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Enterobacter ludwigii has been proven by numerous studies to be an effective plant growth promoter. Enterobacter ludwigii T977 was isolated from leaves of Nicotiana tabacum L. Yunyan 97 which showing high starch degrading ability. The optimal fermentation carbon source of strain T977 was starch, with optimal starch concentration as 2.5 g/L, and the most suitable fermentation nitrogen source for the strain T977 was ammonium acetate, with optimal concentration as 0.25 g/L. The spaying treatment of strain T977 could reduce the starch content of upper leaves from 3.77% to 1.43%, the total sugar and reducing sugar decreased slightly, the starch content of middle leaves decreased from 5.63% to 3.18%, the content of total sugar and reducing sugar increased in middle leaves, and the other chemical components were in the appropriate range. Here, we reported 4.77 MB whole genome of a starch-degrading E. ludwigii T977 that encodes 4501 proteins, 11 α-amylases in GH13 family were identified, and the amylase (GM000159) with signal peptide may play important role in degradation of starch in tobacco leaves. Our study may provide an effective microbiological mean for reducing starch content in tobacco leaves., Competing Interests: Declarations. Ethics approval and consent to participate: Not applicable. Consent for publication: Not applicable. Competing interests: The authors declare no competing interests., (© 2024. The Author(s).)

Background: Enterobacter species are included among the normal human gut microflora and persist in a diverse range of other environmental niches. They have become important opportunistic nosocomial pathogens known to harbour plasmid-mediated multi-class antimicrobial resistance (AMR) determinants. Global AMR surveillance of Enterobacterales isolates shows the genus is second to Klebsiella in terms of frequency of carbapenem resistance. Enterobacter taxonomy is confusing and standard species identification methods are largely inaccurate or insufficient. There are currently 27 named species and a total of 46 taxa in the genus distinguishable via average nucleotide identity (ANI) calculation between pairs of genomic sequences. Here we describe an Enterobacter strain, ECC3473, isolated from the wastewater of an Australian hospital whose species could not be determined by standard methods nor by ribosomal RNA gene multi-locus typing., Aim: To characterise ECC3473 in terms of phenotypic and genotypic antimicrobial resistance, biochemical characteristics and taxonomy as well as to determine the global distribution of the novel species to which it belongs., Methods: Standard broth dilution and disk diffusion were used to determine phenotypic AMR. The strain's complete genome, including plasmids, was obtained following long- and short read sequencing and a novel long/short read hybrid assembly and polishing, and the genomic basis of AMR was determined. Phylogenomic analysis and quantitative measures of relatedness (ANI, digital DNA-DNA hybridisation, and difference in G+C content) were used to study the taxonomic relationship between ECC3473 and Enterobacter type-strains. NCBI and PubMLST databases and the literature were searched for additional members of the novel species to determine its global distribution., Results: ECC3473 is one of 21 strains isolated globally belonging to a novel Enterobacter species for which the name, Enterobacter adelaidei sp. nov. is proposed. The novel species was found to be resilient in its capacity to persist in contaminated water and adaptable in its ability to accumulate multiple transmissible AMR determinants., Conclusion: E. adelaidei sp. nov. may become increasingly important to the dissemination of AMR., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier GmbH.. All rights reserved.)

Background: Bacterial growth rate, commonly reported in terms of doubling time, is frequently determined by one of two techniques: either by measuring optical absorption of a growing culture or by taking samples at different times during their growth phase, diluting them, spreading them on agar plates, incubating them, and counting the colonies that form. Both techniques require measurements of multiple repeats, as well careful assessment of reproducibility and consistency. Existing literature using either technique gives a wide range of growth rate values for even the most extensively studied species of bacteria, such as Escherichia coli, Pseudomonas aeruginosa, and  Staphylococcus aureus. This work aims to apply several methods to reliably determine the growth rate of a recently identified species of Enterobacteriaceae, called Enterobacter sp. SM3, and to compare that rate with that of a well-known wildtype E. coli strain KP437., Results: We extend conventional optical density (OD) measurements to determine the growth rate of Enterobacter sp. SM3. To assess the reliability of this technique, we compare growth rates obtained by fitting the OD data to exponential growth, applying a relative density method, and measuring shifts in OD curves following set factors of dilution. The main source of error in applying the OD technique is due to the reliance on an exponential growth phase with a short span. With proper choice of parameter range, however, we show that these three methods yield consistent results. We also measured the SM3 division rate by counting colony-forming units (CFU) versus time, yielding results consistent with the OD measurements. In lysogeny broth at 37 o C, SM3 divides every 21 ± 3 min, notably faster than the RP437 strain of E. coli, which divides every 29 ± 2 min., Conclusion: The main conclusion of this report is that conventional optical density (OD) measurements and the colony-forming units (CFU) method can yield consistent values of bacterial growth rate. However, to ensure the reproducibility and reliability of the measured growth rate of each bacterial strain, different methods ought to be applied in close comparison. The effort of checking for consistency among multiple techniques, as we have done in this study, is necessary to avoid reporting variable values of doubling time for particular species or strains of bacteria, as seen in the literature., (© 2024. The Author(s).)

Lignin, the second most abundant renewable carbon source on earth, holds significant potential for producing biobased specialty chemicals. However, its complex, highly branched structure, consisting of phenylpropanoic units and strong carbon-carbon and ether bonds, makes it highly resistant to depolymerisation. This recalcitrancy highlights the need to search for robust lignin-degrading microorganisms with potential for use as industrial strains. Bioprospecting for microorganisms from lignin-rich niches is an attractive approach among others. Here, we explored the ligninolytic potential of bacteria isolated from a lignin-rich underground coalmine, the Morupule Coal Mine, in Botswana. Using a culture-dependent approach, we screened for the presence of bacteria that could grow on 2.5% kraft lignin-supplemented media and identified them using 16 S rRNA sequencing. The potential ligninolytic isolates were evaluated for their ability to tolerate industry-associated stressors. We report the isolation of twelve isolates with ligninolytic abilities. Of these, 25% (3) isolates exhibited varying robust ligninolytic ability and tolerance to various industrial stressors. The molecular identification revealed that the isolates belonged to the Enterobacter genus. Two of three isolates had a 16 S rRNA sequence lower than the identity threshold indicating potentially novel species pending further taxonomic review. ATR-FTIR analysis revealed the ligninolytic properties of the isolates by demonstrating structural alterations in lignin, indicating potential KL degradation, while Py-GC/MS identified the resulting biochemicals. These isolates produced chemicals of diverse functional groups and monomers as revealed by both methods. The use of coalmine-associated ligninolytic bacteria in biorefineries has potential., (© 2024. The Author(s).)

Two Enterobacter strains 170198 T and 170250 T were isolated from clinical blood samples from distinct patients in a hospital in Chengdu, China, in 2022. These isolates were subjected to whole-genome sequencing. A phylogenomic tree based on 2,096 concatenated core genes showed that the two strains were clustered within the genus Enterobacter . The average nucleotide identity (ANI) and in silico DNA-DNA hybridization ( is DDH) values between each of the two strains and type strains of all currently known Enterobacter species were determined. The two strains belonged to two novel species as the highest ANI and is DDH values with type strains of all currently known Enterobacter species below the cutoff for species demarcation (96% for ANI and 70% for is DDH). Then the physiological and biochemical studies demonstrated that biochemical features and the profile of whole fatty acids of strains 170198 T and 170250 T were largely consistent with those known Enterobacter species. Nevertheless, the two novel species can be differentiated from all other Enterobacter species by certain biochemical characteristics. In conclusion, 170198 T and 170250 T represent two novel species of the genus Enterobacter , for which we propose Enterobacter chinensis sp. nov. and Enterobacter rongchengensis sp. nov., as the species names. The type strains of Enterobacter chinensis sp. nov., and Enterobacter rongchengensis sp. nov. are 170198 T (=GDMCC 1.3549 T =JCM 35826 T ) and 170250 T (=GDMCC 1.3670 T =JCM 36189 T ), respectively. The two novel species have clinical significance with the ability to cause bloodstream infections.IMPORTANCE Enterobacter is a group of bacteria comprising several common opportunistic pathogens and has a complicated taxonomy. Here, we reported two novel Enterobacter species. We demonstrated that the two novel species can be differentiated from other Enterobacter species by certain phenotypic characteristics and therefore provide information for designing tests for identification. We also showed that strains of the two novel species are able to cause human bloodstream infections and carry multiple virulence factors and therefore are of clinical significance. We highlight that the virulence of Enterobacter is less studied and warrants further exploration. We believe that the findings here are valuable for enhancing the appreciation toward Enterobacter , an important pathogen., Competing Interests: The authors declare no conflict of interest.

Enterobacter species represent widely distributed opportunistic pathogens, commonly associated with plants and humans. In the present study, we performed a detailed molecular characterization as well as genomic study of a type VI secretion system (T6SS) bacterium belonging to member of the family Enterobacteriaceae and named Enterobacter sp. S-33. The comparative sequence analysis of the 16S rRNA gene showed that the strain was closely related to other Enterobacter species. The complete genome of the strain with a genome size of 4.6 Mbp and GC-content of 55.63% was obtained through high-quality sequencing. The genomic analysis with online tools unravelled the various genes belonging to the bacterial secretion system, antibiotic resistance, virulence, efflux pumps, etc. The isolate showed the motility behavior that contributes to Enterobacter persistence in a stressed environment and further supports infections. PCR amplification and further sequencing confirmed the presence of drug-efflux genes acrA, acrB, and outer membrane genes, viz. OmpA, OmpC, and OmpF. The cell surface hydrophobicity and co-aggregation assay against different bacterial strains illustrated its putative pathogenic nature. Genome mining identified various biosynthetic gene clusters (BGCs) corresponding to non-ribosomal proteins (NRPS), siderophore, and arylpolyene production. Briefly, genome sequencing and detailed characterization of environmental Enterobacter isolate will assist in understanding the epidemiology of Enterobacter species, and the further prevention and treatment of infectious diseases caused by these broad-host range species., (© 2023. The Author(s), under exclusive licence to Springer Nature Switzerland AG.)

Objectives: KHM-1-metallo-β-lactamase-producing Enterobacterales strains, of which only a few have been found, were isolated from four inpatients in Osaka, Japan during 2016 to 2020. We compared whole genomes of the four KHM-1-producing isolates, including one Enterobacter hormaechei subsp. hoffmannii, one Escherichia coli, and two Citrobacter freundii., Methods: These isolates were characterized by whole-genome sequencing, comparative analysis of bla KHM-1 -encoding plasmids with earlier reported plasmids, and antimicrobial susceptibility tests., Results: Multilocus sequence typing classified the E. hormaechei subsp. hoffmannii isolate to ST78, the E. coli isolate to ST354, and the two C. freundii isolates to ST95. These isolates harboured various antimicrobial resistance genes aside from bla KHM-1 on their chromosomes and plasmids. In all four isolates, bla KHM-1 was located on 137 kbp to 213 kbp plasmids of IncC replicon type. Although there were common resistance genes such as bla KHM-1 -ISEc68, class I integron cassette, and fosG, the four bla KHM-1 -encoding plasmids were distinguishable into two lineages based on differences of the resistance gene components and their surrounding regions., Conclusion: Because no epidemiological contact was observed among the inpatients, the bla KHM-1 -encoding IncC plasmids might have spread horizontally to multiple bacterial species through repeated recombination and insertion., (Copyright © 2024 The Author(s). Published by Elsevier Ltd.. All rights reserved.)

Despite being one of the most abundant elements in soil, phosphorus (P) often becomes a limiting macronutrient for plants due to its low bioavailability, primarily locked away in insoluble organic and inorganic forms. Phosphate solubilizing and mineralizing bacteria, also called phosphobacteria, isolated from P-deficient soils have emerged as a promising biofertilizer alternative, capable of converting these recalcitrant P forms into plant-available phosphates. Three such phosphobacteria strains-Serratia sp. RJAL6, Klebsiella sp. RCJ4, and Enterobacter sp. 198-previously demonstrated their particular strength as plant growth promoters for wheat, ryegrass, or avocado under abiotic stresses and P deficiency. Comparative genomic analysis of their draft genomes revealed several genes encoding key functionalities, including alkaline phosphatases, isonitrile secondary metabolites, enterobactin biosynthesis and genes associated to the production of indole-3-acetic acid (IAA) and gluconic acid. Moreover, overall genome relatedness indexes (OGRIs) revealed substantial divergence between Serratia sp. RJAL6 and its closest phylogenetic neighbours, Serratia nematodiphila and Serratia bockelmanii. This compelling evidence suggests that RJAL6 merits classification as a novel species. This in silico genomic analysis provides vital insights into the plant growth-promoting capabilities and provenance of these promising PSRB strains. Notably, it paves the way for further characterization and potential application of the newly identified Serratia species as a powerful bioinoculant in future agricultural settings., (© 2024. The Author(s), under exclusive licence to Springer Nature Switzerland AG.)

Objectives: Antimicrobial-resistant bacteria of the order Enterobacterales are emerging threats to global public and animal health, leading to morbidity and mortality. The emergence of antimicrobial-resistant, livestock-associated pathogens is a great public health concern. The genera Enterobacter and Lelliottia are ubiquitous, facultatively anaerobic, motile, non-spore-forming, rod-shaped Gram-negative bacteria belonging to the Enterobacteriaceae family and include pathogens of public health importance. Here, we report the first draft genome sequences of a rare Lelliottia nimipressuralis strain MEZLN61 and two Enterobacter kobei strains MEZEK193 and MEZEK194 in Africa., Methods: The bacteria were isolated from environmental wastewater samples. Bacteria were cultured on nutrient agar, and the pure cultures were subjected to whole-genome sequencing. Genomic DNA was sequenced using an Illumina MiSeq platform. Generated reads were trimmed and subjected to de novo assembly. The assembled contigs were analysed for virulence genes, antimicrobial resistance genes, and extra-chromosomal plasmids, and multilocus sequence typing was performed. To compare the sequenced strains with other, previously sequenced E. kobei and L. nimipressuralis strains, available raw read sequences were downloaded, and all sequence files were treated identically to generate core genome bootstrapped maximum likelihood phylogenetic trees., Results: Whole-genome sequencing analyses identified strain MEZLN61 as L. nimipressuralis and strains MEZEK193 and MEZEK194 as E. kobei. MEZEK193 and MEZEK194 carried genes encoding resistance to fosfomycin (fosA), beta-lactam antibiotics (bla ACT-9 ), and colistin (mcr-9). Additionally, MEZEK193 harboured nine different virulence genes, while MEZEK194 harboured eleven different virulence genes. The phenotypic analysis showed that L. nimipressuralis strain MEZLN61 was susceptible to colistin (2 μg/mL), while E. kobei MEZEK193 (64 μg/mL) and MEZEK194 (32 μg/mL) were resistant to colistin., Conclusion: The genome sequences of strains L. nimipressuralis MEZLN6, E. kobei MEZEK193, and E. kobei MEZEK194 will serve as a reference point for molecular epidemiological studies of L. nimipressuralis and E. kobei in Africa. In addition, this study provides an in-depth analysis of the genomic structure and offers important information that helps clarify the pathogenesis and antimicrobial resistance of L. nimipressuralis and E. kobei. The detection of mcr-9, which is associated with very low-level colistin resistance in Enterobacter species, is alarming and may indicate the undetected dissemination of mcr genes in bacteria of the order Enterobacterales. Continuous monitoring and surveillance of the prevalence of mcr genes and their associated phenotypic changes in clinically important pathogens and environmentally associated bacteria is necessary to control and prevent the spread of colistin resistance., (Copyright © 2023 The Authors. Published by Elsevier Ltd.. All rights reserved.)

An active microbial community of nitrifying and denitrifying bacteria is needed for efficient utilization of nitrogenous compounds from wastewater. In this study, we explored the bacterial community diversity and structure within rivers, treated and untreated wastewater treatment plants (WWTPs) discharging into Lake Victoria. Water samples were collected from rivers and WWTPs that drain into Lake Victoria. Physicochemical analysis was done to determine the level of nutrients or pollutant loading in the samples. Total community DNA was extracted, followed by Illumina high throughput sequencing to determine the total microbial community and abundance. Enrichment and isolation were then done to recover potential nitrifiers and denitrifiers. Physicochemical analysis pointed to high levels total nitrogen and ammonia in both treated and untreated WWTPs as compared to the samples from the lake and rivers. A total of 1,763 operational taxonomic units (OTUs) spread across 26 bacterial phyla were observed with the most dominant phylum being Proteobacteria. We observed a decreasing trend in diversity from the lake, rivers to WWTPs. The genus Planktothrix constituted 19% of the sequence reads in sample J2 collected from the lagoon. All the isolates recovered in this study were affiliated to three genera: Pseudomonas, Klebsiella and Enterobacter in the phylum Proteobacteria. A combination of metagenomic analysis and a culture-dependent approach helped us understand the relative abundance as well as potential nitrifiers and denitrifiers present in different samples. The recovered isolates could be used for in situ removal of nitrogenous compounds from contaminated wastewater., (© 2022. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.)

The taxonomy of the genus Enterobacter can be confusing and has been considerably revised in recent years. We propose a PCR and amplicon sequencing technique based on a partial sequence of the dnaJ gene for species assignment consistent with DNA-DNA digital hybridization (dDDH) and pairwise average nucleotide identity (ANI). We performed a validation of the method by comparing the type strains of each species, sequences obtained from the GenBank database, and clinical specimens. Our results show that the polymorphism of the target sequence of dnaJ allows the identification of species. Using this gene, we assigned the species to 100 strains deposited in the GenBank database that were consistent with the species assignment by dDDH and ANI. The analysis showed that using the partial dnaJ sequence is congruent with WGS as far as correct identification of Enterobacter species is concerned. Finally, we applied our dnaJ method on a national collection of 68 strains identified as Enterobacter isolated from the blood cultures of premature babies using an algorithm based on a type-strain library and the SeqScape software. For the first time, we identified Enterobacter quasihormaechei in blood cultures from four neonatal sepsis cases. We also noticed a higher prevalence of E. bugandensis (36.3%; 32/88) and E. xiangfangensis (46.5%; 41/88). E. bugandensis is a novel species recently described specifically in instances of neonatal sepsis. In conclusion, sequencing a part of the dnaJ gene could be a quick, more economical, and highly discriminating method of identifying Enterobacter species in clinical practice and research. IMPORTANCE We propose a new approach for Enterobacter species identification based on the diversity of the gene encoding the heat shock protein DnaJ. This new tool can be easily implemented in clinical laboratories in addition to identification by MALDI-TOF.

Background and Aims: Bacterial swarming, a collective movement on a surface, has rarely been associated with human pathophysiology. This study aims to define a role for bacterial swarmers in amelioration of intestinal stress., Methods: We developed a polymicrobial plate agar assay to detect swarming and screened mice and humans with intestinal stress and inflammation. From chemically induced colitis in mice, as well as humans with inflammatory bowel disease, we developed techniques to isolate the dominant swarmers. We developed swarm-deficient but growth and swim-competent mutant bacteria as isogenic controls. We performed bacterial reinoculation studies in mice with colitis, fecal 16S, and meta-transcriptomic analyses, as well as in vitro microbial interaction studies., Results: We show that bacterial swarmers are highly predictive of intestinal stress in mice and humans. We isolated a novel Enterobacter swarming strain, SM3, from mouse feces. SM3 and other known commensal swarmers, in contrast to their mutant strains, abrogated intestinal inflammation in mice. Treatment of colitic mice with SM3, but not its mutants, enriched beneficial fecal anaerobes belonging to the family of Bacteroidales S24-7. We observed SM3 swarming associated pathways in the in vivo fecal meta-transcriptomes. In vitro growth of S24-7 was enriched in presence of SM3 or its mutants; however, because SM3, but not mutants, induced S24-7 in vivo, we concluded that swarming plays an essential role in disseminating SM3 in vivo., Conclusions: Overall, our work identified a new but counterintuitive paradigm in which intestinal stress allows for the emergence of swarming bacteria; however, these bacteria act to heal intestinal inflammation., (Copyright © 2021 AGA Institute. Published by Elsevier Inc. All rights reserved.)

Enterobacter is a globally important pathogen. Here we clarify its taxonomy and review recent developments in its resistance to carbapenem and colistin, illustrating that Enterobacter has a large arsenal of mechanisms to grow under antimicrobial pressure. Further studies are required to decipher colistin heteroresistance and understand why certain Enterobacter lineages have emerged clinically., (Copyright © 2020 Elsevier Ltd. All rights reserved.)

Powered by flagella, many bacterial species exhibit collective motion on a solid surface commonly known as swarming. As a natural example of active matter, swarming is also an essential biological phenotype associated with virulence, chemotaxis, and host pathogenesis. Physical changes like cell elongation and hyper-flagellation have been shown to accompany the swarming phenotype. Less studied, however, are the contrasts of collective motion between the swarming cells and their counterpart planktonic cells of comparable cell density. Here, we show that confining bacterial movement in circular microwells allows distinguishing bacterial swarming from collective swimming. On a soft agar plate, a novel bacterial strain Enterobacter sp. SM3 in swarming and planktonic states exhibited different motion patterns when confined to circular microwells of a specific range of sizes. When the confinement diameter was between 40 μm and 90 μm, swarming SM3 formed a single-swirl motion pattern in the microwells whereas planktonic SM3 formed multiple swirls. Similar differential behavior is observed across several other species of gram-negative bacteria. We also observed 'rafting behavior' of swarming bacteria upon dilution. We hypothesize that the rafting behavior might account for the motion pattern difference. We were able to predict these experimental features via numerical simulations where swarming cells are modeled with stronger cell-cell alignment interaction. Our experimental design using PDMS microchip disk arrays enabled us to observe bacterial swarming on murine intestinal surface, suggesting a new method for characterizing bacterial swarming under complex environments, such as in polymicrobial niches, and for in vivo swarming exploration., Competing Interests: WC Weijie Chen, Neha Mani, Jay X. Tang, and Sridhar Mani filed a U.S. patent application (Application No. 63033369). NM, SM, JT Weijie Chen, Neha Mani, Jay X Tang, and Sridhar Mani filed a U.S. patent application (Application No. 63033369). HK, HL No competing interests declared, (© 2021, Chen et al.)

Contamination of ready-to-eat (RTE) foods by pathogenic bacteria may predispose consumers to foodborne diseases. This study investigated the presence of bacterial contaminants and their antibiotic susceptibility patterns in three locally processed RTE foods (eko, fufu and zobo) vended in urban markets in Ogun state, Nigeria. Bacteria isolated from a total of 120 RTE food samples were identified by 16S rRNA gene phylogeny while susceptibility patterns to eight classes of antibiotics were determined by the disc diffusion method. Species belonging to the genera Acinetobacter and Enterobacter were recovered from all RTE food types investigated, Klebsiella and Staphylococcus were recovered from eko and fufu samples, while those of Shigella were recovered from eko samples. Enterobacter hormaechei was the most prevalent species in all three RTE food types. Precisely 99% of 149 isolates were multidrug-resistant, suggesting a high risk for RTE food handlers and consumers. Co-resistance to ampicillin and cephalothin was the most frequently observed resistance phenotype. Results demonstrate that improved hygiene practices by food processors and vendors are urgently required during RTE processing and retail. Also, adequate food safety guidelines, regulation and enforcement by relevant government agencies are needed to improve the safety of RTE foods and ensure the protection of consumer health., (© 2020 The Society for Applied Microbiology.)

Forty-two antibiotic-resistant enterobacteria strains were isolated from fresh produce obtained from the northern German retail market. A polyphasic characterization based on both phenotypic and genotypic methods was used to identify predominant strains as Citrobacter (C.) gillenii, C. portucalensis, Enterobacter (En.) ludwigii, Escherichia (E.) coli and Klebsiella (K.) pneumoniae. 38.1% of the enterobacteria strains were resistant to tetracycline, while 23.8% and 9.5% of strains were resistant to streptomycin and chloramphenicol, respectively. A high percentage of Klebsiella (100%), Enterobacter (57.1%) and Citrobacter (42.9%) strains were also resistant to ampicillin, with some strains showing multiple resistances. For unequivocal species identification, the genomes of thirty strains were sequenced. Multilocus sequence analysis, average nucleotide identity and digital DNA-DNA hybridization showed that Enterobacter strains E1 and E13 were clearly clustered apart from Enterobacter species type strains below the species delineation cutoff values. Thus, strains E1 T (=DSM 111347 T , LMG 31875 T ) represents a novel species proposed as Enterobacter dykesii sp. nov., while strain E13 T (=DSM 110788 T , LMG 31764 T ) represent a novel species proposed as Enterobacter vonholyi sp. nov. Strains often possessed different serine β-lactamase genes, tet(A) and tet(D) tetracycline resistance genes and other acquired antibiotic resistance genes. Typical plasmid replicon types were determined. This study thus accurately identified the enterobacteria from fresh produce as species belonging to the genera Citrobacter, Enterobacter, Escherichia and Klebsiella, but also showed that these can carry potentially transferable antibiotic resistance genes and may thus contribute to the spread of these via the food route., (Copyright © 2020 Elsevier GmbH. All rights reserved.)

Background: Hospital intensive care units (ICUs) are known reservoirs of multidrug resistant nosocomial bacteria. Targeted environmental monitoring of these organisms in health care facilities can strengthen infection control procedures. A routine surveillance of extended spectrum beta-lactamase (ESBL) producers in a large Australian veterinary teaching hospital detected the opportunistic pathogen Enterobacter hormaechei in a hand washing sink of the ICU. The organism persisted for several weeks, despite two disinfection attempts. Four isolates were characterized in this study., Methods: Brilliance-ESBL selective plates were inoculated from environmental swabs collected throughout the hospital. Presumptive identification was done by conventional biochemistry. Genomes of multidrug resistant Enterobacter were entirely sequenced with Illumina and Nanopore platforms. Phylogenetic markers, mobile genetic elements and antimicrobial resistance genes were identified in silico. Antibiograms of isolates and transconjugants were established with Sensititre microdilution plates., Results: The isolates possessed a chromosomal Tn7-associated silver/copper resistance locus and a large IncH12 conjugative plasmid encoding resistance against tellurium, arsenic, mercury and nine classes of antimicrobials. Clusters of antimicrobial resistance genes were associated with class 1 integrons and IS26, IS903 and ISCR transposable elements. The blaSHV-12, qnrB2 and mcr-9.1 genes, respectively conferring resistance to cephalosporins, quinolones and colistin, were present in a locus flanked by two IS903 copies. ESBL production and enrofloxacin resistance were confirmed phenotypically. The isolates appeared susceptible to colistin, possibly reflecting the inducible nature of mcr-9.1., Conclusions: The persistence of this strain in the veterinary hospital represented a risk of further accumulation and dissemination of antimicrobial resistance, prompting a thorough disinfection of the ICU. The organism was not recovered from subsequent environmental swabs, and nosocomial Enterobacter infections were not observed in the hospital during that period. This study shows that targeted routine environmental surveillance programs to track organisms with major resistance phenotypes, coupled with disinfection procedures and follow-up microbiological cultures are useful to control these risks in sensitive areas of large veterinary hospitals.

A strain of thiamethoxam-degrading endophyte, named TMX13, was isolated from roots of mulberry ( Morus alba L.) and was identified as Enterobacter sp. Inoculating Chinese cabbage ( Brassica chinensis L) with strain TMX13- gfp ( gfp -labeled TMX13) could significantly reduce thiamethoxam residues in the aboveground part (edible portion) of the vegetable. The theoretical daily intake (TDI) of thiamethoxam via consumption of TMX13- gfp inoculated Chinese cabbage was 0.17 μg/kg body weight per day, far less than the prescribed acceptable daily intake (ADI) for this pesticide. TMX13- gfp colonization could increase the leaf chlorophyll content and plant biomass and promote the development of plant roots. Compared with the uninoculated treatment, the contents of malondialdehyde (MDA) and hydrogen peroxide (H 2 O 2 ) and the activity of superoxide dismutase (SOD) in leaves of the TMX13- gfp inoculated plants decreased by 18.4%-60.2%, suggesting that TMX13- gfp colonization could alleviate the oxidative stress induced by thiamethoxam exposure. The total amounts of organic acids and amino acids in root exudates from the TMX13- gfp inoculated Chinese cabbage decreased by 9.2% and 85.2%, respectively. Results of this study lead to the conclusion that the isolated endophyte Enterobacter sp. TMX13 could reduce thiamethoxam residues in edible vegetables, promote plant growth, and alleviate the phytotoxic effects induced by thiamethoxam exposure.

Pectinolytic enzymes that catalyze the breakdown of substrates containing pectin are widespread. Pectinases have potential applications in various industries, including food, animal feed, textile, paper, and fuel. In this study, one hundred bacterial isolates were collected from Marand city farmlands (Azarbaijan-E-Sharqi, Iran) and screened by MP medium on the base of pectinase activity considering the significance of pectinases. The results depicted that three isolates showed the most pectinase activity (more massive halo). The biochemical and molecular test results showed that the three screened bacteria were Enterobacter and named Enterobacter sp. MF41, Enterobacter sp. MF84, and Enterobacter sp. MF90. Enterobacter sp. MF84 had the largest halo, so this strain was selected for the study of its produced pectinase. The results exhibited that the produced enzyme has optimum temperature and pH for activity at 30 °C and in 9, respectively. Finally, the enzyme production by Enterobacter sp. MF84 is optimized using response surface methodology (RSM) considering four factors (NH 4 Cl, K 2 HPO 4 , pectin, and incubation time) as variables. The results showed that the optimization procedure increased the enzyme production up to 12 times (from 1.16 to 14.16 U/mg). The Pareto analysis revealed that ammonium chloride has a significant role in decreasing the enzyme production, probably by inducing the nitrification pathway enzymes in the presence of organic nitrogen in Enterobacter sp. MF84.

Bis(2-hydroxyethyl) terephthalate (BHET) is an important compound produced from poly(ethylene terephthalate) (PET) cleavage. It was selected as the representative substance for the study of PET degradation. A bacterial strain HY1 that could degrade BHET was isolated and identified as Enterobacter sp. The optimal temperature and pH for BHET biodegradation were determined to be 30°C and 8.0, respectively. The half-life of degradation was 70.20 h at an initial BHET concentration of 1,000 mg/L. The results of metabolites' analysis by liquid chromatograph-mass spectrometer revealed that BHET was first converted to mono-(2-hydroxyethyl) terephthalate (MHET) and then to terephthalic acid. Furthermore, an esterase-encoding gene, estB, was cloned from strain HY1, and the expressed enzyme EstB was characterized. The esterase has a molecular mass of approximately 25.13 kDa, with an isoelectric point of 4.68. Its optimal pH and temperature were pH 8.0 and 40°C, respectively. The analysis of the enzymatic products showed that EstB could hydrolyze one ester bond of BHET to MHET. To the best of authors' knowledge, this is the first report on the biodegradation characteristics of BHET by a member of the Enterobacter genus., (© 2020 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

Various diseases, including bacterial panicle blight (BPB) and sheath rot, threaten rice production. It has been established that Burkholderia glumae ( B. glumae ) is the causative agent of the above mentioned pathologies. In the present study, antagonistic activity, growth promotion, and the metabolite profiles of two rhizobacteria, isolated in different paddy fields, were assessed against B. glumae . Strains were identified based on 16S rRNA gene sequences, and the phylogenetic analyses showed that both strains belong to the genus Enterobacter , with high similarity to the strain Enterobacter tabaci NR146667.2 (99%). The antagonistic activity was assessed with the disc diffusion method. Active fractions were isolated through a liquid/liquid extraction with ethyl acetate (EtOAc) from the fermentation media, and their antibacterial activities were evaluated following the Clinical and Laboratory Standards Institute (CLSI) guidelines. The Pikovskaya modified medium was used to test the ability of in vitro inorganic phosphorus solubilization, and BSB1 proved to be the best inorganic phosphorus solubilizer, with a solubilization index (SI) of 4.5 ± 0.2. The glass-column fractionation of the EtOAc extracted from BCB11 produced an active fraction (25.9 mg) that inhibited the growth of five B. glumae strains by 85-95%. Further, metabolomic analysis, based on GC-MS, showed 3-phenylpropanoic acid (3-PPA) to be the main compound both in this fraction (46.7%), and in the BSB1 extract (28.6%). This compound showed antibacterial activity against all five strains of B. glumae with a minimum inhibitory concentration (MIC) of 1000 mg/L towards all of them. The results showed that rice rhizosphere microorganisms are a source of compounds that inhibit B. glumae growth and are promising plant growth promoters (PGP).

Patulin contamination is a worldwide concern due to its significant impact on human health. Several yeast strains have been screened for patulin biodegradation; however, little information is available on bacterial strains and their mechanism of degradation. In the present study, we isolated a bacterial strain TT-09 and identified it as Enterobacter cloacae subsp. dissolvens based on the BioLog system and 16S rDNA phylogenetic analysis. The strain was demonstrated to be able to transform patulin into E -ascladiol. Isobaric tags for relative and absolute quantitation and reverse transcription quantitative polymerase chain reaction analyses provided evidence that ribonucleoside diphosphate reductase (NrdA), an important enzyme involved in DNA biosynthesis, plays a crucial role in patulin degradation. Deletion of nrdA resulted in a total loss in the ability to degrade patulin in TT-09. These results indicate a new function for NrdA in mycotoxin biodegradation. The present study provides evidence for understanding a new mechanism of patulin degradation and information that can be used to develop new approaches for managing patulin contamination.

Excessive use of pesticides in agricultural fields is a matter of great concern for living beings as well as the environment across the world, in particular, the third world countries. Therefore, there is an urgent need to find out an effective way to degrade these hazardous chemicals from the soil in an environment-friendly way. In the current project, a bacterial species were isolated through enrichment culture from carbofuran-supplemented rice-field soil and identified as a carbofuran degrader. The rate of carbofuran degradation by this bacterial species was evaluated using reverse-phase high-performance liquid chromatography (RP-HPLC), which confirmed the ability to utilize as a carbon source up to 4 µg/ml of 99% technical grade carbofuran. The morphological, physiological, biochemical characteristics and phylogenetic analysis of the 16S rRNA sequence showed that this strain belongs to the genus of Enterobacter sp. (sequence accession number LC368285 in DDBJ), and the optimum growth condition for the isolated strain was 37°C at pH 7.0. Moreover, an antibiotic sensitivity test showed that it was susceptible to azithromycin, penicillin, ceftazidime, ciprofloxacin, and gentamycin, and the minimal inhibitory concentration value of gentamycin was 400 μg/ml against the bacteria. It shows beyond doubt from the RP-HPLC quantification that the isolated bacterium has the ability to detoxify carbofuran (99% pure). Finally, the obtained results imply that the isolated strain of Enterobacter can be used as a potential and effective carbofuran degrader for bioremediation of contaminated sites through bioaugmentation., (© 2020 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

Objectives: Enterobacter hormaechei is an important causative agent of severe infections in critically ill patients. Aminoglycosides are among the main antibiotics for the treatment of E. hormaechei infections, however the development of antimicrobial resistance is an increasing problem. RmtG is a 16S rRNA methyltransferase, a class of enzymes conferring high-level resistance to clinically relevant aminoglycosides. The aim of this study was to characterise the full genetic context of plasmids harbouring the rmtG gene in two aminoglycoside-resistant E. hormaechei isolated in Brazil., Methods: ThermtG-harbouring plasmids were transferred to an Escherichia coli J53 recipient strain and were fully sequenced using a MiSeq sequencing system. Complete genome assemblies were accomplished using a combination of Newbler v.3.0, SPAdes 3.10.0 and phrap/cross_match programs. Plasmid sequences were annotated using RAST server and were then manually curated using BLAST databases and ISfinder. Easyfig 2.0 was used to map and compare regions of interest containing rmtG in both plasmids., Results: Both isolates carried thermtG gene on an IncA/C plasmid of ˜152kb and ˜235kb, respectively, associated with a Tn3 transposon. The plasmids contain a transfer region as well as genes involved in plasmid stability and resistance to β-lactams, sulfonamides and quaternary ammonium compounds. One of the plasmids also carried the mrk operon encoding type 3 fimbriae., Conclusion: This first detection ofrmtG in E. hormaechei supports the ability for horizontal transfer. The location in complex genetic platforms carried by Tn3 transposons in IncA/C plasmids may facilitate dissemination to other Gram-negative pathogens, further limiting treatment options., (Copyright © 2019. Published by Elsevier Ltd.)

Two novel strains of members of the genus Enterobacter , WCHEs120002 T and WCHEs120003 T , were recovered from the sputum of two patients at a hospital in PR China in 2017. The strains were Gram-stain-negative, facultatively anaerobic, motile and non-spore-forming. The two strains were subjected to whole-genome sequencing. Phylogenetic analysis based on core genes of type strains of species of the family Enterobacteriaceae revealed that the two strains belonged to the genus Enterobacte r but were distinct from any previously known species of the genus. Both average nucleotide identity and in silico DNA-DNA hybridization values between strains WCHEs120002 T and WCHEs120003 T and type strains of all known species of the genus Enterobacter were lower than the recommended thresholds of 95 and 70  %, respectively, for species delineation. The major fatty acids of the two strains were C 16 : 0 , C 17 : 0 cyclo and C 18:1 ω7 c , which are similar to those of other species of the genus Enterobacter . Genomic DNA G+C contents of strains WCHEs120002 T and WCHEs120003 T were 56.09 and 55.91 mol%, respectively. WCHEs120002 T ferments melibiose and sucrose but is negative for d-sorbitol and methyl-α-d-mannopyranoside reactions, which distinguish it from all other species of the genus Enterobacter . WCHEs120003 T can be differentiated from other species of the genus Enterobacter by its ability to ferment potassium gluconate and its negative reactions for d-sorbitol and l-fucose. Genotypic and phenotypic characteristics indicate that strains WCHEs120002 T and WCHEs120003 T represent two novel species of the genus Enterobacter , for which the names Enterobacter wuhouensis sp. nov. and Enterobacter quasihormaechei sp. nov. are proposed, respectively. The type strain of E. wuhouensis sp. nov. is WCHEs120002 T (=GDMCC1.1569 T =NCTC 14273 T ) and the type strain of E. quasihormaechei sp. nov. is WCHEs120003 T (=GDMCC1.1568 T =NCTC 14274 T ).

We performed a comparative genomic analysis to clarify the taxonomic relationship between the two Enterobacter species, Enterobacter tabaci and Enterobacter mori . Whole genome sequences of types strains of the two species became available recently. Average nucleotide identity (ANI) and in silico DNA-DNA hybridization (isDDH) between the two type strains were determined. Type strains of the two species had a 97.25 % ANI and an 80.4 % isDDH value, which are above the well-recognized cutoffs (≥95-96 % ANI and ≥70 % isDDH) for bacterial species delineation. The two strains have similar overall phenotypic characteristics and are clustered together with high bootstrap values in the multi-locus sequence analysis on rpoB , gyrB , infB and atpD housekeeping genes. It therefore becomes evident that the two species actually belong to the same species. E. mori has priority over E. tabaci , therefore we proposed that E. tabaci Duan et al . 2016 is a later heterotypic synonym of E. mori [ 15 ].

A novel oligotrophic bacterium, designated strain CCA6, was isolated from leaf soil collected in Japan. Cells of the strain were found to be a Gram-negative, non-sporulating, motile, rod-shaped bacterium. Strain CCA6 grew at 10-45°C (optimum 20°C) and pH 4.5-10.0 (optimum pH 5.0). The strain was capable of growth in poor-nutrient (oligotrophic) medium, and growth was unaffected by high-nutrient medium. The major fatty acid and predominant quinone system were C 16:0 and ubiquinone-8. Phylogenetic analysis based on 16S rRNA gene sequences indicated strain CCA6 presented as a member of the family Enterobacteriaceae. Multilocus sequence analysis (MLSA) based on fragments of the atpD, gyrB, infB, and rpoB gene sequences was performed to further identify strain CCA6. The MLSA showed clear branching of strain CCA6 with respect to Enterobacter type strains. The complete genome of strain CCA6 consisted of 4,476,585 bp with a G+C content of 54.3% and comprising 4,372 predicted coding sequences. The genome average nucleotide identity values between strain CCA6 and the closest related Enterobacter type strain were <88.02%. Based on its phenotypic, chemotaxonomic and phylogenetic features, strain CCA6 (=HUT 8142 T =KCTC 62525 T ) can be considered as a novel species within the genus Enterobacter with the proposed name Enterobacter oligotrophica., (© 2019 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.)

Objectives: In this study, 77 Enterobacter spp. isolates from a collection of 175 Gram-negative bacilli isolated from Tlemcen University Hospital Center (North-West of Algeria) were tested for antibiotic resistance, biocide tolerance and genetic determinants of antimicrobial resistance., Methods: The isolates were identified by 16S rDNA gene sequencing. Biocide tolerance was determined by broth microdilution, and antibiotic resistance was determined by disk diffusion. Genetic determinants of resistance were studied by PCR amplification using suitable primers., Results: The most common Enterobacter species was Enterobacter cloacae (58.4%), followed by Enterobacter hormaechei (24.7%). The most common antibiotic resistance was to ticarcillin either alone or in combination with clavulanic acid (70.1%), followed by cefepime (68.8%), cefotaxime (63.6%), ceftazidime (54.5%) and gentamicin (54.5%). Tobramycin was active against 87.0% of the isolates. Levels of biocide tolerance were high for hexachlorophene and to a lesser extent for benzalkonium chloride. The extended-spectrum β-lactamase genes bla TEM and bla CTX-M were detected in 44.2% and 36.4% of isolates, respectively. Other antimicrobial resistance genes (ARGs) frequently detected were aac(6')-Ib (57.1%) and sul2 (50.6%). Multidrug-resistant isolates carrying several ARGs were common. Significant positive correlations were detected for efflux pump genes with ARGs and also between ARGs., Conclusion: The results of this study reveal thatEnterobacter spp. isolates from hospital settings are both resistant to clinically-used antibiotics and tolerant to biocides. Biocide tolerance could be an advantage for antibiotic-resistant strains in hospitals., (Copyright © 2019 International Society for Antimicrobial Chemotherapy. Published by Elsevier Ltd. All rights reserved.)

The genus Enterobacter is a member of the ESKAPE group, which contains the major resistant bacterial pathogens. First described in 1960, this group member has proven to be more complex as a result of the exponential evolution of phenotypic and genotypic methods. Today, 22 species belong to the Enterobacter genus. These species are described in the environment and have been reported as opportunistic pathogens in plants, animals, and humans. The pathogenicity/virulence of this bacterium remains rather unclear due to the limited amount of work performed to date in this field. In contrast, its resistance against antibacterial agents has been extensively studied. In the face of antibiotic treatment, it is able to manage different mechanisms of resistance via various local and global regulator genes and the modulation of the expression of different proteins, including enzymes (β-lactamases, etc.) or membrane transporters, such as porins and efflux pumps. During various hospital outbreaks, the Enterobacter aerogenes and E. cloacae complex exhibited a multidrug-resistant phenotype, which has stimulated questions about the role of cascade regulation in the emergence of these well-adapted clones., (Copyright © 2019 American Society for Microbiology.)

Asymptomatic bacteriuria (ASB) has been consistently observed in pregnancy. However, there is a paucity of data on the prevalence and characteristics of extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae in ASB in pregnant women. Therefore, we sought to investigate ESBL-producing and multidrug-resistant Enterobacteriaceae in antenatal women with ASB. Urine samples were collected from 310 asymptomatic pregnant women attending primary antenatal clinics and screened for significant bacteriuria. Isolates of Enterobacteriaceae were phenotypically tested for their ESBL production. ESBL genes (CTX-M, TEM, and SHV genes) were then amplified by polymerase chain reaction (PCR). Multiplex PCRs were used to perform phylogenetic typing of ESBL-producing Escherichia coli isolates and to examine the commonality of sequence type 131 (ST131)-O25b and ST131-O16. A total of 103 (33.2%) pregnant women were positive for significant bacteriuria (80 Enterobacteriaceae). Of these isolates, 32.5% ( n  = 26) were ESBL producers and had a higher rate of multidrug resistance than non-ESBL producers. Genotypic characterization of ESBL-producing isolates showed that 84.6% had the bla CTX-M gene ( bla CTX-M-15  = 77.3%; bla CTX-M-9  = 18.2%). None of the isolates were of the TEM or SHV type. Half of the ESBL-producing E. coli isolates were of the phylogroup B2, and 4 (20%) isolates were of the ST131-O16 clonal subgroup. This study is the first in Egypt to provide evidence for the high prevalence of ESBL-producing Enterobacteriaceae in pregnant women with ASB. It also represents an important step toward genotypic characterization of this resistant form of bacteria, which may be useful for future antimicrobial studies.

Plastic polymers are widely used in agriculture, industry, and our daily life because of their convenient and economic properties. However, pollution caused by plastic polymers, especially polyethylene (PE), affects both animal and human health when they aggregate in the environment, as they are not easily degraded under natural conditions. In this study, Enterobacter sp. D1 was isolated from the guts of wax moth ( Galleria mellonella ). Microbial colonies formed around a PE film after 14 days of cultivation with D1. Roughness, depressions, and cracks were detected on the surface of the PE film by scanning electron microscopy (SEM) and atomic force microscopy (AFM). Fourier transform infrared spectroscopy (FTIR) showed the presence of carbonyl functional groups and ether groups on the PE film that was treated with D1. Liquid chromatography-tandem mass spectrometry (LC-MS) also revealed that the contents of certain alcohols, esters, and acids were increased as a result of the D1 treatment, indicating that oxidation reaction occurred on the surface of the PE film treated with D1 bacteria. These observations confirmed that D1 bacteria has an ability to degrade PE.

An Enterobacter strain, WCHECl-C4, was recovered from a human blood sample in China in 2015. Phylogenetic analysis based on multi-locus sequence analysis of the rpoB, gyrB, infB and atpD housekeeping genes revealed that the strain is distinct from any previously described species of the genus Enterobacter. The whole genome sequence of strain WCHECl-C4 has an 80.48-93.34% average nucleotide identity with those of type strains of all known Enterobacter species. In silico DNA-DNA hybridization (isDDH) values between strain WCHECl-C4 and type strains of all known Enterobacter species range from 23.2 to 52.4%. The major cellular fatty acids of strain WCHECl-C4 are C 16:0 , C 17:0 cyclo and C 18:1 ω7c, which are in the range of Enterobacter species. The genomic DNA G + C content was 55.7 mol%. Strain WCHECl-C4 can be distinguished from all known Enterobacter species by its ability to ferment D-sorbitol, L-rhamnose and melibiose but with a negative Voges-Proskauer reaction. Genotypic and phenotypic characteristics from this study indicate that strain WCHECl-C4 represents a novel species of the genus Enterobacter, for which the name Enterobacter chengduensis sp. nov. is proposed. The type strain is WCHECl-C4 T (= GDMCC1.1216 T  = CCTCC AB 2017105 T  = KCTC 52993 T ).

Plant growth-promoting rhizobacteria are under extensive investigation to supplement the chemical fertilizers due to cost-effective and eco-friendly nature. However, their consistency in heterogeneous soil and diverse ecological settings is unclear. The current study presents in vitro and field evaluation of pre-characterized PGPR strain Enterobacter sp. Fs-11 (GenBank accession # GQ179978) in terms of its potential to enhance sunflower yield and oil contents under diverse environmental conditions. Under in vitro conditions, strain Fs-11 showed optimal growth at a range of temperature (15 to 40 °C) and pH values (6.5 to 8.5). Extracellular and intracellular localizations of the strain Fs-11 in sunflower root cortical cells through transmission electron microscopy confirmed its epiphytic and endophytic colonization patterns, respectively. In field experiments, conducted at three different agro-climatic locations, inoculation of strain Fs-11 at 50% reduced NP fertilizer resulted in a significant increase in growth, achene yield, nutrient uptake, and oil contents. Inoculation also responded significantly in terms of increase in mono- and polyunsaturated fatty acids (oleic and linoleic acids, respectively) without rising saturated fatty acid (palmitic and stearic acids) contents. We concluded that Enterobacter sp. Fs-11 is a potential candidate for biofertilizer formulations to supplement chemical fertilizer requirements of sunflower crop under diverse climatic conditions.

Enterobacter strains 090008 T and 090028 T were recovered from the blood of two different patients at West China Hospital, Chengdu, PR China in 2017. Phylogenetic analysis based on the 16S rRNA gene and multi-locus sequence analysis of the rpoB, gyrB, infB and atpD housekeeping genes revealed that the two strains were distinct from any previously known species of the genus Enterobacter. Both average nucleotide identity (ANI) and in silico DNA-DNA hybridization (isDDH) values between strains 090008 T , 090028 T and type strains of all known Enterobacter species were lower than the cut-off (≥95-96 % for ANI and ≥70 % for isDDH) to define a bacterial species. The major cellular fatty acids of strains 090008 T and 090028 T are C16 : 0, C17 : 0cyclo and C18 : 1ω7c, which are similar to other Enterobacter species, and the genomic DNA G+C content was 55.73 and 55.68 mol%, respectively. Strain 090008 T can be differentiated from other Enterobacter species by its ability to ferment sucrose, melibiose and d-arabitol, but with a negative methyl α-d-mannopyranoside reaction. Strain 090028 T can ferment potassium gluconate, but is negative for l-fucose, mdecarboxylase, deaminase aelibiose and d-sorbitol, which distinguishes it from all other Enterobacter species. Genotypic and phenotypic characteristics indicate that strains 090008 T and 090028 T represent two novel species of the genus Enterobacter, for which the names Enterobacter huaxiensissp. nov. and Enterobacter chuandaensis sp. nov. are proposed, respectively. The type strain of Enterobacter huaxiensissp. nov. is 090008 T (=GDMCC1.1426 T =CCTCC AB 2018174 T =CNCTC 7648 T ) and the type strain of Enterobacter chuandaensissp. nov. is 090028 T (=GDMCC1.1427 T =CCTCC AB 2018173 T =CNCTC 7649 T ).

Introduction: We aimed to demonstrate if fosfomycin tromethamine (FT) treatment could be the treatment of choice in ESBL-producing Enterobacteriaceae strains as an alternative to carbapenem particularly in patients who we would like to treat on an outpatient basis., Methodology: We retrospectively analyzed the medical records of all patients who admitted to infectious disease outpatient clinic with complaints of dysuria and frequency and received FT for lower UTI between May 2016 and May 2017., Results: A total of 48 patients, 19 females (39.6%) and 29 males (60.4%), with a mean age of 62.5 (ranging from 27 to 85) years were included the study. 26 (76.4%) of patients with a history of urinary operation or intervention had also a history of antibiotic use within the past 3 months. The isolated pathogens included Escherichia Coli (n = 32), Klebsiella spp. (n = 12), Enterobacter spp. (n = 4). The overall microbiological response after treatment was 70.8% (34/48) and the clinical response was 75% (36/48). Clinical and microbiological response rates of patients with and without urinary operation/intervention, diabetes mellitus, history of antibiotic use and malignancy were found similar (p > 0.05). However, patients with a urinary stone disease history had significantly higher response rates than those without a urinary stone disease history (P = 0.042)., Conclusion: Oral fosfomycin tromethamine might be the treatment of choice in ESBL-producing enterobactericea related UTIs especially caused by Escherichia Coli., Competing Interests: No Conflict of Interest is declared, (Copyright (c) 2019 Ayhanim Tumturk, Senol Tonyali, Ayse Yasemin Tezer Tekce, Levent Isikay, Hakan Cime.)

Although Enterobacter sp. 532 shows pathogenicity in Bombyx mori, the insecticidal mechanisms are unclear. Here, we identified and characterised an insecticidal protein from Enterobacter. The insecticidal protein was purified from the strain and inoculated into B. mori larvae. Intracellular proteins were prepared, purified and separated by preparative native polyacrylamide gel electrophoresis (PAGE); one protein band had insecticidal activity. Sodium dodecyl sulfate-PAGE showed the presence of several bands, indicating that the insecticidal protein formed a complex. Peptide mass fingerprinting of a prominent 255.3-kDa band revealed 64 peptides that matched one protein with 33.0% sequence coverage. This protein was a homologue of the A component of the toxin complex (Tc), and the VRP1 domain was conserved; thus, the gene was named itcA (insecticidal toxin complex A). In the itcA downstream region, B and C component gene homologues were found, and these genes were located on an 86.2-kb contig sequence. Two repA genes and 27 genes related to conjugation transfer of plasmids were located on the contig, suggesting that the contig originated from a mobilisable plasmid. Therefore, these findings suggested that the strain may have acquired the Tc genes by horizontal transfer. This is the first description of Tc produced by the genus Enterobacter.

Legumes establish symbiotic relationships with different microorganisms, which could function as plant growth promotion microorganisms (PGPM). The finding of new PGPM strains is important to increase plant production avoiding or diminishing the use of industrial fertilizers. Thus, in this work we evaluated the plant growth promotion traits of ten strains isolated from Mimosa pudica root nodules. According to the 16S rDNA sequence, the microorganisms were identified as Enterobacter sp. and Serratia sp. To the best of our knowledge this is the first report describing and endophytic interaction between Mimosa pudica and Enterobacter sp. These strains have some plant growth promoting traits such as phosphate solubilization, auxin production and cellulase and chitinase activity. Strains identified as Serratia sp. inhibited the growth of the phytopathogenic fungi Fusarium sp., and Alternaria solani and the oomycete Phytophthora capsici. According to their biochemical characteristics, three strains were selected to test their plant growth promoting activity in a medium with an insoluble phosphate source. These bacteria show low specificity for their hosts as endophytes, since they were able to colonize two very different legumes: Phaseolus vulgaris and M. pudica. Seedlings of P. vulgaris were inoculated and grown for fifteen days. Enterobacter sp. NOD1 and NOD10, promoted growth as reflected by an increase in shoot height as well as an increase in the size and emergence of the first two trifolia. We could localize NOD5 as an endophyte in roots in P. vulgaris by transforming the strain with a Green Fluorescent Protein carrying plasmid. Experiments of co-inoculation with different Rhizobium etli strains allowed us to discard that NOD5 can fix nitrogen in the nodules formed by a R. etli Fix - strain. The isolates described in this work show biotechnological potential for plant growth promoting activity and production of indoleacetic acid and siderophores., (Copyright © 2018 Elsevier GmbH. All rights reserved.)

An Enterobacter strain, WCHECL1597 T , was recovered from the urine of a patient in China in 2016. Phylogenetic analysis based on its 16S rRNA gene sequence indicated the strain belongs to the genus Enterobacter, while multi-locus sequence analysis of the rpoB, gyrB, infB and atpD housekeeping genes revealed that the strain was distinct from any previously described Enterobacter species. The whole genome sequence of strain WCHECL1597 T had a 79.81-91.49 % average nucleotide identity to those of type strains of all known Enterobacter species. In silico DNA-DNA hybridization values between strain WCHECL1597 T and the type strains of all known Enterobacter species ranged from 22.8 to 45.2 %. The major cellular fatty acids of strain WCHECL1597 T were C16 : 0, C17 : 0cyclo and C18 : 1ω7c, which are in the quantitative range of other Enterobacter species while differentiated by the relatively higher amount (12.3 %) of iso-c16 : 1 I/C14 : 0 3-OH. The genomic DNA G+C content was 55.2 mol%. Strain WCHECL1597 T could be distinguished from all known Enterobacter species by its ability to ferment inositol but with a negative l-rhamnose and d-mannitol reaction. Genotypic and phenotypic characteristics from this study indicate that strain WCHECL1597 T represents a novel species of the genus Enterobacter, for which the name Enterobactersichuanensis sp. nov. is proposed. The type strain is WCHECL1597 T (=GDMCC1.1217 T =CCTCC AB 2017104 T =KCTC 52994 T ).

Sorghum [Sorghum bicolor (L.) Moench] is a multipurpose grass cultivated in drylands due to its adaptation to drought. However the characteristics of sorghum-associated bacteria are not known in the Brazilian drylands. The aim of this study was to isolate and evaluate the plant growth promotion potential bacteria from field-grown sorghum under two irrigation and manure application levels in a Brazilian semi-arid reagion. Sorghum was irrigated with 3 or 1 mm day -1 and fertilized or not with liquid goat manure. Bacteria were obtained from surface-disinfected roots applying two nitrogen-free semi-solid media. The bacteria were evaluated for the presence of nifH gene, 16S rRNA sequences, calcium-phosphate solubilization, production of auxins and siderophores and for sorghum growth promotion. We obtained 20 out of 24 positive bacteria for nifH. The isolates were classified as in six different genera. All isolates produced auxins "in vitro", six bacteria produced siderophores and three Enterobacteriaceae solubilized calcium-phosphate. At least ten bacteria resulted in the increased total N content in the sorghum shoots, comparable to fertilization with 50 mg N plant -1 week -1 and to inoculation with Azospirillum brasilense Ab-V5. Enterobacter sp. ESA 57 was the best sorghum plant-growth promoting bacteria isolated in this study.

Background: The antimicrobial resistance (AMR) phenotypic properties, multiple drug resistance (MDR) gene profiles, and genes related to potential virulence and pathogenic properties of five Enterobacter bugandensis strains isolated from the International Space Station (ISS) were carried out and compared with genomes of three clinical strains. Whole genome sequences of ISS strains were characterized using the hybrid de novo assembly of Nanopore and Illumina reads. In addition to traditional microbial taxonomic approaches, multilocus sequence typing (MLST) analysis was performed to classify the phylogenetic lineage. Agar diffusion discs assay was performed to test antibiotics susceptibility. The draft genomes after assembly and scaffolding were annotated with the Rapid Annotations using Subsystems Technology and RNAmmer servers for downstream analysis., Results: Molecular phylogeny and whole genome analysis of the ISS strains with all publicly available Enterobacter genomes revealed that ISS strains were E. bugandensis and similar to the type strain EB-247 T and two clinical isolates (153&#95;ECLO and MBRL 1077). Comparative genomic analyses of all eight E. bungandensis strains showed, a total of 4733 genes were associated with carbohydrate metabolism (635 genes), amino acid and derivatives (496 genes), protein metabolism (291 genes), cofactors, vitamins, prosthetic groups, pigments (275 genes), membrane transport (247 genes), and RNA metabolism (239 genes). In addition, 112 genes identified in the ISS strains were involved in virulence, disease, and defense. Genes associated with resistance to antibiotics and toxic compounds, including the MDR tripartite system were also identified in the ISS strains. A multiple antibiotic resistance (MAR) locus or MAR operon encoding MarA, MarB, MarC, and MarR, which regulate more than 60 genes, including upregulation of drug efflux systems that have been reported in Escherichia coli K12, was also observed in the ISS strains., Conclusion: Given the MDR results for these ISS Enterobacter genomes and increased chance of pathogenicity (PathogenFinder algorithm with > 79% probability), these species pose important health considerations for future missions. Thorough genomic characterization of the strains isolated from ISS can help to understand the pathogenic potential, and inform future missions, but analyzing them in in-vivo systems is required to discern the influence of microgravity on their pathogenicity.

Background: Travelers' diarrhea (TD) is often caused by enterotoxigenic Escherichia coli, enteroaggregative E. coli, other bacterial pathogens, Norovirus, and occasionally parasites. Nevertheless, standard diagnostic methods fail to identify pathogens in more than 40% of TD patients. It is predicted that new pathogens may be causative agents of the disease., Results: We performed a comprehensive amplicon and whole genome shotgun (WGS) metagenomic study of the fecal microbiomes from 23 TD patients and seven healthy travelers, all of which were negative for the known etiologic agents of TD based on standard microbiological and immunological assays. Abnormal and diverse taxonomic profiles in TD samples were revealed. WGS reads were assembled and the resulting contigs were visualized using multiple query types. A semi-manual workflow was applied to isolate independent genomes from metagenomic pools. A total of 565 genome bins were extracted, 320 of which were complete enough to be characterized as cellular genomes; 160 were viral genomes. We made predictions of the etiology of disease for many of the individual subjects based on the properties and features of the recovered genomes. Multiple patients with low-diversity metagenomes were predominated by one to several E. coli strains. Functional annotation allowed prediction of pathogenic type in many cases. Five patients were co-infected with E. coli and other members of Enterobacteriaceae, including Enterobacter, Klebsiella, and Citrobacter; these may represent blooms of organisms that appear following secretory diarrhea. New "dark matter" microbes were observed in multiple samples. In one, we identified a novel TM7 genome that phylogenetically clustered with a sludge isolate; it carries genes encoding potential virulence factors. In multiple samples, we observed high proportions of putative novel viral genomes, some of which form clusters with the ubiquitous gut virus, crAssphage. The total relative abundance of viruses was significantly higher in healthy travelers versus TD patients., Conclusion: Our study highlights the strength of assembly-based metagenomics, especially the manually curated, visualization-assisted binning of contigs, in resolving unusual and under-characterized pathogenic profiles of human-associated microbiomes. Results show that TD may be polymicrobial, with multiple novel cellular and viral strains as potential players in the diarrheal disease.

We investigated the colistin resistance rate among 356 Enterobacter spp. clinical isolates from eight hospitals in Korea. Antibiotic susceptibility testing was performed by broth microdilution. While 51 of 213 (23.9%) Enterobacter cloacae isolates were colistin-resistant, only six of 143 (4.2%) E. aerogenes isolates showed resistance. We also identified the skip well phenotype in eight E. cloacae and three E. aerogenes isolates. Multilocus sequence typing for E. cloacae and randomly amplified polymorphic DNA analysis and enterobacterial repetitive intergenic consensus PCR for E. aerogenes revealed that clonal spreading of colistin-resistant and skip well Enterobacter spp. isolates had not occurred. In vitro time-kill assays were performed with three colistin-resistant, three skip well, and two colistin-susceptible isolates of E. cloacae and E. aerogenes. Inconsistent results were observed among isolates with skip well phenotypes; while some were eradicated by 2 mg/L colistin, others were not. This suggests that skip well isolates have differentiated into different categories. As the high rates of colistin resistance in E. cloacae detected are of clinical concern, continuous monitoring is warranted. In addition, the clinical implications and mechanisms of the skip well phenotype should be investigated to ensure the appropriate use of colistin against Enterobacter infections.

We performed whole-genome sequencing on 170 clinical carbapenemase-producing Enterobacter spp. isolates collected globally during 2008-2014. The most common carbapenemase was VIM, followed by New Delhi metallo-β-lactamase (NDM), Klebsiella pneumoniae carbapenemase, oxacillin 48, and IMP. The isolates were of predominantly 2 species (E. xiangfangensis and E. hormaechei subsp. steigerwaltii) and 4 global clones (sequence type [ST] 114, ST93, ST90, and ST78) with different clades within ST114 and ST90. Particular genetic structures surrounding carbapenemase genes were circulating locally in various institutions within the same or between different STs in Greece, Guatemala, Italy, Spain, Serbia, and Vietnam. We found a common NDM genetic structure (NDM-GE-U.S.), previously described on pNDM-U.S. from Klebsiella pneumoniae ATCC BAA-214, in 14 different clones obtained from 6 countries spanning 4 continents. Our study highlights the importance of surveillance programs using whole-genome sequencing in providing insight into the molecular epidemiology of carbapenemase-producing Enterobacter spp.

Background: The predominant species in clinical Enterobacter isolates is E. hormaechei . Many articles, clinicians, and GenBank submissions misname these strains as E. cloacae . The lack of sequenced type strains or named species/subspecies for some clades in the E. cloacae complex complicate the issue. Methods: The genomes of the type strains for Enterobacter hormaechei  subsp.  oharae , E .  hormaechei subsp.  steigerwaltii , and E. xiangfangensis , and two strains from Hoffmann clusters III and IV of the E. cloacae complex were sequenced. These genomes, the E .  hormaechei  subsp.  hormaechei type strain, and other available Enterobacter type strains were analysed in conjunction with all extant Enterobacter genomes in NCBI's RefSeq using Average Nucleotide Identity (ANI). Results: There were five recognizable subspecies of E. hormaechei : E. hormaechei subsp. hoffmannii subsp. nov., E. hormaechei subsp. xiangfangensis comb. nov., and the three previously known subspecies. One of the strains sequenced from the E. cloacae complex was not a novel E. hormaechei subspecies but rather a member of a clade of a novel species: E. roggenkampii sp. nov.. E. muelleri was determined to be a later heterotypic synonym of E. asburiae which should take precedence. Conclusion: The phylogeny of the Enterobacter genus, particularly the cloacae complex, was re-evaluated based on the type strain genome sequences and all other available Enterobacter genomes in RefSeq., Competing Interests: No competing interests were disclosed.

Strain PFL01 T was isolated from traditional Korean fermented clam, jogae-jeotgal, and characterized. The strain was a facultative anaerobic, Gram-stain-negative bacterium that was rod-shaped, motile and beige-pigmented. The phylogenetic sequence analysis based on the 16S rRNA gene from PFL01 T revealed that it was closely related to Lelliottia nimipressuralis LMG 10245 T and Lelliottia amnigena LMG 2784 T with 99.3 and 99.3 % sequence identities, respectively. Multilocus sequence type analysis of concatenated partial aptD, gyrB, infB and rpoB gene sequences showed a clear distinction of strain PFL01 T from its closest related type strains. The discrimination was also supported by unique repetitive extragenic palindromic PCR (Rep-PCR, ERIC-PCR) fingerprint patterns. In addition, results from average nucleotide identity analyses with other species were less than 85 %. vitek and API analyses revealed distinct characteristics from other species of Lelliottia. The cellular fatty acid profile of the strain consisted of C16 : 0, cyclo-C17 : 0, C16 : 1ω7c/C16 : 1ω6c and C18 : 1ω7c/C18 : 1ω6c as major components. The whole genome of PFL01 T was 4.6 Mb with a G+C content of 55.3 mol%. Based on these results, strain PFL01 T was classified as a novel species of the genus Lelliottia, for which the name Lelliottia jeotgali sp. nov. is proposed. The type strain in PFL01 T (=KCCM 43247 T =JCM 31901 T ).

Background: The predominant species in clinical Enterobacter isolates is E. hormaechei . Many articles, clinicians, and GenBank submissions misname these strains as E. cloacae . The lack of sequenced type strains or named species/subspecies for some clades in the E. cloacae complex complicate the issue. Methods: The genomes of the type strains for Enterobacter hormaechei  subsp.  oharae , E .  hormaechei subsp.  steigerwaltii , and E. xiangfangensis , and two strains from Hoffmann clusters III and IV of the E. cloacae complex were sequenced. These genomes, the E .  hormaechei  subsp.  hormaechei type strain, and other available Enterobacter type strains were analysed in conjunction with all extant Enterobacter genomes in NCBI's RefSeq using Average Nucleotide Identity (ANI). Results: There were five recognizable subspecies of E. hormaechei : E. hormaechei subsp. hoffmannii subsp. nov., E. hormaechei subsp. xiangfangensis comb. nov., and the three previously known subspecies. One of the strains sequenced from the E. cloacae complex was not a novel E. hormaechei subspecies but rather a member of a clade of a novel species: E. roggenkampii sp. nov.. E. muelleri was determined to be a later heterotypic synonym of E. asburiae which should take precedence. Conclusion: The phylogeny of the Enterobacter genus, particularly the cloacae complex, was re-evaluated based on the type strain genome sequences and all other available Enterobacter genomes in RefSeq., Competing Interests: No competing interests were disclosed.

Although KPC enzymes are most common among carbapenemases produced by Enterobacter cloacae complex globally, the epidemiology varies from one country to another. While previous studies have suggested that IMP enzymes are most common in Japan, detailed analysis has been scarce thus far. Here, we carried out a molecular epidemiological study and plasmid analysis of IMP-1-producing E. cloacae complex isolates collected from three hospitals in central Tokyo using whole-genome sequencing. Seventy-one isolates were classified into several sequence types (STs), and 49 isolates were identified as Enterobacter hormaechei ST78. Isolates of ST78 were divided into three clades by core-genome single nucleotide polymorphism (SNP)-based phylogenetic analysis. Whereas isolates of clade 3 were isolated from only one hospital, isolates of clade 1 and 2 were identified from multiple hospitals. Ten of 12 clade 1 isolates and 1 of 4 clade 2 isolates carried bla IMP-1 on IncHI2 plasmids, with high similarity of genetic structures. In addition, these plasmids shared backbone structures with IncHI2 plasmids carrying bla IMP reported from other countries of the Asia-Pacific region. All isolates of clade 3 except one carried bla IMP-1 in In1426 on IncW plasmids. An isolate of clade 3, which lacked IncW plasmids, carried bla IMP-1 in In1426 on an IncFIB plasmid. These observations suggest that IMP-producing E. cloacae complex isolates with a diversity of host genomic backgrounds have spread in central Tokyo, and they indicate the possible contribution of IncHI2 plasmids toward this phenomenon., (Copyright © 2018 American Society for Microbiology.)

The intestinal microbiota is an important contributor to the health of preterm infants, and may be destabilized by a number of environmental factors and treatment modalities. How to promote the development of a healthy microbiota in preterm infants is largely unknown. We collected fecal samples from 45 breastfed preterm very low birth weight (birth weight < 1500 g) infants from birth until 60 days postnatal age to characterize the intestinal microbiota development during the first weeks of life in preterm infants. Fecal microbiota composition was determined by 16S rRNA amplicon sequencing. The main driver of microbiota development was gestational age; antibiotic use had strong but temporary effects and birth mode had little influence. Microbiota development proceeded in four phases indicated by the dominance of Staphylococcus, Enterococcus, Enterobacter, and finally Bifidobacterium. The Enterococcus phase was only observed among the extremely premature infants and appeared to delay the microbiota succession. The results indicate that hospitalized preterm infants receiving breast milk may develop a normal microbiota resembling that of term infants.

Enterobacter sp. strain FL was newly isolated from activated sludge and exhibited significant capability of auto-aggregation as well as aerobic denitrification. The removal efficiencies of NO 3 - -N, total nitrogen (TN), and TOC by strain FL in batch culture reached 94.6, 63.9, and 72.5% in 24 h, respectively. The production of N 2 O and N 2 in the presence of oxygen demonstrated the occurrence of aerobic denitrification. The auto-aggregation index of strain FL reached 54.3%, suggesting a high tendency that the cells would agglomerate into aggregates. The production of extracellular polymeric substances (EPSs), which were mainly composed of proteins followed by polysaccharides, was considered to be related to the cell aggregation according to Fourier transform infrared (FT-IR) and confocal laser scanning microscopy (CLSM). The proteins in EPS were evenly and tightly combined to cells and altered the protein secondary structures of cell surface from random coils to β-sheets and three-turn helices. The alteration of protein secondary structures of cell surface caused by the proteins in EPS might play a dominant role in the auto-aggregation of strain FL. To further assess the feasibility of strain FL for synthetic wastewater treatment, a sequencing batch reactor (SBR), solely inoculated with strain FL, was conducted. During the 16 running cycles, the removal efficiency of NO 3 - -N was 90.2-99.7% and the auto-aggregation index was stabilized at 35.0-41.5%. The EPS promoted the biomass of strain FL to aggregate in the SBR.