Carbapenemase-producing Enterobacterales Research Articles

Carbapenem- and colistin-resistant Enterobacterales in intensive care unit patients in Mediterranean countries, 2019

IntroductionThe colonization of patients by carbapenemase-producing Enterobacterales (CPE) has been associated with heightened mortality, especially in vulnerable individuals within intensive care units (ICUs). Our study aimed to comprehensively assess CPE prevalence among ICU patients across the Mediterranean region pre-COVID-19, conducting a multicenter prevalence study in the first quarter of 2019.MethodsWe collected clinical data and rectal or fecal samples from 256 ICU patients for CPE testing. Additionally, we performed whole-genome sequencing on 40 representative CPE strains to document their molecular characteristics.ResultsAmong the 256 patients, CPE was detected in 73 samples (28.5%), with prevalence varying from 3.3 to 69.0% across participating centers. We observed 13 colistin-resistant CPE strains, affecting three ICUs. Genetic analysis revealed highly diverse E. coli and K. pneumoniae strains, predominantly from international high-risk clones. Notably, blaOXA-48 and blaNDM-1 were the most prevalent carbapenemase genes. Molecular typing uncovered potential patient clusters in six centers. Significantly, longer hospital stays were associated with increased CPE carriage (p < 0.001). Nine centers across Morocco, Tunisia, Egypt, and Lebanon voluntarily participated.DiscussionOur study provides CPE prevalence in Mediterranean ICUs and reaffirms established CPE presence in this setting but also provides updates on the molecular diversity of CPE strains. These findings highlight the imperative of reinforcing infection control measures in the participating ICUs to curtail escalated mortality rates, and of strictly applying isolation measures around patients originating from the Mediterranean region when transferred to other healthcare institutions.

In vitro pharmacokinetics/pharmacodynamics of FL058 (a novel beta-lactamase inhibitor) combined with meropenem against carbapenemase-producing Enterobacterales

Objective: FL058 is a novel beta-lactamase inhibitor with a broad spectrum of activity and a favorable safety profile. The objective of this study was to evaluate pharmacokinetic/pharmacodynamic (PK/PD) relationships for the combination of FL058 and meropenem in an in vitro infection model.Methods: By simulating human concentration-time profiles in the in vitro model, meropenem combined with FL058 when administered 1 g/0.5 g, 1 g/1 g, 2 g/1 g, and 2 g/2 g q8h by 3-h infusion achieved approximately 2- and 4-log10 kill to KPC/OXA-producing Klebsiella pneumoniae and Escherichia coli; the combination therapy could not inhibit NDM-producing K. pneumoniae but could maintain NDM-producing E. coli around a baseline.Results: The PK/PD indexes that best described the bacterial killing from baseline in log10 CFU/mL at 24 h were the percent time of free drug above the minimal inhibitory concentration (MIC) (%fT > MIC, MIC with FL058 at 4 mg/L) for meropenem and the percent time of free drug above 1 mg/L (%fT > 1 mg/L) for FL058. The targets for achieving a static effect and the 1- and 2-log10 kill were 74, 83, and 99 for %fT > MIC of meropenem and 40, 48, and 64 for %fT > 1 mg/L of FL058, respectively. The PK/PD index of %fT > 1 mg/L can provide a basis for evaluating clinical dosing regimens for FL058 combined with meropenem.Conclusion: FL058 combined with meropenem might be a potential treatment for KPC- and/or OXA-48-producing Enterobacterales infection.

Epidemiology and clinical significance of carbapenemases in Australia: a narrative review.

Carbapenemase-producing gram-negative bacteria (CP-GNB) infections threaten public health with high mortality, morbidity and treatment costs. Although frequencies remain low in Australia (total number of CP-GNB infections reported was 907 in 2022), blaIMP-4 has established low levels of endemicity in many states. Imipenemase metallo-β-lactamase types alone accounted for more than half of all carbapenemases in carbapenemase-producing Enterobacterales isolates in Australia, particularly in Enterobacter cloacae complex. New Delhi metallo-β-lactamase constitutes almost 25% of all carbapenemases in Australia and was identified predominantly in Escherichia coli. The OXA-48-like carbapenemases include almost 10% of all carbapenemases and are mainly seen in Klebsiella pneumoniae and E. coli. Although K. pneumoniae carbapenemase-type carbapenemases are rare in Australia, some local outbreaks have occurred. Most carbapenem-resistant (CR) Pseudomonas aeruginosa strains in Australia do not produce carbapenemases. Finally, OXA-23-like carbapenemases are overwhelmingly positive in CR-Acinetobacter baumannii strains in Australia. Treatment of CR-GNB infections challenges physicians. Of 10 new antibiotics active against at least some CR-GNB infections that are approved by the USFood and Drug Administration, just three are approved for use in Australia. In this context, there is still an unmet need for novel antibacterials that can be used for the treatmentof CR-GNB infections in Australia, as well as a pressing requirement for new mechanisms to 'de-link' antibiotic sales from their availability. In this narrative review, we aim to overview the epidemiology and clinical significance of carbapenem resistance in Australia as it pertains to Enterobacterales, P. aeruginosa and A. baumannii.

Evaluation of the in vitro susceptibility of clinical isolates of NDM-producing Klebsiella pneumoniae to new antibiotics included in a treatment regimen for infections

BackgroundDue to the growing resistance to routinely used antibiotics, the search for new antibiotics or their combinations with effective inhibitors against multidrug-resistant microorganisms is ongoing. In our study, we assessed the in vitro drug susceptibility of Klebsiella pneumoniae strains producing New Delhi metallo-β-lactamases (NDM) to antibiotics included in the Infectious Diseases Society of America (IDSA) and European Society of Clinical Microbiology and Infectious Diseases (ESCMID) recommendations.MethodsA total of 60 strains of NDM-producing K. pneumoniae were obtained from different patients hospitalized at the 4th Military Hospital in Wroclaw between 2019 and 2022 and subjected to drug susceptibility to selected antibiotics, including the effects of drug combinations.ResultsAmong the tested antibiotics, the highest sensitivity (100%) was observed for cefiderocol, eravacycline (interpreted according to the European Committee on Antimicrobial Susceptibility Testing [EUCAST]), and tigecycline. Sensitivity to intravenous fosfomycin varied depending on the method used. Using the “strip stacking” method, determining cumulative sensitivity to ceftazidime/avibactam and aztreonam demonstrated 100% in vitro sensitivity to this combination among the tested strains.ConclusionThe in vitro susceptibility assessment demonstrated that, the best therapeutic option for treating infections caused by carbapenemase-producing strains seems to be a combination of ceftazidime/avibactam with aztreonam. Due to the safety of using both drugs, cost effectiveness, and the broadest indications for use among the tested antibiotics, this therapy should be the first-line treatment for carbapenemase-producing Enterobacterales infections. Nevertheless, a comprehensive evaluation of the efficacy of treating infections caused by NDM-producing K. pneumoniae strains should include not only in vitro susceptibility assessment but also an analysis of clinical cases.

Rapid detection of carbapenemase-producing gram-negative bacteria directly from blood culture bottles for a reliable guided empiric therapy.

Bloodstream infections (BSIs) caused by multidrug-resistant bacteria are a critical life-threatening challenge which necessitates the urgency to trigger life-saving treatment in a timely manner. This study aimed to evaluate the time required for rapid detection of carbapenemase-producing Enterobacterales (CPE) directly from blood culture bottles to optimize empirical treatment of BSI, especially in pediatric and infant patients, using a cost-effective method. This study included 419 Gram-negative bacteria, of which Klebsiella pneumoniae and Escherichia coli were the most common CPE causing BSI in pediatric and neonatal patients. Phenotypic and genotypic resistance of the selected isolates (45 K. pneumoniae and 9 E. coli) were determined by VITEK-2 Compact system and PCR, respectively. BACT/ALERT bottles were spiked with isolates. Finally, colorimetric RESIST-BC assay and Vitek-2 compact system were evaluated for the rapid detection of carbapenem-resistant bacteria directly from positive blood culture bottles. All selected isolates were phenotypically resistant to carbapenems. PCR showed that blaNDM and blaOXA-48 were present in all isolates, blaVIM was present in 44.4%, while blaKPC and blaIMP were entirely absent. The RESIST-BC kit showed good agreement with PCR for blaNDM and blaOXA-48, demonstrating high sensitivity and specificity, but not with blaVIM. These findings point out that RESIST-BC assay demonstrated an exceptionally short detection time for CPE, completing all cases within the first hour after the blood culture bottles flagged positive. It is also superior in providing a cluefor clinicians on antibiotic combinations that can be administered, depending on the type of β-lactamases detected, promptly and efficiently, with low expenses.

Carbapenemase-producing Enterobacterales strains causing infections in companion animals-Portugal.

This is the first study on the prevalence of carbapenemase-producing Enterobacterales (CPE) clinical strains from companion animals in Portugal. Despite the generally low prevalence of CPE in companion animals, it is imperative for veterinary diagnostic laboratories to employ diagnostic methods for carbapenemase detection. The resemblance found in the mobile genetic elements transporting carbapenemase genes between veterinary medicine and human medicine implies a potential circulation within a One Health framework.

The outbreak of multispecies carbapenemase-producing Enterobacterales associated with pediatric ward sinks: IncM1 plasmids act as vehicles for cross-species transmission.

This study describes an outbreak caused by multispecies carbapenemase-producing Enterobacterales (CPE) occurring in a pediatric ward at an academic medical center in Tokyo. The index case involved a 1-year-old boy with Klebsiella variicola (CPE) detected in anal swabs in June 2016. The second case was Klebsiella quasipneumoniae (CPE) occurred in March 2017 followed by further spread, leading to the declaration of an outbreak in April 2017. Extensive environmental and patient microbiological sampling was performed. The relatedness of the isolates was determined using draft-whole-genome sequencing. CPE surveillance cultures of patients and environments were positive in 19 patients and 9 sinks in the ward. The sinks in hospital rooms uninhabited by CPE patients exhibited no positive CPE-positive specimen during the outbreak. All CPE strains analyzed using draft-whole-genome sequencing harbored blaIMP-1, except for one harboring blaIMP-11; these strains harbored identical blaIMP-1-carrying IncM1 plasmids. CPE was detected even after sink replacement; infection-control measures focused on sinks were implemented and the CPE outbreak ended after 7 months. Multiple bacterial species can become CPE via blaIMP-1-carrying IncM1 plasmids of the same origin and spread through sinks in a hospital ward. Thorough infection-control measures implemented as a bundle might be crucial.

Detection of carbapenemase producing enterobacterales using the Modified Hodge Test from clinical isolates in Colombo South Teaching Hospital and Sri Jayewardenepura General Hospital, Sri Lanka in 2017

Introduction: Enterobacterales is a large family of Gram-negative bacilli including many pathogens. Carbapenemase producing Enterobacterales (CPEs) have emerged as a global threat. This study was conducted to detect carbapenemase production by Enterobacterales isolates from clinical specimens and to correlate the occurrence of CPE with age, gender, and duration of hospital stay of the patients included in the study.Methods: A descriptive cross-sectional study was carried out using 120 consecutive, non-repetitive clinical isolates identified as Enterobacterales by the microbiology laboratories of Colombo South Teaching Hospital and Sri Jayewardenepura General Hospital. The demographic data of the patients was gathered and used to analyse the correlation with CPE occurrence. All isolates were identified up to species level using API 20E kits. Screening for detection of carbapenemase was carried out using meropenem, imipenem, and ertapenem disks. The Modified Hodge Test (MHT), which is one of the suggested procedures to determine carbapenemase production, was performed to identify carbapenemase producing isolates.Results: Of the120 isolates, 14 (11.7%) were resistant to at least one of the carbapenems tested. MHT detected carbapenemase production in ten (8.3%) isolates. The majority of these isolates were Klebsiella sp. (6; 60.0%). Of carbapenemase producing isolates, six were from urine specimens (60%). Eight (80.0%) of the CPE harbouring patients were males and eight (80.0%) were aged above 50 years. The mean duration of hospital stay of the patients was 7.2 days (±SD 5.65days).Conclusion: The proportion of CPE was 8.3% according to this study and emphasises the importance of conducting more studies on the prevalence of CPE in Sri Lanka.

The Importance of Carbapenemase-Producing Enterobacterales in African Countries: Evolution and Current Burden

Antimicrobial resistance (AMR) is a worldwide healthcare problem. Multidrug-resistant organisms (MDROs) can spread quickly owing to their resistance mechanisms. Although colonized individuals are crucial for MDRO dissemination, colonizing microbes can lead to symptomatic infections in carriers. Carbapenemase-producing Enterobacterales (CPE) are among the most important MDROs involved in colonizations and infections with severe outcomes. This review aimed to track down the first reports of CPE in Africa, describe their dissemination throughout African countries and summarize the current status of CRE and CPE data, highlighting current knowledge and limitations of reported data. Two database queries were undertaken using Medical Subject Headings (MeSH), employing relevant keywords to identify articles that had as their topics beta-lactamases, carbapenemases and carbapenem resistance pertaining to Africa or African regions and countries. The first information on CPE could be traced back to the mid-2000s, but data for many African countries were established after 2015–2018. Information is presented chronologically for each country. Although no clear conclusions could be drawn for some countries, it was observed that CPE infections and colonizations are present in most African countries and that carbapenem-resistance levels are rising. The most common CPE involved are Klebsiella pneumoniae and Escherichia coli, and the most prevalent carbapenemases are NDM-type and OXA-48-type enzymes. Prophylactic measures, such as screening, are required to combat this phenomenon.

Clinical and genomic characteristics of IMP-producing Enterobacter cloacae complex and Klebsiella pneumoniae.

Carbapenemase-producing Enterobacterales (CPEs) are one of the top priority antimicrobial-resistant pathogens. Among CPEs, those producing acquired metallo-β-lactamases (MBLs) are considered particularly problematic as few agents are active against them. Imipenemase (IMP) is the most frequently encountered acquired MBL in Japan, but comprehensive assessment of clinical and microbiological features of IMP-producing Enterobacterales infection remains scarce. Here, we retrospectively evaluated 62 patients who were hospitalized at a university hospital in Japan and had IMP-producing Enterobacterales from a clinical culture. The isolates were either Enterobacter cloacae complex or Klebsiella pneumoniae, and most of them were isolated from sputum. The majority of K. pneumoniae, but not E. cloacae complex isolates, were susceptible to aztreonam. Sequence type (ST) 78 and ST517 were prevalent for E. cloacae complex and K. pneumoniae, respectively, and all isolates carried blaIMP-1. Twenty-four of the patients were deemed infected with IMP-producing Enterobacterales. Among the infected patients, therapy varied and largely consisted of conventional β-lactam agents, fluoroquinolones, or combinations. Three (13%), five (21%), and nine (38%) of them died by days 14, 30, and 90, respectively. While incremental mortality over 90 days was observed in association with underlying comorbidities, active conventional treatment options were available for most patients with IMP-producing Enterobacterales infections, distinguishing them from more multidrug-resistant CPE infections associated with globally common MBLs, such as New Delhi metallo-β-lactamase (NDM) and Verona integron-encoded metallo-β-lactamase (VIM).

Emergence of pandrug-resistant carbapenemase-producing Enterobacterales in dogs and cats: a cross-sectional study in Egypt.

One of the most important emerging health problems is the increasing role of animals in the rapid global rise in resistance to last-resort antibiotics, such as carbapenems. However, there is limited information on the role of pet animals in harboring and spreading pandrug-resistant (PDR) carbapenemase-producing Enterobacterales (CPE), especially in Egypt. This cross-sectional study was conducted to screen for CPE in healthy and diseased pets using phenotypic and molecular methods and the NG-Test CARBA 5 immunochromatographic assay. Rectal swabs were collected from 62 dogs and 48 cats, incubated overnight in tryptic soy broth containing 10 μg of meropenem disc and subsequently cultured on MacConkey agar supplemented with meropenem (1 mg/L). Sixty-six isolates (60.6%), including 56 Klebsiella pneumoniae, seven Escherichia coli, and three K. oxytoca isolates, were confirmed to be carbapenem-resistant Enterobacterales (CRE) by the disc diffusion method, broth microdilution test, CNPt-direct, and PCR assay targeting carbapenemase genes. Forty-three (65.2%) dogs and 23 (34.8%) cats carried CPE. Of these, 35 (70.0%) were healthy (including 27 dogs and 8 cats) and 31 (52.5%) were diseased (including 16 dogs and 15 cats). bla OXA-181 was the most common gene detected (42/66, 63.6%), followed by bla IMP (40/66, 60.6%), bla OXA-48-like (29/66, 43.9%), bla KPC and bla VIM (20/66, 30.3% each), and bla NDM (17/66, 25.8%). The identified genotypes were bla KPC-2, bla IMP-1, bla VIM-1, bla NDM-1, and bla NDM-5. The CARBA 5 assay showed higher sensitivity and specificity for the detection of NDM, OXA and KPC than that for VIM and IMP genes. Antimicrobial resistance profiles of CRE isolates revealed 20 PDR, 30 extensively drug-resistant (XDR), and 16 multidrug-resistant (MDR) phenotypes. This study provides evidence of colonization with PDR CPE in dogs and cats. To manage the infection or colonization of pets in veterinary clinical settings, extended surveillance systems should be considered, and the use of critical antibiotics should be strictly controlled.

Examining the impact and response to an outbreak of carbapenemase-producing Enterobacterales in a neonatal unit in the United Kingdom: An outbreak report

Background Carbapenemase-producing Enterobacterales (CPE) are a group of Gram-negative bacteria causing global concern due to their resistance to carbapenems. In this report, we detail the learning points from a CPE outbreak in a tertiary neonatal unit (NU) in the UK. Methods Routine surveillance screening (rectal swabs) of babies on the NU identified a potential cluster of CPE carriage. Samples were sent to a reference laboratory for confirmatory testing. Environmental screening and cot mapping were undertaken to determine movements of babies within the unit. Regular audits of cleaning standards, hand hygiene, and maternal hygiene when expressing breast milk were carried out. Results The outbreak lasted 19 weeks. During the outbreak, there were 360 admissions, with 11 babies being colonised with the outbreak strain. Once the outbreak was declared, there were enhanced Infection Prevention and Control (IPC) precautions (including increased environmental and equipment cleaning frequency). CPE screening frequency was increased and cot capacity was reduced. Hand hygiene compliance improved from 92% at the start of the outbreak to 100% by its close. Cleaning standards remained compliant. Maternal hygiene standards varied from 78% to 100%, but no cross-infection links were identified. Environmental screening was negative. No route of cross-infection was identified. Notably, no babies developed invasive CPE infection. Conclusion This is the first report of a CPE outbreak in a UK NU. Although no specific mode of cross-transmission was identified and the outbreak’s end cannot be attributed to any single intervention, the bundle of interventions proved successful after a 5-month period.

The natural history of carbapenemase-producing Enterobacterales: progression from carriage of various carbapenemases to bloodstream infection.

Little is known about the risk of progression from carbapenemase-producing Enterobacterales (CPE) carriage to CPE bloodstream infection (BSI) outside of high-risk settings. We aimed to determine the incidence of CPE BSI among CPE carriers and to assess whether the incidence differed by carbapenemase, species, and setting. We conducted a nationwide population-based retrospective cohort study using national databases. The cohort consisted of all patients in Israel with CPE detected by screening from 1/1/2020 to 10/10/2022. We calculated the cumulative incidence of CPE BSI within 1 year among CPE carriers. We used a competing-risks model with BSI as the outcome and death as the competing risk. The study included 6,828 CPE carriers. The cumulative incidence of CPE BSI was 2.4% (95% CI: 2.1%-2.8%). Compared to KPC, the subhazard of BSI was lower for NDM (aSHR: 0.72, 95% CI: 0.49-1.05) and OXA-48-like (aSHR: 0.60, 95% CI: 0.32-1.12) but these differences did not reach statistical significance. Compared to K. pneumoniae, the subhazard of BSI was lower for carriers of carbapenemase-producing E. coli (aSHR: 0.31, 95% CI: 0.20-0.47). The subhazard of BSI was higher among patients with CPE carriage first detected in intensive care units (aSHR: 2.42, 95% CI: 1.50-3.92) or oncology/hematology wards (aSHR: 3.77, 95% CI: 2.40-5.93) compared to medical wards. The risk of CPE BSI among CPE carriers is lower than previously reported in studies that focused on high-risk patients and settings. The risk of BSI differs significantly by bacterial species and setting, but not by carbapenemase.

Carbapenem- and cefiderocol-resistant Enterobacterales in surface water in Kumasi, Ashanti Region, Ghana.

MDR pathogens including ESBL- and/or carbapenemase-producing Enterobacterales (ESBL-PE and CPE) increasingly occur worldwide in the One Health context. This proof-of-principle study investigated the occurrence of ESBL-PE in surface water in the Ashanti Region in Ghana, sub-Saharan Africa (SSA), and investigated their additional genotypic and phenotypic antimicrobial resistance features as part of the Surveillance Outbreak Response Management and Analysis System (SORMAS). From 75 water samples overall, from nine small to medium-sized river streams and one pond spatially connected to a channelled water stream in the greater area of Kumasi (capital of the Ashanti Region in Ghana) in 2021, we isolated 121 putative ESBL-PE that were subsequently subjected to in-depth genotypic and phenotypic analysis. Of all 121 isolates, Escherichia coli (70.25%) and Klebsiella pneumoniae (23.14%) were the most prevalent bacterial species. In addition to ESBL enzyme-production of mostly the CTX-M-15 type, one-fifth of the isolates carried carbapenemase genes including blaNDM-5. More importantly, susceptibility testing not only confirmed phenotypic carbapenem resistance, but also revealed two isolates resistant to the just recently approved last-resort antibiotic cefiderocol. In addition, we detected several genes associated with heavy metal resistance. ESBL-PE and CPE occur in surface water sources in and around Kumasi in Ghana. Further surveillance and research are needed to not only improve our understanding of their exact prevalence and the reservoir function of water sources in SSA but should include the investigation of cefiderocol-resistant isolates.

Effect of Temperature on Carbapenemase-Encoding Plasmid Transfer in Klebsiella pneumoniae.

Bacteria causing human infections can develop antibiotic resistance due to various factors. Temperature affects bacterial growth and gene transfer; however, studies exploring the association between the changes in local temperature and antibiotic resistance are limited. Here, we investigated the effects of local temperatures on the distribution of antibiotic resistance and transmission of carbapenemase-producing Enterobacterales using the data on Klebsiella pneumoniae from sentinel hospitals in eight regions included in the Korea Global Antimicrobial Resistance Surveillance System between 2017 and 2021. The resistance rates to most antibiotics, including carbapenems, varied significantly according to local temperature (p < 0.047), except for aminoglycosides. Conjugation experiments at various temperatures for strains encoding the carbapenemase gene on a plasmid revealed significant variation in the optimal conjugation temperatures for plasmids carrying blaKPC and blaNDM genes. The optimal conjugation temperatures demonstrating the highest stability for blaKPC- and blaNDM-carrying plasmids were 25 °C (p = 0.030) and 30 °C (p = 0.007), respectively. The stability of blaKPC-IncF was higher at 25 °C than that at 30 °C (p = 0.032) or 37 °C (p = 0.047), while blaKPC-IncX3 exhibited the lowest stability at 37 °C (p = 0.047). blaNDM-IncX3 was more stable at 30 °C than at 37 °C (p = 0.049). These findings suggest that the optimal temperature for carbapenemase gene transmission varied between 25 °C and 30 °C, indicating that warmer seasons promote the transfer of more antibiotic resistance-related genes and highlighting the importance of local temperature in the spread and transmission of plasmids carrying carbapenemases.

Trends of antimicrobial susceptibilities and multidrug-resistant colonization rate in patients transferred from long-term care facilities during 2017-2022: a cross-sectional study.

With the global increase in the older population, the proportion of those receiving care in long-term care facilities (LTCFs) has also been increasing. We assessed the epidemiology, antibiotic susceptibility, and colonization status of drug-resistant organisms in patients transferred from LTCFs. We retrospectively reviewed the medical records of patients transferred from LTCFs between 2017 and 2022. The reasons for admission, antimicrobial susceptibility, and colonization rates of carbapenem-resistant Enterobacterales (CRE), methicillin-resistant Staphylococcus aureus (MRSA), and carbapenem-resistant Acinetobacter baumannii (CRAB) were recorded. We analyzed the susceptibility and colonization rates by year to identify trends. Of the 936 patients transferred from LTCFs, 54.3% were admitted to the intensive care unit and 12.5% died. The most common reason for admission was infection (n = 573, 61.2%), followed by gastrointestinal bleeding (n = 67, 7.2%) and cerebrovascular disorder (n = 65, 6.9%). A total of 452 Enterobacterales strains were isolated, and their susceptibility rates to ciprofloxacin and cefotaxime were 33.3% and 35.6%, respectively. A total of 54.9% were extended-spectrum beta-lactamase-producing strains, and 4.9% of them were carbapenem-resistant, both of which showed an increasing trend (P = 0.024 and P < 0.001, respectively). The prevalence rates of CRE, CRAB, and MRSA colonization were 9.2%, 7.1%, and 23.1%, respectively. CRE colonization showed a significant increase (P < 0.001), with carbapenemase-producing Enterobacterales accounting for 75.9% of cases. Patients transferred from LTCFs are primarily affected by infections and exhibit high resistance rates. The increasing trend in CRE colonization rates each year highlights the need for the implementation of rigorous infection control measures for effective management.

Comparison of clinical outcomes of patients with serial negative surveillance cultures according to a subsequent polymerase chain reaction test for carbapenemase-producing Enterobacterales

The aims of this study were to evaluate the impact of the result of a subsequent polymerase chain reaction (PCR) test for carbapenemase after serial negative surveillance cultures on positive culture conversion in patients with three consecutive negative surveillance cultures for carbapenemase-producing Enterobacterales (CPE), and to identify risk factors for conversion. We performed a retrospective study of patients with positive CPE cultures on CHROMagar KPC medium in a tertiary hospital in Korea from October 2018 to December 2022. A PCR test for the most common carbapenemases in Korea, blaKPC, blaNDM,blaIMP,blaVIM,blaGES, and blaOXA-48 was performed after three consecutive negative rectal swab cultures. We compared the clinical characteristics and outcomes of patients according to whether the follow-up PCR was positive (CNPP) or negative (CNPN). Of 1075 patients with positive CPE cultures, 150 (14.0%) yielded three consecutive negative rectal swab cultures. Of these, 50 (33.3%) were CNPP, and 100 (66.7%) were CNPN. Risk factors associated with a positive PCR result on multivariate analysis were age, central venous catheter, and Escherichia coli infection. CNPP patients were more likely to have positive culture conversion for CPE than CNPN patients (39/44 [88.6%] vs. 21/50 [42.0%], P<0.001). In multivariate analysis, a positive PCR result after surveillance cultures, diabetes mellitus, central venous catheter, and Klebsiella pneumoniae were independent risk factors for culture conversion. CNPP patients have higher rates of culture conversion than CNPN patients, and a follow-up PCR test after serial negative surveillance cultures is useful in deciding whether or not to discontinue contact precautions.

Carba PBP: a novel penicillin-binding protein-based lateral flow assay for rapid phenotypic detection of carbapenemase-producing Enterobacterales.

Rapid phenotypic detection assays, including Carba NP and its variants, are widely applied for clinical diagnosis of carbapenemase-producing Enterobacterales (CPE). However, these tests are based on the acidification of the pH indicator during carbapenem hydrolysis, which limits test sensitivity and speed, especially for the detection of CPE producing low-activity carbapenem (e.g., OXA-48 variants). Herein, we developed a novel rapid and sensitive CPE detection method (Carba PBP) that could measure substrate (meropenem) consumption based on penicillin-binding protein (PBP). Meropenem-specific PBP was used to develop a competitive lateral flow assay (LFA) for meropenem identification. For the detection of carbapenemase activity, meropenem concentration was optimized using a checkerboard assay. The performance of Carba PBP was evaluated and compared with that of Carba NP using a panel of 94 clinical strains characterized by whole-genome sequencing and carbapenem susceptibility test. The limit of detection of PBP-based LFA for meropenem identification was 7 ng mL-1. Using 10 ng mL-1 meropenem as the substrate, Carba PBP and Carba NP could detect 10 ng mL-1 carbapenemase within 25 min and 1,280 ng mL-1 CPE in 2 h, respectively. The sensitivity and specificity were 100% (75/75) and 100% (19/19) for Carba PBP and 85.3% (64/75) and 100% (19/19) for Carba NP, respectively. When compared with Carba NP, Carba PBP showed superior performance in detecting all the tested CPE strains (including OXA-48-like variants) within 25 min and presented two orders of magnitude higher analytical sensitivity, demonstrating potential for clinical diagnosis of CPE. IMPORTANCE This study successfully achieved the goal of carbapenemase activity detection with both high sensitivity and convenience, offering a convenient lateral flow assay for clinical diagnosis of carbapenemase-producing Enterobacterales.

Do we still need Illumina sequencing data? Evaluating Oxford Nanopore Technologies R10.4.1 flow cells and the Rapid v14 library prep kit for Gram negative bacteria whole genome assemblies.

The best whole genome assemblies are currently built from a combination of highly accurate short-read sequencing data and long-read sequencing data that can bridge repetitive and problematic regions. Oxford Nanopore Technologies (ONT) produce long-read sequencing platforms and they are continually improving their technology to obtain higher quality read data that is approaching the quality obtained from short-read platforms such as Illumina. As these innovations continue, we evaluated how much ONT read coverage produced by the Rapid Barcoding Kit v14 (SQK-RBK114) is necessary to generate high-quality hybrid and long-read-only genome assemblies for a panel of carbapenemase-producing Enterobacterales bacterial isolates. We found that 30× long-read coverage is sufficient if Illumina data are available, and that more (at least 100× long-read coverage is recommended for long-read-only assemblies. Illumina polishing is still improving single nucleotide variants (SNVs) and INDELs in long-read-only assemblies. We also examined if antimicrobial resistance genes could be accurately identified in long-read-only data, and found that Flye assemblies regardless of ONT coverage detected>96% of resistance genes at 100% identity and length. Overall, the Rapid Barcoding Kit v14 and long-read-only assemblies can be an optimal sequencing strategy (i.e., plasmid characterization and AMR detection) but finer-scale analyses (i.e., SNV) still benefit from short-read data.

Hospital-wide healthcare-associated carbapenemase-producing Enterobacterales outbreak: risks of electric floor scrubbers in catering facilities and kitchens

BackgroundCarbapenemase-producing Enterobacterales (CPE) are associated with poor clinical outcomes and can spread rapidly in healthcare settings. Environmental reservoirs are increasingly recognised as playing an important part in some nosocomial outbreaks. AimTo describe the investigation and control of a CPE outbreak, lasting several years, across two separate hospital sites within one organisation. MethodsInvestigation of multiple ward level CPE cross-transmissions with a number of sporadic cases. Environmental sampling of ward environments, catering facilities and electric floor scrubbers was undertaken. Findings11 patients over a 19 month period were identified as carrying healthcare associated New Delhi Metallo-beta-lactamase (NDM) producing Enterobacter cloacae, and a further patient carried NDM Escherichia coli. E. cloacae isolates were indistinguishable on pulsed field gel electrophoresis typing, supporting acquisition with a single point source. Environmental sampling found contamination of the electric floor scrubbers used for cleaning the hospital catering facilities and in the associated toilets. Standard outbreak response measures achieved control of ward outbreaks. Sporadic cases and hospital wide cross-transmission were controlled after interventions on the central food-handling unit and by decommissioning affected floor scrubbers. Electric floor scrubbers were found to have the potential to disperse Gram-negative bacteria into the surrounding environment under experimental conditions. ConclusionThis outbreak report demonstrates that catering facilities and kitchens can be involved in widespread healthcare outbreaks of enteric organisms. This is also the first report of the potential role of electric floor scrubbers in causing significant environmental contamination with CPE which may indicate a role in nosocomial transmission.