Comparative genomic analysis of a naturally competent Elizabethkingia anophelis isolated from an eye infection

Population genomics of emerging Elizabethkingia anophelis pathogens reveals potential outbreak and rapid global dissemination

Elizabethkingia anophelis is an emerging species and have increasingly been reported to cause life-threatening infections and even outbreaks in humans. Nevertheless, there is little data regarding the E. anophelis geographical distribution, phylogenetic structure, and transmission across the globe, especially in Asia. We utilize whole genome sequencing (WGS) data to define a global population framework, phylogenetic structure, geographical distribution, and transmission evaluation of E. anophelis pathogens. The geographical distribution diagram revealed the emerging pathogenic bacteria already distributed in various countries worldwide, especially in the USA and China. Strikingly, phylogenetic analysis showed a part of our China original E. anophelis shared the same ancestor with the USA outbreak strain, which implies the possibility of localized outbreaks and global spread. These closer related strains also contained ICEEaI, which might insert into a disrupted DNA repair mutY gene and made the strain more liable to mutation and outbreak infection. BEAST analysis showed that the most recent common ancestor for ICEEaI E. anophelis was dated twelve years ago, and China might be the most likely recent source of this bacteria. Our study sheds light on the potential possibility of E. anophelis causing the large-scale outbreak and rapid global dissemination. Continued genomic surveillance of the dynamics of E. anophelis populations will generate further knowledge for optimizing future prevent global outbreak infections.

Impact of the surrounding environment on antibiotic resistance genes carried by microplastics in mangroves

The pollution of antibiotic resistance genes (ARGs) carried by microplastics (MPs) is a growing concern. Mangroves are located at the intersection of land and sea and are seriously affected by MP pollution. However, few studies have systematic research evaluating the transmission risk of ARGs carried by MPs in mangroves. We conducted in situ experiments by burying five different MPs (polypropylene, high-density polyethylene, polystyrene, polyethylene glycol terephthalate, and polycaprolactone particles) in mangroves with different surrounding environments. A total of 10 genes in the MPs of mangroves were detected using quantitative real-time polymerase chain reactions, including eight ARGs and two mobile genetic elements (MGEs). The abundance of ARGs in Guanhai park mangroves in living areas (GH) was higher than that of Gaoqiao mangroves in protected areas (GQ) and Beiyue dike mangroves in aquaculture pond areas (BY). Pathogenic bacteria, such as Acinetobacter, Bacillus, and Vibrio were found on the MP surfaces of the mangroves. The number of ARGs carried by multiple drug-resistant bacteria in the GH mangroves was greater than that in the GQ and BY mangroves. Moreover, the ARGs carried by MPs in GH mangroves had the highest potential transmission risk by horizontal gene transfer. Sociometric and environmental factors were the main drivers shaping the distribution characteristics of ARGs and MGEs. Polypropylene and high-density polyethylene particles are preferred substrates for obtaining diffuse ARGs. This study investigated the drivers of ARGs in the MPs of mangroves and provided essential guidance on the use and handling of plastics.

Biofilm formation and antibiotic sensitivity in Elizabethkingia anophelis

Elizabethkingia anophelis has recently gained global attention and is emerging as a cause of life-threatening nosocomial infections. The present study aimed to investigate the association between antimicrobial resistance and the ability to form biofilm among E. anophelis isolated from hospitalized patients in China. Over 10 years, a total of 197 non-duplicate E. anophelis strains were collected. Antibiotic susceptibility was determined by the standard agar dilution method as a reference assay according to the Clinical and Laboratory Standards Institute. The biofilm formation ability was assessed using a culture microtiter plate method, which was determined using a crystal violet assay. Culture plate results were cross-checked by scanning electron microscopy imaging analysis. Among the 197 isolates, all were multidrug-resistant, and 20 were extensively drug-resistant. Clinical E. anophelis showed high resistance to current antibiotics, and 99% of the isolates were resistant to at least seven antibiotics. The resistance rate for aztreonam, ceftazidime, imipenem, meropenem, trimethoprim-sulfamethoxazole, cefepime, and tetracycline was high as 100%, 99%, 99%, 99%, 99%, 95%, and 90%, respectively. However, the isolates exhibited the highest susceptibility to minocycline (100%), doxycycline (96%), and rifampin (94%). The biofilm formation results revealed that all strains could form biofilm. Among them, the proportions of strong, medium, and weak biofilm-forming strains were 41%, 42%, and 17%, respectively. Furthermore, the strains forming strong or moderate biofilm presented a statistically significant higher resistance than the weak formers (p < 0.05), especially for piperacillin, piperacillin-tazobactam, cefepime, amikacin, and ciprofloxacin. Although E. anophelis was notoriously resistant to large antibiotics, minocycline, doxycycline, and rifampin showed potent activity against this pathogen. The data in the present report revealed a positive association between biofilm formation and antibiotic resistance, which will provide a foundation for improved therapeutic strategies against E. anophelis infections in the future.

Elizabethkingia Intra-Abdominal Infection and Related Trimethoprim-Sulfamethoxazole Resistance: A Clinical-Genomic Study

(1) Background: Elizabethkingia spp. is an emerging nosocomial pathogen which causes mostly blood stream infection and nosocomial pneumonia. Among Elizabethkingia species, Elizabethkingia anophelis is the major pathogen, but misidentification as Elizabethkingia meningoseptica is a common problem. Elizabethkingia also possesses broad antibiotic resistance, resulting in high morbidity and mortality of the infection. The aim of our study was to review Elizabethkingia intra-abdominal infections and investigate resistance mechanisms against TMP/SMX in Elizabethkingia anophelis by whole genome sequencing. (2) Methods: We retrospectively searched records of patients with Elizabethkingia intra-abdominal infection between 1990 and 2019. We also conducted whole genome sequencing for a TMP/SMX-resistant Elizabethkingia anophelis to identify possible mechanisms of resistance. (3) Results: We identified a total of nine cases of Elizabethkingia intra-abdominal infection in a review of the literature, including our own case. The cases included three biliary tract infections, three CAPD-related infection, two with infected ascites, and two postoperation infections. Host factor, indwelling-catheter, and previous invasive procedure, including surgery, play important roles in Elizabethkingia infection. Removal of the catheter is crucial for successful treatment. Genomic analysis revealed accumulated mutations leading to TMP/SMX-resistance in folP. (4) Conclusions: Patients with underlying disease and indwelling catheter are more susceptible to Elizabethkingia intra-abdominal infection, and successful treatment requires removal of the catheter. The emerging resistance to TMP/SMX may be related to accumulated mutations in folP.

Proteome-wide screening for designing a multi-epitope vaccine against emerging pathogen Elizabethkingia anophelis using immunoinformatic approaches

Elizabethkingia anophelis is an emerging human pathogen causing neonatal meningitis, catheter-associated infections and nosocomial outbreaks with high mortality rates. Besides, they are resistant to most antibiotics used in empirical therapy. In this study, therefore, we used immunoinformatic approaches to design a prophylactic peptide vaccine against E. anophelis as an alternative preventive measure. Initially, cytotoxic T-lymphocyte (CTL), helper T-lymphocyte (HTL), and linear B-lymphocyte (LBL) epitopes were predicted from the highest antigenic protein. The CTL and HTL epitopes together had a population coverage of 99.97% around the world. Eventually, six CTL, seven HTL, and two LBL epitopes were selected and used to construct a multi-epitope vaccine. The vaccine protein was found to be highly immunogenic, non-allergenic, and non-toxic. Codon adaptation and in silico cloning were performed to ensure better expression within E. coli K12 host system. The stability of the vaccine structure was also improved by disulphide bridging. In addition, molecular docking and dynamics simulation revealed strong and stable binding affinity between the vaccine and toll-like receptor 4 (TLR4) molecule. The immune simulation showed higher levels of T-cell and B-cell activities which was in coherence with actual immune response. Repeated exposure simulation resulted in higher clonal selection and faster antigen clearance. Nevertheless, experimental validation is required to ensure the immunogenic potency and safety of this vaccine to control E. anophelis infection in the future.Communicated by Ramaswamy H. Sarma.

Fluoroquinolone resistance in carbapenem-resistant Elizabethkingia anophelis: phenotypic and genotypic characteristics of clinical isolates with topoisomerase mutations and comparative genomic analysis

Background

MDR Elizabethkingia anophelis strains are implicated in an increasing number of healthcare-associated infections worldwide, including a recent cluster of E. anophelis infections in the Midwestern USA associated with significant morbidity and mortality. However, there is minimal information on the antimicrobial susceptibilities of E. anophelis strains or their antimicrobial resistance to carbapenems and fluoroquinolones.

Objectives

Our aim was to examine the susceptibilities and genetic profiles of clinical isolates of E. anophelis from our hospital, characterize their carbapenemase genes and production of MBLs, and determine the mechanism of fluoroquinolone resistance.

Methods

A total of 115 non-duplicated isolates of E. anophelis were examined. MICs of antimicrobial agents were determined using the Sensititre 96-well broth microdilution panel method. QRDR mutations and MBL genes were identified using PCR. MBL production was screened for using a combined disc test.

Results

All E. anophelis isolates harboured the blaGOB and blaB genes with resistance to carbapenems. Antibiotic susceptibility testing indicated different resistance patterns to ciprofloxacin and levofloxacin in most isolates. Sequencing analysis confirmed that a concurrent GyrA amino acid substitution (Ser83Ile or Ser83Arg) in the hotspots of respective QRDRs was primarily responsible for high-level ciprofloxacin/levofloxacin resistance. Only one isolate had no mutation but a high fluoroquinolone MIC.

Conclusions

Our study identified a strong correlation between antibiotic susceptibility profiles and mechanisms of fluoroquinolone resistance among carbapenem-resistant E. anophelis isolates, providing an important foundation for continued surveillance and epidemiological analyses of emerging E. anophelis opportunistic infections. Minocycline or ciprofloxacin has the potential for treatment of severe E. anophelis infections.