Cedecea davisae bacteremia in a neutropenic patient with acute myeloid leukemia

Predicting cancer prognosis and drug response from the tumor microbiome

Tumor gene expression is predictive of patient prognosis in some cancers. However, RNA-seq and whole genome sequencing data contain not only reads from host tumor and normal tissue, but also reads from the tumor microbiome, which can be used to infer the microbial abundances in each tumor. Here, we show that tumor microbial abundances, alone or in combination with tumor gene expression, can predict cancer prognosis and drug response to some extent—microbial abundances are significantly less predictive of prognosis than gene expression, although similarly as predictive of drug response, but in mostly different cancer-drug combinations. Thus, it appears possible to leverage existing sequencing technology, or develop new protocols, to obtain more non-redundant information about prognosis and drug response from RNA-seq and whole genome sequencing experiments than could be obtained from tumor gene expression or genomic data alone.

Computational approaches have been developed to estimate tumor microbial abundances from whole genomic and RNA-sequencing datasets. Here the authors report the predictive value of tumor microbial abundance, alone or in combination with gene expression data, for cancer prognosis and drug response.

The Isolation of Culturable Bacteria in Ixodes ricinus Ticks of a Belgian Peri-Urban Forest Uncovers Opportunistic Bacteria Potentially Important for Public Health

Most bacteria found in ticks are not pathogenic to humans but coexist as endosymbionts and may have effects on tick fitness and pathogen transmission. In this study, we cultured and isolated 78 bacteria from 954 Ixodes ricinus ticks collected in 7 sites of a Belgian peri-urban forest. Most isolated species were non-pathogenic environmental microorganisms, and were from the Firmicutes (69.23%), Actinobacteria (17.95%) and Proteobacteria (3.84%) phyla. One bacterium isolate was particularly noteworthy, Cedecea davisae, a rare opportunistic bacterium, naturally resistant to various antibiotics. It has never been isolated from ticks before and this isolated strain was resistant to ampicillin, cefoxitin and colistin. Although cultivable bacteria do not represent the complete tick microbiota, the sites presented variable bacterial compositions and diversities. This study is a first attempt to describe the culturable microbiota of ticks collected in Belgium. Further collections and analyses of ticks of different species, from various areas and using other bacterial identification methods would strengthen these results. However, they highlight the importance of ticks as potential sentinel for opportunistic bacteria of public health importance.

Genomic Insights into Drug Resistance Determinants in Cedecea neteri, A Rare Opportunistic Pathogen

Cedecea, a genus in the Enterobacteriaceae family, includes several opportunistic pathogens reported to cause an array of sporadic acute infections, most notably of the lung and bloodstream. One species, Cedecea neteri, is associated with cases of bacteremia in immunocompromised hosts and has documented resistance to different antibiotics, including β-lactams and colistin. Despite the potential to inflict serious infections, knowledge about drug resistance determinants in Cedecea is limited. In this study, we utilized whole-genome sequence data available for three environmental strains (SSMD04, M006, ND14a) of C. neteri and various bioinformatics tools to analyze drug resistance genes in this bacterium. All three genomes harbor multiple chromosome-encoded β-lactamase genes. A deeper analysis of β-lactamase genes in SSMD04 revealed four metallo-β-lactamases, a novel variant, and a CMY/ACT-type AmpC putatively regulated by a divergently transcribed AmpR. Homologs of known resistance-nodulation-cell division (RND)-type multidrug efflux pumps such as OqxB, AcrB, AcrD, and MdtBC were also identified. Genomic island prediction for SSMD04 indicated that tolC, involved in drug and toxin export across the outer membrane of Gram-negative bacteria, was acquired by a transposase-mediated genetic transfer mechanism. Our study provides new insights into drug resistance mechanisms of an environmental microorganism capable of behaving as a clinically relevant opportunistic pathogen.

Urinary tract infection by a rare pathogen Cedecea neteri in a pregnant female with Polyhydramnios: rare case report from UAE

BACKGROUND

Cedecea neteri is a gram-negative, oxidase-negative bacillus, a rare pathogen. Few reports are emerging globally about its antimicrobial resistance pattern especially in immunocompromised individuals with comorbidities.

CASE PRESENTATION

In this paper, we report the first case of C. neteri causing urinary tract infection in a pregnant woman at a specialty care hospital in the Northern Emirates of Ras al Khaimah, UAE.

DISCUSSION AND CONCLUSION

C. neteri is a rare and unusual pathogen, unlike routine gram-negative urinary tract pathogens from the family of Enterobacteriaceae and therefore may be missed or misidentified by routine laboratories using conventional microbiology identification techniques. Hence, Cedecea infections may be under-reported. Physicians and microbiology technicians must be aware of such a rare pathogen, as most of the isolates are multi-drug-resistant and require combined antibiotic treatment with beta-lactamase inhibitors and hence pose a treatment challenge especially in immunocompromised patients with comorbidities. In recent years, it has been reported as an emerging opportunistic pathogen.

Expanding spectrum of opportunistic Cedecea infections: Current clinical status and multidrug resistance

Members of the bacterial genus Cedecea cause acute infections worldwide in compromised hosts with serious underlying medical conditions. While global reports of Cedecea infections remain sporadic in the medical literature, cases of multidrug-resistant clinical isolates have been documented each year over the past decade, warranting a comprehensive update on this emerging opportunistic pathogen. Here, we review the clinical manifestations, pathogenesis, natural distribution, epidemiology, and antimicrobial resistance of Cedecea species. Acute infection commonly manifests as bacteremia and pneumonia; however, the spectrum of infectious pathologies associated with Cedecea has expanded to include oral and cutaneous ulcers, orbital cellulitis, and peritonitis. The frequency of resistance among reported clinical isolates was highest to ampicillin, cephalothin, cefoxitin, cefazolin, and ceftazidime. Cedecea isolates harboring metallo-β-lactamases exhibited resistance to carbapenems and fourth-generation cephalosporins. Further research is needed to understand the pathogenicity and multidrug resistance of Cedecea species. Appropriate therapeutic management of Cedecea infections depends on antibiotic susceptibility testing because of variable resistance patterns and the enhanced infection risk in vulnerable populations.

A Rare Case of Cedecea Davisae Bacteremia Presenting as Biliary Sepsis

Cedecea davisae is a gram-negative, non-sporulating motile rod-shaped bacteria of the Enterobacteriaceae family. It is an opportunistic pathogen in advanced-aged patients with many comorbid diseases and the immunosuppressed. To the best of our knowledge, only 12 cases of C. davisae bacteremia have been reported in the literature. Here we discuss the 13th case of C. davisae bacteremia, which is the first reported case presenting as biliary sepsis.

A 41-year-old female, on prednisone for minimal change disease, presented with nausea, vomiting, fever, and diarrhea. She had dry mucous membranes, scleral icterus, and elevated liver enzymes. Blood cultures revealed Cedecea davisae. She improved after management with broad-spectrum antibiotics.

Further studies are needed to understand its role in the mode of transmission, the spectrum of infection, and treatment options. There is a need for physicians to be cognizant of emerging pathogens and address their antibiotic resistance profiles.

Nosocomial pneumonia and sepsis caused by a rare organism Cedecea lapagei in an infant and a review of literature

A late preterm male infant of 36 weeks gestation and a birth weight of 2100 g was admitted on day 35 of life with complaints of respiratory distress and lethargy. He was diagnosed as a case of sepsis screen positive culture negative sepsis and was managed with respiratory support and intravenous antibiotics for 10 days. The infant improved clinically and was on spoon feeds by day 14 of admission. On day 14 of admission, he developed new-onset respiratory distress and was diagnosed as a case of nosocomial pneumonia based on chest radiography findings. The blood culture grew a rare organism Cedecea lapagei and a diagnosis of sepsis was also made. The antibiotics were tailored as per the blood culture sensitivity pattern and the infant had clinical improvement in the next 72 hours.

Urinary Catheter Colonization by Multidrug-Resistant Cedecea neteri in Patient with Benign Prostatic Hyperplasia

Cedecea neteri, a member of the Enterobacteriaceae family, has only been identified as a human pathogen in a few previous clinical cases, thus complicating assessment of this organism's pathogenicity and medical relevance. Documented infections attributed to C. neteri primarily involved bacteremia in severely immunocompromised patients. We report a rare case of urinary catheter colonization by a multidrug-resistant C. neteri strain in a patient of advanced age with benign prostatic hyperplasia and other chronic comorbidities. This C. neteri isolate was resistant or intermediate to second-generation cephalosporins, penicillins, and certain β-lactamase inhibitor/β-lactam combinations. Analysis of whole genome sequence information for a representative C. neteri strain indicated the presence of multiple open reading frames with sequence similarity to β-lactamases, including a chromosome-encoded AmpC β-lactamase and metallo-β-lactamases, consistent with the resistance phenotype of this bacterium. The presence of an AmpR homolog suggests that the C. neteriampC may be inducible in response to β-lactam exposure. Molecular insights into antibiotic resistance traits of this emerging opportunistic pathogen will be important for administering adequate antibiotic treatment to ensure favorable patient outcomes.

Insights into Cedecea neteri strain M006 through complete genome sequence, a rare bacterium from aquatic environment

Cedecea neteri M006 is a rare bacterium typically found as an environmental isolate from the tropical rainforest Sungai Tua waterfall (Gombak, Selangor, Malaysia). It is a Gram-reaction-negative, facultative anaerobic, bacillus. Here, we explore the features of Cedecea neteri M006, together with its genome sequence and annotation. The genome comprised 4,965,436 bp with 4447 protein-coding genes and 103 RNA genes.

Cloning and Characterization of the Autoinducer Synthase Gene from Lipid-Degrading Bacterium Cedecea neteri

The process of intercellular communication among bacteria, termed quorum sensing (QS), is mediated by small diffusible molecules known as the autoinducers. QS allows the population to react to the change of cell density in unison, in processes such as biofilm formation, plasmid conjugation, virulence, motility and root nodulation. In Gram-negative proteobacteria, N-acyl homoserine lactone (AHL) is the common "language" to coordinate gene expression. This signaling molecule is usually synthesized by LuxI-type proteins. We have previously discovered that a rare bacterium, Cedecea neteri, exhibits AHL-type QS activity. With information generated from genome sequencing, we have identified the luxIR gene pair responsible for AHL-type QS and named it cneIR. In this study, we have cloned and expressed the 636 bp luxI homolog in an Escherichia coli host for further characterization. Our findings show that E. coli harboring cneI produced the same AHL profile as the wild type C. neteri, with the synthesis of AHL known as N-butyryl-homoserine lactone. This 25 kDa LuxI homolog shares high similarity with other AHL synthases from closely related species. This work is the first documentation of molecular cloning and characterization of luxI homolog from C. neteri.

Genome analysis of quorum sensing Cedecea neteri SSMD04 leads to identification of its novel signaling synthase (cneI), cognate receptor (cneR) and an orphan receptor

Cedecea neteri is a very rare human pathogen. We have isolated a strain of C. neteri SSMD04 from pickled mackerel sashimi identified using molecular and phenotypics approaches. Using the biosensor Chromobacterium violaceum CV026, we have demonstrated the presence of short chain N-acyl-homoserine lactone (AHL) type quorum sensing (QS) activity in C. neteri SSMD04. Triple quadrupole LC/MS analysis revealed that C. neteri SSMD04 produced short chain N-butyryl-homoserine lactone (C4-HSL). With the available genome information of C. neteri SSMD04, we went on to analyse and identified a pair of luxI/R homologues in this genome that share the highest similarity with croI/R homologues from Citrobacter rodentium. The AHL synthase, which we named cneI(636 bp), was found in the genome sequences of C. neteri SSMD04. At a distance of 8bp from cneI is a sequence encoding a hypothetical protein, potentially the cognate receptor, a luxR homologue which we named it as cneR. Analysis of this protein amino acid sequence reveals two signature domains, the autoinducer-binding domain and the C-terminal effector which is typical characteristic of luxR. In addition, we found that this genome harboured an orphan luxR that is most closely related to easR in Enterobacter asburiae. To our knowledge, this is the first report on the AHL production activity in C. neteri, and the discovery of its luxI/R homologues, the orphan receptor and its whole genome sequence.

First reported case of pneumonia caused by Cedecea lapagei in America

Cedecea represents a genus in the Enterobacteriaceae family that has been rarely associated with human infection. The clinical relevance of Cedecea lapagei has yet to be elucidated. This is the first reported case of pneumonia due to C. lapagei in a patient with acute promyelocytic leukemia.

A rare bacteremia caused by Cedecea davisae in patient with chronic renal disease

Patient:

Female, 77

Final Diagnosis:

Bacteremia

Symptoms:

Chills • diarrhea • fever • nausea

Medication:

—

Clinical Procedure:

X-Ray • CBC • urine and blood cultur

Specialty:

Infectious diseases

Objective:

Rare disease

Background:

Cedecea davisae is a gram negative, oxidase negative bacilli that include 5 species. In the medical literature there are very few reports that describe infections caused by different species of the Cedecea genus.

Case Report:

In this paper we report a fourth case of bacteremia in a 77 year-old patient with a chronic renal disease that was successfully treated with ceftazidim and ciprofloxacin. Additionally, we present a review of all the reported infections that were caused by C. davisae.

Conclusions:

Five cases (not including our report) of Cedecea bacteremia were reported so far. Cedecea infections and particularly C. davisae infections can be difficult to treat due to the antibiotic resistance of the bacterium. Therefore we propose to consider treating C. davisae bacteremia with a combined antibiotic treatment until getting laboratory results for antibiotic-sensitivity tests.

Cedecea davisae's Role in a Polymicrobial Lung Infection in a Cystic Fibrosis Patient

Chronic airway colonization and infection are the hallmark of cystic fibrosis (CF). Staphylococcus aureus, Pseudomonas aeruginosa, and Burkholderia cepacia are well-documented bacterial culprits in this chronic suppurative airway disease. Advanced molecular diagnostics have uncovered a possible role of a larger group of microorganisms in CF. Cedecea is a member of the family Enterobacteriaceae and is an emerging pathogen. We present a case of a polymicrobial healthcare-associated pneumonia in a CF patient caused by Cedecea davisae, among other bacteria.

Bacteraemia due to Cedecea davisae in a patient with sigmoid colon cancer: a case report and brief review of the literature

Cedecea spp. represent a new member of the Enterobacteriaceae family, and although they are commonly described, they have rarely been reported as causes of invasive infection. The species' inherent resistance to antibiotics makes their management extremely challenging, especially in the context of immunocompromise when infections occur. We hereby report a rare case of Cedecea davisae bacteraemia in a patient with stage IV sigmoid colon cancer followed by a brief review of the literature.