A Situation Analysis of the Capacity of Laboratories in Faith-Based Hospitals in Zambia to Conduct Surveillance of Antimicrobial Resistance: Opportunities to Improve Diagnostic Stewardship

Antimicrobial resistance (AMR) is a public health problem exacerbated by the overuse and misuse of antibiotics and the inadequate capacity of laboratories to conduct AMR surveillance. This study assessed the capacity of laboratories in seven faith-based hospitals to conduct AMR testing and surveillance in Zambia. This multi-facility, cross-sectional exploratory study was conducted from February 2024 to April 2024. We collected and analysed data using the self-scoring Laboratory Assessment of Antibiotic Resistance Testing Capacity (LAARC) tool. This study found an average score of 39%, indicating a low capacity of laboratories to conduct AMR surveillance. The highest capacity score was 47%, while the lowest was 25%. Only one hospital had a full capacity (100%) to utilise a laboratory information system (LIS). Three hospitals had a satisfactory capacity to perform data management with scores of 83%, 85%, and 95%. Only one hospital had a full capacity (100%) to process specimens, and only one hospital had good safety requirements for a microbiology laboratory, with a score of 89%. This study demonstrates that all the assessed hospitals had a low capacity to conduct AMR surveillance, which could affect diagnostic stewardship. Therefore, there is an urgent need to strengthen the microbiology capacity of laboratories to enhance AMR surveillance in Zambia.

Cas12a/Guide RNA-Based Platform for Rapidly and Accurately Detecting blaKPC Gene in Carbapenem-Resistant Enterobacterales

Purpose

Accurate detection and identification of pathogens and their associated resistance mechanisms are essential prerequisites for implementing precision medicine in the management of Carbapenem-resistant Enterobacterales (CRE). Among the various resistance mechanisms, the production of KPC carbapenemase is the most prevalent worldwide. Consequently, this study aims to develop a convenient and precise nucleic acid detection platform specifically for the blaKPC gene.

Methods

The initial phase of our research methodology involved developing a CRISPR/Cas12a detection framework, which was achieved by designing highly specific single-guide RNAs (sgRNAs) targeting the blaKPC gene. To enhance the sensitivity of this system, we incorporated three distinct amplification techniques-polymerase chain reaction (PCR), loop-mediated isothermal amplification (LAMP), and recombinase polymerase amplification (RPA)-into the CRISPR/Cas12a framework. Subsequently, we conducted a comparative analysis of the sensitivity and specificity of these three amplification methods when used in combination with the CRISPR/Cas12a system. Additionally, we assessed the clinical applicability of the methodologies by evaluating fluorescence readouts from 80 different clinical isolates. Furthermore, we employed lateral flow assay technology to provide a visual representation of the results, facilitating point-of-care testing.

Results

Following a comparative analysis of the sensitivity and specificity of the three methods, we identified the RPA-Cas12a approach as the optimal detection technique. Our findings demonstrated that the limit of detection (LoD) of the RPA-Cas12a platform was 1 aM (~1 copy/µL) for plasmid DNA and 5 × 10³ fg/µL for genomic DNA. Furthermore, both the sensitivity and specificity of the platform achieved 100% upon validation with 80 clinical isolates.

Conclusion

These findings suggest that the developed RPA-Cas12a platform represents a promising tool for the cost-effective, convenient, and accurate detection of the blaKPC gene.

Sink-traps are a major source for carbapenemase-producing Enterobacteriaceae transmission

OBJECTIVE

We studied the extent of carbapenemase-producing Enterobacteriaceae (CPE) sink contamination and transmission to patients in a nonoutbreak setting.

METHODS

During 2017-2019, 592 patient-room sinks were sampled in 34 departments. Patient weekly rectal swab CPE surveillance was universally performed. Repeated sink sampling was conducted in 9 departments. Isolates from patients and sinks were characterized using pulsed-field gel electrophoresis (PFGE), and pairs of high resemblance were sequenced by Oxford Nanopore and Illumina. Hybrid assembly was used to fully assemble plasmids, which are shared between paired isolates.

RESULTS

In total, 144 (24%) of 592 CPE-contaminated sinks were detected in 25 of 34 departments. Repeated sampling (n = 7,123) revealed that 52%-100% were contaminated at least once during the sampling period. Persistent contamination for >1 year by a dominant strain was common. During the study period, 318 patients acquired CPE. The most common species were Klebsiella pneumoniae, Escherichia coli, and Enterobacter spp. In 127 (40%) patients, a contaminated sink was the suspected source of CPE acquisition. For 20 cases with an identical sink-patient strain, temporal relation suggested sink-to-patient transmission. Hybrid assembly of specific sink-patient isolates revealed that shared plasmids were structurally identical, and SNP differences between shared pairs, along with signatures for potential recombination events, suggests recent sharing of the plasmids.

CONCLUSIONS

CPE-contaminated sinks are an important source of transmission to patients. Although traditionally person-to-person transmission has been considered the main route of CPE transmission, these data suggest a change in paradigm that may influence strategies of preventing CPE dissemination.

Contribution of active surveillance cultures to the control of hospital-acquired carbapenem-resistant Acinetobacter baumannii in an endemic hospital setting

BACKGROUND

Despite the increasing rates of carbapenem-resistant Acinetobacter baumannii (CRAB) carriage among hospitalized patients in endemic settings, the role of active surveillance cultures and cohorting is still debated. We sought to determine the long-term effect of a multifaceted infection-control intervention on the incidence of CRAB in an endemic setting.

METHODS

A prospective, quasi-experimental study was performed at a 670-bed, acute-care hospital. The study consisted of 4 phases. In phase I, basic infection control measures were used. In phase II, CRAB carriers were cohorted in a single ward with dedicated nursing and enhanced environmental cleaning. In phase III large-scale screening in high-risk units was implemented. Phase IV comprised a 15-month follow-up period.

RESULTS

During the baseline period, the mean incidence rate (IDR) of CRAB was 44 per 100,000 patient days (95% CI, 37.7-54.1). No significant decrease was observed during phase II (IDR, 40.8 per 100,000 patient days; 95% CI, 30.0-56.7; P = .97). During phase III, despite high compliance with control measures, ongoing transmission in several wards was observed and the mean IDR was 53.9 per 100,000 patient days (95% CI, 40.5-72.2; P = .55). In phase IV, following the implementation of large-scale screening, a significant decrease in the mean IDR was observed (25.8 per 100,000 patient days; 95% CI, 19.9-33.5; P = .03). An overall reduction of CRAB rate was observed between phase I and phase IV (rate ratio, 0.6; 95% CI, 0.4-0.9; P < .001).

CONCLUSIONS

The comprehensive intervention that included intensified control measures with routine active screening cultures was effective in reducing the incidence of CRAB in an endemic hospital setting.

Global impact of antibacterial resistance in patients with hematologic malignancies and hematopoietic cell transplant recipients

Patients with hematologic malignancies and hematopoietic cell transplant (HCT) recipients are at high risk of developing bacterial infections. These patients may suffer severe consequences from these infections if they do not receive immediate effective therapies, and thus are uniquely threatened by antimicrobial-resistant bacteria. Here, we outline how the emergence of specific resistant bacteria threatens the effectiveness of established approaches to prevent and treat infections in this population. The emergence of fluoroquinolone resistance among Enterobacterales and viridans group streptococci may decrease the effectiveness of fluoroquinolone prophylaxis during neutropenia. The emergence of Enterobacterales that produce extended-spectrum β-lactamases or carbapenemases and of increasingly resistant Pseudomonas aeruginosa may result in neutropenic patients experiencing delayed time to active antibacterial therapy, and consequently worse clinical outcomes. The ability to select targeted antibacterial therapies after the availability of susceptibility data may be limited in patients infected with metallo-β-lactamase-producing Enterobacterales and difficult-to-treat P. aeruginosa. Vancomycin-resistant enterococci and Stenotrophomonas maltophilia can cause breakthrough infections in patients already being treated with broad-spectrum β-lactam antibiotics. Resistance can also limit the ability to provide oral stepdown antibacterial therapy for patients who could otherwise be discharged from hospitalization. We also outline strategies that have the potential to mitigate the negative impact of antimicrobial resistance, including interventions based on active screening for colonization with resistant bacteria and the use of novel rapid diagnostic assays. Additional research is needed to better understand how these strategies can be leveraged to combat the emerging crisis of antimicrobial resistance in patients with hematologic malignancies and HCT recipients.

Healthcare-associated infections and antimicrobial resistance in severe acquired brain injury: a retrospective multicenter study

Background

Recent studies underscore that healthcare-associated infections (HAIs) and multidrug-resistant (MDR) HAIs affect rehabilitation outcomes and hospital length of stay (LOS) for severe acquired brain injury (sABI).

Objective

This study aimed to estimate HAI incidence in different sABI rehabilitation settings and determine risk factors and HAI impact on neuromotor and cognitive recovery.

Methods

We conducted a retrospective multicenter study in two semi-intensive units (SICUs), two high-specialty post-acute units (PAUs), and one long-term care (LTC) rehabilitation facility. Data extraction was performed by experienced clinicians, using a structured Excel file and they agreed upon criteria for case definitions of healthcare. The main outcome measures were the HAI and MDR HAI incidence and the LOS, the functional recovery was measured using the Level of Cognitive Functioning and Disability Rating Scale.

Results

There were 134 sABI participants. The calculation of the probability level was adjusted for three pairwise comparisons among settings (0.05/3 = 0.017). The HAI and MDR HAI incidences were significantly higher in SICU (3.7 and 1.3 per 100 person-days) than in other settings (LTC: 1.9, p = 0.034 and 0.5, p = 0.026; PAU: 1.2, p < 0.001 and 0.3, p < 0.001). HAI and MDR HAI risk variables included older age, an increased number of devices, and carbapenemase-producing Enterobacteriaceae (CPE) colonization, while a high prealbumin plasma value seemed to have a protective effect.

Conclusion

HAIs are related to longer LOS, and colonization is associated with poor prognosis and poor functional outcomes with reduced ability to achieve the cognitive capacity of self-care, employability, and independent living. The need to ensure the protection of non-colonized patients, especially those with severe disabilities on admission, is highlighted.

Impact of intensified prevention measures on rates of hospital-acquired bloodstream infection in medical-surgical intensive care units, Israel, 2011 to 2019

BackgroundCentral line-associated bloodstream infection (CLABSI) is among the most common preventable infectious complications in patients in intensive care units (ICU). In 2011, the Israel National Center for Infection Control initiated a nationwide CLABSI prevention programme.AimTo evaluate the impact of different components of the programme on CLABSI and non-CLABSI rates in medical-surgical ICUs.MethodsWe included data collected from all 29 medical-surgical ICUs in Israel from November 2011 to December 2019. The study period was divided into three phases: I (baseline, initial CLABSI prevention guidelines introduced, initial feedback on rates provided), II (initial guidelines widely implemented, surveillance undertaken, feedback continued) and III (after implementation of additional prevention measures). Interrupted time series analysis was used to compare CLABSI and non-CLABSI rates during the three phases.ResultsThe pooled mean (SD) incidence of CLABSI per 1,000 central line-days dropped from 7.4 (0.38) in phase I to 2.1 (0.13) in phase III (p < 0.001). The incidence rate ratio (IRR) was 0.63 (95% CI: 0.51-0.79) between phases I and II, and 0.78 (95% CI: 0.59-1.02) between phases II and III. The pooled mean (SD) incidence of non-CLABSI per 1,000 patient-days declined from 5.3 (0.24) in phase I to 3.4 (0.13) in phase III (p < 0.001).ConclusionNational CLABSI prevention guidelines, surveillance and feedback resulted in significant reductions in CLABSI and non-CLABSI rates. In the wake of further interventions, significant reduction was achieved in ICUs reporting improvement in the uptake of additional prevention measures.

Rapid detection of carbapenem resistance among gram-negative organisms directly from positive blood culture bottles

Background

Carbapenemase producing gram-negative bacteria (GNB) has become a huge problem in majority of tertiary care centers worldwide. They are associated with very high morbidity and mortality rates, especially when they cause invasive infections. Therefore, rapid detection of these organisms is very important for prompt and adequate antibiotic therapy as well as infection control. The aim of this study was rapid detection of carbapenemase genes and thereby likely carbapenem resistance, 24-48 hours in advance, directly from the positive-flagged blood culture bottles using CHROMagar and Xpert® Carba-R.

Methods

Aspirate from positively flagged blood culture bottles was subjected to differential centrifuge. All gram-negative bacilli on gram stain from the deposit were processed in Xpert® Carba-R and inoculated on CHROMagar. The presence of genes and growth on CHROMagar was compared with carbapenem resistance on VITEK-2 Compact.

Results

A total of 119 GNB isolates were processed. One or more of the carbapenemase genes were detected in 80 isolates. On comparison with VITEK-2 result, 92 samples showed concordance for carbapenem resistance 48 hours in advance. There was discordance in 21 isolates with 12 major errors and 09 minor errors. The sensitivity of direct Xpert® Carba-R test for rapid detection of carbapenem resistance, 48 hours in advance, was 81.42%. The sensitivity of direct CHROMagar test for accurate detection of carbapenem resistance, 24 hours in advance, was 92.06%.

Conclusion

The ability to detect carbapenem resistance with very high accuracy, 48 hours in advance, helps in appropriate antibiotic therapy and implementation of effective infection control practices.

Limiting the Spread of Multidrug-Resistant Bacteria in Low-to-Middle-Income Countries: One Size Does Not Fit All

The spread of multidrug-resistant organisms (MDRO) is associated with additional costs as well as higher morbidity and mortality rates. Risk factors related to the spread of MDRO can be classified into four categories: bacterial, host-related, organizational, and epidemiological. Faced with the severity of the MDRO predicament and its individual and collective consequences, many scientific societies have developed recommendations to help healthcare teams control the spread of MDROs. These international recommendations include a series of control measures based on surveillance cultures and the application of barrier measures, ranging from patients' being isolated in single rooms, to the reinforcement of hand hygiene and implementation of additional contact precautions, to the cohorting of colonized patients in a dedicated unit with or without a dedicated staff. In addition, most policies include the application of an antimicrobial stewardship program. Applying international policies to control the spread of MDROs presents several challenges, particularly in low-to-middle-income countries (LMICs). Through a review of the literature, this work evaluates the real risks of dissemination linked to MDROs and proposes an alternative policy that caters to the means of LMICs. Indeed, sufficient evidence exists to support the theory that high compliance with hand hygiene and antimicrobial stewardship reduces the risk of MDRO transmission. LMICs would therefore be better off adopting such low-cost policies without necessarily having to implement costly isolation protocols or impose additional contact precautions.

Clinical Characteristics, Microbiology, and Risk Factors for Mortality of Pre-Engraftment and Post-Engraftment Bloodstream Infection in Hematopoietic Stem Cell Transplantation Recipients

BACKGROUND

Bloodstream infection (BSI) is a common and serious complication that may lead to high mortality during the different phases after hematopoietic stem cell transplant (HSCT). We investigated BSI in patients undergoing HSCT to provide an appropriate clinical anti-infection experience and improve the prognosis of recipients with BSI after HSCT.

METHODS

A total of 105 patients with BSI after HSCT at our center from January 2015 to June 2020 were included in this retrospective study. We analyzed the clinical and microbiological data, and the risk factors for mortality at 3 months after BSI.

RESULTS

Of the 1141 HSCT recipients, 105 (9.2%) patients presented with 122 episodes of BSI, of which we isolated 85 (65.9%) gram-negative bacteria, 32 (24.8%) gram-positive bacteria and 12 (9.3%) fungi. Multidrug-resistant bacteria (MDR) were more than 70% of all pathogens and carbapenem-resistant organisms (CRO) were 25.6%. There were 55 episodes of BSI in the pre-engraftment phase and 67 episodes in the post-engraftment phase. The mortality of post-engraftment BSI was significantly higher than that of pre-engraftment (56.7% vs 32.7%, p = 0.005). Through multivariate analysis, the independent risk factors for all-cause mortality at 3 months after BSI were higher levels of procalcitonin (PCT), failure to cover appropriate antibiotics timely, and CRO BSI in pre-engraftment period or multidrug-resistant gram-negative bacteria (MDRGNB) BSI in post-engraftment period.

CONCLUSION

Although the incidence of BSI was lower after HSCT, MDR-dominated BSI had a high mortality rate. Rapid identification of infection or pathogens' classification with various testing methods and the more sensible and timely antibiotic cover are critical to the outcome of BSI after HSCT.

Microbial epidemiology and clinical risk factors of carbapenemase-producing Enterobacterales amongst Irish patients from first detection in 2009 until 2020

Background

Carbapenemase producing Enterobacterales (CPE) are major public health threats.

Aim

To review microbial epidemiology of CPE, as well as clinical risk factors and infections, amongst CPE positive patients over 12 years in an Irish tertiary hospital.

Methods

Retrospective observational study of data extracted from a laboratory CPE database, electronic healthcare records and manual review of patient charts. Common risk factors, treatment regimens for all CPE related infections, and clinical outcomes were ascertained.

Findings

Among CPE strains isolated from 460 patients, Klebsiella pneumoniae carbapenemase (KPC) was the carbapenemase most frequently detected, accounting for 87.4% (459) of all CPE enzymes. Citrobacter species 177 (33.7%) were the most common species harbouring this enzyme. 428 CPE positive patients (93%) were identified in the acute hospital setting; the most common risk factor for CPE acquisition was history of hospitalisation, observed in 305 (66%) cases. Thirty patients (6.5%) had confirmed infections post-acquisition, of which four were bloodstream infections. There were 19 subsequent episodes of non CPE-related bacteraemia in this cohort. All causal mortality at 30 days was 41 patients (8.9%). However, clinical review determined that CPE was an indirect associative factor in 8 patient deaths.

Conclusions

In this tertiary hospital setting, microbial epidemiology is changing; with both OXA-48 enzymes and KPC-producing Citrobacter species becoming more prevalent. Whilst the burden of CPE related infections, especially bacteraemia, was low over the study period, it remains critical that basic infection prevention and control practices are adhered to lest the observed changes in epidemiology result in an increase in clinical manifestations.

Effectiveness of Antiepidemic Measures Aimed to Reduce Carbapenemase-Producing Enterobacteriaceae in the Hospital Environment

Purpose

The objective of this study was to evaluate the effectiveness of hospital-based antiepidemic measures aimed at limiting the spread of symptomatic infections and colonization with carbapenem-resistant Enterobacteriaceae (CPE), mainly NDM-producing Klebsiella pneumoniae, with particular emphasis on microbiological screening tests.

Methods

This retrospective study was based on data from 168 hospitals under the supervision of the Provincial Sanitary and Epidemiological Station in Warsaw, Poland, in 2016–2017. Analysis of the effectiveness of antiepidemic procedures focused on the type of implemented antiepidemic procedures, the number of microbiological screening tests per year, the geographic location of the hospitals (inside or outside Warsaw), the timing of the screening tests (on admission to hospital or 48 hours later), and the results of the screening tests.

Results

Rates of proper isolation of patients infected or colonized with an alarm pathogen including NDM-producing K. pneumoniae increased from 38.0% in 2016 to 49.5% in 2017 (p > 0.05). The number of screening tests performed increased by 88% from 68319 in 2016 to 128373 in 2017. The number of epidemic outbreaks of symptomatic infections caused by NDM-producing K. pneumoniae decreased from 11 in 2016 to 7 in 2017 in hospitals in Warsaw, where microbiological screening tests were performed. The number of outbreaks in hospitals outside Warsaw, where the screening tests were not performed or were limited, increased from 8 in 2016 to 24 in 2017.

Conclusion

Screening tests increase the chance of detecting colonization by CPE. The implementation of microbiological screening decreased the risk of epidemic outbreaks of symptomatic infections caused by CPE.

Measuring perception of mental well-being in patients under isolation precautions: a prospective comparative study

OBJECTIVES

Isolation precautions (IP) are applied to prevent transmission of pathogens in healthcare settings. Potential negative health outcomes experienced by patients have been previously described but results remain conflicting. We aimed at evaluating the psychological impact of IP in adult patients in isolation using a novel psychological assessment tool.

STUDY DESIGN

Prospective matched cohort study.

SETTING

Tertiary care centre in Switzerland.

PARTICIPANTS

Hospitalised patients under IP and non-isolated patients were matched by ward, age and illness severity.

OUTCOME MEASURES

We measured surrogates of mental and social well-being by using the Pictorial Representation of Illness and Self Measure (PRISM) instrument once during hospitalisation. PRISM is a visual psychometric instrument that has been validated as a quantitative measure of suffering. Smaller distance in self-to-illness separation (SIS) signifies higher importance for a patient.

RESULTS

156 patients agreed to participate of which 63 were under IP and 93 were matched controls. Median (IQR) duration of isolation was 5 days (2-10). The median SIS (IQR) for perceived inferior nurses' care was 22.8 (18.5-24.3) and 23.8 (23.3-25.5) for isolated and non-isolated patients, respectively (p<0.001). Similarly, median SIS (IQR) was significantly smaller in isolated than non-isolated patients for avoidance by visitors with 17.5 (7.7-22.0) and 22.2 (21.8-22.6), for loneliness with 7.5 (3.6-16.0) and 18 (10.2-21.6) and for feeling impure with 19 (17.0-21.5) and 21.5 (18.9-22.1), respectively (all p values<0.05).

CONCLUSIONS

IP to prevent transmission of pathogens may negatively impact mental and social well-being. Measures to alleviate adverse effects of IP should be taken routinely.

Exploiting genomics to mitigate the public health impact of antimicrobial resistance

Antimicrobial resistance (AMR) is a major global public health threat, which has been largely driven by the excessive use of antimicrobials. Control measures are urgently needed to slow the trajectory of AMR but are hampered by an incomplete understanding of the interplay between pathogens, AMR encoding genes, and mobile genetic elements at a microbial level. These factors, combined with the human, animal, and environmental interactions that underlie AMR dissemination at a population level, make for a highly complex landscape. Whole-genome sequencing (WGS) and, more recently, metagenomic analyses have greatly enhanced our understanding of these processes, and these approaches are informing mitigation strategies for how we better understand and control AMR. This review explores how WGS techniques have advanced global, national, and local AMR surveillance, and how this improved understanding is being applied to inform solutions, such as novel diagnostic methods that allow antimicrobial use to be optimised and vaccination strategies for better controlling AMR. We highlight some future opportunities for AMR control informed by genomic sequencing, along with the remaining challenges that must be overcome to fully realise the potential of WGS approaches for international AMR control.

Overcoming the rising incidence and evolving mechanisms of antibiotic resistance by novel drug delivery approaches - An overview

Antimicrobial resistance is a normal evolutionary process for microorganisms. Antibiotics exerted accelerated selective pressure that hasten bacterial resistance through mutation, and acquisition external genes. These genes often carry multiple antibiotic resistant determinants allowing the recipient microbe an instant "super-bug" status. The extent of Antimicrobial Resistance (AMR) has reached a level of global crisis, existing antimicrobials are no long effective in treating infections caused by AMR pathogens. The great majority of clinically available antimicrobial agents are administered through oral and intra-venous routes. Overcoming antibacterial resistance by novel drug delivery approach offered new hopes, particularly in the treatment of AMR pathogens in sites less assessible through systemic circulation such as the lung and skin. In the current review, we will revisit the mechanism and incidence of important AMR pathogens. Finally, we will discuss novel drug delivery approaches including novel local antibiotic delivery systems, hybrid antibiotics, and nanoparticle-based antibiotic delivery systems.

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 bla_IMP, bla_KPC, bla_NDM, bla_OXA-48, and bla_VIM. 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.

Search and Contain: Impact of an Integrated Genomic and Epidemiological Surveillance and Response Program for Control of Carbapenemase-producing Enterobacterales

BACKGROUND

Multiresistant organisms (MROs) pose a critical threat to public health. Population-based programs for control of MROs such as carbapenemase-producing Enterobacterales (CPE) have emerged and evaluation is needed. We assessed the feasibility and impact of a statewide CPE surveillance and response program deployed across Victoria, Australia (population 6.5 million).

METHODS

A prospective multimodal intervention including active screening, carrier isolation, centralized case investigation, and comparative pathogen genomics was implemented. We analyzed trends in CPE incidence and clinical presentation, risk factors, and local transmission over the program's first 3 years (2016-2018).

RESULTS

CPE case ascertainment increased over the study period to 1.42 cases/100 000 population, linked to increased screening without a concomitant rise in active clinical infections (0.45-0.60 infections/100 000 population, P = .640). KPC-2 infection decreased from 0.29 infections/100 000 population prior to intervention to 0.03 infections/100 000 population in 2018 (P = .003). Comprehensive case investigation identified instances of overseas community acquisition. Median time between isolate referral and genomic and epidemiological assessment for local transmission was 11 days (IQR, 9-14). Prospective surveillance identified numerous small transmission networks (median, 2; range, 1-19 cases), predominantly IMP and KPC, with median pairwise distance of 8 (IQR, 4-13) single nucleotide polymorphisms; low diversity between clusters of the same sequence type suggested genomic cluster definitions alone are insufficient for targeted response.

CONCLUSIONS

We demonstrate the value of centralized CPE control programs to increase case ascertainment, resolve risk factors, and identify local transmission through prospective genomic and epidemiological surveillance; methodologies are transferable to low-prevalence settings and MROs globally.

Multidrug-Resistant Gram-Negative Bacteria: Infection Prevention and Control Update

Multidrug-resistant gram-negative bacteria (MDR-GNB) pose one of the greatest challenges to health care today because of their propensity for human-to-human transmission and lack of therapeutic options. Containing the spread of MDR-GNB is challenging, and the application of multifaceted infection control bundles during an evolving outbreak makes it difficult to measure the relative impact of each measure. This article will review the utility of various infection control measures in containing the spread of various MDR-GNB and will provide the supporting evidence for these interventions.

Adverse Events Associated with Patient Isolation: A Systematic Literature Revue and Meta-analysis

BACKGROUND

Patient isolation is widely recommended and used in healthcare institutions to prevent transmission of MDRO. However, its risk-benefit ratio is debated.

AIM

We undertook a systematic literature review and meta-analysis since 2009 to assess, based on the newly published studies, whether or not there are physical and psychological adverse events associated with patient isolation.

METHODS

Systematic literature review and meta-analysis were performed in accordance with the Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA) guidelines. Studies were systematically searched from PubMed, from the 1^st of may 2009 till the 31^st of January 2020. The concepts of the research questions were defined as: "Adverse events", "patient isolation or cohorting", and "multi-drug resistant organisms colonized or infection patients". Three reviewers independently screened studies and extracted data. All statistical analysis was performed with Stata Software and R.

FINDINGS

After screening titles of 15921 articles, abstracts of 196 and reviewing full texts of 50 studies, we included 19 studies. Studies were divided into 3 groups: 4 qualitative studies, 7 observational studies suitable for meta-analysis and 8 other observational studies. Meta-analysis shows no adverse events related to clinical care or patient's experience associated with patient isolation.

CONCLUSIONS

More studies with correct methodology, including a control group and standardized inclusion criteria, must be conducted to confirm our results.

A systematic review of the effectiveness of cohorting to reduce transmission of healthcare-associated C. difficile and multidrug-resistant organisms

BACKGROUND

Cohorting of patients and staff is a control strategy often used to prevent the spread of infection in healthcare institutions. However, a comprehensive evaluation of cohorting as a prevention approach is lacking.

METHODS

We performed a systematic review of studies that used cohorting as part of an infection control strategy to reduce hospital-acquired infections. We included studies published between 1966 and November 30, 2019, on adult populations hospitalized in acute-care hospitals.

RESULTS

In total, 87 studies met inclusion criteria. Study types were quasi-experimental "before and after" (n = 35), retrospective (n = 49), and prospective (n = 3). Case-control analysis was performed in 7 studies. Cohorting was performed with other infection control strategies in the setting of methicillin-resistant Staphylococcus aureus (MRSA, n = 22), Clostridioides difficile infection (CDI, n = 6), vancomycin-resistant Enterococcus (VRE, n = 17), carbapenem-resistant Enterobacteriaceae infections (CRE, n = 22), A. baumannii (n = 15), and other gram-negative infections (n = 5). Cohorting was performed either simultaneously (56 of 87, 64.4%) or in phases (31 of 87, 35.6%) to help contain transmission. In 60 studies, both patients and staff were cohorted. Most studies (77 of 87, 88.5%) showed a decline in infection or colonization rates after a multifaceted approach that included cohorting as part of the intervention bundle. Hand hygiene compliance improved in approximately half of the studies (8 of 15) during the respective intervention.

CONCLUSION

Cohorting of staff, patients, or both is a frequently used and reasonable component of an enhanced infection control strategy. However, determining the effectiveness of cohorting as a strategy to reduce transmission of MDRO and C. difficile infections is difficult, particularly in endemic situations.

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

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

Does high adherence to contact precautions lead to low in-hospital transmission of multi-drug-resistant micro-organisms in the endemic setting?

BACKGROUND

Conflicting results have been published on the impact of contact precautions (CPs) on reduction of transmission of multi-drug-resistant micro-organisms (MDROs) in the endemic setting. Ambiguous definitions coupled with low adherence partly explain these differences.

AIM

We prospectively monitored the level of adherence to CPs and aimed to relate it to in-hospital transmission of MDROs.

METHODS

Between January 2016 and March 2018, all patients under CPs underwent continuous monitoring of adherence to CPs by routine on-site visits on days 0, 3 and 7 after initiating CPs using a standardized checklist. The protocol included 10 interventions that were routinely checked such as CP sign at the door as well as wearing of gowns and gloves upon entry to the patient room. Patients requiring CPs were defined as colonized or infected with MDROs (meticillin-resistant Staphylococcus aureus (MRSA), non-Escherichia coli extended-spectrum beta lactamase (ESBL) Enterobacterales, vancomycin-resistant enterococci (VRE) and carbapenem-resistant Gram-negative micro-organisms (CRGN)) as well as patients infected with respiratory viruses, norovirus, scabies and hypervirulent strains of Clostridioides difficile.

FINDINGS

Overall, data from 13,756 CP records from 1378 visits of 812 patients were analysed. Adherence varied between 93% and 100% for each intervention, except for "separate space for contaminated material" with an adherence of 5.3-6.1%. The incidence of in-hospital transmission during the study period was extremely low for MRSA, VRE, non-E.coli ESBL Enterobacterales and CRGN with 0.00-0.064 cases/1000 patient days.

CONCLUSION

High adherence coupled with continuous monitoring of CPs correlated with a very low in-hospital transmission rate. These results indicate that CPs are highly effective if routine monitoring of adherence is implemented.

Household transmission of carbapenemase-producing Enterobacteriaceae: a prospective cohort study

OBJECTIVES

To estimate the transmission rate of carbapenemase-producing Enterobacteriaceae (CPE) in households with recently hospitalized CPE carriers.

METHODS

We conducted a prospective case-ascertained cohort study. We identified the presence of CPE in stool samples from index subjects, household contacts and companion animals and environmental samples at regular intervals. Linked transmissions were identified by WGS. A Markov model was constructed to estimate the household transmission potential of CPE.

RESULTS

Ten recently hospitalized index patients and 14 household contacts were included. There were seven households with one contact, two households with two contacts, and one household with three contacts. Index patients were colonized with blaOXA-48-like (n = 4), blaKPC-2 (n = 3), blaIMP (n = 2), and blaNDM-1 (n = 1), distributed among divergent species of Enterobacteriaceae. After a cumulative follow-up time of 9.0 years, three family members (21.4%, 3/14) acquired four different types of CPE in the community (hazard rate of 0.22/year). The probability of CPE transmission from an index patient to a household contact was 10% (95% CI 4%-26%).

CONCLUSIONS

We observed limited transmission of CPE from an index patient to household contacts. Larger studies are needed to understand the factors associated with household transmission of CPE and identify preventive strategies.

A Multispecies Cluster of GES-5 Carbapenemase-Producing Enterobacterales Linked by a Geographically Disseminated Plasmid

BACKGROUND

Early and accurate treatment of infections due to carbapenem-resistant organisms is facilitated by rapid diagnostics, but rare resistance mechanisms can compromise detection. One year after a Guiana Extended-Spectrum (GES)-5 carbapenemase-positive Klebsiella oxytoca infection was identified by whole-genome sequencing (WGS; later found to be part of a cluster of 3 cases), a cluster of 11 patients with GES-5-positive K. oxytoca was identified over 18 weeks in the same hospital.

METHODS

Bacteria were identified by matrix-assisted laser desorption/ionization-time of flight mass spectrometry, antimicrobial susceptibility testing followed European Committee on Antimicrobial Susceptibility Testing guidelines. Ertapenem-resistant isolates were referred to Public Health England for characterization using polymerase chain reaction (PCR) detection of GES, pulsed-field gel electrophoresis (PFGE), and WGS for the second cluster.

RESULTS

The identification of the first GES-5 K. oxytoca isolate was delayed, being identified by WGS. Implementation of a GES-gene PCR informed the occurrence of the second cluster in real time. In contrast to PFGE, WGS phylogenetic analysis refuted an epidemiological link between the 2 clusters; it also suggested a cascade of patient-to-patient transmission in the later cluster. A novel GES-5-encoding plasmid was present in K. oxytoca, Escherichia coli, and Enterobacter cloacae isolates from unlinked patients within the same hospital group and in human and wastewater isolates from 3 hospitals elsewhere in the United Kingdom.

CONCLUSIONS

Genomic sequencing revolutionized the epidemiological understanding of the clusters; it also underlined the risk of covert plasmid propagation in healthcare settings and revealed the national distribution of the resistance-encoding plasmid. Sequencing results also informed and led to the ongoing use of enhanced diagnostic tests for detecting carbapenemases locally and nationally.

Active surveillance of carbapenem-resistant Gram-negative healthcare-associated infections in a low-middle-income country city

Background

Carbapenem-resistance in healthcare-associated infections (HCAIs) is of great concern, and it is urgent to improve surveillance. We aimed to describe and analyze HCAIs trends on Gram-negative antimicrobial susceptibility in a city from a developing country, following the implementation of an active surveillance program.

Methods

This is an aggregated study describing data from 24 hospitals with intensive care units, including a trend analysis by Joinpoint regression between January 2012 and December 2017.

Results

There were 23,578 pathogens in 39,832 HCAIs, from which 16,225 were Gram-negatives (68.8%). Carbapenem susceptibility was lowest in A. baumannii (15.4–25.9%), K. pneumoniae (51.0–55.9%), and P. aeruginosa (64.9–84.1%) and highest in E. coli (96.5–99.2%). Only K. pneumoniae showed a significant Joinpoint at 95% confidence interval: −10.71% (−18.02; −2.75) from 2012 to 2014, p = 0.02, and 6.54% (−2.00; 15.83) from 2015 to 2017, p = 0.12, which was most influenced by urinary tract infections: −9.98% (−16.02; −3.48) from 2012 to 2014, p = 0.01, and 9.66% (−1.75; 22.39) from 2015 to 2017, p = 0.09.

Conclusion

Although we found a significant change toward an improvement in carbapenem susceptibility in K. pneumoniae, resistance is high for most pathogens. These data should encourage health institutions to improve their prevention and control strategies.

Risk factors for the environmental spread of different multidrug-resistant organisms: a prospective cohort study

BACKGROUND

Substantial scientific evidence shows that contamination of environmental surfaces in hospitals plays an important role in the transmission of multidrug-resistant organisms (MDROs). To date, studies have failed to identify the risk factors associated with environmental contamination.

AIM

To evaluate, compare, and identify factors associated with environmental contamination around carriers of different MDROs.

METHODS

This was a prospective cohort study from May 2018 to February 2020. A total of 125 patients were included, having been admitted to Avicenne Hospital and Hotel Dieu de France de Beyrouth Hospital who were faecal carriers of MDROs (extended-spectrum β-lactamase-producing Enterobacterales (ESBL-PE), carbapenemase-producing Enterobacterales (CPE), vancomycin-resistant enterococci (VRE)). For each patient, quantification of MDRO in stool was undertaken, plus a qualitative evaluation of the presence of MDRO in six different environmental sites; and clinical data were collected.

FINDINGS

MDROs comprised ESBL-PE (34%), CPE (45%), and VRE (21%). The most frequent MDRO species was Escherichia coli. Contamination of at least one environmental site was observed for 22 (18%) patients. Only carriage of VanA was associated with a significantly higher risk of dissemination. Having a urinary catheter, carriage of OXA48 and E. coli were protective factors against environmental contamination. There were no significant differences in environmental contamination between E. coli and other Enterobacterales or between ESBL-PE and CPE.

CONCLUSIONS

Hospital environmental contamination rates are substantially higher for patients with VRE, compared to the low environment dissemination rates around ESBL-PE and CPE. Further studies on a larger scale are needed to confirm the validity of our findings.

Clinical and Demographic Characteristics of Patients With a New Diagnosis of Carriage or Clinical Infection With Carbapenemase-Producing Enterobacterales: A Retrospective Study

Background: To examine the clinical, demographic, and microbiologic characteristics of new rectal carbapenemase-producing carbapenem-resistant Enterobacterales (CP-CRE) carriers vs. those with a clinical infection, hospitalized at Padeh-Poriya Medical Center between 2014 and 2017 and to examine the susceptibility profiles of isolates from clinical infections.

Methods: In this retrospective, chart analysis, demographic and clinical data were collected from medical charts of 175 adult patients with either new- onset carbapenemase-producing Enterobacterales (CPE) carriage or clinical CPE infection. Collected data included age, ethnic group, place of residence, hospitalizations in the past 90 days, and 30-day mortality. Microbiological analyses considered bacterial genus, molecular resistance mechanism and antibiotic susceptibility.

Results: A significantly higher percentage (42.4%) of CPE carriers were long-term care facility residents, and had been recently hospitalized (56.3%), as compared to patients with clinical CPE infection (29.2 and 45.9%, respectively). Additionally, we noted a high (58.3%) acquision of CPE in our hospital. The most common bacterial isolate was K. pneumoniae and the most common resistance mechanism was Klebsiella pneumoniae (K. pneumoniae) carbapenemases (KPC). High susceptibility rates to amikacin and chloramphenicol were also noted.

Conclusions: This study reaffirmed the importance of CPE screening and infection control measures. The observed antibiotic susceptibility profile suggests amikacin and chloramphenicol as potential treatments for CPE infection.

The Role of Antibiotic Stewardship and Telemedicine in the Management of Multidrug-Resistant Infections

This article summarizes the literature describing how antimicrobial stewardship and telemedicine interventions affect antimicrobial resistance. Discussion includes why we need stewardship, how to collaborate with team members, and the evidence of stewardship's and telemedicine's impact on resistance.

Agents of Last Resort: An Update on Polymyxin Resistance

Polymyxin resistance is a major public health threat, because the polymyxins represent last-line therapeutics for gram-negative pathogens resistant to essentially all other antibiotics. Minimizing any potential emergence and dissemination of polymyxin resistance relies on an improved understanding of mechanisms of and risk factors for polymyxin resistance, infection prevention and stewardship strategies, together with optimization of dosing of polymyxins (eg, combination regimens).

Molecular Detection and PCR-RFLP Analysis of Mucoviscosity-Associated Gene A (magA) in Clinical Isolates of Multidrug-Resistant Klebsiella pneumoniae in Bangladesh

Background and Objective:

The mucoviscosity associated gene A (magA) in the hypermucoviscous variants of K. pneumoniae is reported to be associated with invasive infections and considered a virulence factor. We sought to analyze the magA genes in K. pneumoniae isolates in the clinical specimen collected from Bangladesh.

Methods:

We established a multicenter cohort of patients with Klebsiella infection hospitalized at 05 different hospitals between September 2016 and April 2017. We collected 313 K. pneumoniae isolates from patients who consented to participate in the study. The isolates were evaluated for harboring the magA genes using a single-tube multiplexed polymerase chain reaction. The magA genes were analyzed by PCR-RFLP technique using two enzymes, namely PciI and SmaI. Antibiogram assay using 12 commercially available antibiotic discs was performed on all the isolates.

Results:

The presence of K. pneumoniae specific gene (ureD) was confirmed in all the isolates. The percentage of isolates harboring the magA gene was 7.34%(23 isolates), the majority of which was collected from the patients admitted in intensive care units (16 isolates, 69.6%), and infectious diseases wards (5 isolates, 21.7%). PCR-RFLP analysis revealed that for 7 out of 23 isolates, where Sma1 could not cleave the magA gene. All the isolates showed resistance to ampicillin, carbenicillin cefradine, chloramphenicol, erythromycin, kanamycin, and sulphamethoxazole, though the extent was varying. However, imipenem showed 100% sensitivity to all the tested isolates.

Conclusion:

This study demonstrates the presence of the magA gene in multidrug-resistant clinical isolates of K. pneumoniae collected from Bangladesh.

Multidrug Resistance (MDR) and Collateral Sensitivity in Bacteria, with Special Attention to Genetic and Evolutionary Aspects and to the Perspectives of Antimicrobial Peptides-A Review

Antibiotic poly-resistance (multidrug-, extreme-, and pan-drug resistance) is controlled by adaptive evolution. Darwinian and Lamarckian interpretations of resistance evolution are discussed. Arguments for, and against, pessimistic forecasts on a fatal “post-antibiotic era” are evaluated. In commensal niches, the appearance of a new antibiotic resistance often reduces fitness, but compensatory mutations may counteract this tendency. The appearance of new antibiotic resistance is frequently accompanied by a collateral sensitivity to other resistances. Organisms with an expanding open pan-genome, such as Acinetobacter baumannii, Pseudomonas aeruginosa, and Klebsiella pneumoniae, can withstand an increased number of resistances by exploiting their evolutionary plasticity and disseminating clonally or poly-clonally. Multidrug-resistant pathogen clones can become predominant under antibiotic stress conditions but, under the influence of negative frequency-dependent selection, are prevented from rising to dominance in a population in a commensal niche. Antimicrobial peptides have a great potential to combat multidrug resistance, since antibiotic-resistant bacteria have shown a high frequency of collateral sensitivity to antimicrobial peptides. In addition, the mobility patterns of antibiotic resistance, and antimicrobial peptide resistance, genes are completely different. The integron trade in commensal niches is fortunately limited by the species-specificity of resistance genes. Hence, we theorize that the suggested post-antibiotic era has not yet come, and indeed might never come.

Risk factors and outcomes of patients colonized with carbapenemase-producing and non–carbapenemase-producing carbapenem-resistant Enterobacteriaceae

Objective:

To compare risk factors and outcome of patients colonized with carbapenemase-producing (CP) carbapenem-resistant Enterobactereaceae (CRE) and non–CP-CRE.

Design:

A comparative historical study.

Setting:

A 1,000-bed tertiary-care university hospital.

Patients:

Adults with CP-CRE positive rectal swab cultures, non–CP-CRE positive rectal swab cultures, and negative rectal swab cultures (non-CRE).

Methods:

CP-CRE and non–CP-CRE colonized adult patients versus patients not colonized with CRE hospitalized during 24 months were included. We identified patients retrospectively through the microbiology laboratory, and we reviewed their files for demographics, underlying diseases, Charlson Index, treatment, and outcome.

Results:

This study included 447 patients for whom a rectal swab for CRE was obtained: 147 positive for CP-CRE, 147 positive for non–CP-CRE, and 147 negative for both. Patients with CP-CRE and non–CP-CRE versus no CRE more frequently resided in nursing homes (P<0.001), received antibiotics 3 months prior to admission (P < .001), and received glucocorticosteroids 3 months prior to admission (P = .047 and P < .001, respectively). Risk factors unique for non–CP-CRE versus CP-CRE colonization included mechanical ventilation and patient movement between hospital departments. Non–CP-CRE was a predictor for mechanical ventilation 2.5 that of CP-CRE colonization. In-hospital mortality was highest among non–CP-CRE–colonized patients. On COX multivariate regression for mortality prediction age, Charlson index and steroid treatment 3 months before admission influenced mortality (P = .027, P = .023, and P = .013, respectively).

Conclusions:

Overlapping and unique risk factors are associated with CP-CRE and non–CP-CRE colonization. Non–CP-CRE colonized patients had a higher in-hospital mortality rate.

The influence of hospital antimicrobial use on carbapenem-non-susceptible Enterobacterales incidence rates according to their mechanism of resistance: a time-series analysis

BACKGROUND

Carbapenem non-susceptible Enterobacterales (CNSE) can be broadly divided into those that produce carbapenemases (carbapenemase-producing Enterobacterales (CPE)), and those that harbour other mechanisms of resistance (non-carbapenemase-producing CNSE (NCP-CNSE)).

AIM

To determine the predictors of CNSE nosocomial incidence rates according to their mechanism of resistance.

METHODS

A time-series analysis was conducted (July 2013 to December 2018) to evaluate the relationship in time between hospital antibiotic use and the percentage of adherence to hand hygiene with the CNSE rates.

FINDINGS

In all, 20,641 non-duplicated Enterobacterales isolates were identified; 2.2% were CNSE. Of these, 48.1% and 51.9% were CPE and NCP-CNSE, respectively. Of the CPE, 78.3% possessed a bla_OXA-232 gene. A transfer function model was identified for CNSE, CPE, and OXA-232 CPE that explained 20.8%, 19.3%, and 24.2% of their variation, respectively. According to the CNSE and CPE models, an increase in piperacillin-tazobactam (TZP) use of 1 defined daily dose (DDD) per 100 hospital patient-days (HPD) would lead to an increase of 0.69 and 0.49 CNSE and CPE cases per 10,000 HPD, respectively. The OXA-232 CPE model estimates that an increase of 1 DDD per 100 HPD of TZP use would lead to an increase of 0.43 OXA-232 CPE cases per 10,000 HPD. A transfer function model was not identified for NCP-CNSE, nor was there an association between the adherence to handhygiene and the CNSE rates.

CONCLUSION

The use of TZP is related in time with the CPE nosocomial rates, mostly explained by its effect on OXA-232 CPE.

Detecting carbapenemase-producing Enterobacterales (CPE): an evaluation of an enhanced CPE infection control and screening programme in acute care

Objectives

The transmission of carbapenemase-producing Enterobacterales (CPE) poses an increasing healthcare challenge. A range of infection prevention activities, including screening and contact precautions, are recommended by international and national guidelines. We evaluated the introduction of an enhanced screening programme in a multisite London hospital group.

Methods

In June 2015, an enhanced CPE policy was launched in response to a local rise in CPE detection. This increased infection prevention measures beyond the national recommendations, with enhanced admission screening, contact tracing and environmental disinfection, improved laboratory protocols and staff/patient education. We report the CPE incidence and trends of CPE in screening and clinical cultures and the adoption of enhanced CPE screening. All non-duplicate CPE isolates identified between April 2014 and March 2018 were included.

Results

The number of CPE screens increased progressively, from 4530 in July 2015 to 10 589 in March 2018. CPE detection increased from 18 patients in July 2015 (1.0 per 1000 admissions) to 50 patients in March 2018 (2.7 per 1000 admissions). The proportion of CPE-positive screening cultures remained at approximately 0.4% throughout, suggesting that whilst the CPE carriage rate was unchanged, carrier identification increased. Also, 123 patients were identified through positive CPE clinical cultures over the study period; there was no significant change in the rate of CPE from clinical cultures per 1000 admissions (P = 0.07).

Conclusions

Our findings suggest that whilst the enhanced screening programme identified a previously undetected reservoir of CPE colonization in our patient population, the rate of detection of CPE in clinical cultures did not increase.

Utilising sigmoid models to predict the spread of antimicrobial resistance at the country level

BackgroundThe spread of antimicrobial resistance (AMR) is of worldwide concern. Public health policymakers and pharmaceutical companies pursuing antibiotic development require accurate predictions about the future spread of AMR.AimWe aimed to identify and model temporal and geographical patterns of AMR spread and to predict future trends based on a slow, intermediate or rapid rise in resistance.MethodsWe obtained data from five antibiotic resistance surveillance projects spanning the years 1997 to 2015. We aggregated the isolate-level or country-level data by country and year to produce country-bacterium-antibiotic class triads. We fitted both linear and sigmoid models to these triads and chose the one with the better fit. For triads that conformed to a sigmoid model, we classified AMR progression into one of three characterising paces: slow, intermediate or fast, based on the sigmoid slope. Within each pace category, average sigmoid models were calculated and validated.ResultsWe constructed a database with 51,670 country-year-bacterium-antibiotic observations, grouped into 7,440 country-bacterium-antibiotic triads. A total of 1,037 triads (14%) met the inclusion criteria. Of these, 326 (31.4%) followed a sigmoid (logistic) pattern over time. Among 107 triads for which both sigmoid and linear models could be fit, the sigmoid model was a better fit in 84%. The sigmoid model deviated from observed data by a median of 6.5%; the degree of deviation was related to the pace of spread.ConclusionWe present a novel method of describing and predicting the spread of antibiotic-resistant organisms.

Evaluation of Xpert Carba-R Assay v.2 to Detect Carbapenemase Genes in Two Hospitals in Korea

Background

As the spread of carbapenemase-producing Enterobacteriaceae poses a critical threat to public health, rapid detection of carbapenemase genes is urgently required for prompt initiation of appropriate antimicrobial therapy and infection control. We evaluated the performance of Xpert Carba-R v.2 (Cepheid, USA) compared with that of culture-based conventional PCR.

Methods

Using the results of 5,479 consecutive clinical rectal swabs, discrepant analysis (enriched culture followed by PCR) was performed for all discordant samples (N=100), which were Carba-R v.2-positive and culture-negative.

Results

Among the samples, 206 carbapenemase genes (3.6%) were detected by Carba-R v.2. The sensitivity and specificity were 95.0% and 98.1%, respectively. The positive predictive value (PPV) and negative predictive value (NPV) were 49.0% and 99.9%, respectively. Following discrepant analysis, the PPV increased to 73.5% and the low PPV (8.1%) of the 86 non-KPC improved to 48.8%. Among the 105 discrepancies, NDM was the most frequently observed (N=56), followed by KPC (N=26), VIM (N=10), IMP (N=8), OXA-48 (N=5). The threshold cycle values between discordant vs. concordant and resolved groups were significantly different (P<0.001).

Conclusions

Carba-R v.2 is a rapid and sensitive method for detecting carbapenemase-encoding genes compared with culture-based conventional PCR. Most of our discrepant results were non-KPC genes. Thus, the clinical significance of the non-KPC positive cases detected by Carba-R v.2 should be investigated. This assay would be useful for deciding whether to isolate pre-exposed patients in hospital settings, based on the high specificity and NPV.

Institutional Burden of Carbapenemase-Producing Enterobacterales: The Effect of Changes in Surveillance Culture Methodology

An essential part of the Israeli intervention program aimed to contain the spread of carbapenemase-producing Enterobacterales (CPE) has been the establishment of national surveillance system, where the institutional rates are determined by both clinical and surveillance cultures. The objectives of the study were to analyze the effect of changes in surveillance culture media on the rates and microbiological characteristics of CPE in a multicenter study. The rates were compared during 2 years in and between four centers. Two centers (Tel-Aviv and Beilinson) had changed their surveillance media to CHROMagar™ mSuperCARBA™ after 1 year, and two centers (Rambam and Hillel-Yaffe) had continued to use CHROMagar KPC. There was an increase in the rates of surveillance CPE in Tel-Aviv and Beilinson following the change in media, whereas the rates remained the same or declined in Rambam and Hillel-Yaffe, respectively. The rates of clinical CPE remained unchanged in Rambam and Hillel-Yaffe, declined in Tel-Aviv, and increased in Beilinson but to a lesser extent compared with the increase in surveillance CPE. The relative composition of the CPE mechanisms and species changed in Tel-Aviv, with an increase in non-Klebsiella pneumoniae species and in carbapenemase other than KPC. Our study shows that changes in surveillance media may contribute to significant changes in the rate of surveillance CPE that may be irrespective of actual epidemiological changes. Therefore, determination of institutional burden of CPE and the assessment of intervention results should be based primarily on the rate of clinical CPE rather than surveillance culture reports.

Precision medicine for the diagnosis and treatment of carbapenem-resistant Enterobacterales: time to think from a different perspective

INTRODUCTION

Carbapenem-resistant Enterobacterales (CRE) represent a global public health problem. Precision medicine (PM) is a multicomponent medical approach that should be used to individualize the management of patients infected with CRE.

AREAS COVERED

Here, we differentiate carbapenem-producing CRE (CP-CRE) from non-CP-CRE and the importance of this distinction in clinical practice. The current phenotypic CRE-case definition and its implications are also discussed. Additionally, we summarize data regarding phenotypic and molecular diagnostic tools and available antibiotics. In order to review the most relevant data, a comprehensive literature search of peer-reviewed articles in PubMed and abstracts presented at high-impact conferences was performed.

EXPERT OPINION

PM in CRE infections entails a multi-step process that includes applying the current phenotypic definition, utilization of the right phenotypic or molecular testing methods, and thorough evaluation of risk factors, source of infection, and comorbidities. A powerful armamentarium is available to treat CRE infections, including recently approved agents. Randomized controlled trials targeting specific pathogens instead of site of infections may be appropriate to fill in the current gaps. In light of the diverse enzymology behind CP-CRE, PM should be employed to provide the best therapy based on the underlying resistance mechanism.

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

BACKGROUND

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

AIM/METHODS

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

FINDINGS

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

CONCLUSION

Local epidemiology and resources must be assessed before implementing cohorting.

Different screening frequencies of carbapenem-resistant Enterobacteriaceae in patients undergoing hematopoietic stem cell transplantation: which one is better?

BACKGROUND

A consensus has been reached that carbapenem-resistant Enterobacteriaceae (CRE) screening in immunosuppressed individuals can reduce the incidence of CRE bloodstream infection (BSI).

METHODS

We retrospectively studied the clinical data of 395 consecutive HSCT patients from September 2017 to April 2019. From September 2017 to June 2018 (period 1), 200 patients received single CRE screening before transplantation. From July 2018 to April 2019 (period 2), 195 patients received continuous weekly CRE screening after admission. For patients colonized with CRE, targeted managements were received: (1) contact precautions and (2) preemptive CRE-targeted treatment if necessary.

RESULTS

During period 1, 3 patients with CRE colonization were detected (1.5%). The CRE BSI rate was 2.0% (4 patients), and the related 30-day mortality was 50.0% (2 out of 4 patients). During period 2, 21 patients with CRE colonization were detected, and the detection rate was significantly higher than that in period 1 (P < 0.001). Of the 21 colonized patients, 4 (19.0%) patients were identified as positive for CRE at the first screening, 5 (23.8%) were identified at the second screening, and the remaining 12 (57.1%) were identified at the third or later screening. The CRE BSI rate decreased to 0.5% (1/195), and there were no CRE-related death. Fifteen colonized patients developed neutropenic fever. Thirteen colonizers were preemptively treated with tigecycline within 24 h of fever onset, and they achieved rapid temperature control. One colonizer received tigecycline later than 48 h after fever onset and ultimately survived due to the addition of polymyxin. The other received tigecycline later than 72 h after fever onset and died of septic shock.

CONCLUSION

The increase in screening frequency contributed to the detection of patients with CRE colonization. Targeted managements for these colonized patients may contribute to reducing the incidence and mortality of CRE BSI, therefore improving the prognosis of patients.

Diagnostic performance of the Xpert Carba-R™ assay directly from rectal swabs for active surveillance of carbapenemase-producing organisms in the largest Brazilian University Hospital

BACKGROUND

The global spread of carbapenemase-producing organisms (CPO) has been considered by international health authorities as a critical public health concern. Brazil has a high CPO prevalence according to distinct publications but many routine microbiology laboratories have only phenotypic resources to evaluate this epidemiological situation, which is time-consuming and detects only carbapenem-resistant isolates missing CPO susceptible expressing a slightly decreased susceptibility. New molecular platforms can detect CPO faster but a local evaluation is essential.

AIM

To evaluate the performance of CPO detection direct from rectal swabs with the Xpert Carba-R™ assay (Cepheid, Sunnyvale, CA) in the largest Brazilian University Hospital.

METHODS

A prospective diagnostic accuracy study of CPO was performed with the collection of rectal swabs from patients admitted into the Intensive Care Unit (ICU) and into the Emergency Department (ED) between April and July 2016. The Xpert Carba-R™ assay results were compared with carbapenem-resistant Enterobacterales (CRE) surveillance cultures plus in-house PCR carbapenemase detection (reference method). In case of discordant results between methods, additional tests were performed. The limit of detection (LoD) for the CRE culture and the Xpert Carba-R™ assay were performed with contrived isolates of known carbapenemases genes.

RESULTS

A total of 921 clinical rectal swabs were analyzed being 21% (196/921) from the ICU and 79% (725/921) from the ED. Overall, the Xpert Carba-R™ assay detected 9.9% (91/921) of CPOs being 9.5% (87/921) positive only for bla_KPC and 0.4% (4/921) positive only for bla_NDM. The reference method detected 9.1% (84/921) CPO being 77 (8.4%) bla_KPC, 5 bla_VIM (0.5%) and 2 bla_NDM (0.2%). No IMP or OXA-48 like gene was detected. Overall, twelve samples, 1.3% (10 bla_KPC, 2 bla_NDM) were Xpert Carba-R™ positive but negative by the reference method. Five isolates (0.5%) were positive for bla_VIM only by in-house PCR and confirmed to be bla_VIM-2 by DNA sequencing. The Kappa value, sensitivity, specificity, positive/negative predictive values and accuracy of the Xpert Carba-R™ assay were; 0.893 (95% confidence interval [CI], 0.842-0.944), 94% (86.7-98.0), 98.6% (97.5-99.3), 86.8% (78.1-93.0), 99.4% (98.6-99.8) and 98.2% (97.3-99.1), respectively. The LoD for bla_KPC of the Xpert Carba-R™ assay and the CRE cultures were 10¹ CFU/swab.

CONCLUSION

The Xpert Carba-R™ assay is an accurate test to detect CPO directly from the rectal swabs with significant lower turnaround time (TAT) when compared to the reference method (CRE culture plus in-house PCR). Xpert Carba-R™ may, therefore, be regarded as a good and fast epidemiological tool.

Whole genome sequencing of carbapenem-resistant Klebsiella pneumoniae: evolutionary analysis for outbreak investigation

Aim: Carbapenemase-resistant Enterobacteriaceae represents a major concern in hospital setting. Materials & methods: The evolutionary history of carbapenem-resistant Klebsiella pneumonia strains was analyzed by core genome multilocus sequence typing and Bayesian phylogenesis by whole genomes sequencing. Results: A great increase carbapenem-resistant K. pneumoniae causing blood stream infection was observed in the years 2015-2016. At multilocus sequence typing (MLST), they were prevalently ST512 and ST101. ST512 were core genome (cg)MLST 53, while ST101 mainly cgMLST453. The minimum-spanning tree, based on cgMLST, showed strains clustering based on the different STs. By Bayesian phylogenetic analysis, maximum clade credibility tree showed that strains were introduced in the year 2005 with the most probable location in the ICU ward. Two outbreaks by ST101 and ST512 strains with Tower T8 as the probable location were evidenced. Conclusion: Molecular epidemiology is a powerful tool to track the way of transmission of resistant bacteria within the hospital setting.

How Introducing a Registry With Automated Alerts for Carbapenem-resistant Enterobacteriaceae (CRE) May Help Control CRE Spread in a Region

BACKGROUND

Regions are considering the use of electronic registries to track patients who carry antibiotic-resistant bacteria, including carbapenem-resistant Enterobacteriaceae (CRE). Implementing such a registry can be challenging and requires time, effort, and resources; therefore, there is a need to better understand the potential impact.

METHODS

We developed an agent-based model of all inpatient healthcare facilities (90 acute care hospitals, 9 long-term acute care hospitals, 351 skilled nursing facilities, and 12 ventilator-capable skilled nursing facilities) in the Chicago metropolitan area, surrounding communities, and patient flow using our Regional Healthcare Ecosystem Analyst software platform. Scenarios explored the impact of a registry that tracked patients carrying CRE to help guide infection prevention and control.

RESULTS

When all Illinois facilities participated (n = 402), the registry reduced the number of new carriers by 11.7% and CRE prevalence by 7.6% over a 3-year period. When 75% of the largest Illinois facilities participated (n = 304), registry use resulted in a 11.6% relative reduction in new carriers (16.9% and 1.2% in participating and nonparticipating facilities, respectively) and 5.0% relative reduction in prevalence. When 50% participated (n = 201), there were 10.7% and 5.6% relative reductions in incident carriers and prevalence, respectively. When 25% participated (n = 101), there was a 9.1% relative reduction in incident carriers (20.4% and 1.6% in participating and nonparticipating facilities, respectively) and 2.8% relative reduction in prevalence.

CONCLUSIONS

Implementing an extensively drug-resistant organism registry reduced CRE spread, even when only 25% of the largest Illinois facilities participated due to patient sharing. Nonparticipating facilities garnered benefits, with reductions in new carriers.