Infection Genetics and Evolution最新文献

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.

The rising frequency of multidrug-resistant (MDR) Acinetobacter baumannii infections represents a significant public health challenge in Bangladesh. Genomic analysis of bacterial pathogens enhances surveillance and control efforts by providing insights into genetic diversity, antimicrobial resistance (AMR) profiles, and transmission dynamics. In this study, we conducted a comprehensive bioinformatic analysis of 82 whole-genome sequences (WGS) of A. baumannii from Bangladesh to understand their genomic epidemiological characteristics. WGS of the MDR and biofilm-forming A. baumannii strain S1C revealed the presence of 28 AMR genes, predicting its pathogenicity and classification within sequence type ST2. Multi-locus sequence typing (MLST) genotyping suggested heterogeneity in the distribution of clinical A. baumannii strains in Bangladesh, with a predominance of ST575. The resistome diversity was evident from the detection of 82 different AMR genes, with antibiotic inactivation being the most prevalent resistance mechanism. All strains were predicted to be multidrug-resistant. The observed virulence genes were associated with immune evasion, biofilm formation, adherence, nutrient acquisition, effector delivery, and other mechanisms. Mobile genetic elements carrying AMR genes were predicted in 68.29% (N = 56) of the genomes. The “open” state of the pan-genome and a high proportion of accessory genes highlighted the genome plasticity and diversity of A. baumannii in Bangladesh. Additionally, phylogenomic analysis indicated clustering of A. baumannii strains into three separate clades according to sequence type. In summary, our findings offer detailed insights into the genomic landscape of A. baumannii in Bangladesh, contributing to our understanding of its epidemiology and pathogenicity and informing strategies to combat this pathogen.

Although we live in the genomic era, the accessibility of the complete genome sequence of Coxiella burnetii, the etiological agent of Q fever, has increased knowledge in the field of genomic diversity of this agent However, it is still somewhat of a “question” microorganism. The epidemiology of Q fever is intricate due to its global distribution, repository and vector variety, as well as absence of surveys defining the dynamic interaction among these factors. Moreover, C. burnetii is a microbial agent that can be utilized as a bioterror weapon. Therefore, typing techniques used to recognize the strains can also be used to trace infections back to their source which is of great significance. In this paper, the latest and current typing techniques of C. burnetii spp. are reviewed illustrating their advantages and constraints. Recently developed multi locus VNTR analysis (MLVA) and single-nucleotide polymorphism (SNP) typing methods are promising in improving diagnostic capacity and enhancing the application of genotyping techniques for molecular epidemiologic surveys of the challenging pathogen. However, most of these studies did not differentiate between C. burnetii and Coxiella-like endosymbionts making it difficult to estimate the potential role that ticks play in the epidemiology of Q fever. Therefore, it is necessary to analyze the vector competence of different tick species to transmit C. burnetii. Knowledge of the vector and reservoir competence of ticks is important for taking adequate preventive measures to limit infection risks. The significant prevalence observed for the IS1111 gene underscores its substantial presence, while other genes display comparatively lower prevalence rates. Methodological variations, particularly between commercial and non-commercial kit-based methods, result in different prevalence outcomes. Variations in sample processing procedures also lead to significant differences in prevalence rates between mechanical and non-mechanical techniques.

Melioidosis is a zoonotic disease, with its outbreaks being rare and indicative of an unusual concurrence of extreme climate and natural environmental factors. An outbreak of melioidosis cases emerged in Hainan following Typhoon “Dianmu” from October to December 2021, presenting an opportunity to identify the environmental sources of infection for these cases due to its nature as a well-defined point-source cluster. To investigate the relationship between the occurrence of these melioidosis cases and the environment, we extracted the entire genome of 25 clinical strains and conducted MLST typing, followed by whole genome sequencing and analysis of molecular genetic information for four ST46 genotypes from these strains. Phylogenetic and evolutionary relationships between Hainan sequence types (STs) and those found in other endemic regions were analyzed using IslandPath-DIMO, PHASTER, e-BURST, PHYLOViZ, and the maximum likelihood method. Notably, a total of 25 clinical strains were identified, encompassing 12 STs (ST46, ST1105, ST1991, ST30, ST1992, ST50, ST164, ST55, ST70, ST1993, ST1545, and ST58), with ST1991, ST1992, and ST1993 being newly discovered subtypes. PHYLOViZ clustering analysis divided the strains into two groups (A and B), both closely related to the Asian region. Phylogenetic tree analysis further revealed that most of the strains in this study were closely related to those found in Australia and Thailand. Analysis of patient information and visits to their residences suggested that contaminated water sources might be the primary source of infection during this outbreak.

Our findings underscore that extreme weather events, such as typhoons, significantly increase the infection rate of B. pseudomallei, along with its genetic diversity, necessitating additional prevention strategies to control these B. pseudomallei infections.

Objective

In Guangdong Province, hepatitis C virus (HCV) had been found to confer resistance to direct-acting antivirals (DAAs). There were few studies of HCV subtypes and resistance-associated substitutions (RASs) of HCV in different high-risk populations. In this study, we aimed to determine the subtype distribution and the RASs in high-risk population groups, including drug users (DU), men who have sex with men (MSM), female sex workers (FSW), and male patients with sexually transmitted diseases (STD) in Guangdong Province (a highly developed province with a large population).

Methods

Using a city-based sampling strategy,1356 samples were obtained from different population groups. Phylogenetic analyses determined subtypes based on Core, NS5B, or NS5A sequences. HCV subtype distribution and RASs in various risk groups and regions were analyzed.

Results

Ten subtypes, of which 6 h and 6 k were novel in Guangdong, were identified. The primary subtype among all risk groups was 6a. RASs in 1b and 3a were different from those observed in other studies. Subtype 3b in western Guangdong was higher than the other three regions. No RASs were found in 6a or any other genotype 6.

Conclusions

The HCV subtypes are expanding in high-risk populations in Guangdong. Drug use by other risk groups and commercial sex by DU may bridge the dissemination of 6a from DU to other populations. The RAS profiles of 1b and 3a differed from those reported in studies conducted in southwestern China. Further research is required to determine the reason for this discrepancy. Moreover, the combination of RASs was high in subtype 3b. To guide HCV treatment of subtype 3b, pretreatment subtyping of HCV genotype 3 should be considered in western cities in the near future.

Purpose

We aimed to characterise Yersinia enterocolitica from human clinical specimens in Switzerland using epidemiological, microbiological and whole-genome sequencing (WGS) data.

Methods

Isolates (n = 149) were collected between January 2019 and December 2023. Epidemiological data was noted and strains were characterized by biochemical and serological typing, antimicrobial susceptibility testing (AST), and WGS-based analysis.

Results

Most of the isolates (86%) were from stool specimens and 52% were from male patients. The patients' median age was 28 years (range < 1–94 years). Typing assigned the isolates to bioserotype 4/O:3 (44%), biotype 1A (34%), bioserotype 2/O:9 (21%), and bioserotype 3/O:3 (1%). WGS identified Y. enterocolitica (n = 147), Y. alsatica (n = 1) and Y. proxima (n = 1). Seven isolates were multidrug resistant (MDR) and harboured plasmid pAB829 carrying aph(3″)-Ib, aph(6)-Id, and tet(Y) (n = 1), pAC120 carrying aph(6)-Id and tet(A) (n = 2), or a 12.6 kb Tn2670-like transposon containing catA1, aadA12, sul1, and qacEΔ1 (n = 4). Virulence factors (VFs) included ail (n = 99), invB, (n = 145), ystA (n = 99), ystB (n = 48) and pYV-associated VFs (n = 93). MLST and cgMLST analysis showed that BT 1A strains consisted of several STs and were highly diverse, whereas BT 2/O:9 strains were all ST12 and clustered closely, and BT 4/O:3 strains mostly belonged to ST18 but were more diverse. SNP analysis revealed two highly clonal BT 4/O:3 subpopulations with wide spatio-temporal distribution.

Conclusions

Y. enterocolitica BT 1A, BT 2/O:9 and BT 4/O:3 are frequently associated with human yersiniosis in Switzerland. WGS-based subtyping of Y. enterocolitica is a powerful tool to explore the genetic diversity and the pathogenic potential of human isolates.

Despite intensive control efforts, Foot and mouth disease (FMD) outbreaks continue to occur regularly in Egypt and resulting in dramatic economic losses to the livestock industry. During 2018 and 2022, FMD was clinically suspected among previously vaccinated cattle in Beheira and Kafr El-Sheikh provinces, Egypt. FMDV RNA was detected in 18 (45%) out of 40 epithelial tissue samples using real-time RT-PCR based on a pan-FMDV primers set. The 2018 outbreak isolates (n = 8) included the FMDV serotypes A and SAT2, whereas all isolates (n = 10) from the 2022 outbreak belonged to the FMDV serotype A. Four selected isolates, designated FMDV/SAT2/EGY/Beheira/2018, FMDV/A/EGY/Kafr El-Sheikh/2018, FMDV/A/EGY/Kafr El-Sheikh/2022 and FMDV/A/EGY/Behiera/2022, were characterized on the basis of partial VP1 gene sequence analysis. The FMDV/SAT2/EGY/Beheira/2018 strain was clustered within the Lib-12 lineage of the topotype VII and shared 79.2–98.4% nucleotide identity with other Egyptian SAT2 strains available in Genbank database. On the other hand, the three FMDV serotype A sequences shared 74.4–99.1% nucleotide identity with each other. Also, they were phylogenetically classified within two distinct topotypes. The FMDV/A/Egy/Kafr El-Sheikh/2018 strain was grouped within the Asian topotype, meanwhile the FMDV/A/EGY/Kafr El-Sheikh/2022 and FMDV/A/EGY/Behiera/2022 strains were grouped together within the genotype IV of the African topotype. Interestingly, the deduced amino acid sequences of the four strains displayed numerous variations in comparison to the vaccine strains currently used in Egypt. In addition, most of these variations were present in prominent antigenic positions in the VP1 protein. These findings raise a crucial need to validate the protective potential of the vaccine strains against the newly emerging FMDV field strains and to update the vaccination strategy accordingly.