Prevalence of, and risk factors for, carriage of carbapenem-resistant Enterobacteriaceae among hospitalized patients in Japan

Minocycline and Omadacycline Resistance Among Carbapenem-Resistant Gram-Negative Bacteria: Antimicrobial Susceptibility Testing and Molecular Characterization

Increasing prevalence of multidrug-resistant infections has rendered the healthcare systems ineffective in managing infectious diseases. Drugs of "last resort" like carbapenems and polymyxins are becoming less effective in the management of antibiotic-resistant Gram-negative bacterial infections, leaving the clinicians with limited choices. Evaluation of the efficacy of other available broad-spectrum antibiotics (belonging to a different class) is warranted as a treatment alternative. The current study was undertaken to evaluate the in vitro antibacterial activity of minocycline and a new drug, omadacycline among carbapenem-resistant Gram-negative bacteria (GNB), isolated from clinical samples (pus and sputum) and to genotypically analyze them. A prospective cross-sectional study was conducted in a 3,200-bedded tertiary care medical center, located in Lucknow in the northern part of India. All the clinical isolates recovered from pus and sputum samples of patients admitted in intensive care units were processed according to the standard protocols. Identification and antibiotic susceptibility testing were performed, and carbapenem-resistant Gram-negative bacteria (CRGNB) showing resistance to minocycline were included in the study. Molecular screening of β-lactamase and tetracycline resistance genes was done by the conventional polymerase chain reaction method. Minimum inhibitory concentration analysis was performed using the broth microdilution technique. Among 700 CRGNB, 15.29% (n = 107/700) were minocycline resistant by disk diffusion method. Genetic analysis demonstrated the presence of tetracycline-resistant genes in about one-third isolates, among which the tet(B) gene was present in 41.12% (n = 44/107). Upon broth microdilution analysis, the overall minimum inhibitory concentration for minocycline was raised, wherein 4.76% (n = 5/107) of our clinical Gram-negative isolates were inhibited at ≤8 mg/L and 15.23% (n = 28/107) were inhibited at ≤16 mg/L. Omadacycline was able to inhibit 13.08% (n = 14/107) of the minocycline-resistant isolates at ≤4 mg/L (susceptible breakpoint for Enterobacterales). Based on the cut-off value proposed, 15.09% (n = 16/107) isolates resistant to minocycline were inhibited by omadacycline. High prevalence of multidrug-resistant bugs entails judicious use of minocycline and omadacycline. The presence of tet genes coexisting with blaNDM and blaOXA in our bacterial isolates shows that the resistance pattern in Gram-negative bacilli is regularly evolving, and a fully functional surveillance program across the health care system is needed to prevent the emergence and spread of antimicrobial resistance.

Epidemiology and outcomes associated with MBL-producing Enterobacterales: A systematic literature review

The increasing prevalence of infections due to metallo-β-lactamase (MBL)-producing Enterobacterales poses a serious concern given the limited treatment options available. This systematic literature review (SLR) describes the molecular epidemiology, geographical distribution, and clinical outcomes of such infections. Systematic searches of literature published between January 2013 and May 2023 were performed, and 39 studies with an MBL sample size of ≥25 isolates and ≥2 well-defined outcomes were eligible. Most of the studies were from Asia (21/39) followed by Europe (11/39) and evaluated more than two species (24/39). Overall, the percentage of MBL-producing isolates ranged from 6.8%-100.0%. Among 6620 MBL-producers, the majority were from Europe (3837/6620; 58.0%), followed by Asia (2079/6620; 31.4%). New Delhi MBL (NDM)-producers (5668/6620; 85.6%) were the most frequent across all regions, with NDM-1 as the common variant. The majority of IMP-producing isolates (586/592; 99.0%) came from Asia, while the majority of VIM-producing isolates were found in Europe (322/371; 86.8%). Studies focused on MBL-specific outcomes (n = 28) reported reduced susceptibility (<80.0%) to most antimicrobials except for colistin and tigecycline. Six studies reported significantly longer hospital and/or ICU stay due to MBL-Enterobacterales compared to other infection groups. Common mortality measures reported were overall mortality (18.8%-57.0%; 9 studies), in-hospital mortality (11.1%-55.3%; 6 studies), and 30-day mortality (0%-36.4%; 7 studies). Previous antibiotic use (9 studies) and hospital and/or ICU stay (8 studies) were common risk factors for colonization/infection and mortality. Reporting of MBL prevalence across regions will provide a better understanding of the infection burden and prevent further spread.

Association between defecation status and the habit of eating vinegar-based dishes in community-dwelling Japanese individuals: a cross-sectional study

Vinegar intake reportedly has an antihypertensive effect and reduces visceral fat. Nonetheless, studies on the form of vinegar intake and its effect on defecation are scarce. This cross-sectional study aimed to investigate the association between the frequency of vinegar-based dish intake and defecation status using data from the Tarumizu cohort study. The participants (n = 1024, 634 women) responded to a health check survey in 2019 using a brief-type self-administered diet history questionnaire. The association between the frequency of vinegar-based dish intake and defecation status was examined using a multivariate logistic regression analysis. Considering confounding factors influencing the defecation status such as sex, age, dietary fiber intake, and medication history, individuals with a habit of eating vinegar-based dishes, such as "sour main dishes" (odds ratio [OR]: 1.38; p = 0.039), "sunomono" (OR: 1.49; p = 0.035), and "salad with sour dressing" (OR: 1.41; p = 0.049), had a significantly higher defecation frequency. No significant association was observed between the habit of eating vinegar-based dishes and the time required for defecation or straining during defecation. Our study showed that the habit of eating vinegar-based dishes was positively associated with defecation status. Our findings may suggest a novel approach for defecation improvement in people with defecation problems.

Systematic review and meta-analysis on the carbapenem-resistant hypervirulent Klebsiella pneumoniae isolates

BACKGROUND

The global dissemination of carbapenem-resistant hypervirulent Klebsiella pneumoniae (CR-hvKp) poses a critical threat to public health. However, comprehensive data on the prevalence and resistance rates of CR-hvKp are limited. This systematic review and meta-analysis aim to estimate the pooled prevalence of carbapenem resistance among hvKp strains and assess the distribution of carbapenemase genes.

MATERIALS AND METHODS

A systematic search of ISI Web of Science, PubMed, and Google Scholar was conducted to identify studies reporting carbapenem resistance rates in hvKp strains. The pooled prevalence of carbapenem resistance and carbapenemase genes was calculated using event rates with 95% confidence intervals.

RESULTS

A total of 36 studies encompassing 1,098 hvKp strains were included. The pooled resistance rates were 49% for imipenem, 53.2% for meropenem, and 38.2% for ertapenem. Carbapenemase gene prevalence was 19.1% for blaVIM, 22.0% for blaNDM, 43.4% for blaOXA-48, and 58.8% for blaKPC.

CONCLUSION

The high prevalence of carbapenem resistance and the widespread distribution of carbapenemase genes among hvKp strains underscore their significant threat to global health. These findings highlight the urgent need for enhanced surveillance, rapid diagnostic tools, and stringent infection control measures to mitigate the spread of CR-hvKp. Future research should focus on understanding resistance mechanisms and developing targeted therapeutic strategies to address this critical challenge.

Clinical effects of non-pharmaceutical interventions for COVID-19 on other nationally notifiable infectious diseases in South Korea

BACKGROUND/AIMS

This study aimed to assess the impact of non-pharmaceutical interventions (NPIs) implemented during the COVID-19 pandemic on nationally notifiable infectious diseases (NNIDs) in South Korea.

METHODS

Long-term data on seven NNIDs from 2018 to 2021 were analyzed to identify trends and change points using a change point detection technique. The timings of the NPI implementations were compared to the identified change points to determine their association.

RESULTS

Varicella, mumps, and scarlet fever showed a significant decrease in incidence following the implementation of NPIs during the COVID-19 pandemic. These diseases, which are primarily transmitted through respiratory droplets, demonstrated a clear response to NPIs. However, carbapenem-resistant Enterobacterales (CRE) showed an increasing trend unrelated to the timing of NPI implementation, suggesting the complex nature of controlling healthcare-associated infections. Hepatitis A, hepatitis C, and scrub typhus did not show significant changes associated with NPIs, likely due to their non-respiratory route of transmission.

CONCLUSION

NPIs effectively controlled NNIDs, particularly those transmitted through respiratory infections. However, the impact varied depending on the disease. Understanding the effectiveness and limitations of NPIs is crucial for developing comprehensive public health strategies during infectious disease outbreaks.

Risk factors and mortality rates of carbapenem-resistant Gram-negative bacterial infections in intensive care units

Background

The prevalence of hospital-acquired infections caused by carbapenem-resistant gram-negative bacteria (CRGNB) is increasing worldwide. Several risk factors have been associated with such infections. The present study aimed to identify risk factors and determine the mortality rates associated with CRGNB infections in intensive care units.

Methods

This retrospective case-control study was conducted at Erciyes University Hospital (Kayseri, Turkey) between January 2017 and December 2021. Demographic and laboratory data were obtained from the Infection Control Committee data and record system. Patients who had CRGNB infection 48-72 h after hospitalization were assigned to the case group, while those who were not infected with CRGNB during hospitalization formed the control group. Risk factors, comorbidity, demographic data, and mortality rates were compared between the two groups.

Results

Approximately 1449 patients (8.97%) were monitored during the active follow-up period; of those, 1171 patients were included in this analysis. CRGNB infection developed in 14 patients (70.00%) who had CRGNB colonization at admission; in 162 (78.26%) were colonized during hospitalization, whereas 515 (54.56%) were not colonized. There was no significant difference in age, sex (male/female) or comorbidities. The total length of hospital stay was statistically significantly longer (P=0.001) in the case group (median: 24 [interquartile range: 3-378] days) than the control group (median: 16 [interquartile range: 3-135] days). The rates of colonization at admission (25.5%; vs. 10.6%, P=0.001) and mortality (64.4% vs. 45.8%, P=0.001) were also significantly higher in the cases than in the control group, respectively. In the univariate analysis, prolonged hospitalization, the time from intensive care unit admission to the development of infection, presence of CRGNB colonization at admission, transfer from other hospitals, previous antibiotic use, enteral nutrition, transfusion, hemodialysis, mechanical ventilation, tracheostomy, reintubation, central venous catheter, arterial catheterization, chest tube, total parenteral nutrition, nasogastric tube use, and bronchoscopy procedures were significantly associated with CRGNB infections (P <0.05). Multivariate analysis identified the total length of stay in the hospital (odds ratio [OR]=1.02; 95% confidence interval [CI]: 1.01 to 1.03; P=0.001), colonization (OR=2.19; 95% CI: 1.53 to 3.13; P=0.001), previous antibiotic use (OR=2.36; 95% CI: 1.53 to 3.62; P=0.001), intubation (OR=1.59; 95% CI: 1.14 to 2.20; P=0.006), tracheostomy (OR=1.42; 95% CI: 1.01 to 1.99; P=0.047), and central venous catheter use (OR=1.62; 95% CI: 1.20 to 2.19; P=0.002) as the most important risk factors for CRGNB infection.

Conclusions

Colonization, previous use of antibiotics, and invasive interventions were recognized as the most important risk factors for infections. Future research should focus on measures for the control of these parameters.

Molecular Epidemiology of Carbapenem-Resistant Klebsiella aerogenes in Japan

Information regarding Klebsiella aerogenes haboring carbapenemase in Japan is limited. A comprehensive nationwide survey was conducted from September 2014 to December 2022, and 67 non-duplicate strains of carbapenem-resistant K. aerogenes were isolated from 57 healthcare facilities in Japan. Through genetic testing and whole-genome sequencing, six strains were found to possess carbapenemases, including imipenemase (IMP)-1, IMP-6, New Delhi metallo-β-lactamase (NDM)-1, and NDM-5. The strain harboring blaNDM-5 was the novel strain ST709, which belongs to the clonal complex of the predominant ST4 in China. The novel integron containing blaIMP-1 featured the oxacillinase-101 gene, which is a previously unreported structure, with an IncN4 plasmid type. However, integrons found in the strains possessing blaIMP-6, which were the most commonly identified, matched those reported domestically in Klebsiella pneumoniae, suggesting the prevalence of identical integrons. Transposons containing blaNDM are similar or identical to the transposon structure of K. aerogenes harboring blaNDM-5 previously reported in Japan, suggesting that the same type of transposon could have been transmitted to K. aerogenes in Japan. This investigation analyzed mobile genetic elements, such as integrons and transposons, to understand the spread of carbapenemases, highlighting the growing challenge of carbapenem-resistant Enterobacterales in Japan and underscoring the critical need for ongoing surveillance to control these pathogens.

Fecal carriage and genetic characteristics of carbapenem-resistant enterobacterales among adults from four provinces of China

Carbapenem-resistant Enterobacterales (CRE) is a global concern. This study investigated the prevalence of fecal colonization carriage and clonal dissemination of CRE among population in four provinces of China. A total of 685 stool samples were collected from four provinces in China. Among these samples, 141 and 544 were obtained from healthy and hospitalized individuals, respectively. The overall fecal carriage rate was 9.6% (65/685) with 4.26% (95% CI: 0.9-7.6) in healthy individuals and 10.84% (95% CI: 8.2-13.5) in hospitalized patients. The highest prevalence was in Henan province (18.35%, 95% CI: 9%-18.7%). Sixty-six CRE isolates were identified in Escherichia coli (56.06%, 37/66), Klebsiella (15.15%, 10/66), Citrobacter (13.63%, 9/66), Enterobacter (12.12%, 8/66), and Atlantibacter (1.51%, 1/66). All CRE strains carried carbapenemase genes and multiple antibiotics resistance genes, blaNDM-5 (77.27%, 51/66) was the most common carbapenemase gene, followed by blaNDM-1 (19.69%, 13/66). Antibiotic resistance genes, including blaIMP-4, and the colistin colistin resistance (mcr-1) gene were also identified. All CRE isolates belonged to different sequence types (STs). ST206 (36.84%, 14/38) in E. coli and ST2270 (60%, 6/10) in Klebsiella were significantly dominant clones. The results indicated the prevalence of CRE fecal carriage among adults of China, mostly blaNDM-producing E coli, which pose significant challenges for clinical management. Screening for CRE colonization is necessary to control infection.

Municipal wastewater monitoring revealed the predominance of bla GES genes with diverse variants among carbapenemase-producing organisms: high occurrence and persistence of Aeromonas caviae harboring the new bla GES variant bla GES-48

IMPORTANCE

The emergence and spread of carbapenemase-producing organisms (CPOs) represent a global health threat because they are associated with limited treatment options and poor clinical outcomes. Wastewater is considered a hotspot for the evolution and dissemination of antimicrobial resistance. Thus, analyses of municipal wastewater are critical for understanding the circulation of these CPOs and carbapenemase genes in local communities, which remains scarcely known in Japan. This study resulted in several key observations: (i) the vast majority of bla GES genes, including six new bla GES variants, and less frequent bla IMP genes were carbapenemase genes encountered exclusively in wastewater influent; (ii) the most dominant CPO species were Aeromonas spp., in which a remarkable diversity of new sequence types was observed; and (iii) CPOs were detected from combined sewer wastewater, but not from separate sewer wastewater, suggesting that the load of CPOs from unrecognized environmental sources could greatly contribute to their detection in influent wastewater.

An observational study on carbapenem-resistant Enterobacterales (CRE) colonisation and subsequent risk of infection in an adult intensive care unit (ICU) at a tertiary care hospital in India

Background

Carbapenem-resistant Enterobacterales (CRE) are a global health problem with a growing prevalence. India has a high prevalence of CRE. CRE infections are difficult to treat, and are associated with significant morbidity and mortality. Colonisation is generally a prerequisite for infection and the prevention of CRE colonisation is key to the prevention of CRE infection.

Objectives

To determine the prevalence of CRE colonisation and subsequent infections in an adult intensive care unit (ICU) in India.

Methods

We conducted a prospective observational study in which perirectal swabs were obtained along with relevant clinical details of consenting adult patients upon ICU admission between January 2019 and August 2020. Rectal screening was performed using MacConkey agar plates with ertapenem disks and further identification was performed using conventional microbiological techniques. Ertapenem minimum inhibitory concentration (MIC) was determined using an epsillometer (E) test. The modified carbapenem inactivation (mCIM) test and EDTA carbapenem inactivation test (eCIM) were performed to confirm carbapenem resistance using the Clinical Laboratory Standards Institute (CLSI) 2020 guidelines.

Results

192 ICU patients were screened for CRE. 37 patients were found to be colonised with CRE. Klebsiella pneumoniae (N=25; 67.6%) was the most frequent CRE isolate, followed by Escherichia coli (N=11; 29.7%) and one Enterobacter species (N=1; 2.7%). 89.2% (33/37) patients developed CRE infection. Pneumonia was the most common CRE infection identified in 12/33 (36.4%) patients.during the hospital stay. The median duration of hospital stay was longer (17 days) for CRE colonised compared to CRE non-colonised patients (9 days) (P<0.001). Death occurred in 27 % (N=10/37) of CRE-colonised patients during the hospital admission.

Conclusion

CRE colonisation is associated with high risk of subsequent CRE infection and longer ICU and hospital admission.

High Prevalence of Carbapenem-Resistant Enterobacterales Colonization Among Intensive Care Unit Patients in a Tertiary Hospital, China

Intestinal colonization with carbapenem-resistant Enterobacterales (CRE) has been shown as a significant risk factor for subsequent CRE infections, especially in intensive care units (ICUs). The aim of this study was to determine the prevalence of intestinal CRE colonization among ICU patients in a Chinese tertiary hospital. Fecal sample screenings for CRE were performed on ICU patients weekly. Antibiotic-susceptibility profile of CRE strains was determined using the Vitek-2 analysis system and broth microdilution method. The carbapenemases of all isolates were determined by phenotypes and genotypes. Clonal relatedness was analyzed by pulsed-field gel electrophoresis (PFGE). Whole-genome sequencing was used to identify the multilocus sequence type (ST), plasmid replicons, and insertion sequences (ISs) of isolates. The overall colonization rate of CRE was 40.4% (82/203). A total of 84 CRE strains were detected, mostly with Klebsiella pneumoniae (92.9%). Antibiotic susceptibility testing profile revealed that 84 CRE strains were resistant to most antibiotics except for tigecycline and colistin. The carbapenemase-encoding genes including blaKPC-2, blaNDM-1, and blaIMP-4 were detected, and blaKPC-2 was the predominant genotype (90.8%). A total of 9 STs were identified among 84 CRE strains, and ST11 was the most common type (83.3%). A variety of mobile genetic elements, including plasmids and ISs, were detected via online tool prediction. PFGE analysis of the 78 K. pneumoniae strains showed 8 different pulsotypes, and pulsotype A was highly prevalent. This study found that the prevalence of CRE colonization was alarmingly high in the ICU, and that effective infection control measures are urgently needed to prevent the dissemination of CRE.

Targeted Infection Control Practices in Japanese Hospitals for Multidrug-Resistant Organisms: Guidance From the Public Health Center

Introduction The study conducted by the Kawaguchi City Public Health Center (PHC) in 2023 on hospital infection control (IC) programs revealed that hospitals can improve their IC programs if the PHC provides training sessions (TSs) that have numerical effects. In this study, we expected that we could help hospitals develop their IC practices by providing targeted guidance. This study aimed to clarify targeted guidance on IC practices and TS programs to develop hospitals'hospitals' IC programs on multidrug-resistant organisms (MDROs) by examining hospitals'hospitals' IC programs in reference to the study conducted in 2023 and other case reports. Methods In June 2022, the Kawaguchi City PHC conducted TSs for 19 hospitals and eight affiliated (AFs) clinics with beds, providing guidelines and practices on infection control (IC) for MDROs. After the TSs, we sent a questionnaire to these hospitals and affiliated clinics. The questionnaire inquired about current and planned IC policies, hand hygiene compliance programs (HHCPs), the usefulness of the TSs conducted by the PHC, and IC programs that the facilities intended to implement or develop in the future. This study examined the relationship between the perceived usefulness of the information provided and the IC programs planned for development, referencing a study conducted in 2023 and other case reports. Results Seventeen hospitals and six AFs with beds responded to the survey, yielding an 85.2% response rate. IC policies for methicillin-resistant Staphylococcus aureus (MRSA) were prepared by 21 hospitals (91.3%), whereas only five hospitals (21.7%) had prepared IC policies for carbapenem-resistant Enterobacteriaceae. Regarding HHCPs, an increase in the availability of alcohol-based hand sanitizer was identified by 17 hospitals (73.9%), while 13 hospitals (56.5%) reported using posters or symbols, 12 hospitals (52.2%) reported using TS and hand sanitizers, and nine hospitals (39.1%) assessed HH compliance and provided feedback. Furthermore, nine hospitals (39.1%) identified HHCPs and Environmental Cleaning (EC) for carbapenemase-producing Enterobacteriaceae (CPE) as useful information. There was a statistically significant association between TSs on HHCPs and the development of new HHCPs (p = 0.027). Additionally, information on EC for CPE was significantly associated with the development of staff cohorting strategies (p = 0.007). However, TS programs were not significantly connected to EC, nor were TSs to be developed. Conclusion The PHC should advise hospitals to assess if their HHCPs effectively contribute to improving HH compliance. It is essential for the PHC to furnish hospitals with resources and information that aid in the development of EC training. Additionally, the PHC should support the creation of specific and effective TS programs focused on EC or TS development. Conducting surveys to identify barriers to implementing staff cohorting strategies is also recommended. We propose that TS programs should include quantifiable data on HHCPs and EC, such as.

Epidemiological Characteristics of Carbapenem-Resistant Enterobacterales in Japan: A Nationwide Analysis of Data from a Clinical Laboratory Center (2016-2022)

In Japan, nationwide epidemiological surveys on carbapenem-resistant Enterobacterales (CREs), including comprehensive information, are scarce, with most data available only through public reports. This study analyzed data on the Enterobacterales family collected from nationwide testing centers between January 2016 and December 2022, focusing on isolates that met the criteria for CRE in Japan based on drug susceptibility. We investigated 5,323,875 Enterobacterales isolates of 12 different species; among 4696 (0.09%) CRE strains, the proportion of major CRE isolates was as follows: Escherichia coli, 31.3%; Klebsiella pneumoniae, 28.0%; Enterobacter cloacae, 18.5%; and Klebsiella aerogenes, 6.7%. Moreover, over a 7-year period, Providencia rettgeri, E. cloacae, K. aerogenes, and K. pneumoniae demonstrated relatively high CRE percentages of 0.6% (156/26,185), 0.47% (869/184,221), 0.28% (313/110,371), and 0.17% (1314/780,958), respectively. The number of CRE strains isolated from different samples was as follows: urine, 2390; respiratory specimens, 1254; stool, 425; blood, 252; others, 375. In the broader context, including colonization, the predominant isolates of CREs collected at nationwide testing centers are E. coli and K. pneumoniae. Furthermore, recently, attention has been directed toward less common CRE species, such as Klebsiella oxytoca and Providencia rettgeri, and thus, it might be necessary to continue monitoring these less common species.

Highly sensitive detection of antimicrobial resistance genes in hospital wastewater using the multiplex hybrid capture target enrichment

Wastewater can be useful in monitoring the spread of antimicrobial resistance (AMR) within a hospital. The abundance of antibiotic resistance genes (ARGs) in hospital effluent was assessed using metagenomic sequencing (mDNA-seq) and hybrid capture (xHYB). mDNA-seq analysis and subsequent xHYB targeted enrichment were conducted on two effluent samples per month from November 2018 to May 2021. Reads per kilobase per million (RPKM) values were calculated for all 1,272 ARGs in the constructed database. The monthly numbers of patients with presumed extended-spectrum β-lactamase (ESBL)-producing and metallo-β-lactamase (MBL)-producing bacteria, methicillin-resistant Staphylococcus aureus (MRSA), and vancomycin-resistant enterococci (VRE) were compared with the monthly RPKM values of blaCTX-M, blaIMP, mecA, vanA, and vanB by xHYB. The average RPKM value for all ARGs detected by xHYB was significantly higher than that of mDNA-seq (665, 225, and 328, respectively, and P < 0.05). The average number of patients with ESBL producers and RPKM values of blaCTX-M-1 genes in 2020 were significantly higher than that in 2019 (17 and 13 patients per month and 921 vs 232 per month, respectively, both P < 0.05). The average numbers of patients with MBL-producers, MRSA, and VRE were 1, 28, and 0 per month, respectively, while the average RPKM values of blaIMP, mecA, vanA, and vanB were 6,163, 6, 0, and 126 per month, respectively. Monitoring ARGs in hospital effluent using xHYB was found to be more useful than conventional mDNA-seq in detecting ARGs including blaCTX-M, blaIMP, and vanB, which are important for infection control.IMPORTANCEEnvironmental ARGs play a crucial role in the emergence and spread of AMR that constitutes a significant global health threat. One major source of ARGs is effluent from healthcare facilities, where patients are frequently administered antimicrobials. Culture-independent methods, including metagenomics, can detect environmental ARGs carried by non-culturable bacteria and extracellular ARGs. mDNA-seq is one of the most comprehensive methods for environmental ARG surveillance; however, its sensitivity is insufficient for wastewater surveillance. This study demonstrates that xHYB appropriately monitors ARGs in hospital effluent for sensitive identification of nosocomial AMR dissemination. Correlations were observed between the numbers of inpatients with antibiotic-resistant bacteria and the ARG RPKM values in hospital effluent over time. ARG surveillance in hospital effluent using the highly sensitive and specific xHYB method could improve our understanding of the emergence and spread of AMR within a hospital.

Establishment of a risk prediction model for multidrug-resistant bacteria in deceased organ donors: a retrospective cohort study in China

Background

Multidrug resistance in bacteria is a serious problem in organ transplantations. This study aimed to identify risk factors and establish a predictive model for screening deceased organ donors for multidrug-resistant (MDR) bacteria.

Methods

A retrospective cohort study was conducted at the First Affiliated Hospital of Zhejiang University School of Medicine from July 1, 2019 to December 31, 2022. The univariate and multivariate logistic regression analysis was used to determine independent risk factors associated with MDR bacteria in organ donors. A nomogram was established based on these risk factors. A calibration plot, receiver operating characteristic (ROC) curve, and decision curve analysis (DCA) were used to estimated the model.

Results

In 164 organ donors, the incidence of MDR bacteria in culture was 29.9%. The duration of antibiotic use ≥3 days (odds ratio [OR] 3.78, 95% confidence interval [CI] 1.62-8.81, p=0.002), length of intensive care unit (ICU) stay per day(OR 1.06, 95% CI 1.02-1.11, p=0.005) and neurosurgery (OR 3.31, 95% CI 1.44-7.58, p=0.005) were significant independent predictive factors for MDR bacteria. The nomogram constructed using these three predictors displayed good predictive ability, with an area under the ROC curve value of 0.79. The calibration curve showed a high consistency between the probabilities and observed values. DCA also revealed the potential clinical usefulness of this nomogram.

Conclusions

The duration of antibiotic use ≥3 days, length of ICU stay and neurosurgery are independent risk factors for MDR bacteria in organ donors. The nomogram can be used to monitor MDR bacteria acquisition risk in organ donors.

The Prevalence of Colonization with Carbapenem-resistant Enterobacteriaceae, E. coli, Klebsiella and Enterobacter, and Related Risk Factors in Children

Background: Carbapenems are broad-spectrum antibiotics used to treat the family of gram-negative Enterobacteriaceae, especially those that are resistant to first-line antibiotics. Because these drugs are usually prescribed as the last line of treatment, resistance to these antibiotics carries irreparable risks to treatment systems, and screening high-risk individuals in medical centers and using infection control measures are critical strategies for eliminating them. Objectives: We investigated the prevalence of colonization of different strains of Enterobacteriaceae, Klebsiella, Enterobacter, and Escherichia coli and their risk factors in hospitalized children. Methods: In this descriptive cross-sectional study, stool samples were taken from patients during the first 48 hours of hospitalization in a tertiary children’s hospital and were cultured on Makcanki culture medium or EMB. Cultured Enterobacteriaceae samples were transferred to Müller-Hinton agar medium, and their antibiotic susceptibility was evaluated with meropenem and imipenem discs by disc diffusion method. In the next step, five common carbapenemase genes, including (VIM, IMP, OXA-48, NDM-1, and SPM-1) were examined by PCR method and reported accordingly. Results: Two hundred and ninety-five stool samples were examined, of which 242 (82%) samples were cultured positively with Enterobacteriaceae. The prevalence of carbapenem resistance was reported to be 37% among 295 samples using the phenotypic method. Resistance rates were high in patients with a history of antibiotic use, with frequent hospitalizations (more than two episodes in the last six months), and in patients with an underlying disease) malignancy, GI diseases, immunodeficiency, neurologic diseases such as cerebral palsy and epilepsy, endocrine diseases. Most of the genes found were OXA-48, followed by IMP and VIM. NDM-1 was found in 3 samples, and SPM was not found in any of the samples. In 13% of resistant samples, more than one carbapenemase gene was found. Conclusions: The results of this study showed that the frequency of carbapenem resistance in stools colonized with Enterobacteriaceae is high in our patients. On the other hand, the presence of carbapenemase genes in these bacteria, which are located on the plasmids that can be rapidly spread in the hospital environment, is an alarm for the hospital infection control committee to take preventive measures in order to prevent the spread of these bacteria in the hospital.

Genomic Insights Into Molecular Characteristics and Phylogenetic Linkage Between the Cases of Carbapenem-Resistant Klebsiella pneumoniae From a Non-tertiary Hospital in China: A Cohort Study

Background: Carbapenem-resistant Klebsiella pneumoniae (CRKP) strains have been listed as one of the major clinical concerns. Objectives: We investigated CPKP isolates from non-tertiary hospitals to find disseminated clones and analyze extensive phenotypic and genetic diversity in this study. Methods: In this cohort study, a total of 49 CRKP isolates from 3 hospitals in the same region were collected in 2021. The prevalence and antimicrobial susceptibility patterns were analyzed. Clinical data were retrieved from electronic medical record systems. The molecular types, antimicrobial resistance (AMR) profiles, plasmid replicons, and virulence factors were analyzed. The maximum-likelihood phylogenetic tree and transmission networks were constructed using single-nucleotide polymorphisms (SNPs). Results: The median age of patients (N = 49) was 66.0 years, and 85.7% were male. The most common CRKP infection was nosocomial pneumonia (75.5%), followed by bacteremia (10.2%). More than 53% of isolates were resistant to ceftazidime-avibactam (CAZ/AVI). Forty-five isolates were successfully sequenced; the predominant carbapenem-resistant gene was blaKPC-2 (93.3%). The 30-day mortality in our cohort was 24.5%. The most dominant sequence type (ST) was ST11 (60.0%), followed by ST15 (13.3%). Whole genome sequencing (WGS) analysis exhibited dissemination of ST11 strain clones, ST420, and ST15 clones, both within and outside the given hospital. Conclusions: In this surveillance study, several dissemination chains of CRKP were discovered in the hospital and the region, as ST11 was the main epidemic clone. Our findings suggest that effective infection control practices and antimicrobial stewardship are needed in non-tertiary hospitals in China.

Isolation of OXA-48-like carbapenemase-producing Escherichia coli susceptible to piperacillin/tazobactam in a Japanese patient without a history of travel abroad

Oxacillinase (OXA)-48-like β-lactamases are the most common carbapenemases in Enterobacterales in certain regions of the world and are being introduced on a regular basis into regions of non-endemicity. Japan has been characterized by low rates of carbapenemase-producing Enterobacterales, and among them, OXA-48-like carbapenemase-producing isolates are extremely rare. Here we describe a Japanese medical worker, without a history of travel abroad, who was diagnosed as having a community-acquired urinary tract infection, and whose urine sample was found to be positive for OXA-48-like carbapenemase-producing Escherichia coli. None of her close contacts had a history of foreign travel, and the same drug-resistant organism was not observed in other patients who had been hospitalized and undergone environmental culture tests in the same medical institution. This isolate was resistant to penicillins, narrow-spectrum cephalosporins, fluoroquinolones, and cefmetazole, but was susceptible to broad-spectrum cephalosporins, piperacillin/tazobactam, and meropenem and displayed reduced susceptibility to imipenem. The modified carbapenem inactivation test supported carbapenemase production, but inhibitor-based synergistic tests yielded negative results of carbapenemase production. Multiplex polymerase chain reaction revealed the presence of the carbapenemase gene (bla_OXA-48) bla_TEM and AmpC β-lactamase gene (bla_DHA). Singleplex polymerase chain reaction targeting the bla_OXA-48 region amplified a product sequencing to nearly the full length (722 bp) and matching 100% with OXA-48. The present case highlights a new concern regarding OXA-48-like carbapenemase-producing Enterobacterales, which remain challenging to detect for clinical laboratories in regions of non-endemicity, and may already be latent in Japan.

Biochemical exploration of β-lactamase inhibitors

The alarming rise of microbial resistance to antibiotics has severely limited the efficacy of current treatment options. The prevalence of β-lactamase enzymes is a significant contributor to the emergence of antibiotic resistance. There are four classes of β-lactamases: A, B, C, and D. Class B is the metallo-β-lactamase, while the rest are serine β-lactamases. The clinical use of β-lactamase inhibitors began as an attempt to combat β-lactamase-mediated resistance. Although β-lactamase inhibitors alone are ineffective against bacteria, research has shown that combining inhibitors with antibiotics is a safe and effective treatment that not only prevents β-lactamase formation but also broadens the range of activity. These inhibitors may cause either temporary or permanent inhibition. The development of new β-lactamase inhibitors will be a primary focus of future research. This study discusses recent advances in our knowledge of the biochemistry behind β-lactam breakdown, with special emphasis on the mechanism of inhibitors for β-lactam complexes with β-lactamase. The study also focuses on the pharmacokinetic and pharmacodynamic properties of all inhibitors and then applies them in clinical settings. Our analysis and discussion of the challenges that exist in designing inhibitors might help pharmaceutical researchers address root issues and develop more effective inhibitors.

Clinical characteristics and treatment of IMP-type carbapenemase-producing Enterobacteriaceae bacteremia: Case series and literature review

BACKGROUND

Several carbapenemases have been identified globally in Enterobacteriaceae. In Japan, IMP-type carbapenemase is the most prevalent, although cases of carbapenemase-producing Enterobacteriaceae (CPE) bacteremia are still scarce. The present case series and literature review aimed to elucidate the clinical characteristics and treatment strategies for IMP-type CPE bacteremia.

METHODS

Clinical data on pediatric cases of IMP-type CPE bacteremia at the Tokyo Metropolitan Children's Medical Center between 2010 and 2020 were collected, and a review of past studies of IMP-type CPE bacteremia has been provided.

RESULTS

Five pediatric episodes of IMP-type CPE bacteremia were identified. Our review of previous literature on IMP-type CPE bacteremia revealed 24 adult patients, but no pediatric patients. All 29 cases had underlying diseases, and 23 (79%) received combination therapy. The median duration of antibiotic therapy was 14 days (interquartile range: 9-14 days). The overall mortality rate was 38% (11/29). The mortality rates associated with monotherapy and combination therapy were 67% (4/6) and 30% (7/23), respectively.

CONCLUSIONS

We report the first case series of IMP-type CPE bacteremia in children. Our review of past studies suggests that combination therapy might lead to better survival outcomes in patients with IMP-type CPE bacteremia. Further research is needed to establish an optimal treatment strategy for IMP-type CPE bacteremia.

Outbreak of KPC-producing Klebsiella pneumoniae at a Portuguese university hospital: Epidemiological characterization and containment measures

Background

KPC-producing K pneumoniae (KPC-Kp) is a public health problem with important clinical and epidemiological implications. We describe an outbreak of KPC-Kp at vascular surgery and neurosurgery wards in a central hospital in Porto, Portugal.

Methods

A case of KPC-Kp was considered to be a patient positive for KPC-Kp with strong epidemiological plausibility of having acquired this microorganism in the affected wards and/or with genetic relationship ≥92% between KPC-Kp isolates. Active surveillance cultures (ASCs) and real-time polymerase chain reaction were used for the detection of carbapenemase genes through rectal swab in a selected population. Molecular analysis was performed using pulsed-field gel electrophoresis at the National Reference Laboratory. Patient risk factors were collected from the electronic medical record system. Information regarding outbreak containment strategy was collected from the Infection Control Unit records.

Results

Of the 16 cases, 11 (69%) were identified through active screening, representing 1.4% of the total 766 ASCs collected. The most frequent risk factors identified were previous admission (63%), antibiotic exposure in the past 6 months (50%), and immunodepression (44%). The length of stay until KPC-Kp detection was high (0-121 days, mean 35.6), as was the total length of stay (5-173 days, mean 56.6). Three patients (19%) were infected by KPC-Kp, 2 of whom died. One previously colonized patient died later because of KPC-Kp infection.

Conclusions

Multifactorial strategy based on contact precautions (with patient and healthcare professional cohorts) and ASC, as well as Antibiotic Stewardship Program reinforcement, allowed to contain this KPC-Kp outbreak.

Structural insights into the substrate specificity of IMP-6 and IMP-1 metallo-β-lactamases

IMP-type metallo-β-lactamases confer resistance to carbapenems and a broad spectrum of β-lactam antibiotics. IMP-6 and IMP-1 differ by only a point mutation: Ser262 in IMP-1 and Gly262 in IMP-6. The kcat/Km values of IMP-1 for imipenem and meropenem are nearly identical; however, for IMP-6, the kcat/Km for meropenem is 7-fold that for imipenem. In clinical practice, this may result in an ineffective therapeutic regimen and, consequently, in treatment failure. Here, we report the crystal structures of IMP-6 and IMP-1 with the same space group and similar cell constants at resolutions of 1.70 and 1.94 Å, respectively. The overall structures of IMP-6 and IMP-1 are similar. However, the loop region (residues 60-66), which participates in substrate binding, is more flexible in IMP-6 than in IMP-1. This difference in flexibility determines the substrate specificity of IMP-type metallo-β-lactamases for imipenem and meropenem. The amino acid at position 262 alters the mobility of His263; this affects the flexibility of the loop via a hydrogen bond with Pro68, which plays the role of a hinge in IMP-type metallo-β-lactamases. The substitution of Pro68 with a glycine elicited an increase in the Km of IMP-6 for imipenem, whereas the affinity for meropenem remained unchanged.

Detection of Enterobacter cloacae complex strain with a blaNDM-1-harboring plasmid from an elderly resident at a long-term care facility in Okayama, Japan

Amidst the global spread of antimicrobial resistance, New Delhi metallo-β-lactamase (NDM)-type carbapenemase-producing Enterobacterales (CPE) remain uncommon in Japan, and the detection of such highly drug-resistant organisms is limited to inbound cases. There is little evidence regarding the prevalence of NDM β-lactamase gene (bla_NDM)-harboring CPE in the domestic community, especially in the provincial cities of Japan. Herein, we report the isolation of a bla_NDM-1-harboring plasmid in Enterobacter cloacae complex strain isolated from an elderly woman without a history of traveling abroad who had resided in a long-term care facility in Okayama, Japan. The multidrug-resistant bla_NDM-harboring CPE isolate was detected in a stool sample of the patient during routine screening at admission. We performed whole-genome sequencing analysis of the isolate using MiSeq (Illumina) and MinION (Oxford Nanopore Technologies) platforms. The isolate was identified as sequence type 171, which has predominantly been reported in the United States and China. The bla_NDM-1 gene was encoded on the 46,161 bp IncX3 plasmid, with sequence similarity to plasmids of similar size isolated from individuals in China. Collectively, the genomic data suggest that an imported CPE isolate may have spread among healthy individuals in the regional area of Japan.

A Longitudinal Study of Spontaneous Gut Decolonization of Carbapenem-resistant Gram-negative Bacteria in Neonatal and Pediatric Patients

BACKGROUND

Antibiotic exposure may convert gut microbiome to reservoir of resistant organisms, including carbapenem-resistant Gram-negative bacteria (CRGNB). Little is known about natural history of spontaneous CRGNB decolonization of neonates/children and their risk to develop CRGNB infections.

METHODS

Patients hospitalized in a tertiary care hospital (1 days to 16 years) found to be CRGNB colonized in weekly surveillance cultures during hospitalization (January 2018 to December 2019) were prospectively followed after discharge with monthly rectal cultures for 12 months after colonization until decolonization (3 consecutive negative rectal cultures, ≥1 week apart). Patient demographics, clinical characteristics and CRGNB infections were recorded. Polymerase chain reaction for carbapenemases was performed in patients colonized, after 3 negative cultures, at the day of the last negative and the day of the first new positive culture.

RESULTS

One-hundred thirty patients (median age, 1.3 months; lower-upper quartile values, 0.8-6.9 months) were studied including 66 neonates (median age, 12.6 days; Q1-Q3, 5-18.5 days). Among patients >30 days old, 51.6% achieved decolonization within 6 months, and among neonates, 91% achieved decolonization within 6 months. By 12th month, 89% of >30 days and 100% of neonates were decolonized. Forty-four (33.9%) patients (59% >30 days and 9% neonates) developed CRGNB infection(s), mainly pneumonia (25%) and bloodstream infection (20.5%). Prolonged colonization (odds ratio [OR], 7.75; 95% confidence interval [CI], 2.10-28.58), duration of broad-spectrum antibiotic use (OR, 1.22; 95% CI, 1.11-1.34) and parenteral nutrition (OR, 4.53; 95% CI, 1.14-17.94) were associated with the development of CRGNB infection. Two patients (1.5%) were found by polymerase chain reaction colonized after 3 negative cultures.

CONCLUSIONS

Spontaneous decolonization occurs in most CRGNB colonized >30 days and all neonates within 12 months. One-third of colonized patients develop CRGNB infection(s). These findings may help optimize duration of contact precautions and empirical antimicrobial therapy for CRGNB colonized pediatric patients.

[Regional dissemination of carbapenem-resistant Enterobacteriaceae accompanying with enhanced resistance in Northern Osaka, Japan]

With the rapid spread of multidrug-resistant bacteria, carbapenem-resistant Enterobacteriaceae (CRE) has been reported worldwide as a major concern because of limited treatment options. Carbapenem resistance is mainly due to carbapenem-ase, a carbapenem-degrading enzyme, which is mainly encoded on a plasmid to spread across bacterial species. However, there have been only small-scale attempts to determine the similarities or accommodations of the plasmids disseminating regionwide. We analysed the 230 CRE isolates carrying bla_IMP from 43 medical facilities in the northern Osaka area focusing on the plasmids, the main carriers of the drug resistance genes. Combination of whole genome sequencing and Southern blotting revealed the predominant dissemination of bla_IMP-6 by the pKPI-6 plasmid among genetically distinct isolates, as well as the emergences of derivatives that acquired various advantages. We iden-tified heteroresistance likely causing stealth transmissions, which was generated by the transcriptional regu-lation of bla_IMP-6, stabilization of bla_IMP-6 through chromosomal integration, enhanced carbapenem resistance through plasmid multimerization, or broadened antimicrobial resistance due to a single point mutation in bla_IMP-6. In this article, I dis-cussed the mechanisms of regional spread of CRE and enhancement of carbapenem resistance providing the insights to prevent their disseminations.

The Antimicrobial Resistance Characteristics of Imipenem-Non-Susceptible, Imipenemase-6-Producing Escherichia coli

Imipenemase-6 (IMP-6) type carbapenemase-producing Enterobacteriaceae is regarded as dangerous due to its unique lack of antimicrobial susceptibility. It is resistant to meropenem (MEPM) but susceptible to imipenem (IPM). In addition to carbapenemase, outer membrane porins and efflux pumps also play roles in carbapenem resistance by reducing the antimicrobial concentration inside cells. Extended-spectrum β-lactamase (ESBL) is transmitted with IMP-6 by the plasmid and broadens the spectrum of antimicrobial resistance. We collected 42 strains of IMP-6-producing Escherichia coli and conducted a molecular analysis of carbapenemase, ESBL, porin, efflux, and epidemiological characteristics using plasmid replicon typing. Among the 42 isolates, 21 strains were susceptible to IPM (50.0%) and 1 (2.4%) to MEPM. Seventeen strains (40.5%) co-produced CTX-M-2 type ESBL. We found that the relative expression of ompC and ompF significantly correlated with the MIC of IPM (p = 0.01 and p = 0.03, respectively). Sixty-eight% of CTX-M-2-non-producing strains had IncI1, which was significantly different from CTX-M-2-producing strains (p < 0.001). In conclusion, 50.0% of our IMP-6-producing strains were non-susceptible to IPM, which is different from the typical pattern and can be attributed to decreased porin expression. Further studies investigating other types of carbapenemase are warranted.

Transmission of NDM-5-Producing and OXA-48-Producing Escherichia coli Sequence Type 648 by International Visitors without Previous Medical Exposure

Carbapenemase-producing Escherichia coli sequence type (ST) 648 strains were isolated from two international visitors without previous medical exposure from Southeast Asian countries in a hospital in Japan. One isolate, FUJ80154, carried bla_NDM-5 in a complex class 1 integron on an IncFIB/FII plasmid; the other isolate, FUJ80155, carried two copies of bla_OXA-48 on the chromosome flanked by IS1R on both sides. The core-genome based-phylogenetic analysis with publicly available genome data of E. coli ST648 carrying bla_NDM-5 or bla_OXA-48-like demonstrated high genetic similarity between FUJ80154 and NDM-5-prooducing E. coli ST648 strains isolated in South and Southeast Asian countries. On the other hand, no closely related isolates of FUJ80155 were identified. In the absence of prior hospitalization overseas, neither patient had qualified for routine screening of multidrug-resistant organisms, and the isolates were incidentally identified in cultures ordered at the discretion of the treating physician.

IMPORTANCE Although patients with history of international hospitalization are often subject to screening for multidrug-resistant organisms, it is unclear whether patients who reside in countries where carbapenemase-producing Enterobacterales (CPE) is endemic but have no history of local hospitalization contribute to the transmission of CPE. In this study, NDM-5-producing and OXA-48-producing Escherichia coli sequence type (ST) 648, a recently recognized high-risk, multidrug-resistant clone, were detected from two overseas visitors without previous medical exposure. The findings of this study suggest that active surveillance culture on admission to hospital may be considered for travelers from countries with endemicity of carbapenem-resistant organisms even without history of local hospitalization and underscore the need to monitor cross-border transmission of high-risk clones, such as carbapenemase-producing E. coli ST648.

Infection Control for a Carbapenem-Resistant Enterobacteriaceae Outbreak in an Advanced Emergency Medical Services Center

BACKGROUND

A carbapenem-resistant Enterobacteriaceae (CRE) outbreak occurred in an advanced emergency medical service center [hereafter referred to as the intensive care unit (ICU)] between 2016 and 2017.

AIM

Our objective was to evaluate the infection control measures for CRE outbreaks.

METHODS

CRE strains were detected in 16 inpatients located at multiple sites. Environmental cultures were performed and CRE strains were detected in 3 of 38 sites tested. Pulsed-field gel electrophoresis (PFGE), multilocus sequence typing (MLST), and detection of β-lactamase genes were performed against 25 CRE strains.

FINDINGS

Molecular typing showed the PFGE patterns of two of four Klebsiella pneumoniae strains were closely related and the same MLST (ST2388), and four of five Enterobacter cloacae strains were closely related and same MLST (ST252). Twenty-three of 25 CRE strains harbored the IMP-1 β-lactamase gene and 15 of 23 CRE strains possessed IncFIIA replicon regions. Despite interventions by the infection control team, new inpatients with the CRE strain continued to appear. Therefore, the ICU was partially closed and the inpatients with CRE were isolated, and the ICU staff was divided into two groups between inpatients with CRE and non-CRE strains to avoid cross-contamination. Although the occurrence of new cases dissipated quickly after the partial closure, a few months were required to eradicate the CRE outbreak.

CONCLUSION

Our data suggest that the various and combined measures that were used for infection control were essential in stopping this CRE outbreak. In particular, partial closure to isolate the ICU and division of the ICU staff were effective.

In Vivo Pharmacodynamics of β-Lactams/Nacubactam against Carbapenem-Resistant and/or Carbapenemase-Producing Enterobacter cloacae and Klebsiella pneumoniae in Murine Pneumonia Model

Carbapenem-resistant Enterobacterales (CRE) and carbapenemase-producing Enterobacterales (CPE) have become global threats. CRE− and CPE− derived infections have been associated with high mortality due to limited treatment options. Nacubactam is a β-lactamase inhibitor and belongs to the new class of diazabicyclooctane. The agent has an in vitro antimicrobial activity against several classes of β-lactamase-producing Enterobacterales. This study evaluated antimicrobial activity of combination therapies including β-lactams (aztreonam, cefepime, and meropenem) and nacubactam against four Enterobacter cloacae and six Klebsiella pneumoniae isolates with murine pneumonia model. Based on changes in bacterial quantity, antimicrobial activities of some regimens were assessed. Combination therapies including β-lactams (aztreonam, cefepime, and meropenem) with nacubactam showed enhanced antimicrobial activity against CRE E. cloacae (−3.70 to −2.08 Δlog₁₀ CFU/lungs) and K. pneumoniae (−4.24 to 1.47 Δlog₁₀ CFU/lungs) with IMP-1, IMP-6, or KPC genes, compared with aztreonam, cefepime, meropenem, and nacubactam monotherapies. Most combination therapies showed bacteriostatic (−3.0 to 0 Δlog₁₀ CFU/lungs) to bactericidal (<−3.0 Δlog₁₀ CFU/lungs) activities against CRE isolates. This study revealed that combination regimens with β-lactams (aztreonam, cefepime, and meropenem) and nacubactam are preferable candidates to treat pneumonia due to CRE and CPE.

Identification and infection control of carbapenem-resistant Enterobacterales in intensive care units

Infections with multidrug-resistant organisms among patients in intensive care units (ICUs) are associated with high mortality. Among multidrug-resistant organisms, carbapenem-resistant Enterobacterales (CRE) harbor important pathogens for healthcare-associated infections, including pneumonia, bacteremia, and urinary tract infections. Risk factors for CRE colonization include underlying comorbid conditions, prior antibiotics exposure, prior use of healthcare facilities, device use, and longer ICU stay. The mortality rate due to invasive CRE infection is 22%–49%, and CRE colonization is associated with an approximately 10-fold increased risk of CRE infection. Infection control measures include hand hygiene, contact precautions, minimizing the use of devices, and environmental control. Additionally, implementing active surveillance of CRE carriage should be considered in ICU settings.

Transmission dynamics of a linear vanA-plasmid during a nosocomial multiclonal outbreak of vancomycin-resistant enterococci in a non-endemic area, Japan

The spread of vancomycin-resistant enterococci (VRE) is a major threat in nosocomial settings. A large-scale multiclonal VRE outbreak has rarely been reported in Japan due to low VRE prevalence. We evaluated the transmission of vancomycin resistance in a multiclonal VRE outbreak, conducted biological and genomic analyses of VRE isolates, and assessed the implemented infection control measures. In total, 149 patients harboring VanA-type VRE were identified from April 2017 to October 2019, with 153 vancomycin-resistant Enterococcus faecium isolated being grouped into 31 pulsotypes using pulsed-field gel electrophoresis, wherein six sequence types belonged to clonal complex 17. Epidemic clones varied throughout the outbreak; however, they all carried vanA-plasmids (pIHVA). pIHVA is a linear plasmid, carrying a unique structural Tn1546 containing vanA; it moves between different Enterococcus spp. by genetic rearrangements. VRE infection incidence among patients in the "hot spot" ward correlated with the local VRE colonization prevalence. Local prevalence also correlated with vancomycin usage in the ward. Transmission of a novel transferrable vanA-plasmid among Enterococcus spp. resulted in genomic diversity in VRE in a non-endemic setting. The prevalence of VRE colonization and vancomycin usage at the ward level may serve as VRE cross-transmission indicators in non-intensive care units for outbreak control.

A prospective surveillance study to determine the prevalence of 16S rRNA methyltransferase-producing Gram-negative bacteria in the UK

OBJECTIVES

To determine the prevalence of 16S rRNA methyltransferase- (16S RMTase-) producing Gram-negative bacteria in patients in the UK and to identify potential risk factors for their acquisition.

METHODS

A 6 month prospective surveillance study was conducted from 1 May to 31 October 2016, wherein 14 hospital laboratories submitted Acinetobacter baumannii, Enterobacterales and Pseudomonas aeruginosa isolates that displayed high-level amikacin resistance according to their testing methods, e.g. no zone of inhibition with amikacin discs. Isolates were linked to patient travel history, medical care abroad, and previous antibiotic exposure using a surveillance questionnaire. In the reference laboratory, isolates confirmed to grow on Mueller-Hinton agar supplemented with 256 mg/L amikacin were screened by PCR for 16S RMTase genes armA, rmtA-rmtH and npmA, and carbapenemase genes (blaKPC, blaNDM, blaOXA-48-like and blaVIM). STs and total antibiotic resistance gene complement were determined via WGS. Prevalence was determined using denominators for each bacterial species provided by participating hospital laboratories.

RESULTS

Eighty-four isolates (44.7%), among 188 submitted isolates, exhibited high-level amikacin resistance (MIC >256 mg/L), and 79 (94.0%) of these harboured 16S RMTase genes. armA (54.4%, 43/79) was the most common, followed by rmtB (17.7%, 14/79), rmtF (13.9%, 11/79), rmtC (12.7%, 10/79) and armA + rmtF (1.3%, 1/79). The overall period prevalence of 16S RMTase-producing Gram-negative bacteria was 0.1% (79/71 063). Potential risk factors identified through multivariate statistical analysis included being male and polymyxin use.

CONCLUSIONS

The UK prevalence of 16S RMTase-producing Gram-negative bacteria is low, but continued surveillance is needed to monitor their spread and inform intervention strategies.

Characterization of bla NDM-5-harbouring Klebsiella pneumoniae sequence type 11 international high-risk clones isolated from clinical samples in Yangon General Hospital, a tertiary-care hospital in Myanmar

Fifteen Klebsiella pneumoniae isolates harbouring bla _NDM genes were identified from blood and sputum specimens of patients at a tertiary-care facility (Yangon General Hospital, Yangon, Myanmar) in 2018. Two of the isolates belonged to sequence type (ST) 11, an international high-risk clone. Whole-genome sequencing and phylogenetic analyses revealed that these two isolates were clustered together with other ST11 isolates originating from other countries. The isolates harboured the bla _NDM-5 gene on an IncFII-type plasmid that is prevalent among carbapenemase-producing Enterobacteriaceae in Yangon but has rarely been found in other ST11 isolates. Our data suggests the regional presence of the ST11 international high-risk clone and its acquisition of an endemic bla _NDM-5-carrying plasmid.

Current situation of carbapenem-resistant Enterobacteriaceae and Acinetobacter in Japan and Southeast Asia

In the recent years, issues related to drug-resistant bacteria have evolved worldwide, and various countermeasures have been taken to control their spread. Among a wide variety of drug-resistant bacterial species, carbapenem-resistant Gram-negative bacteria, including carbapenem-resistant Enterobacteriaceae (CRE) and carbapenem-resistant Acinetobacter baumannii (CRAb), are those for which countermeasures are particularly important. Carbapenems are the last resort antibiotics for any bacterial infection; therefore, infectious diseases caused by these drug-resistant bacteria are difficult to treat. In the case of CRE, since carbapenemases responsible for carbapenem resistance are mostly encoded on transmissible plasmids, it is known that susceptible bacteria can easily become carbapenem-resistant by transfer of plasmids between Enterobacteriaceae. In addition, Enterobacteriaceae are common bacterial species found in the guts of animals, including humans. Acinetobacter is ubiquitously isolated in the environment. Due to these characteristics, it is quite difficult to prevent the intrusion of multi-drug resistant pathogens in hospitals. Therefore, effective countermeasures should be developed and utilized against such dangerous pathogens based on molecular epidemiological analyses. In this review, there are also some examples presented on how to manage to monitor and control those troublesome drug-resistant bacteria conducted in Japan and Southeast Asia.

Community spread and acquisition of clinically relevant Escherichia coli harbouring blaNDM among healthy Japanese residents of Yangon, Myanmar

BACKGROUND

Carbapenemase-producing Enterobacterales (CPE) are spreading in hospitals, environment and retail foods in Yangon, Myanmar.

OBJECTIVES

To investigate whether CPE colonize healthy individuals living in Yangon and whether clinical-related strains are spreading in the community.

METHODS

CPE was isolated from faecal samples obtained from healthy Japanese residents of Yangon with no history of hospitalization. Isolates were subjected to WGS using short- and long-read sequencers and compared with those previously isolated in Yangon.

RESULTS

Six Escherichia coli strains harbouring blaNDM-1 or blaNDM-5 belonging to five different STs-ST10, ST38, ST48, ST410 and ST8453-were isolated from 69 volunteers. The ST38 isolates were related to those previously isolated from retail food in Yangon. The ST410 and ST8453 isolates were highly related to previous Yangon isolates including those of clinical and food origins.

CONCLUSIONS

The analysis suggested the acquisition of blaNDM-positive E. coli, which are disseminating in a clinical setting and through retail foods, by healthy residents in Yangon.

Pharmacodynamic evaluation of meropenem, cefepime, or aztreonam combined with a novel β-lactamase inhibitor, nacubactam, against carbapenem-resistant and/or carbapenemase-producing Klebsiella pneumoniae and Escherichia coli using a murine thigh-infection model

BACKGROUND

Carbapenem-resistant Enterobacterales (CRE) and carbapenemase-producing Enterobacterales (CPE) are difficult to treat and are a serious public health threat. Nacubactam (NAC) is a novel non-β-lactam diazabicyclooctane β-lactamase inhibitor with in vitro activity against some Enterobacterales expressing classes of β-lactamases.

METHODS

The antimicrobial efficacy of meropenem (MEM), cefepime (FEP), and aztreonam (ATM), each in combination with NAC, were assessed in vitro and in vivo against Klebsiella pneumoniae and Escherichia coli. Ten isolates, including CRE and/or CPE with β-lactamase genes, were used in this study. The relationship between phenotype and in vivo efficacy was assessed in a murine neutropenic thigh-infection model. Efficacy was determined by the change in bacterial quantity.

RESULTS

The results of the in vitro study showed the minimum inhibitory concentrations of the combination of NAC with either MEM, FEP, or ATM in a 1:1 ratio were 2 to >128-fold lower than those of MEM, FEP, or ATM alone against CRE+ isolates. In addition, combinations of β-lactams and NAC administered in the murine thigh-infection model showed greater efficacy against CRE+/CPE+, CRE+/CPE-, and CRE-/CPE+ isolates harboring various β-lactamase genes (IMP-1, IMP-6, KPC, DHA-1, or OXA-48) compared with MEM, FEP, ATM, and NAC alone.

CONCLUSION

MEM, FEP, or ATM in combination with NAC showed potent in vivo antimicrobial activity in a murine thigh-infection model caused by K. pneumoniae and E. coli, including CRE and/or CPE isolates. These findings indicate that these combinations of β-lactams and NAC are potential candidates for the treatment of CRE and/or CPE infections.

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.

Multiplex Real-Time PCR Assay for Six Major Carbapenemase Genes

The global dissemination of carbapenemase-producing Enterobacteriaceae (CPE) is a major concern in public health. Due to the existence of the diversity of carbapenemases, development of an easily available, cost-effective multiplex detection assay for CPE is required worldwide. Using clinically available and reliable equipment, COBAS^® z480 (Roche Diagnostics K.K., Tokyo, Japan), we developed a multiplex real-time PCR assay for the detection of two combinations of carbapenemases; first, bla_NDM, bla_KPC, and bla_IMP (Set 1), and second, bla_GES, bla_OXA-48, and bla_VIM (Set 2). We constructed standard curves for each carbapenemase gene using serial dilutions of DNA standards, then applied reference or clinical isolates with each carbapenemase gene to this assay. The multiplex assay showed satisfactory accuracy to detect CPE genes, with the correlation coefficients of greater than 0.99 for all genotypes. The assay appropriately differentiated the reference or clinical strains harboring each carbapenemase gene without cross reactivity. Lastly, the assay successfully detected multiple genes without false-positive reactions by applying six clinical isolates carrying both NDM and OXA-48-like carbapenemase genes. Major advantages of our assay include multiplicity, simple operation, robustness, and speed (1 h). We believe that the multiplex assay potentially contributes to early diagnosis of CPE with a diverse genetic background.

Development of a Nomogram for Carbapenem-Resistant Enterobacteriaceae Acquisition Risk Prediction Among Patients in the Intensive Care Unit of a Secondary Referral Hospital

PURPOSE

This study aimed to identify the risk factors of carbapenem-resistant Enterobacteriaceae (CRE) acquisition to build a nomogram for CRE acquisition risk prediction and evaluate its performance.

METHODS

This unmatched case-control study included 352 adult patients (55 patients and 297 controls) admitted to the intensive care unit (ICU) of a 453-bed secondary referral hospital between January 1, 2018, and September 31, 2019, in Busan, South Korea. The nomogram was built with the identified risk factors using multiple logistic regression analysis. Its performance was analyzed using calibration-in-the-large, the slope of the calibration plot, concordance statistic (c-statistic), and the sensitivity and specificity of the training set, subsets, and a new test set.

RESULTS

The risk factors of CRE acquisition among ICU patients at a secondary referral hospital were Acute Physiology and Chronic Health Evaluation II score at the time of admission, use of a central venous catheter and a nasogastric tube, as well as use of cephalosporin antibiotics. At 20.0% of the predicted CRE acquisition risk in the training set, the calibration-in-the-large was 0, slope of the calibration plot was 1, c-statistic was .93, sensitivity was 85.5%, and specificity was 84.8%. The performance was relatively good in the subsets and new test set.

CONCLUSION

The nomogram can be used to monitor the CRE acquisition risk for ICU patients who have a similar case mix to patients in the study hospitals. Future studies need to involve more rigorous methodology and larger samples.

A Matched Case-Case-Control Study of the Impact of Clinical Outcomes and Risk Factors of Patients with IMP-Type Carbapenemase-Producing Carbapenem-Resistant Enterobacteriaceae in Japan

IMP-type carbapenemase, found in various Gram-negative bacteria, has been increasingly detected worldwide. We aimed to study the outcomes and risk factors for acquisition of IMP-type carbapenemase-producing carbapenem-resistant Enterobacteriaceae (IMP-CRE), as this has not been evaluated in detail. We conducted a matched case-case-control study of patients from whom IMP-CRE isolates were obtained. All patients who tested positive for IMP-CRE were included; they were matched with patients with carbapenem-susceptible Enterobacteriaceae (CSE) and with controls at a ratio of 1:1:2. The risk factors for acquisition for the CRE and CSE groups and mortality rates, which were calculated using multivariate logistic regression models with weighting according to the inverse probability of propensity scores, were compared. In total, 192 patients (96 patients each in the CRE and CSE groups, with 130 Enterobacter cloacae isolates and 62 Klebsiella sp. isolates) were included. The IMP-11 type was present in 43 patients, IMP-1 in 33, and IMP-60 and IMP-66 in 1 each; 31 patients with CRE (32.3%) and 34 with CSE (35.4%) developed infections. Multivariate analysis identified the following independent risk factors: gastrostomy, history of intravenous therapy or hemodialysis, and previous exposure to broad-spectrum β-lactam antibiotics, including penicillin with β-lactamase inhibitors, cephalosporins, and carbapenems. In propensity score-adjusted analysis, mortality rates for the CRE and CSE groups were similar (15.0% and 19.5%, respectively). We found that IMP-CRE may not contribute to worsened clinical outcomes, compared to CSE, and gastrostomy, previous intravenous therapy, hemodialysis, and broad-spectrum antimicrobial exposure were identified as risk factors for CRE isolation. Fluoroquinolone and aminoglycosides are potentially useful antibiotics for IMP-CRE infections.

Deskilled and Rapid Drug-Resistant Gene Detection by Centrifugal Force-Assisted Thermal Convection PCR Device

Here we report the improved Cyclo olefin polymer (COP) microfluidic chip and polymerase chain reaction (PCR) amplification system for point-of-care testing (POCT) in rapid detection of Carbapenem-resistant Enterobacteriaceae (CRE). The PCR solution and thermal cycling is controlled by the relative gravitational acceleration (7G) only and is expected to pose minimal problem in operation by non-expert users. Detection is based on identifying the presence of carbapenemase encoding gene through the corresponding fluorescence signal after amplification. For preliminary tests, the device has been demonstrated to detect bla_IMP-6 from patients stool samples. From the prepared samples, 96.4 fg/µL was detected with good certainty within 15 min (~106 thermocycles,) which is significantly faster than the conventional culture plate method. Moreover, the device is expected to detect other target genes in parallel as determination of the presence of bla_NDM-1 and bla_OXA-23 from control samples has also been demonstrated. With the rising threat of drug-resistant bacteria in global healthcare, this technology can greatly aid the health sector by enabling the appropriate use of antibiotics, accelerating the treatment of carriers, and suppressing the spread.

Prevalence of carbapenem-resistant Enterobacteriaceae and emergence of high rectal colonization rates of blaOXA-181-positive isolates in patients admitted to two major hospital intensive care units in Kuwait

BACKGROUND

Fecal colonization by carbapenem-resistant Enterobacteriaceae (CRE) can be the main reservoir for transmission of these resistant organisms especially in the Intensive Care Units (ICUs).

AIM

This study was conducted to evaluate the rate of rectal carriage and molecular characterization of CRE in patients hospitalized in the ICUs of 2 major hospitals (Adan and Mubarak Al Kabeer Hospitals) in Kuwait.

MATERIALS AND METHODS

Rectal swabs were collected from all patients at admission, 48 h after admission and once weekly from April 2017- March 2018. Initial CRE screening was carried out on MacConkey agar on which meropenem disc 10μg was placed. Identification of isolates was by API 20E. Susceptibility testing was performed using the E-test method. Polymerase chain reaction (PCR) was used to detect the carbapenemase-encoding genes. Clonal relationship was investigated by pulsed-field electrophoresis (PFGE). Genes of blaOXA-181 and blaNDM-5-carrying plasmids were detected in some strains.

RESULTS

A total of 590 patients were recruited into the study. Of these, 58 were positive for CRE, giving a prevalence of 9.8%; 25/320 (7.8%) in Adan and 33/270 (12.2%) in Mubarak Al Kabeer Hospitals. All isolates were resistant to multiple antibiotics. Resistance rates to colistin and tigecycline were 17% and 83%, respectively. Single genes of blaOXA-181 were detected in isolates from 38 (65.5%) out of 58 patients and in 5 patients colonized by blaOXA-48-positive CRE. A combination of 2 genes was detected in 12 isolates; 5 blaKPC-2 and blaOXA-181, 4 blaVIM-1 and blaOXA-181, and 3 blaNDM-5 and blaOXA-181. PFGE showed an overall level of similarity of 38%. Southern hybridization studies localized the blaOXA-181 and blaNDM-5 genes to a large plasmid of 200kb in 3 K. pneumoniae isolates and a small plasmid of 80kb in 2 E. coli isolates, respectively.

CONCLUSION

The prevalence of CRE colonization in the 2 hospital ICUs was relatively high and the emergence of blaOXA-181-mediated CRE is a cause for concern as there is the possibility of rapid horizontal spread among hospital patients in Kuwait. Active surveillance of CRE in the ICUs is highly recommended to stem its spread.

Characterization of the Plasmidome Encoding Carbapenemase and Mechanisms for Dissemination of Carbapenem-Resistant Enterobacteriaceae

Global dissemination of carbapenem-resistant Enterobacteriaceae (CRE) threatens human health by limiting the efficacy of antibiotics even against common bacterial infections. Carbapenem resistance, mainly due to carbapenemase, is generally encoded on plasmids and is spread across bacterial species by conjugation. Most CRE epidemiological studies have analyzed whole genomes or only contigs of CRE isolates. Here, plasmidome analysis on 230 CRE isolates carrying bla_IMP was performed to shed light into the dissemination of a single carbapenemase gene in Osaka, Japan. The predominant dissemination of bla_IMP-6 by the pKPI-6 plasmid among genetically distinct isolates was revealed, as well as the emergences of pKPI-6 derivatives that acquired advantages for further disseminations. Underlying vast clonal dissemination of a carbapenemase-encoding plasmid, heteroresistance was found in CRE offspring, which was generated by the transcriptional regulation of bla_IMP-6, stabilization of bla_IMP-6 through chromosomal integration, or broadened antimicrobial resistance due to a single point mutation in bla_IMP-6.

Carbapenem-resistant Enterobacteriaceae (CRE) infections, high in morbidity and mortality, pose serious clinical challenges due to limited treatment options. A previous CRE surveillance study on 1,507 patients from 43 hospitals in Osaka, Japan, revealed that 12% of patients carried CRE and that 95% of the CRE isolates were IMP-type carbapenemase producers. Here, the mechanisms for this regional dissemination of a single carbapenemase gene were investigated. Since the dissemination of CRE is primarily due to the transmission of carbapenemase genes located on plasmids, we analyzed the plasmidome of 230 CRE isolates carrying bla_IMP by whole-genome sequencing and Southern blotting. bla_IMP-6 was found to be predominantly disseminated among chromosomally distinct isolates through the pKPI-6 plasmid. Underlying the vast clonal dissemination of pKPI-6, various subpopulations deriving from pKPI-6 were identified, which had acquired advantages for the dissemination of CRE isolates. A cluster exhibiting heteroresistance against meropenem by the transcriptional regulation of bla_IMP-6 caused an outbreak likely through covert transmission of bla_IMP-6. For stable carriage of bla_IMP-6, they occasionally integrated bla_IMP-6 on their chromosomes. In addition, we detected one isolate that broadened the range of antimicrobial resistance through a single point mutation in bla_IMP-6 on pKPI-6. Multifaceted analysis of the plasmidome granted us more accurate perspectives on the horizontal spread of CRE isolates, which is difficult to trace only by comparing the whole genomes. This study revealed the predominant spread of a specific carbapenemase-encoding plasmid accompanying the emergence of phenotypically diverse derivatives, which may facilitate further dissemination of CRE in various environments.

IMPORTANCE Global dissemination of carbapenem-resistant Enterobacteriaceae (CRE) threatens human health by limiting the efficacy of antibiotics even against common bacterial infections. Carbapenem resistance, mainly due to carbapenemase, is generally encoded on plasmids and is spread across bacterial species by conjugation. Most CRE epidemiological studies have analyzed whole genomes or only contigs of CRE isolates. Here, plasmidome analysis on 230 CRE isolates carrying bla_IMP was performed to shed light into the dissemination of a single carbapenemase gene in Osaka, Japan. The predominant dissemination of bla_IMP-6 by the pKPI-6 plasmid among genetically distinct isolates was revealed, as well as the emergences of pKPI-6 derivatives that acquired advantages for further disseminations. Underlying vast clonal dissemination of a carbapenemase-encoding plasmid, heteroresistance was found in CRE offspring, which was generated by the transcriptional regulation of bla_IMP-6, stabilization of bla_IMP-6 through chromosomal integration, or broadened antimicrobial resistance due to a single point mutation in bla_IMP-6.

Risk Factors for Carbapenemase-Producing Enterobacterales Infection or Colonization in a Korean Intensive Care Unit: A Case-Control Study

The purpose of this study is to identify the factors related to the infection and/or colonization of carbapenemase-producing Enterobacterales (CPE) based on clinical and microbiological data for patients in the intensive care unit (ICU). All patients admitted to medical ICU were screened for CPE on admission and weekly, and this 1:2 case–control study included patients with CPE identified by screening or clinical cultures from 2017 to 2018. The clonal relatedness was evaluated by pulsed-field gel electrophoresis (PFGE). A total of 45 CPE patients were identified with a prevalence of 3.8%. The most frequent organism was Klebsiella pneumoniae (69%) and the carbapenemases belonged to the class A Klebsiella pneumoniae Carbapenemase (KPC-2) (87%), class B New Delhi Metallo-β-lactamase (NDM) (11%), and Imipenemase (IMP-1) (2%) strains. The PFGE profiles showed two large clustered groups of KPC-2-producing K. pneumoniae. In the multivariate analysis, pneumonia/chronic pulmonary disease, previous fluoroquinolone use, and previous use of nasogastric tube were the significant risk factors for CPE infection or colonization in ICU-admitted patients. Critical illness and underlying medical conditions such as pneumonia/chronic pulmonary disease, antimicrobial selective pressure, and the use of a medical device are identified as risk factors for CPE infection or colonization in ICU. Person to person transmission also contributed.

Development of CRISPR-Cas13a-based antimicrobials capable of sequence-specific killing of target bacteria

The emergence of antimicrobial-resistant bacteria is an increasingly serious threat to global health, necessitating the development of innovative antimicrobials. Here we report the development of a series of CRISPR-Cas13a-based antibacterial nucleocapsids, termed CapsidCas13a(s), capable of sequence-specific killing of carbapenem-resistant Escherichia coli and methicillin-resistant Staphylococcus aureus by recognizing corresponding antimicrobial resistance genes. CapsidCas13a constructs are generated by packaging programmed CRISPR-Cas13a into a bacteriophage capsid to target antimicrobial resistance genes. Contrary to Cas9-based antimicrobials that lack bacterial killing capacity when the target genes are located on a plasmid, the CapsidCas13a(s) exhibit strong bacterial killing activities upon recognizing target genes regardless of their location. Moreover, we also demonstrate that the CapsidCas13a(s) can be applied to detect bacterial genes through gene-specific depletion of bacteria without employing nucleic acid manipulation and optical visualization devices. Our data underscore the potential of CapsidCas13a(s) as both therapeutic agents against antimicrobial-resistant bacteria and nonchemical agents for detection of bacterial genes.

CRISPR technology is emerging as a potential antimicrobial against antimicrobial-resistant bacteria. Here the authors develop a bacteriophage delivered Cas13a system for killing target bacteria and detecting bacterial genes.

Genomic characterisation of a novel plasmid carrying blaIMP-6 of carbapenem-resistant Klebsiella pneumoniae isolated in Osaka, Japan

OBJECTIVES

To analyse plasmids carrying bla_IMP-6 in Klebsiella pneumoniae isolates obtained from multicentre carbapenem-resistant Enterobacteriaceae surveillance.

METHODS

Plasmids harbouring bla_IMP-6 were characterised by the whole-genome sequencing of four Klebsiella pneumoniae isolates carrying bla_IMP-6, and compared with the pKPI-6 plasmid, which is widespread in western Japan, through pulsed-field gel electrophoresis, Southern blotting, bacterial conjugation, and qPCR.

RESULTS

Whole-genome sequencing analysis revealed that three of the four isolates carried approximately 50 kbp plasmids similar to the pKPI-6 plasmid; however, one isolate carried a 250 kbp plasmid harbouring bla_IMP-6 (pE196_IMP6). So far, all of the reported plasmids carrying bla_IMP-6 were similar to the pKPI-6 plasmid, and this plasmid was a novel bla_IMP6-carrier. The size and transferability of this plasmid was confirmed by Southern hybridisation and conjugation experiments. It was demonstrated that the generation of plasmid pE196_IMP6 was due to an intramolecular transposition mediated by IS26, and a homologous recombination between plasmids pKPI-6 and pE013 that was obtained from another carbapenem-resistant Enterobacteriaceae isolate in this analysis. As a result of co-integration with pE013, pE196_IMP6 acquired six additional pairs of type II toxin-antitoxin systems that pKPI-6 does not carry. Transcription of all of the toxin-antitoxin systems were confirmed in an isolate carrying pE196_IMP6 by qPCR.

CONCLUSIONS

This study detected a novel plasmid carrying bla_IMP-6, and revealed the origin of this plasmid. Toxin-antitoxin system acquisition could enable pE196_IMP6 maintenance persistently through successions, even without selection pressure by the clinical usage of antimicrobials, generating broad dissemination and longer carbapenem-resistant Enterobacteriaceae colonisation duration in patients.

Cohorting for preventing the nosocomial spread of Carbapenemase-Producing Enterobacterales, in non-epidemic settings: is it mandatory?

BACKGROUND

Worldwide dissemination of Carbapenemase-Producing Enterobacterales (CPE) has led to national and international guidance recommending the implementation of cohorting in healthcare settings (HS). However, in view of recent data regarding the spread of Extended-spectrum Beta-lactamase-producing Enterobacterales, we may wonder about the usefulness of this measure in a non-outbreak settings; here, individual contact isolation may be sufficient to control the risk of dissemination.

AIM/METHODS

We conducted a narrative review of the literature and discussed the role of cohorting.

FINDINGS

CPE are responsible for outbreaks in HS, which are considered the epicentre of spread of resistance strains. CPE are responsible for adverse effects such as increases in hospital stay and costs, less therapeutic options and thus higher risk of clinical failures and mortality. Environment and materials have also been described contaminated with CPE and can be the source of outbreak. Even if guidelines and publications have supported implementation of cohorting, there are no randomized studies demonstrating the mandatory nature of this measure. Most studies are descriptive and cohorting is usually one of several other measures to control outbreaks. Cohorting is not adapted to all HS, which requires human and material resources. Other measures must be strengthened such as compliance of hand hygiene, antibiotic stewardship and surveillance of contact patients. Individual risk factors of acquisition should also be evaluated.

CONCLUSION

Local epidemiology and resources must be assessed before implementing cohorting.

Trends and molecular characteristics of carbapenemase-producing Enterobacteriaceae in Japanese hospital from 2006 to 2015

BACKGROUND

The increasing number of carbapenemase-producing Enterobacteriaceae (CPE) has become a global problem. Most carbapenemases detected in Japan are imipenemase, which is an imipenem-degrading enzyme with low ability; thus, CPE could have been overlooked. Therefore, this study aimed to detect and analyze CPE, without overlooking CPE showing the low minimum inhibitory concentration phenotype.

METHODS

CPE screening was conducted on 531 ceftazidime-resistant Enterobacteriaceae isolated from Kitasato University Hospital during 2006-2015. We confirmed the presence of the carbapenemase genes (bla_IMP, bla_VIM, bla_KPC, bla_NDM, and bla_OXA-48) by multiplex polymerase chain reaction. The detected CPE strains were analyzed by antimicrobial susceptibility testing, multilocus sequence typing, conjugal experiments, replicon typing, and plasmid profiling by restriction enzyme treatment.

RESULTS

The CPE detection rate in Kitasato University Hospital within the past 10 years was 0.0003% (nine CPE strains). These nine CPE strains were identified to harbor 8 bla_IMP-1 or 1 bla_NDM-5. The CPE strains consisted of five species including Klebsiella pneumoniae and Citrobacter freundii. Six of eight bla_IMP-1 were coded by IncHI2 plasmid, and the other two were coded by IncA/C plasmid. Plasmid profiling revealed that K. pneumoniae and C. freundii isolated from the same patient harbored the same plasmid.

CONCLUSION

The CPE detection rate in this study was significantly lower than those previously reported in Japan. In one case, IncA/C plasmid transmission through different bacterial species within the body was speculated. Although the number of CPE detected was low, these results indicated that the resistance plasmid could spread to other bacterial species.