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Population structure and antibiotic resistance of swine extraintestinal pathogenic Escherichia coli from China
Extraintestinal Pathogenic
Escherichia coli
(ExPEC) pose a significant threat to human and animal health. However, the diversity and antibiotic resistance of animal ExPEC, and their connection to human infections, remain largely unexplored. The study performs large-scale genome sequencing and antibiotic resistance testing of 499 swine-derived ExPEC isolates from China. Results show swine ExPEC are phylogenetically diverse, with over 80% belonging to phylogroups B1 and A. Importantly, 15 swine ExPEC isolates exhibit genetic relatedness to human-origin
E. coli
strains. Additionally, 49 strains harbor toxins typical of enteric
E. coli
pathotypes, implying hybrid pathotypes. Notably, 97% of the total strains are multidrug resistant, including resistance to critical human drugs like third- and fourth-generation cephalosporins. Correspondingly, genomic analysis unveils prevalent antibiotic resistance genes (ARGs), often associated with co-transfer mechanisms. Furthermore, analysis of 20 complete genomes illuminates the transmission pathways of ARGs within swine ExPEC and to human pathogens. For example, the transmission of plasmids co-harboring
fosA3
,
bla
CTX-M-14
, and
mcr-1
genes between swine ExPEC and human-origin
Salmonella enterica
is observed. These findings underscore the importance of monitoring and controlling ExPEC infections in animals, as they can serve as a reservoir of ARGs with the potential to affect human health or even be the origin of pathogens infecting humans.
Extraintestinal pathogenic
E. coli
(ExPEC) is a significant cause of human and animal disease. Here, the authors compile a collection of 499 ExPEC samples from swine in China and characterise their phylogenetic population structure and antibiotic resistance profiles.
Journal Article
Extraintestinal Escherichia coli from camel carcasses: Phylogroups, serotypes, and markers of virulence
Pathogenic Escherichia coli causes infections responsible for economic losses in animal herds worldwide. Although this bacterium is well studied in livestock and poultry, studies of camelid infections caused by extraintestinal pathogenic E. coli (ExPEC) are limited. In this study, a set of ExPEC from camel carcasses (n = 150) was characterized with respect to phylogenetic groups, 162 O serotypes, and 35 virulence-associated genes (VAGs) using PCR screening. ExPEC frequently belonged to phylogroup B1 (58.7%), followed by phylogroups C, A, and B2 (12.7%, 12.0%, and 9.3%, respectively). Additionally, the set of ExPEC contained 36 different serotypes. The ExPEC isolates were found to typically encode ≥5 tested VAGs, particularly those related to adhesion ( afaI , fimA , pap , sfa , tsh ), iron acquisition ( fyuA , iroN , iucC , sitA ), host cell damage ( α-hly , cdt , cnf1 , sat ), invasion ( ibeA ), and bacterial protection ( iss , ompT , traT ). Moreover, ExPEC from camel adults and calves were different from each other. Among isolates from calves, prevalence was significantly higher for phylogroups C (q < 0.001) and E (q < 0.01), and ten VAGs, including fitness factors ( eitA , fepC , fyuA , iroN , iss , iucD , ompT , sitA ), as well as VAGs with stronger link to pathogenicity ( hlyF , and pap ). To identify potential reservoir of camel ExPEC strains, fecal E. coli (n = 139) from healthy camels were also analyzed. Based on the identified characteristics, ExPEC were distinguishable from fecal isolates of healthy camels, suggesting an exogenous source of ExPEC infections, likely transmitted from wild birds and human keepers.
Journal Article
Virulence genes and phylogenetic groups of uropathogenic Escherichia coli isolates from patients with urinary tract infection and uninfected control subjects: a case-control study
Background
Urinary Tract Infection (UTI) is one of the most common bacterial infectious diseases which causes considerable morbidity and costly health problems. Uropathogenic
Escherichia coli
(UPEC), the most common pathogen causing UTI, is a highly heterogeneous group of extraintestinal pathogenic
E. coli
(ExPEC) which may carry a variety of virulence factors and belonging to different phylogenetic backgrounds. The current study aimed to investigate the frequency and association between various virulence factors (VFs) and phylogenetic groups of UPEC and commensal isolates.
Methods
UPEC and commensal
E. coli
strains isolated from UTI and feces of healthy humans were compared for the presence of VFs and phylogenetic groups. Association between virulence genes was investigated and cluster analysis was employed.
Results
According to the results, among a 30 virulence markers tested, the pathogenicity-associated island (PAI)
, pap
AH,
papEF
,
fimH, fyuA
, and
traT
genes prevalence were statistically significant in UPEC isolates. A strong association was found between the B2 and D phylogenetic groups and clinical isolates of UPEC; while, commensal isolates were mostly associated with phylogenetic group A. The aggregated VFs scores were more than twice higher in the UPEC isolates in comparison with the commensal isolates. Interestingly, the B2 group in both UPEC and commensal isolates had the highest VF scores. A strong positive association was found between several virulence genes. The clustering results demonstrated that UPEC or commensal
E. coli
isolates were highly heterogeneous due to different composition of their virulence gene pool and pathogenicity islands.
Conclusion
Genetic structure and VFs of UPEC strains vary from region to region; therefore, to control the UTI, the epidemiological aspects and characterization of the UPEC isolates need to be investigated in different regions. Since UPEC isolates are generally originate from the commensal strains, it may be feasible to reduce the UTI burden by interfering the intestinal colonization, particularly in the highly pathogenic clonal lineages such as B2.
Journal Article
Iceland as Stepping Stone for Spread of Highly Pathogenic Avian Influenza Virus between Europe and North America
Highly pathogenic avian influenza viruses (HPAIVs) of hemagglutinin type H5 and clade 2.3.4.4b have widely spread within the northern hemisphere since 2020 and threaten wild bird populations, as well as poultry production. We present phylogeographic evidence that Iceland has been used as a stepping stone for HPAIV translocation from northern Europe to North America by infected but mobile wild birds. At least 2 independent incursions of HPAIV H5N1 clade 2.3.4.4b assigned to 2 hemagglutinin clusters, B1 and B2, are documented for summer‒autumn 2021 and spring 2022. Spread of HPAIV H5N1 to and among colony-breeding pelagic avian species in Iceland is ongoing. Potentially devastating effects (i.e., local losses >25%) on these species caused by extended HPAIV circulation in space and time are being observed at several affected breeding sites throughout the North Atlantic.
Journal Article
Blight : fungi and the coming pandemic
\"A prescient warning about the mysterious and deadly world of fungi-and how to avert further loss across species, including our own. Fungi are everywhere. Most are harmless; some are helpful. A few are killers. Collectively, infectious fungi are the most devastating agents of disease on earth, and a fungus that can persist in the environment without its host is here to stay. In Blight, Emily Monosson documents how trade, travel, and a changing climate are making us all more vulnerable to invasion. Populations of bats, frogs, and salamanders face extinction. In the Northwest, America's beloved national parks are covered with the spindly corpses of whitebark pines. Food crops are under siege, threatening our coffee, bananas, and wheat-and, more broadly, our global food security. Candida auris, drug-resistant and resilient, infects hospital patients and those with weakened immune systems. Coccidioides, which lives in drier dusty regions, may cause infection in apparently healthy people. The horrors go on. Yet prevention is not impossible. Tracing the history of fungal spread and the most recent discoveries in the field, Monosson meets scientists who are working tirelessly to protect species under threat, and whose innovative approaches to fungal invasion have the potential to save human lives. Delving into case studies at once fascinating, sobering, and hopeful, Blight serves as a wake-up call, a reminder of the delicate interconnectedness of the natural world, and a lesson in seeing life on our planet with renewed humility and awe\"-- Provided by publisher.
Book
Safety, immunogenicity, and preliminary clinical efficacy of a vaccine against extraintestinal pathogenic Escherichia coli in women with a history of recurrent urinary tract infection: a randomised, single-blind, placebo-controlled phase 1b trial
Escherichia coli infections are increasing worldwide in community and hospital settings. The E coli O-antigen is a promising vaccine target. We aimed to assess the safety and immunogenicity of a bioconjugate vaccine containing the O-antigens of four E coli serotypes (ExPEC4V).
In this multicentre phase 1b, first-in-human, single-blind, placebo-controlled trial, we randomly assigned (1:1) healthy adult women with a history of recurrent urinary tract infection (UTI) to receive a single injection of either intramuscular ExPEC4V or placebo. The primary outcome was the incidence of adverse events among vaccine and placebo recipients throughout the study. Secondary outcomes included immunogenicity and antibody functionality, and the incidence of UTIs caused by E coli vaccine serotypes in each group. This study is registered with ClinicalTrials.gov, number NCT02289794.
Between Jan 20, 2014, and Aug 27, 2014, 93 women received target-dose ExPEC4V and 95 received placebo. The vaccine was well tolerated: no vaccine-related serious adverse events occurred. Overall, 56 (60%) target-dose vaccines and 47 (49%) placebo recipients experienced at least one adverse event that was possibly, probably, or certainly related to injection. Vaccination induced significant IgG responses for all serotypes: at day 30 compared with baseline, O1A titres were 4·6 times higher, O2 titres were 9·4 times higher, O6A titres were 4·9 times higher, and O25B titres were 5·9 times higher (overall p<0·0001). Immune responses persisted at 270 days but were lower than those at 30 days. Opsonophagocytic killing activity showed antibody functionality. No reduction in the incidence of UTIs with 103 or more colony-forming units per mL of vaccine-serotype E coli was noted in the vaccine compared with the placebo group (0·149 mean episodes vs 0·146 mean episodes; p=0·522). In post-hoc exploratory analyses of UTIs with higher bacterial counts (≥105 colony-forming units per mL), the number of vaccine serotype UTIs did not differ significantly between groups (0·046 mean episodes in the vaccine group vs 0·110 mean episodes in the placebo group; p=0·074). However, significantly fewer UTIs caused by E coli of any serotype were noted in the vaccine group compared with the placebo group (0·207 mean episodes vs 0·463 mean episodes; p=0·002).
This tetravalent E coli bioconjugate vaccine candidate was well tolerated and elicited functional antibody responses against all vaccine serotypes. Phase 2 studies have been initiated to confirm these findings.
GlycoVaxyn, Janssen Vaccines.
Journal Article