Citrobacter Sedlakii Research Articles

Bla SED-1 beta-lactamase-producing Citrobacter sedlakii isolated from horses and genomic comparison with human-derived isolates.

We aim to detect beta-lactamase-producing Citrobacter sedlakii from horses and compare the genomic characteristics with isolates from humans.Methods and Result: We characterized phenotypically and genotypically nine C. sedlakii isolates from the feces of horses and then compared them to human-derived isolates using whole genome sequencing and phylogenomic methods. Seven isolates (7/9) were ampicillin-resistant, while at least one isolate was resistant to ceftriaxone, gentamicin, meropenem, and streptomycin. All nine isolates were carriers of the chromosomal-mediated blaSED-1 beta-lactamase gene which confer resistance to ampicillin. One isolate was positive for the mcr-9 gene that confers resistance to colistin, and another isolate had the aac(6')-lid gene that confers resistance to aminoglycosides. Seven isolates (7/9) were carriers of genes that confer metal resistance to copper, silver, and arsenic. Phylogenetically, two horse-derived isolates clustered together with two human-derived isolates from the NDARO database. The results from our study provide insight into the antimicrobial susceptibility of C. sedlakii in horses which was previously lacking, and the specific beta-lactamase gene mediating resistance.

Carbapenem-Resistant Enterobacterales in the Western Balkans: Addressing Gaps in European AMR Surveillance Map.

In the context of global efforts to combat antimicrobial resistance (AMR), the importance of comprehensive AMR data is more crucial than ever. AMR surveillance networks, such as the European Antimicrobial Resistance Surveillance Network (EARS-Net) and the Central Asian and European Surveillance of Antimicrobial Resistance (CAESAR), support member states in obtaining high-quality AMR data. Nevertheless, data gaps persist in some countries, including those in the Western Balkans (WBs), a region with high AMR rates. This review analyzed existing research on carbapenem-resistant Enterobacterales (CRE) to better understand the AMR landscape in the WB countries. The most prevalent CRE was Klebsiella pneumoniae, followed by Escherichia coli, Enterobacter cloacae, and Proteus mirabilis, with sporadic cases of Morganella morganii, Providencia spp., Klebsiella oxytoca, and Citrobacter sedlakii. Carbapenemase production was identified as the most common mechanism of carbapenem resistance, but other resistance mechanisms were not investigated. An increasing trend in carbapenem resistance has been observed over the last decade, alongside a shift in carbapenemase epidemiology from the NDM type in 2013-2014 to the OXA-48 type in recent years. Few studies have applied whole-genome sequencing for CRE analysis, which has demonstrated the spread of resistance determinants across different niches and over time, emphasizing the importance of molecular-based research. The overall low number of studies in the WB countries can be attributed to limited resources, highlighting the need for enhanced support in education, training, technology, and equipment to improve data collection and evaluation.

Prevalence of Gram-positive and negative bacteria associated with external ocular infection in Wasit province, Iraq

Abstract Background: In developing countries, ocular infections are a significant public health concern, particularly bacterial infections, which are common. This research aimed to estimate how often Gram-positive and negative bacteria are present in individuals who have external ocular infections in Wasit province. Materials and Methods: One hundred twenty-one eye swabs were gathered from patients with various eye infections in the consulting clinics of AL-Zahra Hospital between October 1, 2021, and March 1, 2022. Various bacterial colonies with different morphological and biochemical characteristics were detected through growth testing. Results: Of all the external ocular samples collected, 56 (46.2%) had a positive culture for bacterial pathogens. Most of the isolated bacteria were Gram-positive, accounting for 73.2% (41 cases) of the total. Coagulase-negative Staphylococci (CoNS) were the most commonly identified Gram-positive bacteria, followed by Staphylococcus epidermidis, Staphylococcus hominis, Staphylococcus haemolyticus, Staphylococcus aureus, Staphylococcus lentus, Staphylococcus hominis spp. Novobiosepticus, Staphylococcus pseudintermedius, Staphylococcus lugdunesis, Staphylococcus gallinarum, Staphylococcus vitulinus, Staphylococcus cohnii, Streptococcus pneumoniae, Kocuria rosea, Micrococcus luteus, Leuconostoc mesenteroides, and, among which, Gram-negative bacteria accounted for 26.8% such as Klebsiella pneumonia, Proteus mirabilis, Enterobacter aerogenes, Pantoea spp., Yersinia enterocolitica, Citrobacter sedlakii, Pseudomonas aeruginosa, Pseudomonas oryzihabitans, and Sphingomonas paucimobilis. DNA extraction and their purity and concentration were confirmed using Nanodrop. A monoplex pattern of polymerase chain reaction (PCR) was employed to detect Gram-positive specific 16S rRNA. Conclusion: A majority of the bacterial strains identified in patients with ocular infections, particularly Gram-positive bacteria, also concluded that the largest percentage of eye infections was for patients who lived in rural areas, this explains the reason for the isolation of some bacterial species that inhabit animals such as S. lentus, S. gallinarum, S. pseudintermedius, S. vitulinus, S. cohnii, and L. mesenteroides. In addition, most of the bacterial species found in patients with eye infections were resistant to multiple drugs, indicating the development of multidrug-resistant bacteria in the study population, also concluded that the most prevalent forms of external ocular infections were blepharitis, followed by conjunctiva.

Genomic insight into transmission mechanisms of carbapenem-producing Citrobacter spp. isolates between the WWTP and connecting rivers

Carbapenem-resistant Enterobacteriaceae (CRE) poses major health risks worldwide. Most studies have focused on carbapenem resistance in Klebsiella pneumoniae and Escherichia coli; however, the occurrence and transmission of carbapenem-resistant Citrobacter spp. (CRCS) are poorly understood. In this study, we investigated the occurrence and potential transmission patterns of CRCS in different functional areas of an urban wastewater treatment plant (WWTP) and connecting rivers during one-year monitoring in Shandong Province, China. In total, 14 CRCS were detected in 376 environmental samples, including those from the WWTP inlet (n = 7), WWTP anaerobic tank (n = 2), and rivers (n = 5). Citrobacter braakii (n = 6) was the dominant subtype among 14 CRCS isolates, followed by Citrobacter freundii (n = 5), Citrobacter sedlakii (n = 2), and Citrobacter werkmanii (n = 1). All CRCS were resistant to imipenem, meropenem, ampicillin, amoxicillin/clavulanic acid, cefotaxime, ceftazidime, trimethoprim/sulfamethoxazole, and ciprofloxacin. Plasmid analysis showed that the blaKPC-2 gene was located on IncN and IncFII (Yp) plasmids, whereas the blaNDM gene was located on IncX3 and IncN2 plasmids. Clonal transmission of CRCS harboring carbapenem genes occurred between the WWTP and connecting rivers on a temporal or spatial scale. High genomic relatedness of NDM-5-producing C. sedlakii was identified between river water and WWTP aerosol, suggesting a potential exposure risk of CRCS for workers and surrounding residents near the WWTP. Furthermore, NDM-5-producing C. sedlakii isolated from rivers was related to C. sedlakii isolated from soil and well water in different regions of China, indicating that NDM-5-producing C. sedlakii may be widespread in China. These findings indicate that rare healthcare-associated pathogens such as CRCS can contribute to widespread carbapenem production in the environment; thus, CRCS should be continuously monitored.

Optimization of textile effluent bacterial treatment and improvement of the process efficiency through SPB1 biosurfactant addition.

The current work aims to optimize biological textile effluent treatment through the use of newly selected bacterial consortia composed of two strains: Citrobacter sedlakii RI11 and Aeromonas veronii GRI. We assessed the effect of SPB1 biosurfactant addition on color removal (CR). The process was optimized by a Box-Bhenken by examining the effect of pH, consortia density and biosurfactant value on treatment efficiency. Firstly, physicochemical analyses of the studied effluent revealed an alkaline pH along with a high content of suspended materials and large amounts of organic matter. Optimal CR and a chemical oxygen demand abatement of about 94 and 86% were obtained when treating the textile effluent at pH 5 with a total optical density of 0.4 and by incorporating 0.01% SPB1 biosurfactant. Additionally, an abolishment of phytotoxicity was registered after treatment optimization. The evaluations of the action mode of both selected bacteria during textile effluent treatment suggested the occurrence of biodegradation phenomena of dyes through enzymatic activities.

Emergence of plasmid-mediated colistin resistance mcr-3.5 gene in Citrobacter amalonaticus and Citrobacter sedlakii isolated from healthy individual in Thailand.

Citrobacter spp. are Gram-negative bacteria commonly found in environments and intestinal tracts of humans and animals. They are generally susceptible to third-generation cephalosporins, carbapenems and colistin. However, several antibiotic resistant genes have been increasingly reported in Citrobacter spp., which leads to the postulation that Citrobacter spp. could potentially be a reservoir for spreading of antimicrobial resistant genes. In this study, we characterized two colistin-resistant Citrobacter spp. isolated from the feces of a healthy individual in Thailand. Based on MALDI-TOF and ribosomal multilocus sequence typing, both strains were identified as Citrobacter sedlakii and Citrobacter amalonaticus. Genomic analysis and S1-nuclease pulsed field gel electrophoresis/DNA hybridization revealed that Citrobacter sedlakii and Citrobacter amalonaticus harbored mcr-3.5 gene on pSY_CS01 and pSY_CA01 plasmids, respectively. Both plasmids belonged to IncFII(pCoo) replicon type, contained the same genetic context (Tn3-IS1-ΔTnAs2-mcr-3.5-dgkA-IS91) and exhibited high transferring frequencies ranging from 1.03×10-4 - 4.6×10-4 CFU/recipient cell Escherichia coli J53. Colistin-MICs of transconjugants increased ≥ 16-fold suggesting that mcr-3.5 on these plasmids can be expressed in other species. However, beside mcr, other major antimicrobial resistant determinants in multidrug resistant Enterobacterales were not found in these two isolates. These findings indicate that mcr gene continued to evolve in the absence of antibiotics selective pressure. Our results also support the hypothesis that Citrobacter could be a reservoir for spreading of antimicrobial resistant genes. To the best of our knowledge, this is the first report that discovered human-derived Citrobacter spp. that harbored mcr but no other major antimicrobial resistant determinants. Also, this is the first report that described the presence of mcr gene in C. sedlakii and mcr-3 in C. amalonaticus.

Timing and Nature of Infections in Multiple Myeloma Patients Treated with Anti-BCMA CAR-T Cells

Introduction: Anti-BCMA CAR-T is a highly effective therapy approved for relapsed/refractory multiple myeloma (MM). Its main toxicities include cytokine release syndrome, neurotoxicity, and cytopenias. Infections are common but not well-studied in this population. In this study, we seek to characterize the timing and nature of infections to better inform appropriate prophylactic measures. Methods: We retrospectively reviewed all MM patients (pts) treated with anti-BCMA CAR-T at Mount Sinai from 2018-2022. Data were collected on baseline characteristics, treatment, disease response, hypogammaglobulinemia (HGG), infections, and prophylactic measures, including intravenous immunoglobulin (IVIg). The study period was from time of CAR-T infusion until progression or death. Chi-squared analysis was used for univariate associations and the Kaplan-Meier method was used for time-to-event calculations. Incidence rates ratios (IRR) were calculated using the exact Poisson method. This study was approved by the Mount Sinai IRB. Results: 80 pts were treated with anti-BCMA CAR-T; the median age was 61 years (range 35-77) and 40% were female. The median time from diagnosis to treatment was 5.1 years, with a median of 5 prior lines of therapy (range 1-18). 71% had high risk cytogenetics, and pts had a median of 2 infections (range 0-8) in the year prior to CAR-T. IVIg was used prophylactically in 95% of pts, usually for at least the first 6 months, and these pts were on IVIg 49% of the total time on study. All patients received prophylaxis for VZV, PCP (if CD4< 200/mm3), and anti-bacterial plus anti-fungal for ANC <500/mm3. Median follow-up was 30.1 months, with ORR of 94%, median PFS of 18.8 months and estimated OS of 70% at 3 years. CRS occurred in 86% (6% grade 3/4), with tocilizumab used in 73% and steroids in 34%. There were a total of 207 infections during 1336 months of follow-up (1.9 per pt-year), including 57 grade 3-5 infections (0.5 per pt-year) among 25 (31%) pts, and 5 (6%) deaths, with infection rates highest in the first 3 months (Figure 1). Deaths from infection occurred at months 3 (bacterial osteomyelitis), 4.6 (COVID-19), 5.3 (bacterial pneumonia), 24.4 (bacterial skin/soft tissue), and 26.4 (fungemia). Infections (all-grade/ grade 3-5) were mostly in the respiratory tract (63%/43%), followed by GI (11%/32%), skin/soft tissue (5%/11%), and bloodstream (5%/21%), and were mostly viral (68%/38%), followed by bacterial (30%/63%) and fungal (2%/5%). Few opportunistic infections occurred, including grade 3 Cryptosporidiosis, grade 3 Citrobacter sedlakii bacteremia, grade 5 Parabacteroides distasonis abscess and osteomyelitis, and grade 5 Saccharomyces fungemia. Of those with follow-up since 2020, 16 (25%) tested positive for SARS-CoV-2, with 4 severe cases including 1 death at 4.6 months (of these, 2 were vaccinated, including the patient who died). Asymptomatic CMV reactivation occurred in 34% and was only treated in 3 patients. 95% developed HGG, with severity difficult to gauge due to routine IVIg use. Immunoglobulin (Ig) recovery occurred at 14.3 months for one uninvolved Ig and 20 months for two uninvolved Igs. Absolute neutrophil count <500/mm3 and absolute lymphocyte count <500/mm3 were each associated with more severe infections (p<0.001). The 26 pts with 1-3 prior lines of therapy (LoT), compared with those with 4+ LoT, had lower overall infection rate (1.68 per pt-year vs 2.42 per pt-year, IRR 0.70, 95% CI [0.51-0.94], p=0.0.013) and grade 3-5 infection rate (0.29 per pt-year vs 0.62 per pt-year, IRR 0.46, 95% CI [0.21-0.91] p=0.016). Discussion: Infections among pts treated with anti-BCMA CAR-T were predominantly viral and occurred in the highest rates in the first 3 months. Neutropenia and lymphopenia, common in the first 3 months, were each associated with more severe infections, emphasizing the need for intensive prophylaxis and close outpatient monitoring during this period. Fungal and other opportunistic infections were rare, although one vaccinated patient died of COVID-19, highlighting the need for passive immunity in this population. Ig recovery occurred at 14.3 months, so the optimal duration of IVIg prophylaxis remains an open question. Of note, pts treated in earlier lines of therapy had significantly fewer infections, including grade 3-5 infections. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

Stabilization of expansive black cotton soil using bioenzymes produced by ureolytic bacteria

Soil stabilization is the art and science of improving the engineering properties of soils. The properties of problematic soils can be improved by blending appropriate amount of insitu soil, aggregates and bioenzymes. In the present study, four bacterial strains: Sporosarcina pasteurii, Bacillus paramycoides, Citrobacter sedlakii, and Enterobacter bugadensis were used to produce bioenzymes using urea supplemented molasses as a substrate via submerged fermentation. The crude bioenzyme was mixed with modified soil blended with 40% black cotton soil, 30% aggregate and 30% river sand; then tested after curing for 7 days. The test results revealed that except soil samples treated with bioenzyme of Enterobacter bugadensis, all treated soil samples showed improved plasticity index (18–55%) and liquid limit (5–44%). Soil samples treated with bioenzyme of Bacillus paramycoides, Citrobacter sedlakii and Sporosarcina pasteurii showed higher CBR values of 12.9%, 12.27%, and 11.95% respectively. On the other hand, free swell showed reduction in soil samples treated with bioenzymes of Sporosarcina pasteurii (47.37%), Bacillus paramycoides (30%), and Citrobacter sedlakii (10.53%). The highest percentage improvement of linear shrinkage was recorded for soil sample treated with bioenzymes of Sporosarcina pasteuri (39.65%), followed by Permazyme (10.44%), Citrobacter sedlakii (8.4%) and Bacillus paramycoides (8.34%). Whereas, the highest percentage improvement in MDD was recorded in permazyme treated soil (11.92%) followed by molasses (8.29%), Bacillus paramycoides (1.92%), and Enterobacter bugadensis (0.73%). The lowest optimum moisture content (9.3%) was recorded in soil treated with permazyme. Triaxial test analysis also showed improvement in both cohesion and angle of friction in bioenzyme treated soils. From the test results it was concluded that it is possible to treat expansive black cotton soils using bioenzymes produced from low cost substrates such as molasses and reduce the cost of construction and environmental carbon emission.

Plasmid Carrying blaCTX-M-15, blaPER-1, and blaTEM-1 Genes in Citrobacter spp. From Regional Hospital in Mexico

Introduction:Citrobacter spp. is an opportunistic bacteria that have been recognized as significant pathogens in patients with underlying diseases or immunocompromised status. The aim of this study was to identify extended-spectrum β-lactamases in clinical isolates of Citrobacter spp.Methods:This cross-sectional study was conducted at Hospital Central “Dr. Ignacio Morones Prieto” in San Luis Potosi, Mexico. Nineteen isolates of Citrobacter spp. were obtained from clinical specimens between April to December 2015. Four isolates were resistant to third-generation cephalosporins. The presence of genes encoding ESBL (blaCTX-M-15, blaTEM-1, blaVEB-1, blaSHV, and blaPER-1) was analyzed by PCR. For this purpose, plasmid DNA was extracted and horizontally transferred to recipient E. coli Top 10.Results:blaCTX-M-15 and blaVEB-1 genes were detected in Citrobacter freundii and Citrobacter sedlakii, whereas blaPER-1 gene was identified in 1 isolate of Citrobacter freundii. In contrast, blaSHV gene was not detected in any isolate. One strain carried blaCTX-M-15, blaTEM-1, blaVEB-1, and blaPER-1 genes, most in a 275-kb plasmid.Conclusion:This study shows the presence of different types of ESBL in clinical isolates of Citrobacter freundii and Citrobacter sedlakii, which confer resistance to broad-spectrum β-lactams. The plasmid identified in this study harboring ESBL genes could play an important role in the dissemination of antibiotic resistance.

A Patient With Multiple Carbapenemase Producers Including an Unusual Citrobacter sedlakii Hosting an IncC bla NDM-1- and armA-carrying Plasmid.

Background.Patients colonized with multiple species of carbapenemase-producing Enterobacterales (CPE) are increasingly observed. This phenomenon can be due to the high local prevalence of these pathogens, the presence of important host risk factors, and the great genetic promiscuity of some carbapenemase genes.Methods.We analyzed 4 CPE (Escherichia coli, Klebsiella pneumoniae, Providencia stuartii, Citrobacter sedlakii), 1 extended-spectrum cephalosporin-resistant K. pneumoniae (ESC-R-Kp), and 1 carbapenemase-producing Acinetobacter baumannii simultaneously isolated from a patient transferred from Macedonia. Susceptibility tests were performed using a microdilution MIC system. The complete genome sequences were obtained by using both short-read and long-read whole-genome sequencing technologies.Results.All CPE presented high-level resistance to all aminoglycosides due to the expression of the armA 16S rRNA methylase. In C. sedlakii and E. coli (ST69), both the carbapenemase blaNDM-1 and armA genes were located on an identical IncC plasmid of type 1a. The K. pneumoniae (ST268) and P. stuartii carried chromosomal blaNDM-1 and blaOXA-48, respectively, while the ESC-R-Kp (ST395) harbored a plasmid-located blaCTX-M-15. In the latter 3 isolates, armA-harboring IncC plasmids similar to plasmids found in C. sedlakii and E. coli were also detected. The A. baumannii strain possessed the blaOXA-40 carbapenemase gene.Conclusions.The characterization of the genetic organization of IncC-type plasmids harbored by 3 different species from the same patient offered insights into the evolution of these broad-host-range plasmids. Moreover, we characterized here the first complete genome sequence of a carbapenemase-producing C. sedlakii strain, providing a reference for future studies on this rarely reported species.

Emergence of IncX3 Plasmid-Harboring blaNDM-5 in a Citrobacter sedlakii Isolated from Outdoor Aerosol in Wastewater Treatment Plant.

A carbapenem-resistant Citrobacter sedlakii strain AA2CS carrying blaNDM-5 was detected in outdoor aerosols of a wastewater treatment plant (WWTP) in China and the whole genome was sequenced subsequently. AA2CS was captured in an aerobic tank with aerosol particles of sizes ranging from 4.7 to 7.0 μm. Besides blaNDM-5, AA2CS also harbored 21 other antibiotic resistance genes and displayed a high level of resistance to ampicillin, cefotaxime, ceftazidime, tetracycline, and meropenem. BlaNDM-5 was located on the IncX3 plasmid (pCSNDM-5) with an IS3000-IS5-blaNDM-5-bleMBL-trpF-dsbD-IS26 structure. pCSNDM-5 was highly homologous to other blaNDM-5-carrying IncX3 plasmids in China and can be transferred to the Escherichia coli recipient J53. To our knowledge, this is the first report of carbapenem-resistant Enterobacteriaceae in outdoor aerosols in WWTPs.

Isolation and Characterization of Urease-Producing Soil Bacteria.

Urease is an enzyme produced by ureolytic microorganisms which hydrolyzes urea into ammonia and carbon dioxide. Microbial urease has wide applications in biotechnology, agriculture, medicine, construction, and geotechnical engineering. Urease-producing microbes can be isolated from different ecosystems such as soil, oceans, and various geological formations. The aim of this study was to isolate and characterize rapid urease-producing bacteria from Ethiopian soils. Using qualitative urease activity assay, twenty urease-producing bacterial isolates were screened and selected. Among these, three expressed urease at high rates as determined by a conductivity assay. The isolates were further characterized with respect to their biochemical, morphological, molecular, and exoenzyme profile characteristics. The active urease-producing bacterial isolates were found to be nonhalophilic to slightly halophilic neutrophiles and aerobic mesophiles with a range of tolerance towards pH (4.0–10.0), NaCl (0.25—5%), and temperature (20–40°C). According to the API ZYM assays, all three isolates were positive for alkaline phosphatase, leucine aryl amidase, acid phosphatase, and naphthol_AS_BI_phosphohydrolase. The closest described relatives of the selected three isolates (Isolate_3, Isolate_7, and Isolate_11) were Bacillus paramycoides, Citrobacter sedlakii, and Enterobacter bugandensis with 16S rRNA gene sequence identity of 99.0, 99.2, and 98.9%, respectively. From the study, it was concluded that the three strains appear to have a relatively higher potential for urease production and be able to grow under a wider range of growth conditions.

Dissemination of blaNDM-5 via IncX3 plasmids in carbapenem-resistant Enterobacteriaceae among humans and in the environment in an intensive vegetable cultivation area in eastern China.

The environment of a large-scale vegetable production area can be exposed to antibiotic residues and antibiotic-resistant bacteria (ARB) via animal manure and irrigation with contaminated water, which can facilitate the dissemination of ARB. However, the occurrence of ARB in plantation areas and their dissemination in this environment remain largely unexplored. In total, 382 samples including those from vegetable (n=106), soil (n=87), well water (n=24), river water (n=20), river sediments (n=20), farmer feces (n=58) and farmer hands (n=67) were collected in 2019 from a large-scale cultivation area in Shandong, China. Selective agar plates were used to screen for carbapenem-resistant Enterobacteriaceae (CRE) and whole-genome sequencing and Southern blotting were used to characterise isolates and mobile genetic elements carrying carbapenem resistance determinants. A total of nine NDM-5-producing isolates of Escherichia coli, Klebsiella pneumoniae, and Citrobacter spp. were identified from environmental sources and human feces, all of which were multidrug-resistant. Single nucleotide polymorphism analysis suggested clonal transmission of carbapenem-resistant Citrobacter sedlakii within greenhouse soils in the area. Eight of the isolates carried closely related or identical IncX3 plasmids carrying blaNDM-5, which were shown to be conjugative via filter mating experiments, indicating the highly transmissible nature of this genetic element. Isolates of E.coli and Citrobacter freundii were detected in the feces of local farm workers and contained similar IncX3 plasmids with blaNDM-5 environmental isolates, suggesting a potential risk of CRE transfer from the work environment to the farm workers. Thus, further research is required to investigate the potential health risks associated with environmental exposure to CRE in vegetable cultivation areas.

Phenotipic Prevalence of Antibiotic Resistance in Gabon

Background: The increasing phenomenon of bacterial resistance to antibiotics is a real public health problem. The main causes are poor management of hygiene and water quality, but also the use of antibiotics without precaution. The objective of this study was to isolate and determine the antibiotic resistance profile of the different bacteria found in the main hospitals and bacteriology laboratories in Gabon. Methods: 6034 samples were taken from hospitals in seven main cities of Gabon, and analyzed according to the usual techniques. The pathogenic strains were identified by Matrix-Assisted Laser Desorption Ionization-Time Of Flight Mass Spectrometry. Antimicrobial susceptibility testing was performed by the agar disc diffusion method, according to the Antibiogram Committee of the French Society for Microbiology guidelines. Results: 974 pathogenic bacterial strains were found, including 890/974 (91.4%) Gram-negative bacilli. The systematic antimicrobial susceptibility testings identified 160/974 (16.4%) multi-resistant strains. Escherichia coli was the most represented species. 12.5% - 25% of Escherichia coli, Klebsiella pneumoniae, Enterobacter cloacae, and Citrobacter sedlakii strains were resistant to amoxicillin + clavulanic acid, third and fourth generation cephalosporins. Aminoglycoside resistance rates of 8.5% - 19% were also noted. 4.5% to 25% of the bacteria found were resistant to quinolones and cotrimoxazole. Resistance rates to carbapenems ranged from 1% to 10.5%. 16% of Staphylococcus aureus were methicillin-resistant (MRSA). Rates of extended spectrum beta-lactamase-producing enterobacteriaceae (ESBL-PE) ranged from 2.5% to 25%. Conclusion: This study showed an increasing evolution of bacterial resistance to antibiotics that are spreading throughout Gabon. This constitutes a threat to the health of Gabonese population.

Citrobacter sedlakii – A rare cause of meningitis and brain abscess in a neonate

Citrobacter sedlakii is a Gram-negative bacillus, usually a non-pathogenic organism, found in human stool. However, it may rarely cause devastating illness in human beings. We are describing a case of C. sedlakii meningitis and brain abscess in a neonate. To the best of our knowledge, this is the second case, of C. sedlakii causing complicated meningitis in a neonate in the world.

Prevalence of β-Lactam Drug-Resistance Genes in Escherichia coli Contaminating Ready-to-Eat Lettuce.

Thirty-four Escherichia coli isolates from 91 ready-to-eat lettuce packages, obtained from local supermarkets in Northern California, were genotyped by multilocus sequence typing, tested for susceptibility to antimicrobial agents, and screened for β-lactamase genes. We found 15 distinct sequence types (STs). Six of these genotypes (ST1198, ST2625, ST2432, ST2819, ST4600, and ST5143) have been reported as pathogens found in human samples. Twenty-six (76%) E. coli isolates were resistant to ampicillin, 17 (50%) to ampicillin/sulbactam, 8 (23%) to cefoxitin, and 7 (20%) to cefuroxime. blaCTX-M was the most prevalent β-lactamase gene, identified in eight (23%) isolates. We identified a class A broad-spectrum β-lactamase SED-1 gene, blaSED, reported by others in Citrobacter sedlakii isolated from bile of a patient. This study found that fresh lettuce carries β-lactam drug-resistant E. coli, which might serve as a reservoir for drug-resistance genes that could potentially be transmitted to pathogens that cause human infections.

Isolation of Lignin-Degrading Bacteria from Different Sources and Testing of Their Ligninolytic Activities

Nine lignin-degrading bacteria were isolated from petroleum-contaminated soil and animal manure samples and characterized by 16S rRNA sequence analysis. Three isolates were identified as Enterobacter cancerogenus, two as Enterobacter ludwigii, one as Citrobacter sedlakii, one as Citrobacter farmeri, one as Klebsiella pneumoniae, and one as Citrobacter murliniae. These bacteria used ligno sulphate as the sole carbon source but did not utilize kraft lignin (KL) as the sole source of carbon and energy. For this reason, basic nutrients, such as 1.0% glucose (w/v) and 0.5% peptone (w/v), were used as additional carbon and nitrogen sources to stimulate bacterial growth for KL decolorization. Under these conditions, the isolates L1, L2, L3, L4, PT21, PT22, PT41, G1, and C1 degraded kraft lignin by 37 %, 14 %, 20%, 43%, 48%, 51%, 28%, 60%, and %99, respectively. The decolorization of Remazol Brilliant Blue R (RBBR) by the isolates was analyzed. The isolates were decolorized at 20-90 % of RBBR, respectively.

Towards Predicting Gut Microbial Metabolism: Integration of Flux Balance Analysis and Untargeted Metabolomics.

Genomics-based metabolic models of microorganisms currently have no easy way of corroborating predicted biomass with the actual metabolites being produced. This study uses untargeted mass spectrometry-based metabolomics data to generate a list of accurate metabolite masses produced from the human commensal bacteria Citrobacter sedlakii grown in the presence of a simple glucose carbon source. A genomics-based flux balance metabolic model of this bacterium was previously generated using the bioinformatics tool PyFBA and phenotypic growth curve data. The high-resolution mass spectrometry data obtained through timed metabolic extractions were integrated with the predicted metabolic model through a program called MS_FBA. This program correlated untargeted metabolomics features from C. sedlakii with 218 of the 699 metabolites in the model using an exact mass match, with 51 metabolites further confirmed using predicted isotope ratios. Over 1400 metabolites were matched with additional metabolites in the ModelSEED database, indicating the need to incorporate more specific gene annotations into the predictive model through metabolomics-guided gap filling.

Investigation of carbon substrate utilization patterns of three ureolytic bacteria

Abstract Bacteria have developed specific substrate utilization profiles which allow them to grow only under specific conditions. They assimilate different organic substrates as carbon and energy sources for their growth and biomass production. In this study the carbon substrate utilization patterns of three bacteria [Bacillus paramycoides (Isolate-3), Citrobacter sedlakii (Isolate-7), and Enterobacter bugadensis (Isolate-11)] were investigated using BIOLOG Gen III microPlate and API strip techniques. These techniques employ various carbon substrates to determine bacterial carbon utilization patterns more quickly, economically, and effectively. Subsequently, biochemical analysis using API 20NE test showed that the three bacterial species were positive for Nitrate reduction, Glucose fermentation, Urease activity, hydrolysis of Esculine, assimilation of N-acetyl-glucosamine, d -maltose and Potassium Gluconate. In addition, the three bacteria assimilated 19 carbon substrates ( d -Glucose, D-Sorbitol, Methyl Pyruvate, Dextrin, d -Maltose, d -Fructose, l -Alanine, l -lactic Acid, d -Gluconic Acid, d -Trehalose, d -Cellobiose, Glycerol, Glucuronamide, l -Glutamic Acid, N-Acetyl- d -Glucosamine, b-Gentiobiose, Acetic Acid, l -Serine, and Inosine) of BIOLOG Gen III MicroPlates. On the other hand, they were all unable to assimilate Tween-40, D-Arabitol, d -Lactic Acid, Methyl Ester, d -Fucose, Quinic Acid, and d -Aspartic Acid. Similarly, API 50CH carbohydrate fermentation analysis showed that the three bacteria intensively metabolized d -Ribose, d -Glucose, d -Fructose, N-Acetyl-Glucosamine, Arbutine, Esculine Citrate, d -Maltose, and d -Trehalose. It was also determined that none of the three bacteria could assimilate Erythritol, l -Xylose, D-Adonitol, Methyl-β- d -Xylopyranoside, l -Sorbose, Methyl-α- d -mannopyranoside, Amygdaline, Inuline, d -Melezitose, Amidon, Glycogene, Xylitol, d -turanose, d -Tagatose, d -Fucose, D-Arabitol, L-Arabitol, and Potassium 5-Ceto-Gluconate. The study revealed that Enterobacter bugadensis and Citrobacter sedlakii exhibited an intensive metabolic activity and strong metabolic correlation than Bacillus paramycoides.

Diversity of carbapenemases in clinical isolates: The emergence of blaVIM-5 in Bangladesh

Global emergence and dissemination of carbapenemases are clinically threatening, notably in countries with endemic blaNDM. To analyze the extent of carbapenemases in Bangladesh, 71 isolates were collected from 7 different clinical sources: wound swab (n = 38), pus (n = 13), urine (n = 9), blood (n = 4), tracheal aspirate (n = 3), pleural fluid (n = 1) and vaginal swab (n = 3) from Dhaka Medical College Hospital, Bangladesh. Among the isolates, 25 were resistant to at least one of the three carbapenems (imipenem, meropenem and doripenem), including 15 being resistant to all. These resistant isolates were identified as Pseudomonas aeruginosa, Acinetobacter baumannii, Klebsiella pneumoniae, P. hibiscicola, Proteus mirabilis, Providencia stuartii and Citrobacter sedlakii. Carbapenemase detection among these 25 isolates varied in individual phenotypic assays (83% in Modified Hodge Test, 50% in Combined Disk Test for Metallo-β-lactamase prediction) as compared with the genotypes observed (96% prevalence of various carbapenemases including blaOXA-1,48, blaNDM-1,5, blaVIM-2,5). blaOXA-48 was the most prevalent gene (84%) followed by blaNDM (72%). Coexistence of multiple gene combination such as blaNDM+blaOXA-48+blaOXA-1 was prevalent (48%). Harborage of blaVIM-5 (n = 1) was characterized for the first time, while blaNDM-5 (n = 5) was reported contemporarily with a recent study in Bangladesh. Presence of plasmids (64%) and integron class 1 (100%) signifies the transferable potential of resistant traits. The emergence of such new variants along with the presence of the mobile genetic elements demands strict surveillance and combating strategies.