Carbapenem-Resistant Enterobacter hormaechei ST1103 with IMP-26 Carbapenemase and ESBL Gene bla SHV-178

Whole-Genome Analysis of Extensively Drug-Resistant Enterobacter hormaechei Isolated from a Patient with Non-Hodgkin's Lymphoma

BACKGROUND

Currently, the Enterobacteriaceae species are responsible for a variety of serious infections and are already considered a global public health problem, especially in underdeveloped countries, where surveillance and monitoring programs are still scarce and limited. Analyses were performed on the complete genome of an extensively antibiotic-resistant strain of Enterobater hormaechei, which was isolated from a patient with non-Hodgkin's lymphoma, who had been admitted to a hospital in the city of Manaus, Brazil.

METHODS

Phenotypical identification and susceptibility tests were performed in automated equipment. Total DNA extraction was performed using the PureLink genomic DNA mini-Kit. The genomic DNA library was prepared with Illumina Microbial Amplicon Prep and sequenced in the MiSeq Illumina Platform. The assembly of the whole-genome and individual analyses of specific resistance genes extracted were carried out using online tools and the Geneious Prime software.

RESULTS

The analyses identified an extensively resistant ST90 clone of E. hormaechei carrying different genes, including blaCTX-M-15, blaGES-2, blaTEM-1A, blaACT-15, blaOXA-1 and blaNDM-1, [aac(3)-IIa, aac(6')-Ian, ant(2″)-Ia], [aac(6')-Ib-cr, (qnrB1)], dfrA25, sul1 and sul2, catB3, fosA, and qnrB, in addition to resistance to chlorhexidine, which is widely used in patient antisepsis.

CONCLUSIONS

These findings highlight the need for actions to control and monitor these pathogens in the hospital environment.

Fosfomycin resistance mechanisms in Enterobacterales: an increasing threat

Antimicrobial resistance is well-known to be a global health and development threat. Due to the decrease of effective antimicrobials, re-evaluation in clinical practice of old antibiotics, as fosfomycin (FOS), have been necessary. FOS is a phosphonic acid derivate that regained interest in clinical practice for the treatment of complicated infection by multi-drug resistant (MDR) bacteria. Globally, FOS resistant Gram-negative pathogens are raising, affecting the public health, and compromising the use of the antibiotic. In particular, the increased prevalence of FOS resistance (FOS^R) profiles among Enterobacterales family is concerning. Decrease in FOS effectiveness can be caused by i) alteration of FOS influx inside bacterial cell or ii) acquiring antimicrobial resistance genes. In this review, we investigate the main components implicated in FOS flow and report specific mutations that affect FOS influx inside bacterial cell and, thus, its effectiveness. FosA enzymes were identified in 1980 from Serratia marcescens but only in recent years the scientific community has started studying their spread. We summarize the global epidemiology of FosA/C2/L1-2 enzymes among Enterobacterales family. To date, 11 different variants of FosA have been reported globally. Among acquired mechanisms, FosA3 is the most spread variant in Enterobacterales, followed by FosA7 and FosA5. Based on recently published studies, we clarify and represent the molecular and genetic composition of fosA/C2 genes enviroment, analyzing the mechanisms by which such genes are slowly transmitting in emerging and high-risk clones, such as E. coli ST69 and ST131, and K. pneumoniae ST11. FOS is indicated as first line option against uncomplicated urinary tract infections and shows remarkable qualities in combination with other antibiotics. A rapid and accurate identification of FOS^R type in Enterobacterales is difficult to achieve due to the lack of commercial phenotypic susceptibility tests and of rapid systems for MIC detection.

Polyclonal Spread of Fosfomycin Resistance among Carbapenemase-Producing Members of the Enterobacterales in the Czech Republic

Fosfomycin (FOS) has been recently reintroduced into clinical practice, but its effectiveness against multidrug-resistant (MDR) Enterobacterales is reduced due to the emergence of FOS resistance. The copresence of carbapenemases and FOS resistance could drastically limit antibiotic treatment. The aims of this study were (i) to investigate fosfomycin susceptibility profiles among carbapenem-resistant Enterobacterales (CRE) in the Czech Republic, (ii) to characterize the genetic environment of fosA genes among the collection, and (iii) to evaluate the presence of amino acid mutations in proteins involved in FOS resistance mechanisms. During the period from December 2018 to February 2022, 293 CRE isolates were collected from different hospitals in the Czech Republic. FOS MICs were assessed by the agar dilution method (ADM), FosA and FosC2 production was detected by the sodium phosphonoformate (PPF) test, and the presence of fosA-like genes was confirmed by PCR. Whole-genome sequencing was conducted with an Illumina NovaSeq 6000 system on selected strains, and the effect of point mutations in the FOS pathway was predicted using PROVEAN. Of these strains, 29% showed low susceptibility to fosfomycin (MIC, ≥16 μg/mL) by ADM. An NDM-producing Escherichia coli sequence type 648 (ST648) strain harbored a fosA10 gene on an IncK plasmid, while a VIM-producing Citrobacter freundii ST673 strain harbored a new fosA7 variant, designated fosA7.9. Analysis of mutations in the FOS pathway revealed several deleterious mutations occurring in GlpT, UhpT, UhpC, CyaA, and GlpR. Results regarding single substitutions in amino acid sequences highlighted a relationship between ST and specific mutations and an enhanced predisposition for certain STs to develop resistance. This study highlights the occurrence of several FOS resistance mechanisms in different clones spreading in the Czech Republic. IMPORTANCE Antimicrobial resistance (AMR) currently represents a concern for human health, and the reintroduction of antibiotics such as fosfomycin into clinical practice can provide further option in treatment of multidrug-resistant (MDR) bacterial infections. However, there is a global increase of fosfomycin-resistant bacteria, reducing its effectiveness. Considering this increase, it is crucial to monitor the spread of fosfomycin resistance in MDR bacteria in clinical settings and to investigate the resistance mechanism at the molecular level. Our study reports a large variety of fosfomycin resistance mechanisms among carbapenemase-producing Enterobacterales (CRE) in the Czech Republic. Our study summarizes the main achievements of our research on the use of molecular technologies, such as next-generation sequencing (NGS), to describe the heterogeneous mechanisms that reduce fosfomycin effectiveness in CRE. The results suggest that a program for widespread monitoring of fosfomycin resistance and epidemiology fosfomycin-resistant organisms can aide timely implementation of countermeasures to maintain the effectiveness of fosfomycin.

Coexistence of blaIMP-4, blaNDM-1 and blaOXA-1 in blaKPC-2-producing Citrobacter freundii of clinical origin in China

Purpose

To explore the genetic characteristics of the IMP-4, NDM-1, OXA-1, and KPC-2 co-producing multidrug-resistant (MDR) clinical isolate, Citrobacter freundii wang9.

Methods

MALDI-TOF MS was used for species identification. PCR and Sanger sequencing analysis were used to identify resistance genes. In addition to agar dilution, broth microdilution was used for antimicrobial susceptibility testing (AST). We performed whole genome sequencing (WGS) of the strains and analyzed the resulting data for drug resistance genes and plasmids. Phylogenetic trees were constructed with maximum likelihood, plotted using MAGA X, and decorated by iTOL.

Results

Citrobacter freundii carrying bla_KPC-2, bla_IMP-4, bla_OXA-1, and bla_NDM-1 are resistant to most antibiotics, intermediate to tigecycline, and only sensitive to polymyxin B, amikacin, and fosfomycin. The bla_IMP-4 coexists with the bla_NDM-1 and the bla_OXA-1 on a novel transferable plasmid variant pwang9-1, located on the integron In1337, transposon TnAS3, and integron In2054, respectively. The gene cassette sequence of integron In1337 is IntI1-bla_IMP-4-qacG2-aacA4'-catB3Δ, while the gene cassette sequence of In2054 is IntI1-aacA4cr-bla_OXA-1-catB3-arr3-qacEΔ1-sul1. The bla_NDM-1 is located on the transposon TnAS3, and its sequence is IS91-sul-ISAba14-aph (3')-VI-IS30-bla_NDM-1-ble-trpF-dsbD-IS91. The bla_KPC-2 is located on the transposon Tn2 of plasmid pwang9-1, and its sequence is klcA-korC-ISkpn6-bla_KPC-2-ISkpn27-tnpR-tnpA. Phylogenetic analysis showed that most of the 34\u00B0C. freundii isolates from China were divided into three clusters. Among them, wang1 and wang9 belong to the same cluster as two strains of C. freundii from environmental samples from Zhejiang.

Conclusion

We found C. freundii carrying bla_IMP-4, bla_NDM-1, bla_OXA-1, and bla_KPC-2 for the first time, and conducted in-depth research on its drug resistance mechanism, molecular transfer mechanism and epidemiology. In particular, we found that bla_IMP-4, bla_OXA-1, and bla_NDM-1 coexisted on a new transferable hybrid plasmid that carried many drug resistance genes and insertion sequences. The plasmid may capture more resistance genes, raising our concern about the emergence of new resistance strains.

Contaminated dicloxacillin capsules as the source of an NDM-5/OXA-48-producing Enterobacter hormaechei ST79 outbreak, Denmark and Iceland, 2022 and 2023

From October 2022 through January 2023, nine patients with NDM-5/OXA-48-carbapenemase-producing Enterobacter hormaechei ST79 were detected in Denmark and subsequently one patient in Iceland. There were no nosocomial links between patients, but they had all been treated with dicloxacillin capsules. An NDM-5/OXA-48-carbapenemase-producing E. hormaechei ST79, identical to patient isolates, was cultured from the surface of dicloxacillin capsules in Denmark, strongly implicating them as the source of the outbreak. Special attention is required to detect the outbreak strain in the microbiology laboratory.

Conventional tobacco products harbor unique and heterogenous microbiomes

While an increasing number of studies have evaluated tobacco microbiomes, comparative microbiome analyses across diverse tobacco products are non-existent. Moreover, to our knowledge, no previous studies have characterized the metabolically-active (live) fraction of tobacco bacterial communities and compared them across products. To address these knowledge gaps, we compared bacterial communities across four commercial products (cigarettes, little cigars, cigarillos and hookah) and one research cigarette product. After total DNA extraction (n = 414) from all samples, the V3V4 region of the 16S rRNA gene was sequenced on the Illumina HiSeq platform. To identify metabolically-active bacterial communities within these products, we applied a coupled 5-bromo-2'-deoxyuridine labeling and sequencing approach to a subset of samples (n = 56). Each tobacco product was characterized by its signature microbiome, along with a shared microbiome across all tobacco products consisting of Pseudomonas aeruginosa, P. putida, P. alcaligenes, Bacillus subtilis, and Klebsiella pneumoniae. Comparing across products (using Linear discriminant analysis Effect Size (LEfSe)), a significantly higher (p < 0.05) relative abundance of Klebsiella and Acinetobacter was observed in commercial cigarettes, while a higher relative abundance of Pseudomonas and Pantoea was observed in research cigarettes. Methylorubrum and Paenibacillus were higher in hookah, and Brevibacillus, Lactobacillus, Bacillus, Lysinibacillus, and Staphylococcus were higher in little cigars and cigarillos. Across all products, the majority of the metabolically-active bacterial communities belonged to the genus Pseudomonas, followed by several genera within the Firmicutes phylum (Bacillus, Terribacillus, and Oceanobacillus). Identification of some metabolically-active pathogens such as Bacillus cereus and Haemophilus parainfluenzae in commercial products is of concern because of the potential for these microorganisms to be transferred to users' respiratory tracts via mainstream smoke. Future work is warranted to evaluate the potential impact of these tobacco bacterial communities on users' oral and lung microbiomes, which play such an important role on the spectrum from health to disease.

Global profiling of antibiotic resistomes in maize rhizospheres

The spreading of antimicrobial resistance (AMR) in crops and food products represents a global concern. In this study, we conducted a survey of resistomes in maize rhizosphere from Michigan, California, the Netherlands, and South Africa, and investigated potential associations with host bacteria and soil management practices in the crop field. For comparison, relative abundance of antibiotic resistance genes (ARGs) is normalized to the size of individual metagenomes. Michigan maize rhizosphere metagenomes showed the highest abundance and diversity of ARGs, with the detection of blaTEM-116, blaACT-4/-6, and FosA2, exhibiting high similarity (≥ 99.0%) to those in animal and human pathogens. This was probably related to the decade-long application of manure/composted manure from antibiotic-treated animals. Moreover, RbpA, vanRO, mtrA, and dfrB were prevalently found across most studied regions, implying their intrinsic origins. Further analysis revealed that RbpA, vanRO, and mtrA are mainly harbored by native Actinobacteria with low mobility since mobile genetic elements were rarely found in their flanking regions. Notably, a group of dfrB genes are adjacent to the recombination binding sites (attC), which together constitute mobile gene cassettes, promoting the transmission from soil bacteria to human pathogens. These results suggest that maize rhizosphere resistomes can be distinctive and affected by many factors, particularly those relevant to agricultural practices.

Paraconexibacter antarcticus sp. nov., a novel actinobacterium isolated from Antarctic tundra soil

A Gram-negative, non-motile, aerobic bacterium, named 02-257^T, was isolated from Antarctic soil. The cells are surrounded by relatively thin capsules and were catalase-positive and oxidase-negative cocci. Growth of strain 02-257^T was observed at 4-35 °C (optimum, 28-30 °C), pH 6.0-8.0 (optimum, pH 6.0) and with 0-1.5% NaCl (optimum, 0 %). Strain 02-257 showed the highest 16S rRNA gene sequence similarity to Paraconexibacter algicola Seoho-28^T (95.06 %). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 02-257^T is a member of a novel species belonging to the clade formed by members of the genus Paraconexibacter in the family Paraconexibacteraceae. The DNA G+C content was 72.9 mol%. Strain 02-257^T contained C_16 : 0-iso (23.0 %), C_{18  :  1} ω9c (13.8 %), C_16 : 0 (12.5 %) and C_17 : 1 ω9c-iso (10.8 %) as major cellular fatty acids and menaquinone MK-7(H₄) was detected as the only isoprenoid quinone. Diphosphatidylglycerol, phosphatidylinositol, phosphatidylinositole mannoside, phosphatidylinositole dimannoside, unidentified phosphoglycolipid, unidentified aminophospholipid, two unidentified phospholipids, three unidentified aminolipids and six unidentified lipids were the major polar lipids. meso-Diaminopimelic acids were the diagnostic diamino acids in the cell-wall peptidoglycan. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain 02-257^T is considered to represent a novel species of the genus Paraconexibacter, for which the name Paraconexibacter antarcticus sp. nov. is proposed. The type strain is 02-257^T (=CCTCC AB 2021030^T=KCTC 49619^T).

Detection of IMP-4 and SFO-1 co-producing ST51 Enterobacter hormaechei clinical isolates

Purpose

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

Methods

MALDI-TOF MS was used for species identification. Antibiotic resistance genes (ARGs) were tested by PCR and Sanger sequencing analysis. In addition to agar dilution, broth microdilution was used for antimicrobial susceptibility testing (AST). Whole-genome sequencing (WGS) analysis was conducted using the Illumina NovaSeq 6000 and Oxford Nanopore platforms. Annotation was performed by RAST on the genome. The phylogenetic tree was achieved using kSNP3.0. Plasmid characterization was conducted using S1-pulsed-field gel electrophoresis (S1-PFGE), Southern blotting, conjugation experiments, and whole genome sequencing (WGS). An in-depth study of the conjugation module was conducted using the OriTFinder website. The genetic context of bla _IMP-4 and bla _SFO-1 was analyzed using BLAST Ring Image Generator (BRIG) and Easyfig 2.3.

Results

YQ13422hy and YQ13530hy, two MDR strains of ST51 E. hormaechei harboring bla _IMP-4 and bla _SFO-1, were identified. They were only sensitive to meropenem, amikacin and polymyxin B, and were resistant to cephalosporins, aztreonam, piperacillin/tazobactam and aminoglycosides, intermediate to imipenem. The genetic context surrounding bla _IMP-4 was 5'CS-hin-1-IS26-IntI1-bla _IMP-4-IS6100-ecoRII. The integron of bla _IMP-4 is In823, which is the array of gene cassettes of 5'CS-bla _IMP-4. Phylogenetic analysis demonstrated that E. hormaechei YQ13422hy and YQ13530hy belonged to the same small clusters with a high degree of homology.

Conclusion

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

Occurrence of Serratia marcescens Carrying blaIMP-26 and mcr-9 in Southern China: New Insights in the Evolution of Megaplasmid IMP-26

The spread of multidrug-resistant enterobacteria strains has posed a significant concern in public health, especially when the strain harbors metallo-beta-lactamase (MBL)-encoding and mobilized colistin resistance (mcr) genes as such genetic components potentially mediate multidrug resistance. Here we report an IncHI2/2A plasmid carrying bla_IMP-26 and mcr-9 in multidrug-resistant Serratia marcescens human isolates YL4. Antimicrobial susceptibility testing was performed by the broth microdilution method. According to the results, S. marcescens YL4 was resistant to several antimicrobials, including β-lactams, fluorquinolones, sulfanilamide, glycylcycline, and aminoglycosides, except for amikacin. To investigate the plasmid further, we conducted whole-genome sequencing and sequence analysis. As shown, S. marcescens YL4 possessed a circular chromosome with 5,171,477 bp length and two plasmids, pYL4.1 (321,744 bp) and pYL4.2 (46,771 bp). Importantly, sharing high similarity with plasmids pZHZJ1 and pIMP-26, pYL4.1 has an IncHI2/2A backbone holding a variable region containing bla_IMP-26, mcr-9, and two copies of bla_TEM-1B. After comprehensively comparing relevant plasmids, we proposed an evolutionary pathway originating from ancestor pZHZJ1. Then, via an acquisition of the mcr-9 element and a few recombination events, this plasmid eventually evolved into pYL4.1 and pIMP-26 through two different pathways. In addition, the phage-like plasmid pYL4.2 also carried a bla_TEM-1B gene. Remarkably, this study first identified a multidrug-resistant S. marcescens strain co-harboring bla_IMP-26 and mcr-9 on a megaplasmid pYL4.1 and also included a proposed evolutionary pathway of epidemic megaplasmids carrying bla_IMP-26.

Molecular Characterization of Antibiotic Resistance and Genetic Diversity of Klebsiella pneumoniae Strains

The aims of this study were the molecular characterization of antibiotic resistance and genotyping of Klebsiella pneumoniae strains isolated from clinical cases in Tehran, Iran. A total of 100 different types of clinical human samples were collected from a major teaching hospital in Tehran, Iran. Bacterial isolates were identified using standard microbiological tests. Antimicrobial susceptibility testing was done according to the latest CLSI guidelines. PCR was used to amplify the gyrA gene in quinolone-resistant isolates and sequencing was performed for the detection of probable mutations between the isolates. The occurrence of plasmid-mediated quinolone resistance genes (qnrA, qnrB, and qnrS) was also investigated by PCR. Finally, genotyping of the strains was performed by PFGE in a standard condition. The susceptibility pattern revealed a high and low level of resistance against meropenem (20%) and trimethoprim (37%), respectively. PCR and sequencing detected mutation in the gyrA gene in 51% of quinolone-resistant K. pneumoniae. According to the susceptibility report, among nalidixic acid-resistant strains, 60.5%, 50%, and 42.9% of isolates contained qnrA, qnrB, and qnrS, respectively. Among ciprofloxacin-resistant strains, qnrA was the most frequent PMQR gene. The PFGE differentiated the strains into 31 different genetic clusters so that the highest number (7/66) was in category A. Our results indicated that the frequency of resistance to various antibiotics particularly trimethoprim, nalidixic acid, and cefoxitin are increasing. The presence of qnr (S and A) genes and point mutation of the gyrA gene were likely to be responsible for the resistance toward nalidixic acid and ciprofloxacin in our strains. Also, the results obtained from genotyping indicated that the K. pneumoniae strains isolated in this study belonged to the diverse clones.

Characterization of persistent organic pollutants and culturable and non-culturable bacterial communities in pulp and paper sludge after secondary treatment

Due to the presence of various organic contaminants, improper disposal of pulp-paper wastewater poses harm to the environment and human health. In this work, pulp-paper sludge (PPS) after secondary treatment were collected from M/s Century Pulp-paper Mills in India, the chemical nature of the organic pollutants was determined after solvent extraction. All the isolates were able to produce lipase (6.34-3.93 U ml^-1) which could account for the different fatty acids detected in the PPS. The dominant strains were in the classes of α and γ Proteobacteria followed by Firmicutes. The Shannon-Weiner diversity indexes for phylotype richness for the culturable and non-culturable bacterial community were 2.01 and 3.01, respectively, indicating the non-culturable bacterial strains has higher species richness and diversity compared to the culturable bacterial strains. However, the culturable strains had higher species evenness (0.94 vs 0.90). Results suggested only a few isolated strains were resistant to the POPs in the PPS, where as non-cultural bacteria survived by entering viable but non-cultural state. The isolated strains (Brevundimonas diminuta, Aeromonas punctata, Enterobacter hormaechei, Citrobacter braakii, Bacillus pumilus and Brevundimonas terrae) are known for their multidrug resistance but their tolerance to POPs have not previously been reported and deserved further investigation. The findings of this research established the presence of POPs which influence the microbial population. Tertiary treatment is recommended prior to the safe disposal of pulp paper mill waste into the environment.

Report on carbapenemase-producing rare sequence types of Escherichia coli and Enterobacter hormaechei

Introduction and Aim: Carbapenem Resistant Enterobacteriaceae (CRE) have emerged at an alarming rate. Multi locus sequence typing (MLST) is an important parameter for identifying drug resistant organisms.  The present study was carried out for elucidating the mechanisms of CRE and MLSTs associated with CRE. Materials and Methods: CRE (n=14) were obtained from various clinical samples and subjected to Rapidec Carba NP (CNP) test and multiplex polymerase chain reaction (M-PCR) and five isolates proceeded for whole genome sequencing (WGS). ?-lactamase (bla) genes were analysed using Resfinder and CARD tool. Bioinformatics tools: mlplasmids, plasmid finder, mobile element finder, and Center for Genomic Epidemiology (CGE) toolbox were used. Results: All isolates (n=14) were positive for CNP and bla genes using M-PCR. Isolates (J21, J22, J23, J27) were identified as Escherichia coli while (J34) was Enterobacter hormaechei. MLST showed E. coli isolates (J21& J22) as ST648; E. coli (J23) was ST940; E. coli (J27) was ST 2851, and E. hormaechei (J34) was closest to ST1325. Genes blaTEM, blaNDM & blaampC were found to be present in all isolates; blaCTX-M was present in all E. coli isolates but not in E. hormaechei. blaOXA was present in E. coli (J23) and in E. hormaechei (J34); while ESBL blaSFO-1 in E. hormaechei (J34). Conclusion: ESBLs (blaTEM & blaCTXM) and metallo beta-lactamase -MBL (blaNDM) cause carbapenem resistance in rare sequence types of E. coli while; ESBL (blaSFO-1) and MBL (blaNDM) cause carbapenem resistance in                             E. hormaechei.

Genomic characterization of high-risk E. coli and E. hormaechei clones recovered from a single tertiary-care hospital in Pakistan

Aims

Spread of carbapenem‐resistant Enterobacterales have become a global problem. We characterized extended‐spectrum β‐lactamase (ESBL)‐producing Enterobacterales from urinary tract infections cases from Allied Hospital Faisalabad, Pakistan.

Methods and Results

Eleven (22%, 11/50) ESBL‐producing Enterobacterales (Escherichia coli; n = 10 and Enterobacter hormaechei; n = 1) were recovered and processed through VITEK‐2, PCR, rep‐PCR followed by whole‐genome sequencing (WGS) of ESBL‐producing Ent. hormaechei and carbapenem‐resistant E. coli isolates. Plasmid transferability of bla_NDM‐1‐producers was assayed by conjugation experiments. All ESBL strains carried the bla_CTX‐M‐15 gene. Of these bla_CTX‐M‐15 producing E. coli, four also carried bla_NDM‐1 located on transferable plasmids. All E. coli strains belonged to ST448 and displayed similar genetic features including genes for antimicrobial resistance, heavy metal, biocides and virulence. Genomic features of a multidrug‐resistant (MDR) Ent. hormaechei were also reported for the first time in Pakistan.

Conclusion

Our findings indicate that bla_NDM‐1 producing E. coli ST448 is a multidrug, heavy metals and biocides‐resistant strain. Therefore, the screening of these isolates may be effective in limiting the MDR bacteria spread in hospitalized patients and within the community.

Significance and Impact of this Study

Spread of multi‐drug‐resistant ESBL‐producing bacteria in the clinical settings of Pakistan is a serious challenge and further limiting treatment options in the country. WGS could be used as a tool in the nationwide antibiotic surveillance programme to explore insights of spread and outbreak.

Isolation, characterization and biocontrol efficacy of a T4-like phage virulent to multidrug-resistant Enterobacter hormaechei

Enterobacter hormaechei is an important emerging pathogen, often exhibiting resistance to multiple clinically important antibiotics. In this study, E. hormaechei was found, for the first time, to be lethal to fish. Bacteriophages are considered potential treatments for bacterial infections. The lytic phage vB_EhoM-IME523 (abbreviated 'IME523') infecting multidrug-resistant E. hormaechei was isolated from hospital sewage. IME523 exhibits T4-like morphology, including a prolate icosahedral head 110 ± 1.89 nm (mean ± SD) long and 82 ± 0.75 nm wide, and a contractile tail of ca. 110 ± 0.91 nm in length. The complete genome length of phage IME523 is 172763 bp, with a G + C content of 39.97%. The whole genome sequence of IME523 has a 93.10% average nucleotide identity (ANI) and a 53.3% in silico DNA-DNA hybridization (isDDH) value with the closest-related Enterobacter phage vB_EclM_CIP9 ('CIP9'). ANI and isDDH values between IME523 and other phages were lower than 78 and 22%, respectively. IME523 and CIP9 formed a monophyletic branch in a phylogenetic tree based on the terminase large subunit, DNA polymerase protein and whole genome phylogenetic analysis. Results suggest that IME523 is a novel species in the subfamily Tevenvirinae and forms a novel genus together with CIP9. No IME523 open reading frame was found to be associated with virulence factors or antibiotic resistance genes. IME523 showed promising protection to zebrafish and brocade carp against E. hormaechei challenge.

Whole Genome Sequencing of Extended-Spectrum- and AmpC- β-Lactamase-Positive Enterobacterales Isolated From Spinach Production in Gauteng Province, South Africa

The increasing occurrence of multidrug-resistant (MDR) extended-spectrum β-lactamase- (ESBL) and/or AmpC β-lactamase- (AmpC) producing Enterobacterales in irrigation water and associated irrigated fresh produce represents risks related to the environment, food safety, and public health. In South Africa, information about the presence of ESBL/AmpC-producing Enterobacterales from non-clinical sources is limited, particularly in the water-plant-food interface. This study aimed to characterize 19 selected MDR ESBL/AmpC-producing Escherichia coli (n=3), Klebsiella pneumoniae (n=5), Serratia fonticola (n=10), and Salmonella enterica (n=1) isolates from spinach and associated irrigation water samples from two commercial spinach production systems within South Africa, using whole genome sequencing (WGS). Antibiotic resistance genes potentially encoding resistance to eight different classes were present, with bla CTX-M-15 being the dominant ESBL encoding gene and bla ACT-types being the dominant AmpC encoding gene detected. A greater number of resistance genes across more antibiotic classes were seen in all the K. pneumoniae strains, compared to the other genera tested. From one farm, bla CTX-M-15-positive K. pneumoniae strains of the same sequence type 985 (ST 985) were present in spinach at harvest and retail samples after processing, suggesting successful persistence of these MDR strains. In addition, ESBL-producing K. pneumoniae ST15, an emerging high-risk clone causing nosocomical outbreaks worldwide, was isolated from irrigation water. Known resistance plasmid replicon types of Enterobacterales including IncFIB, IncFIA, IncFII, IncB/O, and IncHI1B were observed in all strains following analysis with PlasmidFinder. However, bla CTX-M-15 was the only β-lactamase resistance gene associated with plasmids (IncFII and IncFIB) in K. pneumoniae (n=4) strains. In one E. coli and five K. pneumoniae strains, integron In191 was observed. Relevant similarities to human pathogens were predicted with PathogenFinder for all 19 strains, with a confidence of 0.635-0.721 in S. fonticola, 0.852-0.931 in E. coli, 0.796-0.899 in K. pneumoniae, and 0.939 in the S. enterica strain. The presence of MDR ESBL/AmpC-producing E. coli, K. pneumoniae, S. fonticola, and S. enterica with similarities to human pathogens in the agricultural production systems reflects environmental and food contamination mediated by anthropogenic activities, contributing to the spread of antibiotic resistance genes.

Update of the list of QPS-recommended biological agents intentionally added to food or feed as notified to EFSA 14: suitability of taxonomic units notified to EFSA until March 2021

The qualified presumption of safety (QPS) approach was developed to provide a regularly updated generic pre-evaluation of the safety of biological agents, intended for addition to food or feed, to support the work of EFSA's Scientific Panels. The QPS approach is based on an assessment of published data for each agent, with respect to its taxonomic identity, the body of relevant knowledge, safety concerns and occurrence of antimicrobial resistance. Safety concerns identified for a taxonomic unit (TU) are, where possible, confirmed at the species/strain or product level and reflected by 'qualifications'. In the period covered by this statement, no new information was found that would change the status of previously recommended QPS TUs. Schizochytrium limacinum, which is a synonym for Aurantiochytrium limacinum, was added to the QPS list. Of the 78 microorganisms notified to EFSA between October 2020 and March 2021, 71 were excluded; 16 filamentous fungi, 1 Dyella spp., 1 Enterococcus faecium, 7 Escherichia coli, 1 Streptomyces spp., 1 Schizochytrium spp. and 44 TUs that had been previously evaluated. Seven TUs were evaluated: Corynebacterium stationis and Kodamaea ohmeri were re-assessed because an update was requested for the current mandate. Anoxybacillus caldiproteolyticus, Bacillus paralicheniformis, Enterobacter hormaechei, Eremothecium ashbyi and Lactococcus garvieae were assessed for the first time. The following TUs were not recommended for QPS status: A. caldiproteolyticus due to the lack of a body of knowledge in relation to its use in the food or feed chain, E. hormaechei, L. garvieae and K. ohmeri due to their pathogenic potential, E. ashbyi and C. stationis due to a lack of body of knowledge on their occurrence in the food and feed chain and to their pathogenic potential. B. paralicheniformis was recommended for the QPS status with the qualification 'absence of toxigenic activity' and 'absence of genetic information to synthesize bacitracin'.

Role played by the environment in the emergence and spread of antimicrobial resistance (AMR) through the food chain

The role of food-producing environments in the emergence and spread of antimicrobial resistance (AMR) in EU plant-based food production, terrestrial animals (poultry, cattle and pigs) and aquaculture was assessed. Among the various sources and transmission routes identified, fertilisers of faecal origin, irrigation and surface water for plant-based food and water for aquaculture were considered of major importance. For terrestrial animal production, potential sources consist of feed, humans, water, air/dust, soil, wildlife, rodents, arthropods and equipment. Among those, evidence was found for introduction with feed and humans, for the other sources, the importance could not be assessed. Several ARB of highest priority for public health, such as carbapenem or extended-spectrum cephalosporin and/or fluoroquinolone-resistant Enterobacterales (including Salmonella enterica), fluoroquinolone-resistant Campylobacter spp., methicillin-resistant Staphylococcus aureus and glycopeptide-resistant Enterococcus faecium and E. faecalis were identified. Among highest priority ARGs bla CTX -M, bla VIM, bla NDM, bla OXA -48-like, bla OXA -23, mcr, armA, vanA, cfr and optrA were reported. These highest priority bacteria and genes were identified in different sources, at primary and post-harvest level, particularly faeces/manure, soil and water. For all sectors, reducing the occurrence of faecal microbial contamination of fertilisers, water, feed and the production environment and minimising persistence/recycling of ARB within animal production facilities is a priority. Proper implementation of good hygiene practices, biosecurity and food safety management systems is very important. Potential AMR-specific interventions are in the early stages of development. Many data gaps relating to sources and relevance of transmission routes, diversity of ARB and ARGs, effectiveness of mitigation measures were identified. Representative epidemiological and attribution studies on AMR and its effective control in food production environments at EU level, linked to One Health and environmental initiatives, are urgently required.

Endophytic Bacteria Enterobacter hormaechei Fabricated Silver Nanoparticles and Their Antimicrobial Activity

Antimicrobial resistance (AMR), one of the greatest issues for humankind, draws special attention to the scientists formulating new drugs to prevent it. Great emphasis on the biological synthesis of silver nanoparticles (AgNPs) for utilization in single or combinatorial therapy will open up new avenues to the discovery of new antimicrobial drugs. The purpose of this study was to synthesize AgNPs following a green approach by using an endophytic bacterial strain, Enterobacter hormaechei, and to assess their antimicrobial potential against five pathogenic and four multidrug-resistant (MDR) microbes. UV-Vis spectroscopy, fourier-transform infrared spectroscopy (FTIR), transmission electron microscopy (TEM), scanning electron microscopy-energy dispersive X-ray spectroscopy (SEM-EDX), and zeta potential (ζ) were used to characterize the synthesized AgNPs. Endophytic E. hormaechei-mediated AgNPs (Eh-AgNPs) were represented by a strong UV-Vis absorbance peak at 418 nm within 5 min, forming spherical and polydispersed nanoparticles in the size range of 9.91 nm to 92.54 nm. The Eh-AgNPs were moderately stable with a mean ζ value of -19.73 ± 3.94 mV. The presence of amine, amide, and hydroxyl functional groups was observed from FTIR analysis. In comparison to conventional antibiotics, the Eh-AgNPs were more effective against Bacillus cereus (ATCC 10876) and Candida albicans (ATCC 10231), exhibiting 9.14 ± 0.05 mm and 8.24 ± 0.05 mm zones of inhibition (ZOIs), respectively, while displaying effective inhibitory activity with ZOIs ranging from 10.98 ± 0.08 to 13.20 ± 0.07 mm against the MDR bacteria. Eh-AgNP synthesis was rapid and eco-friendly. The results showed that Eh-AgNPs are promising antimicrobial agents that can be used in the development and formulation of new drugs to curb the menace of antimicrobial resistance in pathogenic and MDR microbes.