Carbapenemase-producing Organisms Research Articles

Prevalence of carbapenemase-producing organisms among hospitalized solid organ transplant recipients, five US hospitals, 2019-2020.

Passive reporting to the Centers for Disease Control and Prevention has identified carbapenemase-producing organisms (CPOs) among solid organ transplant (SOT) recipients, potentially representing an emerging source of spread. We analyzed CPO prevalence in wards where SOT recipients receive inpatient care to inform public health action to prevent transmission. From September 2019 to June 2020, five US hospitals conducted consecutive point prevalence surveys (PPS) of all consenting patients admitted to transplant units, regardless of transplant status. We used the Cepheid Xpert Carba-R assay to identify carbapenemase genes (blaKPC , blaNDM , blaVIM , blaIMP , blaOXA-48 ) from rectal swabs. Laboratory-developed molecular tests were used to retrospectively test for a wider range of blaIMP and blaOXA variants. In total, 154 patients were screened and 92 (60%) were SOT recipients. CPOs were detected among 7 (8%) SOT recipients, from two of five screened hospitals: four blaKPC , one blaNDM , and two blaOXA-23 . CPOs were detected in two (3%) of 62 non-transplant patients. In three of five participating hospitals, CPOs were not identified among any patients admitted to transplant units. Longitudinal surveillance in transplant units, as well as PPS in areas with diverse CPO epidemiology, may inform the utility of routine screening in SOT units to prevent the spread of CPOs.

Evaluation of Ceftriaxone-Sulbactam-EDTA Adjuvant Combination against Multidrug Resistant Bacteria in Tertiary Care Hospital, Guntur, Andhra Pradesh, India

Introduction: In India, multiple antibiotic resistances are rapidly growing in the bacterial population with a rising threat to public health. To overcome the effect of extended-spectrum beta-lactamases (ESBL), Metallo beta-lactamases (MBL) and carbapenemaseproducing organisms, very few antibiotics are effective; the need of the hour is a new antibiotic or drug combination. Various studies suggested that antibiotic adjuvant therapies can be an alternate approach to curb the rate of drug resistance in microorganisms. A new antibiotic combination of ceftriaxone+ sulbactam+ EDTA (CSE) has recently been proposed to tackle MDR organisms. Aim: To evaluate the in-vitro efficacy of a new antibiotic adjuvant entity CSE, among the Vitek-2 (Biomerieux, France) confirmed Multidrug Resistant (MDR) strains isolated from specimens of Intensive Care Unit (ICU) patients. Materials and Methods: A cross-sectional descriptive study was conducted on a total of 100 consecutive MDR organisms isolated from specimens of ICU admitted patients in NRI general hospital and super specialty care centre in Guntur district, Andhra Pradesh, India. Bacterial growth on the medium was identified using an automated Vitek-2 system using gram negative and gram positive identification card and Antimicrobial Susceptibility Testing (AST) cards. The isolates were identified as ESBL, MBL, AmpCbeta-lactamase, and carbapenemases producing organisms and tested for sensitivity to CSE drug-using Epsilometer (E)-test strips with Minimum Inhibitory Concentrations (MIC) gradient of 0.016-256 µg/mL, and interpreted as sensitive, and resistant based on breakpoints. A descriptive statistical analysis was done by calculating the frequencies of the variables. Results: The more prevalent MDR pathogens were Escherichia coli (36%), Pseudomonas aeruginosa (18%), Klebsiella pneumoniae (15%), and Proteus species (10%). Among Escherichia coli MDR isolates, 16.7% were ESBL+MBL producing and 83.3% were carbapenemase-producing with good susceptibility to CSE 86.7% and 83.3% respectively. Among Pseudomonas aeruginosa 83.3% of ESBL+MBL and carbapenemase-producing organisms were susceptible to CSE. Overall, 88% of MDR strains were sensitive and 12% were resistant to novel CSE combinations among 100 MDR isolates. Conclusion: The novel antibiotic-adjuvant combination CSE is highly effective (88% susceptibility) against ESBL/MBL, AmpC, and carbapenemase-producing MDR bacteria. The enhanced susceptibility may be due to the synergistic effect of all three molecules in the combination.

Emergence of dual and multicarbapenemase coproducing organisms in the United States.

Carbapenemase-producing organisms commonly carry a single carbapenemase gene conferring resistant to carbapenems and other β-lactam antibiotics. Here, we report rare cases of multidrug-resistant Pseudomonas aeruginosa, Klebsiella pneumoniae, and Acinetobacter baumannii strains that coproduce multiple carbapenemases and exhibit extensive drug resistance. Such resistant strains are rarely identified in the United States.

649. Evaluation of the NG-Test CARBA 5® in Enterobacteriaceae and P. aeruginosa from Clinical Isolates

Abstract Background Identification of carbapenemase-producing organisms like Enterobacteriaceae and P. aeruginosa is important for treatment decisions and infection control. Identification methods require time and technical training. Lateral flow immunoassay NG-Test CARBA 5® exempt these needs. In Mexico there is no evaluation of it on clinical isolates. It is important to define their diagnostic accuracy. Methods We collected 103 clinical strains of Enterobacteriaceae and P. aeruginosa resistant to carbapenems, from 2019 to 2020 from: National Institute of Rehabilitation (INR), National Institute of Cancerology, General Hospital Dr. Manuel Gea González and Hospital Civil de Guadalajara Fray Antonio Mayor. Analyzed in INR’s microbiology laboratory, resistance was corroborated with broth Microdilution Method (CLSI 2020). The carbapenemases was demonstrated by phenotypic methods (CLSI 2021). A homemade PCR was done and sequencing for encoding genes: NDM, KPC, GES, VIM, IMP and OXA-48-like. We analyzed concordance of the NG-Test CARBA 5® versus PCR with kappa coefficient. Results Seven discarded, 96 strains entered the analysis: Enterobacteriaceae (73%), P. aeruginosa (27%) (Table1). The carbapenemase-producing organisms were: 1) 56 Enterobacteriaceae, 30% Class B; 2) 23 P. aeruginosa, 90% Class B. NG-Test CARBA 5® for Enterobacteriaceae demonstrated greater sensitivity, specificity, and NPV (table 2). Kappa coefficient of concordance was 0.92 for Enterobacteriaceae and 0.59 for P. aeruginosa (table 2), and discrepancies in table 3. Sequencing of carbapenemase-producing organisim can be find in table 4. Title 1. Clinical isolates by hospital N: No carbapenem-producing, Gea: General Hospital Dr. Manuel Gea González, Civil GDL: Hospital Civil de Guadalajara, INCAN: National Institute of Cancerology, INR: National Institute of Rehabilitation. Table 3. Discrepancies Enzyme gene secuencing Conclusion The most frequent enzyme were Ambler Class B, consistent with national reports. Sensitivity and specificity was like reported in other series. In P. aeruginosa, errors have already been reported in IMP-type enzymes, ours mainly with IMP-75. To our knowledge there are no reports of the following enzyme variants identified by NG-Test CARBA 5®: KPC-82, VIM-67, IMP-62, and IMP-75. NG-Test CARBA 5® showed high concordance with PCR for Enterobacteriaceae, it has the advantage of being a quick and easy-to-use detection tool. In P. aeruginosa despite the results without solid evidence, we recommend complementing the test with other phenotypic identification tests. Table 2. Kappa Concordance Coefficient of NG-Test CARBA 5® and PCR Se: sensitivity, Sp: specificity, PPV: positive predictive value, NPV: negative predictive value Disclosures All Authors: No reported disclosures

Performance Evaluation of Diagnostic Assays for Detection and Classification of Carbapenemase-Producing Organisms.

Rapid and accurate detection can help optimize patient treatment and improve infection control against nosocomial carbapenemase-producing organisms (CPO). In this study, a total of 217 routine clinical isolates (Enterobacterales and A. baumannii), including 178 CPOs and 39 non-CPOs, were tested to evaluate the performance of six phenotypic carbapenemase detection and classification assays, i.e., BD Phoenix CPO detect panel, Rapidec Carba-NP, O.K.N detection kit, and three carbapenem inactivation methods (CIMs; mCIM, eCIM, sCIM). The overall detection sensitivity and specificity were 98.78% (95.21–99.79%) and 79.49% (63.06–90.13%), respectively, for the BD phoenix CPO P/N test; 91.93% (86.30–95.45%) and 100% (88.83–100%), respectively, for the Rapidec Carba-NP; 98.06% (94.00–99.50%) and 97.44% (84.92–99.87%), respectively, for mCIM; and 96.89% (92.52–98.85%) and 94.87% (81.37–99.11%), respectively, for sCIM. The classification sensitivity and specificity for the BD phoenix CPO Ambler test, the O.K.N detection kit, and the mCIM and eCIM were 56.71% (48.75–64.34%) and 94.87% (81.37–99.11%), 99.28% (95.43–99.96%) and 100% (88.83–100%), and 92.90% (87.35–96.23%) and 97.44% (84.92–99.87%), respectively. All detection assays were reliable in detecting carbapenemase. However, the Rapidec Carba-NP and mCIM were insufficient in detecting OXA-48-like enzymes. The BD phoenix CPO detect panel had a strong ability to detect carbapenemase but failed to classify 48/59 (81.36%) KPC, 8/52 (15.38%) NDM, 8/22 (36.36%) OXA-23-like, and 6/11 (54.55%) dual enzymes. The O.K.N detection kit accurately detected and differentiated KPC, NDM, and OXA-48-like enzymes existing alone or in combination. The results of this study will support reliable laboratory work tools and promote therapeutic and infection control decisions.

Coupling Machine Learning and High Throughput Multiplex Digital PCR Enables Accurate Detection of Carbapenem-Resistant Genes in Clinical Isolates.

Rapid and accurate identification of patients colonised with carbapenemase-producing organisms (CPOs) is essential to adopt prompt prevention measures to reduce the risk of transmission. Recent studies have demonstrated the ability to combine machine learning (ML) algorithms with real-time digital PCR (dPCR) instruments to increase classification accuracy of multiplex PCR assays when using synthetic DNA templates. We sought to determine if this novel methodology could be applied to improve identification of the five major carbapenem-resistant genes in clinical CPO-isolates, which would represent a leap forward in the use of PCR-based data-driven diagnostics for clinical applications. We collected 253 clinical isolates (including 221 CPO-positive samples) and developed a novel 5-plex PCR assay for detection of blaIMP, blaKPC, blaNDM, blaOXA-48, and blaVIM. Combining the recently reported ML method “Amplification and Melting Curve Analysis” (AMCA) with the abovementioned multiplex assay, we assessed the performance of the AMCA methodology in detecting these genes. The improved classification accuracy of AMCA relies on the usage of real-time data from a single-fluorescent channel and benefits from the kinetic/thermodynamic information encoded in the thousands of amplification events produced by high throughput real-time dPCR. The 5-plex showed a lower limit of detection of 10 DNA copies per reaction for each primer set and no cross-reactivity with other carbapenemase genes. The AMCA classifier demonstrated excellent predictive performance with 99.6% (CI 97.8–99.9%) accuracy (only one misclassified sample out of the 253, with a total of 160,041 positive amplification events), which represents a 7.9% increase (p-value <0.05) compared to conventional melting curve analysis. This work demonstrates the use of the AMCA method to increase the throughput and performance of state-of-the-art molecular diagnostic platforms, without hardware modifications and additional costs, thus potentially providing substantial clinical utility on screening patients for CPO carriage.

Quantitative Insights Into β-Lactamase Inhibitor's Contribution in the Treatment of Carbapenemase-Producing Organisms With β-Lactams.

Objectives: Carbapenemase-producing organisms (CPOs) are associated with high mortality rates. The recent development of β-lactamase inhibitors (BLIs) has made it possible to control CPO infections safely and effectively with β-lactams (BLs). This study aims to explicate the quantitative relationship between BLI’s β-lactamase inhibition and CPO’s BL susceptibility restoration, thereby providing the infectious disease society practical scientific grounds for regulating the use of BL/BLI in CPO infection treatment.Methods: A diverse collection of human CPO infection isolates was challenged by three structurally representative BLIs available in the clinic. The resultant β-lactamase inhibition, BL susceptibility restoration, and their correlation were followed quantitatively for each isolate by coupling FIBA (fluorescence identification of β-lactamase activity) and BL antibiotic susceptibility testing.Results: The β-lactamase inhibition and BL susceptibility restoration are positively correlated among CPOs under the treatment of BLIs. Both of them are dependent on the target CPO’s carbapenemase molecular identity. Of note, without sufficient β-lactamase inhibition, CPO’s BL susceptibility restoration is universally low across all tested carbapenemase molecular groups. However, a high degree of β-lactamase inhibition would not necessarily lead to a substantial BL susceptibility restoration in CPO probably due to the existence of non-β-lactamase BL resistance mechanisms.Conclusion: BL/BLI choice and dosing should be guided by quantitative tools that can evaluate the inhibition across the entire β-lactamase background of the CPO upon the BLI administion. Furthermore, rapid molecular diagnostics for BL/BLI resistances, especially those sensitive to β-lactamase independent BL resistance mechanisms, should be exploited to prevent ineffective BL/BLI treatment.

Screening patients at admission to Copenhagen hospitals for carriage of resistant bacteria after contact with healthcare systems abroad, 2016–2019

ObjectivesPatients having previous contact with healthcare systems abroad are routinely screened for resistant bacteria on admission to hospitals in Copenhagen. This study aimed to present carriage prevalence and geographical risk stratification, as well as phenotypic and genotypic characterisation of resistant isolates. MethodsThis study included screening samples analysed at one department of clinical microbiology in Copenhagen from 2016–2019. Patients who had previous contact with healthcare systems abroad within 6 months were screened at admission for methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant Enterococci (VRE) and carbapenemase-producing organisms (CPO). Isolates were characterised phenotypically and by whole-genome sequencing. The relative frequency of positive findings stratified by geographical regions correlated with relative frequency of Danish residents’ travel destinations. ResultsOf 2849 screening sets included in the study, 103 (3.6%) were positive. A total of 120 resistant isolates were detected (36 MRSA, 31 VRE and 53 CPO). The carrier prevalence for MRSA was 1.3%, 1.1% for VRE and 1.5% for CPO. Southern and Western Asia were overrepresented travel destinations in positive screening sets (41%). For VRE, 40% were related to Southern Europe, which also represented 35% of travel destinations. Genotypic characterisation confirmed a heterogenous genomic background reflecting global distribution of resistant clones. ConclusionsExposure targeted screening identified a substantial number of asymptomatic carriers of MRSA, VRE and CPO with heterogenous genetic backgrounds. Although some geographical regions were overrepresented, the complex epidemiology of the different pathogens did not allow a restriction of the screening strategy to certain geographical regions.

Using Molecular Diagnostics to Develop Therapeutic Strategies for Carbapenem-Resistant Gram-Negative Infections.

Infections caused by multidrug-resistant Gram-negative organisms have become a global threat. Such infections can be very difficult to treat, especially when they are caused by carbapenemase-producing organisms (CPO). Since infections caused by CPO tend to have worse outcomes than non-CPO infections, it is important to identify the type of carbapenemase present in the isolate or at least the Ambler Class (i.e., A, B, or D), to optimize therapy. Many of the newer beta-lactam/beta-lactamase inhibitor combinations are not active against organisms carrying Class B metallo-enzymes, so differentiating organisms with Class A or D carbapenemases from those with Class B enzymes rapidly is critical. Using molecular tests to detect and differentiate carbapenem-resistance genes (CRG) in bacterial isolates provides fast and actionable results, but utilization of these tests globally appears to be low. Detecting CRG directly in positive blood culture bottles or in syndromic panels coupled with bacterial identification are helpful when results are positive, however, even negative results can provide guidance for anti-infective therapy for key organism-drug combinations when linked to local epidemiology. This perspective will focus on the reluctance of laboratories to use molecular tests as aids to developing therapeutic strategies for infections caused by carbapenem-resistant organisms and how to overcome that reluctance.

Accuracy of Xpert Carba-R Assay for the Diagnosis of Carbapenemase-Producing Organisms from Rectal Swabs and Clinical Isolates: A Meta-Analysis of Diagnostic Studies

The Cepheid Xpert Carba-R assay has demonstrated a promising value for the detection of carbapenemase-producing organisms, but its diagnostic performance remains unclear. Studies were retrieved from Cochrane Library, EMBASE, and PubMed databases according to predetermined selection criteria. The specificity, sensitivity, negative likelihood ratio, positive likelihood ratio, and area under the summary receiver operating characteristic curves of Xpert Carba-R were analyzed by STATA version 13.0. The quality of each study was examined by Quality Assessment of Diagnostic Accuracy Studies using RevMan version 5.2. In total, 17 unique studies involving 15,972 samples met the inclusion criteria. Nine studies performed Xpert Carba-R on rectal swabs. The pooled sensitivity, specificity, and area under the curve were as follows: 0.95 (95% CI, 0.91-0.97; I2=90.80%), 0.99 (95% CI, 0.97-0.99; I2=97.17%), and 0.99 (95% CI, 0.98-1.00), respectively. The sensitivity and specificity of Xpert Carba-R in high-risk populations were 0.99 (95% CI, 0.76-1.00; I2=78.51%) and 0.98 (95% CI, 0.97-0.99; I2=84.95%), respectively. The sensitivity and specificity in low-prevalence regions were 0.96 (95% CI, 0.88-0.99; I2=74.58%) and 0.99 (95% CI, 0.98-0.99; I2=77.66%), respectively. Eight studies performed Xpert Carba-R on clinical isolates. The pooled sensitivity and specificity were 1.00 (95% CI, 0.97-1.00; I2=97.43%) and 0.98 (95% CI, 0.97-0.99; I2=55.27%), respectively. This meta-analysis indicates that Xpert Carba-R assay has excellent diagnostic accuracy for diagnosing carbapenemase-producing organisms on rectal swabsand clinical isolates, especially for high-risk populations and low-prevalence regions.

Carbapenemase-producing organism (CPO) colonisation at a district general hospital: universal screening may help reduce transmission

SummaryObjectiveAssess the potential of hospital-wide routine screening by determining the prevalence and incidence of carbapenemase-producing organisms (CPOs) isolated from rectal screens at Barnet and Chase Farm Hospitals.Methods3,553 samples were collected between 01/12/2018 and 31/08/2019: from adult critical care wards (universal screening - admission, discharge and weekly), from medical wards with risk-factor based screening according to the prevailing Public Health England (PHE) carbapenemase-producing Enterobacteriaceae (CPE) screening guidelines, or on an ad hoc basis. Prevalence was defined as previously documented positive CPO colonisation, or new positive status, as a proportion of all eligible samples. Incidence was defined as all newly positive patients per 1,000 patient-days.ResultsOverall CPO prevalence was 2.1% (95% CI: 1.61–2.58%). Inpatient prevalence was significantly higher at 2.6% vs outpatient at 0.5% (p < 0.001). Incidence was 0.44 per 1,000 patient-days (95% CI: 0.33–0.57), with a rate ratio between Barnet and Chase Farm of 4.9 (p = 0.013). Incidence was highest where universal screening strategy was applied (3.9 per 1000 patient-days, 95% CI: 2.4–5.91). This was 2.5 times higher than risk-factor based screening (p = 0.005) and 23.5 times that of wards without routine surveillance implemented (p < 0.001).ConclusionSurveillance remains a cornerstone in controlling CPO transmission. Our local incidence, lacking hospital-wide screening, significantly exceeded the reported UK average. Universal screening could help to uncover the true prevalence and incidence of CPO, thereby providing the necessary information to properly control transmission, reducing nosocomial outbreaks and ultimately reducing the overall cost to healthcare.

Antimicrobial resistant bacteria recovered from retail ground meat products in the US include a Raoultella ornithinolytica co-harboring blaKPC-2 and blaNDM-5

Retail beef and pork, including processed products, can serve as vehicles for the zoonotic foodborne transmission of pathogens and antimicrobial resistant bacteria. However, processed and seasoned products like sausages, are not often included in research and surveillance programs. The objective of this study was to investigate retail ground beef and pork, including processed products, for the presence of common foodborne pathogens and antimicrobial resistant bacteria. We purchased 763 packages of fresh and fully cooked retail meat products during 29 visits to 17 grocery stores representing seven major grocery chains located in west and central Ohio. Each package of meat was evaluated for contamination with methicillin-resistant Staphylococcus aureus (MRSA), Salmonella spp., Enterobacteriaceae expressing extended-spectrum cephalosporin resistance, and carbapenemase-producing organisms (CPO). Only 3 of the 144 (2.1%) packages of fully cooked meat products contained any of these organisms, 1 with an extended-spectrum β-lactamase-producing (ESBL) Enterobacteriaceae and 2 with CPO. Among the 619 fresh meat products, we found that 85 (13.7%) packages were contaminated with MRSA, 19 (3.1%) with Salmonella, 136 (22.0%) with Enterobacteriaceae expressing an AmpC (blaCMY) resistance genotype, 25 (4.0%) with Enterobacteriaceae expressing an ESBL (blaCTX-M) resistance genotype, and 31 (5.0%) with CPO, primarily environmental organisms expressing intrinsic carbapenem resistance. However, one CPO, a Raoultella ornithinolytica, isolated from pork sausage co-harbored both blaKPC-2 and blaNDM-5 on IncN and IncX3 plasmids, respectively. Our findings suggest that fresh retail meat, including processed products can be important vehicles for the transmission of foodborne pathogens and antimicrobial resistant bacteria, including those with epidemic carbapenemase-producing genotypes.

Verona Integron-Encoded Metallo-Beta-Lactamase (VIM)–Producing Pseudomonas aeruginosa Outbreak Associated with Acute Care

Background: Contaminated healthcare facility plumbing is increasingly recognized as a source of carbapenemase-producing organisms (CPOs). In August 2019, the Tennessee State Public Health Laboratory identified Tennessee’s twelfth VIM-producing carbapenem-resistant Pseudomonas aeruginosa (VIM-CRPA), from a patient in a long-term acute-care hospital. To determine a potential reservoir, the Tennessee Department of Health (TDH) reviewed healthcare exposures for all cases. Four cases (33%), including the most recent case and earliest from March 2018, had a history of admission to intensive care unit (ICU) room X at acute-care hospital A (ACH A), but the specimens were collected at other facilities. The Public Health Laboratory collaborated with ACH A to assess exposures, perform environmental sampling, and implement control measures. Methods: TDH conducted in-person infection prevention assessments with ACH A, including a review of the water management program. Initial recommendations included placing all patients admitted to room X on contact precautions, screening for CPO on room discharge, daily sink basin and counter cleaning, and other sink hygiene measures. TDH collected environmental and water samples from 5 ICU sinks (ie, the handwashing and bathroom sinks in room X and neighboring room Y [control] and 1 hallway sink) and assessed the presence of VIM-CRPA. Moreover, 5 patients and 4 environmental VIM-CRPA underwent whole-genome sequencing (WGS). Results: From February to June 2020, of 21 patients admitted to room X, 9 (43%) underwent discharge screening and 4 (44%) were colonized with VIM-CRPA. Average room X length of stay was longer for colonized patients (11.3 vs 4.8 days). Drain swabs from room X’s bathroom and handwashing sinks grew VIM-CRPA; VIM-CRPA was not detected in tap water or other swab samples. VIM-CRPA from the environment and patients were sequence type 253 and varied by 0–13 single-nucleotide variants. ACH A replaced room X’s sinks and external plumbing in July. Discharge screening and contact precautions for all patients were discontinued in November, 5 months following the last case and 12 consecutive negative patient discharge screens. Improved sink hygiene and mechanism testing for CRPA from clinical cultures continued, with no new cases identified. Conclusions: An ICU room with a persistently contaminated sink drain was a persistent reservoir of VIM-CRPA. The room X attack rate was high, with VIM-CRPA acquisition occurring in &gt;40% of patients screened. The use of contaminated plumbing fixtures in ACH have the potential to facilitate transmission to patients but may be challenging to identify and remediate. All healthcare facilities should follow sink hygiene best practices.Funding: NoDisclosures: None

Respiratory coinfections in COVID-19 patients evaluated by BioFire Pneumonia Panel

BackgroundRoutine administration of antibacterials in patients with Covid-19 has been a subject of debate, with no solid data about the true prevalence of respiratory coinfections in Covid-19 patients in different geographic areas. The aim of the current study was to identify respiratory coinfections in Covid-19 patients admitted to the hospital and to identify its genetic resistance pattern using the respiratory multiplex polymerase chain reaction (PCR).ResultsThe study included 40 patients, 32 males (80%) and 8 (20%) females with a mean age of 59.3 ± 12.6. Half of the patients had respiratory bacterial coinfections documented by pneumonia (PN) panel. The most common isolate was Klebsiella pneumoniae (10/20, 50%), followed by Acinetobacter calcoaceticus baumanni complex (7/20, 35%). Regarding genetic resistance, thirteen (13/20, 65%) isolates were proven extended spectrum beta lactamase (ESBL)-producing Enterobacteriaceae. Thirteen (13/20, 65%) isolates were proven carbapenemase-producing organisms testing positive for New Delhi metallo-β-lactamase (NDM), oxacillinase β-lactamases (OXA-48), and Verona Integron-Encoded Metallo-β-Lactamase (VIM) (7/20, 35%; 5/20, 25%; 1/20, 5%, respectively). The four isolated Staphylococcus aureus were methicillin-resistant (4/20, 20%).ConclusionIn our cohort, there was 50% rate of bacterial respiratory coinfection in patients with severe Covid-19 admitted to the ICU with high rates of carbapenemase-producing gram-negative bacteria that required escalation of antibacterials and represented a challenge to clinicians.

Preventing a Candida Auris Outbreak at an Acute Care Hospital During the COVID-19 Pandemic

BackgroundCandida auris (C. auris) is a fungal pathogen that recently emerged and rapidly spread around the globe. It is now in California with 74 clinical cases according to the Centers for Disease Control and Prevention (August 31, 2020). C. auris can cause invasive disease with high mortality rates, is frequently resistant to one or more classes of antifungals, and can be difficult to identify. C. auris can also involve prolonged colonization of patients’ skin and contamination of surrounding environments, resulting in hospital outbreaks. The first known clinical case of C. auris in San Diego County was identified in an individual with recent hospitalization outside of the United States. The identification of this clinical case coincided with the first influx of COVID-19 patients.MethodsThe facility's carbapenemase-producing organism (CRO) screening program identified an individual who had recent hospitalization abroad. The patient was placed in a single room in pre-emptive Contact precautions. The patient tested positive for CRO colonization. The public health (PH) authorities asked that the patient be tested for C. auris colonization. While awaiting screening results, the hospital's microbiology laboratory identified C. auris in the patient's wound isolate. The C. auris case prompted the implementation of a robust infection prevention plan in collaboration with PH that included isolation precautions, environmental cleaning and disinfection and education.ResultsThe patient required forty-seven days of hospitalization during the early days of the COVID-19 pandemic. The PH department recommended C. auris colonization screening for selected patients to check for transmission. Neither C. auris colonization nor clinical isolates were identified in the subsequent six months.ConclusionsA strong infection prevention response to the C. auris case prevented a potential outbreak. It is critical that acute-care hospitals are optimized to prevent the spread of C. auris during the COVID-19 pandemic.

Emergence of Morganellaceae Harboring blaIMP-27 Metalloenzyme in Canada.

ABSTRACTIn 2018 to 2019, PCR for carbapenemases in routine Gram-negative isolates submitted to the National Microbiology Laboratory revealed an increase in IMP-type metalloenzyme-positive isolates, mostly among Morganellaceae. Whole-genome sequencing revealed that 23 Morganellaceae harbored blaIMP-27 within a chromosomal Tn7 element. Phylogenomics indicated diversity of isolates but also the presence of a few clonal isolates dispersed geographically. These isolates may be difficult to detect due to carbapenem susceptibility and false-negative results in phenotypic testing.IMPORTANCE Over the last decade or so, the frequency of isolation of clinical carbapenemase-producing organisms (CPOs) has increased among health care-associated infections. This may seriously compromise antimicrobial therapy, as carbapenems are considered the last line of defense against these organisms. The ability of carbapenemases to hydrolyze most β-lactams in addition to the co-occurrence of mechanisms of resistance to other classes of antimicrobials in CPOs can leave few options for treating infections. The class B metalloenzymes are globally distributed carbapenemases, and the most commonly found include the NDM, VIM, and IMP types. Our study describes a sudden emergence of IMP-27-harboring Morganellaceae during 2018 to 2019 in Canada. There is a paucity of literature on IMP-27 isolates, and our data bolster the information on the genetic context, antimicrobial profiles, and phylogenomics of this group of CPOs.

Detection of KPC, NDM and VIM-Producing Organisms Directly from Rectal Swabs by a Multiplex Lateral Flow Immunoassay.

We report a preliminary evaluation of the NG-Test CARBA 5 immunochromatographic assay for detecting carbapenemases directly from rectal swabs on the same day of sampling. Thirty fecal swabs were examined for carbapenemase-producing organisms (CPOs) by conventional culture, PCR, and NG-Test CARBA 5. Each sample was tested by the immunochromatographic assay five times, including direct testing and incubation in trypticase soy broth for 1, 2, 3, and 4 h. Twenty patients yielded CPOs by culture. Immunochromatographic and PCR results were concordant and detected the same 25 carbapenemases (11 KPC, 8 VIM, and 6 NDM). In five cases, we detected co-carriage of KPC and VIM. Compared with PCR, the sensitivity of NG-Test CARBA 5 for the detection of KPC, VIM, and NDM was 80% without incubation, 88% with one hour, 92% with two, and 100% with three hours incubation, while specificity was 100% for all time points. All samples containing adequate fecal content were detected by NG-Test CARBA 5 concordantly with PCR, without incubation. NG-Test CARBA 5 is a reliable test that rapidly detects the presence of carbapenemases at the same day of sampling, directly from rectal swabs. It thus provides early information to guide antimicrobial treatment and infection control interventions.

Molecular characterization of KPC-2-producing Klebsiella pneumoniae ST258 isolated from bovine mastitis.

Bovine mastitis, an inflammation of the mammary gland of dairy cattle, is the most prevalent disease causing economically important losses, reduced milk production, early culling, veterinary expenses, and higher death rates. Bovine mastitis infections are the main cause for the use of antibiotics; however, the emergence of multidrug-resistant bacteria and the poor or nil response to antibiotics has become a critical global health problem. The goal of this study was the characterization of bacterial infections associated with clinical bovine mastitis. All the isolates were multidrug-resistant and were negative for the production of extended spectrum β-lactamases. However, all isolates were identified as carbapenemase-producing organisms by the Carba NP test. The carbapenemase identified was the product of the KPC-2 gene. The isolates were identified as Klebsiella pneumoniae and contained virulence genes for fimbriae, lipopolysaccharides, nitrogen starvation genes, and siderophores. Sixty-nine percent of the KPC-2-producing isolates had the same plasmid profile, although the genetic mobilization of resistance by bacterial conjugation was unsuccessful. The carbapenemase corresponded to the plasmid-borne KPC-2 gene identified by Southern blot hybridization. The assay showed a positive signal in the 90 kb (69% of the isolates), 165 kb (31% of the isolates), and 130 kb (6% of the isolates) plasmids. The IncFIIy and IncFIIk replicons were detected among these K. pneumoniae isolates. The PFGE and MLST analysis showed that all of the isolates are comprised by two clones (A and B) belonging to Sequence Type 258. This is the first report of K. pneumoniae producing carbapenemase KPC-2 isolated from bovine mastitis.

Epidemiology of and risk factors for mortality due to carbapenemase-producing organisms (CPO) in healthcare facilities

SummaryBackgroundCarbapenemase-producing organisms (CPO) have been largely responsible for the extensive spread of carbapenem resistance, and their prevalence is increasing in many parts of the world.AimTo evaluate clinical and molecular epidemiology and mortality associated with CPO among patients.MethodsAll CPO from clinical and long-term healthcare surveillance cultures across Scotland in 2003–2017 were reviewed retrospectively. Polymerase chain reaction was used to detect genes coding for carbapenemases. A generalized linear mixed model was used to identify risk factors for mortality.FindingsIn total, 290 individuals with CPO were identified. The overall incidence increased over time (P<0.001) from 0.02 to 1.38 per 100,000 population between 2003 and 2017. A total of 243 distinct CPO isolates were obtained from 269 isolations in 214 individuals with available metadata. The majority of the isolates were Enterobacterales (206/243, 84.8%), and Klebsiella pneumoniae (65/206, 31.6%) and Enterobacter cloacae (52/206, 25.2%) were the most common species. VIM (75/243, 30.9%) and NDM (56/243, 23.0%) were the most common carbapenemases. The crude 30-day mortality rate was 11.8% (25/211), while the case fatality rate was 5.7% (12/211). Age >60 years [adjusted odds ratio (aOR) 3.36, 95% confidence interval (CI) 1.06–10.63; P=0.033], presence of non-fermenters (aOR 4.88, 95% CI 1.64–14.47; P=0.005), and systemic infection or organ failure (aOR 4.21, 95% CI 1.38–12.81; P=0.032) were independently associated with 30-day mortality.ConclusionThe incidence of CPO in Scotland is low but increasing. Awareness is required that inpatients aged >60 years, patients with systemic infection or organ failure, and patients presenting with non-fermenters are at higher risk of death from CPO.

Standard versus combined chemical, mechanical, and heat decontamination of hospital drains harboring carbapenemase-producing organisms (CPOs): A randomized controlled trial.

We sought to determine whether combined chemical, mechanical, and heat cleaning was superior to standard cleaning for the decontamination of 32 sink and shower drains harboring carbapenemase-producing organisms (CPOs). Of 16 intervention drains, 10 (63%) were decontaminated until day 7 versus 1 (5%) of 16 comparator drains (P = .002). Intensive cleaning may be useful if administered repeatedly in drain-associated CPO outbreaks.