Carbapenem-resistant Enterobacteriaceae Research Articles

Uptake of Revised CLSI Breakpoints and Potential Impact among Hospitals Reporting to The NHSN AR Option, 2022

Background: Antimicrobial susceptibility testing (AST) is critical for detecting antimicrobial resistance (AR) and guiding antimicrobial treatment. The Clinical and Laboratory Standards Institute (CLSI) regularly publishes and revises breakpoints to guide the interpretation of AST results. In 2010–2019, CLSI has lowered many breakpoints for Enterobacterales and Pseudomonas aeruginosa. Timely implementation of updated breakpoints can vary across hospital laboratories, leading to shifts in the interpretation of AST results. This issue is a potential threat to the estimation of national prevalence estimates for AR and limits the comparability of AR data across hospitals. Hospitals submit AST data with clinical laboratory interpretations to the AR Option of CDC’s National Healthcare Safety Network (NHSN). NHSN tracks whether a hospital adopted the revised CLSI breakpoints for six organism-antimicrobial combinations involving AR phenotypes commonly associated with healthcare associated infections through hospital self-reporting status into a structured survey — 2022 NHSN Annual Hospital Survey (Table). For this analysis, we describe the uptake of revised CLSI breakpoints and compare cumulative antibiograms among hospitals that used various breakpoints. Methods: We included hospitals that completed the 2022 NHSN annual survey and submitted data to the NHSN AR Option for at least 9 months in 2022 by November 1, 2023. The percentage of hospitals that implemented CLSI breakpoints, published during 2010–2019, were determined for combinations of antibiotic class, organism, and CLSI revision year (Table). We calculated percent resistance (%R) as the number of isolates meeting AR phenotype definitions divided by the total number of Isolates tested for the following phenotypes: carbapenem-resistant Enterobacterales (CRE) which included E. coli, Klebsiella, and Enterobacter species; extended-spectrum cephalosporin-resistant Enterobacterales (ESC); carbapenem-non-susceptible P. aeruginosa; fluoroquinolone-resistant P. aeruginosa; and fluoroquinolone-resistant Enterobacterales. Results: Among the 741 hospitals included, 75%–93% implemented any of the six revised CLSI breakpoints (Table). The %R was higher among isolates from hospitals that adopted revised breakpoints compared to those that did not (p < 0 .0001). The largest difference was observed for carbapenem-non-susceptible P. aeruginosa (14.91% vs 10.11%). Conclusions: The uptake of revised CLSI breakpoints varied across hospitals, organism-antimicrobial combinations, and CLSI versions. This analysis indicates that the prevalence of AR for corresponding phenotypes could be underestimated if data from hospitals using higher, outdated breakpoints are included. It is important for NHSN to continue tracking breakpoints used in individual hospitals and encourage hospitals to report complete data on the original AST results, such as MIC, to optimize the accuracy of national AR surveillance.

Clusters of emerging multidrug-resistant organisms in US health care facilities during the initial months of the SARS-CoV-2 pandemic

Outbreaks of emerging multidrug-resistant organisms (eMDROs), including carbapenem-resistant Enterobacterales, carbapenem-resistant Acinetobacter baumannii, and Candida auris, have been reported among severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) patients. We describe eMDRO clusters in SARS-CoV-2 units and associated infection control (IC) practices early in the SARS-CoV-2 pandemic. We conducted a retrospective survey of a convenience sample of health departments in 11 states to describe clusters of eMDROs that began before November 1, 2020 and involved SARS-CoV-2 units. Cluster characteristics and IC practices during the cluster period were assessed using a standardized outbreak report form, and descriptive analyses were performed. Overall, 18 eMDRO clusters (10 carbapenem-resistant Enterobacterales, 6 Cauris, 1 carbapenem-resistant Pseudomonas aeruginosa, and 1 carbapenem-resistant A baumannii) in 18 health care facilities involving 397 patients were reported from 10 states. During the cluster period, 60% of facilities reported a shortage of isolation gowns, 69% extended use of gowns, and 67% reported difficulty obtaining preferred disinfectants. Reduced frequency of hand hygiene audits was reported in 85% of acute care hospitals during the cluster period compared with before the pandemic. Changes in IC practices and supply shortages were identified in facilities with eMDRO outbreaks during the SARS-CoV-2 pandemic and might have contributed to eMDRO transmission.

Containment of a KPC-CRE Outbreak Associated with Premise Plumbing in a Long-Term Care Facility— Minnesota, 2022-2023

Background: On March 23, 2022, the Minnesota Department of Health (MDH) was notified of Klebsiella pneumoniae carbapenemase (KPC)-producing Klebsiella oxytoca isolated from a resident’s urine in long-term care facility A (LTCF-A). Carbapenem-resistant Enterobacterales (CRE) are reportable statewide with required isolate submission to MDH Public Health Laboratory (MDH-PHL), where carbapenemase production and mechanism identification is confirmed. Methods: MDH partnered with LTCF-A on a containment response, including infection prevention and control (IPC) measures, KPC-CRE education, and colonization screening. Rectal swabs were screened for carbapenemase genes by real-time PCR (Cepheid Xpert Carba-R), with positive specimens undergoing culture, isolation, and whole genome sequencing (WGS). MDH-PHL conducted WGS including multilocus sequence typing (MLST) and single nucleotide polymorphism (SNP) analysis to describe genetic relationships among isolates. When screening indicated a potential environmental source, due to species diversity and ongoing resident transmission, an environmental screening plan was developed including collection of premise plumbing samples from room faucets, aerators, sinks, toilets, and shared shower drains. Results: KPC-CRE was detected in 23 residents (urine, n=2; rectal swab, n=21) during March 2022–November 2023. 21 isolates comprising 10 Enterobacterales species were cultured from KPC-positive screening specimens. SNP analysis performed on bacteria of the same species demonstrated 5 distinct clusters of relatedness comprising 2-3 residents per cluster (Cluster 1: Klebsiella oxytoca, n=3; Cluster 2: Klebsiella oxytoca, n=3; Cluster 3: Escherichia coli, n=2; Cluster 4: Klebsiella pneumoniae, n=2; Cluster 5: Raoultella planticola, n=2). 7 KPC-positive resident specimens did not yield a culturable organism. KPC-CRE was detected throughout the premise plumbing including 8 of 9 shared shower room drains and 6 of 75 resident room sink drains. WGS and SNP analysis suggest relatedness among resident and environmental KPC-CRE isolates. Gaps in IPC measures including hand hygiene, use of personal protective equipment (PPE), environmental cleaning and disinfection, and sink hygiene practices were observed during onsite assessments. Use of an EPA-registered biofilm disinfectant in facility drains and repeated environmental sampling has demonstrated a decrease in KPC-harboring bacteria within the premise plumbing, but not complete elimination. Conclusion: Containing the spread of KPC-CRE within LTCF-A has been challenging due to environmental reservoirs of KPC-CRE along with insufficient implementation of IPC practices. Continued colonization screening has been necessary to detect newly colonized residents and reinforce efforts to increase IPC compliance. Strict implementation and adherence to IPC measures, including those that minimize the spread of KPC-CRE from facility premise plumbing, are needed to fully halt KPC-CRE transmission within LTCF-A.

Variability of MDRO Reporting Across Tennessee Microbiology Laboratories

Background: Identification and timely reporting of multi-drug resistant organisms (MDROs) drives efficacy of infection prevention efforts. Data on MDRO reporting timeliness and inter-facility variability are limited. Facility-dependent variability in MDRO reporting across Tennessee was examined to identify opportunities for MDRO surveillance improvement. Methods: Data for reported Tennessee MDROs including carbapenem-resistant Enterobacterales (CRE), carbapenem-resistant Acinetobacter baumannii (CRAB), Carbapenem-resistant Pseudomonas aeruginosa (CRPA) and Candida auris, were obtained from the southeast regional Antibiotic Resistance Laboratory Network (ARLN) from 2018-2022, excluding screening and colonization specimens. Variance in days accrued from specimen collection to ARLN receipt was analyzed using one-way analysis of variance (ANOVA) with Tukey’s test (SAS 9.4). Facilities were categorized as fast (1-10 days), slow (11-20 days), or delayed (21-100 days) reporters. Results: There were 9,569 MDRO isolates reported. CRPA was reported faster than other MDROs (p < 0.001), while specimens from West Tennessee compared to other regions (p < 0.001) (Figure) and blood cultures compared to other specimens were reported more slowly (p < 0.001) (Table). There was no difference in reporting times for facilities using on-site microbiology laboratories versus reference laboratories (P = 0.062). Conclusion: MDRO reporting times varied across Tennessee by region, specimen, and organism. Future work to elucidate drivers of variability will consist of surveys and focused interviews with laboratory personnel to identify shared and unique barriers and opportunities for improvement.

Impact of Transitioning to Single-Patient Rooms on Prevention of Multidrug-Resistant Organisms in a Resource-Limited Facility

Background: Healthcare-associated infections (HAI) substantially increase hospital costs and lead to poor patient outcomes, particularly when caused by multidrug-resistant organisms (MDRO). To decrease MDRO transmission, isolation of colonized or infected patients in single rooms is recommended. However, single-patient isolation rooms are expensive to build and often unavailable in resource-limited hospitals. In 2023, an intensive care unit (ICU) at a large Brazilian tertiary hospital relocated from a space with an open floor plan to a newly built location with single-patient rooms. We evaluated the impact of this transition on acquisition of carbapenem-resistant Enterobacterales (CRE) colonization, HAI, and compliance with Hand Hygiene (HH) and Contact Precaution (CP) activities. Methods: We compared rates of CRE colonization acquisition, CRE colonization pressure, HAI, and compliance with HH and CP between pre- (March 1, 2022 – Feb 28, 2023) and post-implementation of single-rooms (March 1, 2023 - October 31, 2023) in a 12-bed surgical ICU. All patients were screened for CRE colonization on admission to the unit and weekly until discharge using rectal swab cultures. Colonization pressure was defined as the ratio of CRE-positive patient-days (PDs) to the total number of PDs. Rates of central-line associated blood-stream infections, ventilator-associated pneumonia, and catheter-associated urinary tract infections were monitored. HH and CP compliance were monitored weekly by infection prevention staff outside of the unit. Poisson regression and multiple linear regression were used to compare rates between pre- and post-implementation periods. Results: Healthcare acquisition of CRE colonization remainedstable between pre- and post-implementation (incidence rate ratio: 0.88 (95%CI, 0.73-1.05; P=0.16) despite an increase in CRE colonization pressure of 8.6% over baseline (from 7.84% pre- to 16.39% post-implementation (95% confidence interval [CI], 4.13-12.96%; P=.001)). The latter was driven by reduced turnover of CRE-colonized patients in the post-implementation period (mean patient-day reduced by 10.33; 95%CI, 3.06-17.61; P=0.006). Incidence of HAIs also remained stable (global incidence 3.12 vs 3.30, pre- and post-intervention, respectively; P=0.2). HH compliance was high prior to the transition (95.7%) and increased slightly but not significantly post-intervention (97.5%; P=0.3). CP compliance improved by 9.83%, especially in gown and glove changes after each patient interaction, from 90.62% pre- to 100% post-implementation (95%CI, 1.52-17.22; P=.02). Conclusion The move to an ICU with exclusively single-patient rooms was associated with increase in CP compliance. This could help explain why HAI incidence and healthcare acquisition of CRE colonization remained stable despite a significant increase in CRE colonization pressure.Disclosure: Matias Salomao: Speaker - Cepheid

Investigation of a Donor-derived Carbapenamase-producing Carbapenem-resistant Enterobacterales Hospital Outbreak

Carbapenamase-producing carbapenem-resistant Enterobacterales (CP-CRE) is an urgent public health threat for healthcare facilities. Solid organ transplant (SOT) recipients carry an increased risk for CRE infection and colonization due to prolonged exposures to antimicrobials, healthcare facilities and immunosuppression. CRE infection in SOT patients is associated with an increase in morbidity and mortality. Here, we describe a hospital outbreak investigation of three cases of New Delhi metallo-beta-lactamase (NDM) - CRE that led to novel findings with implications for further interdisciplinary investigations. An NDM-CRE infection in a critically-ill patient was identified during passive surveillance and prompted an investigation. Previous CP-CRE passive surveillance cases were reviewed. Rectal screening was performed for potentially exposed patients. 403 rectal swabs were tested for carbapenemase genes in active surveillance. Patients identified to have a new NDM-CRE isolate on active or passive surveillance were considered cases and underwent in-depth chart review including possible patient-to-patient exposures, hospital locations, procedures, devices, and consultations. NDM-CRE isolates were sent to the Minnesota Department of Health (MDH) for whole genome sequencing (WGS) to assess relatedness. Five NDM-CRE cases were identified, with all isolates harboring blaNDM including three NDM-Klebsiella pneumoniae (NDM-KP) cases (Figure 1). The first NDM-KP case, patient 1, developed mediastinal infection following lung transplantation. Review of United Network for Organ Sharing revealed that respiratory specimens from patient 1’s donor grew NDM-KP and a bronchial wash at the time of transplant yielded NDM-KP. The second NDM-KP case (patient 3) developed ventilator-associated pneumonia and was found to have used sequentially the same ventilator as patient 1. The third NDM-KP case (patient 4) was detected via rectal swab in active surveillance and shared wound care personnel in common with patients 1 and 3 (Figure 2). WGS demonstrated two single nucleotide polymorphisms (SNP) among all three isolates, strongly suggesting relatedness (Figure 3). Best practices for infection prevention were reviewed with wound care personnel. To date, no further NDM-KP isolates have been identified. Investigation was facilitated by in-depth chart review and WGS via the Central Region Antimicrobial Resistance Laboratory Network at MDH. Detection of the NDM-KP from a lung donor specimen appears genetically linked to clinical isolates in other patients, raising the possibility of a donor-derived hospital outbreak. This investigation is the first to describe a donor-derived NDM outbreak in a healthcare facility. Communication between organ procurement agencies, transplant centers, and infection prevention must be optimized to prevent CRE-associated morbidity in SOT receipts and CRE hospital outbreaks.

Microbiologic Evaluation of Colorectal Surgical Site Infections to Guide Surgical Prophylaxis Recommendations

Background: Use of a combination of parenteral and oral antimicrobial prophylaxis prior to colorectal surgery is recommended to reduce risk of surgical site infection (SSI). Parenteral antibiotic selection is complicated by the need to target organisms likely to cause infection at the surgery site, while mitigating risk of antimicrobial resistance caused by overuse of broad spectrum agents. This study aimed to evaluate microbiologic data from colorectal surgical site infections across an 11-hospital health system. Microbiologic data from SSI events were used to assess continued appropriateness of health system standard recommendations for parenteral antibiotic prophylaxis in colorectal surgery, consisting of either cefazolin with metronidazole or cefoxitin monotherapy. Methods: This multicenter, retrospective, observational study was conducted from January 1, 2019 to March 31, 2023, using data extracted from the National Healthcare Safety Network (NHSN). Microbiologic data from colorectal SSIs from 2019 to 2022 were evaluated for a descriptive review of pathogen and phenotype trends. SSI data excluded patients age < 18 years, those identified as infection present at time of surgery (PATOS), or outpatient procedures. Results: A total of 8059 colorectal procedures were evaluated. Most SSIs were polymicrobial, with at least one pathogen detected in 65% of cases. The most commonly identified organisms were E. coli (22.5%), Enterococcus spp. (19.7%), P. aeruginosa (6.5%), Streptococcus spp. (4.9%), and C. albicans (4.7%). Change over time in antimicrobial-resistant phenotypes from 2019 to 2022 was not statistically significant for extended-spectrum cephalosporin-resistant E. coli (p=0.335), extended-spectrum cephalosporin-resistant K. oxytoca/pneumoniae (p=0.189), multi-drug resistant P. aeruginosa (0.058), methicillin-resistant S. aureus (p=0.906), or among isolates with no identified antimicrobial-resistance phenotype (p=0.096). Among E. coli, change from 2019 to 2022 in cefazolin non-susceptible, ceftriaxone susceptible isolates was not statistically significant (p=0.177). No carbapenem-resistant Enterobacterales isolates were identified among non-PATOS cases. Conclusions: Data does not support a change to broader spectrum agents for colorectal surgery parenteral antimicrobial prophylaxis. Continued use of cefazolin with metronidazole or cefoxitin as IV antibiotic prophylaxis in colorectal surgery is recommended, with ongoing tracking of microbiologic trends and antimicrobial susceptibility.

Whole Genome Sequencing to Identify Multiple Clusters of Carbapenemase-Producing Enterobacterales Cases – Colorado, 2022-2023

Background: The Colorado Department of Public Health and Environment (CDPHE) detected an increase in Klebsiella pneumoniae carbapenemase-producing carbapenem-resistant Enterobacterales (KPC-CRE) infections in October 2022. We investigated patient epidemiological links and isolate relatedness to characterize interfacility transmission of KPC-CRE in the Denver metro area and inform regional prevention strategies. Methods: We defined a case as polymerase chain reaction detection of KPC from clinical or screening specimens collected during January 2022 – January 2023. Cases were identified through statewide CRE surveillance and carbapenemase testing at the CDPHE laboratory and counted once within a 30-day period. Medical records were reviewed to identify healthcare facility admissions and patient facility overlap in the 12 months prior to sample collection. Whole genome sequencing (WGS) was performed for 34 patients with available KPC-CRE isolates using short- and long-read sequencing techniques. We performed multi-locus sequence typing, generated genome phylogenetic trees, and compared plasmid contig sequences to identify relatedness between KPC-CRE isolates. Clusters were defined as ≥2 genetically related isolates of the same organism or carbapenemase plasmid, from different patients. Results: We identified 48 cases (34 clinical and 14 screening) among 39 patients (figure). Patients had a mean age of 52 years (range 16-86) and median of three healthcare facility admissions (range 1-14). Twenty-eight patients (72%) were male. We identified 16 (41%) patients with epidemiological links to one acute care hospital (ACH), 11 (28.2%) patients to one long-term acute care hospital (LTACH), and four (10.2%) patients to each of two ventilator-capable skilled nursing facilities (vSNF). Five distinct clusters of KPC-CRE were identified by WGS among 23 patients (E. hormaechei, two distinct E. cloacae clusters, K. pneumoniae, and K. oxytoca) with linkages to ten healthcare facilities, including two vSNFs, two LTACHs, and six ACHs. Three distinct KPC genes were identified among the clusters: KPC-2, KPC-3, and KPC-4. Genomes assembled from long reads identified identical or similar KPC-gene-containing plasmids across different species or sequence types, suggesting horizontal gene transfer of KPC. Conclusions: Multiple KPC-CRE strains co-circulated and were associated with patient movement between acute and post-acute care settings. WGS allowed us to identify multi-facility clusters. Time and location of carbapenemase acquisition were challenging to determine for genetically related isolates when epidemiologic links could not be determined from medical records. This could be due to undetected cases. We notified healthcare facilities of their shared transmission risk and advocated for improved attention to infection control, carbapenemase screening, and communication upon patient transfer.

VirBR, a transcription regulator, promotes IncX3 plasmid transmission, and persistence of blaNDM-5 in zoonotic bacteria

IncX3 plasmids carrying the New Delhi metallo-β-lactamase-encoding gene, blaNDM-5, are rapidly spreading globally in both humans and animals. Given that carbapenems are listed on the WHO AWaRe watch group and are prohibited for use in animals, the drivers for the successful dissemination of Carbapenem-Resistant Enterobacterales (CRE) carrying blaNDM-5-IncX3 plasmids still remain unknown. We observe that E. coli carrying blaNDM-5-IncX3 can persist in chicken intestines either under the administration of amoxicillin, one of the largest veterinary β-lactams used in livestock, or without any antibiotic pressure. We therefore characterise the blaNDM-5-IncX3 plasmid and identify a transcription regulator, VirBR, that binds to the promoter of the regulator gene actX enhancing the transcription of Type IV secretion systems (T4SS); thereby, promoting conjugation of IncX3 plasmids, increasing pili adhesion capacity and enhancing the colonisation of blaNDM-5-IncX3 transconjugants in animal digestive tracts. Our mechanistic and in-vivo studies identify VirBR as a major factor in the successful spread of blaNDM-5-IncX3 across one-health AMR sectors. Furthermore, VirBR enhances the plasmid conjugation and T4SS expression by the presence of copper and zinc ions, thereby having profound ramifications on the use of universal animal feeds.

Carbapenem-Resistant Enterobacteriaceae Colonization or Infection Was Not Associated with Post-Liver Transplant Graft Failure: An Observational Cohort Study

Introduction: Carbapenem-resistant Enterobacteriaceae (CRE) epidemiology among liver transplant (LT) recipients is variable. We studied the impact of CRE colonization and infection on LT recipients’ outcomes. Methods: This observational cohort study included consecutive adult LT recipients between January 2019 and December 2020 at Curry Cabral Hospital, Lisbon, Portugal. Primary exposures were CRE colonization (rectal swabs under a screening program) and infection within 1 year of index LT. Primary endpoint was graft failure within 1 year of the index LT. Results: Among 209 patients, the median (interquartile range [IQR]) age was 57 (47–64) years and 155 (74.2%) were male. CRE colonization was identified in 28 (13.4%) patients during the first year posttransplant (median [IQR] number of rectal swabs per patient of 4 [2–7]). CRE resistance genes identified were OXA48 in 8 (3.6%) patients, KPC in 19 (67.9%) patients, and VIM in 1 (3.6%) patient. Any bacterial/fungal and CRE infections were diagnosed in 88 (42.1%) and 6 (2.9%) patients, respectively, during the first year posttransplant. After adjusting for confounders, neither CRE colonization (aOR [95% CI] = 1.83 [0.71–4.70]; p = 0.21) nor infection (aOR [95% CI] = 1.35 [0.17–11.06]; p = 0.78) was associated with graft failure within 1 year of index LT. Discussion/Conclusion: Under a screening program, CRE colonization and infection prevalence was low and neither was associated with graft failure.

Optimizing Cefiderocol Dosing Through Population Pharmacokinetic/Pharmacodynamic Simulation: An Assessment of Drug Cost Reductions.

Cefiderocol is a siderophore cephalosporin antibiotic with bactericidal activity against carbapenem-resistant Enterobacterales. However, an efficient dosing strategy is yet to be developed. This study aimed to evaluate efficient lower-dose regimens and estimate potential drug cost reductions. This simulation study used a virtual population of 10,000 resampled individuals based on a reported population pharmacokinetic model. The target index for maximal bactericidal activity was the time for the unbound cefiderocol concentration to be above the minimum inhibitory concentration (TAM_unbound) of 100%, which was determined using a minimum inhibitory concentration distribution or specific value. The probability of achieving 100% TAM_unbound with the standard, low- (reduced by 1 g or one dose), and extended low- (reduced by 2 g or 2 doses) dose regimens was nearly 100%. The lowest probability of achieving 100% TAM_unbound with the extended low-dose regimen at a creatinine clearance range of 90-120 mL/min was 86.4%. The probability of achieving TAM_unbound of 100% was more than 90% for MIC of ≤0.5 mcg/mL with the extended low-dosing regimen. Furthermore, using an efficient dosing regimen reduced the medical costs over a 10-day treatment period for 10 patients, from $122,826.50 to $62,665.69 $ and ¥12,598,187 $ to ¥5,451,173 in the United States and Japan, respectively. A lower dosing regimen for cefiderocol could result in substantial reductions in drug costs while still achieving 100% TAM_unbound.

The scourge of carbapenem resistant Enterobacteriaceae: how to fight back

The Enterobacteriaceae species cause both community acquired and health care associated infections like bloodstream infections, ventilator-associated pneumonia, intra-abdominal infections and urinary tract infections. Carbapenem-resistant Enterobacteriaceae (CRE) have been included in the list of global priority pathogens (GPP) declared by WHO in 2017. These infections pose a serious threat due to the associated significant morbidity and mortality. The mechanisms of antimicrobial resistance in these organisms are numerous; however, β-lactamase genes carried on mobile genetic elements are a key mechanism for the rapid spread of these antibiotic-resistant strains on a global scale. The carbapenem resistance (CR) in Enterobacteriaceae has been recognized for the past two decades, but the carbapenemase-producing Enterobacteriaceae (CPE) has been a more recent issue and is spreading at an alarming pace worldwide. In this article, we conducted a systematic literature search of the PubMed, Embase, Web of Science and Cochrane Library databases to identify relevant studies that reported the epidemiology and the outcomes for hospitalised patients with confirmed infections due to CRE and carbapenem-susceptible Enterobacteriaceae (CSE) published between 1 January 2010 and 30 August 2023.The results emphasize that patients with CRE infection still face a greater risk of mortality and need an urgent need for newer antibiotics and appropriate treatment regimens to reduce the risk of morbidity and mortality.

The Rising Tide of Antibiotic Resistance: A Study on Extended-Spectrum Beta-Lactamase and Carbapenem-Resistant Escherichia coli and Klebsiella pneumoniae.

The global spread of extended-spectrum beta-lactamase (ESBL)-producing and carbapenem-resistant Enterobacterales (CRE) poses a significant concern. Acquisition of antimicrobial resistance genes leads to resistance against several antibiotics, limiting treatment options. We aimed to study ESBL-producing and CRE transmission in clinical settings. From clinical samples, 227 ESBL-producing and CRE isolates were obtained. The isolates were cultured on bacterial media and confirmed by VITEK 2. Antibiograms were tested against several antibiotics using VITEK 2. The acquired resistance genes were identified by PCR. Of the 227 clinical isolates, 145 (63.8%) were Klebsiella pneumoniae and 82 (36.1%) were Escherichia coli; 76 (33.4%) isolates were detected in urine, 57 (25.1%) in pus swabs, and 53 (23.3%) in blood samples. A total of 58 (70.7%) ESBL-producing E. coli were resistant to beta-lactams, except for carbapenems, and 17.2% were amikacin-resistant; 29.2% of E. coli isolates were resistant to carbapenems. A total of 106 (73.1%) ESBL-producing K. pneumoniae were resistant to all beta-lactams, except for carbapenems, and 66.9% to ciprofloxacin; 38 (26.2%) K. pneumoniae were resistant to carbapenems. Colistin emerged as the most effective antibiotic against both bacterial types. Twelve (20.6%) E. coli isolates were positive for blaCTX-M, 11 (18.9%) for blaTEM, and 8 (33.3%) for blaNDM. Forty-six (52.3%) K. pneumoniae isolates had blaCTX-M, 27 (18.6%) blaTEM, and 26 (68.4%) blaNDM. This study found a high prevalence of drug-resistant ESBL-producing and CRE, highlighting the need for targeted antibiotic use to combat resistance.

Activity of Aztreonam/Avibactam and Recently Approved β-Lactamase Inhibitor Combinations against Enterobacterales and Pseudomonas aeruginosa from Intensive Care Unit and Non-Intensive Care Unit Patients.

We evaluated the activities of aztreonam/avibactam and recently approved β-lactamase inhibitor combinations (BLICs) to compare the antimicrobial susceptibility patterns of Enterobacterales and Pseudomonas aeruginosa isolated from intensive care unit (ICU) and non-ICU patients. Clinical isolates (1/patient) were consecutively collected from 72 United States medical centres in 2020-2022 and susceptibility tested by broth microdilution. The results for 5421 isolates from ICU patients were analysed and compared to those for 20,649 isolates from non-ICU patients. Isolates from ventilator-associated pneumonia patients were analysed separately. Aztreonam/avibactam inhibited 100.0%/>99.9% Enterobacterales and 100.0%/98.3% of carbapenem-resistant Enterobacterales (CRE) from ICU/non-ICU patients at ≤8 mg/L, respectively. The CRE susceptibility rates were 88.5%/82.9% for ceftazidime/avibactam, 82.1%/81.2% for meropenem/vaborbactam, and 78.2%/72.6% for imipenem/relebactam among ICU/non-ICU isolates. Among the P. aeruginosa isolates from ICU/non-ICU patients, the susceptibility rates were 96.3%/97.6% for ceftazidime/avibactam, 97.2/98.4% for ceftolozane/tazobactam, 97.1%/98.0% for imipenem/relebactam, 77.8%/84.6% for piperacillin/tazobactam, and 76.9%/85.8% for meropenem; aztreonam/avibactam inhibited 78.0%/81.9% of P. aeruginosa at ≤8 mg/L. In summary, lower susceptibility rates were observed among ICU than non-ICU isolates. Aztreonam/avibactam exhibited potent in vitro activity and broad-spectrum activity against Enterobacterales from ICU and non-ICU patients, including CRE and isolates non-susceptible to newer BLICs. Against P. aeruginosa, aztreonam/avibactam showed a spectrum of activity comparable to that of piperacillin/tazobactam, meropenem, and ceftazidime.

Screening of Carbapenem-Resistant Enterobacteriaceae (CRE) in Stool Samples in Hospitalized Patients: A Study from a Tertiary Care Hospital

Screening of Carbapenem-Resistant Enterobacteriaceae (CRE) in Stool Samples in Hospitalized Patients: A Study from a Tertiary Care Hospital

Genomic Characterization of Multidrug-Resistant Enterobacteriaceae Clinical Isolates from Southern Thailand Hospitals: Unraveling Antimicrobial Resistance and Virulence Mechanisms.

The emergence and spread of antimicrobial resistance (AMR) among Enterobacteriaceae pose significant threats to global public health. In this study, we conducted a short-term surveillance effort in Southern Thailand hospitals to characterize the genomic diversity, AMR profiles, and virulence factors of Enterobacteriaceae strains. We identified 241 carbapenem-resistant Enterobacteriaceae, of which 12 were selected for whole-genome sequencing (WGS) and genome analysis. The strains included Proteus mirabilis, Serratia nevei, Klebsiella variicola, Klebsiella aerogenes, Klebsiella indica, Klebsiella grimontii, Phytobacter ursingii, Phytobacter palmae, Kosakonia spp., and Citrobacter freundii. The strains exhibited high levels of multidrug resistance, including resistance to carbapenem antibiotics. Whole-genome sequencing revealed a diverse array of antimicrobial resistance genes (ARGs), with strains carrying genes for ß-lactamase, efflux pumps, and resistance to other antibiotic classes. Additionally, stress response, metal tolerance, and virulence-associated genes were identified, highlighting the adaptability and pathogenic potential of these strains. A plasmid analysis identified several plasmid replicons, including IncA/C2, IncFIB(K), and Col440I, as well as several plasmids identical to those found globally, indicating the potential for the horizontal gene transfer of ARGs. Importantly, this study also identified a novel species of Kosakonia spp. PSU27, adding to the understanding of the genetic diversity and resistance mechanisms of Enterobacteriaceae in Southern Thailand. The results reported in this study highlight the critical importance of implementing effective antimicrobial management programs and developing innovative treatment approaches to urgently tackle AMR.

The impact of colistin-based regimens on mortality compared to other antimicrobials in patients with carbapenem-resistant Enterobacterales bacteremia in South African hospitals: a cross-sectional study

BackgroundTreatment of carbapenem-resistant Enterobacterales (CRE) infections in low-resource settings is challenging particularly due to limited treatment options. Colistin is the mainstay drug for treatment; however, nephrotoxicity and neurotoxicity make this drug less desirable. Thus, mortality may be higher among patients treated with alternative antimicrobials that are potentially less efficacious than colistin. We assessed mortality in patients with CRE bacteremia treated with colistin-based therapy compared to colistin-sparing therapy.MethodsWe conducted a cross-sectional study using secondary data from a South African national laboratory-based CRE bacteremia surveillance system from January 2015 to December 2020. Patients hospitalized at surveillance sentinel sites with CRE isolated from blood cultures were included. Multivariable logistic regression modeling, with multiple imputations to account for missing data, was conducted to determine the association between in-hospital mortality and colistin-based therapy versus colistin-sparing therapy.ResultsWe included 1 607 case-patients with a median age of 29 years (interquartile range [IQR], 0–52 years) and 53% (857/1 607) male. Klebsiella pneumoniae caused most of the infections (82%, n=1 247), and the most common carbapenemase genes detected were blaOXA-48-like (61%, n=551), and blaNDM (37%, n=333). The overall in-hospital mortality was 31% (504/1 607). Patients treated with colistin-based combination therapy had a lower case fatality ratio (29% [152/521]) compared to those treated with colistin-sparing therapy 32% [352/1 086]) (p=0.18). In our imputed model, compared to colistin-sparing therapy, colistin-based therapy was associated with similar odds of mortality (adjusted odds ratio [aOR] 1.02; 95% confidence interval [CI] 0.78-1.33, p=0.873).ConclusionIn our resource-limited setting, the mortality risk in patients treated with colistin-based therapy was comparable to that of patients treated with colistin-sparing therapy. Given the challenges with colistin treatment and the increasing resistance to alternative agents, further investigations into the benefit of newer antimicrobials for managing CRE infections are needed.

A comparative evaluation of five phenotypic methods for identification of carbapenemase-producing Enterobacteriaceae: a modified carbapenemase detection test.

Rapid detection of carbapenemase-producing Enterobacteriaceae (CPE) is urgently needed to prevent their spread in healthcare settings. Here, we have evaluated the performance of the phenotypic methods for detection of carbapenemase production directly from bacterial cultures. A total of 99 clinical and rectal Enterobacteriaceae isolates were included (81 carrying known carbapenemase-encoding genes and 18 without carbapenemase production). All isolates were subjected to the five phenotypic tests including in-house Carba NP (iCarba NP), modified-Carba NP, E-Test MBL, modified Hodge test (MHT), and commercial combination disk test. Test results were read at different time points for iCarba NP and modified-Carba (1 min, 5 min, 15 min, 1 h and 2 h). The sensitivity and specificity of the iCarba NP were 78.87% and 100%, respectively, whereas those of the modified-Carba NP test were 95.06% and 94.44%, respectively. False-negative results were detected in four OXA-48 isolates with the use of modified-Carba NP, whereas one non-carbapenemase isolate had false-positive results. The sensitivity/specificity was 91.30%/100% and 80.25%/83.33% for the E-Test MBL and MHT, respectively. The sensitivity and specificity of the aminophenylboronic acid synergy test were 100% and 97.94%, respectively, whereas those of the dipicolinic acid synergy test were 82.61% and 96.23%, respectively. Rapid, simple, and reliable methods are needed for laboratory detection of CPE isolates to improve the detection and surveillance of these clinically relevant pathogens in an epidemiological context. We conclude that the modified-Carba NP test can be one of the reliable tests for the prediction of carbapenemase-producing bacteria.IMPORTANCEThe emergence of carbapenem resistance among Gram-negative bacteria is a serious global health threat. Here, we investigate the performance of the five phenotypic assays against carbapenemase-producing and carbapenemase-non-producing Enterobacteriaceae. Accurate and rapid detection of CPE isolates is critically required for clinical management and treatment of infections caused by these organisms. Among the five evaluated phenotypic tests, the mCNP test presented the highest sensitivity (95.06%) and, therefore, can be considered the best test to be used as a screening phenotypic methodology.

Molecular epidemiology and risk factors for carbapenem-resistant Enterobacteriaceae infections during 2020-2021 in Northwest China

Severe infection caused by Carbapenem-resistant Enterobacteriaceae (CRE) is a challenge for clinical anti-infective therapy, and clinical intervention to improve control of CRE is of great significance. The study aims to determine the molecular epidemiology and risk factors of CRE infections to provide evidence for effective control of nosocomial infection in patients with CRE. A total of 192 non-repetitive CRE strains were collected from January 2020 to December 2021 in Northwest China. To explore the risk factors of CRE infection by univariate and Logistic regression analysis, 1:1 case-control study was used to select Carbapenem sensitive Enterobacteriaceae (CSE) infection patients at the same period as the control group. Among the 192 CRE strains, the most common isolates included Klebsiella pneumoniae (Kpn) and Enterobacter cloacae (Ecl). The CRE strain showed the lowest rate of resistance to amikacin at 58.3. 185 CRE strains carried carbapenemase resistance genes of concern in this study. KPC-2 (n=94) was the most common carbapenemase, followed by NDM-1 (n=69), NDM-5 (n=22) and IMP-4 (n=5). OXA-48 and VIM were not detected. And KPC-2 was the most common in all strains. Logistic regression analysis implicated days of invasive ventilator-assisted ventilation (OR=1.452; 95 % CI 1.250～1.686), antibiotic combination therapy (OR=2.149; 95 % CI 1.128～4.094), hypoalbuminemia (OR=6.137; 95 % CI 3.161～11.913), history of immunosuppressant use (OR=25.815; 95 % CI 6.821～97.706) and days of hospitalization (OR=1.020; 95 % CI 1.006～1.035) as independent risk factors associated with CRE infection. Age (OR=0.963; 95% CI 0.943～0.984) and history of hormone use (OR=0.119; 95 % CI 0.028～0.504) were protective factors for CRE infection (P < 0.05). The resistance of commonly used antibiotics in clinical is severe, and CRE strains mainly carry KPC-2 and NDM-1. Multiple risk factors for CRE infection and their control can effectively prevent the spread of CRE.

Comparison of ERIC carbapenem-resistant Enterobacteriaceae test, BD Phoenix CPO detect panel, and NG-test CARBA 5 for the detection of main carbapenemase types of carbapenem-resistant Enterobacterales

BackgroundThis study aimed to assess the performance of three commercial panels, the ERIC Carbapenem-Resistant Enterobacteriaceae Test (ERIC CRE test), the NG-Test CARBA 5 (NG CARBA 5), and the BD Phoenix CPO Detect Panel (CPO panel), for the detection of main types of carbapenemases among carbapenem-resistant Enterobacterales (CRE). MethodsWe collected 502 isolates of carbapenem-resistant Enterobacterales (CRE) demonstrating intermediate or resistant profiles to at least one carbapenem antibiotic (ertapenem, imipenem, meropenem, or doripenem). Carbapenemase genes and their specific types were identified through multiplex PCR and sequencing methods. Subsequently, the ERIC CRE test, CPO panel, and NG CARBA 5 assay were conducted on these isolates, and the results were compared with those obtained from multiplex PCR. ResultsThe results indicated that the ERIC CRE test exhibited an overall sensitivity and specificity of 98.1% and 93.6%, respectively, which were comparable to 99.1% and 90.6% for the NG CARBA 5. However, the CPO panel demonstrated a sensitivity of only 56.2% in identifying Ambler classes, exhibiting the poorest sensitivity for class A. Moreover, while the ERIC CRE test outperformed the NG CARBA 5 in identifying multi-gene isolates with multiple carbapenemase-encoding genes, the CPO panel failed to accurately classify these isolates. ConclusionsOur findings support the utilization of the ERIC CRE test as one of the methods for detecting carbapenemases in clinical laboratories. Nonetheless, further optimization is imperative for the CPO panel to enhance its accuracy in determining carbapenemase classification and address limitations in detecting multi-gene isolates.