Pathogens

Background: Cystic echinococcosis (CE) remains a significant zoonotic burden in the pastoral regions of China. Yili Prefecture in Xinjiang is a high-risk area, yet comprehensive data are lacking on the prevalence and molecular characteristics of Echinococcus granulosus in its primary intermediate host, sheep. Methods: From 2020 to 2024, a total of 2700 sheep livers were visually inspected for hydatid cysts infection at one randomly selected slaughterhouse in each of the nine counties of Yili Prefecture. Ninety cyst-positive samples were subjected to morphological examination and molecular genotyping by amplifying and sequencing the nad2 gene. Results: The overall prevalence of E. granulosus was 22.0% (594/2700). County-level prevalence ranged from 18.3% (Zhaosu County) to 25.7% (Huocheng County), with no significant differences observed among the counties (p > 0.05) except between Huocheng and Zhaosu. Temporally, the annual prevalence fluctuated between 20.2% and 24.2% without a consistent downward trend. Genotyping revealed that the G1 genotype was overwhelmingly dominant (95.2%, 79/83), with a minor circulation of the G3 genotype (4.8%, 4/83). Fourteen haplotypes were identified; Hap1 was the central and predominant haplotype (47.0%, 39/83), found in all counties. Network analysis suggested a recent population expansion of the parasite. Conclusion: This five-year surveillance study reveals a persistently high prevalence and complex genetic diversity of E. granulosus in sheep in Yili Prefecture. The dominance of the zoonotic G1 genotype indicates a substantial public health threat. Our findings provide crucial data for contributing to the development of local control strategies. However, the specific reasons for the high infection rate in sheep remain unclear, as this study did not include examinations of definitive hosts or environmental samples; this gap should be addressed in future research.

Background: Cholera, caused by Vibrio cholerae, remains endemic in many developing countries, including Pakistan. The extensive use of antibiotics has led to the emergence of antimicrobial resistance in V. cholerae, limiting available treatment options. In this study, we performed molecular characterisation of antibiotic-resistant V. cholerae serotype Ogawa isolates from a recent cholera outbreak in Khyber Pakhtunkhwa, Pakistan. Methodology: Suspected cholera stool samples were collected from hospitalised patients at various district hospitals of Khyber Pakhtunkhwa Province (KPK), Pakistan. The samples were transported to the Public Health Reference Microbiology Laboratory at Khyber Medical University, Peshawar. V. cholerae were identified based on colonial morphology, Gram staining, and biochemical tests using EPI 10E. For serotype identification, monovalent antisera were used. Antibiotic susceptibility testing (AST) was performed using CLSI M45 and EUCAST guidelines. DNA was extracted from pure colonies of multidrug-resistant (MDR) V. cholerae and subjected to whole-genome sequencing (WGS) for genomic characterisation using an Illumina MiSeq platform. Results: Of the 350 active diarrheal cases investigated, 70 were confirmed as V. cholerae. The outbreak was initially reported in Dir and was subsequently followed by a high incidence of cholera in the Peshawar district of KPK. All strains belong to the Ogawa serotype, which shows high antibiotic resistance, particularly to ampicillin (n = 62, 88.57%), Sulfamethoxazole/Trimethoprim (n = 60, 85.71%), Erythromycin (n = 59, 84.29%), and Tetracycline (n = 53, 75.71%). The lowest resistance was against Meropenem (n = 1, 1.4%), followed by amikacin (n = 7, 10.0%) and levofloxacin (n = 13, 18.57%). Furthermore, 34 (48.57%) of the isolates were MDR, while 13 (18.57%) were extensively drug-resistant. Six samples were selected for whole-genome sequencing. The selection of six V. cholerae samples for WGS was based on their drug resistance pattern and origin of isolation. At the genomic level, all sequenced V. cholerae strains harboured multiple antimicrobial resistance determinants. Quinolone resistance was associated with mutations and genes in gyrA, gyrB, parC, and parE; resistance to sulfamethoxazole–trimethoprim with folA, folP, and dfr; tetracycline resistance with tetA and tet35; chloramphenicol resistance with catB and S10p; and aminoglycoside resistance with hns, S12p, and gigB. In addition, β-lactam resistance was linked to the presence of efflux and β-lactamase genes, including blaSHV and mox-3. Mutations were identified in gyrA at positions S83I, S177A, and S202A, and in parC at positions S85L and I231V. Collectively, the presence of these resistance determinants likely enables V. cholerae to survive exposure to high concentrations of multiple antibiotics. Conclusions: Our V. cholerae isolates showed close genetic relatedness to previously sequenced strains from Pakistan (2010 and 2022), as well as to recently reported international strains from the USA, Australia, and China. These findings highlight both the long-term persistence of these lineages within Pakistan and their international dissemination, likely facilitated by globalisation.

Bluetongue (BT) is an arthropod-borne viral disease primarily affecting domestic and wild ruminants. In recent years, several BTV serotypes and genotypes have been detected in Israel almost annually, raising questions about their origin and routes of introduction. Some BTV serotypes closely related to those first identified in Israel, including BTV-3, BTV-8, and BTV-12, were subsequently reported in Europe after a delay of several years. In this study, we sequenced the complete genomes of one representative strain of all newly identified Israeli BTV genotypes/serotypes—BTV-1, -4, -5, -8, and -11—first detected between 2021 and 2023. Additionally, complete sequences of enzootic Israeli BTV (2015) and eleven BTV-3 strains (2019–2023), with two representative strains for every year of isolation, except 2021 (three strains), were analyzed using phylogenetic, BLAST, and pairwise identity approaches. Genetic analyses revealed that recently identified Israeli and European BTV strains share common African ancestors, with some genomic “incursions” from Mayotte Island or the Arabian Peninsula. These incursions appeared more frequently in Israeli than in European strains. Nevertheless, nucleotide sequence differences of at least 2–3% across all genes indicate several years of independent evolution. The observed divergence suggests that no direct transmission of BTV occurred between Israel and Europe during the past decade.