In silico discovery of druggable targets in Citrobacter koseri using echinoderm metabolites and molecular dynamics simulation

Citrobacter koseri causes infection in people who are immunocompromised. Without effective antibiotics, these infections can become severe and life-threatening, so effective drugs are essential to treat these infections. Utilizing subtractive genomics, 2699 ORFs were predicted and translated into amino acid sequences. Metabolic pathway analysis and subcellular localization helped define the roles of key bacterial proteins. Two druggable proteins, WP_012000829.1 and WP_275157394.1, were discovered as promising targets. Alpha Fold provided 3D structures, and a library of 1600 echinoderm metabolites was docked against these proteins, with Ampicillin, Levofloxacin, and Doxycycline as controls. Notably, CMNPD13085 and CMNPD15632 exhibited the highest binding affinities for WP_012000829.1 and WP_275157394.1, respectively. Molecular dynamics simulations and MM-GBSA binding free energy complemented docking results. However, acknowledging the reliance on computational validations, the study emphasizes the need for essential in-vitro research to transform these potential inhibitors into therapeutic drugs.

CITROBACTER KOSERI SKIN AND SOFT TISSUE INFECTION COMPLICATED BY ABSCESS FORMATION: A CASE REPORT AND A REVIEW OF LITERATURE

Citrobacter koseri (C. koseri) can lead to severe infections in the neonates, elderly and immunocompromised patients. We describe the first reported case of an axillary abscess due to C. koseri in a healthy adolescent, and review the clinical aspects and associated risk factors of this rare condition.

Z. A, Alhazzani K. Insilico exploration C. koseri ATP synthase inhibitors by pharmacophore-based virtual screening, molecular docking and MD simulation

Citrobacter koseri is a gram-negative rod that causes infections in people who have significant comorbidities and are immunocompromised. Antibiotic-resistant strains are becoming more common, which complicates infection treatment and highlights the need for innovative, effective drugs to fight these resistant strains. The enzyme complex ATP synthase participates in the adenosine triphosphate (ATP) synthesis, the fundamental energy currency of cells. This study used Computer-Aided Drug Design approaches to identify potential inhibitors of C. koseri ATP synthase. SWISS-MODEL was used to predict the 3D structure of C. koseri ATP synthase. A ligand-based pharmacophore model was developed using chemical features of ampicillin. Following ligand-based virtual screening across nine databases, the 2043 screened hits were docked to the ATP synthase active site using the standard precision mode of the glide tool. Based on their binding affinities, the top ten compounds were selected for additional investigation. The binding affinities of the chosen compounds ranged from -10.021 to -8.452 kcal/mol. The top four compounds (PubChem-25230613, PubChem-74936833, CHEMBL263035, PubChem-44208924) with the best ADMET characteristics and binding modes were chosen. Thus, the feasible binding mechanisms of the selected compounds were subjected to stability analysis using the MD Simulation study, which revealed the compounds' stability as potent inhibitors within the protein binding pocket. This computational approach provides important insights into the rational design of novel therapeutics and emphasizes the importance of targeting essential metabolic pathways when combating antibiotic-resistant pathogens. Future experimental validation and optimization of the identified inhibitors is required to determine their efficacy and safety profiles for clinical use.

Osteomyelitis Caused by Citrobacter koseri in a Young Immunocompetent Man

Citrobacter koseri is a non-sporulating, motile, gram-negative, facultative anaerobic bacteria found in various environmental sources, including the human intestine. It is considered an opportunistic infection as it typically causes infection in newborns, elderly, and immunocompromised patients. Common sites of infection are the urinary tract, gastrointestinal system, and respiratory tract in immunocompromised adults, as well as the bloodstream and meninges in newborns. However, osteomyelitis secondary to C. koseri is very rare. We present an unusual case of Citrobacter osteomyelitis in a healthy young man with no identifiable risk factors.

Revolutionizing and identifying novel drug targets in Citrobacter koseri via subtractive proteomics and development of a multi-epitope vaccine using reverse vaccinology and immuno-informatics

Citrobacter koseri is a gram-negative rod that has been linked to infections in people with significant comorbidities and immunocompromised immune systems. It is most commonly known to cause urinary tract infections. Thus, the development of an efficacious C. koseri vaccine is imperative, as the pathogen has acquired resistance to current antibiotics. Subtractive proteomics was employed during this research to identify potential antigenic proteins to design an effective vaccine against C. koseri. The pipeline identified two antigenic proteins as potential vaccine targets: DP-3-O-acyl-N-acetylglucosamine deacetylase and Arabinose 5-phosphate isomerase. B and T cell epitopes from the specific proteins were forecasted employing several immunoinformatic and bioinformatics resources. A vaccine was created using a combination of seven cytotoxic T cell lymphocytes (CTL), five helper T cell lymphocyte (HTL), and seven linear B cell lymphocyte (LBL) epitopes. An adjuvant (β-defensin) was added to the vaccine to enhance immunological responses. The created vaccine was stable for use in humans, highly antigenic, and non-allergenic. The vaccine's molecular and interactions binding affinity with the human immunological receptor TLR3 were studied using MMGBSA, molecular dynamics (MD) simulations, and molecular docking analyses. E. coli (strain-K12) plasmid vector pET-28a (+) was used to examine the ability of the vaccine to be expressed. The vaccine shows great promise in terms of developing protective immunity against diseases, based on the results of these computer experiments. However, in vitro and animal research are required to validate our findings.Communicated by Ramaswamy H. Sarma.

Characterization of an NDM-1-Producing Citrobacter koseri Isolate from China

Purpose

The continuous rise in carbapenemase-producing Enterobacteriaceae infections is a major public health concern. However, there is limited information available on New Delhi metallo-β-lactamase-1 (NDM-1) producing Citrobacter koseri. In this study, we isolated a blaNDM-1-carrying C. koseri from a stool sample of an inpatient. Our aim was to investigate the phenotypic and genomic features of this clinically derived carbapenem-resistant C. koseri isolate and to characterize the transmission pattern of the IncFII/IncN plasmid that carries the blaNDM-1 gene.

Methods and Results

S1-PFGE, Southern blot and conjugation assay confirmed the presence of blaNDM-1 gene in a conjugative plasmid. C. koseri L2395 and transconjugant L2395-EC600 strains showed similar resistance spectrum. Whole-genome analysis revealed that pL2395_NDM is an IncFII/IncN plasmid with a length of 67,839 bp. Moreover, blaNDM-1 gene was found encoded in the ISKpn19-blaNDM-1-ble-tnpF-dsbD-cutA-ISKpn19 cassette array. Phylogenetic analysis revealed that strain L2395 was close to an IMP-4-bearing C. koseri from Australia.

Conclusion

Ongoing surveillance will be essential to control and prevent the spread of carbapenem-resistant Citrobacter spp. in the future.

Infective endocarditis due to Citrobacter koseri following testicular trauma: case report and literature review

Infective endocarditis (IE) is a condition with low prevalence but high mortality rates within intensive care units. Microbiologically, most cases are attributed to Gram-positive cocci, while Gram-negative bacilli are less commonly involved. This case report describes a patient with IE caused by Citrobacter koseri (C. koseri) with secondary bacteremia due to blunt testicular trauma and epididymitis. We conducted a review of the literature to assess the clinical and associated risk factors of this underreported condition. Elderly and urinary tract infections could be associated with this entity. Cefazolin was used as the final targeted treatment. The use of precision medicine in IE is required for specific interventions.

Severe asthma patient with secondary Citrobacter koseri abdominal infection: first case report and review of the literature

Citrobacter koseri (C. koseri) is a Gram-negative, motile, non-spore-forming facultative anaerobic bacillus belonging to the Enterobacteriaceae family. C. koseri typically utilizes citrate as the sole carbon source and constitutes part of the normal gastrointestinal flora in humans and animals. As an opportunistic pathogen, C. koseri infections are mainly observed in neonates, elderly individuals, and immunocompromised hosts. C. koseri has been one of the main etiological agents of neonatal meningitis and cerebral abscess. In recent years, an increasing number of cases have been reported in adults with severe infections caused by C. koseri. Here, we report for the first time a clinical case of concurrent C. koseri intra-abdominal infection in a patient with severe asthma and provide a brief review of the relevant literature. With this report, we hope to increase awareness and alertness among clinicians to the possibility of concurrent infection of gut commensal bacteria in asthmatic patients requiring long-term oral corticosteroid administration.

Citrobacter koseri related abortion and fetal septicemia in cattle

A 31-month-old Holstein dairy cow aborted at 224 days of gestation with ejection of cheese-like lochia. Citrobacter koseri, which commonly exists in the normal flora of human and animal digestive tracts, was isolated from aborted fetal tissues (liver, spleen, kidney, heart, lung, cerebrum, and skeletal muscle) and fetal membranes. Histopathological examination revealed suppurative fibrinous meningoencephalitis of the cerebrum, cerebellum, and brainstem; suppurative bronchopneumonia; suppurative chorioamnionitis; and fibrous splenic serositis. Numerous gram-negative bacilli were detected in the cytoplasm of macrophages and/or neutrophils in these lesions. Bacteriological investigation and immunohistochemical staining identified the bacilli as C. koseri. This is the first report of cattle abortion caused by C. koseri infection in dairy cattle.

Microbial Community Characterization and Molecular Resistance Monitoring in Geriatric Intensive Care Units in China Using mNGS

Background

Surface pathogens in the ICU pose a global public health threat, especially to elderly patients who are immunocompromised. To detect these pathogens, unbiased methods such as metagenomic next-generation sequencing (mNGS) are increasingly utilized for environmental microbiological surveillance.

Methods

In a six-month study from January to July 2022, we investigated microbial communities in Chinese geriatric ICUs by regularly monitoring multiple surfaces at three-month intervals. Using mNGS sequencing, we analyzed microorganisms present at eight specific locations within the ICU. Additionally, we compared pathogen profiles and drug resistance genes between patient cultures and environmental samples collected during the same period.

Results

The microbial composition remained relatively stable over time, but significant differences in alpha diversities were observed among various surfaces such as floors, hands, pumps, trolleys, and ventilator inlets/outlets. Surfaces with high contact frequency for healthcare workers, including workstations, ventilator panels, trolleys, pumps, and beds, harbored pathogenic microorganisms such as Acinetobacter baumannii, Cutibacterium acnes, Staphylococcus haemolyticus, Pseudomonas aeruginosa, and Enterococcus faecium. Acinetobacter baumannii, particularly the carbapenem-resistant strain (CRAB), was the most frequently identified pathogen in geriatric ICU patients regardless of testing method used. The mNGS approach enabled detection of viruses, fungi, and parasites that are challenging to culture. Additionally, an abundance of drug resistance genes was found in almost all environmental samples.

Conclusion

The microbial composition and abundance in the ICU remained relatively constant over time. The floor exhibited the highest microbial diversity and abundance in the ICU environment. Drug-resistant genes in the ICU environment may migrate between patients. Overall, mNGS is an emerging and powerful tool for microbiological monitoring of the hospital environment.

CkP1 bacteriophage, a S16-like myovirus that recognizes Citrobacter koseri lipopolysaccharide through its long tail fibers

Citrobacter koseri is an emerging Gram-negative bacterial pathogen, which causes urinary tract infections. We isolated and characterized a novel S16-like myovirus CKP1 (vB_CkoM_CkP1), infecting C. koseri. CkP1 has a host range covering the whole C. koseri species, i.e., all strains that were tested, but does not infect other species. Its linear 168,463-bp genome contains 291 coding sequences, sharing sequence similarity with the Salmonella phage S16. Based on surface plasmon resonance and recombinant green florescence protein fusions, the tail fiber (gp267) was shown to decorate C. koseri cells, binding with a nanomolar affinity, without the need of accessory proteins. Both phage and the tail fiber specifically bind to bacterial cells by the lipopolysaccharide polymer. We further demonstrate that CkP1 is highly stable towards different environmental conditions of pH and temperatures and is able to control C. koseri cells in urine samples. Altogether, CkP1 features optimal in vitro characteristics to be used both as a control and detection agent towards drug-resistant C. koseri infections. KEY POINTS: • CkP1 infects all C. koseri strains tested • CkP1 recognizes C. koseri lipopolysaccharide through its long tail fiber • Both phage CkP1 and its tail fiber can be used to treat or detect C. koseri pathogens.

Citrobacter koseri: A rare cause of an epidural spinal abscess

Background

Citrobacter koseri, a Gram-negative organism, rarely causes an epidural spinal abscess.

Case Description

A 50-year-old male presented with mild paraparesis attributed to an magnetic resonance (MR)-documented spinal epidural abscess (SEA) at the T10-level. Following surgical debridement, cultures grew C. koseri, a rare Gram-negative organism. The abscess was subsequently managed with a prolonged course of antibiotics resulting in complete symptom and MR-documented radiological resolution.

Conclusion

A 50-year-old male presented with a T10 SEA attributed to a rare Gram-negative organism, C. koseri. The abscess was appropriately managed with surgical decompression/debridement, followed by prolonged antibiotic therapy.

The Effects of Ventilation, Humidity, and Temperature on Bacterial Growth and Bacterial Genera Distribution

BACKGROUND

Bacteria are readily nourished in airtight environments with high humidity, such as storage cabinets, clothing closets, and corners, where ventilation is normally low and humidity is high.

OBJECTIVES

We characterized the role of humidity and ventilation in bacterial growth and genus distribution at different temperatures (26 °C and 34 °C).

METHODS

Fresh pork, which was used as the substrate for bacterial culture, was placed in storage cabinets. Bacterial growth and genera distribution on the surface of pork placed in a storage cabinet under different temperatures (26 °C and 34 °C); relative humidity levels (RH: 50%, 70%, 90%); and ventilation conditions (no ventilation and low, medium, and high levels of ventilation) were assessed by rDNA sequencing.

RESULTS

Increased ventilation and reduced humidity significantly decreased bacterial growth at 26 °C and 34 °C. The contribution of increased ventilation to the reduction in bacterial growth exceeded that of decreased humidity. Ventilation had the greatest effect on reducing bacterial growth compared to the unventilated conditions at 70% RH. At 34 °C, medium and high levels of ventilation were required to reduce bacterial growth. High temperatures greatly increased bacterial growth, but ventilation could reduce the degree of this increase.

Second Trimester Fetal Loss Due to Citrobacter koseri Infection: A Rare Cause of Preterm Premature Rupture of Membranes (PPROM)

Citrobacter koseri is a facultative anaerobic, motile, non-spore-forming Gram-negative bacillus, which belongs to the family of Enterobacteriaceae. Severe infections due to Citrobacter spp. have been reported in the urinary tract, respiratory airways, intra-abdominal organs, skin and soft tissue, eye, bone, bloodstream, and central nervous system. In newborns, C. koseri is a well-known cause of meningitis, cerebral abscesses, brain adhesions, encephalitis, and pneumocephalus. Infection can be acquired through vertical maternal transmission or horizontal hospital settings; however, in many cases, the source is unknown. Preterm premature rupture of membranes (PPROM), caused by C. koseri, has rarely been described. Herein, we describe a case of PPROM at 16 weeks and 3 days of gestation, leading to anhydramnios. The parents opted for legal termination of the pregnancy, as the prognosis was very poor. C. koseri was isolated postmortem from a placental subamniotic swab and parenchymal sample, as well as fetal blood and lung. To the best of our knowledge, this is the first case of early second-trimester PPROM in which C. koseri infection was demonstrated.

Complete genome sequencing and comparative analysis of Citrobacter koseri CKNJ, a strain isolated from patient with endogenous endophthalmitis

Citrobacter koseri is an opportnistic pathogen can cause a variety of diseases. Though the mortality rate of C. koseri infections is high but there is a paucity of clinical information on them. Furthermore, the genomic features of this species are poorly studied. Herein, we presented a patient with endogenous endophthalmitis secondary to septicaemia, and collected a C. koseri isolate, CKNJ, from the blood of the patient. Whole genome sequencing revealed that the CKNJ harbors no plasmid and codes for 67 putative virulence factors. Whole genome SNP-based phylogenetic analysis revealed that strain CKNJ was close to the strains with same isolation sites. Compared to the other sequenced C. koseri chromosomes, CKNJ contains several strain-variable regions, including one prophage and two large genomic islands. The sequencing of the first complete genome of a clinical strain from China should reinforce our understanding of the genomic features and pathogenicity of this invasive infection-causing C. koseri with clinical significance.

CITROBACTER ENDOGENOUS ENDOPHTHALMITIS: A CASE REPORT AND REVIEW OF THE LITERATURE

PURPOSE

We present a case of endogenous endophthalmitis because of an unusual bacterium, Citrobacter koseri.

PATIENT

A 57-year-old woman without previous history of eye surgery or trauma presented with diabetic ketoacidosis and a painful right eye with the reduction of vision. C. koseri was identified in blood culture; thus, a diagnosis of right eye endogenous endophthalmitis was made. Intravenous and intravitreal antibiotics were both started, and vitreous culture further confirmed C. koseri as the causative organism. Computed tomography of the abdomen and pelvis revealed a right C-shaped perinephric abscess, which was drained under ultrasound guidance.

RESULTS

Because of rapid progression to corneal melting, evisceration was performed.

CONCLUSION

Cases of endogenous endophthalmitis caused by Citrobacter are very limited, and a review of all published cases in the English literature and the present case revealed that endogenous Citrobacter endophthalmitis arose almost entirely from Citrobacter renal infection. Early recognition and drainage of renal abscess may lower the chance of uncontrolled infection and endogenous spread to the eyes. Despite prompt and intensive treatment, the clinical outcome of Citrobacter endogenous endophthalmitis seems to be poor.

Genome sequence of carbapenem-resistant Citrobacter koseri carrying blaOXA-181 isolated from sewage sludge

OBJECTIVES

This study reported the resistome content of sewage sludge-isolated carbapenem-resistant Citrobacter koseri (C. koseri) carrying bla_OXA-181. It also provided a general phylogenomic analysis highlighting antibiotic resistance genes (ARGs), plasmids and pathogenicity of C. koseri genomes.

METHODS

The carbapenem-resistantC. koseri AS1 strain was isolated from sewage sludge on CHROMagar™ mSuperCARBA™ media. Whole genome sequencing of C. koseri AS1 was performed using an HiSeq X™ Ten instrument. Additional C. koseri genomes were downloaded from National Center for Biotechnology Information (NCBI). Phylogenomic analysis was established through CSI Phylogeny. ARGs, plasmids and pathogenicity were identified using ResFinder 3.1, PlasmidFinder 2.0 and PathogenFinder 1.1, respectively.

RESULTS

The phylogenomic tree indicated a polyclonal pattern ofC. koseri genomes. Resistome analysis of C. koseri AS1 revealed β-lactam resistance genes (bla_MAL-1 and bla_OXA-181) as well as a fosfomycin resistance gene (fosA7). Three plasmids (ColKP3, ColRNAI and IncX30) were identified in the C. koseri AS1 genome. In addition, 25 ARGs were found in downloaded genomes. Of these, clinically significant ARGs such as bla_KPC-2 and bla_OXA-48 were found in two and four genomes, respectively. Assessment of the genomes using PathogenFinder revealed all genomes as putative human pathogens.

CONCLUSIONS

It is believed that noC. koseri genome has been reported to carry bla_OXA-181; therefore, C. koseri AS1 is the first of its kind. This study also highlighted the resistome contents of C. koseri genomes.

Recurrence of Citrobacter koseri-associated Intra-abdominal Infection 2 Years after Spilled Gallstones during Laparoscopic Cholecystectomy

Spilled gallstones during laparoscopic cholecystectomy (LC) are common. Lost gallstones can lead to complications such as intra-abdominal abscesses, which can occur days, months, or even years after the procedure. Citrobacter koseri belongs to the family of Enterobacteriaceae. It is a low-virulence pathogen; however, it is linked to infections of the urinary tract and abdomen. We report the case of a 70-year-old diabetic male who presented with C. koseri- associated subhepatic abscess. Two years prior, he had emphysematous cholecystitis and liver abscess caused by C. koseri. During his LC, gallstones were spilled in the abdominal cavity and every effort was made to retrieve them. However, 2 years later, an aspiration of the subhepatic abscess revealed cholesterol fragments. We hypothesize that dislodged cholesterol gallstones and bile, contaminated with C. koseri, were the culprits for the appearance of the subhepatic abscess with the same organism 2 years after the LC.

Rectal culture-directed antibiotic prophylaxis before transrectal prostate biopsy: Reduced infectious complications and healthcare costs

BACKGROUND

Transrectal ultrasound-guided prostate biopsy (TUPB) is associated with infectious complications (ICs), which are related to a greater prevalence of ciprofloxacin-resistant bacteria (CRB) in rectal flora. We examined the ICs that occurred in 2 groups: A guided antibiotic prophylaxis (GP) group and an empiric prophylaxis (EP) group. We assessed the financial impact of GP.

MATERIAL AND METHODS

The GP group was studied prospectively (June 2013 to July 2014). We collected rectal cultures (RCs) before the TUPB, which were seeded on selective media with ciprofloxacin to determine the presence of CRB. The patients with sensitive bacteria were administered ciprofloxacin. Patients with resistant bacteria were administered GP according to the RC antibiogram. The EP group was studied retrospectively (January 2011 to June 2009). RCs were not performed, and all patients were treated with ciprofloxacin as prophylaxis. The ICs in both groups were recorded during a period no longer than 30 days following TUPB (electronic medical history).

RESULTS

Three hundred patients underwent TUPB, 145 underwent GP, and 155 underwent EP. In the GP group, 23 patients (15.86%) presented CRB in the RCs. Only one patient (0.7%) experienced a UTI. In the EP group, 26 patients (16.8%) experienced multiple ICs (including 2 cases of sepsis) (P<.005). The estimated total cost, including the management of the ICs, was €57,076 with EP versus €4802.33 with GP. The average cost per patient with EP was €368.23 versus €33.11 with GP. GP achieved an estimated total savings of €52,273.67. Six patients had to undergo GP to prevent an IC.

CONCLUSIONS

GP is associated with a marked decrease in the incidence of ICs caused by CRB and reduced healthcare costs.

In vitro susceptibility and resistance phenotypes in contemporary Citrobacter isolates in a University Hospital in Crete, Greece

BACKGROUND

Data on Citrobacter spp. susceptibility are scarce. We sought to study the evolution in the susceptibility of 385 Citrobacter spp. at the University Hospital of Heraklion, Crete, Greece during a six-year period (2010-2015).

METHODS

Non-duplicate strains isolated from inpatients (intensive care unit, oncology, surgery, internal medicine, paediatrics) and outpatients were studied using Vitek 2. Phenotypic confirmatory tests were applied for detection of β-lactamases and aminoglycoside modifying enzymes.

RESULTS

C. freundii (172, 44.7%) and C. koseri (166, 43.1%) were the most commonly isolated species. C. braakii (34), C. amalonaticus (6), C. youngae (6) and C. sedlakii (1) were the remaining isolates. Colistin and fosfomycin were the most active antibiotics (both 99.2%) followed by carbapenems (99%) aminoglycosides (96.6-98.4%), tigecycline (96.1%), cefepime (94.8%), ciprofloxacin (94.3%), tetracycline (92.7%), trimethoprim/sulphamethoxazole (91.4%), chloramphenicol (88.1%), piperacillin/tazobactam (86.5%) and 3rd generation cephalosporins (85.7%). C. freundii were more resistant than C. koseri. Antibiotic resistance did not increase during the study period for most antibiotics. Lower susceptibility to all antibiotics was observed among multi-drug resistant (MDR) strains. AmpC was the most common resistant mechanism (10.9%); carbapenemases (1.3%) and aminoglycoside modifying enzymes (2.9%) were also detected. All AmpC producers were resistant to cephalosporins but not to carbapenems. In all but one isolates aminoglycoside resistance was accompanied by acquired β-lactamases.

CONCLUSIONS

Although Citrobacter species in general were susceptible, antibiotic susceptibility testing is required for the detection of resistant isolates.