Infection Genetics and Evolution最新文献

In April 2023, an outbreak of acute hepatitis was reported amongst internally displaced persons in the Nazareth community of South Sudan. IgM serology-based screening suggested the likely etiologic agent to be Hepatitis E virus (HEV). In this study, plasma specimens collected from anti-HEV IgM-positive cases were subjected to additional RT-qPCR testing and sequencing of extracted nucleic acids, resulting in the recovery of five full and eight partial HEV genomes. Maximum likelihood phylogenetic reconstruction confirmed the genomes belong to HEV genotype 1. Using distance-based methods, we show that genotype 1 is best split into three sub-genotypes instead of the previously proposed seven, and that these sub-genotypes are geographically restricted. The South Sudanese sequences confidently cluster within sub-genotype 1e, endemic to northeast, central, and east Africa. Bayesian Inference of phylogeny incorporating sampling dates shows that this new outbreak is not directly descended from other recent local outbreaks for which sequence data is available. However, the analysis suggests that sub-genotype 1e has been consistently and cryptically circulating locally for at least the past half century and that the known outbreaks are often not directly descended from one another. The ongoing presence of HEV, combined with poor sanitation and hygiene in the conflict-affected areas in the region, place vulnerable populations at risk for infection and its more serious effects, including progression to fulminant hepatitis.

The human gut presents a complex ecosystem harboring trillions of microorganisms living in close association with each other and the host body. Any perturbation or imbalance of the normal gut microbiota may prove detrimental to human health. Enteric infections and treatment with antibiotics pose major threats to gut microbiota health. Recent genomics-driven research has provided insights into the transmission and evolutionary dynamics of major enteric pathogens such as Escherichia coli, Klebsiella pneumoniae, Vibrio cholerae, Helicobacter pylori and Salmonella spp. Studies entailing the identification of various dominant lineages of some of these organisms based on artificial intelligence and machine learning point to the possibility of a system for prediction of antimicrobial resistance (AMR) as some lineages have a higher propensity to acquire virulence and fitness advantages. This is pertinent in the light of emerging AMR being one of the immediate threats posed by pathogenic bacteria in the form of a multi-layered fitness manifesting as phenotypic drug resistance at the level of clinics and field settings. To develop a holistic or systems-level understanding of such devastating traits, present methodologies need to be advanced with the high throughput techniques integrating community and ecosystem/niche level data across different omics platforms. The next major challenge for public health epidemiologists is understanding the interactions and functioning of these pathogens at the community level, both in the gut and outside. This would provide new insights into the dimensions of enteric bacteria in different environments and niches and would have a plausible impact on infection control strategies in terms of tackling AMR. Hence, the aim of this review is to discuss virulence and AMR in Gram-negative pathogens, the spillover of AMR and methodological advancements aimed at addressing it through a unified One Health framework applicable to the farms, the environment, different clinical settings and the human gut.

Background

Senecavirus A (SVA) is the only member of the genus Senecavirus in the family Picornaviridae, and is one of the pathogens of porcine blistering disease. SVA has been reported in the United States, Canada, China, Thailand, and Colombia.

Methods

In this study, positive SVA infection was detected by RT-PCR in sick materials collected from pig farms of different sizes in Anhui Province.

Results

In this study, a virulent strain of SVA was successfully obtained by viral isolation on BHK21 cells and named SVA-CH-AHAU-1. Meanwhile, a simple, rapid and accurate nano-PCR method for the detection of SVA infection was established in this study, using the recombinant plasmid pClone-SVA-3D as a template.

Conclusions

The complete genome of SVA-CH-AHAU-1 is 7286 bp, including a 5′ non-coding region (UTR), an open reading frame (ORF) of 6546 nucleotides, encoding 2182 amino acids (aa), and a 3’ UTR with Poly(A) features, and phylogenetic analysis showed that this isolate had the highest nucleotide homology (97.9 %) with the US isolate US-15-41901SD. In this study, the virulent strain SVA-CH-AHAU-1 was found to recombine in the ORF region with isolates SVA-CH-SDGT-2017 and SVA/Canada/ON/FMA-2015-0024 T2/2015. The complete genome has been submitted to GeneBank with the accession number OM654411. In addition, our results suggest that the established nano-PCR assay can be used as an economical, reliable and sensitive method for the field diagnosis of SVA method, especially in resource-limited areas.

This study characterised type O foot-and-mouth disease (FMD) viruses recovered from outbreaks that were reported between 2010 and 2019 in the Republic of Korea. We used 96 newly generated whole-genome sequences (WGS) along with 131 already published WGSs from samples collected from countries in East and Southeast Asia. We identified at least eight independent introductions of O/SEA/Mya-98 and O/ME-SA/Ind-2001e FMDV strains into the Republic of Korea during the study period, which were closely related to the sequences of viruses circulating in the East and Southeast Asia neighbourhood with over 97 % nucleotide identity. Spatial-temporal transitions of O/SEA/Mya-98 lineage viruses recovered from the largest outbreak (2014–16) showed that after initial cases were detected within a 15-day period in July 2014, a single introduction of the same virus during December 2014 generated extensive forward virus transmission between farms that lasted until March 2016. We estimated that secondary transmissions were responsible for infection on 44 % FMD affected farms, over a total of 14 generations of infection. We eastimated a median evolutionry rate of 2.51 × 10⁻⁵ nt/site/day, which is similar for other FMD epidemic scenarios. These findings suggest that regular incursions of different FMDV lineages into the Republic of Korea have posed a continuous threat from endemic countries of East and Southeast Asia. These data highlight the importance of active cooperation and information exchange on FMD situation within Asian countries and assessment about the likely risk routes of virus movement is highly necessary to prevent further incursion and virus spread of FMDV in the Republic of Korea.

Mapping tick distribution and pathogens in unexplored areas sheds light on their importance in zoonotic and veterinary contexts. In this study, we performed a comprehensive investigation of the genetic diversity of tick and tick-borne pathogens (TBPs) detection infesting/infecting small ruminants across northern Pakistan. We collected 1587 ixodid ticks from 600 goats and sheep, an overall tick infestation rate of 50.2 %. Notably, gender-based infestation rates were higher in female goats and sheep compared to their male counterparts. Age-wise analysis showed that the tick infestation rate was higher in older animals. This study identified 11 ixodid tick species within three genera: Hyalomma, Haemaphysalis, and Rhipicephalus, which were taxonomically classified using 16S rRNA and cytochrome oxidase I (cox1) molecular markers. Sequence analysis indicated that reported ticks are similar to ixodid species found across various Asian and African countries. Tick-borne pathogens were detected by amplifying 16S rRNA and citrate synthase (gltA) for bacterial pathogens and 18S rRNA for apicomplexan parasites. The present study reported a diverse array of TBPs in ticks from the study area, with Rickettsia massiliae (24.5 %) and Theleria ovis (16.4 %) as the most prevalent bacterial and apicomplexan pathogens. Phylogenetically, detected TBPs shared evolutionary relatedness with identical TBPs from old and new world countries. These findings highlight the presence of zoonotic TBPs in ixodid ticks from Pakistan. In addition, it also provides a foundation for future epidemiological research on ticks and TBPs, emphasizing their relevance in both zoonotic and veterinary contexts.

Molecular data analysis is invaluable in understanding the overall behavior of a rapidly spreading virus population when epidemiological surveillance is problematic. It is also particularly beneficial in describing subgroups within the population, often identified as clades within a phylogenetic tree that represent individuals connected via direct transmission or transmission via differing risk factors in viral spread. However, transmission patterns or viral dynamics within these smaller groups should not be expected to exhibit homogeneous behavior over time. As such, standard phylogenetic approaches that identify clusters based on summary statistics would not be expected to capture dynamic clusters of transmission. We, therefore, sought to evaluate the performance of existing and adapted phylogeny-based cluster identification tools on simulated transmission clusters exhibiting dynamic transmission behavior over time. Despite the complementarity of the tools, we provide strong evidence that novel cluster identification methods are needed for reliable detection of epidemiologically linked individuals, particularly those exhibiting changing transmission dynamics during dynamic outbreak scenarios.

Tick-borne encephalitis virus (TBEV) is a pathogen that causes febrile infectious diseases and neurological damage to humans. TBEVs are prevalent from Europe to Far Eastern Asia, including Northeastern China. The understanding of TBEV phylogeny in China has been limited owing to insufficient genomic data on Chinese TBEV strains. Here, six TBEV strains were isolated from ticks collected in Inner Mongolia. The transmission electron microscopy revealed spherical particles with an enveloped structure of 50–60 nm in diameter. Phylogenetic analysis showed that, two strains were classified as the Siberian subtype, while the remaining four were identified as the Far Eastern subtype. Migration analyses based on TBEV ORF and envelope (E) protein sequences revealed that Chinese TBEV strains were migrated from Russia and/or Kazakhstan into China. Hulun Buir and Mudanjiang, the northeastern region of China, are considered hotspots with multiple import and export routes of Chinese TBEV strains. These results promote the understanding of TBEV genetic variations and phylogeny in China and suggest the importance of improving investigation of TBEV prevalence, which would instrumental for vaccine design strategies and better preparation for controlling TBEV infection in humans.

Hemoplasmas (hemotropic mycoplasmas) are uncultivable wall-less bacteria able to infect mammalian erythrocytes. Hemoplasmas can cause anemia, especially in immunocompromised hosts, predisposing to secondary infections and even leading to death. Between 2017 and 2023, spleen samples of 131 wild Iberian wolves (Canis lupus signatus) of Cantabria (Spain) were screened for Mycoplasma spp. using a real-time PCR able to amplify a 360 bp fragment of the 16S rRNA gene and confirmed by direct Sanger sequencing. Additional conventional PCRs were performed to screen for coinfections by different Mycoplasma species and to discriminate between Mycoplasma haemocanis/haemofelis (Mhc/Mhf). Overall, 24/131 (18.3%) animals were PCR-positive. Biological and environmental factors potentially promoting hemoplasma infection in this species were analyzed. Two different hemoplasma species were detected: Mhc/Mhf (18/131; 13.7%) and Candidatus Mycoplasma haematoparvum (CMhp) (3/131; 2.3%), each with one nucleotide sequence type (ntST); three other sequences were not classified. No Mhc/Mhf and CMhp coinfection were observed. The 12 Mhc/Mhf suitable for ribonuclease P RNA sequencing were confirmed as Mhc. Mhc ntST was 100% identical to a Mhc sequence previously obtained in domestic dogs (Canis lupus familiaris), and in wild Iberian wolves of northwestern Spain (Asturias and Galicia) at a similar prevalence to the one found herein, suggesting a high Mhc genetic homogeneity in this wild population. CMhp ntST was 100% identical to CMhp sequences from domestic dogs. To our knowledge, this is the first description of CMhp in the Iberian wolf. The high genetic similarity observed in Mhc and CMhp sequences, as well as their high similarity with domestic dog sequences, suggest its recent introduction, a high level of intraspecific transmission within the wild wolf population, and likely, interspecific transmission between wolves and domestic dogs.

The microbiota composition of the bovine female reproductive tract influences reproductive efficiency, susceptibility to genital pathogens, and the health of newborn calves. However, knowledge about cervico-vaginal microbiota during gestation is scarce. Therefore, the present study aimed to analyze the taxonomic profile of the cervico-vaginal bovine microbiota throughout pregnancy and after calving using high-throughput sequencing of a fragment of the 16S ribosomal RNA gene.

Healthy nulliparous Holstein heifers (n = 13) with similar age and body conditional score were selected to collect samples from the cervico-vaginal area with a sterile swab at 5 timepoints. We sequenced the V1-V2 region of the 16S ribosomal RNA gene and analyzed data using the DADA2, phyloseq and vegan R Studio packages.

No differences were observed in alpha and beta diversity across sampling points, accounting for the stability of the microbiota throughout pregnancy. The most abundant phyla are Firmicutes, Bacteroidota, Proteobacteria and Actinobacteria, and are present as the main taxa in all five sampling points. Also, several of the least abundant taxa can be observed to change with time.

Our comprehensive study of the cervico-vaginal bacterial microbiota during the gestation period contributes to the knowledge of microbiota dynamics on the bovine reproductive tract during and after pregnancy and can serve as a baseline for future research and the development of potential therapeutic interventions.

The rapid emergence of Extended-spectrum β-lactamase producing Enterobacteriaceae (ESBL-E) is a major global public health concern. Previous studies have identified that intensive medical care of dogs and cats in veterinary hospitals have accelerated the infections and spread of ESBL-E. To investigate the spread of ESBL-E in a veterinary hospital, a total of 202 samples including hospitalized animals, veterinary healthcare workers and environment were collected from a veterinary hospital in Chengdu, China. ESBL-E were identified by antimicrobial susceptibility testing and 16 s rRNA sequencing and were further conducted on ESBL gene detection and multilocus sequence typing (MLST). At last, strains with transmission potential were analyzed by whole genome sequencing (WGS). Our results showed that the overall prevalence of ESBL-positive isolates was 34.7% (70/202), with 55.3% (26/47) in animals, 29.3% (12/41) in healthcare workers and 28.1% (32/114) in environment swabs. Twenty diverse MLST types were detected, with ST744, ST231 as the most prevalent ones. Transmission chains of two ESBL-E.coli (ST744 bla_CTX-M-18, bla_TEM-1) from cat_21 to cat_14, and two ESBL-Kp (ST231 bla_CTX-M-27, bla_TEM-1, bla_SHV-1) from cat_20 to cat_37 were further confirmed by WGS. Furthermore, interdisciplinary investigation and cooperation of AMR are needed to better limit the transmissions of high-risk strains and to implement effective public health interventions.