Nosocomial Outbreak of New Delhi Metallo-β-Lactamase-1-Producing Gram-Negative Bacteria in South Africa: A Case-Control Study

IncX3 plasmid-mediated spread of blaNDM gene in Enterobacteriaceae among children in China

OBJECTIVES

The blaNDM gene was prevalent among children and became the predominant cause of severe infection in infants and children. This study aimed to investigate the epidemiology and molecular characteristics of blaNDM in Enterobacteriaceae among children in China.

METHODS

Carbapenem-resistant Enterobacteriaceae (CRE) were collected in the Children's Hospital of Fudan University from January 2016 to December 2022. Five carbapenemase genes (blaKPC, blaNDM, blaVIM, blaIMP, blaOXA-48) were screened by PCR method. Multilocus sequence typing (MLST) was conducted for phylogenetic analyses. blaNDM-carrying plasmids were typed by PCR-based Incompatibility (Inc) typing method. Moreover, plasmid comparison was performed with 213 publicly available IncX3 plasmids.

RESULTS

A total of 330 CRE strains were enrolled, 96.4% of which carried carbapenemase genes. blaNDM gene accounted for 64.8% (214 strains) and included four variants, including blaNDM-1 (59.8%), blaNDM-5 (39.3%), blaNDM-7 (0.5%), and blaNDM-9 (0.5%). There were no predominant MLST lineages of blaNDM carrying strains. IncX3 was the major plasmid carrying blaNDM-1 (68.0%) and blaNDM-5 (72.6%) and was dominant in blaNDM-Klebsiella penumoniae (79.8%), blaNDM-Escherichia coli (58.2%), and blaNDM-Enterobacter cloacae (61.0%), respectively. Most (79.0%) clinical IncX3 plasmids in the world carried blaNDM, and the prevalence of blaNDM in IncX3 plasmids was more common in China (95.8%) than other countries (58.1%, P <0.01).

CONCLUSION

blaNDM is highly prevalent in CRE among children in China. The spread of blaNDM was mainly mediated by IncX3 plasmids. Surveillance and infection control on the spread of blaNDM among children are important.

Landscape of plasmids encoding β-lactamases in disinfection residual Enterobacteriaceae from wastewater treatment plants

Conventional disinfection processes, such as chlorination and UV radiation, are ineffective in controling antibiotic-resistant bacteria, especially disinfection residual Enterobacteriaceae (DRE) encoding β-lactamases, some of which have been classified as "critical priority pathogens" by the World Health Organization. However, few studies have focused on the transferability, phenotype, and genetic characteristics of DRE-derived plasmids encoding β-lactamases, especially extended-spectrum β-lactamases and carbapenemases. In this study, we isolated 10 typical DRE harboring plasmid-mediated blaNDM, blaCTX-M, or blaTEM in post-disinfection effluent from two wastewater treatment plants (WWTPs), with transfer frequency ranging from 1.69 × 10-6 to 3.02 × 10-5. According to genomic maps of plasmids, all blaNDM and blaTEM were cascaded with IS26, and blaCTX-M was adjacent to ISEcp1 or IS26, indicating the important role of these elements in the movement of β-lactamase-encoding genes. The presence of intact class 1 integrons on pWTPN-01 and pWTPC-03 suggested the ability of these DRE-derived plasmids to integrate other exogenous antibiotic resistance genes (ARGs). The coexistence of antibiotic, disinfectant, and heavy metal resistance genes on the same plasmid (e.g., pWTPT-03) implied the facilitating role of disinfectants and heavy metals in the transmission of DRE-derived ARGs. Notably, two plasmid transconjugants exhibited no discernible competitive fitness cost, suggesting a heightened environmental persistence. Furthermore, enhanced virulence induced by β-lactamase-encoding plasmids in their hosts was confirmed using Galleria mellonella infection models, which might be attributed to plasmid-mediated virulence genes. Overall, this study describes the landscape of β-lactamase-encoding plasmids in DRE, and highlights the urgent need for advanced control of DRE to keep environmental and ecological security.

Epidemiology, risk factors, and clinical outcomes of carbapenem-resistant Enterobacterales in Africa: A systematic review

OBJECTIVES

Carbapenem-resistant Enterobacterales (CRE) commonly cause hospital-acquired infections and hospital outbreaks worldwide, with an alarming increase in Africa, necessitating review of regional CRE epidemiological trends.

METHODS

A systematic review was conducted using PRISMA guidelines, searching PubMed, Scopus and Web of Science databases for studies describing CRE distribution, risk factors for CRE acquisition and clinical outcome of CRE infections in Africa.

RESULTS

One-hundred and sixty-nine studies were included, with the majority from North Africa (92/169, 54.4%). Most studies (136/169; 80.4%) focused only on infection, with a total of 15666 CRE isolates (97.4% clinical infection, 2.6% colonisation). The leading bacterial species included Klebsiella (72.2%), Escherichia coli (13.5%), and Enterobacter (8.3%). The most frequently detected carbapenemases were NDM (43.1%) and OXA-48-like (42.9%). Sequence types were reported in 44 studies, with ST101 and ST147 most commonly reported in K. pneumoniae, and ST410, ST167 and ST38 in E. coli. Previous antibiotic use, prior hospitalisation, surgical procedures, indwelling devices, intensive care unit admission and prolonged hospital stay, were the most frequent factors associated with CRE infection/colonisation. Crude mortality for CRE infection was 37%.

CONCLUSION

Although K. pneumoniae and E. coli remain the most frequent CRE in Africa, observed sequence types are not the commonly reported global 'high-risk' clones. The distribution of species and carbapenemases differs across African regions, while risk factors for CRE colonisation/infection, and patient outcomes are similar to those reported globally. There are limited data on CREs from parts of Africa, highlighting the need to strengthen epidemiologic surveillance programmes in the region.

Antimicrobial Activities of Aztreonam-Avibactam and Comparator Agents against Enterobacterales Analyzed by ICU and Non-ICU Wards, Infection Sources, and Geographic Regions: ATLAS Program 2016-2020

Increasing antimicrobial resistance among multidrug-resistant (MDR), extended-spectrum β-lactamase (ESBL)- and carbapenemase-producing Enterobacterales (CPE), in particular metallo-β-lactamase (MBL)-positive strains, has led to limited treatment options in these isolates. This study evaluated the activity of aztreonam-avibactam (ATM-AVI) and comparator antimicrobials against Enterobacterales isolates and key resistance phenotypes stratified by wards, infection sources and geographic regions as part of the ATLAS program between 2016 and 2020. Minimum inhibitory concentrations (MICs) were determined per Clinical and Laboratory Standards Institute (CLSI) guidelines. The susceptibility of antimicrobials were interpreted using CLSI and European Committee on Antimicrobial Susceptibility Testing (EUCAST) breakpoints. A tentative pharmacokinetic/pharmacodynamic breakpoint of 8 µg/mL was considered for ATM-AVI activity. ATM-AVI inhibited ≥99.2% of Enterobacterales isolates across wards and ≥99.7% isolates across infection sources globally and in all regions at ≤8 µg/mL. For resistance phenotypes, ATM-AVI demonstrated sustained activity across wards and infection sources by inhibiting ≥98.5% and ≥99.1% of multidrug-resistant (MDR) isolates, ≥98.6% and ≥99.1% of ESBL-positive isolates, ≥96.8% and ≥90.9% of carbapenem-resistant (CR) isolates, and ≥96.8% and ≥97.4% of MBL-positive isolates, respectively, at ≤8 µg/mL globally and across regions. Overall, our study demonstrated that ATM-AVI represents an important therapeutic option for infections caused by Enterobacterales, including key resistance phenotypes across different wards and infection sources.

An NDM-Producing Escherichia coli Clinical Isolate Exhibiting Resistance to Cefiderocol and the Combination of Ceftazidime-Avibactam and Aztreonam: Another Step Toward Pan-β-Lactam Resistance

Background

Cefiderocol and ceftazidime-avibactam plus aztreonam (CZA-ATM) are preferred treatment regimens for New Delhi metallo-β-lactamase (NDM)-producing infections.

Methods

We report the case of a US patient who traveled to India to receive a renal transplant. He subsequently experienced pyelonephritis by an NDM-producing Escherichia coli. Broth microdilution and the broth disk elution method indicated resistance to all β-lactams, including cefiderocol and CZA-ATM. Whole-genome sequencing investigations were undertaken to identify resistance mechanisms.

Results

An E. coli isolate belonging to sequence type (ST) 167 containing a bla_NDM-5 gene was identified on a plasmid of the IncFIA/IncFIB/IncFIC replicon groups. When compared with the genome of another ST167 E. coli clinical isolate containing bla_NDM-5 and exhibiting susceptibility to cefiderocol and CZA-ATM, a 12-base pair insertion in ftsI, translating to a 4-amino acid duplication in PBP3, was identified. Moreover, a bla_CMY-59 gene was harbored on an IncI-γ replicon type, and frameshift mutations were identified in the cirA iron transport gene.

Conclusions

This is the first clinical case of a US patient harboring an NDM-producing isolate exhibiting resistance to all available β-lactam agents. The isolate's unexpected resistance to cefiderocol and CZA-ATM was likely due to a combination of (1) a modified PBP3 (increased MICs to both regimens), (2) truncated iron-binding protein (increased cefiderocol MIC), and (3) a bla_CMY gene (reduced CZA-ATM activity). E. coli ST167 clinical isolates harboring bla_NDM-5 genes are a recognized international high-risk clone. When coupled with the additional mechanisms identified in our patient's isolate, which is not uncommon for this high-risk clone, pan-β-lactam resistance may occur.

A case–control study of infections caused by Klebsiella pneumoniae producing New Delhi metallo-beta-lactamase-1: Predictors and outcomes

Introduction

Infections caused by antimicrobial-resistant bacteria are a significant cause of death worldwide, and carbapenemase-producing bacteria are the principal agents. New Delhi metallo-beta-lactamase-1 producing Klebsiella pneumoniae (KP-NDM-1) is an extensively drug-resistant bacterium that has been previously reported in Mexico. Our aim was to conduct a case–control study to describe the risk factors associated with nosocomial infections caused by K. pneumoniae producing NDM-1 in a tertiary-care hospital in Mexico.

Methods

A retrospective case–control study with patients hospitalized from January 2012 to February 2018 at the Hospital Civil de Guadalajara “Fray Antonio Alcalde” was designed. During this period, 139 patients with a culture that was positive for K. pneumoniae NDM-1 (cases) and 486 patients hospitalized in the same department and on the same date as the cases (controls) were included. Data were analyzed using SPSS v. 24, and logistic regression analysis was conducted to calculate the risk factors for KP-NDM-1 infection.

Results

One hundred and thirty-nine case patients with a KP-NDM-1 isolate and 486 control patients were analyzed. In the case group, acute renal failure was a significant comorbidity, hospitalization days were extended, and significantly more deaths occurred. In a multivariate analysis of risk factors, the independent variables included the previous use of antibiotics (odds ratio, OR = 12.252), the use of a urinary catheter (OR = 5.985), the use of a central venous catheter (OR = 5.518), the use of mechanical ventilation (OR = 3.459), and the length of intensive care unit (ICU) stay (OR = 2.334) as predictors of infection with NDM-1 K. pneumoniae.

Conclusion

In this study, the previous use of antibiotics, the use of a urinary catheter, the use of a central venous catheter, the use of mechanical ventilation, and ICU stay were shown to be predictors of infection with NDM-1 K. pneumoniae and were independent risk factors for infection with NDM-1 K. pneumoniae.

In vitro activity of aztreonam/avibactam against isolates of Enterobacterales collected globally from ATLAS in 2019

OBJECTIVES

Infections caused by drug-resistant Enterobacterales including those producing metallo-β-lactamases (MBLs) are particularly challenging due to limited therapeutic options. The drug combination aztreonam/avibactam (ATM-AVI) is under clinical development for treating serious infections caused by these strains. This study assessed the in vitro activity of ATM-AVI against Enterobacterales isolates collected globally in the ATLAS surveillance programme in 2019.

METHODS

Clinical isolates of Enterobacterales (N=18713) including Citrobacter freundii, Citrobacter koseri, Enterobacter cloacae complex, Escherichia coli, Klebsiella aerogenes, Klebsiella oxytoca, Klebsiella pneumoniae, Proteus mirabilis, and Serratia marcescens collected from 232 sites in 2019 were analysed. Antimicrobial susceptibility testing was performed by reference broth microdilution. A pharmacokinetic/pharmacodynamic based breakpoint of 8 mg/L was considered for ATM-AVI activity.

RESULTS

ATM-AVI demonstrated potent antimicrobial activity against all Enterobacterales, with 99.9% isolates inhibited at MIC ≤8 mg/L (MIC₉₀, 0.25 mg/L). MICs ≤8 mg/L (>99.0%) were noted for ATM-AVI across regions worldwide. Among other antimicrobials, amikacin, colistin, imipenem, meropenem, and tigecycline were also active (susceptibility >85.0%) against Enterobacterales. Activity of ATM-AVI was sustained against multi-drug resistant, extended-spectrum β-lactamases producing, and carbapenem-resistant isolates (susceptibility >99%; MIC₉₀, 0.25-0.5 mg/L). Importantly, potent activity for ATM-AVI (>99.0%; MIC_90, 0.5 mg/L) was noted among MBL-positive isolates and those producing other carbapenemases, such as KPC and OXA-48.

CONCLUSIONS

Our results demonstrated that ATM-AVI was highly active against a recent collection of Enterobacterales isolates, including those producing MBLs either alone or in combination with other carbapenemases. Thus, ATM-AVI represents a potential option for treating infections caused by antibiotic-resistant Enterobacterales including MBL-producing strains.

Landscape of genes in hospital wastewater breaking through the defense line of last-resort antibiotics

Hospital wastewater contains abundant antibiotics, antibiotic resistance genes (ARGs), and pathogens. Last-resort antibiotic resistance genes (LARGs) include the New Delhi metallo-β-lactamase gene blaNDM, mobile colistin resistance gene mcr and tigecycline resistance gene tet(X) which confers resistance to carbapenems, colistin and tigecycline. The presence and significance of LARGs in hospital wastewater treatment systems (HWTS) have not yet been systematically explored. Here, LARG variants were shown to be prevalent both influents and effluents of HWTS. A total of 989 Enterobacteriaceae isolates that confer resistance to last-resort antibiotics were collected from effluents and multiple genetic contexts of LARGs were analyzed. LARGs-carrying plasmids were confirmed to show high multidrug phenotypes and transferability. We also discovered the co-occurrence of plasmids harboring blaNDM-1 and mcr-1 in single Escherichia coli, as well as E. coli HM016 containing two unique mcr-1-carrying plasmids. This result might accelerate co-dissemination of LARGs under environmental selection pressure. Different core genetic arrangements in these strains suggest several evolutionary pathways in HWTS. The resistance functions of LARGs were confirmed in vitro and in vivo by mass spectrometry. This study provides novel insights into the diversity, genetic context and function of critical ARGs in HWTS. The results raise the concern that LARGs may further spread into the environment, thus, more stringent discharge standards and regulations for hospital wastewater are urgently needed.

Therapeutic Options for Metallo-β-Lactamase-Producing Enterobacterales

The spread of metallo-β-lactamase (MBL)-producing Enterobacterales worldwide without the simultaneous increase in active antibiotics makes these organisms an urgent public health threat. This review summarizes recent advancements in diagnostic and treatment strategies for infections caused by MBL-producing Enterobacterales. Adequate treatment of patients infected with MBL-producing Enterobacterales relies on detection of the β-lactamase in the clinic. There are several molecular platforms that are currently available to identify clinically relevant MBLs as well as other important serine-β-lactamases. Once detected, there are several antibiotics that have historically been used for the treatment of MBL-producing Enterobacterales. Antimicrobials such as aminoglycosides, tetracyclines, fosfomycin, and polymyxins often show promising in vitro activity though clinical data are currently lacking to support their widespread use. Ceftazidime-avibactam combined with aztreonam is promising for treatment of infections caused by MBL-producing Enterobacterales and currently has the most clinical data of any available antibiotic to support its use. While cefiderocol has displayed promising activity against MBL-producing Enterobacterales in vitro and in preliminary clinical studies, further clinical studies will better shed light on its place in treatment. Lastly, there are several promising MBL inhibitors in the pipeline, which may further improve the treatment of MBL-producing Enterobacterales.

Healthcare-associated outbreaks of bacterial infections in Africa, 2009-2018: A review

BACKGROUND

Healthcare-associated infections (HAIs) are a major global public health problem, increasing the transmission of drug-resistant infections. In Africa, the prevalence of HAIs among all hospital inpatients is estimated to be between 3% and 15%, but outbreaks are infrequently reported. Failure to detect and/or report outbreaks can increase the risk of ongoing infections and recurrent outbreaks.

METHODS

A search of the PubMed, Web of Science, Cochrane Library, and other outbreak databases was performed to identify published literature on bacterial HAI outbreaks in Africa (January 2009 to December 2018). Details of the outbreak characteristics, hospital environment, and the control measures implemented were extracted.

RESULTS

Twenty-two studies published over the 10-year period were identified. These reported 31 distinct outbreaks and a total of 31 causative pathogens, including Klebsiella pneumoniae (six outbreaks, 19%), Staphylococcus aureus (six outbreaks, 19%), and Enterococcus (five outbreaks, 16%). Most outbreaks were reported from university (n = 8, 26%) and tertiary hospitals (n = 11, 55%), from South Africa (n = 9, 41%) and Tunisia (n = 4, 18%). Interventions to control the outbreaks were described in 27 (90%) outbreaks, and all instituted or recommended enhancing hand hygiene and education.

CONCLUSIONS

Few facilities in Africa reported HAI outbreaks over the 10-year period, suggesting substantial under-detection and under-reporting. The quality and timeliness of reporting require improvement to ensure changes in public health practice.

Carbapenem-resistant Enterobacterales bacteriuria and subsequent bacteremia: A population-based study

OBJECTIVE

To describe the epidemiology of carbapenem-resistant Enterobacterales (CRE) bacteriuria and to determine whether urinary catheters increase the risk of subsequent CRE bacteremia.

DESIGN

Using active population- and laboratory-based surveillance we described a cohort of patients with incident CRE bacteriuria and identified risk factors for developing CRE bacteremia within 1 year.

SETTING

The study was conducted among the 8 counties of Georgia Health District 3 (HD3) in Atlanta, Georgia.

PATIENTS

Residents of HD3 with CRE first identified in urine between 2012 and 2017.

RESULTS

We identified 464 patients with CRE bacteriuria (mean yearly incidence, 1.96 cases per 100,000 population). Of 425 with chart review, most had a urinary catheter (56%), and many resided in long-term care facilities (48%), had a Charlson comorbidity index >3 (38%) or a decubitus ulcer (37%). 21 patients (5%) developed CRE bacteremia with the same organism within 1 year. Risk factors for subsequent bacteremia included presence of a urinary catheter (odds ratio [OR], 8.0; 95% confidence interval [CI], 1.8-34.9), central venous catheter (OR, 4.3; 95% CI, 1.7-10.6) or another indwelling device (OR, 4.3; 95% CI, 1.6-11.4), urine culture obtained as an inpatient (OR, 5.7; 95% CI, 1.3-25.9), and being in the ICU in the week prior to urine culture (OR, 2.9; 95% CI, 1.1-7.8). In a multivariable analysis, urinary catheter increased the risk of CRE bacteremia (OR, 5.3; 95% CI, 1.2-23.6).

CONCLUSIONS

In patients with CRE bacteriuria, urinary catheters increase the risk of CRE bacteremia. Future interventions should aim to reduce inappropriate insertion and early removal of urinary catheters.

Genomic and Resistance Epidemiology of Gram-Negative Bacteria in Africa: a Systematic Review and Phylogenomic Analyses from a One Health Perspective

Antibiotic resistance (AR) is one of the major public health threats and challenges to effective containment and treatment of infectious bacterial diseases worldwide. Here, we used different methods to map out the geographical hot spots, sources, and evolutionary epidemiology of AR. Escherichia coli, Klebsiella pneumoniae, Salmonella enterica, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter spp., Neisseria meningitis/gonorrhoeae, Vibrio cholerae, Campylobacter jejuni, etc., were common pathogens shuttling AR genes in Africa. Transmission of the same clones/strains across countries and between animals, humans, plants, and the environment was observed. We recommend Enterobacter spp. or K. pneumoniae as better sentinel species for AR surveillance.

Antibiotic resistance (AR) remains a major threat to public and animal health globally. However, AR ramifications in developing countries are worsened by limited molecular diagnostics, expensive therapeutics, inadequate numbers of skilled clinicians and scientists, and unsanitary environments. The epidemiology of Gram-negative bacteria, their AR genes, and geographical distribution in Africa are described here. Data were extracted and analyzed from English-language articles published between 2015 and December 2019. The genomes and AR genes of the various species, obtained from the Pathosystems Resource Integration Center (PATRIC) and NCBI were analyzed phylogenetically using Randomized Axelerated Maximum Likelihood (RAxML) and annotated with Figtree. The geographic location of resistant clones/clades was mapped manually. Thirty species from 31 countries and 24 genera from 41 countries were analyzed from 146 articles and 3,028 genomes, respectively. Genes mediating resistance to β-lactams (including bla_TEM-1, bla_CTX-M, bla_NDM, bla_IMP, bla_VIM, and bla_OXA-48/181), fluoroquinolones (oqxAB, qnrA/B/D/S, gyrA/B, and parCE mutations, etc.), aminoglycosides (including armA and rmtC/F), sulfonamides (sul1/2/3), trimethoprim (dfrA), tetracycline [tet(A/B/C/D/G/O/M/39)], colistin (mcr-1), phenicols (catA/B, cmlA), and fosfomycin (fosA) were mostly found in Enterobacter spp. and Klebsiella pneumoniae, and also in Serratia marcescens, Escherichia coli, Salmonella enterica, Pseudomonas, Acinetobacter baumannii, etc., on mostly IncF-type, IncX_3/4, ColRNAI, and IncR plasmids, within IntI1 gene cassettes, insertion sequences, and transposons. Clonal and multiclonal outbreaks and dissemination of resistance genes across species and countries and between humans, animals, plants, and the environment were observed; Escherichia coli ST103, K. pneumoniae ST101, S. enterica ST1/2, and Vibrio cholerae ST69/515 were common strains. Most pathogens were of human origin, and zoonotic transmissions were relatively limited.

IMPORTANCE Antibiotic resistance (AR) is one of the major public health threats and challenges to effective containment and treatment of infectious bacterial diseases worldwide. Here, we used different methods to map out the geographical hot spots, sources, and evolutionary epidemiology of AR. Escherichia coli, Klebsiella pneumoniae, Salmonella enterica, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter spp., Neisseria meningitis/gonorrhoeae, Vibrio cholerae, Campylobacter jejuni, etc., were common pathogens shuttling AR genes in Africa. Transmission of the same clones/strains across countries and between animals, humans, plants, and the environment was observed. We recommend Enterobacter spp. or K. pneumoniae as better sentinel species for AR surveillance.

Metallo-β-Lactamases: Structure, Function, Epidemiology, Treatment Options, and the Development Pipeline

Modern medicine is threatened by the global rise of antibiotic resistance, especially among Gram-negative bacteria. Metallo-β-lactamase (MBL) enzymes are a particular concern and are increasingly disseminated worldwide, though particularly in Asia. Many MBL producers have multiple further drug resistances, leaving few obvious treatment options. Nonetheless, and more encouragingly, MBLs may be less effective agents of carbapenem resistance in vivo, under zinc limitation, than in vitro Owing to their unique structure and function and their diversity, MBLs pose a particular challenge for drug development. They evade all recently licensed β-lactam-β-lactamase inhibitor combinations, although several stable agents and inhibitor combinations are at various stages in the development pipeline. These potential therapies, along with the epidemiology of producers and current treatment options, are the focus of this review.

Predictive factors for sepsis by carbapenem resistant Gram-negative bacilli in adult critical patients in Rio de Janeiro: a case-case-control design in a prospective cohort study

Background

Studies have investigated risk factors for infections by specific species of carbapenem-resistant Gram-negative bacilli (CR-GNB), but few considered the group of GNB species and most of them were performed in the setting of bacteremia or hospital infection. This study was implemented to identify risk factors for sepsis by CR- and carbapenem-susceptible (CS) GNB in intensive care unit (ICU) patients to improve management strategies for CR-GNB sepsis.

Methods

We developed a case-case-control study from a prospective cohort of patients with systemic inflammatory response syndrome (SIRS), sepsis-2 or sepsis-3 criteria in which blood and other sample cultures were collected and antimicrobial therapy was instituted, in an adult clinical-surgical ICU, at tertiary public hospital in Rio de Janeiro, from August 2015 through March 2017.

Results

Among the total of 629 ICU admissions followed by 7797 patient-days, after applying inclusion and exclusion criteria we identified 184 patients who developed recurrent or single hospital-acquired sepsis. More than 90% of all evaluable cases of sepsis and 87% of control group fulfilled the modified sepsis-3 definition. Non-fermenting bacilli and ventilator-associated pneumonia predominated as etiology and source of CR-GNB sepsis. While Enterobacteriaceae and intra-abdominal surgical site plus urinary-tract infections prevailed in CS-GNB than CR-GNB sepsis. Carbapenemase production was estimated in 76% of CR-GNB isolates. Multivariate logistic regression analysis revealed previous infection (mostly hospital-acquired bacterial infection or sepsis) (OR = 4.28; 95% CI 1.77–10.35), mechanical ventilation (OR = 4.21; 95% CI 1.17–15.18), carbapenem use (OR = 3.42; 95% CI 1.37–8.52) and length of hospital stay (OR = 1.03; 95% CI 1.01–1.05) as independent risk factors for sepsis by CR-GNB. While ICU readmission (OR = 6.92; 95% CI 1.72–27.78) and nosocomial diarrhea (OR = 5.32; 95% CI 1.07–26.45) were factors associated with CS-GNB sepsis.

Conclusions

The investigation of recurrent and not only bacteremic episodes of sepsis was the differential of this study. The results are in agreement with the basic information in the literature. This may help improve management strategies and future studies on sepsis by CR-GNB.

Risk factors and epidemiologic predictors of blood stream infections with New Delhi Metallo-b-lactamase (NDM-1) producing Enterobacteriaceae

Carbapenem-resistant Enterobacteriaceae conferred by New Delhi metallo-b-lactamase (NDM-1) resistance mechanism are endemic in India and Southeast Asia. An understanding of risk factors for NDM-1 infections is necessary to guide prevention strategies. We performed a retrospective case-control study of patients admitted at Christian Medical College Hospital, Vellore, India between May 2010 and August 2014 with Klebsiella pneumoniae blood stream infection (BSI). We compared patients with BSI caused by NDM-1 producing strains to two control groups: BSI with other multidrug resistant (MDR) strains and BSI with pan-susceptible strains. The study groups were assessed for risk factors for the outcomes: (1) infection with any MDR strain compared to pan-susceptible; and, (2) infection with NDM-1 strain as compared with other MDR and (3) Mortality. A total of 101 patients with BSI with NDM-1 producing Klebsiella pneumoniae were matched to two groups of controls: 112 with non-NDM-1 MDR strains and 101 with pan-susceptible strains. Medical (OR 10.4) and neonatal (OR 0.7) ICU admission, central venous catheter placement (CVC, OR 7.4) predicted MDR BSI. Prior carbapenem use (OR 8.4) and CVC (OR 4.8) predicted acquisition of an NDM-1 strain. Significant predictors for mortality included ICU stay (OR 3.0), mechanical ventilation (OR 3.2), female gender (OR 2.2), diabetes (OR 0.4). CVC placement, prior carbapenem use and ICU admission were significantly associated with BSI with NDM-1 producing and other MDR strains.

Infection control and risk factors for acquisition of carbapenemase-producing enterobacteriaceae. A 5 year (2011-2016) case-control study

Background

Carbapenemase-producing enterobacteriaceae (CPE) are a major threat for severely ill patients. However, only limited data on the epidemiology and on evidence-based infection prevention and control measures are available. The aim of this study was to investigate the epidemiology of patients with CPE, characterizing the CPE isolates by their resistance mechanisms and genetic similarity, to explore risk factors for their acquisition, and to evaluate the effectiveness of the current CPE infection control measures.

Methods

A retrospective case-control study was performed using data from 2011 to 2016 in a 1800-bed academic hospital in Central Europe, where risk-based screening at patients´ admission is performed. Carbapenem resistance mechanisms of all carbapenem resistant enterobacteriaceae from patients admitted during this period were investigated. Clinical data of the CPE-positive patients were analysed and compared to a matched control group (case-control ratio of 1:3). We performed univariate and multivariate statistical analysis to identify risk factors for CPE acquisition.

Results

Of 621,623 admitted patients in the study period, 75 patients with carriage of carbapenem resistant enterobacteriaceae were included (0.12/1000 admittances). Carbapenemase-encoding genes were detected in 77.3% (58/75) of patients with carbapenem-resistant enterobacteriaceae. The enzyme blaOXA-48 was found in 34.5% (20/58), blaKPC in 29.3% (17/58), blaNDM enzymes in 20.7% (12/58) and blaVIM in 8.6% (5/58) of the isolates. The overall mortality among CPE patients was 25.9% (15/58) and attributable mortality of CPE was 53.3% (8/15). Multivariate analysis revealed four risk factors to be independent predictors of CPE carriage: the length of hospital admission > 20 days (AOR: 4.9, 95% CI: 1.4–15.5; P <  0.001), hospital admission within the previous year (AOR: 22.3, 95% CI: 3.9–88.4; P <  0.001), exposure to a healthcare facility in a country with high or unknown carbapenem-resistant enterobacteriaceae prevalence 3 months before admission (AOR: 11.8, 95% CI: 2.2–63.2; P <  0.01) and the use of antibiotics longer than 10 days (AOR: 5.2, 95% CI: 1.4–35.9; P <  0.05). The current risk-based screening strategy at hospital admission could not identify 37 (63.8%) of the 58 CPE-positive patients. Epidemiological investigation and genotyping revealed that no outbreaks due to CPE occurred during this period.

Conclusion

Overall, the CPE carriage rate in patients was very low, the attributable mortality, however, is alarming (53%). BlaOXA-48 and blaKPC were the main cause of carbapenem resistance in enterobacteriaceae. Although the strict application of standard infection control measures was effective for prevention of outbreaks in this setting, an enlarged risk based targeted screening strategy has to be implemented.

Indian consensus on the management of CRE infection in critically ill patients (ICONIC) - India

Background: The increasing burden of carbapenem-resistant Enterobacteriaceae (CRE) carriage and infection in different patient settings in India has created an acute need for guidance for clinicians regarding optimal strategies for the management of CRE infection in critically ill patients. Research design and methods: A multidisciplinary panel of 11 Indian experts in CRE infection assembled for comprehensive discussion and consensus development. The experts developed clinical statements through a systematic review of key literature. Main outcome measures: The panel voted anonymously on 60 clinically relevant questions, through a modified Delphi process. Results: Forty-six key clinical consensus statements (CCS) were proposed. The panel reached a consensus on several important issues, providing recommendations on surveillance, diagnosis, prevention, pharmacokinetic challenges, combination therapy, and cornerstone molecules in CRE infections. The panel also proposed a treatment algorithm for NDM-prevalent settings. Conclusion: These consensus statements may offer clinicians expert guidance on the management of CRE infections. There is a dearth of high-/moderate-level evidence on managing CRE infections; the recommendations presented herein are based on expert opinion.

Prevalence of Antibiotic and Heavy Metal Resistance Determinants and Virulence-Related Genetic Elements in Plasmids of Staphylococcus aureus

The use of antibiotics on a mass scale, particularly in farming, and their release into the environment has led to a rapid emergence of resistant bacteria. Once emerged, resistance determinants are spread by horizontal gene transfer among strains of the same as well as disparate bacterial species. Their accumulation in free-living as well as livestock and community-associated strains results in the widespread multiple-drug resistance among clinically relevant species posing an increasingly pressing problem in healthcare. One of these clinically relevant species is Staphylococcus aureus, a common cause of hospital and community outbreaks. Among the rich diversity of mobile genetic elements regularly occurring in S. aureus such as phages, pathogenicity islands, and staphylococcal cassette chromosomes, plasmids are the major mean for dissemination of resistance determinants and virulence factors. Unfortunately, a vast number of whole-genome sequencing projects does not aim for complete sequence determination, which results in a disproportionately low number of known complete plasmid sequences. To address this problem we determined complete plasmid sequences derived from 18 poultry S. aureus strains and analyzed the prevalence of antibiotic and heavy metal resistance determinants, genes of virulence factors, as well as genetic elements relevant for their maintenance. Some of the plasmids have been reported before and are being found in clinical isolates of strains typical for humans or human ones of livestock origin. This shows that livestock-associated staphylococci are a significant reservoir of resistance determinants and virulence factors. Nevertheless, nearly half of the plasmids were unknown to date. In this group we found a potentially mobilizable plasmid pPA3 being a unique example of accumulation of resistance determinants and virulence factors likely stabilized by a presence of a toxin–antitoxin system.

Emergence of New Delhi Metallo-β-Lactamase (NDM-5) in Klebsiella quasipneumoniae from Neonates in a Nigerian Hospital

Outbreaks of infection occur more often than they are reported in most developing countries, largely due to poor diagnostic services. A Klebsiella species bacteremia outbreak in a newborn unit with high mortality was recently encountered at a location being surveilled for childhood bacteremia. These surveillance efforts offered the opportunity to determine the cause of this neonatal outbreak. In this report, we present the whole-genome sequences of New Delhi metallo-β-lactamase (NDM-5)-containing Klebsiella quasipneumoniae subsp. similipneumoniae bloodstream isolates from a neonatal bacteremia outbreak at a tertiary hospital in Nigeria and as part of the largest collection of K. pneumoniae bloodstream isolates from children in Africa. Comparative analysis of the genetic environment surrounding the NDM-5 genes revealed nearly perfect sequence identity to blaNDM-5-bearing IncX3-type plasmids from other members of the EnterobacteriaceaeIMPORTANCE Carbapenem-resistant Klebsiella pneumoniae is of global health importance, yet there is a paucity of genome-based studies in Africa. Here we report fatal blood-borne NDM-5-producing K. quasipneumoniae subsp. similipneumoniae infections from Nigeria, Africa. New Delhi metallo-β-lactamase (NDM)-producing Klebsiella spp. are responsible for high mortality and morbidity, with the NDM-5 variant showing elevated carbapenem resistance. The prevalence of NDM-5 in Klebsiella has been limited primarily to K. pneumoniae, with only one isolate being collected from Africa. During an outbreak of sepsis in a teaching hospital in Nigeria, five NDM-5-producing K. quasipneumoniae subsp. similipneumoniae sequence type 476 isolates were identified. Given the increased resistance profile of these strains, this study highlights the emerging threat of blaNDM-5 dissemination in hospital environments. The observation of these NDM-5-producing isolates in Africa stresses the urgency to improve monitoring and clinical practices to reduce or prevent the further spread of resistance.

Systematic review in South Africa reveals antibiotic resistance genes shared between clinical and environmental settings

A systematic review was conducted to determine the distribution and prevalence of antibiotic-resistant bacteria (ARB), antimicrobial-resistant genes (ARGs), and antimicrobial-resistant gene determinants (ARGDs) in clinical, environmental, and farm settings and to identify key knowledge gaps in a bid to contain their spread. Fifty-three articles were included. The prevalence of a wide range of antimicrobial-resistant bacteria and their genes was reviewed. Based on the studies reviewed in this systematic review, mutation was found to be the main genetic element investigated. All settings shared 39 ARGs and ARGDs. Despite the fact that ARGs found in clinical settings are present in the environment, in reviewed articles only 12 were found to be shared between environmental and clinical settings; the inclusion of farm settings with these two settings increased this figure to 32. Data extracted from this review revealed farm settings to be one of the main contributors of antibiotic resistance in healthcare settings. ARB, ARGs, and ARGDs were found to be ubiquitous in all settings examined.

Estimating the burden of antimicrobial resistance: a systematic literature review

Background

Accurate estimates of the burden of antimicrobial resistance (AMR) are needed to establish the magnitude of this global threat in terms of both health and cost, and to paramaterise cost-effectiveness evaluations of interventions aiming to tackle the problem. This review aimed to establish the alternative methodologies used in estimating AMR burden in order to appraise the current evidence base.

Methods

MEDLINE, EMBASE, Scopus, EconLit, PubMed and grey literature were searched. English language studies evaluating the impact of AMR (from any microbe) on patient, payer/provider and economic burden published between January 2013 and December 2015 were included. Independent screening of title/abstracts followed by full texts was performed using pre-specified criteria. A study quality score (from zero to one) was derived using Newcastle-Ottawa and Philips checklists. Extracted study data were used to compare study method and resulting burden estimate, according to perspective. Monetary costs were converted into 2013 USD.

Results

Out of 5187 unique retrievals, 214 studies were included. One hundred eighty-seven studies estimated patient health, 75 studies estimated payer/provider and 11 studies estimated economic burden. 64% of included studies were single centre. The majority of studies estimating patient or provider/payer burden used regression techniques. 48% of studies estimating mortality burden found a significant impact from resistance, excess healthcare system costs ranged from non-significance to $1 billion per year, whilst economic burden ranged from $21,832 per case to over $3 trillion in GDP loss. Median quality scores (interquartile range) for patient, payer/provider and economic burden studies were 0.67 (0.56-0.67), 0.56 (0.46-0.67) and 0.53 (0.44-0.60) respectively.

Conclusions

This study highlights what methodological assumptions and biases can occur dependent on chosen outcome and perspective. Currently, there is considerable variability in burden estimates, which can lead in-turn to inaccurate intervention evaluations and poor policy/investment decisions. Future research should utilise the recommendations presented in this review.

Trial registration

This systematic review is registered with PROSPERO (PROSPERO CRD42016037510).

A Systematic Review and Meta-analyses of the Clinical Epidemiology of Carbapenem-Resistant Enterobacteriaceae

Carbapenem-resistant Enterobacteriaceae (CRE) are major health care-associated pathogens and responsible for hospital outbreaks worldwide. To prevent a further increase in CRE infections and to improve infection prevention strategies, it is important to summarize the current knowledge about CRE infection prevention in hospital settings. This systematic review aimed to identify risk factors for CRE acquisition among hospitalized patients. In addition, we summarized the environmental sources/reservoirs and the most successful infection prevention strategies related to CRE. A total of 3,983 potentially relevant articles were identified and screened. Finally, we included 162 studies in the systematic review, of which 69 studies regarding risk factors for CRE acquisition were included in the random-effects meta-analysis studies. The meta-analyses regarding risk factors for CRE acquisition showed that the use of medical devices generated the highest pooled estimate (odds ratio [OR] = 5.09; 95% confidence interval [CI] = 3.38 to 7.67), followed by carbapenem use (OR = 4.71; 95% CI = 3.54 to 6.26). To control hospital outbreaks, bundled interventions, including the use of barrier/contact precautions for patients colonized or infected with CRE, are needed. In addition, it is necessary to optimize the therapeutic approach, which is an important message to infectious disease specialists, who need to be actively involved in a timely manner in the treatment of patients with known CRE infections or suspected carriers of CRE.

Carbapenem-Resistant Enterobacteriaceae: A Strategic Roadmap for Infection Control

The incidence of carbapenem-resistant Enterobacteriaceae (CRE) has increased worldwide with great regional variability. Infections caused by these organisms are associated with crude mortality rates of up to 70%. The spread of CRE in healthcare settings is both an important medical problem and a major global public health threat. All countries are at risk of falling victim to the emergence of CRE; therefore, a preparedness plan is required to avoid the catastrophic natural course of this epidemic. Proactive and adequate preventive measures locally, regionally, and nationally are required to contain the spread of these bacteria. The keys to success in preventing the establishment of CRE endemicity in a region are early detection through targeted laboratory protocols and containment of spread through comprehensive infection control measures. This guideline provides a strategic roadmap for infection control measures based on the best available evidence and expert opinion, to enable preparation of a multifaceted preparedness plan to abort epidemics of CRE. Infect Control Hosp Epidemiol 2017;38:580-594.

Control of carbapenemase-producing Enterobacteriaceae outbreaks in acute settings: an evidence review

BACKGROUND

In recent years, infections with carbapenemase-producing Enterobacteriaceae (CPE) have been increasing globally and present a major public health challenge.

AIM

To review the international literature: (i) to describe CPE outbreaks in acute hospital settings globally; and (ii) to identify the control measures used during these outbreaks and report on their effectiveness.

METHODS

A systematic search of MEDLINE and EMBASE databases, abstract lists for key conferences and reference lists of key reviews was undertaken, and information on unpublished outbreaks was sought for 2000-2015. Where relevant, risk of bias was assessed using the Newcastle-Ottawa scale. A narrative synthesis of the evidence was conducted.

FINDINGS

Ninety-eight outbreaks were eligible. These occurred worldwide, with 53 reports from Europe. The number of cases (CPE infection or colonization) involved in outbreaks varied widely, from two to 803. In the vast majority of outbreaks, multi-component infection control measures were used, commonly including: patient screening; contact precautions (e.g. gowns, gloves); handwashing interventions; staff education or monitoring; enhanced environmental cleaning/decontamination; cohorting of patients and/or staff; and patient isolation. Seven studies were identified as providing the best-available evidence on the effectiveness of control measures. These demonstrated that CPE outbreaks can be controlled successfully using a range of appropriate, commonly used, infection control measures. However, risk of bias was considered relatively high for these studies.

CONCLUSION

The findings indicate that CPE outbreaks can be controlled using combinations of existing measures. However, the quality of the evidence base is weak and further high-quality research is needed, particularly on the effectiveness of individual infection control measures.

Current State of Resistance to Antibiotics of Last-Resort in South Africa: A Review from a Public Health Perspective

A review of the literature was undertaken to delineate the current level and mechanisms of resistance to carbapenems, colistin, and tigecycline in South Africa. Thirty-two English publications and 32 National Institute of Communicable Diseases communiqués identified between early January 2000 and 20 May, 2016 showed substantial reports of NDM (n = 860), OXA-48 (n = 584), VIM (n = 131), and IMP (n = 45) carbapenemases within this period, mainly in Klebsiella pneumoniae (n = 1138), Acinetobacter baumannii (n = 332), Enterobacter cloacae (n = 201), and Serratia marcescens (n = 108). Colistin and tigecycline resistance was prevalent among K. pneumoniae, A. baumannii, S. marcescens, and E. cloacae. The first mcr-1 colistin resistance gene to be detected in South Africa was reported in Escherichia coli from livestock as well as from hospitalized and outpatients. There are increasing reports of NDM and OXA-48 carbapenemases among Enterobacteriaceae and A. baumannii in South Africa. Mcr-1 is now present in South African patients and livestock. Resistance to carbapenems, colistin, and tigecycline restricts infection management options for clinicians.

An Irish outbreak of New Delhi metallo-β-lactamase (NDM)-1 carbapenemase-producing Enterobacteriaceae: increasing but unrecognized prevalence

BACKGROUND

Carbapenemase-producing Enterobacteriaceae (CPE) may cause healthcare-associated infections with high mortality rates. New Delhi metallo-β-lactamase-1 (NDM-1) is among the most recently discovered carbapenemases.

AIM

To report the first outbreak of NDM-1 CPE in Ireland, including microbiological and epidemiological characteristics, and assessing the impact of infection prevention and control measures.

METHODS

This was a retrospective microbiological and epidemiological review. Cases were defined as patients with a CPE-positive culture. Contacts were designated as roommates or ward mates.

FINDINGS

This outbreak involved 10 patients with a median age of 71 years (range: 45-90), located in three separate but affiliated healthcare facilities. One patient was infected (the index case); the nine others were colonized. Nine NDM-1-producing Klebsiella pneumoniae, an NDM-1-producing Escherichia coli and a K. pneumoniae carbapenemase (KPC)-producing Enterobacter cloacae were detected between week 24, 2014 and week 37, 2014. Pulsed-field gel electrophoresis demonstrated similarity. NDM-1-positive isolates were meropenem resistant with minimum inhibitory concentrations (MICs) ranging from 12 to 32 μg/mL. All were tigecycline susceptible (MICs ≤1 μg/mL). One isolate was colistin resistant (MIC 4.0 μg/mL; mcr-1 gene not detected). In 2015, four further NDM-1 isolates were detected.

CONCLUSION

The successful management of this outbreak was achieved via the prompt implementation of enhanced infection prevention and control practices to prevent transmission. These patients did not have a history of travel outside of Ireland, but several had frequent hospitalizations in Ireland, raising concerns regarding the possibility of increasing but unrecognized prevalence of NDM-1 and potential decline in value of travel history as a marker of colonization risk.

The global epidemiology of carbapenemase-producing Enterobacteriaceae

Carbapenemase-producing Enterobacteriaceae (CPE) are an important and increasing threat to global health. Both clonal spread and plasmid-mediated transmission contribute to the ongoing rise in incidence of these bacteria. Among the 4 classes of β-lactamases defined by the Ambler classification system, the carbapenemases that confer carbapenem resistance in Enterobacteriaceae belong to 3 of them: Class A (K. pneumoniae carbapenemases, KPC), Class B (metallo-β-lactamases, MBL including New Delhi metallo-β-lactamases, NDM) and Class D (OXA-48-like carbapenemases). KPC-producing CPE are the most commonly occurring CPE in the United States. MBL-producing CPE have been most commonly associated with the Indian Subcontinent as well as with specific countries in Europe, including Romania, Denmark, Spain, and Hungary. The epicenter of OXA-48-like-producing is in Turkey and surrounding countries. Detailed knowledge of the epidemiology and molecular characteristics of CPE is essential to stem the spread of these pathogens.

Global Dissemination of Carbapenemase-Producing Klebsiella pneumoniae: Epidemiology, Genetic Context, Treatment Options, and Detection Methods

The emergence of carbapenem-resistant Gram-negative pathogens poses a serious threat to public health worldwide. In particular, the increasing prevalence of carbapenem-resistant Klebsiella pneumoniae is a major source of concern. K. pneumoniae carbapenemases (KPCs) and carbapenemases of the oxacillinase-48 (OXA-48) type have been reported worldwide. New Delhi metallo-β-lactamase (NDM) carbapenemases were originally identified in Sweden in 2008 and have spread worldwide rapidly. In this review, we summarize the epidemiology of K. pneumoniae producing three carbapenemases (KPCs, NDMs, and OXA-48-like). Although the prevalence of each resistant strain varies geographically, K. pneumoniae producing KPCs, NDMs, and OXA-48-like carbapenemases have become rapidly disseminated. In addition, we used recently published molecular and genetic studies to analyze the mechanisms by which these three carbapenemases, and major K. pneumoniae clones, such as ST258 and ST11, have become globally prevalent. Because carbapenemase-producing K. pneumoniae are often resistant to most β-lactam antibiotics and many other non-β-lactam molecules, the therapeutic options available to treat infection with these strains are limited to colistin, polymyxin B, fosfomycin, tigecycline, and selected aminoglycosides. Although, combination therapy has been recommended for the treatment of severe carbapenemase-producing K. pneumoniae infections, the clinical evidence for this strategy is currently limited, and more accurate randomized controlled trials will be required to establish the most effective treatment regimen. Moreover, because rapid and accurate identification of the carbapenemase type found in K. pneumoniae may be difficult to achieve through phenotypic antibiotic susceptibility tests, novel molecular detection techniques are currently being developed.

New Delhi Metallo-β-Lactamase-Mediated Carbapenem Resistance: Origin, Diagnosis, Treatment and Public Health Concern

Objective:

To review the origin, diagnosis, treatment and public health concern of New Delhi metallo-β-lactamase (NDM)-producing bacteria.

Data Sources:

We searched database for studies published in English. The database of PubMed from 2007 to 2015 was used to conduct a search using the keyword term “NDM and Acinetobacter or Enterobacteriaceae or Pseudomonas aeruginosa.”

Study Selection:

We collected data including the relevant articles on international transmission, testing methods and treatment strategies of NDM-positive bacteria. Worldwide NDM cases were reviewed based on 22 case reports.

Results:

The first documented case of infection caused by bacteria producing NDM-1 occurred in India, in 2008. Since then, 13 blaNDM variants have been reported. The rise of NDM is not only due to its high rate of genetic transfer among unrelated bacterial species, but also to human factors such as travel, sanitation and food production and preparation. With limited treatment options, scientists try to improve available therapies and create new ones.

Conclusions:

In order to slow down the spread of these NDM-positive bacteria, a series of measures must be implemented. The creation and transmission of blaNDM are potentially global health issues, which are not issues for one country or one medical community, but for global priorities in general and for individual wound care practitioners specifically.