/3) in Niviventer fulvescens. No Paslahepevirus balayani was detected. Additionally, two full-length Rocahepevirus sequences (MSE-17 and LHK-54) and thirty-three partial ORF1 sequences were amplified and determined to be HEV-C1. MSE-17 and LHK-54 shared moderate nucleotide identity (78.9 %-80.3 %) with HEV-C1 isolated in rats and humans. The HEV-C1 isolated from Niviventer fulvescens demonstrated a 100 % nucleotide identity with that from Rattus tanezumi. The rat HEV-C1 sequences isolated in our study and other Asian HEV-C1 sequences were phylogenetically distant from those isolated in North America and Europe. Furthermore, the two full-length sequences isolated in our study had less amino acid substitutions in the motifs of RNA-dependent RNA polymerase domain (F204L and L238F), compared with other Asian sequences. In summary, HEV-C1 commonly spreads in rats in Yunnan province of China. Our findings suggest a spatially associated phylogeny, and potential cross-species transmission of HEV-C1.

Objective: To investigate the distribution and hantavirus (HV) carrying state in host animals of hemorrhagic fever with renal syndrome (HFRS) in Henan Province from 2019 to 2022. Methods: Host animal monitoring was carried out at the monitoring sites of HFRS in Henan Province. The real-time fluorescence quantitative PCR was used to detect hantavirus in rat lungs. The types of hantavirus were analyzed. The positive samples were sequenced and then sequence homology and variation were analyzed. Results: A total of 1 308 rodents were captured from 2019 to 2022, 16 specimens of rat lungs tested positive for hantavirus nucleic acid. The positive rate of HV was 1.22% (16/1 308). According to type, the positive rate of HV in Apodius agrarius was the highest (68.75%, 11/16). According to distribution, the positive rate of HV in field samples was the highest (2.50%, 12/480), and the positive rate of HV in residential samples was 0.53% (4/759). The typing results of 16 positive samples showed that all viruses were hantavirus type Ⅰ (hantaan virus). The positive samples were sequenced and eight S gene fragments (GenBank number: OQ681444-OQ681451) and six M gene fragments (OQ681438-OQ681443) were obtained. The S and M gene fragments were similar to the Shaanxi 84FLi strain and Sichuan SN7 strain. Phylogenetic analysis of S and M gene fragments showed that they all belonged to the hantaan virus-H5 subtype. Amino acid sequence analysis revealed that, compared with the hantaan virus vaccine strain 84FLi, the 74th amino acid encoded by eight S fragments was replaced by aspartamide with serine. Tryptophan was replaced by glycine at the 14th position of Gn region in XC2022047, and isoleucine was replaced by alanine at the 359 position of XC2022022 and XC2022024. Conclusion: The hantavirus carried by host animals in Henan Province from 2019 to 2022 belongs to the type Ⅰ (hantaan virus), and Apodemus agrarius is still the dominant host animal of the hantaan virus. Compared with the vaccine strains, amino acid sites are replaced in the immune epitopes of the S and M gene fragments.
目的： 分析2019—2022年河南省肾综合征出血热（HFRS）宿主动物分布及携带汉坦病毒（HV）情况。 方法： 在河南省HFRS监测点开展宿主动物监测，采用实时荧光定量PCR法检测鼠肺HV，分析河南省鼠类动物携带HV型别，对阳性样本进行测序，分析核苷酸序列的同源性及变异情况。 结果： 2019—2022年共捕鼠1 308只，16份鼠肺HV核酸阳性，鼠HV阳性率为1.22%（16/1 308）。按种类，黑线姬鼠HV阳性率最高（68.75%，11/16）。按分布地，野外鼠HV阳性率最高（2.50%，12/480），居民区鼠HV阳性率为0.53%（4/759）。16份阳性样本分型结果显示，所携带的病毒均属于Ⅰ型汉滩病毒。阳性样本测序后获得8条S基因片段（OQ681444~OQ681451）和6条M基因片段（OQ681438~OQ681443）；S和M基因片段与陕西84FLi株、四川SN7 株相似性较高。S和M基因片段系统进化分析显示，均为汉滩病毒H5基因亚型。氨基酸序列分析显示，与汉滩病毒疫苗株84FLi相比，8条S片段编码氨基酸第74位由天冬酰胺替换为丝氨酸；XC2022047株在Gn区第14位由色氨酸替换为甘氨酸，XC2022022和XC2022024第359位由异亮氨酸替换为丙氨酸。 结论： 2019—2022年河南省宿主动物携带HV属于Ⅰ型汉滩病毒，黑线姬鼠仍然是汉滩病毒的优势宿主。同疫苗株比较，S和M基因片段的免疫表位区均有氨基酸位点替换。.

Objective: To explore the characteristics of natural foci of hemorrhagic fever with renal syndrome (HFRS) in Gansu Province. Methods: The information of HFRS case data and rodent density monitoring data from 2012 to 2022 in Gansu Province were collected and epidemiological methods were used to analyze and investigate the characteristics of the epidemic focus. Results: A total of 869 cases of HFRS were reported, and four patients died from 2012 to 2022. The annual incidence rate is between 0.05 per 100 000 and 1.21 per 100 000. The cases were mainly distributed in the eastern, southeast, southern, and south of the central region of Gansu Province. Most cases were distributed between age 20-60, and the sex ratio was 1.85∶1 (564∶305). Most cases were farmers (61.80%, 537/869), herdsmen (19.79%,172/869) and students (6.33%, 55/869). In a wild rat-type epidemic focus,the incidence peak was from November to January of the following year. The natural rodent hosts of HFRS were Rattus norvegicus, Apodemus agrarius, and Mus musculus. The hantaan virus carriage rates were 2.79% (21/754), 0.42% (5/1 179) and 0.31% (2/643),respectively. Three epidemic foci were defined: two derived from the Pingliang and Gannan prefecture new outbreaks epidemic foci, respectively, while the other was the residue of the Dingxi epidemic focus. Conclusions: The southern, south of the central region and eastern part of Gansu Province are current key HFRS epidemic foci dominated by Rattus norvegicus, Apodemus agrarius, and Mus musculus, respectively. The virus genotype is hantaan virus. Case reporting areas should strengthen epidemic monitoring; the key epidemic areas should strengthen and implement various prevention and control measures to reduce the harm caused by HFRS.
目的： 探讨甘肃省肾综合征出血热（HFRS）自然疫源地现状特征。 方法： 收集2012-2022年甘肃省HFRS病例数据和啮齿类动物（鼠类）密度监测资料，应用流行病学方法分析调查疫源地特征。 结果： 2012-2022年甘肃省共报告HFRS病例869例，死亡4例，年发病率在0.05/10万~1.21/10万之间，病例主要分布于甘肃省东部的平凉市、东南部的天水市、南部的甘南藏族自治州（甘南州），以及中部以南的定西市；20~60岁年龄组居多，男女性别比为1.85∶1（564∶305），职业以农民（61.80%，537/869）、牧民（19.79%，172/869）和学生（6.33%，55/869）为主。野鼠型发病以每年11月至次年1月为高峰。啮齿类宿主动物以褐家鼠、黑线姬鼠和小家鼠为主，汉滩病毒携带率分别为2.79%（21/754）、0.42%（5/1 179）和0.31%（2/643）。甘肃省目前确定了3个疫源地，其中2个分别是平凉市和甘南州的新发疫源地，另1个为定西市的老疫源地。 结论： 甘肃省南部、中部以南和东部地区是目前主要的HFRS疫源地，宿主动物以褐家鼠、黑线姬鼠和小家鼠为主，病毒基因型为汉滩病毒。病例报告地区应加强疫情的监测，疫情重点地区应强化和落实各项预防和控制措施，以减少HFRS带来的危害。.