First description of bla(NDM-1), bla(OXA-48), bla(OXA-181) producing Enterobacteriaceae strains in Romania

Synergistic Combination of Aztreonam and Ceftazidime-Avibactam-A Promising Defense Strategy against OXA-48 + NDM Klebsiella pneumoniae in Romania

With the increasing burden of carbapenem-resistant Klebsiella pneumoniae (CR-Kp), including high rates of healthcare-associated infections, treatment failure, and mortality, a good therapeutic strategy for attacking this multi-resistant pathogen is one of the main goals in current medical practice and necessitates the use of novel antibiotics or new drug combinations.

OBJECTIVES

We reviewed the clinical and microbiological outcomes of seven patients treated at the "Agrippa Ionescu" Clinical Emergency Hospital between October 2023 and January 2024, aiming to demonstrate the synergistic activity of the ceftazidime-avibactam (C/A) plus aztreonam (ATM) combination against the co-producers of blaNDM + blaOXA-48-like CR-Kp.

MATERIAL AND METHODS

Seven CR-Kp with blaNDM and blaOXA-48 as resistance mechanisms were tested. Seven patients treated with C/A + ATM were included. The synergistic activity of C/A + ATM was proven through double-disk diffusion in all seven isolates. Resistance mechanisms like KPC, VIM, OXA-48, NDM, IMP, and CTX-M were assessed through immunochromatography.

RESULTS

With a mean of nine days of treatment with the synergistic combination C/A + ATM, all patients achieved clinical recovery, and five achieved microbiological recovery.

CONCLUSIONS

With the emerging co-occurrence of blaOXA-48 and blaNDM among Kp in Romania, the combination of C/A and ATM could be a promising therapeutic option.

Evolution of Antimicrobial Resistance in Klebsiella pneumoniae over 3 Years (2019-2021) in a Tertiary Hospital in Bucharest, Romania

BACKGROUND

The antimicrobial resistance (AMR) of Klebsiella pneumoniae recorded a steep upward trend over the last two decades, among which carbapenem-resistant Klebsiella pneumoniae (CRKP) is one of the most concerning strains considering the development and spread of AMR. The aim of this study was to analyze the evolution of AMR for Klebsiella pneumoniae and to describe the risk factors of AMR for Klebsiella pneumoniae, including the COVID-19 pandemic.

METHODS

We conducted a retrospective study on Klebsiella pneumoniae non-duplicative isolates collected from patients admitted to a tertiary hospital in Bucharest, Romania, from January 2019 to December 2021. We evaluated AMR changes by comparing resistance between 2019 and the mean of 2020-2021.

RESULTS

The rates of AMR increased for third-generation cephalosporins, carbapenems, aminoglycosides, fluoroquinolones, and colistin and decreased for trimethoprim/sulfamethoxazole (TMP/SMX), 45.7% in 2019 vs. 28.3% in 2021. A longer length of hospital stay (ꭓ2 = 49.68, p < 0.01); recent antibiotic consumption, RR = 1.38, 95% CI [1.21, 1.57]; and recent contact with hospital settings, RR = 1.54, 95% CI [1.32, 1.8] were risk factors for multidrug-resistant (MDR) Klebsiella pneumoniae.

CONCLUSIONS

The AMR of Klebsiella pneumoniae increased during 2020-2021 for most of the potential active antibiotics; only TMP/SMX resistance decreased, and it may represent a treatment option for CRKP or MDR Klebsiella pneumoniae infections. Decreasing the excessive use of antibiotics and the implementation of prevention and control measures in healthcare settings are mandatory for avoiding further increases in the AMR rate of Klebsiella pneumoniae.

Prevalence of carbapenem-resistant and extended-spectrum beta-lactamase-producing Enterobacteriaceae in a teaching hospital in Ghana

BACKGROUND

Carbapenem-resistant Enterobacteriaceae (CRE) and Extended-spectrum beta-lactamase (ESBL) production among Gram-negative Enterobacteriaceae is an increasing global challenge due to the high morbidity and mortality associated with their infections, especially in developing countries where there are little antibiotic treatment options. Despite these challenges, few studies in Ghana have described the burden of CRE. Therefore, this study aimed to determine the prevalence of carbapenem-resistant Enterobacteriaceae isolated from patients at the Cape Coast Teaching Hospital (CCTH) in the Central region of Ghana.

METHODOLOGY/PRINCIPAL FINDINGS

Enterobacteriaceae isolates were collected from April to July 2019 at the bacteriology unit of CCTH using a consecutive sampling method. Isolates were identified by standard microbiological techniques and confirmed using API 20E. Kirby Bauer disc diffusion method was used to determine the antibiogram of isolates. Isolates were also subjected to ESBL testing using the single-disc combination method. Carbapenem-resistant isolates were identified by the Kirby Bauer disc diffusion method and then examined genotypically for the presence of blaKPC-1, blaIMP-1, blaVIM-1, blaNDM-1, and blaOXA-48 genes via polymerase chain reaction (PCR). Of the 230 isolates comprising E. coli (40.9%), Citrobacter spp. (32.6%), K. pneumoniae (9.1%), P. mirabilis (6.1%), P. vulgaris (5.2%), Enterobacter spp (3.5%)., K. oxytoca (2.2%), and Serratia marcenses (0.4%). Most isolates were from urine 162(70.4%) and wound samples. The isolates showed high resistance to ampicillin 171 (74.3%) and cefuroxime 134(58.3%). The prevalence of MDR was 35.2% (81), with E. coli 40(42.6%) being the majority that exhibited MDR. Of the 230 isolates, 113(49.1%) were ESBL producers, with E. coli 54(57.5%) accounting for the majority, while Serratia marcenses was the least. Of the 13 (5.7%) CRE isolates that showed resistance towards carbapenem in the disc diffusion method, 11 showed the presence of the blaNDM-1 gene, while all isolates showed the presence of the blaOXA-48 gene.

CONCLUSION

The prevalence of carbapenem resistance and ESBL-producing Enterobacteriaceae pathogens among patients at the Cape Coast Teaching Hospital is high and alarming. Therefore, it is imperative to consider effective infection prevention and control measures should be implemented at the hospital to prevent the rapid spread of these dangerous organisms.

Antimicrobial Resistance in Romania: Updates on Gram-Negative ESCAPE Pathogens in the Clinical, Veterinary, and Aquatic Sectors

Multidrug-resistant Gram-negative bacteria such as Acinetobacter baumannii, Pseudomonas aeruginosa, and members of the Enterobacterales order are a challenging multi-sectorial and global threat, being listed by the WHO in the priority list of pathogens requiring the urgent discovery and development of therapeutic strategies. We present here an overview of the antibiotic resistance profiles and epidemiology of Gram-negative pathogens listed in the ESCAPE group circulating in Romania. The review starts with a discussion of the mechanisms and clinical significance of Gram-negative bacteria, the most frequent genetic determinants of resistance, and then summarizes and discusses the epidemiological studies reported for A. baumannii, P. aeruginosa, and Enterobacterales-resistant strains circulating in Romania, both in hospital and veterinary settings and mirrored in the aquatic environment. The Romanian landscape of Gram-negative pathogens included in the ESCAPE list reveals that all significant, clinically relevant, globally spread antibiotic resistance genes and carrying platforms are well established in different geographical areas of Romania and have already been disseminated beyond clinical settings.

The threat of carbapenem resistance in Eastern Europe in patients with decompensated cirrhosis admitted to intensive care unit

BACKGROUND

Multidrug-resistant organisms are an increasing concern in patients with decompensated cirrhosis.

AIM

We aimed to evaluate the prevalence of infections with carbapenem-resistant Enterobacteriaceae in patients with decompensated cirrhosis.

METHODS

Patients with decompensated cirrhosis admitted to ICU were included. The isolated Enterobacteriaceae strains were tested for carbapenemase-producing genes using the Roche LightMix® Modular VIM/IMP/NDM/GES/KPC/OXA48-carbapenemase detection kit.

RESULTS

48 culture-positive infections were registered in 75 patients with acutely decompensated cirrhosis. Thirty patients contracted a second infection. 46% of bacteria isolated at admission and 60% of bacteria responsible for infections identified during ICU-stay were multiresistant. ESBL+ Enterobacteriaceae were predominant at admission, while carbapenem-resistance was dominant in both Enterobacteriaceae and Non-Fermenting-Gram-Negative Bacteria responsible for infections diagnosed during hospitalisation. OXA 48 or KPC type carbapenemases were present in 30% of the analyzed Enterobacteriaceae and in 40% of the phenotypically carbapenem-resistant Klebsiella pneumoniae strains. The length of ICU stay was a risk-factor for a second infection (p=0.04). Previous carbapenem usage was associated with occurence of infections with carbapenem-resistant Gram-negative bacteria during hospitalization (p=0.03).

CONCLUSION

The prevalence of infections with carbapenem-resistant Enterobacteriaceae is high in patients with decompensated cirrhosis admitted to ICU. Carbapenemase-producing genes in Enterobacteriaceae in our center are bla_OXA-48 and bla_KPC.

Characterization of Carbapenemase-Producing Klebsiella pneumoniae Isolates from Two Romanian Hospitals Co-Presenting Resistance and Heteroresistance to Colistin

Klebsiella pneumoniae is a notorious human pathogen involved in healthcare-associated infections. The worldwide expansion of infections induced by colistin-resistant and carbapenemase-producing Enterobacterales (CPE) isolates has been increasingly reported. This study aims to analyze the phenotypic and molecular profiles of 10 colistin-resistant (CR) isolates and 2 pairs of colistin-heteroresistant (ChR) (parental and the corresponding resistant mutants) isolates of K. pneumoniae CPE sourced from two hospitals. The phenotypes of strains in the selected collection had been previously characterized. Antimicrobial susceptibility testing was performed using a Vitek 2 Compact system (BioMérieux SA, Marcy l’Etoile, France), the disc diffusion method, and broth microdilution (BMD) for colistin. Whole-genome sequencing (WGS) did not uncover evidence of any mobile colistin resistance (mcr) genes, although the mgrB gene of seven isolates appeared to be disrupted by insertion sequences (ISKpn25 or ISKpn26). Possible deleterious missense mutations were found in phoP (L4F), phoQ (Q426L, L26Q, L224Q, Q317K), pmrB (R256G, P95L, T157P, V352E), and crrB (P151S) genes. The identified isolates belonged to the following clonal lineages: ST101 (n = 6), ST147 (n = 5), ST258 (n = 2), and ST307 (n = 1). All strains harbored IncF plasmids. OXA-48 producers carried IncL and IncR plasmids, while one blaNDM-1 genome was found to harbor IncC plasmids. Ceftazidime–avibactam remains a therapeutic option for KPC-2 and OXA-48 producers. Resistance to meropenem–vaborbactam has emerged in some blakPC-2-carrying isolates. Our study demonstrates that the results of WGS can provide essential evidence for the surveillance of antimicrobial resistance.

Aeromonas dhakensis: Clinical Isolates with High Carbapenem Resistance

Aeromonas dhakensis is ubiquitous in aquatic habitats and can cause life-threatening septicaemia in humans. However, limited data are available on their antimicrobial susceptibility testing (AST) profiles. Hence, we aimed to examine their AST patterns using clinical (n = 94) and non-clinical (n = 23) isolates with dehydrated MicroScan microdilution. Carbapenem resistant isolates were further screened for genes related to carbapenem resistance using molecular assay. The isolates exhibited resistance to imipenem (76.9%), doripenem (62.4%), meropenem (41.9%), trimethoprim/sulfamethoxazole (11.1%), cefotaxime (8.5%), ceftazidime (6%), cefepime (1.7%) and aztreonam (0.9%), whereas all isolates were susceptible to amikacin. Clinical isolates showed significant association with resistance to doripenem, imipenem and meropenem compared to non-clinical isolates. These blacphA were detected in clinical isolates with resistance phenotypes: doripenem (67.2%, 45/67), imipenem (65.9%, 54/82) and meropenem (65.2%, 30/46). Our findings showed that the MicroScan microdilution method is suitable for the detection of carbapenem resistance in both clinical (48.9-87.2%) and non-clinical (4.3-13.0%) isolates. This study revealed that A. dhakensis isolates had relatively high carbapenem resistance, which may lead to potential treatment failure. Continued monitoring of aquatic sources with a larger sample size should be carried out to provide further insights.

Carbapenem resistance determinants in Klebsiella pneumoniae strains isolated from blood cultures-comparative analysis of molecular and phenotypic methods

Introduction: This study provides data on carbapenemases identified in carbapenem-resistant Klebsiella pneumoniae (CR-KP) isolated from blood-cultures by the multiplex molecular method.

Material and method: Between October 2016 and September 2017, 47 non-duplicate Klebsiella pneumoniae (KP) were isolated from blood cultures, from hospitalized patients in the Regional Institute of Gastroenterology and Hepathology, Cluj-Napoca, Romania. Identification and antimicrobial susceptibility tests (AST) were performed by Vitek 2 Compact. The combination disks test (CDT) was used for phenotypic analysis and the LightCycler® Multiplex DNA assay was used to detect and identify the carbapenemases by the LightCycler®z 480 Instrument. The following targets were chosen: blaKPC, blaNDM, blaGES, blaIMP and blaOXA-48 genes and the Cobas® 4800 software variant 2.2.0 was used for the results interpretation.

Results: Taking into consideration the meropenem minimum inhibitory concentration (MIC), 29 KP were susceptible and 18 were not-susceptible (MIC≥0.5 µg ml-1). In the CR-KP group, the CDT identified OXA-48 (10/18) and KPC (7/18) producers. One isolate showed a noninterpretable profile. The multiplex molecular analyses confirmed the carbapenemases production as: 9 CR-KP were KPC and OXA-48 co-producers, 8 were OXA-48 and one was KPC producing strains. In CR-KP group, we found a significant correlation between the CDT and RT-PCR tests results, concerning KPC (p = 0.671). Eight phenotypic results were confirmed by molecular Light-Cycler® Multiplex DNA assay. For CR-KP co-producers (KPC and OXA-48), the CDT could indicate only one carbapenem-hydrolyzing enzyme.

Conclusion: This study highlights the CR-KP co-producers (OXA-48 and KPC). OXA-48-like is more frequently encountered in our area than other carbapenemases.

Five-Year Survey of Asymptomatic Colonization with Multidrug-Resistant Organisms in a Romanian Tertiary Care Hospital

Purpose

To determine the rate of carriage of multidrug-resistant organisms (MDROs) between 2015 and 2019 among patients admitted to the National Institute of Infectious Diseases “Prof. Dr. Matei Balș,” from Bucharest, Romania.

Methods

Nasal, throat, and rectal/perirectal screening swabs were collected either immediately or during the first 24 hours of admission and sent to the microbiology laboratory where the following MDROs were identified: methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant enterococci (VRE), extended-spectrum β-lactamase (ESBL)-producing Enterobacterales, carbapenem-resistant/carbapenemase-producing Enterobacterales (CRE/CPE), multidrug-resistant/extended drug-resistant Acinetobacter baumannii (MDR/XDR-AB), and multidrug-resistant/extended drug-resistant Pseudomonas aeruginosa (MDR/XDR-PA).

Results

A total of 5083 unique patients were screened for MRSA and 5008 for VRE, ESBL/CRE/CPE, MDR/XDR-AB, and MDR/XDR-PA. MRSA was detected in 8.24% of patients, VRE in 17.67%, ESBL Enterobacterales in 25.85%, and CPE in 6.13%. MDR/XDR-AB was found in 1.59% and MDR/XDR-PA in 1.91% of patients. The rates of carriage increased between 2015 and 2019 for MRSA (7.23–7.6%), VRE (9–16.68%), CPE (1.15–6.77%), MDR/XDR-PA (1.15–1.91%), and MDR/XDR-AB (1.15–2.04%). OXA-48-type carbapenemase was predominant in Klebsiella pneumoniae (68.62%) and Escherichia coli (89.47%). CPE bacteria other than Klebsiella pneumoniae and Escherichia coli identified in our study carried mostly metallo-beta-lactamase (n = 28, 84.85%).

Conclusion

In this study, 37% of the unique patients screened over five years were found to be MDRO carriers. The proportion of VRE and CPE rectal carriers increased significantly between 2015 and 2019. The most frequently isolated carbapenemase was the OXA-48 type.

Comparison of Six Phenotypic Assays with Reference Methods for Assessing Colistin Resistance in Clinical Isolates of Carbapenemase-Producing Enterobacterales: Challenges and Opportunities

The global escalation of severe infections due to carbapenemase-producing Enterobacterales (CPE) isolates has prompted increased usage of parenteral colistin. Considering the reported difficulties in assessing their susceptibility to colistin, the purpose of the study was to perform a comparative evaluation of six phenotypic assays—the colistin broth disc elution (CBDE), Vitek 2 Compact (bioMérieux SA, Marcy l’Etoile, France), the Micronaut MIC-Strip Colistin (Merlin Diagnostika GMBH, Bornheim-Hensel, Germany), the gradient diffusion strip Etest (bioMérieux SA, Marcy l’Etoile, France), ChromID Colistin R Agar (COLR) (bioMérieux SA, Marcy l’Etoile, France), and the Rapid Polymyxin NP Test (ELITechGroup, Signes, France)—versus the reference method of broth microdilution (BMD). All false resistance results were further assessed using population analysis profiling (PAP). Ninety-two nonrepetitive clinical CPE strains collected from two hospitals were evaluated. The BMD confirmed 36 (39.13%) isolates susceptible to colistin. According to the BMD, the Micronaut MIC-Strip Colistin, the CBDE, and the COLR medium exhibited category agreement (CA) of 100%. In comparison with the BMD, the highest very major discrepancy (VMD) was noted for Etest (n = 15), and the only false resistance results were recorded for the Rapid Polymyxin NP Test (n = 3). Only the PAP method and the Rapid Polymyxin NP Test were able to detect heteroresistant isolates (n = 2). Thus, there is an urgent need to further optimize the diagnosis strategies for colistin resistance.

Association of Proteus mirabilis and Providencia stuartii Infections with Diabetes

Background and Objectives: Proteus and Providencia are related genera of opportunistic pathogens belonging to the Morganellaceae family, often a cause of infections in the immunocompromised hosts, such as diabetic patients. Their clinical significance has increased due to their intrinsic resistance to polymyxins, which is often associated with acquired resistance mechanisms. In this study we evaluated the infections caused by Proteus mirabilis and Providencia stuartii in two groups of patients, with diabetes (group 1) and without diabetes (group 2) admitted to the intensive care unit and surgical wards. The infections were investigated in terms of infection type, risk factors, clinical course, predictive factors for unfavourable outcomes and antibiotic resistance profile. Materials and Methods: An observational, retrospective, cross-sectional study was conducted, comprising all patients infected with these pathogens. Bacterial identification and antibiotic sensitivity testing were performed using the Vitek2C automated system. Results: Comparison of the two groups showed that the statistically significant common infectious risk factors were found less frequently among diabetic patients when compared with non-diabetic patients, and that antimicrobial resistance was significantly lower in the diabetic patient group. However, survival rates did not differ between the two groups, drawing attention to the implications of diabetes as comorbidity. Additionally, with regard to the antibiotic resistance profile, 38.89% of P. stuartii strains isolated from diabetic patients belonged to the difficult-to-treat (DTR) phenotype, contributing to the severity of these infections compared with those caused by P. mirabilis, of which 32% were wild type strains and 0% were DTR phenotype. The DTR/extended spectrum beta-lactamase producing P. stuartii isolates more than doubled the risk of mortality, while the presence of nasogastric nutrition tripled the risk. Conclusions: P. stuartii infections that occurred in diabetic patients proved to be more difficult to treat, the majority of them being healthcare-associated bacteremias.

Health Care-Acquired Infections in Low- and Middle-Income Countries and the Role of Infection Prevention and Control

Health care-associated infections (HAIs) account for many morbidity and mortality worldwide, with disproportionate adverse effects in low- and middle-income countries (LMIC). Many factors contribute to the impact in LMIC, including lack of infrastructure, inconsistent surveillance, deficiency in trained personnel and infection control programs, and poverty-related factors. Therefore, optimal approaches must be tailored for LMIC and balance effectiveness and cost in the control of HAIs.

Multidrug Resistant Klebsiella pneumoniae ST101 Clone Survival Chain From Inpatients to Hospital Effluent After Chlorine Treatment

In this paper we describe the transmission of a multi-drug resistant Klebsiella pneumoniae ST101 clone from hospital to wastewater and its persistence after chlorine treatment. Water samples from influents and effluents of the sewage tank of an infectious diseases hospital and clinical strains collected from the intra-hospital infections, during a period of 10 days prior to wastewater sampling were analyzed. Antibiotic resistant K. pneumoniae strains from wastewaters were recovered on selective media. Based on antibiotic susceptibility profiles and PCR analyses of antibiotic resistance (AR) genetic background, as well as whole-genome sequencing (Illumina MiSeq) and subsequent bioinformatic analyses, 11 ST101 K. pneumoniae strains isolated from hospital wastewater influent, wastewater effluent and clinical sector were identified as clonally related. The SNP and core genome analyses pointed out that five strains were found to be closely related (with ≤18 SNPs and identical cgMLST profile). The strains belonging to this clone harbored multiple acquired AR genes [bla_CTX–M–15, bla_OXA–48, bla_OXA–1, bla_SHV–106, bla_TEM–150, aac(3)-IIa, aac(6′)-Ib-cr, oqxA10, oqxB17, fosA, catB3, dfrA14, tet(D)] and chromosomal mutations involved in AR (ΔmgrB, ΔompK35, amino acid substitutions in GyrA Ser83Tyr, Asp87Asn, ParC Ser80Tyr). Twenty-nine virulence genes involved in iron acquisition, biofilm and pili formation, adherence, and the type six secretion system – T6SS-III were identified. Our study proves the transmission of MDR K. pneumoniae from hospital to the hospital effluent and its persistence after the chlorine treatment, raising the risk of surface water contamination and further dissemination to different components of the trophic chain, including humans.

Distribution of NDM1 Carbapenemase-Producing Proteeae Strains on High-Risk Hospital Wards

Background

Carbapenem-resistant Proteeae (CRP) is a group of multidrug-resistant (MDR) microorganisms that raise special treatment problems due to their intrinsic resistance to colistin. In this study, our aim is to provide a phenotypic and molecular characterization of the carbapenemases secreted by CRP strains isolated from inpatients from an intensive care unit (ICU) and surgical wards, as well as the identification of the risk factors involved in their acquisition.

Methods

An observational, cross-sectional study was performed which included all Proteeae strains isolated in samples from inpatients on high-risk wards of the largest university hospital in Western Romania, from July 2017 to April 2019. Meropenem-resistant strains (N=65) with MIC ≥16 µg/mL were subjected to a singleplex PCR assay for the detection of blaNDM, blaVIM and blaCTX-M genes. The analysis of risk factors was performed by logistic regression.

Results

Out of 8317 samples that were processed, 400 Proteeae strains were isolated: 64% belonging to the genus Proteus, 26.75% to the genus Providencia and 9.25% to the genus Morganella. Most CRP strains (N=56) were of MBL type, and 55 had the blaNDM gene as the prevalent gene substrate. P. stuartii was the main species that provided the circulating MDR strains. Most CRP strains came from patients admitted to ICU, being isolated mainly from bronchial aspirates and blood cultures. Multivariate analysis revealed 3 independent risk factors – mechanical ventilation>96h (HR: 40.51 [13.65–120.25], p <0.001), tracheostomy (HR: 2.65 [1.14–6.17], p = 0.024) and prolonged antibiotic therapy (HR: 1.01 [1.00–1.02], p = 0.03).

Conclusion

There is a significant increase in the incidence of CR P. stuartii strains, the MBL-blaNDM type being predominant. These strains presented various other resistance mechanisms, being often extremely difficult to treat and led to an excess of lethality of 27.16%.

Molecular epidemiology and the clinical impact of carbapenemase-producing Enterobacterales isolates among adult patients: aspects from a Romanian non-teaching hospital

Introduction: A dramatic increase of infections induced by carbapenemase-producing Enterobacterales (CPE) has been registered worldwide. The aim of this study was to evaluate the molecular epidemiology and the clinical impact of CPE strains isolated from adult inpatients.

Material and methods: A one-year, single-center, retrospective observational study including 34 consecutive patients with 37 non-duplicate CPE strains recovered from clinical specimens was accomplished. The Vitek 2 Compact, M.I.C.Evaluator strips, the modified carbapenem inactivation method (mCIM), and the combination disks test (KPC, MBL, OXA-48 Confirm kit, Rosco Diagnostica) were applied as phenotypic tests. A multiplex polymerase chain reaction (PCR) assay was used for detection of blaKPC, blaNDM, and blaOXA-48-like genes. The clonality was assessed with pulsed-field gel electrophoresis (PFGE).

Results: Klebsiella pneumoniae (n=25) was the most frequent CPE encountered. The carbapenemase types were NDM (n=13), KPC (n=12), and OXA-48-like (n=12). Two distinct clonal clusters were identified among the 12 KPC positive strains. All CPE isolates exhibited non-susceptibility to carbapenems, cephalosporins, ciprofloxacin. Respiratory tract infections (n=16) and hospitalization in the intensive care unit (ICU) (n=14) were dominant. The most common comorbidity was congestive heart failure (n=11). Monotherapy was the main strategy adopted (n=15). Death occurred in 18 patients.

Conclusions: Our analysis underscores the scarcity of antibiotic solutions and high mortality. Monotherapy for urinary tract infections (UTIs) is beneficial. Inter- or intrahospital dissemination of successful epidemic clones is proved. The adequate CPE infections control programs and antimicrobial policies are essential..

Carbapenemase Producing Enterobacterales in Romania: Investigating the Origins

Carbapenemase-producing Enterobacterales (CPE) have emerged and spread in Romania since 2010. According to the reports of the EuSPACE (European survey of carbapenemase-producing Enterobacteriaceae) the epidemio-logical stage of the CPE expansion in Romania has shifted from sporadic occurrence in 2013 directly to inter-regional spread in 2014-2015. In this study we aimed to provide data from the timeframe when the dissemination of the carbapenemase genes in Romania began, by retrospectively analyzing CPE strains in a tertiary care university hospital. During the period of November 2012 – October 2013 we found 107 CPE (8.78%) out of 1219 non-duplicate Enterobacterales strains. 26 isolates of various Enterobacterales species carried blaNDM-1, 83 Klebsiella pneumoniae strains were positive for blaOXA-48-like and 2 of these co-harboured blaNDM-1. The increased incidence of OXA-48 producing K. pneumoniae was linked to a two-peaked hospital outbreak during February and May 2013. The percentage of 24.3% of NDM-1 producers was alarming due to the diversity of involved species and the higher resistance levels to carbapenems compared with blaOXA-48-like gene carriers. Plasmid replicon typing revealed a great diversity of plasmids in NDM-1-positive strains, belonging to incompatibility groups A/C, FII, FIIk, HI2, L and M. The strong connection between certain plasmid groups and host species suggests that the transfer of broad host-range plasmids through conjugation does not play the main role in the successful spread of blaNDM-1 among Enterobacterales species.

Integrating whole-genome sequencing within the National Antimicrobial Resistance Surveillance Program in the Philippines

National networks of laboratory-based surveillance of antimicrobial resistance (AMR) monitor resistance trends and disseminate these data to AMR stakeholders. Whole-genome sequencing (WGS) can support surveillance by pinpointing resistance mechanisms and uncovering transmission patterns. However, genomic surveillance is rare in low- and middle-income countries. Here, we implement WGS within the established Antimicrobial Resistance Surveillance Program of the Philippines via a binational collaboration. In parallel, we characterize bacterial populations of key bug-drug combinations via a retrospective sequencing survey. By linking the resistance phenotypes to genomic data, we reveal the interplay of genetic lineages (strains), AMR mechanisms, and AMR vehicles underlying the expansion of specific resistance phenotypes that coincide with the growing carbapenem resistance rates observed since 2010. Our results enhance our understanding of the drivers of carbapenem resistance in the Philippines, while also serving as the genetic background to contextualize ongoing local prospective surveillance.

Whole genome sequencing snapshot of multi-drug resistant Klebsiella pneumoniae strains from hospitals and receiving wastewater treatment plants in Southern Romania

We report on the genomic characterization of 47 multi-drug resistant, carbapenem resistant and ESBL-producing K. pneumoniae isolates from the influent (I) and effluent (E) of three wastewater treatment plants (WWTPs) and from Romanian hospital units which are discharging the wastewater in the sampled WWTPs. The K. pneumoniae whole genome sequences were analyzed for antibiotic resistance genes (ARGs), virulence genes and sequence types (STs) in order to compare their distribution in C, I and E samples. Both clinical and environmental samples harbored prevalent and widely distributed ESBL genes, i.e. bla_SHV, bla_OXA, bla_TEM and bla_{CTX M}. The most prevalent carbapenemase genes were bla_NDM-1, bla_OXA-48 and bla_KPC-2. They were found in all types of isolates, while bla_OXA-162, a rare bla_OXA-48 variant, was found exclusively in water samples. A higher diversity of carbapenemases genes was seen in wastewater isolates. The aminoglycoside modifying enzymes (AME) genes found in all types of samples were aac(6’), ant(2'')Ia, aph(3'), aaD, aac(3) and aph(6). Quinolone resistance gene qnrS1 and the multi-drug resistance oqxA/B pump gene were found in all samples, while qnrD and qnrB were associated to aquatic isolates. The antiseptics resistance gene qacEdelta1 was found in all samples, while qacE was detected exclusively in the clinical ones. Trimethroprim-sulfamethoxazole (dfrA, sul1 and sul2), tetracyclines (tetA and tetD) and fosfomycin (fosA6, known to be located on a transpozon) resistance genes were found in all samples, while for choramphenicol and macrolides some ARGs were detected in all samples (catA1 and catB3 / mphA), while other (catA2, cmIA5 and aac(6’)Ib / mphE and msrE) only in wastewater samples. The rifampin resistance genes arr2 and 3 (both carried by class I integrons) were detected only in water samples. The highly prevalent ARGs preferentially associating with aquatic versus clinical samples could ascribe potential markers for the aquatic (bla_SHV-145, qacEdelta1, sul1, aadA1, aadA2) and clinical (bla_OXA-1, bla_SHV-106,bla_TEM-150, aac(3)Iia, dfrA14, oqxA10; oqxB17,catB3, tetD) reservoirs of AR. Moreover, some ARGs (oqxA10; bla_SHV-145; bla_SHV-100, aac(6')Il, aph(3')VI, armA, arr2, cmlA5, bla_CMY-4, mphE, msrE, oqxB13, bla_OXA-10) showing decreased prevalence in influent versus effluent wastewater samples could be used as markers for the efficiency of the WWTPs in eliminating AR bacteria and ARGs. The highest number of virulence genes (75) was recorded for the I samples, while for E and C samples it was reduced to half. The most prevalent belong to three functional groups: adherence (fim genes), iron acquisition (ent, fep, fyu, irp and ybt genes) and the secretion system (omp genes). However, none of the genes associated with hypervirulent K. pneumoniae have been found. A total of 14 STs were identified. The most prevalent clones were ST101, ST219 in clinical samples and ST258, ST395 in aquatic isolates. These STs were also the most frequently associated with integrons. ST45 and ST485 were exclusively associated with I samples, ST11, ST35, ST364 with E and ST1564 with C samples. The less frequent ST17 and ST307 aquatic isolates harbored bla_OXA-162, which was co-expressed in our strains with bla_CTX-M-15 and bla_OXA-1.

Contribution of acrB upregulation & OmpC/Ompk36 loss over the presence of blaNDM towards carbapenem resistance development among pathogenic Escherichia coli & Klebsiella spp

Background & objectives:

The global spread of carbapenem-resistant Enterobacteriaceae (CRE) is an emerging clinical problem. Hence, in this study, the plausible role of extended-spectrum beta-lactamases (ESBLs)/carbapenemases, OmpC/Ompk36, acrB and their combinations was explored among CRE.

Methods:

The minimum inhibitory concentration (MIC) of meropenem, enzyme-phenotypes (ESBLs/IR and metallo-beta-lactamase (MBL)/non-MBL carbapenemase), genotypes (bla_TEM,bla_SHV and bla_CTX-M; bla_NDM and bla_VIM;bla_KPC and bla_OXA-48-like variants), acrB and outer membrane protein (OMP) expressions were analyzed with a total of 101 non-duplicate clinical isolates, obtained from various samples of patients visiting two tertiary care units of Eastern India during May 2013 - October 2016. This included Escherichia coli (n=36) and Klebsiella pneumoniae (n=65), categorized into two groups, namely Group I (resistant to all carbapenems; n=93; E. coli=34 and Klebsiella spp.=59) and Group II (non-resistant to all the carbapenems; n=8; E. coli=2 and Klebsiella spp.=6).

Results:

Though 88.17 per cent of Group I isolates exhibited ESBL property, the presence of carbapenemase activity (70.96%) and that of bla_NDM gene (42/66: 63.63%) indicated their contributions towards the emergence of CRE. Further, porin loss and/or efflux pump activation among ESBL/carbapenemase-producing isolates heightened the MIC of meropenem from 64 to 256 mg/l (range exhibited by only ESBL/carbapenemase-producing isolates) to >256 mg/l.

Interpretation & conclusions:

These findings implied the major contribution of porin loss and/or efflux pump activation over the presence of ESBLs/carbapenemases in imparting carbapenem resistance in pathogenic bacteria.

The Global Ascendency of OXA-48-Type Carbapenemases

Surveillance studies have shown that OXA-48-like carbapenemases are the most common carbapenemases in Enterobacterales in certain regions of the world and are being introduced on a regular basis into regions of nonendemicity, where they are responsible for nosocomial outbreaks. OXA-48, OXA-181, OXA-232, OXA-204, OXA-162, and OXA-244, in that order, are the most common enzymes identified among the OXA-48-like carbapenemase group. OXA-48 is associated with different Tn1999 variants on IncL plasmids and is endemic in North Africa and the Middle East. OXA-162 and OXA-244 are derivatives of OXA-48 and are present in Europe. OXA-181 and OXA-232 are associated with ISEcp1, Tn2013 on ColE2, and IncX3 types of plasmids and are endemic in the Indian subcontinent (e.g., India, Bangladesh, Pakistan, and Sri Lanka) and certain sub-Saharan African countries. Overall, clonal dissemination plays a minor role in the spread of OXA-48-like carbapenemases, but certain high-risk clones (e.g., Klebsiella pneumoniae sequence type 147 [ST147], ST307, ST15, and ST14 and Escherichia coli ST38 and ST410) have been associated with the global dispersion of OXA-48, OXA-181, OXA-232, and OXA-204. Chromosomal integration of bla _OXA-48 within Tn6237 occurred among E. coli ST38 isolates, especially in the United Kingdom. The detection of Enterobacterales with OXA-48-like enzymes using phenotypic methods has improved recently but remains challenging for clinical laboratories in regions of nonendemicity. Identification of the specific type of OXA-48-like enzyme requires sequencing of the corresponding genes. Bacteria (especially K. pneumoniae and E. coli) with bla _OXA-48, bla _OXA-181, and bla _OXA-232 are emerging in different parts of the world and are most likely underreported due to problems with the laboratory detection of these enzymes. The medical community should be aware of the looming threat that is posed by bacteria with OXA-48-like carbapenemases.

Molecular characterization of multidrug-resistance in Gram-negative bacteria from the Peshawar teaching hospital, Pakistan

Extended-spectrum β-lactamases, carbapenemases, 16S rRNA methylases conferring pan-drug aminoglycoside resistance and colistin resistance were investigated among Gram-negative bacteria recovered from clinical samples (infections) from 200 individuals hospitalized at the Khyber Teaching Hospital of Peshawar, north Pakistan, from December 2017 to March 2018. Out of 65 isolates recovered, 19% were carbapenem resistant and 16% carried a bla_NDM-1 gene, confirming the widespread distribution of NDM producers in this country. The association of the NDM carbapenem-resistance determinant, together with the extended-spectrum β-lactamase CTX-M-15 and 16S rRNA methylases, was frequent, explaining the multidrug-resistance pattern observed. All isolates remained susceptible to colistin.

Coproduction Of MCR-9 And NDM-1 By Colistin-Resistant Enterobacter hormaechei Isolated From Bloodstream Infection

Background

Colistin acts as the last line of defense against severe infections caused by carbapenem-resistant Enterobacteriaceae. Infections caused by extensively drug-resistant isolates coproducing MCR and carbapenemases have posed a serious public health concern.

Purpose

In this study, we reported the first clinical colistin and carbapenem-resistant Enterobacter hormaechei isolate SCNJ07 coharboring bla _NDM-1 and mcr-9 from a patient with bloodstream infection in China.

Methods

Bacterial antimicrobial susceptibility testing was performed using the broth microdilution method. Conjugation assay was carried out to investigate the transferability of mcr-9 and bla _NDM-1. Whole-genome sequencing of strain SCNJ07 was performed using an Illumina HiSeq system and the genetic characteristics of the mcr-9- and bla _NDM-1-harboring plasmids were analyzed.

Results

Conjugation assays revealed that both bla _NDM-1 and mcr-9 genes could successfully transfer their resistance phenotype to Escherichia coli strain J53. Whole genome sequencing showed that SCNJ07 possessed an FIB36:FIIY4 type self-transmissible plasmid bearing bla _NDM-1, which possessed high similarity to previously reported pRJF866 in China. mcr-9 was located on a ~28-kb self-transmissible plasmid pMCR-SCNJ07 with both IncHI2 and IncR replicons. Two copies of intact IS903 that bracketed a ~8-kb region containing the mcr-9 gene were identified in pMCR-SCNJ07. BLASTn analysis revealed that a number of mcr-9-positive plasmids have been around for a while among Enterobacteriaceae worldwide.

Conclusion

This study reveals the likelihood of a wide dissemination of this newly identified colistin resistance gene mcr-9 among Enterobacteriaceae. Further surveillance is urgently needed to understand the prevalence and dissemination of mcr-9, thereby facilitating establishment of measures to control its spread.

bla NDM-5 carried by a hypervirulent Klebsiella pneumoniae with sequence type 29

Background

A carbapenem-resistant hypermucoviscous Klebsiella pneumoniae isolate was recovered from human sputum.

Methods

Whole genome sequencing of this isolate was carried out to reveal its clonal background, antimicrobial resistance determinants and virulence factors. Virulence assays were performed using wax moth larvae. The transfer of bla_NDM-5 between bacterial strains was tested using conjugation. 59 genome assemblies of ST29 K. pneumoniae and 230 IncX3 plasmids regardless of the carriage of resistance gene were employed for phylogenetic analysis, respectively.

Results

The strain carried a virulence plasmid pVir-SCNJ1 bearing the virulence gene rmpA and exhibited a high virulence in wax moth. This hypervirulent strain belongs to sequence type 29 and carries bla_NDM-5, which is located on a conjugative plasmid, designated pNDM5-SCNJ1, belonging to type IncX3. pNDM5-SCNJ1 was fully sequenced and shows high similarity with pNDM_MGR194, except some deletion inside the ISAba125 region. Phylogenetic analysis of IncX3 plasmids revealed that although bla_NDM-5 can be evolved from bla_NDM-1 via point mutations within some IncX3 plasmids, most of bla_NDM-5-carrying IncX3 plasmids probably have acquired bla_NDM-5 in multiple events.

Conclusions

In this study, we characterized a bla_NDM-5-positive hypervirulent K. pneumoniae of sequence type 29 in China. Our results highlight the need for active surveillance on this lineage of carbapenem-resistant K. pneumoniae.

Electronic supplementary material

The online version of this article (10.1186/s13756-019-0596-1) contains supplementary material, which is available to authorized users.

Antibiotic resistance profiling of pathogenic Enterobacteriaceae from Cluj-Napoca, Romania

Introduction

Members of the family Enterobacteriaceae are commonly identified in the clinical laboratory, being responsible for a substantial range of infections. This study aimed to investigate phenotypic and genotypic resistance traits in pathogenic Enterobacteriaceae isolated from outpatients in Cluj-Napoca, Romania.

Methods

Pathogenic Enterobacteriaceae were isolated from urinary tract infections, wound infections and persistent diarrhea in a private laboratory from Cluj-Napoca, Romania. Bacterial strains were biochemically identified and subjected to antimicrobial susceptibility testing by disk diffusion. The carriage of antibiotic resistance genes and of class 1 integron were assessed by PCR.

Results

E. coli and Enterobacter spp. were the most prevalent pathogens. High levels of resistance were observed against folate pathway inhibitors (74%), fluoroquinolones (49%) and penicillins (44%). The incidence of carbapenem resistance was 3%. The strains displaying phenotypic resistance were able to produce β-lactamase enzymes encoded by bla _TEM, bla _TEM-1, bla _SHV-1 and bla _CTX-M, aminoglycoside modifying enzymes due to the carriage of aac(3)-IIIa, aac(6')-II and aac(6')-Ie-aph(2"), to possess fluoroquinolones resistance due to qnrS DNA gyrase protection proteins and resistance to folate pathway inhibitors due to dihydropteroate synthases encoded by sul1, sul2 and sul3 genes. The high frequency of intI1 integrase was associated to sulphonamide resistance (r=0.48; p<0.001) and also to fluoroquinolone resistance (r=0.27; p=0.011), but no significant associations in the co-occurrence of specific antibiotic resistance genes and intI1 were found in pathogenic Enterobacteriaceae.

Conclusions

An important proportion of pathogenic Enterobacteriaceae were multidrug resistant, due to a wide diversity of mechanisms encoding genetic resistance.

Dissemination of NDM-1 carbapenemase-producer Providencia stuartii strains in Romanian hospitals: a multicentre study

Several Romanian hospitals have noted increasing isolation of Providencia stuartii strains in recent years, with an alarming rate of carbapenem resistance. In order to provide molecular epidemiological data regarding their dissemination, 77 P. stuartii strains collected from five hospitals located in different regions of Romania were analysed. All strains harboured IncA/C plasmid, and 67 carried the blaNDM-1 gene. Six clonal clusters were differentiated by pulsed-field gel electrophoresis. The predominant subtype was found in all five hospitals. Our study highlights the need for efficient infection-control measures, the optimization of antibiotic use and the targeted surveillance for carbapenemase-producing P. stuartii.

Illumina short-read and MinION long-read WGS to characterize the molecular epidemiology of an NDM-1 Serratia marcescens outbreak in Romania

Background and Objectives

Serratia marcescens is an emerging nosocomial pathogen, and the carbapenemase bla_NDM has been reported in several surveys in Romania. We aimed to investigate the molecular epidemiology of S. marcescens in two Romanian hospitals over 2010–15, including a neonatal NDM-1 S. marcescens outbreak.

Methods

Isolates were sequenced using Illumina technology together with carbapenem-non-susceptible NDM-1-positive and NDM-1-negative Klebsiella pneumoniae and Enterobacter cloacae to provide genomic context. A subset was sequenced with MinION to fully resolve NDM-1 plasmid structures. Resistance genes, plasmid replicons and ISs were identified in silico for all isolates; an annotated phylogeny was reconstructed for S. marcescens. Fully resolved study NDM-1 plasmid sequences were compared with the most closely related publicly available NDM-1 plasmid reference.

Results

44/45 isolates were successfully sequenced (S. marcescens, n = 33; K. pneumoniae, n = 7; E. cloacae, n = 4); 10 with MinION. The S. marcescens phylogeny demonstrated several discrete clusters of NDM-1-positive and -negative isolates. All NDM-1-positive isolates across species harboured a pKOX_NDM1-like plasmid; more detailed comparisons of the plasmid structures demonstrated a number of differences, but highlighted the largely conserved plasmid backbones across species and hospital sites.

Conclusions

The molecular epidemiology is most consistent with the importation of a pKOX_NDM1-like plasmid into Romania and its dissemination amongst K. pneumoniae/E. cloacae and subsequently S. marcescens across hospitals. The data suggested multiple acquisitions of this plasmid by S. marcescens in the two hospitals studied; transmission events within centres, including a large outbreak on the Targu Mures neonatal unit; and sharing of the pKOX_NDM1-like plasmid between species within outbreaks.

Resistome of carbapenem- and colistin-resistant Klebsiella pneumoniae clinical isolates

The emergence and dissemination of carbapenemases, bacterial enzymes able to inactivate most β-lactam antibiotics, in Enterobacteriaceae is of increasing concern. The concurrent spread of resistance against colistin, an antibiotic of last resort, further compounds this challenge further. Whole-genome sequencing (WGS) can play a significant role in the rapid and accurate detection/characterization of existing and emergent resistance determinants, an essential aspect of public health surveillance and response activities to combat the spread of antimicrobial resistant bacteria. In the current study, WGS data was used to characterize the genomic content of antimicrobial resistance genes, including those encoding carbapenemases, in 10 multidrug-resistant Klebsiella pneumoniae isolates from Pakistan. These clinical isolates represented five sequence types: ST11 (n = 3 isolates), ST14 (n = 3), ST15 (n = 1), ST101 (n = 2), and ST307 (n = 1). Resistance profiles against 25 clinically-relevant antimicrobials were determined by broth microdilution; resistant phenotypes were observed for at least 15 of the 25 antibiotics tested in all isolates except one. Specifically, 8/10 isolates were carbapenem-resistant and 7/10 isolates were colistin-resistant. The bla_NDM-1 and bla_OXA-48 carbapenemase genes were present in 7/10 and 5/10 isolates, respectively; including 2 isolates carrying both genes. No plasmid-mediated determinants for colistin resistance (e.g. mcr) were detected, but disruptions and mutations in chromosomal loci (i.e. mgrB and pmrB) previously reported to confer colistin resistance were observed. A bla_OXA-48-carrying IncL/M-type plasmid was found in all bla_OXA-48-positive isolates. The application of WGS to molecular epidemiology and surveillance studies, as exemplified here, will provide both a more complete understanding of the global distribution of MDR isolates and a robust surveillance tool useful for detecting emerging threats to public health.

Phenotypic and molecular identification of carbapenemase-producing Enterobacteriaceae - challenges in diagnosis and treatment

Introduction: Infections due to carbapenemase-producing carbapenem-resistant Enterobacteriaceae (CPCRE) are an emerging global public health threat. The purpose of this study was to investigate phenotypic and genotypic features of CP-CRE strains isolated from hospitalized patients. Material and methods: Between 1st of January - 1st of July 2017, in the Department of Microbiology, “Dr. Constantin Opriş” County Emergency Hospital Baia Mare, Romania, 1110 strains of Enterobacteriaceae were isolated from bronchial secretions, urine, wounds and blood cultures. Bacterial identification and antimicrobial susceptibility tests were performed by conventional methods, Vitek 2 Compact and M.I.C.E. strips. We analysed all Enterobacteriaceae strains non-susceptible to carbapenems according to CLSI 2017 criteria. The modified Hodge test (MHT), the modified carbapenem inactivation method (mCIM) and the combination disks test (KPC, MBL, OXA-48 Confirm kit, Rosco Diagnostica) were used for phenotypic confirmation, whereas a multiplex PCR assay for genes blaKPC, blaNDM and blaOXA-48 was used for genetic confirmation. Results: 19 non-duplicate strains isolated from 16 patients were phenotypically identified as CP-CRE: Klebsiella pneumoniae (n=14), Escherichia coli (n=2), Providencia stuartii (n=2) and Serratia marcescens (n=1). Most strains were isolated from bronchial secretions (n=9). The carbapenem-hydrolizing enzymes were identified by the combination disks test as: KPC (n=9), OXA-48-like (n=5) and MBL (n=5). Molecular confirmation was performed in 18 phenotypically positive isolates with 100% concordant results with mCIM and combination disks test. Discrepant results were noticed with the MHT in case of 4 NDM-producers confirmed by PCR. All CP-CRE strains were resistant to all tested cephems. Three out of 9 K. pneumoniae strains tested against colistin were found resistant. Conclusions: The most common carbapenemase detected was KPC. Therapeutic options were limited in all positive cases. Rapid and reliable detection of CP-CRE is critical for preventing the spread of these pathogens

Active surveillance scheme in three Romanian hospitals reveals a high prevalence and variety of carbapenamase-producing Gram-negative bacteria: a pilot study, December 2014 to May 2015

We report the findings of an active surveillance scheme for detection of asymptomatic carriers with carbapenemase-producing Gram-negative bacteria (CP-GNB) in Romanian hospitals. During a pilot study from December 2014 to May 2015, faecal cultures were screened in three hospitals (two large, one medium-size) for patients newly admitted to selected wards or inpatients transferred from other wards to an intensive-care unit. The study revealed a high prevalence of CP-GNB detected in 22/27 and 28/38 of the carbapenem non-susceptible isolates from Hospitals 1 and 3, respectively. CP-GNB identified through faecal screening included NDM-1-producing Serratia marcescens and Klebsiella pneumoniae, OXA-48-producing K. pneumoniae and OXA-23-producing Acinetobacter baumannii. The distribution of the CP-GNB varied between the hospitals, with NDM-1-producing S. marcescens and K. pneumoniae being prevalent in the north-central part of the country and OXA-23/24-producing A. baumannii, OXA-48-producing K.pneumoniae, Morganella morganii and VIM-2-producing Escherichia coli/Pseudomonas aeruginosa detected in the north-east of the country. Conjugation studies showed that carbapenem resistance was transferable and PCR-based replicon typing identified blaNDM-1 on IncFIIs in S. marcescens and K. pneumoniae from Hospital 1 and blaOXA-48 on IncL plasmids in all Klebsiella spp. isolates from Hospitals 1 and 3. Our findings underline the importance of active surveillance for detection of CP-GNB asymptomatic faecal carriers and suggest a likely endemic spread of CP-GNB in Romania.

Implications of direct amplification for measuring antimicrobial resistance using point-of-care devices

Antimicrobial resistance (AMR) is recognized as a global threat to human health. Rapid detection and characterization of AMR is a critical component of most antibiotic stewardship programs. Methods based on amplification of nucleic acids for detection of AMR are generally faster than culture-based approaches but they still require several hours to more than a day due to the need for transporting the sample to a centralized laboratory, processing of sample, and sometimes DNA purification and concentration. Nucleic acids-based point-of-care (POC) devices are capable of rapidly diagnosing antibiotic-resistant infections which may help in making timely and correct treatment decisions. However, for most POC platforms, sample processing for nucleic acids extraction and purification is also generally required prior to amplification. Direct amplification, an emerging possibility for a number of polymerases, has the potential to eliminate these steps without significantly impacting diagnostic performance. This review summarizes direct amplification methods and their implication for rapid measurement of AMR. Future research directions that may further strengthen the possibility of integrating direct amplification methods with POC devices are also summarized.

OXA-48-Carbapenemase-Producing Klebsiella pneumoniae infections - the first cases diagnosed in Romanian National Institute of Infectious Diseases

We report first description of clinical cases of OXA-48 carbapenemase-producing Klebsiella pneumoniae originating from patients hospitalized in the most important Infectious Diseases Hospital from Romania, between December 2012 and March 2013. All strains were isolated from patients who were previously admitted in surgical wards. None of the patients had been admitted in a hospital outside of Romania.

Class 1 integrons in non-clonal multidrug-resistant Acinetobacter baumannii from Iran, description of the new blaIMP-55 allele in In1243

Infections and outbreaks caused by multidrug-resistant Acinetobacter baumannii (MDR-AB) are prevalent and have been reported worldwide over the past 20 or more years. Class 1 integron in MDR-AB plays an important role in the spread of antibiotic resistance in clinical settings. This study has been conducted to evaluate the detection of metallo-β-lactamase, characterization of class 1 integron and determination of clonal relatedness among A. baumannii hospital isolates. Sixty-five clinical isolates of MDR-AB were recovered from two Iranian hospital's intensive care units from February to August 2013. Integrase (intI1) and blaIMP genes were detected in 70.8 % (n=46/65) and 9.23 % (n=6/65) of the isolates using PCR assay, respectively. No other metallo-β-lactamase genes (blaVIM, blaSIM and blaNDM) were detected. PCR sequencing of integron gene cassette revealed the following arrays: blaOXA10-aacA4-blaIMP-55-cmlA5 (as a novel array was designated In1243), aacC1 and aadA1. Analysis of blaIMP gene revealed a new allele designated as blaIMP-55. Gene transfer experiment by conjugation showed the 36 kb conjugative plasmid harbouring In1243. The clonal assessment by repetitive extragenic palindromic PCR demonstrated a high-degree relatedness among the strains, but strains harbouring In1243 displayed a different repetitive extragenic palindromic PCR profile. In this study, we found that a novel class 1 integron (In1243) that encoded a new blaIMP allele resided on a transferable plasmid in non-clonal strains of MDR-AB.

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.

Carbapenemase-producing Enterobacteriaceae: a 2-year surveillance in a hospital in Iaşi, Romania

Aim: Limited information is currently available about the prevalence of carbapenemase-producing Enterobacteriaceae (CPE) in Romania. Materials & methods: Routine tests of 1,993 clinical isolates at a hospital in Iaşi yielded 46 isolates that were resistant to carbapenems. All 46 isolates were phenotypically and genotypically analyzed using VITEK-2 and DNA microarray-based assays. Results: Isolates were assigned to Klebsiella pneumoniae and Enterobacter cloacae. For 39 isolates, carbapenem resistance was confirmed and 37 harbored at least one carbapenem resistance gene. Two isolates were probably resistant due to AmpC β-lactamases in combination with a porin loss. The overall concordance between detected phenotype and genotype was 95%. Conclusion: Our data show that carbapenemase-producing isolates with different underlying resistance mechanisms are still rare in Iaşi, but the global rise of CPE warrants intensified surveillance.

Primer Evaluation for PCR and its Application for Detection of Carbapenemases in Enterobacteriaceae

BACKGROUND

During the last decade, the prevalence of carbapenem-resistant Enterobacteriaceae in human patients has increased. Carbapenemase-producing bacteria are usually multidrug resistant. Therefore, early recognition of carbapenemase producers is critical to prevent their spread.

OBJECTIVES

The objective of this study was to develop the primers for single and/or multiplex PCR amplification assays for simultaneous identification of class A, class B, and class D carbapenem hydrolyzing β-lactamases in Enterobacteriaceae and then to evaluate their efficiency.

MATERIALS AND METHODS

The reference sequences of all genes encoding carbapenemases were downloaded from GenBank. Primers were designed to amplify the following 11 genes: bla KPC, bla OXA, bla VIM, bla NDM, bla IMP, bla SME, bla IMI, bla GES , bla GIM, bla DIM and bla CMY . PCR conditions were tested to amplify fragments of different sizes. Two multiplex PCR sets were created for the detection of clinically important carbapenemases. The third set of primers was included for detection of all known carbapenemases in Enterobacteriaceae. They were evaluated using six reference strains and nine clinical isolates.

RESULTS

Using optimized conditions, all carbapenemase-positive controls yielded predicted amplicon sizes and confirmed the specificity of the primers in single and multiplex PCR.

CONCLUSIONS

We have reported here a reliable method, composed of single and multiplex PCR assays, for screening all clinically known carbapenemases. Primers tested in silico and in vitro may distinguish carbapenem-resistant Enterobacteriaceae and could assist in combating the spread of carbapenem resistance in Enterobacteriaceae.

Carbapenemase-Producing Klebsiella pneumoniae in Romania: A Six-Month Survey

This study presents the first characterization of carbapenem-non-susceptible Klebsiella pneumoniae isolates by means of a structured six-month survey performed in Romania as part of an Europe-wide investigation. Klebsiella pneumoniae clinical isolates from different anatomical sites were tested for antibiotic susceptibility by phenotypic methods and confirmed by PCR for the presence of four carbapenemase genes. Genome macrorestriction fingerprinting with XbaI was used to analyze the relatedness of carbapenemase-producing Klebsiella pneumoniae isolates collected from eight hospitals. Among 75 non-susceptible isolates, 65 were carbapenemase producers. The most frequently identified genotype was OXA-48 (n = 51 isolates), eight isolates were positive for blaNDM-1 gene, four had the blaKPC-2 gene, whereas two were positive for blaVIM-1. The analysis of PFGE profiles of OXA-48 and NDM-1 producing K. pneumoniae suggests inter-hospitals and regional transmission of epidemic clones. This study presents the first description of K. pneumoniae strains harbouring blaKPC-2 and blaVIM-1 genes in Romania. The results of this study highlight the urgent need for the strengthening of hospital infection control measures in Romania in order to curb the further spread of the antibiotic resistance.

Carbapenemase-producing Enterobacteriaceae in Europe: assessment by national experts from 38 countries, May 2015

In 2012, the European Centre for Disease Prevention and Control (ECDC) launched the ‘European survey of carbapenemase-producing Enterobacteriaceae (EuSCAPE)’ project to gain insights into the occurrence and epidemiology of carbapenemase-producing Enterobacteriaceae (CPE), to increase the awareness of the spread of CPE, and to build and enhance the laboratory capacity for diagnosis and surveillance of CPE in Europe. Data collected through a post-EuSCAPE feedback questionnaire in May 2015 documented improvement compared with 2013 in capacity and ability to detect CPE and identify the different carbapenemases genes in the 38 participating countries, thus contributing to their awareness of and knowledge about the spread of CPE. Over the last two years, the epidemiological situation of CPE worsened, in particular with the rapid spread of carbapenem-hydrolysing oxacillinase-48 (OXA-48)- and New Delhi metallo-beta-lactamase (NDM)-producing Enterobacteriaceae. In 2015, 13/38 countries reported inter-regional spread of or an endemic situation for CPE, compared with 6/38 in 2013. Only three countries replied that they had not identified one single case of CPE. The ongoing spread of CPE represents an increasing threat to patient safety in European hospitals, and a majority of countries reacted by establishing national CPE surveillances systems and issuing guidance on control measures for health professionals. However, 14 countries still lacked specific national guidelines for prevention and control of CPE in mid-2015.

Molecular characterization of bacteremic Escherichia coli isolates in Romania

The increasing prevalence of invasive infections caused by antibiotic resistant Escherichia coli strains in Romanian patients, already mentioned in the European reports, requires better knowledge of their specific traits. Thus, a set of 38 E. coli blood isolates, collected between 2010 and 2012 at one of the local hospitals participating into the European Antimicrobial Resistance Surveillance Network, was investigated retrospectively with respect to the phylogenetic origin, extraintestinal virulence-associated markers (i.e. fimH, papC, papG alleles, sfa/foc, afa/dra, hly, cnf1, sat, iucC, fyuA, ibeA), and beta-lactamase encoding genes (i.e. bla CTX-M, bla TEM, and bla SHV alleles). The isolates with extended-spectrum beta-lactamase (ESBL) phenotypes were further characterized using PCR-based replicon typing and multilocus sequencing typing. For ST131 members, pulsed-field gel electrophoresis (PFGE) and PCR-based detection of fimH30 allele were performed. Overall, the isolates were more likely members of the major phylogenetic group A (53 %) and to a lesser extent of groups B2 (29 %), D (10 %), and B1 (8 %). All but three of the virulence markers sought (i.e. papGI, hly, cnf1) were detected with prevalence ranging from 3 % (i.e. ibeA, papGIII) to 87 % (fimH). As expected, the most complex genotypes (four to seven virulence markers) defined the isolates derived from phylogenetic groups B2 and D. ESBL producers were bla CTX-M-15-positive, mostly of phylogroup A (67 %), harboured IncF multireplicon plasmids, and belonged to six sequence types (i.e. ST10, ST131, ST167, ST410, ST540, ST1275). Members of ST10 clonal complex (i.e. ST10, ST167) were the most common. The ST131 isolates belonged to H30 subclone and displayed 74 % similarity at PFGE analysis.

Dissemination of carbapenemase-producing Enterobacteriaceae and Pseudomonas aeruginosa in Romania

Fifteen carbapenemase-producing Enterobacteriaceae isolates and 12 carbapenemase-producing Pseudomonas aeruginosa isolates were recovered from patients hospitalized between August 2011 and March 2013 at the Hospital of Infectious Disease, Cluj-Napoca, Romania. One KPC-, nine NDM-1-, four OXA-48-, and one VIM-4-producing Enterobacteriaceae isolates along with 11 VIM-2-producing and one IMP-13-producing P. aeruginosa isolates were recovered from clinical samples. All carbapenemase genes were located on self-conjugative plasmids and were associated with other resistance determinants, including extended-spectrum β-lactamases and RmtC methylases.

First Report of OXA-181-Producing Escherichia coli in China and Characterization of the Isolate Using Whole-Genome Sequencing

We report the first OXA-181-producing strain in China. blaOXA-181 was found in sequence type 410 (ST410) Escherichia coli strain WCHEC14828 from a Chinese patient without recent travel history. Genome sequencing and conjugation experiments were performed. blaOXA-181 was carried on a 51-kb self-transmissible IncX3 plasmid and was linked with qnrS1, a quinolone resistance gene. blaOXA-181 was introduced onto the IncX3 plasmid from a ColE2-type plasmid, and IncX3 plasmids have the potential to mediate the dissemination of blaOXA-181.

Molecular characterization of carbapenemase production among gram-negative bacteria in saudi arabia

We characterized the molecular basis of carbapenemase production in carbapenem-resistant Gram-negative bacteria isolated from hospitalized patients from Saudi Arabia in the year 2012. Isolates were collected from across the Kingdom and phenotypically tested for carbapenemase production. Polymerase chain reaction detection of carbapenemase genes was also performed. Our results indicate that in Saudi Arabia, OXA-48 and NDM-1 are the dominant carbapenemases among Enterobacteriaceae with low prevalence of VIM. The latter is the most prevalent metallo-beta-lactamase in Pseudomonas aeruginosa, whereas oxacillinases, OXA-23 in particular, are the dominant carbapenemases in Acinetobacter baumannii. No KPC or IMP genes were detected. Our study is the first report of OXA-48, NDM-1, and VIM-4 enzymes in Enterobacter from the Kingdom. Also it is the first report of OXA-72 and NDM-1 in A. baumannii in Saudi Arabia, and the coexistence of blaOXA-23 and blaNDM-1 genes in this species in the country. Awareness of the role of international travel in the spread of carbapenem-resistant determinants in the Kingdom, as well as effective infection control interventions in hospitals and strict antimicrobial stewardship in healthcare facilities and the community are keys to combat the rise of carbapenemase producers in the Kingdom.

Whole-genome assembly of Klebsiella pneumoniae coproducing NDM-1 and OXA-232 carbapenemases using single-molecule, real-time sequencing

The whole-genome sequence of a carbapenem-resistant Klebsiella pneumoniae strain, PittNDM01, which coproduces NDM-1 and OXA-232 carbapenemases, was determined in this study. The use of single-molecule, real-time (SMRT) sequencing provided a closed genome in a single sequencing run. K. pneumoniae PittNDM01 has a single chromosome of 5,348,284 bp and four plasmids: pPKPN1 (283,371 bp), pPKPN2 (103,694 bp), pPKPN3 (70,814 bp), and pPKPN4 (6,141 bp). The contents of the chromosome were similar to that of the K. pneumoniae reference genome strain MGH 78578, with the exception of a large inversion spanning 23.3% of the chromosome. In contrast, three of the four plasmids are unique. The plasmid pPKPN1, an IncHI1B-like plasmid, carries the blaNDM-1, armA, and qnrB1 genes, along with tellurium and mercury resistance operons. blaNDM-1 is carried on a unique structure in which Tn125 is further bracketed by IS26 downstream of a class 1 integron. The IncFIA-like plasmid pPKPN3 also carries an array of resistance elements, including blaCTX-M-15 and a mercury resistance operon. The ColE-type plasmid pPKPN4 carrying blaOXA-232 is identical to a plasmid previously reported from France. SMRT sequencing was useful in resolving the complex bacterial genomic structures in the de novo assemblies.

Molecular screening of carbapenemase-producing Gram-negative strains in Romanian intensive care units during a one year survey

This is the first study, to our knowledge, performed on a significant number of strains (79 carbapenem-resistant Enterobacteriaceae and 84 carbapenem-resistant non-fermenting Gram-negative rods, GNRs) isolated from tissue samples taken from patients in the intensive care units of two large hospitals in Bucharest, Romania, between 2011 and 2012. The results revealed a high prevalence and great diversity of carbapenemase genes (CRG), in both fermenting and non-fermenting Gram-negative carbapenem-resistant strains. The molecular screening of carbapenem-resistant GNRs revealed the presence of worldwide-distributed CRGs (i.e. blaOXA-48 and blaNDM-1 in Enterobacteriaceae and blaOXA-23, blaVIM-4, blaOXA-10-like, blaOXA-60-like, blaSPM-like and blaGES-like in non-fermenting GNRs), reflecting the rapid evolution and spread of carbapenemase producers, particularly in hospitals. Rapid identification of the colonized or infected patients is required, as are epidemiological investigations to establish the local or imported origin of the respective strains.