Clinical Strains of Chryseobacterium and Elizabethkingia spp. Isolated from Pediatric Patients in a University Hospital: Performance of MALDI-TOF MS-Based Identification, Antimicrobial Susceptibilities, and Baseline Patient Characteristics

Elizabethkingia anophelis MSU001 Isolated from Anopheles stephensi: Molecular Characterization and Comparative Genome Analysis

Elizabethkingia anophelis MSU001, isolated from Anopheles stephensi in the laboratory, was characterized by matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-ToF/MS), biochemical testing, and genome sequencing. Average nucleotide identity analysis revealed 99% identity with the type species E. anophelis R26. Phylogenetic placement showed that it formed a clade with other mosquito-associated strains and departed from a clade of clinical isolates. Comparative genome analyses further showed that it shared at least 98.6% of genes with mosquito-associated isolates (except E. anophelis As1), while it shared at most 88.8% of common genes with clinical isolates. Metabolites from MSU001 significantly inhibited growth of E. coli but not the mosquito gut symbionts Serratia marcescens and Asaia sp. W12. Insect-associated E. anophelis carried unique glycoside hydrolase (GH) and auxiliary activities (AAs) encoding genes distinct from those of clinical isolates, indicating their potential role in reshaping chitin structure and other components involved in larval development or formation of the peritrophic matrix. Like other Elizabethkingia, MSU001 also carried abundant genes encoding two-component system proteins (51), transcription factor proteins (188), and DNA-binding proteins (13). E. anophelis MSU001 contains a repertoire of antibiotic resistance genes and several virulence factors. Its potential for opportunistic infections in humans should be further evaluated prior to implementation as a paratransgenesis agent (by transgenesis of a symbiont of the vector).

Emerging Bacterial Pathogens in the COVID-19 Era: Chryseobacterium gleum—A Case in Point

Introduction In the ongoing severe acute respiratory syndrome coronavirus 2 pandemic, a long hospital stay and empirical broad-spectrum antibiotics make the patients prone to acquire nosocomial infections especially with unconventional organisms, and Chryseobacterium gleum is one such rare nosocomial pathogen.

Methods The given study is a case-series-based study conducted from September 2020 to April 2021 in which clinically suspected pneumonia patients who recovered from coronavirus disease 2019 (COVID-19) were included.

Results Seventeen C. gleum isolates were obtained in pure culture from the tracheal aspirates of nine COVID-19 patients (including repeat samples to rule out colonization) within a period of eight months (September 2020–April 2021). Our records showed that there has been an increase in the number of isolates of C. gleum obtained in respiratory samples in 2020. We also did a review of literature of all the cases of C. gleum pneumonia reported till now.

Conclusion To the best of our knowledge, this is the first study reporting the isolation of this rare pathogen from COVID-19 patients with clinical significance in a large cohort of patients. Therefore, it becomes important to consider this pathogen as a significant cause of respiratory infections, especially in patients recovered post COVID-19.

16s rRNA-based phylogenetic analyses of Elizabethkingia anophelis: Detection of Elizabethkingia anophelis, a rare infectious agent from blood and determination of antibiotic susceptibility in Turkey

PURPOSE

Elizabethkingia anophelis was firstly isolated from the midgut of the Anopheles gambiae mosquito in 2011. After this year, it was isolated in some intensive care cases in Africa and Asia. This study, it was aimed to confirm the identification of E. anophelis in the blood of a pediatric patient.

METHODS

After the suspicious bacteria were grown on blood agar, MALDI-TOF MS and 16s rRNA gene sequencing methods were used to identify and an antibiotic susceptibility test was carried out by Vitek 2 Compact system according to the EUCAST. Finally, a phylogenetic tree was created based on the 16s rRNA gene region.

RESULTS

The isolate was identified as E. anophelis by both methods. It was found to be resistant to all beta-lactam antibiotics and also susceptible to ciprofloxacin and levofloxacin. According to the 16S rRNA-based phylogenetic tree, our isolate clustered within a branch containing other E. anophelis.

CONCLUSION

These findings will guide clinicians in choosing which antibiotic to choose if they encounter this agent. Also, the clinicians should be vigilant against this agent, as it is a newly emerging infectious agent in Turkey.

Genomic analysis of Elizabethkingia species from aquatic environments: Evidence for potential clinical transmission

•

Identification of closely related (< 50 SNV) clinical and environmental aquatic Elizabethkingia anophelis isolates.

•

Identification of a provisional novel species Elizabethkingia umaracha.

•

Novel bla_GOB and bla_B carbapenemases and extended spectrum β-lactamase bla_CME alleles identified in Elizabethkingia spp.

•

Analysis of the global phylogeny and pangenome of Elizabethkingia spp.

•

Identification of novel ICE elements carrying uncharacterised genetic cargo in 67 / 94 (71.3%) of the aquatic environments Elizabethkingia spp.

Elizabethkingia species are ubiquitous in aquatic environments, colonize water systems in healthcare settings and are emerging opportunistic pathogens with reports surfacing in 25 countries across six continents. Elizabethkingia infections are challenging to treat, and case fatality rates are high. Chromosomal bla_B, bla_GOB and bla_CME genes encoding carbapenemases and cephalosporinases are unique to Elizabethkingia spp. and reports of concomitant resistance to aminoglycosides, fluoroquinolones and sulfamethoxazole-trimethoprim are known. Here, we characterized whole-genome sequences of 94 Elizabethkingia isolates carrying multiple wide-spectrum metallo-β-lactamase (bla_Band bla_GOB) and extended-spectrum serine‑β-lactamase (bla_CME) genes from Australian aquatic environments and performed comparative phylogenomic analyses against national clinical and international strains. qPCR was performed to quantify the levels of Elizabethkingia species in the source environments. Antibiotic MIC testing revealed significant resistance to carbapenems and cephalosporins but susceptibility to fluoroquinolones, tetracyclines and trimethoprim-sulfamethoxazole. Phylogenetics show that three environmental E. anophelis isolates are closely related to E. anophelis from Australian clinical isolates (∼36 SNPs), and a new species, E. umeracha sp. novel, was discovered. Genomic signatures provide insight into potentially shared origins and a capacity to transfer mobile genetic elements with both national and international isolates.

The Integrative and Conjugative Element ICECspPOL2 Contributes to the Outbreak of Multi-Antibiotic-Resistant Bacteria for Chryseobacterium Spp. and Elizabethkingia Spp

Antibiotic resistance genes (ARGs) and horizontal transfer of ARGs among bacterial species in the environment can have serious clinical implications as such transfers can lead to disease outbreaks from multidrug-resistant (MDR) bacteria. Infections due to antibiotic-resistant Chryseobacterium and Elizabethkingia in intensive care units have been increasing in recent years. In this study, the multi-antibiotic-resistant strain Chryseobacterium sp. POL2 was isolated from the wastewater of a livestock farm. Whole-genome sequencing and annotation revealed that the POL2 genome encodes dozens of ARGs. The integrative and conjugative element (ICE) ICECspPOL2, which encodes ARGs associated with four types of antibiotics, including carbapenem, was identified in the POL2 genome, and phylogenetic affiliation analysis suggested that ICECspPOL2 evolved from related ICEEas of Elizabethkingia spp. Conjugation assays verified that ICECspPOL2 can horizontally transfer to Elizabethkingia species, suggesting that ICECspPOL2 contributes to the dissemination of multiple ARGs among Chryseobacterium spp. and Elizabethkingia spp. Because Elizabethkingia spp. is associated with clinically significant infections and high mortality, there would be challenges to clinical treatment if these bacteria acquire ICECspPOL2 with its multiple ARGs, especially the carbapenem resistance gene. Therefore, the results of this study support the need for monitoring the dissemination of this type of ICE in Chryseobacterium and Elizabethkingia strains to prevent further outbreaks of MDR bacteria. IMPORTANCE Infections with multiple antibiotic-resistant Chryseobacterium and Elizabethkingia in intensive care units have been increasing in recent years. In this study, the mobile integrative and conjugative element ICECspPOL2, which was associated with the transmission of a carbapenem resistance gene, was identified in the genome of the multi-antibiotic-resistant strain Chryseobacterium sp. POL2. ICECspPOL2 is closely related to the ICEEas from Elizabethkingia species, and ICECspPOL2 can horizontally transfer to Elizabethkingia species with the tRNA-Glu-TTC gene as the insertion site. Because Elizabethkingia species are associated with clinically significant infections and high mortality, the ability of ICECspPOL2 to transfer carbapenem resistance from environmental strains of Chryseobacterium to Elizabethkingia is of clinical concern.

Chryseobacterium gleum Causing Healthcare-Associated Pneumonia in an Adult Male With Diffuse Large B Cell Lymphoma

Chryseobacterium species are recognized as an emerging opportunistic bacterial pathogen in nosocomial settings especially in debilitated or immunosuppressed patients and neonates. The ubiquitous distribution in nature, ability to form biofilms with inherent resistance to broad-spectrum antimicrobials, and lack of clinical studies pose a further diagnostic and therapeutic challenge. This case report describes an elderly male with relapsed diffuse large B-cell lymphoma (DLBCL) status post-chemotherapy and radiation who acquired healthcare-associated pneumonia with sputum isolates showing Chryseobacterium gleum and Stenotrophomonas maltophila. It also includes a review of literature compiling all the previously reported cases with antibiotic susceptibilities, clinical picture, and treatment outcomes.

Antimicrobial Activity of Aztreonam in Combination with Old and New β-Lactamase Inhibitors against MBL and ESBL Co-Producing Gram-Negative Clinical Isolates: Possible Options for the Treatment of Complicated Infections

Metallo-β-lactamases (MBLs) are among the most challenging bacterial enzymes to overcome. Aztreonam (ATM) is the only β-lactam not hydrolyzed by MBLs but is often inactivated by co-produced extended-spectrum β-lactamases (ESBL). We assessed the activity of the combination of ATM with old and new β-lactamases inhibitors (BLIs) against MBL and ESBL co-producing Gram-negative clinical isolates. Six Enterobacterales and three non-fermenting bacilli co-producing MBL and ESBL determinants were selected as difficult-to-treat pathogens. ESBLs and MBLs genes were characterized by PCR and sequencing. The activity of ATM in combination with seven different BLIs (clavulanate, sulbactam, tazobactam, vaborbactam, avibactam, relebactam, zidebactam) was assessed by microdilution assay and time–kill curve. ATM plus avibactam was the most effective combination, able to restore ATM susceptibility in four out of nine tested isolates, reaching in some cases a 128-fold reduction of the MIC of ATM. In addition, relebactam and zidebactam showed to be effective, but with lesser reduction of the MIC of ATM. E. meningoseptica and C. indologenes were not inhibited by any ATM–BLI combination. ATM–BLI combinations demonstrated to be promising against MBL and ESBL co-producers, hence providing multiple options for treatment of related infections. However, no effective combination was found for some non-fermentative bacilli, suggesting the presence of additional resistance mechanisms that complicate the choice of an active therapy.

Clinical and molecular characteristics of Chryseobacterium indologenes isolates at a teaching hospital in Shanghai, China

Background

Chryseobacterium indologenes (C. indologenes) has recently emerged as a cause of life-threatening nosocomial infections in humans. This study aims to investigate the clinical characteristics, homology, and antimicrobial patterns of C. indologenes clinical isolates at a teaching hospital in Shanghai, China.

Methods

A total of 135 consecutive non-replicate clinical C. indologenes isolates from January 2010 to December 2018 were collected at a tertiary care university hospital in Shanghai, China. Genetic relatedness of the isolates was performed by pulsed-field gel electrophoresis (PFGE). The antimicrobial susceptibility of these isolates was measured by the microdilution broth method. The prevalence of β-lactamase genes was investigated by polymerase chain reaction (PCR), while the quinolone resistance-determining regions (QRDRs) were sequenced.

Results

All 135 C. indologenes isolates were collected from hospitalized patients with an average age of 55 years. Most of these clinical isolates were derived from ascites (59.3%) or urine (23.7%) specimens. Eighty (80/135) of the strains were classified as clone D by PFGE. In vitro drug susceptibility tests showed that minocycline and trimethoprim-sulfamethoxazole had sound antibacterial effects. However, more than 86% of the tested strains were resistant to cephalosporins (ceftazidime, cefotaxime), β-lactamase/β-lactamase inhibitors (cefoperazone-sulbactam), and carbapenems (meropenem, imipenem). Metallo-β-lactamase bla_IND and type A broad-spectrum β-lactamase genes bla_CIA were present in 135 and 103 isolates, respectively. The clinical strains in our hospital mainly carried bla_IND-2 (89.6%, 121/135). Compared with previous studies, these strains had a high rate of resistance to quinolones. The resistance rates to levofloxacin, ciprofloxacin, norfloxacin, gatifloxacin, and nemonoxacin were as high as 83.7–94.8%. The mutations at Ser83Val, Ser83Tyr, and Asp87Gly in the QRDRs of GyrA were significantly related to the resistance of C. indologenes to levofloxacin. All but one quinolone-resistant strain contained at least one significant mutation.

Conclusions

This study showed a clonal dissemination of C. indologenes isolates in infections at a tertiary care university hospital in Shanghai, China. Minocycline and trimethoprim-sulfamethoxazole had favorable in vitro antibacterial effects. However, the high resistance rate to β-lactams and quinolones was due to carrying β-lactamase (bla_IND, bla_CIA), and mutations in the QRDRs of GyrA.

Chryseobacterium/Elizabethkingia species infections in Saudi Arabia

Objectives:

To describe the epidemiological, clinical, and outcome data of patients infected or colonized with Chryseobacterium/Elizabethkingia spp including antibiotic susceptibility patterns.

Methods:

This retrospective study was conducted at Prince Sultan Military Medical City, Riyadh, Saudi Arabia. All patients infected or colonized by Chryseobacterium /Elizabethkingia spp who were admitted between June 2013 and May 2019 were included. Data were extracted from patient electronic medical records.

Results:

We enrolled 27 patients (13 males and 14 females) with a mean age of 35.6 years. Chryseobacterium/Elizabethkingia spp were isolated from blood cultures (n=13, 48%) and tracheal aspirations (n=11, 41%). The most frequent species isolated was Elizabethkingia meningoseptica (n=22). Although 6 patients were considered colonized, the remaining 21 patients presented with ventilator associated pneumonia (n=9), central line associated bloodstream infection (n=4), septic shock (n=4), or isolated bacteremia (n=4). In 25 cases the infections were health-care related. Three patients (11%) died within 28 days. Twenty-six isolates (96.5%) were resistant to carbapenems. Moxifloxacin and cotrimoxazole were the most active antibiotics.

Conclusion:

Chryseobacterium/Elizabethkingia spp infection is rare, but can be responsible for severe hospital acquired infections. Cotrimoxazole and fluoroquinolone are the most effective antibiotic treatments.

Chryseobacterium gleum Isolation from Respiratory Culture Following Community-Acquired Pneumonia

BACKGROUND Chryseobacterium gleum (C. gleum) is a rare but concerning device-associated infection that can cause urinary tract infections and pneumonia. It produces a biofilm and has intrinsic resistance to a wide array of broad-spectrum agents. Risk factors include neonate or immunocompromised states, intensive care unit admission for more than 21 days, broad-spectrum antibiotic exposure, indwelling devices, and mechanical ventilation. CASE REPORT A 61-year-old cachectic man presented in the United States with community-acquired pneumonia and immediately decompensated, requiring ventilator support. Despite starting broad-spectrum antibiotics, the patient developed fever, leukocytosis, and additional desaturation episodes. The patient's respiratory culture grew numerous C. gleum and few Stenotrophomonas (Xanthomonas) maltophilia. He also had a positive urine streptococcal pneumonia antigen. Broad-spectrum agents were discontinued after prolonged treatment due to a continued worsening clinical picture, and the patient was started on trimethoprim-sulfamethoxazole to cover C. gleum. The patient showed rapid clinical improvement on trimethoprim-sulfamethoxazole, with resolution of symptoms on post-discharge follow-up. CONCLUSIONS To the best of our knowledge, this is the first case report of a documented case of a patient with C. gleum respiratory infection successfully treated solely with trimethoprim-sulfamethoxazole. The expedient identification of C. gleum is essential for proper treatment. The literature has consistently shown isolated respiratory C. gleum strains to be largely susceptible to fluoroquinolones, piperacillin-tazobactam, or trimethoprim-sulfamethoxazole.

Epidemiology of β-Lactamase-Producing Pathogens

β-Lactam antibiotics have been widely used as therapeutic agents for the past 70 years, resulting in emergence of an abundance of β-lactam-inactivating β-lactamases. Although penicillinases in Staphylococcus aureus challenged the initial uses of penicillin, β-lactamases are most important in Gram-negative bacteria, particularly in enteric and nonfermentative pathogens, where collectively they confer resistance to all β-lactam-containing antibiotics. Critical β-lactamases are those enzymes whose genes are encoded on mobile elements that are transferable among species. Major β-lactamase families include plasmid-mediated extended-spectrum β-lactamases (ESBLs), AmpC cephalosporinases, and carbapenemases now appearing globally, with geographic preferences for specific variants. CTX-M enzymes include the most common ESBLs that are prevalent in all areas of the world. In contrast, KPC serine carbapenemases are present more frequently in the Americas, the Mediterranean countries, and China, whereas NDM metallo-β-lactamases are more prevalent in the Indian subcontinent and Eastern Europe. As selective pressure from β-lactam use continues, multiple β-lactamases per organism are increasingly common, including pathogens carrying three different carbapenemase genes. These organisms may be spread throughout health care facilities as well as in the community, warranting close attention to increased infection control measures and stewardship of the β-lactam-containing drugs in an effort to control selection of even more deleterious pathogens.

Comparative genomic analyses reveal diverse virulence factors and antimicrobial resistance mechanisms in clinical Elizabethkingia meningoseptica strains

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.

The draft genomes of Elizabethkingia anophelis of equine origin are genetically similar to three isolates from human clinical specimens

We report the isolation and characterization of two Elizabethkingia anophelis strains (OSUVM-1 and OSUVM-2) isolated from sources associated with horses in Oklahoma. Both strains appeared susceptible to fluoroquinolones and demonstrated high MICs to all cell wall active antimicrobials including vancomycin, along with aminoglycosides, fusidic acid, chloramphenicol, and tetracycline. Typical of the Elizabethkingia, both draft genomes contained multiple copies of β-lactamase genes as well as genes predicted to function in antimicrobial efflux. Phylogenetic analysis of the draft genomes revealed that OSUVM-1 and OSUVM-2 differ by only 6 SNPs and are in a clade with 3 strains of Elizabethkingia anophelis that were responsible for human infections. These findings therefore raise the possibility that Elizabethkingia might have the potential to move between humans and animals in a manner similar to known zoonotic pathogens.