Carbapenem Resistance In Enterobacteriaceae Research Articles

An Investigation Into Carbapenem Resistance in Enterobacteriaceae Among Outpatients With Urinary Tract Infection in Southwestern Uganda

An Investigation Into Carbapenem Resistance in Enterobacteriaceae Among Outpatients With Urinary Tract Infection in Southwestern Uganda

A systematic review and meta-analysis of carbapenem resistance and its possible treatment options with focus on clinical Enterobacteriaceae: Thirty years of development in Pakistan

BackgroundCarbapenem resistance is epidemic worldwide, these last resort antimicrobials are listed in the WHO ‘watch group’ with higher resistance potential. During the years 2017-18 Pakistan Antimicrobial Resistance Surveillance System reported an increase in carbapenem resistance. However, a comprehensive information on prevalence and molecular epidemiology of carbapenem resistance in Pakistan is not available. This systematic review and meta-analysis is aimed to report the current carbapenem resistance situation in Pakistan and its treatment options. MethodsIn this systematic review and meta-analysis, we investigated the pooled prevalence (PPr) of carbapenem resistance in Enterobacteriaceae and non-Enterobacteriaceae by organizing available data, from Web of Science and PubMed by April 2, 2020, in various groups and subgroups including species, years, provinces, extended spectrum β-lactamase production, clinical presentation, carbapenemase and metallo-β-lactamase production, and New Delhi metallo-β-lactamase (NDM) prevalence. Literature review was updated for the studies publisehd by December 07, 2023. Moreover, we descriptively reviewed the molecular epidemiology of carbapenem resistance in Enterobacteriaceae and non-Enterobacteriaceae in Pakistan. Lastly, we statistically explored different treatment options available for carbapenem resistant infections. We used R package ‘metafor’ for performing meta-analysis and influence diagnostics and determining treatment options. ResultsFrom two academic databases Web of Science and PubMed we identified 343 studies. Eighty-eight studies were selected for the systematic review and meta-analysis. Seventy-four studies were selected for phenotypic analysis, 36 for genotypic analysis, and 31 for available treatment options. PPr-ID of 12% [0.12 (0.07, 0.16)] was observed for phenotypic carbapenem resistance in Enterobacteriaceae with more prevalence recorded in Klebsiella pneumoniae 24% [0.24 (0.05, 0.44)] followed by 9% [0.09 (−0.03, 0.20)] in Escherichia coli. During the last two decades we observed a striking increase in carbapenem resistance PPr i.e., from 0% [0.00 (−0.02, 0.03)] to 36% [0.36 (0.17, 0.56)]. blaNDM with PPr 15% [0.15 (0.06, 0.23)] in naive isolates was found to be the fundamental genetic determinant for carbapenem resistance in Enterobacteriaceae in Pakistan. Polymyxin B, colistin, tigecycline, and fosfomycin were identified as the suggested treatment options available for multidrug resistant infections not responding to carbapenems. Various studies reported carbapenem resistance from human, animal, and environment sources. ConclusionIn conclusion, we found that NDM-1 producing carbapenem resistant Enterobacteriaceae are increasing in Pakistan. Meta-analysis showed that metallo-β-lactamases producing E. coli ST405 and K. pneumoniae sequence type11 are the major resistant clones. Number of reported studies in various subgroups and inconsistency in following CLSI guidelines are the potential limitations of this meta-analysis. A National antimicrobial resistance (AMR) surveillance strategy based on One Health is urgently needed to check any future AMR crisis in Pakistan.

Detection Sequencing NDM and blaOXA Genes in Metallo-$\beta$-Lactamase Producing Klebsiella Pneumoniae

The prevalence of Carbapenem-resistance in Enterobacteriaceae is rising worldwide and poses a treatment challenge for healthcare facilities. This study aims to detect a sequence of New Delhi metallo- -lactamase (NDM) and bla OXA-48 gene in metalo-beta-lactamase-producing Klebsiella pneumoniae isolated from a few hospitals in the city of Baghdad. 74 Klebsiella pneumoniae were isolated from 320 clinical samples that were routinely submitted to the diagnostic laboratory of the chosen hospital. These samples included sputum, tissue swabs, folly tips, urine, ear swabs, bloodstream, pus, wound swabs, endotracheal tubes, and body fluids. In this study, 74 isolates were examined for expression of carbapenemase by phenotyping method. The modified Hodge Test (MHT) is utilized for phenotypic detection. MHT was positive for 24 carbapenem-resistant Klebsiella pneumoniae. Genotyping was accomplished by using polymerase chain reaction (PCR) to amplify target genes by employing particular primers. The NDM gene was detected in 19/24 isolates, and the blaOXA-48 gene was detected in 5/24 isolates. The presence of bla NDM and the dangerously high frequency of MBL in the Klebsiella pneumoniae strain are both concerning, and it has been demonstrated to be challenging to treat and inhibit infection.

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

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. 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. 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.

Characterisation of OXA-48-like carbapenemases in Escherichia coli and Klebsiella pneumoniae from North India.

The oxacillinase-48 (OXA-48)-like carbapenemases are class D β-lactamases and increasingly reported in Enterobacterial species. The detection of these carbapenemases is challenging and little information is available on the epidemiology and plasmid characteristics of OXA-48-like carbapenemase producers. We detected the presence of OXA-48-like carbapenemases in 500 clinical isolates of Escherichia coli and Klebsiella pneumoniae, followed by detection of other carbapenemases, extended spectrum β-lactamases (ESBLs) and 16S rRNA methyltransferases in OXA-48 producers. Clonal relatedness was studied using pulsed-field gel electrophoresis (PFGE) and multi-locus sequence typing (MLST). Finally, plasmid characterisation was performed through conjugation experiment, S1-PFGE and Southern hybridisation. Around 40% of E. coli and K. pneumoniae isolates harboured OXA-48-like β-lactamases. Two OXA-48 allele variants, OXA-232 and OXA-181 were detected in our study. OXA-48 producers co-harbored diverse drug-resistant genes belonging to other classes of carbapenemases, ESBLs and 16S rRNA methyltransferases. OXA-48-like carbapenemase producers exhibited high clonal diversity. Bla OXA-48 carrying plasmids were conjugative, untypable and their size was ~ 45kb and ~ 104.5kb in E. coli and K. pneumoniae respectively. In conclusion, OXA-48-like carbapenemases have emerged as major cause of carbapenem resistance in Enterobacteriaceae and probably still being underreported. Strict surveillance and adequate detection methods are needed to prevent the dissemination of OXA-48-like carbapenemases.

Horizontal Transfer of Plasmid Mediated Carbapenem Resistant Genes from Klebsiella pneumoniae to Escherichia coli

Carbapenem resistance among Enterobacteriaceae is an emerging problem worldwide. Klebsiella pneumonia carbapenemase (blaKPC) enzymes are amongst the most common beta-lactamases that have been studied. This broad group of organisms with various resistance mechanisms is associated with increased lengths of hospitalization, costs of medical care, morbidity, and mortality. The global spread of Carbapenem Resistance Enterobacteriaceae (CRE) has largely been attributed to disseminating a dominant strain of Klebsiella pneumoniae producing a serine beta-lactamase, termed as Klebsiella pneumonia carbapenemase (KPC). This study was designed to determine in vitro efficacy of horizontal transfer of plasmid-mediated carbapenem-resistant genes from Klebsiella pneumoniae to Escherichia coli. A total of 30 gram-negative rods from different clinical samples were taken. After preliminary antimicrobial susceptibility screening, isolates that showed a resistance zone were included in the study. These isolates were then subjected to the Modified Hodge test for confirmation of carbapenemase production. Out of 10 isolates, four were positive for carbapenemase production. The plasmid from these resistant strains was transformed into DH5α. RFLP analysis was carried to evaluate these transgenic cells resulted in horizontal gene transfer of resistant plasmid DNA from Klebsiella pneumoniae to Escherichia coli.

Discovery of Quercetin and Its Analogs as Potent OXA-48 Beta-Lactamase Inhibitors.

Carbapenem resistance in Enterobacteriaceae caused by OXA-48 β-lactamase is a growing global health threat and has rapidly spread in many regions of the world. Developing inhibitors is a promising way to overcome antibiotic resistance. However, there are few options for problematic OXA-48. Here we identified quercetin, fisetin, luteolin, 3′,4′,7-trihydroxyflavone, apigenin, kaempferol, and taxifolin as potent inhibitors of OXA-48 with IC50 values ranging from 0.47 to 4.54 μM. Notably, the structure-activity relationship revealed that the substitute hydroxyl groups in the A and B rings of quercetin and its structural analogs improved the inhibitory effect against OXA-48. Mechanism studies including enzymatic kinetic assay, isothermal titration calorimetry (ITC), and surface plasmon resonance (SPR) analysis demonstrated that quercetin reversibly inhibited OXA-48 through a noncompetitive mode. Molecular docking suggested that hydroxyl groups at the 3′, 4′ and 7 positions in flavonoids formed hydrogen-bonding interactions with the side chains of Thr209, Ala194, and Gln193 in OXA-48. Quercetin, fisetin, luteolin, and 3′,4′,7-trihydroxyflavone effectively restored the antibacterial efficacy of piperacillin or imipenem against E. coli producing OXA-48, resulting in 2–8-fold reduction in MIC. Moreover, quercetin combined with piperacillin showed antimicrobial efficacy in mice infection model. These studies provide potential lead compounds for the development of β-lactamase inhibitors and in combination with β-lactams to combat OXA-48 producing pathogen.

Investigation of OXA-23, OXA-24, OXA-40, OXA-51, and OXA-58 Genes in Carbapenem-Resistant Escherichia coli and Klebsiella pneumoniae Isolates from Patients with Urinary Tract Infections

Background: Escherichia coli and Klebsiella pneumoniae are frequently responsible for urinary tract infections (UTIs). The high rate of carbapenem resistance in Enterobacteriaceae has become a global therapeutic concern. Objectives: The study investigated OXA-23, OXA-24, OXA-40, OXA-51, and OXA-58 genes in uropathogenic E. coli and K. pneumoniae isolates. Methods: We isolated 500 uropathogenic isolates of E. coli and K. pneumoniae from patients at Milad Hospital, Tehran, Iran. Antibiotic susceptibility testing was performed using a strip-test method, and the carbapenem-nonsusceptoble isolates were confirmed with an automated antibiotic sensitivity testing system. The OXA genes were determined by multiplex PCR. Molecular typing was performed by multilocus variable-number tandem repeat (VNTR) analysis (MLVA). Results: Out of 500 isolates, 40 (8%) were detected as carbapenem-resistant, including 13 E. coli and 27 K. pneumoniae. All carbapenem-resistant isolates were ESBL-producing and resistant to ceftriaxone, ciprofloxacin, meropenem, ceftazidime, and amoxicillin-clavulanate. Moreover, 46.1% and 26% of carbapenem-insensitive E. coli and K. pneumoniae isolates carried a beta-lactamase-producing gene associated with the OXA-23-like group. Finally, E. coli and K. pneumoniae isolates were divided into two and three MLVA patterns, respectively. Conclusions: This is the first report of OXA-51, 58, and 24 carbapenemases in clinical isolates of E. coli and K. pneumoniae from UTI patients in Iran. Significant differences were seen in OXA-51, 58, and 24 genes between carbapenem-insensitive and carbapenem-sensitive E. coli and K. pneumoniae isolates. Molecular typing suggested the vertical transmission of resistance genes.

High prevalence of fecal carriage of Extended-spectrum beta-lactamase and carbapenemase-producing Enterobacteriaceae among food handlers at the University of Gondar, Northwest Ethiopia.

Fecal carriage of extended-spectrum beta-lactamase and Carbapenemase-producing Enterobacteriaceae is a potential risk for the transmission of infection with resistant strains. Understanding the burden of these resistant strains in asymptomatic people is essential to reduce the chain of infection transmission. However, data on the fecal carriage of Extended-spectrum Beta-lactamase and Carbapenemase-producing Enterobacteriaceae among food handlers were limited in developing countries especially in Ethiopia. The aim of the present study is, therefore, to assess fecal carriage rate, associated factors, and antimicrobial resistance patterns of Extended-spectrum Beta-lactamase and Carbapenemase-producing Enterobacteriaceae among food handlers at the University of Gondar Cafeterias, Northwest Ethiopia. An institution-based cross-sectional study was conducted from February to June 2021 at the University of Gondar cafeterias. A total of 290 stool samples were collected, transported using Cary Blair transport medium, and processed. All isolates were cultured and identified by using MacConkey agar, and routine biochemical tests. Antimicrobial susceptibility testing was done to each isolate following the Kirby Bauer disk diffusion method. If the zone of inhibition was ≤ 22 mm for ceftazidime, ≤25 mm for ceftriaxone, and ≤27 for cefotaxime they were considered as potential ESBL strain and selected for a further phenotypic confirmatory. Moreover, the double-disc diffusion test and the modified carbapenem inactivation method were used for confirmations of Extended-spectrum β-lactamase and Carbapenemase-producing Enterobacteriaceae respectively. If a ≥5mm difference in zone diameter for either antimicrobial agent in combination with clavulanic acid versus the zone diameter of the agent when tested alone (without B-lactamase inhibitor), was confirmed as ESBL-PE and if the zone of inhibition diameter between 6-15mm and 16- 18mm with a pinpoint colony, it was considered as carbapenem resistance Enterobacteriaceae. Data were entered using Epi-data version 4.6 and then exported to SPSS version 26 for analysis. Potential risk factors were assessed using multivariable logistic regression and a p-value less than 0.05 was considered statistically significant. Out of 290 stool samples, 63 (21.7%) and 7 (2.4%) were confirmed as Extended-spectrum β-lactamase and Carbapenemase-producing Enterobacteriaceae. The most predominant ESBL-PE was E. coli 43 (14.8%) followed by K. pneumoniae 17 (5.9%). Most of the Extended-spectrum β-lactamase and Carbapenemase-producing isolates were resistant to tetracycline, cefotaxime, ceftazidime, and ceftriaxone (100% each). In contrast, a low resistance level was recorded for Meropenem and cefoxitin. The overall Multi-drug resistant Enterobacteriaceae (MDR) was 147 (42.3%). Antibiotics usage in the last 3 months and drinking unpasteurized milk were associated with the carriage of the Extended-spectrum beta-lactamase-Producing Enterobacteriaceae. The high fecal carriage rate of Multi-drug resistance isolate, Extended-spectrum β-lactamase, and Carbapenemase-producing Enterobacteriaceae were recorded among food handlers. Therefore, this study gives signals in the spread of drug-resistant bacteria easily to the community. Hence, the need for adjusting and promotion of infection prevention measures to prevent the spread of drug-resistant bacteria should not be underestimated.

In silico Evolution and Comparative Genomic Analysis of IncX3 Plasmids Isolated From China Over Ten Years.

IncX3 plasmids are correlated with the dissemination and acquisition of carbapenem resistance in Enterobacteriaceae and have been prevalent in China over the last 10 years. Since the distribution characteristics of IncX3 plasmids across China as well as their evolutionary traits for 10 years remain unclear, here we conducted a retrospective literature review and in silico comparative analysis of IncX3 plasmids in publicly available IncX3 plasmid genomes. IncX3 plasmids distributed in 17 provinces or cities were extracted for analysis, which tend to be specifically associated with hospital-isolated Escherichia coli ST410 from phylogroup A. Although the backbones of IncX3 plasmids have remained highly conservative over the last 10 years, the blaNDM resistance genetic contexts on these plasmids could fall into five subtypes, among which AR_N1_I has been identified in Enterobacter cloacae174 chromosome and AR_N5_I was simultaneously located on IncF and IncA/C plasmids. This suggests that the blaNDM resistance gene environment can spread between different plasmids, between different bacterial genera, or between strains and plasmids, highlighting that it is imperative to adopt more stringent infection control measures targeting IncX3 plasmid spread.

Detection of KPC-2 gene in K. pneumoniae, E. coli and P. mirabilis isolated from Urine sample of Urinary Tract Infection patients

Background: Carbapenem resistance in Enterobacteriaceae is an uprising problem worldwide. KPC is one of the important mechanisms of resistance in Enterobacteriaceae such as K. pneumoniae. Aims and Objectives: The current research focuses on the frequency of the KPC -2 gene in Enterobacteriaceae isolated from urine samples, as well as antibiotic resistance patterns. Methodology: Antibiotic sensitivity patterns were examined on 53 carbapenem-resistant isolates from the Enterobacteriaceae family. These isolates were subjected to the Modified Hodge Test (MHT) and PCR for KPC 2 gene identification. Results: A total of 150 urine samples were processed for the isolation of the most prevalent Enterobacteriaceae. 125 Gram-negative bacterial isolates were obtained in which the consistency of K. pneumonia was 50(40%),E. colin was 55(44%), and P. mirabilis was 20(16%). The test for susceptibility of antibioticresulted that among50 Klebsiella pneumoniae 40% were resistant to Imipenem, while in E. coli 54.4% and P. mirabilis 30 % were resistant to Imipenem respectively. PCR results show the gene KPC-2 out of 15 (75%) 2 (13.2%) Modified Hodge Test Positive Klebsiella pneumoniae isolates. In total 83.3% (n=25) E. coli Modified Hodge Test positive and for the KPC-2 gene 4% were positive. Conclusion:This research demonstrates that in Enterobacteriaceae there isexistence of carbapenem resistance. Surveillance research and complete antibiotic prescription standards should be established at Pakistan's various hospitals to stop the growth of antibiotic-resistant bacteria. Key Words: Enterobacteriaceae, Urinary Tract Infections, Carbapenem, Modified Hodge test

Epidemiological Characterization of Colistin and Carbapenem Resistant Enterobacteriaceae in a Tertiary: A Hospital from Anhui Province.

PurposeAntimicrobial resistance, especially carbapenem resistance Enterobacteriaceae and plasmid mediated mobile colistin resistance, is a serious issue worldwide. This study was designed to determine the epidemiological characteristics of plasmid mediated colistin resistance and carbapenem resistant Enterobacteriaceae from tertiary A hospital located in Hefei, China.MethodsTotally, 158 carbapenems resistant Enterobacteriaceae (CRE) were screened for antibiotic susceptibility, mcr-1, extended spectrum β-lactamases (ESBLs), metallo-β-lactamases (MBLs), and fosfomycin resistance genes using PCR and sequencing. The sequence types were identified by multilocus sequence typing (MLST). Plasmid profiles were determined by PCR based replicon typing (PBRT), and the plasmid sizes were confirmed by southern blotting.ResultsThe isolates showed high MIC50 and MIC90 for all antimicrobials, except tigecycline, meropenem, and colistin. The main Carbapenemase genes were blaKPC-2 (90.5%), blaNDM-1(3.7%), blaOXA-48(5.6%) and fosA3 (14.5%). The blaCTXM-15 found 36.7%, mcr-1 (3.7%) recorded in six isolates. PBRT revealed blaKPC-2 in K. pneumoniae on IncR, IncFII, and IncA/C. blaNDM-1 in E. coli on IncFII, whereas in E. cloacae noticed on IncHI2 plasmid. mcr-1 was recorded among IncFIIK, IncFII, and IncF in E. coli, K. pneumoniae, and E. cloacae. Resistance genes (mcr-1, blaNDM-1, blaKPC-2) harboring plasmids are successfully trans-conjugant to EC-600. A high incidence of ST11 was observed in K. pneumoniae carbapenem resistant isolates. While in E. coli, multiple STs were identified. However, mcr-1 in ST23 was identified for the first time in Anhui Province. Among Enterobacter cloacae, ST270 detected carrying blaNDM-1. Southern-hybridization confirmed the plasmid sizes 35–150kb.ConclusionThis study indicates the co-carrying of mcr-1, blaKPC-2, and blaNDM-1 among clinical isolates, the prevalence of different Enterobacteriaceae STs is alarming, especially in E. coli. Holding such a resistance profile is a threat for humans and animals, which may be transferred between the strains through plasmid transfusion. Persistent control actions are immediately necessary to combat this hazard.

Carbapenem-Resistant Enterobacteriaceae-Implications for Treating Acute Leukemias, a Subgroup of Hematological Malignancies.

Acute leukemias (AL) are a group of aggressive malignant diseases associated with a high degree of morbidity and mortality. Patients with AL are highly susceptible to infectious diseases due to the disease itself, factors attributed to treatment, and specific individual risk factors. Enterobacteriaceae presence (e.g., Klebsiella pneumonia and Escherichia coli) is a frequent cause of bloodstream infections in AL patients. Carbapenem-resistant Enterobacteriaceae (CRE) is an emerging health problem worldwide; however, the incidence of CRE varies greatly between different regions. Carbapenem resistance in Enterobacteriaceae is caused by different mechanisms, and CRE may display various resistance profiles. Bacterial co-expression of genes conferring resistance to both broad-spectrum β-lactam antibiotics (including carbapenems) and other classes of antibiotics may give rise to multidrug-resistant organisms (MDROs). The spread of CRE represents a major treatment challenge for clinicians due to lack of randomized clinical trials (RCTs), a limited number of antibiotics available, and the side-effects associated with them. Most research concerning CRE infections in AL patients are limited to case reports and retrospective reviews. Current research recommends treatment with older antibiotics, such as polymyxins, fosfomycin, older aminoglycosides, and in some cases carbapenems. To prevent the spread of resistant microbes, it is of pivotal interest to implement antibiotic stewardship to reduce broad-spectrum antibiotic treatment, but without giving too narrow a treatment to neutropenic infected patients.

Pattern of Carbapenem Resistance in Enterobacteriaceae in Rajshahi Medical College Hospital

The global emergence and spread of Carbapenem Resistant Enterobacteriaceae have been threatening the ability to treat an infection. Hence the present study was carried out with the aim to isolate important members of Enterobacteriaceae family with identification of carbapenem resistant isolates among them. The study was done in the Department of Microbiology, Rajshahi Medical College with collaboration of different disciplines of RMCH from January 2019 to December 2019. Samples were collected purposively. Causative organisms were isolated by culture and identified by colonial morphology, gram staining and relevant biochemical tests. Identified Enterobacteriaceae those showed resistance to carbapenem (imipenem, meropenem) were tested phenotypically by Modified Hodge Test (MHT) to see carbapenemase production. A total of 97 Enterobacteriaceae were isolated from 275 samples. E. coli (54.64%) was the most frequent isolate. By Modified Hodge Test, 19(19.59%) bacteria were phenotypically confirmed as Carbapenem Resistant Enterobacteriaceae (CRE). This study signifies that carbapenem resistance is increasing at an alarming rate.
 TAJ 2020; 33(2): 63-68

Epidemiology, risk factors and molecular analysis of carbapenem-resistant Enterobacteriaceae (CRE) in Mthatha, Eastern Cape, South Africa

Background: The emergence of carbapenem resistance in Enterobacteriaceae is an important threat to global health. Reported outcomes of infections with carbapenem-resistant Enterobacteriaceae (CRE) are poor. Commonly used antibiotics are generally inactive against CRE. Therefore, timely detection of CRE is of paramount importance. This study aimed to investigate the resistance genes responsible for CRE in Mthatha and to identify risk factors. Methods and materials: Study design – Prospective cohort study. Study period – 23 April to 27 September 2019. Setting – Eastern Cape province, SA. Study population – All adult and paediatric CRE patients. CRE case definition according to CDC 2018. ID and AST-bioMérieux Vitek 2 system. Detection of the blaOXA-48, blaKPC, blaNDM, and blaVIM by the RESIST-4 OKNV assay (Coris). Patients were interviewed to determine risk factors associated with CRE. Results: Forty-four non-duplicate CRE patients were identified during the study period from microbiology lab at NMAH. Enterobacteriaceae species: K. pneumoniae 22 (61.4%), E. cloacae 10 (22.7%), E. coli 2 (4.5%) and K. oxytoca, P. rettgeri and M. morganii 1 each (4.3%). Adult patient 29 (65.9%0 and paediatric 15 (34.1%). Race: all black patients except one white. CRE genes-blaOXA-48 22 (50%), blaNDM 8 (18.2%), two isolates (4.5%) with both blaOXA and blaNDM. We did not find any blaKPC and blaVIM in our setting and 12 (27.2%) isolates were negative for all OKNV. Outcomes: Demised 18 (40.9%), still admitted in the ward 1 (2.3%), discharged home on basis of clinical grounds 22 (50%) and 3 (6.8%) were transferred back to the district hospitals. HAI in 27 (61.4%) with VAP 8, HABSI 8, CAUTI 5, SSI 3 and CLABSI in 3. Risk factors for CRE acquisition were antibiotic exposure 25 (58.7%), ICU stay 7 (15.9%), received medical care in last 6 months 35 (79.6%) and none travelled outside RSA. HIV positive – 19 (43.2%). Conclusion: In out setting our CRE mortality rate is 40.9%, common CRE genotypes are blaOXA-48 and blaNDM. K. pneumoniae is the most common CRE-producing Enterobacteriaceae and antibiotic exposure is an important risk factor in Mthatha and surrounding areas.

First description of IncX3 NDM-5-producing plasmid within Escherichia coli ST448 in Mali.

Carbapenem resistance in Enterobacteriaceae has become an increasingly worrying threat. So far, no epidemiological data regarding NDM-producing enterobacterial isolates has been available on these strains in West Africa. The aim of this study was to seek for carbapenemase-producing Enterobacteriaceae clinical strains isolated in Bamako Teaching Hospital in Mali. Of 50 strains isolated between May 2016 and September 2016, we found a ST448 E. coli harbouring an IncX3 plasmid with bla NDM-5 embedded in the ΔISAba125-ble MBL structure. This study reports the first description of NDM-5 in Mali isolated in an undescribed ST E. coli in West Africa.

The Predominance of Strain Replacement Among Enterobacteriaceae Pairs With Emerging Carbapenem Resistance During Hospitalization.

Isolates of Enterobacteriaceae collected from the same patient can lose carbapenem susceptibility during antimicrobial therapy, but little attention has been given to how this conversion takes place. In the current study, we retrospectively analyzed microbiological and clinical data from patients with enterobacterial infections at a tertiary hospital in Shanghai, China. After screening 4795 patients and 7120 Enterobacteriaceae isolates over the 3-year study period, we found the change from carbapenem susceptible to carbapenem resistant in 41 pairs of isolates, of which 35 pairs (85.4%) were K. pneumoniae and 25 (61.0%) were from the same anatomic sites. Thirty-six isolate pairs showed different pulsed-field gel electrophoresis patterns between the carbapenem-susceptible and the corresponding resistant strain, and 5 pairs displayed identical pulsed-field gel electrophoresis patterns. Thirty-three (91.7%) of the 36 pairs of Enterobacteriaceae isolates were carbapenem-resistant K. pneumoniae with blaKPC-2, and 28 pairs (90.3%) of K. pneumoniae isolates had different sequence types (STs), with ST11 the most common ST found in carbapenem-resistant K. pneumoniae isolates. Forty of the 41 patients had received antimicrobial therapy such as carbapenems, cephalosporins, and fluoroquinolones, before the isolation of carbapenem-resistant Enterobacteriaceae. These results demonstrated that strain replacement is the main cause of emerging carbapenem resistance in Enterobacteriaceae during hospitalization. The loss of carbapenem susceptibility was not mainly due to in vivo development of carbapenem resistance.

Genetic Factors Associated with Enhanced blaKPC Expression in Tn3/Tn4401 Chimeras.

The expression of the blaKPC gene plays a key role in carbapenem resistance in Enterobacteriaceae However, the genetic regulators of the blaKPC gene have not been completely elucidated, especially the genes in Tn3-Tn4401 chimeras. Two novel Tn3-Tn4401 chimera isoforms were characterized in our hospital, isoform A (CTA), which harbors a 121-bp deletion containing the PX promoter and was present in 22.6% (54/239) of isolates, and isoform C (CTC), which harbors a 624-bp insertion and a P1 promoter deletion and was present in only 1 isolate. The carbapenem MICs of both isoforms were 2-fold or more higher than those of the wild type (Tn3-Tn4401 chimera, CTB), and blaKPC was most highly expressed in CTA. Bioinformatics and 5' rapid amplification of cDNA ends (5' RACE) experiments indicated a novel strong putative promoter, PY, at the 3' end of the ISKpn8 gene. PY mutation nearly abrogated blaKPC expression (P < 0.01) and restored carbapenem susceptibility in all 3 isoforms. Although the mutation of PX or P1 halved blaKPC expression in CTB (P < 0.05), PX deletion caused a 68% increase in blaKPC expression (P = 0.037) in CTA. The level of blaKPC mRNA in CTC was 8-fold higher than that in InCTC, which harbors P1 (P = 0.011). These results suggest that PY is a core promoter of the blaKPC gene in the chimeras and that the deletion of the PX and P1 promoters enhanced gene expression in CTA and CTC, respectively.

Correlation between Bio-Film Formation and Carbapenem Resistant Enterobacteriaceae Isolates Obtained from Various Clinical Specimens

Introduction: The ability to form bio-film is a universal trait of bacteria by attaching to the surfaces. Carbapenem resistance in Enterobacteriaceae might be endorsed by bio-film formation which augmented colonization of pathogens. Aim: To correlate between bio-film formation and carbapenem resistant Enterobacteriaceae isolates obtained from various clinical specimens and to compare the qualitative and quantitative assay for bio-film production. Method: Study was conducted on 150 strains of Enterobacteriaceae isolates. of these, carbapenem resistant Enterobacteriaceae isolates were subjected for bio-film formation by Modified Congo red agar method, tube adherence method and Tissue culture plate method. Results: Carbapenem resistant Enterobacteriaceae strains were found to be 60.66% and the rate of biofilm producers was 75.53% by any of the phenotypic method. Tissue culture plate method was found to be (67.6%) better than Modified Congo Red agar method (54.9%) and Tube adherence method (39.4%). The highest number of bio-film producers was isolated from urinary tract infections (36.61%). Conclusion: TCP method is most reliable, precise and sensitive method for detection of bio-film formation by Enterobacteriaceae isolates and is ideal to use as a general screening tool to detect bio-film production.

Infection control and risk factors for acquisition of carbapenemase-producing enterobacteriaceae. A 5\u2009year (2011\u20132016) case-control study

BackgroundCarbapenemase-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.MethodsA 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.ResultsOf 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.ConclusionOverall, 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.