Elizabethkingia anophelis MSU001 Isolated from Anopheles stephensi: Molecular Characterization and Comparative Genome Analysis
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ABSTRACT:
SUBMITTER: Chen S
PROVIDER: S-EPMC11206156 | biostudies-literature | 2024 May
REPOSITORIES: biostudies-literature
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Project description:Elizabethkingia anophelis has now emerged as an opportunistic human pathogen. However, its mechanisms of transmission remain unexplained. Comparative genomic (CG) analysis of E. anopheles endophthalmitis strain surprisingly found from an eye infection patient with twenty-five other E. anophelis genomes revealed its potential to participate in horizontal gene transfer. CG analysis revealed that the study isolate has an open pan genome and has undergone extensive gene rearrangements. We demonstrate that the strain is naturally competent, hitherto not reported in any members of Elizabethkingia. Presence of competence related genes, mobile genetic elements, Type IV, VI secretory systems and a unique virulence factor arylsulfatase suggests a different lineage of the strain. Deciphering the genome of E. anophelis having a reservoir of antibiotic resistance genes and virulence factors associated with diverse human infections may open up avenues to deal with the myriad of its human infections and devise strategies to combat the pathogen.
| S-EPMC5981450 | biostudies-literature
Project description:Elizabethkingia anophelis is a dominant bacterial species in the gut ecosystem of the malaria vector mosquito Anopheles gambiae. We recently sequenced the genomes of two strains of E. anophelis, R26T and Ag1, isolated from different strains of A. gambiae. The two bacterial strains are identical with a few exceptions. Phylogenetically, Elizabethkingia is closer to Chryseobacterium and Riemerella than to Flavobacterium. In line with other Bacteroidetes known to utilize various polymers in their ecological niches, the E. anophelis genome contains numerous TonB dependent transporters with various substrate specificities. In addition, several genes belonging to the polysaccharide utilization system and the glycoside hydrolase family were identified that could potentially be of benefit for the mosquito carbohydrate metabolism. In agreement with previous reports of broad antibiotic resistance in E. anophelis, a large number of genes encoding efflux pumps and β-lactamases are present in the genome. The component genes of resistance-nodulation-division type efflux pumps were found to be syntenic and conserved in different taxa of Bacteroidetes. The bacterium also displays hemolytic activity and encodes several hemolysins that may participate in the digestion of erythrocytes in the mosquito gut. At the same time, the OxyR regulon and antioxidant genes could provide defense against the oxidative stress that is associated with blood digestion. The genome annotation and comparative genomic analysis revealed functional characteristics associated with the symbiotic relationship with the mosquito host.
| S-EPMC4026382 | biostudies-literature
Project description:We provide complete circularized genome sequences of two mosquito-derived Elizabethkingia anophelis strains with draft sequences currently in the public domain (R26 and Ag1), and two novel E. anophelis strains derived from a different mosquito species, Anopheles sinensis (AR4-6 and AR6-8). The genetic similarity of all four mosquito-derived strains is remarkable.
| S-EPMC5701490 | biostudies-literature
Project description:Acquisition of Elizabethkingia infections in intensive care units (ICUs) has risen in the past decade. Treatment of Elizabethkingia infections is challenging due to the lack of effective therapeutic regimens, leading to a high mortality rate. Elizabethkingia infections have long been attributed to Elizabethkingia meningoseptica. Recently, we used whole-genome sequencing to reveal that E. anophelis is the pathogenic agent for an Elizabethkingia outbreak at two ICUs. We performed comparative genomic analysis of seven hospital-isolated E. anophelis strains with five available Elizabethkingia spp. genomes deposited in the National Center for Biotechnology Information Database. A pan-genomic approach was applied to identify the core- and pan-genome for the Elizabethkingia genus. We showed that unlike the hospital-isolated pathogen E. meningoseptica ATCC 12535 strain, the hospital-isolated E. anophelis strains have genome content and organization similar to the E. anophelis Ag1 and R26 strains isolated from the midgut microbiota of the malaria mosquito vector Anopheles gambiae. Both the core- and accessory genomes of Elizabethkingia spp. possess genes conferring antibiotic resistance and virulence. Our study highlights that E. anophelis is an emerging bacterial pathogen for hospital environments.
| S-EPMC4041001 | biostudies-literature
Project description:Elizabethkingia anophelis is an emerging multidrug-resistant pathogen that causes severe nosocomial and community-acquired infections worldwide. We report the first case of E. anophelis isolation in Russia and the first isolation from raw cow's milk. The ML-44 demonstrated resistance to 28 antimicrobials of 33 tested in the disk-diffusion test. Whole genome-based phylogeny showed ML-44 strain clustered together with the F3201 strain isolated from a human patient in Kuwait in 1982. Both strains were a part of the "endophytica" clade. Another clade was formed by subsp. anophelis strains. Each of the E. anophelis compared genomes carried 18 to 21 antibiotic resistance determinants. The ML-44 chromosome harbored nine efflux system genes and three beta-lactamase genes, along with six other antimicrobial resistance genes. In total, 72 virulence genes were revealed. The set of virulence factors was quite similar between different E. anophelis strains and included LPS and capsule encoded genes, type IV pili, oxidative stress response genes, and genes encoding TIVSS and TVISS effectors. The particular interest caused the mip and zmp1 gene homologs, which can be essential for intracellular survival. In sum, our findings suggest that raw milk might be a source of E. anophelis harboring a set of virulence factors and a broad resistance to generally used antimicrobials.
| S-EPMC9137776 | biostudies-literature
Project description:Elizabethkingia anophelis has become an emerging infection in humans. Recent research has shown that previous reports of E. meningoseptica infections might in fact be caused by E. anophelis. We aimed to investigate the genomic features, phylogenetic relationships, and comparative genomics of this emerging pathogen. Elizabethkingia anophelis strain EM361-97 was isolated from the blood of a cancer patient in Taiwan. The total length of the draft genome was 4,084,052 bp. The whole-genome analysis identified the presence of a number of antibiotic resistance genes, which corresponded with the antibiotic susceptibility phenotype of this strain. Based on the average nucleotide identity, the phylogenetic analysis revealed that E. anophelis EM361-97 was a sister group to E. anophelis FMS-007, which was isolated from a patient with T-cell non-Hodgkin's lymphoma in China. Knowledge of the genomic characteristics and comparative genomics of E. anophelis will provide researchers and clinicians with important information to understand this emerging microorganism.
| S-EPMC5662595 | biostudies-literature
Project description:The recent emergence of Elizabethkingia anophelis as a human pathogen is a major concern for global public health. This organism has the potential to cause severe infections and has inherent antimicrobial resistance. The potential for widespread outbreaks and rapid global spread highlights the critical importance of understanding the biology and transmission dynamics of this infectious agent. We performed a large-scale analysis of available 540 E. anophelis, including one novel strain isolated from raw milk and sequenced in this study. Pan-genome analysis revealed an open and diverse pan-genome in this species, characterized by the presence of many accessory genes. This suggests that the species has a high level of adaptability and can thrive in a variety of environments. Phylogenetic analysis has also revealed a complex population structure, with limited source-lineage correlation. We identified diverse antimicrobial resistance factors, including core-genome and accessory ones often associated with mobile genetic elements within specific lineages. Mobilome analysis revealed a dynamic landscape primarily composed of genetic islands, integrative and conjugative elements, prophage elements, and small portion of plasmids emphasizing a complex mechanism of horizontal gene transfer. Our study underscores the adaptability of E. anophelis, characterized by a diverse range of antimicrobial resistance genes, putative virulence factors, and genes enhancing fitness. This adaptability is also supported by the organism's ability to acquire genetic material through horizontal gene transfer, primarily facilitated by mobile genetic elements such as integrative and conjugative elements (ICEs). The potential for rapid evolution of this emerging pathogen poses a significant challenge to public health efforts.
| S-EPMC11523902 | biostudies-literature
Project description:Flavobacteria (members of the family Flavobacteriaceae) dominate the bacterial community in the Anopheles mosquito midgut. One such commensal, Elizabethkingia anophelis, is closely associated with Anopheles mosquitoes through transstadial persistence (i.e., from one life stage to the next); these and other properties favor its development for paratransgenic applications in control of malaria parasite transmission. However, the physiological requirements of E. anophelis have not been investigated, nor has its capacity to perpetuate despite digestion pressure in the gut been quantified. To this end, we first developed techniques for genetic manipulation of E. anophelis, including selectable markers, reporter systems (green fluorescent protein [GFP] and NanoLuc), and transposons that function in E. anophelis. A flavobacterial expression system based on the promoter PompA was integrated into the E. anophelis chromosome and showed strong promoter activity to drive GFP and NanoLuc reporter production. Introduced, GFP-tagged E. anophelis associated with mosquitoes at successive developmental stages and propagated in Anopheles gambiae and Anopheles stephensi but not in Aedes triseriatus mosquitoes. Feeding NanoLuc-tagged cells to A. gambiae and A. stephensi in the larval stage led to infection rates of 71% and 82%, respectively. In contrast, a very low infection rate (3%) was detected in Aedes triseriatus mosquitoes under the same conditions. Of the initial E. anophelis cells provided to larvae, 23%, 71%, and 85% were digested in A. stephensi, A. gambiae, and Aedes triseriatus, respectively, demonstrating that E. anophelis adapted to various mosquito midgut environments differently. Bacterial cell growth increased up to 3-fold when arginine was supplemented in the defined medium. Furthermore, the number of NanoLuc-tagged cells in A. stephensi significantly increased when arginine was added to a sugar diet, showing it to be an important amino acid for E. anophelis. Animal erythrocytes promoted E. anophelis growth in vivo and in vitro, indicating that this bacterium could obtain nutrients by participating in erythrocyte lysis in the mosquito midgut.
| S-EPMC4345385 | biostudies-literature
Project description:Elizabethkingia anophelis is an emerging pathogen that causes life-threatening infections in neonates and immunocompromised patients. In this study, we performed next-generation sequencing (NGS) to characterize 10 E. anophelis strains isolated from clinical patients in Nantong, China. Core, accessory, and unique genomes were composed of 2,891, 1,633, and 498 genes, respectively. Based on genetic screening for antimicrobial resistance genes (AMRs), all E. anophelis strains carried the same AMRs, including blaB, blaCME, and blaGOB. The virulence factors (VFs) in the 10 strains were classified into 13 functional categories, and the differences between strains were mainly in immune modulation and nutritional/metabolic factor. We further analyzed the genomic features of one of ten strains, NT06 strain. The capsule type of NT06 was X, which is rare among E. anophelis strains. Based on comparative analyses, we first found that NT06 carried the YclNOPQ-like operon, which is the complete transporter for petrobactin, to acquire iron. The genomic features are important for further investigations of epidemiology, resistance, virulence, and to identify appropriate treatments.IMPORTANCEElizabethkingia anophelis strains are opportunistic pathogens causing meningitis, bloodstream infections, and endophthalmitis in vulnerable populations. There is a lack of knowledge of the genetic diversity, presence of antimicrobial resistance genes (AMRs), and virulence factors (VFs) in E. anophelis isolated from clinical patients in China. Based on next-generation sequencing (NGS) and comparative genomic analyses, we determined the genomic features, phylogeny, and diversity of E. anophelis strains isolated from patients and identified a large accessory genome, intrinsic AMRs, and variable VFs. Based on comparative analyses, we identified a key strain, NT06, that carried a unique capsule type of X and the siderophore-mediated iron acquisition system (yclNOPQ-like genes). These findings advance our understanding of the genomic plasticity, evolution, and pathogenicity determinants of E. anophelis.
| S-EPMC11705823 | biostudies-literature
Project description:The complete circularized genome sequences of selected specimens from the largest known Elizabethkingia anophelis outbreak to date are described here. Genomic rearrangements observed among the outbreak strains are discussed.
| S-EPMC4911483 | biostudies-literature