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An atypically large outbreak of Elizabethkingia anophelis infections occurred in Wisconsin. Here we show that it was caused by a single strain with thirteen characteristic genomic regions. Strikingly, the outbreak isolates show an accelerated evolutionary rate and an atypical mutational spectrum. Six phylogenetic sub-clusters with distinctive temporal and geographic dynamics are revealed, and their last common ancestor existed approximately one year before the first recognized human infection. Unlike other E. anophelis , the outbreak strain had a disrupted DNA repair mutY gene caused by insertion of an integrative and conjugative element. This genomic change probably contributed to the high evolutionary rate of the outbreak strain and may have increased its adaptability, as many mutations in protein-coding genes occurred during the outbreak. This unique discovery of an outbreak caused by a naturally occurring mutator bacterial pathogen provides a dramatic example of the potential impact of pathogen evolutionary dynamics on infectious disease epidemiology. Elizabethkingia anophelis is an emerging pathogen of high antimicrobial resistance. Perrin and colleagues sequenced isolates of a 2015/2016 E. anophelis outbreak in Wisconsin and found substantial genetic diversity, accelerated evolutionary rate and a disruptive mutation in the DNA repair gene mutY .

Emergence of tigecycline-resistance tet (X) gene orthologues rendered tigecycline ineffective as last-resort antibiotic. To understand the potential origin and transmission mechanisms of these genes, we survey the prevalence of tet (X) and its orthologues in 2997 clinical E. coli and K. pneumoniae isolates collected nationwide in China with results showing very low prevalence on these two types of strains, 0.32% and 0%, respectively. Further surveillance of tet (X) orthologues in 3692 different clinical Gram-negative bacterial strains collected during 1994–2019 in hospitals in Zhejiang province, China reveals 106 (2.7%) tet (X)-bearing strains with Flavobacteriaceae being the dominant (97/376, 25.8%) bacteria. In addition, tet (X)s are found to be predominantly located on the chromosomes of Flavobacteriaceae and share similar GC-content as Flavobacteriaceae . It also further evolves into different orthologues and transmits among different species. Data from this work suggest that Flavobacteriaceae could be the potential ancestral source of the tigecycline resistance gene tet (X). Emergence of tigecycline-resistance tet (X) genes is of concern. Here, the authors determine tet (X) prevalence in more than 6,000 clinical Gram-negative bacterial isolates collected between 1994 to 2019 in hospitals in China and suggest that Flavobacteriaceae could be the potential ancestral source of the tigecycline resistance genes.

Background: Intestinal microbes play significant roles in fish and can be possibly used as probiotics in aquaculture. In our previous study, Flaviramulus ichthyoenteri Th78 super(T), a novel species in the family Flavobacteriaceae, was isolated from fish intestine and showed strong quorum quenching (QQ) ability. To identify the QQ enzymes in Th78 super(T) and explore the potential roles of Th78 super(T) in fish intestine, we sequenced the genome of Th78 super(T) and performed extensive genomic analysis. Results: An N-acyl homoserine lactonase FiaL belonging to the metallo-[beta]-lactamase superfamily was identified and the QQ activity of heterologously expressed FiaL was confirmed in vitro. FiaL has relatively little similarity to the known lactonases (25.2 ~ 27.9% identity in amino acid sequence). Various digestive enzymes including alginate lyases and lipases can be produced by Th78 super(T), and enzymes essential for production of B vitamins such as biotin, riboflavin and folate are predicted. Genes encoding sialic acid lyases, sialidases, sulfatases and fucosidases, which contribute to utilization of mucus, are present in the genome. In addition, genes related to response to different stresses and gliding motility were also identified. Comparative genome analysis shows that Th78 super(T) has more specific genes involved in carbohydrate transport and metabolism compared to other two isolates in Flavobacteriaceae, both isolated from sediments. Conclusions: The genome of Th78 super(T) exhibits evident advantages for this bacterium to survive in the fish intestine, including production of QQ enzyme, utilization of various nutrients available in the intestine as well as the ability to produce digestive enzymes and vitamins, which also provides an application prospect of Th78 super(T) to be used as a probiotic in aquaculture.

The hospital infection-control team at the National University Hospital of Singapore identified three patients in the cardiothoracic intensive-care unit (ICU) and two patients from the surgical ICU that were colonised with Elizabethkingia during a 3 week period in 2012.1 The Elizabethkingia strains were identified as Elizabethkingia meningoseptica on the basis of matrix-assisted laser desorption-ionisation time-of-flight mass spectrometry analysis.

Three human clinical isolates of bacteria (designated strains Em1, Em2 and Em3) had high average nucleotide identity (ANI) to Elizabethkingia meningoseptica. Their genome sizes (3.89, 4.04 and 4.04 Mb) were comparable to those of other Elizabethkingia species and strains, and exhibited open pan-genome characteristics, with two strains being nearly identical and the third divergent. These strains were susceptible only to trimethoprim/sulfamethoxazole and ciprofloxacin amongst 16 antibiotics in minimum inhibitory tests. The resistome exhibited a high diversity of resistance genes, including 5 different lactamase- and 18 efflux protein- encoding genes. Forty-four genes encoding virulence factors were conserved among the strains. Sialic acid transporters and curli synthesis genes were well conserved in E. meningoseptica but absent in E. anophelis and E. miricola. E. meningoseptica carried several genes contributing to biofilm formation. 58 glycoside hydrolases (GH) and 25 putative polysaccharide utilization loci (PULs) were found. The strains carried numerous genes encoding two-component system proteins (56), transcription factor proteins (187~191), and DNA-binding proteins (6~7). Several prophages and CRISPR/Cas elements were uniquely present in the genomes.

Elizabethkingia miricola is an emerging nosocomial pathogen responsible for meningitis, sepsis, urinary tract infection, pneumonia, and joint infection in humans. These pathogens were also reported to be causal agents for meningitis-like disease in cultured frogs, which displayed high infectivity, mortality, and significant loss. In July 2023, 10 outbreaks of infectious meningitis-like disease in bullfrogs occurred in Tangshan area. To determine the causal agent, 70 diseased frogs from 10 farms were collected for etiological identification. Gram-negative bacilli were isolated from the brain and liver of sick bullfrogs and identified as members of E. miricola by biochemical characterization and 16S rRNA sequencing analysis. A total of 42 strains of E. miricola were isolated and further determined as the etiological agent by reproducing neurological symptoms and deaths in an artificial infection test. A representative isolate, HBTS-1, was picked up for the pathogenicity test, and the data showed that this stain was highly pathogenic to bullfrogs with an LD50 of 3.7 × 105 CFU. Notably, the isolate also showed high pathogenicity to 5-day-old suckling mice, with an LD50 of 3.1 × 106 CFU, indicating its potential threat to mammals. Moreover, all the 42 E. miricola isolates showed resistance to multiple antibotics without an apparent inhibition zone observed in the test, making the choice of antimicrobial therapy challenging. These novel findings prioritized E. miricola as an important zoonotic agent, which may provide a reference for human medicine.

This is the first study to demonstrate a relationship between antagonistic interactions with antibiotic resistance within flavobacterial strains, a component of polar-region microbial mats. These strains were derived from ephemeral freshwater reservoirs, i.e. ponds and streams of the periglacial zone of Ecology Glacier (King George Island, maritime Antarctica). The study demonstrated the strains’ surprisingly high phylogenetic diversity, with 20 species among 50 isolates. Flavobacteria were characterised by different patterns of antagonism and sensitivity to antimicrobials. 29 strains produced substances inhibiting the growth of other isolates, with 21 strains being sensitive to such compounds; 34 strains were multidrug-resistant (MDR). The antibiotic resistance index (ARI) demonstrated a significantly higher proportion of MDR strains and ARI ≥ 0.2 in stream mats (87%) as compared to the strains derived from pond mats (55%). A strong correlation was observed between the strains’ antagonistic potential and antibiotic resistance. An important role in these phenomena is accomplished by the “super bacteria” strains that effectively accumulate numerous traits associated with antagonistic potential and can be involved in the potential transfer of these traits. The results of the study demonstrate that there are individual patterns of antagonistic interactions and antibiotic resistance among the biotic components of mats.

The emergence of antibiotic-resistant Elizabethkingia strains poses a significant challenge in clinical settings. This systematic review and meta-analysis provide a comprehensive assessment of the prevalence of antibiotic resistance among Elizabethkingia isolates across different regions worldwide. A systematic literature search was conducted across PubMed, Embase, Web of Science, and Scopus from 1998 to January 9, 2024, using predefined search strategies. Eligible studies reporting antibiotic resistance in Elizabethkingia were included. A random-effects model was applied to estimate resistance proportions and assess heterogeneity. Additional analyses, including meta-regression, subgroup evaluations, and assessments of outliers and influential studies, were performed to explore resistance trends and evaluate publication bias. Study quality was assessed using the Joanna Briggs Institute Checklist, and all statistical analyses were conducted using R with the metafor package. A total of 1,016 articles were identified, of which 34 studies (47 reports) met the inclusion criteria. The pooled analysis indicated high resistance to ceftazidime (88.5% of isolates, 95% CI: 21.1%-99.5%) with no significant heterogeneity. Resistance to rifampin was 12.5% (95% CI: 5.9%-24.7%), showing substantial heterogeneity, while ciprofloxacin resistance was 27.9% (95% CI: 13.8%-48.4%) with considerable heterogeneity. Among specific antibiotics, cefotaxime resistance was 96.1% (220 isolates), meropenem resistance was 92.4% (353 isolates), and gentamicin resistance was 77.7% (356 isolates). Additionally, sulfamethoxazole resistance was 46.1% (176 out of 360 isolates, 95% CI: 23.5%-70.4%), displaying significant heterogeneity. This study highlights the widespread antibiotic resistance in Elizabethkingia, underscoring the urgent need for targeted treatment strategies and enhanced surveillance programs. The findings emphasize the importance of monitoring local resistance patterns to guide clinical decision-making. Future research should focus on elucidating resistance mechanisms and genetic diversity to develop practical therapeutic approaches and mitigate the global health impact of Elizabethkingia infections.

A comprehensive literature review of cases of Elizabethkingia infection in children characterizes the epidemiology, demographics, clinical presentation, and outcomes. Cases were reported from 1944-2017 (n = 283) demonstrating high mortality that decreased in recent decades, and substantial morbidity among survivors, especially neonates. Abstract Elizabethkingia species often exhibit extensive antibiotic resistance and result in high morbidity and mortality, yet no systematic reviews exist that thoroughly characterize and quantify concerns for infected infants and children. We performed a review of literature and identified an initial 902 articles; 96 articles reporting 283 pediatric cases met our inclusion criteria and were subsequently reviewed. Case reports spanned 28 countries and ranged from 1944 to 2017. Neonatal meningitis remains the most common presentation of this organism in children, along with a range of other clinical manifestations. The majority of reported cases occurred as isolated cases, rather than within outbreaks. Mortality was high but has decreased in recent years, although neurologic sequelae among survivors remains concerning. Child outcomes can be improved through effective prevention measures and early identification and treatment of infected patients.

A novel gliding, Gram-stain-negative, rod-shaped, strictly aerobic bacterium, designated SW4 T , was isolated from seawater in the West Sea, Korea. Strain SW4 T grew optimally at 30 °C, pH 7.5, and NaCl 2% on MA. Phylogenetic analysis based on the 16S rRNA gene placed strain SW4 T in the genus Pontimicrobium within the family Flavobacteriaceae , with its closest relative being Pontimicrobium aquaticum KCTC 72003 T (97.0% similarity). However, genome analysis revealed significant divergence, with average nucleotide identity (ANI) of 81.6% and digital DNA-DNA hybridization (dDDH) value of 24.4%, supporting its designation as a new species. The genome consists of a 3.44 Mb circular chromosome and a plasmid, with a G + C content of 32%. In addition to the physiological distinct characteristics, comparative genomic analysis identified unique genes associated with heavy metal transport, nitrogen and sulfur cycling, oxidative and osmotic stress responses, and numerous carbohydrate-active enzymes that are responsible for polysaccharide degradation and utilization, highlighting its marine adaptation. These findings differentiate strain SW4 T from its closest and only existing species of P. aquaticum at both genomic and phenotypical levels. Based on phenotypic and phylogenetic evidence, we propose the novel species Pontimicrobium maritimus . sp. nov. with the type strain SW4 T (= KCTC 42599 T  = InaCC B 1659 T ).