Precise Species Identification for Enterobacter: a Genome Sequence-Based Study with Reporting of Two Novel Species, Enterobacter quasiroggenkampii sp. nov. and Enterobacter quasimori sp. nov

Clinical emergence of Providencia zhejiangensis sp. nov. and Providencia xihuensis sp. nov.: Genomic insights into antimicrobial resistance and geographical distribution

Members of the genus Providencia are typically opportunistic pathogens that can cause severe infections in immunocompromised hosts. This study identified two Providencia strains, SKLX146130 and SKLX074055, representing novel species designated as Providencia zhejiangensis sp. nov. and Providencia xihuensis sp. nov., respectively. Both strains were isolated from clinical samples, with P. zhejiangensis displaying extensive drug resistance. Our analysis revealed that P. xihuensis is predominantly from China, whereas P. zhejiangensis has a global presence. Meanwhile, our analyses resolved Providencia huashanensis as a later heterotypic synonym of Providencia xianensis. Notably, the strain SKLX146130 from P. zhejiangensis, characterized by carrying multiple acquired resistance determinants including the carbapenemase gene blaNDM-1, belongs to a zoonotic subclade. The genomic analyses of the P. zhejiangensis strain SKLX146130 and Providencia xihuensis strain SKLX074055 showed 79.76-84.55% and 79.85-95.85% average nucleotide identity (ANI), respectively, with other Providencia type strains. In silico DNA-DNA hybridization (dDDH) values ranged from 20.7 to 26.2% and 21.3-64.8%, respectively. These results, along with phenotypic characterization and phylogenetic evidence, confirm that SKLX146130 and SKLX074055 represent two distinct novel species within the genus Providencia. Consequently, we propose the names Providencia zhejiangensis sp. nov. and Providencia xihuensis sp. nov. for these species and call for monitoring these species in clinical infections.

Pan-genome analysis of the Enterobacter hormaechei complex highlights its genomic flexibility and pertinence as a multidrug resistant pathogen

BACKGROUND

Enterobacter hormaechei is of increasing concern as both an opportunistic and nosocomial pathogen, exacerbated by its evolving multidrug resistance. However, its taxonomy remains contentious, and little is known about its pathogenesis and the broader context of its resistome. In this study, a comprehensive comparative genomic analysis was undertaken to address these issues.

RESULTS

Phylogenomic analysis revealed that E. hormaechei represents a complex, comprising three predicted species, E. hormaechei, E. hoffmannii and E. xiangfangensis, with the latter putatively comprising three distinct subspecies, namely oharae, steigerwaltii and xiangfangensis. The species and subspecies all display open and distinct pan-genomes, with diversification driven by an array of mobile genetic elements including numerous plasmid replicons and prophages, integrative conjugative elements (ICE) and transposable elements. These elements have given rise to a broad, relatively conserved set of pathogenicity determinants, but also a variable set of secretion systems. The E. hormaechei complex displays a highly mutable resistome, with most taxa being multidrug resistant.

CONCLUSIONS

This study addressed key issues pertaining to the taxonomy of the E. hormaechei complex, which may contribute towards more accurate identification of strains belonging to this species complex in the clinical setting. The pathogenicity determinants identified in this study could serve as a basis for a deeper understanding of E. hormaechei complex pathogenesis and virulence. The extensive nature of multidrug resistance among E. hormaechei complex strains highlights the need for responsible antibiotic stewardship to ensure effective treatment of these emerging pathogens.

Genomic insights into the taxonomic status and bioactive gene cluster profiling of Bacillus velezensis RVMD2 isolated from desert rock varnish in Ma'an, Jordan

Extreme environments like arid and semi-arid deserts harbor unique microbial diversity, offering rich sources of specialized microbial metabolites. This study explores Bacillus velezensis RVMD2, a strain isolated from rock varnish in the Ma'an Desert, Jordan. The genome was sequenced using the Illumina NextSeq 2000 platform, resulting in a 4,212,579 bp assembly with a GC content of 45.94%. The assembled genome comprises 112 contigs and encodes 4,250 proteins, 77 tRNA genes, and 4 rRNA genes. Phylogenetic analysis of the 16S rRNA gene indicated a 99.84% similarity to previously identified B. velezensis strains. Whole-genome phylogeny using EzBiome, MiGA, and TYGS confirmed its classification as B. velezensis. Functional annotation identified genes involved in carbohydrate metabolism, including 324 carbohydrate-active enzyme (CAZyme) genes, stress response, and secondary metabolite biosynthesis. The genome also contains 50 genes associated with heavy metal resistance and plant growth promotion. Analysis using AntiSMASH identified 12 biosynthetic gene clusters involved in the production of secondary metabolites, including fengycin, surfactin, polyketides, terpenes, and bacteriocins. Notably, several clusters did not match any known sequences, suggesting the presence of potentially novel antimicrobial compounds. The genomic features of RVMD2 highlight its adaptability to extreme environments and its potential for biotechnological applications, including bioremediation and the discovery of novel bioactive metabolites.

Molecular epidemiology and β-lactam resistance mechanisms of Enterobacter cloacae complex isolates obtained from bloodstream infections, Kyoto, Japan

The Enterobacter cloacae complex (ECC) comprises multiple species that require genomic analysis for precise identification. They produce inducible AmpC β-lactamase and may carry acquired β-lactamases, which are responsible for cefotaxime and cefepime resistance. To determine the molecular epidemiology, antimicrobial resistance, and β-lactam resistance mechanisms of the ECC, we conducted whole-genome sequencing analysis, antimicrobial susceptibility testing, and mutation analysis on bloodstream ECC isolates from patients in Kyoto, Japan. In 194 ECC isolates, 13 species and six unnamed taxa were identified, with Enterobacter xiangfangensis (36%) being the most common. A total of 38% of the isolates were nonsusceptible to cefotaxime and presented relatively high nonsusceptibility rates to all antimicrobial agents tested. Among the different species, Enterobacter hoffmannii presented the highest nonsusceptibility rates to both β-lactams and non-β-lactams. Among the cefotaxime-nonsusceptible isolates, 16% harbored genes encoding extended-spectrum β-lactamases (ESBLs), carbapenemase, and/or plasmid-mediated AmpC, and ampC derepression was the predominant resistance mechanism in the remaining isolates. The prevalent sequence types (STs) in cefotaxime-susceptible and cefotaxime-nonsusceptible isolates were different, although some STs were shared by both groups. Cefepime nonsusceptibility was detected in 7% of the isolates and was associated with E. hoffmannii ST78 and E. xiangfangensis ST93, which carry ESBLs. Sixty-four mutants, experimentally obtained from eight cefotaxime-susceptible isolates, had various ampD mutations, and 42% and 99% of the mutants were nonsusceptible to cefepime and piperacillin/tazobactam, respectively, indicating the risks associated with the use of these antimicrobials. Continuous surveillance via genomic and phenotypic analyses is needed to combat antimicrobial resistance in the ECC.IMPORTANCEThe Enterobacter cloacae complex (ECC) is a group of pathogenic bacteria that cause nosocomial infections. The ECC produces chromosomal inducible AmpC β-lactamases, which is associated with treatment failure despite initial susceptibility to third-generation cephalosporins in selected ampC-derepressed mutants. The complex antimicrobial resistance mechanisms of the ECC and challenges in species identification have complicated our understanding of the ECC and the selection of appropriate treatment. In this study, we performed phenotypic, whole-genome sequencing, and mutation analyses among ECC isolates from patients with bloodstream infections to determine the precise molecular-based epidemiology, resistance mechanisms to third-/fourth-generation cephalosporins, specific species and clones that contribute to antimicrobial resistance, and acquisition rates of fourth-generation cephalosporin resistance in ampC-derepressed mutants. These data will help elucidate the local epidemiology and complex β-lactam resistance mechanisms in the ECC and guide appropriate antimicrobial therapy and infection control strategies for ECC-related infections.

First Report of mcr-10 in a Seafood-Borne ESBL-Producing Enterobacter xiangfangensis Strain

mcr-10 is among the growing families of newly identified plasmid-mediated mobile colistin-resistance genes. In this study, we identified an mcr-10 gene in a seafood-borne extended-spectrum β-lactamase (ESBL)-producing Enterobacter xiangfangensis. E. xiangfangensis strain, B12-S77, was subjected to whole genome sequencing using Illumina MiSeq and Oxford Nanopore Technologies. Bioinformatic analysis was performed using tools from the Center for Genomic Epidemiology. The minimum inhibitory concentration (MIC) of 19 antibiotics was determined by the broth microdilution method. Transferability of mcr-10-carrying plasmid was investigated by the conjugation experiment. The strain exhibited a multidrug-resistant (MDR) phenotype against more than three classes of antibiotics but remained susceptible to colistin and polymyxin B. mcr-10 was identified on a fused conjugative plasmid of the IncFIB (K):FII (Yp) backbone adjacent to the XerC-type tyrosine recombinase-gene. At least one insertion sequence (IS) was identified in both the downstream and upstream regions of the xerC-mcr-10 conserved region, indicating that this region may contribute to mcr-10 mobilization or integration into the bacterial genome. The strain belonged to sequence type (ST) 143 and carried the nlpI and mrkA virulence genes, which promote fimbrial adhesion or biofilm formation in enteric bacteria. This report provides novel insights into the emergence of mcr-10 in seafood-borne bacteria, and highlights the importance of surveillance in the seafood supply chain.

Emergence of concurrently transmissible mcr-9 and carbapenemase genes in bloodborne colistin-resistant Enterobacter cloacae complex isolated from ICU patients in Kolkata, India

Colistin resistance in carbapenem-resistant Enterobacter cloacae complex (CR-ECC) infections has grown expeditiously but detecting the underlying mechanism of resistance is often challenging in clinical settings. This study, first of its kind from India, determined the resistance mechanisms and characterized colistin-resistant hospital isolates. Twenty-nine bloodborne CR-ECC isolated from ICU patients of eight tertiary care hospitals in Kolkata, India between 2022 and 2023 were screened for colistin resistance. The plasmid-encoded mcr-9 gene, acrAB-tolC efflux pump (EP) & phoP/Q, and pmr A/B two-component system (TCS) involved in colistin resistance were examined. In addition, AMR gene profiling and molecular subtypes of mcr-9-producing CR-ECC isolates were also investigated. All study isolates showed resistance to ≥5 antimicrobial classes and six (21%) of them were colistin-resistant. The mcr-9 gene transferable by IncHI2-HI2A plasmid was detected in both colistin-resistant (67%) and colistin-sensitive (4%) CR-ECC isolates. The blaNDM-5 gene was significantly (P < 0.05) associated with isolates co-harboring mcr-9 genes. A ≥8-fold increase in minimum inhibitory concentration (MIC)colistin was observed in the mcr-9-producing colistin-sensitive strain after induction. Overexpression of acrA, ramA, soxS, phoP/Q, and pmrA/B genes was found in non-mcr-9-producing colistin-resistant isolates. The resistance to colistin in the wild-type appeared to be mediated in part by the mcr-9 gene, an active EP, and regulatory TCS. The mcr-9-producing isolates were typed into ST932, ST270, and ST1997 by MLST. Heterogeneity (29 pulsotypes; 48.40% similarity coefficient) among the circulating CR-ECC isolates was revealed by PFGE. Robust monitoring of mcr genes in both colistin-resistant and -sensitive strains is warranted to curb the menace of AMR in nosocomial pathogens.

IMPORTANCE

Carbapenem-resistant Enterobacter cloacae complex (CR-ECC) has become a global nosocomial pathogen in last few years. Colistin, the "last resort antibiotic," is being widely used in the treatment of CR-ECC and, consequently, there has been a brisk rise in colistin-resistant CR-ECC isolates. This study was necessitated by the dearth of a comprehensive molecular investigation of colistin-resistant CR-ECC from India. The notorious IncHI2-HI2A plasmid-borne mcr-9 gene along with active acrAB-tolC efflux pump and phoP/Q-pmr A/B two-component system was found to mediate colistin resistance in the study isolates. Interestingly, the mcr-9 gene was also discovered in colistin-sensitive strains and MIC of colistin was found to increase under colistin pressure. Diverse phylogenetic clones along with novel sequence types were detected. This study highlights the necessity for intense monitoring of mcr-9 in conjunction with the existing epidemic clones of CR-ECC strains harboring diverse arrays of transmissible AMR genes.

ESKAPE in China: epidemiology and characteristics of antibiotic resistance

The escalation of antibiotic resistance and the diminishing antimicrobial pipeline have emerged as significant threats to public health. The ESKAPE pathogens - Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp. - were initially identified as critical multidrug-resistant bacteria, demanding urgently effective therapies. Despite the introduction of various new antibiotics and antibiotic adjuvants, such as innovative β-lactamase inhibitors, these organisms continue to pose substantial therapeutic challenges. People's Republic of China, as a country facing a severe bacterial resistance situation, has undergone a series of changes and findings in recent years in terms of the prevalence, transmission characteristics and resistance mechanisms of antibiotic resistant bacteria. The increasing levels of population mobility have not only shaped the unique characteristics of antibiotic resistance prevalence and transmission within People's Republic of China but have also indirectly reflected global patterns of antibiotic-resistant dissemination. What's more, as a vast nation, People's Republic of China exhibits significant variations in the levels of antibiotic resistance and the prevalence characteristics of antibiotic resistant bacteria across different provinces and regions. In this review, we examine the current epidemiology and characteristics of this important group of bacterial pathogens, delving into relevant mechanisms of resistance to recently introduced antibiotics that impact their clinical utility in China.

Molecular detection of Enterobacter hormaechei in bovine respiratory disease

Bovine respiratory disease (BRD) develops from complex interactions among environmental, host and pathogenic factors. This study aimed to phenotypically identify Enterobacter hormaechei isolated from cattle with BRD and assess antimicrobial susceptibility and determining the molecular phylogeny of local E. hormaechei strains. Between November 2023 and March 2024, nasal swabs were collected from 93 cattle with BRD, before culturing for phenotypic analysis, and performing the polymerase chain reaction (PCR) for molecular characterisation. Of the 93 samples evaluated, 15.79% and 24.56% tested positive for E. hormaechei isolates on culture and PCR, respectively. The local isolates exhibited high resistance to amoxicillin, ampicillin, amikacin, nalidixic acid and ceftazidime; high susceptibility to azithromycin, levofloxacin, gentamicin, ofloxacin, cefepime, ceftriaxone, cefotaxime, nitrofurantoin, ceftazidime and ciprofloxacin; and moderate susceptibility to ciprofloxacin, colistin, imipenem and meropenem. Multiple sequence alignment, phylogenetic tree analysis and homology sequence identification, showed that the five positive isolates were similar to the reference isolate. To the best of our knowledge, this is the first time that E. hormaechei has been isolated in cattle with BRD in Iraq. Because phenotype-based assays show limited accuracy to identify species, we recommend molecular and phylogenetic analysis be included in all similar studies in the future.

Comparative genomic characterization of Cellulosimicrobium funkei isolate RVMD1 from Ma'an desert rock varnish challenges Cellulosimicrobium systematics

Desert environments harbor unique microbial communities. This study focuses on Cellulosimicrobium funkei isolate RVMD1, isolated from rock varnish in the Ma'an Desert. Initial identification was achieved using 16S rRNA gene sequencing, followed by whole-genome sequencing (WGS) for comprehensive characterization. The genome comprises 4,264,015 base pairs (857 contigs) with a high G + C content of 74.59%. A total of 4,449 proteins were predicted. Comparative analysis utilizing OrthoANI, ANI, AAI, and dDDH metrics suggests that RVMD1 belongs to the C. cellulans group, with the highest similarity to C. funkei (97.71% ANI). Phylogenomic analysis of 43 Cellulosimicrobium genomes revealed significant heterogeneity within the genus. Our results challenge current systematics, with C. cellulans potentially representing up to 9 distinct genomospecies. Isolate RVMD1 shows genetic adaptations to its desert environment, including genes for denitrification, oxygen and sulfur cycling, and diverse hydrogen metabolism. Pangenomic analysis uncovered a considerable number of unique genes within RVMD1, highlighting its genetic distinctiveness. Gene family expansions suggest evolution in response to stressors like UV radiation and nutrient limitation. This study represents the first whole-genome analysis of a bacterium isolated from Jordanian rock varnish, emphasizing the value of WGS in understanding microbial diversity and adaptation in extreme environments.

Novel multifunctional plant growth-promoting bacteria isolated from the oil palm rhizosphere under long-term organic matter application

Most agricultural products are presently cultivated on marginal lands with poor soil properties and unfavorable environmental conditions (diseases and abiotic stresses), which can threaten plant growth and yield. Plant growth-promoting bacteria (PGPB) are beneficial bacteria that promote plant growth and biomass and act as biocontrols against diseases and stress. However, most isolated PGPBs have a single function and low survival rates owing to their limited growth behaviors. In this study, we isolated multifunctional PGPB from oil palm rhizosphere, quantitatively measured their activities, and evaluated their effectiveness in Brassica rapa (Komatsuna) cultivation. This is the first study to report the isolation of three multifunctional PGPB strains with ammonium production, phosphate-potassium-silicate solubilization, and indole-3-acetic acid (IAA) production from the oil palm rhizosphere, namely Kosakonia oryzendophytica AJLB38, Enterobacter quasimori AJTS77, and Lelliottia jeotgali AJTS83. Additionally, these strains showed antifungal activity against the oil palm pathogen Ganoderma boninense. These strains grow under high temperature, acidic and alkaline pH, and high salt concentration, which would result in their proliferation in various environmental conditions. The cultivation experiments revealed these strains improved the growth and biomass with half the dosage of chemical fertilizer application, which was not significantly different to the full dosage. Furthermore, the overall plant growth-promoting activities in quantitative assays and overall B. rapa growth in cultivation experiments were statistically correlated, which could contribute to the prediction of plant growth promotion without plant cultivation experiments. Thus, the selected PGPB could be valuable as a biofertilizer to improve soil health and quality and promote agricultural sustainability.

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.

VIM-1-producing Enterobacter asburiae with mobile colistin resistance genes from wastewaters

BACKGROUND

Wastewaters are considered as important players in the spread of antimicrobial resistance, thus affecting the health of humans and animals. Here, we focused on wastewaters as a possible source of carbapenemase-producing Enterobacterales for the environment.

METHODS

A total of 180 presumptive coliforms from hospital and municipal wastewaters, and a river in the Czech Republic were obtained by selective cultivation on meropenem-supplemented media and tested for presence of carbapenemase-encoding genes by PCR. Strains carrying genes of interest were characterized by testing antimicrobial susceptibility, carbapenemase production and combination of short- and long- read whole-genome sequencing. The phylogenetic tree including publicly available genomes of Enterobacter asburiae was conducted using Prokka, Roary and RAxML.

RESULTS

Three VIM-producing Enterobacter asburiae isolates, members of the Enterobacter cloacae complex, were detected from hospital and municipal wastewaters, and the river. The blaVIM-1 gene was located within a class 1 integron that was carried by different F-type plasmids and one non-typeable plasmid. Furthermore, one of the isolates carried plasmid-borne colistin-resistance gene mcr-10, while in another isolate chromosomally located mcr-9 without colistin resistance phenotype was detected. In addition, the analysis of 685 publicly available E. asburiae genomes showed they frequently carry carbapenemase genes, highlighting the importance of this species in the emergence of resistance to last-line antibiotics.

CONCLUSION

Our findings pointed out the important contribution of hospital and community wastewaters in transmission of multi-drug resistant pathogens.

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.

Some virulence genes are associated with antibiotic susceptibility in Enterobacter cloacae complex

BACKGROUND

Enterobacter cloacae complex (ECC) including different species are isolated from different human clinical samples. ECC is armed by many different virulence genes (VGs) and they were also classified among ESKAPE group by WHO recently. The present study was designed to find probable association between VGs and antibiotic susceptibility in different ECC species.

METHODS

Forty-five Enterobacter isolates that were harvested from different clinical samples were classified in four different species. Seven VGs were screened by PCR technique and antibiotic susceptibility assessment was performed by disk-diffusion assay.

RESULT

Four Enterobacter species; Enterobacter cloacae (33.3%), Enterobacter hormaechei (55.6%), Enterobacter kobei (6.7%) and Enterobacter roggenkampii (4.4%) were detected. Minimum antibiotic resistance was against carbapenem agents and amikacin even in MDR isolates. 33.3% and 13.3% of isolates were MDR and XDR respectively. The rpoS (97.8%) and csgD (11.1%) showed maximum and minimum frequency respectively. Blood sample isolated were highly virulent but less resistant in comparison to the other sample isolates. The csgA, csgD and iutA genes were associated with cefepime sensitivity.

CONCLUSION

The fepA showed a predictory role for differentiating of E. hormaechei from other species. More evolved iron acquisition system in E. hormaechei was hypothesized. The fepA gene introduced as a suitable target for designing novel anti-virulence/antibiotic agents against E. hormaechei. Complementary studies on other VGs and ARGs and with bigger study population is recommended.

Presence and Role of the Type 3 Fimbria in the Adherence Capacity of Enterobacter hormaechei subsp. hoffmannii

Enterobacter hormaechei, one of the species within the Enterobacter cloacae complex, is a relevant agent of healthcare-associated infections. In addition, it has gained relevance because isolates have shown the capacity to resist several antibiotics, particularly carbapenems. However, knowledge regarding colonization and virulence mechanisms of E. hormaechei has not progressed to the same extent as other Enterobacteriaceae species as Escherichia coli or Klebsiella pneumoniae. Here, we describe the presence and role of the type 3 fimbria, a chaperone-usher assembled fimbria, which was first described in Klebsiella spp., and which has been detected in other representatives of the Enterobacteriaceae family. Eight Chilean E. cloacae isolates were examined, and among them, four E. hormaechei isolates were found to produce the type 3 fimbria. These isolates were identified as E. hormaechei subsp. hoffmannii, one of the five subspecies known. A mutant E. hormaechei subsp. hoffmannii strain lacking the mrkA gene, encoding the major structural subunit, displayed a significantly reduced adherence capacity to a plastic surface and to Caco-2 cells, compared to the wild-type strain. This phenotype of reduced adherence capacity was not observed in the mutant strains complemented with the mrkA gene under the control of an inducible promoter. Therefore, these data suggest a role of the type 3 fimbria in the adherence capacity of E. hormaechei subsp. hoffmannii. A screening in E. hormaechei genomes contained in the NCBI RefSeq Assembly database indicated that the overall presence of the type 3 fimbria is uncommon (5.94-7.37%), although genes encoding the structure were detected in representatives of the five E. hormaechei subspecies. Exploration of complete genomes indicates that, in most of the cases, the mrkABCDF locus, encoding the type 3 fimbria, is located in plasmids. Furthermore, sequence types currently found in healthcare-associated infections were found to harbor genes encoding the type 3 fimbria, mainly ST145, ST78, ST118, ST168, ST66, ST93, and ST171. Thus, although the type 3 fimbria is not widespread among the species, it might be a determinant of fitness for a subset of E. hormaechei representatives.

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.

Whole genome sequence-based molecular characterization of blood isolates of carbapenem-resistant Enterobacter cloacae complex from ICU patients in Kolkata, India, during 2017-2022: emergence of phylogenetically heterogeneous Enterobacter hormaechei subsp. xiangfangensis

Blood-borne infections caused by the carbapenem-resistant Enterobacter cloacae complex (CR-ECC) are major public threats with respect to the challenges encountered during treatment. This study describes the whole genome sequencing-based molecular characteristics of blood isolates (n = 70) of CR-ECC from patients admitted to the intensive care unit of tertiary care hospitals in Kolkata, India, during 2017-2022 with respect to species identification, antimicrobial resistance (AMR) profiling, mechanism of drug resistance, and molecular subtypes. Vitek2 MALDI and species-specific PCR identified Enterobacter hormaechei subsp. xiangfangensis (47.14%) as the emerging CR-ECC subspecies in Kolkata. The predominating carbapenemase and extended-spectrum β-lactamase genes found were blaNDM-1 (51.42%) and blaCTX-M-15 (27%), respectively. Besides, blaNDM-4, blaNDM-5, blaNDM-7, blaCMH-3, blaSFO-1, blaOXA-181, blaOXA-232, blaKPC-3, and blaDHA-7 genes were also detected, which were not previously reported from India. A multitude of Class 1 integrons (including In180, In4874, In4887, and In4888, which were novel) and plasmid replicon types (IncFIB, IncFII, IncX3, IncHI1-HI2, IncC, and IncR) involved in AMR dissemination were identified. Reverse transcription-PCR and western blot revealed that carbapenem resistance in non-carbapenemase-producing CR-ECC isolates was contributed by elevated levels of ampC, overexpression of acrAB, and loss of ompF. A total of 30 distinct sequence types (STs) were ascertained by multi-locus sequence typing; of which, ST2011, ST2018, ST2055, ST2721, and ST2722 were novel STs. Pulsed-field gel electrophoresis analysis showed heterogeneity (69 pulsotypes with a similarity coefficient of 48.40%) among the circulating isolates, suggesting multiple reservoirs of infections in humans. Phylogenetically and genetically diverse CR-ECC with multiple AMR mechanisms mandates close monitoring of nosocomial infections caused by these isolates to forestall the transmission and dissemination of AMR.IMPORTANCEThe emergence and extensive dissemination of the carbapenem-resistant Enterobacter cloacae complex (CR-ECC) have positioned it as a critical nosocomial global pathogen. The dearth of a comprehensive molecular study pertaining to CR-ECC necessitated this study, which is the first of its kind from India. Characterization of blood isolates of CR-ECC over the last 6 years revealed Enterobacter hormaechei subsp. xiangfangensis as the most prevalent subsp., exhibiting resistance to almost all antibiotics currently in use and harboring diverse transmissible carbapenemase genes. Besides the predominating blaNDM-1 and blaCTX-M-15, we document diverse carbapenemase and AmpC genes, such as blaNDM-4, blaNDM-7, blaOXA-181, blaOXA-232, blaKPC-3, blaCMH-3, blaSFO-1, and blaDHA-7, in CR-ECC, which were not previously reported from India. Furthermore, novel integrons and sequence types were identified. Our findings emphasize the need for strengthened vigilance for molecular epidemiological surveillance of CR-ECC due to the presence of epidemic clones with a phylogenetically diverse and wide array of antimicrobial resistance genes in vulnerable populations.

Genomic revisitation and reclassification of the genus Providencia

Members of Providencia, although typically opportunistic, can cause severe infections in immunocompromised hosts. Recent advances in genome sequencing provide an opportunity for more precise study of this genus. In this study, we first identified and characterized a novel species named Providencia zhijiangensis sp. nov. It has ≤88.23% average nucleotide identity (ANI) and ≤31.8% in silico DNA-DNA hybridization (dDDH) values with all known Providencia species, which fall significantly below the species-defining thresholds. Interestingly, we found that Providencia stuartii and Providencia thailandensis actually fall under the same species, evidenced by an ANI of 98.59% and a dDDH value of 90.4%. By fusing ANI with phylogeny, we have reclassified 545 genomes within this genus into 20 species, including seven unnamed taxa (provisionally titled Taxon 1-7), which can be further subdivided into 23 lineages. Pangenomic analysis identified 1,550 genus-core genes in Providencia, with coenzymes being the predominant category at 10.56%, suggesting significant intermediate metabolism activity. Resistance analysis revealed that most lineages of the genus (82.61%, 19/23) carry a high number of antibiotic-resistance genes (ARGs) and display diverse resistance profiles. Notably, the majority of ARGs are located on plasmids, underscoring the significant role of plasmids in the resistance evolution within this genus. Three species or lineages (P. stuartii, Taxon 3, and Providencia hangzhouensis L12) that possess the highest number of carbapenem-resistance genes suggest their potential influence on clinical treatment. These findings underscore the need for continued surveillance and study of this genus, particularly due to their role in harboring antibiotic-resistance genes.

IMPORTANCE

The Providencia genus, known to harbor opportunistic pathogens, has been a subject of interest due to its potential to cause severe infections, particularly in vulnerable individuals. Our research offers groundbreaking insights into this genus, unveiling a novel species, Providencia zhijiangensis sp. nov., and highlighting the need for a re-evaluation of existing classifications. Our comprehensive genomic assessment offers a detailed classification of 545 genomes into distinct species and lineages, revealing the rich biodiversity and intricate species diversity within the genus. The substantial presence of antibiotic-resistance genes in the Providencia genus underscores potential challenges for public health and clinical treatments. Our study highlights the pressing need for increased surveillance and research, enriching our understanding of antibiotic resistance in this realm.

Conserved patterns of sequence diversification provide insight into the evolution of two-component systems in Enterobacteriaceae

Two-component regulatory systems (TCSs) are a major mechanism used by bacteria to sense and respond to their environments. Many of the same TCSs are used by biologically diverse organisms with different regulatory needs, suggesting that the functions of TCS must evolve. To explore this topic, we analysed the amino acid sequence divergence patterns of a large set of broadly conserved TCS across different branches of Enterobacteriaceae, a family of Gram-negative bacteria that includes biomedically important genera such as Salmonella, Escherichia, Klebsiella and others. Our analysis revealed trends in how TCS sequences change across different proteins or functional domains of the TCS, and across different lineages. Based on these trends, we identified individual TCS that exhibit atypical evolutionary patterns. We observed that the relative extent to which the sequence of a given TCS varies across different lineages is generally well conserved, unveiling a hierarchy of TCS sequence conservation with EnvZ/OmpR as the most conserved TCS. We provide evidence that, for the most divergent of the TCS analysed, PmrA/PmrB, different alleles were horizontally acquired by different branches of this family, and that different PmrA/PmrB sequence variants have highly divergent signal-sensing domains. Collectively, this study sheds light on how TCS evolve, and serves as a compendium for how the sequences of the TCS in this family have diverged over the course of evolution.

Genome sequence-based identification of Enterobacter strains and description of Enterobacter pasteurii sp. nov

IMPORTANCE

Accurate taxonomy is essential for microbial biological resource centers, since the microbial resources are often used to support new discoveries and subsequent research. Here, we used genome sequence data, alongside matrix-assisted laser desorption/ionization time-of-flight mass spectrometer biotyper-based protein profiling, to accurately identify six Enterobacter cloacae complex strains. This approach effectively identified distinct species within the E. cloacae complex, including Enterobacter asburiae, "Enterobacter xiangfangensis," and Enterobacter quasihormaechei. Moreover, the study revealed the existence of a novel species within the Enterobacter genus, for which we proposed the name Enterobacter pasteurii sp. nov. In summary, this study demonstrates the significance of adopting a genome sequence-driven taxonomy approach for the precise identification of bacterial strains in a biological resource center and expands our understanding of the E. cloacae complex.

Strategies to Overcome Antimicrobial Resistance in Nosocomial Infections, A Review and Update

Nosocomial infections, also known as healthcare-associated infections, are a significant global concern due to their strong association with high mortality and morbidity in both developed and developing countries. These infections are caused by a variety of pathogens, particularly the ESKAPE group of bacteria, which includes the six pathogens Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp. These bacteria have demonstrated noteworthy resistance to different antibiotics. Antimicrobial resistance mechanisms can manifest in various forms, including restricting drug uptake, modifying drug targets, inactivating drugs, active drug efflux, and biofilm formation. Accordingly, various strategies have been developed to combat antibiotic-resistant bacteria. These strategies encompass the development of new antibiotics, the utilization of bacteriophages that specifically target these bacteria, antimicrobial combination therapy and the use of peptides or enzymes that target the genomes or essential proteins of resistant bacteria. Among promising approaches to overcome antibiotic resistance, the CRISPR/Cas system stands out and offers many advantages. This system enables precise and efficient editing of genetic material at specific locations in the genome. Functioning as a bacterial "adaptive immune system," the CRISPR/Cas system recognizes, degrades, and remembers foreign DNA sequences through the use of spacer DNA segments that are transcribed into CRISPR RNAs (crRNA). This paper has focused on nosocomial infections, specifically the pathogens involved in hospital infections, the mechanisms underlying bacterial resistance, and the strategies currently employed to address this issue. Special emphasis has been placed on the application of CRISPR/Cas technology for overcoming antimicrobial resistance.

Next-Generation Sequencing-Based Identification of Enterobacter hormaechei as Causative Agent of High Mortality Disease in NOD.Cg-PrkdcscidIl2rgtm1Wjl/SzJ (NSG) Mice

NOD.Cg-PrkdcscidIl2rgtm1Wjl/SzJ (NSG) mice, lacking many components of a mature immune system, are at increased risk of disease. General understanding of potential pathogens of these mice is limited. We describe a high mortality disease outbreak caused by an opportunistic bacterial infection in NSG mice. Affected animals exhibited perianal fecal staining, dehydration, and wasting. Histopathologic lesions included a primary necrotizing enterocolitis, with inflammatory and necrotizing lesions also occurring in the liver, kidneys, heart, and brain of some mice. All affected individuals tested negative for known opportunistic pathogens of immunodeficient mice. We initially identified a member of Enterobacter cloacae complex (ECC) in association with the outbreak by traditional diagnostics. ECC was cultured from extraintestinal organs, both with and without histopathologic lesions, suggesting bacteremia. Infrared spectroscopy and MALDI-TOF mass spectrometry demonstrated that isolates from the outbreak shared molecular features and likely a common origin. We subsequently hypothesized that advanced sequencing methods would identify a single species of ECC associated with clinical disease. Using a novel targeted amplicon-based next-generation sequencing assay, we identified Enterobacter hormaechei in association with this outbreak. Knowledge of this organism as a potential opportunistic pathogen in NSG mice is critical for preclinical studies to prevent loss of animals and confounding of research.

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.

Distribution and diversity of type VI secretion system clusters in Enterobacter bugandensis and Enterobacter cloacae

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. Enterobacter 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 Enterobacter species, E. cloacae and E. bugandensis. T6SS clusters are grouped into four types (T6SSi-T6SSiv), 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 T6SSi 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 E. bugandensis clinical isolate for comprehensive in silico 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 Enterobacter T6SSs and reveal new putative effectors that may be important for the interaction of these species with neighbouring cells and their environment.

Application of Next-Generation Sequencing to Enterobacter Hormaechei Subspecies Analysis during a Neonatal Intensive Care Unit Outbreak

INTRODUCTION

The Enterobacter cloacae complex (ECC) species are potential neonatal pathogens, and ECC strains are among the most commonly encountered Enterobacter spp. associated with nosocomial bloodstream infections. Outbreaks caused by ECC can lead to significant morbidity and mortality in susceptible neonates. At the molecular level, ECC exhibits genomic heterogeneity, with six closely related species and subspecies. Genetic variability poses a challenge in accurately identifying outbreaks by determining the clonality of ECC isolates. This difficulty is further compounded by the limitations of the commonly used molecular typing methods, such as pulsed field gel electrophoresis, which do not provide reliable accuracy in distinguishing between ECC strains and can lead to incorrect conclusions. Next-generation sequencing (NGS) offers superior resolution in determining strain relatedness. Therefore, we investigated the clinical pertinence of incorporating NGS into existing bundle measures to enhance patient management during an outbreak of ECC in a level-3 neonatal intensive care unit (NICU) in Germany.

METHODS

As the standard of care, all neonates on the NICU received weekly microbiological swabs (nasopharyngeal and rectal) and analysis of endotracheal secretion, where feasible. During the 2.5-month outbreak, colonisation with ECC was detected in n = 10 neonates. The phylogenetic relationship and potential antimicrobial resistance genes as well as mobile genetic elements were identified via bacterial whole-genome sequencing (WGS) using Illumina MiSeq followed by in silico data analysis.

RESULTS

Although all ECC isolates exhibited almost identical antimicrobial susceptibility patterns, the WGS data revealed the involvement of four different ECC clones. The isolates could be characterised as Enterobacter hormaechei subspecies steigerwaltii (n = 6, clonal), subsp. hoffmannii (n = 3, two clones) and subsp. oharae (n = 1). Despite the collection of environmental samples, no source of this diffuse outbreak could be identified. A new standardised operating procedure was implemented to enhance the management of neonates colonised with MRGN. This collaborative approach involved both parents and medical professionals and successfully prevented further transmission of ECC.

CONCLUSIONS

Initially, it was believed that the NICU outbreak was caused by a single ECC clone due to the similarity in antibiotic resistance. However, our findings show that antibiotic susceptibility patterns can be misleading in investigating outbreaks of multi-drug-resistant ECC. In contrast, bacterial WGS accurately identified ECC at the clonal level, which significantly helped to delineate the nature of the observed outbreak.

Whole-genome sequencing provides insights into a novel species: Providencia hangzhouensis associated with urinary tract infections

Providencia rettgeri is a clinically significant opportunistic pathogen that is involved in urinary tract infections. Due to the resolution limitations of identification, distinguishing P. rettgeri from closely related species is challenging by commercial biochemical test systems. Here, we first reported a novel species, Providencia hangzhouensis, which had been misidentified as P. rettgeri. Exhibiting ≤91.97% average nucleotide identity (ANI) and ≤46.10% in silico DNA-DNA hybridization values with all known Providencia species, P. hangzhouensis falls well beneath the established species-defining thresholds. We conducted a population genomics analysis of P. hangzhouensis isolates worldwide. Our study revealed that P. hangzhouensis has emerged in many countries and has formed several transmission clusters. We found that P. hangzhouensis shared the highest ANI values (91.54% and 91.97%) with P. rettgeri and P. huaxiensis, respectively. The pan-genome analysis revealed that these three species possessed a similar component of pan-genomes. Two genes associated with metabolism, folE2 and ccmM, were identified to be specific to P. hangzhouensis. Furthermore, we also observed that carbapenem-resistance genes frequently occur in P. hangzhouensis with the blaIMP-27 being the most prevalent (46.15%; 36/78). The emergence of P. hangzhouensis is often accompanied by extended-spectrum β-lactamase and carbapenem-resistance genes, and calls for tailored surveillance of this species as a clinically relevant species in the future. IMPORTANCE Our study has identified and characterized a novel species, Providencia hangzhouensis, which is associated with urinary tract infections and was previously misidentified as Providencia rettgeri. Through this study, we have identified specific genes unique to P. hangzhouensis, which could serve as marker genes for rapid PCR identification. Additionally, our findings suggest that the emergence of P. hangzhouensis is often accompanied by extended-spectrum β-lactamase and carbapenem-resistance genes, emphasizing the need for attention to clinical management and the importance of accurate species identification and proper drug use.

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.

Enterobacter pseudoroggenkampii sp. nov. carrying quinolone-resistant gene qnrE recovered from clinical samples in China

Two Enterobacter strains 155092^T and 170,225 were isolated from clinical samples, pus and sputum, from two hospitalised patients separately, in China. Preliminary identification using Vitek II microbiology system assigned the strains to the Enterobacter cloacae complex. The two strains were subjected to genome sequencing and genome-based taxonomy analysis with type strains of all Enterobacter species and those within closely related genera Huaxiibacter, Leclercia, Lelliottia, and Pseudoenterobacter. The average nucleotide identity (ANI) and in silico DNA-DNA hybridisation (isDDH) values between the two strains were 98.35% and 89.4%, respectively, suggesting that they belong to one species. The two strains had the highest ANI (95.02% and 95.04%) with the type strain of Enterobacter quasiroggenkampii. Their highest isDDH values, also seen with the type strain of E. quasiroggenkampii, were 59.5% and 59.8%, well below the 70% cutoff to define species. The two strains were also characterised for morphological and biochemical features by a set of experiments and observations. The abilities of metabolising gelatin and L-rhamnose could differentiate the two strains from all currently known Enterobacter species. Collectively, the two strains represent a novel Enterobacter species, for which we propose Enterobacter pseudoroggenkampii sp. nov. as the species name. The type strain of this novel species is155092^T (= GDMCC 1.3415^T = JCM 35646^T). The two strains also carried multiple virulence factors comprising aerobactin-encoding iucABCD-iutA and salmochelin-encoding iroN. The two strains also had chromosomally located qnrE, a gene associated with reduced susceptibility to quinolones, suggesting that this species is a potential reservoir of qnrE genes.

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.

Acinetobacter nematophilus sp. nov., Alcaligenes nematophilus sp. nov., Enterobacter nematophilus sp. nov., and Kaistia nematophila sp. nov., Isolated from Soil-Borne Nematodes and Proposal for the Elevation of Alcaligenes faecalis subsp. faecalis, Alcaligenes faecalis subsp. parafaecalis, and Alcaligenes faecalis subsp. phenolicus to the Species Level

Four bacterial strains, A-IN1T, A-TC2T, E-TC7T, and K-TC2T, isolated from soil-borne nematodes of the species Oscheius tipulae and Acrobeloides bodenheimeri, were found to represent new species of the genera Acinetobacter, Alcaligenes, Enterobacter, and Kaistia, respectively. In this study, we described these new species using a polyphasic taxonomic approach that included whole-genome and whole-proteome phylogenomic reconstructions, core genome sequence comparisons, and phenotypic characterization. Phylogenomic reconstructions using whole-genome and whole-proteome sequences show that A-IN1T is closely related to Acinetobacter guillouiae DSM 590T and to Acinetobacter bereziniae LMG 1003T. The dDDH values between A-IN1T and these latest strains are 25.1 and 39.6%, respectively, which are below the 70% divergence threshold for prokaryotic species delineation. A-TC2T is closely related to Alcaligenes faecalis subsp. faecalis DSM 30030T and to Alcaligenes faecalis subsp. phenolicus DSM 16503T. The dDDH values between A-TC2T and these latest strains are 47.0 and 66.3%, respectively. In addition, the dDDH values between Alcaligenes faecalis subsp. faecalis DSM 30030T, Alcaligenes faecalis subsp. phenolicus DSM 16503T, and Alcaligenes faecalis subsp. parafaecalis are always lower than 70%, demonstrating that the three strains represent species within the genus Alcaligenes rather than subspecies within Alcaligenes faecalis. E-TC7T is closely related to Enterobacter kobei DSM 13645T, Enterobacter chuandaensis 090028T, and to Enterobacter bugandensis STN0717-56T. The dDDH values between E-TC7T and these strains are 43.5, 42.9, and 63.7%, respectively. K-TC2T is closely related to Kaistia terrae DSM 21341T and to Kaistia defluvii JCM 18034T. The dDDH values between these strains are 29.2 and 30.7%, respectively. Several biochemical tests allow to differentiate the type strains of the newly described species from the type strains of their more closely related species. Based on the results of this polyphasic taxonomic approach, the following new species are proposed: Acinetobacter nematophilus sp. nov. with A-IN1T (=CCM 9231T =CCOS 2018T) as the type strain, Alcaligenes nematophilus sp. nov. with A-TC2T (=CCM 9230T =CCOS 2017T) as the type strain, Enterobacter nematophilus sp. nov. with E-TC7T (=CCM 9232T =CCOS 2020T) as the type strain, and Kaistia nematophila sp. nov. with K-TC2T (=CCM 9239T =CCOS 2022T) as the type strain. In addition, we propose the elevation of Alcaligenes faecalis subsp. faecalis, Alcaligenes faecalis subsp. parafaecalis, and Alcaligenes faecalis subsp. phenolicus to the species level. Therefore, we propose the creation of Alcaligenes parafaecalis sp. nov. with DSM 13975T as the type strain, and Alcaligenes phenolicus sp. nov. with DSM 16503T as the type strain. Our study contributes to a better understanding of the biodiversity and phylogenetic relationships of bacteria associated with soil-borne nematodes.

Comparative genomic analysis provides insight into the phylogeny and potential mechanisms of adaptive evolution of Sphingobacterium sp. CZ-2

Sphingobacterium is a class of Gram-negative, non-fermentative bacilli that have received widespread attention due to their broad ecological distribution and oil degradation ability, but are rarely involved in infections. In this manuscript, a novel Sphingobacterium strain isolated from wildfire-infected tobacco leaves was named Sphingobacterium sp. CZ-2. NGS and TGS sequencing results showed a whole genome of 3.92 Mb with 40.68 mol% GC content and containing 3,462 protein-coding genes, 9 rRNA-coding genes and 50 tRNA-coding genes. Phylogenetic analysis, ANI and dDDH calculations all supported that Sphingobacterium sp. CZ-2 represented a novel species of the genus Sphingobacterium. Analysis of the specific genes of Sphingobacterium sp. CZ-2 by comparative genomics revealed that metal transport proteins encoded by the troD and cusA genes could maintain the balance of heavy metal ion concentrations in the internal environment of bacteria and avoid heavy metal toxicity while meeting the needs of growth and reproduction, and transport proteins encoded by the malG gene could keep nutrients required for the survival of bacteria. Synteny and genome evolutionary analyses of Sphingobacterium strains implicated that the gene family contraction as a major process in genome evolution, with insertional sequences leading to mutations, deletions and reversals of genes that help bacteria to withstand complex environmental changes. Complete genome sequencing and systematic comparative genomic analysis will contribute new insights into the adaptive evolution of this novel species and the genus Sphingobacterium.

High-risk international clones ST66, ST171 and ST78 of Enterobacter cloacae complex causing blood stream infections in Spain and carrying blaOXA-48 with or without mcr-9

BACKGROUND

In the last years, Enterobacter cloacae complex has become an important threat associated with nosocomial infections (including bacteraemia). These bacteria have the ability to acquire mobile genetic elements with antimicrobial resistance genes, reducing the number of therapies available for treatment of the infections they cause. Multidrug resistant isolates of the E. cloacae complex have been causing blood stream infections in a hospital in northern Spain. The aim of this study was to report the spread of E. cloacae complex isolates carrying bla_OXA-48 with or without mcr-9 which were involved in blood stream infections, in a Spanish hospital.

METHODS

All Enterobacter spp. isolates recovered from blood cultures of patients admitted to a tertiary Spanish hospital, over a five-year period were recovered. Of those, OXA-48-producing isolates were selected for further analysis (19 E. xiangfangensis isolates and a single E. hoffmannii). Bacterial identification, antimicrobial susceptibility, DNA sequencing, molecular typing, resistome analysis and plasmid characterization was performed.

RESULTS

20 isolates were positive for bla_OXA-48, harbored by IncL/M plasmids. They belonged to the international high-risk clones ST66, ST171 and ST78. They produced the extended-spectrum β-lactamases CTX-M-15 and/or CTX-M-9 and 40 % of them (n = 8) also carried the mcr-9 gene, located on IncHI2 plasmids. However, they were susceptible to colistin.

CONCLUSION

The presence of bla_OXA-48, together with at least one bla_CTX-M gene in our multidrug resistant high-risk E. cloacae complex clones is worrisome. Also, the additional presence of mcr-9 in some of them is of concern as it could potentially be transferred into other hosts or acquire mutations that might led to emerging colistin resistance. Surveillance systems are essential to detect these difficult-to-treat bacteria which, apart from causing live-threatening infections, can spread important resistance threats.

Update on Accepted Novel Bacterial Isolates Derived from Human Clinical Specimens and Taxonomic Revisions Published in 2020 and 2021

A number of factors, including microbiome analyses and the increased utilization of whole-genome sequencing in the clinical microbiology laboratory, has contributed to the explosion of novel prokaryotic species discovery, as well as bacterial taxonomy revision. This review attempts to summarize such changes relative to human clinical specimens that occurred in 2020 and 2021, per primary publication in the International Journal of Systematic and Evolutionary Microbiology or acceptance on Validation Lists published by the International Journal of Systematic and Evolutionary Microbiology. Of particular significance among valid and effectively published taxa within the past 2 years were novel Corynebacterium spp., coagulase-positive staphylococci, Pandoraea spp., and members of family Yersiniaceae. Noteworthy taxonomic revisions include those within the Bacillus and Lactobacillus genera, family Staphylococcaceae (including unifications of subspecies designations to species level taxa), Elizabethkingia spp., and former members of Clostridium spp. and Bacteroides spp. Revisions within the Brucella genus have the potential to cause deleterious effects unless the relevance of such changes is properly communicated by microbiologists to stakeholders in clinical practice, infection prevention, and public health.

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.

Novel insights related to the rise of KPC-producing Enterobacter cloacae complex strains within the nosocomial niche

According to the World Health Organization, carbapenem-resistant Enterobacteriaceae (CRE) belong to the highest priority group for the development of new antibiotics. Argentina-WHONET data showed that Gram-negative resistance frequencies to imipenem have been increasing since 2010 mostly in two CRE bacteria: Klebsiella pneumoniae and Enterobacter cloacae Complex (ECC). This scenario is mirrored in our hospital. It is known that K. pneumoniae and the ECC coexist in the human body, but little is known about the outcome of these species producing KPC, and colonizing or infecting a patient. We aimed to contribute to the understanding of the rise of the ECC in Argentina, taking as a biological model both a patient colonized with two KPC-producing strains (one Enterobacter hormaechei and one K. pneumoniae) and in vitro competition assays with prevalent KPC-producing ECC (KPC-ECC) versus KPC-producing K. pneumoniae (KPC-Kp) high-risk clones from our institution. A KPC-producing E. hormaechei and later a KPC-Kp strain that colonized a patient shared an identical novel conjugative IncM1 plasmid harboring blaKPC-2. In addition, a total of 19 KPC-ECC and 58 KPC-Kp strains isolated from nosocomial infections revealed that high-risk clones KPC-ECC ST66 and ST78 as well as KPC-Kp ST11 and ST258 were prevalent and selected for competition assays. The competition assays with KCP-ECC ST45, ST66, and ST78 versus KPC-Kp ST11, ST18, and ST258 strains analyzed here showed no statistically significant difference. These assays evidenced that high-risk clones of KPC-ECC and KPC-Kp can coexist in the same hospital environment including the same patient, which explains from an ecological point of view that both species can exchange and share plasmids. These findings offer hints to explain the worldwide rise of KPC-ECC strains based on the ability of some pandemic clones to compete and occupy a certain niche. Taken together, the presence of the same new plasmid and the fitness results that showed that both strains can coexist within the same patient suggest that horizontal genetic transfer of blaKPC-2 within the patient cannot be ruled out. These findings highlight the constant interaction that these two species can keep in the hospital environment, which, in turn, can be related to the spread of KPC.

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.

Genomic Analysis of a mcr-9.1-Harbouring IncHI2-ST1 Plasmid from Enterobacter ludwigii Isolated in Fish Farming

This study analyzed the resistome, virulome and mobilome of an MCR-9-producing Enterobacter sp. identified in a muscle sample of seabream (Sparus aurata), collected in a land tank from multitrophic fish farming production. Average Nucleotide Identity analysis identified INSAq77 at the species level as an Enterobacter ludwigii INSAq77 strain that was resistant to chloramphenicol, florfenicol and fosfomycin and was susceptible to all other antibiotics tested. In silico antimicrobial resistance analyses revealed genes conferring in silico resistance to β-lactams (bla_ACT-88), chloramphenicol (catA4-type), fosfomycin (fosA2-type) and colistin (mcr-9.1), as well as several efflux pumps (e.g., oqxAB-type and mar operon). Further bioinformatics analysis revealed five plasmid replicon types, including the IncHI2/HI2A, which are linked to the worldwide dissemination of the mcr-9 gene in different antibiotic resistance reservoirs. The conserved nickel/copper operon rcnR-rcnA-pcoE-ISSgsp1-pcoS-IS903-mcr-9-wbuC was present, which may play a key role in copper tolerance under anaerobic growth and nickel homeostasis. These results highlight that antibiotic resistance in aquaculture are spreading through food, the environment and humans, which places this research in a One Health context. In fact, colistin is used as a last resort for the treatment of serious infections in clinical settings, thus mcr genes may represent a serious threat to human health.

Colistin Resistance Mechanism in Enterobacter hormaechei subsp. steigerwaltii Isolated from Wild Boar (Sus scrofa) in France

Wild animals may act as efficient antimicrobial-resistance reservoirs and epidemiological links between humans, livestock, and natural environments. By using phenotypic and genotypic characterization, the present study highlighted the occurrence of an antimicrobial-resistant (i.e., amoxicillin, amoxicillin–clavulanic acid, cephalothin, and colistin) Enterobacter hormaechei subsp. steigerwaltii strain in wild boar (Sus scrofa) from France. The molecular analysis conducted showed non-synonymous mutations in the pmrA/pmrB and phoQ/phoP operons and the phoP/Q regulator mgrB gene, leading to colistin resistance. The present data highlight the need for continuous monitoring of multidrug-resistant bacteria in wild animals to limit the spread of these threatening pathogens.

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.

Co-occurrence of dual carbapenemases KPC-2 and OXA-48 with the mobile colistin resistance gene mcr-9.1 in Enterobacter xiangfangensis

Bacterial infections with the genus Enterobacter are notoriously difficult to treat and often associated with resistance to penicillin, aminoglycosides, fluoroquinolones, and third-generation cephalosporins. Also, Enterobacter species have emerged as the third most common hosts for carbapenemases worldwide, forcing the use of colistin as a “last-resort” antibiotic for the treatment. Studies on the population structure of the genus Enterobacter repeatedly detect E. xiangfangensis as a common clinical species present worldwide. Here, we report on the characteristics of an extreme drug-resistant E. xiangfangensis isolate va18651 (ST88), obtained from a cervical swab of an expectant mother. The isolate was resistant to almost all the classes of antibiotics tested, including β-lactams (viz., penicillins, carbapenems, cephalosporin, monobactams, and their combinations), quinolone, aminoglycosides, and sulfonamide/dihydrofolate reductase inhibitor, and exhibited heteroresistance towards colistin. Analysis of its complete genome sequence revealed 37 antibiotic resistance genes (ARGs), including mcr-9.1, bla_KPC-2, and bla_OXA-48, encoded on three of the four different plasmids (cumulative plasmidome size 604,632 bp). An unusually high number of plasmid-based heavy metal resistance gene (HRG) clusters towards silver, arsenate, cadmium, copper, mercury, and tellurite were also detected. Virulence genes (VGs) for the lipopolysaccharide and capsular polysaccharide structures, iron acquisition (iroBCDEN, ent/fep/fes, sitABCD, iut, and fur), and a type VI secretion system, together with motility genes and Type IV pili, were encoded chromosomally. Thus, a unique combination of chromosomally encoded VGs, together with plasmid-encoded ARGs and HRGs, converged to result in an extreme drug-resistant, pathogenic isolate with survival potential in environmental settings. The use of a disinfectant, octenidine, led to its eradication; however, the existence of a highly antibiotic-resistant isolate with significant virulence potential is a matter of concern in public health settings and warrants further surveillance for extreme drug-resistant Enterobacter isolates.

Huaxiibacter chinensis gen. nov., sp. nov., recovered from human sputum

Strain 155047T was recovered from human sputum in China in 2021. Preliminary species identification based on limited phenotypic tests assigned the strain to the genus Enterobacter of the family Enterobacteriaceae . The genome sequence of the strain was obtained and had ≤84.43 % average nucleotide identity (ANI) and ≤26.3 % in silico DNA–DNA hybridization (isDDH) values with the genomes of type strains of known Enterobacteriaceae species. The highest ANI and isDDH matches were with Lelliottia nimipressuralis and Enterobacter asburiae , respectively. The ANI and isDDH values support that the strain belongs to a novel species of the family Enterobacteriaceae . Phylogenomic analysis based on core genes revealed that strain 155047T was located in the Enterobacter–Leclercia–Lelliottia–Pseudenterobacter lineage. The highest ANI and average amino acid identity values between 155047T and any species of the Enterobacter–Leclercia–Lelliottia–Pseudenterobacter lineage were 84.43 % and 90.21 %, respectively, lower than the maximum inter-genus pairwise values. This indicates that 155047T belongs to a novel species of a novel genus in the lineage. Strain 155047T could be differentiated from Enterobacter , Lelliottia , Leclercia and Pseudenterobacter species by a negative reaction for β-galactosidase and the ability to produce acid from l-fucose but not from sucrose. The names Huaxiibacter gen. nov. and Huaxiibacter chinensis sp. nov. are proposed for the novel genus and species, respectively. The type strain is 155047T (= GDMCC 1.2980T=JCM 35262T).

Comparative Genomics Insights into a Novel Biocontrol Agent Paenibacillus peoriae Strain ZF390 against Bacterial Soft Rot

Bacterial soft rot, caused by Pectobacterium brasiliense, can infect several economically important horticultural crops. However, the management strategies available to control this disease are limited. Plant-growth-promoting rhizobacteria (PGPR) have been considered to be promising biocontrol agents. With the aim of obtaining a strain suitable for agricultural applications, 161 strains were isolated from the rhizosphere soil of healthy cucumber plants and screened through plate bioassays and greenhouse tests. Paenibacillus peoriae ZF390 exhibited an eminent control effect against soft rot disease and a broad antagonistic activity spectrum in vitro. Moreover, ZF390 showed good activities of cellulase, protease, and phosphatase and a tolerance of heavy metal. Whole-genome sequencing was performed and annotated to explore the underlying biocontrol mechanisms. Strain ZF390 consists of one 6,193,667 bp circular chromosome and three plasmids. Comparative genome analysis revealed that ZF390 involves ten gene clusters responsible for secondary metabolite antibiotic synthesis, matching its excellent biocontrol activity. Plenty of genes related to plant growth promotion, biofilm formation, and induced systemic resistance were mined to reveal the biocontrol mechanisms that might consist in strain ZF390. Overall, these findings suggest that strain ZF390 could be a potential biocontrol agent in bacterial-soft-rot management, as well as a source of antimicrobial mechanisms for further exploitation.

Monitoring Carbapenem-Resistant Enterobacterales in the Environment to Assess the Spread in the Community

The usefulness of wastewater-based epidemiology (WBE) was proven during the COVID-19 pandemic, and the role of environmental monitoring of emerging infectious diseases has been recognized. In this study, the prevalence of carbapenem-resistant Enterobacterales (CRE) in Japanese environmental samples was measured in the context of applying WBE to CRE. A total of 247 carbapenem-resistant isolates were obtained from wastewater, treated wastewater, and river water. Treated wastewater was shown to be an efficient target for monitoring CRE. The results of the isolate analysis showed that WBE may be applicable to Escherichia coli-carrying New Delhi metallo-β-lactamase (NDM)-type carbapenemase, the Enterobacter cloacae complex and Klebsiella pneumoniae complex-carrying IMP-type carbapenemase. In addition, a certain number of CRE isolated in this study carried Guiana extended spectrum (GES)-type carbapenemase although their clinical importance was unclear. Only a few isolates of Klebsiella aerogenes were obtained from environmental samples in spite of their frequent detection in clinical isolates. Neither the KPC-type, the oxacillinase (OXA)-type nor the VIM-type of carbapenemase was detected in the CRE, which reflected a low regional prevalence. These results indicated the expectation and the limitation of applying WBE to CRE.

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.

Genomic epidemiology, antimicrobial resistance and virulence factors of Enterobacter cloacae complex causing potential community-onset bloodstream infections in a tertiary care hospital of Nepal

Objectives

Community-onset bloodstream infections (BSIs) caused by carbapenemase-producing Enterobacter cloacae complex (ECC) species are increasing internationally. This observation suggests that ECC are emerging pathogens, requiring for detailed understanding on their genomic epidemiology including transmission dynamics and antimicrobial resistance profiles.

Patients and methods

We performed WGS on 79 Enterobacter spp. isolated from the patients with clinically significant BSIs and admitted to emergency department of a major tertiary hospital in Nepal between April 2016 and October 2017.

Results

We identified 5 species and 13 STs of ECC. Enterobacter xiangfangensis ST171, one of the globally emerging carbapenem resistant ECC clones with epidemic potential, was the most prevalent (42%). Phylogenetic analysis showed a large (>19 400 SNPs) core genome SNP distance across major STs, which was minimal (<30 SNPs) among the isolates of each prevalent ST, suggesting the relatively recent importation of major STs followed by local clonal expansions. Genomic evidence for resistance to all major antimicrobial classes except for colistin and macrolides was detected. A limited number of isolates also carried bla NDM-1 (n = 2) and bla OXA-48 (n = 1) carbapenemase genes. Virulence factors encoding siderophores (24%), T6SSD (25%) and fimbriae (54%) were detected.

Conclusions

Our study highlighted that MDR ECC clones are important pathogens of BSIs in community. Though of low prevalence, carbapenem resistance observed in our ECC isolates raised concern about further community dissemination, underscoring the need for community surveillance to identify MDR ECC clones with epidemic potential.

A fatal outbreak of neonatal sepsis caused by mcr-10 carrying Enterobacter kobei in a tertiary care hospital in Nepal

BACKGROUND

Enterobacter kobei is an emerging cause of outbreak of nosocomial infections in neonatal intensive care units (NICUs). Between July and September of 2016, an NICU in a tertiary care hospital of Nepal observed an abrupt increase in the number of neonatal sepsis cases caused by Enterobacter spp. infecting 11 of 23 admitted neonates, 5 of whom died of an exacerbated sepsis.

AIM

Main aims of this study were to confirm the suspected outbreak, identify environmental source of infection, and characterize genetic determinants of antimicrobial resistance (AMR) and virulence of the pathogen.

METHODS

We performed whole genome sequencing of all Enterobacter spp. isolated from blood cultures of septic neonates admitted to NICU between May 2016 and December 2017. Also, an environmental sampling was intensified from fortnightly to weekly during the outbreak.

FINDINGS

The genomic analysis revealed that 10 of 11 non-duplicated E. kobei isolated from neonatal blood cultures between July and September 2016 were clonal, confirming the outbreak. The isolates carried AMR genes including bla_AmpC and mcr-10 conferring reduced susceptibility to carbapenem and colistin respectively. The environmental sampling however failed to isolate any Enterobacter spp. Reinforcement of aseptic protocols in invasive procedures, hand hygiene, environmental decontamination, fumigation, and secluded care of culture positive cases successfully terminated the outbreak.

CONCLUSION

Our study underscored the need to implement stringent infection control measures to prevent infection outbreaks. Further, for the first time, we report the emergence of carbapenem and colistin non-susceptible E. kobei carrying mcr-10 gene as an important cause of nosocomial neonatal sepsis in an NICU.

The Genome of Enterobacter hormaechei Strain MG02, a 2,4-Dichlorophenoxyacetic Acid-Degrading Bacterium Isolated from Brazilian Soil

Enterobacter hormaechei strain MG02 was isolated from a mixed culture collected from soil with a history of pesticide application. This strain degrades 2,4-dichlorophenoxyacetic acid (2,4-D). Here, we report on its genome, which has 4,923,875 bp and 55.4% G+C content.

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.