Review

Authors: Anne Davin-Regli, Jean-Philippe Lavigne, Jean-Marie Pagès...

The genus 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 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 and complex exhibited a multidrug-resistant phenotype, which has stimulated questions about the role of cascade regulation in the emergence of these well-adapted clones.

Topics: Animals; Anti-Bacterial Agents; Drug Resistance, Bacterial; Enterobacter; Enterobacteriaceae Infections; Humans

PubMed: 31315895
DOI: 10.1128/CMR.00002-19

Authors: Mohammed Umar Mustapha, Normala Halimoon, Wan Lutfi Wan Johari...

Extensive use of carbofuran insecticide harms the environment and human health. Carbofuran is an endocrine disruptor and has the highest acute toxicity to humans than all groups of carbamate pesticides used. Carbofuran is highly mobile in soil and soluble in water with a lengthy half-life (50 days). Therefore, it has the potential to contaminate groundwater and nearby water bodies after rainfall events. A bacterial strain BRC05 was isolated from agricultural soil characterized and presumptively identified as sp. The strain was immobilized using gellan gum as an entrapment material. The effect of different heavy metals and the ability of the immobilized cells to degrade carbofuran were compared with their free cell counterparts. The results showed a significant increase in the degradation of carbofuran by immobilized cells compared with freely suspended cells. Carbofuran was completely degraded within 9 h by immobilized cells at 50 mg/L, while it took 12 h for free cells to degrade carbofuran at the same concentration. Besides, the immobilized cells completely degraded carbofuran within 38 h at 100 mg/L. On the other hand, free cells degraded the compound in 68 h. The viability of the freely suspended cell and degradation efficiency was inhibited at a concentration greater than 100 mg/L. Whereas, the immobilized cells almost completely degraded carbofuran at 100 mg/L. At 250 mg/L concentration, the rate of degradation decreased significantly in free cells. The immobilized cells could also be reused for about nine cycles without losing their degradation activity. Hence, the gellan gum-immobilized cells of sp. could be potentially used in the bioremediation of carbofuran in contaminated soil.

Topics: Biodegradation, Environmental; Carbofuran; Cells, Immobilized; Enterobacter; Soil Microbiology

PubMed: 32560037
DOI: 10.3390/molecules25122771

Authors: Amy J G Anderson, Becca Morrell, Guillermo Lopez Campos...

Gram-negative bacteria use type VI secretion systems (T6SSs) to antagonize neighbouring cells. Although primarily involved in bacterial competition, the T6SS is also implicated in pathogenesis, biofilm formation and ion scavenging. species belong to the ESKAPE pathogens, and while their antibiotic resistance has been well studied, less is known about their pathogenesis. Here, we investigated the distribution and diversity of T6SS components in isolates of two clinically relevant species, and . T6SS clusters are grouped into four types (T6SS-T6SS), of which type i can be further divided into six subtypes (i1, i2, i3, i4a, i4b, i5). Analysis of a curated dataset of 31 strains demonstrated that most of them encode T6SS clusters belonging to the T6SS type. All T6SS-positive strains possessed a conserved i3 cluster, and many harboured one or two additional i2 clusters. These clusters were less conserved, and some strains displayed evidence of deletion. We focused on a pathogenic clinical isolate for comprehensive effector prediction, with comparative analyses across the 31 isolates. Several new effector candidates were identified, including an evolved VgrG with a metallopeptidase domain and a Tse6-like protein. Additional effectors included an anti-eukaryotic catalase (KatN), M23 peptidase, PAAR and VgrG proteins. Our findings highlight the diversity of T6SSs and reveal new putative effectors that may be important for the interaction of these species with neighbouring cells and their environment.

Topics: Enterobacter cloacae; Type VI Secretion Systems; Peptide Hydrolases; Enterobacter

PubMed: 38054968
DOI: 10.1099/mgen.0.001148

Authors: Zhichen Zhu, Xiaofang Xie, Hua Yu...

Epidemiological characteristics and molecular features of carbapenem-resistant (CR-) species remain unclear in China. In this study, we performed a genomic study on 92 isolates from -caused infections from a multicenter study in China. Whole genome sequencing (WGS) was used to determine the genome sequence of 92 non-duplicated CR- strains collected from multiple tertiary health centres. The precise species of strains were identified by average nucleotide identity (ANI) and in silico DNA-DNA hybridization (isDDH). Molecular features of high-risk CR- sequence type (ST) lineages and carbapenemase-encoding plasmids were determined. The result revealed that the most common human-source CR- species in China was (66/92, 71.93%), and the proportion of carbapenemase-producing (CP-) in CR- was high (72/92, 78.26%) in comparison to other global regions. Furthermore, ST171 and ST116 were the major lineages of CP- strains, and ST171 was more likely to cause infections in older patients. Genomic analysis also highlighted the likelihood of intra-hospital/inter-hospital clonal transmission of ST171 and ST116 . In addition, the -harbouring IncX3-type plasmid was identified as the prevalent carbapenemase-encoding plasmid carried by CR- strains, and was experimentally confirmed to be able to self-transfer with high frequency. This study detailed the genomic and clinical characteristics of CR- in China in the form of multicenter for the first time. The high risk of carbapenemase-producing ST171 and ST116 , and the -harbouring IncX3-type plasmid were detected and emphasized.

Topics: Aged; Humans; Bacterial Proteins; beta-Lactamases; Carbapenem-Resistant Enterobacteriaceae; China; Enterobacter; Enterobacteriaceae Infections; Genomics; Microbial Sensitivity Tests; Plasmids

PubMed: 36382635
DOI: 10.1080/22221751.2022.2148562

Authors: Yanling He, Yuling Xiao, Yu Feng...

Two strains 170198 and 170250 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 . The average nucleotide identity (ANI) and DNA-DNA hybridization (DDH) values between each of the two strains and type strains of all currently known species were determined. The two strains belonged to two novel species as the highest ANI and DDH values with type strains of all currently known species below the cutoff for species demarcation (96% for ANI and 70% for DDH). Then the physiological and biochemical studies demonstrated that biochemical features and the profile of whole fatty acids of strains 170198 and 170250 were largely consistent with those known species. Nevertheless, the two novel species can be differentiated from all other species by certain biochemical characteristics. In conclusion, 170198 and 170250 represent two novel species of the genus , for which we propose sp. nov. and sp. nov., as the species names. The type strains of sp. nov., and sp. nov. are 170198 (=GDMCC 1.3549=JCM 35826) and 170250 (=GDMCC 1.3670=JCM 36189), respectively. The two novel species have clinical significance with the ability to cause bloodstream infections.IMPORTANCE is a group of bacteria comprising several common opportunistic pathogens and has a complicated taxonomy. Here, we reported two novel species. We demonstrated that the two novel species can be differentiated from other 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 is less studied and warrants further exploration. We believe that the findings here are valuable for enhancing the appreciation toward , an important pathogen.

Topics: Enterobacter; Humans; Enterobacteriaceae Infections; Phylogeny; Virulence Factors; China; Fatty Acids; DNA, Bacterial; Bacterial Typing Techniques; Anti-Bacterial Agents; Whole Genome Sequencing; Microbial Sensitivity Tests; Nucleic Acid Hybridization; RNA, Ribosomal, 16S; Genome, Bacterial; Female; Male

PubMed: 38916331
DOI: 10.1128/spectrum.00292-24

Authors: Jie Qiao, Haoyu Ge, Hao Xu...

PURPOSE

To explore the genetic characteristics of the IMP-4 and SFO-1 co-producing multidrug-resistant (MDR) clinical isolates, YQ13422hy and YQ13530hy.

METHODS

MALDI-TOF MS was used for species identification. Antibiotic resistance genes (ARGs) were tested by PCR and Sanger sequencing analysis. In addition to agar dilution, broth microdilution was used for antimicrobial susceptibility testing (AST). Whole-genome sequencing (WGS) analysis was conducted using the Illumina NovaSeq 6000 and Oxford Nanopore platforms. Annotation was performed by RAST on the genome. The phylogenetic tree was achieved using kSNP3.0. Plasmid characterization was conducted using S1-pulsed-field gel electrophoresis (S1-PFGE), Southern blotting, conjugation experiments, and whole genome sequencing (WGS). An in-depth study of the conjugation module was conducted using the OriTFinder website. The genetic context of and was analyzed using BLAST Ring Image Generator (BRIG) and Easyfig 2.3.

RESULTS

YQ13422hy and YQ13530hy, two MDR strains of ST51 harboring and , were identified. They were only sensitive to meropenem, amikacin and polymyxin B, and were resistant to cephalosporins, aztreonam, piperacillin/tazobactam and aminoglycosides, intermediate to imipenem. The genetic context surrounding was 5'CS--IS-In- -IS-. The integron of is In, which is the array of gene cassettes of 5'CS- . Phylogenetic analysis demonstrated that YQ13422hy and YQ13530hy belonged to the same small clusters with a high degree of homology.

CONCLUSION

This observation revealed the dissemination of the gene in in China. We found that and co-exist in MDR clinical isolates. This work showed a transferable IncN-type plasmid carrying the resistance gene in . We examined the potential resistance mechanisms of pYQ13422-IMP-4 and pYQ13422-SFO-1, along with their detailed genetic contexts.

Topics: Anti-Bacterial Agents; beta-Lactamases; Enterobacter; Phylogeny

PubMed: 36389152
DOI: 10.3389/fcimb.2022.998578

Authors: Dziyana Shymialevich, Stanisław Błażejak, Paulina Średnicka...

Due to the high microbiological contamination of raw food materials and the increase in the incidence of multidrug-resistant bacteria, new methods of ensuring microbiological food safety are being sought. One solution may be to use bacteriophages (so-called phages) as natural bacterial enemies. Therefore, the aim of this study was the biological and genomic characterization of three newly isolated - and -specific virulent bacteriophages as potential candidates for food biocontrol. Serratia phage KKP_3708 (vB_Sli-IAFB_3708), Serratia phage KKP_3709 (vB_Sma-IAFB_3709), and Enterobacter phage KKP_3711 (vB_Ecl-IAFB_3711) were isolated from municipal sewage against strain KKP 3654, strain KKP 3687, and strain KKP 3684, respectively. The effect of phage addition at different multiplicity of infection (MOI) rates on the growth kinetics of the bacterial hosts was determined using a Bioscreen C Pro growth analyzer. The phages retained high activity in a wide temperature range (from -20 °C to 60 °C) and active acidity values (pH from 3 to 12). Based on transmission electron microscopy (TEM) imaging and whole-genome sequencing (WGS), the isolated bacteriophages belong to the tailed bacteriophages from the class. Genomic analysis revealed that the phages have linear double-stranded DNA of size 40,461 bp (Serratia phage KKP_3708), 67,890 bp (Serratia phage KKP_3709), and 113,711 bp (Enterobacter phage KKP_3711). No virulence, toxins, or antibiotic resistance genes were detected in the phage genomes. The lack of lysogenic markers indicates that all three bacteriophages may be potential candidates for food biocontrol.

Topics: Bacteriophages; Genome, Viral; Serratia; Enterobacter; Genomics; Phylogeny; Sewage; Virulence

PubMed: 38892136
DOI: 10.3390/ijms25115944

Authors: Santi M Mandal, Shalley Sharma, Anil Kumar Pinnaka...

BACKGROUND

Increasing multidrug-resistance in bacteria resulted in a greater need to find alternative antimicrobial substances that can be used for clinical applications or preservation of food and dairy products. Research on antimicrobial peptides including lipopeptides exhibiting both narrow and broad spectrum inhibition activities is increasing in the recent past. Therefore, the present study was aimed at isolation and characterization of antimicrobial lipopeptide producing bacterial strains from fecal contaminated soil sample.

RESULTS

The phenotypic and 16S rRNA gene sequence analysis of all isolates identified them as different species of Gram-negative genera Citrobacter and Enterobacter. They exhibited common phenotypic traits like citrate utilization, oxidase negative and facultative anaerobic growth. The HPLC analysis of solvent extracts obtained from cell free fermented broth revealed the presence of multiple antimicrobial lipopeptides. The comprehensive mass spectral analysis (MALDI-TOF MS and GC-MS) of HPLC purified fractions of different isolates revealed that the lipopeptides varied in their molecular weight between (m/z) 607.21 to 1536.16 Da. Isomers of mass ion m/z 984/985 Da was produced by all strains. The 1495 Da lipopeptides produced by strains S-3 and S-11 were fengycin analogues and most active against all strains. While amino acid analysis of lipopeptides suggested most of them had similar composition as in iturins, fengycins, kurstakins and surfactins, differences in their β-hydroxy fatty acid content proposed them to be isoforms of these lipopeptides.

CONCLUSION

Although antimicrobial producing strains can be used as biocontrol agents in food preservation, strains with ability to produce multiple antimicrobial lipopeptides have potential applications in biotechnology sectors such as pharmaceutical and cosmetic industry. This is the first report on antibacterial lipopeptides production by strains of Citrobacter and Enterobacter.

Topics: Anti-Bacterial Agents; Bacterial Typing Techniques; Chromatography, High Pressure Liquid; Citrobacter; Cluster Analysis; Culture Media; DNA, Bacterial; DNA, Ribosomal; Enterobacter; Humans; Lipopeptides; Mass Spectrometry; Molecular Sequence Data; Molecular Weight; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology

PubMed: 23834699
DOI: 10.1186/1471-2180-13-152

Authors: Chih-Ming Chen, Hui-Ling Tang, Ying-Tsong Chen...

Carbapenem-resistant complex is a significant global healthcare threat, particularly carbapenemase-producing (CPEH). From January 2017 to January 2021, twenty-two CPEH isolates from a regional teaching hospital in central Taiwan were identified with the carriage of carbapenemase genes , and predominantly . Over 80% of these CPEH strains clustered into the high-risk ST78 lineage, carrying a IncL plasmid (pOXA48-CREH), nearly identical to the endemic plasmid pOXA48-KP in ST11 . This OXA-48-producing ST78 lineage disseminated clonally from 2018 to 2021 and transferred pOXA48-CREH to ST66 and ST90 . An IMP-8-producing ST78 strain harbouring a -carrying pIncHI2 plasmid appeared in 2018, and by late 2020, a KPC-2-producing ST78 strain was identified after acquiring a novel -carrying IncFII plasmid. These findings suggest that the high-risk ST78 lineage of . has emerged as the primary driver behind the transmission of CPEH ST78 has not only acquired various carbapenemase-gene-carrying plasmids but has also facilitated the transfer of pOXA48-CREH to other lineages. Continuous genomic surveillance and targeted interventions are urgently needed to control the spread of emerging CPEH clones in hospital settings.

Topics: Taiwan; beta-Lactamases; Humans; Enterobacter; Enterobacteriaceae Infections; Plasmids; Bacterial Proteins; Anti-Bacterial Agents; Microbial Sensitivity Tests; Hospitals; Carbapenem-Resistant Enterobacteriaceae

PubMed: 39258852
DOI: 10.1080/22221751.2024.2404165

Authors: Yu Feng, Ya Hu, Zhiyong Zong...

We performed whole-genome sequencing for 17 Enterobacter clinical strains and analyzed all available Enterobacter genomes and those of its closely related genera ( = 3,389) from NCBI. The exact origins of plasmid-borne and genes are Enterobacter cloacae and Enterobacter roggenkampii, respectively, while plasmid-borne genes originated from multiple other Enterobacter species, including Enterobacter xiangfangensis, Enterobacter hoffmannii, Enterobacter asburiae, Enterobacter ludwigii, and Enterobacter kobei. The genus Enterobacter represents a large reservoir of plasmid-borne AmpC β-lactamase.

Topics: Bacterial Proteins; Enterobacter; Enterobacter cloacae; Microbial Sensitivity Tests; Plasmids; beta-Lactamases

PubMed: 34516244
DOI: 10.1128/AAC.01596-21