Population genetics of the nomenspecies Enterobacter cloacae

Enterobacter adelaidei sp. nov. Isolation of an extensively drug resistant strain from hospital wastewater in Australia and the global distribution of the species

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.

Two novel Enterobacter species, Enterobacter chinensis sp. nov. and Enterobacter rongchengensis sp. nov., recovered from clinical samples carrying multiple virulence factors

Two Enterobacter strains 170198T and 170250T 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 (isDDH) 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 isDDH values with type strains of all currently known Enterobacter species below the cutoff for species demarcation (96% for ANI and 70% for isDDH). Then the physiological and biochemical studies demonstrated that biochemical features and the profile of whole fatty acids of strains 170198T and 170250T 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, 170198T and 170250T 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 170198T (=GDMCC 1.3549T=JCM 35826T) and 170250T (=GDMCC 1.3670T=JCM 36189T), respectively. The two novel species have clinical significance with the ability to cause bloodstream infections.IMPORTANCEEnterobacter 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.

Genome sequence-based species classification of Enterobacter cloacae complex: a study among clinical isolates

Accurate species-level identification of Enterobacter cloacae complex (ECC) is crucial for related research. The classification of ECC is based on strain-to-strain phylogenetic congruence, as well as genomic features including average nucleotide identity (ANI) and digitalized DNA-DNA hybridization (dDDH). ANI and dDDH derived from whole-genome sequencing have emerged as a reliable metric for assessing genetic relatedness between genomes and are increasingly recognized as a standard for species delimitation. Up to now, there are two different classification methods for ECC. The first one categorizes E. hormaechei, a species within ECC, into five subspecies (E. hormaechei subsp. steigerwaltii, subsp. oharae, subsp. xiangfangensis, subsp. hoffmannii, and subsp. hormaechei). The second classifies E. hormaechei as three species: E. hormaechei, "E. xiangfangensis," "E. hoffmanii." While the former is well-accepted in the academic area, the latter may have a greater ability to distinguish different species of ECC. To assess the suitability of these identification criteria for clinical ECC isolates, we conducted a comprehensive analysis involving phylogenetic analysis, ANI and dDDH value alignment, virulence gene identification, and capsule typing on 256 clinical ECC strains isolated from the bloodstream. Our findings indicated that the method of categorizing E. hormaechei into five subspecies has better correlation and consistency with the molecular characteristics of clinical ECC isolates, as evidenced by phylogenetic analysis, virulence genes, and capsule typing. Therefore, the subspecies-based classification method appears more suitable for taxonomic assignments of clinical ECC isolates.

IMPORTANCE

Standardizing taxonomy of the Enterobacter cloacae complex (ECC) is necessary for data integration across diverse studies. The study utilized whole-genome data to accurately identify 256 clinical ECC isolated from bloodstream infections using average nucleotide identity (ANI), digitalized DNA-DNA hybridization (dDDH), and phylogenetic analysis. Through comprehensive assessments including phylogenetic analysis, ANI and dDDH comparisons, virulence gene, and capsule typing of the 256 clinical isolates, it was concluded that the classification method based on subspecies exhibited better correlation and consistency with the molecular characteristics of clinical ECC isolates. In summary, this research contributes to the precise identification of clinical ECC at the species level and expands our understanding of ECC.

Carbapenem-Resistant Enterobacter cloacae Complex in Southwest China: Molecular Characteristics and Risk Factors Caused by NDM Producers

Purpose

The isolation rate of carbapenem-resistant Enterobacter cloacae complex (CREC) is continuously increasing. The aims of this study were to investigate the molecular characteristics and risk factors associated with CREC infections.

Methods

Bacterial species were identified using the matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) (Bruker Daltonik GmbH, Bremen, Germany), and the hsp60 gene was utilized for further typing. Antimicrobial susceptibilities were assessed through the MicroScan WalkAway 96 Plus system (Siemens, Germany) and the microbroth dilution method. Antimicrobial resistance genes were screened through polymerase chain reaction (PCR), while the homologous relationship was assessed using multilocus sequence typing (MLST). Conjugation experiments were performed to verify whether the plasmid could be transferred. Additionally, logistic regression model was employed to analyze risk factors for CREC infections.

Results

32 strains of CREC bacteria were isolated during the study, yet only 20 were retained for preservation. While the isolates demonstrated resistance to the majority of antibiotics, they exhibited high sensitivity to polymyxin B and tigecycline. All isolates carried the blaNDM resistance gene, including 13 blaNDM-1 isolates and 7 blaNDM-5 isolates. MLST homology analysis revealed the presence of seven known ST types and one new ST type. Conjugation experiments confirmed that 13 isolates were capable of transferring the blaNDM resistance gene to Escherichia coli strain EC600. Single-factor analysis identified multiple primary risk factors for CREC infection, but multivariate analysis did not reveal independent risk factors.

Conclusion

This study investigates the molecular characteristics and risk factors associated with CREC infections. The detection rate of CREC strains in our hospital is continuously rising and homology analysis suggested that strains might spread in our hospital, emphasizing the importance of implementing effective preventive measures to control the horizontal transmission of plasmid-mediated antimicrobial resistance genes.

Analysis of the transmission chain of carbapenem-resistant Enterobacter cloacae complex infections in clinical, intestinal and healthcare settings in Zhejiang province, China (2022-2023)

Considerable attention is given to intensive care unit-acquired infections; however, research on the transmission dynamics of multichain carbapenemase-resistant Enterobacter cloacae complex (CRECC) outbreaks remains elusive. A total of 118 non-duplicated CRECC strains were isolated from the clinical, intestinal, and hospital sewage samples collected from Zhejiang province of China during 2022-2023. A total of 64 CRECC strains were isolated from the hospital sewage samples, and their prevalence increased from 10.0 % (95 % confidence interval, CI = 0.52-45.8 %) in 2022 to 63.6 % (95 % CI = 31.6-87.6 %) in 2023. Species-specific identification revealed that Enterobacter hormaechei was the predominant CRECC species isolated in this study (53.4 %, 95 % CI = 44.0-62.6 %). The antimicrobial susceptibility profiles indicated that all 118 CRECC strains conferred high-level resistance to β-lactam antibiotics, ceftacillin/avibactam, and polymyxin. Furthermore, all CRECC strains exhibited resistance to β-lactams, quinolones, and fosfomycin, with a higher colistin resistance rate observed in the hospital sewage samples (67.2 %, 95 % CI = 54.2-78.1 %). Several antibiotic resistance genes were identified in CRECC strains, including Class A carbapenemases (blaKPC-2) and Class B carbapenemases (blaNDM-1/blaIMP), but not Class D carbapenemases. The WGS analysis showed that the majority of the CRECC strains carried carbapenemase-encoding genes, with blaNDM-1 being the most prevalent (86.9 %, 95 % CI = 77.4-92.9 %). Furthermore, sequence typing revealed that the isolated CRECC strains belonged to diverse sequence types (STs), among which ST418 was the most prevalent blaNDM-positive strain. The high risk of carbapenemase-producing ST418 E. hormaechei and the blaNDM-harboring IncFIB-type plasmid (81.4 %, 95 % CI = 72.9-87.7 %) were detected and emphasized in this study. This study provides valuable insights into the prevalence, antimicrobial resistance, genomic characteristics, and plasmid analysis of CRECC strains in diverse populations and environments. The clonal relatedness analysis showed sporadic clonal transmission of ST418 E. hormaechei strains, supporting inter-hospital transmission.

Complete genome sequence of multidrug-resistant Enterobacter roggenkampii 0-E

Here, we present the complete 4.77 Mb genome of Enterobacter roggenkampii 0-E assembled with Oxford Nanopore long reads. This genome harbors 19 antimicrobial resistance genes, including ramA and marA decreasing permeability to carbapenems. This genome adds novel knowledge on emerging multidrug resistance in the Enterobacter cloacae species complex.

Extensively drug-resistant Enterobacter ludwigii co-harbouring MCR-9 and a multicopy of blaIMP-1 in South Korea

In this study, we describe an Enterobacter ludwigii clinical isolate that is resistant to both carbapenems and colistin in South Korea. Antimicrobial susceptibility testing revealed that E. ludwigii CRE2104-31 was non-susceptible to all tested antibiotics except fosfomycin. Whole genome sequencing identified a 323-kbp IncHI2 plasmid, pCRE2104-31a, that was co-harbouring mobile colistin resistance (mcr)-9.1 and blaIMP-1. In comparison with other full plasmids, pCRE2104-31a exhibited the closest similarity to a plasmid from the Klebsiella pneumoniae strain CNR48 from France, with 19.9% query coverage and 99% identity. Notably, we observed five tandem repeats of blaIMP-1 and aac(6')-Il genes, accompanied by multiple attCs within a class I integron on the Tn402-like transposon. The unit of blaIMP-1-attC-aac(6')-Il-attC might have accumulated due to multiple convergent events. In addition to mcr-9.1 and blaIMP-1, various other antibiotic resistance-associated genes were identified in the plasmid, as follows: blaTEM-1B, aph(3')-I, aph(3')-Ia, aac(6')-Il, aac(6')-IIc, aac(6')-IIa, aph(6)-Id, aph(3'')-Ib, aadA2b, aac(6')-Ib3, sul, dfrA19, qnrB2, aac(6')-Ib-cr, ere(A), and qacE. A conjugation assay showed that the mcr-9.1/blaIMP-1-co-bearing plasmid was self-transmissible to E. coli J53. However, colistin and carbapenem resistance could not be transferred to E. coli due to high incompatibility. The convergence of mcr and carbapenemase genes is thought to be host-dependent among Enterobacteriaceae. The emergence of extensively drug-resistant E. ludwigii co-harbouring MCR-9.1 and a multicopy of blaIMP-1 would pose a significant threat within the compatible Enterobacteriaceae.

Enterobacter cloacae from urinary tract infections: frequency, protein analysis, and antimicrobial resistance

The genus Enterobacter belongs to the ESKAPE group, which includes Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp. This group is characterized by the development of resistance to various antibiotics. In recent years, Enterobacter cloacae (E. cloacae) has emerged as a clinically important pathogen responsible for a wide range of healthcare-associated illnesses. Identifying Enterobacter species can be challenging due to their similar phenotypic characteristics. The emergence of multidrug-resistant E. cloacae is also a significant problem in healthcare settings. Therefore, our study aimed to identify and differentiate E. cloacae using Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) as a fast and precise proteomic analytical technique. We also tested hospital-acquired E. cloacae isolates that produce Extended-spectrum beta-lactamases (ESBL) against commonly used antibiotics for treating urinary tract infections (UTIs). We used a total of 189 E. cloacae isolates from 2300 urine samples of patients with UTIs in our investigation. We employed culturing techniques, as well as the BD Phoenix™ automated identification system (Becton, Dickinson) and Analytical Profile Index (API) system for the biochemical identification of E. cloacae isolates. We used the MALDI Biotyper (MBT) device for peptide mass fingerprinting analysis of all isolates. We utilized the single peak intensities and Principal Component Analysis (PCA) created by MBT Compass software to discriminate and cluster the E. cloacae isolates. Additionally, we evaluated the sensitivity and resistance of ESBL-E. cloacae isolates using the Kirby Bauer method. Out of the 189 E. cloacae isolates, the BD Phoenix system correctly identified 180 (95.24%) isolates, while the API system correctly identified 165 (87.30%) isolates. However, the MBT accurately identified 185 (98.95%) isolates with a score of 2.00 or higher. PCA positively discriminated the identified E. cloacae isolates into one group, and prominent peaks were noticed between 4230 mass-to-charge ratio (m/z) and 8500 m/z. The ESBL-E. cloacae isolates exhibited a higher degree of resistance to ampicillin, amoxicillin-clavulanate, cephalothin, cefuroxime, and cefoxitin. Several isolates were susceptible to carbapenems (meropenem, imipenem, and ertapenem); however, potential future resistance against carbapenems should be taken into consideration. In conclusion, MALDI-TOF MS is a powerful and precise technology that can be routinely used to recognize and differentiate various pathogens in clinical samples. Additionally, the growing antimicrobial resistance of this bacterium may pose a significant risk to human health.

Isolation and draft genome sequence of Enterobacter asburiae strain i6 amenable to genetic manipulation

Enterobacter asburiae is a species of Gram-negative bacteria that is found in soil, water, and sewage. E. asburiae is generally considered to be an opportunistic pathogen, but has also been reported as a plant growth-promoting bacterium (PGPB), which may have beneficial effects on plant growth and development. However, genetic analysis of E. asburiae has been limited, possibly due to its redundant enzymes that digest exogenous DNA in the cell. Here, an E. asburiae strain i6 was isolated from soil in Nara, Japan. This strain was amenable to transformation and the one-step gene inactivation method based on λ Red recombinase. The transformation efficiency of the i6 strain with the 10 kb plasmid DNA pCF430 was at least four orders of magnitude higher than that of the previously sequenced E. asburiae strain ATCC 35953, which could not be transformed with the same plasmid DNA. A draft genome sequence of the i6 strain was determined and deposited into the database, allowing several factors that may determine transformation efficiency to be perturbed and tested. Together with the amenability of the i6 strain to genetic manipulation, the information from the i6 genome will facilitate characterization and fine-tuning of the beneficial and detrimental traits of this species.

Clinical and Microbiological Characteristics of Bacteremia Caused by Carbapenemase-producing Enterobacterales in Minami Ibaraki Area, Japan

Although recent propagation of carbapenemase-producing Enterobacterales (CPE) has become a problem worldwide, the picture of CPE infection in Japan has not fully been elucidated. In this study, we examined clinical and microbiological characteristics of invasive CPE infection occurring at 8 hospitals in Minami Ibaraki Area between July 2001 to June 2017. Of 7294 Enterobacterales strains isolated from independent cases of bacteremia and/or meningitis, 10 (0.14%) were CPE (8 Enterobacter cloacae-complex, 1 Escherichia coli, and 1 Edwardsiella tarda）, all of which had the blaIMP-1 gene and susceptible to gentamicin and trimethoprim/sulfamethoxazole. These strains were isolated from 7 adult and 2 infant bacteremia (1 infant patient developed CPE bacteremia twice) after 2007. The most common portal of entry was intravenous catheters. All of the adult patients were recovered, while the infant patients eventually died. Genomic analyses showed that the 8 E. cloacae-complex strains were classified into 5 groups, each of which was exclusively detected in specific facilities at intervals of up to 3 years, suggesting persistent colonization in the facilities. This study showed that invasive CPE infection in the area was rare, caused by IMP-1-type CPE having susceptibility to various antibiotics, and nonfatal among adult patients.

Surface water in Lower Saxony: A reservoir for multidrug-resistant Enterobacterales

The emergence of extended-spectrum β-lactamase and carbapenemase-producing Enterobacterales (ESBL-E and CPE, respectively) is a threat to modern medicine, as infections become increasingly difficult to treat. These bacteria have been detected in aquatic environments, which raises concerns about the potential spread of antibiotic resistance through water. Therefore, we investigated the occurrence of ESBL-E and CPE in surface water in Lower Saxony, Germany, using phenotypic and genotypic methods. Water samples were collected from two rivers, five water canals near farms, and 18 swimming lakes. ESBL-E and CPE were isolated from these samples using filters and selective agars. All isolates were analyzed by whole genome sequencing. Multidrug-resistant Enterobacterales were detected in 4/25 (16%) water bodies, including 1/2 rivers, 2/5 water canals and 1/18 lakes. Among all samples, isolates belonging to five different species/species complexes were detected: Escherichia coli (n = 10), Enterobacter cloacae complex (n = 4), Citrobacter freundii (n = 3), Citrobacter braakii (n = 2), and Klebsiella pneumoniae (n = 2). Of the 21 isolates, 13 (62%) were resistant at least to 3rd generation cephalosporins and eight (38%) additionally to carbapenems. CPE isolates harbored blaKPC-2 (n = 5), blaKPC-2 and blaVIM-1 (n = 2), or blaOXA-181 (n = 1); additionally, mcr-9 was detected in one isolate. Two out of eight CPE isolates were resistant to cefiderocol and two to colistin. Resistance to 3rd generation cephalosporins was mediated by ESBL (n = 10) or AmpC (n = 3). The presence of AmpC-producing Enterobacterales, ESBL-E and CPE in northern German surface water samples is alarming and highlights the importance of aquatic environments as a potential source of MDR bacteria.

Emergence of OXA-48-producing Enterobacter hormaechei in a Swiss companion animal clinic and their genetic relationship to clinical human isolates

BACKGROUND

Enterobacter hormaechei producing the carbapenemase OXA-48 was identified repeatedly in infections in companion animals hospitalized at a Swiss veterinary clinic where OXA-48-producing Klebsiella pneumoniae was previously reported.

OBJECTIVES

To determine the genetic relatedness of animal and human E. hormaechei strains collected in Switzerland during 2017-22 and their mobile genetic elements.

METHODS

Hybrid assemblies for phylogenetic and comparative analysis of animal (n = 9) and human (n = 25) isolates were obtained by sequencing with Illumina, PacBio and Oxford Nanopore Technologies. Antimicrobial susceptibility was tested by broth microdilution.

RESULTS

The animal strains were identified as E. hormaechei subsp. xiangfangensis ST114 (n = 6) and ST418 (n = 2), and E. hormaechei subsp. hoffmannii ST78 (n = 1). Human E. hormaechei belonged to subspecies steigerwaltii (n = 10), xiangfangensis (n = 13), hoffmannii (n = 1) and hormaechei (n = 1), with a heterogeneous ST distribution differing from the animal strains, except for two ST114. Core-gene SNP analysis confirmed the clonality of the animal ST114 and ST418 isolates (0 to 10 SNPs), and close relatedness of animal and human ST114 strains (80-120 SNPs). The strains harboured the blaOXA-48 gene on ca. 63 kb IncL-type plasmids (n = 27); on ca. 72 kb IncL plasmids co-harbouring blaCTX-M-14 (n = 2); and on ca. 150-180 kb IncFIB (n = 4) or hybrid IncFIB/IncL (n = 1) plasmids. The blaOXA-48-harbouring plasmids and the blaDHA-1-carrying ISCR1 element in one animal ST114 and both ST418 clones were likely acquired from previously spreading K. pneumoniae strains.

CONCLUSIONS

Common ecological niches favour the spread of plasmid-borne carbapenemases among Enterobacterales and the emergence of MDR E. hormaechei clones.

Metagenomic next-generation sequencing of bronchoalveolar lavage fluid in non-severe and severe pneumonia patients

Metagenomic next-generation sequencing (mNGS) is widely used as a more promising technology than conventional tests. However, its clinical utility in the context of bronchoalveolar lavage fluid (BALF) samples for discriminating between non-severe and severe pneumonia is not well established. Thus, this study aimed to investigate the diagnostic performance of mNGS on BALF samples from 100 individuals suspected of pneumonia, and compared it with conventional microbiological tests (CMT) of BALF samples and the final clinical diagnosis. Twenty-seven cases of non-severe pneumonia and 73 cases of severe pneumonia patients were finally clinically diagnosed. Among 100 cases, diagnostic performance of mNGS and culture showed a significant difference; 65 cases had the same sample types, of which 25 cases were diagnosed as positive by mNGS only (38.46%) and 1 was diagnosed as positive by culture only (1.54%). Moreover, 24 cases were diagnosed positive in both mNGS and culture (36.92%) and 15 cases tested negative in both mNGS and culture (23.08%). Among 35 cases, 28 out of 35 cases were diagnosed as positive by mNGS, while only 4 out of 35 cases were diagnosed as positive by the indirect immunofluorescence method (IIFT). In addition, the positive rate of mNGS was higher than that of culture in cases regardless of prior antibiotic exposure. Mixed pathogens were found to be significantly more prevalent in severe pneumonia patients than in non-severe pneumonia patients. Importantly, among 38 cases who were diagnosed solely by mNGS, 25 patients experienced an improved outcome after physicians changed the therapy according to the mNGS results. In conclusion, the results showed that mNGS of BALF represents a potentially effective tool for detection of mixed pathogens in severe pneumonia.

Gastropods as a source for fecal indicator bacteria in drinking water

Microbial water quality is routinely examined using the fecal indicator bacteria Escherichia coli, coliform bacteria and enterococci. Several practical cases in German drinking water distribution systems indicated invertebrates such as insects or gastropods as a source for the microbiological deterioration. Therefore, we examined three genera of Gastropoda (Arion, Helix and Cepaea) for the presence of fecal indictor bacteria in excreta using standard methods. Enterococci and coliform bacteria were detected in high concentrations (mean values of 1.5 × 106 and 6.3 × 106 per gram feces, respectively). E. coli was also detected, still specification revealed that what was assigned by standard ISO-methods to be E. coli was indeed a novel species of Buttiauxella, exhibiting β-D-glucuronidase activity, thus, explaining the false-positive results. Microbiome analyses confirmed the cultural results. Enterobacteriaceae were dominant in the samples, yet only very few sequences could be assigned to Escherichia. Our study suggests, that enterococci and coliform bacteria are an integral component in the gastropod microbiome, whereas E. coli might be derived from other sources with gastropods being a vector. The results further indicate, that the current concept of fecal indicator bacteria needs to be extended, as not only humans and homeothermic animals could be a source for fecal indictor bacteria, but also gastropods need to be taken into consideration.

Comparison of prevalence, resistance, biofilm-forming ability and virulence between carbapenem-non-susceptible and carbepenem-susceptible Enterobacter cloacae complex in clusters

OBJECTIVES

This study aimed to explore differences in prevalence, resistance, biofilm-forming ability and virulence between carbapenem-non-susceptible and carbapenem-susceptible Enterobacter cloacae complex (ECC) in different clusters.

METHODS

Ninety-one carbapenem-non-susceptible isolates and an equal number of carbapenem-susceptible isolates and their clinical information were collected from a university teaching hospital in China. The strains were divided into different clusters based on hsp60 analysis. The agar dilution method was used to determine the minimum inhibitory concentrations of common antibiotics. The crystal violet assay was used to measure biofilm-forming ability. The Galleria mellonella infection model and polymerase chain reaction of virulence genes were used to evaluate virulence.

RESULTS

The isolates were divided into 12 clusters based on hsp60 analysis. Cluster VIII accounted for a greater proportion of carbapenem-non-susceptible isolates than the other clusters. The same clusters exhibited different resistance rates in carbapenem-non-susceptible and carbapenem-susceptible isolates. Moreover, carbapenem-non-susceptible isolates carried fewer virulence genes than carbapenem-susceptible isolates, and carbapenem-non-susceptible isolates in cluster II in did not carry the detected virulence genes. Virulence of carbapenem-non-susceptible and carbapenem-susceptible isolates differed significantly in clusters I, III, VIII and IX, as evaluated using the G. mellonella infection model. Carbapenem-non-susceptible isolates in cluster VIII showed higher prevalence, resistance, biofilm-forming ability and pathogenicity compared with the other clusters.

CONCLUSIONS

The study findings indicate the need to identify subgroups of ECC, and provide better advice and guidance for the use of carbapenems.

High prevalence of colistin heteroresistance in specific species and lineages of Enterobacter cloacae complex derived from human clinical specimens

BACKGROUND

Colistin (CST) is a last-line drug for multidrug-resistant Gram-negative bacterial infections. CST-heteroresistant Enterobacter cloacae complex (ECC) has been isolated. However, integrated analysis of epidemiology and resistance mechanisms based on the complete ECC species identification has not been performed.

METHODS

Clinical isolates identified as "E. cloacae complex" by MALDI-TOF MS Biotyper Compass in a university hospital in Japan were analyzed. Minimum inhibitory concentrations of CST were determined by the broth microdilution method. The population analysis profiling (PAP) was performed for detecting the heteroresistant phenotype. The heat shock protein 60 (hsp60) cluster was determined from its partial nucleotide sequence. From the data of whole-genome sequencing, average nucleotide identity (ANI) for determining ECC species, multilocus sequence type, core genome single-nucleotide-polymorphism-based phylogenetic analysis were performed. phoPQ-, eptA-, and arnT-deleted mutants were established to evaluate the mechanism underlying colistin heteroresistance. The arnT mRNA expression levels were determined by reverse transcription quantitative PCR.

RESULTS

Thirty-eight CST-resistant isolates, all of which exhibited the heteroresistant phenotype by PAP, were found from 138 ECC clinical isolates (27.5%). The prevalence of CST-resistant isolates did not significantly differ among the origin of specimens (29.0%, 27.8%, and 20.2% for respiratory, urine, and blood specimens, respectively). hsp60 clusters, core genome phylogeny, and ANI revealed that the CST-heteroresistant isolates were found in all or most of Enterobacter roggenkampii (hsp60 cluster IV), Enterobacter kobei (cluster II), Enterobacter chuandaensis (clusters III and IX), and Enterobacter cloacae subspecies (clusters XI and XII). No heteroresistant isolates were found in Enterobacter hormaechei subspecies (clusters VIII, VI, and III) and Enterobacter ludwigii (cluster V). CST-induced mRNA upregulation of arnT, which encodes 4-amino-4-deoxy-L-arabinose transferase, was observed in the CST-heteroresistant isolates, and it is mediated by phoPQ pathway. Isolates possessing mcr-9 and mcr-10 (3.6% and 5.6% of total ECC isolates, respectively) exhibited similar CST susceptibility and PAP compared with mcr-negative isolates.

CONCLUSIONS

Significant prevalence (approximately 28%) of CST heteroresistance is observed in ECC clinical isolates, and they are accumulated in specific species and lineages. Heteroresistance is occurred by upregulation of arnT mRNA induced by CST. Acquisition of mcr genes contributes less to CST resistance in ECC.

Phenotypic and Molecular Characterization of an Enterobacter ludwigii Clinical Isolate Carrying a Plasmid-Mediated blaIMI-6 Gene

We report a plasmid-encoded IMI-6 carbapenemase in a clinical isolate of Enterobacter ludwigii from Spain. The isolate belongs to ST641 and was susceptible to expanded-spectrum cephalosporins and resistant to carbapenems. The modified carbapenem inactivation method (mCIM) test was positive, but β-Carba was negative. Whole-genome sequencing identified the blaIMI-6 gene located in a conjugative IncFIIY plasmid and associated with the LysR-like regulator imiR. Both genes were bracketed by an ISEclI-like insertion sequence and a putatively defective ISEc36 insertion sequence. IMPORTANCE IMI carbapenemases confer an unusual resistance pattern of susceptibility to broad-spectrum cephalosporins and piperacillin-tazobactam but decreased susceptibility to carbapenems, which may make them difficult to detect in routine practice. Commercially available molecular methods for the detection of carbapenemases in clinical laboratories do not usually include blaIMI genes, which could contribute to the hidden dissemination of bacteria producing these enzymes. Techniques should be implemented to detect minor carbapenemases that are not very frequent in our environment and control their dissemination.

Temocillin Resistance in the Enterobacter cloacae Complex Is Conferred by a Single Point Mutation in BaeS, Leading to Overexpression of the AcrD Efflux Pump

The Enterobacter cloacae complex (ECC) has become a major opportunistic pathogen with antimicrobial resistance issues. Temocillin, an "old" carboxypenicillin that is remarkably stable toward β-lactamases, has been used as an alternative for the treatment of multidrug-resistant ECC infections. Here, we aimed at deciphering the never-investigated mechanisms of temocillin resistance acquisition in Enterobacterales. By comparative genomic analysis of two clonally related ECC clinical isolates, one susceptible (Temo_S [MIC of 4 mg/L]) and the other resistant (Temo_R [MIC of 32 mg/L]), we found that they differed by only 14 single-nucleotide polymorphisms, including one nonsynonymous mutation (Thr175Pro) in the two-component system (TCS) sensor histidine kinase BaeS. By site-directed mutagenesis in Escherichia coli CFT073, we demonstrated that this unique change in BaeS was responsible for a significant (16-fold) increase in temocillin MIC. Since the BaeSR TCS regulates the expression of two resistance-nodulation-cell division (RND)-type efflux pumps (namely, AcrD and MdtABCD) in E. coli and Salmonella, we demonstrated by quantitative reverse transcription-PCR that mdtB, baeS, and acrD genes were significantly overexpressed (15-, 11-, and 3-fold, respectively) in Temo_R. To confirm the role of each efflux pump in this mechanism, multicopy plasmids harboring mdtABCD or acrD were introduced into either Temo_S or the reference strain E. cloacae subsp. cloacae ATCC 13047. Interestingly, only the overexpression of acrD conferred a significant increase (from 8- to 16-fold) of the temocillin MIC. Altogether, we have shown that temocillin resistance in the ECC can result from a single BaeS alteration, likely resulting in the permanent phosphorylation of BaeR and leading to AcrD overexpression and temocillin resistance through enhanced active efflux.

Automatic Discrimination of Species within the Enterobacter cloacae Complex Using Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry and Supervised Algorithms

The Enterobacter cloacae complex (ECC) encompasses heterogeneous clusters of species that have been associated with nosocomial outbreaks. These species may have different acquired antimicrobial resistance and virulence mechanisms, and their identification is challenging. This study aims to develop predictive models based on matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) profiles and machine learning for species-level identification. A total of 219 ECC and 118 Klebsiella aerogenes clinical isolates from three hospitals were included. The capability of the proposed method to differentiate the most common ECC species (Enterobacter asburiae, Enterobacter kobei, Enterobacter hormaechei, Enterobacter roggenkampii, Enterobacter ludwigii, and Enterobacter bugandensis) and K. aerogenes was demonstrated by applying unsupervised hierarchical clustering with principal-component analysis (PCA) preprocessing. We observed a distinctive clustering of E. hormaechei and K. aerogenes and a clear trend for the rest of the ECC species to be differentiated over the development data set. Thus, we developed supervised, nonlinear predictive models (support vector machine with radial basis function and random forest). The external validation of these models with protein spectra from two participating hospitals yielded 100% correct species-level assignment for E. asburiae, E. kobei, and E. roggenkampii and between 91.2% and 98.0% for the remaining ECC species; with data analyzed in the three participating centers, the accuracy was close to 100%. Similar results were obtained with the Mass Spectrometric Identification (MSI) database developed recently (https://msi.happy-dev.fr) except in the case of E. hormaechei, which was more accurately identified with the random forest algorithm. In short, MALDI-TOF MS combined with machine learning was demonstrated to be a rapid and accurate method for the differentiation of ECC species.

Complete Genome Sequence of Enterobacter roggenkampii RX.G5M56, a C1-Metabolizing Strain from a Freshwater Stream in Hong Kong

The C1-metabolizing strain Enterobacter roggenkampii RX.G5M56 was isolated from a freshwater stream in Hong Kong. Its complete genome, a single chromosome of 4,772,201 bp (GC content of 56.05%), was established through hybrid assembly.

Draft genome sequence of Enterobacter chengduensis ECC445, isolated from fresh water in the West Indies

OBJECTIVES

The Enterobacter cloacae complex is considered an important opportunistic pathogen. It comprises many members that remain difficult to delineate by phenotypic approaches. Despite its importance in human infection, there is a lack of information on associated members in other compartments. Here we report the first de novo assembled and annotated whole-genome sequence of a E. chengduensis strain isolated from the environment.

DATA DESCRIPTION

ECC445 specimen was isolated in 2018 from a drinking water catchment point in Guadeloupe. It was clearly related to E. chengduensis species according to hsp60 typing and genomic comparison. Its whole-genome sequence is 5,211,280-bp long divided into 68 contigs, and presents a G + C content of 55.78%. This genome and associated datasets provided here will serve as a useful resource for further analyses of this rarely reported Enterobacter species.

Acquisition of Enterobacterales carrying the colistin resistance gene mcr following travel to the tropics

BACKGROUND

Colistin is an antibiotic of last resort in the management of highly drug-resistant Enterobacterales infections. Travel to some destinations presents a high risk of acquiring multidrug-resistant Enterobacterales, but little data are available on the risk of acquiring colistin-resistant strains. Here, we use the VOYAG-R sample collection (2012-2013) in order to evaluate the rate of acquisition of colistin-resistant Enterobacterales, excluding species with intrinsic resistance (CRE), following travel to tropical regions.

METHODS

A total of 574 frozen stool samples of travellers returning from tropical regions were screened for colistin-resistant strains using ChromID Colistin R agar (bioMerieux®) after pre-enrichment culture with 1 mg/L of colistin. Genomes were obtained by Illumina sequencing and genetic determinants of colistin resistance (mutational events and mcr genes) were searched.

RESULTS

A total of 22 travellers (3.8%) acquired colistin-resistant Enterobacterales carrying an mcr gene. Acquisition rates varied between visited regions: 9.2% (18/195) for Asia (southeast Asia: 17/18), 2.2% (4/184) for Latin America (Peru: 4/4) and 0% from Africa (0/195). Acquired strains were predominantly Escherichia coli (92%) and carried mostly the mcr-1 variant (83%). Escherichia coli strains belonged mainly to commensal phylogroups A and B1, and were genetically highly diverse (5 non-clonal sequence type (ST)10 and 17 ST singletons). Only four non mcr colistin-resistant strains (two E. coli and two Enterobacter cloacae complex) were identified. Among all the strains, two also carried extended-spectrum beta-lactamase genes.

CONCLUSIONS

Travel to tropical regions, and particularly to Southeast Asia, is a risk factor for the acquisition of mcr-carrying Enterobacterales. This study highlights the community dissemination of mcr in humans as early as 2012, 4 years prior to its first published description.

Whole Genome-Based Characterization of Multidrug Resistant Enterobacter and Klebsiella aerogenes Isolates from Lebanon

Enterobacter spp. and Klebsiella aerogenes are rod-shaped Gram-negative opportunistic pathogens. This study aimed at the molecular and genomic characterization of multidrug resistant Enterobacter spp. and K. aerogenes isolates recovered from hospitalized patients in a tertiary care hospital in Lebanon. A total of 59 Enterobacter spp. clinical isolates consisting of 41 carbapenem-resistant and 18 susceptible by Etest were included in this study. Genotypic identification through whole-genome sequencing (WGS) was performed and confirmed in silico. Resistance and plasmid profiles were studied using ResFinder4.0 and Plasmid-Finder2.1. Multilocus sequence typing (MLST) was used to determine the isolates' clonality. Using the average nucleotide identity (ANI) we identified and confirmed that 47 (80%) isolates were E. hormaechei, 11 (18%) were Klebsiella aerogenes and 1 (2%) was an E. cloacae. Carbapenem-resistance was detected among 41 isolates all showing an MIC₉₀ of ≥ 32 μg/mL for ertapenem, imipenem, and meropenem. bla_NDM-1 (58.5%), bla_ACT-16 (54%), and bla_OXA-1 (54%) were the most common detected β-lactamases, while bla_CTX-M-15 (68%) was the main detected extended-spectrum β-lactamase (ESBL) encoding gene. Chromosomal ampC, carbapenemase encoding genes, and porin modifications were among the detected carbapenem resistance determinants. The carbapenemase encoding genes were linked to three well-defined plasmid Inc groups, IncFII/IncFIB, IncX3, and IncL. MLST typing revealed the diversity within the studied isolates, with ST114 being the most common among the studied E. hormaechei.: The spread of carbapenem-resistant isolates in clinical settings in Lebanon is a serious challenge. Screening and continuous monitoring through WGS analysis could effectively limit the dissemination of drug-resistant isolates in hospitalized patients. IMPORTANCE Drug resistance is an increasing global public health threat that involves most disease-causing organisms and antimicrobial drugs. Drug-resistant organisms spread in health care settings, and resistance to multiple drugs is common. Our study demonstrated the mechanisms leading to resistance against the last resort antimicrobial agents among members of the Enterobacteriaceae family. The spread of carbapenem-resistant bacteria in clinical settings is a serious challenge. Screening and continuous monitoring could effectively limit the dissemination of drug-resistant isolates in hospitalized patients.

The transmittable through stinging microbiota differs between honeybees and wasps: a potentially greater microbial risk of the wasp sting for humans

The present research investigated whether accidental contact through stinging with honeybees, wasps, and hornets could represent a microbial hazard for humans. It has been previously suggested that such contact may transmit pathogens causing infections that could even be fatal for some susceptible individuals. Stinging simulation experiments were performed in the lab with live insects collected from the environment in Lemnos Island (north-eastern Greece), while different selective agar media targeting some clinically important bacteria (i.e., Staphylococcus aureus, Streptococcus pyogenes, Enterococcus faecalis/faecium, and Pseudomonas aeruginosa) were used as substrates for microbial recovery and identification. Results revealed none of the target pathogenic bacterial species in the honeybee samples, with bacilli, staphylococci, and micrococci dominating their surveyed microbiota. However, most of the suspect colonies isolated from wasps and hornets belonged to important hygienic indicators (i.e., enterococci, Proteus mirabilis, and coliforms), implying possible contact of these insects with fecal origin materials. To sum up, the microbiota that may be transmitted to humans through stinging appears to differ between honeybees and wasps/hornets, while the isolation from the latter samples of some other important opportunistic pathogens, such as Enterobacter spp. and Klebsiella spp., also known for multidrug resistance, could be an additional reason of concern.

Resolving colistin resistance and heteroresistance in Enterobacter species

Species within the Enterobacter cloacae complex (ECC) include globally important nosocomial pathogens. A three-year study of ECC in Germany identified Enterobacter xiangfangensis as the most common species (65.5%) detected, a result replicated by examining a global pool of 3246 isolates. Antibiotic resistance profiling revealed widespread resistance and heteroresistance to the antibiotic colistin and detected the mobile colistin resistance (mcr)-9 gene in 19.2% of all isolates. We show that resistance and heteroresistance properties depend on the chromosomal arnBCADTEF gene cassette whose products catalyze transfer of L-Ara4N to lipid A. Using comparative genomics, mutational analysis, and quantitative lipid A profiling we demonstrate that intrinsic lipid A modification levels are genospecies-dependent and governed by allelic variations in phoPQ and mgrB, that encode a two-component sensor-activator system and specific inhibitor peptide. By generating phoPQ chimeras and combining them with mgrB alleles, we show that interactions at the pH-sensing interface of the sensory histidine kinase phoQ dictate arnBCADTEF expression levels. To minimize therapeutic failures, we developed an assay that accurately detects colistin resistance levels for any ECC isolate.

Species identification, antibiotic resistance, and virulence in Enterobacter cloacae complex clinical isolates from South Korea

This study aimed to identify the species of Enterobacter cloacae complex (ECC) isolates and compare the genotype, antibiotic resistance, and virulence among them. A total of 183 ECC isolates were collected from patients in eight hospitals in South Korea. Based on partial sequences of hsp60 and phylogenetic analysis, all ECC isolates were identified as nine species and six subspecies. Enterobacter hormaechei was the predominant species (47.0%), followed by Enterobacter kobei, Enterobacter asburiae, Enterobacter ludiwigii, and Enterobacter roggenkampii. Multilocus sequence typing analysis revealed that dissemination was not limited to a few clones, but E. hormaechei subsp. xiangfangensis, E. hormaechei subsp. steigerwaltii, and E. ludwigii formed large clonal complexes. Antibiotic resistance rates were different between the ECC species. In particular, E. asburiae, E. kobei, E. roggenkampii, and E. cloacae isolates were highly resistant to colistin, whereas most E. hormaechei and E. ludwigii isolates were susceptible to colistin. Virulence was evaluated through serum bactericidal assay and the Galleria mellonella larvae infection model. Consistency in the results between the serum resistance and the G. mellonella larvae infection assay was observed. Serum bactericidal assay showed that E. hormaechei, E. kobei, and E. ludwigii were significantly more virulent than E. asburiae and E. roggenkampii. In this study, we identified the predominant ECC species in South Korea and observed the differences in antibiotic resistance and virulence between the species. Our findings suggest that correct species identification, as well as continuous monitoring is crucial in clinical settings.

Cross-Over Pathogenic Bacteria Detected in Infected Tomatoes (Solanum lycopersicum L.) and Peppers (Capsicum annuum L.) in Bulgaria

The ability of certain human pathogens to adapt to plants without losing their virulence toward people is a major concern today. Thus, the aim of the present work was the investigation of the presence of cross-over pathogenic bacteria in infected tomato and pepper plants. The objects of the study were 21 samples from seven different parts of the plants and three from tomato rhizosphere. In total, 26 strains were isolated, identified by MALDI-TOF, and phenotypically characterized. The PCR amplification of the rpoB gene was applied as an approach for the rapid detection of cross-over pathogens in plant samples. A great bacterial diversity was revealed from tomato samples as nine species were identified (Leclercia adecarboxylata, Pseudesherichia vulneris, Enterobacter cancerogenus, Enterobacter cloacae, Enterobacter bugandensis, Acinetobacter calcoaceticus, Pantoea agglomerans, Pantoea ananatis, and Pectobacterium carotovorum). Polymicrobial contaminations were observed in samples T2 (tomato flower) and T10 (tomato fruit). Five species were identified from pepper samples (P. agglomerans, L. adecarboxylata, Pseudomonas sp., Pseudomonas putida, and Enterococcus sp.). Antibiotic resistance patterns were assigned in accordance with EFSA recommendations. All isolates showed varying resistance to the tested antibiotics. The genetic basis for the phenotypic antibiotic resistance was not revealed. No genes for the virulence factors were found among the population. To our knowledge, this is the first overall investigation of tomato and pepper cross-over pathogenic bacterial populations in Bulgaria.

Genomic landscape of blaGES-5- and blaGES-24-harboring Gram-negative bacteria from hospital wastewater: emergence of class 3 integron-associated blaGES-24 genes

OBJECTIVES

This study aimed to characterize Gram negative bacteria carrying bla_GES carbapenemase genes detected in wastewater from a hospital with no history of detection of clinical isolates producing GES carbapenemases.

METHODS

Six hospital effluent samples were screened for carbapenemase-producing organisms (CPO) using CHROMagar mSuperCARBA and MacConkey agar with 1 µg/mL imipenem. Polymerase chain reaction (PCR) amplification and sequencing of carbapenemase genes, multilocus sequence typing, antimicrobial susceptibility testing, and whole-genome sequencing were performed.

RESULTS

Among 21 CPO isolates, 11 Klebsiella spp. and 5 Enterobacter kobei isolates carried bla_GES-24, and 4 E. roggenkampii and 1 Pseudomonas aeruginosa isolates carried bla_GES-5. Genomic analysis of 8 representative isolates comprising 6 bla_GES-24-positive and 2 bla_GES-5-positive revealed that class 3 integrons with complete or defective Tn402-like transposition modules were predominantly associated with two tandem copies of bla_GES-24. Furthermore, a total of 5 new class 3 integrons, In3-18 to In3-22, were identified among 5 bla_GES-24 and 1 bla_GES-5 plasmids. One strain each of K. pneumoniae subsp. pneumoniae and K. quasipneumoniae subsp. similipneumoniae harboring bla_GES-24 plasmids also carried a rare bla_VEB-1-positive class 1 integron on a non-typeable plasmid, where these bla_VEB-1 plasmids had high sequence similarity. Virulence gene profiles differed between Klebsiella spp. and Enterobacter spp.; the former harbored type III fimbriae cluster, salmochelin, and T6SS type i2 gene clusters, while the latter had curli pili operon, aerobactin, T2SS gene clusters, and T6SS type i3 gene clusters.

CONCLUSION

Our findings confirmed the linkage of bla_GES-24 with rare Tn402-like class 3 integrons and the structural diversity of their gene cassette arrays.

Emergence of a Novel Lineage and Wide Spread of a blaCTX-M-15/IncHI2/ST1 Plasmid among Nosocomial Enterobacter in Guadeloupe

Between April 2018 and August 2019, a total of 135 strains of Enterobacter cloacae complex (ECC) were randomly collected at the University Hospital Center of Guadeloupe to investigate the structure and diversity of the local bacterial population. These nosocomial isolates were initially identified genetically by the hsp60 typing method, which revealed the clinical relevance of E. xiangfangensis (n = 69). Overall, 57/94 of the third cephalosporin-resistant strains were characterized as extended-spectrum-β-lactamase (ESBL) producers, and their whole-genome was sequenced using Illumina technology to determine the clonal relatedness and diffusion of resistance genes. We found limited genetic diversity among sequence types (STs). ST114 (n = 13), ST1503 (n = 9), ST53 (n = 5) and ST113 (n = 4), which belong to three different Enterobacter species, were the most prevalent among the 57 ESBL producers. The blaCTXM-15 gene was the most prevalent ESBL determinant (56/57) and was in most cases associated with IncHI2/ST1 plasmid replicon carriage (36/57). To fully characterize this predominant blaCTXM-15/IncHI2/ST1 plasmid, four isolates from different lineages were also sequenced using Oxford Nanopore sequencing technology to generate long-reads. Hybrid sequence analyses confirmed the circulation of a well-conserved plasmid among ECC members. In addition, the novel ST1503 and its associated species (ECC taxon 4) were analyzed, in view of its high prevalence in nosocomial infections. These genetic observations confirmed the overall incidence of nosocomial ESBL Enterobacteriaceae infections acquired in this hospital during the study period, which was clearly higher in Guadeloupe (1.59/1000 hospitalization days) than in mainland France (0.52/1,000 hospitalization days). This project revealed issues and future challenges for the management and surveillance of nosocomial and multidrug-resistant Enterobacter in the Caribbean.

Exploring Cluster-Dependent Antibacterial Activities and Resistance Pathways of NOSO-502 and Colistin against Enterobacter cloacae Complex Species

The Enterobacter cloacae complex (ECC) is a group of diverse environmental and clinically relevant bacterial species associated with a variety of infections in humans. ECC have emerged as one of the leading causes of nosocomial infections worldwide. The purpose of this paper is to evaluate the activity of NOSO-502 and colistin (CST) against a panel of ECC clinical isolates, including different Hoffmann's clusters strains, and to investigate the associated resistance mechanisms. NOSO-502 is the first preclinical candidate of a novel antibiotic class, the odilorhabdins (ODLs). MIC₅₀ and MIC₉₀ of NOSO-502 against ECC are 1 μg/mL and 2 μg/mL, respectively, with a MIC range from 0.5 μg/mL to 32 μg/mL. Only strains belonging to clusters XI and XII showed decreased susceptibility to both NOSO-502 and CST while isolates from clusters I, II, IV, and IX were only resistant to CST. To understand this phenomenon, E. cloacae ATCC 13047 from cluster XI was chosen for further study. Results revealed that the two-component system ECL_01761-ECL_01762 (ortholog of CrrAB from Klebsiella pneumoniae) induces NOSO-502 hetero-resistance by expression regulation of the ECL_01758 efflux pump component (ortholog of KexD from K. pneumoniae) which could compete with AcrB to work with the multidrug efflux pump proteins AcrA and TolC. In E. cloacae ATCC 13047, CST-hetero-resistance is conferred via modification of the lipid A by addition of 4-amino-4-deoxy-l-arabinose controlled by PhoPQ. We identified that the response regulator ECL_01761 is also involved in this resistance pathway by regulating the expression of the ECL_01760 membrane transporter.

The Resistance Mechanisms and Clinical Impact of Resistance to the Third Generation Cephalosporins in Species of Enterobacter cloacae Complex in Taiwan

Enterobacter cloacae complex (ECC) is ubiquitous in the environment and is an important pathogen causing nosocomial infections. Because routine methods used in clinical laboratories cannot identify species within ECC, the clinical significance of each species within ECC is less known. We applied hsp60 gene sequencing to identify the species/clusters of ECC and detected β-lactamase genes and class 1 integrons with PCR for 184 clinical ECC isolates in Taiwan from 2013 to 2014 to investigate the clinical impact of species within ECC. The four most common clusters were E. hormaechei subsp. steigerwaltii (cluster VIII) (29.9%), E. hormaechei subsp. oharae (cluster VI) (20.1%), E. cloacae subsp. cloacae (cluster XI) (12%), and E. kobei (cluster II) (10.3%). E. hormaechei, which consisted of four clusters (clusters III, VI, VII, and VIII), is the predominant species and accounted for 57.1% of the isolates. The ceftazidime resistance rate was 27.2%, and the ceftriaxone resistance rate was 29.3%. Resistance to third generation cephalosporin was associated with a higher 30-day mortality rate. In total, 5 (2.7%), 24 (13.0%), and 1 (0.5%) isolates carried ESBL, AmpC, and carbapenemase genes, respectively. Class 1 integrons were present in 24.5% of the isolates, and most of the cassettes pertain to antibiotic resistance. Resistance to third generation cephalosporins, multidrug resistance, and class 1 integrons were significantly more in E. hormaechei (clusters III, VI, VII, and VIII) than in the other species. The 30-day mortality rate and 100-day mortality did not differ significantly between patients with E. hormaechei and those with infections with the other species. In conclusion, the distribution of third generation cephalosporin resistance, multidrug resistance, and class 1 integrons were uneven among Enterobacter species. The resistance to third generation cephalosporins possessed significant impact on patient outcome.

Functional Annotation of Hypothetical Proteins From the Enterobacter cloacae B13 Strain and Its Association With Pathogenicity

Enterobacter cloacae B13 strain is a rod-shaped gram-negative bacterium that belongs to the Enterobacteriaceae family. It can cause respiratory and urinary tract infections, and is responsible for several outbreaks in hospitals. E. cloacae has become an important pathogen and an emerging global threat because of its opportunistic and multidrug resistant ability. However, little knowledge is present about a large portion of its proteins and functions. Therefore, functional annotation of the hypothetical proteins (HPs) can provide an improved understanding of this organism and its virulence activity. The workflow in the study included several bioinformatic tools which were utilized to characterize functions, family and domains, subcellular localization, physiochemical properties, and protein-protein interactions. The E. cloacae B13 strain has overall 604 HPs, among which 78 were functionally annotated with high confidence. Several proteins were identified as enzymes, regulatory, binding, and transmembrane proteins with essential functions. Furthermore, 23 HPs were predicted to be virulent factors. These virulent proteins are linked to pathogenesis with their contribution to biofilm formation, quorum sensing, 2-component signal transduction or secretion. Better knowledge about the HPs’ characteristics and functions will provide a greater overview of the proteome. Moreover, it will help against E. cloacae in neonatal intensive care unit (NICU) outbreaks and nosocomial infections.

Colistin Susceptibility in Companion Animal-Derived Escherichia coli, Klebsiella spp., and Enterobacter spp. in Japan: Frequent Isolation of Colistin-Resistant Enterobacter cloacae Complex

Transmission of colistin-resistant Enterobacterales from companion animals to humans poses a clinical risk as colistin is a last-line antimicrobial agent for treatment of multidrug-resistant Gram-negative bacteria including Enterobacterales. In this study, we investigated the colistin susceptibility of 285 Enterobacterales (including 140 Escherichia coli, 86 Klebsiella spp., and 59 Enterobacter spp.) isolated from companion animals in Japan. We further characterized colistin-resistant isolates by multilocus sequence typing (MLST), phylogenetic analysis of hsp60 sequences, and population analysis profiling, to evaluate the potential clinical risk of companion animal-derived colistin-resistant Enterobacterales to humans in line with the One Health approach. All E. coli isolates were susceptible to colistin, and only one Klebsiella spp. isolate (1.2%, 1/86 isolates) was colistin resistant. Enterobacter spp. isolates were frequently colistin resistant (20.3%, 12/59 isolates). In colistin-resistant Enterobacter spp., all except one isolate exhibited colistin heteroresistance by population analysis profiling. These colistin-heteroresistant isolates belonged to clusters I, II, IV, VIII, and XII based on hsp60 phylogeny. MLST analysis revealed that 12 colistin-resistant Enterobacter spp. belonged to the Enterobacter cloacae complex; five Enterobacter kobei (four ST591 and one ST1577), three Enterobacter asburiae (one ST562 and two ST1578), two Enterobacter roggenkampii (ST606 and ST1576), and Enterobacter hormaechei (ST1579) and E. cloacae (ST765) (each one strain). Forty-two percent of the colistin-resistant E. cloacae complex isolates (predominantly ST562 and ST591) belonged to lineages with human clinical isolates. Four E. kobei ST591 isolates were resistant to third-generation cephalosporines, aminoglycosides, and fluroquinolones but remained susceptible to carbapenems. In conclusion, our study is the first to our knowledge to report the frequent isolation of the colistin-resistant E. cloacae complex from companion animals. Furthermore, a subset of isolates belonged to human-associated lineages with resistance to multiple classes of antibiotics. These data warrant monitoring carriage of the colistin-resistant E. cloacae complex in companion animals as part of a domestic infection control procedure in line with the One Health approach.

Phenotypic and Genotypic Characterization of Multidrug-Resistant Enterobacter hormaechei Carrying qnrS Gene Isolated from Chicken Feed in China

Multidrug resistance (MDR) in Enterobacteriaceae including resistance to quinolones is rising worldwide. The plasmid-mediated quinolone resistance (PMQR) gene qnrS is prevalent in Enterobacteriaceae. However, the qnrS gene is rarely found in Enterobacter hormaechei (E. hormaechei). Here, we reported one multidrug resistant E. hormaechei strain M1 carrying the qnrS1 and blaTEM-1 genes. This study was to analyze the characteristics of MDR E. hormaechei strain M1. The E. hormaechei strain M1 was identified as Enterobacter cloacae complex by biochemical assay and 16S rRNA sequencing. The whole genome was sequenced by the Oxford Nanopore method. Taxonomy of the E. hormaechei was based on multilocus sequence typing (MLST). The qnrS with the other antibiotic resistance genes were coexisted on IncF plasmid (pM1). Besides, the virulence factors associated with pathogenicity were also located on pM1. The qnrS1 gene was located between insertion element IS2A (upstream) and transposition element ISKra4 (downstream). The comparison result of IncF plasmids revealed that they had a common plasmid backbone. Susceptibility experiment revealed that the E. hormaechei M1 showed extensive resistance to the clinical antimicrobials. The conjugation transfer was performed by filter membrane incubation method. The competition and plasmid stability assays suggested the host bacteria carrying qnrS had an energy burden. As far as we know, this is the first report that E. hormaechei carrying qnrS was isolated from chicken feed. The chicken feed and poultry products could serve as a vehicle for these MDR bacteria, which could transfer between animals and humans through the food chain. We need to pay close attention to the epidemiology of E. hormaechei and prevent their further dissemination. IMPORTANCE Enterobacter hormaechei is an opportunistic pathogen. It can cause infections in humans and animals. Plasmid-mediated quinolone resistance (PMQR) gene qnrS can be transferred intergenus, which is leading to increase the quinolone resistance levels in Enterobacteriaceae. Chicken feed could serve as a vehicle for the MDR E. hormaechei. Therefore, antibiotic-resistance genes (ARGs) might be transferred to the intestinal flora after entering the gastrointestinal tract with the feed. Furthermore, antibiotic-resistant bacteria (ARB) were also excreted into environment with feces, posing a huge threat to public health. This requires us to monitor the ARB and antibiotic-resistant plasmids in the feed. Here, we demonstrated the characteristics of one MDR E. hormaechei isolate from chicken feed. The plasmid carrying the qnrS gene is a conjugative plasmid with transferability. The presence of plasmid carrying antibiotic-resistance genes requires the maintenance of antibiotic pressure. In addition, the E. hormaechei M1 belonged to new sequence type (ST). These data show the MDR E. hormaechei M1 is a novel strain that requires our further research.

Cluster Differences in Antibiotic Resistance, Biofilm Formation, Mobility, and Virulence of Clinical Enterobacter cloacae Complex

Due to the lack of research on the characteristics of different clusters of Enterobacter cloacae complex (ECC), this study aimed to characterize and explore the differences among species of the ECC. An analysis based on hsp60 showed that Enterobacter hormaechei was predominant in ECC. Interestingly, the antibiotic resistance rates of clusters were different, among which E. hormaechei subsp. steigerwaltii (cluster VIII) and Enterobacter cloacae IX (cluster IX) possessed high resistant rates to ciprofloxacin and levofloxacin, but cluster II (Enterobacter kobei) had low resistant rates. Cluster II exhibited a strong biofilm formation ability. Different motility and protease production ability were shown for distinct clusters. A PCR analysis showed that clusters I, III, VI, VIII, and IX carried more virulence genes, while cluster II had fewer. Clusters I, VIII, and IX with high pathogenicity were evaluated using the Galleria mellonella infection model. Thus, the characteristics of resistance, biofilm-forming ability, mobility, and virulence differed among the clusters. The strains were divided into 12 subgroups based on hsp60. The main clusters of ECC clinical strains were I, II, III, VI, VIII, and IX, among which IX, VIII, and I were predominant with high resistance and pathogenicity, and cluster II (E. kobei) was a special taxon with a strong biofilm formation ability under nutrient deficiency, but was associated with low resistance, virulence, and pathogenicity. Hence, clinical classification methods to identify ECC subgroups are an urgent requirement to guide the treatment of clinical infections.

Immunopathological Changes Post-Infection with Enterobacter cloacae in Rabbits

Nosocomial infections have serious effects on health conditions in humans and animals. The present study aimed to investigate the pathogenesis of Enterobacter cloacae post intraperitoneal inoculation in rabbits to investigate the immunological and possible pathological effects. A total of 42 rabbits were randomly divided into two equal groups (n=21). The first group was inoculated with 3×10⁸ CFU/ml of the virulent isolate of E. cloacae intraperitoneally (IP), while the second group was injected IP with phosphate buffer saline and considered a control negative group. The animals were sacrificed at different time post-infection at 48/72 h, and at day 7 post-bacterial inoculation. The results revealed a significant increase in the concentration of TNF-α, especially in the infected groups. In addition, there were different pathological lesions in different organs of animals, mainly in the infected groups, which represents by vascular congestion and edema with polymorphoneutrophiles infiltration in the lungs, kidneys, and heart. This study is considered the first trial which aimed to observe the pathological changes of E. cloacae in vital organs in rabbits.

Comparative resistome and virulome analysis of clinical NDM-1 producing carbapenem-resistant Enterobacter cloacae complex

OBJECTIVES

Enterobacter cloacae complex (ECC), are causatives of hospital-acquired infections (HAI). The antimicrobial resistance (AMR) and virulence and profiling of ECC promotes our knowledge to be further implemented for their elimination in clinical settings.

METHOD

We assembled the whole genome of four clinical Carbapenem-resistant ECC (CR-ECC) and characterized their AMR and virulence profiles using whole genome sequencing (WGS).

RESULTS

The chromosome length of scaled from minimum 3,949,952 bp (for P2) to maximum 4,976,575 bp (for P3). P1 and P2 belonged to ST182. P3 and P4 belonged to ST477 and ST134, respectively. The bla_CTX-M-15 gene was detected in P1 plamsid. P1 and P4 harbored the bla_TEM-1 and bla_OXA-1 genes. bla_NDM-1 was found in P1, P3 and P4. No bla_OXA-48, bla_KPC, bla_VIM and bla_IMP were identified. The plasmids were non-transferrable and had IncFIB, IncFII, Col and IncC incompatibility groups (Inc). Class 1 integron was deteceted in all strains. Genes related to biofilms, adhesins, siderophores (aerobactin, enterobactin and salmochelin), intrinsic antimicrobial efflux pumps, secretory systems type I to VI, environmental and antibiotic stress response regulators, outer membrane proteins (OMPs) and heavy metals (copper, tellurite, arsenic and zinc) resistance were found in the strains. The number of positive virulence factors was higher for P1 to that of other strains.

CONCLUSION

The accumulation of AMR genes in Enterobacter spp. and their high endurance in hostile environments is a serious health problem. More genomic investigations are required in to determine their AMR and virulence genetic reservoirs at the global level.

Molecular Epidemiology, Risk Factors and Clinical Outcomes of Carbapenem-Nonsusceptible Enterobacter cloacae Complex Infections in a Taiwan University Hospital

The genus Enterobacter is a member of the ESKAPE group, which contains the major resistant bacterial pathogens. Enterobacter cloacae complex (ECC) has emerged as a clinically significant cause of a wide variety of nosocomial infections. Carbapenem-nonsusceptible Enterobacter cloacae complex (CnsECC) has become an emerging threat to public health but there is still a lack of comprehensive molecular and clinical epidemiological analysis. A total of 157 CnsECC isolates were recovered during October 2011 to August 2017. hsp60 gene sequencing and pulsed-field gel electrophoresis (PFGE) were applied to discriminate the species, genetic clusters and clonal relatedness. All the isolates were subjected to polymerase chain reaction (PCR) analysis for carbapenemase, AmpC-type β-lactamase, and extended spectrum β-lactamase (ESBL) genes. Clinical data were collected on all patients for comparing clinical risks and outcomes between patients with carbapenemase-producing (CP)-CnsECC compared with non-CP-CnsECC infection. The most commonly identified species was E. hormaechei subsp. hoffmannii (47.1%), followed by E. hormaechei subsp. steigerwaltii (24.8%). Different species of CnsECC isolates showed heterogeneity in resistance patterns to piperacillin/tazobactam, cefepime and levofloxacin. In the present study, we observed that E. hormaechei subsp. hoffmannii was characterized with higher cefepime and levofloxacin resistance rate but lower piperacillin/tazobactam resistance rate relative to other species of CnsECC. CP-CnsECC comprised 41.1% (65 isolates) and all of these isolates carried IMP-8. In this study, 98% of patients had antimicrobial therapy prior to culture, with a total of 57/150 (38%) patients being exposed to carbapenems. Chronic pulmonary disease (OR: 2.51, 95% CI: 1.25–5.06), received ventilator support (OR: 5.54, 95% CI: 2.25–12.03), steroid exposure (OR: 3.88, 95% CI: 1.91–7.88) and carbapenems exposure (OR: 2.17, 95% CI: 1.10–4.25) were considered risk factors associated with CP-CnsECC infection. The results suggest that CP-CnsECC are associated with poorer outcomes including in-hospital mortality, 30-day mortality and 100-day mortality. Our study provides insights into the epidemic potential of IMP-8-producing E. cloacae for healthcare-associated infections and underscores the importance of understanding underlying resistance mechanisms of CnsECC to direct antibiotic treatment decisions.

Emergence of VIM-producing Enterobacter cloacae complex in France between 2015 and 2018

OBJECTIVES

To genetically characterize VIM-producing Enterobacter cloacae complex (ECC) isolates recovered in France from 2015 to 2018.

METHODS

WGS, species determination, MLST, clonal relationship and genetic characterization were performed on 149 VIM-producing ECC isolates.

RESULTS

Among VIM-producing Enterobacterales, the prevalence of ECC increased drastically from 6% in 2012 to 52% in 2018. The most prevalent species were Enterobacter hormaechei subsp. hoffmannii (40.9%), E. hormaechei subsp. steigerwaltii (21.5%), E. hormaechei subsp. xiangfangensis (14.8%) and ECC clade S (17.4%). Major STs were ST-873 (17.5%), ST-66 (12.1%), ST-78 (9.4%), ST-419 (8.1%), ST-145 (4.7%), ST-50 (4.0%), ST-118 (4.0%) and ST-168 (4.0%). Finally, six different integrons were identified, with some being specific to a given blaVIM variant (In916 with blaVIM-1-aacA4'-aphA15-aadA1-catB2 and In416 with blaVIM-4-aacA7-dfrA1b-aadA1b-smr2 genes).

CONCLUSIONS

This study demonstrated the genetic diversity among VIM-producing ECC isolates, indicating that their spread is not linked to a single clone.

dnaJ: a New Approach to Identify Species within the Genus Enterobacter

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.

Enterobacter cloacae Complex and CTX-M Extended-Spectrum β-Lactamases in Algeria

We evaluated the β-lactam resistance phenotypes of clinical and environmental strains of the Enterobacter cloacae complex (ECC) isolated from three Algerian hospitals. The first combination of API 20E, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), and hsp60 genetic clustering methodologies were carried out for the identification of ECC strains. Our research showed that API 20E and MALDI TOF MS are satisfactory in genus identification of ECC strains, but sequence-based methods are then necessary to discriminate the species and subspecies levels. Among 36 ECC strains, 94.44% belonged to Enterobacter hormaechei species. Twenty-five isolates clustered with the reference strain of E. hormaechei subsp. xiangfangensis, making it the most frequently isolated subspecies. Enterobacter kobei was found only once (2.77%). All ECC isolates were phenotypically extended-spectrum β-lactamase (ESBL) producers and were resistant to ticarcillin, piperacillin, cefoxitin, cefotaxime, ceftazidime, ceftriaxone, and aztreonam, but susceptible to ertapenem and imipenem. The genetic analyses only allowed the detection of resistance genes of the CTX-M-1 group (32 strains, 88.9%), including CTX-M-15 (30 strains), CTX-M-3 (1 strain), and CTX-M-22 (1 strain). We report for the first time the detection of CTX-M-22 among ECC strains in an Algerian hospital (Tlemcen hospital). None of the isolated strains harbored CTX-M-2, CTX-M-9, or CTX-M-8/25 group genes. In this review, we address recent comparison in the identification methods of multidrug-resistant E. cloacae complex in Algeria, focusing also on the CTX-M ESBLs. This represents a serious public health challenge, which requires the clarification of the current situation and warrants the reinforcement of hygiene measures in the Algerian hospitals.

Bacteriophages PɸEn-CL and PɸEn-HO can eliminate MDR Enterobacter cloacae and Enterobacter hormaechei isolated from burn wound infections without toxicity for human skin cells

The prevalence of multidrug-resistant (MDR) strains has caused serious problems in the treatment of burn infections. MDR Enterobactercloacae and Enterobacterhormaechei have been defined as the causative agents of nosocomial infections in burn patients. In this situation, examination of phages side effects on human cell lines before any investigation on human or animal that can provide beneficial information about the safety of isolated phages. The aim of this study was to isolate and identify the specific bacteriophages on MDR E. cloacae and E. hormaechei isolated from burn wounds and to analyze the efficacy, cell viability and cell cytotoxicity of phages on A-375 and HFSF-PI cell lines by MTT (3-(4, 5-dimethylthiazol-2-yl)2,5-diphenyl-tetrazolium bromide) colorimetric assay and lactate dehydrogenase (LDH) release assay. Phages were isolated from urban sewage Isfahan, Iran. Enterobactercloacae strain Iau-EC100 (GenBank accession number: MZ314381) and E. hormaechei strain Iau-EHO100 (GenBank accession number: MZ348826) were sensitive to the isolated phages. Transmission electron microscopy (TEM) results revealed that PɸEn-CL and PɸEn-HO that were described had the morphologies of Myovirus and Inovirus, respectively. Overall, MTT and LDH assays showed moderate to excellent correlation in the evaluation of cytotoxicity of isolated phages. The results of MTT and LDH assays showed that, phages PɸEn-CL and PɸEn-HO had no significant toxicity effect on A375 and HFSF-PI 3 cells. Phage PɸEn-HO had a better efficacy on the two tested cell lines than other phage. Our results indicated that, there were significant differences between the two cytotoxicity assays in phage treatment compared to control.

Structure and genetics of the O-antigen of Enterobacter cloacae K7 containing di-N-acetylpseudaminic acid

The O-antigen (O-polysaccharide) is an essential component of lipopolysaccharide on the surface of Gram-negative bacteria and plays an important role in interaction with host organisms. In this study, we investigated the chemical structure and characterized the gene cluster of Enterobacter cloacae K7 O-antigen. As judged by sugar analyses along with NMR spectroscopy data, E. cloacae K7 antigen has a tetrasaccharide O-unit with the following structure: →8)-β-Psep5Ac7Ac-(2 → 2)-β-l-Rhap-(1 → 4)-α-l-Rhap-(1 → 3)-α-d-Galp-(1→ The O-antigen gene cluster of E. cloacae K7 between conserved genes galF and gnd was sequenced. Most genes necessary for the O-antigen synthesis were found in the cluster and their functions were tentatively assigned by comparison with sequences in the available databases.

Whole Genome Sequencing Based Taxonomic Classification, and Comparative Genomic Analysis of Potentially Human Pathogenic Enterobacter spp. Isolated from Chlorinated Wastewater in the North West Province, South Africa

Comparative genomics, in particular, pan-genome analysis, provides an in-depth understanding of the genetic variability and dynamics of a bacterial species. Coupled with whole-genome-based taxonomic analysis, these approaches can help to provide comprehensive, detailed insights into a bacterial species. Here, we report whole-genome-based taxonomic classification and comparative genomic analysis of potential human pathogenic Enterobacter hormaechei subsp. hoffmannii isolated from chlorinated wastewater. Genome Blast Distance Phylogeny (GBDP), digital DNA-DNA hybridization (dDDH), and average nucleotide identity (ANI) confirmed the identity of the isolates. The algorithm PathogenFinder predicted the isolates to be human pathogens with a probability of greater than 0.78. The potential pathogenic nature of the isolates was supported by the presence of biosynthetic gene clusters (BGCs), aerobactin, and aryl polyenes (APEs), which are known to be associated with pathogenic/virulent strains. Moreover, analysis of the genome sequences of the isolates reflected the presence of an arsenal of virulence factors and antibiotic resistance genes that augment the predictions of the algorithm PathogenFinder. The study comprehensively elucidated the genomic features of pathogenic Enterobacter isolates from wastewaters, highlighting the role of wastewaters in the dissemination of pathogenic microbes, and the need for monitoring the effectiveness of the wastewater treatment process.

Draft Genome Sequence of Enterobacter oligotrophicus, Isolated from the Microbiome of a Lizard in the Caribbean

Here, we describe the genome sequence of ECC486. This Enterobacter oligotrophicus strain was isolated from a wild specimen of Anolis marmoratus speciosus, a lizard endemic to the territory of Guadeloupe (French West Indies). Its draft genome sequence consists of 40 contigs and contains a total of 4,504,233 bp, with a G+C content of 54.1%.

Presence of 2-hydroxymyristate on endotoxins is associated with death in neonates with Enterobacter cloacae complex septic shock

Enterobacter cloacae complex species are involved in infections among critically ill patients. After a recent E.cloacae outbreak of fulminant neonatal septic shock, we conducted a study to determine whether septic shock severity and its lethal consequence are related to structural features of the endotoxin (lipopolysaccharide [LPS]) of the strains isolated from hospitalized infants and more specifically its lipid A region. It appeared that the LPSs are very heterogeneous, carrying fifteen different molecular species of lipid A. The virulence was correlated with a structural feature identified by matrix-assisted laser desorption ionization–time of flight mass spectrometry and gas chromatography coupled with mass spectrometry: the presence of 2-hydroxymyristic acid as a secondary substituent in lipid A. This is the first published evidence linking LPS structural moiety to neonatal sepsis outcome and opens the possibility of using this fatty acid marker as a detection tool for high-risk patients, which could help reduce their mortality.

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Fifteen different molecular species of lipid A is found in E. cloacae complex

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2-Hydroxymyristate moiety on Lipid A is a virulence marker of the E. cloacae complex

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Presence of 2-hydroxymyristate is associated with mortality in neonatal sepsis

Revisiting Species Identification within the Enterobacter cloacae Complex by Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is commonly used by clinical microbiology laboratories to identify pathogens, despite some limitations of the technique. The Enterobacter cloacae complex (ECC) taxonomy has recently been expanded, leading to uncertain identification of some species within the ECC when commercial MALDI-TOF MS is used. This technique is especially unsuited in the case of E. hormaechei, the main species responsible for infections and one of the most prone, within the ECC, to acquire antibiotic resistance. Hence, rapid and reliable identification at the species level could improve patient management. Here, we evaluated the performance of the Bruker Microflex MALDI-TOF MS instrument to identify ECC isolates using two databases and algorithms in comparison to the hsp60 gene sequencing reference method: the Bruker database included in the MALDI Biotyper software and an extensive online database coupled to an original Mass Spectrometric Identification (MSI) algorithm. Among a panel of 94 ECC isolates tested in triplicate, the online database coupled to MSI software allowed the highest rate of identification at the species level (92%) compared to the MALDI Biotyper database (25%), especially for the species E. hormaechei (97% versus 20%). We show that by creating a database of MALDI-TOF reference spectral profiles with a high number of representatives associated with the performant MSI software, we were able to substantially improve the identification of the E. cloacae complex members, with only 8% of isolates misidentified at the species level. This online database is available through a free online MSI application (https://msi.happy-dev.fr/). IMPORTANCE Creation of a database of MALDI-TOF reference spectral profiles with a high number of representatives associated with the performant MSI software enables substantial improvement in identification of E. cloacae complex members. Moreover, this online database is available through a free online MSI application (https://msi.happy-dev.fr/).

Evidence of an epidemic spread of KPC-producing Enterobacterales in Czech hospitals

The aim of the present study is to describe the ongoing spread of the KPC-producing strains, which is evolving to an epidemic in Czech hospitals. During the period of 2018-2019, a total of 108 KPC-producing Enterobacterales were recovered from 20 hospitals. Analysis of long-read sequencing data revealed the presence of several types of blaKPC-carrying plasmids; 19 out of 25 blaKPC-carrying plasmids could be assigned to R (n = 12), N (n = 5), C (n = 1) and P6 (n = 1) incompatibility (Inc) groups. Five of the remaining blaKPC-carrying plasmids were multireplicon, while one plasmid couldn't be typed. Additionally, phylogenetic analysis confirmed the spread of blaKPC-carrying plasmids among different clones of diverse Enterobacterales species. Our findings demonstrated that the increased prevalence of KPC-producing isolates was due to plasmids spreading among different species. In some districts, the local dissemination of IncR and IncN plasmids was observed. Additionally, the ongoing evolution of blaKPC-carrying plasmids, through genetic rearrangements, favours the preservation and further dissemination of these mobile genetic elements. Therefore, the situation should be monitored, and immediate infection control should be implemented in hospitals reporting KPC-producing strains.

Identification of qnrE3 and qnrE4, New Transferable Quinolone Resistance qnrE Family Genes Originating from Enterobacter mori and Enterobacter asburiae, Respectively

The qnrE family was designated in 2017. To date, two qnrE alleles have been discovered that are carried by plasmids. Here, we identified a new quinolone resistance gene, qnrE3, in the chromosome of Enterobacter mori clinical isolate 08-091 in China. qnrE3 conferred decreased susceptibility to fluoroquinolones, similar to qnrE1 and qnrE2. To investigate the precise origin of qnrE1, qnrE2, and qnrE3, 79 qnrE-bearing strains producing 30 qnrE variants were retrieved from the NCBI database. Phylogenetic analysis illustrated two major clusters, QnrE_Emo and QnrE_Eas, produced mainly by the E. mori and E. asburiae strains, respectively. Comparison of the genetic context of qnrE alleles demonstrated that qnrE3 and qnrE_Eas2 alleles presumably were captured by ISEcp1 and mobilized from the E. mori and E. asburiae strains to the E. xiangfangensis and Escherichia coli strains, respectively. qnrE_Eas2 was proposed to be named qnrE4, since it has spread to another genus. All the qnrE alleles were harbored by the Enterobacter species, except those captured by ISEcp1 and mobilized into other species of Enterobacterales. E. mori is probably the source of qnrE1 to qnrE3 alleles, and E. asburiae is the reservoir of qnrE4.