Molecular epidemiological analysis and risk factors for acquisition of carbapenemase-producing Enterobacter cloacae complex in a Japanese university hospital

Clinical Characteristics, Prognosis and Treatment of Bloodstream Infections with Enterobacter Cloacae Complex in a Chinese Tertiary Hospital: A Retrospective Study

Objective

This research aimed to analyze the clinical characteristics, prognosis, and antimicrobial treatment of bloodstream infections (BSI) caused by Enterobacter cloacae complex (ECC).

Methods

The clinical data of patients with bloodstream infections caused by Enterobacter cloacae complex from April 2017 to June 2023 were collected retrospectively. These data were then analyzed in subgroups based on the detection results of extended-spectrum β-lactamase (ESBL), 30-day mortality, and the type of antimicrobial agent used (β-lactam/β-lactamase inhibitor combinations (BLICs) or carbapenems).

Results

The proportion of ESBL-producing Enterobacter cloacae complex was 32.5% (37/114). Meanwhile, ICU admission, receiving surgical treatment within 3 months, and biliary tract infection were identified as risk factors for ESBL-producing ECC-BSI. Additionally, immunocompromised status and Sequential Organ Failure Assessment (SOFA) score ≥ 6.0 were identified as independent risk factors of 30-day mortality in patients with ECC-BSI (n = 108). Further analysis in BSI patients caused by non-ESBL-producing ECC revealed that patients treated with BLICs (n = 45) had lower SOFA scores and lower incidence of hypoproteinemia and sepsis compared with patients treated with carbapenems (n = 20). Moreover, in non-ESBL-producing ECC-BSI patients, the univariate Cox regression analysis indicated a significantly lower 30-day mortality rate in patients treated with BLICs compared to those treated with carbapenems (hazard ratios (HR) [95% CI] 0.190 [0.055-0.662], P = 0.009; adjusted HR [95% CI] 0.106 [0.013-0.863], P = 0.036).

Conclusion

This study investigated the factors influencing the susceptibility to infection by ESBL-producing strains and risk factors for 30-day mortality in ECC-BSI patients. The results revealed that ESBL-negative ECC-BSI patients treated with BLICs exhibited significantly lower 30-day mortality compared to those treated with carbapenems. BLICs were found to be more effective in ECC-BSI patients with milder disease (ESBL-negative and SOFA ≤6.0).

Burden of Antimicrobial Resistance in Japan: A Systematic Literature Review and Meta-Analysis

INTRODUCTION

Antimicrobial resistance (AMR) is one of the most serious public health challenges worldwide, including in Japan. However, there is limited evidence assessing the AMR burden in Japan. Thus, this systematic literature review (SLR) and meta-analysis (MA) were conducted to assess the clinical and economic burden of AMR in Japan.

METHODS

Comprehensive literature searches were performed on EMBASE, MEDLINE, the Cochrane Library, and ICHUSHI between 2012 and 2022 following the Preferred Reporting Items for Systematic Reviews and Meta-Analysis guidelines. MA estimated a pooled effect between the two comparative arms (AMR vs. non-AMR). The results were reported in measures of odds ratios (ORs) for in-hospital mortality and in standardized mean differences (SMDs) for length of stay (LOS) and direct medical costs.

RESULTS

Literature searches identified 1256 de-duplicated records, of which 56 observational studies (English, n = 35; Japanese, n = 21) were included. Of note, twenty-two studies (39.3%) compared the AMR group with non-AMR group. In the SLR, in-hospital mortality, LOS, and direct medical costs were higher in the AMR group compared to the non-AMR group. Eight studies were selected for the MA. In the AMR group, the pooled estimate showed a statistically higher in-hospital mortality [random effect (RE)-OR 2.25, 95% CI 1.34-3.79; I2 = 89%; τ2 = 0.2257, p < 0.01], LOS (RE-SMD 0.37, 95% CI  - 0.09-0.84; I2 = 99%; τ2 = 0.3600, p < 0.01), and direct medical cost (RE-SMD 0.53, 95% CI 0.43-0.62; I2 = 0.0%; τ2 = 0.0, p = 0.88) versus the non-AMR group.

CONCLUSION

Our study presents an overview of the clinical and economic burden of AMR in Japan. Patients with AMR infections experience significantly higher in-hospital mortality, LOS, and direct medical costs compared with patients without AMR infections.

Association of short-course antimicrobial therapy and bacterial resistance in acute cholangitis: Retrospective cohort study

Background and study aims Although the number of resistant bacteria tends to increase with prolonged antimicrobial therapy, no studies have examined the relationship between the duration of antimicrobial therapy and increase in the number of resistant bacteria in acute cholangitis. We hypothesized that the short-term administration of antimicrobial agents in acute cholangitis would suppress bacterial resistance. Patients and methods This was a single-center, retrospective, observational study of patients with acute cholangitis admitted between January 2018 and June 2020 who met the following criteria: successful biliary drainage, positive blood or bile cultures, bacteria identified from cultures sensitive to antimicrobials, and subsequent cholangitis recurrence by January 2022. The patients were divided into two groups: those whose causative organisms at the time of recurrence became resistant to the antimicrobial agents used at the time of initial admission (resistant group) and those who remained susceptible (susceptible group). Multivariate analysis was used to examine risk factors associated with the development of resistant pathogens. Multivariate analysis investigated antibiotics used with the length of 3 days or shorter after endoscopic retrograde cholangiopancreatography (ERCP) and previously reported risk factors for the development of bacterial resistance. Results In total, 89 eligible patients were included in this study. There were no significant differences in patient background or ERCP findings between the groups. The use of antibiotics, completed within 3 days after ERCP, was associated with a lower risk of developing bacterial resistance (odds ratio, 0.17; 95% confidence interval, 0.04-0.65; P =0.01). Conclusions In acute cholangitis, the administration of antimicrobials within 3 days of ERCP may suppress the development of resistant bacteria.

Draft Genome Sequence of Enterobacter cloacae S23 a Plant Growth-promoting Passenger Endophytic Bacterium Isolated from Groundnut Nodule Possesses Stress Tolerance Traits

Aim

This study aims to reveal the passenger endophytic bacterium Enterobacter cloacae S23 isolated from groundnut nodules and to underpin the molecular mechanism and genes responsible for abiotic stress tolerance.

Background

A variety of microorganisms that contribute to nodulation and encourage plant development activity in addition to the nodulating Rhizobium. Passenger endophytes (PE) are endophytes that accidentally penetrate the plant without any selective pressure keeping them in the interior tissue of the plant. PE possesses characteristics that encourage plant development and boost output while reducing pathogen infection and improving biotic and abiotic stress tolerance. However, there is a lack of molecular evidence on the passenger endophyte-mediated alleviation of abiotic stresses.

Objective

This study was formulated to reveal the draft genome sequence of Enterobacter cloacae S23, as well as genes and characteristics involved in plant growth promotion and stress tolerance.

Method

The data were submitted to PATRIC and the TORMES-1.0 Unicyclker tools were used to conduct a complete genome study of Enterobacter cloacae S23. The TORMES-1.0 platform was used to process the reads. RAST tool kit (RASTtk) was used to annotate the S23 sequence. The plant growth-promoting traits such as indole acetic acid production, siderophore secretion, production of extracellular polysaccharides, biofilm formation, phosphate solubilization, and accumulation of osmolytes were examined under normal, 7% NaCl and 30% polyethylene glycol amended conditions to determine their ability to withstand salt and moisture stressed conditions, respectively.

Result

We report the size of Enterobacter cloacae S23 is 4.82Mb which contains 4511 protein-coding sequences, 71 transfer RNA genes, and 3 ribosomal RNA with a G+C content of DNA is 55.10%. Functional analysis revealed that most of the genes are involved in the metabolism of amino acids, cofactors, vitamins, stress response, nutrient solubilization (kdp, pho, pst), biofilm formation (pga) IAA production (trp), siderophore production (luc, fhu, fep, ent, ybd), defense, and virulence. The result revealed that E. cloacae S23 exhibited multiple plant growth-promoting traits under abiotic stress conditions.

Conclusion

Our research suggested that the discovery of anticipated genes and metabolic pathways might characterise this bacterium as an environmentally friendly bioresource to support groundnut growth through several mechanisms of action under multi-stresses.

Diagnostic Performance of BD Phoenix CPO Detect Panels for Detection and Classification of Carbapenemase-Producing Gram-Negative Bacteria

BD Phoenix CPO Detect panels can identify and classify carbapenemase-producing organisms (CPOs) simultaneously with antimicrobial susceptibility testing (AST) for Gram-negative bacteria. Detection and classification of carbapenemase producers were performed using the BD Phoenix CPO Detect panels NMIC/ID-441 for Enterobacterales, NMIC/ID-442 for nonfermenting bacteria, and NMIC-440 for both. The results were compared with those obtained using comparator methods. A total of 133 strains (32 Klebsiella pneumoniae, 37 Enterobacter cloacae complex, 33 Pseudomonas aeruginosa, and 31 Acinetobacter baumannii complex strains), including 60 carbapenemase producers (54 imipenemases [IMPs] and 6 OXA type), were analyzed. Using panels NMIC-440 and NMIC/ID-441 or NMIC/ID-442, all 54 IMP producers were accurately identified as CPOs (positive percent agreement [PPA], 100.0%; 54/54). Among the 54 IMP producers identified as CPOs using panels NMIC-440 and NMIC/ID-441, 12 and 14 Enterobacterales were not resistant to carbapenem, respectively. Among all 54 IMP producers, 48 (88.9%; 48/54) were correctly classified as Ambler class B using panel NMIC-440. Using panels NMIC-440 and NMIC/ID-442, all four OXA-23-like carbapenemase-producing A. baumannii complex strains (100.0%, 4/4) were correctly identified as CPOs, and three (75.0%, 3/4) were precisely classified as class D using panel NMIC-440. Both carbapenemase producers harboring the blaISAba1-OXA-51-like gene were incorrectly identified as non-CPOs using panels NMIC-440 and NMIC/ID-442. For detecting carbapenemase producers, the overall PPA and negative percent agreement (NPA) between panel NMIC-440 and the comparator methods were 96.7% (58/60) and 71.2% (52/73), respectively, and the PPA and NPA between panels NMIC/ID-441 or NMIC/ID-442 and the comparator methods were 96.7% (58/60) and 74.0% (54/73), respectively. BD Phoenix CPO Detect panels can successfully screen carbapenemase producers, particularly IMP producers, regardless of the presence of carbapenem resistance and can be beneficial in routine AST workflows. IMPORTANCE Simple and efficient screening methods of detecting carbapenemase producers are required. BD Phoenix CPO Detect panels effectively screened carbapenemase producers, particularly IMP producers, with a high overall PPA. As the panels enable automatic screening for carbapenemase producers simultaneously with AST, the workflow from AST to confirmatory testing for carbapenemase production can be shortened. In addition, because carbapenem resistance varies among carbapenemase producers, the BD Phoenix CPO Detect panels, which can screen carbapenemase producers regardless of carbapenem susceptibility, can contribute to the accurate detection of carbapenemase producers. Our results report that these panels can help streamline the AST workflow before confirmatory testing for carbapenemase production in routine microbiological tests.

Genomic and clinical characteristics of carbapenem-resistant Enterobacter cloacae complex isolates collected in a Chinese tertiary hospital during 2013-2021

Objective

To analyze the molecular epidemiology of carbapenem-resistant Enterobacter cloacae complex (CREC) by whole-genome sequencing and to explore its clinical characteristics.

Methods

Enterobacter cloacae complex isolates collected in a tertiary hospital during 2013-2021 were subjected to whole-genome sequencing to determine the distribution of antimicrobial resistance genes (ARGs), sequence types (STs), and plasmid replicons. A phylogenetic tree of the CREC strains was constructed based on the whole-genome sequences to analyze their relationships. Clinical patient information was collected for risk factor analysis.

Results

Among the 51 CREC strains collected, blaNDM-1 (n = 42, 82.4%) was the main carbapenem-hydrolyzing β-lactamase (CHβL), followed by blaIMP-4 (n = 11, 21.6%). Several other extended-spectrum β-lactamase-encoding genes were also identified, with blaSHV-12 (n = 30, 58.8%) and blaTEM-1B (n = 24, 47.1%) being the predominant ones. Multi-locus sequence typing revealed 25 distinct STs, and ST418 (n = 12, 23.5%) was the predominant clone. Plasmid analysis identified 15 types of plasmid replicons, among which IncHI2 (n = 33, 64.7%) and IncHI2A (n = 33, 64.7%) were the main ones. Risk factor analysis showed that intensive care unit (ICU) admission, autoimmune disease, pulmonary infection, and previous corticosteroid use within 1 month were major risk factors for acquiring CREC. Logistic regression analysis showed that ICU admission was an independent risk factor for CREC acquisition and was closely related with acquiring infection by CREC with ST418.

Conclusion

BlaNDM-1 and blaIMP-4 were the predominant carbapenem resistance genes. ST418 carrying BlaNDM-1 not only was the main clone, but also circulated in the ICU of our hospital during 2019-2021, which highlights the necessity for surveillance of this strain in the ICU. Furthermore, patients with risk factors for CREC acquisition, including ICU admission, autoimmune disease, pulmonary infection, and previous corticosteroid use within 1 month, need to be closely monitored for CREC infection.

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.

Molecular characterization of NDM-1-producing carbapenem-resistant E. cloacae complex from a tertiary hospital in Chongqing, China

Background

The aim of this study was to clarify the molecular characterization of NDM-1-producing carbapenem-resistant Enterobacter cloacae complex (CREL) at a teaching hospital in Chongqing, China.

Methods

Antimicrobial susceptibility and resistance genes were analyzed. Epidemiological relationship was analyzed by pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). Conjugation experiments were performed to determine the transferability of plasmids. Whole-genome sequencing (WGS) of strains was implemented, and the genetic environment of the blaNDM-1- and mcr-9-carrying plasmids was analyzed.

Results

A total of 10 blaNDM-1-positive CREL isolates were identified. All isolates harbored multiple resistance genes. ECL68 and ECL78 co-produce blaNDM-1 and mcr-9. Among the four different sequence types (STs) detected, ST1466 was assigned as a novel ST. Six isolates exhibited highly similar PFGE patterns. Conjugation assay proved that all plasmids containing blaNDM-1 or mcr-9 could be transferred to the recipient Escherichia coli. WGS indicated that blaNDM-1 genes were carried by diverse plasmids, including IncHI2/IncN, IncX3, and one unclassified plasmid type. The backbone structure of these plasmids is involved in replication initiation (repAB), partitioning (parABM), and conjugation/type IV secretion (tra/virB). Analysis of the genetic environment showed that blaNDM-1 in three plasmids exhibited a highly similar structure to protype Tn125. Co-existence of blaNDM-1 and the colistin resistance gene mcr-9 was detected in the two isolates, ECL68 and ECL78. In ECL68, blaNDM-1 and mcr-9 were present on the same plasmid while located in two separate plasmids in ECL78. The genetic environment of mcr-9 was organized as IS26-wbuC-mcr-9-IS903-pcoS-pcoE-rcnA-rcnR, and the two-component system encoding genes qseC and qseB was not found in two plasmids, which could explain mcr-9-harboring strains’ colistin susceptibility.

Conclusions

We first report a nosocomial outbreak of NDM-1-producing E. cloacae complex ST177 in China. Conjugative plasmids contributed to the horizontal transfer of antibiotic resistance genes. The prevalence and even coexistence of blaNDM-1 and mcr-9 may further threaten public health. Our results highlight further surveillance for blaNDM-1, and mcr-9 is essential to prevent its dissemination.

＜Editors' Choice＞ Multicenter survey for carbapenemase-producing Enterobacterales in central Japan

Carbapenemase-producing Enterobacterales (CPE) raise concerns about the treatment options for infectious diseases and infection control. We conducted a multicenter study to clarify the molecular epidemiology of CPE in the Aichi Prefecture during the first 3-month period from 2015 to 2019. Carbapenemase production was screened using a modified carbapenem inactivation method, and the genotypes of the carbapenemase genes were determined by polymerase chain reaction sequencing. Genetic relatedness was analyzed using multilocus sequence typing (MLST). Twenty-four hospitals participated in this study. Of the 56,494 Enterobacterales strains detected during the study period, 341 (0.6%) that met the susceptibility criteria were analyzed. Sixty-five of the 341 strains were determined to be CPE, with an incidence rate of 0.12% (65/56,494). The bacterial species responsible for CPE were Klebsiella pneumoniae (n = 24), Enterobacter cloacae complex (n = 23), Klebsiella oxytoca (n = 10), and Escherichia coli (n = 8). Most of the carbapenemase genotypes were IMP-1 (58/65), and only three were IMP-6 types. Three E. coli strains that produced NDM-5 were detected. MLST analysis showed that Sequence type (ST) 78 was predominant in E. cloacae complex CPE (14/23, 60.9%). Meanwhile, various STs were detected in carbapenemase-producing (CP) K. pneumoniae, of which ST37 and ST517 were the most common. The incidence rate of CPE in this region was comparable to national data. This 3-month surveillance revealed the spread of ST78 of CP E. cloacae complex and ST517 and ST592 of CP K. pneumoniae across hospitals, indicating the need to strengthen regional infection control programs.

Clinical characteristics and treatment outcomes of carbapenem-resistant Enterobacterales infections in Japan

OBJECTIVES

The dissemination of difficult-to-treat carbapenem-resistant Enterobacterales (CRE) is of great concern. We clarified the risk factors underlying CRE infection mortality in Japan.

METHODS

We conducted a retrospective, multicentre, observational cohort study of patients with CRE infections at 28 university hospitals from September 2014 to December 2016, using the Japanese National Surveillance criteria. Clinical information, including patient background, type of infection, antibiotic treatment, and treatment outcome, was collected. The carbapenemase genotype was determined using PCR sequencing. Multivariate analysis was performed to identify the risk factors for 28-day mortality.

RESULTS

Among the 179 patients enrolled, 65 patients (36.3%) had bloodstream infections, with 37 (20.7%) infections occurring due to carbapenemase-producing Enterobacterales (CPE); all carbapenemases were of IMP-type (IMP-1: 32, IMP-6: 5). Two-thirds of CPE were identified as Enterobacter cloacae complex. Combination therapy was administered only in 46 patients (25.7%), and the 28-day mortality rate was 14.3%. Univariate analysis showed that solid metastatic cancer, Charlson Comorbidity Index ≥3, bloodstream infection, pneumonia, or empyema, central venous catheters, mechanical ventilation, and prior use of quinolones were significant risk factors for mortality. Multivariate analysis revealed that mechanical ventilation (OR: 6.71 [1.42-31.6], P = 0.016), solid metastatic cancers (OR: 5.63 [1.38-23.0], P = 0.016), and bloodstream infections (OR: 3.49 [1.02-12.0], P = 0.046) were independent risk factors for 28-day mortality.

CONCLUSION

The significant risk factors for 28-day mortality in patients with CRE infections in Japan are mechanical ventilation, solid metastatic cancers, and bloodstream infections.

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.

Effect of Antibiotic Resistance of Pathogens on Initial Antibiotic Therapy for Patients With Cholangitis

Objectives

Considering that pathogens resistant to initial antibiotic therapies for cholangitis can affect mortality rates, appropriate initial empiric antibiotic therapy is important. However, evidence regarding the influence of pathogens resistant to initial antibiotics in patients with cholangitis who have undergone early endoscopic retrograde cholangiopancreatography (ERCP) is limited, and the conditions in several cases can improve with early ERCP even when pathogens resistant to initial antibiotics are detected on time. Therefore, this study aimed to assess the influence of pathogens resistant to initial antibiotics on the course of cholangitis in patients undergoing early ERCP.

Materials and methods

Patients (n=266) with positive blood or bile culture results treated with early ERCP were divided into those with cultures that were resistant to the initial antibiotics (antibiotic-resistant group; n=66; 24.8%) and those with cultures that were sensitive to the initial antibiotics (antibiotic-sensitive group; n=200; 75.2%). The duration of hospitalization, in-hospital mortality rates due to cholangitis, rates of increased disease severity, and complications during hospitalization were studied.

Results

Enterococcus, Enterobacter, Citrobacter, and Pseudomonas species showed high resistance to several antibiotics. No significant between-group differences were found in the duration of hospitalization, in-hospital mortality rates due to cholangitis, and rates of increased disease severity. However, the rate of post-ERCP cholecystitis was significantly higher in the antibiotic-resistant group than in the antibiotic-sensitive group (p=0.0245).

Conclusions

Even if the initial antibiotics were ineffective, the rate of fatal outcomes did not increase among patients with cholangitis who had undergone early ERCP. However, when initial antibiotics were ineffective, the frequency of post-ERCP cholecystitis increased even after early bile duct decompression.

Molecular epidemiology of Enterobacter cloacae complex isolates with reduced carbapenem susceptibility recovered by blood culture

The Enterobacter cloacae complex (ECC) is one of the most common causes of bacteremia and leads to poor clinical outcomes. The aim of this study was to clarify the antimicrobial susceptibility profiles and genetic backgrounds of non-carbapenemase-producing reduced-carbapenem-susceptible (RCS) ECC blood isolates in Japan using agar dilution antimicrobial susceptibility testing, whole-genome sequencing, and quantitative polymerase chain reaction for assays of ampC, ompC and ompF transcripts. Forty-two ECC blood isolates were categorized into RCS and carbapenem-susceptible groups based on imipenem minimum inhibitory concentration. RCS ECC blood isolates belonged to distinct species and sequence types and produced varying class C β-lactamases. The E. roggenkampii, E. asburiae, and E. bugandensis isolates belonged only to the RCS group. Some E. hormaecheii ssp. steigerwaltii isolates of the RCS group exhibited AmpC overexpression caused by amino acid substitutions in AmpD and AmpR along with ompF gene downregulation. These findings suggest that non-carbapenemase-producing RCS ECC blood isolates are genetically diverse.

Institutional outbreak involving multiple clades of IMP-producing Enterobacter cloacae complex sequence type 78 at a cancer center in Tokyo, Japan

Background

Information about the clinical and microbiological characteristics of IMP-producing Enterobacterales has been limited. Here, we describe an institutional outbreak of IMP-producing Enterobacter cloacae complex (ECC) involving multiple clades of ECC sequence type (ST) 78 strains.

Methods

Antimicrobial susceptibility testing, whole-genome sequencing, and conjugation experiments of 18 IMP-producing ECC strains isolated during four-year study period were performed. Species and subspecies were determined by average nucleotide identity analysis and clonal relatedness of the isolates was analyzed with multilocus sequence typing and core-genome single nucleotide polymorphism (SNP) analysis. Relevant clinical information was extracted from medical records.

Results

Fourteen of 18 IMP-producing ECC isolates were determined as Enterobacter hormaechei ST78. Sixteen isolates, including 13 isolates belonging to ST78, carried bla_IMP-1 in In316-like class 1 integron and also carried IncHI2 plasmids. Conjugation experiments were successful for 12 isolates carrying bla_IMP-1 on IncHI2 plasmids and for an isolate carrying bla_IMP-11 on an IncL/M plasmid. Although isolation of ST78 strains was clustered in a 14-months period suggesting nosocomial transmission, these strains were subdivided into three clades by SNP analysis: clade A (n = 10), clade B (n = 1), clade C (n = 3). A part of clonal relatedness was unexpected by the epidemiological information at the time of isolation of the strains. Most of the IMP-producing ECC strains were susceptible to non-β-lactam antibiotics and had relatively low minimum inhibitory concentrations to carbapenems (≤4 μg/mL). Five of six infections caused by IMP-producing ECC were treated successfully.

Conclusions

Whole-genome sequencing analysis revealed the outbreak was caused by three different clades of ST78 strains, where patients had favorable treatment outcome of the infections compared with that caused by Enterobacterales producing other carbapenemases, possibly due to their non-multidrug-resistant phenotype.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12879-021-05952-9.

Acquisition of MDR-GNB in hospital settings: a systematic review and meta-analysis focusing on ESBL-E

INTRODUCTION

Extended-spectrum beta-lactamase-producing Enterobacterales (ESBL-E) and other multi-drug-resistant Gram-negative bacteria (MDR-GNB) have disseminated globally since their discovery in the late 20^th century. Various infection prevention and control measures are in place to prevent nosocomial transmission of these organisms, but their efficacy remains disputed. New literature has emerged in recent years providing further evidence which can be used to formulate effective strategies to tackle this issue in the future.

METHODS

A systematic review was performed to characterize the prevalence of colonization of multi-drug-resistant organisms and subsequent acquisition of these organisms within hospital settings. A meta-analysis was performed to characterize the prevalence and acquisition of ESBL-E in Europe and North America.

RESULTS

Twenty-eight studies fulfilled the inclusion criteria. Escherichia coli formed the main burden of MDR-GNB colonization worldwide. Patient-to-patient transmission of ESBL-E was found to be rare, but increased transmissibility of Klebsiella pneumoniae was described over E. coli. Within European and North American healthcare settings, a meta-analysis of eight studies identified a pooled prevalence of ESBL-E on admission to hospital of 7.91% and an acquisition rate of 3.73%.

DISCUSSION

Low prevalence at the point of hospital admission and insufficient evidence of patient-to-patient transmission suggests that infection prevention and control measures such as universal surveillance screening and single-room isolation are unlikely to be practical or effective interventions in reducing the overall burden of ESBL-E in hospitals, in line with current European guidelines. Instead, it is argued that efforts should be placed on controlling the spread of these organisms and other MDR-GNB in the community, predominantly long-term care facilities.

Carbapenem-Resistant Enterobacter cloacae Causing Nosocomial Infections in Southwestern China: Molecular Epidemiology, Risk Factors, and Predictors of Mortality

Background

The emergence and spread of carbapenem-resistant Enterobacter cloacae (CR-ECL) have posed a serious threat to clinical management. This retrospective study assessed the epidemiological characteristics of CR-ECL to explore the risk factors and predictors of mortality in patients with CR-ECL infection.

Methods

We performed a retrospective 1:2 case-control study of hospitalized patients from January 2014 to December 2017. A total of 85 consecutive unique CR-ECL strains comprised the case group, and 170 matched patients with carbapenem-susceptible Enterobacter cloacae (CS-ECL) infection at the same period as the control group. Isolates were screened for potential resistance genes by polymerase chain reaction (PCR) and molecular typing was performed by multilocus sequence typing (MLST).

Results

The results of drug resistance gene detection showed that blaNDM-1 was the most common carbapenem resistance gene. The MLST results showed that ST51 was the predominant epidemic type, followed by ST88. ICU admission (P<0.001), drainage tube (P=0.002), central venous catheter (P=0.005), and carbapenem exposure (P=0.003) were independent risk factors for CR-ECL infection. Significant predictors for 28-day mortality included solid tumours (P=0.005), septic shock (P=0.019), and mechanical ventilation (P=0.027).

Conclusion

Our study indicated that ST51 and ST88, which are closely related, were the predominant epidemic types of CR-ECL producing blaNDM-1 in southwestern China. Strengthening the surveillance of patients with solid tumours, septic shock and mechanical ventilation is an urgent need.

Carbapenemase-producing Enterobacteriaceae - once positive always positive?

PURPOSE OF REVIEW

This review provides an overview of gastrointestinal tract colonization with carbapenemase-producing Enterobacteriaceae (CPE), including risk factors for colonization, determinants for duration of colonization, and whether patients can decolonize, either spontaneously or via targeted interventions.

RECENT FINDINGS

CPE colonization is disseminating globally with increasing numbers of carbapenemases being identified in increasing patient cohorts. Numerous risk factors including repeated healthcare contact, patient co-morbidities and international travel have all been linked to increased rates of colonization. Duration of colonization has been investigated in various healthcare settings and ranges many months or even years. Although new methods for expediting decolonization are being investigated, including faecal microbiota transplantation, high quality evidence of impact is lacking.

SUMMARY

Current evidence indicates that CPE colonization usually persists throughout the duration of most hospital admissions, although the majority of patients will subsequently spontaneously decolonize. Difficulties remain in determining the point at which patients can be considered decolonized because of the lack acceptable criteria for defining eradication. This has significance implications for infection prevention and control measures during the initial and subsequent hospital admissions. Strategies to reduce the healthcare burden of CPE colonization continue to rely predominantly on preventing acquisition, whereas decolonization efforts remain a focus of research.

IMP-68, a Novel IMP-Type Metallo-β-Lactamase in Imipenem-Susceptible Klebsiella pneumoniae

We recently detected a novel variant of an IMP-type metallo-β-lactamase gene (bla _IMP-68) from meropenem-resistant but imipenem-susceptible Klebsiella pneumoniae TA6363 isolated in Tokyo, Japan. bla _IMP-68 encodes a Ser262Gly point mutant of IMP-11, and transformation experiments showed that bla _IMP-68 increased the MIC of carbapenems in recipient strains, whereas the MIC of imipenem was not greatly increased relative to that of other carbapenems, including meropenem. Kinetics experiments showed that IMP-68 imipenem-hydrolyzing activity was lower than that for other carbapenems, suggesting that the antimicrobial susceptibility profile of TA6363 originated from IMP-68 substrate specificity. Whole-genome sequencing showed that bla _IMP-68 is harbored by the class 1 integron located on the IncL/M plasmid pTMTA63632 (88,953 bp), which was transferable via conjugation. The presence of plasmid-borne bla _IMP-68 is notable, because it conferred antimicrobial resistance to carbapenems, except for imipenem, on Enterobacteriaceae and will likely affect treatment plans using antibacterial agents in clinical settings.IMPORTANCE IMP-type metallo-β-lactamases comprise one group of the "Big 5" carbapenemases. Here, a novel bla _IMP-68 gene encoding IMP-68 (harboring a Ser262Gly point mutant of IMP-11) was discovered from meropenem-resistant but imipenem-susceptible Klebsiella pneumoniae TA6363. The Ser262Gly substitution was previously identified as important for substrate specificity according to a study of other IMP variants, including IMP-6. We confirmed that IMP-68 exhibited weaker imipenem-hydrolyzing activity than that for other carbapenems, demonstrating that the antimicrobial susceptibility profile of TA6363 originated from IMP-68 substrate specificity, with this likely to affect treatment strategies using antibacterial agents in clinical settings. Notably, the carbapenem resistance conferred by IMP-68 was undetectable based on the MIC of imipenem as a carbapenem representative, which demonstrates a comparable antimicrobial susceptibility profile to IMP-6-producing Enterobacteriaceae that previously spread in Japan due to lack of awareness of its existence.